-- dump date 20120504_160906 -- class Genbank::CDS -- table cds -- table main -- field 1 id -- field 2 GI -- field 3 GeneID -- field 4 chrom_position -- field 5 chromosome -- field 6 codon_start -- field 7 contig -- field 8 description -- field 9 end_pos -- field 10 gene -- field 11 gene_id -- field 12 name -- field 13 organism -- field 14 product -- field 15 protein_id -- field 16 start_pos -- field 17 strand -- field 18 taxid -- field 19 type -- header -- id GI GeneID chrom_position chromosome codon_start contig description end_pos gene gene_id name organism product protein_id start_pos strand taxid type YP_165274.1 56694929 3194636 1..1869 1 NC_003911.11 GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs; tRNA uridine 5-carboxymethylaminomethyl modification protein GidA 1869 gidA 3194636 gidA Ruegeria pomeroyi DSS-3 tRNA uridine 5-carboxymethylaminomethyl modification protein GidA YP_165274.1 1 D 246200 CDS YP_165275.1 56694930 3194097 1866..2480 1 NC_003911.11 identified by match to protein family HMM PF02527; match to protein family HMM TIGR00138; glucose-inhibited division protein B 2480 gidB 3194097 gidB Ruegeria pomeroyi DSS-3 glucose-inhibited division protein B YP_165275.1 1866 D 246200 CDS YP_165276.1 56694931 3196454 2473..3276 1 NC_003911.11 identified by similarity to SP:O05189; match to protein family HMM PF01656; chromosome partitioning protein ParA 3276 parA 3196454 parA Ruegeria pomeroyi DSS-3 chromosome partitioning protein ParA YP_165276.1 2473 D 246200 CDS YP_165277.1 56694932 3192954 3299..4189 1 NC_003911.11 identified by similarity to SP:O05190; match to protein family HMM PF02195; match to protein family HMM TIGR00180; chromosome partitioning protein parB 4189 parB 3192954 parB Ruegeria pomeroyi DSS-3 chromosome partitioning protein parB YP_165277.1 3299 D 246200 CDS YP_165278.1 56694933 3196415 complement(4179..4532) 1 NC_003911.11 identified by similarity to GB:AAN55061.1; match to protein family HMM PF04304; hypothetical protein 4532 3196415 SPO0005 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165278.1 4179 R 246200 CDS YP_165279.1 56694934 3196529 complement(4536..5693) 1 NC_003911.11 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 5693 3196529 SPO0006 Ruegeria pomeroyi DSS-3 coproporphyrinogen III oxidase YP_165279.1 4536 R 246200 CDS YP_165280.1 56694935 3196546 complement(5683..6297) 1 NC_003911.11 HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine; deoxyribonucleotide triphosphate pyrophosphatase 6297 3196546 SPO0007 Ruegeria pomeroyi DSS-3 deoxyribonucleotide triphosphate pyrophosphatase YP_165280.1 5683 R 246200 CDS YP_165281.1 56694936 3193125 complement(6294..7007) 1 NC_003911.11 RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs; ribonuclease PH 7007 rph 3193125 rph Ruegeria pomeroyi DSS-3 ribonuclease PH YP_165281.1 6294 R 246200 CDS YP_165282.1 56694937 3195247 7130..8194 1 NC_003911.11 Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons; heat-inducible transcription repressor 8194 hrcA 3195247 hrcA Ruegeria pomeroyi DSS-3 heat-inducible transcription repressor YP_165282.1 7130 D 246200 CDS YP_165283.1 56694938 3195554 8205..8768 1 NC_003911.11 identified by match to protein family HMM PF01025; co-chaperone GrpE 8768 grpE 3195554 grpE Ruegeria pomeroyi DSS-3 co-chaperone GrpE YP_165283.1 8205 D 246200 CDS YP_165284.1 56694939 3194479 complement(8822..11455) 1 NC_003911.11 This protein performs the mismatch recognition step during the DNA repair process; DNA mismatch repair protein MutS 11455 mutS 3194479 mutS Ruegeria pomeroyi DSS-3 DNA mismatch repair protein MutS YP_165284.1 8822 R 246200 CDS YP_165285.1 56694940 3194690 11598..13853 1 NC_003911.11 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate; malic enzyme 13853 maeB 3194690 maeB Ruegeria pomeroyi DSS-3 malic enzyme YP_165285.1 11598 D 246200 CDS YP_165286.1 56694941 3194154 13857..14729 1 NC_003911.11 identified by similarity to SP:P05054; match to protein family HMM PF00294; ribokinase 14729 rbsK 3194154 rbsK Ruegeria pomeroyi DSS-3 ribokinase YP_165286.1 13857 D 246200 CDS YP_165287.1 56694942 3196173 complement(14726..15388) 1 NC_003911.11 identified by similarity to SP:Q93P63; match to protein family HMM PF01625; match to protein family HMM TIGR00401; methionine-S-sulfoxide reductase 15388 msrA-1 3196173 msrA-1 Ruegeria pomeroyi DSS-3 methionine-S-sulfoxide reductase YP_165287.1 14726 R 246200 CDS YP_165288.1 56694943 3192837 15491..16264 1 NC_003911.11 hypothetical protein 16264 3192837 SPO0015 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165288.1 15491 D 246200 CDS YP_165289.1 56694944 3194043 complement(16332..16613) 1 NC_003911.11 identified by match to protein family HMM PF02036; sterol carrier protein 16613 3194043 SPO0016 Ruegeria pomeroyi DSS-3 sterol carrier protein YP_165289.1 16332 R 246200 CDS YP_165290.1 56694945 3194316 complement(16689..17132) 1 NC_003911.11 identified by similarity to GB:BAC49462.1; hypothetical protein 17132 3194316 SPO0017 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165290.1 16689 R 246200 CDS YP_165291.1 56694946 3192922 complement(17129..18358) 1 NC_003911.11 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase 18358 argG 3192922 argG Ruegeria pomeroyi DSS-3 argininosuccinate synthase YP_165291.1 17129 R 246200 CDS YP_165292.1 56694947 3194726 18450..19280 1 NC_003911.11 hypothetical protein 19280 3194726 SPO0019 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165292.1 18450 D 246200 CDS YP_165293.1 56694948 3193232 19338..20564 1 NC_003911.11 catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic; threonine dehydratase 20564 ilvA 3193232 ilvA Ruegeria pomeroyi DSS-3 threonine dehydratase YP_165293.1 19338 D 246200 CDS YP_165294.1 56694949 3196142 complement(20571..20924) 1 NC_003911.11 identified by match to protein family HMM PF01627; Hpt domain-containing protein 20924 3196142 SPO0021 Ruegeria pomeroyi DSS-3 Hpt domain-containing protein YP_165294.1 20571 R 246200 CDS YP_165295.1 56694950 3194721 21005..22342 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF07228; response regulator 22342 3194721 SPO0022 Ruegeria pomeroyi DSS-3 response regulator YP_165295.1 21005 D 246200 CDS YP_165296.1 56694951 3194753 complement(22329..22781) 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX family hydrolase 22781 3194753 SPO0023 Ruegeria pomeroyi DSS-3 NUDIX family hydrolase YP_165296.1 22329 R 246200 CDS YP_165297.1 56694952 3194665 22858..23838 1 NC_003911.11 identified by similarity to SP:P45803; match to protein family HMM PF01430; chaperonin, 33 kDa 23838 hslO 3194665 hslO Ruegeria pomeroyi DSS-3 chaperonin, 33 kDa YP_165297.1 22858 D 246200 CDS YP_165298.1 56694953 3193819 23855..24427 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX family hydrolase 24427 3193819 SPO0025 Ruegeria pomeroyi DSS-3 NUDIX family hydrolase YP_165298.1 23855 D 246200 CDS YP_165299.1 56694954 3195220 24424..25578 1 NC_003911.11 identified by match to protein family HMM PF01743; poly(A) polymerase 25578 3195220 SPO0026 Ruegeria pomeroyi DSS-3 poly(A) polymerase YP_165299.1 24424 D 246200 CDS YP_165300.1 56694955 3196318 25770..27608 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter transmembrane ATP-binding protein 27608 3196318 SPO0027 Ruegeria pomeroyi DSS-3 ABC transporter transmembrane ATP-binding protein YP_165300.1 25770 D 246200 CDS YP_165301.1 56694956 3194381 27605..29437 1 NC_003911.11 identified by similarity to GB:BAB70471.1; match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter transmembrane ATP-binding protein 29437 3194381 SPO0028 Ruegeria pomeroyi DSS-3 ABC transporter transmembrane ATP-binding protein YP_165301.1 27605 D 246200 CDS YP_165302.1 56694957 3196355 29456..30709 1 NC_003911.11 identified by similarity to SP:P55135; 23S rRNA (uracil-5-)-methyltransferase RumA 30709 rumA 3196355 rumA Ruegeria pomeroyi DSS-3 23S rRNA (uracil-5-)-methyltransferase RumA YP_165302.1 29456 D 246200 CDS YP_165303.1 56694958 3195038 30727..31503 1 NC_003911.11 identified by similarity to GB:CAD24429.1; match to protein family HMM PF00520; voltage-gated sodium channel 31503 3195038 SPO0030 Ruegeria pomeroyi DSS-3 voltage-gated sodium channel YP_165303.1 30727 D 246200 CDS YP_165304.1 56694959 3194916 31478..32086 1 NC_003911.11 identified by match to protein family HMM PF03734; ErfK/YbiS/YcfS/YnhG family protein 32086 3194916 SPO0031 Ruegeria pomeroyi DSS-3 ErfK/YbiS/YcfS/YnhG family protein YP_165304.1 31478 D 246200 CDS YP_165305.1 56694960 3194226 complement(32070..32372) 1 NC_003911.11 hypothetical protein 32372 3194226 SPO0032 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165305.1 32070 R 246200 CDS YP_165306.1 56694961 3196462 32458..33366 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 33366 3196462 SPO0033 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165306.1 32458 D 246200 CDS YP_165307.1 56694962 3193208 complement(33377..34816) 1 NC_003911.11 identified by similarity to GB:AAM48703.1; hypothetical protein 34816 3193208 SPO0034 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165307.1 33377 R 246200 CDS YP_165308.1 56694963 3193855 complement(34823..36502) 1 NC_003911.11 identified by match to protein family HMM PF02485; core-2/I-branching enzyme family protein 36502 3193855 SPO0035 Ruegeria pomeroyi DSS-3 core-2/I-branching enzyme family protein YP_165308.1 34823 R 246200 CDS YP_165309.1 56694964 3195595 complement(36520..37542) 1 NC_003911.11 identified by similarity to GB:CAC46616.1; hypothetical protein 37542 3195595 SPO0036 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165309.1 36520 R 246200 CDS YP_165310.1 56694965 3195218 complement(37703..38752) 1 NC_003911.11 identified by similarity to GB:CAC46616.1; hypothetical protein 38752 3195218 SPO0037 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165310.1 37703 R 246200 CDS YP_165311.1 56694966 3196170 complement(38766..39566) 1 NC_003911.11 CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS; 3-deoxy-manno-octulosonate cytidylyltransferase 39566 kdsB 3196170 kdsB Ruegeria pomeroyi DSS-3 3-deoxy-manno-octulosonate cytidylyltransferase YP_165311.1 38766 R 246200 CDS YP_165312.1 56694967 3194237 complement(39567..40364) 1 NC_003911.11 identified by similarity to SP:P22255; match to protein family HMM PF00459; match to protein family HMM TIGR01331; 3'(2'),5'-bisphosphate nucleotidase 40364 cysQ 3194237 cysQ Ruegeria pomeroyi DSS-3 3'(2'),5'-bisphosphate nucleotidase YP_165312.1 39567 R 246200 CDS YP_165313.1 56694968 3195714 40483..41304 1 NC_003911.11 ABC transporter permease 41304 3195714 SPO0040 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_165313.1 40483 D 246200 CDS YP_165314.1 56694969 3192766 41301..41885 1 NC_003911.11 identified by similarity to PIR:E82361; hypothetical protein 41885 3192766 SPO0041 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165314.1 41301 D 246200 CDS YP_165315.1 56694970 3194568 complement(41882..42478) 1 NC_003911.11 identified by similarity to SP:P05050; match to protein family HMM PF03171; alkylated DNA repair protein 42478 3194568 SPO0042 Ruegeria pomeroyi DSS-3 alkylated DNA repair protein YP_165315.1 41882 R 246200 CDS YP_165316.1 56694971 3195579 42698..44611 1 NC_003911.11 heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE; multiple copies in some bacteria; molecular chaperone DnaK 44611 dnaK 3195579 dnaK Ruegeria pomeroyi DSS-3 molecular chaperone DnaK YP_165316.1 42698 D 246200 CDS YP_165317.1 56694972 3196511 44687..45832 1 NC_003911.11 chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion; molecular chaperone DnaJ 45832 dnaJ 3196511 dnaJ Ruegeria pomeroyi DSS-3 molecular chaperone DnaJ YP_165317.1 44687 D 246200 CDS YP_165318.1 56694973 3196387 46122..46925 1 NC_003911.11 identified by similarity to SP:P76422; match to protein family HMM TIGR00097; phosphomethylpyrimidine kinase 46925 thiD 3196387 thiD Ruegeria pomeroyi DSS-3 phosphomethylpyrimidine kinase YP_165318.1 46122 D 246200 CDS YP_165319.1 56694974 3194412 46922..47899 1 NC_003911.11 identified by match to protein family HMM PF01266; thiamine biosynthesis oxidoreductase ThiO 47899 3194412 SPO0046 Ruegeria pomeroyi DSS-3 thiamine biosynthesis oxidoreductase ThiO YP_165319.1 46922 D 246200 CDS YP_165320.1 56698725 3196328 47883..48077 1 NC_003911.11 identified by match to protein family HMM PF02597; match to protein family HMM TIGR01683; thiamine biosynthesis protein ThiS 48077 thiS 3196328 thiS Ruegeria pomeroyi DSS-3 thiamine biosynthesis protein ThiS YP_165320.1 47883 D 246200 CDS YP_165321.1 56694975 3195546 48081..48845 1 NC_003911.11 functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate; thiazole synthase 48845 thiG 3195546 thiG Ruegeria pomeroyi DSS-3 thiazole synthase YP_165321.1 48081 D 246200 CDS YP_165322.1 56694976 3194380 48842..49438 1 NC_003911.11 Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate; thiamine-phosphate pyrophosphorylase 49438 thiE 3194380 thiE Ruegeria pomeroyi DSS-3 thiamine-phosphate pyrophosphorylase YP_165322.1 48842 D 246200 CDS YP_165323.1 56694977 3194908 49417..50400 1 NC_003911.11 identified by match to protein family HMM PF00899; match to protein family HMM PF05237; thiamine biosynthesis protein ThiF 50400 3194908 SPO0049 Ruegeria pomeroyi DSS-3 thiamine biosynthesis protein ThiF YP_165323.1 49417 D 246200 CDS YP_165324.1 56694978 3192843 50309..51349 1 NC_003911.11 Assignment based partly on membership in ABC transporter gene cluster.; ABC transporter substrate-binding protein 51349 3192843 SPO0050 Ruegeria pomeroyi DSS-3 ABC transporter substrate-binding protein YP_165324.1 50309 D 246200 CDS YP_165325.1 56694979 3194303 51382..52026 1 NC_003911.11 identified by match to protein family HMM PF03070; TENA/THI-4 family protein 52026 3194303 SPO0051 Ruegeria pomeroyi DSS-3 TENA/THI-4 family protein YP_165325.1 51382 D 246200 CDS YP_165326.1 56694980 3193579 51960..52751 1 NC_003911.11 identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 52751 3193579 SPO0052 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_165326.1 51960 D 246200 CDS YP_165327.1 56694981 3196528 52706..53482 1 NC_003911.11 identified by match to protein family HMM PF00528; ABC transporter permease 53482 3196528 SPO0053 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_165327.1 52706 D 246200 CDS YP_165328.1 56694982 3195576 53600..54274 1 NC_003911.11 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase; DNA repair protein RadC 54274 radC 3195576 radC Ruegeria pomeroyi DSS-3 DNA repair protein RadC YP_165328.1 53600 D 246200 CDS YP_165329.1 56694983 3194535 complement(54337..55893) 1 NC_003911.11 identified by match to protein family HMM PF00691; OmpA domain-containing protein 55893 3194535 SPO0055 Ruegeria pomeroyi DSS-3 OmpA domain-containing protein YP_165329.1 54337 R 246200 CDS YP_165330.1 56694984 3193841 55908..56147 1 NC_003911.11 hypothetical protein 56147 3193841 SPO0056 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165330.1 55908 D 246200 CDS YP_165331.1 56694985 3194508 complement(57011..59716) 1 NC_003911.11 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins; preprotein translocase subunit SecA 59716 secA 3194508 secA Ruegeria pomeroyi DSS-3 preprotein translocase subunit SecA YP_165331.1 57011 R 246200 CDS YP_165332.1 56694986 3196485 59912..60742 1 NC_003911.11 identified by match to protein family HMM PF00639; peptidyl-prolyl cis-trans isomerase domain-containing protein 60742 3196485 SPO0058 Ruegeria pomeroyi DSS-3 peptidyl-prolyl cis-trans isomerase domain-containing protein YP_165332.1 59912 D 246200 CDS YP_165333.1 56694987 3193952 60750..61976 1 NC_003911.11 bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate; bifunctional ornithine acetyltransferase/N-acetylglutamate synthase 61976 argJ 3193952 argJ Ruegeria pomeroyi DSS-3 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase YP_165333.1 60750 D 246200 CDS YP_165334.1 56694988 3196202 61973..62371 1 NC_003911.11 identified by match to protein family HMM PF00293; match to protein family HMM TIGR00586; mutator mutT protein 62371 mutT 3196202 mutT Ruegeria pomeroyi DSS-3 mutator mutT protein YP_165334.1 61973 D 246200 CDS YP_165335.1 56694989 3193823 complement(62848..65355) 1 NC_003911.11 Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex; translation initiation factor IF-2 65355 infB 3193823 infB Ruegeria pomeroyi DSS-3 translation initiation factor IF-2 YP_165335.1 62848 R 246200 CDS YP_165336.1 56694990 3194394 complement(65364..65987) 1 NC_003911.11 identified by similarity to GB:AAK22031.1; match to protein family HMM PF04296; hypothetical protein 65987 3194394 SPO0062 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165336.1 65364 R 246200 CDS YP_165337.1 56694991 3196304 complement(66012..67637) 1 NC_003911.11 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA 67637 nusA 3196304 nusA Ruegeria pomeroyi DSS-3 transcription elongation factor NusA YP_165337.1 66012 R 246200 CDS YP_165338.1 56694992 3194733 complement(67637..68263) 1 NC_003911.11 in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins; hypothetical protein 68263 3194733 SPO0064 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165338.1 67637 R 246200 CDS YP_165339.1 56694993 3192830 complement(68420..69241) 1 NC_003911.11 peptide/opine/nickel uptake ABC transporter substrate-binding protein 69241 3192830 SPO0065 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter substrate-binding protein YP_165339.1 68420 R 246200 CDS YP_165340.1 56694994 3193990 complement(69238..70188) 1 NC_003911.11 identified by match to protein family HMM PF00561; match to protein family HMM TIGR01249; proline iminopeptidase 70188 pip 3193990 pip Ruegeria pomeroyi DSS-3 proline iminopeptidase YP_165340.1 69238 R 246200 CDS YP_165341.1 56694995 3196541 70268..71014 1 NC_003911.11 Involved in ubiquinone biosynthesis; 3-demethylubiquinone-9 3-methyltransferase 71014 ubiG 3196541 ubiG Ruegeria pomeroyi DSS-3 3-demethylubiquinone-9 3-methyltransferase YP_165341.1 70268 D 246200 CDS YP_165342.1 56694996 3195175 complement(71105..71545) 1 NC_003911.11 transcriptional regulator 71545 3195175 SPO0068 Ruegeria pomeroyi DSS-3 transcriptional regulator YP_165342.1 71105 R 246200 CDS YP_165343.1 56694997 3192744 complement(71558..72388) 1 NC_003911.11 identified by match to protein family HMM PF00795; carbon-nitrogen family hydrolase 72388 3192744 SPO0069 Ruegeria pomeroyi DSS-3 carbon-nitrogen family hydrolase YP_165343.1 71558 R 246200 CDS YP_165344.1 56694998 3196331 complement(72385..72645) 1 NC_003911.11 identified by match to protein family HMM PF00462; match to protein family HMM TIGR02181; glutaredoxin 72645 3196331 SPO0070 Ruegeria pomeroyi DSS-3 glutaredoxin YP_165344.1 72385 R 246200 CDS YP_165345.1 56694999 3194872 complement(72738..73466) 1 NC_003911.11 identified by similarity to GB:AAK22815.1; competence protein F 73466 3194872 SPO0071 Ruegeria pomeroyi DSS-3 competence protein F YP_165345.1 72738 R 246200 CDS YP_165346.1 56695000 3194699 73483..74316 1 NC_003911.11 identified by similarity to GB:CAE26039.1; hypothetical protein 74316 3194699 SPO0072 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165346.1 73483 D 246200 CDS YP_165347.1 56695001 3192903 74429..75424 1 NC_003911.11 protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic; ferrochelatase 75424 hemH 3192903 hemH Ruegeria pomeroyi DSS-3 ferrochelatase YP_165347.1 74429 D 246200 CDS YP_165348.1 56695002 3194101 complement(75521..75706) 1 NC_003911.11 hypothetical protein 75706 3194101 SPO0074 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165348.1 75521 R 246200 CDS YP_165349.1 56695003 3193322 complement(75848..76474) 1 NC_003911.11 identified by match to protein family HMM PF03734; ErfK/YbiS/YcfS/YnhG family protein 76474 3193322 SPO0075 Ruegeria pomeroyi DSS-3 ErfK/YbiS/YcfS/YnhG family protein YP_165349.1 75848 R 246200 CDS YP_165350.1 56695004 3195730 76609..77127 1 NC_003911.11 lipoprotein 77127 3195730 SPO0076 Ruegeria pomeroyi DSS-3 lipoprotein YP_165350.1 76609 D 246200 CDS YP_165351.1 56695005 3193872 complement(77195..77659) 1 NC_003911.11 identified by match to protein family HMM PF00359; match to protein family HMM TIGR01419; PTS transporter subunit IIA-like nitrogen-regulatory protein PtsN 77659 ptsN 3193872 ptsN Ruegeria pomeroyi DSS-3 PTS transporter subunit IIA-like nitrogen-regulatory protein PtsN YP_165351.1 77195 R 246200 CDS YP_165352.1 56695006 3194769 complement(77723..78286) 1 NC_003911.11 identified by match to protein family HMM PF02482; match to protein family HMM TIGR00741; ribosomal subunit interface protein 78286 3194769 SPO0078 Ruegeria pomeroyi DSS-3 ribosomal subunit interface protein YP_165352.1 77723 R 246200 CDS YP_165353.1 56695008 3196351 complement(78536..79294) 1 NC_003911.11 identified by similarity to GB:AAM48706.1; match to protein family HMM PF00005; ABC transporter ATP-binding protein 79294 3196351 SPO0079 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_165353.1 78536 R 246200 CDS YP_165354.1 56695007 3195158 complement(79294..79785) 1 NC_003911.11 identified by match to protein family HMM PF03968; hypothetical protein 79785 3195158 SPO0080 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165354.1 79294 R 246200 CDS YP_165355.1 56695009 3195608 complement(79789..80397) 1 NC_003911.11 identified by similarity to GB:AAM48708.1; hypothetical protein 80397 3195608 SPO0081 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165355.1 79789 R 246200 CDS YP_165356.1 56695011 3196256 complement(80401..81369) 1 NC_003911.11 identified by similarity to SP:P45395; match to protein family HMM PF00571; match to protein family HMM PF01380; match to protein family HMM TIGR00393; arabinose 5-phosphate isomerase 81369 kdsD 3196256 kdsD Ruegeria pomeroyi DSS-3 arabinose 5-phosphate isomerase YP_165356.1 80401 R 246200 CDS YP_165357.1 56695010 3193828 complement(81366..81980) 1 NC_003911.11 identified by match to protein family HMM PF01612; exonuclease 81980 3193828 SPO0083 Ruegeria pomeroyi DSS-3 exonuclease YP_165357.1 81366 R 246200 CDS YP_165358.1 56695012 3194160 complement(82247..83701) 1 NC_003911.11 catalyzes the formation of betaine from betaine aldehyde; betaine aldehyde dehydrogenase 83701 betB 3194160 betB Ruegeria pomeroyi DSS-3 betaine aldehyde dehydrogenase YP_165358.1 82247 R 246200 CDS YP_165359.1 56695013 3192846 83874..84212 1 NC_003911.11 identified by similarity to GB:CAE29577.1; hypothetical protein 84212 3192846 SPO0085 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165359.1 83874 D 246200 CDS YP_165360.1 56695014 3193941 84326..85588 1 NC_003911.11 identified by similarity to GB:CAC41759.1; lipoprotein 85588 3193941 SPO0086 Ruegeria pomeroyi DSS-3 lipoprotein YP_165360.1 84326 D 246200 CDS YP_165361.1 56695015 3195276 85616..86671 1 NC_003911.11 hypothetical protein 86671 3195276 SPO0087 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165361.1 85616 D 246200 CDS YP_165362.1 56695016 3196530 86668..88158 1 NC_003911.11 identified by similarity to GB:BAB51963.1; hypothetical protein 88158 3196530 SPO0088 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165362.1 86668 D 246200 CDS YP_165363.1 56695017 3196117 88160..89155 1 NC_003911.11 identified by similarity to GB:CAE32220.1; hypothetical protein 89155 3196117 SPO0089 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165363.1 88160 D 246200 CDS YP_165364.1 56695018 3196424 89159..90235 1 NC_003911.11 identified by similarity to GB:CAE37570.1; hypothetical protein 90235 3196424 SPO0090 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165364.1 89159 D 246200 CDS YP_165365.1 56695019 3195736 complement(90242..91147) 1 NC_003911.11 identified by match to protein family HMM PF00581; rhodanese-like domain-containing protein 91147 3195736 SPO0091 Ruegeria pomeroyi DSS-3 rhodanese-like domain-containing protein YP_165365.1 90242 R 246200 CDS YP_165366.1 56695021 3196517 complement(91224..92447) 1 NC_003911.11 identified by similarity to SP:P36928; molecular chaperone DnaK 92447 3196517 SPO0092 Ruegeria pomeroyi DSS-3 molecular chaperone DnaK YP_165366.1 91224 R 246200 CDS YP_165367.1 56695020 3195369 92595..93185 1 NC_003911.11 identified by similarity to SP:P21369; match to protein family HMM PF00857; pyrazinamidase/nicotinamidase 93185 pncA 3195369 pncA Ruegeria pomeroyi DSS-3 pyrazinamidase/nicotinamidase YP_165367.1 92595 D 246200 CDS YP_165368.1 56695022 3196418 93264..95495 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF00785; match to protein family HMM PF00989; match to protein family HMM PF02518; match to protein family HMM TIGR00229; sensory box sensor histidine kinase/response regulator 95495 3196418 SPO0094 Ruegeria pomeroyi DSS-3 sensory box sensor histidine kinase/response regulator YP_165368.1 93264 D 246200 CDS YP_165369.1 56695023 3194607 95526..96869 1 NC_003911.11 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase 96869 pncB 3194607 pncB Ruegeria pomeroyi DSS-3 nicotinate phosphoribosyltransferase YP_165369.1 95526 D 246200 CDS YP_165370.1 56695024 3194541 complement(96926..97840) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 97840 3194541 SPO0096 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165370.1 96926 R 246200 CDS YP_165371.1 56695025 3196084 complement(97843..99294) 1 NC_003911.11 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 99294 3196084 SPO0097 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_165371.1 97843 R 246200 CDS YP_165372.1 56695026 3194676 complement(99759..101357) 1 NC_003911.11 identified by match to protein family HMM PF00005; peptide/opine/nickel uptake ABC transporter ATP-binding protein 101357 3194676 SPO0098 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter ATP-binding protein YP_165372.1 99759 R 246200 CDS YP_165373.1 56695027 3193770 complement(101354..102169) 1 NC_003911.11 identified by match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease 102169 3193770 SPO0099 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter permease YP_165373.1 101354 R 246200 CDS YP_165374.1 56695028 3194346 complement(102166..103113) 1 NC_003911.11 identified by match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease 103113 3194346 SPO0100 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter permease YP_165374.1 102166 R 246200 CDS YP_165375.1 56695029 3196223 complement(103222..104709) 1 NC_003911.11 identified by match to protein family HMM PF00496; peptide/opine/nickel uptake ABC transporter substrate-binding protein 104709 3196223 SPO0101 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter substrate-binding protein YP_165375.1 103222 R 246200 CDS YP_165376.1 56695030 3194680 104880..105719 1 NC_003911.11 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate; 3-methyl-2-oxobutanoate hydroxymethyltransferase 105719 panB 3194680 panB Ruegeria pomeroyi DSS-3 3-methyl-2-oxobutanoate hydroxymethyltransferase YP_165376.1 104880 D 246200 CDS YP_165377.1 56695031 3195525 105716..106573 1 NC_003911.11 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine; pantoate--beta-alanine ligase 106573 panC 3195525 panC Ruegeria pomeroyi DSS-3 pantoate--beta-alanine ligase YP_165377.1 105716 D 246200 CDS YP_165378.1 56695032 3194950 106644..108122 1 NC_003911.11 identified by match to protein family HMM PF00370; match to protein family HMM PF02782; match to protein family HMM TIGR01311; glycerol kinase 108122 glpK 3194950 glpK Ruegeria pomeroyi DSS-3 glycerol kinase YP_165378.1 106644 D 246200 CDS YP_165379.1 56695033 3196392 complement(108119..109378) 1 NC_003911.11 identified by match to protein family HMM PF01360; hypothetical protein 109378 3196392 SPO0105 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165379.1 108119 R 246200 CDS YP_165380.1 56695034 3194930 complement(109440..110210) 1 NC_003911.11 identified by similarity to SP:Q9A321; match to protein family HMM PF03883; hypothetical protein 110210 3194930 SPO0106 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165380.1 109440 R 246200 CDS YP_165381.1 56695035 3194995 complement(110244..112283) 1 NC_003911.11 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF00570; match to protein family HMM TIGR00614; match to protein family HMM TIGR01389; ATP-dependent DNA helicase RecQ 112283 recQ 3194995 recQ Ruegeria pomeroyi DSS-3 ATP-dependent DNA helicase RecQ YP_165381.1 110244 R 246200 CDS YP_165382.1 56698707 3196275 complement(112680..112952) 1 NC_003911.11 identified by similarity to GB:AAR33383.1; transposase, truncation 112952 3196275 SPO0108 Ruegeria pomeroyi DSS-3 transposase, truncation YP_165382.1 112680 R 246200 CDS YP_165383.1 56695036 3193800 complement(113139..114266) 1 NC_003911.11 identified by match to protein family HMM PF01061; hypothetical protein 114266 3193800 SPO0109 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165383.1 113139 R 246200 CDS YP_165384.1 56695037 3194511 complement(114268..116994) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF01061; ABC transporter ATP-binding protein/permease 116994 3194511 SPO0110 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein/permease YP_165384.1 114268 R 246200 CDS YP_165385.1 56695038 3194548 complement(116991..118055) 1 NC_003911.11 identified by similarity to PIR:H82993; hypothetical protein 118055 3194548 SPO0111 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165385.1 116991 R 246200 CDS YP_165386.1 56695039 3192952 118243..120084 1 NC_003911.11 identified by match to protein family HMM PF07167; poly(3-hydroxyalkanoate) polymerase 120084 3192952 SPO0112 Ruegeria pomeroyi DSS-3 poly(3-hydroxyalkanoate) polymerase YP_165386.1 118243 D 246200 CDS YP_165387.1 56695040 3196492 120115..120879 1 NC_003911.11 Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-ACP reductase 120879 fabI-1 3196492 fabI-1 Ruegeria pomeroyi DSS-3 enoyl-ACP reductase YP_165387.1 120115 D 246200 CDS YP_165388.1 56695041 3194359 120897..121097 1 NC_003911.11 hypothetical protein 121097 3194359 SPO0114 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165388.1 120897 D 246200 CDS YP_165389.1 56695042 3194439 121130..122524 1 NC_003911.11 Catalyses the synthesis of acetylphosphate from acetyl-CoA and inorganic phosphate; bifunctional enoyl-CoA hydratase/phosphate acetyltransferase 122524 3194439 SPO0115 Ruegeria pomeroyi DSS-3 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase YP_165389.1 121130 D 246200 CDS YP_165390.1 56695043 3192885 122521..123705 1 NC_003911.11 identified by match to protein family HMM PF00871; match to protein family HMM TIGR00016; acetate kinase 123705 ackA 3192885 ackA Ruegeria pomeroyi DSS-3 acetate kinase YP_165390.1 122521 D 246200 CDS YP_165391.1 56695044 3196217 126237..127478 1 NC_003911.11 hypothetical protein 127478 3196217 SPO0118 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165391.1 126237 D 246200 CDS YP_165392.1 56695045 3195575 complement(127691..128194) 1 NC_003911.11 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 128194 3195575 SPO0119 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_165392.1 127691 R 246200 CDS YP_165393.1 56695046 3194375 128242..129201 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 129201 3194375 SPO0120 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165393.1 128242 D 246200 CDS YP_165394.1 56695047 3194448 complement(130161..130448) 1 NC_003911.11 identified by match to protein family HMM PF02325; hypothetical protein 130448 3194448 SPO0122 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165394.1 130161 R 246200 CDS YP_165395.1 56695048 3194881 130602..131966 1 NC_003911.11 identified by match to protein family HMM PF07690; hypothetical protein 131966 3194881 SPO0123 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165395.1 130602 D 246200 CDS YP_165396.1 56695049 3196344 131966..132847 1 NC_003911.11 D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm; penicillin-insensitive murein endopeptidase 132847 mepA 3196344 mepA Ruegeria pomeroyi DSS-3 penicillin-insensitive murein endopeptidase YP_165396.1 131966 D 246200 CDS YP_165397.1 56695050 3193228 132820..133704 1 NC_003911.11 identified by similarity to PIR:F98281; hypothetical protein 133704 3193228 SPO0125 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165397.1 132820 D 246200 CDS YP_165398.1 56695051 3194605 133714..134445 1 NC_003911.11 identified by match to protein family HMM PF02592; match to protein family HMM TIGR00697; hypothetical protein 134445 3194605 SPO0126 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165398.1 133714 D 246200 CDS YP_165399.1 56695052 3196191 134704..135123 1 NC_003911.11 identified by similarity to GB:AAM35138.1; match to protein family HMM PF00472; peptidyl-tRNA hydrolase domain-containing protein 135123 3196191 SPO0127 Ruegeria pomeroyi DSS-3 peptidyl-tRNA hydrolase domain-containing protein YP_165399.1 134704 D 246200 CDS YP_165400.1 56695053 3196090 135168..135923 1 NC_003911.11 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 135923 fabG 3196090 fabG Ruegeria pomeroyi DSS-3 3-ketoacyl-ACP reductase YP_165400.1 135168 D 246200 CDS YP_165401.1 56695054 3194709 135951..136958 1 NC_003911.11 identified by match to protein family HMM PF03576; T4 family peptidase 136958 3194709 SPO0129 Ruegeria pomeroyi DSS-3 T4 family peptidase YP_165401.1 135951 D 246200 CDS YP_165402.1 56695055 3194236 137081..137494 1 NC_003911.11 identified by match to protein family HMM PF00034; cytochrome c family protein 137494 3194236 SPO0130 Ruegeria pomeroyi DSS-3 cytochrome c family protein YP_165402.1 137081 D 246200 CDS YP_165403.1 56695056 3194796 137668..138210 1 NC_003911.11 identified by similarity to SP:P26173; match to protein family HMM PF00293; match to protein family HMM TIGR02150; isopentyl-diphosphate delta-isomerase 138210 3194796 SPO0131 Ruegeria pomeroyi DSS-3 isopentyl-diphosphate delta-isomerase YP_165403.1 137668 D 246200 CDS YP_165404.1 56695057 3196450 complement(138223..140442) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF02518; sensor histidine kinase/response regulator 140442 3196450 SPO0132 Ruegeria pomeroyi DSS-3 sensor histidine kinase/response regulator YP_165404.1 138223 R 246200 CDS YP_165405.1 56695058 3194066 140575..146001 1 NC_003911.11 identified by match to protein family HMM PF00024; match to protein family HMM PF01835; match to protein family HMM PF07703; PAN domain-containing protein 146001 3194066 SPO0133 Ruegeria pomeroyi DSS-3 PAN domain-containing protein YP_165405.1 140575 D 246200 CDS YP_165406.1 56695059 3196545 145998..146564 1 NC_003911.11 identified by similarity to GB:BAB50328.1; hypothetical protein 146564 3196545 SPO0134 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165406.1 145998 D 246200 CDS YP_165407.1 56695060 3195559 146554..148593 1 NC_003911.11 identified by similarity to SP:P76577; match to protein family HMM PF00905; match to protein family HMM PF00912; match to protein family HMM TIGR02073; penicillin-binding protein 1C 148593 pbpC 3195559 pbpC Ruegeria pomeroyi DSS-3 penicillin-binding protein 1C YP_165407.1 146554 D 246200 CDS YP_165408.1 56695061 3193811 complement(148600..150645) 1 NC_003911.11 identified by similarity to GB:BAC47727.1; hypothetical protein 150645 3193811 SPO0136 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165408.1 148600 R 246200 CDS YP_165409.1 56695062 3192756 complement(150642..153404) 1 NC_003911.11 identified by similarity to PIR:D97630; match to protein family HMM TIGR02226; hypothetical protein 153404 3192756 SPO0137 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165409.1 150642 R 246200 CDS YP_165410.1 56695063 3193576 complement(153401..154276) 1 NC_003911.11 identified by similarity to GB:AAN30463.1; hypothetical protein 154276 3193576 SPO0138 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165410.1 153401 R 246200 CDS YP_165411.1 56695064 3196129 complement(154273..155280) 1 NC_003911.11 MoxR family ATPase 155280 3196129 SPO0139 Ruegeria pomeroyi DSS-3 MoxR family ATPase YP_165411.1 154273 R 246200 CDS YP_165412.1 56695065 3194666 155346..155927 1 NC_003911.11 identified by similarity to PIR:E83277; match to protein family HMM PF06938; hypothetical protein 155927 3194666 SPO0140 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165412.1 155346 D 246200 CDS YP_165413.1 56695066 3196273 complement(155946..156515) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA binding protein 156515 3196273 SPO0141 Ruegeria pomeroyi DSS-3 DNA binding protein YP_165413.1 155946 R 246200 CDS YP_165414.1 56695067 3196131 156963..158138 1 NC_003911.11 catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA; beta-ketothiolase 158138 bktB 3196131 bktB Ruegeria pomeroyi DSS-3 beta-ketothiolase YP_165414.1 156963 D 246200 CDS YP_165415.1 56695068 3193922 complement(158208..159194) 1 NC_003911.11 identified by match to protein family HMM PF00037; (Fe-S)-binding protein 159194 3193922 SPO0143 Ruegeria pomeroyi DSS-3 (Fe-S)-binding protein YP_165415.1 158208 R 246200 CDS YP_165416.1 56695069 3194970 complement(159233..160762) 1 NC_003911.11 identified by similarity to SP:P27854; match to protein family HMM PF03109; match to protein family HMM TIGR01982; 2-polyprenylphenol 6-hydroxylase 160762 ubiB 3194970 ubiB Ruegeria pomeroyi DSS-3 2-polyprenylphenol 6-hydroxylase YP_165416.1 159233 R 246200 CDS YP_165417.1 56695070 3193275 complement(160766..161539) 1 NC_003911.11 identified by similarity to SP:P27851; match to protein family HMM PF01209; match to protein family HMM TIGR01934; ubiquinone/menaquinone biosynthesis methyltransferase UbiE 161539 ubiE 3193275 ubiE Ruegeria pomeroyi DSS-3 ubiquinone/menaquinone biosynthesis methyltransferase UbiE YP_165417.1 160766 R 246200 CDS YP_165418.1 56695071 3194954 161604..162455 1 NC_003911.11 Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases; formamidopyrimidine-DNA glycosylase 162455 mutM 3194954 mutM Ruegeria pomeroyi DSS-3 formamidopyrimidine-DNA glycosylase YP_165418.1 161604 D 246200 CDS YP_165419.1 56695072 3193769 162522..163298 1 NC_003911.11 identified by similarity to SP:P14604; match to protein family HMM PF00378; enoyl-CoA hydratase 163298 3193769 SPO0147 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_165419.1 162522 D 246200 CDS YP_165420.1 56695073 3195937 163518..163781 1 NC_003911.11 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 163781 rpsT 3195937 rpsT Ruegeria pomeroyi DSS-3 30S ribosomal protein S20 YP_165420.1 163518 D 246200 CDS YP_165421.1 56695074 3194668 164331..165737 1 NC_003911.11 binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself.; chromosome replication initiator DnaA 165737 dnaA 3194668 dnaA Ruegeria pomeroyi DSS-3 chromosome replication initiator DnaA YP_165421.1 164331 D 246200 CDS YP_165422.1 56695075 3195527 165999..167117 1 NC_003911.11 binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta 167117 dnaN 3195527 dnaN Ruegeria pomeroyi DSS-3 DNA polymerase III subunit beta YP_165422.1 165999 D 246200 CDS YP_165423.1 56695076 3196176 167177..168277 1 NC_003911.11 Required for DNA replication; binds preferentially to single-stranded, linear DNA; recombination protein F 168277 recF 3196176 recF Ruegeria pomeroyi DSS-3 recombination protein F YP_165423.1 167177 D 246200 CDS YP_165424.1 56695077 3193950 168274..168894 1 NC_003911.11 identified by match to protein family HMM PF01810; amino acid transporter LysE 168894 3193950 SPO0152 Ruegeria pomeroyi DSS-3 amino acid transporter LysE YP_165424.1 168274 D 246200 CDS YP_165425.1 56695078 3194138 complement(168887..169474) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 169474 3194138 SPO0153 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_165425.1 168887 R 246200 CDS YP_165426.1 56695079 3196293 169581..170174 1 NC_003911.11 identified by similarity to SP:P45245; match to protein family HMM PF02525; quinone family NAD(P)H dehydrogenase 170174 3196293 SPO0154 Ruegeria pomeroyi DSS-3 quinone family NAD(P)H dehydrogenase YP_165426.1 169581 D 246200 CDS YP_165427.1 56695080 3194940 170259..172676 1 NC_003911.11 negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B 172676 gyrB 3194940 gyrB Ruegeria pomeroyi DSS-3 DNA gyrase subunit B YP_165427.1 170259 D 246200 CDS YP_165428.1 56695081 3195211 complement(172724..174295) 1 NC_003911.11 identified by similarity to SP:P38035; match to protein family HMM PF00158; transcriptional regulator RtcR 174295 rtcR 3195211 rtcR Ruegeria pomeroyi DSS-3 transcriptional regulator RtcR YP_165428.1 172724 R 246200 CDS YP_165429.1 56695082 3195479 174344..176026 1 NC_003911.11 identified by match to protein family HMM PF05731; TROVE domain-containing protein 176026 3195479 SPO0157 Ruegeria pomeroyi DSS-3 TROVE domain-containing protein YP_165429.1 174344 D 246200 CDS YP_165430.1 56695083 3196417 177007..178419 1 NC_003911.11 identified by similarity to PIR:D75521; hypothetical protein 178419 3196417 SPO0160 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165430.1 177007 D 246200 CDS YP_165431.1 56695084 3196211 complement(178533..179147) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator 179147 3196211 SPO0161 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_165431.1 178533 R 246200 CDS YP_165432.1 56695085 3194449 179479..179967 1 NC_003911.11 identified by similarity to GB:AAQ59886.1; hypothetical protein 179967 3194449 SPO0162 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165432.1 179479 D 246200 CDS YP_165433.1 56695086 3194882 180023..182494 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF00989; match to protein family HMM PF02518; match to protein family HMM TIGR00229; sensory box histidine kinase/response regulator 182494 3194882 SPO0163 Ruegeria pomeroyi DSS-3 sensory box histidine kinase/response regulator YP_165433.1 180023 D 246200 CDS YP_165434.1 56695087 3194895 complement(182491..184470) 1 NC_003911.11 identified by match to protein family HMM PF00070; match to protein family HMM PF00724; oxidoreductase, FMN-binding/pyridine nucleotide-disulfide oxidoreductase 184470 3194895 SPO0164 Ruegeria pomeroyi DSS-3 oxidoreductase, FMN-binding/pyridine nucleotide-disulfide oxidoreductase YP_165434.1 182491 R 246200 CDS YP_165435.1 56695088 3194960 complement(184467..185198) 1 NC_003911.11 pyrroline-5-carboxylate reductase 185198 3194960 SPO0165 Ruegeria pomeroyi DSS-3 pyrroline-5-carboxylate reductase YP_165435.1 184467 R 246200 CDS YP_165436.1 56695089 3195336 complement(185200..187245) 1 NC_003911.11 identified by similarity to SP:O87278; match to protein family HMM PF00724; N-methylproline demethylase 187245 3195336 SPO0166 Ruegeria pomeroyi DSS-3 N-methylproline demethylase YP_165436.1 185200 R 246200 CDS YP_165437.1 56695090 3195109 complement(187255..188823) 1 NC_003911.11 identified by match to protein family HMM PF06253; trimethylamine methyltransferase 188823 3195109 SPO0167 Ruegeria pomeroyi DSS-3 trimethylamine methyltransferase YP_165437.1 187255 R 246200 CDS YP_165438.1 56695091 3193023 188930..189568 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 189568 3193023 SPO0168 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_165438.1 188930 D 246200 CDS YP_165439.1 56695092 3195096 189622..190320 1 NC_003911.11 identified by match to protein family HMM PF01464; Slt family transglycosylase 190320 3195096 SPO0169 Ruegeria pomeroyi DSS-3 Slt family transglycosylase YP_165439.1 189622 D 246200 CDS YP_165440.1 56695093 3193109 190330..192417 1 NC_003911.11 membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA 192417 flhA 3193109 flhA Ruegeria pomeroyi DSS-3 flagellar biosynthesis protein FlhA YP_165440.1 190330 D 246200 CDS YP_165441.1 56695094 3193095 192414..193187 1 NC_003911.11 identified by similarity to SP:P35537; similarity to SP:Q45975; match to protein family HMM PF01311; flagellar biosynthetic protein FliR 193187 fliR 3193095 fliR Ruegeria pomeroyi DSS-3 flagellar biosynthetic protein FliR YP_165441.1 192414 D 246200 CDS YP_165442.1 56695095 3195100 193184..194272 1 NC_003911.11 membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB 194272 flhB 3195100 flhB Ruegeria pomeroyi DSS-3 flagellar biosynthesis protein FlhB YP_165442.1 193184 D 246200 CDS YP_165443.1 56695096 3195174 194266..194679 1 NC_003911.11 hypothetical protein 194679 3195174 SPO0173 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165443.1 194266 D 246200 CDS YP_165444.1 56695097 3195169 complement(194774..195310) 1 NC_003911.11 hypothetical protein 195310 3195169 SPO0174 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165444.1 194774 R 246200 CDS YP_165445.1 56695098 3195762 complement(195319..196059) 1 NC_003911.11 part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod; flagellar basal body L-ring protein 196059 flgH 3195762 flgH Ruegeria pomeroyi DSS-3 flagellar basal body L-ring protein YP_165445.1 195319 R 246200 CDS YP_165446.1 56695099 3195181 complement(196056..196472) 1 NC_003911.11 required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA 196472 flgA 3195181 flgA Ruegeria pomeroyi DSS-3 flagellar basal body P-ring biosynthesis protein FlgA YP_165446.1 196056 R 246200 CDS YP_165447.1 56695100 3195735 complement(196472..197257) 1 NC_003911.11 makes up the distal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagella; flagellar basal body rod protein FlgG 197257 flgG 3195735 flgG Ruegeria pomeroyi DSS-3 flagellar basal body rod protein FlgG YP_165447.1 196472 R 246200 CDS YP_165448.1 56695101 3194052 complement(197281..197931) 1 NC_003911.11 FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of this and other flagella genes; flagellar basal body rod protein FlgF 197931 flgF 3194052 flgF Ruegeria pomeroyi DSS-3 flagellar basal body rod protein FlgF YP_165448.1 197281 R 246200 CDS YP_165449.1 56695102 3194330 complement(197995..198267) 1 NC_003911.11 identified by similarity to SP:P35535; match to protein family HMM PF01313; match to protein family HMM TIGR01402; flagellar biosynthetic protein FliQ 198267 fliQ 3194330 fliQ Ruegeria pomeroyi DSS-3 flagellar biosynthetic protein FliQ YP_165449.1 197995 R 246200 CDS YP_165450.1 56695103 3196430 complement(198271..198561) 1 NC_003911.11 forms a junction between the M-ring and FlgB during flagella biosynthesis; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella; flagellar hook-basal body protein FliE 198561 fliE 3196430 fliE Ruegeria pomeroyi DSS-3 flagellar hook-basal body protein FliE YP_165450.1 198271 R 246200 CDS YP_165451.1 56695104 3192784 complement(198574..198981) 1 NC_003911.11 with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC 198981 flgC 3192784 flgC Ruegeria pomeroyi DSS-3 flagellar basal body rod protein FlgC YP_165451.1 198574 R 246200 CDS YP_165452.1 56695105 3192893 complement(198978..199394) 1 NC_003911.11 with FlgF and C makes up the proximal portion of the flagellar basal body rod; flagellar basal-body rod protein FlgB 199394 flgB 3192893 flgB Ruegeria pomeroyi DSS-3 flagellar basal-body rod protein FlgB YP_165452.1 198978 R 246200 CDS YP_165453.1 56695106 3195322 199455..200792 1 NC_003911.11 identified by similarity to SP:P26465; match to protein family HMM PF00006; match to protein family HMM TIGR01026; H+-transporting two-sector ATPase, flagellum-specific 200792 fliI 3195322 fliI Ruegeria pomeroyi DSS-3 H+-transporting two-sector ATPase, flagellum-specific YP_165453.1 199455 D 246200 CDS YP_165454.1 56695107 3193797 complement(200811..202328) 1 NC_003911.11 identified by match to protein family HMM PF01970; hypothetical protein 202328 3193797 SPO0184 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165454.1 200811 R 246200 CDS YP_165455.1 56695108 3194629 complement(202330..202956) 1 NC_003911.11 hypothetical protein 202956 3194629 SPO0185 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165455.1 202330 R 246200 CDS YP_165456.1 56695109 3195491 complement(203121..204098) 1 NC_003911.11 identified by match to protein family HMM PF03401; hypothetical protein 204098 3195491 SPO0186 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165456.1 203121 R 246200 CDS YP_165457.1 56695110 3193850 204208..204873 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator 204873 3193850 SPO0187 Ruegeria pomeroyi DSS-3 DNA-binding response regulator YP_165457.1 204208 D 246200 CDS YP_165458.1 56695111 3195286 204870..206255 1 NC_003911.11 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase 206255 3195286 SPO0188 Ruegeria pomeroyi DSS-3 sensor histidine kinase YP_165458.1 204870 D 246200 CDS YP_165459.1 56695112 3195068 206225..207250 1 NC_003911.11 identified by similarity to GB:AAM42620.1; hypothetical protein 207250 3195068 SPO0189 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165459.1 206225 D 246200 CDS YP_165460.1 56695113 3195583 207330..208943 1 NC_003911.11 identified by match to protein family HMM PF00732; match to protein family HMM PF05199; GMC family oxidoreductase 208943 3195583 SPO0190 Ruegeria pomeroyi DSS-3 GMC family oxidoreductase YP_165460.1 207330 D 246200 CDS YP_165461.1 56695114 3194641 209006..209863 1 NC_003911.11 identified by similarity to SP:P09349; chemotaxis protein MotB 209863 motB 3194641 motB Ruegeria pomeroyi DSS-3 chemotaxis protein MotB YP_165461.1 209006 D 246200 CDS YP_165462.1 56695115 3195683 209965..211260 1 NC_003911.11 identified by similarity to SP:O07884; match to protein family HMM PF00460; match to protein family HMM PF06429; flagellar hook protein FlgE 211260 3195683 SPO0192 Ruegeria pomeroyi DSS-3 flagellar hook protein FlgE YP_165462.1 209965 D 246200 CDS YP_165463.1 56695116 3195278 211299..212750 1 NC_003911.11 with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK 212750 flgK 3195278 flgK Ruegeria pomeroyi DSS-3 flagellar hook-associated protein FlgK YP_165463.1 211299 D 246200 CDS YP_165464.1 56695117 3194464 212754..213761 1 NC_003911.11 flagellar hook-associated protein FlgL family protein 213761 3194464 SPO0194 Ruegeria pomeroyi DSS-3 flagellar hook-associated protein FlgL family protein YP_165464.1 212754 D 246200 CDS YP_165465.1 56695118 3193009 213758..214858 1 NC_003911.11 part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum; flagellar basal body P-ring biosynthesis protein FlgA 214858 flgI 3193009 flgI Ruegeria pomeroyi DSS-3 flagellar basal body P-ring biosynthesis protein FlgA YP_165465.1 213758 D 246200 CDS YP_165466.1 56695119 3195673 complement(215016..215759) 1 NC_003911.11 FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP 215759 fliP 3195673 fliP Ruegeria pomeroyi DSS-3 flagellar biosynthesis protein FliP YP_165466.1 215016 R 246200 CDS YP_165467.1 56695120 3196056 complement(215756..216085) 1 NC_003911.11 identified by similarity to SP:Q03593; match to protein family HMM PF01052; flagellar motor switch protein FliN 216085 fliN 3196056 fliN Ruegeria pomeroyi DSS-3 flagellar motor switch protein FliN YP_165467.1 215756 R 246200 CDS YP_165468.1 56695121 3196035 complement(216042..216632) 1 NC_003911.11 ABC transporter ATP-binding protein, flagellar 216632 3196035 SPO0198 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein, flagellar YP_165468.1 216042 R 246200 CDS YP_165469.1 56695122 3192761 complement(216632..218236) 1 NC_003911.11 the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod; flagellar MS-ring protein 218236 fliF 3192761 fliF Ruegeria pomeroyi DSS-3 flagellar MS-ring protein YP_165469.1 216632 R 246200 CDS YP_165470.1 56695123 3195727 218355..218861 1 NC_003911.11 identified by similarity to SP:P34008; match to protein family HMM PF03748; flagellar basal body protein FliL 218861 fliL 3195727 fliL Ruegeria pomeroyi DSS-3 flagellar basal body protein FliL YP_165470.1 218355 D 246200 CDS YP_165471.1 56695124 3195986 218871..219290 1 NC_003911.11 identified by similarity to GB:AAF27716.1; hypothetical protein 219290 3195986 SPO0201 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165471.1 218871 D 246200 CDS YP_165472.1 56695125 3194244 219287..219877 1 NC_003911.11 identified by similarity to PIR:E83956; hypothetical protein 219877 3194244 SPO0202 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165472.1 219287 D 246200 CDS YP_165473.1 56695126 3195632 219941..220810 1 NC_003911.11 With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine; flagellar motor protein MotA 220810 motA 3195632 motA Ruegeria pomeroyi DSS-3 flagellar motor protein MotA YP_165473.1 219941 D 246200 CDS YP_165474.1 56695127 3196368 220807..223038 1 NC_003911.11 hypothetical protein 223038 3196368 SPO0204 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165474.1 220807 D 246200 CDS YP_165475.1 56695128 3196222 complement(223341..224723) 1 NC_003911.11 identified by similarity to GB:AAO56546.1; match to protein family HMM PF03972; MmgE/PrpD family protein 224723 3196222 SPO0205 Ruegeria pomeroyi DSS-3 MmgE/PrpD family protein YP_165475.1 223341 R 246200 CDS YP_165476.1 56695129 3194494 224915..225808 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 225808 3194494 SPO0206 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165476.1 224915 D 246200 CDS YP_165477.1 56695130 3195798 complement(225805..228222) 1 NC_003911.11 identified by match to protein family HMM PF01266; match to protein family HMM PF01571; glycine cleavage system protein T 228222 3195798 SPO0207 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_165477.1 225805 R 246200 CDS YP_165478.1 56695131 3192860 228804..230498 1 NC_003911.11 identified by match to protein family HMM PF02690; Na/Pi-cotransporter family protein 230498 3192860 SPO0209 Ruegeria pomeroyi DSS-3 Na/Pi-cotransporter family protein YP_165478.1 228804 D 246200 CDS YP_165479.1 56695132 3195751 complement(230495..231598) 1 NC_003911.11 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase 231598 leuB 3195751 leuB Ruegeria pomeroyi DSS-3 3-isopropylmalate dehydrogenase YP_165479.1 230495 R 246200 CDS YP_165480.1 56695133 3196243 complement(231701..232597) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 232597 3196243 SPO0211 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165480.1 231701 R 246200 CDS YP_165481.1 56695134 3194278 232647..233597 1 NC_003911.11 identified by similarity to PIR:G97622; hypothetical protein 233597 3194278 SPO0212 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165481.1 232647 D 246200 CDS YP_165482.1 56695135 3195593 complement(233547..234620) 1 NC_003911.11 identified by similarity to GB:AAM40439.1; hypothetical protein 234620 3195593 SPO0213 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165482.1 233547 R 246200 CDS YP_165483.1 56695136 3196489 complement(234617..235450) 1 NC_003911.11 hypothetical protein 235450 3196489 SPO0214 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165483.1 234617 R 246200 CDS YP_165484.1 56695137 3194679 complement(235799..236404) 1 NC_003911.11 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit 236404 leuD 3194679 leuD Ruegeria pomeroyi DSS-3 isopropylmalate isomerase small subunit YP_165484.1 235799 R 246200 CDS YP_165485.1 56695138 3195137 complement(236489..237895) 1 NC_003911.11 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 237895 leuC-1 3195137 leuC-1 Ruegeria pomeroyi DSS-3 isopropylmalate isomerase large subunit YP_165485.1 236489 R 246200 CDS YP_165486.1 56695139 3196527 complement(237948..238112) 1 NC_003911.11 hypothetical protein 238112 3196527 SPO0217 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165486.1 237948 R 246200 CDS YP_165487.1 56695140 3193938 238133..239485 1 NC_003911.11 identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS 239485 3193938 SPO0218 Ruegeria pomeroyi DSS-3 mechanosensitive ion channel MscS YP_165487.1 238133 D 246200 CDS YP_165488.1 56695141 3195586 239625..240011 1 NC_003911.11 identified by match to protein family HMM PF02410; match to protein family HMM TIGR00090; iojap family protein 240011 3195586 SPO0219 Ruegeria pomeroyi DSS-3 iojap family protein YP_165488.1 239625 D 246200 CDS YP_165489.1 56695142 3196019 240058..240528 1 NC_003911.11 SPOUT methyltransferase; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA; rRNA large subunit methyltransferase 240528 3196019 SPO0220 Ruegeria pomeroyi DSS-3 rRNA large subunit methyltransferase YP_165489.1 240058 D 246200 CDS YP_165490.1 56695143 3196497 240537..241022 1 NC_003911.11 identified by similarity to GB:CAE38612.1; hypothetical protein 241022 3196497 SPO0221 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165490.1 240537 D 246200 CDS YP_165491.1 56695144 3196062 complement(241109..242224) 1 NC_003911.11 identified by similarity to SP:P30234; match to protein family HMM PF01262; match to protein family HMM PF05222; match to protein family HMM TIGR00518; alanine dehydrogenase 242224 ald 3196062 ald Ruegeria pomeroyi DSS-3 alanine dehydrogenase YP_165491.1 241109 R 246200 CDS YP_165492.1 56695145 3196105 242364..242822 1 NC_003911.11 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 242822 3196105 SPO0223 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_165492.1 242364 D 246200 CDS YP_165493.1 56695146 3196455 242986..243903 1 NC_003911.11 identified by similarity to GB:AAN87337.1; match to protein family HMM PF03976; polyphosphate kinase 243903 3196455 SPO0224 Ruegeria pomeroyi DSS-3 polyphosphate kinase YP_165493.1 242986 D 246200 CDS YP_165494.1 56695147 3195104 complement(243987..244499) 1 NC_003911.11 transcriptional regulator 244499 3195104 SPO0225 Ruegeria pomeroyi DSS-3 transcriptional regulator YP_165494.1 243987 R 246200 CDS YP_165495.1 56695148 3194470 244548..245786 1 NC_003911.11 cytochrome P450 family protein 245786 3194470 SPO0226 Ruegeria pomeroyi DSS-3 cytochrome P450 family protein YP_165495.1 244548 D 246200 CDS YP_165496.1 56695149 3196495 complement(245787..247157) 1 NC_003911.11 identified by similarity to GB:AAF15370.1; match to protein family HMM PF00353; PaxA 247157 3196495 SPO0227 Ruegeria pomeroyi DSS-3 PaxA YP_165496.1 245787 R 246200 CDS YP_165497.1 56695150 3196464 247265..248473 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 248473 3196464 SPO0228 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165497.1 247265 D 246200 CDS YP_165498.1 56695151 3196118 complement(248574..248780) 1 NC_003911.11 a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA; 30S ribosomal protein S21 248780 rpsU 3196118 rpsU Ruegeria pomeroyi DSS-3 30S ribosomal protein S21 YP_165498.1 248574 R 246200 CDS YP_165499.1 56695152 3195644 248890..249570 1 NC_003911.11 identified by similarity to GB:AAK25258.1; hypothetical protein 249570 3195644 SPO0230 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165499.1 248890 D 246200 CDS YP_165500.1 56695153 3193028 249647..250630 1 NC_003911.11 identified by match to protein family HMM PF00107; alcohol dehydrogenase 250630 3193028 SPO0231 Ruegeria pomeroyi DSS-3 alcohol dehydrogenase YP_165500.1 249647 D 246200 CDS YP_165501.1 56695154 3194003 250710..251693 1 NC_003911.11 identified by similarity to SP:P40783; match to protein family HMM PF00107; quinone oxidoreductase 251693 3194003 SPO0232 Ruegeria pomeroyi DSS-3 quinone oxidoreductase YP_165501.1 250710 D 246200 CDS YP_165502.1 56695155 3195984 251746..252174 1 NC_003911.11 identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator 252174 3195984 SPO0233 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_165502.1 251746 D 246200 CDS YP_165503.1 56695156 3196075 252290..253396 1 NC_003911.11 identified by similarity to GB:BAB51119.1; hypothetical protein 253396 3196075 SPO0234 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165503.1 252290 D 246200 CDS YP_165504.1 56695157 3196441 253400..254914 1 NC_003911.11 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 254914 3196441 SPO0235 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_165504.1 253400 D 246200 CDS YP_165505.1 56695158 3194627 complement(255034..255972) 1 NC_003911.11 identified by similarity to SP:P37965; match to protein family HMM PF03009; glycerophosphoryl diester phosphodiesterase 255972 3194627 SPO0236 Ruegeria pomeroyi DSS-3 glycerophosphoryl diester phosphodiesterase YP_165505.1 255034 R 246200 CDS YP_165506.1 56695159 3196148 complement(255969..257024) 1 NC_003911.11 part of the UgpABCE glycerol-3-phosphate uptake system; glycerol-3-phosphate transporter ATP-binding subunit 257024 ugpC 3196148 ugpC Ruegeria pomeroyi DSS-3 glycerol-3-phosphate transporter ATP-binding subunit YP_165506.1 255969 R 246200 CDS YP_165507.1 56695160 3192706 complement(257035..257886) 1 NC_003911.11 identified by similarity to SP:P10906; match to protein family HMM PF00528; SN-glycerol-3-phosphate ABC transporter permease 257886 ugpE 3192706 ugpE Ruegeria pomeroyi DSS-3 SN-glycerol-3-phosphate ABC transporter permease YP_165507.1 257035 R 246200 CDS YP_165508.1 56695161 3195670 complement(257886..258806) 1 NC_003911.11 identified by similarity to SP:P10905; match to protein family HMM PF00528; SN-glycerol-3-phosphate ABC transporter permease 258806 ugpA 3195670 ugpA Ruegeria pomeroyi DSS-3 SN-glycerol-3-phosphate ABC transporter permease YP_165508.1 257886 R 246200 CDS YP_165509.1 56695162 3196154 complement(258851..260236) 1 NC_003911.11 identified by similarity to SP:P10904; match to protein family HMM PF01547; SN-glycerol-3-phophate ABC transporter substrate-binding protein 260236 ugpB 3196154 ugpB Ruegeria pomeroyi DSS-3 SN-glycerol-3-phophate ABC transporter substrate-binding protein YP_165509.1 258851 R 246200 CDS YP_165510.1 56695163 3194549 260302..261231 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 261231 3194549 SPO0241 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165510.1 260302 D 246200 CDS YP_165511.1 56695164 3196253 complement(267660..269588) 1 NC_003911.11 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase 269588 dxs 3196253 dxs Ruegeria pomeroyi DSS-3 1-deoxy-D-xylulose-5-phosphate synthase YP_165511.1 267660 R 246200 CDS YP_165512.1 56695165 3196371 complement(269616..270482) 1 NC_003911.11 identified by similarity to GB:BAA96458.1; match to protein family HMM PF00348; farnesyl diphosphate synthase 270482 ispA 3196371 ispA Ruegeria pomeroyi DSS-3 farnesyl diphosphate synthase YP_165512.1 269616 R 246200 CDS YP_165513.1 56695166 3196276 complement(270485..270703) 1 NC_003911.11 identified by match to protein family HMM PF02609; match to protein family HMM TIGR01280; exodeoxyribonuclease VII small subunit 270703 xseB 3196276 xseB Ruegeria pomeroyi DSS-3 exodeoxyribonuclease VII small subunit YP_165513.1 270485 R 246200 CDS YP_165514.1 56695167 3196238 complement(270724..271650) 1 NC_003911.11 identified by match to protein family HMM PF00850; histone deacetylase 271650 3196238 SPO0250 Ruegeria pomeroyi DSS-3 histone deacetylase YP_165514.1 270724 R 246200 CDS YP_165515.1 56695168 3196152 complement(271676..272377) 1 NC_003911.11 identified by similarity to SP:P31079; match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator PetR 272377 petR 3196152 petR Ruegeria pomeroyi DSS-3 DNA-binding response regulator PetR YP_165515.1 271676 R 246200 CDS YP_165516.1 56695169 3195959 complement(272374..272886) 1 NC_003911.11 identified by similarity to SP:P31078; match to protein family HMM PF01047; transcriptional regulator PetP 272886 petP 3195959 petP Ruegeria pomeroyi DSS-3 transcriptional regulator PetP YP_165516.1 272374 R 246200 CDS YP_165517.1 56695170 3194036 273044..273910 1 NC_003911.11 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase 273910 ilvE 3194036 ilvE Ruegeria pomeroyi DSS-3 branched-chain amino acid aminotransferase YP_165517.1 273044 D 246200 CDS YP_165518.1 56695171 3196543 complement(273966..274406) 1 NC_003911.11 identified by similarity to GB:AAC38562.1; match to protein family HMM PF02566; organic hydroperoxide resistance protein 274406 ohr 3196543 ohr Ruegeria pomeroyi DSS-3 organic hydroperoxide resistance protein YP_165518.1 273966 R 246200 CDS YP_165519.1 56695172 3196321 274505..274942 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 274942 3196321 SPO0255 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_165519.1 274505 D 246200 CDS YP_165520.1 56695173 3194099 complement(274955..275284) 1 NC_003911.11 identified by match to protein family HMM PF00127; plastocyanin/azurin family copper binding protein 275284 3194099 SPO0256 Ruegeria pomeroyi DSS-3 plastocyanin/azurin family copper binding protein YP_165520.1 274955 R 246200 CDS YP_165521.1 56695174 3195225 complement(275275..275799) 1 NC_003911.11 identified by similarity to PIR:A96030; hypothetical protein 275799 3195225 SPO0257 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165521.1 275275 R 246200 CDS YP_165522.1 56695175 3195966 275937..276917 1 NC_003911.11 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 276917 3195966 SPO0258 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_165522.1 275937 D 246200 CDS YP_165523.1 56695176 3194001 276985..277395 1 NC_003911.11 identified by similarity to GB:CAE32384.1; hypothetical protein 277395 3194001 SPO0259 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165523.1 276985 D 246200 CDS YP_165524.1 56695177 3194912 277569..279137 1 NC_003911.11 identified by similarity to SP:P42251; match to protein family HMM PF00245; match to protein family HMM TIGR01409; alkaline phosphatase 279137 3194912 SPO0260 Ruegeria pomeroyi DSS-3 alkaline phosphatase YP_165524.1 277569 D 246200 CDS YP_165525.1 56695178 3196288 complement(279220..280086) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 280086 3196288 SPO0261 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165525.1 279220 R 246200 CDS YP_165526.1 56695179 3196500 complement(280092..280691) 1 NC_003911.11 identified by match to protein family HMM PF02572; match to protein family HMM TIGR00708; cob(I)alamin adenosyltransferase 280691 cobO 3196500 cobO Ruegeria pomeroyi DSS-3 cob(I)alamin adenosyltransferase YP_165526.1 280092 R 246200 CDS YP_165527.1 56695180 3192897 complement(280748..281791) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 281791 3192897 SPO0263 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165527.1 280748 R 246200 CDS YP_165528.1 56695181 3193993 281790..283121 1 NC_003911.11 identified by match to protein family HMM PF02515; CaiB/BaiF family protein 283121 3193993 SPO0264 Ruegeria pomeroyi DSS-3 CaiB/BaiF family protein YP_165528.1 281790 D 246200 CDS YP_165529.1 56695182 3193839 complement(283122..284063) 1 NC_003911.11 identified by similarity to GB:AAA99820.1; match to protein family HMM PF03547; auxin efflux carrier protein 284063 3193839 SPO0265 Ruegeria pomeroyi DSS-3 auxin efflux carrier protein YP_165529.1 283122 R 246200 CDS YP_165530.1 56695183 3196435 complement(284060..284764) 1 NC_003911.11 identified by match to protein family HMM PF01966; HD domain-containing protein 284764 3196435 SPO0266 Ruegeria pomeroyi DSS-3 HD domain-containing protein YP_165530.1 284060 R 246200 CDS YP_165531.1 56695184 3196504 complement(284706..285806) 1 NC_003911.11 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase 285806 aroC 3196504 aroC Ruegeria pomeroyi DSS-3 chorismate synthase YP_165531.1 284706 R 246200 CDS YP_165532.2 161598435 3195724 complement(285959..286399) 1 NC_003911.11 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not; riboflavin synthase subunit beta 286399 ribH-1 3195724 ribH-1 Ruegeria pomeroyi DSS-3 riboflavin synthase subunit beta YP_165532.2 285959 R 246200 CDS YP_165533.1 56695186 3195962 286691..287305 1 NC_003911.11 identified by match to protein family HMM PF04299; negative transcriptional regulator 287305 3195962 SPO0269 Ruegeria pomeroyi DSS-3 negative transcriptional regulator YP_165533.1 286691 D 246200 CDS YP_165534.1 56695187 3194841 287383..287994 1 NC_003911.11 identified by match to protein family HMM PF02798; glutathione S-transferase 287994 3194841 SPO0270 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_165534.1 287383 D 246200 CDS YP_165535.1 56695188 3196282 288197..288760 1 NC_003911.11 identified by match to protein family HMM PF00355; match to protein family HMM TIGR01409; match to protein family HMM TIGR01416; ubiquinol-cytochrome c reductase, iron-sulfur subunit 288760 petA 3196282 petA Ruegeria pomeroyi DSS-3 ubiquinol-cytochrome c reductase, iron-sulfur subunit YP_165535.1 288197 D 246200 CDS YP_165536.1 56695189 3195221 288773..290101 1 NC_003911.11 identified by similarity to SP:P05418; match to protein family HMM PF00032; match to protein family HMM PF00033; ubiquinol--cytochrome c reductase, cytochrome B 290101 petB 3195221 petB Ruegeria pomeroyi DSS-3 ubiquinol--cytochrome c reductase, cytochrome B YP_165536.1 288773 D 246200 CDS YP_165537.1 56695190 3194314 290120..290983 1 NC_003911.11 identified by similarity to SP:Q02760; match to protein family HMM PF02167; ubiquinol--cytochrome c reductase, cytochrome c1 290983 petC 3194314 petC Ruegeria pomeroyi DSS-3 ubiquinol--cytochrome c reductase, cytochrome c1 YP_165537.1 290120 D 246200 CDS YP_165538.1 56695191 3196540 291065..291460 1 NC_003911.11 identified by similarity to GB:BAC74098.1; hypothetical protein 291460 3196540 SPO0274 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165538.1 291065 D 246200 CDS YP_165539.1 56695192 3196491 291467..292033 1 NC_003911.11 identified by match to protein family HMM PF01292; cytochrome b 292033 3196491 SPO0275 Ruegeria pomeroyi DSS-3 cytochrome b YP_165539.1 291467 D 246200 CDS YP_165540.1 56695193 3196434 292054..292551 1 NC_003911.11 identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 292551 3196434 SPO0276 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_165540.1 292054 D 246200 CDS YP_165541.1 56695195 3196395 complement(292631..293887) 1 NC_003911.11 identified by match to protein family HMM PF00919; match to protein family HMM PF04055; match to protein family HMM TIGR00089; match to protein family HMM TIGR01579; MiaB-like tRNA modifying enzyme 293887 3196395 SPO0277 Ruegeria pomeroyi DSS-3 MiaB-like tRNA modifying enzyme YP_165541.1 292631 R 246200 CDS YP_165542.1 56695194 3196503 complement(293884..294693) 1 NC_003911.11 identified by similarity to SP:P08885; match to protein family HMM PF01678; match to protein family HMM TIGR00652; diaminopimelate epimerase 294693 dapF 3196503 dapF Ruegeria pomeroyi DSS-3 diaminopimelate epimerase YP_165542.1 293884 R 246200 CDS YP_165543.1 56698708 3196279 295170..295337 1 NC_003911.11 identified by similarity to GB:AAC43509.1; transposase, truncation 295337 3196279 SPO0280 Ruegeria pomeroyi DSS-3 transposase, truncation YP_165543.1 295170 D 246200 CDS YP_165544.1 56695196 3195726 complement(295450..295923) 1 NC_003911.11 identified by similarity to GB:BAC93558.1; hypothetical protein 295923 3195726 SPO0281 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165544.1 295450 R 246200 CDS YP_165545.1 56695197 3196323 complement(296104..296379) 1 NC_003911.11 hypothetical protein 296379 3196323 SPO0282 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165545.1 296104 R 246200 CDS YP_165546.1 56695198 3195725 complement(296376..296987) 1 NC_003911.11 identified by similarity to GB:CAE28560.1; match to protein family HMM PF02660; match to protein family HMM TIGR00023; hypothetical protein 296987 3195725 SPO0283 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165546.1 296376 R 246200 CDS YP_165547.1 56695199 3195702 complement(296987..298276) 1 NC_003911.11 identified by similarity to SP:P46538; match to protein family HMM PF01979; match to protein family HMM TIGR00857; dihydroorotase, multifunctional complex type 298276 3195702 SPO0284 Ruegeria pomeroyi DSS-3 dihydroorotase, multifunctional complex type YP_165547.1 296987 R 246200 CDS YP_165548.1 56695200 3193013 complement(298273..298659) 1 NC_003911.11 hypothetical protein 298659 3193013 SPO0285 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165548.1 298273 R 246200 CDS YP_165549.1 56695201 3194341 complement(298644..299168) 1 NC_003911.11 hypothetical protein 299168 3194341 SPO0286 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165549.1 298644 R 246200 CDS YP_165550.1 56695202 3196460 complement(299165..300100) 1 NC_003911.11 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase 300100 pyrB 3196460 pyrB Ruegeria pomeroyi DSS-3 aspartate carbamoyltransferase YP_165550.1 299165 R 246200 CDS YP_165551.1 56695203 3196228 300846..301631 1 NC_003911.11 identified by similarity to GB:CAD29336.1; match to protein family HMM PF03167; match to protein family HMM TIGR00758; uracil-DNA glycosylase 301631 udgA 3196228 udgA Ruegeria pomeroyi DSS-3 uracil-DNA glycosylase YP_165551.1 300846 D 246200 CDS YP_165552.1 56695204 3196135 301631..302230 1 NC_003911.11 identified by match to protein family HMM PF00149; Ser/Thr protein phosphatase 302230 3196135 SPO0289 Ruegeria pomeroyi DSS-3 Ser/Thr protein phosphatase YP_165552.1 301631 D 246200 CDS YP_165553.1 56695205 3195828 302227..302847 1 NC_003911.11 identified by match to protein family HMM PF01810; transmembrane amino acid efflux protein 302847 3195828 SPO0290 Ruegeria pomeroyi DSS-3 transmembrane amino acid efflux protein YP_165553.1 302227 D 246200 CDS YP_165554.1 56695206 3196337 302852..303394 1 NC_003911.11 identified by similarity to SP:P30746; match to protein family HMM PF00994; match to protein family HMM TIGR00177; molybdenum cofactor biosynthesis protein B 303394 3196337 SPO0291 Ruegeria pomeroyi DSS-3 molybdenum cofactor biosynthesis protein B YP_165554.1 302852 D 246200 CDS YP_165555.1 56695207 3193281 303491..304948 1 NC_003911.11 identified by match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 304948 3193281 SPO0292 Ruegeria pomeroyi DSS-3 RND family efflux transporter MFP subunit YP_165555.1 303491 D 246200 CDS YP_165556.1 56695208 3194582 304955..308356 1 NC_003911.11 identified by match to protein family HMM PF00873; AcrB/AcrD/AcrF family transporter 308356 3194582 SPO0293 Ruegeria pomeroyi DSS-3 AcrB/AcrD/AcrF family transporter YP_165556.1 304955 D 246200 CDS YP_165557.1 56695209 3196361 complement(308364..308783) 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX family hydrolase 308783 3196361 SPO0294 Ruegeria pomeroyi DSS-3 NUDIX family hydrolase YP_165557.1 308364 R 246200 CDS YP_165558.1 56695210 3193762 complement(308787..309605) 1 NC_003911.11 identified by similarity to GB:BAC46756.1; hypothetical protein 309605 3193762 SPO0295 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165558.1 308787 R 246200 CDS YP_165559.1 56695211 3195560 309710..310294 1 NC_003911.11 identified by similarity to GB:BAC46757.1; match to protein family HMM PF02622; hypothetical protein 310294 3195560 SPO0296 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165559.1 309710 D 246200 CDS YP_165560.1 56695212 3193859 complement(310446..311396) 1 NC_003911.11 identified by match to protein family HMM PF01300; match to protein family HMM PF03481; match to protein family HMM TIGR00057; Sua5/YciO/YrdC family protein 311396 3193859 SPO0297 Ruegeria pomeroyi DSS-3 Sua5/YciO/YrdC family protein YP_165560.1 310446 R 246200 CDS YP_165561.1 56695213 3193203 311525..313228 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 313228 3193203 SPO0298 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_165561.1 311525 D 246200 CDS YP_165562.1 56695214 3193047 313225..314274 1 NC_003911.11 identified by match to protein family HMM PF00753; metallo-beta-lactamase 314274 3193047 SPO0299 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_165562.1 313225 D 246200 CDS YP_165563.1 56695215 3196352 314278..314733 1 NC_003911.11 hypothetical protein 314733 3196352 SPO0300 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165563.1 314278 D 246200 CDS YP_165564.1 56695216 3196120 314804..316648 1 NC_003911.11 identified by match to protein family HMM PF03009; glycerophosphoryl diester phosphodiesterase 316648 3196120 SPO0301 Ruegeria pomeroyi DSS-3 glycerophosphoryl diester phosphodiesterase YP_165564.1 314804 D 246200 CDS YP_165565.1 56695217 3194544 316617..317195 1 NC_003911.11 identified by similarity to GB:CAE78911.1; hypothetical protein 317195 3194544 SPO0302 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165565.1 316617 D 246200 CDS YP_165566.1 56695218 3196055 317258..317392 1 NC_003911.11 cytochrome c oxidase subunit IV 317392 3196055 SPO0303 Ruegeria pomeroyi DSS-3 cytochrome c oxidase subunit IV YP_165566.1 317258 D 246200 CDS YP_165567.1 56695219 3193909 317412..318029 1 NC_003911.11 lipoprotein 318029 3193909 SPO0304 Ruegeria pomeroyi DSS-3 lipoprotein YP_165567.1 317412 D 246200 CDS YP_165568.1 56695220 3193808 complement(318368..319084) 1 NC_003911.11 identified by match to protein family HMM PF03591; AzlC family protein 319084 3193808 SPO0305 Ruegeria pomeroyi DSS-3 AzlC family protein YP_165568.1 318368 R 246200 CDS YP_165569.1 56695221 3192759 319140..320021 1 NC_003911.11 identified by match to protein family HMM PF02634; match to protein family HMM TIGR00129; formate dehydrogenase accessory protein FdhD 320021 fdhD 3192759 fdhD Ruegeria pomeroyi DSS-3 formate dehydrogenase accessory protein FdhD YP_165569.1 319140 D 246200 CDS YP_165570.1 56695222 3193793 320619..321254 1 NC_003911.11 in Escherichia coli MobA links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide during molybdenum cofactor biosynthesis; molybdopterin-guanine dinucleotide biosynthesis protein MobA 321254 mobA 3193793 mobA Ruegeria pomeroyi DSS-3 molybdopterin-guanine dinucleotide biosynthesis protein MobA YP_165570.1 320619 D 246200 CDS YP_165571.1 56695223 3193692 321251..321742 1 NC_003911.11 identified by similarity to SP:P32125; match to protein family HMM PF03205; match to protein family HMM TIGR00176; molybdopterin-guanine dinucleotide biosynthesis protein B 321742 mobB 3193692 mobB Ruegeria pomeroyi DSS-3 molybdopterin-guanine dinucleotide biosynthesis protein B YP_165571.1 321251 D 246200 CDS YP_165572.1 56695224 3192816 321739..322539 1 NC_003911.11 identified by similarity to GB:AAK23994.1; hypothetical protein 322539 3192816 SPO0309 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165572.1 321739 D 246200 CDS YP_165573.1 56695225 3194185 322536..323795 1 NC_003911.11 is involved in the formation of active molybdenum cofactor and the chelation of molybdenum; molybdopterin biosynthesis protein MoeA 323795 moeA 3194185 moeA Ruegeria pomeroyi DSS-3 molybdopterin biosynthesis protein MoeA YP_165573.1 322536 D 246200 CDS YP_165574.1 56695226 3194146 complement(323819..324826) 1 NC_003911.11 hypothetical protein 324826 3194146 SPO0311 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165574.1 323819 R 246200 CDS YP_165575.1 56695227 3194600 complement(324840..325310) 1 NC_003911.11 necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus; transcription elongation factor GreA 325310 greA 3194600 greA Ruegeria pomeroyi DSS-3 transcription elongation factor GreA YP_165575.1 324840 R 246200 CDS YP_165576.1 56695228 3194049 complement(325446..325826) 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 325826 3194049 SPO0313 Ruegeria pomeroyi DSS-3 glyoxalase YP_165576.1 325446 R 246200 CDS YP_165577.1 56695229 3194247 325911..326366 1 NC_003911.11 identified by match to protein family HMM PF00376; match to protein family HMM TIGR01950; redox-sensitive transcriptional activator SoxR 326366 soxR 3194247 soxR Ruegeria pomeroyi DSS-3 redox-sensitive transcriptional activator SoxR YP_165577.1 325911 D 246200 CDS YP_165578.1 56695230 3194162 complement(326374..326682) 1 NC_003911.11 identified by similarity to GB:AAM41091.1; match to protein family HMM TIGR02118; hypothetical protein 326682 3194162 SPO0315 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165578.1 326374 R 246200 CDS YP_165579.1 56695231 3192928 326914..328560 1 NC_003911.11 identified by similarity to SP:Q16134; match to protein family HMM PF05187; electrotransfer ubiquinone oxidoreductase 328560 3192928 SPO0316 Ruegeria pomeroyi DSS-3 electrotransfer ubiquinone oxidoreductase YP_165579.1 326914 D 246200 CDS YP_165580.1 56695232 3195165 328606..330441 1 NC_003911.11 identified by similarity to GB:CAE26481.1; match to protein family HMM PF00515; hypothetical protein 330441 3195165 SPO0317 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165580.1 328606 D 246200 CDS YP_165581.1 56695233 3193014 330431..331270 1 NC_003911.11 identified by match to protein family HMM PF00288; match to protein family HMM TIGR00154; 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 331270 ispE 3193014 ispE Ruegeria pomeroyi DSS-3 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase YP_165581.1 330431 D 246200 CDS YP_165582.1 56695234 3194982 complement(331351..332349) 1 NC_003911.11 identified by similarity to GB:CAD24417.1; match to protein family HMM PF00348; decaprenyl diphosphate synthase 332349 ddsA 3194982 ddsA Ruegeria pomeroyi DSS-3 decaprenyl diphosphate synthase YP_165582.1 331351 R 246200 CDS YP_165583.1 56695235 3192970 332406..332621 1 NC_003911.11 identified by similarity to GB:CAC45419.1; hypothetical protein 332621 3192970 SPO0320 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165583.1 332406 D 246200 CDS YP_165584.1 56695236 3193164 332618..333391 1 NC_003911.11 identified by similarity to GB:CAD24416.1; hypothetical protein 333391 3193164 SPO0321 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165584.1 332618 D 246200 CDS YP_165585.1 56695237 3193178 333505..333669 1 NC_003911.11 identified by similarity to PIR:AE3289; match to protein family HMM PF04325; hypothetical protein 333669 3193178 SPO0322 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165585.1 333505 D 246200 CDS YP_165586.1 56695238 3193016 complement(333666..334532) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 334532 3193016 SPO0323 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165586.1 333666 R 246200 CDS YP_165587.1 56695239 3194175 complement(334529..335476) 1 NC_003911.11 Glycine cleavage system transcriptional activator; activates the gcvTHP operon in the presence of glycine and represses the operon in its absence; DNA-binding transcriptional activator GcvA 335476 3194175 SPO0324 Ruegeria pomeroyi DSS-3 DNA-binding transcriptional activator GcvA YP_165587.1 334529 R 246200 CDS YP_165588.1 56695240 3193146 complement(335827..336549) 1 NC_003911.11 identified by similarity to SP:P23238; match to protein family HMM PF00106; match to protein family HMM TIGR01829; acetoacetyl-CoA reductase 336549 phbB 3193146 phbB Ruegeria pomeroyi DSS-3 acetoacetyl-CoA reductase YP_165588.1 335827 R 246200 CDS YP_165589.1 56695241 3194058 complement(336736..337911) 1 NC_003911.11 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; in Rhizobia and Ralstonia is involved in PHB biosynthesis; acetyl-CoA acetyltransferase 337911 phbA 3194058 phbA Ruegeria pomeroyi DSS-3 acetyl-CoA acetyltransferase YP_165589.1 336736 R 246200 CDS YP_165590.1 56695242 3195449 complement(338082..338921) 1 NC_003911.11 identified by match to protein family HMM PF00563; diguanylate phosphodiesterase 338921 3195449 SPO0327 Ruegeria pomeroyi DSS-3 diguanylate phosphodiesterase YP_165590.1 338082 R 246200 CDS YP_165591.1 56695243 3192694 complement(339136..340068) 1 NC_003911.11 identified by similarity to GB:BAB48523.1; hypothetical protein 340068 3192694 SPO0328 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165591.1 339136 R 246200 CDS YP_165592.1 56695244 3193423 complement(340065..340484) 1 NC_003911.11 hypothetical protein 340484 3193423 SPO0329 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165592.1 340065 R 246200 CDS YP_165593.1 56695245 3195929 340918..341967 1 NC_003911.11 identified by similarity to SP:P14532; match to protein family HMM PF03150; cytochrome c peroxidase 341967 ccpA 3195929 ccpA Ruegeria pomeroyi DSS-3 cytochrome c peroxidase YP_165593.1 340918 D 246200 CDS YP_165594.1 56695246 3194061 complement(342014..342577) 1 NC_003911.11 identified by similarity to SP:P43221; thiol:disulfide interchange protein 342577 3194061 SPO0331 Ruegeria pomeroyi DSS-3 thiol:disulfide interchange protein YP_165594.1 342014 R 246200 CDS YP_165595.1 56695247 3196544 342602..343993 1 NC_003911.11 catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase 343993 argH 3196544 argH Ruegeria pomeroyi DSS-3 argininosuccinate lyase YP_165595.1 342602 D 246200 CDS YP_165596.1 56695248 3196542 343990..344172 1 NC_003911.11 lipoprotein 344172 3196542 SPO0333 Ruegeria pomeroyi DSS-3 lipoprotein YP_165596.1 343990 D 246200 CDS YP_165597.1 56695249 3195501 344379..345644 1 NC_003911.11 identified by match to protein family HMM PF00278; match to protein family HMM PF02784; match to protein family HMM TIGR01048; diaminopimelate decarboxylase 345644 lysA 3195501 lysA Ruegeria pomeroyi DSS-3 diaminopimelate decarboxylase YP_165597.1 344379 D 246200 CDS YP_165598.1 56695250 3196168 345684..348242 1 NC_003911.11 hypothetical protein 348242 3196168 SPO0335 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165598.1 345684 D 246200 CDS YP_165599.1 56695251 3196186 complement(348262..349101) 1 NC_003911.11 identified by match to protein family HMM TIGR02098; hypothetical protein 349101 3196186 SPO0336 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165599.1 348262 R 246200 CDS YP_165600.1 56695252 3196289 349240..349971 1 NC_003911.11 identified by similarity to SP:P10115; match to protein family HMM PF00005; cell division ATP-binding protein FtsE 349971 ftsE 3196289 ftsE Ruegeria pomeroyi DSS-3 cell division ATP-binding protein FtsE YP_165600.1 349240 D 246200 CDS YP_165601.1 56695253 3196209 349968..350867 1 NC_003911.11 identified by match to protein family HMM PF02687; cell division permease FtsX 350867 3196209 SPO0338 Ruegeria pomeroyi DSS-3 cell division permease FtsX YP_165601.1 349968 D 246200 CDS YP_165602.1 56695254 3196208 350864..351595 1 NC_003911.11 identified by match to protein family HMM PF01553; acyltransferase 351595 3196208 SPO0339 Ruegeria pomeroyi DSS-3 acyltransferase YP_165602.1 350864 D 246200 CDS YP_165603.1 56695257 3196204 complement(351721..353109) 1 NC_003911.11 identified by match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM TIGR01350; 2-oxoglutarate dehydrogenase E3 353109 lpdA 3196204 lpdA Ruegeria pomeroyi DSS-3 2-oxoglutarate dehydrogenase E3 YP_165603.1 351721 R 246200 CDS YP_165604.1 56695256 3196182 353124..353468 1 NC_003911.11 hypothetical protein 353468 3196182 SPO0341 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165604.1 353124 D 246200 CDS YP_165605.1 56695255 3196194 complement(353181..353450) 1 NC_003911.11 hypothetical protein 353450 3196194 SPO0342 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165605.1 353181 R 246200 CDS YP_165606.1 56695258 3196189 complement(353635..354831) 1 NC_003911.11 component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA; dihydrolipoamide succinyltransferase 354831 sucB 3196189 sucB Ruegeria pomeroyi DSS-3 dihydrolipoamide succinyltransferase YP_165606.1 353635 R 246200 CDS YP_165607.1 56695259 3196406 complement(355147..358104) 1 NC_003911.11 SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide; 2-oxoglutarate dehydrogenase E1 358104 sucA 3196406 sucA Ruegeria pomeroyi DSS-3 2-oxoglutarate dehydrogenase E1 YP_165607.1 355147 R 246200 CDS YP_165608.1 56695260 3196205 complement(358880..359431) 1 NC_003911.11 identified by similarity to GB:AAN82305.1; match to protein family HMM PF05656; hypothetical protein 359431 3196205 SPO0345 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165608.1 358880 R 246200 CDS YP_165609.1 56695261 3196431 complement(359481..360365) 1 NC_003911.11 identified by similarity to SP:P07459; match to protein family HMM PF00549; match to protein family HMM PF02629; match to protein family HMM TIGR01019; succinyl-CoA synthase subunit alpha 360365 sucD 3196431 sucD Ruegeria pomeroyi DSS-3 succinyl-CoA synthase subunit alpha YP_165609.1 359481 R 246200 CDS YP_165610.1 56695262 3196412 complement(360913..362106) 1 NC_003911.11 catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta 362106 sucC 3196412 sucC Ruegeria pomeroyi DSS-3 succinyl-CoA synthetase subunit beta YP_165610.1 360913 R 246200 CDS YP_165611.1 56695263 3196422 362383..363507 1 NC_003911.11 hypothetical protein 363507 3196422 SPO0348 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165611.1 362383 D 246200 CDS YP_165612.1 56695264 3196445 complement(363558..364520) 1 NC_003911.11 Catalyzes the reversible oxidation of malate to oxaloacetate; malate dehydrogenase 364520 mdh 3196445 mdh Ruegeria pomeroyi DSS-3 malate dehydrogenase YP_165612.1 363558 R 246200 CDS YP_165613.1 56695265 3196429 364683..365438 1 NC_003911.11 identified by match to protein family HMM PF01925; hypothetical protein 365438 3196429 SPO0350 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165613.1 364683 D 246200 CDS YP_165614.1 56695266 3196453 complement(365521..365835) 1 NC_003911.11 identified by similarity to GB:CAC45660.1; hypothetical protein 365835 3196453 SPO0351 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165614.1 365521 R 246200 CDS YP_165615.1 56695267 3196439 366147..367004 1 NC_003911.11 identified by similarity to SP:P77770; citrate lyase subunit beta 367004 citE 3196439 citE Ruegeria pomeroyi DSS-3 citrate lyase subunit beta YP_165615.1 366147 D 246200 CDS YP_165616.1 56695268 3196459 367011..367565 1 NC_003911.11 identified by match to protein family HMM PF07298; NnrU family protein 367565 3196459 SPO0353 Ruegeria pomeroyi DSS-3 NnrU family protein YP_165616.1 367011 D 246200 CDS YP_165617.1 56695269 3196257 367576..367782 1 NC_003911.11 identified by similarity to PIR:AE3561; hypothetical protein 367782 3196257 SPO0354 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165617.1 367576 D 246200 CDS YP_165618.1 56695270 3196452 367782..368810 1 NC_003911.11 identified by similarity to GB:AAK25618.1; hypothetical protein 368810 3196452 SPO0355 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165618.1 367782 D 246200 CDS YP_165619.1 56695271 3196463 368789..369547 1 NC_003911.11 identified by similarity to GB:BAC61369.1; hypothetical protein 369547 3196463 SPO0356 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165619.1 368789 D 246200 CDS YP_165620.1 56695272 3196456 369582..370244 1 NC_003911.11 identified by match to protein family HMM PF00092; von Willebrand factor A 370244 3196456 SPO0357 Ruegeria pomeroyi DSS-3 von Willebrand factor A YP_165620.1 369582 D 246200 CDS YP_165621.1 56695273 3196468 370463..370849 1 NC_003911.11 identified by match to protein family HMM PF01127; succinate dehydrogenase, cytochrome b556 subunit 370849 sdhC 3196468 sdhC Ruegeria pomeroyi DSS-3 succinate dehydrogenase, cytochrome b556 subunit YP_165621.1 370463 D 246200 CDS YP_165622.1 56695274 3196461 370862..371233 1 NC_003911.11 identified by similarity to GB:AAC17941.1; succinate dehydrogenase, hydrophobic membrane anchor protein 371233 sdhD 3196461 sdhD Ruegeria pomeroyi DSS-3 succinate dehydrogenase, hydrophobic membrane anchor protein YP_165622.1 370862 D 246200 CDS YP_165623.1 56695275 3196466 371250..373055 1 NC_003911.11 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; succinate dehydrogenase flavoprotein subunit 373055 sdhA 3196466 sdhA Ruegeria pomeroyi DSS-3 succinate dehydrogenase flavoprotein subunit YP_165623.1 371250 D 246200 CDS YP_165624.1 56695276 3196472 373340..374119 1 NC_003911.11 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase; succinate dehydrogenase iron-sulfur subunit 374119 sdhB 3196472 sdhB Ruegeria pomeroyi DSS-3 succinate dehydrogenase iron-sulfur subunit YP_165624.1 373340 D 246200 CDS YP_165625.1 56695277 3196478 374164..376323 1 NC_003911.11 identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 376323 3196478 SPO0362 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_165625.1 374164 D 246200 CDS YP_165626.1 56695278 3196486 376576..376791 1 NC_003911.11 hypothetical protein 376791 3196486 SPO0363 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165626.1 376576 D 246200 CDS YP_165627.1 56695279 3196498 377206..378387 1 NC_003911.11 identified by match to protein family HMM PF00278; match to protein family HMM PF02784; decarboxylase, pyridoxal-dependent 378387 3196498 SPO0364 Ruegeria pomeroyi DSS-3 decarboxylase, pyridoxal-dependent YP_165627.1 377206 D 246200 CDS YP_165628.1 56695280 3196506 378468..379325 1 NC_003911.11 identified by similarity to PIR:G97525; hypothetical protein 379325 3196506 SPO0365 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165628.1 378468 D 246200 CDS YP_165629.1 56695281 3196509 complement(379410..380120) 1 NC_003911.11 catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate; purine nucleoside phosphorylase 380120 deoD 3196509 deoD Ruegeria pomeroyi DSS-3 purine nucleoside phosphorylase YP_165629.1 379410 R 246200 CDS YP_165630.1 56695282 3196512 complement(380136..380453) 1 NC_003911.11 identified by match to protein family HMM PF00816; H-NS family DNA-binding protein 380453 3196512 SPO0367 Ruegeria pomeroyi DSS-3 H-NS family DNA-binding protein YP_165630.1 380136 R 246200 CDS YP_165631.1 56695283 3196514 complement(380565..382565) 1 NC_003911.11 identified by similarity to SP:Q49115; match to protein family HMM PF01642; match to protein family HMM PF02310; match to protein family HMM TIGR00640; match to protein family HMM TIGR00641; methylmalonyl-CoA mutase 382565 3196514 SPO0368 Ruegeria pomeroyi DSS-3 methylmalonyl-CoA mutase YP_165631.1 380565 R 246200 CDS YP_165632.1 56695284 3196523 382532..384115 1 NC_003911.11 identified by similarity to SP:P00482; match to protein family HMM PF01553; acyltransferase 384115 3196523 SPO0369 Ruegeria pomeroyi DSS-3 acyltransferase YP_165632.1 382532 D 246200 CDS YP_165633.1 56695285 3196525 384226..385512 1 NC_003911.11 identified by match to protein family HMM PF00107; match to protein family HMM TIGR01751; crotonyl-CoA reductase 385512 ccrA 3196525 ccrA Ruegeria pomeroyi DSS-3 crotonyl-CoA reductase YP_165633.1 384226 D 246200 CDS YP_165634.1 56695286 3196532 385883..386602 1 NC_003911.11 identified by match to protein family HMM PF00196; match to protein family HMM PF03472; LuxR family transcriptional regulator 386602 luxR-1 3196532 luxR-1 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_165634.1 385883 D 246200 CDS YP_165635.1 56695287 3196537 386685..387323 1 NC_003911.11 identified by match to protein family HMM PF00765; autoinducer synthesis protein 387323 3196537 SPO0372 Ruegeria pomeroyi DSS-3 autoinducer synthesis protein YP_165635.1 386685 D 246200 CDS YP_165636.1 56695288 3196397 387521..388918 1 NC_003911.11 helicase, ATP-dependent 388918 3196397 SPO0373 Ruegeria pomeroyi DSS-3 helicase, ATP-dependent YP_165636.1 387521 D 246200 CDS YP_165637.1 56695289 3196206 complement(389073..389870) 1 NC_003911.11 identified by similarity to GB:CAE26256.1; hypothetical protein 389870 3196206 SPO0374 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165637.1 389073 R 246200 CDS YP_165638.1 56695290 3196372 complement(389848..390798) 1 NC_003911.11 identified by match to protein family HMM PF01925; hypothetical protein 390798 3196372 SPO0375 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165638.1 389848 R 246200 CDS YP_165639.1 56695291 3194229 complement(390860..391828) 1 NC_003911.11 identified by match to protein family HMM PF02653; sugar ABC transporter permease 391828 3194229 SPO0376 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_165639.1 390860 R 246200 CDS YP_165640.1 56695292 3194004 complement(391825..392919) 1 NC_003911.11 identified by match to protein family HMM PF02653; sugar ABC transporter permease 392919 3194004 SPO0377 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_165640.1 391825 R 246200 CDS YP_165641.1 56695293 3192747 complement(392919..394448) 1 NC_003911.11 identified by match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein 394448 3192747 SPO0378 Ruegeria pomeroyi DSS-3 sugar ABC transporter ATP-binding protein YP_165641.1 392919 R 246200 CDS YP_165642.1 56695294 3196193 complement(394572..395570) 1 NC_003911.11 identified by match to protein family HMM PF02608; sugar ABC transporter periplasmic sugar-binding protein 395570 3196193 SPO0379 Ruegeria pomeroyi DSS-3 sugar ABC transporter periplasmic sugar-binding protein YP_165642.1 394572 R 246200 CDS YP_165643.1 56695295 3195351 complement(395729..396142) 1 NC_003911.11 identified by similarity to SP:P09453; match to protein family HMM PF00583; ribosomal-protein-alanine acetyltransferase 396142 3195351 SPO0380 Ruegeria pomeroyi DSS-3 ribosomal-protein-alanine acetyltransferase YP_165643.1 395729 R 246200 CDS YP_165644.1 56695296 3194018 complement(396139..396729) 1 NC_003911.11 identified by match to protein family HMM PF00814; protease 396729 3194018 SPO0381 Ruegeria pomeroyi DSS-3 protease YP_165644.1 396139 R 246200 CDS YP_165645.1 56695297 3196136 complement(396719..397282) 1 NC_003911.11 identified by match to protein family HMM PF01106; NifU domain-containing protein 397282 3196136 SPO0382 Ruegeria pomeroyi DSS-3 NifU domain-containing protein YP_165645.1 396719 R 246200 CDS YP_165646.1 56695298 3196394 complement(397406..398020) 1 NC_003911.11 identified by similarity to SP:P41407; match to protein family HMM PF02525; ACP phosphodieterase 398020 3196394 SPO0383 Ruegeria pomeroyi DSS-3 ACP phosphodieterase YP_165646.1 397406 R 246200 CDS YP_165647.1 56695299 3194611 398149..398739 1 NC_003911.11 identified by similarity to GB:BAC89223.1; match to protein family HMM PF07336; hypothetical protein 398739 3194611 SPO0384 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165647.1 398149 D 246200 CDS YP_165648.1 56695300 3196516 complement(398793..399386) 1 NC_003911.11 identified by match to protein family HMM PF01323; 2-hydroxychromene-2-carboxylate isomerase 399386 3196516 SPO0385 Ruegeria pomeroyi DSS-3 2-hydroxychromene-2-carboxylate isomerase YP_165648.1 398793 R 246200 CDS YP_165649.1 56695301 3196363 complement(399394..399864) 1 NC_003911.11 identified by match to protein family HMM PF00582; universal stress family protein 399864 3196363 SPO0386 Ruegeria pomeroyi DSS-3 universal stress family protein YP_165649.1 399394 R 246200 CDS YP_165650.1 56695302 3196034 complement(399889..400953) 1 NC_003911.11 hypothetical protein 400953 3196034 SPO0387 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165650.1 399889 R 246200 CDS YP_165651.1 56695303 3192972 complement(400950..401813) 1 NC_003911.11 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; aminotransferase 401813 3192972 SPO0388 Ruegeria pomeroyi DSS-3 aminotransferase YP_165651.1 400950 R 246200 CDS YP_165652.1 56695304 3196281 complement(401873..402334) 1 NC_003911.11 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 402334 3196281 SPO0389 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_165652.1 401873 R 246200 CDS YP_165653.1 56695305 3195417 402464..403513 1 NC_003911.11 identified by match to protein family HMM PF00208; match to protein family HMM PF02812; glutamate/leucine/phenylalanine/valine dehydrogenase 403513 3195417 SPO0390 Ruegeria pomeroyi DSS-3 glutamate/leucine/phenylalanine/valine dehydrogenase YP_165653.1 402464 D 246200 CDS YP_165654.1 56695306 3196315 complement(403532..404017) 1 NC_003911.11 identified by similarity to SP:P47233; match to protein family HMM PF00903; biphenyl-2,3-diol 1,2-dioxygenase III 404017 bphC3 3196315 bphC3 Ruegeria pomeroyi DSS-3 biphenyl-2,3-diol 1,2-dioxygenase III YP_165654.1 403532 R 246200 CDS YP_165655.1 56695307 3196317 complement(404139..405155) 1 NC_003911.11 catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; tryptophanyl-tRNA synthetase 405155 trpS 3196317 trpS Ruegeria pomeroyi DSS-3 tryptophanyl-tRNA synthetase YP_165655.1 404139 R 246200 CDS YP_165656.1 56695308 3196163 405115..405927 1 NC_003911.11 identified by match to protein family HMM PF01694; rhomboid family protein 405927 3196163 SPO0393 Ruegeria pomeroyi DSS-3 rhomboid family protein YP_165656.1 405115 D 246200 CDS YP_165657.1 56695309 3196232 complement(405948..406139) 1 NC_003911.11 identified by similarity to GB:CAE09894.1; hypothetical protein 406139 3196232 SPO0394 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165657.1 405948 R 246200 CDS YP_165658.1 56695310 3196147 complement(406211..406795) 1 NC_003911.11 identified by match to protein family HMM PF00027; cyclic nucleotide-binding protein 406795 3196147 SPO0395 Ruegeria pomeroyi DSS-3 cyclic nucleotide-binding protein YP_165658.1 406211 R 246200 CDS YP_165659.1 56695311 3193673 complement(406792..408333) 1 NC_003911.11 identified by similarity to SP:O05467; match to protein family HMM PF03023; match to protein family HMM TIGR01695; integral membrane protein MviN 408333 mviN 3193673 mviN Ruegeria pomeroyi DSS-3 integral membrane protein MviN YP_165659.1 406792 R 246200 CDS YP_165660.1 56695312 3195406 complement(408330..411056) 1 NC_003911.11 catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein; PII uridylyl-transferase 411056 glnD 3195406 glnD Ruegeria pomeroyi DSS-3 PII uridylyl-transferase YP_165660.1 408330 R 246200 CDS YP_165661.1 56695313 3196178 complement(411124..412299) 1 NC_003911.11 identified by similarity to GB:BAC45936.1; hypothetical protein 412299 3196178 SPO0398 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165661.1 411124 R 246200 CDS YP_165662.1 56695314 3195371 412384..413241 1 NC_003911.11 identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096; tetrapyrrole methylase 413241 3195371 SPO0399 Ruegeria pomeroyi DSS-3 tetrapyrrole methylase YP_165662.1 412384 D 246200 CDS YP_165663.1 56695315 3195920 413243..413614 1 NC_003911.11 identified by similarity to GB:AAN66948.1; match to protein family HMM PF02021; hypothetical protein 413614 3195920 SPO0400 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165663.1 413243 D 246200 CDS YP_165664.1 56695316 3196266 413677..414609 1 NC_003911.11 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione; glutathione synthetase 414609 gshB 3196266 gshB Ruegeria pomeroyi DSS-3 glutathione synthetase YP_165664.1 413677 D 246200 CDS YP_165665.1 56695317 3196310 complement(414677..416191) 1 NC_003911.11 identified by similarity to SP:P45049; match to protein family HMM PF01078; match to protein family HMM TIGR00368; competence protein ComM 416191 comM 3196310 comM Ruegeria pomeroyi DSS-3 competence protein ComM YP_165665.1 414677 R 246200 CDS YP_165666.1 56695318 3196259 complement(416250..417134) 1 NC_003911.11 identified by similarity to GB:CAD13614.1; hypothetical protein 417134 3196259 SPO0403 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165666.1 416250 R 246200 CDS YP_165667.1 56695319 3196408 complement(417186..417764) 1 NC_003911.11 identified by match to protein family HMM PF00300; phosphoglycerate mutase 417764 3196408 SPO0404 Ruegeria pomeroyi DSS-3 phosphoglycerate mutase YP_165667.1 417186 R 246200 CDS YP_165668.1 56695320 3196251 complement(417761..418285) 1 NC_003911.11 identified by match to protein family HMM PF02283; cobinamide kinase/cobinamide phosphate guanyltransferase 418285 3196251 SPO0405 Ruegeria pomeroyi DSS-3 cobinamide kinase/cobinamide phosphate guanyltransferase YP_165668.1 417761 R 246200 CDS YP_165669.1 56695321 3196326 418384..419262 1 NC_003911.11 binds with the catalytic core of RNA polymerase to produce the holoenzyme; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma-32 is responsible for the expression of heat shock promoters; there are paralogs in Rhizobium and Sinorhizobium; the proteins in this cluster act as secondary heat shock sigma factors; the Rhizobium sigma-32 factor may also be involved in exopolysaccharide production; RNA polymerase factor sigma-32 419262 rpoH2 3196326 rpoH2 Ruegeria pomeroyi DSS-3 RNA polymerase factor sigma-32 YP_165669.1 418384 D 246200 CDS YP_165670.1 56695322 3196229 419259..420083 1 NC_003911.11 identified by similarity to PIR:E83058; hypothetical protein 420083 3196229 SPO0407 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165670.1 419259 D 246200 CDS YP_165671.1 56695323 3196298 420163..421359 1 NC_003911.11 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine; bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase 421359 coaBC 3196298 coaBC Ruegeria pomeroyi DSS-3 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase YP_165671.1 420163 D 246200 CDS YP_165672.1 56695324 3196171 421423..421878 1 NC_003911.11 catalyzes the formation of dUMP from dUTP; deoxyuridine 5'-triphosphate nucleotidohydrolase 421878 dut 3196171 dut Ruegeria pomeroyi DSS-3 deoxyuridine 5'-triphosphate nucleotidohydrolase YP_165672.1 421423 D 246200 CDS YP_165673.1 56695325 3196134 421878..422918 1 NC_003911.11 identified by match to protein family HMM PF00899; match to protein family HMM PF05237; molybdopterin biosynthesis protein MoeB 422918 3196134 SPO0410 Ruegeria pomeroyi DSS-3 molybdopterin biosynthesis protein MoeB YP_165673.1 421878 D 246200 CDS YP_165674.1 56695326 3193668 422854..423549 1 NC_003911.11 hypothetical protein 423549 3193668 SPO0411 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165674.1 422854 D 246200 CDS YP_165675.1 56695327 3196398 complement(423669..424136) 1 NC_003911.11 hypothetical protein 424136 3196398 SPO0412 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165675.1 423669 R 246200 CDS YP_165676.1 56695328 3196400 complement(424229..425440) 1 NC_003911.11 identified by match to protein family HMM PF01053; Cys/Met metabolism PLP-dependent enzyme family protein 425440 3196400 SPO0413 Ruegeria pomeroyi DSS-3 Cys/Met metabolism PLP-dependent enzyme family protein YP_165676.1 424229 R 246200 CDS YP_165677.1 56695329 3196255 425562..427577 1 NC_003911.11 identified by similarity to SP:P27236; match to protein family HMM PF01432; peptidyl-dipeptidase 427577 3196255 SPO0414 Ruegeria pomeroyi DSS-3 peptidyl-dipeptidase YP_165677.1 425562 D 246200 CDS YP_165678.1 56695330 3196539 complement(427642..428589) 1 NC_003911.11 identified by match to protein family HMM PF02826; D-isomer specific 2-hydroxyacid dehydrogenase 428589 3196539 SPO0415 Ruegeria pomeroyi DSS-3 D-isomer specific 2-hydroxyacid dehydrogenase YP_165678.1 427642 R 246200 CDS YP_165679.1 56695331 3195922 complement(428594..429733) 1 NC_003911.11 identified by similarity to SP:P15035; match to protein family HMM PF01098; match to protein family HMM TIGR02210; rod shape-determining protein MreD 429733 mreD 3195922 mreD Ruegeria pomeroyi DSS-3 rod shape-determining protein MreD YP_165679.1 428594 R 246200 CDS YP_165680.1 56695332 3196071 complement(429730..431676) 1 NC_003911.11 identified by similarity to SP:P08150; match to protein family HMM PF00905; match to protein family HMM PF03717; penicillin-binding protein 2 431676 pbpA 3196071 pbpA Ruegeria pomeroyi DSS-3 penicillin-binding protein 2 YP_165680.1 429730 R 246200 CDS YP_165681.1 56695333 3196538 complement(431678..432214) 1 NC_003911.11 identified by similarity to GB:CAE53834.1; hypothetical protein 432214 3196538 SPO0418 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165681.1 431678 R 246200 CDS YP_165682.1 56695334 3194068 complement(432207..433142) 1 NC_003911.11 in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall; rod shape-determining protein MreC 433142 mreC 3194068 mreC Ruegeria pomeroyi DSS-3 rod shape-determining protein MreC YP_165682.1 432207 R 246200 CDS YP_165683.1 56695335 3194772 complement(433204..434250) 1 NC_003911.11 functions in MreBCD complex in some organisms; rod shape-determining protein MreB 434250 mreB 3194772 mreB Ruegeria pomeroyi DSS-3 rod shape-determining protein MreB YP_165683.1 433204 R 246200 CDS YP_165684.1 56695336 3192983 434416..435201 1 NC_003911.11 hypothetical protein 435201 3192983 SPO0421 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165684.1 434416 D 246200 CDS YP_165685.1 56695337 3193656 complement(435291..436865) 1 NC_003911.11 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase 436865 leuA 3193656 leuA Ruegeria pomeroyi DSS-3 2-isopropylmalate synthase YP_165685.1 435291 R 246200 CDS YP_165686.1 56695338 3192695 complement(437092..437673) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 437673 3192695 SPO0423 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_165686.1 437092 R 246200 CDS YP_165687.1 56695339 3192742 437751..438938 1 NC_003911.11 identified by match to protein family HMM PF07690; hypothetical protein 438938 3192742 SPO0424 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165687.1 437751 D 246200 CDS YP_165688.1 56695340 3192656 complement(438976..440388) 1 NC_003911.11 identified by match to protein family HMM PF02493; MORN repeat-containing protein 440388 3192656 SPO0425 Ruegeria pomeroyi DSS-3 MORN repeat-containing protein YP_165688.1 438976 R 246200 CDS YP_165689.1 56695341 3192654 440542..442200 1 NC_003911.11 NH(3)-dependent; catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers; NAD synthetase 442200 nadE 3192654 nadE Ruegeria pomeroyi DSS-3 NAD synthetase YP_165689.1 440542 D 246200 CDS YP_165690.1 56695342 3193641 442341..443000 1 NC_003911.11 hypothetical protein 443000 3193641 SPO0427 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165690.1 442341 D 246200 CDS YP_165691.1 56695343 3192889 443116..444447 1 NC_003911.11 identified by similarity to GB:AAA86752.1; match to protein family HMM PF01266; amino acid deaminase 444447 3192889 SPO0428 Ruegeria pomeroyi DSS-3 amino acid deaminase YP_165691.1 443116 D 246200 CDS YP_165692.1 56695344 3193104 complement(444464..445396) 1 NC_003911.11 identified by match to protein family HMM PF00753; match to protein family HMM TIGR01409; metallo-beta-lactamase 445396 3193104 SPO0429 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_165692.1 444464 R 246200 CDS YP_165693.1 56695345 3192955 445622..446953 1 NC_003911.11 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 446953 gltX 3192955 gltX Ruegeria pomeroyi DSS-3 glutamyl-tRNA synthetase YP_165693.1 445622 D 246200 CDS YP_165694.1 56695346 3193635 complement(447047..447616) 1 NC_003911.11 identified by similarity to PIR:E82090; hypothetical protein 447616 3193635 SPO0431 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165694.1 447047 R 246200 CDS YP_165695.1 56695347 3193691 447721..448167 1 NC_003911.11 identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738; rrf2 family protein 448167 3193691 SPO0432 Ruegeria pomeroyi DSS-3 rrf2 family protein YP_165695.1 447721 D 246200 CDS YP_165696.1 56695348 3195618 complement(448191..450707) 1 NC_003911.11 identified by match to protein family HMM PF02687; ABC transporter permease 450707 3195618 SPO0433 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_165696.1 448191 R 246200 CDS YP_165697.1 56695350 3194411 complement(450704..451399) 1 NC_003911.11 ABC transporter ATP-binding protein 451399 3194411 SPO0434 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_165697.1 450704 R 246200 CDS YP_165698.1 56695349 3194389 451448..452083 1 NC_003911.11 identified by similarity to SP:P29679; acyl-CoA thioesterase 452083 3194389 SPO0435 Ruegeria pomeroyi DSS-3 acyl-CoA thioesterase YP_165698.1 451448 D 246200 CDS YP_165699.1 56695351 3192880 452085..452702 1 NC_003911.11 identified by similarity to PIR:AC2205; hypothetical protein 452702 3192880 SPO0436 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165699.1 452085 D 246200 CDS YP_165700.1 56695352 3192720 complement(452742..452948) 1 NC_003911.11 cold shock family protein 452948 3192720 SPO0437 Ruegeria pomeroyi DSS-3 cold shock family protein YP_165700.1 452742 R 246200 CDS YP_165701.1 56695353 3192946 complement(453151..453708) 1 NC_003911.11 ErfK/YbiS/YcfS/YnhG family protein 453708 3192946 SPO0438 Ruegeria pomeroyi DSS-3 ErfK/YbiS/YcfS/YnhG family protein YP_165701.1 453151 R 246200 CDS YP_165702.1 56695354 3193493 complement(453771..454187) 1 NC_003911.11 hypothetical protein 454187 3193493 SPO0439 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165702.1 453771 R 246200 CDS YP_165703.1 56695355 3196114 454260..454676 1 NC_003911.11 thioesterase 454676 3196114 SPO0440 Ruegeria pomeroyi DSS-3 thioesterase YP_165703.1 454260 D 246200 CDS YP_165704.1 56695356 3192927 454811..455152 1 NC_003911.11 hypothetical protein 455152 3192927 SPO0441 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165704.1 454811 D 246200 CDS YP_165705.1 56695357 3193475 455224..455649 1 NC_003911.11 thioredoxin 455649 3193475 SPO0442 Ruegeria pomeroyi DSS-3 thioredoxin YP_165705.1 455224 D 246200 CDS YP_165706.1 56695358 3193659 455724..455942 1 NC_003911.11 identified by similarity to GB:BAC62291.1; hypothetical protein 455942 3193659 SPO0443 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165706.1 455724 D 246200 CDS YP_165707.1 56695359 3194282 complement(455955..456170) 1 NC_003911.11 hypothetical protein 456170 3194282 SPO0444 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165707.1 455955 R 246200 CDS YP_165708.1 56695360 3193470 456283..456858 1 NC_003911.11 identified by similarity to GB:AAQ60337.1; hypothetical protein 456858 3193470 SPO0445 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165708.1 456283 D 246200 CDS YP_165709.1 56695361 3193465 complement(456890..458665) 1 NC_003911.11 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence; ABC transporter ATP-binding protein 458665 3193465 SPO0446 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_165709.1 456890 R 246200 CDS YP_165710.1 56695362 3193325 458806..459792 1 NC_003911.11 hypothetical protein 459792 3193325 SPO0447 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165710.1 458806 D 246200 CDS YP_165711.1 56695363 3192916 459926..460420 1 NC_003911.11 MOSC domain-containing protein 460420 3192916 SPO0448 Ruegeria pomeroyi DSS-3 MOSC domain-containing protein YP_165711.1 459926 D 246200 CDS YP_165712.1 56695364 3193074 460454..461095 1 NC_003911.11 transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria; nicotinic acid mononucleotide adenylyltransferase 461095 nadD 3193074 nadD Ruegeria pomeroyi DSS-3 nicotinic acid mononucleotide adenylyltransferase YP_165712.1 460454 D 246200 CDS YP_165713.1 56695365 3193421 complement(461048..461875) 1 NC_003911.11 hypothetical protein 461875 3193421 SPO0450 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165713.1 461048 R 246200 CDS YP_165714.1 56695366 3193279 461960..463450 1 NC_003911.11 identified by match to protein family HMM PF02113; match to protein family HMM TIGR00666; D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase 463450 dacB 3193279 dacB Ruegeria pomeroyi DSS-3 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase YP_165714.1 461960 D 246200 CDS YP_165715.1 56695367 3193518 complement(463501..463923) 1 NC_003911.11 identified by similarity to PIR:AD3572; hypothetical protein 463923 3193518 SPO0452 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165715.1 463501 R 246200 CDS YP_165716.1 56695368 3192993 complement(464016..464474) 1 NC_003911.11 identified by similarity to GB:AAM06297.1; hypothetical protein 464474 3192993 SPO0453 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165716.1 464016 R 246200 CDS YP_165717.1 56695369 3193773 464569..465450 1 NC_003911.11 LysR family transcriptional regulator 465450 3193773 SPO0454 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165717.1 464569 D 246200 CDS YP_165718.1 56695370 3196262 465480..467126 1 NC_003911.11 class I; LysRS1; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine; lysyl-tRNA synthetase 467126 lysK 3196262 lysK Ruegeria pomeroyi DSS-3 lysyl-tRNA synthetase YP_165718.1 465480 D 246200 CDS YP_165719.1 56695371 3193501 467225..467545 1 NC_003911.11 hypothetical protein 467545 3193501 SPO0456 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165719.1 467225 D 246200 CDS YP_165720.1 56695372 3193703 467598..467999 1 NC_003911.11 identified by similarity to GB:BAC47480.1; hypothetical protein 467999 3193703 SPO0457 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165720.1 467598 D 246200 CDS YP_165721.1 56695374 3193456 complement(467966..470359) 1 NC_003911.11 hypothetical protein 470359 3193456 SPO0458 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165721.1 467966 R 246200 CDS YP_165722.1 56695373 3192963 468056..470425 1 NC_003911.11 hypothetical protein 470425 3192963 SPO0459 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165722.1 468056 D 246200 CDS YP_165723.1 56695375 3193316 complement(470475..471332) 1 NC_003911.11 hypothetical protein 471332 3193316 SPO0460 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165723.1 470475 R 246200 CDS YP_165724.1 56695376 3193709 471280..471909 1 NC_003911.11 ParA family protein 471909 3193709 SPO0461 Ruegeria pomeroyi DSS-3 ParA family protein YP_165724.1 471280 D 246200 CDS YP_165725.1 56695377 3192854 471959..472285 1 NC_003911.11 antibiotic biosynthesis monooxygenase domain-containing protein 472285 3192854 SPO0462 Ruegeria pomeroyi DSS-3 antibiotic biosynthesis monooxygenase domain-containing protein YP_165725.1 471959 D 246200 CDS YP_165726.1 56695378 3195754 472365..472772 1 NC_003911.11 universal stress family protein 472772 3195754 SPO0463 Ruegeria pomeroyi DSS-3 universal stress family protein YP_165726.1 472365 D 246200 CDS YP_165727.1 56695379 3195342 472839..473417 1 NC_003911.11 hypothetical protein 473417 3195342 SPO0464 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165727.1 472839 D 246200 CDS YP_165728.1 56695380 3193344 complement(473414..473896) 1 NC_003911.11 identified by match to protein family HMM PF01243; pyridoxamine 5'-phosphate oxidase 473896 3193344 SPO0465 Ruegeria pomeroyi DSS-3 pyridoxamine 5'-phosphate oxidase YP_165728.1 473414 R 246200 CDS YP_165729.1 56695381 3193634 complement(473906..474685) 1 NC_003911.11 identified by similarity to SP:P21501; formate/nitrate transporter 474685 3193634 SPO0466 Ruegeria pomeroyi DSS-3 formate/nitrate transporter YP_165729.1 473906 R 246200 CDS YP_165730.1 56695382 3193960 complement(474743..475453) 1 NC_003911.11 GntR family transcriptional regulator 475453 3193960 SPO0467 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_165730.1 474743 R 246200 CDS YP_165731.1 56695383 3195430 475557..476012 1 NC_003911.11 identified by similarity to SP:P16685; alkylphosphonate utilization protein PhnG 476012 phnG 3195430 phnG Ruegeria pomeroyi DSS-3 alkylphosphonate utilization protein PhnG YP_165731.1 475557 D 246200 CDS YP_165732.1 56695384 3193639 476009..476587 1 NC_003911.11 identified by similarity to SP:P16686; carbon-phosphorus lyase complex subunit 476587 phnH 3193639 phnH Ruegeria pomeroyi DSS-3 carbon-phosphorus lyase complex subunit YP_165732.1 476009 D 246200 CDS YP_165733.1 56695385 3192943 476591..477682 1 NC_003911.11 identified by similarity to SP:P16687; alkylphosphonate utilization protein PhnI 477682 phnI 3192943 phnI Ruegeria pomeroyi DSS-3 alkylphosphonate utilization protein PhnI YP_165733.1 476591 D 246200 CDS YP_165734.1 56695386 3193860 477762..478598 1 NC_003911.11 identified by similarity to SP:P16688; alkylphosphonate utilization protein PhnJ 478598 phnJ 3193860 phnJ Ruegeria pomeroyi DSS-3 alkylphosphonate utilization protein PhnJ YP_165734.1 477762 D 246200 CDS YP_165735.1 56695387 3193357 478684..479454 1 NC_003911.11 identified by similarity to SP:P16678; phosphonate C-P lyase system protein PhnK 479454 phnK 3193357 phnK Ruegeria pomeroyi DSS-3 phosphonate C-P lyase system protein PhnK YP_165735.1 478684 D 246200 CDS YP_165736.1 56695388 3195983 479522..480205 1 NC_003911.11 identified by similarity to SP:P16679; alkylphosphonate utilization protein PhnL 480205 phnL 3195983 phnL Ruegeria pomeroyi DSS-3 alkylphosphonate utilization protein PhnL YP_165736.1 479522 D 246200 CDS YP_165737.1 56695389 3195461 480202..480750 1 NC_003911.11 identified by similarity to SP:P16690; alkylphosphonate utilization protein PhnN 480750 phnN 3195461 phnN Ruegeria pomeroyi DSS-3 alkylphosphonate utilization protein PhnN YP_165737.1 480202 D 246200 CDS YP_165738.1 56695390 3195260 complement(480732..481415) 1 NC_003911.11 identified by similarity to GB:AAN29788.1; hypothetical protein 481415 3195260 SPO0475 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165738.1 480732 R 246200 CDS YP_165739.1 56695391 3195241 481469..482611 1 NC_003911.11 identified by similarity to SP:P16689; alkylphosphonate utilization protein PhnM 482611 phnM 3195241 phnM Ruegeria pomeroyi DSS-3 alkylphosphonate utilization protein PhnM YP_165739.1 481469 D 246200 CDS YP_165740.1 56695392 3195249 complement(482616..483182) 1 NC_003911.11 hypothetical protein 483182 3195249 SPO0477 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165740.1 482616 R 246200 CDS YP_165741.1 56695393 3195989 483205..483456 1 NC_003911.11 hypothetical protein 483456 3195989 SPO0478 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165741.1 483205 D 246200 CDS YP_165742.1 56695394 3195622 483607..484674 1 NC_003911.11 identified by similarity to GB:AAF61102.1; ISSpo8, transposase 484674 3195622 SPO0479 Ruegeria pomeroyi DSS-3 ISSpo8, transposase YP_165742.1 483607 D 246200 CDS YP_165743.1 56695395 3195280 complement(485499..485975) 1 NC_003911.11 acetyltransferase 485975 3195280 SPO0481 Ruegeria pomeroyi DSS-3 acetyltransferase YP_165743.1 485499 R 246200 CDS YP_165744.1 56695396 3195294 complement(485983..486294) 1 NC_003911.11 NADH-ubiquinone oxidoreductase 486294 3195294 SPO0482 Ruegeria pomeroyi DSS-3 NADH-ubiquinone oxidoreductase YP_165744.1 485983 R 246200 CDS YP_165745.1 56695397 3195475 complement(486480..487127) 1 NC_003911.11 microcystin dependent protein 487127 3195475 SPO0483 Ruegeria pomeroyi DSS-3 microcystin dependent protein YP_165745.1 486480 R 246200 CDS YP_165746.1 56695398 3195307 487568..488410 1 NC_003911.11 one of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation; 50S ribosomal protein L2 488410 rplB 3195307 rplB Ruegeria pomeroyi DSS-3 50S ribosomal protein L2 YP_165746.1 487568 D 246200 CDS YP_165747.1 56695399 3195270 488414..488692 1 NC_003911.11 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 488692 rpsS 3195270 rpsS Ruegeria pomeroyi DSS-3 30S ribosomal protein S19 YP_165747.1 488414 D 246200 CDS YP_165748.1 56695400 3195009 488696..489076 1 NC_003911.11 binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center; 50S ribosomal protein L22 489076 rplV 3195009 rplV Ruegeria pomeroyi DSS-3 50S ribosomal protein L22 YP_165748.1 488696 D 246200 CDS YP_165749.1 56695401 3195573 489076..489783 1 NC_003911.11 forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation; 30S ribosomal protein S3 489783 rpsC 3195573 rpsC Ruegeria pomeroyi DSS-3 30S ribosomal protein S3 YP_165749.1 489076 D 246200 CDS YP_165750.1 56695402 3195318 489796..490209 1 NC_003911.11 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 490209 rplP 3195318 rplP Ruegeria pomeroyi DSS-3 50S ribosomal protein L16 YP_165750.1 489796 D 246200 CDS YP_165751.1 56695403 3193409 complement(491490..492839) 1 NC_003911.11 ISSpo2, transposase 492839 3193409 SPO0489 Ruegeria pomeroyi DSS-3 ISSpo2, transposase YP_165751.1 491490 R 246200 CDS YP_165752.1 56695404 3195633 493432..494433 1 NC_003911.11 identified by similarity to GB:AAO08434.1; calcium-binding domain-containing protein 494433 3195633 SPO0490 Ruegeria pomeroyi DSS-3 calcium-binding domain-containing protein YP_165752.1 493432 D 246200 CDS YP_165753.1 56695405 3195948 494436..495119 1 NC_003911.11 identified by similarity to GB:CAE79871.1; hypothetical protein 495119 3195948 SPO0491 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165753.1 494436 D 246200 CDS YP_165754.1 56695406 3195349 495649..496491 1 NC_003911.11 identified by similarity to GB:BAC74954.1; cyclic nucleotide-binding protein 496491 3195349 SPO0492 Ruegeria pomeroyi DSS-3 cyclic nucleotide-binding protein YP_165754.1 495649 D 246200 CDS YP_165755.1 56695407 3195500 496675..496875 1 NC_003911.11 one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 496875 rpmC 3195500 rpmC Ruegeria pomeroyi DSS-3 50S ribosomal protein L29 YP_165755.1 496675 D 246200 CDS YP_165756.1 56695408 3194784 496888..497118 1 NC_003911.11 primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17 497118 rpsQ 3194784 rpsQ Ruegeria pomeroyi DSS-3 30S ribosomal protein S17 YP_165756.1 496888 D 246200 CDS YP_165757.1 56695409 3195401 497221..497589 1 NC_003911.11 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 497589 rplN 3195401 rplN Ruegeria pomeroyi DSS-3 50S ribosomal protein L14 YP_165757.1 497221 D 246200 CDS YP_165758.1 56695410 3195436 497592..497903 1 NC_003911.11 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 497903 rplX 3195436 rplX Ruegeria pomeroyi DSS-3 50S ribosomal protein L24 YP_165758.1 497592 D 246200 CDS YP_165759.1 56695411 3195440 497896..498456 1 NC_003911.11 part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13; 50S ribosomal protein L5 498456 rplE 3195440 rplE Ruegeria pomeroyi DSS-3 50S ribosomal protein L5 YP_165759.1 497896 D 246200 CDS YP_165760.1 56695412 3196049 498474..498779 1 NC_003911.11 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif; 30S ribosomal protein S14 498779 rpsN 3196049 rpsN Ruegeria pomeroyi DSS-3 30S ribosomal protein S14 YP_165760.1 498474 D 246200 CDS YP_165761.1 56695413 3195046 498792..499184 1 NC_003911.11 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 499184 rpsH 3195046 rpsH Ruegeria pomeroyi DSS-3 30S ribosomal protein S8 YP_165761.1 498792 D 246200 CDS YP_165762.1 56695414 3195456 499197..499730 1 NC_003911.11 ribosomal protein L6 appears to have arisen as a result of an ancient gene duplication as based on structural comparison of the Bacillus stearothermophilus protein; RNA-binding appears to be in the C-terminal domain; mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain; it has been localized to a region between the base of the L7/L12 stalk and the central protuberance; 50S ribosomal protein L6 499730 rplF 3195456 rplF Ruegeria pomeroyi DSS-3 50S ribosomal protein L6 YP_165762.1 499197 D 246200 CDS YP_165763.1 56695415 3196026 499742..500101 1 NC_003911.11 binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 500101 rplR 3196026 rplR Ruegeria pomeroyi DSS-3 50S ribosomal protein L18 YP_165763.1 499742 D 246200 CDS YP_165764.1 56695416 3195459 500214..500786 1 NC_003911.11 located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance; 30S ribosomal protein S5 500786 rpsE 3195459 rpsE Ruegeria pomeroyi DSS-3 30S ribosomal protein S5 YP_165764.1 500214 D 246200 CDS YP_165765.1 56695417 3195239 500799..500987 1 NC_003911.11 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 500987 rpmD 3195239 rpmD Ruegeria pomeroyi DSS-3 50S ribosomal protein L30 YP_165765.1 500799 D 246200 CDS YP_165766.1 56695418 3196030 complement(501390..501515) 1 NC_003911.11 hypothetical protein 501515 3196030 SPO0504 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165766.1 501390 R 246200 CDS YP_165767.1 56695419 3195630 502782..503432 1 NC_003911.11 identified by similarity to SP:P19946; 50S ribosomal protein L15 503432 rplO 3195630 rplO Ruegeria pomeroyi DSS-3 50S ribosomal protein L15 YP_165767.1 502782 D 246200 CDS YP_165768.1 56695420 3194103 503545..504912 1 NC_003911.11 forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase; preprotein translocase subunit SecY 504912 secY 3194103 secY Ruegeria pomeroyi DSS-3 preprotein translocase subunit SecY YP_165768.1 503545 D 246200 CDS YP_165769.1 56695421 3195636 504909..505550 1 NC_003911.11 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 505550 adk 3195636 adk Ruegeria pomeroyi DSS-3 adenylate kinase YP_165769.1 504909 D 246200 CDS YP_165770.1 56695422 3194553 505599..506672 1 NC_003911.11 identified by similarity to PIR:AB2876; hypothetical protein 506672 3194553 SPO0508 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165770.1 505599 D 246200 CDS YP_165771.1 56695423 3195393 506867..507235 1 NC_003911.11 located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA; 30S ribosomal protein S13 507235 rpsM 3195393 rpsM Ruegeria pomeroyi DSS-3 30S ribosomal protein S13 YP_165771.1 506867 D 246200 CDS YP_165772.1 56695424 3195723 507251..507643 1 NC_003911.11 located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3; 30S ribosomal protein S11 507643 rpsK 3195723 rpsK Ruegeria pomeroyi DSS-3 30S ribosomal protein S11 YP_165772.1 507251 D 246200 CDS YP_165773.1 56695425 3193120 507760..508776 1 NC_003911.11 catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Dimerization of the alpha subunit is the first step in the sequential assembly of subunits to form the holoenzyme; DNA-directed RNA polymerase subunit alpha 508776 rpoA 3193120 rpoA Ruegeria pomeroyi DSS-3 DNA-directed RNA polymerase subunit alpha YP_165773.1 507760 D 246200 CDS YP_165774.1 56695426 3195334 508954..509376 1 NC_003911.11 is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 509376 rplQ 3195334 rplQ Ruegeria pomeroyi DSS-3 50S ribosomal protein L17 YP_165774.1 508954 D 246200 CDS YP_165775.1 56695427 3194712 509484..509891 1 NC_003911.11 identified by similarity to GB:BAC52410.1; hypothetical protein 509891 3194712 SPO0513 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165775.1 509484 D 246200 CDS YP_165776.1 56695428 3196017 509955..511337 1 NC_003911.11 serine protease 511337 3196017 SPO0514 Ruegeria pomeroyi DSS-3 serine protease YP_165776.1 509955 D 246200 CDS YP_165777.1 56695429 3194720 511341..512657 1 NC_003911.11 recombination factor protein RarA 512657 3194720 SPO0515 Ruegeria pomeroyi DSS-3 recombination factor protein RarA YP_165777.1 511341 D 246200 CDS YP_165778.1 56695430 3196070 512820..513863 1 NC_003911.11 identified by similarity to SP:P23851; ribosomal large subunit pseudouridine synthase C 513863 rluC 3196070 rluC Ruegeria pomeroyi DSS-3 ribosomal large subunit pseudouridine synthase C YP_165778.1 512820 D 246200 CDS YP_165779.1 56695431 3195802 513860..514531 1 NC_003911.11 HAD family hydrolase 514531 3195802 SPO0517 Ruegeria pomeroyi DSS-3 HAD family hydrolase YP_165779.1 513860 D 246200 CDS YP_165780.1 56695432 3192817 514528..515244 1 NC_003911.11 identified by similarity to GB:BAC50629.1; hypothetical protein 515244 3192817 SPO0518 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165780.1 514528 D 246200 CDS YP_165781.1 56695433 3195297 515315..516457 1 NC_003911.11 glutamate/glutamine/aspartate/asparagine ABC transporter substrate-binding protein 516457 3195297 SPO0519 Ruegeria pomeroyi DSS-3 glutamate/glutamine/aspartate/asparagine ABC transporter substrate-binding protein YP_165781.1 515315 D 246200 CDS YP_165782.1 56695434 3194763 516592..517860 1 NC_003911.11 identified by similarity to SP:Q52664; glutamate/glutamine/aspartate/asparagine ABC transporter permease 517860 3194763 SPO0520 Ruegeria pomeroyi DSS-3 glutamate/glutamine/aspartate/asparagine ABC transporter permease YP_165782.1 516592 D 246200 CDS YP_165783.1 56695435 3194506 517862..519175 1 NC_003911.11 identified by similarity to SP:Q52665; glutamate/glutamine/aspartate/asparagine ABC transporter permease 519175 3194506 SPO0521 Ruegeria pomeroyi DSS-3 glutamate/glutamine/aspartate/asparagine ABC transporter permease YP_165783.1 517862 D 246200 CDS YP_165784.1 56695436 3196183 519186..519977 1 NC_003911.11 identified by similarity to SP:Q52666; glutamate/glutamine/aspartate/asparagine ABC transporter ATP-binding protein 519977 3196183 SPO0522 Ruegeria pomeroyi DSS-3 glutamate/glutamine/aspartate/asparagine ABC transporter ATP-binding protein YP_165784.1 519186 D 246200 CDS YP_165785.1 56695437 3195243 complement(520026..520535) 1 NC_003911.11 phosphoglycerate mutase 520535 3195243 SPO0523 Ruegeria pomeroyi DSS-3 phosphoglycerate mutase YP_165785.1 520026 R 246200 CDS YP_165786.1 56695438 3194837 complement(520532..521167) 1 NC_003911.11 identified by similarity to GB:BAB48651.1; hypothetical protein 521167 3194837 SPO0524 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165786.1 520532 R 246200 CDS YP_165787.1 56695439 3194956 complement(521164..521958) 1 NC_003911.11 sterol desaturase-like protein 521958 3194956 SPO0525 Ruegeria pomeroyi DSS-3 sterol desaturase-like protein YP_165787.1 521164 R 246200 CDS YP_165788.1 56695440 3195896 complement(522016..522879) 1 NC_003911.11 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase 522879 argB 3195896 argB Ruegeria pomeroyi DSS-3 acetylglutamate kinase YP_165788.1 522016 R 246200 CDS YP_165789.1 56695441 3194658 522955..523722 1 NC_003911.11 short chain dehydrogenase/reductase oxidoreductase 523722 3194658 SPO0527 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_165789.1 522955 D 246200 CDS YP_165790.1 56695442 3195914 complement(523761..525158) 1 NC_003911.11 hypothetical protein 525158 3195914 SPO0528 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165790.1 523761 R 246200 CDS YP_165791.1 56695443 3196479 complement(525224..525592) 1 NC_003911.11 hypothetical protein 525592 3196479 SPO0529 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165791.1 525224 R 246200 CDS YP_165792.1 56695444 3194815 complement(525589..526242) 1 NC_003911.11 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential; ribosome biogenesis GTP-binding protein YsxC 526242 engB 3194815 engB Ruegeria pomeroyi DSS-3 ribosome biogenesis GTP-binding protein YsxC YP_165792.1 525589 R 246200 CDS YP_165793.1 56695445 3194917 complement(526239..526976) 1 NC_003911.11 MOSC domain-containing protein 526976 3194917 SPO0531 Ruegeria pomeroyi DSS-3 MOSC domain-containing protein YP_165793.1 526239 R 246200 CDS YP_165794.1 56695446 3195935 complement(526973..528802) 1 NC_003911.11 functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria; inner membrane protein translocase component YidC 528802 3195935 SPO0532 Ruegeria pomeroyi DSS-3 inner membrane protein translocase component YidC YP_165794.1 526973 R 246200 CDS YP_165795.1 56695447 3195906 complement(528927..530468) 1 NC_003911.11 diguanylate cyclase 530468 3195906 SPO0533 Ruegeria pomeroyi DSS-3 diguanylate cyclase YP_165795.1 528927 R 246200 CDS YP_165796.1 56695448 3195432 complement(530541..531425) 1 NC_003911.11 TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs; C32 tRNA thiolase 531425 3195432 SPO0534 Ruegeria pomeroyi DSS-3 C32 tRNA thiolase YP_165796.1 530541 R 246200 CDS YP_165797.1 56695449 3195517 complement(531470..532399) 1 NC_003911.11 K+-dependent Na+/Ca+ exchanger-like protein 532399 3195517 SPO0535 Ruegeria pomeroyi DSS-3 K+-dependent Na+/Ca+ exchanger-like protein YP_165797.1 531470 R 246200 CDS YP_165798.1 56695450 3195209 complement(532528..532785) 1 NC_003911.11 identified by similarity to GB:CAE35356.1; hypothetical protein 532785 3195209 SPO0536 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165798.1 532528 R 246200 CDS YP_165799.1 56695451 3195555 complement(532846..533271) 1 NC_003911.11 ribonuclease P protein component 533271 3195555 SPO0537 Ruegeria pomeroyi DSS-3 ribonuclease P protein component YP_165799.1 532846 R 246200 CDS YP_165800.2 161598434 3195490 complement(533296..533430) 1 NC_003911.11 in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 533430 rpmH 3195490 rpmH Ruegeria pomeroyi DSS-3 50S ribosomal protein L34 YP_165800.2 533296 R 246200 CDS YP_165801.1 56695453 3194861 533672..534469 1 NC_003911.11 hypothetical protein 534469 3194861 SPO0539 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165801.1 533672 D 246200 CDS YP_165802.1 56695454 3195222 534469..535887 1 NC_003911.11 identified by similarity to SP:P17239; mercuric reductase 535887 3195222 SPO0540 Ruegeria pomeroyi DSS-3 mercuric reductase YP_165802.1 534469 D 246200 CDS YP_165803.1 56695455 3195574 535901..537286 1 NC_003911.11 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase 537286 3195574 SPO0541 Ruegeria pomeroyi DSS-3 sensor histidine kinase YP_165803.1 535901 D 246200 CDS YP_165804.1 56695456 3194211 complement(537802..539055) 1 NC_003911.11 identified by similarity to GB:CAD14035.1; hypothetical protein 539055 3194211 SPO0543 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165804.1 537802 R 246200 CDS YP_165805.1 56695457 3195841 complement(539068..541503) 1 NC_003911.11 glycine cleavage system protein T 541503 3195841 SPO0544 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_165805.1 539068 R 246200 CDS YP_165806.1 56695458 3194622 541827..544025 1 NC_003911.11 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion; excinuclease ABC subunit B 544025 uvrB 3194622 uvrB Ruegeria pomeroyi DSS-3 excinuclease ABC subunit B YP_165806.1 541827 D 246200 CDS YP_165807.1 56695459 3195284 544149..544619 1 NC_003911.11 hypothetical protein 544619 3195284 SPO0546 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165807.1 544149 D 246200 CDS YP_165808.1 56695460 3194705 complement(544720..545253) 1 NC_003911.11 identified by similarity to PIR:H83501; hypothetical protein 545253 3194705 SPO0547 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165808.1 544720 R 246200 CDS YP_165809.1 56695461 3193736 545461..545724 1 NC_003911.11 hypothetical protein 545724 3193736 SPO0548 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165809.1 545461 D 246200 CDS YP_165810.1 56695462 3195285 complement(545732..546238) 1 NC_003911.11 identified by similarity to PIR:G97668; hypothetical protein 546238 3195285 SPO0549 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165810.1 545732 R 246200 CDS YP_165811.1 56695463 3195961 complement(546205..546969) 1 NC_003911.11 identified by similarity to PIR:E95936; hypothetical protein 546969 3195961 SPO0550 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165811.1 546205 R 246200 CDS YP_165812.1 56695464 3195452 complement(546966..548105) 1 NC_003911.11 identified by similarity to PIR:B97670; hypothetical protein 548105 3195452 SPO0551 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165812.1 546966 R 246200 CDS YP_165813.1 56695465 3193954 complement(548102..548686) 1 NC_003911.11 phosphoglycerate mutase 548686 3193954 SPO0552 Ruegeria pomeroyi DSS-3 phosphoglycerate mutase YP_165813.1 548102 R 246200 CDS YP_165814.1 56695466 3195963 complement(548683..549762) 1 NC_003911.11 group 1 family glycosyltransferase 549762 3195963 SPO0553 Ruegeria pomeroyi DSS-3 group 1 family glycosyltransferase YP_165814.1 548683 R 246200 CDS YP_165815.1 56695467 3195640 complement(549765..551009) 1 NC_003911.11 glycoside hydrolase 551009 3195640 SPO0554 Ruegeria pomeroyi DSS-3 glycoside hydrolase YP_165815.1 549765 R 246200 CDS YP_165816.1 56695468 3193898 complement(551006..552220) 1 NC_003911.11 identified by similarity to GB:BAB50184.1; hypothetical protein 552220 3193898 SPO0555 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165816.1 551006 R 246200 CDS YP_165817.1 56695469 3195062 complement(552230..553540) 1 NC_003911.11 UDP-glucose/GDP-mannose dehydrogenase 553540 3195062 SPO0556 Ruegeria pomeroyi DSS-3 UDP-glucose/GDP-mannose dehydrogenase YP_165817.1 552230 R 246200 CDS YP_165818.1 56695470 3193953 553643..556090 1 NC_003911.11 mechanosensitive ion channel MscS 556090 3193953 SPO0557 Ruegeria pomeroyi DSS-3 mechanosensitive ion channel MscS YP_165818.1 553643 D 246200 CDS YP_165819.1 56695471 3193760 complement(556181..557332) 1 NC_003911.11 identified by similarity to SP:P42063; oligopeptide ABC transporter permease 557332 3193760 SPO0558 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter permease YP_165819.1 556181 R 246200 CDS YP_165820.1 56695472 3193982 complement(557329..558357) 1 NC_003911.11 identified by similarity to SP:P42062; oligopeptide ABC transporter permease 558357 3193982 SPO0559 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter permease YP_165820.1 557329 R 246200 CDS YP_165821.1 56695473 3193966 complement(558370..560286) 1 NC_003911.11 identified by similarity to GB:BAB50197.1; oligopeptide ABC transporter periplasmic oligopeptide-binding protein 560286 3193966 SPO0560 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter periplasmic oligopeptide-binding protein YP_165821.1 558370 R 246200 CDS YP_165822.1 56695474 3193858 562276..562797 1 NC_003911.11 identified by similarity to GB:BAB50200.1; hypothetical protein 562797 3193858 SPO0562 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165822.1 562276 D 246200 CDS YP_165823.1 56695475 3193873 562898..563527 1 NC_003911.11 identified by similarity to SP:Q12390; glutathione S-transferase 563527 3193873 SPO0563 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_165823.1 562898 D 246200 CDS YP_165824.1 56695476 3193816 563719..566127 1 NC_003911.11 glycine cleavage system protein T 566127 3193816 SPO0564 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_165824.1 563719 D 246200 CDS YP_165825.1 56695477 3193832 566124..567647 1 NC_003911.11 trimethylamine methyltransferase 567647 3193832 SPO0565 Ruegeria pomeroyi DSS-3 trimethylamine methyltransferase YP_165825.1 566124 D 246200 CDS YP_165826.1 56695478 3193829 567710..568333 1 NC_003911.11 TetR family transcriptional regulator 568333 3193829 SPO0566 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_165826.1 567710 D 246200 CDS YP_165827.1 56695479 3194259 568330..569634 1 NC_003911.11 oxidoreductase, FAD-binding 569634 3194259 SPO0567 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_165827.1 568330 D 246200 CDS YP_165828.1 56695480 3194242 complement(569856..573269) 1 NC_003911.11 catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; 2-oxoacid ferredoxin oxidoreductase 573269 3194242 SPO0568 Ruegeria pomeroyi DSS-3 2-oxoacid ferredoxin oxidoreductase YP_165828.1 569856 R 246200 CDS YP_165829.1 56695481 3193796 573420..573878 1 NC_003911.11 AsnC family transcriptional regulator 573878 3193796 SPO0569 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_165829.1 573420 D 246200 CDS YP_165830.1 56695482 3193963 574060..576396 1 NC_003911.11 identified by similarity to GB:CAD14776.1; hypothetical protein 576396 3193963 SPO0570 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165830.1 574060 D 246200 CDS YP_165831.1 56695483 3194013 576430..581301 1 NC_003911.11 PKD domain-containing protein 581301 3194013 SPO0571 Ruegeria pomeroyi DSS-3 PKD domain-containing protein YP_165831.1 576430 D 246200 CDS YP_165832.1 56695484 3194243 581384..583099 1 NC_003911.11 guanylate cyclase 583099 3194243 SPO0572 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_165832.1 581384 D 246200 CDS YP_165833.1 56695485 3193880 complement(583202..583597) 1 NC_003911.11 identified by similarity to GB:AAQ87470.1; hypothetical protein 583597 3193880 SPO0573 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165833.1 583202 R 246200 CDS YP_165834.1 56695486 3193862 583707..586805 1 NC_003911.11 ABC transporter transmembrane ATP-binding protein 586805 3193862 SPO0574 Ruegeria pomeroyi DSS-3 ABC transporter transmembrane ATP-binding protein YP_165834.1 583707 D 246200 CDS YP_165835.1 56695488 3194165 complement(586901..588058) 1 NC_003911.11 acyl-CoA dehydrogenase 588058 acdA-1 3194165 acdA-1 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_165835.1 586901 R 246200 CDS YP_165836.1 56695487 3193916 complement(588055..588684) 1 NC_003911.11 identified by similarity to GB:AAS05297.1; TetR family transcriptional regulator 588684 3193916 SPO0576 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_165836.1 588055 R 246200 CDS YP_165837.1 56695489 3194204 588798..590561 1 NC_003911.11 identified by similarity to PIR:D83286; hypothetical protein 590561 3194204 SPO0577 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165837.1 588798 D 246200 CDS YP_165838.1 56695490 3194171 590574..592193 1 NC_003911.11 identified by similarity to GB:BAB16296.1; acetyl-CoA carboxylase carboxyltransferase 592193 3194171 SPO0578 Ruegeria pomeroyi DSS-3 acetyl-CoA carboxylase carboxyltransferase YP_165838.1 590574 D 246200 CDS YP_165839.1 56695491 3193852 592193..594175 1 NC_003911.11 identified by similarity to GB:BAB16297.1; acetyl-CoA carboxylase, biotin carboxylase 594175 3193852 SPO0579 Ruegeria pomeroyi DSS-3 acetyl-CoA carboxylase, biotin carboxylase YP_165839.1 592193 D 246200 CDS YP_165840.1 56695492 3193969 594172..595302 1 NC_003911.11 2-nitropropane dioxygenase 595302 3193969 SPO0580 Ruegeria pomeroyi DSS-3 2-nitropropane dioxygenase YP_165840.1 594172 D 246200 CDS YP_165841.1 56695493 3192697 595305..596096 1 NC_003911.11 identified by similarity to GB:CAB95889.1; hypothetical protein 596096 3192697 SPO0581 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165841.1 595305 D 246200 CDS YP_165842.1 56695494 3194156 596201..597358 1 NC_003911.11 acyl-CoA dehydrogenase 597358 acdA-2 3194156 acdA-2 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_165842.1 596201 D 246200 CDS YP_165843.1 56695495 3194065 complement(597541..598422) 1 NC_003911.11 LysR family transcriptional regulator 598422 3194065 SPO0583 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165843.1 597541 R 246200 CDS YP_165844.1 56695496 3193806 598520..599683 1 NC_003911.11 identified by similarity to SP:Q06191; aspartate aminotransferase 599683 aspC-1 3193806 aspC-1 Ruegeria pomeroyi DSS-3 aspartate aminotransferase YP_165844.1 598520 D 246200 CDS YP_165845.1 56695497 3194057 599693..601915 1 NC_003911.11 dehydrogenase/transketolase 601915 3194057 SPO0585 Ruegeria pomeroyi DSS-3 dehydrogenase/transketolase YP_165845.1 599693 D 246200 CDS YP_165846.1 56695498 3193757 601912..602949 1 NC_003911.11 identified by similarity to PIR:T00580; acyl carrier protein 602949 3193757 SPO0586 Ruegeria pomeroyi DSS-3 acyl carrier protein YP_165846.1 601912 D 246200 CDS YP_165847.1 56695499 3193649 602993..604270 1 NC_003911.11 identified by similarity to GB:CAC46788.1; hypothetical protein 604270 3193649 SPO0587 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165847.1 602993 D 246200 CDS YP_165848.1 56695500 3193919 complement(604264..605175) 1 NC_003911.11 LysR family transcriptional regulator 605175 3193919 SPO0588 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165848.1 604264 R 246200 CDS YP_165849.1 56695501 3192824 605197..608469 1 NC_003911.11 oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein 608469 3192824 SPO0589 Ruegeria pomeroyi DSS-3 oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein YP_165849.1 605197 D 246200 CDS YP_165850.1 56695502 3193422 complement(608479..609507) 1 NC_003911.11 LacI family transcriptional regulator 609507 hpsR 3193422 hpsR Ruegeria pomeroyi DSS-3 LacI family transcriptional regulator YP_165850.1 608479 R 246200 CDS YP_165851.1 56695503 3193906 609873..611018 1 NC_003911.11 identified by similarity to SP:P37735; dihydroxypropanesulfonateTRAP transporter 611018 hpsK 3193906 hpsK Ruegeria pomeroyi DSS-3 dihydroxypropanesulfonateTRAP transporter YP_165851.1 609873 D 246200 CDS YP_165852.1 56695504 3193787 611098..611640 1 NC_003911.11 dihydroxypropanesulfonateTRAP transporter 611640 hpsL 3193787 hpsL Ruegeria pomeroyi DSS-3 dihydroxypropanesulfonateTRAP transporter YP_165852.1 611098 D 246200 CDS YP_165853.1 56695505 3195982 611651..612979 1 NC_003911.11 dihydroxypropanesulfonateTRAP transporter 612979 hpsM 3195982 hpsM Ruegeria pomeroyi DSS-3 dihydroxypropanesulfonateTRAP transporter YP_165853.1 611651 D 246200 CDS YP_165854.1 56695506 3193878 612992..614299 1 NC_003911.11 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; dihydroxypropanesulfonate-3-dehydrogenase 614299 hpsN 3193878 hpsN Ruegeria pomeroyi DSS-3 dihydroxypropanesulfonate-3-dehydrogenase YP_165854.1 612992 D 246200 CDS YP_165855.1 56695507 3193226 614292..615053 1 NC_003911.11 identified by similarity to SP:P50199; R or S-dihydroxypropanesulfonate-2-dehydrogenase 615053 hpsO 3193226 hpsO Ruegeria pomeroyi DSS-3 R or S-dihydroxypropanesulfonate-2-dehydrogenase YP_165855.1 614292 D 246200 CDS YP_165856.1 56695508 3193939 615050..616048 1 NC_003911.11 S or R-dihydroxypropanesulfonate-2-dehydrogenase 616048 hpsP 3193939 hpsP Ruegeria pomeroyi DSS-3 S or R-dihydroxypropanesulfonate-2-dehydrogenase YP_165856.1 615050 D 246200 CDS YP_165857.1 56695509 3193130 616052..616456 1 NC_003911.11 UspA family stress protein 616456 hpsQ 3193130 hpsQ Ruegeria pomeroyi DSS-3 UspA family stress protein YP_165857.1 616052 D 246200 CDS YP_165858.1 56695510 3196027 616497..617612 1 NC_003911.11 membrane-bound sulfolactate dehydrogenase 617612 slcD 3196027 slcD Ruegeria pomeroyi DSS-3 membrane-bound sulfolactate dehydrogenase YP_165858.1 616497 D 246200 CDS YP_165859.1 56695511 3192836 complement(617619..618467) 1 NC_003911.11 agmatinase 618467 speB-1 3192836 speB-1 Ruegeria pomeroyi DSS-3 agmatinase YP_165859.1 617619 R 246200 CDS YP_165860.1 56695512 3193162 complement(618464..619642) 1 NC_003911.11 carboxynorspermidine decarboxylase 619642 nspC 3193162 nspC Ruegeria pomeroyi DSS-3 carboxynorspermidine decarboxylase YP_165860.1 618464 R 246200 CDS YP_165861.1 56695513 3193831 complement(619738..620949) 1 NC_003911.11 saccharopine dehydrogenase 620949 3193831 SPO0601 Ruegeria pomeroyi DSS-3 saccharopine dehydrogenase YP_165861.1 619738 R 246200 CDS YP_165862.1 56695514 3193886 complement(620975..622960) 1 NC_003911.11 catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis; arginine decarboxylase 622960 speA 3193886 speA Ruegeria pomeroyi DSS-3 arginine decarboxylase YP_165862.1 620975 R 246200 CDS YP_165863.1 56695515 3192733 complement(623033..623347) 1 NC_003911.11 identified by similarity to PIR:AH0077; hypothetical protein 623347 3192733 SPO0603 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165863.1 623033 R 246200 CDS YP_165864.1 56695516 3192988 complement(623376..623753) 1 NC_003911.11 identified by similarity to GB:BAC62948.1; hypothetical protein 623753 3192988 SPO0604 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165864.1 623376 R 246200 CDS YP_165865.1 56695517 3193745 complement(623756..624208) 1 NC_003911.11 MarR family transcriptional regulator 624208 3193745 SPO0605 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_165865.1 623756 R 246200 CDS YP_165866.1 56695518 3195886 624481..626169 1 NC_003911.11 identified by similarity to PIR:C95874; hypothetical protein 626169 3195886 SPO0606 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165866.1 624481 D 246200 CDS YP_165867.1 56695519 3195347 626169..627194 1 NC_003911.11 identified by similarity to GB:CAB71312.1; proline racemase 627194 3195347 SPO0607 Ruegeria pomeroyi DSS-3 proline racemase YP_165867.1 626169 D 246200 CDS YP_165868.1 56695520 3195271 627308..629086 1 NC_003911.11 Assignment partly based on location in sugar transporter operon.; sugar ABC transporter periplasmic sugar-binding protein 629086 3195271 SPO0608 Ruegeria pomeroyi DSS-3 sugar ABC transporter periplasmic sugar-binding protein YP_165868.1 627308 D 246200 CDS YP_165869.1 56695521 3195033 629201..630265 1 NC_003911.11 Assignment partly based on location in sugar transport operon.; sugar ABC transporter ATP-binding protein 630265 3195033 SPO0609 Ruegeria pomeroyi DSS-3 sugar ABC transporter ATP-binding protein YP_165869.1 629201 D 246200 CDS YP_165870.1 56695522 3194437 630273..631358 1 NC_003911.11 Assignment partly based on location in sugar transport operon.; sugar ABC transporter ATP-binding protein 631358 3194437 SPO0610 Ruegeria pomeroyi DSS-3 sugar ABC transporter ATP-binding protein YP_165870.1 630273 D 246200 CDS YP_165871.1 56695523 3195016 631355..632218 1 NC_003911.11 Assignment partly based on location in sugar transport operon.; identified by similarity to PIR:T46751; sugar ABC transporter permease 632218 3195016 SPO0611 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_165871.1 631355 D 246200 CDS YP_165872.1 56695524 3193837 632230..633027 1 NC_003911.11 Assignment partly based on location in sugar transport operon.; sugar ABC transporter permease 633027 3193837 SPO0612 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_165872.1 632230 D 246200 CDS YP_165873.1 56695525 3195703 633027..633305 1 NC_003911.11 identified by similarity to GB:BAB48242.1; hypothetical protein 633305 3195703 SPO0613 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165873.1 633027 D 246200 CDS YP_165874.1 56695526 3195955 633393..633788 1 NC_003911.11 identified by similarity to SP:P06555; transcriptional regulator 633788 3195955 SPO0614 Ruegeria pomeroyi DSS-3 transcriptional regulator YP_165874.1 633393 D 246200 CDS YP_165875.1 56698726 3196484 633778..634911 1 NC_003911.11 identified by similarity to GB:CAD73596.1; hypothetical protein 634911 3196484 SPO0615 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165875.1 633778 D 246200 CDS YP_165876.1 56695527 3195107 634997..635989 1 NC_003911.11 zinc-binding dehydrogenase oxidoreductase 635989 3195107 SPO0616 Ruegeria pomeroyi DSS-3 zinc-binding dehydrogenase oxidoreductase YP_165876.1 634997 D 246200 CDS YP_165877.1 56695528 3195131 complement(636308..637354) 1 NC_003911.11 AraC family transcriptional regulator 637354 3195131 SPO0618 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_165877.1 636308 R 246200 CDS YP_165878.1 56695529 3194955 637522..638718 1 NC_003911.11 sterol desaturase 638718 3194955 SPO0619 Ruegeria pomeroyi DSS-3 sterol desaturase YP_165878.1 637522 D 246200 CDS YP_165879.1 56695530 3195691 638752..639378 1 NC_003911.11 identified by similarity to GB:BAC91031.1; hypothetical protein 639378 3195691 SPO0620 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165879.1 638752 D 246200 CDS YP_165880.1 56695531 3195217 639827..641368 1 NC_003911.11 ankyrin repeat-containing protein 641368 3195217 SPO0621 Ruegeria pomeroyi DSS-3 ankyrin repeat-containing protein YP_165880.1 639827 D 246200 CDS YP_165881.1 56695532 3194020 complement(641833..642891) 1 NC_003911.11 ISSpo1, transposase 642891 3194020 SPO0622 Ruegeria pomeroyi DSS-3 ISSpo1, transposase YP_165881.1 641833 R 246200 CDS YP_165882.1 56698709 3196274 complement(642986..643534) 1 NC_003911.11 cytochrome c oxidase domain-containing protein 643534 3196274 SPO0623 Ruegeria pomeroyi DSS-3 cytochrome c oxidase domain-containing protein YP_165882.1 642986 R 246200 CDS YP_165883.1 56695533 3195267 complement(643541..644167) 1 NC_003911.11 identified by similarity to PIR:B75629; hypothetical protein 644167 3195267 SPO0624 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165883.1 643541 R 246200 CDS YP_165884.1 56695534 3195188 complement(648529..649044) 1 NC_003911.11 transposase, degenerate 649044 3195188 SPO0628 Ruegeria pomeroyi DSS-3 transposase, degenerate YP_165884.1 648529 R 246200 CDS YP_165885.1 56695535 3194515 complement(650052..650945) 1 NC_003911.11 identified by similarity to GB:AAN56319.1; ISSpo3, transposase 650945 3194515 SPO0629 Ruegeria pomeroyi DSS-3 ISSpo3, transposase YP_165885.1 650052 R 246200 CDS YP_165886.1 56695536 3194691 complement(652365..652889) 1 NC_003911.11 hypothetical protein 652889 3194691 SPO0631 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165886.1 652365 R 246200 CDS YP_165887.1 56695537 3194128 653027..654013 1 NC_003911.11 Involved in the metabolism of aromatic amino acids; 2-hydroxyacid dehydrogenase 654013 3194128 SPO0632 Ruegeria pomeroyi DSS-3 2-hydroxyacid dehydrogenase YP_165887.1 653027 D 246200 CDS YP_165888.1 56695538 3194587 654249..656042 1 NC_003911.11 identified by similarity to SP:P54422; gamma-glutamyltranspeptidase 656042 ggt 3194587 ggt Ruegeria pomeroyi DSS-3 gamma-glutamyltranspeptidase YP_165888.1 654249 D 246200 CDS YP_165889.1 56695539 3195266 656146..657543 1 NC_003911.11 oxidoreductase, FAD-binding 657543 3195266 SPO0634 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_165889.1 656146 D 246200 CDS YP_165890.1 56695540 3195325 657754..660261 1 NC_003911.11 glycine cleavage system protein T 660261 3195325 SPO0635 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_165890.1 657754 D 246200 CDS YP_165891.1 56695541 3195627 complement(660314..660850) 1 NC_003911.11 EF hand domain-containing protein 660850 3195627 SPO0636 Ruegeria pomeroyi DSS-3 EF hand domain-containing protein YP_165891.1 660314 R 246200 CDS YP_165892.1 56695542 3194193 complement(660904..661020) 1 NC_003911.11 hypothetical protein 661020 3194193 SPO0637 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165892.1 660904 R 246200 CDS YP_165893.1 56695543 3195719 complement(661053..661670) 1 NC_003911.11 identified by similarity to GB:AAO90814.1; hypothetical protein 661670 3195719 SPO0638 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165893.1 661053 R 246200 CDS YP_165894.1 56695544 3194616 661739..662596 1 NC_003911.11 LysR family transcriptional regulator 662596 3194616 SPO0639 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165894.1 661739 D 246200 CDS YP_165895.1 56695546 3195051 complement(662593..662928) 1 NC_003911.11 alkylhydroperoxidase 662928 3195051 SPO0640 Ruegeria pomeroyi DSS-3 alkylhydroperoxidase YP_165895.1 662593 R 246200 CDS YP_165896.1 56695545 3195244 complement(662997..663647) 1 NC_003911.11 identified by similarity to GB:AAP57703.1; hypothetical protein 663647 3195244 SPO0641 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165896.1 662997 R 246200 CDS YP_165897.1 56695547 3195488 complement(663644..664714) 1 NC_003911.11 oxidoreductase, FAD-binding 664714 3195488 SPO0642 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_165897.1 663644 R 246200 CDS YP_165898.1 56695548 3195705 complement(664711..665649) 1 NC_003911.11 aldo/keto reductase 665649 3195705 SPO0643 Ruegeria pomeroyi DSS-3 aldo/keto reductase YP_165898.1 664711 R 246200 CDS YP_165899.1 56695549 3195619 665747..666202 1 NC_003911.11 identified by similarity to GB:BAC48747.1; hypothetical protein 666202 3195619 SPO0644 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165899.1 665747 D 246200 CDS YP_165900.1 56695550 3194633 666206..667444 1 NC_003911.11 identified by similarity to GB:BAC48748.1; multidrug resistance efflux pump 667444 3194633 SPO0645 Ruegeria pomeroyi DSS-3 multidrug resistance efflux pump YP_165900.1 666206 D 246200 CDS YP_165901.1 56695551 3195864 complement(667490..667897) 1 NC_003911.11 identified by similarity to GB:AAQ61228.1; hypothetical protein 667897 3195864 SPO0646 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165901.1 667490 R 246200 CDS YP_165902.1 56695552 3192754 complement(667894..668199) 1 NC_003911.11 hypothetical protein 668199 3192754 SPO0647 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165902.1 667894 R 246200 CDS YP_165903.1 56695553 3195807 complement(668375..669448) 1 NC_003911.11 bmp family protein 669448 3195807 SPO0648 Ruegeria pomeroyi DSS-3 bmp family protein YP_165903.1 668375 R 246200 CDS YP_165904.1 56695554 3195273 complement(669502..670422) 1 NC_003911.11 Assignment based partly on membership in sugar ABC transporter operon; sugar ABC transporter permease 670422 3195273 SPO0649 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_165904.1 669502 R 246200 CDS YP_165905.1 56695555 3194022 complement(670426..671508) 1 NC_003911.11 Assignment based partly on membership in sugar ABC transporter operon; sugar ABC transporter permease 671508 3194022 SPO0650 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_165905.1 670426 R 246200 CDS YP_165906.1 56695556 3195876 complement(671563..673080) 1 NC_003911.11 sugar ABC transporter ATP-binding protein 673080 3195876 SPO0651 Ruegeria pomeroyi DSS-3 sugar ABC transporter ATP-binding protein YP_165906.1 671563 R 246200 CDS YP_165907.1 56695557 3194591 complement(673077..674045) 1 NC_003911.11 identified by similarity to GB:CAB41849.1; xanthine dehydrogenase accessory factor 674045 xdhC 3194591 xdhC Ruegeria pomeroyi DSS-3 xanthine dehydrogenase accessory factor YP_165907.1 673077 R 246200 CDS YP_165908.1 56695558 3194183 complement(674035..676365) 1 NC_003911.11 identified by similarity to GB:CAA04470.2; xanthine dehydrogenase subunit B 676365 xdhB 3194183 xdhB Ruegeria pomeroyi DSS-3 xanthine dehydrogenase subunit B YP_165908.1 674035 R 246200 CDS YP_165909.1 56695559 3195620 complement(676362..677747) 1 NC_003911.11 identified by similarity to GB:CAA04469.1; xanthine dehydrogenase, A subunit 677747 xdhA 3195620 xdhA Ruegeria pomeroyi DSS-3 xanthine dehydrogenase, A subunit YP_165909.1 676362 R 246200 CDS YP_165910.1 56695560 3195387 complement(678063..678827) 1 NC_003911.11 identified by similarity to PIR:D95421; hypothetical protein 678827 3195387 SPO0655 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165910.1 678063 R 246200 CDS YP_165911.1 56695561 3194643 678963..682526 1 NC_003911.11 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase; DNA polymerase III subunit alpha 682526 dnaE 3194643 dnaE Ruegeria pomeroyi DSS-3 DNA polymerase III subunit alpha YP_165911.1 678963 D 246200 CDS YP_165912.1 56695562 3193738 complement(682533..683429) 1 NC_003911.11 metallochaperone 683429 naaT 3193738 naaT Ruegeria pomeroyi DSS-3 metallochaperone YP_165912.1 682533 R 246200 CDS YP_165913.1 56695563 3195737 complement(683429..685072) 1 NC_003911.11 N-acetyltaurine amidohydrolas 685072 naaS 3195737 naaS Ruegeria pomeroyi DSS-3 N-acetyltaurine amidohydrolas YP_165913.1 683429 R 246200 CDS YP_165914.1 56695564 3193567 685171..686103 1 NC_003911.11 LysR family transcriptional regulator 686103 naaR 3193567 naaR Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165914.1 685171 D 246200 CDS YP_165915.1 56695565 3194493 686223..687797 1 NC_003911.11 N-acetyltaurine ABC transporter substrate-binding protein 687797 naaA 3194493 naaA Ruegeria pomeroyi DSS-3 N-acetyltaurine ABC transporter substrate-binding protein YP_165915.1 686223 D 246200 CDS YP_165916.1 56695566 3195988 687865..688842 1 NC_003911.11 identified by similarity to SP:P42062; N-acetyltaurine 688842 naaB 3195988 naaB Ruegeria pomeroyi DSS-3 N-acetyltaurine YP_165916.1 687865 D 246200 CDS YP_165917.1 56695567 3194688 688839..689726 1 NC_003911.11 identified by similarity to SP:P42063; N-acetyltaurine ABC transporter permease 689726 naaB' 3194688 naaB' Ruegeria pomeroyi DSS-3 N-acetyltaurine ABC transporter permease YP_165917.1 688839 D 246200 CDS YP_165918.1 56695568 3195712 689663..690715 1 NC_003911.11 identified by similarity to SP:P26905; N-acetyltaurine ABC transporter ATP-binding protein 690715 naaC 3195712 naaC Ruegeria pomeroyi DSS-3 N-acetyltaurine ABC transporter ATP-binding protein YP_165918.1 689663 D 246200 CDS YP_165919.1 56695569 3194255 690716..691714 1 NC_003911.11 identified by similarity to SP:P42065; N-acetyltaurine ABC transporter ATP-binding protein 691714 naaC' 3194255 naaC' Ruegeria pomeroyi DSS-3 N-acetyltaurine ABC transporter ATP-binding protein YP_165919.1 690716 D 246200 CDS YP_165920.1 56695570 3195981 complement(691743..691937) 1 NC_003911.11 identified by similarity to SP:Q89SJ8; SlyX protein 691937 3195981 SPO0665 Ruegeria pomeroyi DSS-3 SlyX protein YP_165920.1 691743 R 246200 CDS YP_165921.1 56695571 3195344 692042..692845 1 NC_003911.11 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 692845 3195344 SPO0666 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_165921.1 692042 D 246200 CDS YP_165922.1 56695572 3192980 692935..694422 1 NC_003911.11 catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG; histidyl-tRNA synthetase 694422 hisS 3192980 hisS Ruegeria pomeroyi DSS-3 histidyl-tRNA synthetase YP_165922.1 692935 D 246200 CDS YP_165923.1 56695573 3193863 694419..695507 1 NC_003911.11 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine; ATP phosphoribosyltransferase 695507 hisZ 3193863 hisZ Ruegeria pomeroyi DSS-3 ATP phosphoribosyltransferase YP_165923.1 694419 D 246200 CDS YP_165924.1 56695574 3195758 695504..696196 1 NC_003911.11 short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ; ATP phosphoribosyltransferase 696196 hisG 3195758 hisG Ruegeria pomeroyi DSS-3 ATP phosphoribosyltransferase YP_165924.1 695504 D 246200 CDS YP_165925.1 56695575 3195523 complement(696285..699590) 1 NC_003911.11 DNA polymerase III subunit alpha 699590 3195523 SPO0670 Ruegeria pomeroyi DSS-3 DNA polymerase III subunit alpha YP_165925.1 696285 R 246200 CDS YP_165926.1 56695576 3195816 complement(699587..700960) 1 NC_003911.11 identified by similarity to GB:BAB51085.1; hypothetical protein 700960 3195816 SPO0671 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165926.1 699587 R 246200 CDS YP_165927.1 56695577 3195663 complement(700980..701555) 1 NC_003911.11 identified by similarity to PIR:AH2953; hypothetical protein 701555 3195663 SPO0672 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165927.1 700980 R 246200 CDS YP_165928.1 56695578 3195442 complement(701701..703098) 1 NC_003911.11 identified by similarity to SP:Q9APM5; taurine--pyruvate aminotransferase 703098 tpa 3195442 tpa Ruegeria pomeroyi DSS-3 taurine--pyruvate aminotransferase YP_165928.1 701701 R 246200 CDS YP_165929.1 56695579 3195870 703493..704503 1 NC_003911.11 Assignment partly based on membership in taurine ABC transporter gene cluster.; identified by similarity to SP:Q47537; taurine ABC transporter periplasmic taurine-binding protein 704503 tauA 3195870 tauA Ruegeria pomeroyi DSS-3 taurine ABC transporter periplasmic taurine-binding protein YP_165929.1 703493 D 246200 CDS YP_165930.1 56695580 3194041 704612..705418 1 NC_003911.11 identified by similarity to SP:Q47538; taurine ABC transporter ATP-binding protein 705418 tauB 3194041 tauB Ruegeria pomeroyi DSS-3 taurine ABC transporter ATP-binding protein YP_165930.1 704612 D 246200 CDS YP_165931.1 56695581 3195375 705817..706689 1 NC_003911.11 identified by similarity to SP:Q47539; taurine ABC transporter permease 706689 tauC 3195375 tauC Ruegeria pomeroyi DSS-3 taurine ABC transporter permease YP_165931.1 705817 D 246200 CDS YP_165932.1 56695582 3195740 706831..708459 1 NC_003911.11 activates fatty acids by binding to coenzyme A; acyl-CoA synthetase 708459 3195740 SPO0677 Ruegeria pomeroyi DSS-3 acyl-CoA synthetase YP_165932.1 706831 D 246200 CDS YP_165933.1 56695583 3195947 complement(708546..709505) 1 NC_003911.11 identified by similarity to SP:Q9BSE5; agmatinase 709505 3195947 SPO0678 Ruegeria pomeroyi DSS-3 agmatinase YP_165933.1 708546 R 246200 CDS YP_165934.1 56695584 3196015 complement(709636..710277) 1 NC_003911.11 identified by similarity to SP:O43708; maleylacetoacetate isomerase 710277 hmgC 3196015 hmgC Ruegeria pomeroyi DSS-3 maleylacetoacetate isomerase YP_165934.1 709636 R 246200 CDS YP_165935.1 56695585 3195869 complement(710424..710969) 1 NC_003911.11 glyoxalase 710969 3195869 SPO0680 Ruegeria pomeroyi DSS-3 glyoxalase YP_165935.1 710424 R 246200 CDS YP_165936.1 56695586 3195879 complement(710975..711169) 1 NC_003911.11 identified by similarity to GB:CAE31393.1; hypothetical protein 711169 3195879 SPO0681 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165936.1 710975 R 246200 CDS YP_165937.1 56695587 3195775 complement(711175..712836) 1 NC_003911.11 FAD-dependent oxidoreductase 712836 3195775 SPO0682 Ruegeria pomeroyi DSS-3 FAD-dependent oxidoreductase YP_165937.1 711175 R 246200 CDS YP_165938.1 56695588 3196052 complement(713009..713959) 1 NC_003911.11 metallo-beta-lactamase 713959 3196052 SPO0683 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_165938.1 713009 R 246200 CDS YP_165939.1 56695589 3195669 complement(713963..714322) 1 NC_003911.11 glyoxalase 714322 3195669 SPO0684 Ruegeria pomeroyi DSS-3 glyoxalase YP_165939.1 713963 R 246200 CDS YP_165940.1 56695590 3194878 complement(714330..715583) 1 NC_003911.11 fumarylacetoacetase 715583 hmgB 3194878 hmgB Ruegeria pomeroyi DSS-3 fumarylacetoacetase YP_165940.1 714330 R 246200 CDS YP_165941.1 56695591 3194373 complement(715657..717012) 1 NC_003911.11 An oxygenase that acts to open the ring of homogentisate formingmaleylacetoacetate as part of the catabolism of L-tyrosine and L-phenylalanine; homogentisate 1,2-dioxygenase 717012 hmgA 3194373 hmgA Ruegeria pomeroyi DSS-3 homogentisate 1,2-dioxygenase YP_165941.1 715657 R 246200 CDS YP_165942.1 56695592 3195872 717071..717523 1 NC_003911.11 MarR family transcriptional regulator 717523 3195872 SPO0687 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_165942.1 717071 D 246200 CDS YP_165943.1 56695593 3195979 717598..718845 1 NC_003911.11 guanylate cyclase 718845 3195979 SPO0688 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_165943.1 717598 D 246200 CDS YP_165944.1 56695594 3194579 complement(718846..719655) 1 NC_003911.11 identified by similarity to GB:AAK24136.1; hypothetical protein 719655 3194579 SPO0689 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165944.1 718846 R 246200 CDS YP_165945.1 56698710 3196285 complement(720123..720452) 1 NC_003911.11 identified by similarity to GB:BAC48339.1; hypothetical protein 720452 3196285 SPO0690 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165945.1 720123 R 246200 CDS YP_165946.1 56695595 3195765 complement(720511..721416) 1 NC_003911.11 Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome; GTP-binding protein Era 721416 era 3195765 era Ruegeria pomeroyi DSS-3 GTP-binding protein Era YP_165946.1 720511 R 246200 CDS YP_165947.1 56695596 3193482 721599..722984 1 NC_003911.11 identified by similarity to GB:AAD24211.1; multicopper oxidase 722984 3193482 SPO0692 Ruegeria pomeroyi DSS-3 multicopper oxidase YP_165947.1 721599 D 246200 CDS YP_165948.1 56695597 3194836 complement(723039..724733) 1 NC_003911.11 identified by similarity to GB:AAL17673.1; isobutyryl-CoA dehydrogenase 724733 3194836 SPO0693 Ruegeria pomeroyi DSS-3 isobutyryl-CoA dehydrogenase YP_165948.1 723039 R 246200 CDS YP_165949.1 56695598 3194169 complement(724858..725421) 1 NC_003911.11 hypothetical protein 725421 3194169 SPO0694 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165949.1 724858 R 246200 CDS YP_165950.1 56695599 3194399 complement(725430..725723) 1 NC_003911.11 hypothetical protein 725723 3194399 SPO0695 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165950.1 725430 R 246200 CDS YP_165951.1 56695601 3194867 complement(726145..727224) 1 NC_003911.11 identified by similarity to SP:P09833; molybdate ABC transporter ATP-binding protein 727224 modC 3194867 modC Ruegeria pomeroyi DSS-3 molybdate ABC transporter ATP-binding protein YP_165951.1 726145 R 246200 CDS YP_165952.1 56695600 3194843 complement(727221..727913) 1 NC_003911.11 part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE; molybdate ABC transporter permease 727913 modB 3194843 modB Ruegeria pomeroyi DSS-3 molybdate ABC transporter permease YP_165952.1 727221 R 246200 CDS YP_165953.1 56695602 3193763 complement(727917..728681) 1 NC_003911.11 identified by similarity to SP:P37329; molybdate ABC transporter periplasmic molybdate-binding protein 728681 modA 3193763 modA Ruegeria pomeroyi DSS-3 molybdate ABC transporter periplasmic molybdate-binding protein YP_165953.1 727917 R 246200 CDS YP_165954.1 56695603 3193318 complement(728732..729154) 1 NC_003911.11 identified by similarity to SP:P46930; molybdenum-binding transcriptional regulator 729154 3193318 SPO0700 Ruegeria pomeroyi DSS-3 molybdenum-binding transcriptional regulator YP_165954.1 728732 R 246200 CDS YP_165955.1 56695604 3195539 complement(729188..730213) 1 NC_003911.11 glyceraldehyde-3-phosphate dehydrogenase, type I 730213 gap-1 3195539 gap-1 Ruegeria pomeroyi DSS-3 glyceraldehyde-3-phosphate dehydrogenase, type I YP_165955.1 729188 R 246200 CDS YP_165956.1 56695605 3195845 complement(730361..731347) 1 NC_003911.11 oligopeptide ABC transporter ATP-binding protein 731347 3195845 SPO0702 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter ATP-binding protein YP_165956.1 730361 R 246200 CDS YP_165957.1 56695606 3195190 complement(731344..732339) 1 NC_003911.11 oligopeptide ABC transporter ATP-binding protein 732339 3195190 SPO0703 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter ATP-binding protein YP_165957.1 731344 R 246200 CDS YP_165958.1 56695607 3194918 complement(732336..733460) 1 NC_003911.11 identified by similarity to SP:P42063; oligopeptide ABC transporter permease 733460 3194918 SPO0704 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter permease YP_165958.1 732336 R 246200 CDS YP_165959.1 56695608 3195945 complement(733465..734469) 1 NC_003911.11 Assignment partly based on location in oligopeptide ABC transport gene cluster; oligopeptide ABC transporter permease 734469 3195945 SPO0705 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter permease YP_165959.1 733465 R 246200 CDS YP_165960.1 56695609 3195934 complement(734530..736569) 1 NC_003911.11 Assignment partly based on location in oligopeptide ABC transporter gene cluster.; identified by similarity to SP:Q9X4Y1; oligopeptide ABC transporter periplasmic oligopeptide-binding protein 736569 3195934 SPO0706 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter periplasmic oligopeptide-binding protein YP_165960.1 734530 R 246200 CDS YP_165961.1 56695610 3193428 complement(736566..737441) 1 NC_003911.11 DeoR family transcriptional regulator 737441 3193428 SPO0707 Ruegeria pomeroyi DSS-3 DeoR family transcriptional regulator YP_165961.1 736566 R 246200 CDS YP_165962.1 56695611 3195213 737679..739049 1 NC_003911.11 identified by similarity to GB:AAF98391.2; invasion protein IbeA 739049 3195213 SPO0708 Ruegeria pomeroyi DSS-3 invasion protein IbeA YP_165962.1 737679 D 246200 CDS YP_165963.1 56695612 3195361 complement(739100..740698) 1 NC_003911.11 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase 740698 pckA 3195361 pckA Ruegeria pomeroyi DSS-3 phosphoenolpyruvate carboxykinase YP_165963.1 739100 R 246200 CDS YP_165964.1 56695613 3195446 741039..741743 1 NC_003911.11 identified by similarity to SP:P50350; DNA-binding response regulator ChvI 741743 chvI 3195446 chvI Ruegeria pomeroyi DSS-3 DNA-binding response regulator ChvI YP_165964.1 741039 D 246200 CDS YP_165965.1 56695614 3195818 741777..743486 1 NC_003911.11 sensor histidine kinase ChvG 743486 chvG 3195818 chvG Ruegeria pomeroyi DSS-3 sensor histidine kinase ChvG YP_165965.1 741777 D 246200 CDS YP_165966.1 56695615 3192731 743434..743952 1 NC_003911.11 identified by similarity to SP:O34483; Hpr serine kinase/phosphatase domain-containing protein 743952 3192731 SPO0712 Ruegeria pomeroyi DSS-3 Hpr serine kinase/phosphatase domain-containing protein YP_165966.1 743434 D 246200 CDS YP_165967.2 161598433 3194619 743957..744838 1 NC_003911.11 hypothetical protein 744838 3194619 SPO0713 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165967.2 743957 D 246200 CDS YP_165968.1 56695617 3195950 744835..745227 1 NC_003911.11 PTS system mannose subfamily IIA subunit 745227 3195950 SPO0714 Ruegeria pomeroyi DSS-3 PTS system mannose subfamily IIA subunit YP_165968.1 744835 D 246200 CDS YP_165969.1 56695618 3195949 745244..745513 1 NC_003911.11 phosphocarrier protein HPr 745513 3195949 SPO0715 Ruegeria pomeroyi DSS-3 phosphocarrier protein HPr YP_165969.1 745244 D 246200 CDS YP_165970.1 56695619 3195913 745552..746439 1 NC_003911.11 identified by similarity to PIR:D82434; hypothetical protein 746439 3195913 SPO0716 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165970.1 745552 D 246200 CDS YP_165971.1 56695620 3195358 complement(746531..747406) 1 NC_003911.11 converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase 747406 bhbD 3195358 bhbD Ruegeria pomeroyi DSS-3 3-hydroxybutyryl-CoA dehydrogenase YP_165971.1 746531 R 246200 CDS YP_165972.1 56695621 3195680 747563..748405 1 NC_003911.11 identified by similarity to GB:AAK08138.1; hypothetical protein 748405 3195680 SPO0718 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165972.1 747563 D 246200 CDS YP_165973.1 56695622 3194972 complement(748465..749394) 1 NC_003911.11 identified by similarity to SP:P38974; electron transfer flavoprotein subunit alpha 749394 etfA 3194972 etfA Ruegeria pomeroyi DSS-3 electron transfer flavoprotein subunit alpha YP_165973.1 748465 R 246200 CDS YP_165974.1 56695623 3195524 complement(749394..750152) 1 NC_003911.11 identified by similarity to SP:P38975; electron transfer flavoprotein subunit beta 750152 etfB 3195524 etfB Ruegeria pomeroyi DSS-3 electron transfer flavoprotein subunit beta YP_165974.1 749394 R 246200 CDS YP_165975.1 56695624 3195237 750351..750716 1 NC_003911.11 glyoxalase 750716 3195237 SPO0721 Ruegeria pomeroyi DSS-3 glyoxalase YP_165975.1 750351 D 246200 CDS YP_165976.1 56695625 3195264 complement(750883..751455) 1 NC_003911.11 ATP:cob(I)alamin adenosyltransferase 751455 3195264 SPO0722 Ruegeria pomeroyi DSS-3 ATP:cob(I)alamin adenosyltransferase YP_165976.1 750883 R 246200 CDS YP_165977.1 56695626 3195661 complement(751459..751659) 1 NC_003911.11 identified by similarity to PIR:C98285; hypothetical protein 751659 3195661 SPO0723 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165977.1 751459 R 246200 CDS YP_165978.1 56695627 3195854 complement(751738..752565) 1 NC_003911.11 short chain dehydrogenase/reductase oxidoreductase 752565 3195854 SPO0724 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_165978.1 751738 R 246200 CDS YP_165979.1 56695628 3195493 752176..753495 1 NC_003911.11 hypothetical protein 753495 3195493 SPO0725 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165979.1 752176 D 246200 CDS YP_165980.1 56695629 3193734 753492..755840 1 NC_003911.11 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A 755840 parC 3193734 parC Ruegeria pomeroyi DSS-3 DNA topoisomerase IV subunit A YP_165980.1 753492 D 246200 CDS YP_165981.1 56695630 3194576 755809..756531 1 NC_003911.11 hypothetical protein 756531 3194576 SPO0727 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165981.1 755809 D 246200 CDS YP_165982.1 56695631 3195418 756639..757814 1 NC_003911.11 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 757814 tuf-1 3195418 tuf-1 Ruegeria pomeroyi DSS-3 elongation factor Tu YP_165982.1 756639 D 246200 CDS YP_165983.1 56695632 3193804 complement(758046..758747) 1 NC_003911.11 identified by similarity to GB:AAK22291.1; hypothetical protein 758747 3193804 SPO0729 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165983.1 758046 R 246200 CDS YP_165984.1 56695633 3193942 759232..760005 1 NC_003911.11 identified by similarity to SP:P09392; match to protein family HMM PF00455; glycerol-3-phosphate regulon repressor 760005 glpR 3193942 glpR Ruegeria pomeroyi DSS-3 glycerol-3-phosphate regulon repressor YP_165984.1 759232 D 246200 CDS YP_165985.1 56695634 3195024 759998..761569 1 NC_003911.11 in Escherichia coli this homodimeric enzyme is expressed under aerobic conditions; anaerobic expression is repressed by the arcAB system; converts sn-glycerol-3-phosphate and ubiquinone-8 to dihydroxy acetone phosphate and ubiquinol-8; associates with the cytoplasmic membrane; glycerol-3-phosphate dehydrogenase 761569 glpD 3195024 glpD Ruegeria pomeroyi DSS-3 glycerol-3-phosphate dehydrogenase YP_165985.1 759998 D 246200 CDS YP_165986.1 56695635 3195013 complement(761582..762559) 1 NC_003911.11 identified by similarity to GB:AAC36352.1; match to protein family HMM PF00561; esterase 762559 3195013 SPO0733 Ruegeria pomeroyi DSS-3 esterase YP_165986.1 761582 R 246200 CDS YP_165987.1 56695636 3194222 complement(762661..763461) 1 NC_003911.11 identified by similarity to SP:P76086; PaaX domain-containing protein 763461 3194222 SPO0734 Ruegeria pomeroyi DSS-3 PaaX domain-containing protein YP_165987.1 762661 R 246200 CDS YP_165988.1 56695637 3194459 complement(763540..765561) 1 NC_003911.11 catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA; bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase 765561 paaZ 3194459 paaZ Ruegeria pomeroyi DSS-3 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase YP_165988.1 763540 R 246200 CDS YP_165989.1 56695638 3194675 complement(765718..767070) 1 NC_003911.11 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM 767070 3194675 SPO0736 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_165989.1 765718 R 246200 CDS YP_165990.1 56695639 3194388 complement(767067..767573) 1 NC_003911.11 TRAP dicarboxylate transporter subunit DctQ 767573 3194388 SPO0737 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctQ YP_165990.1 767067 R 246200 CDS YP_165991.1 56695640 3194986 complement(767630..768649) 1 NC_003911.11 identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 768649 3194986 SPO0738 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctP YP_165991.1 767630 R 246200 CDS YP_165992.1 56695641 3193505 complement(768721..770766) 1 NC_003911.11 identified by match to protein family HMM PF00378; match to protein family HMM PF00725; match to protein family HMM PF02737; enoyl-CoA hydratase 770766 3193505 SPO0739 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_165992.1 768721 R 246200 CDS YP_165993.1 56695642 3195412 770869..771654 1 NC_003911.11 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 771654 paaB 3195412 paaB Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_165993.1 770869 D 246200 CDS YP_165994.1 56695643 3195354 771657..772085 1 NC_003911.11 identified by similarity to SP:P76084; match to protein family HMM PF03061; match to protein family HMM TIGR00369; phenylacetic acid degradation protein PaaD 772085 paaD 3195354 paaD Ruegeria pomeroyi DSS-3 phenylacetic acid degradation protein PaaD YP_165994.1 771657 D 246200 CDS YP_165995.1 56695644 3195746 772101..773411 1 NC_003911.11 identified by similarity to GB:AAF26285.1; match to protein family HMM TIGR02155; phenylacetate-CoA ligase 773411 paaF 3195746 paaF Ruegeria pomeroyi DSS-3 phenylacetate-CoA ligase YP_165995.1 772101 D 246200 CDS YP_165996.1 56695645 3195010 773415..774011 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 774011 3195010 SPO0743 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_165996.1 773415 D 246200 CDS YP_165997.1 56695646 3194876 complement(774970..776691) 1 NC_003911.11 identified by similarity to GB:CAE30152.1; hypothetical protein 776691 3194876 SPO0744 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165997.1 774970 R 246200 CDS YP_165998.1 56695647 3195150 complement(776692..778908) 1 NC_003911.11 hypothetical protein 778908 3195150 SPO0745 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165998.1 776692 R 246200 CDS YP_165999.1 56695648 3195844 complement(778868..780238) 1 NC_003911.11 identified by similarity to PIR:C83621; hypothetical protein 780238 3195844 SPO0746 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165999.1 778868 R 246200 CDS YP_166000.1 56695649 3195070 780325..782022 1 NC_003911.11 identified by match to protein family HMM PF03098; peroxidase 782022 3195070 SPO0747 Ruegeria pomeroyi DSS-3 peroxidase YP_166000.1 780325 D 246200 CDS YP_166001.1 56695650 3194477 complement(782079..783101) 1 NC_003911.11 hypothetical protein 783101 3194477 SPO0748 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166001.1 782079 R 246200 CDS YP_166002.1 56695651 3194870 complement(783082..783651) 1 NC_003911.11 identified by similarity to PIR:AE2995; hypothetical protein 783651 3194870 SPO0749 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166002.1 783082 R 246200 CDS YP_166003.1 56695652 3195197 784282..785040 1 NC_003911.11 identified by similarity to GB:CAE14641.1; hypothetical protein 785040 3195197 SPO0750 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166003.1 784282 D 246200 CDS YP_166004.1 56695653 3194759 complement(785123..786295) 1 NC_003911.11 identified by match to protein family HMM PF00211; guanylate cyclase 786295 3194759 SPO0751 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_166004.1 785123 R 246200 CDS YP_166005.1 56695654 3194813 complement(786573..787331) 1 NC_003911.11 phenylacetic acid degradation protein 787331 3194813 SPO0752 Ruegeria pomeroyi DSS-3 phenylacetic acid degradation protein YP_166005.1 786573 R 246200 CDS YP_166006.1 56695655 3195933 complement(787342..788415) 1 NC_003911.11 identified by similarity to SP:P76081; match to protein family HMM PF00111; match to protein family HMM PF00175; match to protein family HMM PF00970; match to protein family HMM TIGR02160; phenylacetic acid degradation oxidoreductase PaaK 788415 paaK 3195933 paaK Ruegeria pomeroyi DSS-3 phenylacetic acid degradation oxidoreductase PaaK YP_166006.1 787342 R 246200 CDS YP_166007.1 56695656 3195585 complement(788426..788887) 1 NC_003911.11 identified by similarity to SP:P76080; match to protein family HMM PF01883; match to protein family HMM TIGR02159; phenylacetic acid degradation protein PaaJ 788887 paaJ 3195585 paaJ Ruegeria pomeroyi DSS-3 phenylacetic acid degradation protein PaaJ YP_166007.1 788426 R 246200 CDS YP_166008.1 56695657 3195321 complement(788892..789653) 1 NC_003911.11 identified by similarity to SP:P76079; match to protein family HMM PF05138; match to protein family HMM TIGR02158; phenylacetic acid degradation protein PaaI 789653 paaI 3195321 paaI Ruegeria pomeroyi DSS-3 phenylacetic acid degradation protein PaaI YP_166008.1 788892 R 246200 CDS YP_166009.1 56695658 3195639 complement(789653..789937) 1 NC_003911.11 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation; phenylacetate-CoA oxygenase subunit PaaB 789937 paaB 3195639 paaB Ruegeria pomeroyi DSS-3 phenylacetate-CoA oxygenase subunit PaaB YP_166009.1 789653 R 246200 CDS YP_166010.1 56695659 3195813 complement(790031..791023) 1 NC_003911.11 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; phenylacetate-CoA oxygenase subunit PaaA 791023 paaA 3195813 paaA Ruegeria pomeroyi DSS-3 phenylacetate-CoA oxygenase subunit PaaA YP_166010.1 790031 R 246200 CDS YP_166011.1 56695660 3195388 complement(791039..792241) 1 NC_003911.11 catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA; beta-ketoadipyl CoA thiolase 792241 3195388 SPO0758 Ruegeria pomeroyi DSS-3 beta-ketoadipyl CoA thiolase YP_166011.1 791039 R 246200 CDS YP_166012.1 56695661 3195677 complement(792463..792786) 1 NC_003911.11 hypothetical protein 792786 3195677 SPO0759 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166012.1 792463 R 246200 CDS YP_166013.1 56695662 3195183 complement(792824..793219) 1 NC_003911.11 identified by match to protein family HMM PF02627; match to protein family HMM TIGR00778; alkylhydroperoxidase 793219 3195183 SPO0760 Ruegeria pomeroyi DSS-3 alkylhydroperoxidase YP_166013.1 792824 R 246200 CDS YP_166014.1 56695663 3193876 complement(793223..794041) 1 NC_003911.11 identified by match to protein family HMM PF04199; match to protein family HMM TIGR01409; cyclase 794041 3193876 SPO0761 Ruegeria pomeroyi DSS-3 cyclase YP_166014.1 793223 R 246200 CDS YP_166015.1 56695664 3195565 794236..794886 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 794886 3195565 SPO0762 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_166015.1 794236 D 246200 CDS YP_166016.1 56695665 3195600 complement(794968..795681) 1 NC_003911.11 identified by match to protein family HMM PF00117; glutamine amidotransferase 795681 3195600 SPO0763 Ruegeria pomeroyi DSS-3 glutamine amidotransferase YP_166016.1 794968 R 246200 CDS YP_166017.1 56695666 3195602 795780..797039 1 NC_003911.11 identified by match to protein family HMM PF00067; cytochrome P450 family protein 797039 3195602 SPO0764 Ruegeria pomeroyi DSS-3 cytochrome P450 family protein YP_166017.1 795780 D 246200 CDS YP_166018.1 56695667 3195087 797079..798368 1 NC_003911.11 identified by match to protein family HMM PF00120; glutamine synthetase 798368 3195087 SPO0765 Ruegeria pomeroyi DSS-3 glutamine synthetase YP_166018.1 797079 D 246200 CDS YP_166019.1 56695668 3195760 798379..798693 1 NC_003911.11 identified by match to protein family HMM PF00111; (Fe-S)-binding protein 798693 3195760 SPO0766 Ruegeria pomeroyi DSS-3 (Fe-S)-binding protein YP_166019.1 798379 D 246200 CDS YP_166020.1 56695669 3195905 798878..799570 1 NC_003911.11 identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 799570 3195905 SPO0767 Ruegeria pomeroyi DSS-3 FkbM family methyltransferase YP_166020.1 798878 D 246200 CDS YP_166021.1 56695670 3195953 complement(799573..800346) 1 NC_003911.11 identified by match to protein family HMM PF01614; IclR family transcriptional regulator 800346 3195953 SPO0768 Ruegeria pomeroyi DSS-3 IclR family transcriptional regulator YP_166021.1 799573 R 246200 CDS YP_166022.1 56695671 3195678 800420..801460 1 NC_003911.11 identified by match to protein family HMM PF03401; hypothetical protein 801460 3195678 SPO0769 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166022.1 800420 D 246200 CDS YP_166023.1 56695672 3194213 801482..802048 1 NC_003911.11 hypothetical protein 802048 3194213 SPO0770 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166023.1 801482 D 246200 CDS YP_166024.1 56695673 3195171 802048..803667 1 NC_003911.11 identified by match to protein family HMM PF01970; hypothetical protein 803667 3195171 SPO0771 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166024.1 802048 D 246200 CDS YP_166025.1 56695674 3194899 803809..805905 1 NC_003911.11 identified by match to protein family HMM PF00378; match to protein family HMM PF00725; match to protein family HMM PF02737; enoyl-CoA hydratase 805905 3194899 SPO0772 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_166025.1 803809 D 246200 CDS YP_166026.1 56695675 3192775 805905..807080 1 NC_003911.11 identified by match to protein family HMM PF00108; match to protein family HMM PF02803; match to protein family HMM TIGR01930; acetyl-CoA acyltransferase/thiolase 807080 3192775 SPO0773 Ruegeria pomeroyi DSS-3 acetyl-CoA acyltransferase/thiolase YP_166026.1 805905 D 246200 CDS YP_166027.1 56695676 3195860 807187..808377 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 808377 3195860 SPO0774 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_166027.1 807187 D 246200 CDS YP_166028.1 56695677 3193308 808383..809510 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 809510 3193308 SPO0775 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_166028.1 808383 D 246200 CDS YP_166029.1 56695678 3195863 809491..809916 1 NC_003911.11 identified by match to protein family HMM PF03061; match to protein family HMM TIGR00369; hypothetical protein 809916 3195863 SPO0776 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166029.1 809491 D 246200 CDS YP_166030.1 56695679 3194199 809916..810683 1 NC_003911.11 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 810683 3194199 SPO0777 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_166030.1 809916 D 246200 CDS YP_166031.1 56695680 3194774 810706..812196 1 NC_003911.11 identified by similarity to SP:P94547; match to protein family HMM PF00501; long-chain-fatty-acid--CoA ligase 812196 3194774 SPO0778 Ruegeria pomeroyi DSS-3 long-chain-fatty-acid--CoA ligase YP_166031.1 810706 D 246200 CDS YP_166032.1 56695681 3195182 complement(812452..813141) 1 NC_003911.11 identified by match to protein family HMM PF00834; match to protein family HMM TIGR01163; ribulose-phosphate 3-epimerase 813141 rpe 3195182 rpe Ruegeria pomeroyi DSS-3 ribulose-phosphate 3-epimerase YP_166032.1 812452 R 246200 CDS YP_166033.1 56695682 3195497 813316..814137 1 NC_003911.11 identified by similarity to SP:P16677; match to protein family HMM PF00005; phosphonate ABC transporter ATP-binding protein 814137 phoC 3195497 phoC Ruegeria pomeroyi DSS-3 phosphonate ABC transporter ATP-binding protein YP_166033.1 813316 D 246200 CDS YP_166034.1 56695683 3194026 814166..815101 1 NC_003911.11 identified by similarity to SP:P16682; phosphonate ABC transporter periplasmic phosphonate-binding protein 815101 phnD 3194026 phnD Ruegeria pomeroyi DSS-3 phosphonate ABC transporter periplasmic phosphonate-binding protein YP_166034.1 814166 D 246200 CDS YP_166035.1 56695684 3195615 815167..816048 1 NC_003911.11 identified by similarity to SP:P16683; match to protein family HMM PF00528; phosphonate ABC transporter permease 816048 phoE 3195615 phoE Ruegeria pomeroyi DSS-3 phosphonate ABC transporter permease YP_166035.1 815167 D 246200 CDS YP_166036.1 56695685 3195365 816045..817415 1 NC_003911.11 identified by similarity to PIR:H95946; match to protein family HMM PF00528; phosphonate ABC transporter permease 817415 phnE 3195365 phnE Ruegeria pomeroyi DSS-3 phosphonate ABC transporter permease YP_166036.1 816045 D 246200 CDS YP_166037.1 56695686 3195036 817437..818051 1 NC_003911.11 identified by similarity to SP:P26838; match to protein family HMM PF00132; chloramphenicol acetyltransferase 818051 3195036 SPO0784 Ruegeria pomeroyi DSS-3 chloramphenicol acetyltransferase YP_166037.1 817437 D 246200 CDS YP_166038.1 56695687 3195078 818129..818983 1 NC_003911.11 2-dehydro-3-deoxygalactonokinase 818983 3195078 SPO0785 Ruegeria pomeroyi DSS-3 2-dehydro-3-deoxygalactonokinase YP_166038.1 818129 D 246200 CDS YP_166039.1 56695688 3195875 819040..819444 1 NC_003911.11 identified by match to protein family HMM PF03061; thioesterase 819444 3195875 SPO0786 Ruegeria pomeroyi DSS-3 thioesterase YP_166039.1 819040 D 246200 CDS YP_166040.1 56695689 3194551 complement(819426..820082) 1 NC_003911.11 catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate; phosphoglycolate phosphatase 820082 gph-1 3194551 gph-1 Ruegeria pomeroyi DSS-3 phosphoglycolate phosphatase YP_166040.1 819426 R 246200 CDS YP_166041.1 56695690 3195040 complement(820377..821297) 1 NC_003911.11 identified by match to protein family HMM PF00753; match to protein family HMM TIGR01409; metallo-beta-lactamase 821297 3195040 SPO0788 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_166041.1 820377 R 246200 CDS YP_166042.1 56695691 3195095 821481..821648 1 NC_003911.11 identified by similarity to GB:AAQ61556.1; hypothetical protein 821648 3195095 SPO0789 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166042.1 821481 D 246200 CDS YP_166043.1 56695692 3193737 821645..822088 1 NC_003911.11 hypothetical protein 822088 3193737 SPO0790 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166043.1 821645 D 246200 CDS YP_166044.1 56695693 3194770 complement(822093..825149) 1 NC_003911.11 identified by match to protein family HMM PF00202; match to protein family HMM PF01551; hypothetical protein 825149 3194770 SPO0791 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166044.1 822093 R 246200 CDS YP_166045.1 56695694 3194481 complement(825265..826137) 1 NC_003911.11 identified by match to protein family HMM PF03446; match to protein family HMM TIGR00872; match to protein family HMM TIGR00873; 6-phosphogluconate dehydrogenase 826137 3194481 SPO0792 Ruegeria pomeroyi DSS-3 6-phosphogluconate dehydrogenase YP_166045.1 825265 R 246200 CDS YP_166046.1 56695695 3194968 complement(826233..826622) 1 NC_003911.11 identified by match to protein family HMM PF00376; match to protein family HMM TIGR02044; Cu(I)-responsive transcriptional regulator 826622 cueR 3194968 cueR Ruegeria pomeroyi DSS-3 Cu(I)-responsive transcriptional regulator YP_166046.1 826233 R 246200 CDS YP_166047.1 56695696 3193988 complement(826633..829119) 1 NC_003911.11 identified by similarity to SP:P37279; match to protein family HMM PF00122; match to protein family HMM PF00403; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01511; match to protein family HMM TIGR01525; copper-translocating P-type ATPase 829119 3193988 SPO0794 Ruegeria pomeroyi DSS-3 copper-translocating P-type ATPase YP_166047.1 826633 R 246200 CDS YP_166048.1 56695697 3195238 complement(829201..829956) 1 NC_003911.11 identified by similarity to PIR:E83152; match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 829956 3195238 SPO0795 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_166048.1 829201 R 246200 CDS YP_166049.1 56695698 3195367 complement(829953..830876) 1 NC_003911.11 identified by similarity to GB:BAC72444.1; hypothetical protein 830876 3195367 SPO0796 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166049.1 829953 R 246200 CDS YP_166050.1 56695699 3194595 complement(830873..831775) 1 NC_003911.11 identified by match to protein family HMM PF01758; bile acid transporter family protein 831775 3194595 SPO0797 Ruegeria pomeroyi DSS-3 bile acid transporter family protein YP_166050.1 830873 R 246200 CDS YP_166051.1 56695700 3195453 complement(831772..833088) 1 NC_003911.11 identified by similarity to GB:AAS47561.1; monooxygenase domain-containing protein 833088 3195453 SPO0798 Ruegeria pomeroyi DSS-3 monooxygenase domain-containing protein YP_166051.1 831772 R 246200 CDS YP_166052.1 56695701 3195157 833156..833818 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 833818 3195157 SPO0799 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_166052.1 833156 D 246200 CDS YP_166053.1 56695702 3195931 complement(833887..835335) 1 NC_003911.11 identified by similarity to GB:AAC13371.1; match to protein family HMM PF00884; choline sulfatase 835335 3195931 SPO0800 Ruegeria pomeroyi DSS-3 choline sulfatase YP_166053.1 833887 R 246200 CDS YP_166054.1 56695703 3193580 complement(835353..836960) 1 NC_003911.11 identified by similarity to PIR:T08074; match to protein family HMM PF00501; 4-coumarate--CoA ligase 836960 fadD 3193580 fadD Ruegeria pomeroyi DSS-3 4-coumarate--CoA ligase YP_166054.1 835353 R 246200 CDS YP_166055.1 56695704 3195039 837242..838918 1 NC_003911.11 in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins; 30S ribosomal protein S1 838918 rpsA 3195039 rpsA Ruegeria pomeroyi DSS-3 30S ribosomal protein S1 YP_166055.1 837242 D 246200 CDS YP_166056.1 56695705 3193570 complement(839256..839723) 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX domain-containing protein 839723 3193570 SPO0803 Ruegeria pomeroyi DSS-3 NUDIX domain-containing protein YP_166056.1 839256 R 246200 CDS YP_166057.1 56695706 3195204 840121..840405 1 NC_003911.11 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit beta 840405 ihfB 3195204 ihfB Ruegeria pomeroyi DSS-3 integration host factor subunit beta YP_166057.1 840121 D 246200 CDS YP_166058.1 56695707 3195956 840409..840765 1 NC_003911.11 identified by similarity to GB:CAE25511.1; hypothetical protein 840765 3195956 SPO0805 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166058.1 840409 D 246200 CDS YP_166059.1 56695708 3195077 840774..841424 1 NC_003911.11 catalyzes the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)-anthranilate in tryptophan biosynthesis; N-(5'-phosphoribosyl)anthranilate isomerase 841424 trpF 3195077 trpF Ruegeria pomeroyi DSS-3 N-(5'-phosphoribosyl)anthranilate isomerase YP_166059.1 840774 D 246200 CDS YP_166060.1 56695709 3195097 841540..841719 1 NC_003911.11 hypothetical protein 841719 3195097 SPO0807 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166060.1 841540 D 246200 CDS YP_166061.1 56695710 3193893 841825..843075 1 NC_003911.11 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 843075 trpB 3193893 trpB Ruegeria pomeroyi DSS-3 tryptophan synthase subunit beta YP_166061.1 841825 D 246200 CDS YP_166062.1 56695711 3195611 complement(843088..843465) 1 NC_003911.11 identified by similarity to GB:AAD29263.1; hypothetical protein 843465 3195611 SPO0809 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166062.1 843088 R 246200 CDS YP_166063.1 56695712 3193861 complement(843475..844638) 1 NC_003911.11 identified by similarity to GB:BAA01524.1; match to protein family HMM PF00144; 6-aminohexanoate-dimer hydrolase 844638 3193861 SPO0810 Ruegeria pomeroyi DSS-3 6-aminohexanoate-dimer hydrolase YP_166063.1 843475 R 246200 CDS YP_166064.1 56695713 3195572 complement(844717..845436) 1 NC_003911.11 Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase 845436 pth 3195572 pth Ruegeria pomeroyi DSS-3 peptidyl-tRNA hydrolase YP_166064.1 844717 R 246200 CDS YP_166065.1 56695714 3194994 complement(845578..846201) 1 NC_003911.11 the Ctc family of proteins consists of two types, one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response; 50S ribosomal protein L25 846201 rplY 3194994 rplY Ruegeria pomeroyi DSS-3 50S ribosomal protein L25 YP_166065.1 845578 R 246200 CDS YP_166066.1 56695715 3195125 complement(846327..847490) 1 NC_003911.11 identified by similarity to SP:P46454; match to protein family HMM PF01070; L-lactate dehydrogenase 847490 3195125 SPO0813 Ruegeria pomeroyi DSS-3 L-lactate dehydrogenase YP_166066.1 846327 R 246200 CDS YP_166067.1 56695716 3195110 847599..848042 1 NC_003911.11 identified by match to protein family HMM PF01575; acyl dehydratase MaoC 848042 3195110 SPO0814 Ruegeria pomeroyi DSS-3 acyl dehydratase MaoC YP_166067.1 847599 D 246200 CDS YP_166068.1 56695717 3195134 complement(848046..848837) 1 NC_003911.11 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha 848837 trpA 3195134 trpA Ruegeria pomeroyi DSS-3 tryptophan synthase subunit alpha YP_166068.1 848046 R 246200 CDS YP_166069.1 56695718 3195164 complement(848916..849404) 1 NC_003911.11 identified by similarity to GB:AAN66362.1; hypothetical protein 849404 3195164 SPO0816 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166069.1 848916 R 246200 CDS YP_166070.1 56695719 3195076 849588..850685 1 NC_003911.11 translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1; GTP-dependent nucleic acid-binding protein EngD 850685 ychF 3195076 ychF Ruegeria pomeroyi DSS-3 GTP-dependent nucleic acid-binding protein EngD YP_166070.1 849588 D 246200 CDS YP_166071.1 56695720 3195152 complement(850682..851281) 1 NC_003911.11 identified by similarity to GB:AAL18255.1; match to protein family HMM PF01124; MAPEG family protein 851281 3195152 SPO0818 Ruegeria pomeroyi DSS-3 MAPEG family protein YP_166071.1 850682 R 246200 CDS YP_166072.1 56695721 3195939 851411..852577 1 NC_003911.11 identified by match to protein family HMM PF01979; amidohydrolase 852577 3195939 SPO0819 Ruegeria pomeroyi DSS-3 amidohydrolase YP_166072.1 851411 D 246200 CDS YP_166073.1 56695722 3195002 852622..853734 1 NC_003911.11 identified by match to protein family HMM PF02515; CAIB/BAIF family protein 853734 3195002 SPO0820 Ruegeria pomeroyi DSS-3 CAIB/BAIF family protein YP_166073.1 852622 D 246200 CDS YP_166074.1 56695723 3194566 complement(853729..854166) 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 854166 3194566 SPO0821 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_166074.1 853729 R 246200 CDS YP_166075.1 56695724 3194996 complement(854229..854960) 1 NC_003911.11 identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 854960 3194996 SPO0822 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_166075.1 854229 R 246200 CDS YP_166076.1 56695725 3194473 complement(854923..855696) 1 NC_003911.11 identified by similarity to SP:P22730; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 855696 3194473 SPO0823 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_166076.1 854923 R 246200 CDS YP_166077.1 56695726 3195212 complement(855693..857537) 1 NC_003911.11 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 857537 3195212 SPO0824 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_166077.1 855693 R 246200 CDS YP_166078.1 56695727 3195410 complement(857605..858915) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF01094; branched-chain amino acid ABC transporter substrate-binding protein 858915 3195410 SPO0825 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter substrate-binding protein YP_166078.1 857605 R 246200 CDS YP_166079.1 56695728 3195398 complement(858912..859493) 1 NC_003911.11 identified by similarity to GB:AAR38363.1; match to protein family HMM PF06684; hypothetical protein 859493 3195398 SPO0826 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166079.1 858912 R 246200 CDS YP_166080.1 56695729 3195119 complement(859490..860077) 1 NC_003911.11 identified by similarity to GB:AAR38364.1; match to protein family HMM PF06684; hypothetical protein 860077 3195119 SPO0827 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166080.1 859490 R 246200 CDS YP_166081.1 56695730 3195052 complement(860064..860933) 1 NC_003911.11 identified by similarity to GB:AAR38365.1; hypothetical protein 860933 3195052 SPO0828 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166081.1 860064 R 246200 CDS YP_166082.1 56695731 3195138 complement(860930..862423) 1 NC_003911.11 identified by similarity to GB:AAR38366.1; hypothetical protein 862423 3195138 SPO0829 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166082.1 860930 R 246200 CDS YP_166083.1 56695732 3195146 complement(862416..865163) 1 NC_003911.11 identified by match to protein family HMM PF00111; match to protein family HMM PF01315; match to protein family HMM PF01799; match to protein family HMM PF02738; xanthine dehydrogenase, small/large subunits 865163 3195146 SPO0830 Ruegeria pomeroyi DSS-3 xanthine dehydrogenase, small/large subunits YP_166083.1 862416 R 246200 CDS YP_166084.1 56695733 3195136 complement(865160..865987) 1 NC_003911.11 identified by match to protein family HMM PF00941; xanthine dehydrogenase, medium subunit 865987 3195136 SPO0831 Ruegeria pomeroyi DSS-3 xanthine dehydrogenase, medium subunit YP_166084.1 865160 R 246200 CDS YP_166085.1 56695734 3195123 866161..867018 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 867018 3195123 SPO0832 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_166085.1 866161 D 246200 CDS YP_166086.1 56695735 3195069 867103..868806 1 NC_003911.11 identified by similarity to GB:AAN03798.1; match to protein family HMM PF01257; match to protein family HMM PF01512; formate dehydrogenase subunit beta 868806 3195069 SPO0833 Ruegeria pomeroyi DSS-3 formate dehydrogenase subunit beta YP_166086.1 867103 D 246200 CDS YP_166087.1 56695736 3194589 868808..871585 1 NC_003911.11 identified by match to protein family HMM PF00037; match to protein family HMM PF00111; match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; match to protein family HMM TIGR01591; formate dehydrogenase subunit alpha 871585 3194589 SPO0834 Ruegeria pomeroyi DSS-3 formate dehydrogenase subunit alpha YP_166087.1 868808 D 246200 CDS YP_166088.1 56695737 3195133 871766..872560 1 NC_003911.11 identified by similarity to GB:AAC38443.1; match to protein family HMM PF04199; cyclase 872560 3195133 SPO0835 Ruegeria pomeroyi DSS-3 cyclase YP_166088.1 871766 D 246200 CDS YP_166089.1 56695738 3193050 872582..873097 1 NC_003911.11 identified by similarity to GB:BAB48851.1; hypothetical protein 873097 3193050 SPO0836 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166089.1 872582 D 246200 CDS YP_166090.1 56695739 3194988 873206..874339 1 NC_003911.11 hypothetical protein 874339 3194988 SPO0837 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166090.1 873206 D 246200 CDS YP_166091.1 56695740 3195690 874894..875658 1 NC_003911.11 identified by match to protein family HMM PF02397; sugar transferase 875658 3195690 SPO0838 Ruegeria pomeroyi DSS-3 sugar transferase YP_166091.1 874894 D 246200 CDS YP_166092.1 56695741 3195974 875694..876629 1 NC_003911.11 identified by similarity to SP:Q45409; exopolysaccharide biosynthesis domain-containing protein 876629 3195974 SPO0839 Ruegeria pomeroyi DSS-3 exopolysaccharide biosynthesis domain-containing protein YP_166092.1 875694 D 246200 CDS YP_166093.1 56695742 3195379 876722..878005 1 NC_003911.11 identified by match to protein family HMM PF02706; chain length determinant protein 878005 3195379 SPO0840 Ruegeria pomeroyi DSS-3 chain length determinant protein YP_166093.1 876722 D 246200 CDS YP_166094.1 56695743 3192809 complement(878016..879374) 1 NC_003911.11 identified by match to protein family HMM PF01943; polysaccharide biosynthesis protein 879374 3192809 SPO0841 Ruegeria pomeroyi DSS-3 polysaccharide biosynthesis protein YP_166094.1 878016 R 246200 CDS YP_166095.1 56695744 3195858 879591..880796 1 NC_003911.11 identified by match to protein family HMM PF00534; glycoside hydrolase 880796 3195858 SPO0842 Ruegeria pomeroyi DSS-3 glycoside hydrolase YP_166095.1 879591 D 246200 CDS YP_166096.1 56695745 3195596 complement(880836..881681) 1 NC_003911.11 identified by match to protein family HMM PF00535; glycosyl transferase family protein 881681 3195596 SPO0843 Ruegeria pomeroyi DSS-3 glycosyl transferase family protein YP_166096.1 880836 R 246200 CDS YP_166097.1 56695746 3195861 complement(881678..884215) 1 NC_003911.11 hypothetical protein 884215 3195861 SPO0844 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166097.1 881678 R 246200 CDS YP_166098.1 56695747 3194383 complement(884212..885159) 1 NC_003911.11 hypothetical protein 885159 3194383 SPO0845 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166098.1 884212 R 246200 CDS YP_166099.1 56695748 3193236 complement(885191..885862) 1 NC_003911.11 identified by similarity to GB:AAG43513.1; match to protein family HMM PF01648; phosphopantetheinyl transferase PptA 885862 3193236 SPO0846 Ruegeria pomeroyi DSS-3 phosphopantetheinyl transferase PptA YP_166099.1 885191 R 246200 CDS YP_166100.1 56695749 3195891 complement(885859..890463) 1 NC_003911.11 identified by similarity to GB:CAC01603.1; match to protein family HMM PF00296; match to protein family HMM PF00501; match to protein family HMM PF00550; match to protein family HMM PF00551; match to protein family HMM PF02911; match to protein family HMM TIGR01733; non-ribosomal peptide synthetase 890463 3195891 SPO0847 Ruegeria pomeroyi DSS-3 non-ribosomal peptide synthetase YP_166100.1 885859 R 246200 CDS YP_166101.1 56695750 3193835 complement(890460..891467) 1 NC_003911.11 identified by match to protein family HMM PF00535; glycosyl transferase family protein 891467 3193835 SPO0848 Ruegeria pomeroyi DSS-3 glycosyl transferase family protein YP_166101.1 890460 R 246200 CDS YP_166102.1 56695751 3193890 complement(891472..897897) 1 NC_003911.11 identified by similarity to GB:CAD70195.1; match to protein family HMM PF00109; match to protein family HMM PF00550; match to protein family HMM PF00698; match to protein family HMM PF00975; match to protein family HMM PF02801; non-ribosomal peptide synthase 897897 3193890 SPO0849 Ruegeria pomeroyi DSS-3 non-ribosomal peptide synthase YP_166102.1 891472 R 246200 CDS YP_166103.1 56695752 3195681 complement(898157..899653) 1 NC_003911.11 hypothetical protein 899653 3195681 SPO0850 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166103.1 898157 R 246200 CDS YP_166104.1 56695753 3193690 899799..900551 1 NC_003911.11 identified by similarity to GB:BAC55144.1; match to protein family HMM PF03808; match to protein family HMM TIGR00696; WecB/TagA/CpsF family glycosyl transferase 900551 3193690 SPO0851 Ruegeria pomeroyi DSS-3 WecB/TagA/CpsF family glycosyl transferase YP_166104.1 899799 D 246200 CDS YP_166105.1 56695754 3195862 complement(900554..902653) 1 NC_003911.11 identified by match to protein family HMM PF01408; Gfo/Idh/MocA family oxidoreductase 902653 3195862 SPO0852 Ruegeria pomeroyi DSS-3 Gfo/Idh/MocA family oxidoreductase YP_166105.1 900554 R 246200 CDS YP_166106.1 56695755 3195817 complement(902661..903626) 1 NC_003911.11 identified by match to protein family HMM PF00535; glycosyl transferase family protein 903626 3195817 SPO0853 Ruegeria pomeroyi DSS-3 glycosyl transferase family protein YP_166106.1 902661 R 246200 CDS YP_166107.1 56695756 3195928 complement(903623..904702) 1 NC_003911.11 identified by match to protein family HMM PF00534; glycoside hydrolase 904702 3195928 SPO0854 Ruegeria pomeroyi DSS-3 glycoside hydrolase YP_166107.1 903623 R 246200 CDS YP_166108.1 56695757 3193306 904917..906365 1 NC_003911.11 identified by similarity to SP:P09099; match to protein family HMM PF00370; match to protein family HMM PF02782; match to protein family HMM TIGR01312; xylulokinase 906365 xylB 3193306 xylB Ruegeria pomeroyi DSS-3 xylulokinase YP_166108.1 904917 D 246200 CDS YP_166109.1 56695758 3195629 906362..907666 1 NC_003911.11 catalyzes the interconversion of D-xylose to D-xylulose; xylose isomerase 907666 xylA 3195629 xylA Ruegeria pomeroyi DSS-3 xylose isomerase YP_166109.1 906362 D 246200 CDS YP_166110.1 56695759 3195652 907689..908624 1 NC_003911.11 identified by match to protein family HMM PF01263; aldose 1-epimerase 908624 galM 3195652 galM Ruegeria pomeroyi DSS-3 aldose 1-epimerase YP_166110.1 907689 D 246200 CDS YP_166111.1 56695760 3194938 908621..909919 1 NC_003911.11 identified by similarity to SP:Q49128; methylamine utilization protein MauG 909919 3194938 SPO0858 Ruegeria pomeroyi DSS-3 methylamine utilization protein MauG YP_166111.1 908621 D 246200 CDS YP_166112.1 56695761 3195384 complement(909977..911506) 1 NC_003911.11 identified by match to protein family HMM PF01839; hypothetical protein 911506 3195384 SPO0859 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166112.1 909977 R 246200 CDS YP_166113.1 56695762 3195885 complement(911496..912692) 1 NC_003911.11 identified by similarity to SP:P16557; match to protein family HMM PF00480; xylose repressor 912692 3195885 SPO0860 Ruegeria pomeroyi DSS-3 xylose repressor YP_166113.1 911496 R 246200 CDS YP_166114.1 56695763 3195789 912912..913940 1 NC_003911.11 identified by similarity to SP:P37387; match to protein family HMM PF00532; xylose ABC transporter periplasmic xylose-binding protein 913940 xylF 3195789 xylF Ruegeria pomeroyi DSS-3 xylose ABC transporter periplasmic xylose-binding protein YP_166114.1 912912 D 246200 CDS YP_166115.1 56695764 3195938 914007..915305 1 NC_003911.11 identified by similarity to SP:P37389; match to protein family HMM PF02653; xylose ABC transporter permease 915305 xylH 3195938 xylH Ruegeria pomeroyi DSS-3 xylose ABC transporter permease YP_166115.1 914007 D 246200 CDS YP_166116.1 56695765 3195820 915302..916072 1 NC_003911.11 identified by match to protein family HMM PF00005; xylose ABC transporter ATP-binding protein 916072 xylG 3195820 xylG Ruegeria pomeroyi DSS-3 xylose ABC transporter ATP-binding protein YP_166116.1 915302 D 246200 CDS YP_166117.1 56695766 3195769 916075..916998 1 NC_003911.11 glucokinase 916998 3195769 SPO0864 Ruegeria pomeroyi DSS-3 glucokinase YP_166117.1 916075 D 246200 CDS YP_166118.1 56695767 3195791 916989..917981 1 NC_003911.11 identified by match to protein family HMM PF01408; match to protein family HMM PF02894; Gfo/Idh/MocA family oxidoreductase 917981 3195791 SPO0865 Ruegeria pomeroyi DSS-3 Gfo/Idh/MocA family oxidoreductase YP_166118.1 916989 D 246200 CDS YP_166119.1 56695768 3195728 complement(918039..919829) 1 NC_003911.11 identified by match to protein family HMM PF01019; gamma-glutamyltranspeptidase 919829 3195728 SPO0866 Ruegeria pomeroyi DSS-3 gamma-glutamyltranspeptidase YP_166119.1 918039 R 246200 CDS YP_166120.1 56695769 3195346 complement(919833..923915) 1 NC_003911.11 identified by similarity to GB:AAN29006.1; match to protein family HMM PF04357; hypothetical protein 923915 3195346 SPO0867 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166120.1 919833 R 246200 CDS YP_166121.1 56695770 3195797 complement(923915..925720) 1 NC_003911.11 identified by match to protein family HMM PF01103; OMP85 family outer membrane protein 925720 3195797 SPO0868 Ruegeria pomeroyi DSS-3 OMP85 family outer membrane protein YP_166121.1 923915 R 246200 CDS YP_166122.1 56695771 3194596 complement(925865..927094) 1 NC_003911.11 identified by match to protein family HMM PF00034; match to protein family HMM PF06181; hypothetical protein 927094 3194596 SPO0869 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166122.1 925865 R 246200 CDS YP_166123.1 56695772 3193205 927189..928112 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 928112 3193205 SPO0870 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_166123.1 927189 D 246200 CDS YP_166124.1 56695773 3195386 complement(928331..928687) 1 NC_003911.11 identified by match to protein family HMM PF00576; transthyretin family protein 928687 3195386 SPO0871 Ruegeria pomeroyi DSS-3 transthyretin family protein YP_166124.1 928331 R 246200 CDS YP_166125.1 56695774 3195926 928972..930387 1 NC_003911.11 polysaccharide deacetylase 930387 3195926 SPO0872 Ruegeria pomeroyi DSS-3 polysaccharide deacetylase YP_166125.1 928972 D 246200 CDS YP_166126.1 56695775 3195530 930384..930872 1 NC_003911.11 catalyzes the formation of glyoxylate from (S)-ureidoglycolate; ureidoglycolate hydrolase 930872 allA 3195530 allA Ruegeria pomeroyi DSS-3 ureidoglycolate hydrolase YP_166126.1 930384 D 246200 CDS YP_166127.1 56695776 3195822 930939..932351 1 NC_003911.11 identified by match to protein family HMM PF00860; match to protein family HMM TIGR00801; xanthine/uracil permease 932351 3195822 SPO0874 Ruegeria pomeroyi DSS-3 xanthine/uracil permease YP_166127.1 930939 D 246200 CDS YP_166128.1 56695777 3195512 complement(932526..933509) 1 NC_003911.11 identified by match to protein family HMM PF00044; match to protein family HMM PF02800; glyceraldehyde-3-phosphate dehydrogenase, type I 933509 gap-2 3195512 gap-2 Ruegeria pomeroyi DSS-3 glyceraldehyde-3-phosphate dehydrogenase, type I YP_166128.1 932526 R 246200 CDS YP_166129.1 56695778 3195641 complement(933712..934539) 1 NC_003911.11 identified by similarity to GB:BAB51632.1; match to protein family HMM PF06038; hypothetical protein 934539 3195641 SPO0876 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166129.1 933712 R 246200 CDS YP_166130.1 56695779 3193998 934903..936054 1 NC_003911.11 identified by similarity to GB:AAM05262.1; hypothetical protein 936054 3193998 SPO0877 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166130.1 934903 D 246200 CDS YP_166131.1 56695780 3195867 936297..936656 1 NC_003911.11 identified by similarity to SP:P23884; match to protein family HMM PF01597; match to protein family HMM TIGR00527; glycine cleavage system H protein 936656 gcvH-1 3195867 gcvH-1 Ruegeria pomeroyi DSS-3 glycine cleavage system H protein YP_166131.1 936297 D 246200 CDS YP_166132.1 56695781 3194469 936870..938105 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 938105 3194469 SPO0879 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_166132.1 936870 D 246200 CDS YP_166133.1 56695782 3193980 938111..938902 1 NC_003911.11 identified by similarity to PIR:T36459; hypothetical protein 938902 3193980 SPO0880 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166133.1 938111 D 246200 CDS YP_166134.1 56695783 3192876 complement(938910..939143) 1 NC_003911.11 hypothetical protein 939143 3192876 SPO0881 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166134.1 938910 R 246200 CDS YP_166135.1 56695784 3194505 939782..940129 1 NC_003911.11 hypothetical protein 940129 3194505 SPO0882 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166135.1 939782 D 246200 CDS YP_166136.1 56695785 3194120 940268..940918 1 NC_003911.11 identified by similarity to GB:CAE26317.1; hypothetical protein 940918 3194120 SPO0883 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166136.1 940268 D 246200 CDS YP_166137.1 56695786 3195246 940903..941802 1 NC_003911.11 identified by match to protein family HMM PF03824; hypothetical protein 941802 3195246 SPO0884 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166137.1 940903 D 246200 CDS YP_166138.1 56695787 3195895 complement(941799..942734) 1 NC_003911.11 identified by match to protein family HMM PF00561; alpha/beta hydrolase 942734 3195895 SPO0885 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_166138.1 941799 R 246200 CDS YP_166139.1 56695788 3195778 942925..943212 1 NC_003911.11 10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring; co-chaperonin GroES 943212 groES 3195778 groES Ruegeria pomeroyi DSS-3 co-chaperonin GroES YP_166139.1 942925 D 246200 CDS YP_166140.1 56695789 3194998 943275..944915 1 NC_003911.11 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is not essential for growth; molecular chaperone GroEL 944915 groEL 3194998 groEL Ruegeria pomeroyi DSS-3 molecular chaperone GroEL YP_166140.1 943275 D 246200 CDS YP_166141.1 56695790 3195231 945190..945660 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 945660 3195231 SPO0888 Ruegeria pomeroyi DSS-3 acetyltransferase YP_166141.1 945190 D 246200 CDS YP_166142.1 56695791 3195642 945708..946550 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 946550 3195642 SPO0889 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166142.1 945708 D 246200 CDS YP_166143.1 56695792 3193652 946589..947362 1 NC_003911.11 identified by similarity to GB:AAM73853.1; lipase 947362 3193652 SPO0890 Ruegeria pomeroyi DSS-3 lipase YP_166143.1 946589 D 246200 CDS YP_166144.1 56695793 3195911 947359..948507 1 NC_003911.11 identified by similarity to SP:P16689; match to protein family HMM PF01979; alkylphosphonate utilization protein PhnM 948507 3195911 SPO0891 Ruegeria pomeroyi DSS-3 alkylphosphonate utilization protein PhnM YP_166144.1 947359 D 246200 CDS YP_166145.1 56695794 3194564 complement(948640..949713) 1 NC_003911.11 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway; phosphoribosylaminoimidazole carboxylase ATPase subunit 949713 purK 3194564 purK Ruegeria pomeroyi DSS-3 phosphoribosylaminoimidazole carboxylase ATPase subunit YP_166145.1 948640 R 246200 CDS YP_166146.1 56695795 3195654 complement(949706..950194) 1 NC_003911.11 identified by similarity to SP:P09028; match to protein family HMM PF00731; match to protein family HMM TIGR01162; phosphoribosylaminoimidazole carboxylase catalytic subunit 950194 purE 3195654 purE Ruegeria pomeroyi DSS-3 phosphoribosylaminoimidazole carboxylase catalytic subunit YP_166146.1 949706 R 246200 CDS YP_166147.1 56695796 3195333 complement(950284..950535) 1 NC_003911.11 identified by similarity to GB:BAC52375.1; match to protein family HMM PF04325; hypothetical protein 950535 3195333 SPO0894 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166147.1 950284 R 246200 CDS YP_166148.1 56695797 3195429 950677..951090 1 NC_003911.11 identified by match to protein family HMM PF00011; heat shock protein 20 951090 3195429 SPO0895 Ruegeria pomeroyi DSS-3 heat shock protein 20 YP_166148.1 950677 D 246200 CDS YP_166149.1 56695798 3194196 951094..951318 1 NC_003911.11 identified by similarity to GB:AAK25555.1; hypothetical protein 951318 3194196 SPO0896 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166149.1 951094 D 246200 CDS YP_166150.1 56695799 3195731 951414..952292 1 NC_003911.11 identified by match to protein family HMM PF02567; match to protein family HMM TIGR00654; PhzF family phenazine biosynthesis protein 952292 3195731 SPO0897 Ruegeria pomeroyi DSS-3 PhzF family phenazine biosynthesis protein YP_166150.1 951414 D 246200 CDS YP_166151.1 56695800 3195946 952299..953159 1 NC_003911.11 identified by similarity to PIR:AH1879; hypothetical protein 953159 3195946 SPO0898 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166151.1 952299 D 246200 CDS YP_166152.1 56695801 3195994 953214..954386 1 NC_003911.11 hypothetical protein 954386 3195994 SPO0899 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166152.1 953214 D 246200 CDS YP_166153.1 56695802 3193730 complement(954455..956164) 1 NC_003911.11 in Rhizobium meliloti this protein is involved in the synthesis of nodulation factors that are active on the roots of alfalfa; catalyzes formation of activated sulfate intermediate; converts ATP and sulfate to diphosphate and adenylylsulfate and then ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; the activated intermediate is transferred to the nodulation factors by NodH; may interact with NodP and NodQ; similar to the CysD and CysN proteins from Escherichia coli involved in cysteine biosynthesis; bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase 956164 sat 3193730 sat Ruegeria pomeroyi DSS-3 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase YP_166153.1 954455 R 246200 CDS YP_166154.1 56695803 3194090 complement(956356..958053) 1 NC_003911.11 identified by match to protein family HMM PF00111; match to protein family HMM PF00211; guanylate cyclase 958053 3194090 SPO0901 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_166154.1 956356 R 246200 CDS YP_166155.1 56695804 3195584 complement(958113..958577) 1 NC_003911.11 identified by similarity to GB:AAM35160.1; hypothetical protein 958577 3195584 SPO0902 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166155.1 958113 R 246200 CDS YP_166156.1 56695805 3195877 complement(958582..959523) 1 NC_003911.11 identified by match to protein family HMM PF00070; match to protein family HMM TIGR01292; thioredoxin-disulfide reductase 959523 trxB 3195877 trxB Ruegeria pomeroyi DSS-3 thioredoxin-disulfide reductase YP_166156.1 958582 R 246200 CDS YP_166157.1 56695806 3195548 959740..960240 1 NC_003911.11 identified by similarity to SP:P37403; match to protein family HMM PF01037; leucine-responsive regulatory protein 960240 3195548 SPO0904 Ruegeria pomeroyi DSS-3 leucine-responsive regulatory protein YP_166157.1 959740 D 246200 CDS YP_166158.1 56695807 3194209 complement(960339..961124) 1 NC_003911.11 identified by similarity to PIR:T03518; hypothetical protein 961124 3194209 SPO0905 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166158.1 960339 R 246200 CDS YP_166159.1 56695808 3195910 complement(961875..962630) 1 NC_003911.11 identified by similarity to GB:CAC46924.1; match to protein family HMM PF02578; match to protein family HMM TIGR00726; hypothetical protein 962630 3195910 SPO0906 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166159.1 961875 R 246200 CDS YP_166160.1 56695809 3195997 complement(962627..963694) 1 NC_003911.11 identified by similarity to GB:BAB49749.1; match to protein family HMM PF02636; hypothetical protein 963694 3195997 SPO0907 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166160.1 962627 R 246200 CDS YP_166161.1 56695810 3196007 complement(963691..964578) 1 NC_003911.11 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 964578 lgt 3196007 lgt Ruegeria pomeroyi DSS-3 prolipoprotein diacylglyceryl transferase YP_166161.1 963691 R 246200 CDS YP_166162.1 56695811 3195193 964675..964923 1 NC_003911.11 identified by similarity to GB:CAC46921.1; match to protein family HMM PF04380; hypothetical protein 964923 3195193 SPO0909 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166162.1 964675 D 246200 CDS YP_166163.1 56695812 3193477 965251..965751 1 NC_003911.11 identified by similarity to GB:CAE29805.1; hypothetical protein 965751 3193477 SPO0910 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166163.1 965251 D 246200 CDS YP_166164.1 56695813 3193059 965770..966606 1 NC_003911.11 catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase 966606 proC 3193059 proC Ruegeria pomeroyi DSS-3 pyrroline-5-carboxylate reductase YP_166164.1 965770 D 246200 CDS YP_166165.1 56695814 3196065 966599..966937 1 NC_003911.11 identified by similarity to SP:P37584; match to protein family HMM PF01588; chaperonin csaA 966937 csaA 3196065 csaA Ruegeria pomeroyi DSS-3 chaperonin csaA YP_166165.1 966599 D 246200 CDS YP_166166.1 56695815 3196166 966937..967890 1 NC_003911.11 identified by match to protein family HMM PF00389; match to protein family HMM PF02826; D-isomer specific 2-hydroxyacid dehydrogenase 967890 3196166 SPO0913 Ruegeria pomeroyi DSS-3 D-isomer specific 2-hydroxyacid dehydrogenase YP_166166.1 966937 D 246200 CDS YP_166167.1 56695816 3195435 complement(968104..968700) 1 NC_003911.11 catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase 968700 tdk 3195435 tdk Ruegeria pomeroyi DSS-3 thymidine kinase YP_166167.1 968104 R 246200 CDS YP_166168.1 56695817 3196143 968966..969526 1 NC_003911.11 identified by similarity to PIR:AB2631; hypothetical protein 969526 3196143 SPO0915 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166168.1 968966 D 246200 CDS YP_166169.1 56695818 3196080 969637..970500 1 NC_003911.11 identified by similarity to GB:AAS41921.1; hypothetical protein 970500 3196080 SPO0916 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166169.1 969637 D 246200 CDS YP_166170.1 56695819 3196074 970668..971045 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 971045 3196074 SPO0917 Ruegeria pomeroyi DSS-3 glyoxalase YP_166170.1 970668 D 246200 CDS YP_166171.1 56695820 3195073 complement(971105..972232) 1 NC_003911.11 catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs; 3-oxoacyl-ACP synthase 972232 fabH-1 3195073 fabH-1 Ruegeria pomeroyi DSS-3 3-oxoacyl-ACP synthase YP_166171.1 971105 R 246200 CDS YP_166172.1 56695821 3196050 972396..972869 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 972869 3196050 SPO0919 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_166172.1 972396 D 246200 CDS YP_166173.1 56695822 3193025 972903..973904 1 NC_003911.11 identified by match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 973904 3193025 SPO0920 Ruegeria pomeroyi DSS-3 RND family efflux transporter MFP subunit YP_166173.1 972903 D 246200 CDS YP_166174.1 56695823 3196016 973916..976948 1 NC_003911.11 identified by match to protein family HMM PF00873; AcrB/AcrD/AcrF family transporter 976948 3196016 SPO0921 Ruegeria pomeroyi DSS-3 AcrB/AcrD/AcrF family transporter YP_166174.1 973916 D 246200 CDS YP_166175.1 56695824 3195428 complement(976963..977373) 1 NC_003911.11 identified by similarity to PIR:D83152; match to protein family HMM PF00903; hypothetical protein 977373 3195428 SPO0922 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166175.1 976963 R 246200 CDS YP_166176.1 56695825 3195282 complement(977565..980933) 1 NC_003911.11 four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity; carbamoyl phosphate synthase large subunit 980933 carB 3195282 carB Ruegeria pomeroyi DSS-3 carbamoyl phosphate synthase large subunit YP_166176.1 977565 R 246200 CDS YP_166177.1 56695826 3194612 981130..982251 1 NC_003911.11 catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine; aminodeoxychorismate synthase 982251 pabB 3194612 pabB Ruegeria pomeroyi DSS-3 aminodeoxychorismate synthase YP_166177.1 981130 D 246200 CDS YP_166178.1 56695827 3194864 982206..982853 1 NC_003911.11 identified by similarity to GB:CAC47377.1; hypothetical protein 982853 3194864 SPO0925 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166178.1 982206 D 246200 CDS YP_166179.1 56695828 3194889 983055..984836 1 NC_003911.11 catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes; aspartyl-tRNA synthetase 984836 aspS 3194889 aspS Ruegeria pomeroyi DSS-3 aspartyl-tRNA synthetase YP_166179.1 983055 D 246200 CDS YP_166180.1 56695829 3194999 984839..985012 1 NC_003911.11 hypothetical protein 985012 3194999 SPO0927 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166180.1 984839 D 246200 CDS YP_166181.1 56695830 3195291 complement(984844..985557) 1 NC_003911.11 hypothetical protein 985557 3195291 SPO0928 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166181.1 984844 R 246200 CDS YP_166182.1 56695831 3195463 complement(985559..986191) 1 NC_003911.11 Possibly an isoschizomer of M.MboI found in Moraxella bovis.; identified by match to protein family HMM PF05063; type II DNA modification methyltransferase 986191 3195463 SPO0929 Ruegeria pomeroyi DSS-3 type II DNA modification methyltransferase YP_166182.1 985559 R 246200 CDS YP_166183.1 56695832 3196319 complement(986386..986493) 1 NC_003911.11 hypothetical protein 986493 3196319 SPO0930 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166183.1 986386 R 246200 CDS YP_166184.1 56695833 3193727 complement(986495..987214) 1 NC_003911.11 identified by match to protein family HMM PF00072; response regulator 987214 3193727 SPO0931 Ruegeria pomeroyi DSS-3 response regulator YP_166184.1 986495 R 246200 CDS YP_166185.1 56695834 3194735 987345..987755 1 NC_003911.11 identified by similarity to GB:AAK52053.1; match to protein family HMM PF00903; methylmalonyl-CoA epimerase 987755 3194735 SPO0932 Ruegeria pomeroyi DSS-3 methylmalonyl-CoA epimerase YP_166185.1 987345 D 246200 CDS YP_166186.1 56695835 3195403 987789..988064 1 NC_003911.11 identified by similarity to GB:BAB48740.1; hypothetical protein 988064 3195403 SPO0933 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166186.1 987789 D 246200 CDS YP_166187.1 56695836 3194914 complement(988097..988792) 1 NC_003911.11 hypothetical protein 988792 3194914 SPO0934 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166187.1 988097 R 246200 CDS YP_166188.1 56695837 3195763 complement(988789..989367) 1 NC_003911.11 identified by match to protein family HMM PF00881; nitroreductase 989367 3195763 SPO0935 Ruegeria pomeroyi DSS-3 nitroreductase YP_166188.1 988789 R 246200 CDS YP_166189.1 56695838 3196043 989512..989697 1 NC_003911.11 hypothetical protein 989697 3196043 SPO0936 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166189.1 989512 D 246200 CDS YP_166190.1 56695839 3194129 989745..990023 1 NC_003911.11 identified by similarity to SP:Q9Z854; match to protein family HMM PF02594; hypothetical protein 990023 3194129 SPO0937 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166190.1 989745 D 246200 CDS YP_166191.1 56695840 3195799 complement(990027..990296) 1 NC_003911.11 hypothetical protein 990296 3195799 SPO0938 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166191.1 990027 R 246200 CDS YP_166192.1 56695841 3195502 990386..991102 1 NC_003911.11 identified by match to protein family HMM PF01435; M48 family peptidase 991102 3195502 SPO0939 Ruegeria pomeroyi DSS-3 M48 family peptidase YP_166192.1 990386 D 246200 CDS YP_166193.1 56695842 3196047 991099..991467 1 NC_003911.11 identified by similarity to PIR:T27104; match to protein family HMM PF01205; hypothetical protein 991467 3196047 SPO0940 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166193.1 991099 D 246200 CDS YP_166194.1 56695843 3195366 991539..991790 1 NC_003911.11 hypothetical protein 991790 3195366 SPO0941 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166194.1 991539 D 246200 CDS YP_166195.1 56695844 3194871 991821..992078 1 NC_003911.11 hypothetical protein 992078 3194871 SPO0942 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166195.1 991821 D 246200 CDS YP_166196.1 56695845 3194179 complement(992079..992321) 1 NC_003911.11 identified by similarity to GB:AAO38330.1; hypothetical protein 992321 3194179 SPO0943 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166196.1 992079 R 246200 CDS YP_166197.1 56695846 3196011 complement(993168..994568) 1 NC_003911.11 catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; ribosomal protein S12 methylthiotransferase 994568 rimO 3196011 rimO Ruegeria pomeroyi DSS-3 ribosomal protein S12 methylthiotransferase YP_166197.1 993168 R 246200 CDS YP_166198.1 56695847 3194777 994657..996594 1 NC_003911.11 identified by match to protein family HMM PF05170; AsmA family protein 996594 3194777 SPO0945 Ruegeria pomeroyi DSS-3 AsmA family protein YP_166198.1 994657 D 246200 CDS YP_166199.1 56695848 3195637 complement(996822..998261) 1 NC_003911.11 identified by similarity to SP:P26276; match to protein family HMM PF00408; match to protein family HMM PF02878; match to protein family HMM PF02879; match to protein family HMM PF02880; phosphomannomutase 998261 algC 3195637 algC Ruegeria pomeroyi DSS-3 phosphomannomutase YP_166199.1 996822 R 246200 CDS YP_166200.1 56695849 3195476 complement(998339..999172) 1 NC_003911.11 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis; 2-dehydro-3-deoxyphosphooctonate aldolase 999172 kdsA 3195476 kdsA Ruegeria pomeroyi DSS-3 2-dehydro-3-deoxyphosphooctonate aldolase YP_166200.1 998339 R 246200 CDS YP_166201.1 56695850 3193114 complement(999177..1000355) 1 NC_003911.11 capsule polysaccharide exporter 1000355 kpsE 3193114 kpsE Ruegeria pomeroyi DSS-3 capsule polysaccharide exporter YP_166201.1 999177 R 246200 CDS YP_166202.1 56695851 3193970 complement(1000873..1001586) 1 NC_003911.11 identified by similarity to SP:P10640; match to protein family HMM PF00005; capsular polysaccharide export ATP-binding protein 1001586 kpsT 3193970 kpsT Ruegeria pomeroyi DSS-3 capsular polysaccharide export ATP-binding protein YP_166202.1 1000873 R 246200 CDS YP_166203.1 56695852 3193379 1001795..1002421 1 NC_003911.11 identified by similarity to GB:CAD29336.1; match to protein family HMM PF03167; uracil-DNA glycosylase 1002421 3193379 SPO0950 Ruegeria pomeroyi DSS-3 uracil-DNA glycosylase YP_166203.1 1001795 D 246200 CDS YP_166204.1 56695853 3195105 1002390..1003178 1 NC_003911.11 hypothetical protein 1003178 3195105 SPO0951 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166204.1 1002390 D 246200 CDS YP_166205.1 56695854 3195207 1003206..1004636 1 NC_003911.11 hypothetical protein 1004636 3195207 SPO0952 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166205.1 1003206 D 246200 CDS YP_166206.1 56695855 3195255 complement(1004465..1005343) 1 NC_003911.11 YghU; B2989; one of eight glutathione transferases from E. coli; glutathione S-transferase 1005343 3195255 SPO0953 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_166206.1 1004465 R 246200 CDS YP_166207.1 56695856 3195543 1005566..1006090 1 NC_003911.11 identified by similarity to PIR:E82434; hypothetical protein 1006090 3195543 SPO0954 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166207.1 1005566 D 246200 CDS YP_166208.1 56695857 3194212 1006275..1008170 1 NC_003911.11 identified by match to protein family HMM PF01979; amidohydrolase 1008170 3194212 SPO0955 Ruegeria pomeroyi DSS-3 amidohydrolase YP_166208.1 1006275 D 246200 CDS YP_166209.1 56695858 3195214 complement(1008222..1008818) 1 NC_003911.11 identified by similarity to PIR:AI3454; hypothetical protein 1008818 3195214 SPO0956 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166209.1 1008222 R 246200 CDS YP_166210.1 56695859 3195509 1008968..1009759 1 NC_003911.11 identified by match to protein family HMM PF01061; ABC transporter permease 1009759 3195509 SPO0957 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_166210.1 1008968 D 246200 CDS YP_166211.1 56695860 3192875 complement(1009820..1011052) 1 NC_003911.11 hypothetical protein 1011052 3192875 SPO0958 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166211.1 1009820 R 246200 CDS YP_166212.1 56695861 3195638 complement(1011250..1012266) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 1012266 3195638 SPO0959 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166212.1 1011250 R 246200 CDS YP_166213.1 56695862 3195781 complement(1012299..1012664) 1 NC_003911.11 identified by match to protein family HMM PF00376; MerR family transcriptional regulator 1012664 3195781 SPO0960 Ruegeria pomeroyi DSS-3 MerR family transcriptional regulator YP_166213.1 1012299 R 246200 CDS YP_166214.1 56695863 3194644 1012748..1013005 1 NC_003911.11 identified by similarity to PIR:B86741; hypothetical protein 1013005 3194644 SPO0961 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166214.1 1012748 D 246200 CDS YP_166215.1 56695864 3194580 1013246..1014421 1 NC_003911.11 DapATase; functions in arginine biosynthetic pathway; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine; acetylornithine transaminase 1014421 argD 3194580 argD Ruegeria pomeroyi DSS-3 acetylornithine transaminase YP_166215.1 1013246 D 246200 CDS YP_166216.1 56695865 3195160 1014510..1015436 1 NC_003911.11 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase 1015436 argF 3195160 argF Ruegeria pomeroyi DSS-3 ornithine carbamoyltransferase YP_166216.1 1014510 D 246200 CDS YP_166217.1 56695866 3194685 1015554..1016471 1 NC_003911.11 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis; N-acetyl-gamma-glutamyl-phosphate reductase 1016471 argC-1 3194685 argC-1 Ruegeria pomeroyi DSS-3 N-acetyl-gamma-glutamyl-phosphate reductase YP_166217.1 1015554 D 246200 CDS YP_166218.1 56695867 3196036 1016468..1017358 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 1017358 3196036 SPO0965 Ruegeria pomeroyi DSS-3 acetyltransferase YP_166218.1 1016468 D 246200 CDS YP_166219.1 56695868 3194571 1017416..1018411 1 NC_003911.11 catalyzes the formation of 2-dehydropantoate from (R)-pantoate; 2-dehydropantoate 2-reductase 1018411 panE-1 3194571 panE-1 Ruegeria pomeroyi DSS-3 2-dehydropantoate 2-reductase YP_166219.1 1017416 D 246200 CDS YP_166220.1 56695869 3196041 complement(1018497..1019975) 1 NC_003911.11 identified by match to protein family HMM PF01384; phosphate transporter family protein 1019975 3196041 SPO0967 Ruegeria pomeroyi DSS-3 phosphate transporter family protein YP_166220.1 1018497 R 246200 CDS YP_166221.1 56695870 3195155 complement(1020068..1020526) 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX family hydrolase 1020526 3195155 SPO0968 Ruegeria pomeroyi DSS-3 NUDIX family hydrolase YP_166221.1 1020068 R 246200 CDS YP_166222.1 56695871 3195594 1021580..1022275 1 NC_003911.11 porin involved in osmoregulation allowing water to move into and out of the cell in response to osmotic pressure; aquaporin Z 1022275 apqZ 3195594 apqZ Ruegeria pomeroyi DSS-3 aquaporin Z YP_166222.1 1021580 D 246200 CDS YP_166223.1 56695872 3195473 1022390..1023994 1 NC_003911.11 identified by match to protein family HMM PF00732; match to protein family HMM PF05199; GMC family oxidoreductase 1023994 3195473 SPO0971 Ruegeria pomeroyi DSS-3 GMC family oxidoreductase YP_166223.1 1022390 D 246200 CDS YP_166224.1 56695873 3192888 complement(1024037..1026487) 1 NC_003911.11 identified by match to protein family HMM PF00271; match to protein family HMM PF04408; match to protein family HMM TIGR01970; ATP-dependent helicase HrpB 1026487 hrpB 3192888 hrpB Ruegeria pomeroyi DSS-3 ATP-dependent helicase HrpB YP_166224.1 1024037 R 246200 CDS YP_166225.1 56695874 3194801 1026711..1027688 1 NC_003911.11 functions in transport of arginine/ornithine; inner membrane ATPase that cleaves ATP and phosphorylates two periplasmic proteins that function as two distinct transport systems, the AO (arginine and ornithine) and LAO (lysine, arginine, and ornithine) periplasmic binding proteins; arginine/ornithine transport system ATPase 1027688 3194801 SPO0973 Ruegeria pomeroyi DSS-3 arginine/ornithine transport system ATPase YP_166225.1 1026711 D 246200 CDS YP_166226.1 56695875 3194737 1027916..1028203 1 NC_003911.11 required for 70S ribosome assembly; 50S ribosomal protein L28 1028203 rpmB 3194737 rpmB Ruegeria pomeroyi DSS-3 50S ribosomal protein L28 YP_166226.1 1027916 D 246200 CDS YP_166227.1 56695876 3195494 1028308..1028754 1 NC_003911.11 hypothetical protein 1028754 3195494 SPO0975 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166227.1 1028308 D 246200 CDS YP_166228.1 56695877 3195975 1028800..1029279 1 NC_003911.11 identified by match to protein family HMM PF04314; hypothetical protein 1029279 3195975 SPO0976 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166228.1 1028800 D 246200 CDS YP_166229.1 56695878 3195980 complement(1029330..1030364) 1 NC_003911.11 identified by match to protein family HMM PF02423; ornithine cyclodeaminase/mu-crystallin family protein 1030364 3195980 SPO0977 Ruegeria pomeroyi DSS-3 ornithine cyclodeaminase/mu-crystallin family protein YP_166229.1 1029330 R 246200 CDS YP_166230.1 56695879 3195581 complement(1030331..1031029) 1 NC_003911.11 Modulates the activities of several enzymes which are inactive in their acetylated form; NAD-dependent deacetylase 1031029 3195581 SPO0978 Ruegeria pomeroyi DSS-3 NAD-dependent deacetylase YP_166230.1 1030331 R 246200 CDS YP_166231.1 56695880 3195056 1031074..1031535 1 NC_003911.11 identified by similarity to SP:P53433; match to protein family HMM PF01451; low molecular weight phosphotyrosine protein phosphatase 1031535 3195056 SPO0979 Ruegeria pomeroyi DSS-3 low molecular weight phosphotyrosine protein phosphatase YP_166231.1 1031074 D 246200 CDS YP_166232.1 56695881 3193747 complement(1031810..1032769) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1032769 3193747 SPO0980 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_166232.1 1031810 R 246200 CDS YP_166233.1 56695882 3193830 1032853..1034154 1 NC_003911.11 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 1034154 hisD 3193830 hisD Ruegeria pomeroyi DSS-3 histidinol dehydrogenase YP_166233.1 1032853 D 246200 CDS YP_166234.1 56695883 3195259 complement(1034805..1036106) 1 NC_003911.11 hypothetical protein 1036106 3195259 SPO0982 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166234.1 1034805 R 246200 CDS YP_166235.1 56695884 3194387 1036159..1037958 1 NC_003911.11 binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA 1037958 lepA 3194387 lepA Ruegeria pomeroyi DSS-3 GTP-binding protein LepA YP_166235.1 1036159 D 246200 CDS YP_166236.1 56695885 3194603 complement(1038962..1039759) 1 NC_003911.11 identified by similarity to SP:P39832; match to protein family HMM PF00950; zinc ABC transporter permease 1039759 znuB 3194603 znuB Ruegeria pomeroyi DSS-3 zinc ABC transporter permease YP_166236.1 1038962 R 246200 CDS YP_166237.1 56695886 3195402 complement(1039756..1040526) 1 NC_003911.11 identified by similarity to SP:P52648; match to protein family HMM PF00005; zinc ABC transporter ATP-binding protein 1040526 znuC 3195402 znuC Ruegeria pomeroyi DSS-3 zinc ABC transporter ATP-binding protein YP_166237.1 1039756 R 246200 CDS YP_166238.1 56695887 3195534 complement(1040523..1041002) 1 NC_003911.11 Part of a zinc ABC transporter gene cluster.; identified by similarity to SP:P32692; zinc uptake regulation protein 1041002 zur 3195534 zur Ruegeria pomeroyi DSS-3 zinc uptake regulation protein YP_166238.1 1040523 R 246200 CDS YP_166239.1 56695888 3194922 1041090..1042058 1 NC_003911.11 identified by similarity to SP:P39172; match to protein family HMM PF01297; zinc ABC transporter periplasmic zinc-binding protein 1042058 znuA 3194922 znuA Ruegeria pomeroyi DSS-3 zinc ABC transporter periplasmic zinc-binding protein YP_166239.1 1041090 D 246200 CDS YP_166240.1 56695889 3196004 complement(1042071..1043129) 1 NC_003911.11 identified by similarity to SP:P33015; match to protein family HMM PF04143; hypothetical protein 1043129 3196004 SPO0988 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166240.1 1042071 R 246200 CDS YP_166241.1 56695890 3195455 complement(1043193..1043579) 1 NC_003911.11 identified by match to protein family HMM PF01022; transcriptional regulator SoxR 1043579 3195455 SPO0989 Ruegeria pomeroyi DSS-3 transcriptional regulator SoxR YP_166241.1 1043193 R 246200 CDS YP_166242.1 56695891 3195943 complement(1043673..1044050) 1 NC_003911.11 identified by similarity to GB:AAO11779.1; regulatory protein SoxS 1044050 soxS 3195943 soxS Ruegeria pomeroyi DSS-3 regulatory protein SoxS YP_166242.1 1043673 R 246200 CDS YP_166243.1 56695892 3193615 1044146..1044883 1 NC_003911.11 identified by similarity to GB:AAF99429.1; match to protein family HMM PF02683; sulfur oxidation V protein 1044883 soxV 3193615 soxV Ruegeria pomeroyi DSS-3 sulfur oxidation V protein YP_166243.1 1044146 D 246200 CDS YP_166244.1 56695893 3194811 1044911..1045486 1 NC_003911.11 identified by similarity to GB:CAB94378.1; thioredoxin 1045486 soxW 3194811 soxW Ruegeria pomeroyi DSS-3 thioredoxin YP_166244.1 1044911 D 246200 CDS YP_166245.1 56695894 3195339 1045605..1046090 1 NC_003911.11 identified by similarity to GB:CAB94379.1; match to protein family HMM PF00034; monoheme cytochrome c SoxX 1046090 soxX 3195339 soxX Ruegeria pomeroyi DSS-3 monoheme cytochrome c SoxX YP_166245.1 1045605 D 246200 CDS YP_166246.1 56695895 3194856 1046133..1046549 1 NC_003911.11 with SoxZ catalyzes the oxidation of sulfur compounds; sulfur oxidation protein SoxY 1046549 soxY 3194856 soxY Ruegeria pomeroyi DSS-3 sulfur oxidation protein SoxY YP_166246.1 1046133 D 246200 CDS YP_166247.1 56695896 3195930 1046583..1046912 1 NC_003911.11 identified by similarity to GB:CAB94381.1; sulfur oxidation Z protein 1046912 soxZ 3195930 soxZ Ruegeria pomeroyi DSS-3 sulfur oxidation Z protein YP_166247.1 1046583 D 246200 CDS YP_166248.1 56695897 3194976 1046990..1047841 1 NC_003911.11 identified by similarity to GB:AAF99434.1; diheme cytochrome c SoxA 1047841 soxA 3194976 soxA Ruegeria pomeroyi DSS-3 diheme cytochrome c SoxA YP_166248.1 1046990 D 246200 CDS YP_166249.1 56695898 3194111 1047943..1049646 1 NC_003911.11 identified by similarity to GB:CAA55824.2; match to protein family HMM PF00149; match to protein family HMM PF02872; match to protein family HMM TIGR01409; sulfur oxidation B protein 1049646 soxB 3194111 soxB Ruegeria pomeroyi DSS-3 sulfur oxidation B protein YP_166249.1 1047943 D 246200 CDS YP_166250.1 56695899 3195075 1049725..1051008 1 NC_003911.11 identified by similarity to PIR:T46965; match to protein family HMM PF00174; match to protein family HMM PF03404; match to protein family HMM TIGR01409; sulfur oxidation molybdopterin C protein 1051008 soxC 3195075 soxC Ruegeria pomeroyi DSS-3 sulfur oxidation molybdopterin C protein YP_166250.1 1049725 D 246200 CDS YP_166251.1 56695900 3195695 1050992..1052035 1 NC_003911.11 identified by similarity to PIR:T46966; match to protein family HMM PF00034; diheme cytochrome c SoxD 1052035 soxD 3195695 soxD Ruegeria pomeroyi DSS-3 diheme cytochrome c SoxD YP_166251.1 1050992 D 246200 CDS YP_166252.1 56695901 3194630 1052039..1052749 1 NC_003911.11 identified by match to protein family HMM PF00034; diheme cytochrome c SoxE 1052749 soxE 3194630 soxE Ruegeria pomeroyi DSS-3 diheme cytochrome c SoxE YP_166252.1 1052039 D 246200 CDS YP_166253.1 56695902 3194648 1052788..1054050 1 NC_003911.11 identified by similarity to GB:CAA55826.2; sulfur oxidation F protein 1054050 soxF 3194648 soxF Ruegeria pomeroyi DSS-3 sulfur oxidation F protein YP_166253.1 1052788 D 246200 CDS YP_166254.1 56695903 3195743 complement(1054075..1055079) 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 1055079 3195743 SPO1002 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_166254.1 1054075 R 246200 CDS YP_166255.1 56695904 3193881 1055324..1055953 1 NC_003911.11 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit 1055953 clpP 3193881 clpP Ruegeria pomeroyi DSS-3 ATP-dependent Clp protease proteolytic subunit YP_166255.1 1055324 D 246200 CDS YP_166256.1 56695905 3195507 1056087..1057361 1 NC_003911.11 binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX 1057361 clpX 3195507 clpX Ruegeria pomeroyi DSS-3 ATP-dependent protease ATP-binding subunit ClpX YP_166256.1 1056087 D 246200 CDS YP_166257.1 56695906 3194692 1057373..1057888 1 NC_003911.11 identified by match to protein family HMM PF01042; endoribonuclease L-PSP 1057888 3194692 SPO1005 Ruegeria pomeroyi DSS-3 endoribonuclease L-PSP YP_166257.1 1057373 D 246200 CDS YP_166258.1 56695907 3196053 1057980..1058363 1 NC_003911.11 Provides the input to the respiratory chain from the NAD-linked dehydrogenases of the citric acid cycle. The complex couples the oxidation of NADH and the reduction of ubiquinone, to the generation of a proton gradient which is then used for ATP synthesis; NADH dehydrogenase 1058363 3196053 SPO1006 Ruegeria pomeroyi DSS-3 NADH dehydrogenase YP_166258.1 1057980 D 246200 CDS YP_166259.1 56695908 3195753 1058374..1058829 1 NC_003911.11 identified by match to protein family HMM PF02470; hypothetical protein 1058829 3195753 SPO1007 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166259.1 1058374 D 246200 CDS YP_166260.1 56695909 3194292 1058826..1059185 1 NC_003911.11 identified by similarity to GB:AAN29832.1; hypothetical protein 1059185 3194292 SPO1008 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166260.1 1058826 D 246200 CDS YP_166261.1 56695910 3194540 complement(1059149..1059781) 1 NC_003911.11 leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys; leucyl/phenylalanyl-tRNA--protein transferase 1059781 aat 3194540 aat Ruegeria pomeroyi DSS-3 leucyl/phenylalanyl-tRNA--protein transferase YP_166261.1 1059149 R 246200 CDS YP_166262.1 56695911 3195480 complement(1059833..1061182) 1 NC_003911.11 an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism; acetyl-CoA carboxylase biotin carboxylase subunit 1061182 accC 3195480 accC Ruegeria pomeroyi DSS-3 acetyl-CoA carboxylase biotin carboxylase subunit YP_166262.1 1059833 R 246200 CDS YP_166263.1 56695912 3195545 complement(1061193..1061687) 1 NC_003911.11 identified by match to protein family HMM PF00364; match to protein family HMM TIGR00531; acetyl-CoA carboxylase, biotin carboxyl carrier protein 1061687 accB 3195545 accB Ruegeria pomeroyi DSS-3 acetyl-CoA carboxylase, biotin carboxyl carrier protein YP_166263.1 1061193 R 246200 CDS YP_166264.1 56695914 3194617 complement(1061835..1062371) 1 NC_003911.11 identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 1062371 3194617 SPO1012 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_166264.1 1061835 R 246200 CDS YP_166265.1 56695913 3195826 1062462..1063622 1 NC_003911.11 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; acetyl-CoA acetyltransferase 1063622 3195826 SPO1013 Ruegeria pomeroyi DSS-3 acetyl-CoA acetyltransferase YP_166265.1 1062462 D 246200 CDS YP_166266.1 56695915 3195103 1063619..1065127 1 NC_003911.11 identified by match to protein family HMM PF00501; AMP-binding protein 1065127 3195103 SPO1014 Ruegeria pomeroyi DSS-3 AMP-binding protein YP_166266.1 1063619 D 246200 CDS YP_166267.1 56695916 3193768 1065124..1065927 1 NC_003911.11 identified by similarity to SP:O86034; match to protein family HMM PF00106; 3-hydroxybutyrate dehydrogenase 1065927 3193768 SPO1015 Ruegeria pomeroyi DSS-3 3-hydroxybutyrate dehydrogenase YP_166267.1 1065124 D 246200 CDS YP_166268.1 56695917 3194536 complement(1065929..1066909) 1 NC_003911.11 hypothetical protein 1066909 3194536 SPO1016 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166268.1 1065929 R 246200 CDS YP_166269.1 56695918 3195692 complement(1066986..1067741) 1 NC_003911.11 Assignment partly based on location in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1067741 3195692 SPO1017 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_166269.1 1066986 R 246200 CDS YP_166270.1 56695919 3195795 complement(1067811..1068566) 1 NC_003911.11 identified by similarity to SP:P22730; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1068566 3195795 SPO1018 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_166270.1 1067811 R 246200 CDS YP_166271.1 56695920 3195228 complement(1068579..1069781) 1 NC_003911.11 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1069781 3195228 SPO1019 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_166271.1 1068579 R 246200 CDS YP_166272.1 56695921 3195954 complement(1069785..1070825) 1 NC_003911.11 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1070825 3195954 SPO1020 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_166272.1 1069785 R 246200 CDS YP_166273.1 56695922 3195562 complement(1070921..1072273) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM TIGR01409; branched-chain amino acid ABC transporter substrate-binding protein 1072273 3195562 SPO1021 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter substrate-binding protein YP_166273.1 1070921 R 246200 CDS YP_166274.1 56695923 3193733 1072502..1073800 1 NC_003911.11 identified by match to protein family HMM PF01381; transcriptional regulator 1073800 3193733 SPO1022 Ruegeria pomeroyi DSS-3 transcriptional regulator YP_166274.1 1072502 D 246200 CDS YP_166275.1 56695924 3195651 1073886..1074266 1 NC_003911.11 identified by match to protein family HMM PF00072; response regulator 1074266 3195651 SPO1023 Ruegeria pomeroyi DSS-3 response regulator YP_166275.1 1073886 D 246200 CDS YP_166276.1 56695925 3195598 1074263..1074568 1 NC_003911.11 hypothetical protein 1074568 3195598 SPO1024 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166276.1 1074263 D 246200 CDS YP_166277.1 56695926 3194941 1074565..1077243 1 NC_003911.11 identified by match to protein family HMM PF00512; match to protein family HMM PF02518; sensor histidine kinase 1077243 3194941 SPO1025 Ruegeria pomeroyi DSS-3 sensor histidine kinase YP_166277.1 1074565 D 246200 CDS YP_166278.1 56695927 3196067 1077322..1078488 1 NC_003911.11 hypothetical protein 1078488 3196067 SPO1026 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166278.1 1077322 D 246200 CDS YP_166279.1 56695928 3195967 complement(1078508..1078939) 1 NC_003911.11 identified by similarity to PIR:T10511; match to protein family HMM PF04273; match to protein family HMM TIGR01244; hypothetical protein 1078939 3195967 SPO1027 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166279.1 1078508 R 246200 CDS YP_166280.1 56695929 3194527 complement(1078949..1079380) 1 NC_003911.11 identified by match to protein family HMM PF04143; hypothetical protein 1079380 3194527 SPO1028 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166280.1 1078949 R 246200 CDS YP_166281.1 56695930 3195195 complement(1079380..1079808) 1 NC_003911.11 identified by match to protein family HMM PF04143; hypothetical protein 1079808 3195195 SPO1029 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166281.1 1079380 R 246200 CDS YP_166282.1 56695931 3194430 complement(1079849..1080766) 1 NC_003911.11 identified by match to protein family HMM PF00753; metallo-beta-lactamase 1080766 3194430 SPO1030 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_166282.1 1079849 R 246200 CDS YP_166283.1 56695932 3195824 1080814..1081185 1 NC_003911.11 hypothetical protein 1081185 3195824 SPO1031 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166283.1 1080814 D 246200 CDS YP_166284.1 56695933 3195849 complement(1081210..1081431) 1 NC_003911.11 hypothetical protein 1081431 3195849 SPO1032 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166284.1 1081210 R 246200 CDS YP_166285.1 56695934 3194604 1081578..1081838 1 NC_003911.11 identified by similarity to GB:BAB50739.1; hypothetical protein 1081838 3194604 SPO1033 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166285.1 1081578 D 246200 CDS YP_166286.1 56695935 3195486 complement(1081875..1082750) 1 NC_003911.11 hypothetical protein 1082750 3195486 SPO1034 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166286.1 1081875 R 246200 CDS YP_166287.1 56695936 3195462 1083132..1084376 1 NC_003911.11 identified by match to protein family HMM PF00589; phage integrase site specific recombinase 1084376 3195462 SPO1036 Ruegeria pomeroyi DSS-3 phage integrase site specific recombinase YP_166287.1 1083132 D 246200 CDS YP_166288.1 56695937 3195599 1084691..1086001 1 NC_003911.11 hypothetical protein 1086001 3195599 SPO1037 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166288.1 1084691 D 246200 CDS YP_166289.1 56695938 3195978 complement(1085995..1086156) 1 NC_003911.11 hypothetical protein 1086156 3195978 SPO1038 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166289.1 1085995 R 246200 CDS YP_166290.1 56695939 3194771 1087398..1088780 1 NC_003911.11 identified by similarity to GB:CAE33998.1; hypothetical protein 1088780 3194771 SPO1039 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166290.1 1087398 D 246200 CDS YP_166291.1 56695940 3195173 1088777..1089391 1 NC_003911.11 hypothetical protein 1089391 3195173 SPO1040 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166291.1 1088777 D 246200 CDS YP_166292.1 56695941 3195335 1089461..1089865 1 NC_003911.11 hypothetical protein 1089865 3195335 SPO1041 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166292.1 1089461 D 246200 CDS YP_166293.1 56695942 3196006 1089858..1090526 1 NC_003911.11 hypothetical protein 1090526 3196006 SPO1042 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166293.1 1089858 D 246200 CDS YP_166294.1 56695943 3193491 1090717..1090953 1 NC_003911.11 hypothetical protein 1090953 3193491 SPO1043 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166294.1 1090717 D 246200 CDS YP_166295.1 56695944 3193542 1091162..1092196 1 NC_003911.11 identified by similarity to GB:BAC45394.1; hypothetical protein 1092196 3193542 SPO1044 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166295.1 1091162 D 246200 CDS YP_166296.1 56698729 3196334 1092791..1093339 1 NC_003911.11 hypothetical protein 1093339 3196334 SPO1045 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166296.1 1092791 D 246200 CDS YP_166297.1 56698728 3196181 1093332..1094060 1 NC_003911.11 hypothetical protein 1094060 3196181 SPO1046 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166297.1 1093332 D 246200 CDS YP_166298.1 56698727 3196332 1094205..1095173 1 NC_003911.11 identified by match to protein family HMM PF00078; RNA-dependent DNA polymerase 1095173 3196332 SPO1047 Ruegeria pomeroyi DSS-3 RNA-dependent DNA polymerase YP_166298.1 1094205 D 246200 CDS YP_166299.1 56695945 3194608 1095296..1096321 1 NC_003911.11 hypothetical protein 1096321 3194608 SPO1048 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166299.1 1095296 D 246200 CDS YP_166300.1 56695946 3194254 1096391..1097512 1 NC_003911.11 identified by match to protein family HMM PF00145; match to protein family HMM TIGR00675; C-5 cytosine-specific family DNA methylase 1097512 3194254 SPO1049 Ruegeria pomeroyi DSS-3 C-5 cytosine-specific family DNA methylase YP_166300.1 1096391 D 246200 CDS YP_166301.1 56695947 3194594 1098451..1099539 1 NC_003911.11 identified by match to protein family HMM PF00589; phage integrase site specific recombinase 1099539 3194594 SPO1050 Ruegeria pomeroyi DSS-3 phage integrase site specific recombinase YP_166301.1 1098451 D 246200 CDS YP_166302.1 56695948 3195200 complement(1100582..1101598) 1 NC_003911.11 hypothetical protein 1101598 3195200 SPO1051 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166302.1 1100582 R 246200 CDS YP_166303.1 56695949 3194086 complement(1102078..1102485) 1 NC_003911.11 hypothetical protein 1102485 3194086 SPO1052 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166303.1 1102078 R 246200 CDS YP_166304.1 56695950 3195709 complement(1105457..1105987) 1 NC_003911.11 identified by similarity to PIR:H75269; hypothetical protein 1105987 3195709 SPO1053 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166304.1 1105457 R 246200 CDS YP_166305.1 56695951 3193822 complement(1106015..1106524) 1 NC_003911.11 identified by similarity to PIR:AB1950; hypothetical protein 1106524 3193822 SPO1054 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166305.1 1106015 R 246200 CDS YP_166306.1 56695952 3195744 complement(1106581..1107015) 1 NC_003911.11 hypothetical protein 1107015 3195744 SPO1055 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166306.1 1106581 R 246200 CDS YP_166307.1 56695953 3195606 complement(1107039..1107866) 1 NC_003911.11 identified by similarity to GB:BAB50720.1; hypothetical protein 1107866 3195606 SPO1056 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166307.1 1107039 R 246200 CDS YP_166308.1 56695954 3195397 1108042..1109040 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM TIGR01199; AraC family transcriptional regulator 1109040 3195397 SPO1057 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_166308.1 1108042 D 246200 CDS YP_166309.1 56695955 3195055 complement(1109195..1110070) 1 NC_003911.11 identified by similarity to GB:CAA74897.1; match to protein family HMM PF03279; acyltransferase 1110070 3195055 SPO1058 Ruegeria pomeroyi DSS-3 acyltransferase YP_166309.1 1109195 R 246200 CDS YP_166310.1 56695956 3195072 1110768..1112879 1 NC_003911.11 identified by match to protein family HMM PF00069; serine/threonine protein kinase 1112879 3195072 SPO1059 Ruegeria pomeroyi DSS-3 serine/threonine protein kinase YP_166310.1 1110768 D 246200 CDS YP_166311.1 56695957 3195704 1112983..1114359 1 NC_003911.11 hypothetical protein 1114359 3195704 SPO1060 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166311.1 1112983 D 246200 CDS YP_166312.1 56695958 3196002 1114443..1115543 1 NC_003911.11 identified by match to protein family HMM PF01476; LysM domain-containing protein 1115543 3196002 SPO1061 Ruegeria pomeroyi DSS-3 LysM domain-containing protein YP_166312.1 1114443 D 246200 CDS YP_166313.1 56695959 3195421 1115805..1116899 1 NC_003911.11 identified by match to protein family HMM PF01476; LysM domain-containing protein 1116899 3195421 SPO1062 Ruegeria pomeroyi DSS-3 LysM domain-containing protein YP_166313.1 1115805 D 246200 CDS YP_166314.1 56695960 3195805 1117059..1117895 1 NC_003911.11 identified by similarity to GB:AAS02340.1; hypothetical protein 1117895 3195805 SPO1063 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166314.1 1117059 D 246200 CDS YP_166315.1 56695961 3194190 1117879..1118835 1 NC_003911.11 serine/threonine protein phosphatase 1118835 3194190 SPO1064 Ruegeria pomeroyi DSS-3 serine/threonine protein phosphatase YP_166315.1 1117879 D 246200 CDS YP_166316.1 56695962 3195532 1118838..1120214 1 NC_003911.11 hypothetical protein 1120214 3195532 SPO1065 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166316.1 1118838 D 246200 CDS YP_166317.1 56695963 3192819 complement(1120242..1121030) 1 NC_003911.11 hypothetical protein 1121030 3192819 SPO1066 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166317.1 1120242 R 246200 CDS YP_166318.1 56695964 3194131 complement(1121069..1121482) 1 NC_003911.11 hypothetical protein 1121482 3194131 SPO1067 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166318.1 1121069 R 246200 CDS YP_166319.1 56695965 3195556 complement(1121522..1122424) 1 NC_003911.11 identified by similarity to GB:CAE10435.1; hypothetical protein 1122424 3195556 SPO1068 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166319.1 1121522 R 246200 CDS YP_166320.1 56695966 3194725 complement(1122421..1124523) 1 NC_003911.11 hypothetical protein 1124523 3194725 SPO1069 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166320.1 1122421 R 246200 CDS YP_166321.1 56695967 3194756 complement(1125279..1126940) 1 NC_003911.11 proposed role in polysaccahride synthesis; FAD-binding dehydrogenase 1126940 3194756 SPO1070 Ruegeria pomeroyi DSS-3 FAD-binding dehydrogenase YP_166321.1 1125279 R 246200 CDS YP_166322.1 56695968 3195404 complement(1127009..1127743) 1 NC_003911.11 Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group; glutamine amidotransferase 1127743 3195404 SPO1071 Ruegeria pomeroyi DSS-3 glutamine amidotransferase YP_166322.1 1127009 R 246200 CDS YP_166323.1 56695969 3195080 complement(1127946..1128686) 1 NC_003911.11 identified by similarity to PIR:AC3292; match to protein family HMM PF01709; match to protein family HMM TIGR01033; hypothetical protein 1128686 3195080 SPO1072 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166323.1 1127946 R 246200 CDS YP_166324.1 56695970 3195338 1128890..1129834 1 NC_003911.11 identified by match to protein family HMM PF03401; hypothetical protein 1129834 3195338 SPO1073 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166324.1 1128890 D 246200 CDS YP_166325.1 56695971 3195168 1129842..1130273 1 NC_003911.11 hypothetical protein 1130273 3195168 SPO1074 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166325.1 1129842 D 246200 CDS YP_166326.1 56695972 3194391 1130297..1131802 1 NC_003911.11 identified by match to protein family HMM PF01970; hypothetical protein 1131802 3194391 SPO1075 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166326.1 1130297 D 246200 CDS YP_166327.1 56695973 3192906 1131862..1133637 1 NC_003911.11 identified by match to protein family HMM PF02080; TrkA domain-containing protein 1133637 3192906 SPO1076 Ruegeria pomeroyi DSS-3 TrkA domain-containing protein YP_166327.1 1131862 D 246200 CDS YP_166328.1 56695974 3195236 complement(1133708..1134400) 1 NC_003911.11 identified by match to protein family HMM PF00881; nitroreductase 1134400 3195236 SPO1077 Ruegeria pomeroyi DSS-3 nitroreductase YP_166328.1 1133708 R 246200 CDS YP_166329.1 56695975 3194722 complement(1134438..1135322) 1 NC_003911.11 specific inhibitor of chromosomal initiation of replication in vitro; binds the three 13-mers in the origin (oriC) to block initiation of replication; also controls genes involved in arginine transport; chromosome replication initiation inhibitor protein 1135322 3194722 SPO1078 Ruegeria pomeroyi DSS-3 chromosome replication initiation inhibitor protein YP_166329.1 1134438 R 246200 CDS YP_166330.1 56695976 3193931 1135414..1136025 1 NC_003911.11 identified by similarity to SP:P94633; match to protein family HMM PF01810; L-lysine exporter 1136025 3193931 SPO1079 Ruegeria pomeroyi DSS-3 L-lysine exporter YP_166330.1 1135414 D 246200 CDS YP_166331.1 56695977 3195295 1136078..1137004 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 1137004 3195295 SPO1080 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166331.1 1136078 D 246200 CDS YP_166332.1 56695978 3194677 1137018..1137476 1 NC_003911.11 identified by similarity to GB:AAM82654.1; hypothetical protein 1137476 3194677 SPO1081 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166332.1 1137018 D 246200 CDS YP_166333.1 56695979 3195688 1137532..1138110 1 NC_003911.11 HTH-type; bet1; Repressor involved in choline regulation of the bet genes; transcriptional regulator BetI 1138110 betI 3195688 betI Ruegeria pomeroyi DSS-3 transcriptional regulator BetI YP_166333.1 1137532 D 246200 CDS YP_166334.1 56695980 3195014 1138107..1139615 1 NC_003911.11 identified by similarity to SP:O69787; match to protein family HMM PF00884; choline sulfatase 1139615 betC-1 3195014 betC-1 Ruegeria pomeroyi DSS-3 choline sulfatase YP_166334.1 1138107 D 246200 CDS YP_166335.1 56695981 3194664 1139766..1140125 1 NC_003911.11 identified by similarity to GB:CAC41724.1; hypothetical protein 1140125 3194664 SPO1084 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166335.1 1139766 D 246200 CDS YP_166336.1 56695982 3195172 complement(1140146..1140952) 1 NC_003911.11 identified by similarity to GB:CAE29266.1; hypothetical protein 1140952 3195172 SPO1085 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166336.1 1140146 R 246200 CDS YP_166337.1 56695983 3193964 complement(1141118..1141699) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 1141699 3193964 SPO1086 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_166337.1 1141118 R 246200 CDS YP_166338.1 56695984 3195815 1141865..1143067 1 NC_003911.11 hypothetical protein 1143067 3195815 SPO1087 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166338.1 1141865 D 246200 CDS YP_166339.1 56695985 3195720 1143150..1144808 1 NC_003911.11 catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine; choline dehydrogenase 1144808 betA 3195720 betA Ruegeria pomeroyi DSS-3 choline dehydrogenase YP_166339.1 1143150 D 246200 CDS YP_166340.1 56695986 3193441 1144931..1145170 1 NC_003911.11 identified by similarity to GB:AAN33382.1; match to protein family HMM PF04325; hypothetical protein 1145170 3193441 SPO1089 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166340.1 1144931 D 246200 CDS YP_166341.1 56695987 3195215 complement(1145243..1146640) 1 NC_003911.11 identified by match to protein family HMM PF01381; match to protein family HMM PF06114; DNA-binding protein 1146640 3195215 SPO1090 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_166341.1 1145243 R 246200 CDS YP_166342.1 56695988 3193826 complement(1146710..1146997) 1 NC_003911.11 identified by similarity to GB:AAG42024.1; match to protein family HMM PF03795; hypothetical protein 1146997 3193826 SPO1091 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166342.1 1146710 R 246200 CDS YP_166343.1 56695989 3194862 1147095..1147997 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1147997 3194862 SPO1092 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_166343.1 1147095 D 246200 CDS YP_166344.1 56695990 3194409 complement(1147941..1149146) 1 NC_003911.11 identified by match to protein family HMM TIGR00710; Bcr/CflA subfamily drug resistance transporter 1149146 3194409 SPO1093 Ruegeria pomeroyi DSS-3 Bcr/CflA subfamily drug resistance transporter YP_166344.1 1147941 R 246200 CDS YP_166345.1 56695991 3195272 1149329..1150861 1 NC_003911.11 identified by similarity to PIR:T42208; match to protein family HMM PF01039; propionyl-CoA carboxylase subunit beta 1150861 pccB 3195272 pccB Ruegeria pomeroyi DSS-3 propionyl-CoA carboxylase subunit beta YP_166345.1 1149329 D 246200 CDS YP_166346.1 56695992 3195281 1151639..1152133 1 NC_003911.11 identified by similarity to GB:BAC50887.1; hypothetical protein 1152133 3195281 SPO1095 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166346.1 1151639 D 246200 CDS YP_166347.1 56695993 3194202 1152824..1152961 1 NC_003911.11 lipoprotein 1152961 3194202 SPO1096 Ruegeria pomeroyi DSS-3 lipoprotein YP_166347.1 1152824 D 246200 CDS YP_166348.1 56695994 3195852 1153031..1153390 1 NC_003911.11 identified by similarity to PIR:C98286; hypothetical protein 1153390 3195852 SPO1097 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166348.1 1153031 D 246200 CDS YP_166349.1 56695995 3194937 complement(1153471..1154610) 1 NC_003911.11 identified by similarity to GB:AAM43280.1; hypothetical protein 1154610 3194937 SPO1098 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166349.1 1153471 R 246200 CDS YP_166350.1 56695996 3194396 1155083..1155205 1 NC_003911.11 hypothetical protein 1155205 3194396 SPO1099 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166350.1 1155083 D 246200 CDS YP_166351.1 56695997 3195626 1155270..1155473 1 NC_003911.11 lipoprotein 1155473 3195626 SPO1100 Ruegeria pomeroyi DSS-3 lipoprotein YP_166351.1 1155270 D 246200 CDS YP_166352.1 56695998 3193848 1155594..1157639 1 NC_003911.11 identified by similarity to SP:P14882; match to protein family HMM PF00289; match to protein family HMM PF00364; match to protein family HMM PF02785; match to protein family HMM PF02786; propionyl-CoA carboxylase subunit alpha 1157639 pccA 3193848 pccA Ruegeria pomeroyi DSS-3 propionyl-CoA carboxylase subunit alpha YP_166352.1 1155594 D 246200 CDS YP_166353.1 56695999 3194810 1157644..1158165 1 NC_003911.11 lipoprotein 1158165 3194810 SPO1102 Ruegeria pomeroyi DSS-3 lipoprotein YP_166353.1 1157644 D 246200 CDS YP_166354.1 56696000 3195337 complement(1158182..1158766) 1 NC_003911.11 hypothetical protein 1158766 3195337 SPO1103 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166354.1 1158182 R 246200 CDS YP_166355.1 56696001 3195234 1158731..1159732 1 NC_003911.11 hypothetical protein 1159732 3195234 SPO1104 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166355.1 1158731 D 246200 CDS YP_166356.1 56696002 3196172 1159698..1161827 1 NC_003911.11 MDM; functions in conversion of succinate to propionate; methylmalonyl-CoA mutase 1161827 3196172 SPO1105 Ruegeria pomeroyi DSS-3 methylmalonyl-CoA mutase YP_166356.1 1159698 D 246200 CDS YP_166357.1 56696003 3194681 1161906..1162559 1 NC_003911.11 identified by similarity to PIR:B75327; hypothetical protein 1162559 3194681 SPO1106 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166357.1 1161906 D 246200 CDS YP_166358.1 56696004 3196164 1162556..1163050 1 NC_003911.11 identified by similarity to SP:P21861; match to protein family HMM PF00583; phosphinothricin N-acetyltransferase 1163050 3196164 SPO1107 Ruegeria pomeroyi DSS-3 phosphinothricin N-acetyltransferase YP_166358.1 1162556 D 246200 CDS YP_166359.1 56696005 3195067 1163091..1163771 1 NC_003911.11 identified by similarity to SP:P31680; match to protein family HMM PF00226; DnaJ-like protein DjlA 1163771 3195067 SPO1108 Ruegeria pomeroyi DSS-3 DnaJ-like protein DjlA YP_166359.1 1163091 D 246200 CDS YP_166360.1 56696006 3195812 1163776..1164789 1 NC_003911.11 identified by match to protein family HMM PF03372; hypothetical protein 1164789 3195812 SPO1109 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166360.1 1163776 D 246200 CDS YP_166361.1 56696007 3196144 1165314..1166216 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1166216 3196144 SPO1110 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_166361.1 1165314 D 246200 CDS YP_166362.1 56696008 3195111 1166294..1167121 1 NC_003911.11 identified by similarity to GB:CAE33489.1; match to protein family HMM PF07286; hypothetical protein 1167121 3195111 SPO1111 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166362.1 1166294 D 246200 CDS YP_166363.1 56696009 3195696 1167143..1168180 1 NC_003911.11 identified by match to protein family HMM PF03480; TRAP transporter, periplasmic protein 1168180 3195696 SPO1112 Ruegeria pomeroyi DSS-3 TRAP transporter, periplasmic protein YP_166363.1 1167143 D 246200 CDS YP_166364.1 56696010 3195613 1168219..1168752 1 NC_003911.11 Assignment based partly on membership in a TRAP-T gene trio.; identified by similarity to GB:CAE33493.1; TRAP transporter, transmembrane protein 1168752 3195613 SPO1113 Ruegeria pomeroyi DSS-3 TRAP transporter, transmembrane protein YP_166364.1 1168219 D 246200 CDS YP_166365.1 56696011 3193589 1168749..1170035 1 NC_003911.11 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM 1170035 3193589 SPO1114 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_166365.1 1168749 D 246200 CDS YP_166366.1 56696012 3193929 1170039..1170692 1 NC_003911.11 identified by similarity to GB:CAE33491.1; hypothetical protein 1170692 3193929 SPO1115 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166366.1 1170039 D 246200 CDS YP_166367.1 56696013 3195847 complement(1170850..1172775) 1 NC_003911.11 hypothetical protein 1172775 3195847 SPO1116 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166367.1 1170850 R 246200 CDS YP_166368.1 56696014 3195224 complement(1173336..1174880) 1 NC_003911.11 identified by match to protein family HMM PF02541; Ppx/GppA phosphatase 1174880 3195224 SPO1117 Ruegeria pomeroyi DSS-3 Ppx/GppA phosphatase YP_166368.1 1173336 R 246200 CDS YP_166369.1 56696015 3196130 complement(1174942..1175619) 1 NC_003911.11 identified by similarity to GB:BAC49388.1; hypothetical protein 1175619 3196130 SPO1118 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166369.1 1174942 R 246200 CDS YP_166370.1 56696016 3192989 complement(1175620..1176687) 1 NC_003911.11 identified by match to protein family HMM PF01594; hypothetical protein 1176687 3192989 SPO1119 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166370.1 1175620 R 246200 CDS YP_166371.1 56696017 3193090 1176927..1177682 1 NC_003911.11 identified by similarity to PIR:T10512; hypothetical protein 1177682 3193090 SPO1120 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166371.1 1176927 D 246200 CDS YP_166372.1 56696018 3195540 1177999..1179393 1 NC_003911.11 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase 1179393 proS 3195540 proS Ruegeria pomeroyi DSS-3 prolyl-tRNA synthetase YP_166372.1 1177999 D 246200 CDS YP_166373.1 56696019 3193001 complement(1179398..1179763) 1 NC_003911.11 hypothetical protein 1179763 3193001 SPO1122 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166373.1 1179398 R 246200 CDS YP_166374.1 56696020 3196122 1179969..1181312 1 NC_003911.11 identified by similarity to SP:P75956; match to protein family HMM PF02687; lipoprotein releasing system transmembrane protein LolE 1181312 lolE 3196122 lolE Ruegeria pomeroyi DSS-3 lipoprotein releasing system transmembrane protein LolE YP_166374.1 1179969 D 246200 CDS YP_166375.1 56696021 3195423 1181305..1181991 1 NC_003911.11 identified by similarity to SP:P75957; match to protein family HMM PF00005; lipoprotein releasing system ATP-binding protein 1181991 lolD 3195423 lolD Ruegeria pomeroyi DSS-3 lipoprotein releasing system ATP-binding protein YP_166375.1 1181305 D 246200 CDS YP_166376.1 56696022 3196116 1182006..1182461 1 NC_003911.11 hypothetical protein 1182461 3196116 SPO1125 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166376.1 1182006 D 246200 CDS YP_166377.1 56696023 3195907 1182487..1182879 1 NC_003911.11 cytochrome c family protein 1182879 3195907 SPO1126 Ruegeria pomeroyi DSS-3 cytochrome c family protein YP_166377.1 1182487 D 246200 CDS YP_166378.1 56696024 3193945 1182895..1183302 1 NC_003911.11 identified by match to protein family HMM PF00034; cytochrome c family protein 1183302 3193945 SPO1127 Ruegeria pomeroyi DSS-3 cytochrome c family protein YP_166378.1 1182895 D 246200 CDS YP_166379.1 56696025 3195112 complement(1183370..1184170) 1 NC_003911.11 hypothetical protein 1184170 3195112 SPO1128 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166379.1 1183370 R 246200 CDS YP_166380.1 56696026 3196109 complement(1184211..1184873) 1 NC_003911.11 identified by similarity to PIR:D83497; hypothetical protein 1184873 3196109 SPO1129 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166380.1 1184211 R 246200 CDS YP_166381.1 56696027 3196096 complement(1184936..1185343) 1 NC_003911.11 identified by match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase 1185343 3196096 SPO1130 Ruegeria pomeroyi DSS-3 thioesterase YP_166381.1 1184936 R 246200 CDS YP_166382.1 56696028 3196089 1185539..1186549 1 NC_003911.11 identified by match to protein family HMM PF04069; glycine betaine/proline ABC transporter substrate-binding protein 1186549 3196089 SPO1131 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter substrate-binding protein YP_166382.1 1185539 D 246200 CDS YP_166383.1 56696029 3196091 1186559..1187611 1 NC_003911.11 identified by similarity to SP:P46920; match to protein family HMM PF00005; glycine betaine/proline ABC transporter ATP-binding protein 1187611 3196091 SPO1132 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter ATP-binding protein YP_166383.1 1186559 D 246200 CDS YP_166384.1 56696030 3196072 1187608..1189671 1 NC_003911.11 identified by similarity to SP:P14176; match to protein family HMM PF00528; glycine betaine/proline ABC transporter permease 1189671 3196072 SPO1133 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter permease YP_166384.1 1187608 D 246200 CDS YP_166385.1 56696031 3195924 1189756..1190424 1 NC_003911.11 identified by match to protein family HMM PF07298; NnrU family protein 1190424 3195924 SPO1134 Ruegeria pomeroyi DSS-3 NnrU family protein YP_166385.1 1189756 D 246200 CDS YP_166386.1 56696032 3193578 1190456..1191007 1 NC_003911.11 identified by similarity to PIR:AB3629; hypothetical protein 1191007 3193578 SPO1135 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166386.1 1190456 D 246200 CDS YP_166387.1 56696033 3195074 complement(1191289..1192662) 1 NC_003911.11 identified by match to protein family HMM PF00202; hypothetical protein 1192662 3195074 SPO1136 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166387.1 1191289 R 246200 CDS YP_166388.1 56696034 3194046 complement(1192817..1194292) 1 NC_003911.11 identified by similarity to SP:P25526; match to protein family HMM PF00171; match to protein family HMM TIGR01780; succinate-semialdehyde dehydrogenase 1194292 gabD-1 3194046 gabD-1 Ruegeria pomeroyi DSS-3 succinate-semialdehyde dehydrogenase YP_166388.1 1192817 R 246200 CDS YP_166389.1 56696035 3193874 complement(1194420..1194899) 1 NC_003911.11 identified by match to protein family HMM PF01037; amino acid metabolism regulator 1194899 asnC 3193874 asnC Ruegeria pomeroyi DSS-3 amino acid metabolism regulator YP_166389.1 1194420 R 246200 CDS YP_166390.1 56696036 3195186 complement(1194911..1195903) 1 NC_003911.11 identified by match to protein family HMM PF04952; ectoine utilization protein EutE 1195903 3195186 SPO1139 Ruegeria pomeroyi DSS-3 ectoine utilization protein EutE YP_166390.1 1194911 R 246200 CDS YP_166391.1 56696037 3195544 complement(1195907..1197094) 1 NC_003911.11 identified by similarity to SP:P55667; ectoine utilization protein EutD 1197094 3195544 SPO1140 Ruegeria pomeroyi DSS-3 ectoine utilization protein EutD YP_166391.1 1195907 R 246200 CDS YP_166392.1 56696038 3195478 complement(1197114..1198148) 1 NC_003911.11 cyclodeaminase; ectoine utilization protein EutC 1198148 3195478 SPO1141 Ruegeria pomeroyi DSS-3 ectoine utilization protein EutC YP_166392.1 1197114 R 246200 CDS YP_166393.1 56696039 3193370 complement(1198099..1199106) 1 NC_003911.11 catalyzes the formation of 2-oxobutanoate from L-threonine; involved in ectoine utilization; threonine dehydratase 1199106 eutB 3193370 eutB Ruegeria pomeroyi DSS-3 threonine dehydratase YP_166393.1 1198099 R 246200 CDS YP_166394.1 56696040 3194757 complement(1199124..1199888) 1 NC_003911.11 identified by match to protein family HMM PF01177; ectoine utilization protein EutA 1199888 3194757 SPO1143 Ruegeria pomeroyi DSS-3 ectoine utilization protein EutA YP_166394.1 1199124 R 246200 CDS YP_166395.1 56696041 3192648 complement(1199897..1200334) 1 NC_003911.11 identified by match to protein family HMM PF00582; universal stress protein family protein 1200334 3192648 SPO1144 Ruegeria pomeroyi DSS-3 universal stress protein family protein YP_166395.1 1199897 R 246200 CDS YP_166396.1 56696042 3195851 complement(1200347..1201633) 1 NC_003911.11 identified by match to protein family HMM PF00597; match to protein family HMM PF06808; match to protein family HMM TIGR00786; ectoin/5-hydroxyectoin TRAP transporter periplasmic binding protein 1201633 uehC 3195851 uehC Ruegeria pomeroyi DSS-3 ectoin/5-hydroxyectoin TRAP transporter periplasmic binding protein YP_166396.1 1200347 R 246200 CDS YP_166397.1 56696043 3195006 complement(1201644..1202210) 1 NC_003911.11 identified by match to protein family HMM PF04290; ectoin/5-hydroxyectoin TRAP transporter small integral membrane protein 1202210 uehB 3195006 uehB Ruegeria pomeroyi DSS-3 ectoin/5-hydroxyectoin TRAP transporter small integral membrane protein YP_166397.1 1201644 R 246200 CDS YP_166398.1 56696044 3195242 complement(1202280..1203299) 1 NC_003911.11 identified by similarity to SP:P37735; match to protein family HMM PF03480; ectoin/5-hydroxyectoin TRAP transporter large integral membrane protein 1203299 uehA 3195242 uehA Ruegeria pomeroyi DSS-3 ectoin/5-hydroxyectoin TRAP transporter large integral membrane protein YP_166398.1 1202280 R 246200 CDS YP_166399.1 56696045 3195381 complement(1203397..1204791) 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1204791 gntR 3195381 gntR Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_166399.1 1203397 R 246200 CDS YP_166400.1 56696046 3195708 1205883..1206656 1 NC_003911.11 identified by match to protein family HMM PF00588; match to protein family HMM TIGR00186; RNA methyltransferase 1206656 3195708 SPO1150 Ruegeria pomeroyi DSS-3 RNA methyltransferase YP_166400.1 1205883 D 246200 CDS YP_166401.1 56696047 3194323 1206671..1206976 1 NC_003911.11 hypothetical protein 1206976 3194323 SPO1151 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166401.1 1206671 D 246200 CDS YP_166402.1 56696048 3195020 1207067..1207525 1 NC_003911.11 identified by similarity to PIR:E82434; match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1207525 3195020 SPO1152 Ruegeria pomeroyi DSS-3 twin-arginine translocation pathway signal sequence domain-containing protein YP_166402.1 1207067 D 246200 CDS YP_166403.1 56696049 3193315 1207721..1208197 1 NC_003911.11 identified by match to protein family HMM PF02629; CoA-binding domain-containing protein 1208197 3193315 SPO1153 Ruegeria pomeroyi DSS-3 CoA-binding domain-containing protein YP_166403.1 1207721 D 246200 CDS YP_166404.1 56696050 3194032 complement(1208194..1208754) 1 NC_003911.11 lipoprotein 1208754 3194032 SPO1154 Ruegeria pomeroyi DSS-3 lipoprotein YP_166404.1 1208194 R 246200 CDS YP_166405.1 56696051 3194083 complement(1208815..1209132) 1 NC_003911.11 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis; phosphoribosyl-ATP pyrophosphatase 1209132 hisE 3194083 hisE Ruegeria pomeroyi DSS-3 phosphoribosyl-ATP pyrophosphatase YP_166405.1 1208815 R 246200 CDS YP_166406.1 56696052 3195843 complement(1209129..1209890) 1 NC_003911.11 catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase; imidazole glycerol phosphate synthase subunit HisF 1209890 hisF 3195843 hisF Ruegeria pomeroyi DSS-3 imidazole glycerol phosphate synthase subunit HisF YP_166406.1 1209129 R 246200 CDS YP_166407.1 56696053 3195045 complement(1209924..1210418) 1 NC_003911.11 identified by similarity to GB:BAC46085.1; hypothetical protein 1210418 3195045 SPO1157 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166407.1 1209924 R 246200 CDS YP_166408.1 56696054 3195806 complement(1210495..1211217) 1 NC_003911.11 catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide; 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 1211217 hisA 3195806 hisA Ruegeria pomeroyi DSS-3 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase YP_166408.1 1210495 R 246200 CDS YP_166409.1 56696055 3194740 1211350..1211748 1 NC_003911.11 identified by similarity to GB:AAN29556.1; hypothetical protein 1211748 3194740 SPO1159 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166409.1 1211350 D 246200 CDS YP_166410.1 56696056 3193244 complement(1211792..1212328) 1 NC_003911.11 identified by similarity to GB:AAM73219.1; hypothetical protein 1212328 3193244 SPO1160 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166410.1 1211792 R 246200 CDS YP_166411.1 56696057 3193382 1212347..1213138 1 NC_003911.11 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 1213138 3193382 SPO1161 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_166411.1 1212347 D 246200 CDS YP_166412.1 56696058 3195662 complement(1213227..1213865) 1 NC_003911.11 with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide; imidazole glycerol phosphate synthase subunit HisH 1213865 hisH 3195662 hisH Ruegeria pomeroyi DSS-3 imidazole glycerol phosphate synthase subunit HisH YP_166412.1 1213227 R 246200 CDS YP_166413.1 56696059 3195098 complement(1213865..1214452) 1 NC_003911.11 catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis; imidazoleglycerol-phosphate dehydratase 1214452 hisB 3195098 hisB Ruegeria pomeroyi DSS-3 imidazoleglycerol-phosphate dehydratase YP_166413.1 1213865 R 246200 CDS YP_166414.1 56696060 3194632 1214565..1214852 1 NC_003911.11 identified by similarity to PIR:A97666; hypothetical protein 1214852 3194632 SPO1164 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166414.1 1214565 D 246200 CDS YP_166415.1 56696061 3195889 complement(1214839..1215612) 1 NC_003911.11 identified by similarity to GB:BAB52792.1; hypothetical protein 1215612 3195889 SPO1165 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166415.1 1214839 R 246200 CDS YP_166416.1 56696062 3195918 complement(1215666..1217018) 1 NC_003911.11 identified by match to protein family HMM PF00202; aminotransferase 1217018 3195918 SPO1166 Ruegeria pomeroyi DSS-3 aminotransferase YP_166416.1 1215666 R 246200 CDS YP_166417.1 56696063 3194788 1217387..1217911 1 NC_003911.11 identified by similarity to PIR:D95307; hypothetical protein 1217911 3194788 SPO1168 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166417.1 1217387 D 246200 CDS YP_166418.1 56696064 3195551 complement(1218331..1221768) 1 NC_003911.11 biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate; pyruvate carboxylase 1221768 pyc 3195551 pyc Ruegeria pomeroyi DSS-3 pyruvate carboxylase YP_166418.1 1218331 R 246200 CDS YP_166419.1 56696065 3194219 complement(1221906..1223021) 1 NC_003911.11 identified by match to protein family HMM PF01070; FMN-dependent alpha-hydroxy acid dehydrogenase 1223021 3194219 SPO1172 Ruegeria pomeroyi DSS-3 FMN-dependent alpha-hydroxy acid dehydrogenase YP_166419.1 1221906 R 246200 CDS YP_166420.1 56696066 3195229 complement(1223161..1224957) 1 NC_003911.11 identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254; diguanylate cyclase 1224957 3195229 SPO1173 Ruegeria pomeroyi DSS-3 diguanylate cyclase YP_166420.1 1223161 R 246200 CDS YP_166421.1 56696067 3195921 1225205..1227544 1 NC_003911.11 identified by match to protein family HMM PF00580; DNA helicase II 1227544 3195921 SPO1174 Ruegeria pomeroyi DSS-3 DNA helicase II YP_166421.1 1225205 D 246200 CDS YP_166422.1 56696068 3192965 complement(1227563..1228426) 1 NC_003911.11 hypothetical protein 1228426 3192965 SPO1175 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166422.1 1227563 R 246200 CDS YP_166423.1 56696069 3195151 complement(1228427..1229203) 1 NC_003911.11 identified by match to protein family HMM PF00149; Ser/Thr protein phosphatase 1229203 3195151 SPO1176 Ruegeria pomeroyi DSS-3 Ser/Thr protein phosphatase YP_166423.1 1228427 R 246200 CDS YP_166424.1 56696070 3194542 complement(1229631..1229855) 1 NC_003911.11 identified by similarity to GB:BAB50586.1; match to protein family HMM PF06568; hypothetical protein 1229855 3194542 SPO1177 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166424.1 1229631 R 246200 CDS YP_166425.1 56696071 3193765 1230789..1231292 1 NC_003911.11 MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ 1231292 3193765 SPO1178 Ruegeria pomeroyi DSS-3 cell division protein MraZ YP_166425.1 1230789 D 246200 CDS YP_166426.1 56696072 3193020 1231297..1232292 1 NC_003911.11 identified by similarity to SP:P60391; match to protein family HMM PF01795; match to protein family HMM TIGR00006; S-adenosyl-methyltransferase MraW 1232292 mraW 3193020 mraW Ruegeria pomeroyi DSS-3 S-adenosyl-methyltransferase MraW YP_166426.1 1231297 D 246200 CDS YP_166427.1 56696073 3194791 1232289..1232657 1 NC_003911.11 identified by similarity to GB:BAB48908.1; hypothetical protein 1232657 3194791 SPO1180 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166427.1 1232289 D 246200 CDS YP_166428.1 56696074 3195148 1232654..1234441 1 NC_003911.11 identified by similarity to SP:P11882; match to protein family HMM PF00905; match to protein family HMM PF03717; penicillin-binding protein 1234441 3195148 SPO1181 Ruegeria pomeroyi DSS-3 penicillin-binding protein YP_166428.1 1232654 D 246200 CDS YP_166429.1 56696075 3194562 1234460..1235941 1 NC_003911.11 involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate; UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase 1235941 murE 3194562 murE Ruegeria pomeroyi DSS-3 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase YP_166429.1 1234460 D 246200 CDS YP_166430.1 56696076 3193363 1235938..1237332 1 NC_003911.11 identified by similarity to SP:P11880; match to protein family HMM PF01225; match to protein family HMM PF02875; match to protein family HMM TIGR01143; UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase 1237332 murF 3193363 murF Ruegeria pomeroyi DSS-3 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase YP_166430.1 1235938 D 246200 CDS YP_166431.1 56696077 3194606 1237348..1238430 1 NC_003911.11 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase 1238430 mraY 3194606 mraY Ruegeria pomeroyi DSS-3 phospho-N-acetylmuramoyl-pentapeptide- transferase YP_166431.1 1237348 D 246200 CDS YP_166432.1 56696078 3194062 1238573..1239373 1 NC_003911.11 hypothetical protein 1239373 3194062 SPO1185 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166432.1 1238573 D 246200 CDS YP_166433.1 56696079 3195360 1239345..1240469 1 NC_003911.11 identified by similarity to PIR:AG2285; match to protein family HMM PF00515; hypothetical protein 1240469 3195360 SPO1186 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166433.1 1239345 D 246200 CDS YP_166434.1 56696080 3195454 1240536..1241936 1 NC_003911.11 UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase 1241936 murD 3195454 murD Ruegeria pomeroyi DSS-3 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase YP_166434.1 1240536 D 246200 CDS YP_166435.1 56696081 3194363 complement(1242072..1243292) 1 NC_003911.11 identified by similarity to PIR:E97432; match to protein family HMM PF03486; match to protein family HMM TIGR00275; hypothetical protein 1243292 3194363 SPO1188 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166435.1 1242072 R 246200 CDS YP_166436.1 56696082 3194007 complement(1243312..1244196) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 1244196 3194007 SPO1189 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166436.1 1243312 R 246200 CDS YP_166437.1 56696083 3193777 complement(1244296..1244658) 1 NC_003911.11 identified by match to protein family HMM PF01638; transcriptional regulator family protein 1244658 3193777 SPO1190 Ruegeria pomeroyi DSS-3 transcriptional regulator family protein YP_166437.1 1244296 R 246200 CDS YP_166438.1 56696084 3193256 1244786..1245400 1 NC_003911.11 identified by similarity to SP:P39100; match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 1245400 gst 3193256 gst Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_166438.1 1244786 D 246200 CDS YP_166439.1 56696085 3194240 1245397..1245783 1 NC_003911.11 identified by similarity to GB:AAK24936.1; hypothetical protein 1245783 3194240 SPO1192 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166439.1 1245397 D 246200 CDS YP_166440.1 56696086 3194260 1245844..1246050 1 NC_003911.11 identified by match to protein family HMM PF01361; match to protein family HMM TIGR00013; 4-oxalocrotonate tautomerase 1246050 3194260 SPO1193 Ruegeria pomeroyi DSS-3 4-oxalocrotonate tautomerase YP_166440.1 1245844 D 246200 CDS YP_166441.1 56696087 3193181 1246139..1247380 1 NC_003911.11 identified by similarity to SP:P16457; match to protein family HMM PF01098; cell division protein FtsW 1247380 3193181 SPO1194 Ruegeria pomeroyi DSS-3 cell division protein FtsW YP_166441.1 1246139 D 246200 CDS YP_166442.1 56696088 3193006 1247394..1248491 1 NC_003911.11 UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis; UDPdiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase 1248491 murG 3193006 murG Ruegeria pomeroyi DSS-3 UDPdiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase YP_166442.1 1247394 D 246200 CDS YP_166443.1 56696089 3192978 1248488..1249885 1 NC_003911.11 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis; UDP-N-acetylmuramate--L-alanine ligase 1249885 murC 3192978 murC Ruegeria pomeroyi DSS-3 UDP-N-acetylmuramate--L-alanine ligase YP_166443.1 1248488 D 246200 CDS YP_166444.1 56696090 3193190 1249978..1251186 1 NC_003911.11 identified by match to protein family HMM PF00324; amino acid permease 1251186 3193190 SPO1197 Ruegeria pomeroyi DSS-3 amino acid permease YP_166444.1 1249978 D 246200 CDS YP_166445.1 56696091 3194119 1251431..1251676 1 NC_003911.11 identified by similarity to GB:BAC67841.1; hypothetical protein 1251676 3194119 SPO1198 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166445.1 1251431 D 246200 CDS YP_166446.1 56696092 3192865 1251913..1252227 1 NC_003911.11 hypothetical protein 1252227 3192865 SPO1199 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166446.1 1251913 D 246200 CDS YP_166447.1 56696093 3193384 1252296..1253222 1 NC_003911.11 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase 1253222 murB 3193384 murB Ruegeria pomeroyi DSS-3 UDP-N-acetylenolpyruvoylglucosamine reductase YP_166447.1 1252296 D 246200 CDS YP_166448.1 56696094 3192915 1253322..1254242 1 NC_003911.11 D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli; D-alanine--D-alanine ligase 1254242 ddl 3192915 ddl Ruegeria pomeroyi DSS-3 D-alanine--D-alanine ligase YP_166448.1 1253322 D 246200 CDS YP_166449.1 56696095 3193369 1254230..1255237 1 NC_003911.11 identified by match to protein family HMM PF03799; cell division protein FtsQ 1255237 3193369 SPO1202 Ruegeria pomeroyi DSS-3 cell division protein FtsQ YP_166449.1 1254230 D 246200 CDS YP_166450.1 56696096 3193675 1255243..1256580 1 NC_003911.11 identified by match to protein family HMM PF02491; match to protein family HMM TIGR01174; cell division protein FtsA 1256580 ftsA 3193675 ftsA Ruegeria pomeroyi DSS-3 cell division protein FtsA YP_166450.1 1255243 D 246200 CDS YP_166451.1 56696097 3193425 1256978..1258606 1 NC_003911.11 GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function; cell division protein FtsZ 1258606 ftsZ 3193425 ftsZ Ruegeria pomeroyi DSS-3 cell division protein FtsZ YP_166451.1 1256978 D 246200 CDS YP_166452.1 56696098 3193410 1258819..1259739 1 NC_003911.11 zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis; UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase 1259739 lpxC 3193410 lpxC Ruegeria pomeroyi DSS-3 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase YP_166452.1 1258819 D 246200 CDS YP_166453.1 56696099 3192904 1259890..1260744 1 NC_003911.11 identified by similarity to SP:Q50985; match to protein family HMM PF03696; competence lipoprotein ComL 1260744 3192904 SPO1206 Ruegeria pomeroyi DSS-3 competence lipoprotein ComL YP_166453.1 1259890 D 246200 CDS YP_166454.1 56696100 3192969 1260784..1262433 1 NC_003911.11 identified by match to protein family HMM TIGR00634; DNA repair protein RecN 1262433 recN 3192969 recN Ruegeria pomeroyi DSS-3 DNA repair protein RecN YP_166454.1 1260784 D 246200 CDS YP_166455.1 56696101 3192751 1262479..1264224 1 NC_003911.11 identified by match to protein family HMM PF00654; voltage-gated chloride channel family protein 1264224 3192751 SPO1208 Ruegeria pomeroyi DSS-3 voltage-gated chloride channel family protein YP_166455.1 1262479 D 246200 CDS YP_166456.1 56696102 3193817 1264368..1265816 1 NC_003911.11 identified by match to protein family HMM PF07171; match to protein family HMM PF07364; MlrC domain-containing protein 1265816 3193817 SPO1209 Ruegeria pomeroyi DSS-3 MlrC domain-containing protein YP_166456.1 1264368 D 246200 CDS YP_166457.1 56696103 3192737 1265972..1267567 1 NC_003911.11 identified by similarity to SP:P75797; match to protein family HMM PF00496; oligopeptide ABC transporter periplasmic oligopeptide-binding protein 1267567 3192737 SPO1210 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter periplasmic oligopeptide-binding protein YP_166457.1 1265972 D 246200 CDS YP_166458.1 56696104 3193723 1267642..1268583 1 NC_003911.11 identified by match to protein family HMM PF00528; oligopeptide ABC transporter permease 1268583 3193723 SPO1211 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter permease YP_166458.1 1267642 D 246200 CDS YP_166459.1 56696105 3193116 1268583..1269485 1 NC_003911.11 identified by similarity to SP:P42063; match to protein family HMM PF00528; oligopeptide ABC transporter permease 1269485 3193116 SPO1212 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter permease YP_166459.1 1268583 D 246200 CDS YP_166460.1 56696106 3193925 1269469..1271139 1 NC_003911.11 Substrate assignment partly based on location in oligopeptide ABC transporter gene cluster.; identified by similarity to SP:P75796; match to protein family HMM PF00005; oligopeptide ABC transporter ATP-binding protein 1271139 3193925 SPO1213 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter ATP-binding protein YP_166460.1 1269469 D 246200 CDS YP_166461.1 56696107 3193697 1271143..1272312 1 NC_003911.11 identified by similarity to PIR:I40762; match to protein family HMM PF01546; match to protein family HMM TIGR01891; hippurate hydrolase 1272312 3193697 SPO1214 Ruegeria pomeroyi DSS-3 hippurate hydrolase YP_166461.1 1271143 D 246200 CDS YP_166462.1 56696108 3193545 1272318..1273448 1 NC_003911.11 catalyzes the release of C-terminal glutamate residues from N-acylating moieties; carboxypeptidase 1273448 3193545 SPO1215 Ruegeria pomeroyi DSS-3 carboxypeptidase YP_166462.1 1272318 D 246200 CDS YP_166463.1 56696109 3192714 complement(1274319..1275038) 1 NC_003911.11 hypothetical protein 1275038 3192714 SPO1216 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166463.1 1274319 R 246200 CDS YP_166464.1 56696110 3193779 1275144..1275398 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 1275398 3193779 SPO1217 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_166464.1 1275144 D 246200 CDS YP_166465.1 56696111 3193761 complement(1277271..1278860) 1 NC_003911.11 identified by match to protein family HMM PF00589; phage integrase site specific recombinase 1278860 3193761 SPO1218 Ruegeria pomeroyi DSS-3 phage integrase site specific recombinase YP_166465.1 1277271 R 246200 CDS YP_166466.1 56698711 3196333 1279111..1280238 1 NC_003911.11 identified by match to protein family HMM PF00589; phage integrase site specific recombinase 1280238 3196333 SPO1219 Ruegeria pomeroyi DSS-3 phage integrase site specific recombinase YP_166466.1 1279111 D 246200 CDS YP_166467.1 56696112 3193935 complement(1280321..1280677) 1 NC_003911.11 hypothetical protein 1280677 3193935 SPO1220 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166467.1 1280321 R 246200 CDS YP_166468.1 56696113 3193786 1280672..1282654 1 NC_003911.11 hypothetical protein 1282654 3193786 SPO1221 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166468.1 1280672 D 246200 CDS YP_166469.1 56696114 3193810 complement(1283506..1284990) 1 NC_003911.11 identified by match to protein family HMM PF00239; match to protein family HMM PF07508; resolvase site-specific recombinase 1284990 3193810 SPO1222 Ruegeria pomeroyi DSS-3 resolvase site-specific recombinase YP_166469.1 1283506 R 246200 CDS YP_166470.1 56696115 3193168 complement(1285246..1286073) 1 NC_003911.11 hypothetical protein 1286073 3193168 SPO1223 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166470.1 1285246 R 246200 CDS YP_166471.1 56696116 3192942 complement(1286092..1287255) 1 NC_003911.11 identified by similarity to GB:BAB66386.1; hypothetical protein 1287255 3192942 SPO1224 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166471.1 1286092 R 246200 CDS YP_166472.1 56696117 3193780 1287409..1287987 1 NC_003911.11 identified by similarity to GB:AAQ58890.1; hypothetical protein 1287987 3193780 SPO1225 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166472.1 1287409 D 246200 CDS YP_166473.1 56696118 3193968 1288109..1289455 1 NC_003911.11 lipoprotein 1289455 3193968 SPO1226 Ruegeria pomeroyi DSS-3 lipoprotein YP_166473.1 1288109 D 246200 CDS YP_166474.1 56696119 3193891 1290725..1291075 1 NC_003911.11 identified by similarity to GB:AAQ58888.1; hypothetical protein 1291075 3193891 SPO1227 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166474.1 1290725 D 246200 CDS YP_166475.1 56696120 3194108 1291062..1291544 1 NC_003911.11 hypothetical protein 1291544 3194108 SPO1228 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166475.1 1291062 D 246200 CDS YP_166476.1 56696121 3193870 1292517..1292876 1 NC_003911.11 hypothetical protein 1292876 3193870 SPO1229 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166476.1 1292517 D 246200 CDS YP_166477.1 56696122 3194728 1292876..1295182 1 NC_003911.11 identified by similarity to PIR:T31014; hypothetical protein 1295182 3194728 SPO1230 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166477.1 1292876 D 246200 CDS YP_166478.1 56696123 3193972 1295431..1296327 1 NC_003911.11 hypothetical protein 1296327 3193972 SPO1231 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166478.1 1295431 D 246200 CDS YP_166479.1 56696124 3193871 complement(1296349..1296696) 1 NC_003911.11 identified by similarity to SP:P42505; match to protein family HMM PF00816; H-NS family DNA-binding protein 1296696 3193871 SPO1232 Ruegeria pomeroyi DSS-3 H-NS family DNA-binding protein YP_166479.1 1296349 R 246200 CDS YP_166480.1 56696125 3194015 1297126..1300509 1 NC_003911.11 hypothetical protein 1300509 3194015 SPO1233 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166480.1 1297126 D 246200 CDS YP_166481.1 56698730 3196336 1300861..1301811 1 NC_003911.11 identified by similarity to GB:AAO28025.1; hypothetical protein 1301811 3196336 SPO1234 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166481.1 1300861 D 246200 CDS YP_166482.1 56696126 3192647 1302040..1303836 1 NC_003911.11 identified by similarity to GB:CAE15648.1; hypothetical protein 1303836 3192647 SPO1235 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166482.1 1302040 D 246200 CDS YP_166483.1 56696127 3193015 1303933..1305291 1 NC_003911.11 hypothetical protein 1305291 3193015 SPO1236 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166483.1 1303933 D 246200 CDS YP_166484.1 56696128 3194555 complement(1305533..1306843) 1 NC_003911.11 hypothetical protein 1306843 3194555 SPO1237 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166484.1 1305533 R 246200 CDS YP_166485.1 56696129 3193027 1307788..1308441 1 NC_003911.11 identified by match to protein family HMM PF01135; protein-L-isoaspartate O-methyltransferase 1308441 pcm-1 3193027 pcm-1 Ruegeria pomeroyi DSS-3 protein-L-isoaspartate O-methyltransferase YP_166485.1 1307788 D 246200 CDS YP_166486.1 56696130 3195283 1308540..1309958 1 NC_003911.11 identified by match to protein family HMM PF02321; match to protein family HMM TIGR01844; TolC family type I secretion outer membrane protein 1309958 3195283 SPO1240 Ruegeria pomeroyi DSS-3 TolC family type I secretion outer membrane protein YP_166486.1 1308540 D 246200 CDS YP_166487.1 56696131 3193017 1310034..1310963 1 NC_003911.11 identified by similarity to GB:AAK23300.1; hypothetical protein 1310963 3193017 SPO1241 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166487.1 1310034 D 246200 CDS YP_166488.1 56696132 3193022 complement(1310964..1312421) 1 NC_003911.11 catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation; cobyric acid synthase 1312421 cobQ 3193022 cobQ Ruegeria pomeroyi DSS-3 cobyric acid synthase YP_166488.1 1310964 R 246200 CDS YP_166489.1 56696133 3194786 complement(1312625..1313164) 1 NC_003911.11 identified by similarity to GB:AAR38391.1; hypothetical protein 1313164 3194786 SPO1243 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166489.1 1312625 R 246200 CDS YP_166490.1 56696134 3193034 1313163..1313726 1 NC_003911.11 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 1313726 efp 3193034 efp Ruegeria pomeroyi DSS-3 elongation factor P YP_166490.1 1313163 D 246200 CDS YP_166491.1 56696135 3193048 complement(1313798..1314730) 1 NC_003911.11 identified by match to protein family HMM PF00664; ABC transporter permease 1314730 3193048 SPO1245 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_166491.1 1313798 R 246200 CDS YP_166492.1 56696136 3193070 complement(1314759..1315493) 1 NC_003911.11 identified by match to protein family HMM PF01571; glycine cleavage system protein T 1315493 3193070 SPO1246 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_166492.1 1314759 R 246200 CDS YP_166493.1 56696137 3193977 1315573..1316253 1 NC_003911.11 identified by match to protein family HMM PF00535; glycosyl transferase family protein 1316253 3193977 SPO1247 Ruegeria pomeroyi DSS-3 glycosyl transferase family protein YP_166493.1 1315573 D 246200 CDS YP_166494.1 56696138 3192675 1317572..1319986 1 NC_003911.11 identified by similarity to SP:P43671; paraquat-inducible protein 1319986 3192675 SPO1249 Ruegeria pomeroyi DSS-3 paraquat-inducible protein YP_166494.1 1317572 D 246200 CDS YP_166495.1 56696139 3193790 1319990..1320547 1 NC_003911.11 identified by similarity to GB:AAQ60217.1; match to protein family HMM PF03886; lipoprotein 1320547 3193790 SPO1250 Ruegeria pomeroyi DSS-3 lipoprotein YP_166495.1 1319990 D 246200 CDS YP_166496.1 56696140 3193140 complement(1320544..1321305) 1 NC_003911.11 hypothetical protein 1321305 3193140 SPO1251 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166496.1 1320544 R 246200 CDS YP_166497.1 56696141 3193815 complement(1321425..1321550) 1 NC_003911.11 hypothetical protein 1321550 3193815 SPO1252 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166497.1 1321425 R 246200 CDS YP_166498.1 56696142 3192730 complement(1322648..1324606) 1 NC_003911.11 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B 1324606 parE 3192730 parE Ruegeria pomeroyi DSS-3 DNA topoisomerase IV subunit B YP_166498.1 1322648 R 246200 CDS YP_166499.1 56696143 3194147 complement(1324740..1325333) 1 NC_003911.11 hypothetical protein 1325333 3194147 SPO1254 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166499.1 1324740 R 246200 CDS YP_166500.1 56696144 3193846 1325382..1326056 1 NC_003911.11 identified by match to protein family HMM TIGR01926; alkylhydroperoxidase 1326056 3193846 SPO1255 Ruegeria pomeroyi DSS-3 alkylhydroperoxidase YP_166500.1 1325382 D 246200 CDS YP_166501.1 56696145 3194096 1326265..1327299 1 NC_003911.11 identified by similarity to GB:AAN87337.1; match to protein family HMM PF03976; polyphosphate kinase 1327299 ppk2 3194096 ppk2 Ruegeria pomeroyi DSS-3 polyphosphate kinase YP_166501.1 1326265 D 246200 CDS YP_166502.1 56696146 3194291 complement(1327302..1327913) 1 NC_003911.11 identified by match to protein family HMM PF02798; glutathione S-transferase 1327913 3194291 SPO1257 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_166502.1 1327302 R 246200 CDS YP_166503.1 56696147 3193923 complement(1327910..1328809) 1 NC_003911.11 identified by match to protein family HMM PF00561; alpha/beta hydrolase 1328809 3193923 SPO1258 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_166503.1 1327910 R 246200 CDS YP_166504.1 56696148 3192687 complement(1328806..1329441) 1 NC_003911.11 identified by similarity to GB:AAN30332.1; hypothetical protein 1329441 3192687 SPO1259 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166504.1 1328806 R 246200 CDS YP_166505.1 56696149 3194224 1329564..1330904 1 NC_003911.11 identified by similarity to SP:P37340; match to protein family HMM PF01554; match to protein family HMM TIGR00797; MATE efflux family protein 1330904 3194224 SPO1260 Ruegeria pomeroyi DSS-3 MATE efflux family protein YP_166505.1 1329564 D 246200 CDS YP_166506.1 56696150 3194465 1331077..1331619 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1331619 3194465 SPO1261 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_166506.1 1331077 D 246200 CDS YP_166507.1 56696151 3192911 1331616..1332515 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 1332515 3192911 SPO1262 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166507.1 1331616 D 246200 CDS YP_166508.1 56696152 3194023 complement(1332653..1333054) 1 NC_003911.11 hypothetical protein 1333054 3194023 SPO1263 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166508.1 1332653 R 246200 CDS YP_166509.1 56696153 3194016 complement(1333071..1334273) 1 NC_003911.11 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase 1334273 aspC-2 3194016 aspC-2 Ruegeria pomeroyi DSS-3 aspartate aminotransferase YP_166509.1 1333071 R 246200 CDS YP_166510.1 56696154 3194460 1334366..1334758 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 1334758 3194460 SPO1265 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_166510.1 1334366 D 246200 CDS YP_166511.1 56696155 3194734 1334755..1335012 1 NC_003911.11 identified by match to protein family HMM PF03937; hypothetical protein 1335012 3194734 SPO1266 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166511.1 1334755 D 246200 CDS YP_166512.1 56696156 3192807 1335135..1335587 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1335587 3192807 SPO1267 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_166512.1 1335135 D 246200 CDS YP_166513.1 56696157 3192996 complement(1335581..1336345) 1 NC_003911.11 lipoprotein 1336345 3192996 SPO1268 Ruegeria pomeroyi DSS-3 lipoprotein YP_166513.1 1335581 R 246200 CDS YP_166514.1 56696158 3193381 complement(1336342..1337037) 1 NC_003911.11 identified by similarity to GB:BAB50411.1; hypothetical protein 1337037 3193381 SPO1269 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166514.1 1336342 R 246200 CDS YP_166515.1 56696159 3193319 complement(1337034..1337462) 1 NC_003911.11 identified by match to protein family HMM PF00903; lactoylglutathione lyase 1337462 3193319 SPO1270 Ruegeria pomeroyi DSS-3 lactoylglutathione lyase YP_166515.1 1337034 R 246200 CDS YP_166516.1 56696160 3193752 complement(1337529..1338932) 1 NC_003911.11 hypothetical protein 1338932 3193752 SPO1271 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166516.1 1337529 R 246200 CDS YP_166517.1 56696161 3194028 complement(1338938..1340065) 1 NC_003911.11 hypothetical protein 1340065 3194028 SPO1272 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166517.1 1338938 R 246200 CDS YP_166518.1 56696162 3194823 1340119..1341096 1 NC_003911.11 flavin dependent thymidylate synthase; ThyX; thymidylate synthase complementing protein; catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate; the enzyme from Mycobacterium tuberculosis forms homotetramers; uses FAD as a cofactor; FAD-dependent thymidylate synthase 1341096 thyX 3194823 thyX Ruegeria pomeroyi DSS-3 FAD-dependent thymidylate synthase YP_166518.1 1340119 D 246200 CDS YP_166519.1 56696163 3193771 1341164..1342057 1 NC_003911.11 hypothetical protein 1342057 3193771 SPO1274 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166519.1 1341164 D 246200 CDS YP_166520.1 56696164 3194159 complement(1342151..1342357) 1 NC_003911.11 identified by match to protein family HMM PF00313; cold shock family protein 1342357 3194159 SPO1275 Ruegeria pomeroyi DSS-3 cold shock family protein YP_166520.1 1342151 R 246200 CDS YP_166521.1 56696165 3193983 1342577..1342894 1 NC_003911.11 identified by match to protein family HMM PF03960; ArsC family protein 1342894 3193983 SPO1276 Ruegeria pomeroyi DSS-3 ArsC family protein YP_166521.1 1342577 D 246200 CDS YP_166522.1 56696166 3193038 1342943..1343311 1 NC_003911.11 hypothetical protein 1343311 3193038 SPO1277 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166522.1 1342943 D 246200 CDS YP_166523.1 56696167 3194345 complement(1343352..1343915) 1 NC_003911.11 identified by similarity to GB:AAK25219.1; hypothetical protein 1343915 3194345 SPO1278 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166523.1 1343352 R 246200 CDS YP_166524.1 56696168 3194144 complement(1343890..1344672) 1 NC_003911.11 identified by similarity to GB:CAE43198.1; hypothetical protein 1344672 3194144 SPO1279 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166524.1 1343890 R 246200 CDS YP_166525.1 56696169 3194268 complement(1344669..1345547) 1 NC_003911.11 identified by similarity to SP:Q92W37; match to protein family HMM PF05114; hypothetical protein 1345547 3194268 SPO1280 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166525.1 1344669 R 246200 CDS YP_166526.1 56696170 3194277 complement(1345624..1345935) 1 NC_003911.11 identified by similarity to GB:CAE31790.1; hypothetical protein 1345935 3194277 SPO1281 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166526.1 1345624 R 246200 CDS YP_166527.1 56696171 3194092 complement(1346148..1348094) 1 NC_003911.11 catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); threonyl-tRNA synthetase 1348094 thrS 3194092 thrS Ruegeria pomeroyi DSS-3 threonyl-tRNA synthetase YP_166527.1 1346148 R 246200 CDS YP_166528.1 56696172 3194775 complement(1348253..1348666) 1 NC_003911.11 identified by similarity to GB:BAC49624.1; hypothetical protein 1348666 3194775 SPO1283 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166528.1 1348253 R 246200 CDS YP_166529.1 56696173 3194238 complement(1348663..1349406) 1 NC_003911.11 identified by match to protein family HMM PF01022; match to protein family HMM PF05146; ArsR family transcriptional regulator 1349406 3194238 SPO1284 Ruegeria pomeroyi DSS-3 ArsR family transcriptional regulator YP_166529.1 1348663 R 246200 CDS YP_166530.1 56696174 3194274 1349522..1350265 1 NC_003911.11 identified by similarity to GB:CAE25485.1; hypothetical protein 1350265 3194274 SPO1285 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166530.1 1349522 D 246200 CDS YP_166531.1 56696175 3193324 1350265..1351257 1 NC_003911.11 identified by similarity to GB:BAB47950.1; hypothetical protein 1351257 3193324 SPO1286 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166531.1 1350265 D 246200 CDS YP_166532.1 56696176 3192997 1351257..1351685 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 1351685 3192997 SPO1287 Ruegeria pomeroyi DSS-3 glyoxalase YP_166532.1 1351257 D 246200 CDS YP_166533.1 56696177 3194302 1351685..1352317 1 NC_003911.11 identified by similarity to GB:CAC41730.1; hypothetical protein 1352317 3194302 SPO1288 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166533.1 1351685 D 246200 CDS YP_166534.1 56696178 3193667 1352390..1353094 1 NC_003911.11 identified by match to protein family HMM PF00561; alpha/beta hydrolase 1353094 3193667 SPO1289 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_166534.1 1352390 D 246200 CDS YP_166535.1 56696179 3192655 complement(1353085..1353669) 1 NC_003911.11 identified by similarity to PIR:D83123; hypothetical protein 1353669 3192655 SPO1290 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166535.1 1353085 R 246200 CDS YP_166536.1 56696180 3193958 complement(1353672..1354946) 1 NC_003911.11 identified by similarity to GB:BAA33394.1; match to protein family HMM PF06850; match to protein family HMM TIGR01849; polyhydroxyalkanoate depolymerase 1354946 phaZ 3193958 phaZ Ruegeria pomeroyi DSS-3 polyhydroxyalkanoate depolymerase YP_166536.1 1353672 R 246200 CDS YP_166537.1 56696181 3194012 1355058..1356860 1 NC_003911.11 identified by match to protein family HMM PF07167; match to protein family HMM TIGR01838; poly(3-hydroxyalkanoate) polymerase 1356860 phaC 3194012 phaC Ruegeria pomeroyi DSS-3 poly(3-hydroxyalkanoate) polymerase YP_166537.1 1355058 D 246200 CDS YP_166538.1 56696182 3193788 1356992..1357438 1 NC_003911.11 identified by similarity to GB:BAA77258.1; phasin, PhaP 1357438 phaP 3193788 phaP Ruegeria pomeroyi DSS-3 phasin, PhaP YP_166538.1 1356992 D 246200 CDS YP_166539.1 56696183 3194014 1357700..1358257 1 NC_003911.11 identified by match to protein family HMM TIGR01848; polyhydroxyalkanoate synthesis repressor PhaR 1358257 3194014 SPO1294 Ruegeria pomeroyi DSS-3 polyhydroxyalkanoate synthesis repressor PhaR YP_166539.1 1357700 D 246200 CDS YP_166540.1 56696184 3193776 complement(1358270..1359562) 1 NC_003911.11 identified by match to protein family HMM PF01041; aminotransferase 1359562 3193776 SPO1295 Ruegeria pomeroyi DSS-3 aminotransferase YP_166540.1 1358270 R 246200 CDS YP_166541.1 56696185 3193820 complement(1362412..1363401) 1 NC_003911.11 identified by match to protein family HMM PF00248; oxidoreductase, aldo/keto reductase 1363401 3193820 SPO1298 Ruegeria pomeroyi DSS-3 oxidoreductase, aldo/keto reductase YP_166541.1 1362412 R 246200 CDS YP_166542.1 56698712 3196258 1363484..1364311 1 NC_003911.11 identified by match to protein family HMM PF00126; LysR family transcriptional regulator 1364311 3196258 SPO1299 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_166542.1 1363484 D 246200 CDS YP_166543.1 56696186 3193789 complement(1364561..1365919) 1 NC_003911.11 identified by match to protein family HMM PF00120; glutamine synthetase 1365919 3193789 SPO1300 Ruegeria pomeroyi DSS-3 glutamine synthetase YP_166543.1 1364561 R 246200 CDS YP_166544.1 56696187 3194907 complement(1365921..1366601) 1 NC_003911.11 identified by match to protein family HMM PF00117; glutamine amidotransferase 1366601 3194907 SPO1301 Ruegeria pomeroyi DSS-3 glutamine amidotransferase YP_166544.1 1365921 R 246200 CDS YP_166545.1 56696188 3193944 complement(1366663..1368003) 1 NC_003911.11 identified by match to protein family HMM PF00120; glutamine synthetase 1368003 3193944 SPO1302 Ruegeria pomeroyi DSS-3 glutamine synthetase YP_166545.1 1366663 R 246200 CDS YP_166546.1 56696189 3193802 complement(1368111..1369169) 1 NC_003911.11 identified by similarity to GB:BAB91123.1; match to protein family HMM PF01266; fructosyl-amino acid oxidase 1369169 3193802 SPO1303 Ruegeria pomeroyi DSS-3 fructosyl-amino acid oxidase YP_166546.1 1368111 R 246200 CDS YP_166547.1 56696190 3193749 complement(1369179..1369988) 1 NC_003911.11 identified by similarity to SP:P02912; match to protein family HMM PF00528; match to protein family HMM TIGR01726; His/Glu/Gln/Arg/opine family ABC transporter permease 1369988 3193749 SPO1304 Ruegeria pomeroyi DSS-3 His/Glu/Gln/Arg/opine family ABC transporter permease YP_166547.1 1369179 R 246200 CDS YP_166548.1 56696191 3193894 complement(1369985..1370872) 1 NC_003911.11 identified by similarity to PIR:T44455; match to protein family HMM PF00528; ABC transporter permease 1370872 3193894 SPO1305 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_166548.1 1369985 R 246200 CDS YP_166549.1 56696192 3194724 complement(1370957..1371769) 1 NC_003911.11 identified by similarity to SP:P35120; similarity to PIR:T44454; match to protein family HMM PF00497; His/Glu/Gln/Arg/opine family ABC transporter substrate-binding protein 1371769 3194724 SPO1306 Ruegeria pomeroyi DSS-3 His/Glu/Gln/Arg/opine family ABC transporter substrate-binding protein YP_166549.1 1370957 R 246200 CDS YP_166550.1 56696193 3193924 complement(1371711..1372487) 1 NC_003911.11 identified by similarity to SP:P07109; match to protein family HMM PF00005; His/Glu/Gln/Arg/opine family ABC transporter ATP-binding protein 1372487 3193924 SPO1307 Ruegeria pomeroyi DSS-3 His/Glu/Gln/Arg/opine family ABC transporter ATP-binding protein YP_166550.1 1371711 R 246200 CDS YP_166551.1 56696194 3193748 complement(1372597..1373349) 1 NC_003911.11 identified by similarity to PIR:F83007; hypothetical protein 1373349 3193748 SPO1308 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166551.1 1372597 R 246200 CDS YP_166552.1 56696195 3193754 complement(1373346..1373783) 1 NC_003911.11 identified by similarity to GB:CAC47662.1; match to protein family HMM PF07049; hypothetical protein 1373783 3193754 SPO1309 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166552.1 1373346 R 246200 CDS YP_166553.1 56696196 3192770 complement(1373810..1374253) 1 NC_003911.11 identified by similarity to GB:BAB50927.1; match to protein family HMM PF07049; hypothetical protein 1374253 3192770 SPO1310 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166553.1 1373810 R 246200 CDS YP_166554.1 56696197 3193783 1374686..1375726 1 NC_003911.11 identified by match to protein family HMM PF01244; renal dipeptidase 1375726 3193783 SPO1311 Ruegeria pomeroyi DSS-3 renal dipeptidase YP_166554.1 1374686 D 246200 CDS YP_166555.1 56696198 3193759 complement(1375919..1377562) 1 NC_003911.11 CTP synthase; CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer; CTP synthetase 1377562 pyrG 3193759 pyrG Ruegeria pomeroyi DSS-3 CTP synthetase YP_166555.1 1375919 R 246200 CDS YP_166556.1 56696199 3193914 complement(1377725..1378090) 1 NC_003911.11 identified by match to protein family HMM PF03840; match to protein family HMM TIGR00810; preprotein translocase subunit SecG 1378090 secG 3193914 secG Ruegeria pomeroyi DSS-3 preprotein translocase subunit SecG YP_166556.1 1377725 R 246200 CDS YP_166557.1 56696200 3193903 1378242..1378856 1 NC_003911.11 identified by similarity to SP:P97051; match to protein family HMM PF02979; match to protein family HMM TIGR01323; nitrile hydratase subunit alpha 1378856 nthA 3193903 nthA Ruegeria pomeroyi DSS-3 nitrile hydratase subunit alpha YP_166557.1 1378242 D 246200 CDS YP_166558.1 56696201 3195537 1378853..1379527 1 NC_003911.11 identified by similarity to SP:P97052; nitrile hydratase subunit beta 1379527 nthB 3195537 nthB Ruegeria pomeroyi DSS-3 nitrile hydratase subunit beta YP_166558.1 1378853 D 246200 CDS YP_166559.1 56696202 3194498 1379524..1379856 1 NC_003911.11 identified by similarity to GB:BAC49761.1; hypothetical protein 1379856 3194498 SPO1316 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166559.1 1379524 D 246200 CDS YP_166560.1 56696203 3192887 complement(1379867..1380100) 1 NC_003911.11 identified by similarity to PIR:H81075; hypothetical protein 1380100 3192887 SPO1317 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166560.1 1379867 R 246200 CDS YP_166561.1 56696204 3193892 complement(1380100..1381392) 1 NC_003911.11 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase 1381392 purA 3193892 purA Ruegeria pomeroyi DSS-3 adenylosuccinate synthetase YP_166561.1 1380100 R 246200 CDS YP_166562.1 56696205 3193961 1381548..1381943 1 NC_003911.11 hypothetical protein 1381943 3193961 SPO1319 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166562.1 1381548 D 246200 CDS YP_166563.1 56696206 3193947 complement(1382017..1384080) 1 NC_003911.11 lipoprotein 1384080 3193947 SPO1320 Ruegeria pomeroyi DSS-3 lipoprotein YP_166563.1 1382017 R 246200 CDS YP_166564.1 56696207 3192704 1384220..1384912 1 NC_003911.11 identified by match to protein family HMM PF04263; thiamine pyrophosphokinase 1384912 3192704 SPO1321 Ruegeria pomeroyi DSS-3 thiamine pyrophosphokinase YP_166564.1 1384220 D 246200 CDS YP_166565.1 56696208 3193946 complement(1384857..1385771) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 1385771 3193946 SPO1322 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166565.1 1384857 R 246200 CDS YP_166566.1 56696209 3193948 complement(1385906..1387279) 1 NC_003911.11 identified by similarity to SP:O53614; match to protein family HMM PF03313; match to protein family HMM PF03315; match to protein family HMM TIGR00720; L-serine ammonia-lyase 1387279 sdaA 3193948 sdaA Ruegeria pomeroyi DSS-3 L-serine ammonia-lyase YP_166566.1 1385906 R 246200 CDS YP_166567.1 56696210 3193987 complement(1387281..1387982) 1 NC_003911.11 identified by match to protein family HMM PF02798; glutathione S-transferase 1387982 3193987 SPO1324 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_166567.1 1387281 R 246200 CDS YP_166568.1 56696211 3193716 complement(1388090..1388536) 1 NC_003911.11 lipoprotein 1388536 3193716 SPO1325 Ruegeria pomeroyi DSS-3 lipoprotein YP_166568.1 1388090 R 246200 CDS YP_166569.1 56696212 3193949 1388612..1389043 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1389043 3193949 SPO1326 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_166569.1 1388612 D 246200 CDS YP_166570.1 56696213 3193647 1389138..1389926 1 NC_003911.11 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway; ribose-5-phosphate isomerase A 1389926 rpiA 3193647 rpiA Ruegeria pomeroyi DSS-3 ribose-5-phosphate isomerase A YP_166570.1 1389138 D 246200 CDS YP_166571.1 56696214 3193528 1390068..1391426 1 NC_003911.11 identified by match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM TIGR01424; glutathione-disulfide reductase 1391426 gor 3193528 gor Ruegeria pomeroyi DSS-3 glutathione-disulfide reductase YP_166571.1 1390068 D 246200 CDS YP_166572.1 56696215 3193619 1391501..1392652 1 NC_003911.11 identified by similarity to SP:P25662; match to protein family HMM PF01145; match to protein family HMM TIGR01933; HflK protein 1392652 3193619 SPO1329 Ruegeria pomeroyi DSS-3 HflK protein YP_166572.1 1391501 D 246200 CDS YP_166573.1 56696216 3193971 1392652..1393527 1 NC_003911.11 identified by match to protein family HMM PF01145; match to protein family HMM TIGR01932; HflC protein 1393527 hflC 3193971 hflC Ruegeria pomeroyi DSS-3 HflC protein YP_166573.1 1392652 D 246200 CDS YP_166574.1 56696217 3194009 1393603..1394889 1 NC_003911.11 hypothetical protein 1394889 3194009 SPO1331 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166574.1 1393603 D 246200 CDS YP_166575.1 56696218 3193426 1394886..1395083 1 NC_003911.11 identified by similarity to GB:BAB48824.1; hypothetical protein 1395083 3193426 SPO1332 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166575.1 1394886 D 246200 CDS YP_166576.1 56696219 3194011 1395279..1396736 1 NC_003911.11 identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037; serine protease 1396736 3194011 SPO1333 Ruegeria pomeroyi DSS-3 serine protease YP_166576.1 1395279 D 246200 CDS YP_166577.1 56696220 3193721 1396733..1397173 1 NC_003911.11 hypothetical protein 1397173 3193721 SPO1334 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166577.1 1396733 D 246200 CDS YP_166578.1 56696221 3193756 complement(1397382..1398050) 1 NC_003911.11 identified by match to protein family HMM PF00027; match to protein family HMM PF00325; Crp/Fnr family transcriptional regulator 1398050 3193756 SPO1335 Ruegeria pomeroyi DSS-3 Crp/Fnr family transcriptional regulator YP_166578.1 1397382 R 246200 CDS YP_166579.1 56696222 3195515 complement(1398127..1398738) 1 NC_003911.11 identified by match to protein family HMM PF04279; intracellular septation protein A 1398738 ispZ 3195515 ispZ Ruegeria pomeroyi DSS-3 intracellular septation protein A YP_166579.1 1398127 R 246200 CDS YP_166580.1 56696223 3193439 complement(1398756..1399658) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 1399658 3193439 SPO1337 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166580.1 1398756 R 246200 CDS YP_166581.1 56696224 3192959 complement(1400200..1401372) 1 NC_003911.11 identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM TIGR00064; signal recognition particle-docking protein FtsY 1401372 ftsY 3192959 ftsY Ruegeria pomeroyi DSS-3 signal recognition particle-docking protein FtsY YP_166581.1 1400200 R 246200 CDS YP_166582.1 56696225 3192917 complement(1401434..1402072) 1 NC_003911.11 hypothetical protein 1402072 3192917 SPO1340 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166582.1 1401434 R 246200 CDS YP_166583.1 56696226 3194344 1402098..1403183 1 NC_003911.11 identified by match to protein family HMM PF00487; alkane-1 monooxygenase 1403183 3194344 SPO1341 Ruegeria pomeroyi DSS-3 alkane-1 monooxygenase YP_166583.1 1402098 D 246200 CDS YP_166584.1 56696227 3193677 1403217..1403609 1 NC_003911.11 hypothetical protein 1403609 3193677 SPO1342 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166584.1 1403217 D 246200 CDS YP_166585.1 56696228 3192776 complement(1403684..1404325) 1 NC_003911.11 identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 1404325 3192776 SPO1343 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_166585.1 1403684 R 246200 CDS YP_166586.1 56696229 3193062 complement(1404325..1405773) 1 NC_003911.11 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides; exodeoxyribonuclease VII large subunit 1405773 xseA 3193062 xseA Ruegeria pomeroyi DSS-3 exodeoxyribonuclease VII large subunit YP_166586.1 1404325 R 246200 CDS YP_166587.1 56696230 3192964 1405900..1407162 1 NC_003911.11 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase 1407162 purD 3192964 purD Ruegeria pomeroyi DSS-3 phosphoribosylamine--glycine ligase YP_166587.1 1405900 D 246200 CDS YP_166588.1 56696231 3192660 1407319..1407933 1 NC_003911.11 identified by match to protein family HMM PF00196; match to protein family HMM TIGR00229; LuxR family transcriptional regulator 1407933 3192660 SPO1346 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_166588.1 1407319 D 246200 CDS YP_166589.1 56696232 3193670 complement(1407941..1408873) 1 NC_003911.11 hypothetical protein 1408873 3193670 SPO1347 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166589.1 1407941 R 246200 CDS YP_166590.1 56696233 3195755 complement(1408873..1409196) 1 NC_003911.11 identified by match to protein family HMM PF00111; (Fe-S)-binding protein 1409196 3195755 SPO1348 Ruegeria pomeroyi DSS-3 (Fe-S)-binding protein YP_166590.1 1408873 R 246200 CDS YP_166591.1 56696234 3193126 1409382..1409909 1 NC_003911.11 lipoprotein 1409909 3193126 SPO1349 Ruegeria pomeroyi DSS-3 lipoprotein YP_166591.1 1409382 D 246200 CDS YP_166592.1 56696235 3193698 complement(1409922..1410035) 1 NC_003911.11 hypothetical protein 1410035 3193698 SPO1350 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166592.1 1409922 R 246200 CDS YP_166593.1 56696236 3193007 1410221..1411411 1 NC_003911.11 identified by match to protein family HMM PF01053; match to protein family HMM TIGR01325; O-succinylhomoserine sulfhydrylase 1411411 metZ 3193007 metZ Ruegeria pomeroyi DSS-3 O-succinylhomoserine sulfhydrylase YP_166593.1 1410221 D 246200 CDS YP_166594.1 56696237 3193416 1411589..1412692 1 NC_003911.11 similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis; GTP cyclohydrolase 1412692 3193416 SPO1352 Ruegeria pomeroyi DSS-3 GTP cyclohydrolase YP_166594.1 1411589 D 246200 CDS YP_166595.1 56696238 3192781 1413474..1414922 1 NC_003911.11 identified by similarity to GB:BAA31229.1; match to protein family HMM PF02386; Trk system potassium uptake protein TrkH 1414922 trkH-1 3192781 trkH-1 Ruegeria pomeroyi DSS-3 Trk system potassium uptake protein TrkH YP_166595.1 1413474 D 246200 CDS YP_166596.1 56696239 3192792 complement(1415023..1416942) 1 NC_003911.11 identified by match to protein family HMM PF01471; peptidoglycan binding domain-containing protein 1416942 3192792 SPO1354 Ruegeria pomeroyi DSS-3 peptidoglycan binding domain-containing protein YP_166596.1 1415023 R 246200 CDS YP_166597.1 56696240 3194795 1416986..1417921 1 NC_003911.11 glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit alpha 1417921 glyQ 3194795 glyQ Ruegeria pomeroyi DSS-3 glycyl-tRNA synthetase subunit alpha YP_166597.1 1416986 D 246200 CDS YP_166598.1 56696241 3194785 1417947..1418633 1 NC_003911.11 identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 1418633 3194785 SPO1356 Ruegeria pomeroyi DSS-3 FkbM family methyltransferase YP_166598.1 1417947 D 246200 CDS YP_166599.1 56696242 3192724 1419209..1420420 1 NC_003911.11 identified by similarity to SP:P19933; match to protein family HMM PF03616; match to protein family HMM TIGR00210; sodium/glutamate symporter 1420420 gltS 3192724 gltS Ruegeria pomeroyi DSS-3 sodium/glutamate symporter YP_166599.1 1419209 D 246200 CDS YP_166600.1 56696243 3194984 1420430..1422637 1 NC_003911.11 glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit beta 1422637 glyS 3194984 glyS Ruegeria pomeroyi DSS-3 glycyl-tRNA synthetase subunit beta YP_166600.1 1420430 D 246200 CDS YP_166601.1 56696244 3193323 1422758..1425382 1 NC_003911.11 catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate phosphate dikinase 1425382 ppdK 3193323 ppdK Ruegeria pomeroyi DSS-3 pyruvate phosphate dikinase YP_166601.1 1422758 D 246200 CDS YP_166602.1 56696245 3193026 1425556..1426200 1 NC_003911.11 identified by similarity to SP:P50739; hypothetical protein 1426200 3193026 SPO1360 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166602.1 1425556 D 246200 CDS YP_166603.1 56696246 3193079 1426278..1427654 1 NC_003911.11 identified by match to protein family HMM PF00394; multicopper oxidase domain-containing protein 1427654 3193079 SPO1361 Ruegeria pomeroyi DSS-3 multicopper oxidase domain-containing protein YP_166603.1 1426278 D 246200 CDS YP_166604.1 56696247 3193448 1427754..1428674 1 NC_003911.11 identified by match to protein family HMM TIGR00526; dihydroneopterin aldolase 1428674 3193448 SPO1362 Ruegeria pomeroyi DSS-3 dihydroneopterin aldolase YP_166604.1 1427754 D 246200 CDS YP_166605.1 56696248 3194284 1428875..1429669 1 NC_003911.11 identified by match to protein family HMM PF00809; match to protein family HMM TIGR01496; dihydropteroate synthase 1429669 folP 3194284 folP Ruegeria pomeroyi DSS-3 dihydropteroate synthase YP_166605.1 1428875 D 246200 CDS YP_166606.1 56696249 3195909 1429708..1431054 1 NC_003911.11 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase 1431054 glmM 3195909 glmM Ruegeria pomeroyi DSS-3 phosphoglucosamine mutase YP_166606.1 1429708 D 246200 CDS YP_166607.1 56696250 3193269 complement(1431592..1432512) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 1432512 3193269 SPO1365 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166607.1 1431592 R 246200 CDS YP_166608.1 56696251 3193655 complement(1432639..1433661) 1 NC_003911.11 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis; ketol-acid reductoisomerase 1433661 ilvC 3193655 ilvC Ruegeria pomeroyi DSS-3 ketol-acid reductoisomerase YP_166608.1 1432639 R 246200 CDS YP_166609.1 56696252 3193388 1433793..1434248 1 NC_003911.11 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 1434248 3193388 SPO1367 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_166609.1 1433793 D 246200 CDS YP_166610.1 56696253 3193664 1434245..1434703 1 NC_003911.11 identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator 1434703 3193664 SPO1368 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_166610.1 1434245 D 246200 CDS YP_166611.1 56696254 3193707 complement(1434700..1435401) 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1435401 3193707 SPO1369 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_166611.1 1434700 R 246200 CDS YP_166612.1 56696255 3193653 1435912..1437039 1 NC_003911.11 identified by match to protein family HMM PF00266; aminotransferase 1437039 3193653 SPO1370 Ruegeria pomeroyi DSS-3 aminotransferase YP_166612.1 1435912 D 246200 CDS YP_166613.1 56696256 3193144 complement(1437104..1438300) 1 NC_003911.11 identified by similarity to SP:P25534; match to protein family HMM PF01360; match to protein family HMM TIGR01988; 2-octaprenyl-6-methoxyphenyl hydroxylase 1438300 3193144 SPO1371 Ruegeria pomeroyi DSS-3 2-octaprenyl-6-methoxyphenyl hydroxylase YP_166613.1 1437104 R 246200 CDS YP_166614.1 56696257 3193040 complement(1438378..1438626) 1 NC_003911.11 hypothetical protein 1438626 3193040 SPO1372 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166614.1 1438378 R 246200 CDS YP_166615.1 56696258 3192938 1438825..1440393 1 NC_003911.11 identified by similarity to GB:BAB81303.1; hypothetical protein 1440393 3192938 SPO1373 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166615.1 1438825 D 246200 CDS YP_166616.1 56696259 3194368 complement(1440400..1441044) 1 NC_003911.11 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01509; match to protein family HMM TIGR01993; pyrimidine 5'-nucleotidase 1441044 3194368 SPO1374 Ruegeria pomeroyi DSS-3 pyrimidine 5'-nucleotidase YP_166616.1 1440400 R 246200 CDS YP_166617.1 56696260 3192851 1441145..1441795 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1441795 3192851 SPO1375 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_166617.1 1441145 D 246200 CDS YP_166618.1 56696261 3193431 complement(1441842..1443794) 1 NC_003911.11 identified by match to protein family HMM PF00535; match to protein family HMM PF05157; glycosyl transferase family protein 1443794 3193431 SPO1376 Ruegeria pomeroyi DSS-3 glycosyl transferase family protein YP_166618.1 1441842 R 246200 CDS YP_166619.1 56696262 3193092 complement(1443878..1445044) 1 NC_003911.11 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers; carbamoyl phosphate synthase small subunit 1445044 carA 3193092 carA Ruegeria pomeroyi DSS-3 carbamoyl phosphate synthase small subunit YP_166619.1 1443878 R 246200 CDS YP_166620.1 56696263 3192721 1445233..1445712 1 NC_003911.11 identified by match to protein family HMM PF02637; GatB/YqeY domain-containing protein 1445712 3192721 SPO1378 Ruegeria pomeroyi DSS-3 GatB/YqeY domain-containing protein YP_166620.1 1445233 D 246200 CDS YP_166621.1 56696264 3193212 complement(1446295..1447089) 1 NC_003911.11 identified by match to protein family HMM PF02153; prephenate dehydrogenase 1447089 3193212 SPO1379 Ruegeria pomeroyi DSS-3 prephenate dehydrogenase YP_166621.1 1446295 R 246200 CDS YP_166622.1 56696265 3193075 complement(1447210..1447707) 1 NC_003911.11 identified by similarity to GB:BAB50627.1; hypothetical protein 1447707 3193075 SPO1380 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166622.1 1447210 R 246200 CDS YP_166623.1 56696266 3195114 complement(1447722..1448198) 1 NC_003911.11 identified by similarity to PIR:E98182; hypothetical protein 1448198 3195114 SPO1381 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166623.1 1447722 R 246200 CDS YP_166624.1 56696267 3193704 complement(1448269..1449195) 1 NC_003911.11 hypothetical protein 1449195 3193704 SPO1382 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166624.1 1448269 R 246200 CDS YP_166625.1 56696268 3192919 complement(1449390..1451048) 1 NC_003911.11 identified by similarity to SP:P33517; match to protein family HMM PF00115; cytochrome c oxidase, aa3-type, subunit I 1451048 ctaD 3192919 ctaD Ruegeria pomeroyi DSS-3 cytochrome c oxidase, aa3-type, subunit I YP_166625.1 1449390 R 246200 CDS YP_166626.1 56696269 3194561 complement(1451287..1451748) 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1451748 3194561 SPO1384 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_166626.1 1451287 R 246200 CDS YP_166627.1 56696270 3194033 complement(1451745..1452893) 1 NC_003911.11 identified by match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1452893 3194033 SPO1385 Ruegeria pomeroyi DSS-3 twin-arginine translocation pathway signal sequence domain-containing protein YP_166627.1 1451745 R 246200 CDS YP_166628.1 56696271 3193526 1453104..1453526 1 NC_003911.11 identified by match to protein family HMM PF01230; HIT family protein 1453526 3193526 SPO1386 Ruegeria pomeroyi DSS-3 HIT family protein YP_166628.1 1453104 D 246200 CDS YP_166629.1 56696272 3192909 1453606..1454568 1 NC_003911.11 identified by similarity to SP:P13512; match to protein family HMM PF01545; match to protein family HMM TIGR01297; cation efflux system protein 1454568 3192909 SPO1387 Ruegeria pomeroyi DSS-3 cation efflux system protein YP_166629.1 1453606 D 246200 CDS YP_166630.1 56696273 3193520 1454801..1456573 1 NC_003911.11 identified by similarity to GB:BAC51348.1; match to protein family HMM PF00196; match to protein family HMM PF00561; LuxR family transcriptional regulator 1456573 3193520 SPO1388 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_166630.1 1454801 D 246200 CDS YP_166631.1 56696274 3195079 complement(1456579..1457229) 1 NC_003911.11 lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein; lipoate-protein ligase B 1457229 lipB 3195079 lipB Ruegeria pomeroyi DSS-3 lipoate-protein ligase B YP_166631.1 1456579 R 246200 CDS YP_166632.1 56696275 3193424 complement(1457276..1457935) 1 NC_003911.11 identified by match to protein family HMM PF01323; thioredoxin 1457935 3193424 SPO1390 Ruegeria pomeroyi DSS-3 thioredoxin YP_166632.1 1457276 R 246200 CDS YP_166633.1 56696276 3192953 complement(1458355..1458801) 1 NC_003911.11 identified by match to protein family HMM PF02627; match to protein family HMM TIGR00778; alkylhydroperoxidase 1458801 3192953 SPO1392 Ruegeria pomeroyi DSS-3 alkylhydroperoxidase YP_166633.1 1458355 R 246200 CDS YP_166634.1 56696277 3194989 1458889..1459383 1 NC_003911.11 identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738; Rrf2 family protein 1459383 3194989 SPO1393 Ruegeria pomeroyi DSS-3 Rrf2 family protein YP_166634.1 1458889 D 246200 CDS YP_166635.1 56696278 3193523 1459532..1461655 1 NC_003911.11 identified by match to protein family HMM PF00144; match to protein family HMM PF00353; beta-lactamase 1461655 3193523 SPO1394 Ruegeria pomeroyi DSS-3 beta-lactamase YP_166635.1 1459532 D 246200 CDS YP_166636.1 56696279 3193084 1461711..1462940 1 NC_003911.11 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 1462940 3193084 SPO1395 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_166636.1 1461711 D 246200 CDS YP_166637.1 56696280 3193516 complement(1462852..1464129) 1 NC_003911.11 identified by similarity to GB:AAK38164.1; transporter 1464129 3193516 SPO1396 Ruegeria pomeroyi DSS-3 transporter YP_166637.1 1462852 R 246200 CDS YP_166638.1 56696281 3193043 complement(1464160..1467288) 1 NC_003911.11 identified by match to protein family HMM PF00873; match to protein family HMM TIGR00915; hydrophobe/amphiphile efflux-1 family protein 1467288 3193043 SPO1397 Ruegeria pomeroyi DSS-3 hydrophobe/amphiphile efflux-1 family protein YP_166638.1 1464160 R 246200 CDS YP_166639.1 56696282 3193300 complement(1467292..1468551) 1 NC_003911.11 identified by match to protein family HMM PF00529; match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 1468551 3193300 SPO1398 Ruegeria pomeroyi DSS-3 RND family efflux transporter MFP subunit YP_166639.1 1467292 R 246200 CDS YP_166640.1 56696283 3193694 1468642..1469613 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 1469613 3193694 SPO1399 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_166640.1 1468642 D 246200 CDS YP_166641.1 56696284 3193317 1469684..1470442 1 NC_003911.11 identified by match to protein family HMM PF05853; hypothetical protein 1470442 3193317 SPO1400 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166641.1 1469684 D 246200 CDS YP_166642.1 56696285 3193648 1470439..1471761 1 NC_003911.11 identified by match to protein family HMM PF00202; hypothetical protein 1471761 3193648 SPO1401 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166642.1 1470439 D 246200 CDS YP_166643.1 56696286 3193633 1471842..1472129 1 NC_003911.11 hypothetical protein 1472129 3193633 SPO1402 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166643.1 1471842 D 246200 CDS YP_166644.1 56696287 3193132 complement(1472241..1473959) 1 NC_003911.11 methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content; methionyl-tRNA synthetase 1473959 metG 3193132 metG Ruegeria pomeroyi DSS-3 methionyl-tRNA synthetase YP_166644.1 1472241 R 246200 CDS YP_166645.1 56696288 3193534 complement(1474041..1475267) 1 NC_003911.11 identified by similarity to GB:BAB53930.1; hypothetical protein 1475267 3193534 SPO1404 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166645.1 1474041 R 246200 CDS YP_166646.1 56696289 3194620 1475741..1477204 1 NC_003911.11 identified by match to protein family HMM PF00264; tyrosinase domain-containing protein 1477204 3194620 SPO1405 Ruegeria pomeroyi DSS-3 tyrosinase domain-containing protein YP_166646.1 1475741 D 246200 CDS YP_166647.1 56696290 3193446 1477201..1478067 1 NC_003911.11 hypothetical protein 1478067 3193446 SPO1406 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166647.1 1477201 D 246200 CDS YP_166648.1 56696291 3193443 complement(1478180..1478482) 1 NC_003911.11 identified by similarity to GB:BAD02216.1; hypothetical protein 1478482 3193443 SPO1407 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166648.1 1478180 R 246200 CDS YP_166649.1 56696292 3193242 1478481..1479509 1 NC_003911.11 identified by similarity to SP:P33643; match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005; ribosomal large subunit pseudouridine synthase D 1479509 rluD 3193242 rluD Ruegeria pomeroyi DSS-3 ribosomal large subunit pseudouridine synthase D YP_166649.1 1478481 D 246200 CDS YP_166650.1 56696293 3195142 1479660..1480556 1 NC_003911.11 binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters; RNA polymerase factor sigma-32 1480556 rpoH-2 3195142 rpoH-2 Ruegeria pomeroyi DSS-3 RNA polymerase factor sigma-32 YP_166650.1 1479660 D 246200 CDS YP_166651.1 56696294 3195128 complement(1480689..1481867) 1 NC_003911.11 identified by match to protein family HMM PF01244; renal dipeptidase 1481867 3195128 SPO1410 Ruegeria pomeroyi DSS-3 renal dipeptidase YP_166651.1 1480689 R 246200 CDS YP_166652.1 56696295 3193724 1482007..1482276 1 NC_003911.11 identified by match to protein family HMM PF01258; hypothetical protein 1482276 3193724 SPO1411 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166652.1 1482007 D 246200 CDS YP_166653.1 56696296 3193196 1482323..1482505 1 NC_003911.11 DNA modification methyltransferase domain-containing protein 1482505 3193196 SPO1412 Ruegeria pomeroyi DSS-3 DNA modification methyltransferase domain-containing protein YP_166653.1 1482323 D 246200 CDS YP_166654.1 56696297 3193066 complement(1483569..1485389) 1 NC_003911.11 identified by match to protein family HMM PF01432; oligoendopeptidase F 1485389 pepF 3193066 pepF Ruegeria pomeroyi DSS-3 oligoendopeptidase F YP_166654.1 1483569 R 246200 CDS YP_166655.1 56696298 3193148 complement(1485525..1486487) 1 NC_003911.11 identified by match to protein family HMM PF00561; alpha/beta hydrolase 1486487 3193148 SPO1414 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_166655.1 1485525 R 246200 CDS YP_166656.1 56696299 3192760 complement(1486487..1486777) 1 NC_003911.11 identified by match to protein family HMM PF02036; sterol carrier family protein 1486777 3192760 SPO1415 Ruegeria pomeroyi DSS-3 sterol carrier family protein YP_166656.1 1486487 R 246200 CDS YP_166657.1 56696300 3193065 1486857..1487426 1 NC_003911.11 identified by match to protein family HMM PF00515; hypothetical protein 1487426 3193065 SPO1416 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166657.1 1486857 D 246200 CDS YP_166658.1 56696301 3192722 1487460..1490339 1 NC_003911.11 identified by match to protein family HMM PF00271; helicase 1490339 3192722 SPO1417 Ruegeria pomeroyi DSS-3 helicase YP_166658.1 1487460 D 246200 CDS YP_166659.1 56696302 3192801 1490346..1490648 1 NC_003911.11 identified by match to protein family HMM PF01479; S4 domain-containing protein 1490648 3192801 SPO1418 Ruegeria pomeroyi DSS-3 S4 domain-containing protein YP_166659.1 1490346 D 246200 CDS YP_166660.1 56696303 3192740 1490784..1491122 1 NC_003911.11 identified by match to protein family HMM PF00037; (Fe-S)-binding protein 1491122 3192740 SPO1419 Ruegeria pomeroyi DSS-3 (Fe-S)-binding protein YP_166660.1 1490784 D 246200 CDS YP_166661.1 56696304 3192823 1491414..1491923 1 NC_003911.11 identified by match to protein family HMM PF02559; CarD family transcriptional regulator 1491923 3192823 SPO1420 Ruegeria pomeroyi DSS-3 CarD family transcriptional regulator YP_166661.1 1491414 D 246200 CDS YP_166662.1 56696305 3192796 1492040..1492813 1 NC_003911.11 identified by match to protein family HMM PF00520; cation channel family protein 1492813 3192796 SPO1421 Ruegeria pomeroyi DSS-3 cation channel family protein YP_166662.1 1492040 D 246200 CDS YP_166663.1 56696306 3193304 complement(1492825..1493589) 1 NC_003911.11 identified by match to protein family HMM PF02654; match to protein family HMM TIGR00317; cobalamin 5'-phosphate synthase 1493589 3193304 SPO1422 Ruegeria pomeroyi DSS-3 cobalamin 5'-phosphate synthase YP_166663.1 1492825 R 246200 CDS YP_166664.1 56696307 3195790 1493668..1494678 1 NC_003911.11 catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 1494678 cobT 3195790 cobT Ruegeria pomeroyi DSS-3 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase YP_166664.1 1493668 D 246200 CDS YP_166665.1 56696308 3193373 complement(1494719..1496599) 1 NC_003911.11 identified by similarity to SP:P03819; match to protein family HMM PF02254; match to protein family HMM TIGR00932; glutathione-regulated potassium-efflux system protein 1496599 3193373 SPO1424 Ruegeria pomeroyi DSS-3 glutathione-regulated potassium-efflux system protein YP_166665.1 1494719 R 246200 CDS YP_166666.1 56696309 3194790 complement(1496619..1497074) 1 NC_003911.11 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 1497074 3194790 SPO1425 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_166666.1 1496619 R 246200 CDS YP_166667.1 56696310 3193684 1497219..1498319 1 NC_003911.11 identified by similarity to SP:P80064; match to protein family HMM PF00903; match to protein family HMM TIGR01263; 4-hydroxyphenylpyruvate dioxygenase 1498319 hppD 3193684 hppD Ruegeria pomeroyi DSS-3 4-hydroxyphenylpyruvate dioxygenase YP_166667.1 1497219 D 246200 CDS YP_166668.1 56696311 3195589 complement(1498437..1500689) 1 NC_003911.11 hypothetical protein 1500689 3195589 SPO1427 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166668.1 1498437 R 246200 CDS YP_166669.1 56696312 3193489 1499940..1500860 1 NC_003911.11 hypothetical protein 1500860 3193489 SPO1428 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166669.1 1499940 D 246200 CDS YP_166670.1 56696313 3194723 1500857..1501555 1 NC_003911.11 identified by similarity to SP:Q57099; match to protein family HMM PF04402; outer membrane protein, 28Kda 1501555 omp28 3194723 omp28 Ruegeria pomeroyi DSS-3 outer membrane protein, 28Kda YP_166670.1 1500857 D 246200 CDS YP_166671.1 56696314 3195017 1501651..1502868 1 NC_003911.11 identified by similarity to GB:AAB84282.1; antibiotic efflux protein 1502868 3195017 SPO1430 Ruegeria pomeroyi DSS-3 antibiotic efflux protein YP_166671.1 1501651 D 246200 CDS YP_166672.1 56696315 3193072 complement(1502903..1504195) 1 NC_003911.11 identified by similarity to GB:BAB68505.1; match to protein family HMM PF01053; match to protein family HMM TIGR01326; O-acetylhomoserine aminocarboxypropyltransferase 1504195 3193072 SPO1431 Ruegeria pomeroyi DSS-3 O-acetylhomoserine aminocarboxypropyltransferase YP_166672.1 1502903 R 246200 CDS YP_166673.1 56696316 3192727 complement(1504401..1504799) 1 NC_003911.11 identified by match to protein family HMM PF00581; rhodanese domain-containing protein 1504799 3192727 SPO1432 Ruegeria pomeroyi DSS-3 rhodanese domain-containing protein YP_166673.1 1504401 R 246200 CDS YP_166674.1 56696317 3194752 1504914..1505960 1 NC_003911.11 identified by match to protein family HMM PF00248; aldo/keto reductase 1505960 3194752 SPO1433 Ruegeria pomeroyi DSS-3 aldo/keto reductase YP_166674.1 1504914 D 246200 CDS YP_166675.1 56696318 3195356 complement(1506043..1507032) 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 1507032 3195356 SPO1434 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_166675.1 1506043 R 246200 CDS YP_166676.1 56696319 3194678 1507175..1508080 1 NC_003911.11 identified by match to protein family HMM PF05853; hypothetical protein 1508080 3194678 SPO1435 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166676.1 1507175 D 246200 CDS YP_166677.1 56696320 3193457 1508173..1509636 1 NC_003911.11 Converts (S)-3-hydroxyacyl-CoA to 3-oxyacyl-CoA; may also act as a thioesterase; bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase 1509636 3193457 SPO1436 Ruegeria pomeroyi DSS-3 bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase YP_166677.1 1508173 D 246200 CDS YP_166678.1 56696321 3193485 1509633..1510394 1 NC_003911.11 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 1510394 fabG 3193485 fabG Ruegeria pomeroyi DSS-3 3-ketoacyl-ACP reductase YP_166678.1 1509633 D 246200 CDS YP_166679.1 56696322 3195373 complement(1510501..1510770) 1 NC_003911.11 identified by similarity to GB:BAC50099.1; hypothetical protein 1510770 3195373 SPO1438 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166679.1 1510501 R 246200 CDS YP_166680.1 56696323 3194906 complement(1510771..1511622) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA binding protein 1511622 3194906 SPO1439 Ruegeria pomeroyi DSS-3 DNA binding protein YP_166680.1 1510771 R 246200 CDS YP_166681.1 56696324 3193463 1511739..1511942 1 NC_003911.11 identified by similarity to PIR:E84256; hypothetical protein 1511942 3193463 SPO1440 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166681.1 1511739 D 246200 CDS YP_166682.1 56696325 3194121 1511935..1512837 1 NC_003911.11 identified by match to protein family HMM PF00487; fatty acid desaturase 1512837 3194121 SPO1441 Ruegeria pomeroyi DSS-3 fatty acid desaturase YP_166682.1 1511935 D 246200 CDS YP_166683.1 56696326 3193660 1512858..1513760 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 1513760 3193660 SPO1442 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166683.1 1512858 D 246200 CDS YP_166684.1 56696327 3193638 complement(1513975..1515390) 1 NC_003911.11 identified by similarity to SP:P25888; match to protein family HMM PF00270; match to protein family HMM PF00271; ATP-dependent RNA helicase RhlE 1515390 rhlE 3193638 rhlE Ruegeria pomeroyi DSS-3 ATP-dependent RNA helicase RhlE YP_166684.1 1513975 R 246200 CDS YP_166685.1 56696328 3194035 complement(1515581..1516549) 1 NC_003911.11 hypothetical protein 1516549 3194035 SPO1444 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166685.1 1515581 R 246200 CDS YP_166686.1 56696329 3193229 complement(1516571..1517293) 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 1517293 3193229 SPO1445 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_166686.1 1516571 R 246200 CDS YP_166687.1 56696330 3193476 complement(1517290..1518066) 1 NC_003911.11 identified by match to protein family HMM PF04199; cyclase 1518066 3193476 SPO1446 Ruegeria pomeroyi DSS-3 cyclase YP_166687.1 1517290 R 246200 CDS YP_166688.1 56696331 3193167 complement(1518063..1519358) 1 NC_003911.11 identified by match to protein family HMM PF00106; match to protein family HMM PF01796; short chain dehydrogenase/reductase oxidoreductase 1519358 3193167 SPO1447 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_166688.1 1518063 R 246200 CDS YP_166689.1 56696332 3193455 complement(1519316..1520494) 1 NC_003911.11 identified by similarity to GB:BAC48694.1; hypothetical protein 1520494 3193455 SPO1448 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166689.1 1519316 R 246200 CDS YP_166690.1 56696333 3192939 complement(1520491..1522140) 1 NC_003911.11 identified by match to protein family HMM PF00501; AMP-binding protein 1522140 3192939 SPO1449 Ruegeria pomeroyi DSS-3 AMP-binding protein YP_166690.1 1520491 R 246200 CDS YP_166691.1 56696334 3194761 complement(1522101..1522577) 1 NC_003911.11 identified by match to protein family HMM PF00866; aromatic 1,2-dioxygenase subunit beta 1522577 3194761 SPO1450 Ruegeria pomeroyi DSS-3 aromatic 1,2-dioxygenase subunit beta YP_166691.1 1522101 R 246200 CDS YP_166692.1 56696337 3192871 complement(1522595..1523920) 1 NC_003911.11 identified by match to protein family HMM PF00355; match to protein family HMM PF00848; aromatic 1,2-dioxygenase subunit alpha 1523920 3192871 SPO1451 Ruegeria pomeroyi DSS-3 aromatic 1,2-dioxygenase subunit alpha YP_166692.1 1522595 R 246200 CDS YP_166693.1 56696335 3193179 complement(1523932..1524858) 1 NC_003911.11 identified by match to protein family HMM PF00111; match to protein family HMM PF00175; oxidoreductase 1524858 3193179 SPO1452 Ruegeria pomeroyi DSS-3 oxidoreductase YP_166693.1 1523932 R 246200 CDS YP_166694.1 56696336 3192646 1524926..1525384 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1525384 3192646 SPO1453 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_166694.1 1524926 D 246200 CDS YP_166695.1 56696338 3195742 1525447..1526514 1 NC_003911.11 identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 1526514 3195742 SPO1454 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctP YP_166695.1 1525447 D 246200 CDS YP_166696.1 56696339 3193986 1526568..1527065 1 NC_003911.11 TRAP dicarboxylate transporter subunit DctQ 1527065 3193986 SPO1455 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctQ YP_166696.1 1526568 D 246200 CDS YP_166697.1 56696340 3193613 1527062..1528375 1 NC_003911.11 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP C4-dicarboxylate transport system permease DctM 1528375 3193613 SPO1456 Ruegeria pomeroyi DSS-3 TRAP C4-dicarboxylate transport system permease DctM YP_166697.1 1527062 D 246200 CDS YP_166698.1 56696341 3195591 complement(1528378..1528809) 1 NC_003911.11 identified by match to protein family HMM PF03061; thioesterase 1528809 3195591 SPO1457 Ruegeria pomeroyi DSS-3 thioesterase YP_166698.1 1528378 R 246200 CDS YP_166699.1 56696342 3193389 1528988..1529467 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1529467 3193389 SPO1458 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_166699.1 1528988 D 246200 CDS YP_166700.1 56696343 3192907 1529475..1531622 1 NC_003911.11 identified by similarity to SP:O07835; match to protein family HMM PF02775; indolepyruvate oxidoreductase, IorA subunit 1531622 3192907 SPO1459 Ruegeria pomeroyi DSS-3 indolepyruvate oxidoreductase, IorA subunit YP_166700.1 1529475 D 246200 CDS YP_166701.1 56696344 3193712 1531619..1533172 1 NC_003911.11 Involved in the incorporation of exogenous aryl acids in the biosynthesis of aromatic amino acids: catalysis of the ferredoxin-dependent oxidative decarboxylation of arylpyruvates.; indolepyruvate oxidoreductase subunit B 1533172 3193712 SPO1460 Ruegeria pomeroyi DSS-3 indolepyruvate oxidoreductase subunit B YP_166701.1 1531619 D 246200 CDS YP_166702.1 56696345 3193221 1533243..1534046 1 NC_003911.11 identified by similarity to GB:BAC48692.1; hypothetical protein 1534046 3193221 SPO1461 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166702.1 1533243 D 246200 CDS YP_166703.1 56696346 3193387 1534089..1535336 1 NC_003911.11 identified by match to protein family HMM PF00691; OmpA family protein 1535336 3193387 SPO1462 Ruegeria pomeroyi DSS-3 OmpA family protein YP_166703.1 1534089 D 246200 CDS YP_166704.1 56696347 3195607 complement(1535349..1536686) 1 NC_003911.11 identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM 1536686 3195607 SPO1463 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_166704.1 1535349 R 246200 CDS YP_166705.1 56696348 3193586 complement(1536714..1537217) 1 NC_003911.11 TRAP dicarboxylate transporter subunit DctQ 1537217 3193586 SPO1464 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctQ YP_166705.1 1536714 R 246200 CDS YP_166706.1 56696349 3193271 complement(1537282..1538310) 1 NC_003911.11 identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 1538310 3193271 SPO1465 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctP YP_166706.1 1537282 R 246200 CDS YP_166707.1 56696350 3193032 1538519..1539598 1 NC_003911.11 identified by similarity to SP:Q44297; opine dehydrogenase 1539598 3193032 SPO1466 Ruegeria pomeroyi DSS-3 opine dehydrogenase YP_166707.1 1538519 D 246200 CDS YP_166708.1 56696351 3193135 1539600..1540583 1 NC_003911.11 converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase 1540583 3193135 SPO1467 Ruegeria pomeroyi DSS-3 3-hydroxybutyryl-CoA dehydrogenase YP_166708.1 1539600 D 246200 CDS YP_166709.1 56696352 3193376 complement(1540668..1541756) 1 NC_003911.11 identified by match to protein family HMM PF00155; aminotransferase 1541756 3193376 SPO1468 Ruegeria pomeroyi DSS-3 aminotransferase YP_166709.1 1540668 R 246200 CDS YP_166710.1 56696353 3194803 complement(1541807..1543195) 1 NC_003911.11 identified by similarity to GB:AAF19054.1; match to protein family HMM PF00890; 3-ketosteroid dehydrogenase 1543195 3194803 SPO1469 Ruegeria pomeroyi DSS-3 3-ketosteroid dehydrogenase YP_166710.1 1541807 R 246200 CDS YP_166711.1 56696354 3195000 complement(1543179..1544042) 1 NC_003911.11 identified by similarity to SP:Q56062; isocitrate lyase 1544042 3195000 SPO1470 Ruegeria pomeroyi DSS-3 isocitrate lyase YP_166711.1 1543179 R 246200 CDS YP_166712.1 56696355 3195693 complement(1544039..1544659) 1 NC_003911.11 identified by match to protein family HMM PF00857; isochorismatase 1544659 3195693 SPO1471 Ruegeria pomeroyi DSS-3 isochorismatase YP_166712.1 1544039 R 246200 CDS YP_166713.1 56696356 3194486 complement(1544656..1546722) 1 NC_003911.11 identified by similarity to SP:Q01262; match to protein family HMM PF01968; match to protein family HMM PF05378; hydantoin utilization protein A 1546722 hyuA 3194486 hyuA Ruegeria pomeroyi DSS-3 hydantoin utilization protein A YP_166713.1 1544656 R 246200 CDS YP_166714.1 56696357 3192767 complement(1546719..1548413) 1 NC_003911.11 identified by similarity to SP:Q01263; match to protein family HMM PF02538; hydantoin utilization protein B 1548413 3192767 SPO1473 Ruegeria pomeroyi DSS-3 hydantoin utilization protein B YP_166714.1 1546719 R 246200 CDS YP_166715.1 56696358 3193108 complement(1548410..1548976) 1 NC_003911.11 tautomerase 1548976 3193108 SPO1474 Ruegeria pomeroyi DSS-3 tautomerase YP_166715.1 1548410 R 246200 CDS YP_166716.1 56696359 3195561 1549109..1549888 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1549888 3195561 SPO1475 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_166716.1 1549109 D 246200 CDS YP_166717.1 56696360 3192795 1549934..1551292 1 NC_003911.11 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 1551292 leuC-2 3192795 leuC-2 Ruegeria pomeroyi DSS-3 isopropylmalate isomerase large subunit YP_166717.1 1549934 D 246200 CDS YP_166718.1 56696361 3193666 1551292..1551903 1 NC_003911.11 identified by similarity to SP:P30126; match to protein family HMM PF00694; match to protein family HMM TIGR00171; 3-isopropylmalate dehydratase small subunit 1551903 leuD-2 3193666 leuD-2 Ruegeria pomeroyi DSS-3 3-isopropylmalate dehydratase small subunit YP_166718.1 1551292 D 246200 CDS YP_166719.1 56696362 3192773 1552129..1552764 1 NC_003911.11 Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor is involved in heat shock and oxidative stress response; RNA polymerase sigma factor RpoE 1552764 3192773 SPO1478 Ruegeria pomeroyi DSS-3 RNA polymerase sigma factor RpoE YP_166719.1 1552129 D 246200 CDS YP_166720.1 56696363 3192763 1552761..1553396 1 NC_003911.11 identified by similarity to SP:P40685; transcriptional activator 1553396 3192763 SPO1479 Ruegeria pomeroyi DSS-3 transcriptional activator YP_166720.1 1552761 D 246200 CDS YP_166721.1 56696364 3192762 complement(1553536..1554261) 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 1554261 3192762 SPO1480 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_166721.1 1553536 R 246200 CDS YP_166722.1 56696365 3194384 complement(1554258..1555130) 1 NC_003911.11 identified by similarity to GB:AAQ64061.1; hypothetical protein 1555130 3194384 SPO1481 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166722.1 1554258 R 246200 CDS YP_166723.1 56696366 3195829 1555154..1556497 1 NC_003911.11 identified by similarity to PIR:F97597; hypothetical protein 1556497 3195829 SPO1482 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166723.1 1555154 D 246200 CDS YP_166724.1 56696367 3193601 1556436..1557593 1 NC_003911.11 identified by similarity to SP:P30010; match to protein family HMM PF02353; cyclopropane-fatty-acyl-phospholipid synthase 1557593 3193601 SPO1483 Ruegeria pomeroyi DSS-3 cyclopropane-fatty-acyl-phospholipid synthase YP_166724.1 1556436 D 246200 CDS YP_166725.1 56696368 3195081 1557586..1558080 1 NC_003911.11 identified by similarity to GB:AAO56021.1; hypothetical protein 1558080 3195081 SPO1484 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166725.1 1557586 D 246200 CDS YP_166726.1 56696369 3192937 1558077..1559306 1 NC_003911.11 identified by similarity to SP:P96792; sodium:galactoside symporter family protein 1559306 3192937 SPO1485 Ruegeria pomeroyi DSS-3 sodium:galactoside symporter family protein YP_166726.1 1558077 D 246200 CDS YP_166727.1 56696370 3195706 1559303..1559863 1 NC_003911.11 identified by similarity to GB:AAN56374.1; hypothetical protein 1559863 3195706 SPO1486 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166727.1 1559303 D 246200 CDS YP_166728.1 56696371 3192691 1559898..1560632 1 NC_003911.11 hypothetical protein 1560632 3192691 SPO1487 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166728.1 1559898 D 246200 CDS YP_166729.1 56696372 3193437 1560881..1561597 1 NC_003911.11 identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 1561597 3193437 SPO1488 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_166729.1 1560881 D 246200 CDS YP_166730.1 56696373 3194684 1561657..1563036 1 NC_003911.11 catalyzes the formation of indole-3-acetic acid from indole-3-acetamide; indole acetimide hydrolase 1563036 3194684 SPO1489 Ruegeria pomeroyi DSS-3 indole acetimide hydrolase YP_166730.1 1561657 D 246200 CDS YP_166731.1 56696374 3192765 1563063..1564214 1 NC_003911.11 identified by similarity to GB:BAA11039.1; regulatory protein 1564214 3192765 SPO1490 Ruegeria pomeroyi DSS-3 regulatory protein YP_166731.1 1563063 D 246200 CDS YP_166732.1 56696375 3192820 1564225..1565073 1 NC_003911.11 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1565073 3192820 SPO1491 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_166732.1 1564225 D 246200 CDS YP_166733.1 56696376 3192679 1565048..1566796 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease/ATP-binding protein 1566796 3192679 SPO1492 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease/ATP-binding protein YP_166733.1 1565048 D 246200 CDS YP_166734.1 56696377 3194547 1566793..1567476 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1567476 3194547 SPO1493 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_166734.1 1566793 D 246200 CDS YP_166735.1 56696378 3193598 1567665..1569029 1 NC_003911.11 This may represent a duplication of NahD in which the N-terminus copy has diverged more from NahD than the C-terminus copy.; identified by match to protein family HMM PF01323; 2-hydroxychromene-2-carboxylate isomerase 1569029 3193598 SPO1494 Ruegeria pomeroyi DSS-3 2-hydroxychromene-2-carboxylate isomerase YP_166735.1 1567665 D 246200 CDS YP_166736.1 56696379 3195004 1569268..1569975 1 NC_003911.11 identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 1569975 3195004 SPO1495 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_166736.1 1569268 D 246200 CDS YP_166737.1 56696380 3193089 1569983..1572346 1 NC_003911.11 identified by match to protein family HMM PF02687; ABC transporter permease 1572346 3193089 SPO1496 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_166737.1 1569983 D 246200 CDS YP_166738.1 56696381 3192753 1572343..1573593 1 NC_003911.11 identified by match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 1573593 3192753 SPO1497 Ruegeria pomeroyi DSS-3 RND family efflux transporter MFP subunit YP_166738.1 1572343 D 246200 CDS YP_166739.1 56696382 3195115 complement(1573629..1575137) 1 NC_003911.11 identified by similarity to SP:P14407; match to protein family HMM PF05681; match to protein family HMM PF05683; match to protein family HMM TIGR00722; match to protein family HMM TIGR00723; fumarate hydratase, class I 1575137 3195115 SPO1498 Ruegeria pomeroyi DSS-3 fumarate hydratase, class I YP_166739.1 1573629 R 246200 CDS YP_166740.1 56696383 3192676 1575373..1576266 1 NC_003911.11 identified by match to protein family HMM PF00561; alpha/beta hydrolase 1576266 3192676 SPO1499 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_166740.1 1575373 D 246200 CDS YP_166741.1 56696384 3195721 complement(1576263..1577387) 1 NC_003911.11 identified by similarity to SP:P27507; match to protein family HMM PF04055; match to protein family HMM TIGR02109; pyrroloquinoline quinone biosynthesis protein PqqE 1577387 pqqE 3195721 pqqE Ruegeria pomeroyi DSS-3 pyrroloquinoline quinone biosynthesis protein PqqE YP_166741.1 1576263 R 246200 CDS YP_166742.1 56696385 3193984 complement(1577452..1577739) 1 NC_003911.11 identified by similarity to SP:P27506; match to protein family HMM PF05402; coenzyme PQQ synthesis protein D 1577739 pqqD 3193984 pqqD Ruegeria pomeroyi DSS-3 coenzyme PQQ synthesis protein D YP_166742.1 1577452 R 246200 CDS YP_166743.1 56696386 3194751 complement(1577736..1578461) 1 NC_003911.11 Required in the synthesis of PPQ, but its exact function is unknown; pyrroloquinoline quinone biosynthesis protein PqqC 1578461 pqqC 3194751 pqqC Ruegeria pomeroyi DSS-3 pyrroloquinoline quinone biosynthesis protein PqqC YP_166743.1 1577736 R 246200 CDS YP_166744.1 56696387 3192929 complement(1578458..1579345) 1 NC_003911.11 possibly involved in transport of pyrroloquinoline quinone transport; pyrroloquinoline quinone biosynthesis protein PqqB 1579345 pqqB 3192929 pqqB Ruegeria pomeroyi DSS-3 pyrroloquinoline quinone biosynthesis protein PqqB YP_166744.1 1578458 R 246200 CDS YP_166745.1 56696388 3193989 complement(1579373..1579480) 1 NC_003911.11 identified by match to protein family HMM TIGR02107; coenzyme PQQ biosynthesis protein A 1579480 pqqA 3193989 pqqA Ruegeria pomeroyi DSS-3 coenzyme PQQ biosynthesis protein A YP_166745.1 1579373 R 246200 CDS YP_166746.1 56696389 3194858 complement(1579566..1581779) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF02518; sensor histidine kinase/response regulator 1581779 3194858 SPO1505 Ruegeria pomeroyi DSS-3 sensor histidine kinase/response regulator YP_166746.1 1579566 R 246200 CDS YP_166747.1 56696390 3195065 complement(1581786..1582955) 1 NC_003911.11 identified by similarity to GB:AAL30776.1; GfdT protein 1582955 3195065 SPO1506 Ruegeria pomeroyi DSS-3 GfdT protein YP_166747.1 1581786 R 246200 CDS YP_166748.1 56696391 3193082 complement(1582986..1583690) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator 1583690 3193082 SPO1507 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_166748.1 1582986 R 246200 CDS YP_166749.1 56696392 3193500 complement(1583913..1585733) 1 NC_003911.11 identified by similarity to SP:Q9Z4J7; match to protein family HMM PF01011; quinoprotein ethanol dehydrogenase 1585733 3193500 SPO1508 Ruegeria pomeroyi DSS-3 quinoprotein ethanol dehydrogenase YP_166749.1 1583913 R 246200 CDS YP_166750.1 56696393 3193361 complement(1585981..1586388) 1 NC_003911.11 identified by match to protein family HMM PF00034; cytochrome c family protein 1586388 3193361 SPO1509 Ruegeria pomeroyi DSS-3 cytochrome c family protein YP_166750.1 1585981 R 246200 CDS YP_166751.1 56696394 3193955 complement(1586503..1587294) 1 NC_003911.11 identified by match to protein family HMM PF01061; ABC transporter permease 1587294 3193955 SPO1510 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_166751.1 1586503 R 246200 CDS YP_166752.1 56696395 3192674 complement(1587291..1588022) 1 NC_003911.11 identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 1588022 3192674 SPO1511 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_166752.1 1587291 R 246200 CDS YP_166753.1 56696396 3193981 complement(1588019..1588465) 1 NC_003911.11 identified by similarity to PIR:D95864; hypothetical protein 1588465 3193981 SPO1512 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166753.1 1588019 R 246200 CDS YP_166754.1 56696397 3193418 complement(1588479..1589435) 1 NC_003911.11 identified by similarity to GB:AAM77056.1; hypothetical protein 1589435 3193418 SPO1513 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166754.1 1588479 R 246200 CDS YP_166755.1 56696398 3193537 complement(1589441..1590622) 1 NC_003911.11 identified by similarity to PIR:B95864; hypothetical protein 1590622 3193537 SPO1514 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166755.1 1589441 R 246200 CDS YP_166756.1 56696399 3194727 1590779..1591453 1 NC_003911.11 identified by similarity to GB:AAC79658.1; cytochrome c550 1591453 3194727 SPO1515 Ruegeria pomeroyi DSS-3 cytochrome c550 YP_166756.1 1590779 D 246200 CDS YP_166757.1 56696400 3193614 1591450..1592364 1 NC_003911.11 amino acid ABC transporter substrate-binding protein 1592364 3193614 SPO1516 Ruegeria pomeroyi DSS-3 amino acid ABC transporter substrate-binding protein YP_166757.1 1591450 D 246200 CDS YP_166758.1 56696401 3193185 1592481..1593005 1 NC_003911.11 identified by similarity to GB:CAB76249.1; match to protein family HMM PF06240; carbon monoxide dehydrogenase operon G protein 1593005 coxG 3193185 coxG Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase operon G protein YP_166758.1 1592481 D 246200 CDS YP_166759.1 56696402 3193851 1593042..1593527 1 NC_003911.11 identified by similarity to SP:P19921; match to protein family HMM PF00111; match to protein family HMM PF01799; carbon-monoxide dehydrogenase, small subunit 1593527 coxS-1 3193851 coxS-1 Ruegeria pomeroyi DSS-3 carbon-monoxide dehydrogenase, small subunit YP_166759.1 1593042 D 246200 CDS YP_166760.1 56696403 3193481 1593624..1595990 1 NC_003911.11 identified by similarity to SP:P19913; match to protein family HMM PF01315; match to protein family HMM PF02738; carbon monoxide dehydrogenase, large subunit 1595990 coxL-1 3193481 coxL-1 Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase, large subunit YP_166760.1 1593624 D 246200 CDS YP_166761.1 56696404 3195391 1596090..1596872 1 NC_003911.11 identified by similarity to SP:P19920; match to protein family HMM PF00941; carbon monoxide dehydrogenase, medium subunit 1596872 3195391 SPO1520 Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase, medium subunit YP_166761.1 1596090 D 246200 CDS YP_166762.1 56696405 3193080 complement(1596963..1599032) 1 NC_003911.11 identified by similarity to SP:Q00790; regulatory protein 1599032 3193080 SPO1521 Ruegeria pomeroyi DSS-3 regulatory protein YP_166762.1 1596963 R 246200 CDS YP_166763.1 56696406 3195687 1599214..1599801 1 NC_003911.11 identified by similarity to GB:BAC51459.1; hypothetical protein 1599801 3195687 SPO1522 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166763.1 1599214 D 246200 CDS YP_166764.1 56696407 3192986 complement(1599809..1600765) 1 NC_003911.11 identified by match to protein family HMM PF00753; match to protein family HMM TIGR01409; metallo-beta-lactamase 1600765 3192986 SPO1523 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_166764.1 1599809 R 246200 CDS YP_166765.1 56696408 3192789 complement(1600765..1601547) 1 NC_003911.11 identified by similarity to GB:AAN68285.1; hypothetical protein 1601547 3192789 SPO1524 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166765.1 1600765 R 246200 CDS YP_166766.1 56696409 3195090 complement(1601623..1604829) 1 NC_003911.11 identified by match to protein family HMM PF00873; AcrB/AcrD/AcrF family transporter 1604829 3195090 SPO1525 Ruegeria pomeroyi DSS-3 AcrB/AcrD/AcrF family transporter YP_166766.1 1601623 R 246200 CDS YP_166767.1 56696410 3193490 complement(1604822..1605802) 1 NC_003911.11 identified by similarity to SP:P75830; match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 1605802 3193490 SPO1526 Ruegeria pomeroyi DSS-3 RND family efflux transporter MFP subunit YP_166767.1 1604822 R 246200 CDS YP_166768.1 56696411 3193219 complement(1605949..1606545) 1 NC_003911.11 identified by similarity to GB:CAF18626.1; hypothetical protein 1606545 3193219 SPO1527 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166768.1 1605949 R 246200 CDS YP_166769.1 56696412 3193688 complement(1606542..1608782) 1 NC_003911.11 identified by similarity to GB:AAQ00309.1; hypothetical protein 1608782 3193688 SPO1528 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166769.1 1606542 R 246200 CDS YP_166770.1 56696413 3193414 complement(1608788..1609501) 1 NC_003911.11 identified by similarity to GB:BAC14468.1; hypothetical protein 1609501 3193414 SPO1529 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166770.1 1608788 R 246200 CDS YP_166771.1 56696414 3193864 complement(1609667..1611196) 1 NC_003911.11 integral membrane protein MviN 1611196 3193864 SPO1530 Ruegeria pomeroyi DSS-3 integral membrane protein MviN YP_166771.1 1609667 R 246200 CDS YP_166772.1 56696415 3193060 1611310..1612476 1 NC_003911.11 identified by similarity to GB:BAC73064.1; hypothetical protein 1612476 3193060 SPO1531 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166772.1 1611310 D 246200 CDS YP_166773.1 56696416 3193644 complement(1613519..1614226) 1 NC_003911.11 hypothetical protein 1614226 3193644 SPO1532 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166773.1 1613519 R 246200 CDS YP_166774.1 56696417 3194817 complement(1614257..1615399) 1 NC_003911.11 identified by match to protein family HMM PF00534; glycoside hydrolase 1615399 3194817 SPO1533 Ruegeria pomeroyi DSS-3 glycoside hydrolase YP_166774.1 1614257 R 246200 CDS YP_166775.1 56696418 3193330 1615633..1616832 1 NC_003911.11 identified by match to protein family HMM PF02397; sugar transferase 1616832 3193330 SPO1534 Ruegeria pomeroyi DSS-3 sugar transferase YP_166775.1 1615633 D 246200 CDS YP_166776.1 56696419 3193462 1616839..1618122 1 NC_003911.11 identified by match to protein family HMM PF01522; polysaccharide deacetylase 1618122 3193462 SPO1535 Ruegeria pomeroyi DSS-3 polysaccharide deacetylase YP_166776.1 1616839 D 246200 CDS YP_166777.1 56696420 3192728 1618119..1619354 1 NC_003911.11 identified by match to protein family HMM PF00534; group 1 family glycosyltransferase 1619354 3192728 SPO1536 Ruegeria pomeroyi DSS-3 group 1 family glycosyltransferase YP_166777.1 1618119 D 246200 CDS YP_166778.1 56696421 3193358 1619351..1620322 1 NC_003911.11 identified by match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1620322 3193358 SPO1537 Ruegeria pomeroyi DSS-3 twin-arginine translocation pathway signal sequence domain-containing protein YP_166778.1 1619351 D 246200 CDS YP_166779.1 56696422 3193413 1620325..1622094 1 NC_003911.11 identified by match to protein family HMM PF02706; chain length determinant protein 1622094 3193413 SPO1538 Ruegeria pomeroyi DSS-3 chain length determinant protein YP_166779.1 1620325 D 246200 CDS YP_166780.1 56696423 3193345 1622091..1623488 1 NC_003911.11 identified by match to protein family HMM PF04932; O-antigen polymerase 1623488 3193345 SPO1539 Ruegeria pomeroyi DSS-3 O-antigen polymerase YP_166780.1 1622091 D 246200 CDS YP_166781.1 56696424 3192699 1623485..1624627 1 NC_003911.11 identified by match to protein family HMM PF00535; glycosyl transferase family protein 1624627 3192699 SPO1540 Ruegeria pomeroyi DSS-3 glycosyl transferase family protein YP_166781.1 1623485 D 246200 CDS YP_166782.1 56696425 3192693 complement(1624752..1625663) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1625663 3192693 SPO1541 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_166782.1 1624752 R 246200 CDS YP_166783.1 56696426 3195063 1625777..1626835 1 NC_003911.11 identified by match to protein family HMM PF01244; renal dipeptidase 1626835 3195063 SPO1542 Ruegeria pomeroyi DSS-3 renal dipeptidase YP_166783.1 1625777 D 246200 CDS YP_166784.1 56696427 3193888 1626885..1628489 1 NC_003911.11 identified by match to protein family HMM PF00496; peptide/opine/nickel uptake ABC transporter substrate-binding protein 1628489 3193888 SPO1543 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter substrate-binding protein YP_166784.1 1626885 D 246200 CDS YP_166785.1 56696428 3192711 1628490..1629548 1 NC_003911.11 identified by similarity to SP:P37316; match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease 1629548 3192711 SPO1544 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter permease YP_166785.1 1628490 D 246200 CDS YP_166786.1 56696429 3192782 1629545..1630459 1 NC_003911.11 identified by similarity to SP:P37315; match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease 1630459 3192782 SPO1545 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter permease YP_166786.1 1629545 D 246200 CDS YP_166787.1 56696430 3194487 1630456..1631310 1 NC_003911.11 identified by similarity to SP:P24136; match to protein family HMM PF00005; peptide/opine/nickel uptake ABC transporter ATP-binding protein 1631310 3194487 SPO1546 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter ATP-binding protein YP_166787.1 1630456 D 246200 CDS YP_166788.1 56696431 3192874 1631307..1632071 1 NC_003911.11 identified by match to protein family HMM PF00005; peptide/opine/nickel uptake ABC transporter ATP-binding protein 1632071 3192874 SPO1547 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter ATP-binding protein YP_166788.1 1631307 D 246200 CDS YP_166789.1 56696432 3193272 1632385..1633386 1 NC_003911.11 identified by match to protein family HMM PF04069; glycine betaine/proline ABC transporter substrate-binding protein 1633386 3193272 SPO1548 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter substrate-binding protein YP_166789.1 1632385 D 246200 CDS YP_166790.1 56696433 3193478 1633461..1634483 1 NC_003911.11 identified by similarity to SP:P46920; match to protein family HMM PF00005; glycine betaine/proline ABC transporter ATP-binding protein 1634483 3193478 SPO1549 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter ATP-binding protein YP_166790.1 1633461 D 246200 CDS YP_166791.1 56696434 3193160 1634483..1636459 1 NC_003911.11 identified by similarity to SP:P46921; match to protein family HMM PF00528; glycine betaine/proline ABC transporter permease 1636459 3193160 SPO1550 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter permease YP_166791.1 1634483 D 246200 CDS YP_166792.1 56696435 3193211 complement(1636630..1637982) 1 NC_003911.11 identified by similarity to PIR:JC7986; flavin-containing monooxygenase 1637982 3193211 SPO1551 Ruegeria pomeroyi DSS-3 flavin-containing monooxygenase YP_166792.1 1636630 R 246200 CDS YP_166793.1 56696436 3192999 1638115..1639449 1 NC_003911.11 ABC transporter substrate-binding protein 1639449 3192999 SPO1552 Ruegeria pomeroyi DSS-3 ABC transporter substrate-binding protein YP_166793.1 1638115 D 246200 CDS YP_166794.1 56696437 3193827 complement(1639494..1640213) 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1640213 3193827 SPO1553 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_166794.1 1639494 R 246200 CDS YP_166795.1 56696438 3195092 complement(1640347..1642062) 1 NC_003911.11 identified by match to protein family HMM PF00909; ammonium transporter 1642062 3195092 SPO1554 Ruegeria pomeroyi DSS-3 ammonium transporter YP_166795.1 1640347 R 246200 CDS YP_166796.1 56696439 3194780 1642162..1643844 1 NC_003911.11 identified by similarity to GB:AAN03798.1; match to protein family HMM PF01257; match to protein family HMM PF01512; formate dehydrogenase subunit beta 1643844 3194780 SPO1555 Ruegeria pomeroyi DSS-3 formate dehydrogenase subunit beta YP_166796.1 1642162 D 246200 CDS YP_166797.1 56696440 3193002 1643846..1646626 1 NC_003911.11 identified by match to protein family HMM PF00037; match to protein family HMM PF00111; match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; match to protein family HMM TIGR01591; formate dehydrogenase subunit alpha 1646626 3193002 SPO1556 Ruegeria pomeroyi DSS-3 formate dehydrogenase subunit alpha YP_166797.1 1643846 D 246200 CDS YP_166798.1 56696441 3194762 1646655..1648331 1 NC_003911.11 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase 1648331 fhs-1 3194762 fhs-1 Ruegeria pomeroyi DSS-3 formate--tetrahydrofolate ligase YP_166798.1 1646655 D 246200 CDS YP_166799.1 56696442 3193429 1648391..1648696 1 NC_003911.11 identified by match to protein family HMM PF01817; match to protein family HMM TIGR01803; chorismate mutase 1648696 3193429 SPO1558 Ruegeria pomeroyi DSS-3 chorismate mutase YP_166799.1 1648391 D 246200 CDS YP_166800.1 56696443 3194901 1648760..1649650 1 NC_003911.11 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate; bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 1649650 3194901 SPO1559 Ruegeria pomeroyi DSS-3 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase YP_166800.1 1648760 D 246200 CDS YP_166801.1 56696444 3193492 1649647..1650525 1 NC_003911.11 identified by match to protein family HMM PF00763; match to protein family HMM PF02882; folD bifunctional protein 1650525 folD 3193492 folD Ruegeria pomeroyi DSS-3 folD bifunctional protein YP_166801.1 1649647 D 246200 CDS YP_166802.1 56696445 3193188 complement(1650542..1651387) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 1651387 3193188 SPO1561 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166802.1 1650542 R 246200 CDS YP_166803.1 56696446 3192949 1652735..1653880 1 NC_003911.11 identified by match to protein family HMM PF01571; glycine cleavage system T protein 1653880 3192949 SPO1562 Ruegeria pomeroyi DSS-3 glycine cleavage system T protein YP_166803.1 1652735 D 246200 CDS YP_166804.1 56696447 3193408 1653926..1654378 1 NC_003911.11 identified by match to protein family HMM PF01152; hypothetical protein 1654378 3193408 SPO1563 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166804.1 1653926 D 246200 CDS YP_166805.1 56696448 3192931 complement(1654384..1655658) 1 NC_003911.11 identified by match to protein family HMM PF05161; MOFRL domain-containing protein 1655658 3192931 SPO1564 Ruegeria pomeroyi DSS-3 MOFRL domain-containing protein YP_166805.1 1654384 R 246200 CDS YP_166806.1 56696449 3193772 complement(1655645..1656622) 1 NC_003911.11 identified by similarity to SP:O53078; citrate lyase 1656622 3193772 SPO1565 Ruegeria pomeroyi DSS-3 citrate lyase YP_166806.1 1655645 R 246200 CDS YP_166807.1 56696450 3193657 complement(1656751..1657365) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator 1657365 3193657 SPO1566 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_166807.1 1656751 R 246200 CDS YP_166808.1 56696451 3192808 1657594..1658841 1 NC_003911.11 aminotransferase 1658841 3192808 SPO1567 Ruegeria pomeroyi DSS-3 aminotransferase YP_166808.1 1657594 D 246200 CDS YP_166809.1 56696452 3193005 1658883..1660082 1 NC_003911.11 catalyzes the formation of malyl-CoA from malate and CoA; malate--CoA ligase subunit beta 1660082 sucC 3193005 sucC Ruegeria pomeroyi DSS-3 malate--CoA ligase subunit beta YP_166809.1 1658883 D 246200 CDS YP_166810.1 56696453 3193138 1660079..1660969 1 NC_003911.11 Catalyzes the only substrate-level phosphorylation in the TCA cycle; succinyl-CoA synthetase subunit alpha 1660969 3193138 SPO1569 Ruegeria pomeroyi DSS-3 succinyl-CoA synthetase subunit alpha YP_166810.1 1660079 D 246200 CDS YP_166811.1 56696454 3192973 1660969..1661961 1 NC_003911.11 Involved in the metabolism of aromatic amino acids; 2-hydroxyacid dehydrogenase 1661961 3192973 SPO1570 Ruegeria pomeroyi DSS-3 2-hydroxyacid dehydrogenase YP_166811.1 1660969 D 246200 CDS YP_166812.1 56696455 3192821 1661961..1664600 1 NC_003911.11 identified by match to protein family HMM PF00311; phosphoenolpyruvate carboxylase 1664600 ppc 3192821 ppc Ruegeria pomeroyi DSS-3 phosphoenolpyruvate carboxylase YP_166812.1 1661961 D 246200 CDS YP_166813.1 56696456 3194742 1664626..1665921 1 NC_003911.11 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 1665921 glyA 3194742 glyA Ruegeria pomeroyi DSS-3 serine hydroxymethyltransferase YP_166813.1 1664626 D 246200 CDS YP_166814.1 56696457 3192810 complement(1665986..1667314) 1 NC_003911.11 identified by similarity to SP:P31592; match to protein family HMM PF00120; match to protein family HMM PF03951; glutamine synthetase 1667314 glnT 3192810 glnT Ruegeria pomeroyi DSS-3 glutamine synthetase YP_166814.1 1665986 R 246200 CDS YP_166815.1 56696458 3193151 complement(1667388..1668740) 1 NC_003911.11 identified by match to protein family HMM PF01645; glutamate synthase 1668740 3193151 SPO1574 Ruegeria pomeroyi DSS-3 glutamate synthase YP_166815.1 1667388 R 246200 CDS YP_166816.1 56696459 3195021 complement(1668748..1669425) 1 NC_003911.11 identified by match to protein family HMM PF01493; FwdC/FmdC family protein 1669425 3195021 SPO1575 Ruegeria pomeroyi DSS-3 FwdC/FmdC family protein YP_166816.1 1668748 R 246200 CDS YP_166817.1 56696460 3195025 complement(1669426..1670355) 1 NC_003911.11 identified by match to protein family HMM PF00310; glutamine amidotransferase 1670355 3195025 SPO1576 Ruegeria pomeroyi DSS-3 glutamine amidotransferase YP_166817.1 1669426 R 246200 CDS YP_166818.1 56696461 3193726 complement(1670500..1670718) 1 NC_003911.11 hypothetical protein 1670718 3193726 SPO1577 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166818.1 1670500 R 246200 CDS YP_166819.1 56696462 3193288 complement(1670731..1672104) 1 NC_003911.11 identified by match to protein family HMM PF00909; ammonium transporter 1672104 3193288 SPO1578 Ruegeria pomeroyi DSS-3 ammonium transporter YP_166819.1 1670731 R 246200 CDS YP_166820.1 56696463 3192995 1672349..1673494 1 NC_003911.11 identified by match to protein family HMM PF01571; glycine cleavage system protein T 1673494 3192995 SPO1579 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_166820.1 1672349 D 246200 CDS YP_166821.1 56696464 3193265 1673539..1674180 1 NC_003911.11 identified by similarity to GB:BAB53453.1; hypothetical protein 1674180 3193265 SPO1580 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166821.1 1673539 D 246200 CDS YP_166822.1 56696465 3193252 1674177..1675163 1 NC_003911.11 identified by match to protein family HMM PF00111; match to protein family HMM PF00175; oxidoreductase 1675163 3193252 SPO1581 Ruegeria pomeroyi DSS-3 oxidoreductase YP_166822.1 1674177 D 246200 CDS YP_166823.1 56696466 3193341 1675175..1676242 1 NC_003911.11 identified by similarity to GB:BAB53455.1; hypothetical protein 1676242 3193341 SPO1582 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166823.1 1675175 D 246200 CDS YP_166824.1 56696467 3193299 complement(1676294..1676947) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 1676947 3193299 SPO1583 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_166824.1 1676294 R 246200 CDS YP_166825.1 56696468 3192827 1677085..1678074 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 1678074 3192827 SPO1584 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_166825.1 1677085 D 246200 CDS YP_166826.1 56696469 3192866 complement(1678075..1678635) 1 NC_003911.11 identified by match to protein family HMM PF04268; match to protein family HMM TIGR01375; sarcosine oxidase subunit gamma 1678635 3192866 SPO1585 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit gamma YP_166826.1 1678075 R 246200 CDS YP_166827.1 56696470 3192653 complement(1678628..1681579) 1 NC_003911.11 identified by similarity to SP:Q46337; match to protein family HMM PF01571; match to protein family HMM TIGR01372; sarcosine oxidase subunit alpha 1681579 3192653 SPO1586 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit alpha YP_166827.1 1678628 R 246200 CDS YP_166828.1 56696471 3193198 complement(1681576..1681863) 1 NC_003911.11 identified by similarity to SP:Q46336; match to protein family HMM PF04267; sarcosine oxidase subunit delta 1681863 3193198 SPO1587 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit delta YP_166828.1 1681576 R 246200 CDS YP_166829.1 56696472 3192812 complement(1681877..1683127) 1 NC_003911.11 identified by similarity to SP:P40875; match to protein family HMM TIGR01373; sarcosine oxidase subunit beta 1683127 3192812 SPO1588 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit beta YP_166829.1 1681877 R 246200 CDS YP_166830.1 56696473 3195047 complement(1683246..1683629) 1 NC_003911.11 identified by match to protein family HMM PF02627; carboxymuconolactone decarboxylase 1683629 3195047 SPO1589 Ruegeria pomeroyi DSS-3 carboxymuconolactone decarboxylase YP_166830.1 1683246 R 246200 CDS YP_166831.1 56696474 3193705 complement(1683694..1684785) 1 NC_003911.11 identified by match to protein family HMM PF00355; Rieske (2Fe-2S) domain-containing protein 1684785 3193705 SPO1590 Ruegeria pomeroyi DSS-3 Rieske (2Fe-2S) domain-containing protein YP_166831.1 1683694 R 246200 CDS YP_166832.1 56696475 3193142 complement(1684791..1685678) 1 NC_003911.11 identified by match to protein family HMM PF01380; SIS domain-containing protein 1685678 3193142 SPO1591 Ruegeria pomeroyi DSS-3 SIS domain-containing protein YP_166832.1 1684791 R 246200 CDS YP_166833.1 56696476 3193241 1685750..1688206 1 NC_003911.11 identified by match to protein family HMM PF01571; glycine cleavage system protein T 1688206 3193241 SPO1592 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_166833.1 1685750 D 246200 CDS YP_166834.1 56696477 3193186 1688221..1689285 1 NC_003911.11 identified by match to protein family HMM PF00107; alcohol dehydrogenase 1689285 3193186 SPO1593 Ruegeria pomeroyi DSS-3 alcohol dehydrogenase YP_166834.1 1688221 D 246200 CDS YP_166835.1 56696478 3193978 1689282..1690388 1 NC_003911.11 identified by similarity to SP:P27099; match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase 1690388 3193978 SPO1594 Ruegeria pomeroyi DSS-3 mandelate racemase YP_166835.1 1689282 D 246200 CDS YP_166836.1 56696479 3192788 1690385..1691488 1 NC_003911.11 identified by similarity to SP:P95608; match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase 1691488 3192788 SPO1595 Ruegeria pomeroyi DSS-3 mandelate racemase YP_166836.1 1690385 D 246200 CDS YP_166837.1 56696480 3193536 1691493..1692098 1 NC_003911.11 identified by similarity to GB:CAE27785.1; hypothetical protein 1692098 3193536 SPO1596 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166837.1 1691493 D 246200 CDS YP_166838.1 56696481 3195552 1692095..1693369 1 NC_003911.11 identified by similarity to SP:P48247; match to protein family HMM PF00202; glutamate-1-semialdehyde 2,1-aminomutase 1693369 hemL 3195552 hemL Ruegeria pomeroyi DSS-3 glutamate-1-semialdehyde 2,1-aminomutase YP_166838.1 1692095 D 246200 CDS YP_166839.1 56696482 3194840 complement(1693554..1694387) 1 NC_003911.11 identified by similarity to GB:CAE31122.1; hypothetical protein 1694387 3194840 SPO1598 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166839.1 1693554 R 246200 CDS YP_166840.1 56696483 3193606 complement(1694413..1695750) 1 NC_003911.11 identified by match to protein family HMM PF03972; MmgE/PrpD family protein 1695750 3193606 SPO1599 Ruegeria pomeroyi DSS-3 MmgE/PrpD family protein YP_166840.1 1694413 R 246200 CDS YP_166841.1 56696484 3193497 complement(1695747..1696592) 1 NC_003911.11 identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase 1696592 3193497 SPO1600 Ruegeria pomeroyi DSS-3 fumarylacetoacetate hydrolase YP_166841.1 1695747 R 246200 CDS YP_166842.1 56696485 3193337 complement(1696589..1697524) 1 NC_003911.11 identified by match to protein family HMM PF02558; match to protein family HMM TIGR00745; 2-dehydropantoate 2-reductase 1697524 panE-2 3193337 panE-2 Ruegeria pomeroyi DSS-3 2-dehydropantoate 2-reductase YP_166842.1 1696589 R 246200 CDS YP_166843.1 56696486 3195011 complement(1697521..1699029) 1 NC_003911.11 identified by match to protein family HMM PF06253; trimethylamine methyltransferase 1699029 3195011 SPO1602 Ruegeria pomeroyi DSS-3 trimethylamine methyltransferase YP_166843.1 1697521 R 246200 CDS YP_166844.1 56696487 3193995 complement(1699026..1700078) 1 NC_003911.11 identified by match to protein family HMM PF02615; malate/L-lactate dehydrogenase 1700078 3193995 SPO1603 Ruegeria pomeroyi DSS-3 malate/L-lactate dehydrogenase YP_166844.1 1699026 R 246200 CDS YP_166845.1 56696488 3195655 1700190..1701119 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1701119 3195655 SPO1604 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_166845.1 1700190 D 246200 CDS YP_166846.1 56696489 3194695 complement(1701082..1702764) 1 NC_003911.11 identified by similarity to GB:BAB49910.1; hypothetical protein 1702764 3194695 SPO1605 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166846.1 1701082 R 246200 CDS YP_166847.1 56696490 3192957 complement(1702821..1703840) 1 NC_003911.11 identified by similarity to SP:P23861; match to protein family HMM PF01547; spermidine/putrescine ABC transporter substrate-binding protein 1703840 potD 3192957 potD Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter substrate-binding protein YP_166847.1 1702821 R 246200 CDS YP_166848.1 56696491 3192984 complement(1703859..1704662) 1 NC_003911.11 identified by similarity to SP:P31136; match to protein family HMM PF00528; spermidine/putrescine ABC transporter permease 1704662 3192984 SPO1607 Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter permease YP_166848.1 1703859 R 246200 CDS YP_166849.1 56696492 3192873 complement(1704655..1705566) 1 NC_003911.11 identified by similarity to SP:P23860; match to protein family HMM PF00528; spermidine/putrescine ABC transporter permease 1705566 potB 3192873 potB Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter permease YP_166849.1 1704655 R 246200 CDS YP_166850.1 56696493 3193682 complement(1705570..1706670) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF03459; match to protein family HMM TIGR01187; spermidine/putrescine ABC transporter ATP-binding component 1706670 potA 3193682 potA Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter ATP-binding component YP_166850.1 1705570 R 246200 CDS YP_166851.1 56696494 3193663 1706791..1707582 1 NC_003911.11 identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 1707582 3193663 SPO1610 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_166851.1 1706791 D 246200 CDS YP_166852.1 56696495 3192661 1707651..1708880 1 NC_003911.11 identified by similarity to GB:CAE10095.1; hypothetical protein 1708880 3192661 SPO1611 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166852.1 1707651 D 246200 CDS YP_166853.1 56696496 3193599 1708920..1710209 1 NC_003911.11 identified by similarity to GB:AAK03561.1; match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1710209 3193599 SPO1612 Ruegeria pomeroyi DSS-3 twin-arginine translocation pathway signal sequence domain-containing protein YP_166853.1 1708920 D 246200 CDS YP_166854.1 56696497 3193396 1710222..1710596 1 NC_003911.11 identified by similarity to SP:Q9CKX3; hypothetical protein 1710596 3193396 SPO1613 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166854.1 1710222 D 246200 CDS YP_166855.1 56696498 3193631 1710770..1711204 1 NC_003911.11 identified by similarity to GB:AAM72242.1; hypothetical protein 1711204 3193631 SPO1614 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166855.1 1710770 D 246200 CDS YP_166856.1 56696499 3192905 1711334..1712008 1 NC_003911.11 identified by match to protein family HMM PF00027; cyclic nucleotide-binding protein 1712008 3192905 SPO1615 Ruegeria pomeroyi DSS-3 cyclic nucleotide-binding protein YP_166856.1 1711334 D 246200 CDS YP_166857.1 56696500 3193134 complement(1712041..1712931) 1 NC_003911.11 identified by match to protein family HMM PF04397; transcriptional regulator 1712931 3193134 SPO1616 Ruegeria pomeroyi DSS-3 transcriptional regulator YP_166857.1 1712041 R 246200 CDS YP_166858.1 56696501 3193097 1713363..1716374 1 NC_003911.11 identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 1716374 3193097 SPO1617 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_166858.1 1713363 D 246200 CDS YP_166859.1 56696502 3192800 1716368..1716964 1 NC_003911.11 hypothetical protein 1716964 3192800 SPO1618 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166859.1 1716368 D 246200 CDS YP_166860.1 56696503 3192920 1716958..1717341 1 NC_003911.11 identified by similarity to GB:CAE07324.1; hypothetical protein 1717341 3192920 SPO1619 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166860.1 1716958 D 246200 CDS YP_166861.1 56696504 3193719 complement(1717383..1717970) 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 1717970 3193719 SPO1620 Ruegeria pomeroyi DSS-3 glyoxalase YP_166861.1 1717383 R 246200 CDS YP_166862.1 56696505 3193406 complement(1718117..1718467) 1 NC_003911.11 TfoX domain-containing protein 1718467 3193406 SPO1621 Ruegeria pomeroyi DSS-3 TfoX domain-containing protein YP_166862.1 1718117 R 246200 CDS YP_166863.1 56696506 3192858 1718611..1719903 1 NC_003911.11 identified by match to protein family HMM PF00067; cytochrome P450 family protein 1719903 3192858 SPO1622 Ruegeria pomeroyi DSS-3 cytochrome P450 family protein YP_166863.1 1718611 D 246200 CDS YP_166864.1 56696507 3194307 complement(1719919..1721289) 1 NC_003911.11 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase 1721289 3194307 SPO1623 Ruegeria pomeroyi DSS-3 sensor histidine kinase YP_166864.1 1719919 R 246200 CDS YP_166865.1 56696508 3193367 complement(1721282..1721962) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator 1721962 3193367 SPO1624 Ruegeria pomeroyi DSS-3 DNA-binding response regulator YP_166865.1 1721282 R 246200 CDS YP_166866.1 56696509 3192705 complement(1722127..1723563) 1 NC_003911.11 identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037; serine protease 1723563 3192705 SPO1625 Ruegeria pomeroyi DSS-3 serine protease YP_166866.1 1722127 R 246200 CDS YP_166867.1 56696510 3193076 1724415..1728230 1 NC_003911.11 identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 1728230 3193076 SPO1626 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_166867.1 1724415 D 246200 CDS YP_166868.1 56696511 3193486 complement(1728320..1728916) 1 NC_003911.11 hypothetical protein 1728916 3193486 SPO1627 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166868.1 1728320 R 246200 CDS YP_166869.1 56696512 3193115 complement(1728948..1731356) 1 NC_003911.11 identified by match to protein family HMM PF01266; match to protein family HMM PF01571; glycine cleavage system protein T 1731356 3193115 SPO1628 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_166869.1 1728948 R 246200 CDS YP_166870.1 56696513 3192834 1731481..1732731 1 NC_003911.11 identified by similarity to GB:AAN68935.1; hypothetical protein 1732731 3192834 SPO1629 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166870.1 1731481 D 246200 CDS YP_166871.1 56696514 3193364 complement(1732715..1734346) 1 NC_003911.11 hypothetical protein 1734346 3193364 SPO1630 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166871.1 1732715 R 246200 CDS YP_166872.1 56696515 3193722 complement(1734343..1735650) 1 NC_003911.11 identified by match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471; hypothetical protein 1735650 3193722 SPO1631 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166872.1 1734343 R 246200 CDS YP_166873.1 56696516 3193328 complement(1735714..1736673) 1 NC_003911.11 identified by similarity to SP:P21891; match to protein family HMM PF00589; match to protein family HMM PF02899; tyrosine recombinase XerD 1736673 xerD 3193328 xerD Ruegeria pomeroyi DSS-3 tyrosine recombinase XerD YP_166873.1 1735714 R 246200 CDS YP_166874.1 56696517 3193010 1737148..1738335 1 NC_003911.11 hypothetical protein 1738335 3193010 SPO1633 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166874.1 1737148 D 246200 CDS YP_166875.1 56696518 3194890 1738445..1739032 1 NC_003911.11 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis; shikimate kinase 1739032 aroK 3194890 aroK Ruegeria pomeroyi DSS-3 shikimate kinase YP_166875.1 1738445 D 246200 CDS YP_166876.1 56696519 3192771 1739034..1740146 1 NC_003911.11 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase 1740146 aroB 3192771 aroB Ruegeria pomeroyi DSS-3 3-dehydroquinate synthase YP_166876.1 1739034 D 246200 CDS YP_166877.1 56696520 3192829 complement(1740157..1741227) 1 NC_003911.11 identified by match to protein family HMM PF00571; match to protein family HMM PF02163; SREBP protease 1741227 3192829 SPO1636 Ruegeria pomeroyi DSS-3 SREBP protease YP_166877.1 1740157 R 246200 CDS YP_166878.1 56696521 3193067 complement(1741243..1741785) 1 NC_003911.11 identified by similarity to SP:P02339; match to protein family HMM PF00436; match to protein family HMM TIGR00621; single-strand binding protein 1741785 ssb 3193067 ssb Ruegeria pomeroyi DSS-3 single-strand binding protein YP_166878.1 1741243 R 246200 CDS YP_166879.1 56696522 3193449 1741995..1742573 1 NC_003911.11 identified by match to protein family HMM PF01464; transglycosylase 1742573 3193449 SPO1638 Ruegeria pomeroyi DSS-3 transglycosylase YP_166879.1 1741995 D 246200 CDS YP_166880.1 56696523 3193174 1742777..1743238 1 NC_003911.11 identified by similarity to GB:AAK18170.1; FadB domain-containing protein 1743238 3193174 SPO1639 Ruegeria pomeroyi DSS-3 FadB domain-containing protein YP_166880.1 1742777 D 246200 CDS YP_166881.1 56696524 3194706 complement(1743226..1744155) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1744155 3194706 SPO1640 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_166881.1 1743226 R 246200 CDS YP_166882.1 56696525 3192663 1744264..1745460 1 NC_003911.11 identified by match to protein family HMM PF00144; beta-lactamase 1745460 3192663 SPO1641 Ruegeria pomeroyi DSS-3 beta-lactamase YP_166882.1 1744264 D 246200 CDS YP_166883.1 56696526 3193291 complement(1745477..1746055) 1 NC_003911.11 hypothetical protein 1746055 3193291 SPO1642 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166883.1 1745477 R 246200 CDS YP_166884.1 56696527 3193350 complement(1746137..1747537) 1 NC_003911.11 identified by match to protein family HMM PF05694; selenium-binding protein 1747537 3193350 SPO1643 Ruegeria pomeroyi DSS-3 selenium-binding protein YP_166884.1 1746137 R 246200 CDS YP_166885.1 56696528 3195301 complement(1747689..1749470) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide/dipeptide ABC transporter ATP-binding protein 1749470 3195301 SPO1644 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter ATP-binding protein YP_166885.1 1747689 R 246200 CDS YP_166886.1 56696530 3193177 complement(1749467..1750342) 1 NC_003911.11 identified by similarity to SP:P37315; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 1750342 3193177 SPO1645 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter permease YP_166886.1 1749467 R 246200 CDS YP_166887.1 56696529 3193053 complement(1750339..1751286) 1 NC_003911.11 identified by match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 1751286 3193053 SPO1646 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter permease YP_166887.1 1750339 R 246200 CDS YP_166888.1 56696531 3193305 1751479..1753137 1 NC_003911.11 identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; oligopeptide/dipeptide ABC transporter substrate-binding protein 1753137 3193305 SPO1647 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter substrate-binding protein YP_166888.1 1751479 D 246200 CDS YP_166889.1 56696532 3193889 1753243..1754346 1 NC_003911.11 identified by match to protein family HMM PF01571; glycine cleavage system protein T 1754346 3193889 SPO1648 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_166889.1 1753243 D 246200 CDS YP_166890.1 56696533 3193403 1754354..1755715 1 NC_003911.11 identified by similarity to GB:AAF98391.2; invasion protein IbeA 1755715 3193403 SPO1649 Ruegeria pomeroyi DSS-3 invasion protein IbeA YP_166890.1 1754354 D 246200 CDS YP_166891.1 56696534 3193112 1755718..1755828 1 NC_003911.11 hypothetical protein 1755828 3193112 SPO1650 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166891.1 1755718 D 246200 CDS YP_166892.1 56696535 3192673 1755968..1756324 1 NC_003911.11 hypothetical protein 1756324 3192673 SPO1651 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166892.1 1755968 D 246200 CDS YP_166893.1 56696536 3192868 1756358..1756930 1 NC_003911.11 identified by similarity to GB:CAF32821.1; transposase, truncation 1756930 3192868 SPO1652 Ruegeria pomeroyi DSS-3 transposase, truncation YP_166893.1 1756358 D 246200 CDS YP_166894.1 56696537 3192994 1761171..1761857 1 NC_003911.11 hypothetical protein 1761857 3192994 SPO1655 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166894.1 1761171 D 246200 CDS YP_166895.1 56696538 3192700 complement(1761894..1764113) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide/dipeptide ABC transporter ATP-binding protein 1764113 3192700 SPO1656 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter ATP-binding protein YP_166895.1 1761894 R 246200 CDS YP_166896.1 56696539 3192684 complement(1764115..1765317) 1 NC_003911.11 identified by match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 1765317 3192684 SPO1657 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter permease YP_166896.1 1764115 R 246200 CDS YP_166897.1 56696540 3195345 complement(1765332..1766378) 1 NC_003911.11 identified by similarity to SP:P42062; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 1766378 3195345 SPO1658 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter permease YP_166897.1 1765332 R 246200 CDS YP_166898.1 56696541 3193539 complement(1766522..1768348) 1 NC_003911.11 identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; oligopeptide/dipeptide ABC transporter substrate-binding protein 1768348 3193539 SPO1659 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter substrate-binding protein YP_166898.1 1766522 R 246200 CDS YP_166899.1 56696542 3193230 complement(1768418..1769224) 1 NC_003911.11 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 1769224 3193230 SPO1660 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_166899.1 1768418 R 246200 CDS YP_166900.1 56696543 3192726 complement(1769266..1770141) 1 NC_003911.11 IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity; tRNA delta(2)-isopentenylpyrophosphate transferase 1770141 miaA 3192726 miaA Ruegeria pomeroyi DSS-3 tRNA delta(2)-isopentenylpyrophosphate transferase YP_166900.1 1769266 R 246200 CDS YP_166901.1 56696544 3192709 1770258..1771013 1 NC_003911.11 Catalyzes the phosphorylation of UMP to UDP; uridylate kinase 1771013 pyrH 3192709 pyrH Ruegeria pomeroyi DSS-3 uridylate kinase YP_166901.1 1770258 D 246200 CDS YP_166902.1 56696545 3192678 1771076..1771771 1 NC_003911.11 hypothetical protein 1771771 3192678 SPO1663 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166902.1 1771076 D 246200 CDS YP_166903.1 56696546 3193529 1771943..1772506 1 NC_003911.11 Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs; ribosome recycling factor 1772506 frr 3193529 frr Ruegeria pomeroyi DSS-3 ribosome recycling factor YP_166903.1 1771943 D 246200 CDS YP_166904.1 56696547 3194281 1772517..1773248 1 NC_003911.11 identified by match to protein family HMM PF01255; match to protein family HMM TIGR00055; UDP diphosphate synthase 1773248 uppS 3194281 uppS Ruegeria pomeroyi DSS-3 UDP diphosphate synthase YP_166904.1 1772517 D 246200 CDS YP_166905.1 56696548 3193513 1773245..1774027 1 NC_003911.11 identified by similarity to SP:P06466; match to protein family HMM PF01148; phosphatidate cytidylyltransferase 1774027 cdsA 3193513 cdsA Ruegeria pomeroyi DSS-3 phosphatidate cytidylyltransferase YP_166905.1 1773245 D 246200 CDS YP_166906.1 56696549 3194834 1774027..1775214 1 NC_003911.11 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate; 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1775214 dxr 3194834 dxr Ruegeria pomeroyi DSS-3 1-deoxy-D-xylulose 5-phosphate reductoisomerase YP_166906.1 1774027 D 246200 CDS YP_166907.1 56696550 3195245 1775219..1776589 1 NC_003911.11 identified by match to protein family HMM PF00595; match to protein family HMM PF02163; match to protein family HMM TIGR00054; zinc metalloprotease 1776589 3195245 SPO1668 Ruegeria pomeroyi DSS-3 zinc metalloprotease YP_166907.1 1775219 D 246200 CDS YP_166908.1 56696551 3193515 1776689..1776814 1 NC_003911.11 hypothetical protein 1776814 3193515 SPO1669 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166908.1 1776689 D 246200 CDS YP_166909.1 56696552 3193626 1776944..1779307 1 NC_003911.11 identified by match to protein family HMM PF01103; match to protein family HMM PF07244; OMP85 family outer membrane protein 1779307 3193626 SPO1670 Ruegeria pomeroyi DSS-3 OMP85 family outer membrane protein YP_166909.1 1776944 D 246200 CDS YP_166910.1 56696553 3195422 1779315..1779887 1 NC_003911.11 hypothetical protein 1779887 3195422 SPO1671 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166910.1 1779315 D 246200 CDS YP_166911.1 56696554 3192982 1779981..1780454 1 NC_003911.11 in Pseudomonas aeruginosa this enzyme is a trimer of dimers; essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP; (3R)-hydroxymyristoyl-ACP dehydratase 1780454 fabZ 3192982 fabZ Ruegeria pomeroyi DSS-3 (3R)-hydroxymyristoyl-ACP dehydratase YP_166911.1 1779981 D 246200 CDS YP_166912.1 56696555 3193293 1780451..1781236 1 NC_003911.11 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase 1781236 lpxA 3193293 lpxA Ruegeria pomeroyi DSS-3 UDP-N-acetylglucosamine acyltransferase YP_166912.1 1780451 D 246200 CDS YP_166913.1 56696556 3194991 1781238..1782032 1 NC_003911.11 identified by similarity to GB:CAE28351.1; hypothetical protein 1782032 3194991 SPO1674 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166913.1 1781238 D 246200 CDS YP_166914.1 56696557 3194064 1781984..1783189 1 NC_003911.11 identified by similarity to SP:P10441; match to protein family HMM PF02684; match to protein family HMM TIGR00215; lipid-A-disaccharide synthase 1783189 lpxB 3194064 lpxB Ruegeria pomeroyi DSS-3 lipid-A-disaccharide synthase YP_166914.1 1781984 D 246200 CDS YP_166915.1 56696558 3192948 complement(1783186..1783698) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 1783698 3192948 SPO1676 Ruegeria pomeroyi DSS-3 acetyltransferase YP_166915.1 1783186 R 246200 CDS YP_166916.1 56696559 3192677 complement(1783688..1784815) 1 NC_003911.11 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA 1784815 mnmA 3192677 mnmA Ruegeria pomeroyi DSS-3 tRNA-specific 2-thiouridylase MnmA YP_166916.1 1783688 R 246200 CDS YP_166917.1 56696560 3192768 1784961..1785242 1 NC_003911.11 identified by similarity to PIR:AE3305; hypothetical protein 1785242 3192768 SPO1678 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166917.1 1784961 D 246200 CDS YP_166918.1 56696561 3194546 1785341..1786057 1 NC_003911.11 identified by similarity to SP:Q45994; match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator CtrA 1786057 ctrA 3194546 ctrA Ruegeria pomeroyi DSS-3 DNA-binding response regulator CtrA YP_166918.1 1785341 D 246200 CDS YP_166919.1 56696562 3192682 1786196..1788415 1 NC_003911.11 identified by match to protein family HMM PF00533; match to protein family HMM PF01653; match to protein family HMM PF03119; match to protein family HMM PF03120; match to protein family HMM TIGR00575; NAD-dependent DNA ligase 1788415 ligA 3192682 ligA Ruegeria pomeroyi DSS-3 NAD-dependent DNA ligase YP_166919.1 1786196 D 246200 CDS YP_166920.1 56696563 3193560 1788412..1790502 1 NC_003911.11 catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG 1790502 recG 3193560 recG Ruegeria pomeroyi DSS-3 ATP-dependent DNA helicase RecG YP_166920.1 1788412 D 246200 CDS YP_166921.1 56696564 3192900 1790617..1790739 1 NC_003911.11 hypothetical protein 1790739 3192900 SPO1682 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166921.1 1790617 D 246200 CDS YP_166922.1 56696565 3193123 complement(1790995..1791447) 1 NC_003911.11 identified by similarity to GB:AAK22449.1; hypothetical protein 1791447 3193123 SPO1683 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166922.1 1790995 R 246200 CDS YP_166923.1 56696566 3195450 1791515..1791874 1 NC_003911.11 identified by match to protein family HMM PF01502; phosphoribosyl-AMP cyclohydrolase 1791874 hisI 3195450 hisI Ruegeria pomeroyi DSS-3 phosphoribosyl-AMP cyclohydrolase YP_166923.1 1791515 D 246200 CDS YP_166924.1 56696567 3192785 complement(1791878..1792717) 1 NC_003911.11 identified by match to protein family HMM PF00749; tRNA synthetase, class I family protein 1792717 3192785 SPO1685 Ruegeria pomeroyi DSS-3 tRNA synthetase, class I family protein YP_166924.1 1791878 R 246200 CDS YP_166925.1 56696568 3193555 complement(1792746..1794095) 1 NC_003911.11 TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine; tRNA (uracil-5-)-methyltransferase Gid 1794095 gid 3193555 gid Ruegeria pomeroyi DSS-3 tRNA (uracil-5-)-methyltransferase Gid YP_166925.1 1792746 R 246200 CDS YP_166926.1 56696569 3193602 complement(1794417..1795202) 1 NC_003911.11 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 1795202 3193602 SPO1687 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_166926.1 1794417 R 246200 CDS YP_166927.1 56696570 3193708 1795261..1795704 1 NC_003911.11 identified by similarity to GB:AAN29721.1; match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase 1795704 3193708 SPO1688 Ruegeria pomeroyi DSS-3 thioesterase YP_166927.1 1795261 D 246200 CDS YP_166928.1 56696571 3193559 complement(1795773..1796000) 1 NC_003911.11 identified by similarity to PIR:AE2803; hypothetical protein 1796000 3193559 SPO1689 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166928.1 1795773 R 246200 CDS YP_166929.1 56696572 3194963 1796102..1797505 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1797505 3194963 SPO1690 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_166929.1 1796102 D 246200 CDS YP_166930.1 56696573 3193556 1797669..1798127 1 NC_003911.11 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 1798127 rplM 3193556 rplM Ruegeria pomeroyi DSS-3 50S ribosomal protein L13 YP_166930.1 1797669 D 246200 CDS YP_166931.1 56696574 3193551 1798133..1798615 1 NC_003911.11 forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 1798615 rpsI 3193551 rpsI Ruegeria pomeroyi DSS-3 30S ribosomal protein S9 YP_166931.1 1798133 D 246200 CDS YP_166932.1 56696575 3194945 1799149..1800744 1 NC_003911.11 identified by similarity to GB:AAR33500.1; hypothetical protein 1800744 3194945 SPO1693 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166932.1 1799149 D 246200 CDS YP_166933.1 56698731 3196343 1802181..1803143 1 NC_003911.11 identified by match to protein family HMM PF00294; carbohydrate kinase 1803143 3196343 SPO1694 Ruegeria pomeroyi DSS-3 carbohydrate kinase YP_166933.1 1802181 D 246200 CDS YP_166934.1 56696576 3192787 1804224..1806323 1 NC_003911.11 identified by similarity to SP:Q01262; match to protein family HMM PF01968; match to protein family HMM PF05378; hydantoin utilization protein 1806323 3192787 SPO1695 Ruegeria pomeroyi DSS-3 hydantoin utilization protein YP_166934.1 1804224 D 246200 CDS YP_166935.1 56696577 3195350 1806320..1807969 1 NC_003911.11 identified by match to protein family HMM PF02538; hydantoinase/oxoprolinase 1807969 3195350 SPO1696 Ruegeria pomeroyi DSS-3 hydantoinase/oxoprolinase YP_166935.1 1806320 D 246200 CDS YP_166936.1 56696578 3193553 1807966..1809048 1 NC_003911.11 identified by match to protein family HMM PF00155; aminotransferase, classes I and II 1809048 3193553 SPO1697 Ruegeria pomeroyi DSS-3 aminotransferase, classes I and II YP_166936.1 1807966 D 246200 CDS YP_166937.1 56696579 3193468 1809064..1809789 1 NC_003911.11 identified by match to protein family HMM PF01177; Asp/Glu/Hydantoin racemase 1809789 3193468 SPO1698 Ruegeria pomeroyi DSS-3 Asp/Glu/Hydantoin racemase YP_166937.1 1809064 D 246200 CDS YP_166938.1 56696580 3193547 1809786..1811132 1 NC_003911.11 identified by match to protein family HMM PF03972; MmgE/PrpD family protein 1811132 3193547 SPO1699 Ruegeria pomeroyi DSS-3 MmgE/PrpD family protein YP_166938.1 1809786 D 246200 CDS YP_166939.1 56696581 3193595 1811125..1812093 1 NC_003911.11 identified by match to protein family HMM PF02826; D-isomer specific 2-hydroxyacid dehydrogenase 1812093 3193595 SPO1700 Ruegeria pomeroyi DSS-3 D-isomer specific 2-hydroxyacid dehydrogenase YP_166939.1 1811125 D 246200 CDS YP_166940.1 56696582 3193676 1812104..1812997 1 NC_003911.11 identified by match to protein family HMM PF00701; dihydrodipicolinate synthase 1812997 3193676 SPO1701 Ruegeria pomeroyi DSS-3 dihydrodipicolinate synthase YP_166940.1 1812104 D 246200 CDS YP_166941.1 56696583 3194828 complement(1813320..1814963) 1 NC_003911.11 identified by similarity to GB:BAC48815.1; hypothetical protein 1814963 3194828 SPO1702 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166941.1 1813320 R 246200 CDS YP_166942.1 56696584 3193546 complement(1814968..1817448) 1 NC_003911.11 identified by match to protein family HMM PF02515; CaiB/BaiF family protein 1817448 3193546 SPO1703 Ruegeria pomeroyi DSS-3 CaiB/BaiF family protein YP_166942.1 1814968 R 246200 CDS YP_166943.1 56696585 3193594 1817549..1818472 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 1818472 3193594 SPO1704 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_166943.1 1817549 D 246200 CDS YP_166944.1 56696586 3193591 1819114..1820538 1 NC_003911.11 phage head morphogenesis domain-containing protein 1820538 3193591 SPO1705 Ruegeria pomeroyi DSS-3 phage head morphogenesis domain-containing protein YP_166944.1 1819114 D 246200 CDS YP_166945.1 56696587 3195008 complement(1823098..1823793) 1 NC_003911.11 identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1823793 3195008 SPO1707 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_166945.1 1823098 R 246200 CDS YP_166946.1 56698737 3196350 complement(1823797..1824537) 1 NC_003911.11 identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1824537 3196350 SPOA0447 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_166946.1 1823797 R 246200 CDS YP_166947.1 56696588 3193583 complement(1824534..1825763) 1 NC_003911.11 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1825763 3193583 SPO1708 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_166947.1 1824534 R 246200 CDS YP_166948.1 56696589 3195518 complement(1825767..1827722) 1 NC_003911.11 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1827722 3195518 SPO1709 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_166948.1 1825767 R 246200 CDS YP_166949.1 56696590 3193581 complement(1827788..1829122) 1 NC_003911.11 Assignment based partly on membership in branched-chain amino acid ABC transporter gene cluster; branched-chain amino acid ABC transporter substrate-binding protein 1829122 3193581 SPO1710 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter substrate-binding protein YP_166949.1 1827788 R 246200 CDS YP_166950.1 56696591 3193571 1829519..1830292 1 NC_003911.11 identified by match to protein family HMM PF01774; urease accessory protein UreD 1830292 ureD 3193571 ureD Ruegeria pomeroyi DSS-3 urease accessory protein UreD YP_166950.1 1829519 D 246200 CDS YP_166951.1 56696592 3193563 1830294..1830596 1 NC_003911.11 identified by match to protein family HMM PF00547; match to protein family HMM TIGR00193; urease subunit gamma 1830596 ureA 3193563 ureA Ruegeria pomeroyi DSS-3 urease subunit gamma YP_166951.1 1830294 D 246200 CDS YP_166952.1 56698732 3196338 1830773..1831078 1 NC_003911.11 identified by similarity to GB:BAB21066.1; match to protein family HMM PF00699; match to protein family HMM TIGR00192; urease subunit beta 1831078 ureB 3196338 ureB Ruegeria pomeroyi DSS-3 urease subunit beta YP_166952.1 1830773 D 246200 CDS YP_166953.1 56696593 3192899 1831078..1832787 1 NC_003911.11 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits; urease subunit alpha 1832787 ureC 3192899 ureC Ruegeria pomeroyi DSS-3 urease subunit alpha YP_166953.1 1831078 D 246200 CDS YP_166954.1 56696594 3193558 1832799..1833248 1 NC_003911.11 identified by similarity to SP:P18317; match to protein family HMM PF02814; match to protein family HMM PF05194; urease accessory protein ureE 1833248 ureE 3193558 ureE Ruegeria pomeroyi DSS-3 urease accessory protein ureE YP_166954.1 1832799 D 246200 CDS YP_166955.1 56696595 3192879 1833232..1833885 1 NC_003911.11 identified by match to protein family HMM PF01730; urease accessory protein UreF 1833885 ureF 3192879 ureF Ruegeria pomeroyi DSS-3 urease accessory protein UreF YP_166955.1 1833232 D 246200 CDS YP_166956.1 56696596 3193533 1833882..1834529 1 NC_003911.11 identified by match to protein family HMM PF01495; match to protein family HMM TIGR00101; urease accessory protein UreG 1834529 ureG 3193533 ureG Ruegeria pomeroyi DSS-3 urease accessory protein UreG YP_166956.1 1833882 D 246200 CDS YP_166957.1 56696597 3194250 complement(1834693..1835868) 1 NC_003911.11 hypothetical protein 1835868 3194250 SPO1718 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166957.1 1834693 R 246200 CDS YP_166958.1 56698718 3196272 complement(1837668..1837859) 1 NC_003911.11 identified by similarity to SP:P39140; match to protein family HMM PF02796; resolvase site-specific recombinase 1837859 3196272 SPO3897 Ruegeria pomeroyi DSS-3 resolvase site-specific recombinase YP_166958.1 1837668 R 246200 CDS YP_166959.1 56696598 3193582 complement(1838069..1839346) 1 NC_003911.11 identified by match to protein family HMM PF00597; match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM 1839346 3193582 SPO1719 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_166959.1 1838069 R 246200 CDS YP_166960.1 56696599 3193024 complement(1839351..1839851) 1 NC_003911.11 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ 1839851 3193024 SPO1720 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctQ YP_166960.1 1839351 R 246200 CDS YP_166961.1 56696600 3193550 complement(1839928..1840950) 1 NC_003911.11 identified by match to protein family HMM PF03480; match to protein family HMM TIGR00787; TRAP dicarboxylate transporter subunit DctP 1840950 3193550 SPO1721 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctP YP_166961.1 1839928 R 246200 CDS YP_166962.1 56696601 3193054 complement(1840901..1841641) 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1841641 3193054 SPO1722 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_166962.1 1840901 R 246200 CDS YP_166963.1 56696602 3193519 1841740..1842951 1 NC_003911.11 catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate; mannonate dehydratase 1842951 uxuA 3193519 uxuA Ruegeria pomeroyi DSS-3 mannonate dehydratase YP_166963.1 1841740 D 246200 CDS YP_166964.1 56696603 3193566 1842948..1844432 1 NC_003911.11 identified by similarity to SP:P39160; match to protein family HMM PF01232; D-mannonate oxidoreductase 1844432 uxuB 3193566 uxuB Ruegeria pomeroyi DSS-3 D-mannonate oxidoreductase YP_166964.1 1842948 D 246200 CDS YP_166965.1 56696604 3195564 complement(1845036..1845779) 1 NC_003911.11 identified by similarity to GB:CAD15199.1; hypothetical protein 1845779 3195564 SPO1725 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166965.1 1845036 R 246200 CDS YP_166966.1 56696605 3193527 complement(1845847..1846458) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 1846458 3193527 SPO3896 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_166966.1 1845847 R 246200 CDS YP_166967.1 56696606 3193544 complement(1846451..1847356) 1 NC_003911.11 identified by similarity to GB:AAN87337.1; match to protein family HMM PF03976; polyphosphate kinase 1847356 3193544 SPO1727 Ruegeria pomeroyi DSS-3 polyphosphate kinase YP_166967.1 1846451 R 246200 CDS YP_166968.1 56696607 3193393 complement(1847375..1848322) 1 NC_003911.11 identified by similarity to GB:AAC36352.1; match to protein family HMM PF00561; esterase 1848322 3193393 SPO1728 Ruegeria pomeroyi DSS-3 esterase YP_166968.1 1847375 R 246200 CDS YP_166969.1 56696608 3194898 complement(1848329..1849267) 1 NC_003911.11 catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase 1849267 metA 3194898 metA Ruegeria pomeroyi DSS-3 homoserine O-succinyltransferase YP_166969.1 1848329 R 246200 CDS YP_166970.1 56696609 3192707 complement(1849853..1851508) 1 NC_003911.11 identified by match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644; single-stranded-DNA-specific exonuclease RecJ 1851508 recJ 3192707 recJ Ruegeria pomeroyi DSS-3 single-stranded-DNA-specific exonuclease RecJ YP_166970.1 1849853 R 246200 CDS YP_166971.1 56696610 3193511 complement(1851701..1852654) 1 NC_003911.11 type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese; fructose 1,6-bisphosphatase II 1852654 glpX 3193511 glpX Ruegeria pomeroyi DSS-3 fructose 1,6-bisphosphatase II YP_166971.1 1851701 R 246200 CDS YP_166972.1 56696611 3193343 complement(1852754..1854040) 1 NC_003911.11 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase 1854040 hom 3193343 hom Ruegeria pomeroyi DSS-3 homoserine dehydrogenase YP_166972.1 1852754 R 246200 CDS YP_166973.1 56696612 3195711 complement(1854142..1854477) 1 NC_003911.11 hypothetical protein 1854477 3195711 SPO1735 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166973.1 1854142 R 246200 CDS YP_166974.1 56696613 3193150 1854520..1855104 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 1855104 3193150 SPO1736 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_166974.1 1854520 D 246200 CDS YP_166975.1 56696614 3193290 complement(1855180..1856091) 1 NC_003911.11 identified by match to protein family HMM PF02678; match to protein family HMM PF05726; pirin 1856091 3193290 SPO1737 Ruegeria pomeroyi DSS-3 pirin YP_166975.1 1855180 R 246200 CDS YP_166976.1 56696615 3192799 complement(1856210..1857394) 1 NC_003911.11 identified by similarity to GB:AAO60101.1; match to protein family HMM PF00037; match to protein family HMM PF03860; dehalogenase 1857394 3192799 SPO1738 Ruegeria pomeroyi DSS-3 dehalogenase YP_166976.1 1856210 R 246200 CDS YP_166977.1 56696616 3193165 1857384..1857971 1 NC_003911.11 hypothetical protein 1857971 3193165 SPO1739 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166977.1 1857384 D 246200 CDS YP_166978.1 56696617 3193469 complement(1857975..1858550) 1 NC_003911.11 identified by similarity to PIR:F97376; hypothetical protein 1858550 3193469 SPO1740 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166978.1 1857975 R 246200 CDS YP_166979.1 56696618 3193390 complement(1858531..1859064) 1 NC_003911.11 identified by similarity to GB:CAE29115.1; hypothetical protein 1859064 3193390 SPO1741 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166979.1 1858531 R 246200 CDS YP_166980.1 56696619 3193561 complement(1859061..1860737) 1 NC_003911.11 identified by similarity to GB:BAB54226.1; hypothetical protein 1860737 3193561 SPO1742 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166980.1 1859061 R 246200 CDS YP_166981.1 56696620 3192979 1861061..1862491 1 NC_003911.11 identified by similarity to SP:P96110; match to protein family HMM PF00208; match to protein family HMM PF02812; glutamate dehydrogenase 1862491 3192979 SPO1743 Ruegeria pomeroyi DSS-3 glutamate dehydrogenase YP_166981.1 1861061 D 246200 CDS YP_166982.1 56696621 3193224 1862691..1863944 1 NC_003911.11 identified by similarity to SP:P40875; match to protein family HMM PF01266; match to protein family HMM TIGR01373; sarcosine oxidase subunit beta 1863944 3193224 SPO1744 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit beta YP_166982.1 1862691 D 246200 CDS YP_166983.1 56696622 3192833 1864000..1864263 1 NC_003911.11 identified by similarity to SP:Q46336; match to protein family HMM PF04267; sarcosine oxidase subunit delta 1864263 3192833 SPO1745 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit delta YP_166983.1 1864000 D 246200 CDS YP_166984.1 56696623 3193191 1864260..1867193 1 NC_003911.11 identified by similarity to SP:Q46337; match to protein family HMM PF01571; match to protein family HMM TIGR01372; sarcosine oxidase subunit alpha 1867193 3193191 SPO1746 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit alpha YP_166984.1 1864260 D 246200 CDS YP_166985.1 56696624 3193268 1867162..1867731 1 NC_003911.11 identified by match to protein family HMM PF04268; sarcosine oxidase subunit gamma 1867731 3193268 SPO1747 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit gamma YP_166985.1 1867162 D 246200 CDS YP_166986.1 56696625 3196013 1867767..1868063 1 NC_003911.11 hypothetical protein 1868063 3196013 SPO1748 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166986.1 1867767 D 246200 CDS YP_166987.1 56696626 3195570 1868156..1870105 1 NC_003911.11 synthesizes RNA primers at the replication forks; DNA primase 1870105 dnaG 3195570 dnaG Ruegeria pomeroyi DSS-3 DNA primase YP_166987.1 1868156 D 246200 CDS YP_166988.1 56696627 3193502 1870217..1872199 1 NC_003911.11 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria; RNA polymerase sigma factor RpoD 1872199 rpoD 3193502 rpoD Ruegeria pomeroyi DSS-3 RNA polymerase sigma factor RpoD YP_166988.1 1870217 D 246200 CDS YP_166989.1 56696628 3192777 1872471..1872884 1 NC_003911.11 hypothetical protein 1872884 3192777 SPO1751 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166989.1 1872471 D 246200 CDS YP_166990.1 56696629 3193331 1872904..1873314 1 NC_003911.11 identified by similarity to PIR:D97619; match to protein family HMM PF01894; match to protein family HMM TIGR00149; hypothetical protein 1873314 3193331 SPO1752 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166990.1 1872904 D 246200 CDS YP_166991.1 56696630 3192977 1873443..1873913 1 NC_003911.11 identified by similarity to GB:BAC44848.1; match to protein family HMM PF03477; match to protein family HMM TIGR00244; transcriptional regulator NrdR 1873913 nrdR 3192977 nrdR Ruegeria pomeroyi DSS-3 transcriptional regulator NrdR YP_166991.1 1873443 D 246200 CDS YP_166992.1 56696631 3193058 1873910..1875004 1 NC_003911.11 identified by similarity to SP:P25539; match to protein family HMM PF00383; match to protein family HMM PF01872; match to protein family HMM TIGR00227; match to protein family HMM TIGR00326; riboflavin biosynthesis protein RibD 1875004 ribD 3193058 ribD Ruegeria pomeroyi DSS-3 riboflavin biosynthesis protein RibD YP_166992.1 1873910 D 246200 CDS YP_166993.1 56696632 3192840 complement(1875208..1877211) 1 NC_003911.11 identified by similarity to SP:P42217; match to protein family HMM PF05159; capsular polysaccharide export protein KpsC 1877211 kpsC 3192840 kpsC Ruegeria pomeroyi DSS-3 capsular polysaccharide export protein KpsC YP_166993.1 1875208 R 246200 CDS YP_166994.1 56696633 3192729 complement(1877215..1878348) 1 NC_003911.11 identified by match to protein family HMM PF02563; polysaccharide biosynthesis/export protein 1878348 3192729 SPO1756 Ruegeria pomeroyi DSS-3 polysaccharide biosynthesis/export protein YP_166994.1 1877215 R 246200 CDS YP_166995.1 56696634 3193254 complement(1878444..1879736) 1 NC_003911.11 identified by similarity to SP:P42218; match to protein family HMM PF05159; capsular polysaccharide export protein KpsS 1879736 kpsS 3193254 kpsS Ruegeria pomeroyi DSS-3 capsular polysaccharide export protein KpsS YP_166995.1 1878444 R 246200 CDS YP_166996.1 56696635 3193450 1879735..1879902 1 NC_003911.11 hypothetical protein 1879902 3193450 SPO1758 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166996.1 1879735 D 246200 CDS YP_166997.1 56696636 3193407 1879908..1880495 1 NC_003911.11 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha 1880495 ribE 3193407 ribE Ruegeria pomeroyi DSS-3 riboflavin synthase subunit alpha YP_166997.1 1879908 D 246200 CDS YP_166998.1 56696637 3192748 1880499..1881071 1 NC_003911.11 hypothetical protein 1881071 3192748 SPO1760 Ruegeria pomeroyi DSS-3 hypothetical protein YP_166998.1 1880499 D 246200 CDS YP_166999.1 56696638 3193366 1881259..1882380 1 NC_003911.11 identified by match to protein family HMM PF00925; match to protein family HMM PF00926; match to protein family HMM TIGR00506; 3,4-dihydroxy-2-butanone 4-phosphate synthase 1882380 3193366 SPO1761 Ruegeria pomeroyi DSS-3 3,4-dihydroxy-2-butanone 4-phosphate synthase YP_166999.1 1881259 D 246200 CDS YP_167000.1 56696639 3192913 1882382..1882933 1 NC_003911.11 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not; 6,7-dimethyl-8-ribityllumazine synthase 1882933 ribH 3192913 ribH Ruegeria pomeroyi DSS-3 6,7-dimethyl-8-ribityllumazine synthase YP_167000.1 1882382 D 246200 CDS YP_167001.1 56696640 3193374 1882930..1883412 1 NC_003911.11 identified by similarity to SP:P04381; match to protein family HMM PF01029; match to protein family HMM TIGR01951; transcription antitermination factor NusB 1883412 nusB 3193374 nusB Ruegeria pomeroyi DSS-3 transcription antitermination factor NusB YP_167001.1 1882930 D 246200 CDS YP_167002.1 56696641 3195163 complement(1883585..1884361) 1 NC_003911.11 identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 1884361 3195163 SPO1764 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_167002.1 1883585 R 246200 CDS YP_167003.1 56696642 3193385 1884458..1884763 1 NC_003911.11 identified by similarity to GB:CAE26745.1; hypothetical protein 1884763 3193385 SPO1765 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167003.1 1884458 D 246200 CDS YP_167004.1 56696643 3194650 1885036..1885488 1 NC_003911.11 identified by similarity to GB:CAA06860.1; hypothetical protein 1885488 3194650 SPO1766 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167004.1 1885036 D 246200 CDS YP_167005.1 56696644 3193625 1885835..1886317 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 1886317 3193625 SPO1767 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167005.1 1885835 D 246200 CDS YP_167006.1 56696645 3194626 complement(1886497..1887588) 1 NC_003911.11 hypothetical protein 1887588 3194626 SPO1769 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167006.1 1886497 R 246200 CDS YP_167007.1 56696646 3193295 1887615..1888205 1 NC_003911.11 hypothetical protein 1888205 3193295 SPO1770 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167007.1 1887615 D 246200 CDS YP_167008.1 56696647 3194565 complement(1888276..1889535) 1 NC_003911.11 identified by match to protein family HMM PF00597; match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM 1889535 3194565 SPO1771 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_167008.1 1888276 R 246200 CDS YP_167009.1 56696648 3195263 complement(1889532..1890110) 1 NC_003911.11 TRAP dicarboxylate transporter subunit DctQ 1890110 3195263 SPO1772 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctQ YP_167009.1 1889532 R 246200 CDS YP_167010.1 56696649 3192797 complement(1890141..1891124) 1 NC_003911.11 identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 1891124 3192797 SPO1773 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctP YP_167010.1 1890141 R 246200 CDS YP_167011.1 56696650 3192877 complement(1891175..1891717) 1 NC_003911.11 catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde in the final enzymatic step of quinolinate biosynthesis; 3-hydroxyanthranilate 3,4-dioxygenase 1891717 3192877 SPO1774 Ruegeria pomeroyi DSS-3 3-hydroxyanthranilate 3,4-dioxygenase YP_167011.1 1891175 R 246200 CDS YP_167012.1 56696651 3195305 1891953..1892672 1 NC_003911.11 identified by similarity to GB:CAE42879.1; hypothetical protein 1892672 3195305 SPO1775 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167012.1 1891953 D 246200 CDS YP_167013.1 56696652 3193113 1892849..1894186 1 NC_003911.11 function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase 1894186 3193113 SPO1776 Ruegeria pomeroyi DSS-3 oxidoreductase YP_167013.1 1892849 D 246200 CDS YP_167014.1 56696653 3193314 1894229..1895533 1 NC_003911.11 catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines; dihydropyrimidine dehydrogenase 1895533 3193314 SPO1777 Ruegeria pomeroyi DSS-3 dihydropyrimidine dehydrogenase YP_167014.1 1894229 D 246200 CDS YP_167015.1 56696654 3193235 complement(1895588..1895818) 1 NC_003911.11 hypothetical protein 1895818 3193235 SPO1778 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167015.1 1895588 R 246200 CDS YP_167016.1 56696655 3193122 1895936..1897216 1 NC_003911.11 major facilitator transporter 1897216 3193122 SPO1779 Ruegeria pomeroyi DSS-3 major facilitator transporter YP_167016.1 1895936 D 246200 CDS YP_167017.1 56696656 3194887 complement(1897197..1897814) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 1897814 3194887 SPO1780 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_167017.1 1897197 R 246200 CDS YP_167018.1 56696657 3193623 1897978..1899228 1 NC_003911.11 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase 1899228 3193623 SPO1781 Ruegeria pomeroyi DSS-3 allantoate amidohydrolase YP_167018.1 1897978 D 246200 CDS YP_167019.1 56696658 3193696 1899283..1899600 1 NC_003911.11 hypothetical protein 1899600 3193696 SPO1782 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167019.1 1899283 D 246200 CDS YP_167020.1 56696659 3192976 1899626..1901080 1 NC_003911.11 catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase 1901080 hydA 3192976 hydA Ruegeria pomeroyi DSS-3 phenylhydantoinase YP_167020.1 1899626 D 246200 CDS YP_167021.1 56696660 3193645 complement(1901086..1901499) 1 NC_003911.11 identified by similarity to GB:BAB48956.1; hypothetical protein 1901499 3193645 SPO1784 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167021.1 1901086 R 246200 CDS YP_167022.1 56696661 3193055 1901532..1902335 1 NC_003911.11 identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 1902335 3193055 SPO1785 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_167022.1 1901532 D 246200 CDS YP_167023.1 56696662 3193336 1902369..1903361 1 NC_003911.11 identified by match to protein family HMM PF00528; ABC transporter permease 1903361 3193336 SPO1786 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_167023.1 1902369 D 246200 CDS YP_167024.1 56696663 3192738 1903423..1904301 1 NC_003911.11 identified by match to protein family HMM PF00528; ABC transporter permease 1904301 3192738 SPO1787 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_167024.1 1903423 D 246200 CDS YP_167025.1 56696664 3192831 1904267..1905361 1 NC_003911.11 ABC transporter substrate-binding protein 1905361 3192831 SPO1788 Ruegeria pomeroyi DSS-3 ABC transporter substrate-binding protein YP_167025.1 1904267 D 246200 CDS YP_167026.1 56696665 3193479 1905532..1906245 1 NC_003911.11 identified by similarity to GB:CAC40783.1; match to protein family HMM PF00528; sulfate/tungstate ABC transporter permease 1906245 3193479 SPO1789 Ruegeria pomeroyi DSS-3 sulfate/tungstate ABC transporter permease YP_167026.1 1905532 D 246200 CDS YP_167027.1 56696666 3196221 1906238..1906972 1 NC_003911.11 identified by similarity to GB:CAC40784.1; match to protein family HMM PF00005; sulfate/tungstate ABC transporter ATP-binding protein 1906972 3196221 SPO1790 Ruegeria pomeroyi DSS-3 sulfate/tungstate ABC transporter ATP-binding protein YP_167027.1 1906238 D 246200 CDS YP_167028.1 56696667 3195511 1906992..1907807 1 NC_003911.11 identified by similarity to GB:CAC40782.1; match to protein family HMM PF01547; sulfate/tungstate ABC transporter substrate-binding protein 1907807 3195511 SPO1791 Ruegeria pomeroyi DSS-3 sulfate/tungstate ABC transporter substrate-binding protein YP_167028.1 1906992 D 246200 CDS YP_167029.1 56696668 3193420 complement(1907919..1908791) 1 NC_003911.11 identified by match to protein family HMM TIGR01764; excisionase 1908791 3193420 SPO1792 Ruegeria pomeroyi DSS-3 excisionase YP_167029.1 1907919 R 246200 CDS YP_167030.1 56696669 3193683 complement(1908914..1910263) 1 NC_003911.11 identified by match to protein family HMM PF00034; match to protein family HMM PF00400; hypothetical protein 1910263 3193683 SPO1793 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167030.1 1908914 R 246200 CDS YP_167031.1 56696670 3193031 complement(1910179..1911360) 1 NC_003911.11 identified by match to protein family HMM TIGR01583; formate dehydrogenase subunit gamma 1911360 3193031 SPO1794 Ruegeria pomeroyi DSS-3 formate dehydrogenase subunit gamma YP_167031.1 1910179 R 246200 CDS YP_167032.1 56696671 3193506 complement(1911485..1912078) 1 NC_003911.11 identified by similarity to SP:P27273; match to protein family HMM PF00037; formate dehydrogenase, iron-sulfur subunit 1912078 3193506 SPO1795 Ruegeria pomeroyi DSS-3 formate dehydrogenase, iron-sulfur subunit YP_167032.1 1911485 R 246200 CDS YP_167033.1 56696672 3193356 complement(1912091..1914985) 1 NC_003911.11 identified by similarity to PIR:S18213; match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; match to protein family HMM TIGR01409; formate dehydrogenase subunit alpha 1914985 3193356 SPO1796 Ruegeria pomeroyi DSS-3 formate dehydrogenase subunit alpha YP_167033.1 1912091 R 246200 CDS YP_167034.1 56696673 3192921 complement(1915092..1915283) 1 NC_003911.11 identified by match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1915283 3192921 SPO1797 Ruegeria pomeroyi DSS-3 twin-arginine translocation pathway signal sequence domain-containing protein YP_167034.1 1915092 R 246200 CDS YP_167035.1 56696674 3193220 complement(1915351..1915962) 1 NC_003911.11 identified by match to protein family HMM PF06192; chaperone TorD 1915962 3193220 SPO1798 Ruegeria pomeroyi DSS-3 chaperone TorD YP_167035.1 1915351 R 246200 CDS YP_167036.1 56696675 3193349 complement(1915966..1916595) 1 NC_003911.11 hypothetical protein 1916595 3193349 SPO1799 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167036.1 1915966 R 246200 CDS YP_167037.1 56696676 3193680 1917429..1919378 1 NC_003911.11 identified by match to protein family HMM PF00037; (Fe-S)-binding protein 1919378 3193680 SPO1800 Ruegeria pomeroyi DSS-3 (Fe-S)-binding protein YP_167037.1 1917429 D 246200 CDS YP_167038.1 56696677 3195510 complement(1919486..1920214) 1 NC_003911.11 identified by similarity to SP:P24059; hypothetical protein 1920214 3195510 SPO1801 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167038.1 1919486 R 246200 CDS YP_167039.1 56696678 3193608 1920259..1920480 1 NC_003911.11 identified by similarity to PIR:H95364; hypothetical protein 1920480 3193608 SPO1802 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167039.1 1920259 D 246200 CDS YP_167040.1 56696679 3192975 1920477..1921538 1 NC_003911.11 Mrp/NBP35 family protein 1921538 3192975 SPO1803 Ruegeria pomeroyi DSS-3 Mrp/NBP35 family protein YP_167040.1 1920477 D 246200 CDS YP_167041.1 56696680 3193128 1921535..1922242 1 NC_003911.11 identified by similarity to GB:BAC50748.1; hypothetical protein 1922242 3193128 SPO1804 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167041.1 1921535 D 246200 CDS YP_167042.1 56696681 3193110 1922239..1922718 1 NC_003911.11 hypothetical protein 1922718 3193110 SPO1805 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167042.1 1922239 D 246200 CDS YP_167043.1 56696682 3192890 complement(1922858..1923358) 1 NC_003911.11 identified by match to protein family HMM PF01613; flavin reductase domain-containing protein 1923358 3192890 SPO1806 Ruegeria pomeroyi DSS-3 flavin reductase domain-containing protein YP_167043.1 1922858 R 246200 CDS YP_167044.1 56696683 3193715 complement(1923541..1924953) 1 NC_003911.11 identified by match to protein family HMM PF00929; match to protein family HMM TIGR00573; DNA polymerase III subunit epsilon 1924953 3193715 SPO1807 Ruegeria pomeroyi DSS-3 DNA polymerase III subunit epsilon YP_167044.1 1923541 R 246200 CDS YP_167045.1 56696684 3194750 complement(1924955..1925506) 1 NC_003911.11 identified by similarity to GB:AAD22393.1; hypothetical protein 1925506 3194750 SPO1808 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167045.1 1924955 R 246200 CDS YP_167046.1 56696685 3193042 complement(1925559..1927382) 1 NC_003911.11 identified by match to protein family HMM PF00027; match to protein family HMM PF00571; match to protein family HMM PF03445; nucleotidyltransferase/CBS/cyclic nucleotide-binding domain-containing protein 1927382 3193042 SPO1809 Ruegeria pomeroyi DSS-3 nucleotidyltransferase/CBS/cyclic nucleotide-binding domain-containing protein YP_167046.1 1925559 R 246200 CDS YP_167047.1 56696686 3192878 complement(1927492..1929276) 1 NC_003911.11 identified by match to protein family HMM PF00474; sodium/solute symporter family protein 1929276 3192878 SPO1810 Ruegeria pomeroyi DSS-3 sodium/solute symporter family protein YP_167047.1 1927492 R 246200 CDS YP_167048.1 56696687 3194297 complement(1929283..1929567) 1 NC_003911.11 identified by similarity to GB:CAE09733.1; hypothetical protein 1929567 3194297 SPO1811 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167048.1 1929283 R 246200 CDS YP_167049.1 56696688 3193471 complement(1929739..1930407) 1 NC_003911.11 identified by similarity to SP:P10772; match to protein family HMM PF00406; match to protein family HMM PF05191; match to protein family HMM TIGR01351; adenylate kinase 1930407 adk-2 3193471 adk-2 Ruegeria pomeroyi DSS-3 adenylate kinase YP_167049.1 1929739 R 246200 CDS YP_167050.1 56696689 3192793 complement(1930433..1932397) 1 NC_003911.11 identified by similarity to SP:P27550; match to protein family HMM PF00501; acetyl-coenzyme A synthetase 1932397 acs 3192793 acs Ruegeria pomeroyi DSS-3 acetyl-coenzyme A synthetase YP_167050.1 1930433 R 246200 CDS YP_167051.1 56696690 3193194 1932854..1933870 1 NC_003911.11 identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 1933870 3193194 SPO1814 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctP YP_167051.1 1932854 D 246200 CDS YP_167052.1 56696691 3193096 1933945..1934580 1 NC_003911.11 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ 1934580 3193096 SPO1815 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctQ YP_167052.1 1933945 D 246200 CDS YP_167053.1 56696692 3192985 1934567..1935976 1 NC_003911.11 identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM 1935976 3192985 SPO1816 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_167053.1 1934567 D 246200 CDS YP_167054.1 56696693 3195314 1936040..1936789 1 NC_003911.11 identified by match to protein family HMM PF01925; hypothetical protein 1936789 3195314 SPO1817 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167054.1 1936040 D 246200 CDS YP_167055.1 56696694 3193672 1936854..1937642 1 NC_003911.11 identified by match to protein family HMM PF01925; hypothetical protein 1937642 3193672 SPO1818 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167055.1 1936854 D 246200 CDS YP_167056.1 56696695 3195317 complement(1937847..1938674) 1 NC_003911.11 identified by similarity to GB:AAN52089.1; match to protein family HMM PF00149; phosphodiesterase 1938674 3195317 SPO1819 Ruegeria pomeroyi DSS-3 phosphodiesterase YP_167056.1 1937847 R 246200 CDS YP_167057.1 56696696 3193496 complement(1938786..1940033) 1 NC_003911.11 identified by similarity to SP:P10904; match to protein family HMM PF01547; sugar ABC transporter periplasmic sugar-binding protein 1940033 3193496 SPO1820 Ruegeria pomeroyi DSS-3 sugar ABC transporter periplasmic sugar-binding protein YP_167057.1 1938786 R 246200 CDS YP_167058.1 56696697 3192715 complement(1940135..1940815) 1 NC_003911.11 identified by match to protein family HMM PF00528; sugar ABC transporter permease 1940815 3192715 SPO1821 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_167058.1 1940135 R 246200 CDS YP_167059.1 56696698 3194949 complement(1941094..1942035) 1 NC_003911.11 identified by match to protein family HMM PF00528; sugar ABC transporter permease 1942035 3194949 SPO1822 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_167059.1 1941094 R 246200 CDS YP_167060.1 56696699 3194693 complement(1942037..1943194) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF03459; sugar ABC transporter ATP-binding protein 1943194 3194693 SPO1823 Ruegeria pomeroyi DSS-3 sugar ABC transporter ATP-binding protein YP_167060.1 1942037 R 246200 CDS YP_167061.1 56696700 3193604 1943307..1944179 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1944179 3193604 SPO1824 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167061.1 1943307 D 246200 CDS YP_167062.1 56696701 3194357 complement(1944190..1945491) 1 NC_003911.11 glutamine synthetase 1945491 3194357 SPO1825 Ruegeria pomeroyi DSS-3 glutamine synthetase YP_167062.1 1944190 R 246200 CDS YP_167063.1 56696702 3194888 complement(1945493..1946335) 1 NC_003911.11 identified by match to protein family HMM PF01380; match to protein family HMM PF01418; RpiR family transcriptional regulator 1946335 3194888 SPO1826 Ruegeria pomeroyi DSS-3 RpiR family transcriptional regulator YP_167063.1 1945493 R 246200 CDS YP_167064.1 56696703 3192701 1946349..1947188 1 NC_003911.11 identified by match to protein family HMM PF05013; N-formylglutamate amidohydrolase 1947188 3192701 SPO1827 Ruegeria pomeroyi DSS-3 N-formylglutamate amidohydrolase YP_167064.1 1946349 D 246200 CDS YP_167065.1 56696704 3193702 1947185..1947826 1 NC_003911.11 identified by match to protein family HMM PF00857; isochorismatase 1947826 3193702 SPO1828 Ruegeria pomeroyi DSS-3 isochorismatase YP_167065.1 1947185 D 246200 CDS YP_167066.1 56696705 3192665 1947819..1948544 1 NC_003911.11 identified by similarity to SP:P21629; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1948544 3192665 SPO1829 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_167066.1 1947819 D 246200 CDS YP_167067.1 56696706 3193071 1948576..1949730 1 NC_003911.11 identified by similarity to SP:P21175; match to protein family HMM PF01094; branched-chain amino acid ABC transporter periplasmic branched-chain amino acid binding protein 1949730 3193071 SPO1830 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter periplasmic branched-chain amino acid binding protein YP_167067.1 1948576 D 246200 CDS YP_167068.1 56696707 3192764 1949792..1950490 1 NC_003911.11 identified by similarity to SP:P22731; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1950490 livF-1 3192764 livF-1 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_167068.1 1949792 D 246200 CDS YP_167069.1 56696708 3192828 1950492..1951388 1 NC_003911.11 identified by similarity to SP:P08340; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1951388 3192828 SPO1832 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_167069.1 1950492 D 246200 CDS YP_167070.1 56696709 3194492 1951385..1952404 1 NC_003911.11 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1952404 3194492 SPO1833 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_167070.1 1951385 D 246200 CDS YP_167071.1 56696710 3193637 1952414..1953352 1 NC_003911.11 identified by match to protein family HMM PF03069; acetamidase/formamidase 1953352 3193637 SPO1834 Ruegeria pomeroyi DSS-3 acetamidase/formamidase YP_167071.1 1952414 D 246200 CDS YP_167072.1 56696711 3194807 complement(1953388..1954389) 1 NC_003911.11 identified by similarity to GB:AAC04471.1; match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein 1954389 3194807 SPO1835 Ruegeria pomeroyi DSS-3 sugar ABC transporter ATP-binding protein YP_167072.1 1953388 R 246200 CDS YP_167073.1 56696712 3193706 complement(1954391..1955419) 1 NC_003911.11 identified by match to protein family HMM PF01408; Gfo/Idh/MocA family oxidoreductase 1955419 3193706 SPO1836 Ruegeria pomeroyi DSS-3 Gfo/Idh/MocA family oxidoreductase YP_167073.1 1954391 R 246200 CDS YP_167074.1 56696713 3193145 complement(1955416..1956255) 1 NC_003911.11 identified by match to protein family HMM PF00528; sugar ABC transporter permease 1956255 3193145 SPO1837 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_167074.1 1955416 R 246200 CDS YP_167075.1 56696714 3193662 complement(1956268..1957182) 1 NC_003911.11 identified by similarity to SP:P29823; match to protein family HMM PF00528; sugar ABC transporter permease 1957182 3193662 SPO1838 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_167075.1 1956268 R 246200 CDS YP_167076.1 56696715 3193267 complement(1957239..1958489) 1 NC_003911.11 identified by similarity to SP:Q00749; match to protein family HMM PF01547; sugar ABC transporter periplasmic sugar-binding protein 1958489 3193267 SPO1839 Ruegeria pomeroyi DSS-3 sugar ABC transporter periplasmic sugar-binding protein YP_167076.1 1957239 R 246200 CDS YP_167077.1 56696716 3192849 complement(1958486..1959394) 1 NC_003911.11 catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway; N-acetylmuramic acid 6-phosphate etherase 1959394 murQ 3192849 murQ Ruegeria pomeroyi DSS-3 N-acetylmuramic acid 6-phosphate etherase YP_167077.1 1958486 R 246200 CDS YP_167078.1 56696717 3194707 1959554..1960444 1 NC_003911.11 identified by match to protein family HMM PF01869; BadF/BadG/BcrA/BcrD ATPase 1960444 3194707 SPO1841 Ruegeria pomeroyi DSS-3 BadF/BadG/BcrA/BcrD ATPase YP_167078.1 1959554 D 246200 CDS YP_167079.1 56696718 3195848 1960441..1961217 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1961217 3195848 SPO1842 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_167079.1 1960441 D 246200 CDS YP_167080.1 56696719 3193173 1961226..1962257 1 NC_003911.11 identified by match to protein family HMM PF01380; SIS domain-containing protein 1962257 3193173 SPO1843 Ruegeria pomeroyi DSS-3 SIS domain-containing protein YP_167080.1 1961226 D 246200 CDS YP_167081.1 56696720 3192869 1962254..1963399 1 NC_003911.11 identified by similarity to SP:P15300; match to protein family HMM PF01979; match to protein family HMM TIGR00221; N-acetylglucosamine-6-phosphate deacetylase 1963399 nagA 3192869 nagA Ruegeria pomeroyi DSS-3 N-acetylglucosamine-6-phosphate deacetylase YP_167081.1 1962254 D 246200 CDS YP_167082.1 56696721 3193400 complement(1963574..1965676) 1 NC_003911.11 identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; molybdopterin-binding oxidoreductase 1965676 3193400 SPO1845 Ruegeria pomeroyi DSS-3 molybdopterin-binding oxidoreductase YP_167082.1 1963574 R 246200 CDS YP_167083.1 56696722 3193624 complement(1965749..1966909) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF01094; branched-chain amino acid ABC transporter substrate-binding protein 1966909 3193624 SPO1846 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter substrate-binding protein YP_167083.1 1965749 R 246200 CDS YP_167084.1 56696723 3193687 complement(1966939..1968825) 1 NC_003911.11 identified by match to protein family HMM PF00501; AMP-binding protein 1968825 3193687 SPO1847 Ruegeria pomeroyi DSS-3 AMP-binding protein YP_167084.1 1966939 R 246200 CDS YP_167085.1 56696724 3194806 complement(1968843..1969616) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1969616 3194806 SPO1848 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_167085.1 1968843 R 246200 CDS YP_167086.1 56696725 3193037 complement(1969613..1970377) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1970377 3193037 SPO1849 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_167086.1 1969613 R 246200 CDS YP_167087.1 56696726 3192662 complement(1970374..1971471) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1971471 3192662 SPO1850 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_167087.1 1970374 R 246200 CDS YP_167088.1 56696727 3193102 complement(1971476..1972351) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1972351 3193102 SPO1851 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_167088.1 1971476 R 246200 CDS YP_167089.1 56696728 3192686 complement(1972430..1973458) 1 NC_003911.11 identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase 1973458 3192686 SPO1852 Ruegeria pomeroyi DSS-3 zinc-binding dehydrogenase oxidoreductase YP_167089.1 1972430 R 246200 CDS YP_167090.1 56696729 3193248 complement(1973477..1974118) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 1974118 3193248 SPO1853 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_167090.1 1973477 R 246200 CDS YP_167091.1 56696730 3193286 1974322..1974792 1 NC_003911.11 identified by similarity to GB:CAD18588.1; hypothetical protein 1974792 3193286 SPO1854 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167091.1 1974322 D 246200 CDS YP_167092.1 56696731 3193099 complement(1974867..1975550) 1 NC_003911.11 hypothetical protein 1975550 3193099 SPO1855 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167092.1 1974867 R 246200 CDS YP_167093.1 56696732 3195275 1975957..1976811 1 NC_003911.11 identified by match to protein family HMM PF03631; match to protein family HMM TIGR00765; ribonuclease BN 1976811 3195275 SPO1856 Ruegeria pomeroyi DSS-3 ribonuclease BN YP_167093.1 1975957 D 246200 CDS YP_167094.1 56696733 3193189 1976918..1977220 1 NC_003911.11 hypothetical protein 1977220 3193189 SPO1857 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167094.1 1976918 D 246200 CDS YP_167095.1 56696734 3195971 complement(1977167..1977868) 1 NC_003911.11 identified by match to protein family HMM PF01728; ribosomal RNA large subunit methyltransferase J 1977868 rrmJ 3195971 rrmJ Ruegeria pomeroyi DSS-3 ribosomal RNA large subunit methyltransferase J YP_167095.1 1977167 R 246200 CDS YP_167096.1 56696735 3195288 complement(1977989..1979101) 1 NC_003911.11 identified by match to protein family HMM PF02541; Ppx/GppA phosphatase 1979101 3195288 SPO1859 Ruegeria pomeroyi DSS-3 Ppx/GppA phosphatase YP_167096.1 1977989 R 246200 CDS YP_167097.1 56696736 3195716 1979284..1981167 1 NC_003911.11 identified by match to protein family HMM PF05787; match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1981167 3195716 SPO1860 Ruegeria pomeroyi DSS-3 twin-arginine translocation pathway signal sequence domain-containing protein YP_167097.1 1979284 D 246200 CDS YP_167098.1 56696737 3193225 1981420..1981716 1 NC_003911.11 identified by similarity to GB:BAB48658.1; hypothetical protein 1981716 3193225 SPO1861 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167098.1 1981420 D 246200 CDS YP_167099.1 56696738 3192752 1981743..1982672 1 NC_003911.11 identified by similarity to PIR:B97532; MetF-like protein 1982672 3192752 SPO1862 Ruegeria pomeroyi DSS-3 MetF-like protein YP_167099.1 1981743 D 246200 CDS YP_167100.1 56696739 3192958 1982683..1983744 1 NC_003911.11 catalyzes the transfer of the N5-methyl group from (6S)-methyl tetrahydrofolate to the cobalt center of a corrinoid iron-sulfur protein; methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase 1983744 3192958 SPO1863 Ruegeria pomeroyi DSS-3 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase YP_167100.1 1982683 D 246200 CDS YP_167101.1 56696740 3193210 complement(1983863..1984102) 1 NC_003911.11 hypothetical protein 1984102 3193210 SPO1864 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167101.1 1983863 R 246200 CDS YP_167102.1 56696741 3192774 complement(1984235..1986256) 1 NC_003911.11 catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase; transketolase 1986256 tkt 3192774 tkt Ruegeria pomeroyi DSS-3 transketolase YP_167102.1 1984235 R 246200 CDS YP_167103.1 56696742 3193238 1986524..1987405 1 NC_003911.11 hypothetical protein 1987405 3193238 SPO1866 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167103.1 1986524 D 246200 CDS YP_167104.1 56696743 3193472 1987405..1987800 1 NC_003911.11 identified by similarity to GB:AAK25209.1; hypothetical protein 1987800 3193472 SPO1867 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167104.1 1987405 D 246200 CDS YP_167105.1 56696744 3192918 complement(1987932..1988294) 1 NC_003911.11 identified by match to protein family HMM TIGR00365; glutaredoxin-like protein 1988294 3192918 SPO1868 Ruegeria pomeroyi DSS-3 glutaredoxin-like protein YP_167105.1 1987932 R 246200 CDS YP_167106.1 56696745 3192908 complement(1988361..1988597) 1 NC_003911.11 identified by match to protein family HMM PF01722; BolA family protein 1988597 3192908 SPO1869 Ruegeria pomeroyi DSS-3 BolA family protein YP_167106.1 1988361 R 246200 CDS YP_167107.1 56696746 3194711 complement(1988722..1990881) 1 NC_003911.11 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis; phosphoribosylformylglycinamidine synthase II 1990881 purL 3194711 purL Ruegeria pomeroyi DSS-3 phosphoribosylformylglycinamidine synthase II YP_167107.1 1988722 R 246200 CDS YP_167108.1 56696747 3193943 complement(1991015..1993288) 1 NC_003911.11 identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS 1993288 3193943 SPO1871 Ruegeria pomeroyi DSS-3 mechanosensitive ion channel MscS YP_167108.1 1991015 R 246200 CDS YP_167109.1 56696748 3195605 complement(1993553..1994488) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1994488 3195605 SPO1872 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167109.1 1993553 R 246200 CDS YP_167110.1 56696749 3192932 1994630..1998049 1 NC_003911.11 Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; indolepyruvate ferredoxin oxidoreductase 1998049 3192932 SPO1873 Ruegeria pomeroyi DSS-3 indolepyruvate ferredoxin oxidoreductase YP_167110.1 1994630 D 246200 CDS YP_167111.1 56696750 3193459 1998130..1999008 1 NC_003911.11 identified by match to protein family HMM PF01553; acyltransferase domain-containing protein 1999008 3193459 SPO1874 Ruegeria pomeroyi DSS-3 acyltransferase domain-containing protein YP_167111.1 1998130 D 246200 CDS YP_167112.1 56696751 3193464 1999017..1999826 1 NC_003911.11 identified by similarity to SP:P48797; match to protein family HMM PF01177; match to protein family HMM TIGR00067; glutamate racemase 1999826 murI 3193464 murI Ruegeria pomeroyi DSS-3 glutamate racemase YP_167112.1 1999017 D 246200 CDS YP_167113.1 56696752 3193483 1999917..2000945 1 NC_003911.11 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate; N-acetyl-gamma-glutamyl-phosphate reductase 2000945 argC 3193483 argC Ruegeria pomeroyi DSS-3 N-acetyl-gamma-glutamyl-phosphate reductase YP_167113.1 1999917 D 246200 CDS YP_167114.1 56696753 3192772 2000953..2001396 1 NC_003911.11 CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane; cytochrome c-type biogenesis protein CcmE 2001396 ccmE 3192772 ccmE Ruegeria pomeroyi DSS-3 cytochrome c-type biogenesis protein CcmE YP_167114.1 2000953 D 246200 CDS YP_167115.1 56696754 3193467 2001542..2002153 1 NC_003911.11 identified by similarity to GB:AAF26222.1; match to protein family HMM PF05838; hypothetical protein 2002153 3193467 SPO1878 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167115.1 2001542 D 246200 CDS YP_167116.1 56696756 3193253 complement(2002126..2002818) 1 NC_003911.11 hypothetical protein 2002818 3193253 SPO1879 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167116.1 2002126 R 246200 CDS YP_167117.1 56696755 3192786 2002798..2004762 1 NC_003911.11 identified by similarity to SP:Q00500; match to protein family HMM PF01578; match to protein family HMM TIGR00353; cytochrome c-type biogenesis protein CcmF 2004762 ccmF 3192786 ccmF Ruegeria pomeroyi DSS-3 cytochrome c-type biogenesis protein CcmF YP_167117.1 2002798 D 246200 CDS YP_167118.1 56696757 3193434 2004759..2005211 1 NC_003911.11 identified by match to protein family HMM PF03918; cytochrome c biogenesis family protein 2005211 3193434 SPO1881 Ruegeria pomeroyi DSS-3 cytochrome c biogenesis family protein YP_167118.1 2004759 D 246200 CDS YP_167119.1 56696758 3193419 2005288..2006064 1 NC_003911.11 identified by match to protein family HMM PF00378; enoyl-CoA hydratase 2006064 3193419 SPO1882 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_167119.1 2005288 D 246200 CDS YP_167120.1 56696759 3193204 2006114..2007667 1 NC_003911.11 identified by similarity to SP:O43464; hypothetical protein 2007667 3193204 SPO1883 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167120.1 2006114 D 246200 CDS YP_167121.1 56696760 3193239 complement(2007677..2008696) 1 NC_003911.11 catalyzes the formation of methionine from L-homocysteine and S-adenosyl-L-methionine; methionine synthase I 2008696 3193239 SPO1884 Ruegeria pomeroyi DSS-3 methionine synthase I YP_167121.1 2007677 R 246200 CDS YP_167122.1 56696761 3192659 complement(2008757..2010664) 1 NC_003911.11 hypothetical protein 2010664 3192659 SPO1885 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167122.1 2008757 R 246200 CDS YP_167123.1 56696762 3193466 complement(2010734..2011051) 1 NC_003911.11 identified by similarity to GB:CAC46350.1; match to protein family HMM PF07345; hypothetical protein 2011051 3193466 SPO1886 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167123.1 2010734 R 246200 CDS YP_167124.1 56696763 3193415 2011211..2011966 1 NC_003911.11 catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase; phosphoribosylaminoimidazole-succinocarboxamide synthase 2011966 purC 3193415 purC Ruegeria pomeroyi DSS-3 phosphoribosylaminoimidazole-succinocarboxamide synthase YP_167124.1 2011211 D 246200 CDS YP_167125.1 56696764 3193488 2012153..2012383 1 NC_003911.11 identified by match to protein family HMM PF02700; match to protein family HMM TIGR00302; phosphoribosylformylglycinamidine synthase, PurS protein 2012383 purS 3193488 purS Ruegeria pomeroyi DSS-3 phosphoribosylformylglycinamidine synthase, PurS protein YP_167125.1 2012153 D 246200 CDS YP_167126.1 56696765 3192783 2012387..2013430 1 NC_003911.11 identified by match to protein family HMM PF00107; alcohol dehydrogenase 2013430 3192783 SPO1889 Ruegeria pomeroyi DSS-3 alcohol dehydrogenase YP_167126.1 2012387 D 246200 CDS YP_167127.1 56696766 3193087 2013443..2014111 1 NC_003911.11 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis; phosphoribosylformylglycinamidine synthase I 2014111 purQ 3193087 purQ Ruegeria pomeroyi DSS-3 phosphoribosylformylglycinamidine synthase I YP_167127.1 2013443 D 246200 CDS YP_167128.1 56696767 3192652 2014148..2015917 1 NC_003911.11 identified by similarity to SP:P13633; match to protein family HMM PF00512; match to protein family HMM PF02518; C4-dicarboxylate transport sensor protein DctB 2015917 3192652 SPO1891 Ruegeria pomeroyi DSS-3 C4-dicarboxylate transport sensor protein DctB YP_167128.1 2014148 D 246200 CDS YP_167129.1 56696768 3193394 2015932..2017266 1 NC_003911.11 identified by similarity to SP:P13632; match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954; match to protein family HMM TIGR01199; C4-dicarboxylate transport transcriptional regulatory protein DctD 2017266 dctD-1 3193394 dctD-1 Ruegeria pomeroyi DSS-3 C4-dicarboxylate transport transcriptional regulatory protein DctD YP_167129.1 2015932 D 246200 CDS YP_167130.1 56696769 3192750 2017824..2020805 1 NC_003911.11 identified by match to protein family HMM TIGR00757; ribonuclease 2020805 3192750 SPO1893 Ruegeria pomeroyi DSS-3 ribonuclease YP_167130.1 2017824 D 246200 CDS YP_167131.1 56696770 3194393 complement(2020838..2021071) 1 NC_003911.11 identified by similarity to SP:P37618; match to protein family HMM PF01206; SirA family protein 2021071 3194393 SPO1895 Ruegeria pomeroyi DSS-3 SirA family protein YP_167131.1 2020838 R 246200 CDS YP_167132.1 56696771 3195230 2021197..2021949 1 NC_003911.11 identified by similarity to GB:AAF26218.1; match to protein family HMM PF02683; cytochrome c-type biogenesis protein CcdA 2021949 ccdA 3195230 ccdA Ruegeria pomeroyi DSS-3 cytochrome c-type biogenesis protein CcdA YP_167132.1 2021197 D 246200 CDS YP_167133.1 56696772 3192857 2022105..2023337 1 NC_003911.11 identified by similarity to PIR:AF3633; hypothetical protein 2023337 3192857 SPO1897 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167133.1 2022105 D 246200 CDS YP_167134.1 56696773 3193352 2023334..2024686 1 NC_003911.11 identified by match to protein family HMM PF00067; cytochrome P450 family protein 2024686 3193352 SPO1898 Ruegeria pomeroyi DSS-3 cytochrome P450 family protein YP_167134.1 2023334 D 246200 CDS YP_167135.1 56696774 3193495 2024755..2025636 1 NC_003911.11 catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis; fructose-1,6-bisphosphate aldolase 2025636 fda 3193495 fda Ruegeria pomeroyi DSS-3 fructose-1,6-bisphosphate aldolase YP_167135.1 2024755 D 246200 CDS YP_167136.1 56696775 3195713 complement(2025682..2026290) 1 NC_003911.11 identified by similarity to SP:P05100; match to protein family HMM PF03352; DNA-3-methyladenine glycosylase I 2026290 tag 3195713 tag Ruegeria pomeroyi DSS-3 DNA-3-methyladenine glycosylase I YP_167136.1 2025682 R 246200 CDS YP_167137.1 56696776 3193100 complement(2026287..2026586) 1 NC_003911.11 identified by similarity to GB:AAQ61811.1; hypothetical protein 2026586 3193100 SPO1901 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167137.1 2026287 R 246200 CDS YP_167138.1 56696777 3193487 complement(2026599..2027174) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 2027174 3193487 SPO1902 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_167138.1 2026599 R 246200 CDS YP_167139.1 56696778 3195550 complement(2027240..2027461) 1 NC_003911.11 identified by similarity to GB:CAC46714.1; hypothetical protein 2027461 3195550 SPO1903 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167139.1 2027240 R 246200 CDS YP_167140.1 56696779 3193630 complement(2027458..2027634) 1 NC_003911.11 identified by similarity to GB:AAK23509.1; hypothetical protein 2027634 3193630 SPO1904 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167140.1 2027458 R 246200 CDS YP_167141.1 56696780 3193215 complement(2027634..2028983) 1 NC_003911.11 class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle; fumarate hydratase 2028983 fumC 3193215 fumC Ruegeria pomeroyi DSS-3 fumarate hydratase YP_167141.1 2027634 R 246200 CDS YP_167142.1 56696781 3192841 2029197..2029748 1 NC_003911.11 hypothetical protein 2029748 3192841 SPO1906 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167142.1 2029197 D 246200 CDS YP_167143.1 56696782 3193447 complement(2029818..2030273) 1 NC_003911.11 identified by similarity to GB:AAK24073.1; hypothetical protein 2030273 3193447 SPO1907 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167143.1 2029818 R 246200 CDS YP_167144.1 56696783 3195788 complement(2030354..2031724) 1 NC_003911.11 identified by similarity to SP:P17551; match to protein family HMM PF02417; chromate transporter 2031724 3195788 SPO1908 Ruegeria pomeroyi DSS-3 chromate transporter YP_167144.1 2030354 R 246200 CDS YP_167145.1 56696784 3192894 complement(2031767..2032222) 1 NC_003911.11 identified by similarity to PIR:AB2272; hypothetical protein 2032222 3192894 SPO1909 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167145.1 2031767 R 246200 CDS YP_167146.1 56696785 3193353 complement(2032765..2033016) 1 NC_003911.11 hypothetical protein 2033016 3193353 SPO1911 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167146.1 2032765 R 246200 CDS YP_167147.1 56696786 3192669 complement(2033030..2033761) 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 2033761 3192669 SPO1912 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_167147.1 2033030 R 246200 CDS YP_167148.1 56696787 3192947 2033984..2035078 1 NC_003911.11 DmdA; DMSP demethylase; in Silicibacter knockout of this gene results in an inability to convert DMSP to methanethiol which is restored with a cloned copy of the gene; dimethyl sulfoniopropionate demethylase 2035078 dmdA 3192947 dmdA Ruegeria pomeroyi DSS-3 dimethyl sulfoniopropionate demethylase YP_167148.1 2033984 D 246200 CDS YP_167149.1 56696788 3192712 2035156..2036148 1 NC_003911.11 identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase 2036148 3192712 SPO1914 Ruegeria pomeroyi DSS-3 zinc-binding dehydrogenase oxidoreductase YP_167149.1 2035156 D 246200 CDS YP_167150.1 56696789 3193227 complement(2036201..2036584) 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 2036584 3193227 SPO1915 Ruegeria pomeroyi DSS-3 glyoxalase YP_167150.1 2036201 R 246200 CDS YP_167151.1 56696790 3192708 2036724..2037947 1 NC_003911.11 identified by match to protein family HMM PF00266; class V aminotransferase 2037947 3192708 SPO1916 Ruegeria pomeroyi DSS-3 class V aminotransferase YP_167151.1 2036724 D 246200 CDS YP_167152.1 56696791 3192692 2037997..2039442 1 NC_003911.11 identified by similarity to SP:P00914; match to protein family HMM PF00875; match to protein family HMM PF03441; deoxyribodipyrimidine photolyase 2039442 phrB 3192692 phrB Ruegeria pomeroyi DSS-3 deoxyribodipyrimidine photolyase YP_167152.1 2037997 D 246200 CDS YP_167153.1 56696792 3195566 2039492..2040706 1 NC_003911.11 identified by match to protein family HMM PF02353; cyclopropane-fatty-acyl-phospholipid synthase 2040706 cfa 3195566 cfa Ruegeria pomeroyi DSS-3 cyclopropane-fatty-acyl-phospholipid synthase YP_167153.1 2039492 D 246200 CDS YP_167154.1 56696793 3193833 2040718..2041158 1 NC_003911.11 identified by similarity to GB:AAB95446.1; tellurite resistance protein 2041158 trgA 3193833 trgA Ruegeria pomeroyi DSS-3 tellurite resistance protein YP_167154.1 2040718 D 246200 CDS YP_167155.1 56696794 3195180 2041159..2042304 1 NC_003911.11 identified by similarity to GB:AAB95442.1; match to protein family HMM PF00293; match to protein family HMM TIGR00052; tellurite resistance protein 2042304 trgB 3195180 trgB Ruegeria pomeroyi DSS-3 tellurite resistance protein YP_167155.1 2041159 D 246200 CDS YP_167156.1 56696795 3194670 2042389..2043423 1 NC_003911.11 CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis; cysteine synthase A 2043423 3194670 SPO1921 Ruegeria pomeroyi DSS-3 cysteine synthase A YP_167156.1 2042389 D 246200 CDS YP_167157.1 56696796 3193175 2043404..2045836 1 NC_003911.11 identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS 2045836 3193175 SPO1922 Ruegeria pomeroyi DSS-3 mechanosensitive ion channel MscS YP_167157.1 2043404 D 246200 CDS YP_167158.1 56696797 3193618 2045826..2046548 1 NC_003911.11 identified by similarity to GB:CAC46199.1; hypothetical protein 2046548 3193618 SPO1923 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167158.1 2045826 D 246200 CDS YP_167159.1 56696798 3193453 complement(2047083..2047958) 1 NC_003911.11 hypothetical protein 2047958 3193453 SPO1925 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167159.1 2047083 R 246200 CDS YP_167160.1 56696799 3193163 complement(2047955..2050852) 1 NC_003911.11 identified by similarity to GB:AAK22811.1; hypothetical protein 2050852 3193163 SPO1926 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167160.1 2047955 R 246200 CDS YP_167161.1 56698719 3196263 complement(2052890..2053081) 1 NC_003911.11 identified by similarity to SP:P12552; match to protein family HMM PF05930; DNA-binding protein 2053081 3196263 SPO3898 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_167161.1 2052890 R 246200 CDS YP_167162.1 56696800 3194586 complement(2053837..2055057) 1 NC_003911.11 identified by match to protein family HMM PF00589; phage integrase site specific recombinase 2055057 3194586 SPO1927 Ruegeria pomeroyi DSS-3 phage integrase site specific recombinase YP_167162.1 2053837 R 246200 CDS YP_167163.1 56696801 3192805 complement(2055392..2055997) 1 NC_003911.11 identified by match to protein family HMM PF05951; match to protein family HMM TIGR01409; Tat pathway signal sequence domain-containing protein 2055997 3192805 SPO1928 Ruegeria pomeroyi DSS-3 Tat pathway signal sequence domain-containing protein YP_167163.1 2055392 R 246200 CDS YP_167164.1 56696802 3193273 2056316..2057929 1 NC_003911.11 identified by match to protein family HMM PF01471; peptidoglycan binding protein 2057929 3193273 SPO1929 Ruegeria pomeroyi DSS-3 peptidoglycan binding protein YP_167164.1 2056316 D 246200 CDS YP_167165.1 56696803 3192672 2057964..2059055 1 NC_003911.11 identified by match to protein family HMM PF00132; match to protein family HMM PF04613; match to protein family HMM TIGR01853; UDP-3-O-3-hydroxymyristoyl glucosamine N-acyltransferase 2059055 lpxD 3192672 lpxD Ruegeria pomeroyi DSS-3 UDP-3-O-3-hydroxymyristoyl glucosamine N-acyltransferase YP_167165.1 2057964 D 246200 CDS YP_167166.1 56696804 3193176 2059087..2059344 1 NC_003911.11 identified by similarity to SP:P20804; match to protein family HMM PF00550; acyl carrier protein 2059344 3193176 SPO1931 Ruegeria pomeroyi DSS-3 acyl carrier protein YP_167166.1 2059087 D 246200 CDS YP_167167.1 56696805 3193139 2059353..2060561 1 NC_003911.11 identified by match to protein family HMM PF00109; match to protein family HMM PF02801; beta-ketoacyl synthase 2060561 3193139 SPO1932 Ruegeria pomeroyi DSS-3 beta-ketoacyl synthase YP_167167.1 2059353 D 246200 CDS YP_167168.1 56696806 3193077 complement(2060640..2061314) 1 NC_003911.11 identified by match to protein family HMM PF06776; invasion associated family protein 2061314 3193077 SPO1933 Ruegeria pomeroyi DSS-3 invasion associated family protein YP_167168.1 2060640 R 246200 CDS YP_167169.1 56696807 3192689 2061709..2063262 1 NC_003911.11 identified by similarity to PIR:B97464; match to protein family HMM PF05872; hypothetical protein 2063262 3192689 SPO1934 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167169.1 2061709 D 246200 CDS YP_167170.1 56696808 3193517 complement(2063401..2064705) 1 NC_003911.11 identified by similarity to SP:P22729; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 2064705 3193517 SPO1935 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_167170.1 2063401 R 246200 CDS YP_167171.1 56696809 3192832 complement(2064702..2065712) 1 NC_003911.11 identified by similarity to SP:P08340; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 2065712 3192832 SPO1936 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_167171.1 2064702 R 246200 CDS YP_167172.1 56696810 3193285 complement(2065716..2066546) 1 NC_003911.11 identified by similarity to SP:P22731; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 2066546 3193285 SPO1937 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_167172.1 2065716 R 246200 CDS YP_167173.1 56696811 3193021 complement(2066543..2067433) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 2067433 3193021 SPO1938 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_167173.1 2066543 R 246200 CDS YP_167174.1 56696812 3193383 complement(2067471..2068664) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF01094; branched-chain amino acid ABC transporter substrate-binding protein 2068664 3193383 SPO1939 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter substrate-binding protein YP_167174.1 2067471 R 246200 CDS YP_167175.1 56696813 3193184 2068824..2069936 1 NC_003911.11 identified by similarity to GB:CAC46907.1; hypothetical protein 2069936 3193184 SPO1940 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167175.1 2068824 D 246200 CDS YP_167176.1 56696814 3193292 complement(2070049..2071026) 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 2071026 3193292 SPO1941 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_167176.1 2070049 R 246200 CDS YP_167177.1 56696815 3193118 2071198..2072595 1 NC_003911.11 identified by match to protein family HMM PF01474; match to protein family HMM TIGR01358; 3-deoxy-7-phosphoheptulonate synthase 2072595 3193118 SPO1942 Ruegeria pomeroyi DSS-3 3-deoxy-7-phosphoheptulonate synthase YP_167177.1 2071198 D 246200 CDS YP_167178.1 56696816 3192872 complement(2072666..2073358) 1 NC_003911.11 identified by similarity to PIR:C97571; hypothetical protein 2073358 3192872 SPO1943 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167178.1 2072666 R 246200 CDS YP_167179.1 56696817 3193035 2073600..2074490 1 NC_003911.11 identified by match to protein family HMM PF03755; match to protein family HMM TIGR00255; hypothetical protein 2074490 3193035 SPO1944 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167179.1 2073600 D 246200 CDS YP_167180.1 56696818 3193183 2074509..2075150 1 NC_003911.11 Essential for recycling GMP and indirectly, cGMP; guanylate kinase 2075150 gmk 3193183 gmk Ruegeria pomeroyi DSS-3 guanylate kinase YP_167180.1 2074509 D 246200 CDS YP_167181.1 56696819 3193643 2075147..2075671 1 NC_003911.11 identified by match to protein family HMM PF00132; transferase 2075671 3193643 SPO1946 Ruegeria pomeroyi DSS-3 transferase YP_167181.1 2075147 D 246200 CDS YP_167182.1 56696820 3193213 2075688..2076734 1 NC_003911.11 identified by similarity to SP:P23621; match to protein family HMM PF00512; match to protein family HMM PF02518; phosphate regulon sensor histidine kinase 2076734 3193213 SPO1947 Ruegeria pomeroyi DSS-3 phosphate regulon sensor histidine kinase YP_167182.1 2075688 D 246200 CDS YP_167183.1 56696821 3194730 2076961..2078001 1 NC_003911.11 phosphate ABC transporter substrate-binding protein 2078001 pstS 3194730 pstS Ruegeria pomeroyi DSS-3 phosphate ABC transporter substrate-binding protein YP_167183.1 2076961 D 246200 CDS YP_167184.1 56696822 3193326 2078079..2079554 1 NC_003911.11 identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138; phosphate ABC transporter permease 2079554 pstC 3193326 pstC Ruegeria pomeroyi DSS-3 phosphate ABC transporter permease YP_167184.1 2078079 D 246200 CDS YP_167185.1 56696823 3192719 2079551..2080903 1 NC_003911.11 identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974; phosphate ABC transporter permease 2080903 pstA 3192719 pstA Ruegeria pomeroyi DSS-3 phosphate ABC transporter permease YP_167185.1 2079551 D 246200 CDS YP_167186.1 56696824 3195194 2080887..2081714 1 NC_003911.11 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation; phosphate transporter ATP-binding protein 2081714 pstB 3195194 pstB Ruegeria pomeroyi DSS-3 phosphate transporter ATP-binding protein YP_167186.1 2080887 D 246200 CDS YP_167187.1 56696825 3192941 2081732..2082433 1 NC_003911.11 identified by match to protein family HMM PF01895; match to protein family HMM TIGR02135; phosphate transport system regulatory protein PhoU 2082433 phoU 3192941 phoU Ruegeria pomeroyi DSS-3 phosphate transport system regulatory protein PhoU YP_167187.1 2081732 D 246200 CDS YP_167188.1 56696826 3193549 2082449..2083138 1 NC_003911.11 identified by similarity to SP:P08402; match to protein family HMM PF00072; match to protein family HMM PF00486; phosphate regulon transcriptional regulatory protein PhoB 2083138 phoB 3193549 phoB Ruegeria pomeroyi DSS-3 phosphate regulon transcriptional regulatory protein PhoB YP_167188.1 2082449 D 246200 CDS YP_167189.1 56696827 3192743 complement(2083157..2084068) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2084068 3192743 SPO1954 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167189.1 2083157 R 246200 CDS YP_167190.1 56696828 3192934 2084084..2085394 1 NC_003911.11 identified by similarity to SP:Q92947; match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF02771; glutaryl-CoA dehydrogenase 2085394 gcdH 3192934 gcdH Ruegeria pomeroyi DSS-3 glutaryl-CoA dehydrogenase YP_167190.1 2084084 D 246200 CDS YP_167191.1 56696829 3193371 2085537..2087285 1 NC_003911.11 identified by match to protein family HMM PF00916; match to protein family HMM PF01740; match to protein family HMM TIGR00815; sulfate permease 2087285 sulP 3193371 sulP Ruegeria pomeroyi DSS-3 sulfate permease YP_167191.1 2085537 D 246200 CDS YP_167192.1 56696830 3192968 2087518..2088288 1 NC_003911.11 identified by similarity to GB:AAR05249.1; match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2088288 3192968 SPO1957 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_167192.1 2087518 D 246200 CDS YP_167193.1 56696831 3192914 complement(2088285..2089154) 1 NC_003911.11 identified by similarity to SP:P23911; match to protein family HMM PF02551; match to protein family HMM TIGR00189; acyl-CoA thioesterase 2089154 3192914 SPO1958 Ruegeria pomeroyi DSS-3 acyl-CoA thioesterase YP_167193.1 2088285 R 246200 CDS YP_167194.1 56696832 3193701 complement(2089171..2091132) 1 NC_003911.11 AcsA; in Sinorhizobium meliloti this enzyme is required for acetoacetate activation; similar to acetyl-CoA synthase; acetoacetyl-CoA synthetase 2091132 3193701 SPO1959 Ruegeria pomeroyi DSS-3 acetoacetyl-CoA synthetase YP_167194.1 2089171 R 246200 CDS YP_167195.1 56696833 3193532 complement(2091123..2092358) 1 NC_003911.11 identified by match to protein family HMM PF00144; beta-lactamase 2092358 3193532 SPO1960 Ruegeria pomeroyi DSS-3 beta-lactamase YP_167195.1 2091123 R 246200 CDS YP_167196.1 56696834 3193069 complement(2092464..2093234) 1 NC_003911.11 identified by match to protein family HMM PF01614; IclR family transcriptional regulator 2093234 3193069 SPO1961 Ruegeria pomeroyi DSS-3 IclR family transcriptional regulator YP_167196.1 2092464 R 246200 CDS YP_167197.1 56696835 3193362 complement(2093261..2094289) 1 NC_003911.11 identified by match to protein family HMM PF01636; phosphotransferase 2094289 3193362 SPO1962 Ruegeria pomeroyi DSS-3 phosphotransferase YP_167197.1 2093261 R 246200 CDS YP_167198.1 56696836 3194758 complement(2094300..2094950) 1 NC_003911.11 identified by match to protein family HMM PF00300; phosphoglycerate mutase 2094950 3194758 SPO1963 Ruegeria pomeroyi DSS-3 phosphoglycerate mutase YP_167198.1 2094300 R 246200 CDS YP_167199.1 56696837 3192749 complement(2094954..2095955) 1 NC_003911.11 identified by similarity to GB:AAL02322.2; hypothetical protein 2095955 3192749 SPO1964 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167199.1 2094954 R 246200 CDS YP_167200.1 56696838 3193695 complement(2095969..2096898) 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2096898 3193695 SPO1965 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_167200.1 2095969 R 246200 CDS YP_167201.1 56696839 3192838 complement(2096909..2097727) 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2097727 3192838 SPO1966 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_167201.1 2096909 R 246200 CDS YP_167202.1 56696840 3192803 complement(2097737..2098852) 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF02771; acyl-CoA dehydrogenase 2098852 3192803 SPO1967 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_167202.1 2097737 R 246200 CDS YP_167203.1 56696841 3192936 complement(2098858..2100015) 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 2100015 3192936 SPO1968 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_167203.1 2098858 R 246200 CDS YP_167204.1 56696842 3193674 2100154..2101146 1 NC_003911.11 identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase 2101146 3193674 SPO1969 Ruegeria pomeroyi DSS-3 zinc-binding dehydrogenase oxidoreductase YP_167204.1 2100154 D 246200 CDS YP_167205.1 56696843 3193170 complement(2101153..2101809) 1 NC_003911.11 identified by match to protein family HMM PF00300; phosphoglycerate mutase 2101809 3193170 SPO1970 Ruegeria pomeroyi DSS-3 phosphoglycerate mutase YP_167205.1 2101153 R 246200 CDS YP_167206.1 56696844 3193616 2101866..2102690 1 NC_003911.11 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 2102690 3193616 SPO1971 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_167206.1 2101866 D 246200 CDS YP_167207.1 56696845 3193445 2102697..2103203 1 NC_003911.11 identified by similarity to SP:P25200; match to protein family HMM PF01575; nodulation protein N 2103203 3193445 SPO1972 Ruegeria pomeroyi DSS-3 nodulation protein N YP_167207.1 2102697 D 246200 CDS YP_167208.1 56696846 3193440 2103300..2103752 1 NC_003911.11 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis; 3-dehydroquinate dehydratase 2103752 aroQ 3193440 aroQ Ruegeria pomeroyi DSS-3 3-dehydroquinate dehydratase YP_167208.1 2103300 D 246200 CDS YP_167209.1 56696847 3193044 2103755..2104504 1 NC_003911.11 identified by match to protein family HMM PF00196; match to protein family HMM PF03472; LuxR family transcriptional regulator 2104504 3193044 SPO1974 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_167209.1 2103755 D 246200 CDS YP_167210.1 56696848 3192723 complement(2104998..2105873) 1 NC_003911.11 EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu; elongation factor Ts 2105873 tsf 3192723 tsf Ruegeria pomeroyi DSS-3 elongation factor Ts YP_167210.1 2104998 R 246200 CDS YP_167211.1 56696849 3192960 complement(2105951..2106724) 1 NC_003911.11 one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit; 30S ribosomal protein S2 2106724 rpsB 3192960 rpsB Ruegeria pomeroyi DSS-3 30S ribosomal protein S2 YP_167211.1 2105951 R 246200 CDS YP_167212.1 56696850 3192745 2107034..2108089 1 NC_003911.11 hypothetical protein 2108089 3192745 SPO1977 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167212.1 2107034 D 246200 CDS YP_167213.1 56696851 3195265 2108083..2109255 1 NC_003911.11 hypothetical protein 2109255 3195265 SPO1978 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167213.1 2108083 D 246200 CDS YP_167214.1 56696852 3193119 complement(2109260..2110093) 1 NC_003911.11 identified by match to protein family HMM PF01553; acyltransferase 2110093 3193119 SPO1979 Ruegeria pomeroyi DSS-3 acyltransferase YP_167214.1 2109260 R 246200 CDS YP_167215.1 56696853 3193154 complement(2110096..2110851) 1 NC_003911.11 identified by similarity to PIR:AB3477; hypothetical protein 2110851 3193154 SPO1980 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167215.1 2110096 R 246200 CDS YP_167216.1 56696854 3194789 complement(2110844..2110963) 1 NC_003911.11 hypothetical protein 2110963 3194789 SPO1981 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167216.1 2110844 R 246200 CDS YP_167217.1 56696856 3194201 complement(2110960..2111199) 1 NC_003911.11 hypothetical protein 2111199 3194201 SPO1982 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167217.1 2110960 R 246200 CDS YP_167218.1 56696855 3193572 2111191..2111787 1 NC_003911.11 identified by similarity to PIR:AB3305; hypothetical protein 2111787 3193572 SPO1983 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167218.1 2111191 D 246200 CDS YP_167219.1 56696857 3193622 complement(2111788..2113041) 1 NC_003911.11 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase 2113041 proA 3193622 proA Ruegeria pomeroyi DSS-3 gamma-glutamyl phosphate reductase YP_167219.1 2111788 R 246200 CDS YP_167220.1 56696858 3193117 complement(2113096..2114202) 1 NC_003911.11 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase 2114202 proB 3193117 proB Ruegeria pomeroyi DSS-3 gamma-glutamyl kinase YP_167220.1 2113096 R 246200 CDS YP_167221.1 56696859 3193499 complement(2114190..2115224) 1 NC_003911.11 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE 2115224 obgE 3193499 obgE Ruegeria pomeroyi DSS-3 GTPase ObgE YP_167221.1 2114190 R 246200 CDS YP_167222.1 56696861 3193182 complement(2115261..2115797) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 2115797 3193182 SPO1987 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167222.1 2115261 R 246200 CDS YP_167223.1 56696860 3192898 complement(2115794..2116474) 1 NC_003911.11 identified by match to protein family HMM PF01810; amino acid transporter LysE 2116474 3192898 SPO1988 Ruegeria pomeroyi DSS-3 amino acid transporter LysE YP_167223.1 2115794 R 246200 CDS YP_167224.1 56696862 3195614 complement(2116505..2116774) 1 NC_003911.11 involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 2116774 rpmA 3195614 rpmA Ruegeria pomeroyi DSS-3 50S ribosomal protein L27 YP_167224.1 2116505 R 246200 CDS YP_167225.1 56696863 3193713 complement(2116786..2117367) 1 NC_003911.11 fusion of ribosomal protein L21 and COG3743; 50S ribosomal protein L21 2117367 rplU 3193713 rplU Ruegeria pomeroyi DSS-3 50S ribosomal protein L21 YP_167225.1 2116786 R 246200 CDS YP_167226.1 56696864 3195563 complement(2117632..2118438) 1 NC_003911.11 hypothetical protein 2118438 3195563 SPO1991 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167226.1 2117632 R 246200 CDS YP_167227.1 56696865 3192966 complement(2118435..2119274) 1 NC_003911.11 hypothetical protein 2119274 3192966 SPO1992 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167227.1 2118435 R 246200 CDS YP_167228.1 56696866 3194056 complement(2119882..2121195) 1 NC_003911.11 identified by match to protein family HMM PF00529; match to protein family HMM TIGR01843; HlyD family type I secretion membrane fusion protein 2121195 3194056 SPO1994 Ruegeria pomeroyi DSS-3 HlyD family type I secretion membrane fusion protein YP_167228.1 2119882 R 246200 CDS YP_167229.1 56696867 3192680 complement(2121199..2123004) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter ATP-binding protein/permease 2123004 3192680 SPO1995 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein/permease YP_167229.1 2121199 R 246200 CDS YP_167230.1 56696868 3194745 complement(2123136..2123981) 1 NC_003911.11 identified by similarity to GB:CAE79871.1; hypothetical protein 2123981 3194745 SPO1996 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167230.1 2123136 R 246200 CDS YP_167231.1 56696869 3193524 2123980..2124903 1 NC_003911.11 hypothetical protein 2124903 3193524 SPO1997 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167231.1 2123980 D 246200 CDS YP_167232.1 56696870 3195734 2124900..2125643 1 NC_003911.11 hypothetical protein 2125643 3195734 SPO1998 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167232.1 2124900 D 246200 CDS YP_167233.1 56696871 3193334 complement(2125795..2128956) 1 NC_003911.11 hypothetical protein 2128956 3193334 SPO1999 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167233.1 2125795 R 246200 CDS YP_167234.1 56696872 3193577 complement(2129470..2129823) 1 NC_003911.11 identified by match to protein family HMM PF01042; endoribonuclease L-PSP 2129823 3193577 SPO2000 Ruegeria pomeroyi DSS-3 endoribonuclease L-PSP YP_167234.1 2129470 R 246200 CDS YP_167235.1 56696873 3193574 complement(2129839..2130939) 1 NC_003911.11 identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding 2130939 3193574 SPO2001 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_167235.1 2129839 R 246200 CDS YP_167236.1 56696874 3192741 complement(2130936..2131961) 1 NC_003911.11 identified by similarity to SP:Q48935; match to protein family HMM PF00850; acetylpolyamine aminohydrolase 2131961 3192741 SPO2002 Ruegeria pomeroyi DSS-3 acetylpolyamine aminohydrolase YP_167236.1 2130936 R 246200 CDS YP_167237.1 56696875 3193588 complement(2131958..2132437) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 2132437 3193588 SPO2003 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167237.1 2131958 R 246200 CDS YP_167238.1 56696876 3193552 complement(2132437..2133363) 1 NC_003911.11 identified by similarity to GB:BAB47761.1; match to protein family HMM PF05853; hypothetical protein 2133363 3193552 SPO2004 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167238.1 2132437 R 246200 CDS YP_167239.1 56696877 3192725 complement(2133365..2134696) 1 NC_003911.11 identified by match to protein family HMM PF00202; class III aminotransferase 2134696 3192725 SPO2005 Ruegeria pomeroyi DSS-3 class III aminotransferase YP_167239.1 2133365 R 246200 CDS YP_167240.1 56696878 3195227 complement(2134698..2135774) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01187; spermidine/putrescine ABC transporter ATP-binding protein 2135774 3195227 SPO2006 Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter ATP-binding protein YP_167240.1 2134698 R 246200 CDS YP_167241.1 56696879 3192716 complement(2135835..2136986) 1 NC_003911.11 identified by match to protein family HMM PF01547; match to protein family HMM TIGR01409; spermidine/putrescine ABC transporter substrate-binding protein 2136986 3192716 SPO2007 Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter substrate-binding protein YP_167241.1 2135835 R 246200 CDS YP_167242.1 56696880 3192658 complement(2137028..2137813) 1 NC_003911.11 identified by similarity to SP:P23859; match to protein family HMM PF00528; spermidine/putrescine ABC transporter permease 2137813 3192658 SPO2008 Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter permease YP_167242.1 2137028 R 246200 CDS YP_167243.1 56696881 3193121 complement(2137813..2138730) 1 NC_003911.11 Assignment based partly on membership in spermidine/putrescine ABC transporter gene cluster; identified by match to protein family HMM PF00528; spermidine/putrescine ABC transporter permease 2138730 3193121 SPO2009 Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter permease YP_167243.1 2137813 R 246200 CDS YP_167244.1 56696882 3193266 2138773..2139741 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2139741 3193266 SPO2010 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167244.1 2138773 D 246200 CDS YP_167245.1 56696883 3193590 2140917..2142413 1 NC_003911.11 hypothetical protein 2142413 3193590 SPO2013 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167245.1 2140917 D 246200 CDS YP_167246.1 56696884 3193329 complement(2142515..2143735) 1 NC_003911.11 identified by match to protein family HMM PF00266; match to protein family HMM TIGR01979; cysteine desulfurase 2143735 sufS 3193329 sufS Ruegeria pomeroyi DSS-3 cysteine desulfurase YP_167246.1 2142515 R 246200 CDS YP_167247.1 56696885 3194782 complement(2143728..2144315) 1 NC_003911.11 hypothetical protein 2144315 3194782 SPO2015 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167247.1 2143728 R 246200 CDS YP_167248.1 56696886 3193019 complement(2144312..2144797) 1 NC_003911.11 hypothetical protein 2144797 3193019 SPO2016 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167248.1 2144312 R 246200 CDS YP_167249.1 56696887 3193302 complement(2144797..2146077) 1 NC_003911.11 identified by match to protein family HMM PF01458; match to protein family HMM TIGR01981; FeS assembly protein SufD 2146077 3193302 SPO2017 Ruegeria pomeroyi DSS-3 FeS assembly protein SufD YP_167249.1 2144797 R 246200 CDS YP_167250.1 56696888 3193375 complement(2146077..2146832) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01978; FeS assembly ATPase SufC 2146832 sufC 3193375 sufC Ruegeria pomeroyi DSS-3 FeS assembly ATPase SufC YP_167250.1 2146077 R 246200 CDS YP_167251.1 56696889 3193133 complement(2146845..2147681) 1 NC_003911.11 identified by similarity to GB:AAA16052.1; exoV domain-containing protein 2147681 3193133 SPO2019 Ruegeria pomeroyi DSS-3 exoV domain-containing protein YP_167251.1 2146845 R 246200 CDS YP_167252.1 56696890 3192886 complement(2147683..2148612) 1 NC_003911.11 identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 2148612 3192886 SPO2020 Ruegeria pomeroyi DSS-3 FkbM family methyltransferase YP_167252.1 2147683 R 246200 CDS YP_167253.1 56696891 3193078 complement(2148629..2148943) 1 NC_003911.11 identified by similarity to SP:Q8D461; match to protein family HMM PF01906; hypothetical protein 2148943 3193078 SPO2021 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167253.1 2148629 R 246200 CDS YP_167254.1 56696892 3192961 complement(2148971..2149576) 1 NC_003911.11 hypothetical protein 2149576 3192961 SPO2022 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167254.1 2148971 R 246200 CDS YP_167255.1 56696893 3193051 complement(2149615..2151135) 1 NC_003911.11 with SufCD activates cysteine desulfurase SufS; cysteine desulfurase 2151135 sufB 3193051 sufB Ruegeria pomeroyi DSS-3 cysteine desulfurase YP_167255.1 2149615 R 246200 CDS YP_167256.1 56696894 3193530 complement(2152297..2152755) 1 NC_003911.11 identified by similarity to GB:AAN17744.1; match to protein family HMM PF02082; match to protein family HMM TIGR00738; iron-sulfur cluster assembly transcription factor IscR 2152755 3193530 SPO2025 Ruegeria pomeroyi DSS-3 iron-sulfur cluster assembly transcription factor IscR YP_167256.1 2152297 R 246200 CDS YP_167257.1 56696895 3193991 2152941..2153594 1 NC_003911.11 identified by similarity to GB:BAB47692.1; hypothetical protein 2153594 3193991 SPO2026 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167257.1 2152941 D 246200 CDS YP_167258.1 56696896 3194779 2153594..2153833 1 NC_003911.11 hypothetical protein 2153833 3194779 SPO2027 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167258.1 2153594 D 246200 CDS YP_167259.1 56696897 3193187 2153830..2154990 1 NC_003911.11 identified by match to protein family HMM PF01966; HD domain-containing protein 2154990 3193187 SPO2028 Ruegeria pomeroyi DSS-3 HD domain-containing protein YP_167259.1 2153830 D 246200 CDS YP_167260.1 56696898 3193636 complement(2155218..2156012) 1 NC_003911.11 identified by match to protein family HMM PF00310; glutamine amidotransferase 2156012 3193636 SPO2029 Ruegeria pomeroyi DSS-3 glutamine amidotransferase YP_167260.1 2155218 R 246200 CDS YP_167261.1 56696899 3193155 2156239..2156574 1 NC_003911.11 identified by similarity to SP:P23895; match to protein family HMM PF00893; SMR family multidrug efflux pump 2156574 3193155 SPO2030 Ruegeria pomeroyi DSS-3 SMR family multidrug efflux pump YP_167261.1 2156239 D 246200 CDS YP_167262.1 56696900 3193107 2156688..2158508 1 NC_003911.11 identified by match to protein family HMM PF00009; match to protein family HMM PF00679; match to protein family HMM PF03144; match to protein family HMM TIGR00231; match to protein family HMM TIGR01394; GTP-binding protein TypA 2158508 typA 3193107 typA Ruegeria pomeroyi DSS-3 GTP-binding protein TypA YP_167262.1 2156688 D 246200 CDS YP_167263.1 56696901 3192791 complement(2158606..2158893) 1 NC_003911.11 identified by similarity to GB:CAC41768.1; match to protein family HMM PF07045; hypothetical protein 2158893 3192791 SPO2032 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167263.1 2158606 R 246200 CDS YP_167264.1 56696902 3195191 complement(2158898..2161570) 1 NC_003911.11 Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; alanyl-tRNA synthetase 2161570 alaS 3195191 alaS Ruegeria pomeroyi DSS-3 alanyl-tRNA synthetase YP_167264.1 2158898 R 246200 CDS YP_167265.1 56696903 3193665 complement(2161731..2162774) 1 NC_003911.11 catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs; recombinase A 2162774 recA 3193665 recA Ruegeria pomeroyi DSS-3 recombinase A YP_167265.1 2161731 R 246200 CDS YP_167266.1 56696904 3193654 2162985..2163578 1 NC_003911.11 hypothetical protein 2163578 3193654 SPO2035 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167266.1 2162985 D 246200 CDS YP_167267.1 56696905 3193689 complement(2163585..2165891) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF02518; match to protein family HMM TIGR00229; sensory box sensor histidine kianse/response regulator 2165891 3193689 SPO2036 Ruegeria pomeroyi DSS-3 sensory box sensor histidine kianse/response regulator YP_167267.1 2163585 R 246200 CDS YP_167268.1 56696906 3193597 complement(2165997..2167172) 1 NC_003911.11 identified by match to protein family HMM PF01189; NOL1/NOP2/sun family protein 2167172 3193597 SPO2037 Ruegeria pomeroyi DSS-3 NOL1/NOP2/sun family protein YP_167268.1 2165997 R 246200 CDS YP_167269.1 56696907 3195226 complement(2167176..2167961) 1 NC_003911.11 identified by match to protein family HMM PF00753; metallo-beta-lactamase 2167961 3195226 SPO2038 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_167269.1 2167176 R 246200 CDS YP_167270.1 56696908 3195341 complement(2167961..2169409) 1 NC_003911.11 identified by match to protein family HMM PF00478; match to protein family HMM PF00571; match to protein family HMM TIGR01302; inosine-5'-monophosphate dehydrogenase 2169409 guaB 3195341 guaB Ruegeria pomeroyi DSS-3 inosine-5'-monophosphate dehydrogenase YP_167270.1 2167961 R 246200 CDS YP_167271.1 56696909 3193159 2169594..2170751 1 NC_003911.11 identified by match to protein family HMM PF02515; CaiB/BaiF family protein 2170751 3193159 SPO2040 Ruegeria pomeroyi DSS-3 CaiB/BaiF family protein YP_167271.1 2169594 D 246200 CDS YP_167272.1 56696910 3192814 2170882..2172921 1 NC_003911.11 identified by match to protein family HMM PF00111; (Fe-S)-binding protein 2172921 3192814 SPO2041 Ruegeria pomeroyi DSS-3 (Fe-S)-binding protein YP_167272.1 2170882 D 246200 CDS YP_167273.1 56696911 3193585 2172943..2173800 1 NC_003911.11 identified by match to protein family HMM PF01209; UbiE/COQ5 family methlytransferase 2173800 3193585 SPO2042 Ruegeria pomeroyi DSS-3 UbiE/COQ5 family methlytransferase YP_167273.1 2172943 D 246200 CDS YP_167274.1 56696912 3193611 2174023..2174442 1 NC_003911.11 lipoprotein 2174442 3193611 SPO2044 Ruegeria pomeroyi DSS-3 lipoprotein YP_167274.1 2174023 D 246200 CDS YP_167275.1 56696913 3195206 complement(2174589..2176208) 1 NC_003911.11 identified by similarity to SP:Q00594; 3-methylmercaptopropionyl-CoA ligase 2176208 dmdB 3195206 dmdB Ruegeria pomeroyi DSS-3 3-methylmercaptopropionyl-CoA ligase YP_167275.1 2174589 R 246200 CDS YP_167276.1 56696914 3195577 complement(2176372..2177991) 1 NC_003911.11 functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family; glucose-6-phosphate isomerase 2177991 pgi 3195577 pgi Ruegeria pomeroyi DSS-3 glucose-6-phosphate isomerase YP_167276.1 2176372 R 246200 CDS YP_167277.1 56696915 3194880 complement(2178001..2178672) 1 NC_003911.11 identified by match to protein family HMM TIGR01198; 6-phosphogluconolactonase 2178672 pgl 3194880 pgl Ruegeria pomeroyi DSS-3 6-phosphogluconolactonase YP_167277.1 2178001 R 246200 CDS YP_167278.1 56696916 3193693 complement(2178669..2180126) 1 NC_003911.11 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase 2180126 zwf-1 3193693 zwf-1 Ruegeria pomeroyi DSS-3 glucose-6-phosphate 1-dehydrogenase YP_167278.1 2178669 R 246200 CDS YP_167279.1 56696917 3195256 2180180..2181238 1 NC_003911.11 identified by match to protein family HMM PF04055; radical SAM domain-containing protein 2181238 3195256 SPO2049 Ruegeria pomeroyi DSS-3 radical SAM domain-containing protein YP_167279.1 2180180 D 246200 CDS YP_167280.1 56696918 3192804 complement(2181311..2181580) 1 NC_003911.11 identified by similarity to SP:P12288; match to protein family HMM PF06233; Usg 2181580 3192804 SPO2050 Ruegeria pomeroyi DSS-3 Usg YP_167280.1 2181311 R 246200 CDS YP_167281.1 56696919 3193149 2181848..2184523 1 NC_003911.11 negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A 2184523 gyrA 3193149 gyrA Ruegeria pomeroyi DSS-3 DNA gyrase subunit A YP_167281.1 2181848 D 246200 CDS YP_167282.1 56696920 3194951 2184627..2184977 1 NC_003911.11 hypothetical protein 2184977 3194951 SPO2052 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167282.1 2184627 D 246200 CDS YP_167283.1 56696921 3193386 complement(2185071..2186540) 1 NC_003911.11 identified by match to protein family HMM PF02074; thermostable carboxypeptidase 2186540 3193386 SPO2053 Ruegeria pomeroyi DSS-3 thermostable carboxypeptidase YP_167283.1 2185071 R 246200 CDS YP_167284.1 56696922 3193327 complement(2186547..2187620) 1 NC_003911.11 identified by match to protein family HMM PF02628; cytochrome c oxidase assembly protein 2187620 3193327 SPO2054 Ruegeria pomeroyi DSS-3 cytochrome c oxidase assembly protein YP_167284.1 2186547 R 246200 CDS YP_167285.1 56696923 3193313 complement(2187757..2188503) 1 NC_003911.11 identified by match to protein family HMM PF00588; match to protein family HMM TIGR00050; RNA methyltransferase 2188503 3193313 SPO2055 Ruegeria pomeroyi DSS-3 RNA methyltransferase YP_167285.1 2187757 R 246200 CDS YP_167286.1 56696924 3194714 2188790..2189410 1 NC_003911.11 identified by similarity to SP:P39594; thiamine-phosphate pyrophosphorylase 2189410 3194714 SPO2056 Ruegeria pomeroyi DSS-3 thiamine-phosphate pyrophosphorylase YP_167286.1 2188790 D 246200 CDS YP_167287.1 56696925 3193029 complement(2189419..2190591) 1 NC_003911.11 hypothetical protein 2190591 3193029 SPO2057 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167287.1 2189419 R 246200 CDS YP_167288.1 56696926 3193461 2190590..2191357 1 NC_003911.11 identified by similarity to GB:BAC89701.1; hypothetical protein 2191357 3193461 SPO2058 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167288.1 2190590 D 246200 CDS YP_167289.1 56696927 3193538 2191417..2192259 1 NC_003911.11 identified by match to protein family HMM PF02798; glutathione S-transferase 2192259 3193538 SPO2059 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_167289.1 2191417 D 246200 CDS YP_167290.1 56696928 3194812 2192314..2193207 1 NC_003911.11 identified by match to protein family HMM PF00294; PfkB family kinase 2193207 3194812 SPO2060 Ruegeria pomeroyi DSS-3 PfkB family kinase YP_167290.1 2192314 D 246200 CDS YP_167291.1 56696929 3193592 2193204..2194118 1 NC_003911.11 identified by match to protein family HMM PF04227; indigoidine synthase A family protein 2194118 3193592 SPO2061 Ruegeria pomeroyi DSS-3 indigoidine synthase A family protein YP_167291.1 2193204 D 246200 CDS YP_167292.1 56696930 3193433 2194196..2194870 1 NC_003911.11 identified by similarity to GB:AAQ61403.1; match to protein family HMM PF04367; hypothetical protein 2194870 3193433 SPO2062 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167292.1 2194196 D 246200 CDS YP_167293.1 56696931 3193283 2194867..2195373 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 2195373 3193283 SPO2063 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167293.1 2194867 D 246200 CDS YP_167294.1 56696932 3193098 complement(2195370..2196401) 1 NC_003911.11 identified by match to protein family HMM PF01734; patatin family phospholipase 2196401 3193098 SPO2064 Ruegeria pomeroyi DSS-3 patatin family phospholipase YP_167294.1 2195370 R 246200 CDS YP_167295.1 56696933 3193339 complement(2196494..2197267) 1 NC_003911.11 identified by similarity to SP:O86034; match to protein family HMM PF00106; match to protein family HMM TIGR01963; D-beta-hydroxybutyrate dehydrogenase 2197267 bdh-1 3193339 bdh-1 Ruegeria pomeroyi DSS-3 D-beta-hydroxybutyrate dehydrogenase YP_167295.1 2196494 R 246200 CDS YP_167296.1 56696934 3193685 2197677..2199491 1 NC_003911.11 identified by match to protein family HMM PF00496; ABC transporter substrate-binding protein 2199491 3193685 SPO2066 Ruegeria pomeroyi DSS-3 ABC transporter substrate-binding protein YP_167296.1 2197677 D 246200 CDS YP_167297.1 56696935 3193845 2199640..2199864 1 NC_003911.11 identified by similarity to GB:BAC46738.1; hypothetical protein 2199864 3193845 SPO2067 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167297.1 2199640 D 246200 CDS YP_167298.1 56696936 3193401 complement(2199868..2200491) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 2200491 3193401 SPO2068 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_167298.1 2199868 R 246200 CDS YP_167299.1 56696937 3193610 2200556..2202073 1 NC_003911.11 identified by similarity to GB:AAA92151.1; match to protein family HMM PF00501; benzoate-coenzyme A ligase 2202073 3193610 SPO2069 Ruegeria pomeroyi DSS-3 benzoate-coenzyme A ligase YP_167299.1 2200556 D 246200 CDS YP_167300.1 56696938 3193085 2202070..2202726 1 NC_003911.11 identified by match to protein family HMM PF01323; DSBA-like thioredoxin family protein 2202726 3193085 SPO2070 Ruegeria pomeroyi DSS-3 DSBA-like thioredoxin family protein YP_167300.1 2202070 D 246200 CDS YP_167301.1 56696939 3193264 2202805..2204013 1 NC_003911.11 identified by similarity to SP:P28246; match to protein family HMM PF00083; match to protein family HMM TIGR00710; Bcr/CflA subfamily drug resistance transporter 2204013 3193264 SPO2071 Ruegeria pomeroyi DSS-3 Bcr/CflA subfamily drug resistance transporter YP_167301.1 2202805 D 246200 CDS YP_167302.1 56696940 3193603 2204065..2205738 1 NC_003911.11 identified by match to protein family HMM PF00515; hypothetical protein 2205738 3193603 SPO2072 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167302.1 2204065 D 246200 CDS YP_167303.1 56696941 3193157 2205699..2206394 1 NC_003911.11 hypothetical protein 2206394 3193157 SPO2073 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167303.1 2205699 D 246200 CDS YP_167304.1 56696942 3193158 complement(2206464..2209892) 1 NC_003911.11 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF02559; match to protein family HMM PF03461; match to protein family HMM TIGR00580; transcription-repair coupling factor 2209892 mfd 3193158 mfd Ruegeria pomeroyi DSS-3 transcription-repair coupling factor YP_167304.1 2206464 R 246200 CDS YP_167305.1 56696943 3194746 complement(2209947..2210471) 1 NC_003911.11 identified by similarity to GB:AAL26882.1; hypothetical protein 2210471 3194746 SPO2075 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167305.1 2209947 R 246200 CDS YP_167306.1 56696944 3193195 2210595..2211593 1 NC_003911.11 catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase 2211593 hemB 3193195 hemB Ruegeria pomeroyi DSS-3 delta-aminolevulinic acid dehydratase YP_167306.1 2210595 D 246200 CDS YP_167307.1 56696945 3193725 2211735..2212307 1 NC_003911.11 twin-arginine translocation pathway signal sequence domain-containing protein 2212307 3193725 SPO2077 Ruegeria pomeroyi DSS-3 twin-arginine translocation pathway signal sequence domain-containing protein YP_167307.1 2211735 D 246200 CDS YP_167308.1 56696946 3192839 2212452..2214920 1 NC_003911.11 identified by similarity to SP:P07941; match to protein family HMM PF01804; penicillin amidase 2214920 3192839 SPO2078 Ruegeria pomeroyi DSS-3 penicillin amidase YP_167308.1 2212452 D 246200 CDS YP_167309.1 56696947 3193397 2214924..2216108 1 NC_003911.11 Na(+)/H(+) antiporter-like protein 2216108 3193397 SPO2079 Ruegeria pomeroyi DSS-3 Na(+)/H(+) antiporter-like protein YP_167309.1 2214924 D 246200 CDS YP_167310.1 56696948 3195610 complement(2216093..2217367) 1 NC_003911.11 identified by similarity to SP:P25519; match to protein family HMM TIGR00231; GTP-binding protein HflX 2217367 hflX 3195610 hflX Ruegeria pomeroyi DSS-3 GTP-binding protein HflX YP_167310.1 2216093 R 246200 CDS YP_167311.1 56696949 3193311 complement(2217364..2217603) 1 NC_003911.11 Stimulates the elongation of poly(A) tails; RNA-binding protein Hfq 2217603 hfq 3193311 hfq Ruegeria pomeroyi DSS-3 RNA-binding protein Hfq YP_167311.1 2217364 R 246200 CDS YP_167312.1 56696950 3193259 complement(2217741..2219276) 1 NC_003911.11 identified by similarity to SP:P21166; match to protein family HMM PF02386; Trk system potassium uptake protein TrkH 2219276 trkH-2 3193259 trkH-2 Ruegeria pomeroyi DSS-3 Trk system potassium uptake protein TrkH YP_167312.1 2217741 R 246200 CDS YP_167313.1 56696951 3192863 complement(2219276..2220652) 1 NC_003911.11 involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain; potassium transporter peripheral membrane protein 2220652 trkA 3192863 trkA Ruegeria pomeroyi DSS-3 potassium transporter peripheral membrane protein YP_167313.1 2219276 R 246200 CDS YP_167314.1 56696952 3192956 2220715..2221230 1 NC_003911.11 hypothetical protein 2221230 3192956 SPO2084 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167314.1 2220715 D 246200 CDS YP_167315.1 56696953 3192664 complement(2221246..2222658) 1 NC_003911.11 identified by similarity to SP:Q04849; match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954; match to protein family HMM TIGR01199; nitrogen assimilation regulatory protein NtrX 2222658 ntrX 3192664 ntrX Ruegeria pomeroyi DSS-3 nitrogen assimilation regulatory protein NtrX YP_167315.1 2221246 R 246200 CDS YP_167316.1 56696954 3192681 complement(2222655..2224940) 1 NC_003911.11 identified by similarity to SP:Q04850; match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; match to protein family HMM TIGR00229; nitrogen regulation protein ntrY 2224940 ntrY 3192681 ntrY Ruegeria pomeroyi DSS-3 nitrogen regulation protein ntrY YP_167316.1 2222655 R 246200 CDS YP_167317.1 56696955 3195357 complement(2225040..2226413) 1 NC_003911.11 identified by similarity to SP:P45671; match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954; match to protein family HMM TIGR01199; nitrogen regulation protein NtrC 2226413 ntrC 3195357 ntrC Ruegeria pomeroyi DSS-3 nitrogen regulation protein NtrC YP_167317.1 2225040 R 246200 CDS YP_167318.1 56696956 3193223 complement(2226413..2227492) 1 NC_003911.11 identified by similarity to SP:P09431; match to protein family HMM PF00512; match to protein family HMM PF02518; nitrogen regulation protein NtrB 2227492 ntrB 3193223 ntrB Ruegeria pomeroyi DSS-3 nitrogen regulation protein NtrB YP_167318.1 2226413 R 246200 CDS YP_167319.1 56696957 3193240 complement(2227489..2228472) 1 NC_003911.11 identified by similarity to SP:Q08111; match to protein family HMM PF01207; match to protein family HMM TIGR00737; tRNA-dihydrouridine synthase 2228472 3193240 SPO2089 Ruegeria pomeroyi DSS-3 tRNA-dihydrouridine synthase YP_167319.1 2227489 R 246200 CDS YP_167320.1 56696958 3193402 2228508..2229800 1 NC_003911.11 identified by similarity to GB:AAN30040.1; match to protein family HMM PF01128; match to protein family HMM PF02542; match to protein family HMM TIGR00151; match to protein family HMM TIGR00453; 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2229800 ispDF 3193402 ispDF Ruegeria pomeroyi DSS-3 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase YP_167320.1 2228508 D 246200 CDS YP_167321.1 56696959 3192901 2229797..2230294 1 NC_003911.11 identified by similarity to SP:P18200; match to protein family HMM PF04608; phosphatidylglycerophosphatase 2230294 3192901 SPO2091 Ruegeria pomeroyi DSS-3 phosphatidylglycerophosphatase YP_167321.1 2229797 D 246200 CDS YP_167322.1 56696960 3193111 2230291..2230770 1 NC_003911.11 identified by match to protein family HMM PF02464; match to protein family HMM TIGR00199; competence/damage inducible protein CinA 2230770 3193111 SPO2092 Ruegeria pomeroyi DSS-3 competence/damage inducible protein CinA YP_167322.1 2230291 D 246200 CDS YP_167323.1 56696961 3194760 2230811..2232106 1 NC_003911.11 identified by match to protein family HMM PF00909; match to protein family HMM TIGR00836; ammonium transporter 2232106 amt-1 3194760 amt-1 Ruegeria pomeroyi DSS-3 ammonium transporter YP_167323.1 2230811 D 246200 CDS YP_167324.1 56696962 3193351 complement(2232174..2232686) 1 NC_003911.11 identified by similarity to GB:AAK38651.1; ACT domain-containing protein 2232686 3193351 SPO2094 Ruegeria pomeroyi DSS-3 ACT domain-containing protein YP_167324.1 2232174 R 246200 CDS YP_167325.1 56696963 3193629 complement(2232782..2234077) 1 NC_003911.11 identified by match to protein family HMM PF03972; MmgE/PrpD family protein 2234077 3193629 SPO2095 Ruegeria pomeroyi DSS-3 MmgE/PrpD family protein YP_167325.1 2232782 R 246200 CDS YP_167326.1 56696964 3193710 complement(2234124..2234570) 1 NC_003911.11 identified by match to protein family HMM PF03654; aromatic-rich family protein 2234570 3193710 SPO2096 Ruegeria pomeroyi DSS-3 aromatic-rich family protein YP_167326.1 2234124 R 246200 CDS YP_167327.1 56696965 3194848 2234645..2235187 1 NC_003911.11 identified by similarity to SP:P37171; match to protein family HMM PF00156; match to protein family HMM TIGR01203; hypoxanthine phosphoribosyltransferase 2235187 hpt 3194848 hpt Ruegeria pomeroyi DSS-3 hypoxanthine phosphoribosyltransferase YP_167327.1 2234645 D 246200 CDS YP_167328.1 56696966 3192912 complement(2235249..2236100) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2236100 3192912 SPO2098 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167328.1 2235249 R 246200 CDS YP_167329.1 56696967 3192870 2236210..2236686 1 NC_003911.11 identified by similarity to SP:Q53142; match to protein family HMM PF01322; cytochrome c-554 2236686 cycF 3192870 cycF Ruegeria pomeroyi DSS-3 cytochrome c-554 YP_167329.1 2236210 D 246200 CDS YP_167330.1 56696968 3193411 2236745..2237629 1 NC_003911.11 identified by similarity to SP:Q53143; match to protein family HMM PF00034; diheme cytochrome c-type 2237629 cycG 3193411 cycG Ruegeria pomeroyi DSS-3 diheme cytochrome c-type YP_167330.1 2236745 D 246200 CDS YP_167331.1 56696969 3192825 complement(2237607..2238779) 1 NC_003911.11 identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase 2238779 3192825 SPO2101 Ruegeria pomeroyi DSS-3 amidohydrolase YP_167331.1 2237607 R 246200 CDS YP_167332.1 56696970 3193172 complement(2238776..2239726) 1 NC_003911.11 catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group; lipoyl synthase 2239726 lipA 3193172 lipA Ruegeria pomeroyi DSS-3 lipoyl synthase YP_167332.1 2238776 R 246200 CDS YP_167333.1 56696971 3193320 2239931..2240479 1 NC_003911.11 identified by similarity to PIR:S39907; match to protein family HMM PF00578; anti-oxidant AhpCTSA family protein 2240479 3193320 SPO2103 Ruegeria pomeroyi DSS-3 anti-oxidant AhpCTSA family protein YP_167333.1 2239931 D 246200 CDS YP_167334.1 56696972 3192864 2240640..2241104 1 NC_003911.11 identified by similarity to GB:AAK22261.1; hypothetical protein 2241104 3192864 SPO2104 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167334.1 2240640 D 246200 CDS YP_167335.1 56696973 3193609 complement(2241182..2242147) 1 NC_003911.11 identified by similarity to SP:P52677; match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2242147 3193609 SPO2105 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167335.1 2241182 R 246200 CDS YP_167336.1 56696974 3193011 complement(2242171..2243325) 1 NC_003911.11 identified by similarity to GB:CAE27296.1; hypothetical protein 2243325 3193011 SPO2106 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167336.1 2242171 R 246200 CDS YP_167337.1 56696975 3192855 2243536..2243877 1 NC_003911.11 hypothetical protein 2243877 3192855 SPO2107 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167337.1 2243536 D 246200 CDS YP_167338.1 56696976 3195647 complement(2243870..2245414) 1 NC_003911.11 identified by match to protein family HMM PF06253; trimethylamine methyltransferase 2245414 3195647 SPO2108 Ruegeria pomeroyi DSS-3 trimethylamine methyltransferase YP_167338.1 2243870 R 246200 CDS YP_167339.1 56696977 3193064 2245651..2247210 1 NC_003911.11 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase 2247210 guaA 3193064 guaA Ruegeria pomeroyi DSS-3 GMP synthase YP_167339.1 2245651 D 246200 CDS YP_167340.1 56696978 3193391 2247244..2248110 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 2248110 3193391 SPO2110 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167340.1 2247244 D 246200 CDS YP_167341.1 56696979 3193347 2248223..2249362 1 NC_003911.11 identified by match to protein family HMM PF03349; OmpP1/FadL/TodX family outer membrane transporter 2249362 3193347 SPO2111 Ruegeria pomeroyi DSS-3 OmpP1/FadL/TodX family outer membrane transporter YP_167341.1 2248223 D 246200 CDS YP_167342.1 56696980 3193460 2249417..2250316 1 NC_003911.11 identified by match to protein family HMM PF00892; transmembrane drug/metabolite transporter family protein 2250316 3193460 SPO2112 Ruegeria pomeroyi DSS-3 transmembrane drug/metabolite transporter family protein YP_167342.1 2249417 D 246200 CDS YP_167343.1 56696981 3192971 2250313..2251236 1 NC_003911.11 hypothetical protein 2251236 3192971 SPO2113 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167343.1 2250313 D 246200 CDS YP_167344.1 56696982 3193260 2251862..2252440 1 NC_003911.11 identified by match to protein family HMM PF00597; DedA family protein 2252440 3193260 SPO2116 Ruegeria pomeroyi DSS-3 DedA family protein YP_167344.1 2251862 D 246200 CDS YP_167345.1 56696983 3195631 2252440..2252901 1 NC_003911.11 identified by match to protein family HMM PF02600; DsbB family disulfide bond formation protein 2252901 3195631 SPO2117 Ruegeria pomeroyi DSS-3 DsbB family disulfide bond formation protein YP_167345.1 2252440 D 246200 CDS YP_167346.1 56696984 3195643 complement(2253001..2253426) 1 NC_003911.11 identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator 2253426 3195643 SPO2118 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_167346.1 2253001 R 246200 CDS YP_167347.1 56696985 3193436 2253447..2254460 1 NC_003911.11 identified by similarity to SP:Q59174; match to protein family HMM PF00491; match to protein family HMM TIGR01229; arginase 2254460 rocF 3193436 rocF Ruegeria pomeroyi DSS-3 arginase YP_167347.1 2253447 D 246200 CDS YP_167348.1 56696986 3194700 2254457..2255386 1 NC_003911.11 identified by match to protein family HMM PF02274; amidinotransferase 2255386 3194700 SPO2120 Ruegeria pomeroyi DSS-3 amidinotransferase YP_167348.1 2254457 D 246200 CDS YP_167349.1 56696987 3192981 2255383..2256447 1 NC_003911.11 catalyzes the formation of L-proline from L-ornithine; ornithine cyclodeaminase 2256447 arcB 3192981 arcB Ruegeria pomeroyi DSS-3 ornithine cyclodeaminase YP_167349.1 2255383 D 246200 CDS YP_167350.1 56696988 3192690 2256609..2256944 1 NC_003911.11 identified by match to protein family HMM PF03831; match to protein family HMM TIGR00686; alkylphosphonate utilization protein PhnA 2256944 phnA 3192690 phnA Ruegeria pomeroyi DSS-3 alkylphosphonate utilization protein PhnA YP_167350.1 2256609 D 246200 CDS YP_167351.1 56696989 3193103 complement(2256948..2257532) 1 NC_003911.11 identified by match to protein family HMM PF01844; HNH endonuclease 2257532 3193103 SPO2123 Ruegeria pomeroyi DSS-3 HNH endonuclease YP_167351.1 2256948 R 246200 CDS YP_167352.1 56696990 3192861 2257748..2258350 1 NC_003911.11 identified by match to protein family HMM PF00849; match to protein family HMM TIGR00093; RNA pseudouridylate synthase 2258350 3192861 SPO2124 Ruegeria pomeroyi DSS-3 RNA pseudouridylate synthase YP_167352.1 2257748 D 246200 CDS YP_167353.1 56696991 3193458 complement(2258355..2258852) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 2258852 3193458 SPO2125 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167353.1 2258355 R 246200 CDS YP_167354.1 56696992 3195484 complement(2258849..2259514) 1 NC_003911.11 identified by match to protein family HMM PF02230; phospholipase/carboxylesterase 2259514 3195484 SPO2126 Ruegeria pomeroyi DSS-3 phospholipase/carboxylesterase YP_167354.1 2258849 R 246200 CDS YP_167355.1 56696993 3193412 complement(2259511..2260143) 1 NC_003911.11 identified by match to protein family HMM PF00730; DNA-3-methyladenine glycosylase II 2260143 3193412 SPO2127 Ruegeria pomeroyi DSS-3 DNA-3-methyladenine glycosylase II YP_167355.1 2259511 R 246200 CDS YP_167356.1 56696994 3193805 2260247..2261464 1 NC_003911.11 identified by similarity to GB:CAE30241.1; transporter 2261464 3193805 SPO2128 Ruegeria pomeroyi DSS-3 transporter YP_167356.1 2260247 D 246200 CDS YP_167357.1 56696995 3194891 complement(2261595..2262377) 1 NC_003911.11 identified by similarity to PIR:F87495; hypothetical protein 2262377 3194891 SPO2129 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167357.1 2261595 R 246200 CDS YP_167358.1 56696996 3192780 complement(2262374..2264008) 1 NC_003911.11 catalyzes the formation of 2-isopropylmalate from 1-methyl-2-oxobutanoate and acetyl-CoA; alpha-isopropylmalate synthase 2264008 3192780 SPO2130 Ruegeria pomeroyi DSS-3 alpha-isopropylmalate synthase YP_167358.1 2262374 R 246200 CDS YP_167359.1 56696997 3193717 complement(2264124..2265521) 1 NC_003911.11 identified by similarity to SP:P21888; match to protein family HMM PF01406; match to protein family HMM TIGR00435; cysteinyl-tRNA synthetase 2265521 cysS 3193717 cysS Ruegeria pomeroyi DSS-3 cysteinyl-tRNA synthetase YP_167359.1 2264124 R 246200 CDS YP_167360.1 56696998 3192683 2265779..2266966 1 NC_003911.11 identified by similarity to SP:Q56232; match to protein family HMM PF00155; aspartate aminotransferase 2266966 aspC-3 3192683 aspC-3 Ruegeria pomeroyi DSS-3 aspartate aminotransferase YP_167360.1 2265779 D 246200 CDS YP_167361.1 56696999 3193812 complement(2267010..2267546) 1 NC_003911.11 identified by similarity to GB:AAL60203.1; hypothetical protein 2267546 3193812 SPO2133 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167361.1 2267010 R 246200 CDS YP_167362.1 56697000 3193504 2267949..2269493 1 NC_003911.11 identified by match to protein family HMM PF06253; trimethylamine methyltransferase 2269493 3193504 SPO2134 Ruegeria pomeroyi DSS-3 trimethylamine methyltransferase YP_167362.1 2267949 D 246200 CDS YP_167363.1 56697001 3193454 complement(2269551..2269796) 1 NC_003911.11 identified by similarity to GB:BAC50222.1; hypothetical protein 2269796 3193454 SPO2135 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167363.1 2269551 R 246200 CDS YP_167364.1 56697002 3192806 complement(2270351..2273995) 1 NC_003911.11 Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 2273995 nrdJ 3192806 nrdJ Ruegeria pomeroyi DSS-3 ribonucleotide-diphosphate reductase subunit alpha YP_167364.1 2270351 R 246200 CDS YP_167365.1 56697003 3195477 2274542..2274985 1 NC_003911.11 lipoprotein 2274985 3195477 SPO2137 Ruegeria pomeroyi DSS-3 lipoprotein YP_167365.1 2274542 D 246200 CDS YP_167366.1 56697004 3194744 complement(2275116..2275583) 1 NC_003911.11 identified by similarity to GB:CAE27967.1; match to protein family HMM PF02643; hypothetical protein 2275583 3194744 SPO2139 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167366.1 2275116 R 246200 CDS YP_167367.1 56697005 3193503 complement(2275594..2276121) 1 NC_003911.11 identified by similarity to SP:P32081; similarity to SP:P36997; match to protein family HMM PF00313; cold shock DNA-binding domain-containing protein 2276121 3193503 SPO2140 Ruegeria pomeroyi DSS-3 cold shock DNA-binding domain-containing protein YP_167367.1 2275594 R 246200 CDS YP_167368.1 56697006 3193231 complement(2276242..2276871) 1 NC_003911.11 identified by match to protein family HMM PF01243; pyridoxamine 5''-phosphate oxidase 2276871 3193231 SPO2141 Ruegeria pomeroyi DSS-3 pyridoxamine 5''-phosphate oxidase YP_167368.1 2276242 R 246200 CDS YP_167369.1 56697007 3192884 2276982..2277788 1 NC_003911.11 Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-ACP reductase 2277788 fabI-2 3192884 fabI-2 Ruegeria pomeroyi DSS-3 enoyl-ACP reductase YP_167369.1 2276982 D 246200 CDS YP_167370.1 56697008 3192842 2277802..2278317 1 NC_003911.11 catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively; xanthine-guanine phosphoribosyltransferase 2278317 gpt 3192842 gpt Ruegeria pomeroyi DSS-3 xanthine-guanine phosphoribosyltransferase YP_167370.1 2277802 D 246200 CDS YP_167371.1 56697009 3193068 2278388..2279563 1 NC_003911.11 identified by match to protein family HMM PF00155; hypothetical protein 2279563 3193068 SPO2144 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167371.1 2278388 D 246200 CDS YP_167372.1 56697010 3192930 2279655..2281499 1 NC_003911.11 identified by similarity to PIR:T46851; hypothetical protein 2281499 3192930 SPO2145 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167372.1 2279655 D 246200 CDS YP_167373.1 56697011 3192794 2281509..2283020 1 NC_003911.11 with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine; anthranilate synthase component I 2283020 trpE 3192794 trpE Ruegeria pomeroyi DSS-3 anthranilate synthase component I YP_167373.1 2281509 D 246200 CDS YP_167374.1 56697012 3193480 2283020..2283544 1 NC_003911.11 identified by similarity to GB:CAC47284.1; match to protein family HMM PF05962; hypothetical protein 2283544 3193480 SPO2147 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167374.1 2283020 D 246200 CDS YP_167375.1 56697013 3192649 complement(2283631..2285076) 1 NC_003911.11 hypothetical protein 2285076 3192649 SPO2148 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167375.1 2283631 R 246200 CDS YP_167376.1 56697014 3192657 2285237..2285818 1 NC_003911.11 TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity; anthranilate synthase component II 2285818 trpG 3192657 trpG Ruegeria pomeroyi DSS-3 anthranilate synthase component II YP_167376.1 2285237 D 246200 CDS YP_167377.1 56697015 3192757 2285815..2286834 1 NC_003911.11 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate; anthranilate phosphoribosyltransferase 2286834 trpD 3192757 trpD Ruegeria pomeroyi DSS-3 anthranilate phosphoribosyltransferase YP_167377.1 2285815 D 246200 CDS YP_167378.1 56697016 3194776 2286831..2287643 1 NC_003911.11 involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water; indole-3-glycerol phosphate synthase 2287643 trpC 3194776 trpC Ruegeria pomeroyi DSS-3 indole-3-glycerol phosphate synthase YP_167378.1 2286831 D 246200 CDS YP_167379.1 56697017 3192710 2287643..2288116 1 NC_003911.11 MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis; molybdenum cofactor biosynthesis protein MoaC 2288116 moaC 3192710 moaC Ruegeria pomeroyi DSS-3 molybdenum cofactor biosynthesis protein MoaC YP_167379.1 2287643 D 246200 CDS YP_167380.1 56697018 3195433 2288113..2289282 1 NC_003911.11 identified by match to protein family HMM PF00994; match to protein family HMM PF03453; match to protein family HMM PF03454; match to protein family HMM TIGR00177; molybdenum cofactor biosynthesis protein A 2289282 moaA 3195433 moaA Ruegeria pomeroyi DSS-3 molybdenum cofactor biosynthesis protein A YP_167380.1 2288113 D 246200 CDS YP_167381.1 56697019 3193214 2289362..2290057 1 NC_003911.11 Represses a number of genes involved in the response to DNA damage; LexA repressor 2290057 lexA 3193214 lexA Ruegeria pomeroyi DSS-3 LexA repressor YP_167381.1 2289362 D 246200 CDS YP_167382.1 56697020 3193627 complement(2290065..2292095) 1 NC_003911.11 competence protein 2292095 3193627 SPO2155 Ruegeria pomeroyi DSS-3 competence protein YP_167382.1 2290065 R 246200 CDS YP_167383.1 56697021 3192862 2292177..2293583 1 NC_003911.11 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 2293583 gltX 3192862 gltX Ruegeria pomeroyi DSS-3 glutamyl-tRNA synthetase YP_167383.1 2292177 D 246200 CDS YP_167384.1 56697022 3193605 2293707..2295002 1 NC_003911.11 identified by similarity to SP:P00891; match to protein family HMM PF00285; match to protein family HMM TIGR01798; citrate synthase I 2295002 gltA 3193605 gltA Ruegeria pomeroyi DSS-3 citrate synthase I YP_167384.1 2293707 D 246200 CDS YP_167385.1 56697023 3196471 2295317..2296498 1 NC_003911.11 hypothetical protein 2296498 3196471 SPO2158 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167385.1 2295317 D 246200 CDS YP_167386.1 56697024 3193372 complement(2296512..2297696) 1 NC_003911.11 identified by similarity to PIR:B97447; match to protein family HMM PF04055; radical SAM domain-containing protein 2297696 3193372 SPO2159 Ruegeria pomeroyi DSS-3 radical SAM domain-containing protein YP_167386.1 2296512 R 246200 CDS YP_167387.1 56697025 3193365 2297868..2298566 1 NC_003911.11 identified by similarity to SP:O93657; match to protein family HMM PF02310; match to protein family HMM PF02607; corrinoid methyltransferase 2298566 3193365 SPO2160 Ruegeria pomeroyi DSS-3 corrinoid methyltransferase YP_167387.1 2297868 D 246200 CDS YP_167388.1 56697026 3192967 2298744..2299784 1 NC_003911.11 identified by similarity to PIR:T03518; hypothetical protein 2299784 3192967 SPO2161 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167388.1 2298744 D 246200 CDS YP_167389.1 56697027 3193686 2299870..2300532 1 NC_003911.11 identified by similarity to GB:BAB48654.1; hypothetical protein 2300532 3193686 SPO2162 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167389.1 2299870 D 246200 CDS YP_167390.1 56697029 3193243 complement(2300559..2301188) 1 NC_003911.11 identified by similarity to PIR:AC3193; hypothetical protein 2301188 3193243 SPO2163 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167390.1 2300559 R 246200 CDS YP_167391.1 56697028 3193342 2301282..2301992 1 NC_003911.11 identified by similarity to PIR:AB3193; hypothetical protein 2301992 3193342 SPO2164 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167391.1 2301282 D 246200 CDS YP_167392.1 56697030 3195531 complement(2301997..2302407) 1 NC_003911.11 identified by match to protein family HMM PF02657; Fe-S metabolism associated family protein 2302407 3195531 SPO2165 Ruegeria pomeroyi DSS-3 Fe-S metabolism associated family protein YP_167392.1 2301997 R 246200 CDS YP_167393.1 56697031 3192718 2302553..2303077 1 NC_003911.11 lipoprotein 2303077 3192718 SPO2166 Ruegeria pomeroyi DSS-3 lipoprotein YP_167393.1 2302553 D 246200 CDS YP_167394.1 56697032 3193200 complement(2303155..2304312) 1 NC_003911.11 identified by match to protein family HMM PF01612; match to protein family HMM TIGR01388; ribonuclease D 2304312 rnd 3193200 rnd Ruegeria pomeroyi DSS-3 ribonuclease D YP_167394.1 2303155 R 246200 CDS YP_167395.1 56697033 3193498 complement(2304432..2305028) 1 NC_003911.11 identified by similarity to SP:P08179; match to protein family HMM PF00551; match to protein family HMM TIGR00639; phosphoribosylglycinamide formyltransferase 2305028 purN 3193498 purN Ruegeria pomeroyi DSS-3 phosphoribosylglycinamide formyltransferase YP_167395.1 2304432 R 246200 CDS YP_167396.1 56697034 3193262 complement(2305025..2306071) 1 NC_003911.11 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase 2306071 purM 3193262 purM Ruegeria pomeroyi DSS-3 phosphoribosylaminoimidazole synthetase YP_167396.1 2305025 R 246200 CDS YP_167397.1 56697035 3194651 complement(2306176..2307150) 1 NC_003911.11 identified by similarity to GB:AAR21562.1; match to protein family HMM PF00753; match to protein family HMM TIGR01409; metallo-beta-lactamase 2307150 3194651 SPO2170 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_167397.1 2306176 R 246200 CDS YP_167398.1 56697036 3193209 2307258..2308181 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2308181 3193209 SPO2171 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167398.1 2307258 D 246200 CDS YP_167399.1 56697037 3192848 complement(2308313..2309638) 1 NC_003911.11 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase 2309638 3192848 SPO2173 Ruegeria pomeroyi DSS-3 sensor histidine kinase YP_167399.1 2308313 R 246200 CDS YP_167400.1 56697038 3193247 2309680..2310597 1 NC_003911.11 identified by match to protein family HMM PF00753; metallo-beta-lactamase 2310597 3193247 SPO2174 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_167400.1 2309680 D 246200 CDS YP_167401.1 56697039 3195312 2311560..2312672 1 NC_003911.11 identified by similarity to SP:P77535; match to protein family HMM PF01594; hypothetical protein 2312672 3195312 SPO2176 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167401.1 2311560 D 246200 CDS YP_167402.1 56697040 3193192 2312693..2313799 1 NC_003911.11 identified by similarity to SP:P39067; match to protein family HMM PF00850; acetoin utilization protein AcuC 2313799 acuC 3193192 acuC Ruegeria pomeroyi DSS-3 acetoin utilization protein AcuC YP_167402.1 2312693 D 246200 CDS YP_167403.1 56697041 3194660 2313848..2315260 1 NC_003911.11 catalyzes the transfer of a phosphatidyl group to phosphodidylglycerol to form cardiolipin (diphosphatidylglycerol); cardiolipin synthetase 2315260 cls 3194660 cls Ruegeria pomeroyi DSS-3 cardiolipin synthetase YP_167403.1 2313848 D 246200 CDS YP_167404.1 56697042 3193617 complement(2315271..2315705) 1 NC_003911.11 identified by similarity to GB:BAB52889.1; hypothetical protein 2315705 3193617 SPO2179 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167404.1 2315271 R 246200 CDS YP_167405.1 56697044 3193435 complement(2315802..2316107) 1 NC_003911.11 hypothetical protein 2316107 3193435 SPO2180 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167405.1 2315802 R 246200 CDS YP_167406.1 56697043 3194674 2316132..2316920 1 NC_003911.11 identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 2316920 3194674 SPO2181 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_167406.1 2316132 D 246200 CDS YP_167407.1 56697045 3192736 2316917..2319331 1 NC_003911.11 identified by match to protein family HMM PF02687; permease 2319331 3192736 SPO2182 Ruegeria pomeroyi DSS-3 permease YP_167407.1 2316917 D 246200 CDS YP_167408.1 56697046 3193399 2319315..2320364 1 NC_003911.11 identified by similarity to GB:AAK90829.1; hypothetical protein 2320364 3193399 SPO2183 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167408.1 2319315 D 246200 CDS YP_167409.1 56697047 3192671 complement(2320417..2321469) 1 NC_003911.11 identified by similarity to SP:P55495; hypothetical protein 2321469 3192671 SPO2184 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167409.1 2320417 R 246200 CDS YP_167410.1 56697048 3193417 complement(2321564..2322001) 1 NC_003911.11 identified by match to protein family HMM PF00582; universal stress protein family protein 2322001 3193417 SPO2185 Ruegeria pomeroyi DSS-3 universal stress protein family protein YP_167410.1 2321564 R 246200 CDS YP_167411.1 56697049 3193091 complement(2321998..2324607) 1 NC_003911.11 identified by match to protein family HMM PF06808; match to protein family HMM TIGR02123; TRAP transporter, 4TM/12TM fusion protein 2324607 3193091 SPO2186 Ruegeria pomeroyi DSS-3 TRAP transporter, 4TM/12TM fusion protein YP_167411.1 2321998 R 246200 CDS YP_167412.1 56697050 3192688 complement(2324731..2325732) 1 NC_003911.11 identified by similarity to SP:P12920; match to protein family HMM TIGR02122; TRAP transporter solute receptor TAXI family protein 2325732 3192688 SPO2187 Ruegeria pomeroyi DSS-3 TRAP transporter solute receptor TAXI family protein YP_167412.1 2324731 R 246200 CDS YP_167413.1 56697051 3194655 complement(2325957..2326376) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 2326376 3194655 SPO2188 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167413.1 2325957 R 246200 CDS YP_167414.1 56697052 3193169 complement(2326570..2327034) 1 NC_003911.11 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 2327034 3193169 SPO2189 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_167414.1 2326570 R 246200 CDS YP_167415.1 56697053 3193905 complement(2327119..2327820) 1 NC_003911.11 identified by match to protein family HMM PF00392; histidine utilization repressor 2327820 hutC 3193905 hutC Ruegeria pomeroyi DSS-3 histidine utilization repressor YP_167415.1 2327119 R 246200 CDS YP_167416.1 56697054 3193081 2327900..2329207 1 NC_003911.11 catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway; imidazolonepropionase 2329207 hutI 3193081 hutI Ruegeria pomeroyi DSS-3 imidazolonepropionase YP_167416.1 2327900 D 246200 CDS YP_167417.1 56697055 3192758 2329204..2330742 1 NC_003911.11 catalyzes the degradation of histidine to urocanate and ammmonia; histidine ammonia-lyase 2330742 hutH 3192758 hutH Ruegeria pomeroyi DSS-3 histidine ammonia-lyase YP_167417.1 2329204 D 246200 CDS YP_167418.1 56698738 3196342 2330739..2331554 1 NC_003911.11 identified by match to protein family HMM PF05013; match to protein family HMM TIGR02017; N-formylglutamate amidohydrolase 2331554 hutG 3196342 hutG Ruegeria pomeroyi DSS-3 N-formylglutamate amidohydrolase YP_167418.1 2330739 D 246200 CDS YP_167419.1 56697056 3194783 2331557..2333239 1 NC_003911.11 catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism; urocanate hydratase 2333239 hutU 3194783 hutU Ruegeria pomeroyi DSS-3 urocanate hydratase YP_167419.1 2331557 D 246200 CDS YP_167420.1 56697057 3192698 2333251..2334612 1 NC_003911.11 catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate; N-formimino-L-glutamate deiminase 2334612 hutF 3192698 hutF Ruegeria pomeroyi DSS-3 N-formimino-L-glutamate deiminase YP_167420.1 2333251 D 246200 CDS YP_167421.1 56697058 3194647 2334740..2335882 1 NC_003911.11 identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase 2335882 3194647 SPO2195 Ruegeria pomeroyi DSS-3 amidohydrolase YP_167421.1 2334740 D 246200 CDS YP_167422.1 56697059 3192935 2335885..2337078 1 NC_003911.11 catalyzes the formation of pyruvate from 2,3-diaminopropionate; diaminopropionate ammonia-lyase 2337078 3192935 SPO2196 Ruegeria pomeroyi DSS-3 diaminopropionate ammonia-lyase YP_167422.1 2335885 D 246200 CDS YP_167423.1 56697060 3192867 complement(2337097..2338077) 1 NC_003911.11 identified by similarity to PIR:H75411; match to protein family HMM PF05661; hypothetical protein 2338077 3192867 SPO2197 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167423.1 2337097 R 246200 CDS YP_167424.1 56697061 3192734 2338261..2339262 1 NC_003911.11 identified by match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534; glyceraldehyde-3-phosphate dehydrogenase, type I 2339262 gap-3 3192734 gap-3 Ruegeria pomeroyi DSS-3 glyceraldehyde-3-phosphate dehydrogenase, type I YP_167424.1 2338261 D 246200 CDS YP_167425.1 56697062 3194935 2339278..2339481 1 NC_003911.11 hypothetical protein 2339481 3194935 SPO2199 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167425.1 2339278 D 246200 CDS YP_167426.1 56697063 3193063 complement(2339581..2340078) 1 NC_003911.11 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase 2340078 coaD 3193063 coaD Ruegeria pomeroyi DSS-3 phosphopantetheine adenylyltransferase YP_167426.1 2339581 R 246200 CDS YP_167427.1 56697064 3192666 complement(2340172..2340606) 1 NC_003911.11 identified by match to protein family HMM PF00571; hypothetical protein 2340606 3192666 SPO2201 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167427.1 2340172 R 246200 CDS YP_167428.1 56697065 3194869 complement(2340667..2341569) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2341569 3194869 SPO2202 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167428.1 2340667 R 246200 CDS YP_167429.1 56697066 3194905 2341675..2343174 1 NC_003911.11 identified by similarity to SP:P28810; match to protein family HMM PF00171; match to protein family HMM TIGR01722; methylmalonate-semialdehyde dehydrogenase 2343174 mmsA 3194905 mmsA Ruegeria pomeroyi DSS-3 methylmalonate-semialdehyde dehydrogenase YP_167429.1 2341675 D 246200 CDS YP_167430.1 56697067 3195192 complement(2343235..2343735) 1 NC_003911.11 identified by similarity to GB:AAM72242.1; hypothetical protein 2343735 3195192 SPO2204 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167430.1 2343235 R 246200 CDS YP_167431.1 56697068 3194713 2343876..2344526 1 NC_003911.11 identified by match to protein family HMM PF03734; ErfK/YbiS/YcfS/YnhG family protein 2344526 3194713 SPO2205 Ruegeria pomeroyi DSS-3 ErfK/YbiS/YcfS/YnhG family protein YP_167431.1 2343876 D 246200 CDS YP_167432.1 56697069 3194915 complement(2344523..2344993) 1 NC_003911.11 hypothetical protein 2344993 3194915 SPO2206 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167432.1 2344523 R 246200 CDS YP_167433.1 56697070 3194879 complement(2345034..2345492) 1 NC_003911.11 hypothetical protein 2345492 3194879 SPO2207 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167433.1 2345034 R 246200 CDS YP_167434.1 56697071 3194896 complement(2345609..2346454) 1 NC_003911.11 identified by similarity to GB:BAB53466.1; hypothetical protein 2346454 3194896 SPO2208 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167434.1 2345609 R 246200 CDS YP_167435.1 56697072 3194886 2346548..2347702 1 NC_003911.11 ATP-dependent carboxylate-amine ligase; carboxylate-amine ligase 2347702 3194886 SPO2209 Ruegeria pomeroyi DSS-3 carboxylate-amine ligase YP_167435.1 2346548 D 246200 CDS YP_167436.1 56697073 3194855 complement(2347766..2349916) 1 NC_003911.11 identified by match to protein family HMM PF02012; BNR/Asp-box repeat-containing protein 2349916 3194855 SPO2210 Ruegeria pomeroyi DSS-3 BNR/Asp-box repeat-containing protein YP_167436.1 2347766 R 246200 CDS YP_167437.1 56697074 3194875 2350328..2351470 1 NC_003911.11 identified by similarity to SP:Q9UKU7; match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF02771; acyl-CoA dehydrogenase 2351470 3194875 SPO2211 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_167437.1 2350328 D 246200 CDS YP_167438.1 56697075 3195378 2351478..2352524 1 NC_003911.11 identified by match to protein family HMM PF00378; enoyl-CoA hydratase 2352524 3195378 SPO2212 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_167438.1 2351478 D 246200 CDS YP_167439.1 56697076 3192822 2352521..2353393 1 NC_003911.11 identified by similarity to SP:P28811; match to protein family HMM PF03446; match to protein family HMM TIGR01692; 3-hydroxyisobutyrate dehydrogenase 2353393 mmsB-1 3192822 mmsB-1 Ruegeria pomeroyi DSS-3 3-hydroxyisobutyrate dehydrogenase YP_167439.1 2352521 D 246200 CDS YP_167440.1 56697077 3194829 complement(2353972..2355468) 1 NC_003911.11 identified by similarity to SP:O69787; match to protein family HMM PF00884; choline sulfatase 2355468 betC-2 3194829 betC-2 Ruegeria pomeroyi DSS-3 choline sulfatase YP_167440.1 2353972 R 246200 CDS YP_167441.1 56697078 3194851 complement(2355531..2356112) 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 2356112 3194851 SPO2215 Ruegeria pomeroyi DSS-3 glyoxalase YP_167441.1 2355531 R 246200 CDS YP_167442.1 56697079 3193962 complement(2356164..2356949) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 2356949 3193962 SPO2216 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_167442.1 2356164 R 246200 CDS YP_167443.1 56697080 3195603 complement(2357103..2357516) 1 NC_003911.11 hypothetical protein 2357516 3195603 SPO2217 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167443.1 2357103 R 246200 CDS YP_167444.1 56697081 3194701 complement(2357532..2360447) 1 NC_003911.11 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate; excinuclease ABC subunit A 2360447 uvrA 3194701 uvrA Ruegeria pomeroyi DSS-3 excinuclease ABC subunit A YP_167444.1 2357532 R 246200 CDS YP_167445.1 56697082 3194768 2360617..2360976 1 NC_003911.11 identified by match to protein family HMM PF00581; rhodanese-like domain-containing protein 2360976 3194768 SPO2219 Ruegeria pomeroyi DSS-3 rhodanese-like domain-containing protein YP_167445.1 2360617 D 246200 CDS YP_167446.1 56697083 3194845 complement(2360983..2361633) 1 NC_003911.11 identified by similarity to GB:BAB53751.1; hypothetical protein 2361633 3194845 SPO2220 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167446.1 2360983 R 246200 CDS YP_167447.1 56697084 3194696 2361733..2363430 1 NC_003911.11 identified by match to protein family HMM PF00092; von Willebrand factor A 2363430 3194696 SPO2221 Ruegeria pomeroyi DSS-3 von Willebrand factor A YP_167447.1 2361733 D 246200 CDS YP_167448.1 56697085 3194814 complement(2363490..2364884) 1 NC_003911.11 E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase 2364884 3194814 SPO2222 Ruegeria pomeroyi DSS-3 dihydrolipoamide dehydrogenase YP_167448.1 2363490 R 246200 CDS YP_167449.1 56697086 3194747 2365060..2365491 1 NC_003911.11 hypothetical protein 2365491 3194747 SPO2223 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167449.1 2365060 D 246200 CDS YP_167450.1 56697087 3194710 complement(2365502..2366083) 1 NC_003911.11 identified by similarity to GB:BAC46583.1; match to protein family HMM PF06041; hypothetical protein 2366083 3194710 SPO2224 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167450.1 2365502 R 246200 CDS YP_167451.1 56697088 3194883 complement(2366199..2367461) 1 NC_003911.11 hypothetical protein 2367461 3194883 SPO2225 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167451.1 2366199 R 246200 CDS YP_167452.1 56697089 3194698 complement(2367563..2368612) 1 NC_003911.11 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine--tRNA ribosyltransferase-isomerase 2368612 queA 3194698 queA Ruegeria pomeroyi DSS-3 S-adenosylmethionine--tRNA ribosyltransferase-isomerase YP_167452.1 2367563 R 246200 CDS YP_167453.1 56697090 3194005 complement(2368682..2372104) 1 NC_003911.11 identified by similarity to GB:BAC49590.1; hypothetical protein 2372104 3194005 SPO2227 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167453.1 2368682 R 246200 CDS YP_167454.1 56697091 3194741 2372166..2372627 1 NC_003911.11 identified by match to protein family HMM PF00578; AhpC/TSA family protein 2372627 3194741 SPO2228 Ruegeria pomeroyi DSS-3 AhpC/TSA family protein YP_167454.1 2372166 D 246200 CDS YP_167455.1 56697092 3194288 2372624..2373460 1 NC_003911.11 identified by similarity to PIR:G97580; match to protein family HMM PF04305; hypothetical protein 2373460 3194288 SPO2229 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167455.1 2372624 D 246200 CDS YP_167456.1 56697093 3194885 2373484..2374977 1 NC_003911.11 identified by match to protein family HMM PF01551; M24/M37 family peptidase 2374977 3194885 SPO2230 Ruegeria pomeroyi DSS-3 M24/M37 family peptidase YP_167456.1 2373484 D 246200 CDS YP_167457.1 56697094 3194027 2374967..2375482 1 NC_003911.11 identified by match to protein family HMM PF04519; hypothetical protein 2375482 3194027 SPO2231 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167457.1 2374967 D 246200 CDS YP_167458.1 56697095 3194697 complement(2375617..2376603) 1 NC_003911.11 hypothetical protein 2376603 3194697 SPO2232 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167458.1 2375617 R 246200 CDS YP_167459.1 56697096 3194792 complement(2376704..2377249) 1 NC_003911.11 identified by match to protein family HMM PF00160; cyclophilin type peptidyl-prolyl cis-trans isomerase 2377249 3194792 SPO2233 Ruegeria pomeroyi DSS-3 cyclophilin type peptidyl-prolyl cis-trans isomerase YP_167459.1 2376704 R 246200 CDS YP_167460.1 56697097 3194048 complement(2377242..2377748) 1 NC_003911.11 identified by match to protein family HMM PF00160; cyclophilin type peptidyl-prolyl cis-trans isomerase 2377748 3194048 SPO2234 Ruegeria pomeroyi DSS-3 cyclophilin type peptidyl-prolyl cis-trans isomerase YP_167460.1 2377242 R 246200 CDS YP_167461.1 56697098 3194419 2377881..2379077 1 NC_003911.11 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase 2379077 pgk 3194419 pgk Ruegeria pomeroyi DSS-3 phosphoglycerate kinase YP_167461.1 2377881 D 246200 CDS YP_167462.1 56697099 3194717 complement(2379090..2379257) 1 NC_003911.11 hypothetical protein 2379257 3194717 SPO2236 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167462.1 2379090 R 246200 CDS YP_167463.1 56697100 3194597 complement(2379254..2379514) 1 NC_003911.11 hypothetical protein 2379514 3194597 SPO2237 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167463.1 2379254 R 246200 CDS YP_167464.1 56697101 3193222 2379647..2380579 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2380579 3193222 SPO2238 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167464.1 2379647 D 246200 CDS YP_167465.1 56697102 3195489 2380704..2381003 1 NC_003911.11 identified by similarity to GB:AAN30050.1; hypothetical protein 2381003 3195489 SPO2239 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167465.1 2380704 D 246200 CDS YP_167466.1 56697103 3192883 2381179..2382171 1 NC_003911.11 identified by similarity to SP:Q9R9N5; match to protein family HMM PF00676; pyruvate dehydrogenase complex, E1 component subunit alpha 2382171 pdhA 3192883 pdhA Ruegeria pomeroyi DSS-3 pyruvate dehydrogenase complex, E1 component subunit alpha YP_167466.1 2381179 D 246200 CDS YP_167467.1 56697104 3194559 2382186..2383565 1 NC_003911.11 catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acetyltransferase within the complex. The E1 component of the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase(E2) and lipoamide dehydrogenase; pyruvate dehydrogenase subunit beta 2383565 pdhB 3194559 pdhB Ruegeria pomeroyi DSS-3 pyruvate dehydrogenase subunit beta YP_167467.1 2382186 D 246200 CDS YP_167468.1 56697105 3194537 2383578..2384891 1 NC_003911.11 identified by match to protein family HMM PF00198; match to protein family HMM PF00364; match to protein family HMM PF02817; match to protein family HMM TIGR01349; branched-chain alpha-keto acid dehydrogenase subunit E2 2384891 pdhC 3194537 pdhC Ruegeria pomeroyi DSS-3 branched-chain alpha-keto acid dehydrogenase subunit E2 YP_167468.1 2383578 D 246200 CDS YP_167469.1 56697106 3194045 complement(2385038..2386612) 1 NC_003911.11 hypothetical protein 2386612 3194045 SPO2243 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167469.1 2385038 R 246200 CDS YP_167470.1 56697107 3193794 complement(2386575..2388632) 1 NC_003911.11 hypothetical protein 2388632 3193794 SPO2244 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167470.1 2386575 R 246200 CDS YP_167471.1 56697108 3194943 2389149..2390372 1 NC_003911.11 identified by similarity to GB:BAB53127.1; hypothetical protein 2390372 3194943 SPO2245 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167471.1 2389149 D 246200 CDS YP_167472.1 56697109 3194926 complement(2390631..2391695) 1 NC_003911.11 identified by similarity to SP:P37887; match to protein family HMM PF00291; match to protein family HMM TIGR01136; match to protein family HMM TIGR01139; cysteine synthase A 2391695 cysK 3194926 cysK Ruegeria pomeroyi DSS-3 cysteine synthase A YP_167472.1 2390631 R 246200 CDS YP_167473.1 56697110 3193744 complement(2391975..2392787) 1 NC_003911.11 identified by similarity to SP:P05796; match to protein family HMM PF00132; match to protein family HMM PF06426; match to protein family HMM TIGR01172; serine O-acetyltransferase 2392787 cysE 3193744 cysE Ruegeria pomeroyi DSS-3 serine O-acetyltransferase YP_167473.1 2391975 R 246200 CDS YP_167474.1 56697111 3192739 2392851..2393210 1 NC_003911.11 identified by similarity to SP:P18274; dnaK suppressor protein 2393210 3192739 SPO2248 Ruegeria pomeroyi DSS-3 dnaK suppressor protein YP_167474.1 2392851 D 246200 CDS YP_167475.1 56697112 3194468 complement(2393191..2393487) 1 NC_003911.11 hypothetical protein 2393487 3194468 SPO2249 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167475.1 2393191 R 246200 CDS YP_167476.1 56697113 3194538 complement(2393491..2397417) 1 NC_003911.11 identified by similarity to PIR:G97477; hypothetical protein 2397417 3194538 SPO2250 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167476.1 2393491 R 246200 CDS YP_167477.1 56697114 3194932 complement(2397417..2397863) 1 NC_003911.11 identified by similarity to PIR:F97477; hypothetical protein 2397863 3194932 SPO2251 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167477.1 2397417 R 246200 CDS YP_167478.1 56697115 3194927 complement(2397860..2398747) 1 NC_003911.11 identified by similarity to GB:CAE27346.1; hypothetical protein 2398747 3194927 SPO2252 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167478.1 2397860 R 246200 CDS YP_167479.1 56697116 3193321 complement(2398747..2399379) 1 NC_003911.11 identified by similarity to PIR:D97477; hypothetical protein 2399379 3193321 SPO2253 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167479.1 2398747 R 246200 CDS YP_167480.1 56697117 3193867 complement(2400044..2400253) 1 NC_003911.11 identified by similarity to GB:CAE27342.1; hypothetical protein 2400253 3193867 SPO2255 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167480.1 2400044 R 246200 CDS YP_167481.1 56697118 3194276 complement(2400250..2400570) 1 NC_003911.11 hypothetical protein 2400570 3194276 SPO2256 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167481.1 2400250 R 246200 CDS YP_167482.1 56697119 3193233 complement(2400573..2400986) 1 NC_003911.11 identified by match to protein family HMM TIGR02126; TP901-1 family major tail protein 2400986 3193233 SPO2257 Ruegeria pomeroyi DSS-3 TP901-1 family major tail protein YP_167482.1 2400573 R 246200 CDS YP_167483.1 56697120 3193956 complement(2401011..2401424) 1 NC_003911.11 identified by similarity to GB:AAN29524.1; hypothetical protein 2401424 3193956 SPO2258 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167483.1 2401011 R 246200 CDS YP_167484.1 56697121 3194085 complement(2401421..2401759) 1 NC_003911.11 identified by match to protein family HMM TIGR01563; head-tail adaptor 2401759 3194085 SPO2259 Ruegeria pomeroyi DSS-3 head-tail adaptor YP_167484.1 2401421 R 246200 CDS YP_167485.1 56697122 3193896 complement(2401756..2402370) 1 NC_003911.11 identified by similarity to GB:AAN29521.1; match to protein family HMM TIGR02215; hypothetical protein 2402370 3193896 SPO2260 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167485.1 2401756 R 246200 CDS YP_167486.1 56697123 3192998 complement(2402520..2403698) 1 NC_003911.11 identified by match to protein family HMM PF05065; match to protein family HMM TIGR01554; HK97 family major capsid protein 2403698 3192998 SPO2261 Ruegeria pomeroyi DSS-3 HK97 family major capsid protein YP_167486.1 2402520 R 246200 CDS YP_167487.1 56697124 3195355 complement(2403732..2404289) 1 NC_003911.11 identified by match to protein family HMM PF04586; match to protein family HMM TIGR01543; HK97 family phage prohead protease 2404289 3195355 SPO2262 Ruegeria pomeroyi DSS-3 HK97 family phage prohead protease YP_167487.1 2403732 R 246200 CDS YP_167488.1 56697125 3193792 complement(2404318..2404548) 1 NC_003911.11 hypothetical protein 2404548 3193792 SPO2263 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167488.1 2404318 R 246200 CDS YP_167489.1 56697126 3193535 complement(2404535..2405707) 1 NC_003911.11 identified by match to protein family HMM PF04860; match to protein family HMM TIGR01537; HK97 family portal protein 2405707 3193535 SPO2264 Ruegeria pomeroyi DSS-3 HK97 family portal protein YP_167489.1 2404535 R 246200 CDS YP_167490.1 56697127 3194781 complement(2405833..2407059) 1 NC_003911.11 identified by similarity to GB:AAF13179.1; terminase large subunit 2407059 3194781 SPO2266 Ruegeria pomeroyi DSS-3 terminase large subunit YP_167490.1 2405833 R 246200 CDS YP_167491.1 56697128 3193057 complement(2407112..2407837) 1 NC_003911.11 hypothetical protein 2407837 3193057 SPO2267 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167491.1 2407112 R 246200 CDS YP_167492.1 56697129 3192769 2407713..2408099 1 NC_003911.11 identified by similarity to GB:AAK25445.1; hypothetical protein 2408099 3192769 SPO2268 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167492.1 2407713 D 246200 CDS YP_167493.1 56697130 3193651 complement(2408460..2408984) 1 NC_003911.11 identified by similarity to GB:BAB49728.1; hypothetical protein 2408984 3193651 SPO2269 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167493.1 2408460 R 246200 CDS YP_167494.1 56697131 3194329 complement(2409460..2410614) 1 NC_003911.11 identified by similarity to GB:AAK23657.1; match to protein family HMM PF02618; match to protein family HMM TIGR00247; hypothetical protein 2410614 3194329 SPO2270 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167494.1 2409460 R 246200 CDS YP_167495.1 56697132 3194842 complement(2410614..2411879) 1 NC_003911.11 FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP; 3-oxoacyl-ACP synthase 2411879 fabF 3194842 fabF Ruegeria pomeroyi DSS-3 3-oxoacyl-ACP synthase YP_167495.1 2410614 R 246200 CDS YP_167496.1 56697133 3193857 complement(2412015..2412758) 1 NC_003911.11 identified by similarity to SP:P26720; match to protein family HMM PF00977; phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase 2412758 3193857 SPO2272 Ruegeria pomeroyi DSS-3 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase YP_167496.1 2412015 R 246200 CDS YP_167497.1 56697134 3193882 complement(2412853..2413392) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 2413392 3193882 SPO2273 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167497.1 2412853 R 246200 CDS YP_167498.1 56697135 3193338 complement(2413533..2413766) 1 NC_003911.11 carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein 2413766 acpP 3193338 acpP Ruegeria pomeroyi DSS-3 acyl carrier protein YP_167498.1 2413533 R 246200 CDS YP_167499.1 56697136 3194395 complement(2413979..2414716) 1 NC_003911.11 identified by match to protein family HMM PF00106; match to protein family HMM TIGR01830; 3-oxoacyl-ACP reductase 2414716 fabG 3194395 fabG Ruegeria pomeroyi DSS-3 3-oxoacyl-ACP reductase YP_167499.1 2413979 R 246200 CDS YP_167500.1 56697137 3194285 complement(2414774..2415712) 1 NC_003911.11 identified by similarity to SP:P71019; match to protein family HMM PF00698; match to protein family HMM TIGR00128; ACP S-malonyltransferase 2415712 fabD 3194285 fabD Ruegeria pomeroyi DSS-3 ACP S-malonyltransferase YP_167500.1 2414774 R 246200 CDS YP_167501.1 56697138 3194621 2415874..2417091 1 NC_003911.11 identified by match to protein family HMM PF01292; match to protein family HMM PF04264; cytochrome 2417091 3194621 SPO2277 Ruegeria pomeroyi DSS-3 cytochrome YP_167501.1 2415874 D 246200 CDS YP_167502.1 56697139 3194495 complement(2417264..2418736) 1 NC_003911.11 hypothetical protein 2418736 3194495 SPO2278 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167502.1 2417264 R 246200 CDS YP_167503.1 56697140 3192651 complement(2418954..2419532) 1 NC_003911.11 identified by similarity to GB:AAQ60940.1; match to protein family HMM PF04264; hypothetical protein 2419532 3192651 SPO2279 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167503.1 2418954 R 246200 CDS YP_167504.1 56697141 3193206 complement(2419670..2420395) 1 NC_003911.11 hypothetical protein 2420395 3193206 SPO2280 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167504.1 2419670 R 246200 CDS YP_167505.1 56697142 3194317 2420491..2420844 1 NC_003911.11 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 2420844 rpsF 3194317 rpsF Ruegeria pomeroyi DSS-3 30S ribosomal protein S6 YP_167505.1 2420491 D 246200 CDS YP_167506.1 56697143 3193473 2420872..2421099 1 NC_003911.11 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit; 30S ribosomal protein S18 2421099 rpsR 3193473 rpsR Ruegeria pomeroyi DSS-3 30S ribosomal protein S18 YP_167506.1 2420872 D 246200 CDS YP_167507.1 56697144 3192811 2421112..2421714 1 NC_003911.11 in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 2421714 rplI 3192811 rplI Ruegeria pomeroyi DSS-3 50S ribosomal protein L9 YP_167507.1 2421112 D 246200 CDS YP_167508.1 56697145 3194230 2421897..2422370 1 NC_003911.11 identified by match to protein family HMM PF01464; transglycosylase 2422370 3194230 SPO2284 Ruegeria pomeroyi DSS-3 transglycosylase YP_167508.1 2421897 D 246200 CDS YP_167509.1 56697146 3194528 2422764..2423168 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 2423168 3194528 SPO2285 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_167509.1 2422764 D 246200 CDS YP_167510.1 56697147 3194844 2423208..2423909 1 NC_003911.11 identified by match to protein family HMM PF00196; match to protein family HMM PF03472; LuxR family transcriptional regulator 2423909 luxR-2 3194844 luxR-2 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_167510.1 2423208 D 246200 CDS YP_167511.1 56697148 3193562 2424015..2424875 1 NC_003911.11 identified by match to protein family HMM PF00765; autoinducer synthesis protein 2424875 3193562 SPO2287 Ruegeria pomeroyi DSS-3 autoinducer synthesis protein YP_167511.1 2424015 D 246200 CDS YP_167512.1 56697149 3194965 complement(2424967..2426298) 1 NC_003911.11 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor 2426298 tig 3194965 tig Ruegeria pomeroyi DSS-3 trigger factor YP_167512.1 2424967 R 246200 CDS YP_167513.1 56697150 3194334 complement(2426489..2427751) 1 NC_003911.11 identified by similarity to PIR:E82389; hypothetical protein 2427751 3194334 SPO2289 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167513.1 2426489 R 246200 CDS YP_167514.1 56697151 3193920 2427851..2429167 1 NC_003911.11 hypothetical protein 2429167 3193920 SPO2290 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167514.1 2427851 D 246200 CDS YP_167515.1 56697152 3193936 2429724..2430233 1 NC_003911.11 identified by similarity to GB:AAR38409.1; hypothetical protein 2430233 3193936 SPO2292 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167515.1 2429724 D 246200 CDS YP_167516.1 56697153 3194194 complement(2430230..2431900) 1 NC_003911.11 identified by similarity to GB:AAQ18205.1; match to protein family HMM PF01256; match to protein family HMM PF03853; match to protein family HMM TIGR00196; match to protein family HMM TIGR00197; hypothetical protein 2431900 3194194 SPO2293 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167516.1 2430230 R 246200 CDS YP_167517.1 56698713 3196300 2432038..2432376 1 NC_003911.11 identified by match to protein family HMM PF00543; nitrogen regulatory protein P-II 2432376 glnB-1 3196300 glnB-1 Ruegeria pomeroyi DSS-3 nitrogen regulatory protein P-II YP_167517.1 2432038 D 246200 CDS YP_167518.1 56697154 3194467 2432409..2433815 1 NC_003911.11 identified by similarity to SP:P06201; match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653; glutamine synthetase, type I 2433815 glnA 3194467 glnA Ruegeria pomeroyi DSS-3 glutamine synthetase, type I YP_167518.1 2432409 D 246200 CDS YP_167519.1 56697155 3195415 2433950..2434792 1 NC_003911.11 hypothetical protein 2434792 3195415 SPO2296 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167519.1 2433950 D 246200 CDS YP_167520.1 56697156 3195519 2434985..2435911 1 NC_003911.11 hypothetical protein 2435911 3195519 SPO2297 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167520.1 2434985 D 246200 CDS YP_167521.1 56697157 3193282 complement(2435967..2436704) 1 NC_003911.11 identified by similarity to GB:BAC90287.1; hypothetical protein 2436704 3193282 SPO2298 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167521.1 2435967 R 246200 CDS YP_167522.1 56697158 3193310 2436996..2438177 1 NC_003911.11 identified by match to protein family HMM PF00557; M24 family metallopeptidase 2438177 3193310 SPO2299 Ruegeria pomeroyi DSS-3 M24 family metallopeptidase YP_167522.1 2436996 D 246200 CDS YP_167523.1 56697159 3193061 complement(2438202..2438393) 1 NC_003911.11 hypothetical protein 2438393 3193061 SPO2300 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167523.1 2438202 R 246200 CDS YP_167524.1 56697160 3194936 2438618..2439838 1 NC_003911.11 identified by match to protein family HMM PF02566; osmC-like family protein 2439838 3194936 SPO2301 Ruegeria pomeroyi DSS-3 osmC-like family protein YP_167524.1 2438618 D 246200 CDS YP_167525.1 56697161 3195485 complement(2439904..2440491) 1 NC_003911.11 identified by match to protein family HMM PF02632; bioY family protein 2440491 3195485 SPO2302 Ruegeria pomeroyi DSS-3 bioY family protein YP_167525.1 2439904 R 246200 CDS YP_167526.1 56697162 3193368 complement(2440568..2440990) 1 NC_003911.11 identified by similarity to PIR:T36819; hypothetical protein 2440990 3193368 SPO2303 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167526.1 2440568 R 246200 CDS YP_167527.1 56697163 3194293 complement(2440987..2441385) 1 NC_003911.11 hypothetical protein 2441385 3194293 SPO2304 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167527.1 2440987 R 246200 CDS YP_167528.1 56697164 3195293 2441408..2442712 1 NC_003911.11 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 2442712 purB 3195293 purB Ruegeria pomeroyi DSS-3 adenylosuccinate lyase YP_167528.1 2441408 D 246200 CDS YP_167529.1 56697165 3193297 2442758..2442979 1 NC_003911.11 hypothetical protein 2442979 3193297 SPO2306 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167529.1 2442758 D 246200 CDS YP_167530.1 56697166 3194491 2443074..2443628 1 NC_003911.11 identified by similarity to GB:BAB49208.1; hypothetical protein 2443628 3194491 SPO2307 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167530.1 2443074 D 246200 CDS YP_167531.1 56697167 3194628 2443771..2444820 1 NC_003911.11 identified by similarity to SP:P23448; match to protein family HMM PF01706; flagellar motor switch protein FliG 2444820 fliG 3194628 fliG Ruegeria pomeroyi DSS-3 flagellar motor switch protein FliG YP_167531.1 2443771 D 246200 CDS YP_167532.1 56697168 3194267 2444866..2445849 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 2445849 3194267 SPO2309 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167532.1 2444866 D 246200 CDS YP_167533.1 56697169 3193277 2445859..2446785 1 NC_003911.11 identified by similarity to SP:P24187; match to protein family HMM PF03279; lipid A biosynthesis lauroyl acyltransferase 2446785 3193277 SPO2310 Ruegeria pomeroyi DSS-3 lipid A biosynthesis lauroyl acyltransferase YP_167533.1 2445859 D 246200 CDS YP_167534.1 56697170 3194732 complement(2446786..2447670) 1 NC_003911.11 identified by similarity to GB:CAC47807.1; match to protein family HMM PF06764; hypothetical protein 2447670 3194732 SPO2311 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167534.1 2446786 R 246200 CDS YP_167535.1 56697171 3193296 2447736..2450426 1 NC_003911.11 Catalyzes the conversion of citrate to isocitrate; aconitate hydratase 2450426 acnA 3193296 acnA Ruegeria pomeroyi DSS-3 aconitate hydratase YP_167535.1 2447736 D 246200 CDS YP_167536.1 56697172 3194102 2450606..2450923 1 NC_003911.11 hypothetical protein 2450923 3194102 SPO2313 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167536.1 2450606 D 246200 CDS YP_167537.1 56697173 3194354 complement(2450992..2451531) 1 NC_003911.11 identified by match to protein family HMM TIGR00385; DsbE subfamily periplasmic protein thiol:disulfide oxidoreductase 2451531 3194354 SPO2314 Ruegeria pomeroyi DSS-3 DsbE subfamily periplasmic protein thiol:disulfide oxidoreductase YP_167537.1 2450992 R 246200 CDS YP_167538.1 56697174 3195309 complement(2451679..2452452) 1 NC_003911.11 identified by similarity to SP:P33929; match to protein family HMM PF01578; match to protein family HMM TIGR01191; heme exporter protein CcmC 2452452 ccmC 3195309 ccmC Ruegeria pomeroyi DSS-3 heme exporter protein CcmC YP_167538.1 2451679 R 246200 CDS YP_167539.1 56697175 3193255 complement(2452498..2453154) 1 NC_003911.11 identified by similarity to SP:P33930; match to protein family HMM PF03379; match to protein family HMM TIGR01190; heme exporter protein CcmB 2453154 ccmB 3193255 ccmB Ruegeria pomeroyi DSS-3 heme exporter protein CcmB YP_167539.1 2452498 R 246200 CDS YP_167540.1 56697176 3194563 complement(2453151..2453765) 1 NC_003911.11 ATP-binding protein; required for proper cytochrome c maturation; cytochrome c biogenesis protein CcmA 2453765 ccmA 3194563 ccmA Ruegeria pomeroyi DSS-3 cytochrome c biogenesis protein CcmA YP_167540.1 2453151 R 246200 CDS YP_167541.1 56697177 3194592 complement(2453905..2454258) 1 NC_003911.11 identified by similarity to GB:AAB61905.1; match to protein family HMM PF04635; hypothetical protein 2454258 3194592 SPO2318 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167541.1 2453905 R 246200 CDS YP_167542.1 56697178 3193261 complement(2454260..2455015) 1 NC_003911.11 identified by similarity to GB:BAC45969.1; match to protein family HMM PF01925; hypothetical protein 2455015 3193261 SPO2319 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167542.1 2454260 R 246200 CDS YP_167543.1 56697179 3193136 complement(2455085..2456053) 1 NC_003911.11 forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF; preprotein translocase subunit SecF 2456053 secF 3193136 secF Ruegeria pomeroyi DSS-3 preprotein translocase subunit SecF YP_167543.1 2455085 R 246200 CDS YP_167544.1 56697180 3194904 complement(2456055..2457716) 1 NC_003911.11 part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; preprotein translocase subunit SecD 2457716 secD 3194904 secD Ruegeria pomeroyi DSS-3 preprotein translocase subunit SecD YP_167544.1 2456055 R 246200 CDS YP_167545.1 56697181 3194318 complement(2457745..2458110) 1 NC_003911.11 identified by match to protein family HMM PF02699; match to protein family HMM TIGR00739; preprotein translocase subunit YajC 2458110 yajC 3194318 yajC Ruegeria pomeroyi DSS-3 preprotein translocase subunit YajC YP_167545.1 2457745 R 246200 CDS YP_167546.1 56697182 3194610 2458194..2459810 1 NC_003911.11 identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS 2459810 3194610 SPO2323 Ruegeria pomeroyi DSS-3 mechanosensitive ion channel MscS YP_167546.1 2458194 D 246200 CDS YP_167547.1 56697183 3194625 2459957..2460373 1 NC_003911.11 identified by similarity to GB:BAB50081.1; hypothetical protein 2460373 3194625 SPO2324 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167547.1 2459957 D 246200 CDS YP_167548.1 56697184 3194584 2460515..2461807 1 NC_003911.11 catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; seryl-tRNA synthetase 2461807 serS 3194584 serS Ruegeria pomeroyi DSS-3 seryl-tRNA synthetase YP_167548.1 2460515 D 246200 CDS YP_167549.1 56697185 3194602 complement(2461847..2462536) 1 NC_003911.11 hypothetical protein 2462536 3194602 SPO2326 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167549.1 2461847 R 246200 CDS YP_167550.1 56697186 3192895 complement(2462563..2463546) 1 NC_003911.11 identified by match to protein family HMM PF00487; fatty acid desaturase 2463546 3192895 SPO2327 Ruegeria pomeroyi DSS-3 fatty acid desaturase YP_167550.1 2462563 R 246200 CDS YP_167551.1 56697187 3194590 complement(2463747..2465210) 1 NC_003911.11 EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains; GTP-binding protein EngA 2465210 engA 3194590 engA Ruegeria pomeroyi DSS-3 GTP-binding protein EngA YP_167551.1 2463747 R 246200 CDS YP_167552.1 56697188 3193836 complement(2465260..2466537) 1 NC_003911.11 identified by match to protein family HMM PF01011; PQQ repeat-containing protein 2466537 3193836 SPO2329 Ruegeria pomeroyi DSS-3 PQQ repeat-containing protein YP_167552.1 2465260 R 246200 CDS YP_167553.1 56697189 3194583 complement(2466641..2467417) 1 NC_003911.11 hypothetical protein 2467417 3194583 SPO2330 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167553.1 2466641 R 246200 CDS YP_167554.1 56697190 3193452 2467487..2468791 1 NC_003911.11 identified by match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 2468791 3193452 SPO2331 Ruegeria pomeroyi DSS-3 RND family efflux transporter MFP subunit YP_167554.1 2467487 D 246200 CDS YP_167555.1 56697191 3194573 2468788..2472567 1 NC_003911.11 AcrB/AcrD/AcrF family transporter 2472567 3194573 SPO2332 Ruegeria pomeroyi DSS-3 AcrB/AcrD/AcrF family transporter YP_167555.1 2468788 D 246200 CDS YP_167556.1 56697192 3194552 2472669..2473028 1 NC_003911.11 hypothetical protein 2473028 3194552 SPO2333 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167556.1 2472669 D 246200 CDS YP_167557.1 56697193 3194054 complement(2473038..2474666) 1 NC_003911.11 identified by match to protein family HMM PF02517; CAAX amino terminal protease 2474666 3194054 SPO2334 Ruegeria pomeroyi DSS-3 CAAX amino terminal protease YP_167557.1 2473038 R 246200 CDS YP_167558.1 56697194 3192746 complement(2474742..2476571) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter ATP-binding protein/permease 2476571 3192746 SPO2335 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein/permease YP_167558.1 2474742 R 246200 CDS YP_167559.1 56697195 3194558 complement(2476640..2478298) 1 NC_003911.11 identified by match to protein family HMM PF01476; lysM domain-containing protein 2478298 3194558 SPO2336 Ruegeria pomeroyi DSS-3 lysM domain-containing protein YP_167559.1 2476640 R 246200 CDS YP_167560.1 56697196 3194047 2478424..2478975 1 NC_003911.11 identified by match to protein family HMM PF03641; match to protein family HMM TIGR00730; decarboxylase 2478975 3194047 SPO2337 Ruegeria pomeroyi DSS-3 decarboxylase YP_167560.1 2478424 D 246200 CDS YP_167561.1 56697197 3194765 complement(2478912..2479832) 1 NC_003911.11 identified by similarity to SP:P27844; match to protein family HMM PF00892; match to protein family HMM TIGR00688; protein RarD 2479832 rarD-1 3194765 rarD-1 Ruegeria pomeroyi DSS-3 protein RarD YP_167561.1 2478912 R 246200 CDS YP_167562.1 56697198 3194933 complement(2479902..2480672) 1 NC_003911.11 identified by match to protein family HMM PF00378; enoyl-CoA hydratase 2480672 3194933 SPO2339 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_167562.1 2479902 R 246200 CDS YP_167563.1 56697199 3194900 complement(2480854..2481453) 1 NC_003911.11 identified by similarity to SP:P09157; superoxide dismutase, Fe 2481453 sodB 3194900 sodB Ruegeria pomeroyi DSS-3 superoxide dismutase, Fe YP_167563.1 2480854 R 246200 CDS YP_167564.1 56697200 3194072 2481555..2482307 1 NC_003911.11 identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 2482307 3194072 SPO2341 Ruegeria pomeroyi DSS-3 FkbM family methyltransferase YP_167564.1 2481555 D 246200 CDS YP_167565.1 56697201 3194186 complement(2482748..2483182) 1 NC_003911.11 hypothetical protein 2483182 3194186 SPO2342 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167565.1 2482748 R 246200 CDS YP_167566.1 56697202 3195568 complement(2483207..2483656) 1 NC_003911.11 hypothetical protein 2483656 3195568 SPO2343 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167566.1 2483207 R 246200 CDS YP_167567.1 56697203 3194262 complement(2484213..2484779) 1 NC_003911.11 identified by similarity to SP:Q46338; match to protein family HMM PF04268; sarcosine oxidase subunit gamma 2484779 3194262 SPO2344 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit gamma YP_167567.1 2484213 R 246200 CDS YP_167568.1 56697204 3193813 complement(2484772..2487804) 1 NC_003911.11 identified by similarity to SP:Q46337; match to protein family HMM PF01571; match to protein family HMM TIGR01372; sarcosine oxidase subunit alpha 2487804 3193813 SPO2345 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit alpha YP_167568.1 2484772 R 246200 CDS YP_167569.1 56697205 3193543 complement(2487850..2488179) 1 NC_003911.11 identified by similarity to SP:Q46336; match to protein family HMM PF04267; sarcosine oxidase subunit delta 2488179 3193543 SPO2346 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit delta YP_167569.1 2487850 R 246200 CDS YP_167570.1 56697206 3193514 complement(2488757..2489149) 1 NC_003911.11 identified by similarity to GB:BAB54267.1; hypothetical protein 2489149 3193514 SPO2347 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167570.1 2488757 R 246200 CDS YP_167571.1 56697207 3193974 complement(2489175..2490476) 1 NC_003911.11 identified by similarity to SP:P40875; match to protein family HMM PF01266; match to protein family HMM TIGR01373; sarcosine oxidase subunit beta 2490476 3193974 SPO2348 Ruegeria pomeroyi DSS-3 sarcosine oxidase subunit beta YP_167571.1 2489175 R 246200 CDS YP_167572.1 56697208 3195443 2490597..2491832 1 NC_003911.11 identified by similarity to SP:P45400; cytochrome c-type biogenesis protein CycH 2491832 cycH 3195443 cycH Ruegeria pomeroyi DSS-3 cytochrome c-type biogenesis protein CycH YP_167572.1 2490597 D 246200 CDS YP_167573.1 56697209 3194839 2491829..2492293 1 NC_003911.11 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function; Holliday junction resolvase-like protein 2492293 3194839 SPO2350 Ruegeria pomeroyi DSS-3 Holliday junction resolvase-like protein YP_167573.1 2491829 D 246200 CDS YP_167574.1 56697210 3193565 2492307..2492540 1 NC_003911.11 identified by similarity to GB:BAB48126.1; match to protein family HMM PF06945; hypothetical protein 2492540 3193565 SPO2351 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167574.1 2492307 D 246200 CDS YP_167575.1 56697211 3194059 complement(2492612..2494006) 1 NC_003911.11 identified by similarity to SP:P55127; match to protein family HMM PF00353; type I secretion target repeat-containing protein 2494006 3194059 SPO2352 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_167575.1 2492612 R 246200 CDS YP_167576.1 56698736 3196490 complement(2494151..2494936) 1 NC_003911.11 hypothetical protein 2494936 3196490 SPO2353 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167576.1 2494151 R 246200 CDS YP_167577.1 56697212 3194755 complement(2494930..2495754) 1 NC_003911.11 identified by match to protein family HMM PF01925; hypothetical protein 2495754 3194755 SPO2354 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167577.1 2494930 R 246200 CDS YP_167578.1 56697213 3194809 complement(2495995..2496801) 1 NC_003911.11 identified by match to protein family HMM PF01614; isethionate dissimilation regulator 2496801 iseR 3194809 iseR Ruegeria pomeroyi DSS-3 isethionate dissimilation regulator YP_167578.1 2495995 R 246200 CDS YP_167579.1 56697214 3194820 complement(2496837..2498198) 1 NC_003911.11 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; isethionate TRAP transporter 2498198 iseM 3194820 iseM Ruegeria pomeroyi DSS-3 isethionate TRAP transporter YP_167579.1 2496837 R 246200 CDS YP_167580.1 56697215 3194893 complement(2498209..2498763) 1 NC_003911.11 identified by match to protein family HMM PF04290; isethionate TRAP transporter 2498763 iseL 3194893 iseL Ruegeria pomeroyi DSS-3 isethionate TRAP transporter YP_167580.1 2498209 R 246200 CDS YP_167581.1 56697216 3194653 complement(2498972..2500204) 1 NC_003911.11 identified by match to protein family HMM PF03480; match to protein family HMM TIGR01409; isethionate TRAP transporter 2500204 iseK 3194653 iseK Ruegeria pomeroyi DSS-3 isethionate TRAP transporter YP_167581.1 2498972 R 246200 CDS YP_167582.1 56697217 3192668 2500332..2501939 1 NC_003911.11 identified by match to protein family HMM PF00732; match to protein family HMM PF05199; isethionate dehydrogenase 2501939 iseJ 3192668 iseJ Ruegeria pomeroyi DSS-3 isethionate dehydrogenase YP_167582.1 2500332 D 246200 CDS YP_167583.1 56697218 3194743 complement(2503503..2505671) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase/response regulator 2505671 3194743 SPO2361 Ruegeria pomeroyi DSS-3 sensor histidine kinase/response regulator YP_167583.1 2503503 R 246200 CDS YP_167584.1 56697219 3194657 complement(2505668..2506669) 1 NC_003911.11 identified by similarity to SP:Q52663; amino acid ABC transporter substrate-binding protein 2506669 3194657 SPO2362 Ruegeria pomeroyi DSS-3 amino acid ABC transporter substrate-binding protein YP_167584.1 2505668 R 246200 CDS YP_167585.1 56697220 3194824 complement(2506666..2507559) 1 NC_003911.11 identified by match to protein family HMM PF00702; match to protein family HMM TIGR00338; match to protein family HMM TIGR01488; phosphoserine phosphatase 2507559 serB-1 3194824 serB-1 Ruegeria pomeroyi DSS-3 phosphoserine phosphatase YP_167585.1 2506666 R 246200 CDS YP_167586.1 56697221 3192845 2507889..2508902 1 NC_003911.11 identified by similarity to SP:Q52663; amino acid ABC transporter substrate-binding protein 2508902 3192845 SPO2364 Ruegeria pomeroyi DSS-3 amino acid ABC transporter substrate-binding protein YP_167586.1 2507889 D 246200 CDS YP_167587.1 56697222 3194682 2508969..2510141 1 NC_003911.11 identified by similarity to SP:Q52664; match to protein family HMM PF00528; match to protein family HMM TIGR01726; amino acid ABC transporter permease 2510141 3194682 SPO2365 Ruegeria pomeroyi DSS-3 amino acid ABC transporter permease YP_167587.1 2508969 D 246200 CDS YP_167588.1 56697223 3193628 2510119..2511246 1 NC_003911.11 identified by similarity to SP:Q52665; match to protein family HMM PF00528; match to protein family HMM TIGR01726; amino acid ABC transporter permease 2511246 3193628 SPO2366 Ruegeria pomeroyi DSS-3 amino acid ABC transporter permease YP_167588.1 2510119 D 246200 CDS YP_167589.1 56697224 3193012 2511266..2512036 1 NC_003911.11 identified by similarity to SP:Q52666; match to protein family HMM PF00005; amino acid ABC transporter ATP-binding protein 2512036 3193012 SPO2367 Ruegeria pomeroyi DSS-3 amino acid ABC transporter ATP-binding protein YP_167589.1 2511266 D 246200 CDS YP_167590.1 56697225 3195298 2512088..2513695 1 NC_003911.11 identified by match to protein family HMM PF02690; Na/Pi-cotransporter family protein 2513695 3195298 SPO2368 Ruegeria pomeroyi DSS-3 Na/Pi-cotransporter family protein YP_167590.1 2512088 D 246200 CDS YP_167591.1 56697226 3194639 2513756..2514418 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator 2514418 3194639 SPO2369 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_167591.1 2513756 D 246200 CDS YP_167592.1 56697227 3193444 complement(2514751..2516337) 1 NC_003911.11 identified by similarity to SP:P30144; match to protein family HMM PF01235; match to protein family HMM TIGR00835; sodium:alanine symporter family protein 2516337 3193444 SPO2370 Ruegeria pomeroyi DSS-3 sodium:alanine symporter family protein YP_167592.1 2514751 R 246200 CDS YP_167593.1 56697228 3194860 complement(2516319..2516753) 1 NC_003911.11 identified by match to protein family HMM PF00582; universal stress protein family protein 2516753 3194860 SPO2371 Ruegeria pomeroyi DSS-3 universal stress protein family protein YP_167593.1 2516319 R 246200 CDS YP_167594.1 56697229 3193856 2516900..2517355 1 NC_003911.11 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 2517355 3193856 SPO2372 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_167594.1 2516900 D 246200 CDS YP_167595.1 56697230 3192850 complement(2517367..2517783) 1 NC_003911.11 identified by similarity to PIR:B98206; match to protein family HMM PF00903; hypothetical protein 2517783 3192850 SPO2373 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167595.1 2517367 R 246200 CDS YP_167596.1 56697231 3194172 complement(2517869..2518903) 1 NC_003911.11 identified by similarity to SP:Q8X5V6; match to protein family HMM PF01207; match to protein family HMM TIGR00742; tRNA-dihydrouridine synthase A 2518903 3194172 SPO2374 Ruegeria pomeroyi DSS-3 tRNA-dihydrouridine synthase A YP_167596.1 2517869 R 246200 CDS YP_167597.1 56697232 3192717 complement(2520538..2521002) 1 NC_003911.11 identified by match to protein family HMM PF02629; CoA-binding domain-containing protein 2521002 3192717 SPO2376 Ruegeria pomeroyi DSS-3 CoA-binding domain-containing protein YP_167597.1 2520538 R 246200 CDS YP_167598.1 56697233 3193359 complement(2521006..2521404) 1 NC_003911.11 identified by match to protein family HMM PF00111; ferredoxin 2521404 3193359 SPO2377 Ruegeria pomeroyi DSS-3 ferredoxin YP_167598.1 2521006 R 246200 CDS YP_167599.1 56697234 3194894 complement(2521401..2522750) 1 NC_003911.11 identified by match to protein family HMM PF05694; selenium-binding protein 2522750 3194894 SPO2378 Ruegeria pomeroyi DSS-3 selenium-binding protein YP_167599.1 2521401 R 246200 CDS YP_167600.1 56697235 3195664 complement(2523564..2524730) 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF02771; acyl-CoA dehydrogenase 2524730 3195664 SPO2380 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_167600.1 2523564 R 246200 CDS YP_167601.1 56697236 3192856 complement(2524849..2525784) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2525784 3192856 SPO2381 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167601.1 2524849 R 246200 CDS YP_167602.1 56697237 3192847 2526033..2526986 1 NC_003911.11 identified by similarity to GB:CAE42344.1; match to protein family HMM PF03401; tricarboxylate transporter family protein 2526986 3192847 SPO2382 Ruegeria pomeroyi DSS-3 tricarboxylate transporter family protein YP_167602.1 2526033 D 246200 CDS YP_167603.1 56697238 3193046 2527016..2527504 1 NC_003911.11 hypothetical protein 2527504 3193046 SPO2383 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167603.1 2527016 D 246200 CDS YP_167604.1 56697239 3192798 2527492..2529066 1 NC_003911.11 identified by match to protein family HMM PF01970; tricarboxylate transporter family protein 2529066 3192798 SPO2384 Ruegeria pomeroyi DSS-3 tricarboxylate transporter family protein YP_167604.1 2527492 D 246200 CDS YP_167605.1 56697240 3192974 2529082..2530812 1 NC_003911.11 identified by similarity to SP:P51853; match to protein family HMM PF00205; match to protein family HMM PF02776; benzaldehyde lyase 2530812 3192974 SPO2385 Ruegeria pomeroyi DSS-3 benzaldehyde lyase YP_167605.1 2529082 D 246200 CDS YP_167606.1 56697241 3194640 2530812..2531141 1 NC_003911.11 identified by similarity to GB:AAM35187.1; hypothetical protein 2531141 3194640 SPO2386 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167606.1 2530812 D 246200 CDS YP_167607.1 56697242 3193395 2531150..2532556 1 NC_003911.11 identified by match to protein family HMM PF01565; match to protein family HMM PF02913; oxidoreductase, FAD-binding 2532556 3193395 SPO2387 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_167607.1 2531150 D 246200 CDS YP_167608.1 56697243 3194440 2532582..2533223 1 NC_003911.11 identified by similarity to SP:P27847; match to protein family HMM PF01810; LysE family translocator protein 2533223 3194440 SPO2388 Ruegeria pomeroyi DSS-3 LysE family translocator protein YP_167608.1 2532582 D 246200 CDS YP_167609.1 56697244 3194863 2533224..2535506 1 NC_003911.11 identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM TIGR00509; molybdopterin-binding oxidoreductase 2535506 3194863 SPO2389 Ruegeria pomeroyi DSS-3 molybdopterin-binding oxidoreductase YP_167609.1 2533224 D 246200 CDS YP_167610.1 56697245 3194646 2537527..2538186 1 NC_003911.11 identified by match to protein family HMM PF00589; phage integrase site specific recombinase 2538186 3194646 SPO2390 Ruegeria pomeroyi DSS-3 phage integrase site specific recombinase YP_167610.1 2537527 D 246200 CDS YP_167611.1 56697246 3194637 complement(2538865..2538969) 1 NC_003911.11 hypothetical protein 2538969 3194637 SPO2392 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167611.1 2538865 R 246200 CDS YP_167612.1 56697247 3194846 complement(2539789..2540241) 1 NC_003911.11 identified by similarity to GB:CAB76249.1; match to protein family HMM PF06240; carbon monoxide dehydrogenase G protein 2540241 3194846 SPO2393 Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase G protein YP_167612.1 2539789 R 246200 CDS YP_167613.1 56697248 3193728 complement(2540453..2541235) 1 NC_003911.11 identified by similarity to GB:CAB76248.1; match to protein family HMM PF02625; carbon monoxide dehydrogenase F protein 2541235 coxF 3193728 coxF Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase F protein YP_167613.1 2540453 R 246200 CDS YP_167614.1 56697249 3194529 complement(2541232..2542413) 1 NC_003911.11 identified by similarity to GB:CAB76247.1; match to protein family HMM PF05762; carbon monoxide dehydrogenase E protein 2542413 coxE 3194529 coxE Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase E protein YP_167614.1 2541232 R 246200 CDS YP_167615.1 56697250 3192987 complement(2542410..2543312) 1 NC_003911.11 identified by similarity to GB:CAA57830.1; carbon monoxide dehydrogenase D protein 2543312 coxD 3192987 coxD Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase D protein YP_167615.1 2542410 R 246200 CDS YP_167616.1 56697251 3194835 complement(2543344..2545773) 1 NC_003911.11 identified by similarity to SP:P19919; match to protein family HMM PF01315; match to protein family HMM PF02738; carbon monoxide dehydrogenase, large subunit 2545773 coxL-2 3194835 coxL-2 Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase, large subunit YP_167616.1 2543344 R 246200 CDS YP_167617.1 56697252 3194614 complement(2545770..2546264) 1 NC_003911.11 identified by similarity to SP:P19921; match to protein family HMM PF00111; match to protein family HMM PF01799; carbon monoxide dehydrogenase, small subunit 2546264 coxS-2 3194614 coxS-2 Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase, small subunit YP_167617.1 2545770 R 246200 CDS YP_167618.1 56697253 3194034 complement(2546278..2547132) 1 NC_003911.11 identified by similarity to SP:P19920; match to protein family HMM PF00941; match to protein family HMM PF03450; carbon monoxide dehydrogenase, medium subunit 2547132 coxM 3194034 coxM Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase, medium subunit YP_167618.1 2546278 R 246200 CDS YP_167619.1 56697254 3193853 complement(2547244..2548365) 1 NC_003911.11 identified by similarity to GB:CAB76246.1; match to protein family HMM PF03707; carbon monoxide dehydrogenase operon C protein 2548365 coxC 3193853 coxC Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase operon C protein YP_167619.1 2547244 R 246200 CDS YP_167620.1 56697255 3193807 complement(2548868..2552137) 1 NC_003911.11 identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 2552137 3193807 SPO2401 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_167620.1 2548868 R 246200 CDS YP_167621.1 56697256 3193564 2554589..2554693 1 NC_003911.11 hypothetical protein 2554693 3193564 SPO2403 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167621.1 2554589 D 246200 CDS YP_167622.1 56697257 3194572 complement(2555372..2556031) 1 NC_003911.11 identified by match to protein family HMM PF00589; phage integrase site specific recombinase 2556031 3194572 SPO2405 Ruegeria pomeroyi DSS-3 phage integrase site specific recombinase YP_167622.1 2555372 R 246200 CDS YP_167623.1 56698735 3196314 2556700..2557140 1 NC_003911.11 identified by similarity to PIR:F95919; ISSpo6, transposase orf A 2557140 3196314 SPO2406 Ruegeria pomeroyi DSS-3 ISSpo6, transposase orf A YP_167623.1 2556700 D 246200 CDS YP_167624.1 56697258 3193340 2557085..2557660 1 NC_003911.11 identified by similarity to GB:CAC47676.1; ISSpo6, transposase orfB 2557660 3193340 SPO2407 Ruegeria pomeroyi DSS-3 ISSpo6, transposase orfB YP_167624.1 2557085 D 246200 CDS YP_167625.1 56697259 3194825 complement(2559208..2559843) 1 NC_003911.11 hypothetical protein 2559843 3194825 SPO2408 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167625.1 2559208 R 246200 CDS YP_167626.1 56697260 3192703 complement(2560699..2561466) 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2561466 3192703 SPO2409 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_167626.1 2560699 R 246200 CDS YP_167627.1 56697261 3192713 complement(2561463..2563244) 1 NC_003911.11 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase 2563244 3192713 SPO2410 Ruegeria pomeroyi DSS-3 dihydroxy-acid dehydratase YP_167627.1 2561463 R 246200 CDS YP_167628.1 56697262 3194822 2563267..2563821 1 NC_003911.11 hypothetical protein 2563821 3194822 SPO2411 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167628.1 2563267 D 246200 CDS YP_167629.1 56697263 3192853 2563843..2564538 1 NC_003911.11 identified by similarity to GB:BAB21456.3; aldolase 2564538 3192853 SPO2412 Ruegeria pomeroyi DSS-3 aldolase YP_167629.1 2563843 D 246200 CDS YP_167630.1 56697264 3194827 2564548..2565300 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2565300 3194827 SPO2413 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_167630.1 2564548 D 246200 CDS YP_167631.1 56697265 3194010 complement(2565441..2566610) 1 NC_003911.11 identified by match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase 2566610 3194010 SPO2414 Ruegeria pomeroyi DSS-3 mandelate racemase YP_167631.1 2565441 R 246200 CDS YP_167632.1 56697266 3193600 complement(2566607..2567521) 1 NC_003911.11 identified by match to protein family HMM PF05721; phytanoyl-CoA dioxygenase 2567521 3193600 SPO2415 Ruegeria pomeroyi DSS-3 phytanoyl-CoA dioxygenase YP_167632.1 2566607 R 246200 CDS YP_167633.1 56697267 3194997 complement(2567541..2568452) 1 NC_003911.11 identified by similarity to SP:P23523; 3-hydroxyisobutyrate dehydrogenase 2568452 3194997 SPO2416 Ruegeria pomeroyi DSS-3 3-hydroxyisobutyrate dehydrogenase YP_167633.1 2567541 R 246200 CDS YP_167634.1 56697268 3192778 complement(2568543..2569304) 1 NC_003911.11 catalyzes the formation of 5-dehydro-D-gluconate from D-gluconate; gluconate 5-dehydrogenase 2569304 idnO 3192778 idnO Ruegeria pomeroyi DSS-3 gluconate 5-dehydrogenase YP_167634.1 2568543 R 246200 CDS YP_167635.1 56697269 3194808 2569503..2570105 1 NC_003911.11 identified by match to protein family HMM PF01810; amino acid transporter LysE 2570105 3194808 SPO2418 Ruegeria pomeroyi DSS-3 amino acid transporter LysE YP_167635.1 2569503 D 246200 CDS YP_167636.1 56697270 3195201 2570166..2571317 1 NC_003911.11 identified by similarity to GB:CAB55723.1; hypothetical protein 2571317 3195201 SPO2419 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167636.1 2570166 D 246200 CDS YP_167637.1 56697271 3194444 2571466..2572380 1 NC_003911.11 identified by similarity to SP:P37647; match to protein family HMM PF00294; 2-dehydro-3-deoxygluconokinase 2572380 kdgK 3194444 kdgK Ruegeria pomeroyi DSS-3 2-dehydro-3-deoxygluconokinase YP_167637.1 2571466 D 246200 CDS YP_167638.1 56697272 3193263 2572377..2573345 1 NC_003911.11 identified by similarity to PIR:B96013; hypothetical protein 2573345 3193263 SPO2421 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167638.1 2572377 D 246200 CDS YP_167639.1 56697274 3194503 complement(2573459..2574400) 1 NC_003911.11 identified by match to protein family HMM PF00389; match to protein family HMM PF02826; D-isomer specific 2-hydroxyacid dehydrogenase 2574400 3194503 SPO2422 Ruegeria pomeroyi DSS-3 D-isomer specific 2-hydroxyacid dehydrogenase YP_167639.1 2573459 R 246200 CDS YP_167640.1 56697273 3194787 2574536..2574799 1 NC_003911.11 identified by similarity to SP:O58489; hypothetical protein 2574799 3194787 SPO2423 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167640.1 2574536 D 246200 CDS YP_167641.1 56697275 3193193 2574813..2575862 1 NC_003911.11 identified by similarity to SP:P39346; match to protein family HMM PF00107; L-idonate 5-dehydrogenase 2575862 idnD 3193193 idnD Ruegeria pomeroyi DSS-3 L-idonate 5-dehydrogenase YP_167641.1 2574813 D 246200 CDS YP_167642.1 56697276 3193039 2575872..2576699 1 NC_003911.11 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase 2576699 aroE 3193039 aroE Ruegeria pomeroyi DSS-3 shikimate 5-dehydrogenase YP_167642.1 2575872 D 246200 CDS YP_167643.1 56697277 3194474 complement(2576701..2577588) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 2577588 3194474 SPO2426 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167643.1 2576701 R 246200 CDS YP_167644.1 56697278 3193137 complement(2577596..2578318) 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2578318 3193137 SPO2427 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_167644.1 2577596 R 246200 CDS YP_167645.1 56697279 3194447 complement(2578315..2579223) 1 NC_003911.11 identified by match to protein family HMM PF03446; 6-phosphogluconate dehydrogenase 2579223 3194447 SPO2428 Ruegeria pomeroyi DSS-3 6-phosphogluconate dehydrogenase YP_167645.1 2578315 R 246200 CDS YP_167646.1 56697280 3194475 complement(2579220..2580284) 1 NC_003911.11 identified by match to protein family HMM PF01408; match to protein family HMM PF02894; Gfo/Idh/MocA family oxidoreductase 2580284 3194475 SPO2429 Ruegeria pomeroyi DSS-3 Gfo/Idh/MocA family oxidoreductase YP_167646.1 2579220 R 246200 CDS YP_167647.1 56697281 3195425 complement(2580281..2581774) 1 NC_003911.11 identified by match to protein family HMM PF04292; match to protein family HMM PF04295; UxaA family hydrolase 2581774 3195425 SPO2430 Ruegeria pomeroyi DSS-3 UxaA family hydrolase YP_167647.1 2580281 R 246200 CDS YP_167648.1 56697282 3193883 complement(2581865..2583493) 1 NC_003911.11 identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM 2583493 3193883 SPO2431 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_167648.1 2581865 R 246200 CDS YP_167649.1 56697283 3194673 complement(2583495..2584103) 1 NC_003911.11 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ 2584103 3194673 SPO2432 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctQ YP_167649.1 2583495 R 246200 CDS YP_167650.1 56697284 3195176 complement(2584432..2585604) 1 NC_003911.11 identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 2585604 3195176 SPO2433 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctP YP_167650.1 2584432 R 246200 CDS YP_167651.1 56697285 3193671 2585641..2586348 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 2586348 3193671 SPO2434 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_167651.1 2585641 D 246200 CDS YP_167652.1 56697286 3194708 2586391..2587236 1 NC_003911.11 identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase 2587236 3194708 SPO2435 Ruegeria pomeroyi DSS-3 fumarylacetoacetate hydrolase YP_167652.1 2586391 D 246200 CDS YP_167653.1 56697287 3194123 complement(2587546..2589984) 1 NC_003911.11 identified by match to protein family HMM PF01266; match to protein family HMM PF01571; FAD-dependent oxidoreductase 2589984 3194123 SPO2436 Ruegeria pomeroyi DSS-3 FAD-dependent oxidoreductase YP_167653.1 2587546 R 246200 CDS YP_167654.1 56697288 3194574 complement(2590024..2590806) 1 NC_003911.11 identified by match to protein family HMM PF01177; Asp/Glu/Hydantoin racemase 2590806 3194574 SPO2437 Ruegeria pomeroyi DSS-3 Asp/Glu/Hydantoin racemase YP_167654.1 2590024 R 246200 CDS YP_167655.1 56697289 3194661 complement(2590809..2591696) 1 NC_003911.11 identified by match to protein family HMM PF05721; phytanoyl-CoA dioxygenase 2591696 3194661 SPO2438 Ruegeria pomeroyi DSS-3 phytanoyl-CoA dioxygenase YP_167655.1 2590809 R 246200 CDS YP_167656.1 56697290 3194570 2591937..2592704 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 2592704 3194570 SPO2439 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_167656.1 2591937 D 246200 CDS YP_167657.1 56697291 3195873 2592712..2593866 1 NC_003911.11 identified by match to protein family HMM PF00557; M24 family metallopeptidase 2593866 3195873 SPO2440 Ruegeria pomeroyi DSS-3 M24 family metallopeptidase YP_167657.1 2592712 D 246200 CDS YP_167658.1 56697292 3192732 2594080..2595054 1 NC_003911.11 identified by similarity to GB:AAF78097.1; match to protein family HMM PF04069; glycine betaine/L-proline ABC transporter substrate-binding protein 2595054 3192732 SPO2441 Ruegeria pomeroyi DSS-3 glycine betaine/L-proline ABC transporter substrate-binding protein YP_167658.1 2594080 D 246200 CDS YP_167659.1 56697293 3195170 2595168..2596199 1 NC_003911.11 identified by similarity to SP:P14176; match to protein family HMM PF00528; glycine betaine/proline ABC transporter permease 2596199 3195170 SPO2442 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter permease YP_167659.1 2595168 D 246200 CDS YP_167660.1 56697294 3194609 2596211..2597272 1 NC_003911.11 identified by similarity to SP:P46920; match to protein family HMM PF00005; glycine betaine/proline ABC transporter ATP-binding protein 2597272 3194609 SPO2443 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter ATP-binding protein YP_167660.1 2596211 D 246200 CDS YP_167661.1 56697295 3194414 complement(2597384..2597806) 1 NC_003911.11 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase 2597806 ndk 3194414 ndk Ruegeria pomeroyi DSS-3 nucleoside diphosphate kinase YP_167661.1 2597384 R 246200 CDS YP_167662.1 56697296 3195902 complement(2597933..2599198) 1 NC_003911.11 identified by match to protein family HMM TIGR00710; Bcr/CflA subfamily drug resistance transporter 2599198 3195902 SPO2445 Ruegeria pomeroyi DSS-3 Bcr/CflA subfamily drug resistance transporter YP_167662.1 2597933 R 246200 CDS YP_167663.1 56697297 3194578 2599240..2601090 1 NC_003911.11 identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 2601090 3194578 SPO2446 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_167663.1 2599240 D 246200 CDS YP_167664.1 56697298 3195776 2601045..2601569 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 2601569 3195776 SPO2447 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167664.1 2601045 D 246200 CDS YP_167665.1 56697299 3194075 2601566..2602186 1 NC_003911.11 identified by match to protein family HMM PF01914; match to protein family HMM TIGR00427; multiple antibiotic resistance protein MarC 2602186 3194075 SPO2448 Ruegeria pomeroyi DSS-3 multiple antibiotic resistance protein MarC YP_167665.1 2601566 D 246200 CDS YP_167666.1 56697300 3194569 2602226..2602807 1 NC_003911.11 hypothetical protein 2602807 3194569 SPO2449 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167666.1 2602226 D 246200 CDS YP_167667.1 56697301 3194002 2602907..2603659 1 NC_003911.11 identified by match to protein family HMM PF01177; Asp/Glu/Hydantoin racemase 2603659 3194002 SPO2450 Ruegeria pomeroyi DSS-3 Asp/Glu/Hydantoin racemase YP_167667.1 2602907 D 246200 CDS YP_167668.1 56697302 3194053 complement(2603669..2604433) 1 NC_003911.11 identified by match to protein family HMM PF01553; acyltransferase 2604433 3194053 SPO2451 Ruegeria pomeroyi DSS-3 acyltransferase YP_167668.1 2603669 R 246200 CDS YP_167669.1 56697303 3192881 complement(2604620..2605084) 1 NC_003911.11 binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB; DNA polymerase III subunit chi 2605084 3192881 SPO2452 Ruegeria pomeroyi DSS-3 DNA polymerase III subunit chi YP_167669.1 2604620 R 246200 CDS YP_167670.1 56697304 3192926 complement(2605089..2606570) 1 NC_003911.11 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase 2606570 pepA 3192926 pepA Ruegeria pomeroyi DSS-3 leucyl aminopeptidase YP_167670.1 2605089 R 246200 CDS YP_167671.1 56697305 3194435 2606803..2607900 1 NC_003911.11 identified by match to protein family HMM PF03739; YjgP/YjgQ family permease 2607900 3194435 SPO2454 Ruegeria pomeroyi DSS-3 YjgP/YjgQ family permease YP_167671.1 2606803 D 246200 CDS YP_167672.1 56697306 3193355 2607900..2610056 1 NC_003911.11 identified by similarity to SP:P31554; organic solvent tolerance protein 2610056 3193355 SPO2455 Ruegeria pomeroyi DSS-3 organic solvent tolerance protein YP_167672.1 2607900 D 246200 CDS YP_167673.1 56697307 3194958 2610041..2611279 1 NC_003911.11 peptidyl-prolyl cis-trans isomerase domain-containing protein 2611279 3194958 SPO2456 Ruegeria pomeroyi DSS-3 peptidyl-prolyl cis-trans isomerase domain-containing protein YP_167673.1 2610041 D 246200 CDS YP_167674.1 56697308 3195279 2611284..2612243 1 NC_003911.11 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate); 4-hydroxythreonine-4-phosphate dehydrogenase 2612243 pdxA 3195279 pdxA Ruegeria pomeroyi DSS-3 4-hydroxythreonine-4-phosphate dehydrogenase YP_167674.1 2611284 D 246200 CDS YP_167675.1 56697309 3192940 2612325..2613164 1 NC_003911.11 catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases A1518 and A1519 in 16S rRNA; mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin; dimethyladenosine transferase 2613164 ksgA 3192940 ksgA Ruegeria pomeroyi DSS-3 dimethyladenosine transferase YP_167675.1 2612325 D 246200 CDS YP_167676.1 56697310 3194624 complement(2613332..2614042) 1 NC_003911.11 identified by similarity to PIR:H98216; hypothetical protein 2614042 3194624 SPO2459 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167676.1 2613332 R 246200 CDS YP_167677.1 56697311 3193801 complement(2614200..2615015) 1 NC_003911.11 identified by match to protein family HMM TIGR00536; HemK family modification methylase 2615015 3193801 SPO2460 Ruegeria pomeroyi DSS-3 HemK family modification methylase YP_167677.1 2614200 R 246200 CDS YP_167678.1 56697312 3194030 complement(2615039..2616094) 1 NC_003911.11 recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1; this protein is similar to release factor 2; peptide chain release factor 1 2616094 prfA 3194030 prfA Ruegeria pomeroyi DSS-3 peptide chain release factor 1 YP_167678.1 2615039 R 246200 CDS YP_167679.1 56697313 3193596 2616122..2616451 1 NC_003911.11 identified by similarity to GB:CAC45916.1; hypothetical protein 2616451 3193596 SPO2462 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167679.1 2616122 D 246200 CDS YP_167680.1 56697314 3193346 complement(2616392..2616796) 1 NC_003911.11 identified by similarity to GB:CAE21209.1; hypothetical protein 2616796 3193346 SPO2463 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167680.1 2616392 R 246200 CDS YP_167681.1 56697315 3194037 complement(2616800..2617747) 1 NC_003911.11 identified by similarity to SP:Q9BSE5; match to protein family HMM PF00491; match to protein family HMM TIGR01230; agmatinase 2617747 speB-2 3194037 speB-2 Ruegeria pomeroyi DSS-3 agmatinase YP_167681.1 2616800 R 246200 CDS YP_167682.1 56697316 3194567 complement(2617832..2618371) 1 NC_003911.11 identified by similarity to GB:AAO54462.1; hypothetical protein 2618371 3194567 SPO2465 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167682.1 2617832 R 246200 CDS YP_167683.1 56697317 3192696 2618411..2618788 1 NC_003911.11 identified by similarity to GB:AAN68182.1; match to protein family HMM PF00903; glyoxalase 2618788 3192696 SPO2466 Ruegeria pomeroyi DSS-3 glyoxalase YP_167683.1 2618411 D 246200 CDS YP_167684.1 56697318 3193270 complement(2618829..2619812) 1 NC_003911.11 catalyzes the formation of putrescine from agmatine; agmatinase 2619812 speB-3 3193270 speB-3 Ruegeria pomeroyi DSS-3 agmatinase YP_167684.1 2618829 R 246200 CDS YP_167685.1 56697319 3193766 complement(2619858..2621021) 1 NC_003911.11 identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase 2621021 3193766 SPO2468 Ruegeria pomeroyi DSS-3 amidohydrolase YP_167685.1 2619858 R 246200 CDS YP_167686.1 56697320 3194456 2621087..2621908 1 NC_003911.11 functions in degradation of stringent response intracellular messenger ppGpp; in Escherichia coli this gene is co-transcribed with the toxin/antitoxin genes mazEF; activity of MazG is inhibited by MazEF in vitro; ppGpp inhibits mazEF expression; MazG thus works in limiting the toxic activity of the MazF toxin induced during starvation; MazG also interacts with the GTPase Era; nucleoside triphosphate pyrophosphohydrolase 2621908 mazG 3194456 mazG Ruegeria pomeroyi DSS-3 nucleoside triphosphate pyrophosphohydrolase YP_167686.1 2621087 D 246200 CDS YP_167687.1 56697321 3193287 2622032..2622973 1 NC_003911.11 identified by match to protein family HMM PF01156; inosine-uridine preferring nucleoside hydrolase 2622973 iunH 3193287 iunH Ruegeria pomeroyi DSS-3 inosine-uridine preferring nucleoside hydrolase YP_167687.1 2622032 D 246200 CDS YP_167688.1 56697322 3194164 2622970..2623419 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 2623419 3194164 SPO2471 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167688.1 2622970 D 246200 CDS YP_167689.1 56697323 3194051 complement(2623477..2623791) 1 NC_003911.11 identified by similarity to GB:BAC45440.1; hypothetical protein 2623791 3194051 SPO2472 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167689.1 2623477 R 246200 CDS YP_167690.1 56697324 3194523 complement(2623763..2624524) 1 NC_003911.11 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01428; match to protein family HMM TIGR01493; haloacid dehalogenase 2624524 3194523 SPO2473 Ruegeria pomeroyi DSS-3 haloacid dehalogenase YP_167690.1 2623763 R 246200 CDS YP_167691.1 56697325 3193003 complement(2624682..2625959) 1 NC_003911.11 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase 2625959 eno 3193003 eno Ruegeria pomeroyi DSS-3 phosphopyruvate hydratase YP_167691.1 2624682 R 246200 CDS YP_167692.1 56697326 3194446 complement(2626109..2627044) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 2627044 3194446 SPO2475 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167692.1 2626109 R 246200 CDS YP_167693.1 56697327 3194512 2627224..2627541 1 NC_003911.11 lipoprotein 2627541 3194512 SPO2476 Ruegeria pomeroyi DSS-3 lipoprotein YP_167693.1 2627224 D 246200 CDS YP_167694.1 56697328 3194017 complement(2627656..2628069) 1 NC_003911.11 identified by match to protein family HMM PF01475; FUR family transcriptional regulator 2628069 3194017 SPO2477 Ruegeria pomeroyi DSS-3 FUR family transcriptional regulator YP_167694.1 2627656 R 246200 CDS YP_167695.1 56697329 3194429 complement(2629710..2630141) 1 NC_003911.11 identified by similarity to PIR:E87313; match to protein family HMM PF06172; hypothetical protein 2630141 3194429 SPO2479 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167695.1 2629710 R 246200 CDS YP_167696.1 56697330 3193161 2630167..2631612 1 NC_003911.11 identified by similarity to SP:Q89MQ0; match to protein family HMM PF02696; hypothetical protein 2631612 3193161 SPO2480 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167696.1 2630167 D 246200 CDS YP_167697.1 56697331 3194428 complement(2631700..2632605) 1 NC_003911.11 identified by match to protein family HMM PF00892; drug/metabolite exporter family protein 2632605 3194428 SPO2481 Ruegeria pomeroyi DSS-3 drug/metabolite exporter family protein YP_167697.1 2631700 R 246200 CDS YP_167698.1 56697332 3194431 2632691..2633392 1 NC_003911.11 identified by match to protein family HMM PF03372; hypothetical protein 2633392 3194431 SPO2482 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167698.1 2632691 D 246200 CDS YP_167699.1 56697333 3193994 complement(2633490..2634572) 1 NC_003911.11 catalyzes hydrolysis of 1,6-anhydro bond of anyhydro-N-acetylmuramic acid (anhMurNAc) and phosphorylates anhMurNAc to produce N-acetyl-muramate-6-phosphate; involved in murein recycling; anhydro-N-acetylmuramic acid kinase 2634572 anmK 3193994 anmK Ruegeria pomeroyi DSS-3 anhydro-N-acetylmuramic acid kinase YP_167699.1 2633490 R 246200 CDS YP_167700.1 56697334 3194517 2634665..2635912 1 NC_003911.11 identified by similarity to SP:P00951; match to protein family HMM PF00579; match to protein family HMM TIGR00234; tyrosyl-tRNA synthetase 2635912 tyrS 3194517 tyrS Ruegeria pomeroyi DSS-3 tyrosyl-tRNA synthetase YP_167700.1 2634665 D 246200 CDS YP_167701.1 56697335 3194526 complement(2636011..2636133) 1 NC_003911.11 hypothetical protein 2636133 3194526 SPO2485 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167701.1 2636011 R 246200 CDS YP_167702.1 56698733 3196341 2636180..2637082 1 NC_003911.11 identified by similarity to GB:AAL49478.1; hypothetical protein 2637082 3196341 SPO2486 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167702.1 2636180 D 246200 CDS YP_167703.1 56697336 3194504 2637110..2637865 1 NC_003911.11 identified by similarity to SP:O02691; match to protein family HMM PF00106; 3-hydroxyacyl-CoA dehydrogenase 2637865 3194504 SPO2487 Ruegeria pomeroyi DSS-3 3-hydroxyacyl-CoA dehydrogenase YP_167703.1 2637110 D 246200 CDS YP_167704.1 56697337 3194472 complement(2637887..2639695) 1 NC_003911.11 identified by similarity to SP:P43672; match to protein family HMM PF00005; ABC transporter ATP-binding protein 2639695 3194472 SPO2488 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_167704.1 2637887 R 246200 CDS YP_167705.1 56697339 3194454 complement(2639748..2640539) 1 NC_003911.11 identified by similarity to GB:BAC75021.1; hypothetical protein 2640539 3194454 SPO2489 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167705.1 2639748 R 246200 CDS YP_167706.1 56697338 3195382 complement(2640575..2641042) 1 NC_003911.11 identified by match to protein family HMM PF04355; SmpA/OmlA family lipoprotein 2641042 3195382 SPO2490 Ruegeria pomeroyi DSS-3 SmpA/OmlA family lipoprotein YP_167706.1 2640575 R 246200 CDS YP_167707.1 56697340 3194514 2641058..2641666 1 NC_003911.11 identified by similarity to GB:BAB54306.1; hypothetical protein 2641666 3194514 SPO2491 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167707.1 2641058 D 246200 CDS YP_167708.1 56698714 3196294 2641875..2642081 1 NC_003911.11 some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 2642081 rpmF 3196294 rpmF Ruegeria pomeroyi DSS-3 50S ribosomal protein L32 YP_167708.1 2641875 D 246200 CDS YP_167709.1 56697341 3194463 2642106..2643221 1 NC_003911.11 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY; glycerol-3-phosphate acyltransferase PlsX 2643221 plsX 3194463 plsX Ruegeria pomeroyi DSS-3 glycerol-3-phosphate acyltransferase PlsX YP_167709.1 2642106 D 246200 CDS YP_167710.1 56697342 3194497 2643227..2644198 1 NC_003911.11 identified by similarity to SP:P24249; match to protein family HMM TIGR00747; 3-oxoacyl-ACP synthase 2644198 fabH-2 3194497 fabH-2 Ruegeria pomeroyi DSS-3 3-oxoacyl-ACP synthase YP_167710.1 2643227 D 246200 CDS YP_167711.1 56697343 3194426 2644283..2644585 1 NC_003911.11 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit alpha 2644585 ihfA 3194426 ihfA Ruegeria pomeroyi DSS-3 integration host factor subunit alpha YP_167711.1 2644283 D 246200 CDS YP_167712.1 56697344 3194501 2644604..2645335 1 NC_003911.11 identified by match to protein family HMM PF00376; MerR family transcriptional regulator 2645335 3194501 SPO2496 Ruegeria pomeroyi DSS-3 MerR family transcriptional regulator YP_167712.1 2644604 D 246200 CDS YP_167713.1 56697345 3194232 2645535..2646614 1 NC_003911.11 Catalyzes the deamination of dCTP to form dUTP; 2'-deoxycytidine 5'-triphosphate deaminase 2646614 3194232 SPO2498 Ruegeria pomeroyi DSS-3 2'-deoxycytidine 5'-triphosphate deaminase YP_167713.1 2645535 D 246200 CDS YP_167714.1 56697346 3194235 complement(2646625..2646882) 1 NC_003911.11 hypothetical protein 2646882 3194235 SPO2499 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167714.1 2646625 R 246200 CDS YP_167715.1 56697347 3194127 complement(2646909..2647565) 1 NC_003911.11 identified by match to protein family HMM PF04079; match to protein family HMM TIGR00281; segregation and condensation protein B 2647565 scpB 3194127 scpB Ruegeria pomeroyi DSS-3 segregation and condensation protein B YP_167715.1 2646909 R 246200 CDS YP_167716.1 56697348 3194256 complement(2647562..2648407) 1 NC_003911.11 identified by match to protein family HMM PF02616; segregation and condensation protein A 2648407 scpA 3194256 scpA Ruegeria pomeroyi DSS-3 segregation and condensation protein A YP_167716.1 2647562 R 246200 CDS YP_167717.1 56697349 3194406 complement(2648343..2649350) 1 NC_003911.11 identified by similarity to SP:P75949; match to protein family HMM PF00933; beta-N-acetylhexosaminidase 2649350 3194406 SPO2502 Ruegeria pomeroyi DSS-3 beta-N-acetylhexosaminidase YP_167717.1 2648343 R 246200 CDS YP_167718.1 56697350 3195472 complement(2649347..2650573) 1 NC_003911.11 hypothetical protein 2650573 3195472 SPO2503 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167718.1 2649347 R 246200 CDS YP_167719.1 56697351 3193911 complement(2650533..2652278) 1 NC_003911.11 catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class-I aminoacyl-tRNA synthetase; arginyl-tRNA synthetase 2652278 argS 3193911 argS Ruegeria pomeroyi DSS-3 arginyl-tRNA synthetase YP_167719.1 2650533 R 246200 CDS YP_167720.1 56697352 3194081 complement(2652350..2653507) 1 NC_003911.11 identified by match to protein family HMM PF01966; match to protein family HMM TIGR01353; deoxyguanosinetriphosphate triphosphohydrolase 2653507 3194081 SPO2505 Ruegeria pomeroyi DSS-3 deoxyguanosinetriphosphate triphosphohydrolase YP_167720.1 2652350 R 246200 CDS YP_167721.1 56697353 3194098 2653583..2653906 1 NC_003911.11 identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049; Iron-sulfur cluster assembly family protein 2653906 3194098 SPO2506 Ruegeria pomeroyi DSS-3 Iron-sulfur cluster assembly family protein YP_167721.1 2653583 D 246200 CDS YP_167722.1 56697354 3194507 complement(2653910..2654803) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 2654803 3194507 SPO2507 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167722.1 2653910 R 246200 CDS YP_167723.1 56697355 3195529 complement(2655936..2656421) 1 NC_003911.11 identified by similarity to GB:AAQ93629.1; hypothetical protein 2656421 3195529 SPO2508 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167723.1 2655936 R 246200 CDS YP_167724.1 56697356 3194499 2656690..2657496 1 NC_003911.11 identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633; exodeoxyribonuclease III 2657496 xth 3194499 xth Ruegeria pomeroyi DSS-3 exodeoxyribonuclease III YP_167724.1 2656690 D 246200 CDS YP_167725.1 56697357 3194349 complement(2657585..2658751) 1 NC_003911.11 identified by similarity to SP:P23262; match to protein family HMM PF01360; salicylate hydroxylase 2658751 nahG 3194349 nahG Ruegeria pomeroyi DSS-3 salicylate hydroxylase YP_167725.1 2657585 R 246200 CDS YP_167726.1 56697358 3194221 complement(2658830..2659306) 1 NC_003911.11 identified by similarity to SP:P18274; match to protein family HMM PF01258; dnaK suppressor protein 2659306 3194221 SPO2511 Ruegeria pomeroyi DSS-3 dnaK suppressor protein YP_167726.1 2658830 R 246200 CDS YP_167727.1 56697359 3194308 2659642..2660487 1 NC_003911.11 identified by similarity to GB:CAA57830.1; match to protein family HMM PF00004; ATPase AAA 2660487 3194308 SPO2512 Ruegeria pomeroyi DSS-3 ATPase AAA YP_167727.1 2659642 D 246200 CDS YP_167728.1 56697360 3194524 2660655..2662100 1 NC_003911.11 identified by similarity to GB:CAE27057.1; hypothetical protein 2662100 3194524 SPO2513 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167728.1 2660655 D 246200 CDS YP_167729.1 56697361 3195383 2662116..2662283 1 NC_003911.11 hypothetical protein 2662283 3195383 SPO2514 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167729.1 2662116 D 246200 CDS YP_167730.1 56697362 3194071 2662288..2663472 1 NC_003911.11 identified by similarity to GB:BAB50733.1; hypothetical protein 2663472 3194071 SPO2515 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167730.1 2662288 D 246200 CDS YP_167731.1 56697363 3194413 complement(2663517..2663708) 1 NC_003911.11 hypothetical protein 2663708 3194413 SPO2516 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167731.1 2663517 R 246200 CDS YP_167732.1 56697364 3194332 2663950..2664636 1 NC_003911.11 identified by match to protein family HMM PF01435; M48 family peptidase 2664636 3194332 SPO2517 Ruegeria pomeroyi DSS-3 M48 family peptidase YP_167732.1 2663950 D 246200 CDS YP_167733.1 56697365 3194432 2664633..2665637 1 NC_003911.11 identified by match to protein family HMM PF00296; luciferase 2665637 3194432 SPO2518 Ruegeria pomeroyi DSS-3 luciferase YP_167733.1 2664633 D 246200 CDS YP_167734.1 56697366 3194275 complement(2665629..2666183) 1 NC_003911.11 identified by similarity to GB:CAE41104.1; hypothetical protein 2666183 3194275 SPO2519 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167734.1 2665629 R 246200 CDS YP_167735.1 56697367 3194087 complement(2666180..2667391) 1 NC_003911.11 identified by similarity to PIR:D83601; hypothetical protein 2667391 3194087 SPO2520 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167735.1 2666180 R 246200 CDS YP_167736.1 56697368 3194418 complement(2667431..2668207) 1 NC_003911.11 lipoprotein 2668207 3194418 SPO2521 Ruegeria pomeroyi DSS-3 lipoprotein YP_167736.1 2667431 R 246200 CDS YP_167737.1 56697369 3194522 complement(2668336..2668611) 1 NC_003911.11 hypothetical protein 2668611 3194522 SPO2522 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167737.1 2668336 R 246200 CDS YP_167738.1 56697370 3194476 complement(2668595..2671396) 1 NC_003911.11 identified by match to protein family HMM PF03710; glutamate-ammonia ligase adenylyltransferase 2671396 glnE 3194476 glnE Ruegeria pomeroyi DSS-3 glutamate-ammonia ligase adenylyltransferase YP_167738.1 2668595 R 246200 CDS YP_167739.1 56697371 3194170 2671479..2671952 1 NC_003911.11 identified by match to protein family HMM PF04073; prolyl-tRNA synthetase 2671952 3194170 SPO2524 Ruegeria pomeroyi DSS-3 prolyl-tRNA synthetase YP_167739.1 2671479 D 246200 CDS YP_167740.1 56697372 3194335 complement(2671962..2672108) 1 NC_003911.11 hypothetical protein 2672108 3194335 SPO2525 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167740.1 2671962 R 246200 CDS YP_167741.1 56697373 3195899 complement(2672618..2672830) 1 NC_003911.11 hypothetical protein 2672830 3195899 SPO2526 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167741.1 2672618 R 246200 CDS YP_167742.1 56697374 3194246 complement(2675136..2676575) 1 NC_003911.11 identified by similarity to SP:P13397; match to protein family HMM PF01425; 6-aminohexanoate-cyclic-dimer hydrolase 2676575 nylA 3194246 nylA Ruegeria pomeroyi DSS-3 6-aminohexanoate-cyclic-dimer hydrolase YP_167742.1 2675136 R 246200 CDS YP_167743.1 56697375 3194385 complement(2676621..2678336) 1 NC_003911.11 activates fatty acids by binding to coenzyme A; AMP-binding protein 2678336 3194385 SPO2528 Ruegeria pomeroyi DSS-3 AMP-binding protein YP_167743.1 2676621 R 246200 CDS YP_167744.1 56697376 3195465 complement(2678340..2680004) 1 NC_003911.11 identified by similarity to GB:BAB49910.1; hypothetical protein 2680004 3195465 SPO2529 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167744.1 2678340 R 246200 CDS YP_167745.1 56697377 3194189 complement(2680001..2681023) 1 NC_003911.11 identified by similarity to SP:P22729; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 2681023 3194189 SPO2530 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_167745.1 2680001 R 246200 CDS YP_167746.1 56697378 3194466 complement(2681020..2681898) 1 NC_003911.11 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 2681898 3194466 SPO2531 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_167746.1 2681020 R 246200 CDS YP_167747.1 56697379 3194978 complement(2681902..2682618) 1 NC_003911.11 identified by similarity to SP:P22731; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 2682618 3194978 SPO2532 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_167747.1 2681902 R 246200 CDS YP_167748.1 56697380 3193897 complement(2682615..2683382) 1 NC_003911.11 identified by similarity to SP:P21629; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 2683382 3193897 SPO2533 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_167748.1 2682615 R 246200 CDS YP_167749.1 56697381 3194352 complement(2683390..2684709) 1 NC_003911.11 Assignment partly based on membership in an branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF01094; match to protein family HMM TIGR01409; branched-chain amino acid ABC transporter periplasmic branched-chain amino acid-binding protein 2684709 3194352 SPO2534 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter periplasmic branched-chain amino acid-binding protein YP_167749.1 2683390 R 246200 CDS YP_167750.1 56697382 3194445 complement(2684729..2685844) 1 NC_003911.11 identified by match to protein family HMM PF00850; histone deacetylase/AcuC/AphA family protein 2685844 3194445 SPO2535 Ruegeria pomeroyi DSS-3 histone deacetylase/AcuC/AphA family protein YP_167750.1 2684729 R 246200 CDS YP_167751.1 56697383 3194231 2686001..2686738 1 NC_003911.11 identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 2686738 3194231 SPO2536 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_167751.1 2686001 D 246200 CDS YP_167752.1 56697384 3194453 complement(2687189..2687308) 1 NC_003911.11 hypothetical protein 2687308 3194453 SPO2537 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167752.1 2687189 R 246200 CDS YP_167753.1 56697385 3194069 complement(2687395..2688636) 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 2688636 3194069 SPO2538 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_167753.1 2687395 R 246200 CDS YP_167754.1 56697386 3194407 complement(2688666..2690213) 1 NC_003911.11 identified by match to protein family HMM PF00501; AMP-binding protein 2690213 3194407 SPO2539 Ruegeria pomeroyi DSS-3 AMP-binding protein YP_167754.1 2688666 R 246200 CDS YP_167755.1 56697387 3194166 complement(2690237..2691607) 1 NC_003911.11 identified by match to protein family HMM PF00289; match to protein family HMM PF02785; match to protein family HMM PF02786; carbamoyl-phosphate synthase 2691607 3194166 SPO2540 Ruegeria pomeroyi DSS-3 carbamoyl-phosphate synthase YP_167755.1 2690237 R 246200 CDS YP_167756.1 56697388 3194433 complement(2691615..2693171) 1 NC_003911.11 identified by similarity to GB:AAD28194.1; match to protein family HMM PF01039; propionyl-CoA carboxylase 2693171 3194433 SPO2541 Ruegeria pomeroyi DSS-3 propionyl-CoA carboxylase YP_167756.1 2691615 R 246200 CDS YP_167757.1 56697389 3194425 2693316..2693543 1 NC_003911.11 identified by match to protein family HMM PF00364; biotin/lipoate binding domain-containing protein 2693543 3194425 SPO2542 Ruegeria pomeroyi DSS-3 biotin/lipoate binding domain-containing protein YP_167757.1 2693316 D 246200 CDS YP_167758.1 56697390 3195990 2693584..2694333 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 2694333 3195990 SPO2543 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_167758.1 2693584 D 246200 CDS YP_167759.1 56697391 3194450 complement(2694321..2695226) 1 NC_003911.11 identified by match to protein family HMM PF04909; amidohydrolase 2695226 3194450 SPO2544 Ruegeria pomeroyi DSS-3 amidohydrolase YP_167759.1 2694321 R 246200 CDS YP_167760.1 56697392 3194296 complement(2695285..2696328) 1 NC_003911.11 identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 2696328 3194296 SPO2545 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctP YP_167760.1 2695285 R 246200 CDS YP_167761.1 56697393 3194374 complement(2696374..2696886) 1 NC_003911.11 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ 2696886 3194374 SPO2546 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctQ YP_167761.1 2696374 R 246200 CDS YP_167762.1 56697394 3194452 complement(2696888..2698201) 1 NC_003911.11 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM 2698201 3194452 SPO2547 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_167762.1 2696888 R 246200 CDS YP_167763.1 56697395 3194298 2698322..2699314 1 NC_003911.11 identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase 2699314 3194298 SPO2548 Ruegeria pomeroyi DSS-3 zinc-binding dehydrogenase oxidoreductase YP_167763.1 2698322 D 246200 CDS YP_167764.1 56697396 3194116 2699321..2700352 1 NC_003911.11 identified by match to protein family HMM PF01636; phosphotransferase 2700352 3194116 SPO2549 Ruegeria pomeroyi DSS-3 phosphotransferase YP_167764.1 2699321 D 246200 CDS YP_167765.1 56697397 3194265 complement(2700409..2701122) 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 2701122 3194265 SPO2550 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_167765.1 2700409 R 246200 CDS YP_167766.1 56697398 3194153 complement(2701142..2702098) 1 NC_003911.11 identified by similarity to SP:P42065; match to protein family HMM PF00005; match to protein family HMM TIGR01727; peptide/opine/nickel uptake ABC transporter ATP-binding protein 2702098 3194153 SPO2551 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter ATP-binding protein YP_167766.1 2701142 R 246200 CDS YP_167767.1 56697399 3193129 complement(2702098..2703963) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF00528; match to protein family HMM TIGR01727; peptide/opine/nickel ABC transporter permease/ATP-binding protein 2703963 3193129 SPO2552 Ruegeria pomeroyi DSS-3 peptide/opine/nickel ABC transporter permease/ATP-binding protein YP_167767.1 2702098 R 246200 CDS YP_167768.1 56697400 3194148 complement(2703960..2704907) 1 NC_003911.11 identified by similarity to SP:P37316; match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease 2704907 3194148 SPO2553 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter permease YP_167768.1 2703960 R 246200 CDS YP_167769.1 56697401 3195667 complement(2704968..2706599) 1 NC_003911.11 identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; peptide/opine/nickel uptake ABC transporter substrate-binding protein 2706599 3195667 SPO2554 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter substrate-binding protein YP_167769.1 2704968 R 246200 CDS YP_167770.1 56697402 3194095 2706647..2707312 1 NC_003911.11 identified by similarity to GB:CAE35155.1; hypothetical protein 2707312 3194095 SPO2555 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167770.1 2706647 D 246200 CDS YP_167771.1 56697403 3194325 2707305..2708534 1 NC_003911.11 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase 2708534 3194325 SPO2556 Ruegeria pomeroyi DSS-3 allantoate amidohydrolase YP_167771.1 2707305 D 246200 CDS YP_167772.1 56697404 3194423 2710773..2711729 1 NC_003911.11 identified by similarity to SP:Q01578; match to protein family HMM PF03758; gluconolactonase 2711729 gnl 3194423 gnl Ruegeria pomeroyi DSS-3 gluconolactonase YP_167772.1 2710773 D 246200 CDS YP_167773.1 56697405 3194136 2711726..2712625 1 NC_003911.11 identified by similarity to SP:P23523; match to protein family HMM PF03446; 2-hydroxy-3-oxopropionate reductase 2712625 garR 3194136 garR Ruegeria pomeroyi DSS-3 2-hydroxy-3-oxopropionate reductase YP_167773.1 2711726 D 246200 CDS YP_167774.1 56697406 3194091 2712622..2713854 1 NC_003911.11 identified by match to protein family HMM PF07005; hypothetical protein 2713854 3194091 SPO2561 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167774.1 2712622 D 246200 CDS YP_167775.1 56697407 3194080 2713851..2714498 1 NC_003911.11 identified by similarity to SP:P11550; match to protein family HMM PF00596; aldolase 2714498 fucA 3194080 fucA Ruegeria pomeroyi DSS-3 aldolase YP_167775.1 2713851 D 246200 CDS YP_167776.1 56697408 3194109 2714495..2715250 1 NC_003911.11 identified by similarity to SP:P30147; hydroxypyruvate isomerase 2715250 3194109 SPO2563 Ruegeria pomeroyi DSS-3 hydroxypyruvate isomerase YP_167776.1 2714495 D 246200 CDS YP_167777.1 56697409 3194642 2715970..2716074 1 NC_003911.11 hypothetical protein 2716074 3194642 SPO2564 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167777.1 2715970 D 246200 CDS YP_167778.1 56697410 3194286 2716361..2717443 1 NC_003911.11 EngC; RsgA; CpgA; circularly permuted GTPase; ribosome small subunit-dependent GTPase A; has the pattern G4-G1-G3 as opposed to other GTPases; interacts strongly with 30S ribosome which stimulates GTPase activity; ribosome-associated GTPase 2717443 3194286 SPO2565 Ruegeria pomeroyi DSS-3 ribosome-associated GTPase YP_167778.1 2716361 D 246200 CDS YP_167779.1 56697411 3194139 2717430..2718215 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 2718215 3194139 SPO2566 Ruegeria pomeroyi DSS-3 glyoxalase YP_167779.1 2717430 D 246200 CDS YP_167780.1 56697412 3194104 2719098..2719547 1 NC_003911.11 identified by similarity to GB:CAE26557.1; hypothetical protein 2719547 3194104 SPO2567 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167780.1 2719098 D 246200 CDS YP_167781.1 56697413 3194509 2719605..2720042 1 NC_003911.11 identified by match to protein family HMM PF06271; RDD family protein 2720042 3194509 SPO2568 Ruegeria pomeroyi DSS-3 RDD family protein YP_167781.1 2719605 D 246200 CDS YP_167782.2 161598432 3194485 2720118..2720939 1 NC_003911.11 Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate; arginyl-tRNA-protein transferase 2720939 ate 3194485 ate Ruegeria pomeroyi DSS-3 arginyl-tRNA-protein transferase YP_167782.2 2720118 D 246200 CDS YP_167783.1 56697415 3194518 2720944..2721324 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 2721324 3194518 SPO2570 Ruegeria pomeroyi DSS-3 glyoxalase YP_167783.1 2720944 D 246200 CDS YP_167784.1 56697416 3194458 complement(2721521..2723875) 1 NC_003911.11 identified by match to protein family HMM PF06808; TRAP C4-dicarboxylate transport system permease DctM 2723875 3194458 SPO2571 Ruegeria pomeroyi DSS-3 TRAP C4-dicarboxylate transport system permease DctM YP_167784.1 2721521 R 246200 CDS YP_167785.1 56697417 3194417 complement(2723893..2724588) 1 NC_003911.11 hypothetical protein 2724588 3194417 SPO2572 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167785.1 2723893 R 246200 CDS YP_167786.1 56697418 3194455 complement(2724935..2726020) 1 NC_003911.11 identified by match to protein family HMM PF03480; match to protein family HMM TIGR01409; solute-binding family 7 protein 2726020 3194455 SPO2573 Ruegeria pomeroyi DSS-3 solute-binding family 7 protein YP_167786.1 2724935 R 246200 CDS YP_167787.1 56697419 3194482 2726110..2727714 1 NC_003911.11 identified by similarity to SP:P13799; match to protein family HMM PF02518; sensor histidine kinase 2727714 3194482 SPO2574 Ruegeria pomeroyi DSS-3 sensor histidine kinase YP_167787.1 2726110 D 246200 CDS YP_167788.1 56697420 3194300 2727711..2728361 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator 2728361 3194300 SPO2575 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_167788.1 2727711 D 246200 CDS YP_167789.1 56697421 3194063 complement(2728313..2728930) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 2728930 3194063 SPO2576 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_167789.1 2728313 R 246200 CDS YP_167790.1 56697422 3194451 2729048..2730136 1 NC_003911.11 hypothetical protein 2730136 3194451 SPO2577 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167790.1 2729048 D 246200 CDS YP_167791.1 56697423 3194403 2730491..2732242 1 NC_003911.11 catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; acetolactate synthase 3 catalytic subunit 2732242 ilvB 3194403 ilvB Ruegeria pomeroyi DSS-3 acetolactate synthase 3 catalytic subunit YP_167791.1 2730491 D 246200 CDS YP_167792.1 56697424 3194513 2732312..2732872 1 NC_003911.11 with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit; acetolactate synthase 3 regulatory subunit 2732872 ilvH 3194513 ilvH Ruegeria pomeroyi DSS-3 acetolactate synthase 3 regulatory subunit YP_167792.1 2732312 D 246200 CDS YP_167793.1 56697425 3194294 complement(2732884..2733252) 1 NC_003911.11 hypothetical protein 2733252 3194294 SPO2580 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167793.1 2732884 R 246200 CDS YP_167794.1 56697426 3194420 2733470..2734267 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 2734267 3194420 SPO2581 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_167794.1 2733470 D 246200 CDS YP_167795.1 56697427 3194434 complement(2734309..2735088) 1 NC_003911.11 hypothetical protein 2735088 3194434 SPO2582 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167795.1 2734309 R 246200 CDS YP_167796.1 56697428 3194443 complement(2735120..2736523) 1 NC_003911.11 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia; amidase 2736523 3194443 SPO2583 Ruegeria pomeroyi DSS-3 amidase YP_167796.1 2735120 R 246200 CDS YP_167797.1 56697429 3194489 2736658..2737089 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 2737089 3194489 SPO2584 Ruegeria pomeroyi DSS-3 glyoxalase YP_167797.1 2736658 D 246200 CDS YP_167798.1 56697430 3194310 complement(2737185..2738312) 1 NC_003911.11 recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1; peptide chain release factor 2 2738312 prfB 3194310 prfB Ruegeria pomeroyi DSS-3 peptide chain release factor 2 YP_167798.1 2737185 R 246200 CDS YP_167799.1 56697431 3194270 2738544..2740535 1 NC_003911.11 identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 2740535 3194270 SPO2586 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_167799.1 2738544 D 246200 CDS YP_167800.1 56697432 3194379 complement(2740529..2743015) 1 NC_003911.11 identified by match to protein family HMM PF00905; match to protein family HMM PF00912; match to protein family HMM TIGR02074; penicillin-binding protein 1A 2743015 mrca 3194379 mrca Ruegeria pomeroyi DSS-3 penicillin-binding protein 1A YP_167800.1 2740529 R 246200 CDS YP_167801.1 56697433 3194149 complement(2743172..2744389) 1 NC_003911.11 identified by match to protein family HMM PF01520; N-acetylmuramoyl-L-alanine amidase 2744389 3194149 SPO2588 Ruegeria pomeroyi DSS-3 N-acetylmuramoyl-L-alanine amidase YP_167801.1 2743172 R 246200 CDS YP_167802.1 56697434 3194336 complement(2744451..2745620) 1 NC_003911.11 identified by match to protein family HMM PF00155; aminotransferase, classes I and II 2745620 3194336 SPO2589 Ruegeria pomeroyi DSS-3 aminotransferase, classes I and II YP_167802.1 2744451 R 246200 CDS YP_167803.1 56697435 3194322 2745619..2746968 1 NC_003911.11 identified by match to protein family HMM PF01435; M48 family peptidase 2746968 3194322 SPO2590 Ruegeria pomeroyi DSS-3 M48 family peptidase YP_167803.1 2745619 D 246200 CDS YP_167804.1 56697436 3194331 2746965..2747723 1 NC_003911.11 identified by similarity to PIR:A49232; match to protein family HMM PF01323; hypothetical protein 2747723 3194331 SPO2591 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167804.1 2746965 D 246200 CDS YP_167805.1 56697437 3194333 complement(2747794..2748582) 1 NC_003911.11 identified by similarity to SP:P14489; beta-lactamase 2748582 3194333 SPO2592 Ruegeria pomeroyi DSS-3 beta-lactamase YP_167805.1 2747794 R 246200 CDS YP_167806.1 56697438 3194319 2748813..2749073 1 NC_003911.11 hypothetical protein 2749073 3194319 SPO2593 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167806.1 2748813 D 246200 CDS YP_167807.1 56697439 3194269 complement(2749081..2750208) 1 NC_003911.11 catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis; 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 2750208 ispG 3194269 ispG Ruegeria pomeroyi DSS-3 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase YP_167807.1 2749081 R 246200 CDS YP_167808.1 56697440 3194312 2750263..2751501 1 NC_003911.11 hypothetical protein 2751501 3194312 SPO2595 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167808.1 2750263 D 246200 CDS YP_167809.1 56697441 3194287 complement(2751613..2752836) 1 NC_003911.11 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 2752836 hemA-1 3194287 hemA-1 Ruegeria pomeroyi DSS-3 5-aminolevulinate synthase YP_167809.1 2751613 R 246200 CDS YP_167810.1 56697442 3194364 2753156..2754544 1 NC_003911.11 identified by match to protein family HMM PF01546; hypothetical protein 2754544 3194364 SPO2597 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167810.1 2753156 D 246200 CDS YP_167811.1 56697443 3193249 complement(2754573..2755532) 1 NC_003911.11 hypothetical protein 2755532 3193249 SPO2598 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167811.1 2754573 R 246200 CDS YP_167812.1 56697444 3194283 complement(2755967..2756905) 1 NC_003911.11 identified by match to protein family HMM PF02678; match to protein family HMM PF05726; pirin 2756905 3194283 SPO2601 Ruegeria pomeroyi DSS-3 pirin YP_167812.1 2755967 R 246200 CDS YP_167813.1 56697445 3194348 complement(2757005..2757877) 1 NC_003911.11 identified by match to protein family HMM PF01380; match to protein family HMM PF01418; RpiR family transcriptional regulator 2757877 3194348 SPO2602 Ruegeria pomeroyi DSS-3 RpiR family transcriptional regulator YP_167813.1 2757005 R 246200 CDS YP_167814.1 56697446 3194115 2757973..2758767 1 NC_003911.11 identified by match to protein family HMM PF05013; N-formylglutamate amidohydrolase 2758767 3194115 SPO2603 Ruegeria pomeroyi DSS-3 N-formylglutamate amidohydrolase YP_167814.1 2757973 D 246200 CDS YP_167815.1 56697447 3194271 2758784..2759320 1 NC_003911.11 identified by similarity to GB:BAB51666.1; hypothetical protein 2759320 3194271 SPO2604 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167815.1 2758784 D 246200 CDS YP_167816.1 56697448 3194272 2759322..2760647 1 NC_003911.11 identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM 2760647 3194272 SPO2605 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_167816.1 2759322 D 246200 CDS YP_167817.1 56697449 3194261 2760702..2761736 1 NC_003911.11 identified by match to protein family HMM PF03480; match to protein family HMM TIGR01409; solute-binding family 7 protein 2761736 3194261 SPO2606 Ruegeria pomeroyi DSS-3 solute-binding family 7 protein YP_167817.1 2760702 D 246200 CDS YP_167818.1 56697450 3194398 2761834..2763189 1 NC_003911.11 identified by similarity to GB:CAC81335.1; match to protein family HMM PF00120; gamma-glutamylisopropylamide synthetase 2763189 3194398 SPO2607 Ruegeria pomeroyi DSS-3 gamma-glutamylisopropylamide synthetase YP_167818.1 2761834 D 246200 CDS YP_167819.1 56697451 3194203 2763260..2764669 1 NC_003911.11 identified by similarity to GB:CAC81341.1; match to protein family HMM PF00171; aldehyde dehydrogenase 2764669 3194203 SPO2608 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_167819.1 2763260 D 246200 CDS YP_167820.1 56697452 3194197 2764675..2765820 1 NC_003911.11 identified by match to protein family HMM PF00465; alcohol dehydrogenase 2765820 3194197 SPO2609 Ruegeria pomeroyi DSS-3 alcohol dehydrogenase YP_167820.1 2764675 D 246200 CDS YP_167821.1 56697453 3194415 2765921..2766709 1 NC_003911.11 identified by similarity to GB:CAD17488.1; hypothetical protein 2766709 3194415 SPO2610 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167821.1 2765921 D 246200 CDS YP_167822.1 56697454 3194174 complement(2766944..2767219) 1 NC_003911.11 DNA-binding protein HU 2767219 3194174 SPO2612 Ruegeria pomeroyi DSS-3 DNA-binding protein HU YP_167822.1 2766944 R 246200 CDS YP_167823.1 56697455 3194158 complement(2767583..2769994) 1 NC_003911.11 identified by match to protein family HMM PF00004; match to protein family HMM PF02190; match to protein family HMM PF05362; match to protein family HMM TIGR00763; ATP-dependent protease La 2769994 lon 3194158 lon Ruegeria pomeroyi DSS-3 ATP-dependent protease La YP_167823.1 2767583 R 246200 CDS YP_167824.1 56697456 3194143 complement(2770257..2770940) 1 NC_003911.11 hypothetical protein 2770940 3194143 SPO2614 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167824.1 2770257 R 246200 CDS YP_167825.1 56697457 3194140 complement(2770956..2772032) 1 NC_003911.11 identified by match to protein family HMM PF00724; Oye family NADH-dependent flavin oxidoreductase 2772032 3194140 SPO2615 Ruegeria pomeroyi DSS-3 Oye family NADH-dependent flavin oxidoreductase YP_167825.1 2770956 R 246200 CDS YP_167826.1 56697458 3193294 complement(2772306..2773436) 1 NC_003911.11 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr); queuine tRNA-ribosyltransferase 2773436 tgt 3193294 tgt Ruegeria pomeroyi DSS-3 queuine tRNA-ribosyltransferase YP_167826.1 2772306 R 246200 CDS YP_167827.1 56697459 3194402 2773612..2774502 1 NC_003911.11 identified by match to protein family HMM PF01145; hypothetical protein 2774502 3194402 SPO2617 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167827.1 2773612 D 246200 CDS YP_167828.1 56697460 3194133 2774502..2774774 1 NC_003911.11 identified by similarity to PIR:C75311; hypothetical protein 2774774 3194133 SPO2618 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167828.1 2774502 D 246200 CDS YP_167829.1 56697461 3194220 2774919..2775281 1 NC_003911.11 identified by similarity to GB:AAK23834.1; match to protein family HMM PF01883; hypothetical protein 2775281 3194220 SPO2619 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167829.1 2774919 D 246200 CDS YP_167830.1 56697462 3195353 2775573..2775947 1 NC_003911.11 identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049; iron-sulfur cluster assembly accessory protein 2775947 3195353 SPO2620 Ruegeria pomeroyi DSS-3 iron-sulfur cluster assembly accessory protein YP_167830.1 2775573 D 246200 CDS YP_167831.1 56697463 3194114 2776049..2776804 1 NC_003911.11 identified by match to protein family HMM PF00121; match to protein family HMM TIGR00419; triosephosphate isomerase 2776804 tpiA 3194114 tpiA Ruegeria pomeroyi DSS-3 triosephosphate isomerase YP_167831.1 2776049 D 246200 CDS YP_167832.1 56697464 3194167 2776814..2777329 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 2777329 3194167 SPO2622 Ruegeria pomeroyi DSS-3 acetyltransferase YP_167832.1 2776814 D 246200 CDS YP_167833.1 56697465 3194124 complement(2777347..2777964) 1 NC_003911.11 identified by match to protein family HMM PF01810; amino acid transporter LysE 2777964 3194124 SPO2623 Ruegeria pomeroyi DSS-3 amino acid transporter LysE YP_167833.1 2777347 R 246200 CDS YP_167834.1 56697466 3194355 2778084..2778539 1 NC_003911.11 identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator 2778539 3194355 SPO2624 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_167834.1 2778084 D 246200 CDS YP_167835.1 56697467 3194100 2778591..2779244 1 NC_003911.11 identified by similarity to GB:AAM40972.1; hypothetical protein 2779244 3194100 SPO2625 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167835.1 2778591 D 246200 CDS YP_167836.1 56697468 3194079 complement(2779290..2780687) 1 NC_003911.11 identified by match to protein family HMM PF00597; match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP C4-dicarboxylate transport system permease DctM 2780687 3194079 SPO2626 Ruegeria pomeroyi DSS-3 TRAP C4-dicarboxylate transport system permease DctM YP_167836.1 2779290 R 246200 CDS YP_167837.1 56697469 3194181 complement(2780687..2781358) 1 NC_003911.11 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ 2781358 3194181 SPO2627 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctQ YP_167837.1 2780687 R 246200 CDS YP_167838.1 56697470 3194093 complement(2781431..2782432) 1 NC_003911.11 identified by similarity to SP:P37735; match to protein family HMM PF03480; match to protein family HMM TIGR00787; TRAP transporter solute receptor DctP family protein 2782432 3194093 SPO2628 Ruegeria pomeroyi DSS-3 TRAP transporter solute receptor DctP family protein YP_167838.1 2781431 R 246200 CDS YP_167839.1 56697471 3194353 complement(2782760..2783989) 1 NC_003911.11 identified by similarity to SP:P13632; match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954; match to protein family HMM TIGR01199; C4-dicarboxylate transport transcriptional regulatory protein 2783989 3194353 SPO2629 Ruegeria pomeroyi DSS-3 C4-dicarboxylate transport transcriptional regulatory protein YP_167839.1 2782760 R 246200 CDS YP_167840.1 56697472 3194082 complement(2783986..2785722) 1 NC_003911.11 identified by similarity to SP:P13633; match to protein family HMM PF00512; match to protein family HMM PF02518; C4-dicarboxylate transport sensor protein 2785722 3194082 SPO2630 Ruegeria pomeroyi DSS-3 C4-dicarboxylate transport sensor protein YP_167840.1 2783986 R 246200 CDS YP_167841.1 56697473 3193957 complement(2785776..2786237) 1 NC_003911.11 identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator 2786237 3193957 SPO2631 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_167841.1 2785776 R 246200 CDS YP_167842.1 56697474 3194076 2786378..2787154 1 NC_003911.11 identified by match to protein family HMM PF00590; match to protein family HMM TIGR01469; uroporphyrin-III C-methyltransferase 2787154 cobA-1 3194076 cobA-1 Ruegeria pomeroyi DSS-3 uroporphyrin-III C-methyltransferase YP_167842.1 2786378 D 246200 CDS YP_167843.1 56697475 3194478 2787154..2787468 1 NC_003911.11 identified by similarity to GB:CAE29655.1; hypothetical protein 2787468 3194478 SPO2633 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167843.1 2787154 D 246200 CDS YP_167844.1 56697476 3195199 2787532..2789196 1 NC_003911.11 identified by match to protein family HMM PF01077; match to protein family HMM PF03460; sulfite reductase 2789196 3195199 SPO2634 Ruegeria pomeroyi DSS-3 sulfite reductase YP_167844.1 2787532 D 246200 CDS YP_167845.1 56697477 3194868 2789186..2789947 1 NC_003911.11 catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite; phosphoadenosine phosphosulfate reductase 2789947 cysH 3194868 cysH Ruegeria pomeroyi DSS-3 phosphoadenosine phosphosulfate reductase YP_167845.1 2789186 D 246200 CDS YP_167846.1 56697478 3194525 2789944..2790351 1 NC_003911.11 identified by similarity to PIR:AF3472; hypothetical protein 2790351 3194525 SPO2636 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167846.1 2789944 D 246200 CDS YP_167847.1 56697479 3194521 2790466..2791299 1 NC_003911.11 identified by similarity to SP:Q44532; match to protein family HMM PF00970; ferredoxin-NADP reductase 2791299 3194521 SPO2637 Ruegeria pomeroyi DSS-3 ferredoxin-NADP reductase YP_167847.1 2790466 D 246200 CDS YP_167848.1 56697480 3195359 2791446..2791994 1 NC_003911.11 IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits; translation initiation factor IF-3 2791994 infC 3195359 infC Ruegeria pomeroyi DSS-3 translation initiation factor IF-3 YP_167848.1 2791446 D 246200 CDS YP_167849.1 56697481 3194500 complement(2792216..2793256) 1 NC_003911.11 identified by match to protein family HMM PF00994; molybdopterin biosynthesis protein 2793256 3194500 SPO2639 Ruegeria pomeroyi DSS-3 molybdopterin biosynthesis protein YP_167849.1 2792216 R 246200 CDS YP_167850.1 56697482 3194410 complement(2793253..2794233) 1 NC_003911.11 identified by match to protein family HMM PF02625; XdhC/CoxI family protein 2794233 3194410 SPO2640 Ruegeria pomeroyi DSS-3 XdhC/CoxI family protein YP_167850.1 2793253 R 246200 CDS YP_167851.1 56697483 3194490 complement(2794401..2794994) 1 NC_003911.11 hypothetical protein 2794994 3194490 SPO2641 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167851.1 2794401 R 246200 CDS YP_167852.1 56697484 3194132 complement(2794998..2795582) 1 NC_003911.11 identified by similarity to GB:BAC48787.1; match to protein family HMM PF04143; hypothetical protein 2795582 3194132 SPO2642 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167852.1 2794998 R 246200 CDS YP_167853.1 56697485 3194422 complement(2795667..2796755) 1 NC_003911.11 hypothetical protein 2796755 3194422 SPO2643 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167853.1 2795667 R 246200 CDS YP_167854.1 56697486 3194184 complement(2796752..2798014) 1 NC_003911.11 identified by match to protein family HMM PF05762; von Willebrand factor A 2798014 3194184 SPO2644 Ruegeria pomeroyi DSS-3 von Willebrand factor A YP_167854.1 2796752 R 246200 CDS YP_167855.1 56697487 3194400 2798051..2799034 1 NC_003911.11 identified by similarity to SP:P39790; S2 family protease 2799034 3194400 SPO2645 Ruegeria pomeroyi DSS-3 S2 family protease YP_167855.1 2798051 D 246200 CDS YP_167856.1 56697488 3194401 complement(2799128..2800036) 1 NC_003911.11 identified by similarity to GB:CAE29242.1; hypothetical protein 2800036 3194401 SPO2646 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167856.1 2799128 R 246200 CDS YP_167857.1 56697489 3194214 2800112..2801329 1 NC_003911.11 identified by similarity to PIR:F95909; hypothetical protein 2801329 3194214 SPO2647 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167857.1 2800112 D 246200 CDS YP_167858.1 56697490 3194320 2801326..2802015 1 NC_003911.11 hypothetical protein 2802015 3194320 SPO2648 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167858.1 2801326 D 246200 CDS YP_167859.1 56697491 3194366 2802015..2804396 1 NC_003911.11 identified by similarity to GB:CAB52234.1; hypothetical protein 2804396 3194366 SPO2649 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167859.1 2802015 D 246200 CDS YP_167860.1 56697492 3194280 2804400..2805098 1 NC_003911.11 identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 2805098 3194280 SPO2650 Ruegeria pomeroyi DSS-3 FkbM family methyltransferase YP_167860.1 2804400 D 246200 CDS YP_167861.1 56697493 3195392 2805105..2806184 1 NC_003911.11 identified by match to protein family HMM PF00535; glycosyl transferase family protein 2806184 3195392 SPO2651 Ruegeria pomeroyi DSS-3 glycosyl transferase family protein YP_167861.1 2805105 D 246200 CDS YP_167862.1 56697494 3194078 2806270..2807229 1 NC_003911.11 hypothetical protein 2807229 3194078 SPO2652 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167862.1 2806270 D 246200 CDS YP_167863.1 56697495 3194392 2807766..2808806 1 NC_003911.11 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 2808806 3194392 SPO2653 Ruegeria pomeroyi DSS-3 dihydroorotase YP_167863.1 2807766 D 246200 CDS YP_167864.1 56697496 3194223 2808884..2809561 1 NC_003911.11 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate; orotate phosphoribosyltransferase 2809561 pyrE 3194223 pyrE Ruegeria pomeroyi DSS-3 orotate phosphoribosyltransferase YP_167864.1 2808884 D 246200 CDS YP_167865.1 56697497 3194228 2809757..2811247 1 NC_003911.11 unwinds double stranded DNA; replicative DNA helicase 2811247 dnaB 3194228 dnaB Ruegeria pomeroyi DSS-3 replicative DNA helicase YP_167865.1 2809757 D 246200 CDS YP_167866.1 56697498 3194313 complement(2811257..2812147) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2812147 3194313 SPO2656 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167866.1 2811257 R 246200 CDS YP_167867.2 161598431 3194361 2812318..2813325 1 NC_003911.11 catalyzes the formation of pyruvate from D-cysteine; D-cysteine desulfhydrase 2813325 3194361 SPO2657 Ruegeria pomeroyi DSS-3 D-cysteine desulfhydrase YP_167867.2 2812318 D 246200 CDS YP_167868.1 56697500 3194326 2813357..2814220 1 NC_003911.11 Assignment based partly on membership in glutamate/aspartate ABC transporter gene cluster.; identified by similarity to SP:P37902; match to protein family HMM PF00497; glutamate/aspartate ABC transporter substrate-binding protein 2814220 gltI 3194326 gltI Ruegeria pomeroyi DSS-3 glutamate/aspartate ABC transporter substrate-binding protein YP_167868.1 2813357 D 246200 CDS YP_167869.1 56697501 3194077 2814287..2815003 1 NC_003911.11 Assignment based partly on membership in glutamate/aspartate ABC transporter gene cluster.; identified by similarity to SP:P41074; match to protein family HMM PF00528; match to protein family HMM TIGR01726; glutamate/aspartate ABC transporter permease 2815003 gltJ 3194077 gltJ Ruegeria pomeroyi DSS-3 glutamate/aspartate ABC transporter permease YP_167869.1 2814287 D 246200 CDS YP_167870.1 56697502 3195471 2815007..2815663 1 NC_003911.11 identified by similarity to SP:P41075; match to protein family HMM PF00528; match to protein family HMM TIGR01726; glutamate/aspartate ABC transporter permease 2815663 gltK 3195471 gltK Ruegeria pomeroyi DSS-3 glutamate/aspartate ABC transporter permease YP_167870.1 2815007 D 246200 CDS YP_167871.1 56697503 3194378 2815660..2816388 1 NC_003911.11 identified by similarity to SP:P41076; match to protein family HMM PF00005; glutamate/aspartate ABC transporter ATP-binding protein 2816388 gltL 3194378 gltL Ruegeria pomeroyi DSS-3 glutamate/aspartate ABC transporter ATP-binding protein YP_167871.1 2815660 D 246200 CDS YP_167872.1 56697504 3194173 complement(2816520..2817977) 1 NC_003911.11 Contains tandem repeat of aspartate racemase domain. Aspartate racemase is normally a homodimer.; identified by similarity to PIR:T08467; match to protein family HMM PF01177; match to protein family HMM TIGR00035; aspartate racemase 2817977 3194173 SPO2662 Ruegeria pomeroyi DSS-3 aspartate racemase YP_167872.1 2816520 R 246200 CDS YP_167873.1 56697505 3194328 complement(2817974..2819344) 1 NC_003911.11 catalyzes the formation of fumarate from aspartate; aspartate ammonia-lyase 2819344 aspA 3194328 aspA Ruegeria pomeroyi DSS-3 aspartate ammonia-lyase YP_167873.1 2817974 R 246200 CDS YP_167874.1 56697506 3194234 complement(2819355..2820122) 1 NC_003911.11 identified by similarity to SP:P27675; match to protein family HMM PF00005; polar amino acid ABC transporter ATP-binding protein 2820122 3194234 SPO2664 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter ATP-binding protein YP_167874.1 2819355 R 246200 CDS YP_167875.1 56697507 3193105 complement(2820124..2820918) 1 NC_003911.11 Assignment partly based on membership in polar amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease 2820918 3193105 SPO2665 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter permease YP_167875.1 2820124 R 246200 CDS YP_167876.1 56697508 3194168 complement(2820995..2821798) 1 NC_003911.11 identified by similarity to SP:P41074; match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease 2821798 3194168 SPO2666 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter permease YP_167876.1 2820995 R 246200 CDS YP_167877.1 56697509 3193739 complement(2821816..2822649) 1 NC_003911.11 Assignment partly based on membership in polar amino acid ABC transporter gene cluster and on multiple alignment to members of TCDB family 3.A.1.3.; identified by similarity to SP:P37902; match to protein family HMM PF00497; polar amino acid ABC transporter substrate-binding protein 2822649 3193739 SPO2667 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter substrate-binding protein YP_167877.1 2821816 R 246200 CDS YP_167878.1 56697510 3194134 2822841..2823734 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2823734 3194134 SPO2668 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_167878.1 2822841 D 246200 CDS YP_167879.1 56697511 3193427 2823920..2824873 1 NC_003911.11 identified by match to protein family HMM PF03171; 2OG-Fe(II) oxygenase 2824873 3193427 SPO2669 Ruegeria pomeroyi DSS-3 2OG-Fe(II) oxygenase YP_167879.1 2823920 D 246200 CDS YP_167880.1 56697512 3193741 2824893..2826026 1 NC_003911.11 identified by similarity to SP:P29743; match to protein family HMM PF00842; match to protein family HMM PF01168; match to protein family HMM TIGR00492; alanine racemase 2826026 alr 3193741 alr Ruegeria pomeroyi DSS-3 alanine racemase YP_167880.1 2824893 D 246200 CDS YP_167881.1 56697513 3194118 2826023..2826805 1 NC_003911.11 identified by similarity to GB:AAD17958.1; match to protein family HMM PF02405; match to protein family HMM TIGR00056; hypothetical protein 2826805 3194118 SPO2671 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167881.1 2826023 D 246200 CDS YP_167882.1 56697514 3194342 2826802..2827551 1 NC_003911.11 identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 2827551 3194342 SPO2672 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_167882.1 2826802 D 246200 CDS YP_167883.1 56697515 3193927 2827548..2828051 1 NC_003911.11 identified by match to protein family HMM PF04403; paraquat-inducible protein A 2828051 3193927 SPO2673 Ruegeria pomeroyi DSS-3 paraquat-inducible protein A YP_167883.1 2827548 D 246200 CDS YP_167884.1 56697516 3193849 2828263..2829624 1 NC_003911.11 Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents; DNA repair protein RadA 2829624 radA 3193849 radA Ruegeria pomeroyi DSS-3 DNA repair protein RadA YP_167884.1 2828263 D 246200 CDS YP_167885.1 56697517 3195324 2829667..2830221 1 NC_003911.11 identified by similarity to SP:P08550; match to protein family HMM PF02674; colicin V production protein CvpA 2830221 3195324 SPO2675 Ruegeria pomeroyi DSS-3 colicin V production protein CvpA YP_167885.1 2829667 D 246200 CDS YP_167886.1 56697518 3194306 2830468..2831040 1 NC_003911.11 hypothetical protein 2831040 3194306 SPO2676 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167886.1 2830468 D 246200 CDS YP_167887.1 56697519 3194339 2831183..2832655 1 NC_003911.11 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase 2832655 purF 3194339 purF Ruegeria pomeroyi DSS-3 amidophosphoribosyltransferase YP_167887.1 2831183 D 246200 CDS YP_167888.1 56697520 3193758 2832800..2833048 1 NC_003911.11 hypothetical protein 2833048 3193758 SPO2678 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167888.1 2832800 D 246200 CDS YP_167889.1 56697521 3194315 2833090..2833734 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2833734 3194315 SPO2679 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_167889.1 2833090 D 246200 CDS YP_167890.1 56697522 3193735 complement(2833789..2834631) 1 NC_003911.11 identified by similarity to GB:BAB48529.1; match to protein family HMM PF05673; hypothetical protein 2834631 3193735 SPO2680 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167890.1 2833789 R 246200 CDS YP_167891.1 56697523 3194249 complement(2834750..2835688) 1 NC_003911.11 identified by match to protein family HMM PF00902; match to protein family HMM TIGR00945; twin-arginine translocation protein TatC 2835688 tatC 3194249 tatC Ruegeria pomeroyi DSS-3 twin-arginine translocation protein TatC YP_167891.1 2834750 R 246200 CDS YP_167892.1 56697524 3194245 complement(2835685..2836143) 1 NC_003911.11 identified by match to protein family HMM PF02416; match to protein family HMM TIGR01410; twin-arginine translocation protein TatB 2836143 tatB 3194245 tatB Ruegeria pomeroyi DSS-3 twin-arginine translocation protein TatB YP_167892.1 2835685 R 246200 CDS YP_167893.1 56697525 3195048 complement(2836150..2836365) 1 NC_003911.11 identified by match to protein family HMM PF02416; twin arginine-targeting protein translocase 2836365 3195048 SPO2683 Ruegeria pomeroyi DSS-3 twin arginine-targeting protein translocase YP_167893.1 2836150 R 246200 CDS YP_167894.1 56697526 3194241 2836590..2836889 1 NC_003911.11 identified by similarity to GB:BAC96491.1; hypothetical protein 2836889 3194241 SPO2684 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167894.1 2836590 D 246200 CDS YP_167895.1 56697527 3193908 2836955..2837620 1 NC_003911.11 hypothetical protein 2837620 3193908 SPO2685 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167895.1 2836955 D 246200 CDS YP_167896.1 56697528 3195390 complement(2837760..2838950) 1 NC_003911.11 identified by match to protein family HMM PF01476; match to protein family HMM PF01551; LysM/M23/M37 peptidase 2838950 3195390 SPO2686 Ruegeria pomeroyi DSS-3 LysM/M23/M37 peptidase YP_167896.1 2837760 R 246200 CDS YP_167897.1 56697529 3193932 complement(2839029..2839676) 1 NC_003911.11 identified by match to protein family HMM PF01135; match to protein family HMM TIGR00080; protein-L-isoaspartate O-methyltransferase 2839676 pcm-2 3193932 pcm-2 Ruegeria pomeroyi DSS-3 protein-L-isoaspartate O-methyltransferase YP_167897.1 2839029 R 246200 CDS YP_167898.1 56697530 3194205 complement(2839673..2840455) 1 NC_003911.11 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE 2840455 surE 3194205 surE Ruegeria pomeroyi DSS-3 stationary phase survival protein SurE YP_167898.1 2839673 R 246200 CDS YP_167899.1 56697531 3194206 complement(2840667..2841764) 1 NC_003911.11 identified by similarity to SP:P21410; match to protein family HMM PF00005; iron ABC transporter ATP-binding protein 2841764 3194206 SPO2689 Ruegeria pomeroyi DSS-3 iron ABC transporter ATP-binding protein YP_167899.1 2840667 R 246200 CDS YP_167900.1 56697532 3194178 complement(2841855..2842910) 1 NC_003911.11 identified by similarity to GB:CAB61860.1; hypothetical protein 2842910 3194178 SPO2690 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167900.1 2841855 R 246200 CDS YP_167901.1 56697533 3195053 complement(2843069..2844175) 1 NC_003911.11 identified by similarity to GB:CAD72185.1; hypothetical protein 2844175 3195053 SPO2691 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167901.1 2843069 R 246200 CDS YP_167902.1 56697534 3194152 complement(2844179..2844958) 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2844958 3194152 SPO2692 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_167902.1 2844179 R 246200 CDS YP_167903.1 56697535 3193843 2845138..2846148 1 NC_003911.11 identified by similarity to GB:AAN33954.1; hypothetical protein 2846148 3193843 SPO2693 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167903.1 2845138 D 246200 CDS YP_167904.1 56697536 3194273 2846275..2846718 1 NC_003911.11 identified by match to protein family HMM PF01322; cytochrome c' 2846718 3194273 SPO2694 Ruegeria pomeroyi DSS-3 cytochrome c' YP_167904.1 2846275 D 246200 CDS YP_167905.1 56697537 3194161 2846764..2848371 1 NC_003911.11 identified by similarity to SP:Q56121; match to protein family HMM PF00009; match to protein family HMM PF03144; match to protein family HMM TIGR00231; match to protein family HMM TIGR00503; peptide chain release factor 3 2848371 3194161 SPO2695 Ruegeria pomeroyi DSS-3 peptide chain release factor 3 YP_167905.1 2846764 D 246200 CDS YP_167906.1 56697538 3194125 complement(2848417..2849544) 1 NC_003911.11 identified by match to protein family HMM PF00144; beta-lactamase 2849544 3194125 SPO2696 Ruegeria pomeroyi DSS-3 beta-lactamase YP_167906.1 2848417 R 246200 CDS YP_167907.1 56697539 3194122 complement(2849547..2851640) 1 NC_003911.11 identified by similarity to GB:AAN69320.1; similarity to GB:BAC79255.1; match to protein family HMM PF02629; acyl-CoA synthetase 2851640 3194122 SPO2697 Ruegeria pomeroyi DSS-3 acyl-CoA synthetase YP_167907.1 2849547 R 246200 CDS YP_167908.1 56697540 3193764 complement(2851637..2852797) 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 2852797 3193764 SPO2698 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_167908.1 2851637 R 246200 CDS YP_167909.1 56697541 3194110 complement(2852811..2853608) 1 NC_003911.11 identified by match to protein family HMM PF00528; opine/polyamine ABC transporter permease 2853608 3194110 SPO2699 Ruegeria pomeroyi DSS-3 opine/polyamine ABC transporter permease YP_167909.1 2852811 R 246200 CDS YP_167910.1 56697542 3194367 complement(2853605..2854483) 1 NC_003911.11 identified by match to protein family HMM PF00528; opine/polyamine ABC transporter permease 2854483 3194367 SPO2700 Ruegeria pomeroyi DSS-3 opine/polyamine ABC transporter permease YP_167910.1 2853605 R 246200 CDS YP_167911.1 56697543 3194107 complement(2854509..2855618) 1 NC_003911.11 identified by match to protein family HMM TIGR01409; opine/polyamine ABC transporter substrate-binding protein 2855618 3194107 SPO2701 Ruegeria pomeroyi DSS-3 opine/polyamine ABC transporter substrate-binding protein YP_167911.1 2854509 R 246200 CDS YP_167912.1 56697544 3194356 complement(2855698..2856699) 1 NC_003911.11 identified by match to protein family HMM PF00005; opine/polyamine ABC transporter ATP-binding protein 2856699 3194356 SPO2702 Ruegeria pomeroyi DSS-3 opine/polyamine ABC transporter ATP-binding protein YP_167912.1 2855698 R 246200 CDS YP_167913.1 56697545 3194386 complement(2856700..2857590) 1 NC_003911.11 identified by similarity to PIR:G82972; match to protein family HMM PF05853; hypothetical protein 2857590 3194386 SPO2703 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167913.1 2856700 R 246200 CDS YP_167914.1 56697546 3194351 2857726..2858811 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 2858811 3194351 SPO2704 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_167914.1 2857726 D 246200 CDS YP_167915.1 56697547 3194362 complement(2858777..2859730) 1 NC_003911.11 identified by match to protein family HMM PF00725; match to protein family HMM PF02737; 3-hydroxyacyl-CoA dehydrogenase 2859730 3194362 SPO2705 Ruegeria pomeroyi DSS-3 3-hydroxyacyl-CoA dehydrogenase YP_167915.1 2858777 R 246200 CDS YP_167916.1 56697548 3193838 complement(2859727..2860548) 1 NC_003911.11 catalyzes the dehydration of L-carnitinyl-CoA to crotonobetainyl-CoA; carnitinyl-CoA dehydratase 2860548 caiD-1 3193838 caiD-1 Ruegeria pomeroyi DSS-3 carnitinyl-CoA dehydratase YP_167916.1 2859727 R 246200 CDS YP_167917.1 56697549 3194309 complement(2860545..2861579) 1 NC_003911.11 identified by match to protein family HMM PF00296; luciferase 2861579 3194309 SPO2707 Ruegeria pomeroyi DSS-3 luciferase YP_167917.1 2860545 R 246200 CDS YP_167918.1 56697550 3194155 complement(2861607..2863088) 1 NC_003911.11 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 2863088 3194155 SPO2708 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_167918.1 2861607 R 246200 CDS YP_167919.1 56697551 3194321 2863232..2863636 1 NC_003911.11 endoribonuclease L-PSP 2863636 3194321 SPO2709 Ruegeria pomeroyi DSS-3 endoribonuclease L-PSP YP_167919.1 2863232 D 246200 CDS YP_167920.1 56697552 3194382 2863636..2864442 1 NC_003911.11 identified by similarity to GB:AAR21628.1; match to protein family HMM PF00561; 3-oxoadipate enol-lactonase 2864442 3194382 SPO2710 Ruegeria pomeroyi DSS-3 3-oxoadipate enol-lactonase YP_167920.1 2863636 D 246200 CDS YP_167921.1 56697553 3194295 2864439..2866550 1 NC_003911.11 identified by match to protein family HMM PF01613; match to protein family HMM PF02515; CaiB/BaiF family protein 2866550 3194295 SPO2711 Ruegeria pomeroyi DSS-3 CaiB/BaiF family protein YP_167921.1 2864439 D 246200 CDS YP_167922.1 56697554 3194347 2866564..2867178 1 NC_003911.11 identified by similarity to PIR:C95315; match to protein family HMM PF06684; hypothetical protein 2867178 3194347 SPO2712 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167922.1 2866564 D 246200 CDS YP_167923.1 56697555 3194324 complement(2867244..2869202) 1 NC_003911.11 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; in some organisms, there are paralogous proteins that have been found to be nonessential but do function in secretion of a subset of exported proteins; preprotein translocase subunit SecA 2869202 secA 3194324 secA Ruegeria pomeroyi DSS-3 preprotein translocase subunit SecA YP_167923.1 2867244 R 246200 CDS YP_167924.1 56697556 3194299 complement(2869195..2871342) 1 NC_003911.11 identified by similarity to GB:CAD78905.1; match to protein family HMM PF02163; M50 family peptidase 2871342 3194299 SPO2714 Ruegeria pomeroyi DSS-3 M50 family peptidase YP_167924.1 2869195 R 246200 CDS YP_167925.1 56697557 3194305 complement(2871339..2873192) 1 NC_003911.11 identified by match to protein family HMM PF01590; GAF domain-containing protein 2873192 3194305 SPO2715 Ruegeria pomeroyi DSS-3 GAF domain-containing protein YP_167925.1 2871339 R 246200 CDS YP_167926.1 56697558 3194248 complement(2873400..2897681) 1 NC_003911.11 identified by match to protein family HMM PF00353; match to protein family HMM PF02412; match to protein family HMM TIGR01409; match to protein family HMM TIGR01451; type I secretion target repeat-containing protein 2897681 3194248 SPO2716 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_167926.1 2873400 R 246200 CDS YP_167927.1 56697559 3194210 2897729..2898511 1 NC_003911.11 identified by similarity to GB:AAC97196.1; match to protein family HMM PF07277; protein SapC protein 2898511 3194210 SPO2717 Ruegeria pomeroyi DSS-3 protein SapC protein YP_167927.1 2897729 D 246200 CDS YP_167928.1 56697560 3196028 2898520..2899335 1 NC_003911.11 identified by similarity to GB:CAD84993.1; hypothetical protein 2899335 3196028 SPO2718 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167928.1 2898520 D 246200 CDS YP_167929.1 56697561 3194253 complement(2899435..2900271) 1 NC_003911.11 identified by similarity to GB:AAN87700.1; hypothetical protein 2900271 3194253 SPO2719 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167929.1 2899435 R 246200 CDS YP_167930.1 56697562 3194216 complement(2901443..2902948) 1 NC_003911.11 hypothetical protein 2902948 3194216 SPO2720 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167930.1 2901443 R 246200 CDS YP_167931.1 56697563 3194239 2903106..2903702 1 NC_003911.11 hypothetical protein 2903702 3194239 SPO2721 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167931.1 2903106 D 246200 CDS YP_167932.1 56697564 3194251 2903699..2904058 1 NC_003911.11 hypothetical protein 2904058 3194251 SPO2722 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167932.1 2903699 D 246200 CDS YP_167933.1 56697565 3194207 2904055..2905611 1 NC_003911.11 hypothetical protein 2905611 3194207 SPO2723 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167933.1 2904055 D 246200 CDS YP_167934.1 56697566 3194200 2906229..2910770 1 NC_003911.11 hypothetical protein 2910770 3194200 SPO2724 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167934.1 2906229 D 246200 CDS YP_167935.1 56697567 3194187 complement(2911529..2911627) 1 NC_003911.11 hypothetical protein 2911627 3194187 SPO2725 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167935.1 2911529 R 246200 CDS YP_167936.1 56697568 3194195 complement(2912002..2913927) 1 NC_003911.11 hypothetical protein 2913927 3194195 SPO2726 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167936.1 2912002 R 246200 CDS YP_167937.1 56697569 3195694 complement(2917912..2918346) 1 NC_003911.11 identified by similarity to PIR:F97477; hypothetical protein 2918346 3195694 SPO2729 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167937.1 2917912 R 246200 CDS YP_167938.1 56697570 3193875 complement(2918343..2918549) 1 NC_003911.11 identified by similarity to PIR:H97795; hypothetical protein 2918549 3193875 SPO2730 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167938.1 2918343 R 246200 CDS YP_167939.1 56697571 3194188 2918831..2919400 1 NC_003911.11 identified by match to protein family HMM PF01609; ISSpo7, transposase 2919400 3194188 SPO2731 Ruegeria pomeroyi DSS-3 ISSpo7, transposase YP_167939.1 2918831 D 246200 CDS YP_167940.1 56697572 3194088 2920543..2923245 1 NC_003911.11 identified by match to protein family HMM PF02384; match to protein family HMM PF02506; match to protein family HMM TIGR00497; type I restriction-modification system, M subunit 2923245 hsdM 3194088 hsdM Ruegeria pomeroyi DSS-3 type I restriction-modification system, M subunit YP_167940.1 2920543 D 246200 CDS YP_167941.1 56697573 3194163 2923238..2924542 1 NC_003911.11 identified by similarity to SP:P05719; match to protein family HMM PF01420; type I restriction-modification system subunit S 2924542 hsdS 3194163 hsdS Ruegeria pomeroyi DSS-3 type I restriction-modification system subunit S YP_167941.1 2923238 D 246200 CDS YP_167942.1 56697574 3194130 2924539..2927922 1 NC_003911.11 identified by match to protein family HMM PF04313; match to protein family HMM TIGR00348; type I restriction-modification system, R subunit 2927922 hsdR 3194130 hsdR Ruegeria pomeroyi DSS-3 type I restriction-modification system, R subunit YP_167942.1 2924539 D 246200 CDS YP_167943.1 56698720 3196260 2927919..2928632 1 NC_003911.11 identified by similarity to GB:BAD02160.1; match to protein family HMM PF01863; hypothetical protein 2928632 3196260 SPO3899 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167943.1 2927919 D 246200 CDS YP_167944.1 56697575 3194141 2928710..2929648 1 NC_003911.11 identified by similarity to GB:CAD79234.1; hypothetical protein 2929648 3194141 SPO2736 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167944.1 2928710 D 246200 CDS YP_167945.1 56697576 3194126 2930229..2931110 1 NC_003911.11 lipoprotein 2931110 3194126 SPO2738 Ruegeria pomeroyi DSS-3 lipoprotein YP_167945.1 2930229 D 246200 CDS YP_167946.1 56697577 3194117 2931128..2932294 1 NC_003911.11 identified by similarity to SP:P08506; match to protein family HMM PF00768; D-alanyl-D-alanine carboxypeptidase 2932294 3194117 SPO2739 Ruegeria pomeroyi DSS-3 D-alanyl-D-alanine carboxypeptidase YP_167946.1 2931128 D 246200 CDS YP_167947.1 56697578 3194112 2932291..2932926 1 NC_003911.11 identified by match to protein family HMM PF02223; match to protein family HMM TIGR00041; thymidylate kinase 2932926 tmk 3194112 tmk Ruegeria pomeroyi DSS-3 thymidylate kinase YP_167947.1 2932291 D 246200 CDS YP_167948.1 56697579 3194106 2932923..2934044 1 NC_003911.11 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA; DNA polymerase III subunit delta' 2934044 3194106 SPO2741 Ruegeria pomeroyi DSS-3 DNA polymerase III subunit delta' YP_167948.1 2932923 D 246200 CDS YP_167949.1 56697580 3194150 2934041..2934856 1 NC_003911.11 identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010; TatD family hydrolase 2934856 3194150 SPO2742 Ruegeria pomeroyi DSS-3 TatD family hydrolase YP_167949.1 2934041 D 246200 CDS YP_167950.1 56697581 3194145 2934853..2935653 1 NC_003911.11 identified by similarity to GB:AAK23796.1; hypothetical protein 2935653 3194145 SPO2743 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167950.1 2934853 D 246200 CDS YP_167951.1 56697582 3194137 2935709..2936641 1 NC_003911.11 identified by similarity to GB:AAC45458.1; match to protein family HMM PF03547; malonate transporter 2936641 3194137 SPO2744 Ruegeria pomeroyi DSS-3 malonate transporter YP_167951.1 2935709 D 246200 CDS YP_167952.1 56697583 3195380 2936614..2937381 1 NC_003911.11 identified by similarity to GB:AAS06255.1; hypothetical protein 2937381 3195380 SPO2745 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167952.1 2936614 D 246200 CDS YP_167953.1 56697584 3194135 complement(2937384..2938670) 1 NC_003911.11 hypothetical protein 2938670 3194135 SPO2746 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167953.1 2937384 R 246200 CDS YP_167954.1 56697585 3194094 complement(2938818..2939885) 1 NC_003911.11 identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254; diguanylate cyclase 2939885 3194094 SPO2747 Ruegeria pomeroyi DSS-3 diguanylate cyclase YP_167954.1 2938818 R 246200 CDS YP_167955.1 56697586 3193937 complement(2939891..2940478) 1 NC_003911.11 identified by similarity to PIR:AG2090; hypothetical protein 2940478 3193937 SPO2748 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167955.1 2939891 R 246200 CDS YP_167956.1 56697587 3195145 complement(2940566..2942341) 1 NC_003911.11 identified by similarity to GB:AAQ58806.1; hypothetical protein 2942341 3195145 SPO2749 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167956.1 2940566 R 246200 CDS YP_167957.1 56697588 3194084 complement(2942424..2943983) 1 NC_003911.11 identified by match to protein family HMM PF06253; trimethylamine methyltransferase 2943983 3194084 SPO2750 Ruegeria pomeroyi DSS-3 trimethylamine methyltransferase YP_167957.1 2942424 R 246200 CDS YP_167958.1 56697589 3194073 complement(2944100..2944789) 1 NC_003911.11 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549; HAD-superfamily hydrolase 2944789 3194073 SPO2751 Ruegeria pomeroyi DSS-3 HAD-superfamily hydrolase YP_167958.1 2944100 R 246200 CDS YP_167959.1 56697590 3194067 complement(2944829..2945110) 1 NC_003911.11 identified by similarity to GB:AAN33802.1; hypothetical protein 2945110 3194067 SPO2752 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167959.1 2944829 R 246200 CDS YP_167960.1 56697591 3193997 2945206..2946594 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00990; match to protein family HMM TIGR00254; diguanylate cyclase, /response regulator 2946594 3193997 SPO2753 Ruegeria pomeroyi DSS-3 diguanylate cyclase, /response regulator YP_167960.1 2945206 D 246200 CDS YP_167961.1 56697592 3193992 complement(2946591..2947061) 1 NC_003911.11 identified by similarity to GB:AAK24713.1; hypothetical protein 2947061 3193992 SPO2754 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167961.1 2946591 R 246200 CDS YP_167962.1 56697593 3193866 complement(2947062..2947430) 1 NC_003911.11 hypothetical protein 2947430 3193866 SPO2755 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167962.1 2947062 R 246200 CDS YP_167963.1 56697594 3193973 complement(2947414..2948016) 1 NC_003911.11 Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; RNA polymerase sigma factor 2948016 3193973 SPO2756 Ruegeria pomeroyi DSS-3 RNA polymerase sigma factor YP_167963.1 2947414 R 246200 CDS YP_167964.1 56697595 3195800 complement(2948022..2948501) 1 NC_003911.11 identified by match to protein family HMM PF00036; EF hand domain-containing protein 2948501 3195800 SPO2757 Ruegeria pomeroyi DSS-3 EF hand domain-containing protein YP_167964.1 2948022 R 246200 CDS YP_167965.1 56697596 3193844 2948736..2949128 1 NC_003911.11 identified by similarity to GB:CAE28567.1; hypothetical protein 2949128 3193844 SPO2758 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167965.1 2948736 D 246200 CDS YP_167966.1 56697597 3193778 2949152..2949859 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX family hydrolase 2949859 3193778 SPO2759 Ruegeria pomeroyi DSS-3 NUDIX family hydrolase YP_167966.1 2949152 D 246200 CDS YP_167967.1 56697598 3193750 complement(2949942..2951609) 1 NC_003911.11 identified by match to protein family HMM PF00753; match to protein family HMM PF07521; metallo-beta-lactamase 2951609 3193750 SPO2760 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_167967.1 2949942 R 246200 CDS YP_167968.1 56697599 3194372 complement(2951606..2952385) 1 NC_003911.11 type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP; pantothenate kinase 2952385 3194372 SPO2761 Ruegeria pomeroyi DSS-3 pantothenate kinase YP_167968.1 2951606 R 246200 CDS YP_167969.1 56697600 3193847 complement(2952399..2953148) 1 NC_003911.11 identified by match to protein family HMM PF02237; match to protein family HMM PF03099; match to protein family HMM TIGR00121; biotin--acetyl-CoA-carboxylase ligase 2953148 3193847 SPO2762 Ruegeria pomeroyi DSS-3 biotin--acetyl-CoA-carboxylase ligase YP_167969.1 2952399 R 246200 CDS YP_167970.1 56697601 3194358 complement(2953207..2954649) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit N 2954649 nuoN 3194358 nuoN Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit N YP_167970.1 2953207 R 246200 CDS YP_167971.1 56697602 3193979 complement(2954665..2956206) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit M 2956206 nuoM 3193979 nuoM Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit M YP_167971.1 2954665 R 246200 CDS YP_167972.1 56697603 3195784 complement(2956206..2958350) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L 2958350 nuoL 3195784 nuoL Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit L YP_167972.1 2956206 R 246200 CDS YP_167973.1 56697604 3193895 complement(2958357..2958662) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit K 2958662 nuoK 3193895 nuoK Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit K YP_167973.1 2958357 R 246200 CDS YP_167974.1 56697605 3193743 complement(2958741..2959343) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J 2959343 nuoJ 3193743 nuoJ Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit J YP_167974.1 2958741 R 246200 CDS YP_167975.1 56697606 3193751 complement(2959340..2959759) 1 NC_003911.11 identified by match to protein family HMM PF02627; 4-carboxymuconolactone decarboxylase 2959759 3193751 SPO2768 Ruegeria pomeroyi DSS-3 4-carboxymuconolactone decarboxylase YP_167975.1 2959340 R 246200 CDS YP_167976.1 56697607 3193996 complement(2959756..2960625) 1 NC_003911.11 identified by similarity to GB:AAN30033.1; hypothetical protein 2960625 3193996 SPO2769 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167976.1 2959756 R 246200 CDS YP_167977.1 56697608 3193825 complement(2960622..2961116) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I 2961116 nuoI 3193825 nuoI Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit I YP_167977.1 2960622 R 246200 CDS YP_167978.1 56697609 3193632 complement(2961113..2961328) 1 NC_003911.11 hypothetical protein 2961328 3193632 SPO2771 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167978.1 2961113 R 246200 CDS YP_167979.1 56697610 3193930 complement(2961330..2962367) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H 2962367 nuoH 3193930 nuoH Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit H YP_167979.1 2961330 R 246200 CDS YP_167980.1 56697611 3194961 complement(2962374..2962760) 1 NC_003911.11 lipoprotein 2962760 3194961 SPO2773 Ruegeria pomeroyi DSS-3 lipoprotein YP_167980.1 2962374 R 246200 CDS YP_167981.1 56697612 3193753 complement(2962757..2964781) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit G 2964781 nuoG 3193753 nuoG Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit G YP_167981.1 2962757 R 246200 CDS YP_167982.1 56697613 3193661 complement(2964785..2965291) 1 NC_003911.11 identified by similarity to SP:P29909; hypothetical protein 2965291 3193661 SPO2775 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167982.1 2964785 R 246200 CDS YP_167983.1 56697614 3193620 complement(2965288..2965671) 1 NC_003911.11 hypothetical protein 2965671 3193620 SPO2776 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167983.1 2965288 R 246200 CDS YP_167984.1 56697615 3193143 complement(2965668..2966966) 1 NC_003911.11 part of NADH-ubiquinone oxidoreductase complex I; shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase; NADH dehydrogenase I subunit F 2966966 nuoF 3193143 nuoF Ruegeria pomeroyi DSS-3 NADH dehydrogenase I subunit F YP_167984.1 2965668 R 246200 CDS YP_167985.1 56697616 3193276 complement(2966976..2967221) 1 NC_003911.11 identified by similarity to SP:P29907; hypothetical protein 2967221 3193276 SPO2778 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167985.1 2966976 R 246200 CDS YP_167986.1 56697617 3193333 complement(2967225..2967671) 1 NC_003911.11 hypothetical protein 2967671 3193333 SPO2779 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167986.1 2967225 R 246200 CDS YP_167987.1 56697618 3193152 complement(2967694..2968938) 1 NC_003911.11 catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit E 2968938 nuoE 3193152 nuoE Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit E YP_167987.1 2967694 R 246200 CDS YP_167988.1 56697619 3192802 complement(2968964..2969275) 1 NC_003911.11 lipoprotein 2969275 3192802 SPO2781 Ruegeria pomeroyi DSS-3 lipoprotein YP_167988.1 2968964 R 246200 CDS YP_167989.1 56697620 3193679 complement(2969272..2970489) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D 2970489 nuoD 3193679 nuoD Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit D YP_167989.1 2969272 R 246200 CDS YP_167990.1 56697621 3195925 complement(2970565..2970702) 1 NC_003911.11 hypothetical protein 2970702 3195925 SPO2783 Ruegeria pomeroyi DSS-3 hypothetical protein YP_167990.1 2970565 R 246200 CDS YP_167991.1 56697622 3193202 complement(2970881..2971483) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit C 2971483 nuoC 3193202 nuoC Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit C YP_167991.1 2970881 R 246200 CDS YP_167992.1 56697623 3193700 complement(2971496..2972050) 1 NC_003911.11 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen; NADH dehydrogenase subunit B 2972050 nuoB 3193700 nuoB Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit B YP_167992.1 2971496 R 246200 CDS YP_167993.1 56697624 3193166 complement(2972020..2972385) 1 NC_003911.11 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit A 2972385 nuoA 3193166 nuoA Ruegeria pomeroyi DSS-3 NADH dehydrogenase subunit A YP_167993.1 2972020 R 246200 CDS YP_167994.1 56697625 3193392 complement(2972571..2973359) 1 NC_003911.11 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 2973359 3193392 SPO2787 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_167994.1 2972571 R 246200 CDS YP_167995.1 56697626 3193250 complement(2973426..2974280) 1 NC_003911.11 catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA; hydroxymethylglutaryl-CoA lyase 2974280 mvaB 3193250 mvaB Ruegeria pomeroyi DSS-3 hydroxymethylglutaryl-CoA lyase YP_167995.1 2973426 R 246200 CDS YP_167996.1 56697627 3193216 complement(2974346..2976283) 1 NC_003911.11 identified by similarity to SP:Q96RQ3; match to protein family HMM PF00289; match to protein family HMM PF00364; match to protein family HMM PF02785; match to protein family HMM PF02786; methylcrotonyl-CoA carboxylase subunit alpha 2976283 mccA 3193216 mccA Ruegeria pomeroyi DSS-3 methylcrotonyl-CoA carboxylase subunit alpha YP_167996.1 2974346 R 246200 CDS YP_167997.1 56698721 3196312 complement(2976302..2976868) 1 NC_003911.11 identified by match to protein family HMM PF00565; thermonuclease 2976868 3196312 SPO3900 Ruegeria pomeroyi DSS-3 thermonuclease YP_167997.1 2976302 R 246200 CDS YP_167998.1 56697628 3192650 complement(2976955..2978559) 1 NC_003911.11 identified by similarity to SP:Q9HCC0; match to protein family HMM PF01039; methylcrotonyl-CoA carboxylase subunit beta 2978559 mccB 3192650 mccB Ruegeria pomeroyi DSS-3 methylcrotonyl-CoA carboxylase subunit beta YP_167998.1 2976955 R 246200 CDS YP_167999.1 56697629 3193312 complement(2978556..2980088) 1 NC_003911.11 identified by similarity to SP:P39062; match to protein family HMM PF00501; acetyl-coenzyme A synthetase 2980088 acsA 3193312 acsA Ruegeria pomeroyi DSS-3 acetyl-coenzyme A synthetase YP_167999.1 2978556 R 246200 CDS YP_168000.1 56697630 3193377 2980256..2980861 1 NC_003911.11 identified by similarity to SP:P17266; match to protein family HMM PF03922; outer membrane protein OmpW 2980861 ompW 3193377 ompW Ruegeria pomeroyi DSS-3 outer membrane protein OmpW YP_168000.1 2980256 D 246200 CDS YP_168001.1 56697631 3193199 complement(2980923..2982086) 1 NC_003911.11 identified by similarity to SP:P26440; match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF02771; isovaleryl-CoA dehydrogenase 2982086 ivD 3193199 ivD Ruegeria pomeroyi DSS-3 isovaleryl-CoA dehydrogenase YP_168001.1 2980923 R 246200 CDS YP_168002.1 56697632 3194799 complement(2982120..2982236) 1 NC_003911.11 hypothetical protein 2982236 3194799 SPO2794 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168002.1 2982120 R 246200 CDS YP_168003.1 56697633 3193246 complement(2982241..2983431) 1 NC_003911.11 identified by match to protein family HMM PF01041; aminotransferase 2983431 3193246 SPO2795 Ruegeria pomeroyi DSS-3 aminotransferase YP_168003.1 2982241 R 246200 CDS YP_168004.1 56697634 3194599 complement(2983505..2984167) 1 NC_003911.11 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01449; match to protein family HMM TIGR01509; match to protein family HMM TIGR01549; phosphoglycolate phosphatase 2984167 gph-2 3194599 gph-2 Ruegeria pomeroyi DSS-3 phosphoglycolate phosphatase YP_168004.1 2983505 R 246200 CDS YP_168005.1 56697635 3193284 2984286..2985638 1 NC_003911.11 forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis; bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 2985638 glmU 3193284 glmU Ruegeria pomeroyi DSS-3 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase YP_168005.1 2984286 D 246200 CDS YP_168006.1 56697636 3193124 2985719..2986405 1 NC_003911.11 identified by similarity to PIR:AG1725; hypothetical protein 2986405 3193124 SPO2798 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168006.1 2985719 D 246200 CDS YP_168007.1 56697637 3196169 2986945..2987952 1 NC_003911.11 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A 2987952 moaA 3196169 moaA Ruegeria pomeroyi DSS-3 molybdenum cofactor biosynthesis protein A YP_168007.1 2986945 D 246200 CDS YP_168008.1 56697638 3195810 2987956..2989254 1 NC_003911.11 identified by similarity to SP:P23282; match to protein family HMM PF04413; 3-deoxy-D-manno-octulosonic acid transferase 2989254 kdtA 3195810 kdtA Ruegeria pomeroyi DSS-3 3-deoxy-D-manno-octulosonic acid transferase YP_168008.1 2987956 D 246200 CDS YP_168009.1 56697639 3193131 2989254..2990309 1 NC_003911.11 identified by similarity to SP:O68547; match to protein family HMM PF00534; lipopolysaccharide core biosynthesis mannosyltransferase 2990309 lpcC 3193131 lpcC Ruegeria pomeroyi DSS-3 lipopolysaccharide core biosynthesis mannosyltransferase YP_168009.1 2989254 D 246200 CDS YP_168010.1 56697640 3196174 2990371..2991426 1 NC_003911.11 identified by match to protein family HMM PF02608; bmp family protein 2991426 3196174 SPO2802 Ruegeria pomeroyi DSS-3 bmp family protein YP_168010.1 2990371 D 246200 CDS YP_168011.1 56697641 3193000 2991469..2992986 1 NC_003911.11 identified by match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein 2992986 3193000 SPO2803 Ruegeria pomeroyi DSS-3 sugar ABC transporter ATP-binding protein YP_168011.1 2991469 D 246200 CDS YP_168012.1 56697642 3196167 2992983..2994056 1 NC_003911.11 identified by match to protein family HMM PF02653; sugar ABC transporter permease 2994056 3196167 SPO2804 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_168012.1 2992983 D 246200 CDS YP_168013.1 56697643 3195022 2994053..2994997 1 NC_003911.11 identified by match to protein family HMM PF02653; sugar ABC transporter permease 2994997 3195022 SPO2805 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_168013.1 2994053 D 246200 CDS YP_168014.1 56697644 3196165 2995007..2996299 1 NC_003911.11 Catalyzes the deamination of cytosine to uracil and ammonia; cytosine deaminase 2996299 3196165 SPO2806 Ruegeria pomeroyi DSS-3 cytosine deaminase YP_168014.1 2995007 D 246200 CDS YP_168015.1 56697645 3196159 2996358..2996996 1 NC_003911.11 identified by similarity to GB:AAQ87176.1; hypothetical protein 2996996 3196159 SPO2807 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168015.1 2996358 D 246200 CDS YP_168016.1 56697646 3194441 complement(2997045..2998208) 1 NC_003911.11 identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase 2998208 3194441 SPO2808 Ruegeria pomeroyi DSS-3 amidohydrolase YP_168016.1 2997045 R 246200 CDS YP_168017.1 56697647 3193033 complement(2998230..2999399) 1 NC_003911.11 identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase 2999399 3193033 SPO2809 Ruegeria pomeroyi DSS-3 amidohydrolase YP_168017.1 2998230 R 246200 CDS YP_168018.1 56697648 3193307 complement(2999414..3000577) 1 NC_003911.11 identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase 3000577 3193307 SPO2810 Ruegeria pomeroyi DSS-3 amidohydrolase YP_168018.1 2999414 R 246200 CDS YP_168019.1 56697649 3196157 complement(3000608..3001774) 1 NC_003911.11 identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase 3001774 3196157 SPO2811 Ruegeria pomeroyi DSS-3 amidohydrolase YP_168019.1 3000608 R 246200 CDS YP_168020.1 56697650 3196162 complement(3001939..3003105) 1 NC_003911.11 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase 3003105 argE-1 3196162 argE-1 Ruegeria pomeroyi DSS-3 acetylornithine deacetylase YP_168020.1 3001939 R 246200 CDS YP_168021.1 56697651 3194980 complement(3003109..3004974) 1 NC_003911.11 identified by match to protein family HMM PF00005; peptide/nickel/opine uptake ABC transporter ATP-binding protein 3004974 3194980 SPO2813 Ruegeria pomeroyi DSS-3 peptide/nickel/opine uptake ABC transporter ATP-binding protein YP_168021.1 3003109 R 246200 CDS YP_168022.1 56697652 3196158 3005240..3006961 1 NC_003911.11 identified by similarity to SP:P42061; match to protein family HMM PF00496; peptide/opine/nickel uptake ABC transporter substrate-binding protein 3006961 3196158 SPO2814 Ruegeria pomeroyi DSS-3 peptide/opine/nickel uptake ABC transporter substrate-binding protein YP_168022.1 3005240 D 246200 CDS YP_168023.1 56697653 3195376 3007058..3008065 1 NC_003911.11 identified by similarity to SP:P42062; match to protein family HMM PF00528; peptide/nickel/opine uptake ABC transporter permease 3008065 3195376 SPO2815 Ruegeria pomeroyi DSS-3 peptide/nickel/opine uptake ABC transporter permease YP_168023.1 3007058 D 246200 CDS YP_168024.1 56697654 3196150 3008040..3008969 1 NC_003911.11 identified by similarity to SP:P42063; match to protein family HMM PF00528; peptide/nickel/opine uptake ABC transporter permease 3008969 3196150 SPO2816 Ruegeria pomeroyi DSS-3 peptide/nickel/opine uptake ABC transporter permease YP_168024.1 3008040 D 246200 CDS YP_168025.1 56697655 3196153 3009179..3010252 1 NC_003911.11 identified by similarity to GB:CAE29903.1; match to protein family HMM PF04143; hypothetical protein 3010252 3196153 SPO2817 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168025.1 3009179 D 246200 CDS YP_168026.1 56697656 3196140 complement(3010188..3011468) 1 NC_003911.11 identified by similarity to GB:CAE26946.1; hypothetical protein 3011468 3196140 SPO2818 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168026.1 3010188 R 246200 CDS YP_168027.1 56697657 3196151 complement(3011655..3013088) 1 NC_003911.11 identified by match to protein family HMM PF02233; NAD(P) transhydrogenase subunit beta 3013088 pntB 3196151 pntB Ruegeria pomeroyi DSS-3 NAD(P) transhydrogenase subunit beta YP_168027.1 3011655 R 246200 CDS YP_168028.1 56697658 3193432 complement(3013102..3014673) 1 NC_003911.11 forms a tetramer composed of 2 alpha subunits and 2 beta subunits in the inner membrane; involved in catalyzing transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm; NAD(P) transhydrogenase subunit alpha 3014673 pntA 3193432 pntA Ruegeria pomeroyi DSS-3 NAD(P) transhydrogenase subunit alpha YP_168028.1 3013102 R 246200 CDS YP_168029.1 56697659 3195154 complement(3014804..3015253) 1 NC_003911.11 identified by match to protein family HMM PF04140; isoprenylcysteine carboxyl methyltransferase 3015253 3195154 SPO2821 Ruegeria pomeroyi DSS-3 isoprenylcysteine carboxyl methyltransferase YP_168029.1 3014804 R 246200 CDS YP_168030.1 56697660 3196141 complement(3015442..3016389) 1 NC_003911.11 identified by similarity to GB:CAD33969.1; soxH protein-like protein 3016389 3196141 SPO2822 Ruegeria pomeroyi DSS-3 soxH protein-like protein YP_168030.1 3015442 R 246200 CDS YP_168031.1 56697661 3195434 3016510..3017262 1 NC_003911.11 identified by similarity to SP:O86034; match to protein family HMM PF00106; D-beta-hydroxybutyrate dehydrogenase 3017262 bdh-2 3195434 bdh-2 Ruegeria pomeroyi DSS-3 D-beta-hydroxybutyrate dehydrogenase YP_168031.1 3016510 D 246200 CDS YP_168032.1 56697662 3196138 3017478..3018683 1 NC_003911.11 identified by similarity to SP:Q16719; match to protein family HMM TIGR01814; kynureninase 3018683 kynU 3196138 kynU Ruegeria pomeroyi DSS-3 kynureninase YP_168032.1 3017478 D 246200 CDS YP_168033.1 56697663 3196133 complement(3018691..3019269) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 3019269 3196133 SPO2825 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_168033.1 3018691 R 246200 CDS YP_168034.1 56697664 3195329 3019391..3019855 1 NC_003911.11 identified by similarity to SP:Q51697; match to protein family HMM PF00111; match to protein family HMM PF01799; isoquinoline 1-oxidoreductase subunit alpha 3019855 iorA 3195329 iorA Ruegeria pomeroyi DSS-3 isoquinoline 1-oxidoreductase subunit alpha YP_168034.1 3019391 D 246200 CDS YP_168035.1 56697665 3196127 3019859..3022099 1 NC_003911.11 identified by similarity to SP:Q51698; match to protein family HMM PF02738; match to protein family HMM TIGR01409; isoquinoline 1-oxidoreductase subunit beta 3022099 3196127 SPO2827 Ruegeria pomeroyi DSS-3 isoquinoline 1-oxidoreductase subunit beta YP_168035.1 3019859 D 246200 CDS YP_168036.1 56697666 3196124 3022301..3024379 1 NC_003911.11 identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 3024379 3196124 SPO2828 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_168036.1 3022301 D 246200 CDS YP_168037.1 56697667 3196125 complement(3024665..3026080) 1 NC_003911.11 identified by similarity to SP:O85304; match to protein family HMM PF03577; dipeptidase domain-containing protein 3026080 3196125 SPO2829 Ruegeria pomeroyi DSS-3 dipeptidase domain-containing protein YP_168037.1 3024665 R 246200 CDS YP_168038.1 56697668 3196123 complement(3026077..3027693) 1 NC_003911.11 identified by similarity to GB:AAN53028.1; hypothetical protein 3027693 3196123 SPO2830 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168038.1 3026077 R 246200 CDS YP_168039.1 56697669 3196112 complement(3027690..3028676) 1 NC_003911.11 identified by similarity to SP:P42065; match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide ABC transporter ATP-binding protein 3028676 3196112 SPO2831 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter ATP-binding protein YP_168039.1 3027690 R 246200 CDS YP_168040.1 56697670 3193803 complement(3028673..3029647) 1 NC_003911.11 identified by similarity to SP:P24136; similarity to SP:P26905; match to protein family HMM PF00005; match to protein family HMM TIGR01727; dipeptide ABC transporter ATP-binding protein 3029647 3193803 SPO2832 Ruegeria pomeroyi DSS-3 dipeptide ABC transporter ATP-binding protein YP_168040.1 3028673 R 246200 CDS YP_168041.1 56697671 3196113 complement(3029644..3030522) 1 NC_003911.11 identified by match to protein family HMM PF00528; dipeptide ABC transporter permease 3030522 3196113 SPO2833 Ruegeria pomeroyi DSS-3 dipeptide ABC transporter permease YP_168041.1 3029644 R 246200 CDS YP_168042.1 56697672 3196110 complement(3030533..3031477) 1 NC_003911.11 Assignment partly based on membership in dipeptide ABC transporter gene cluster.; identified by similarity to SP:P37316; match to protein family HMM PF00528; dipeptide ABC transporter permease 3031477 3196110 SPO2834 Ruegeria pomeroyi DSS-3 dipeptide ABC transporter permease YP_168042.1 3030533 R 246200 CDS YP_168043.1 56697673 3196108 complement(3031553..3033121) 1 NC_003911.11 Assignment partly based on membership in dipeptide ABC transporter gene cluster.; identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; dipeptide ABC transporter substrate-binding protein 3033121 3196108 SPO2835 Ruegeria pomeroyi DSS-3 dipeptide ABC transporter substrate-binding protein YP_168043.1 3031553 R 246200 CDS YP_168044.1 56697674 3196095 3033296..3034087 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 3034087 3196095 SPO2836 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_168044.1 3033296 D 246200 CDS YP_168045.1 56697675 3196107 complement(3034345..3035124) 1 NC_003911.11 identified by similarity to GB:BAB51661.1; hypothetical protein 3035124 3196107 SPO2837 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168045.1 3034345 R 246200 CDS YP_168046.1 56697676 3196102 complement(3035247..3035672) 1 NC_003911.11 identified by similarity to GB:BAB50596.1; match to protein family HMM PF03928; hypothetical protein 3035672 3196102 SPO2838 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168046.1 3035247 R 246200 CDS YP_168047.1 56697677 3196099 complement(3035758..3037905) 1 NC_003911.11 catalyzes the formation of malate from glyoxylate and acetyl-CoA; malate synthase G 3037905 glcB 3196099 glcB Ruegeria pomeroyi DSS-3 malate synthase G YP_168047.1 3035758 R 246200 CDS YP_168048.1 56697678 3196098 3038169..3038918 1 NC_003911.11 identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254; diguanylate cyclase 3038918 3196098 SPO2840 Ruegeria pomeroyi DSS-3 diguanylate cyclase YP_168048.1 3038169 D 246200 CDS YP_168049.1 56697679 3196093 3039024..3041576 1 NC_003911.11 identified by similarity to SP:P37893; match to protein family HMM PF01433; aminopeptidase 3041576 pepN 3196093 pepN Ruegeria pomeroyi DSS-3 aminopeptidase YP_168049.1 3039024 D 246200 CDS YP_168050.1 56697680 3193251 3041580..3042320 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 3042320 3193251 SPO2842 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_168050.1 3041580 D 246200 CDS YP_168051.1 56697681 3194263 3042280..3042759 1 NC_003911.11 hypothetical protein 3042759 3194263 SPO2843 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168051.1 3042280 D 246200 CDS YP_168052.1 56697682 3196086 complement(3042304..3043290) 1 NC_003911.11 hypothetical protein 3043290 3196086 SPO2844 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168052.1 3042304 R 246200 CDS YP_168053.1 56697683 3193510 3042731..3044167 1 NC_003911.11 hypothetical protein 3044167 3193510 SPO2845 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168053.1 3042731 D 246200 CDS YP_168054.1 56697684 3192933 complement(3044170..3045012) 1 NC_003911.11 identified by similarity to GB:BAC88423.1; hypothetical protein 3045012 3192933 SPO2846 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168054.1 3044170 R 246200 CDS YP_168055.1 56697685 3196088 3045154..3046665 1 NC_003911.11 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit B 3046665 gatB 3196088 gatB Ruegeria pomeroyi DSS-3 aspartyl/glutamyl-tRNA amidotransferase subunit B YP_168055.1 3045154 D 246200 CDS YP_168056.1 56697686 3195451 3046930..3047457 1 NC_003911.11 identified by similarity to SP:P51702; hypothetical protein 3047457 3195451 SPO2848 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168056.1 3046930 D 246200 CDS YP_168057.1 56697687 3196082 complement(3047454..3047708) 1 NC_003911.11 identified by similarity to SP:P15298; match to protein family HMM PF01722; BolA protein, truncation 3047708 3196082 SPO2849 Ruegeria pomeroyi DSS-3 BolA protein, truncation YP_168057.1 3047454 R 246200 CDS YP_168058.1 56697688 3193976 3047852..3048472 1 NC_003911.11 identified by match to protein family HMM PF00226; DnaJ domain-containing protein 3048472 3193976 SPO2850 Ruegeria pomeroyi DSS-3 DnaJ domain-containing protein YP_168058.1 3047852 D 246200 CDS YP_168059.1 56697689 3194180 complement(3048465..3049628) 1 NC_003911.11 identified by similarity to PIR:T03518; hypothetical protein 3049628 3194180 SPO2851 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168059.1 3048465 R 246200 CDS YP_168060.1 56697690 3196079 3049641..3050243 1 NC_003911.11 identified by similarity to SP:P94139; CzcN domain-containing protein 3050243 3196079 SPO2852 Ruegeria pomeroyi DSS-3 CzcN domain-containing protein YP_168060.1 3049641 D 246200 CDS YP_168061.1 56697691 3196078 3050260..3051369 1 NC_003911.11 identified by match to protein family HMM PF06383; match to protein family HMM TIGR01650; cobalt chelatase, CobS subunit 3051369 3196078 SPO2853 Ruegeria pomeroyi DSS-3 cobalt chelatase, CobS subunit YP_168061.1 3050260 D 246200 CDS YP_168062.1 56697692 3195120 3051366..3051809 1 NC_003911.11 identified by similarity to SP:P43270; match to protein family HMM PF00565; thermonuclease 3051809 nucH 3195120 nucH Ruegeria pomeroyi DSS-3 thermonuclease YP_168062.1 3051366 D 246200 CDS YP_168063.1 56697693 3193907 3051930..3053807 1 NC_003911.11 identified by similarity to SP:P29934; match to protein family HMM TIGR01651; cobalt chelatase large subunit 3053807 3193907 SPO2855 Ruegeria pomeroyi DSS-3 cobalt chelatase large subunit YP_168063.1 3051930 D 246200 CDS YP_168064.1 56697694 3196073 complement(3053979..3054365) 1 NC_003911.11 hypothetical protein 3054365 3196073 SPO2856 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168064.1 3053979 R 246200 CDS YP_168065.1 56697695 3193785 3054457..3056247 1 NC_003911.11 identified by match to protein family HMM PF00557; M24 family metallopeptidase 3056247 3193785 SPO2857 Ruegeria pomeroyi DSS-3 M24 family metallopeptidase YP_168065.1 3054457 D 246200 CDS YP_168066.1 56697696 3196044 3056331..3056675 1 NC_003911.11 identified by similarity to GB:BAC50981.1; match to protein family HMM PF04248; hypothetical protein 3056675 3196044 SPO2858 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168066.1 3056331 D 246200 CDS YP_168067.1 56697697 3195745 complement(3056743..3057705) 1 NC_003911.11 identified by similarity to SP:P23523; 3-hydroxyisobutyrate dehydrogenase 3057705 3195745 SPO2859 Ruegeria pomeroyi DSS-3 3-hydroxyisobutyrate dehydrogenase YP_168067.1 3056743 R 246200 CDS YP_168068.1 56697698 3196029 3057925..3058809 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3058809 3196029 SPO2860 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168068.1 3057925 D 246200 CDS YP_168069.1 56697699 3195757 3059175..3059573 1 NC_003911.11 identified by similarity to PIR:AE2921; hypothetical protein 3059573 3195757 SPO2861 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168069.1 3059175 D 246200 CDS YP_168070.1 56697700 3195686 3059577..3060632 1 NC_003911.11 identified by similarity to SP:P29937; match to protein family HMM PF02492; match to protein family HMM PF07683; CobW 3060632 3195686 SPO2862 Ruegeria pomeroyi DSS-3 CobW YP_168070.1 3059577 D 246200 CDS YP_168071.1 56697701 3193474 3060642..3063935 1 NC_003911.11 with CobST catalyzes the formation of cobyrinic acid a,c-diamide from hydrogenobyrinic acid a,c-diamide in an ATP-dependent manner; involved in porphyrin and chlorophyll metabolism; vitamin B12 metabolism; cobaltochelatase subunit CobN 3063935 cobN 3193474 cobN Ruegeria pomeroyi DSS-3 cobaltochelatase subunit CobN YP_168071.1 3060642 D 246200 CDS YP_168072.1 56697702 3195892 3063932..3065059 1 NC_003911.11 identified by similarity to SP:P21637; match to protein family HMM PF03460; CobG 3065059 3195892 SPO2864 Ruegeria pomeroyi DSS-3 CobG YP_168072.1 3063932 D 246200 CDS YP_168073.1 56697703 3195717 3065059..3065688 1 NC_003911.11 catalyzes the interconversion of precorrin-8X and hydrogenobyrinate; precorrin-8X methylmutase 3065688 cobH 3195717 cobH Ruegeria pomeroyi DSS-3 precorrin-8X methylmutase YP_168073.1 3065059 D 246200 CDS YP_168074.1 56697704 3196061 3065685..3066413 1 NC_003911.11 identified by match to protein family HMM PF00590; match to protein family HMM TIGR01467; precorrin-2 C(20)-methyltransferase 3066413 cobI 3196061 cobI Ruegeria pomeroyi DSS-3 precorrin-2 C(20)-methyltransferase YP_168074.1 3065685 D 246200 CDS YP_168075.1 56697705 3195887 3066410..3067162 1 NC_003911.11 identified by match to protein family HMM PF00590; match to protein family HMM TIGR01466; precorrin-3B C(17)-methyltransferase 3067162 cobJ 3195887 cobJ Ruegeria pomeroyi DSS-3 precorrin-3B C(17)-methyltransferase YP_168075.1 3066410 D 246200 CDS YP_168076.1 56697706 3193607 complement(3067135..3067887) 1 NC_003911.11 CobK/CbiJ; there are 2 pathways for cobalamin (vitamin B12) production, one aerobic (ex. P. denitrificans), the other anaerobic (ex. S. typhimurium); the CobK/CbiJ perform similar reactions in both; the anaerobic pathway includes the use of a chelated cobalt ion in order for ring contraction to occur; CobK thus converts precorrin 6 into dihydro-precorrin 6 while CbiJ converts cobalt-precorrin 6 into cobalt-deihydro-precorrin 6; cobalt-precorrin-6x reductase 3067887 cobK 3193607 cobK Ruegeria pomeroyi DSS-3 cobalt-precorrin-6x reductase YP_168076.1 3067135 R 246200 CDS YP_168077.1 56697707 3195658 3067886..3069085 1 NC_003911.11 identified by match to protein family HMM PF00590; match to protein family HMM TIGR01468; precorrin-6Y C5,15-methyltransferase 3069085 cobL 3195658 cobL Ruegeria pomeroyi DSS-3 precorrin-6Y C5,15-methyltransferase YP_168077.1 3067886 D 246200 CDS YP_168078.1 56697708 3193799 3069082..3069450 1 NC_003911.11 cobalamin biosynthesis domain-containing protein 3069450 3193799 SPO2870 Ruegeria pomeroyi DSS-3 cobalamin biosynthesis domain-containing protein YP_168078.1 3069082 D 246200 CDS YP_168079.1 56697709 3195679 3069447..3070241 1 NC_003911.11 identified by match to protein family HMM PF00590; match to protein family HMM TIGR01465; precorrin-4 C(11)-methyltransferase 3070241 cobM 3195679 cobM Ruegeria pomeroyi DSS-3 precorrin-4 C(11)-methyltransferase YP_168079.1 3069447 D 246200 CDS YP_168080.1 56697710 3195029 3070255..3071550 1 NC_003911.11 responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid; cobyrinic acid a,c-diamide synthase 3071550 cobB 3195029 cobB Ruegeria pomeroyi DSS-3 cobyrinic acid a,c-diamide synthase YP_168080.1 3070255 D 246200 CDS YP_168081.1 56697711 3195129 3071547..3072275 1 NC_003911.11 catalyzes 2 sequential methylations, the formation of precorrin-1 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and uroporphyrin III, and the formation of precorrin-2 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and precorrin-1; uroporphyrin-III C-methyltransferase 3072275 cobA-2 3195129 cobA-2 Ruegeria pomeroyi DSS-3 uroporphyrin-III C-methyltransferase YP_168081.1 3071547 D 246200 CDS YP_168082.1 56697712 3195028 3072268..3073011 1 NC_003911.11 catalyzes the formation of precorrin 6x from precorrin 5; precorrin 6A synthase 3073011 cobF 3195028 cobF Ruegeria pomeroyi DSS-3 precorrin 6A synthase YP_168082.1 3072268 D 246200 CDS YP_168083.1 56697713 3195277 3073278..3073472 1 NC_003911.11 identified by similarity to GB:AAO56638.1; hypothetical protein 3073472 3195277 SPO2875 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168083.1 3073278 D 246200 CDS YP_168084.1 56697714 3196051 3073476..3074174 1 NC_003911.11 hypothetical protein 3074174 3196051 SPO2876 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168084.1 3073476 D 246200 CDS YP_168085.1 56697715 3195965 3074238..3074732 1 NC_003911.11 identified by similarity to PIR:T36736; hypothetical protein 3074732 3195965 SPO2877 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168085.1 3074238 D 246200 CDS YP_168086.1 56697716 3194483 complement(3074720..3075112) 1 NC_003911.11 identified by similarity to GB:BAC48526.1; hypothetical protein 3075112 3194483 SPO2878 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168086.1 3074720 R 246200 CDS YP_168087.1 56697717 3196058 complement(3075132..3076049) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3076049 3196058 SPO2879 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168087.1 3075132 R 246200 CDS YP_168088.1 56697718 3195767 complement(3076116..3076943) 1 NC_003911.11 catalyzes the formation of L-aspartate to iminoaspartate in NAD(+) biosynthesis; L-aspartate dehydrogenase 3076943 3195767 SPO2880 Ruegeria pomeroyi DSS-3 L-aspartate dehydrogenase YP_168088.1 3076116 R 246200 CDS YP_168089.1 56697719 3195830 3076961..3079156 1 NC_003911.11 identified by match to protein family HMM PF01315; match to protein family HMM PF02738; xanthine dehydrogenase, large subunit 3079156 3195830 SPO2881 Ruegeria pomeroyi DSS-3 xanthine dehydrogenase, large subunit YP_168089.1 3076961 D 246200 CDS YP_168090.1 56697720 3195005 3079198..3080106 1 NC_003911.11 identified by match to protein family HMM PF00701; dihydrodipicolinate synthase 3080106 3195005 SPO2882 Ruegeria pomeroyi DSS-3 dihydrodipicolinate synthase YP_168090.1 3079198 D 246200 CDS YP_168091.1 56697721 3195043 complement(3080178..3081728) 1 NC_003911.11 thiamine-pyrophosphate requiring enzyme; hypothetical protein 3081728 3195043 SPO2883 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168091.1 3080178 R 246200 CDS YP_168092.1 56697722 3195617 3081815..3082330 1 NC_003911.11 hypothetical protein 3082330 3195617 SPO2884 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168092.1 3081815 D 246200 CDS YP_168093.1 56697723 3194852 3082404..3084023 1 NC_003911.11 identified by similarity to SP:P27696; match to protein family HMM PF00205; match to protein family HMM PF02776; acetolactate synthase, catabolic 3084023 3194852 SPO2885 Ruegeria pomeroyi DSS-3 acetolactate synthase, catabolic YP_168093.1 3082404 D 246200 CDS YP_168094.1 56697724 3195912 3084010..3085203 1 NC_003911.11 identified by match to protein family HMM PF02515; CAIB/BAIF family protein 3085203 3195912 SPO2886 Ruegeria pomeroyi DSS-3 CAIB/BAIF family protein YP_168094.1 3084010 D 246200 CDS YP_168095.1 56697725 3195942 3085381..3086751 1 NC_003911.11 identified by similarity to GB:CAE31162.1; hypothetical protein 3086751 3195942 SPO2887 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168095.1 3085381 D 246200 CDS YP_168096.1 56697726 3195018 3086755..3088005 1 NC_003911.11 hypothetical protein 3088005 3195018 SPO2888 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168096.1 3086755 D 246200 CDS YP_168097.1 56697727 3195856 3088002..3089501 1 NC_003911.11 involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan; glucan biosynthesis protein G 3089501 mdoG 3195856 mdoG Ruegeria pomeroyi DSS-3 glucan biosynthesis protein G YP_168097.1 3088002 D 246200 CDS YP_168098.1 56697728 3195836 3089489..3091372 1 NC_003911.11 necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 3091372 3195836 SPO2890 Ruegeria pomeroyi DSS-3 glucosyltransferase MdoH YP_168098.1 3089489 D 246200 CDS YP_168099.1 56697729 3193257 complement(3091377..3092195) 1 NC_003911.11 identified by similarity to GB:AAA85939.1; hypothetical protein 3092195 3193257 SPO2891 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168099.1 3091377 R 246200 CDS YP_168100.1 56697730 3195135 complement(3092192..3092674) 1 NC_003911.11 identified by similarity to GB:AAM38343.1; hypothetical protein 3092674 3195135 SPO2892 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168100.1 3092192 R 246200 CDS YP_168101.1 56697731 3195927 3092895..3095804 1 NC_003911.11 subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved with K+; monovalent cation/H+ antiporter subunit A 3095804 phaA 3195927 phaA Ruegeria pomeroyi DSS-3 monovalent cation/H+ antiporter subunit A YP_168101.1 3092895 D 246200 CDS YP_168102.1 56697732 3195466 3095806..3096165 1 NC_003911.11 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; monovalent cation/H+ antiporter subunit C 3096165 3195466 SPO2894 Ruegeria pomeroyi DSS-3 monovalent cation/H+ antiporter subunit C YP_168102.1 3095806 D 246200 CDS YP_168103.1 56697733 3195796 3096162..3097709 1 NC_003911.11 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone; monovalent cation/H+ antiporter subunit D 3097709 phaD 3195796 phaD Ruegeria pomeroyi DSS-3 monovalent cation/H+ antiporter subunit D YP_168103.1 3096162 D 246200 CDS YP_168104.1 56697734 3194369 3097706..3098203 1 NC_003911.11 subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport; monovalent cation/H+ antiporter subunit E 3098203 phaE 3194369 phaE Ruegeria pomeroyi DSS-3 monovalent cation/H+ antiporter subunit E YP_168104.1 3097706 D 246200 CDS YP_168105.1 56697735 3196005 3098200..3098472 1 NC_003911.11 subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport; monovalent cation/H+ antiporter subunit F 3098472 phaF 3196005 phaF Ruegeria pomeroyi DSS-3 monovalent cation/H+ antiporter subunit F YP_168105.1 3098200 D 246200 CDS YP_168106.1 56697736 3196008 3098480..3098866 1 NC_003911.11 subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport; monovalent cation/H+ antiporter subunit G 3098866 phaG 3196008 phaG Ruegeria pomeroyi DSS-3 monovalent cation/H+ antiporter subunit G YP_168106.1 3098480 D 246200 CDS YP_168107.1 56697737 3196021 3098871..3101030 1 NC_003911.11 identified by match to protein family HMM PF00070; match to protein family HMM PF02769; selenide,water dikinase 3101030 3196021 SPO2899 Ruegeria pomeroyi DSS-3 selenide,water dikinase YP_168107.1 3098871 D 246200 CDS YP_168108.1 56697738 3195834 complement(3101186..3102238) 1 NC_003911.11 catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA; tRNA 2-selenouridine synthase 3102238 3195834 SPO2900 Ruegeria pomeroyi DSS-3 tRNA 2-selenouridine synthase YP_168108.1 3101186 R 246200 CDS YP_168109.1 56697739 3195289 complement(3102276..3102941) 1 NC_003911.11 identified by similarity to GB:AAR33375.1; match to protein family HMM PF02586; hypothetical protein 3102941 3195289 SPO2901 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168109.1 3102276 R 246200 CDS YP_168110.1 56697740 3194613 complement(3102951..3103580) 1 NC_003911.11 identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 3103580 3194613 SPO2902 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_168110.1 3102951 R 246200 CDS YP_168111.1 56697741 3193569 3103734..3105482 1 NC_003911.11 identified by match to protein family HMM PF00515; match to protein family HMM PF00685; TPR/sulfotransferase domain-containing protein 3105482 3193569 SPO2903 Ruegeria pomeroyi DSS-3 TPR/sulfotransferase domain-containing protein YP_168111.1 3103734 D 246200 CDS YP_168112.1 56697742 3195528 complement(3105486..3107060) 1 NC_003911.11 identified by match to protein family HMM PF00149; match to protein family HMM PF02872; Ser/Thr protein phosphatase/nucleotidase 3107060 3195528 SPO2904 Ruegeria pomeroyi DSS-3 Ser/Thr protein phosphatase/nucleotidase YP_168112.1 3105486 R 246200 CDS YP_168113.1 56697743 3193245 3107178..3107516 1 NC_003911.11 identified by similarity to GB:CAC45122.1; match to protein family HMM PF06108; hypothetical protein 3107516 3193245 SPO2905 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168113.1 3107178 D 246200 CDS YP_168114.1 56697744 3193030 3107513..3107944 1 NC_003911.11 identified by similarity to GB:CAE26026.1; hypothetical protein 3107944 3193030 SPO2906 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168114.1 3107513 D 246200 CDS YP_168115.1 56697745 3195368 3107947..3108999 1 NC_003911.11 catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors; dihydroorotate dehydrogenase 2 3108999 pyrD 3195368 pyrD Ruegeria pomeroyi DSS-3 dihydroorotate dehydrogenase 2 YP_168115.1 3107947 D 246200 CDS YP_168116.1 56697746 3194113 3108996..3109340 1 NC_003911.11 identified by match to protein family HMM PF03960; match to protein family HMM TIGR00014; arsenate reductase 3109340 arsC-1 3194113 arsC-1 Ruegeria pomeroyi DSS-3 arsenate reductase YP_168116.1 3108996 D 246200 CDS YP_168117.1 56697747 3193509 complement(3109324..3110649) 1 NC_003911.11 identified by similarity to SP:P28303; match to protein family HMM PF01554; match to protein family HMM TIGR00797; DNA-damage-inducible protein F 3110649 dinF 3193509 dinF Ruegeria pomeroyi DSS-3 DNA-damage-inducible protein F YP_168117.1 3109324 R 246200 CDS YP_168118.1 56697748 3195853 complement(3110657..3111175) 1 NC_003911.11 identified by match to protein family HMM PF03061; thioesterase 3111175 3195853 SPO2910 Ruegeria pomeroyi DSS-3 thioesterase YP_168118.1 3110657 R 246200 CDS YP_168119.1 56697749 3196069 complement(3111177..3111647) 1 NC_003911.11 identified by match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase 3111647 3196069 SPO2911 Ruegeria pomeroyi DSS-3 thioesterase YP_168119.1 3111177 R 246200 CDS YP_168120.1 56697750 3195835 3111714..3112082 1 NC_003911.11 identified by match to protein family HMM PF00376; MerR family transcriptional regulator 3112082 3195835 SPO2912 Ruegeria pomeroyi DSS-3 MerR family transcriptional regulator YP_168120.1 3111714 D 246200 CDS YP_168121.1 56697751 3196022 3112203..3112397 1 NC_003911.11 hypothetical protein 3112397 3196022 SPO2913 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168121.1 3112203 D 246200 CDS YP_168122.1 56697752 3194350 3112617..3113018 1 NC_003911.11 identified by match to protein family HMM PF00376; MerR family transcriptional regulator 3113018 3194350 SPO2914 Ruegeria pomeroyi DSS-3 MerR family transcriptional regulator YP_168122.1 3112617 D 246200 CDS YP_168123.1 56697753 3194663 3113063..3114844 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 3114844 3194663 SPO2915 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_168123.1 3113063 D 246200 CDS YP_168124.1 56697754 3194645 3114899..3115111 1 NC_003911.11 hypothetical protein 3115111 3194645 SPO2916 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168124.1 3114899 D 246200 CDS YP_168125.1 56697755 3195269 3115377..3116018 1 NC_003911.11 identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 3116018 3195269 SPO2917 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_168125.1 3115377 D 246200 CDS YP_168126.1 56697756 3195219 3116029..3117240 1 NC_003911.11 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; acetyl-CoA acetyltransferase 3117240 3195219 SPO2918 Ruegeria pomeroyi DSS-3 acetyl-CoA acetyltransferase YP_168126.1 3116029 D 246200 CDS YP_168127.1 56697757 3195612 3117240..3117728 1 NC_003911.11 identified by similarity to GB:BAC49273.1; hypothetical protein 3117728 3195612 SPO2919 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168127.1 3117240 D 246200 CDS YP_168128.1 56697758 3193840 3117721..3119922 1 NC_003911.11 identified by similarity to SP:P77399; match to protein family HMM PF00378; match to protein family HMM PF00725; match to protein family HMM PF02737; fatty oxidation complex subunit alpha 3119922 fabJ-1 3193840 fabJ-1 Ruegeria pomeroyi DSS-3 fatty oxidation complex subunit alpha YP_168128.1 3117721 D 246200 CDS YP_168129.1 56697759 3194656 complement(3119991..3120725) 1 NC_003911.11 identified by similarity to GB:AAA70414.1; hypothetical protein 3120725 3194656 SPO2921 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168129.1 3119991 R 246200 CDS YP_168130.1 56697760 3194198 complement(3120897..3121544) 1 NC_003911.11 identified by similarity to PIR:B95911; hypothetical protein 3121544 3194198 SPO2922 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168130.1 3120897 R 246200 CDS YP_168131.1 56697761 3194176 complement(3121576..3122484) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 3122484 3194176 SPO2923 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168131.1 3121576 R 246200 CDS YP_168132.1 56697762 3194377 3122519..3123658 1 NC_003911.11 identified by similarity to GB:BAC52505.1; hypothetical protein 3123658 3194377 SPO2924 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168132.1 3122519 D 246200 CDS YP_168133.1 56697763 3195162 3123695..3124933 1 NC_003911.11 hypothetical protein 3124933 3195162 SPO2925 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168133.1 3123695 D 246200 CDS YP_168134.1 56697764 3193814 complement(3124964..3125596) 1 NC_003911.11 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase 3125596 upp 3193814 upp Ruegeria pomeroyi DSS-3 uracil phosphoribosyltransferase YP_168134.1 3124964 R 246200 CDS YP_168135.1 56697765 3195857 complement(3125593..3126594) 1 NC_003911.11 catalyzes the formation of inosine from adenosine; adenosine deaminase 3126594 add 3195857 add Ruegeria pomeroyi DSS-3 adenosine deaminase YP_168135.1 3125593 R 246200 CDS YP_168136.1 56697766 3194718 complement(3126591..3127802) 1 NC_003911.11 catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose; phosphopentomutase 3127802 deoB 3194718 deoB Ruegeria pomeroyi DSS-3 phosphopentomutase YP_168136.1 3126591 R 246200 CDS YP_168137.1 56697767 3195037 complement(3127799..3129109) 1 NC_003911.11 Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate; thymidine phosphorylase 3129109 deoA 3195037 deoA Ruegeria pomeroyi DSS-3 thymidine phosphorylase YP_168137.1 3127799 R 246200 CDS YP_168138.1 56697768 3194421 complement(3129113..3129505) 1 NC_003911.11 identified by similarity to SP:P19079; match to protein family HMM PF00383; match to protein family HMM TIGR01354; cytidine deaminase 3129505 cdd 3194421 cdd Ruegeria pomeroyi DSS-3 cytidine deaminase YP_168138.1 3129113 R 246200 CDS YP_168139.1 56697769 3195901 complement(3129647..3130831) 1 NC_003911.11 identified by similarity to GB:BAC50887.1; hypothetical protein 3130831 3195901 SPO2931 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168139.1 3129647 R 246200 CDS YP_168140.1 56697770 3193912 3130877..3133150 1 NC_003911.11 NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate; malic enzyme 3133150 3193912 SPO2932 Ruegeria pomeroyi DSS-3 malic enzyme YP_168140.1 3130877 D 246200 CDS YP_168141.1 56697771 3195759 3133193..3133582 1 NC_003911.11 identified by similarity to GB:BAB50467.1; match to protein family HMM PF04828; hypothetical protein 3133582 3195759 SPO2933 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168141.1 3133193 D 246200 CDS YP_168142.1 56697772 3194703 3133807..3135696 1 NC_003911.11 identified by similarity to SP:P77495; match to protein family HMM PF00501; propionate--CoA ligase 3135696 prpE 3194703 prpE Ruegeria pomeroyi DSS-3 propionate--CoA ligase YP_168142.1 3133807 D 246200 CDS YP_168143.1 56697774 3192991 3135853..3136878 1 NC_003911.11 hypothetical protein 3136878 3192991 SPO2936 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168143.1 3135853 D 246200 CDS YP_168144.1 56697773 3195292 3135866..3136321 1 NC_003911.11 hypothetical protein 3136321 3195292 SPO2935 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168144.1 3135866 D 246200 CDS YP_168145.1 56697775 3194060 3136878..3137450 1 NC_003911.11 identified by match to protein family HMM PF02630; SCO1/SenC family protein 3137450 3194060 SPO2937 Ruegeria pomeroyi DSS-3 SCO1/SenC family protein YP_168145.1 3136878 D 246200 CDS YP_168146.1 56697776 3192685 3137529..3138959 1 NC_003911.11 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia; amidase 3138959 3192685 SPO2938 Ruegeria pomeroyi DSS-3 amidase YP_168146.1 3137529 D 246200 CDS YP_168147.1 56697777 3196038 complement(3139264..3140025) 1 NC_003911.11 catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase 3140025 ppnK 3196038 ppnK Ruegeria pomeroyi DSS-3 inorganic polyphosphate/ATP-NAD kinase YP_168147.1 3139264 R 246200 CDS YP_168148.1 56697778 3193885 3140194..3141489 1 NC_003911.11 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 3141489 glyA 3193885 glyA Ruegeria pomeroyi DSS-3 serine hydroxymethyltransferase YP_168148.1 3140194 D 246200 CDS YP_168149.1 56697779 3194532 3141625..3142434 1 NC_003911.11 hypothetical protein 3142434 3194532 SPO2941 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168149.1 3141625 D 246200 CDS YP_168150.1 56697780 3193921 complement(3142503..3143000) 1 NC_003911.11 hypothetical protein 3143000 3193921 SPO2942 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168150.1 3142503 R 246200 CDS YP_168151.1 56697781 3194598 3142980..3143738 1 NC_003911.11 identified by match to protein family HMM PF00561; alpha/beta hydrolase 3143738 3194598 SPO2943 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_168151.1 3142980 D 246200 CDS YP_168152.1 56697782 3195495 complement(3143883..3144107) 1 NC_003911.11 hypothetical protein 3144107 3195495 SPO2944 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168152.1 3143883 R 246200 CDS YP_168153.1 56697783 3193049 complement(3144147..3144530) 1 NC_003911.11 identified by match to protein family HMM PF00581; rhodanese-like domain-containing protein 3144530 3193049 SPO2945 Ruegeria pomeroyi DSS-3 rhodanese-like domain-containing protein YP_168153.1 3144147 R 246200 CDS YP_168154.1 56697784 3193335 complement(3144632..3146119) 1 NC_003911.11 identified by similarity to GB:AAB50013.1; monooxygenase domain-containing protein 3146119 3193335 SPO2946 Ruegeria pomeroyi DSS-3 monooxygenase domain-containing protein YP_168154.1 3144632 R 246200 CDS YP_168155.1 56697785 3195198 complement(3146135..3146596) 1 NC_003911.11 identified by match to protein family HMM PF00190; cupin 3146596 3195198 SPO2947 Ruegeria pomeroyi DSS-3 cupin YP_168155.1 3146135 R 246200 CDS YP_168156.1 56697786 3194866 3146698..3147744 1 NC_003911.11 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 3147744 3194866 SPO2948 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_168156.1 3146698 D 246200 CDS YP_168157.1 56697787 3195985 complement(3147750..3148094) 1 NC_003911.11 identified by match to protein family HMM PF01042; endoribonuclease L-PSP 3148094 3195985 SPO2949 Ruegeria pomeroyi DSS-3 endoribonuclease L-PSP YP_168157.1 3147750 R 246200 CDS YP_168158.1 56697788 3192735 complement(3148164..3149345) 1 NC_003911.11 identified by similarity to GB:AAQ65571.1; match to protein family HMM PF04536; hypothetical protein 3149345 3192735 SPO2950 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168158.1 3148164 R 246200 CDS YP_168159.1 56697789 3195747 complement(3149400..3150179) 1 NC_003911.11 identified by similarity to PIR:G97655; match to protein family HMM PF03724; hypothetical protein 3150179 3195747 SPO2951 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168159.1 3149400 R 246200 CDS YP_168160.1 56697790 3194539 complement(3150256..3152034) 1 NC_003911.11 identified by match to protein family HMM PF02080; TrkA domain-containing protein 3152034 3194539 SPO2952 Ruegeria pomeroyi DSS-3 TrkA domain-containing protein YP_168160.1 3150256 R 246200 CDS YP_168161.1 56697791 3194948 complement(3152142..3152954) 1 NC_003911.11 identified by match to protein family HMM PF00149; Ser/Thr protein phosphatase 3152954 3194948 SPO2953 Ruegeria pomeroyi DSS-3 Ser/Thr protein phosphatase YP_168161.1 3152142 R 246200 CDS YP_168162.1 56697792 3194884 complement(3153136..3153693) 1 NC_003911.11 identified by match to protein family HMM PF01812; 5-formyltetrahydrofolate cyclo-ligase 3153693 3194884 SPO2954 Ruegeria pomeroyi DSS-3 5-formyltetrahydrofolate cyclo-ligase YP_168162.1 3153136 R 246200 CDS YP_168163.1 56697793 3193018 complement(3153702..3155093) 1 NC_003911.11 identified by match to protein family HMM PF00571; match to protein family HMM PF01769; match to protein family HMM PF03448; match to protein family HMM TIGR00400; magnesium transporter 3155093 mgtE 3193018 mgtE Ruegeria pomeroyi DSS-3 magnesium transporter YP_168163.1 3153702 R 246200 CDS YP_168164.1 56697794 3193915 3155229..3156512 1 NC_003911.11 Catalyzes the deamination of guanine; guanine deaminase 3156512 3193915 SPO2956 Ruegeria pomeroyi DSS-3 guanine deaminase YP_168164.1 3155229 D 246200 CDS YP_168165.1 56697795 3194390 complement(3156593..3157927) 1 NC_003911.11 catalyzes the transformation of hydroxyatrazine to N-isopropylammelide and ethylamine in the atrazine degradation pathway.; hydroxydechloroatrazine ethylaminohydrolase 3157927 3194390 SPO2957 Ruegeria pomeroyi DSS-3 hydroxydechloroatrazine ethylaminohydrolase YP_168165.1 3156593 R 246200 CDS YP_168166.1 56697796 3192910 complement(3158044..3158835) 1 NC_003911.11 identified by match to protein family HMM PF00459; match to protein family HMM TIGR02067; inositol monophosphatase 3158835 3192910 SPO2958 Ruegeria pomeroyi DSS-3 inositol monophosphatase YP_168166.1 3158044 R 246200 CDS YP_168167.1 56697797 3193965 complement(3158885..3159256) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 3159256 3193965 SPO2959 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_168167.1 3158885 R 246200 CDS YP_168168.1 56697798 3192815 3159607..3160563 1 NC_003911.11 identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase 3160563 3192815 SPO2960 Ruegeria pomeroyi DSS-3 zinc-binding dehydrogenase oxidoreductase YP_168168.1 3159607 D 246200 CDS YP_168169.1 56697799 3195732 complement(3160726..3161604) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3161604 3195732 SPO2961 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168169.1 3160726 R 246200 CDS YP_168170.1 56697800 3195533 3161684..3161935 1 NC_003911.11 identified by similarity to GB:AAO55291.1; hypothetical protein 3161935 3195533 SPO2962 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168170.1 3161684 D 246200 CDS YP_168171.1 56697801 3195811 3162085..3162894 1 NC_003911.11 identified by match to protein family HMM PF01027; hypothetical protein 3162894 3195811 SPO2963 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168171.1 3162085 D 246200 CDS YP_168172.1 56697802 3194953 complement(3162966..3163616) 1 NC_003911.11 hypothetical protein 3163616 3194953 SPO2964 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168172.1 3162966 R 246200 CDS YP_168173.1 56698715 3195427 complement(3163621..3163788) 1 NC_003911.11 in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif; 50S ribosomal protein L33 3163788 rpmG 3195427 rpmG Ruegeria pomeroyi DSS-3 50S ribosomal protein L33 YP_168173.1 3163621 R 246200 CDS YP_168174.1 56697803 3194805 complement(3164377..3165051) 1 NC_003911.11 identified by match to protein family HMM PF01510; N-acetylmuramoyl-L-alanine amidase 3165051 3194805 SPO2967 Ruegeria pomeroyi DSS-3 N-acetylmuramoyl-L-alanine amidase YP_168174.1 3164377 R 246200 CDS YP_168175.1 56697804 3194533 complement(3165058..3165969) 1 NC_003911.11 hypothetical protein 3165969 3194533 SPO2968 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168175.1 3165058 R 246200 CDS YP_168176.1 56697805 3194340 complement(3165885..3167375) 1 NC_003911.11 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit A 3167375 gatA 3194340 gatA Ruegeria pomeroyi DSS-3 aspartyl/glutamyl-tRNA amidotransferase subunit A YP_168176.1 3165885 R 246200 CDS YP_168177.1 56697806 3194892 complement(3167379..3167666) 1 NC_003911.11 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain; aspartyl/glutamyl-tRNA amidotransferase subunit C 3167666 gatC 3194892 gatC Ruegeria pomeroyi DSS-3 aspartyl/glutamyl-tRNA amidotransferase subunit C YP_168177.1 3167379 R 246200 CDS YP_168178.1 56697807 3195761 complement(3167743..3168894) 1 NC_003911.11 identified by match to protein family HMM TIGR01409; hypothetical protein 3168894 3195761 SPO2971 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168178.1 3167743 R 246200 CDS YP_168179.1 56697808 3194601 complement(3169010..3169492) 1 NC_003911.11 hypothetical protein 3169492 3194601 SPO2972 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168179.1 3169010 R 246200 CDS YP_168180.1 56697809 3194830 complement(3171756..3173042) 1 NC_003911.11 identified by similarity to GB:CAE27781.1; hypothetical protein 3173042 3194830 SPO2974 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168180.1 3171756 R 246200 CDS YP_168181.1 56697810 3195343 complement(3173116..3173763) 1 NC_003911.11 identified by similarity to GB:BAB51018.1; hypothetical protein 3173763 3195343 SPO2975 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168181.1 3173116 R 246200 CDS YP_168182.1 56697811 3195253 3173821..3174513 1 NC_003911.11 identified by match to protein family HMM PF00753; metallo-beta-lactamase 3174513 3195253 SPO2976 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_168182.1 3173821 D 246200 CDS YP_168183.1 56697812 3195656 3174604..3175593 1 NC_003911.11 identified by match to protein family HMM PF00211; guanylate cyclase 3175593 3195656 SPO2977 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_168183.1 3174604 D 246200 CDS YP_168184.1 56697813 3193901 3175590..3176549 1 NC_003911.11 identified by match to protein family HMM PF00211; guanylate cyclase 3176549 3193901 SPO2978 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_168184.1 3175590 D 246200 CDS YP_168185.1 56697814 3194461 complement(3176649..3177098) 1 NC_003911.11 hypothetical protein 3177098 3194461 SPO2979 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168185.1 3176649 R 246200 CDS YP_168186.1 56697815 3195665 complement(3177095..3178111) 1 NC_003911.11 identified by match to protein family HMM PF04371; peptidyl-arginine deiminase 3178111 3195665 SPO2980 Ruegeria pomeroyi DSS-3 peptidyl-arginine deiminase YP_168186.1 3177095 R 246200 CDS YP_168187.1 56697816 3195363 complement(3178253..3180013) 1 NC_003911.11 identified by similarity to GB:CAC67530.1; hypothetical protein 3180013 3195363 SPO2981 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168187.1 3178253 R 246200 CDS YP_168188.1 56697817 3195084 complement(3180077..3180550) 1 NC_003911.11 identified by match to protein family HMM PF01980; match to protein family HMM TIGR00104; hypothetical protein 3180550 3195084 SPO2982 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168188.1 3180077 R 246200 CDS YP_168189.1 56697818 3195951 complement(3180552..3181031) 1 NC_003911.11 identified by match to protein family HMM PF00383; cytidine and deoxycytidylate deaminase 3181031 3195951 SPO2983 Ruegeria pomeroyi DSS-3 cytidine and deoxycytidylate deaminase YP_168189.1 3180552 R 246200 CDS YP_168190.1 56697819 3195842 3181093..3182256 1 NC_003911.11 identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093; RNA pseudouridylate synthase 3182256 3195842 SPO2984 Ruegeria pomeroyi DSS-3 RNA pseudouridylate synthase YP_168190.1 3181093 D 246200 CDS YP_168191.1 56697820 3195187 3182433..3183332 1 NC_003911.11 hypothetical protein 3183332 3195187 SPO2985 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168191.1 3182433 D 246200 CDS YP_168192.1 56697821 3195536 3183358..3184548 1 NC_003911.11 identified by similarity to GB:AAB93480.1; tellurite resistance protein 3184548 3195536 SPO2986 Ruegeria pomeroyi DSS-3 tellurite resistance protein YP_168192.1 3183358 D 246200 CDS YP_168193.1 56697822 3195941 3184553..3185515 1 NC_003911.11 identified by similarity to GB:AAB93481.1; lipoprotein 3185515 3195941 SPO2987 Ruegeria pomeroyi DSS-3 lipoprotein YP_168193.1 3184553 D 246200 CDS YP_168194.1 56697823 3194853 3185543..3186658 1 NC_003911.11 identified by similarity to GB:CAD18447.1; hypothetical protein 3186658 3194853 SPO2988 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168194.1 3185543 D 246200 CDS YP_168195.1 56697824 3195445 3186722..3187210 1 NC_003911.11 identified by similarity to SP:P16670; match to protein family HMM PF01292; cytochrome b562 3187210 3195445 SPO2989 Ruegeria pomeroyi DSS-3 cytochrome b562 YP_168195.1 3186722 D 246200 CDS YP_168196.1 56697825 3195624 3187214..3188341 1 NC_003911.11 identified by similarity to PIR:F83875; hypothetical protein 3188341 3195624 SPO2990 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168196.1 3187214 D 246200 CDS YP_168197.1 56697826 3195936 3188990..3189685 1 NC_003911.11 identified by match to protein family HMM PF00881; nitroreductase 3189685 3195936 SPO2991 Ruegeria pomeroyi DSS-3 nitroreductase YP_168197.1 3188990 D 246200 CDS YP_168198.1 56697827 3195426 3189696..3190133 1 NC_003911.11 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine; D-tyrosyl-tRNA(Tyr) deacylase 3190133 dtd 3195426 dtd Ruegeria pomeroyi DSS-3 D-tyrosyl-tRNA(Tyr) deacylase YP_168198.1 3189696 D 246200 CDS YP_168199.1 56697828 3195514 3190130..3191236 1 NC_003911.11 identified by match to protein family HMM PF05161; MOFRL family protein 3191236 3195514 SPO2993 Ruegeria pomeroyi DSS-3 MOFRL family protein YP_168199.1 3190130 D 246200 CDS YP_168200.1 56697829 3195156 3191281..3193281 1 NC_003911.11 identified by similarity to PIR:I40217; match to protein family HMM PF02129; match to protein family HMM TIGR00976; X-Pro dipeptidyl-peptidase 3193281 3195156 SPO2994 Ruegeria pomeroyi DSS-3 X-Pro dipeptidyl-peptidase YP_168200.1 3191281 D 246200 CDS YP_168201.1 56697830 3195604 3193314..3194990 1 NC_003911.11 identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; peptide/nickel/opine uptake ABC transporter substrate-binding protein 3194990 3195604 SPO2995 Ruegeria pomeroyi DSS-3 peptide/nickel/opine uptake ABC transporter substrate-binding protein YP_168201.1 3193314 D 246200 CDS YP_168202.1 56697831 3194971 3195010..3195966 1 NC_003911.11 identified by match to protein family HMM PF00528; peptide/nickel/opine uptake ABC transporter permease 3195966 3194971 SPO2996 Ruegeria pomeroyi DSS-3 peptide/nickel/opine uptake ABC transporter permease YP_168202.1 3195010 D 246200 CDS YP_168203.1 56697832 3194534 3195963..3196778 1 NC_003911.11 identified by similarity to SP:P37315; match to protein family HMM PF00528; peptide/nickel/opine uptake ABC transporter permease 3196778 3194534 SPO2997 Ruegeria pomeroyi DSS-3 peptide/nickel/opine uptake ABC transporter permease YP_168203.1 3195963 D 246200 CDS YP_168204.1 56697833 3195482 3196775..3198412 1 NC_003911.11 identified by match to protein family HMM PF00005; peptide/nickel/opine uptake ABC transporter ATP-binding protein 3198412 3195482 SPO2998 Ruegeria pomeroyi DSS-3 peptide/nickel/opine uptake ABC transporter ATP-binding protein YP_168204.1 3196775 D 246200 CDS YP_168205.1 56697834 3195973 complement(3198458..3199708) 1 NC_003911.11 hypothetical protein 3199708 3195973 SPO2999 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168205.1 3198458 R 246200 CDS YP_168206.1 56697835 3195085 3199824..3200759 1 NC_003911.11 identified by similarity to GB:BAB51623.1; hypothetical protein 3200759 3195085 SPO3000 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168206.1 3199824 D 246200 CDS YP_168207.1 56697836 3195083 3200818..3201375 1 NC_003911.11 hypothetical protein 3201375 3195083 SPO3001 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168207.1 3200818 D 246200 CDS YP_168208.1 56697837 3192925 complement(3201378..3202301) 1 NC_003911.11 identified by similarity to GB:AAC38151.1; lipase 3202301 3192925 SPO3002 Ruegeria pomeroyi DSS-3 lipase YP_168208.1 3201378 R 246200 CDS YP_168209.1 56697838 3194560 complement(3202319..3204244) 1 NC_003911.11 activates fatty acids by binding to coenzyme A; AMP-binding protein 3204244 3194560 SPO3003 Ruegeria pomeroyi DSS-3 AMP-binding protein YP_168209.1 3202319 R 246200 CDS YP_168210.1 56697839 3195316 complement(3204434..3204862) 1 NC_003911.11 identified by match to protein family HMM PF01476; match to protein family HMM PF04972; LysM domain/BON superfamily protein 3204862 3195316 SPO3004 Ruegeria pomeroyi DSS-3 LysM domain/BON superfamily protein YP_168210.1 3204434 R 246200 CDS YP_168211.1 56697840 3195372 complement(3204929..3206860) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter ATP-binding protein/permease 3206860 3195372 SPO3005 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein/permease YP_168211.1 3204929 R 246200 CDS YP_168212.1 56697841 3194987 complement(3207376..3207954) 1 NC_003911.11 identified by match to protein family HMM PF00515; hypothetical protein 3207954 3194987 SPO3008 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168212.1 3207376 R 246200 CDS YP_168213.1 56697842 3194689 complement(3207967..3208455) 1 NC_003911.11 identified by similarity to SP:Q52710; match to protein family HMM PF01037; match to protein family HMM TIGR01199; proline dehydrogenase 3208455 putR 3194689 putR Ruegeria pomeroyi DSS-3 proline dehydrogenase YP_168213.1 3207967 R 246200 CDS YP_168214.1 56697843 3193507 3208560..3211964 1 NC_003911.11 proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the protein from Pseudomonas does not have this domain; bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase 3211964 putA 3193507 putA Ruegeria pomeroyi DSS-3 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase YP_168214.1 3208560 D 246200 CDS YP_168215.1 56697844 3195499 3212088..3212831 1 NC_003911.11 identified by match to protein family HMM PF01694; rhomboid family protein 3212831 3195499 SPO3011 Ruegeria pomeroyi DSS-3 rhomboid family protein YP_168215.1 3212088 D 246200 CDS YP_168216.1 56697845 3192702 complement(3212902..3213687) 1 NC_003911.11 identified by similarity to SP:P22783; match to protein family HMM PF00459; inositol monophosphatase 3213687 3192702 SPO3012 Ruegeria pomeroyi DSS-3 inositol monophosphatase YP_168216.1 3212902 R 246200 CDS YP_168217.1 56697846 3194024 3213862..3214902 1 NC_003911.11 identified by match to protein family HMM PF00107; L4BD family NADP-dependent oxidoreductase 3214902 3194024 SPO3013 Ruegeria pomeroyi DSS-3 L4BD family NADP-dependent oxidoreductase YP_168217.1 3213862 D 246200 CDS YP_168218.1 56697847 3194800 3215138..3215497 1 NC_003911.11 hypothetical protein 3215497 3194800 SPO3014 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168218.1 3215138 D 246200 CDS YP_168219.1 56697848 3193156 complement(3215540..3216445) 1 NC_003911.11 identified by similarity to SP:P19797; match to protein family HMM PF00126; match to protein family HMM PF03466; transcriptional regulator MetR 3216445 metR 3193156 metR Ruegeria pomeroyi DSS-3 transcriptional regulator MetR YP_168219.1 3215540 R 246200 CDS YP_168220.1 56697849 3193512 3216495..3217418 1 NC_003911.11 identified by similarity to SP:P00394; match to protein family HMM PF02219; match to protein family HMM TIGR00676; 5,10-methylenetetrahydrofolate reductase 3217418 metF 3193512 metF Ruegeria pomeroyi DSS-3 5,10-methylenetetrahydrofolate reductase YP_168220.1 3216495 D 246200 CDS YP_168221.1 56697850 3193926 3217480..3217965 1 NC_003911.11 identified by similarity to SP:P76084; match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase 3217965 3193926 SPO3017 Ruegeria pomeroyi DSS-3 thioesterase YP_168221.1 3217480 D 246200 CDS YP_168222.1 56697851 3194044 complement(3218169..3219248) 1 NC_003911.11 identified by similarity to GB:AAK24661.1; hypothetical protein 3219248 3194044 SPO3018 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168222.1 3218169 R 246200 CDS YP_168223.1 56697852 3195542 complement(3219223..3221514) 1 NC_003911.11 identified by match to protein family HMM PF01315; match to protein family HMM PF02738; xanthine dehydrogenase, large subunit 3221514 3195542 SPO3019 Ruegeria pomeroyi DSS-3 xanthine dehydrogenase, large subunit YP_168223.1 3219223 R 246200 CDS YP_168224.1 56697853 3195801 complement(3221652..3223289) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3223289 3195801 SPO3020 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168224.1 3221652 R 246200 CDS YP_168225.1 56697854 3193928 3223313..3224281 1 NC_003911.11 identified by match to protein family HMM PF05721; phytanoyl-CoA dioxygenase 3224281 3193928 SPO3021 Ruegeria pomeroyi DSS-3 phytanoyl-CoA dioxygenase YP_168225.1 3223313 D 246200 CDS YP_168226.1 56697855 3194327 3224640..3227702 1 NC_003911.11 valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain; valyl-tRNA synthetase 3227702 valS 3194327 valS Ruegeria pomeroyi DSS-3 valyl-tRNA synthetase YP_168226.1 3224640 D 246200 CDS YP_168227.1 56697856 3194397 3227728..3228114 1 NC_003911.11 identified by similarity to PIR:C83757; hypothetical protein 3228114 3194397 SPO3023 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168227.1 3227728 D 246200 CDS YP_168228.1 56697857 3192818 3228187..3229584 1 NC_003911.11 identified by match to protein family HMM PF00211; match to protein family HMM PF00561; adenylate cyclase 3229584 3192818 SPO3024 Ruegeria pomeroyi DSS-3 adenylate cyclase YP_168228.1 3228187 D 246200 CDS YP_168229.1 56697858 3195331 complement(3229758..3230540) 1 NC_003911.11 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 3230540 3195331 SPO3025 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_168229.1 3229758 R 246200 CDS YP_168230.1 56697859 3194929 complement(3230614..3231789) 1 NC_003911.11 identified by match to protein family HMM PF03088; strictosidine synthase 3231789 3194929 SPO3026 Ruegeria pomeroyi DSS-3 strictosidine synthase YP_168230.1 3230614 R 246200 CDS YP_168231.1 56697860 3195868 3231741..3232883 1 NC_003911.11 catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate; histidinol-phosphate aminotransferase 3232883 3195868 SPO3027 Ruegeria pomeroyi DSS-3 histidinol-phosphate aminotransferase YP_168231.1 3231741 D 246200 CDS YP_168232.1 56697861 3195179 3232907..3233113 1 NC_003911.11 hypothetical protein 3233113 3195179 SPO3028 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168232.1 3232907 D 246200 CDS YP_168233.1 56697862 3193073 complement(3233121..3234329) 1 NC_003911.11 identified by similarity to SP:O08374; match to protein family HMM PF00266; serine--glyoxylate transaminase 3234329 3193073 SPO3029 Ruegeria pomeroyi DSS-3 serine--glyoxylate transaminase YP_168233.1 3233121 R 246200 CDS YP_168234.1 56697863 3193541 3234424..3236394 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF00664; efflux ABC transporter transmembrane ATP-binding protein 3236394 3193541 SPO3030 Ruegeria pomeroyi DSS-3 efflux ABC transporter transmembrane ATP-binding protein YP_168234.1 3234424 D 246200 CDS YP_168235.1 56697864 3195167 complement(3236472..3237104) 1 NC_003911.11 identified by similarity to SP:P10177; match to protein family HMM PF01081; match to protein family HMM TIGR01182; 2-dehydro-3-deoxyphosphooctonate aldolase 3237104 eda-1 3195167 eda-1 Ruegeria pomeroyi DSS-3 2-dehydro-3-deoxyphosphooctonate aldolase YP_168235.1 3236472 R 246200 CDS YP_168236.1 56697865 3193093 complement(3237108..3238913) 1 NC_003911.11 catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate; phosphogluconate dehydratase 3238913 edd 3193093 edd Ruegeria pomeroyi DSS-3 phosphogluconate dehydratase YP_168236.1 3237108 R 246200 CDS YP_168237.1 56697866 3194581 complement(3238916..3240367) 1 NC_003911.11 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase 3240367 zwf-2 3194581 zwf-2 Ruegeria pomeroyi DSS-3 glucose-6-phosphate 1-dehydrogenase YP_168237.1 3238916 R 246200 CDS YP_168238.1 56697867 3194964 complement(3241134..3243377) 1 NC_003911.11 identified by similarity to SP:P37177; match to protein family HMM PF00391; match to protein family HMM PF01590; match to protein family HMM PF02896; match to protein family HMM PF05524; match to protein family HMM TIGR01417; phosphoenolpyruvate-protein phosphotransferase 3243377 3194964 SPO3034 Ruegeria pomeroyi DSS-3 phosphoenolpyruvate-protein phosphotransferase YP_168238.1 3241134 R 246200 CDS YP_168239.1 56697868 3194877 complement(3243425..3244663) 1 NC_003911.11 identified by match to protein family HMM PF00696; match to protein family HMM PF01842; match to protein family HMM TIGR00656; match to protein family HMM TIGR00657; aspartate kinase 3244663 3194877 SPO3035 Ruegeria pomeroyi DSS-3 aspartate kinase YP_168239.1 3243425 R 246200 CDS YP_168240.1 56697869 3193678 complement(3245171..3247231) 1 NC_003911.11 identified by match to protein family HMM PF00753; metallo-beta-lactamase 3247231 3193678 SPO3036 Ruegeria pomeroyi DSS-3 metallo-beta-lactamase YP_168240.1 3245171 R 246200 CDS YP_168241.1 56697870 3195987 3247808..3248617 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00126; LysR family transcriptional regulator 3248617 3195987 SPO3037 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168241.1 3247808 D 246200 CDS YP_168242.1 56697871 3195648 complement(3248605..3251301) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase/response regulator 3251301 3195648 SPO3038 Ruegeria pomeroyi DSS-3 sensor histidine kinase/response regulator YP_168242.1 3248605 R 246200 CDS YP_168243.1 56697872 3195535 complement(3251298..3252041) 1 NC_003911.11 polar amino acid ABC transporter substrate-binding protein 3252041 3195535 SPO3039 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter substrate-binding protein YP_168243.1 3251298 R 246200 CDS YP_168244.1 56697873 3194731 3252210..3253043 1 NC_003911.11 identified by match to protein family HMM PF00497; polar amino acid ABC transporter substrate-binding protein 3253043 3194731 SPO3040 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter substrate-binding protein YP_168244.1 3252210 D 246200 CDS YP_168245.1 56697874 3194370 3253047..3253826 1 NC_003911.11 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease 3253826 3194370 SPO3041 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter permease YP_168245.1 3253047 D 246200 CDS YP_168246.1 56697875 3195792 3253816..3254703 1 NC_003911.11 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease 3254703 3195792 SPO3042 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter permease YP_168246.1 3253816 D 246200 CDS YP_168247.1 56697876 3193767 3254716..3255465 1 NC_003911.11 identified by similarity to SP:P27675; match to protein family HMM PF00005; glutamine ABC transporter ATP-binding protein 3255465 glnQ 3193767 glnQ Ruegeria pomeroyi DSS-3 glutamine ABC transporter ATP-binding protein YP_168247.1 3254716 D 246200 CDS YP_168248.1 56697877 3195235 3255584..3256588 1 NC_003911.11 identified by match to protein family HMM PF00126; LysR family transcriptional regulator 3256588 3195235 SPO3044 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168248.1 3255584 D 246200 CDS YP_168249.1 56697878 3195044 complement(3256591..3257394) 1 NC_003911.11 identified by match to protein family HMM PF00117; glutamine amidotransferase 3257394 3195044 SPO3045 Ruegeria pomeroyi DSS-3 glutamine amidotransferase YP_168249.1 3256591 R 246200 CDS YP_168250.1 56697879 3196059 complement(3257440..3259527) 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide ABC transporter ATP-binding protein 3259527 3196059 SPO3046 Ruegeria pomeroyi DSS-3 oligopeptide ABC transporter ATP-binding protein YP_168250.1 3257440 R 246200 CDS YP_168251.1 56697880 3194946 complement(3259539..3260744) 1 NC_003911.11 identified by similarity to SP:P37315; match to protein family HMM PF00528; dipeptide ABC transporter permease 3260744 3194946 SPO3047 Ruegeria pomeroyi DSS-3 dipeptide ABC transporter permease YP_168251.1 3259539 R 246200 CDS YP_168252.1 56697881 3195850 complement(3260757..3261896) 1 NC_003911.11 Assignment partly based on membership in dipeptide ABC transporter gene cluster.; identified by match to protein family HMM PF00528; dipeptide ABC transporter permease 3261896 3195850 SPO3048 Ruegeria pomeroyi DSS-3 dipeptide ABC transporter permease YP_168252.1 3260757 R 246200 CDS YP_168253.1 56697882 3194967 complement(3261914..3263584) 1 NC_003911.11 Assignment partly based on membership in dipeptide ABC transporter gene cluster.; identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; dipeptide ABC transporter substrate-binding protein 3263584 3194967 SPO3049 Ruegeria pomeroyi DSS-3 dipeptide ABC transporter substrate-binding protein YP_168253.1 3261914 R 246200 CDS YP_168254.1 56697883 3195202 complement(3263848..3263940) 1 NC_003911.11 hypothetical protein 3263940 3195202 SPO3050 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168254.1 3263848 R 246200 CDS YP_168255.1 56697884 3195567 complement(3264047..3264685) 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 3264685 3195567 SPO3051 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase oxidoreductase YP_168255.1 3264047 R 246200 CDS YP_168256.1 56697885 3194919 complement(3264687..3265112) 1 NC_003911.11 identified by similarity to GB:AAK22812.1; match to protein family HMM PF06676; hypothetical protein 3265112 3194919 SPO3052 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168256.1 3264687 R 246200 CDS YP_168257.1 56697886 3195185 complement(3265164..3265664) 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX domain-containing protein 3265664 3195185 SPO3053 Ruegeria pomeroyi DSS-3 NUDIX domain-containing protein YP_168257.1 3265164 R 246200 CDS YP_168258.1 56697887 3195102 complement(3265729..3266490) 1 NC_003911.11 identified by similarity to GB:CAD71689.1; hypothetical protein 3266490 3195102 SPO3054 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168258.1 3265729 R 246200 CDS YP_168259.1 56697888 3195050 complement(3266540..3267028) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3267028 3195050 SPO3055 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168259.1 3266540 R 246200 CDS YP_168260.1 56697889 3194911 3267112..3267717 1 NC_003911.11 identified by similarity to GB:AAN29988.1; hypothetical protein 3267717 3194911 SPO3056 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168260.1 3267112 D 246200 CDS YP_168261.1 56697890 3194767 3267717..3268355 1 NC_003911.11 identified by similarity to GB:AAN77593.1; match to protein family HMM PF00132; streptogramin acetyltransferase 3268355 3194767 SPO3057 Ruegeria pomeroyi DSS-3 streptogramin acetyltransferase YP_168261.1 3267717 D 246200 CDS YP_168262.1 56697891 3195722 complement(3268484..3270118) 1 NC_003911.11 identified by match to protein family HMM PF00916; match to protein family HMM PF01740; sulfate transporter family protein 3270118 3195722 SPO3058 Ruegeria pomeroyi DSS-3 sulfate transporter family protein YP_168262.1 3268484 R 246200 CDS YP_168263.1 56697892 3195041 3270279..3270860 1 NC_003911.11 hypothetical protein 3270860 3195041 SPO3059 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168263.1 3270279 D 246200 CDS YP_168264.1 56697893 3195483 3270937..3271809 1 NC_003911.11 Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate; 5'-methylthioadenosine phosphorylase 3271809 mtaP 3195483 mtaP Ruegeria pomeroyi DSS-3 5'-methylthioadenosine phosphorylase YP_168264.1 3270937 D 246200 CDS YP_168265.1 56697894 3195315 3273089..3273562 1 NC_003911.11 identified by similarity to PIR:H95891; hypothetical protein 3273562 3195315 SPO3062 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168265.1 3273089 D 246200 CDS YP_168266.1 56697895 3194819 3273593..3274252 1 NC_003911.11 identified by similarity to SP:P27847; match to protein family HMM PF01810; transmembrane efflux protein 3274252 3194819 SPO3063 Ruegeria pomeroyi DSS-3 transmembrane efflux protein YP_168266.1 3273593 D 246200 CDS YP_168267.1 56697896 3193784 complement(3274249..3274482) 1 NC_003911.11 identified by similarity to GB:AAM37286.1; hypothetical protein 3274482 3193784 SPO3064 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168267.1 3274249 R 246200 CDS YP_168268.1 56697897 3194279 3274481..3274648 1 NC_003911.11 hypothetical protein 3274648 3194279 SPO3065 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168268.1 3274481 D 246200 CDS YP_168269.1 56697898 3195689 3274764..3275303 1 NC_003911.11 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 3275303 apt 3195689 apt Ruegeria pomeroyi DSS-3 adenine phosphoribosyltransferase YP_168269.1 3274764 D 246200 CDS YP_168270.1 56697899 3193056 complement(3275373..3276785) 1 NC_003911.11 identified by match to protein family HMM PF01565; match to protein family HMM PF02913; oxidoreductase, FAD-binding 3276785 3193056 SPO3067 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_168270.1 3275373 R 246200 CDS YP_168271.1 56697900 3193522 complement(3276824..3277672) 1 NC_003911.11 identified by similarity to GB:CAC47333.1; hypothetical protein 3277672 3193522 SPO3068 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168271.1 3276824 R 246200 CDS YP_168272.1 56697901 3195952 complement(3277751..3278335) 1 NC_003911.11 identified by similarity to SP:P09454; match to protein family HMM PF00583; ribosomal-protein-alanine acetyltransferase 3278335 3195952 SPO3069 Ruegeria pomeroyi DSS-3 ribosomal-protein-alanine acetyltransferase YP_168272.1 3277751 R 246200 CDS YP_168273.1 56697902 3196066 complement(3278335..3279597) 1 NC_003911.11 identified by match to protein family HMM PF00675; match to protein family HMM PF05193; M16 family peptidase 3279597 3196066 SPO3070 Ruegeria pomeroyi DSS-3 M16 family peptidase YP_168273.1 3278335 R 246200 CDS YP_168274.1 56697903 3196057 complement(3279594..3280985) 1 NC_003911.11 catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase 3280985 thrC 3196057 thrC Ruegeria pomeroyi DSS-3 threonine synthase YP_168274.1 3279594 R 246200 CDS YP_168275.1 56697904 3196001 complement(3280991..3281662) 1 NC_003911.11 SURF1 family protein 3281662 3196001 SPO3072 Ruegeria pomeroyi DSS-3 SURF1 family protein YP_168275.1 3280991 R 246200 CDS YP_168276.1 56697905 3195972 complement(3281848..3282663) 1 NC_003911.11 identified by match to protein family HMM PF00510; cytochrome c oxidase subunit III 3282663 ctaE 3195972 ctaE Ruegeria pomeroyi DSS-3 cytochrome c oxidase subunit III YP_168276.1 3281848 R 246200 CDS YP_168277.1 56697906 3195127 complement(3282686..3283261) 1 NC_003911.11 involved in the insertion of copper into subunit I of cytochrome C oxidase; cytochrome C oxidase assembly protein 3283261 ctaG 3195127 ctaG Ruegeria pomeroyi DSS-3 cytochrome C oxidase assembly protein YP_168277.1 3282686 R 246200 CDS YP_168278.1 56697907 3196009 complement(3283425..3284381) 1 NC_003911.11 converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase 3284381 cyoE 3196009 cyoE Ruegeria pomeroyi DSS-3 protoheme IX farnesyltransferase YP_168278.1 3283425 R 246200 CDS YP_168279.1 56697908 3196014 complement(3284469..3285305) 1 NC_003911.11 identified by similarity to SP:P08306; match to protein family HMM PF00116; match to protein family HMM PF02790; cytochrome c oxidase subunit II 3285305 ctaC 3196014 ctaC Ruegeria pomeroyi DSS-3 cytochrome c oxidase subunit II YP_168279.1 3284469 R 246200 CDS YP_168280.1 56697909 3195320 3285483..3286904 1 NC_003911.11 identified by similarity to SP:P46473; match to protein family HMM PF01523; TldD/PmbA family protein 3286904 3195320 SPO3077 Ruegeria pomeroyi DSS-3 TldD/PmbA family protein YP_168280.1 3285483 D 246200 CDS YP_168281.1 56697910 3195908 3287129..3288277 1 NC_003911.11 identified by match to protein family HMM PF02481; match to protein family HMM TIGR00732; DNA processing protein DprA 3288277 3195908 SPO3078 Ruegeria pomeroyi DSS-3 DNA processing protein DprA YP_168281.1 3287129 D 246200 CDS YP_168282.1 56697911 3196046 3288441..3291083 1 NC_003911.11 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I 3291083 topA 3196046 topA Ruegeria pomeroyi DSS-3 DNA topoisomerase I YP_168282.1 3288441 D 246200 CDS YP_168283.1 56697912 3196045 complement(3291105..3291686) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 3291686 3196045 SPO3080 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_168283.1 3291105 R 246200 CDS YP_168284.1 56697913 3196033 3291754..3292179 1 NC_003911.11 identified by match to protein family HMM PF00903; glyoxalase 3292179 3196033 SPO3081 Ruegeria pomeroyi DSS-3 glyoxalase YP_168284.1 3291754 D 246200 CDS YP_168285.1 56697914 3195964 3292312..3293016 1 NC_003911.11 identified by similarity to GB:CAA51372.1; match to protein family HMM PF01144; 3-oxoadipate CoA-succinyl transferase subunit alpha 3293016 dxnG 3195964 dxnG Ruegeria pomeroyi DSS-3 3-oxoadipate CoA-succinyl transferase subunit alpha YP_168285.1 3292312 D 246200 CDS YP_168286.1 56697915 3195832 3293020..3293646 1 NC_003911.11 identified by similarity to GB:CAA51373.1; match to protein family HMM PF01144; 3-oxoadipate CoA-succinyl transferase subunit beta 3293646 dxnH 3195832 dxnH Ruegeria pomeroyi DSS-3 3-oxoadipate CoA-succinyl transferase subunit beta YP_168286.1 3293020 D 246200 CDS YP_168287.1 56697916 3194944 complement(3293700..3294638) 1 NC_003911.11 identified by match to protein family HMM PF01464; Slt family transglycosylase 3294638 3194944 SPO3084 Ruegeria pomeroyi DSS-3 Slt family transglycosylase YP_168287.1 3293700 R 246200 CDS YP_168288.1 56697917 3194217 3294900..3295088 1 NC_003911.11 hypothetical protein 3295088 3194217 SPO3085 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168288.1 3294900 D 246200 CDS YP_168289.1 56697918 3195786 3295503..3296420 1 NC_003911.11 identified by match to protein family HMM PF06981; CpaB family protein 3296420 3195786 SPO3086 Ruegeria pomeroyi DSS-3 CpaB family protein YP_168289.1 3295503 D 246200 CDS YP_168290.1 56697919 3195838 3296595..3298022 1 NC_003911.11 identified by match to protein family HMM PF00263; type II/III secretion system protein 3298022 3195838 SPO3087 Ruegeria pomeroyi DSS-3 type II/III secretion system protein YP_168290.1 3296595 D 246200 CDS YP_168291.1 56697920 3195419 3298030..3298665 1 NC_003911.11 identified by match to protein family HMM PF00691; OmpA family protein 3298665 3195419 SPO3088 Ruegeria pomeroyi DSS-3 OmpA family protein YP_168291.1 3298030 D 246200 CDS YP_168292.1 56697921 3195468 3298759..3300087 1 NC_003911.11 ATPase 3300087 3195468 SPO3089 Ruegeria pomeroyi DSS-3 ATPase YP_168292.1 3298759 D 246200 CDS YP_168293.1 56697922 3195634 3300112..3301551 1 NC_003911.11 identified by similarity to GB:AAN75211.1; match to protein family HMM PF00437; type II/IV secretion system protein 3301551 3195634 SPO3090 Ruegeria pomeroyi DSS-3 type II/IV secretion system protein YP_168293.1 3300112 D 246200 CDS YP_168294.1 56697923 3195470 3301563..3302531 1 NC_003911.11 identified by match to protein family HMM PF00482; TadC family type II/IV secretion system protein 3302531 3195470 SPO3091 Ruegeria pomeroyi DSS-3 TadC family type II/IV secretion system protein YP_168294.1 3301563 D 246200 CDS YP_168295.1 56697924 3193575 3302542..3303522 1 NC_003911.11 identified by match to protein family HMM PF00482; TadC family type II/IV secretion system protein 3303522 3193575 SPO3092 Ruegeria pomeroyi DSS-3 TadC family type II/IV secretion system protein YP_168295.1 3302542 D 246200 CDS YP_168296.1 56697925 3194457 3303527..3304117 1 NC_003911.11 identified by similarity to GB:CAE29125.1; match to protein family HMM PF00515; hypothetical protein 3304117 3194457 SPO3093 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168296.1 3303527 D 246200 CDS YP_168297.1 56697926 3193127 3304147..3304995 1 NC_003911.11 lipoprotein 3304995 3193127 SPO3094 Ruegeria pomeroyi DSS-3 lipoprotein YP_168297.1 3304147 D 246200 CDS YP_168298.1 56697927 3194502 3305000..3305545 1 NC_003911.11 hypothetical protein 3305545 3194502 SPO3095 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168298.1 3305000 D 246200 CDS YP_168299.1 56697928 3192896 3305583..3306971 1 NC_003911.11 identified by similarity to GB:BAC95426.1; hypothetical protein 3306971 3192896 SPO3096 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168299.1 3305583 D 246200 CDS YP_168300.1 56697929 3195882 3306968..3307777 1 NC_003911.11 identified by similarity to GB:AAA50312.1; 3-hydroxyisobutyrate dehydrogenase 3307777 mmsB-2 3195882 mmsB-2 Ruegeria pomeroyi DSS-3 3-hydroxyisobutyrate dehydrogenase YP_168300.1 3306968 D 246200 CDS YP_168301.1 56697930 3195597 3307859..3310267 1 NC_003911.11 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; DEAD/DEAH box helicase 3310267 3195597 SPO3098 Ruegeria pomeroyi DSS-3 DEAD/DEAH box helicase YP_168301.1 3307859 D 246200 CDS YP_168302.1 56697931 3195840 3310309..3310971 1 NC_003911.11 identified by similarity to GB:BAC46414.1; hypothetical protein 3310971 3195840 SPO3099 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168302.1 3310309 D 246200 CDS YP_168303.1 56697932 3194942 complement(3310968..3311711) 1 NC_003911.11 identified by similarity to GB:AAN30398.1; hypothetical protein 3311711 3194942 SPO3100 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168303.1 3310968 R 246200 CDS YP_168304.1 56697933 3193798 complement(3311973..3312863) 1 NC_003911.11 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate; bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 3312863 3193798 SPO3101 Ruegeria pomeroyi DSS-3 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase YP_168304.1 3311973 R 246200 CDS YP_168305.1 56697934 3193669 complement(3312927..3313232) 1 NC_003911.11 identified by match to protein family HMM PF01817; match to protein family HMM TIGR01803; chorismate mutase 3313232 3193669 SPO3102 Ruegeria pomeroyi DSS-3 chorismate mutase YP_168305.1 3312927 R 246200 CDS YP_168306.1 56697935 3195304 complement(3313292..3314968) 1 NC_003911.11 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase 3314968 fhs-2 3195304 fhs-2 Ruegeria pomeroyi DSS-3 formate--tetrahydrofolate ligase YP_168306.1 3313292 R 246200 CDS YP_168307.1 56697936 3193714 complement(3315135..3315713) 1 NC_003911.11 identified by match to protein family HMM PF03473; MOSC domain-containing protein 3315713 3193714 SPO3104 Ruegeria pomeroyi DSS-3 MOSC domain-containing protein YP_168307.1 3315135 R 246200 CDS YP_168308.1 56697937 3195808 complement(3315827..3317746) 1 NC_003911.11 identified by similarity to GB:CAB51029.1; match to protein family HMM PF00004; match to protein family HMM PF01434; match to protein family HMM PF06480; match to protein family HMM TIGR01241; ATP-dependent metalloprotease FtsH 3317746 ftsH 3195808 ftsH Ruegeria pomeroyi DSS-3 ATP-dependent metalloprotease FtsH YP_168308.1 3315827 R 246200 CDS YP_168309.1 56697938 3194218 complement(3317819..3319078) 1 NC_003911.11 identified by match to protein family HMM PF01171; PP-loop family protein 3319078 3194218 SPO3106 Ruegeria pomeroyi DSS-3 PP-loop family protein YP_168309.1 3317819 R 246200 CDS YP_168310.1 56697939 3193940 complement(3319069..3319884) 1 NC_003911.11 identified by similarity to GB:AAO57429.1; hypothetical protein 3319884 3193940 SPO3107 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168310.1 3319069 R 246200 CDS YP_168311.1 56697940 3194177 complement(3319889..3320434) 1 NC_003911.11 identified by similarity to SP:P07176; match to protein family HMM PF00691; peptidoglycan-associated lipoprotein 3320434 pal 3194177 pal Ruegeria pomeroyi DSS-3 peptidoglycan-associated lipoprotein YP_168311.1 3319889 R 246200 CDS YP_168312.1 56697941 3193729 complement(3320487..3321806) 1 NC_003911.11 forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA; translocation protein TolB 3321806 tolB 3193729 tolB Ruegeria pomeroyi DSS-3 translocation protein TolB YP_168312.1 3320487 R 246200 CDS YP_168313.1 56697942 3193280 complement(3321803..3322945) 1 NC_003911.11 TonB domain-containing protein 3322945 3193280 SPO3110 Ruegeria pomeroyi DSS-3 TonB domain-containing protein YP_168313.1 3321803 R 246200 CDS YP_168314.1 56697943 3193621 complement(3322955..3323434) 1 NC_003911.11 identified by match to protein family HMM PF02472; biopolymer ExbD/TolR family transporter 3323434 3193621 SPO3111 Ruegeria pomeroyi DSS-3 biopolymer ExbD/TolR family transporter YP_168314.1 3322955 R 246200 CDS YP_168315.1 56697944 3194798 complement(3323438..3324133) 1 NC_003911.11 identified by similarity to SP:P05828; match to protein family HMM PF01618; proton transporter TolQ 3324133 tolQ 3194798 tolQ Ruegeria pomeroyi DSS-3 proton transporter TolQ YP_168315.1 3323438 R 246200 CDS YP_168316.1 56697945 3195232 complement(3324241..3324624) 1 NC_003911.11 identified by match to protein family HMM PF03061; match to protein family HMM TIGR00051; hypothetical protein 3324624 3195232 SPO3113 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168316.1 3324241 R 246200 CDS YP_168317.1 56697946 3195659 complement(3324621..3325418) 1 NC_003911.11 hypothetical protein 3325418 3195659 SPO3114 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168317.1 3324621 R 246200 CDS YP_168318.1 56697947 3194519 complement(3325427..3326452) 1 NC_003911.11 promotes strand exchange during homologous recombination; RuvAB complex promotes branch migration; RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences; forms hexameric rings around opposite DNA arms; requires ATP for branch migration and orientation of RuvAB complex determines direction of migration; Holliday junction DNA helicase RuvB 3326452 ruvB 3194519 ruvB Ruegeria pomeroyi DSS-3 Holliday junction DNA helicase RuvB YP_168318.1 3325427 R 246200 CDS YP_168319.1 56697949 3193593 complement(3326499..3327173) 1 NC_003911.11 plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA 3327173 ruvA 3193593 ruvA Ruegeria pomeroyi DSS-3 Holliday junction DNA helicase RuvA YP_168319.1 3326499 R 246200 CDS YP_168320.1 56697948 3195558 complement(3327170..3327667) 1 NC_003911.11 endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity; Holliday junction resolvase 3327667 ruvC 3195558 ruvC Ruegeria pomeroyi DSS-3 Holliday junction resolvase YP_168320.1 3327170 R 246200 CDS YP_168321.1 56697950 3195407 3327999..3328217 1 NC_003911.11 identified by similarity to GB:CAC46124.1; match to protein family HMM PF06568; hypothetical protein 3328217 3195407 SPO3118 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168321.1 3327999 D 246200 CDS YP_168322.1 56697951 3195431 complement(3328300..3328656) 1 NC_003911.11 hypothetical protein 3328656 3195431 SPO3119 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168322.1 3328300 R 246200 CDS YP_168323.1 56697952 3195458 complement(3328744..3329622) 1 NC_003911.11 identified by similarity to SP:P28637; match to protein family HMM PF06325; 50S ribosomal protein L11 methyltransferase 3329622 3195458 SPO3120 Ruegeria pomeroyi DSS-3 50S ribosomal protein L11 methyltransferase YP_168323.1 3328744 R 246200 CDS YP_168324.1 56697953 3195252 complement(3329622..3331016) 1 NC_003911.11 identified by match to protein family HMM PF01554; MATE efflux family protein 3331016 3195252 SPO3121 Ruegeria pomeroyi DSS-3 MATE efflux family protein YP_168324.1 3329622 R 246200 CDS YP_168325.1 56697954 3194442 complement(3331021..3332253) 1 NC_003911.11 identified by similarity to GB:BAC62827.1; hypothetical protein 3332253 3194442 SPO3122 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168325.1 3331021 R 246200 CDS YP_168326.1 56697955 3195313 3332423..3333487 1 NC_003911.11 identified by similarity to SP:P33015; match to protein family HMM PF04143; hypothetical protein 3333487 3195313 SPO3123 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168326.1 3332423 D 246200 CDS YP_168327.1 56697956 3195035 3333559..3333978 1 NC_003911.11 identified by similarity to GB:CAC46680.1; match to protein family HMM PF03640; hypothetical protein 3333978 3195035 SPO3124 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168327.1 3333559 D 246200 CDS YP_168328.1 56697957 3196068 3333994..3334512 1 NC_003911.11 identified by match to protein family HMM PF04542; match to protein family HMM PF04545; match to protein family HMM TIGR01199; ECF subfamily RNA polymerase sigma factor 3334512 3196068 SPO3125 Ruegeria pomeroyi DSS-3 ECF subfamily RNA polymerase sigma factor YP_168328.1 3333994 D 246200 CDS YP_168329.1 56697958 3196054 3334509..3335255 1 NC_003911.11 identified by similarity to GB:AAF81073.1; sigma factor regulator PrtR 3335255 3196054 SPO3126 Ruegeria pomeroyi DSS-3 sigma factor regulator PrtR YP_168329.1 3334509 D 246200 CDS YP_168330.1 56697959 3196031 complement(3335405..3337615) 1 NC_003911.11 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA 3337615 priA 3196031 priA Ruegeria pomeroyi DSS-3 primosome assembly protein PriA YP_168330.1 3335405 R 246200 CDS YP_168331.1 56697960 3196037 3337734..3338387 1 NC_003911.11 similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity; translaldolase 3338387 fsaB 3196037 fsaB Ruegeria pomeroyi DSS-3 translaldolase YP_168331.1 3337734 D 246200 CDS YP_168332.1 56697961 3196018 3338609..3339316 1 NC_003911.11 identified by similarity to GB:AAK22332.1; hypothetical protein 3339316 3196018 SPO3129 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168332.1 3338609 D 246200 CDS YP_168333.1 56697962 3196023 3339313..3340233 1 NC_003911.11 site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs; site-specific tyrosine recombinase XerC 3340233 xerC 3196023 xerC Ruegeria pomeroyi DSS-3 site-specific tyrosine recombinase XerC YP_168333.1 3339313 D 246200 CDS YP_168334.1 56697963 3196010 3340305..3341012 1 NC_003911.11 identified by similarity to SP:Q9KJY8; match to protein family HMM PF01066; phosphatidylcholine synthase 3341012 pcs 3196010 pcs Ruegeria pomeroyi DSS-3 phosphatidylcholine synthase YP_168334.1 3340305 D 246200 CDS YP_168335.1 56697964 3196003 complement(3340978..3341601) 1 NC_003911.11 identified by similarity to GB:AAQ87450.1; hypothetical protein 3341601 3196003 SPO3132 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168335.1 3340978 R 246200 CDS YP_168336.1 56697965 3195623 complement(3341598..3342056) 1 NC_003911.11 hypothetical protein 3342056 3195623 SPO3133 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168336.1 3341598 R 246200 CDS YP_168337.1 56697966 3195793 complement(3342125..3342577) 1 NC_003911.11 identified by similarity to SP:P11742; match to protein family HMM PF01035; match to protein family HMM TIGR00589; methylated-DNA--protein-cysteine methyltransferase 3342577 ogt 3195793 ogt Ruegeria pomeroyi DSS-3 methylated-DNA--protein-cysteine methyltransferase YP_168337.1 3342125 R 246200 CDS YP_168338.1 56697967 3195001 complement(3342717..3343679) 1 NC_003911.11 identified by match to protein family HMM PF03576; T4 family peptidase 3343679 3195001 SPO3135 Ruegeria pomeroyi DSS-3 T4 family peptidase YP_168338.1 3342717 R 246200 CDS YP_168339.1 56697968 3193197 complement(3343681..3346593) 1 NC_003911.11 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase type 1 subfamily; some organisms carry two different copies of this enzyme; isoleucyl-tRNA synthetase 3346593 ileS 3193197 ileS Ruegeria pomeroyi DSS-3 isoleucyl-tRNA synthetase YP_168339.1 3343681 R 246200 CDS YP_168340.1 56697969 3193732 3346819..3347406 1 NC_003911.11 hypothetical protein 3347406 3193732 SPO3137 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168340.1 3346819 D 246200 CDS YP_168341.1 56697970 3194008 complement(3347426..3348136) 1 NC_003911.11 identified by similarity to GB:BAC19465.1; match to protein family HMM PF01988; hypothetical protein 3348136 3194008 SPO3138 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168341.1 3347426 R 246200 CDS YP_168342.1 56697971 3195521 3348262..3348669 1 NC_003911.11 hypothetical protein 3348669 3195521 SPO3139 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168342.1 3348262 D 246200 CDS YP_168343.1 56697972 3195685 complement(3348764..3349774) 1 NC_003911.11 identified by similarity to GB:BAB48295.1; match to protein family HMM TIGR01620; hypothetical protein 3349774 3195685 SPO3140 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168343.1 3348764 R 246200 CDS YP_168344.1 56697973 3195890 complement(3349759..3350199) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3350199 3195890 SPO3141 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168344.1 3349759 R 246200 CDS YP_168345.1 56697974 3194588 complement(3350196..3351611) 1 NC_003911.11 identified by similarity to GB:CAC46385.1; hypothetical protein 3351611 3194588 SPO3142 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168345.1 3350196 R 246200 CDS YP_168346.1 56697975 3193303 3351843..3352631 1 NC_003911.11 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A 3352631 truA 3193303 truA Ruegeria pomeroyi DSS-3 tRNA pseudouridine synthase A YP_168346.1 3351843 D 246200 CDS YP_168347.1 56697976 3195898 complement(3352586..3353293) 1 NC_003911.11 identified by similarity to GB:BAB48071.1; hypothetical protein 3353293 3195898 SPO3144 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168347.1 3352586 R 246200 CDS YP_168348.1 56697977 3195420 3353376..3354392 1 NC_003911.11 identified by similarity to PIR:AD2899; match to protein family HMM PF07446; GumN family protein 3354392 3195420 SPO3145 Ruegeria pomeroyi DSS-3 GumN family protein YP_168348.1 3353376 D 246200 CDS YP_168349.1 56697978 3195676 3354395..3355390 1 NC_003911.11 identified by match to protein family HMM PF07446; GumN family protein 3355390 3195676 SPO3146 Ruegeria pomeroyi DSS-3 GumN family protein YP_168349.1 3354395 D 246200 CDS YP_168350.1 56697979 3195814 3355493..3356413 1 NC_003911.11 catalyzes the hydrolysis of pyrophosphate to phosphate; manganese-dependent inorganic pyrophosphatase 3356413 ppaC 3195814 ppaC Ruegeria pomeroyi DSS-3 manganese-dependent inorganic pyrophosphatase YP_168350.1 3355493 D 246200 CDS YP_168351.1 56697980 3195248 complement(3356468..3357163) 1 NC_003911.11 hypothetical protein 3357163 3195248 SPO3148 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168351.1 3356468 R 246200 CDS YP_168352.1 56697981 3194850 complement(3357283..3357741) 1 NC_003911.11 identified by similarity to GB:CAE31907.1; match to protein family HMM PF04828; hypothetical protein 3357741 3194850 SPO3149 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168352.1 3357283 R 246200 CDS YP_168353.1 56697982 3195903 3357794..3358711 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 3358711 3195903 SPO3150 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_168353.1 3357794 D 246200 CDS YP_168354.1 56697983 3194029 3358735..3359667 1 NC_003911.11 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01459; match to protein family HMM TIGR01460; HAD family hydrolase 3359667 3194029 SPO3151 Ruegeria pomeroyi DSS-3 HAD family hydrolase YP_168354.1 3358735 D 246200 CDS YP_168355.1 56697984 3194659 3359719..3360213 1 NC_003911.11 identified by match to protein family HMM PF01575; acyl dehydratase MaoC 3360213 3194659 SPO3152 Ruegeria pomeroyi DSS-3 acyl dehydratase MaoC YP_168355.1 3359719 D 246200 CDS YP_168356.1 56697985 3195915 3360454..3362145 1 NC_003911.11 identified by similarity to GB:BAA61829.1; match to protein family HMM PF00173; match to protein family HMM PF01360; monooxygenase 3362145 3195915 SPO3153 Ruegeria pomeroyi DSS-3 monooxygenase YP_168356.1 3360454 D 246200 CDS YP_168357.1 56697986 3195108 3362242..3363174 1 NC_003911.11 identified by similarity to SP:P73651; match to protein family HMM PF01687; match to protein family HMM PF06574; match to protein family HMM TIGR00083; riboflavin biosynthesis protein RibF 3363174 ribF 3195108 ribF Ruegeria pomeroyi DSS-3 riboflavin biosynthesis protein RibF YP_168357.1 3362242 D 246200 CDS YP_168358.1 56697987 3193398 3363171..3363641 1 NC_003911.11 identified by similarity to SP:O68068; match to protein family HMM PF05779; hypothetical protein 3363641 3193398 SPO3155 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168358.1 3363171 D 246200 CDS YP_168359.1 56697988 3195878 3363641..3364678 1 NC_003911.11 identified by similarity to SP:O50584; L-threonine aldolase 3364678 3195878 SPO3156 Ruegeria pomeroyi DSS-3 L-threonine aldolase YP_168359.1 3363641 D 246200 CDS YP_168360.1 56697989 3195998 complement(3364767..3365585) 1 NC_003911.11 identified by match to protein family HMM PF00561; alpha/beta hydrolase 3365585 3195998 SPO3157 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_168360.1 3364767 R 246200 CDS YP_168361.1 56697990 3195660 complement(3365582..3366184) 1 NC_003911.11 identified by similarity to SP:Q51948; match to protein family HMM PF01323; 2-hydroxychromene-2-carboxylate isomerase 3366184 nahD 3195660 nahD Ruegeria pomeroyi DSS-3 2-hydroxychromene-2-carboxylate isomerase YP_168361.1 3365582 R 246200 CDS YP_168362.1 56697991 3193207 3366292..3367311 1 NC_003911.11 identified by match to protein family HMM PF00156; match to protein family HMM TIGR01251; ribose-phosphate pyrophosphokinase 3367311 prs 3193207 prs Ruegeria pomeroyi DSS-3 ribose-phosphate pyrophosphokinase YP_168362.1 3366292 D 246200 CDS YP_168363.1 56697992 3195764 complement(3367394..3367762) 1 NC_003911.11 identified by similarity to GB:CAA67912.1; hypothetical protein 3367762 3195764 SPO3160 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168363.1 3367394 R 246200 CDS YP_168364.1 56697993 3195323 complement(3367873..3368283) 1 NC_003911.11 produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex; ATP synthase F0F1 subunit epsilon 3368283 atpC 3195323 atpC Ruegeria pomeroyi DSS-3 ATP synthase F0F1 subunit epsilon YP_168364.1 3367873 R 246200 CDS YP_168365.1 56697994 3194225 complement(3368296..3369720) 1 NC_003911.11 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit; ATP synthase F0F1 subunit beta 3369720 atpD 3194225 atpD Ruegeria pomeroyi DSS-3 ATP synthase F0F1 subunit beta YP_168365.1 3368296 R 246200 CDS YP_168366.1 56697995 3195916 complement(3369740..3370615) 1 NC_003911.11 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit; ATP synthase F0F1 subunit gamma 3370615 atpG 3195916 atpG Ruegeria pomeroyi DSS-3 ATP synthase F0F1 subunit gamma YP_168366.1 3369740 R 246200 CDS YP_168367.1 56697996 3195837 complement(3370628..3372166) 1 NC_003911.11 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit; ATP synthase F0F1 subunit alpha 3372166 atpA 3195837 atpA Ruegeria pomeroyi DSS-3 ATP synthase F0F1 subunit alpha YP_168367.1 3370628 R 246200 CDS YP_168368.1 56697997 3195251 complement(3372167..3372727) 1 NC_003911.11 identified by similarity to SP:P05437; match to protein family HMM PF00213; match to protein family HMM TIGR01145; ATP synthase subunit delta 3372727 atpH 3195251 atpH Ruegeria pomeroyi DSS-3 ATP synthase subunit delta YP_168368.1 3372167 R 246200 CDS YP_168369.1 56697998 3195825 3373134..3374081 1 NC_003911.11 hypothetical protein 3374081 3195825 SPO3166 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168369.1 3373134 D 246200 CDS YP_168370.1 56697999 3192859 complement(3374090..3374842) 1 NC_003911.11 identified by similarity to PIR:AC3001; hypothetical protein 3374842 3192859 SPO3167 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168370.1 3374090 R 246200 CDS YP_168371.1 56698000 3195448 3374903..3375670 1 NC_003911.11 identified by match to protein family HMM PF00753; hydroxyacylglutathione hydrolase 3375670 3195448 SPO3168 Ruegeria pomeroyi DSS-3 hydroxyacylglutathione hydrolase YP_168371.1 3374903 D 246200 CDS YP_168372.1 56698001 3195159 3375845..3378172 1 NC_003911.11 identified by similarity to SP:P15716; match to protein family HMM PF00004; match to protein family HMM PF02861; ATP-dependent Clp protease ATP-binding subunit ClpA 3378172 clpA 3195159 clpA Ruegeria pomeroyi DSS-3 ATP-dependent Clp protease ATP-binding subunit ClpA YP_168372.1 3375845 D 246200 CDS YP_168373.1 56698002 3195302 3378391..3379131 1 NC_003911.11 identified by match to protein family HMM PF01551; M24/M37 family peptidase 3379131 3195302 SPO3170 Ruegeria pomeroyi DSS-3 M24/M37 family peptidase YP_168373.1 3378391 D 246200 CDS YP_168374.1 56698003 3195866 complement(3379134..3381434) 1 NC_003911.11 identified by match to protein family HMM PF00691; hypothetical protein 3381434 3195866 SPO3171 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168374.1 3379134 R 246200 CDS YP_168375.1 56698004 3195210 complement(3381438..3382619) 1 NC_003911.11 identified by similarity to GB:BAC46776.1; hypothetical protein 3382619 3195210 SPO3172 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168375.1 3381438 R 246200 CDS YP_168376.1 56698005 3195821 complement(3382690..3383223) 1 NC_003911.11 identified by similarity to SP:P39163; match to protein family HMM PF04752; cation transport protein ChaC 3383223 3195821 SPO3173 Ruegeria pomeroyi DSS-3 cation transport protein ChaC YP_168376.1 3382690 R 246200 CDS YP_168377.1 56698006 3195803 3383232..3384287 1 NC_003911.11 identified by similarity to GB:AAK24192.1; hypothetical protein 3384287 3195803 SPO3174 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168377.1 3383232 D 246200 CDS YP_168378.1 56698007 3195827 complement(3384303..3385163) 1 NC_003911.11 identified by similarity to GB:AAO55033.1; hypothetical protein 3385163 3195827 SPO3175 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168378.1 3384303 R 246200 CDS YP_168379.1 56698008 3195700 complement(3385160..3386083) 1 NC_003911.11 dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate; cyclohexadienyl dehydrogenase 3386083 3195700 SPO3176 Ruegeria pomeroyi DSS-3 cyclohexadienyl dehydrogenase YP_168379.1 3385160 R 246200 CDS YP_168380.1 56698009 3195649 complement(3386080..3387195) 1 NC_003911.11 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase 3387195 hisC 3195649 hisC Ruegeria pomeroyi DSS-3 histidinol-phosphate aminotransferase YP_168380.1 3386080 R 246200 CDS YP_168381.1 56698010 3194038 complement(3387232..3388647) 1 NC_003911.11 hypothetical protein 3388647 3194038 SPO3178 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168381.1 3387232 R 246200 CDS YP_168382.1 56698011 3195646 3388753..3389211 1 NC_003911.11 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 3389211 3195646 SPO3179 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_168382.1 3388753 D 246200 CDS YP_168383.1 56698012 3195196 complement(3389208..3389657) 1 NC_003911.11 identified by match to protein family HMM PF02502; match to protein family HMM TIGR00689; match to protein family HMM TIGR01120; ribose 5-phosphate isomerase B 3389657 rpiB 3195196 rpiB Ruegeria pomeroyi DSS-3 ribose 5-phosphate isomerase B YP_168383.1 3389208 R 246200 CDS YP_168384.1 56698013 3195804 complement(3389785..3390405) 1 NC_003911.11 primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination; 30S ribosomal protein S4 3390405 rpsD 3195804 rpsD Ruegeria pomeroyi DSS-3 30S ribosomal protein S4 YP_168384.1 3389785 R 246200 CDS YP_168385.1 56698014 3195015 complement(3390607..3391671) 1 NC_003911.11 identified by similarity to PIR:T03518; hypothetical protein 3391671 3195015 SPO3182 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168385.1 3390607 R 246200 CDS YP_168386.1 56698015 3195771 3391910..3393943 1 NC_003911.11 identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; molybdopterin-binding oxidoreductase 3393943 3195771 SPO3183 Ruegeria pomeroyi DSS-3 molybdopterin-binding oxidoreductase YP_168386.1 3391910 D 246200 CDS YP_168387.1 56698016 3195787 complement(3393940..3394647) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3394647 3195787 SPO3184 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168387.1 3393940 R 246200 CDS YP_168388.1 56698017 3195733 3394736..3396139 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 3396139 3195733 SPO3185 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_168388.1 3394736 D 246200 CDS YP_168389.1 56698018 3195144 complement(3396229..3398064) 1 NC_003911.11 identified by similarity to SP:P54417; match to protein family HMM PF02028; glycine betaine transporter 3398064 opuD 3195144 opuD Ruegeria pomeroyi DSS-3 glycine betaine transporter YP_168389.1 3396229 R 246200 CDS YP_168390.1 56698019 3195794 complement(3398172..3399185) 1 NC_003911.11 identified by match to protein family HMM PF02615; (2R)-3-sulfolactate dehydrogenase 3399185 comC 3195794 comC Ruegeria pomeroyi DSS-3 (2R)-3-sulfolactate dehydrogenase YP_168390.1 3398172 R 246200 CDS YP_168391.1 56698020 3194729 complement(3399198..3399830) 1 NC_003911.11 identified by similarity to GB:AAN68298.1; hypothetical protein 3399830 3194729 SPO3188 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168391.1 3399198 R 246200 CDS YP_168392.1 56698021 3193083 complement(3399827..3401515) 1 NC_003911.11 identified by similarity to GB:AAN68299.1; hypothetical protein 3401515 3193083 SPO3189 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168392.1 3399827 R 246200 CDS YP_168393.1 56698022 3195752 complement(3401521..3402501) 1 NC_003911.11 identified by match to protein family HMM PF01244; renal dipeptidase 3402501 3195752 SPO3190 Ruegeria pomeroyi DSS-3 renal dipeptidase YP_168393.1 3401521 R 246200 CDS YP_168394.1 56698024 3194957 complement(3402498..3403949) 1 NC_003911.11 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 3403949 3194957 SPO3191 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_168394.1 3402498 R 246200 CDS YP_168395.1 56698023 3195508 3404052..3404924 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3404924 3195508 SPO3192 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168395.1 3404052 D 246200 CDS YP_168396.1 56698025 3195823 complement(3404928..3405359) 1 NC_003911.11 identified by similarity to GB:BAB48214.1; hypothetical protein 3405359 3195823 SPO3193 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168396.1 3404928 R 246200 CDS YP_168397.1 56698026 3192944 3405491..3407773 1 NC_003911.11 identified by match to protein family HMM PF02867; ribonucleoside-diphosphate reductase 3407773 3192944 SPO3194 Ruegeria pomeroyi DSS-3 ribonucleoside-diphosphate reductase YP_168397.1 3405491 D 246200 CDS YP_168398.1 56698027 3195671 3408049..3409143 1 NC_003911.11 identified by match to protein family HMM PF00850; histone deacetylase 3409143 3195671 SPO3195 Ruegeria pomeroyi DSS-3 histone deacetylase YP_168398.1 3408049 D 246200 CDS YP_168399.1 56698028 3195505 3409228..3409953 1 NC_003911.11 involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA; DNA repair protein RecO 3409953 recO 3195505 recO Ruegeria pomeroyi DSS-3 DNA repair protein RecO YP_168399.1 3409228 D 246200 CDS YP_168400.1 56698029 3194966 complement(3409937..3410332) 1 NC_003911.11 identified by similarity to GB:BAB54274.1; hypothetical protein 3410332 3194966 SPO3197 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168400.1 3409937 R 246200 CDS YP_168401.1 56698030 3195258 complement(3410341..3411018) 1 NC_003911.11 identified by similarity to SP:P05797; match to protein family HMM PF00035; match to protein family HMM PF00636; ribonuclease III 3411018 rnc 3195258 rnc Ruegeria pomeroyi DSS-3 ribonuclease III YP_168401.1 3410341 R 246200 CDS YP_168402.1 56698031 3194337 complement(3411015..3411854) 1 NC_003911.11 identified by match to protein family HMM PF00717; match to protein family HMM TIGR02227; signal peptidase I 3411854 lepB 3194337 lepB Ruegeria pomeroyi DSS-3 signal peptidase I YP_168402.1 3411015 R 246200 CDS YP_168403.1 56698032 3195332 complement(3411888..3412334) 1 NC_003911.11 Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids; 4'-phosphopantetheinyl transferase 3412334 acpS 3195332 acpS Ruegeria pomeroyi DSS-3 4'-phosphopantetheinyl transferase YP_168403.1 3411888 R 246200 CDS YP_168404.1 56698033 3195698 complement(3412399..3413145) 1 NC_003911.11 involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase 3413145 pdxJ 3195698 pdxJ Ruegeria pomeroyi DSS-3 pyridoxine 5'-phosphate synthase YP_168404.1 3412399 R 246200 CDS YP_168405.1 56698034 3194593 complement(3413181..3413837) 1 NC_003911.11 identified by similarity to PIR:G97485; hypothetical protein 3413837 3194593 SPO3202 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168405.1 3413181 R 246200 CDS YP_168406.1 56698035 3193258 complement(3413869..3416061) 1 NC_003911.11 identified by similarity to SP:P17580; match to protein family HMM PF01842; match to protein family HMM PF01966; match to protein family HMM PF02824; match to protein family HMM PF04607; match to protein family HMM TIGR00691; guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase 3416061 3193258 SPO3203 Ruegeria pomeroyi DSS-3 guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase YP_168406.1 3413869 R 246200 CDS YP_168407.1 56698036 3195699 complement(3416030..3416383) 1 NC_003911.11 Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits; DNA-directed RNA polymerase subunit omega 3416383 rpoZ 3195699 rpoZ Ruegeria pomeroyi DSS-3 DNA-directed RNA polymerase subunit omega YP_168407.1 3416030 R 246200 CDS YP_168408.1 56698037 3195424 complement(3416475..3417041) 1 NC_003911.11 identified by match to protein family HMM PF01288; match to protein family HMM TIGR01498; 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase 3417041 folK 3195424 folK Ruegeria pomeroyi DSS-3 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase YP_168408.1 3416475 R 246200 CDS YP_168409.1 56698038 3195756 3417180..3417752 1 NC_003911.11 identified by similarity to GB:AAK23529.1; match to protein family HMM PF01936; hypothetical protein 3417752 3195756 SPO3206 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168409.1 3417180 D 246200 CDS YP_168410.1 56698039 3195859 3417945..3418895 1 NC_003911.11 catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway; 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 3418895 ispH 3195859 ispH Ruegeria pomeroyi DSS-3 4-hydroxy-3-methylbut-2-enyl diphosphate reductase YP_168410.1 3417945 D 246200 CDS YP_168411.1 56698040 3195682 3418892..3419521 1 NC_003911.11 identified by match to protein family HMM PF00043; glutathione S-transferase 3419521 3195682 SPO3208 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_168411.1 3418892 D 246200 CDS YP_168412.1 56698041 3195674 3419588..3420202 1 NC_003911.11 identified by match to protein family HMM PF01810; amino acid transporter LysE 3420202 3195674 SPO3209 Ruegeria pomeroyi DSS-3 amino acid transporter LysE YP_168412.1 3419588 D 246200 CDS YP_168413.1 56698042 3195113 3420199..3420651 1 NC_003911.11 identified by similarity to GB:AAK24940.1; hypothetical protein 3420651 3195113 SPO3210 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168413.1 3420199 D 246200 CDS YP_168414.1 56698043 3195855 3420624..3421241 1 NC_003911.11 identified by similarity to GB:AAK23900.1; hypothetical protein 3421241 3195855 SPO3211 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168414.1 3420624 D 246200 CDS YP_168415.1 56698044 3195666 3421234..3421701 1 NC_003911.11 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H 3421701 rnhA 3195666 rnhA Ruegeria pomeroyi DSS-3 ribonuclease H YP_168415.1 3421234 D 246200 CDS YP_168416.1 56698045 3195578 3421698..3422327 1 NC_003911.11 identified by similarity to PIR:F97377; match to protein family HMM PF03458; hypothetical protein 3422327 3195578 SPO3213 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168416.1 3421698 D 246200 CDS YP_168417.1 56698046 3194436 complement(3422394..3422633) 1 NC_003911.11 hypothetical protein 3422633 3194436 SPO3214 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168417.1 3422394 R 246200 CDS YP_168418.1 56698047 3195122 complement(3422635..3422877) 1 NC_003911.11 hypothetical protein 3422877 3195122 SPO3215 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168418.1 3422635 R 246200 CDS YP_168419.1 56698048 3195992 complement(3422885..3423790) 1 NC_003911.11 identified by similarity to SP:O85732; match to protein family HMM PF00551; match to protein family HMM PF02911; match to protein family HMM TIGR00460; methionyl-tRNA formyltransferase 3423790 fmt 3195992 fmt Ruegeria pomeroyi DSS-3 methionyl-tRNA formyltransferase YP_168419.1 3422885 R 246200 CDS YP_168420.1 56698049 3194969 complement(3423795..3424292) 1 NC_003911.11 identified by match to protein family HMM PF01327; match to protein family HMM TIGR00079; peptide deformylase 3424292 def-1 3194969 def-1 Ruegeria pomeroyi DSS-3 peptide deformylase YP_168420.1 3423795 R 246200 CDS YP_168421.1 56698050 3195601 complement(3424289..3424786) 1 NC_003911.11 identified by match to protein family HMM PF01327; match to protein family HMM TIGR00079; peptide deformylase 3424786 def-2 3195601 def-2 Ruegeria pomeroyi DSS-3 peptide deformylase YP_168421.1 3424289 R 246200 CDS YP_168422.1 56698051 3193782 complement(3424783..3425301) 1 NC_003911.11 identified by match to protein family HMM PF01327; match to protein family HMM TIGR00079; peptide deformylase 3425301 def-3 3193782 def-3 Ruegeria pomeroyi DSS-3 peptide deformylase YP_168422.1 3424783 R 246200 CDS YP_168423.1 56698052 3195058 3425383..3426573 1 NC_003911.11 identified by match to protein family HMM PF00155; aminotransferase, classes I and II 3426573 3195058 SPO3220 Ruegeria pomeroyi DSS-3 aminotransferase, classes I and II YP_168423.1 3425383 D 246200 CDS YP_168424.1 56698053 3193910 complement(3426645..3426995) 1 NC_003911.11 hypothetical protein 3426995 3193910 SPO3221 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168424.1 3426645 R 246200 CDS YP_168425.1 56698054 3195783 3427198..3428187 1 NC_003911.11 identified by similarity to PIR:T45023; hypothetical protein 3428187 3195783 SPO3222 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168425.1 3427198 D 246200 CDS YP_168426.1 56698055 3195254 complement(3428169..3428531) 1 NC_003911.11 identified by match to protein family HMM PF00072; response regulator 3428531 3195254 SPO3223 Ruegeria pomeroyi DSS-3 response regulator YP_168426.1 3428169 R 246200 CDS YP_168427.1 56698056 3195395 3428717..3429706 1 NC_003911.11 identified by similarity to SP:P21633; cobalamin biosynthetic protein CobC 3429706 cobC 3195395 cobC Ruegeria pomeroyi DSS-3 cobalamin biosynthetic protein CobC YP_168427.1 3428717 D 246200 CDS YP_168428.1 56698057 3195582 3429703..3430623 1 NC_003911.11 CobD; CbiD in Salmonella; converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group; cobalamin biosynthesis protein 3430623 cobD 3195582 cobD Ruegeria pomeroyi DSS-3 cobalamin biosynthesis protein YP_168428.1 3429703 D 246200 CDS YP_168429.1 56698058 3195541 3430655..3431818 1 NC_003911.11 identified by similarity to PIR:D97614; hypothetical protein 3431818 3195541 SPO3226 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168429.1 3430655 D 246200 CDS YP_168430.1 56698059 3195290 complement(3431828..3432190) 1 NC_003911.11 hypothetical protein 3432190 3195290 SPO3227 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168430.1 3431828 R 246200 CDS YP_168431.1 56698060 3194939 complement(3432247..3435702) 1 NC_003911.11 identified by similarity to GB:CAD66603.1; match to protein family HMM PF02463; match to protein family HMM PF02483; match to protein family HMM PF06470; SMC protein 3435702 3194939 SPO3228 Ruegeria pomeroyi DSS-3 SMC protein YP_168431.1 3432247 R 246200 CDS YP_168432.1 56698061 3194343 complement(3435831..3436247) 1 NC_003911.11 lipoprotein 3436247 3194343 SPO3229 Ruegeria pomeroyi DSS-3 lipoprotein YP_168432.1 3435831 R 246200 CDS YP_168433.1 56698062 3192779 complement(3436267..3437475) 1 NC_003911.11 identified by match to protein family HMM PF00155; aminotransferase, classes I and II 3437475 3192779 SPO3230 Ruegeria pomeroyi DSS-3 aminotransferase, classes I and II YP_168433.1 3436267 R 246200 CDS YP_168434.1 56698063 3194672 3437629..3438399 1 NC_003911.11 identified by similarity to SP:P06957; match to protein family HMM PF00392; pyruvate dehydrogenase complex repressor 3438399 pdhR 3194672 pdhR Ruegeria pomeroyi DSS-3 pyruvate dehydrogenase complex repressor YP_168434.1 3437629 D 246200 CDS YP_168435.1 56698064 3195968 3438399..3438887 1 NC_003911.11 hypothetical protein 3438887 3195968 SPO3232 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168435.1 3438399 D 246200 CDS YP_168436.1 56698065 3194903 complement(3438997..3439569) 1 NC_003911.11 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel.; ATP synthase F0F1 subunit B 3439569 atpF 3194903 atpF Ruegeria pomeroyi DSS-3 ATP synthase F0F1 subunit B YP_168436.1 3438997 R 246200 CDS YP_168437.1 56698066 3195208 complement(3439575..3440120) 1 NC_003911.11 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B' is part of the membrane proton channel.; ATP synthase F0F1 subunit B' 3440120 3195208 SPO3234 Ruegeria pomeroyi DSS-3 ATP synthase F0F1 subunit B' YP_168437.1 3439575 R 246200 CDS YP_168438.1 56698067 3195970 complement(3440207..3440431) 1 NC_003911.11 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0; ATP synthase F0F1 subunit C 3440431 atpE 3195970 atpE Ruegeria pomeroyi DSS-3 ATP synthase F0F1 subunit C YP_168438.1 3440207 R 246200 CDS YP_168439.1 56698068 3195250 complement(3440508..3441278) 1 NC_003911.11 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0; ATP synthase F0F1 subunit A 3441278 atpB 3195250 atpB Ruegeria pomeroyi DSS-3 ATP synthase F0F1 subunit A YP_168439.1 3440508 R 246200 CDS YP_168440.1 56698069 3195738 complement(3441281..3441634) 1 NC_003911.11 identified by similarity to GB:CAA72980.1; ATP synthase F0 subunit I 3441634 atpI 3195738 atpI Ruegeria pomeroyi DSS-3 ATP synthase F0 subunit I YP_168440.1 3441281 R 246200 CDS YP_168441.1 56698070 3194039 3441856..3442197 1 NC_003911.11 identified by match to protein family HMM PF01022; ArsR family transcriptional regulator 3442197 3194039 SPO3238 Ruegeria pomeroyi DSS-3 ArsR family transcriptional regulator YP_168441.1 3441856 D 246200 CDS YP_168442.1 56698071 3194921 complement(3442207..3443106) 1 NC_003911.11 identified by similarity to GB:CAE09829.1; match to protein family HMM PF00892; hypothetical protein 3443106 3194921 SPO3239 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168442.1 3442207 R 246200 CDS YP_168443.1 56698072 3195785 complement(3443094..3443972) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3443972 3195785 SPO3240 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168443.1 3443094 R 246200 CDS YP_168444.1 56698073 3194669 3444135..3444881 1 NC_003911.11 Asp/Glu/Hydantoin racemase 3444881 3194669 SPO3241 Ruegeria pomeroyi DSS-3 Asp/Glu/Hydantoin racemase YP_168444.1 3444135 D 246200 CDS YP_168445.1 56698074 3195370 complement(3444931..3445494) 1 NC_003911.11 identified by similarity to GB:CAC47762.1; match to protein family HMM PF04073; prolyl-tRNA synthetase 3445494 3195370 SPO3242 Ruegeria pomeroyi DSS-3 prolyl-tRNA synthetase YP_168445.1 3444931 R 246200 CDS YP_168446.1 56698075 3193531 3445790..3446842 1 NC_003911.11 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate; quinolinate synthetase 3446842 nadA 3193531 nadA Ruegeria pomeroyi DSS-3 quinolinate synthetase YP_168446.1 3445790 D 246200 CDS YP_168447.1 56698076 3195460 3446850..3448400 1 NC_003911.11 catalyzes the formation of oxaloacetate from L-aspartate; L-aspartate oxidase 3448400 3195460 SPO3244 Ruegeria pomeroyi DSS-3 L-aspartate oxidase YP_168447.1 3446850 D 246200 CDS YP_168448.1 56698077 3195118 3448397..3449263 1 NC_003911.11 identified by similarity to SP:P39666; match to protein family HMM PF01729; match to protein family HMM PF02749; match to protein family HMM TIGR00078; nicotinate-nucleotide pyrophosphorylase 3449263 nadC 3195118 nadC Ruegeria pomeroyi DSS-3 nicotinate-nucleotide pyrophosphorylase YP_168448.1 3448397 D 246200 CDS YP_168449.1 56698078 3195205 3449530..3451062 1 NC_003911.11 identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM PF02978; match to protein family HMM TIGR00959; signal recognition particle protein 3451062 ffh 3195205 ffh Ruegeria pomeroyi DSS-3 signal recognition particle protein YP_168449.1 3449530 D 246200 CDS YP_168450.1 56698079 3193451 3451064..3451606 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3451606 3193451 SPO3247 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168450.1 3451064 D 246200 CDS YP_168451.1 56698080 3195240 3451603..3452139 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3452139 3195240 SPO3248 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168451.1 3451603 D 246200 CDS YP_168452.1 56698081 3195057 3452136..3452645 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3452645 3195057 SPO3249 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168452.1 3452136 D 246200 CDS YP_168453.1 56698082 3194854 3452642..3453160 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3453160 3194854 SPO3250 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168453.1 3452642 D 246200 CDS YP_168454.1 56698083 3195657 3453157..3453759 1 NC_003911.11 identified by similarity to PIR:B97652; hypothetical protein 3453759 3195657 SPO3251 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168454.1 3453157 D 246200 CDS YP_168455.1 56698084 3195299 3453764..3454060 1 NC_003911.11 catalyzes the interconversion of chorismate to prephenate; chorismate mutase 3454060 3195299 SPO3252 Ruegeria pomeroyi DSS-3 chorismate mutase YP_168455.1 3453764 D 246200 CDS YP_168456.1 56698085 3195394 3454125..3454490 1 NC_003911.11 binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity; 30S ribosomal protein S16 3454490 rpsP 3195394 rpsP Ruegeria pomeroyi DSS-3 30S ribosomal protein S16 YP_168456.1 3454125 D 246200 CDS YP_168457.1 56698086 3195300 3454502..3455137 1 NC_003911.11 identified by similarity to PIR:S52225; match to protein family HMM PF00881; cobalamin biosynthesis protein BluB 3455137 bluB 3195300 bluB Ruegeria pomeroyi DSS-3 cobalamin biosynthesis protein BluB YP_168457.1 3454502 D 246200 CDS YP_168458.1 56698087 3194913 3455284..3455787 1 NC_003911.11 Essential for efficient processing of 16S rRNA; 16S rRNA-processing protein RimM 3455787 rimM 3194913 rimM Ruegeria pomeroyi DSS-3 16S rRNA-processing protein RimM YP_168458.1 3455284 D 246200 CDS YP_168459.1 56698088 3193045 complement(3456324..3456545) 1 NC_003911.11 RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome; 50S ribosomal protein L31 3456545 rpmE 3193045 rpmE Ruegeria pomeroyi DSS-3 50S ribosomal protein L31 YP_168459.1 3456324 R 246200 CDS YP_168460.1 56698089 3195464 complement(3456557..3456940) 1 NC_003911.11 this protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site; 50S ribosomal protein L19 3456940 rplS 3195464 rplS Ruegeria pomeroyi DSS-3 50S ribosomal protein L19 YP_168460.1 3456557 R 246200 CDS YP_168461.1 56698090 3193153 3457342..3458151 1 NC_003911.11 identified by match to protein family HMM PF01183; glycosyl hydrolase 3458151 3193153 SPO3258 Ruegeria pomeroyi DSS-3 glycosyl hydrolase YP_168461.1 3457342 D 246200 CDS YP_168462.1 56698091 3195328 3458262..3458993 1 NC_003911.11 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA; tRNA (guanine-N(1)-)-methyltransferase 3458993 trmD 3195328 trmD Ruegeria pomeroyi DSS-3 tRNA (guanine-N(1)-)-methyltransferase YP_168462.1 3458262 D 246200 CDS YP_168463.1 56698092 3195779 3459026..3459808 1 NC_003911.11 identified by similarity to GB:AAD44211.1; methyltransferase-like protein 3459808 3195779 SPO3260 Ruegeria pomeroyi DSS-3 methyltransferase-like protein YP_168463.1 3459026 D 246200 CDS YP_168464.1 56698093 3194736 complement(3459931..3460599) 1 NC_003911.11 identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 3460599 3194736 SPO3261 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_168464.1 3459931 R 246200 CDS YP_168465.1 56698094 3193711 3460699..3461157 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 3461157 3193711 SPO3262 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_168465.1 3460699 D 246200 CDS YP_168466.1 56698095 3195377 3461163..3461615 1 NC_003911.11 hypothetical protein 3461615 3195377 SPO3263 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168466.1 3461163 D 246200 CDS YP_168467.1 56698096 3195303 complement(3468359..3468955) 1 NC_003911.11 in Escherichia coli this inner membrane protein was found to anchor the periplasmic catalytic oxidoreductase YedY; sulfite oxidase activity not demonstrated; contains heme; sulfite oxidase subunit YedZ 3468955 3195303 SPO3270 Ruegeria pomeroyi DSS-3 sulfite oxidase subunit YedZ YP_168467.1 3468359 R 246200 CDS YP_168468.1 56698097 3195130 complement(3468959..3469858) 1 NC_003911.11 in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ; sulfite oxidase subunit YedY 3469858 3195130 SPO3271 Ruegeria pomeroyi DSS-3 sulfite oxidase subunit YedY YP_168468.1 3468959 R 246200 CDS YP_168469.1 56698098 3193642 complement(3469965..3471551) 1 NC_003911.11 identified by match to protein family HMM PF01645; glutamate synthase 3471551 3193642 SPO3272 Ruegeria pomeroyi DSS-3 glutamate synthase YP_168469.1 3469965 R 246200 CDS YP_168470.1 56698099 3194952 3471517..3472068 1 NC_003911.11 hypothetical protein 3472068 3194952 SPO3273 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168470.1 3471517 D 246200 CDS YP_168471.1 56698100 3195991 3472122..3472562 1 NC_003911.11 hypothetical protein 3472562 3195991 SPO3274 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168471.1 3472122 D 246200 CDS YP_168472.1 56698101 3195960 complement(3472566..3473261) 1 NC_003911.11 identified by similarity to GB:CAE20608.1; hypothetical protein 3473261 3195960 SPO3275 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168472.1 3472566 R 246200 CDS YP_168473.1 56698102 3195262 complement(3473444..3476062) 1 NC_003911.11 identified by similarity to SP:P03815; match to protein family HMM PF00004; match to protein family HMM PF02861; ATP-dependent Clp protease, ATP-binding subunit ClpB 3476062 clpB 3195262 clpB Ruegeria pomeroyi DSS-3 ATP-dependent Clp protease, ATP-binding subunit ClpB YP_168473.1 3473444 R 246200 CDS YP_168474.1 56698103 3195438 3476266..3476538 1 NC_003911.11 identified by similarity to GB:AAN69029.1; hypothetical protein 3476538 3195438 SPO3277 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168474.1 3476266 D 246200 CDS YP_168475.1 56698104 3195326 3476646..3477380 1 NC_003911.11 OMP decarboxylase; OMPDCase; OMPdecase; type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase; orotidine 5'-phosphate decarboxylase 3477380 pyrF 3195326 pyrF Ruegeria pomeroyi DSS-3 orotidine 5'-phosphate decarboxylase YP_168475.1 3476646 D 246200 CDS YP_168476.1 56698105 3194631 complement(3477706..3478155) 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX domain-containing protein 3478155 3194631 SPO3279 Ruegeria pomeroyi DSS-3 NUDIX domain-containing protein YP_168476.1 3477706 R 246200 CDS YP_168477.1 56698106 3193147 3478224..3479486 1 NC_003911.11 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function; DNA polymerase IV 3479486 3193147 SPO3280 Ruegeria pomeroyi DSS-3 DNA polymerase IV YP_168477.1 3478224 D 246200 CDS YP_168478.1 56698107 3195088 3479535..3480032 1 NC_003911.11 identified by similarity to SP:Q02886; match to protein family HMM PF05163; DinB family protein 3480032 3195088 SPO3281 Ruegeria pomeroyi DSS-3 DinB family protein YP_168478.1 3479535 D 246200 CDS YP_168479.1 56698108 3195780 complement(3480049..3480909) 1 NC_003911.11 identified by match to protein family HMM PF05013; N-formylglutamate amidohydrolase 3480909 3195780 SPO3282 Ruegeria pomeroyi DSS-3 N-formylglutamate amidohydrolase YP_168479.1 3480049 R 246200 CDS YP_168480.2 161598429 3196292 3481212..3481337 1 NC_003911.11 smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group do not have the motif; 50S ribosomal protein L36 3481337 rpmJ 3196292 rpmJ Ruegeria pomeroyi DSS-3 50S ribosomal protein L36 YP_168480.2 3481212 D 246200 CDS YP_168481.1 56698109 3194928 3481443..3483047 1 NC_003911.11 hypothetical protein 3483047 3194928 SPO3285 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168481.1 3481443 D 246200 CDS YP_168482.1 56698110 3193868 3483233..3484840 1 NC_003911.11 identified by similarity to SP:P51691; match to protein family HMM PF00884; arylsulfatase 3484840 atsA 3193868 atsA Ruegeria pomeroyi DSS-3 arylsulfatase YP_168482.1 3483233 D 246200 CDS YP_168483.1 56698111 3195059 3484905..3485954 1 NC_003911.11 identified by match to protein family HMM PF01547; ferric iron ABC transporter periplasmic ferric iron-binding protein 3485954 3195059 SPO3287 Ruegeria pomeroyi DSS-3 ferric iron ABC transporter periplasmic ferric iron-binding protein YP_168483.1 3484905 D 246200 CDS YP_168484.1 56698112 3195715 complement(3486032..3487729) 1 NC_003911.11 identified by match to protein family HMM PF00528; ferric iron ABC transporter permease 3487729 3195715 SPO3288 Ruegeria pomeroyi DSS-3 ferric iron ABC transporter permease YP_168484.1 3486032 R 246200 CDS YP_168485.1 56698113 3195940 complement(3487873..3489090) 1 NC_003911.11 identified by similarity to GB:AAF26285.1; phenylacetate-CoA ligase 3489090 3195940 SPO3289 Ruegeria pomeroyi DSS-3 phenylacetate-CoA ligase YP_168485.1 3487873 R 246200 CDS YP_168486.1 56698114 3194371 complement(3489105..3489941) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 3489941 3194371 SPO3290 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_168486.1 3489105 R 246200 CDS YP_168487.1 56698115 3195772 complement(3490052..3491335) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; branched-chain amino acid ABC transporter periplasmic branched-chain amino acid binding protein 3491335 3195772 SPO3291 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter periplasmic branched-chain amino acid binding protein YP_168487.1 3490052 R 246200 CDS YP_168488.1 56698116 3195143 complement(3491418..3492494) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 3492494 3195143 SPO3292 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_168488.1 3491418 R 246200 CDS YP_168489.1 56698117 3194019 complement(3492498..3492755) 1 NC_003911.11 identified by similarity to GB:AAM36995.1; hypothetical protein 3492755 3194019 SPO3293 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168489.1 3492498 R 246200 CDS YP_168490.1 56698118 3195900 complement(3492834..3493820) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 3493820 3195900 SPO3294 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_168490.1 3492834 R 246200 CDS YP_168491.1 56698119 3195184 complement(3493862..3494746) 1 NC_003911.11 Assignment partly based on membership in branched-chain amino acid ABC transporter gene cluster.; identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 3494746 3195184 SPO3295 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_168491.1 3493862 R 246200 CDS YP_168492.1 56698120 3195178 complement(3494774..3496747) 1 NC_003911.11 identified by match to protein family HMM PF00501; AMP-binding protein 3496747 3195178 SPO3296 Ruegeria pomeroyi DSS-3 AMP-binding protein YP_168492.1 3494774 R 246200 CDS YP_168493.1 56698121 3193612 3497068..3498966 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF02518; sensory box histidine kinase/response regulator 3498966 3193612 SPO3297 Ruegeria pomeroyi DSS-3 sensory box histidine kinase/response regulator YP_168493.1 3497068 D 246200 CDS YP_168494.1 56698122 3195116 3498963..3499670 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator 3499670 3195116 SPO3298 Ruegeria pomeroyi DSS-3 DNA-binding response regulator YP_168494.1 3498963 D 246200 CDS YP_168495.1 56698123 3195569 complement(3499657..3500241) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 3500241 3195569 SPO3299 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_168495.1 3499657 R 246200 CDS YP_168496.1 56698124 3193720 3500355..3500747 1 NC_003911.11 identified by similarity to PIR:AD0744; hypothetical protein 3500747 3193720 SPO3300 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168496.1 3500355 D 246200 CDS YP_168497.1 56698125 3195650 complement(3500757..3501623) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3501623 3195650 SPO3301 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168497.1 3500757 R 246200 CDS YP_168498.1 56698126 3193380 3501641..3502009 1 NC_003911.11 identified by similarity to GB:BAC50637.1; hypothetical protein 3502009 3193380 SPO3302 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168498.1 3501641 D 246200 CDS YP_168499.1 56698127 3195538 complement(3502019..3502714) 1 NC_003911.11 identified by match to protein family HMM PF00657; GDSL-like lipase/acylhydrolase 3502714 3195538 SPO3303 Ruegeria pomeroyi DSS-3 GDSL-like lipase/acylhydrolase YP_168499.1 3502019 R 246200 CDS YP_168500.1 56698128 3194634 complement(3502814..3503998) 1 NC_003911.11 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase 3503998 3194634 SPO3304 Ruegeria pomeroyi DSS-3 allantoate amidohydrolase YP_168500.1 3502814 R 246200 CDS YP_168501.1 56698129 3193278 3504162..3504812 1 NC_003911.11 identified by match to protein family HMM PF00300; phosphoglycerate mutase 3504812 3193278 SPO3305 Ruegeria pomeroyi DSS-3 phosphoglycerate mutase YP_168501.1 3504162 D 246200 CDS YP_168502.1 56698130 3195327 3504822..3505436 1 NC_003911.11 identified by similarity to GB:AAC44159.1; match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 3505436 3195327 SPO3306 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_168502.1 3504822 D 246200 CDS YP_168503.1 56698131 3194227 3505451..3506503 1 NC_003911.11 identified by similarity to SP:P43065; match to protein family HMM PF01262; match to protein family HMM PF05222; saccharopine dehydrogenase 3506503 3194227 SPO3307 Ruegeria pomeroyi DSS-3 saccharopine dehydrogenase YP_168503.1 3505451 D 246200 CDS YP_168504.1 56698132 3193887 3506500..3506751 1 NC_003911.11 identified by similarity to GB:BAC51725.1; hypothetical protein 3506751 3193887 SPO3308 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168504.1 3506500 D 246200 CDS YP_168505.1 56698133 3195590 3506765..3507907 1 NC_003911.11 identified by similarity to SP:Q9P4R4; match to protein family HMM PF03435; saccharopine dehydrogenase 3507907 3195590 SPO3309 Ruegeria pomeroyi DSS-3 saccharopine dehydrogenase YP_168505.1 3506765 D 246200 CDS YP_168506.1 56698134 3195089 complement(3508018..3508335) 1 NC_003911.11 identified by similarity to GB:BAC53154.1; hypothetical protein 3508335 3195089 SPO3310 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168506.1 3508018 R 246200 CDS YP_168507.1 56698135 3195580 3508498..3509571 1 NC_003911.11 identified by similarity to SP:P06134; match to protein family HMM PF01035; match to protein family HMM PF02805; match to protein family HMM TIGR00589; ADA regulatory protein 3509571 3195580 SPO3311 Ruegeria pomeroyi DSS-3 ADA regulatory protein YP_168507.1 3508498 D 246200 CDS YP_168508.1 56698136 3195447 3509568..3510335 1 NC_003911.11 identified by similarity to GB:CAC41875.1; hypothetical protein 3510335 3195447 SPO3312 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168508.1 3509568 D 246200 CDS YP_168509.1 56698137 3194719 complement(3510359..3510928) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 3510928 3194719 SPO3313 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_168509.1 3510359 R 246200 CDS YP_168510.1 56698138 3195012 3511107..3512939 1 NC_003911.11 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 3512939 ilvD 3195012 ilvD Ruegeria pomeroyi DSS-3 dihydroxy-acid dehydratase YP_168510.1 3511107 D 246200 CDS YP_168511.1 56698139 3195904 complement(3513089..3514018) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3514018 3195904 SPO3315 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168511.1 3513089 R 246200 CDS YP_168512.1 56698140 3195094 3514119..3515087 1 NC_003911.11 hypothetical protein 3515087 3195094 SPO3316 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168512.1 3514119 D 246200 CDS YP_168513.1 56698141 3195977 3515662..3516219 1 NC_003911.11 transcriptional regulator 3516219 3195977 SPO3317 Ruegeria pomeroyi DSS-3 transcriptional regulator YP_168513.1 3515662 D 246200 CDS YP_168514.1 56698142 3195149 complement(3516235..3517053) 1 NC_003911.11 identified by similarity to GB:AAH10441.1; hypothetical protein 3517053 3195149 SPO3318 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168514.1 3516235 R 246200 CDS YP_168515.1 56698143 3192790 3517201..3518778 1 NC_003911.11 identified by similarity to GB:AAC44018.1; match to protein family HMM PF02485; EpsK domain-containing protein 3518778 3192790 SPO3319 Ruegeria pomeroyi DSS-3 EpsK domain-containing protein YP_168515.1 3517201 D 246200 CDS YP_168516.1 56698144 3195071 complement(3518860..3519504) 1 NC_003911.11 identified by similarity to GB:AAO54466.1; hypothetical protein 3519504 3195071 SPO3320 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168516.1 3518860 R 246200 CDS YP_168517.1 56698145 3193442 complement(3519515..3519781) 1 NC_003911.11 hypothetical protein 3519781 3193442 SPO3321 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168517.1 3519515 R 246200 CDS YP_168518.1 56698146 3193809 complement(3519783..3521132) 1 NC_003911.11 identified by similarity to GB:CAC46971.1; hypothetical protein 3521132 3193809 SPO3322 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168518.1 3519783 R 246200 CDS YP_168519.1 56698147 3195782 complement(3521993..3523930) 1 NC_003911.11 identified by similarity to GB:CAC46974.1; hypothetical protein 3523930 3195782 SPO3323 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168519.1 3521993 R 246200 CDS YP_168520.1 56698148 3192826 complement(3523998..3525119) 1 NC_003911.11 identified by similarity to GB:CAC46975.1; hypothetical protein 3525119 3192826 SPO3324 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168520.1 3523998 R 246200 CDS YP_168521.1 56698149 3195126 complement(3525534..3526613) 1 NC_003911.11 identified by similarity to GB:BAB49806.1; hypothetical protein 3526613 3195126 SPO3325 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168521.1 3525534 R 246200 CDS YP_168522.1 56698150 3195082 3526803..3527144 1 NC_003911.11 identified by similarity to GB:BAB54345.1; match to protein family HMM PF05899; hypothetical protein 3527144 3195082 SPO3326 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168522.1 3526803 D 246200 CDS YP_168523.1 56698151 3195993 complement(3527205..3528422) 1 NC_003911.11 identified by similarity to SP:P38488; match to protein family HMM PF00557; match to protein family HMM PF01321; creatinase 3528422 3195993 SPO3327 Ruegeria pomeroyi DSS-3 creatinase YP_168523.1 3527205 R 246200 CDS YP_168524.1 56698152 3194993 3528642..3530153 1 NC_003911.11 identified by similarity to SP:P25526; match to protein family HMM PF00171; match to protein family HMM TIGR01780; succinate-semialdehyde dehydrogenase 3530153 gabD-2 3194993 gabD-2 Ruegeria pomeroyi DSS-3 succinate-semialdehyde dehydrogenase YP_168524.1 3528642 D 246200 CDS YP_168525.1 56698153 3194838 complement(3530160..3530561) 1 NC_003911.11 identified by match to protein family HMM PF00042; globin domain-containing protein 3530561 3194838 SPO3329 Ruegeria pomeroyi DSS-3 globin domain-containing protein YP_168525.1 3530160 R 246200 CDS YP_168526.1 56698154 3193934 complement(3530661..3532919) 1 NC_003911.11 identified by similarity to SP:P21499; match to protein family HMM PF00575; match to protein family HMM PF00773; match to protein family HMM TIGR00358; match to protein family HMM TIGR02063; ribonuclease R 3532919 rnr 3193934 rnr Ruegeria pomeroyi DSS-3 ribonuclease R YP_168526.1 3530661 R 246200 CDS YP_168527.1 56698155 3193508 complement(3532951..3533562) 1 NC_003911.11 identified by similarity to GB:AAN40802.1; match to protein family HMM PF05143; hypothetical protein 3533562 3193508 SPO3331 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168527.1 3532951 R 246200 CDS YP_168528.1 56698156 3192962 complement(3533572..3534714) 1 NC_003911.11 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.; succinyl-diaminopimelate desuccinylase 3534714 dapE 3192962 dapE Ruegeria pomeroyi DSS-3 succinyl-diaminopimelate desuccinylase YP_168528.1 3533572 R 246200 CDS YP_168529.1 56698157 3193884 3535008..3536594 1 NC_003911.11 identified by similarity to GB:AAR38409.1; hypothetical protein 3536594 3193884 SPO3333 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168529.1 3535008 D 246200 CDS YP_168530.1 56698158 3194360 3536521..3537690 1 NC_003911.11 hypothetical protein 3537690 3194360 SPO3334 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168530.1 3536521 D 246200 CDS YP_168531.1 56698159 3194025 3537829..3538914 1 NC_003911.11 identified by similarity to SP:P10344; match to protein family HMM PF00497; glutamine ABC transporter periplasmic glutamine-binding protein 3538914 3194025 SPO3335 Ruegeria pomeroyi DSS-3 glutamine ABC transporter periplasmic glutamine-binding protein YP_168531.1 3537829 D 246200 CDS YP_168532.1 56698160 3195748 complement(3538921..3539262) 1 NC_003911.11 hypothetical protein 3539262 3195748 SPO3336 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168532.1 3538921 R 246200 CDS YP_168533.1 56698161 3195457 complement(3539336..3540163) 1 NC_003911.11 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway; 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase 3540163 dapD 3195457 dapD Ruegeria pomeroyi DSS-3 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase YP_168533.1 3539336 R 246200 CDS YP_168534.1 56698162 3195697 complement(3540260..3541216) 1 NC_003911.11 identified by match to protein family HMM PF04055; match to protein family HMM PF06968; match to protein family HMM TIGR00433; biotin synthase 3541216 bioB 3195697 bioB Ruegeria pomeroyi DSS-3 biotin synthase YP_168534.1 3540260 R 246200 CDS YP_168535.1 56698163 3195106 complement(3541209..3541796) 1 NC_003911.11 identified by match to protein family HMM PF02632; bioY family protein 3541796 3195106 SPO3339 Ruegeria pomeroyi DSS-3 bioY family protein YP_168535.1 3541209 R 246200 CDS YP_168536.1 56698164 3194992 complement(3541920..3542519) 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 3542519 3194992 SPO3340 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_168536.1 3541920 R 246200 CDS YP_168537.1 56698165 3195019 complement(3542565..3543485) 1 NC_003911.11 catalyzes the formation of 2-oxobutanoate from L-threonine; threonine dehydratase 3543485 3195019 SPO3341 Ruegeria pomeroyi DSS-3 threonine dehydratase YP_168537.1 3542565 R 246200 CDS YP_168538.1 56698166 3195439 3543541..3544416 1 NC_003911.11 identified by match to protein family HMM PF03641; match to protein family HMM TIGR00730; decarboxylase 3544416 3195439 SPO3342 Ruegeria pomeroyi DSS-3 decarboxylase YP_168538.1 3543541 D 246200 CDS YP_168539.1 56698168 3194050 complement(3544432..3544704) 1 NC_003911.11 hypothetical protein 3544704 3194050 SPO3343 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168539.1 3544432 R 246200 CDS YP_168540.1 56698167 3195049 3544879..3545994 1 NC_003911.11 catalyzes the formation of cysteine and 2-oxobutanoate from cystathionine; cystathionine gamma-lyase 3545994 3195049 SPO3344 Ruegeria pomeroyi DSS-3 cystathionine gamma-lyase YP_168540.1 3544879 D 246200 CDS YP_168541.1 56698169 3192667 complement(3545997..3546422) 1 NC_003911.11 hypothetical protein 3546422 3192667 SPO3345 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168541.1 3545997 R 246200 CDS YP_168542.1 56698170 3195026 complement(3546460..3547641) 1 NC_003911.11 identified by match to protein family HMM PF04055; match to protein family HMM TIGR00048; radical SAM protein 3547641 3195026 SPO3346 Ruegeria pomeroyi DSS-3 radical SAM protein YP_168542.1 3546460 R 246200 CDS YP_168543.1 56698171 3194376 complement(3547811..3548197) 1 NC_003911.11 identified by similarity to SP:P42879; hypothetical protein 3548197 3194376 SPO3347 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168543.1 3547811 R 246200 CDS YP_168544.1 56698172 3193088 complement(3548233..3548772) 1 NC_003911.11 identified by similarity to GB:CAD85590.1; hypothetical protein 3548772 3193088 SPO3348 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168544.1 3548233 R 246200 CDS YP_168545.1 56698173 3195547 3548954..3549952 1 NC_003911.11 identified by similarity to GB:AAF00929.1; match to protein family HMM PF06089; L-asparaginase 3549952 3195547 SPO3349 Ruegeria pomeroyi DSS-3 L-asparaginase YP_168545.1 3548954 D 246200 CDS YP_168546.1 56698174 3194831 complement(3549959..3550273) 1 NC_003911.11 identified by similarity to GB:BAB50844.1; hypothetical protein 3550273 3194831 SPO3350 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168546.1 3549959 R 246200 CDS YP_168547.1 56698175 3193865 complement(3550310..3550744) 1 NC_003911.11 identified by similarity to PIR:G96031; match to protein family HMM PF05146; Aha1 domain-containing protein 3550744 3193865 SPO3351 Ruegeria pomeroyi DSS-3 Aha1 domain-containing protein YP_168547.1 3550310 R 246200 CDS YP_168548.1 56698176 3194804 complement(3550732..3551079) 1 NC_003911.11 identified by match to protein family HMM PF01022; ArsR family transcriptional regulator 3551079 3194804 SPO3352 Ruegeria pomeroyi DSS-3 ArsR family transcriptional regulator YP_168548.1 3550732 R 246200 CDS YP_168549.1 56698177 3195675 complement(3551105..3552013) 1 NC_003911.11 identified by match to protein family HMM PF00702; match to protein family HMM TIGR00338; match to protein family HMM TIGR01488; phosphoserine phosphatase 3552013 serB-2 3195675 serB-2 Ruegeria pomeroyi DSS-3 phosphoserine phosphatase YP_168549.1 3551105 R 246200 CDS YP_168550.1 56698178 3195374 3552346..3553527 1 NC_003911.11 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; phosphoserine aminotransferase 3553527 3195374 SPO3354 Ruegeria pomeroyi DSS-3 phosphoserine aminotransferase YP_168550.1 3552346 D 246200 CDS YP_168551.1 56698179 3194715 3553615..3555210 1 NC_003911.11 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate; D-3-phosphoglycerate dehydrogenase 3555210 serA 3194715 serA Ruegeria pomeroyi DSS-3 D-3-phosphoglycerate dehydrogenase YP_168551.1 3553615 D 246200 CDS YP_168552.1 56698180 3195330 complement(3555263..3555646) 1 NC_003911.11 identified by similarity to GB:BAB50697.1; hypothetical protein 3555646 3195330 SPO3356 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168552.1 3555263 R 246200 CDS YP_168553.1 56698181 3194934 3555752..3556747 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3556747 3194934 SPO3357 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168553.1 3555752 D 246200 CDS YP_168554.1 56698182 3194865 3556744..3557478 1 NC_003911.11 identified by similarity to GB:AAC46052.1; match to protein family HMM PF00149; serine/threonine protein phosphatase 3557478 3194865 SPO3358 Ruegeria pomeroyi DSS-3 serine/threonine protein phosphatase YP_168554.1 3556744 D 246200 CDS YP_168555.1 56698183 3195944 complement(3557551..3558594) 1 NC_003911.11 converts threonine and NAD to 1,2-amino-3-oxobutanoate and NADH; functions in threonine catabolism; L-threonine 3-dehydrogenase 3558594 tdh 3195944 tdh Ruegeria pomeroyi DSS-3 L-threonine 3-dehydrogenase YP_168555.1 3557551 R 246200 CDS YP_168556.1 56698184 3195774 complement(3558594..3559778) 1 NC_003911.11 catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine; 2-amino-3-ketobutyrate CoA ligase 3559778 kbl 3195774 kbl Ruegeria pomeroyi DSS-3 2-amino-3-ketobutyrate CoA ligase YP_168556.1 3558594 R 246200 CDS YP_168557.1 56698185 3195177 complement(3559874..3561112) 1 NC_003911.11 identified by similarity to GB:BAB51420.1; match to protein family HMM PF02646; RmuC domain-containing protein 3561112 3195177 SPO3361 Ruegeria pomeroyi DSS-3 RmuC domain-containing protein YP_168557.1 3559874 R 246200 CDS YP_168558.1 56698186 3194545 complement(3561170..3563035) 1 NC_003911.11 This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex; DNA mismatch repair protein 3563035 mutL 3194545 mutL Ruegeria pomeroyi DSS-3 DNA mismatch repair protein YP_168558.1 3561170 R 246200 CDS YP_168559.1 56698187 3195117 complement(3563304..3564233) 1 NC_003911.11 identified by similarity to GB:AAK33470.1; match to protein family HMM PF00950; zinc/manganese/iron ABC transporter permease 3564233 3195117 SPO3363 Ruegeria pomeroyi DSS-3 zinc/manganese/iron ABC transporter permease YP_168559.1 3563304 R 246200 CDS YP_168560.1 56698188 3193234 complement(3564230..3565435) 1 NC_003911.11 identified by similarity to GB:AAS11742.1; match to protein family HMM PF00950; zinc/manganese/iron ABC transporter permease 3565435 3193234 SPO3364 Ruegeria pomeroyi DSS-3 zinc/manganese/iron ABC transporter permease YP_168560.1 3564230 R 246200 CDS YP_168561.1 56698189 3193094 complement(3565440..3566243) 1 NC_003911.11 identified by similarity to SP:P96117; match to protein family HMM PF00005; zinc/manganese/iron ABC transporter ATP-binding protein 3566243 3193094 SPO3365 Ruegeria pomeroyi DSS-3 zinc/manganese/iron ABC transporter ATP-binding protein YP_168561.1 3565440 R 246200 CDS YP_168562.1 56698190 3194816 complement(3566247..3567200) 1 NC_003911.11 identified by similarity to SP:P96116; match to protein family HMM PF01297; zinc/manganese/iron ABC transporter periplasmic zinc/manganese/iron-binding protein 3567200 3194816 SPO3366 Ruegeria pomeroyi DSS-3 zinc/manganese/iron ABC transporter periplasmic zinc/manganese/iron-binding protein YP_168562.1 3566247 R 246200 CDS YP_168563.1 56698191 3195831 3567556..3568389 1 NC_003911.11 identified by match to protein family HMM PF01791; match to protein family HMM TIGR00126; deoxyribose-phosphate aldolase 3568389 deoC 3195831 deoC Ruegeria pomeroyi DSS-3 deoxyribose-phosphate aldolase YP_168563.1 3567556 D 246200 CDS YP_168564.1 56698192 3194554 3568476..3570809 1 NC_003911.11 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 3570809 3194554 SPO3368 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_168564.1 3568476 D 246200 CDS YP_168565.1 56698193 3194749 3570837..3571649 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase 3571649 3194749 SPO3369 Ruegeria pomeroyi DSS-3 short chain dehydrogenase YP_168565.1 3570837 D 246200 CDS YP_168566.1 56698194 3195880 complement(3571747..3573057) 1 NC_003911.11 identified by match to protein family HMM PF00675; match to protein family HMM PF05193; M16 family peptidase 3573057 3195880 SPO3370 Ruegeria pomeroyi DSS-3 M16 family peptidase YP_168566.1 3571747 R 246200 CDS YP_168567.1 56698195 3195729 complement(3573054..3574403) 1 NC_003911.11 identified by match to protein family HMM PF00675; match to protein family HMM PF05193; M16 family peptidase 3574403 3195729 SPO3371 Ruegeria pomeroyi DSS-3 M16 family peptidase YP_168567.1 3573054 R 246200 CDS YP_168568.1 56698196 3193171 complement(3574476..3575048) 1 NC_003911.11 hypothetical protein 3575048 3193171 SPO3372 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168568.1 3574476 R 246200 CDS YP_168569.1 56698197 3195474 complement(3575045..3575518) 1 NC_003911.11 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase 3575518 lspA 3195474 lspA Ruegeria pomeroyi DSS-3 lipoprotein signal peptidase YP_168569.1 3575045 R 246200 CDS YP_168570.1 56698198 3195268 complement(3575518..3577107) 1 NC_003911.11 involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase 3577107 purH 3195268 purH Ruegeria pomeroyi DSS-3 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase YP_168570.1 3575518 R 246200 CDS YP_168571.1 56698199 3195874 complement(3577130..3578851) 1 NC_003911.11 identified by similarity to GB:BAB50839.1; hypothetical protein 3578851 3195874 SPO3375 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168571.1 3577130 R 246200 CDS YP_168572.1 56698200 3195741 complement(3578939..3580210) 1 NC_003911.11 identified by similarity to SP:P36929; match to protein family HMM PF01029; match to protein family HMM PF01189; ribosomal RNA small subunit methyltransferase B 3580210 3195741 SPO3376 Ruegeria pomeroyi DSS-3 ribosomal RNA small subunit methyltransferase B YP_168572.1 3578939 R 246200 CDS YP_168573.1 56698201 3195362 3580305..3580487 1 NC_003911.11 identified by similarity to GB:AAN30707.1; hypothetical protein 3580487 3195362 SPO3377 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168573.1 3580305 D 246200 CDS YP_168574.1 56698202 3195628 3580575..3581747 1 NC_003911.11 identified by match to protein family HMM PF03594; match to protein family HMM TIGR00843; benzoate transporter 3581747 3195628 SPO3378 Ruegeria pomeroyi DSS-3 benzoate transporter YP_168574.1 3580575 D 246200 CDS YP_168575.1 56698203 3195027 complement(3581744..3582586) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3582586 3195027 SPO3379 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168575.1 3581744 R 246200 CDS YP_168576.1 56698204 3194530 3582708..3583844 1 NC_003911.11 identified by similarity to SP:P80193; match to protein family HMM PF03322; gamma-butyrobetaine hydroxylase 3583844 3194530 SPO3380 Ruegeria pomeroyi DSS-3 gamma-butyrobetaine hydroxylase YP_168576.1 3582708 D 246200 CDS YP_168577.1 56698205 3195957 3583841..3584431 1 NC_003911.11 identified by similarity to GB:BAB48813.1; hypothetical protein 3584431 3195957 SPO3381 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168577.1 3583841 D 246200 CDS YP_168578.1 56698206 3194405 complement(3584584..3586023) 1 NC_003911.11 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 3586023 3194405 SPO3382 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_168578.1 3584584 R 246200 CDS YP_168579.1 56698207 3195770 3586245..3586898 1 NC_003911.11 identified by similarity to GB:BAC00970.1; match to protein family HMM PF00578; thiol-specific antioxidant protein 3586898 3195770 SPO3383 Ruegeria pomeroyi DSS-3 thiol-specific antioxidant protein YP_168579.1 3586245 D 246200 CDS YP_168580.1 56698208 3195846 3586953..3587609 1 NC_003911.11 identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 3587609 3195846 SPO3384 Ruegeria pomeroyi DSS-3 FkbM family methyltransferase YP_168580.1 3586953 D 246200 CDS YP_168581.1 56698209 3195653 complement(3587617..3588438) 1 NC_003911.11 identified by match to protein family HMM PF01755; glycosyl transferase family protein 3588438 3195653 SPO3385 Ruegeria pomeroyi DSS-3 glycosyl transferase family protein YP_168581.1 3587617 R 246200 CDS YP_168582.1 56698210 3195287 complement(3588477..3588959) 1 NC_003911.11 hypothetical protein 3588959 3195287 SPO3386 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168582.1 3588477 R 246200 CDS YP_168583.1 56698211 3194424 complement(3588946..3590337) 1 NC_003911.11 identified by similarity to GB:AAK01513.1; hypothetical protein 3590337 3194424 SPO3387 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168583.1 3588946 R 246200 CDS YP_168584.1 56698212 3194977 complement(3590395..3591018) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 3591018 3194977 SPO3388 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_168584.1 3590395 R 246200 CDS YP_168585.1 56698213 3195958 complement(3591258..3593402) 1 NC_003911.11 identified by similarity to SP:P05055; match to protein family HMM PF00013; match to protein family HMM PF00575; match to protein family HMM PF01138; match to protein family HMM PF03725; match to protein family HMM PF03726; polynucleotide phosphorylase 3593402 pnp 3195958 pnp Ruegeria pomeroyi DSS-3 polynucleotide phosphorylase YP_168585.1 3591258 R 246200 CDS YP_168586.1 56698214 3193902 complement(3593615..3594139) 1 NC_003911.11 identified by similarity to PIR:AH2948; hypothetical protein 3594139 3193902 SPO3390 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168586.1 3593615 R 246200 CDS YP_168587.1 56698215 3195274 3594307..3595152 1 NC_003911.11 identified by similarity to GB:AAC99764.1; match to protein family HMM PF01531; alpha-1,2-fucosyltransferase 3595152 3195274 SPO3391 Ruegeria pomeroyi DSS-3 alpha-1,2-fucosyltransferase YP_168587.1 3594307 D 246200 CDS YP_168588.1 56698216 3194821 complement(3595235..3595882) 1 NC_003911.11 identified by similarity to SP:P39219; match to protein family HMM PF00849; ribosomal large subunit pseudouridine synthase A 3595882 rluA 3194821 rluA Ruegeria pomeroyi DSS-3 ribosomal large subunit pseudouridine synthase A YP_168588.1 3595235 R 246200 CDS YP_168589.1 56698217 3195153 3595986..3596396 1 NC_003911.11 identified by similarity to GB:BAC68979.1; hypothetical protein 3596396 3195153 SPO3393 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168589.1 3595986 D 246200 CDS YP_168590.1 56698218 3194404 3596429..3597130 1 NC_003911.11 identified by match to protein family HMM PF00657; GDSL-like lipase/acylhydrolase 3597130 3194404 SPO3394 Ruegeria pomeroyi DSS-3 GDSL-like lipase/acylhydrolase YP_168590.1 3596429 D 246200 CDS YP_168591.1 56698219 3194510 complement(3597088..3597987) 1 NC_003911.11 identified by similarity to SP:P27844; match to protein family HMM PF00892; match to protein family HMM TIGR00688; protein RarD 3597987 rarD-2 3194510 rarD-2 Ruegeria pomeroyi DSS-3 protein RarD YP_168591.1 3597088 R 246200 CDS YP_168592.1 56698220 3195707 complement(3598191..3600641) 1 NC_003911.11 identified by match to protein family HMM PF01266; match to protein family HMM PF01571; FAD-dependent oxidoreductase 3600641 3195707 SPO3396 Ruegeria pomeroyi DSS-3 FAD-dependent oxidoreductase YP_168592.1 3598191 R 246200 CDS YP_168593.1 56698221 3194496 complement(3600729..3601697) 1 NC_003911.11 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 3601697 3194496 SPO3397 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_168593.1 3600729 R 246200 CDS YP_168594.1 56698222 3195042 complement(3601725..3602621) 1 NC_003911.11 identified by match to protein family HMM PF02574; homocysteine S-methyltransferase 3602621 3195042 SPO3398 Ruegeria pomeroyi DSS-3 homocysteine S-methyltransferase YP_168594.1 3601725 R 246200 CDS YP_168595.1 56698223 3195141 complement(3602618..3603685) 1 NC_003911.11 identified by match to protein family HMM PF00107; alcohol dehydrogenase 3603685 3195141 SPO3399 Ruegeria pomeroyi DSS-3 alcohol dehydrogenase YP_168595.1 3602618 R 246200 CDS YP_168596.1 56698224 3193141 complement(3603682..3606129) 1 NC_003911.11 identified by match to protein family HMM PF01571; glycine cleavage system protein T 3606129 3193141 SPO3400 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_168596.1 3603682 R 246200 CDS YP_168597.1 56698225 3195023 complement(3606139..3606510) 1 NC_003911.11 identified by similarity to GB:BAB48331.1; match to protein family HMM PF04828; hypothetical protein 3606510 3195023 SPO3401 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168597.1 3606139 R 246200 CDS YP_168598.1 56698226 3195516 complement(3606514..3607137) 1 NC_003911.11 identified by similarity to SP:P27847; match to protein family HMM PF01810; amino acid transporter LysE 3607137 3195516 SPO3402 Ruegeria pomeroyi DSS-3 amino acid transporter LysE YP_168598.1 3606514 R 246200 CDS YP_168599.1 56698227 3195093 complement(3607148..3607717) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 3607717 3195093 SPO3403 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_168599.1 3607148 R 246200 CDS YP_168600.1 56698228 3195592 3607935..3608207 1 NC_003911.11 identified by similarity to GB:AAQ58177.1; match to protein family HMM PF06961; hypothetical protein 3608207 3195592 SPO3404 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168600.1 3607935 D 246200 CDS YP_168601.1 56698229 3195526 complement(3608184..3608636) 1 NC_003911.11 identified by similarity to GB:AAM38460.1; hypothetical protein 3608636 3195526 SPO3405 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168601.1 3608184 R 246200 CDS YP_168602.1 56698230 3195364 complement(3608707..3609303) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 3609303 3195364 SPO3406 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_168602.1 3608707 R 246200 CDS YP_168603.1 56698231 3194638 3609403..3609768 1 NC_003911.11 hypothetical protein 3609768 3194638 SPO3407 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168603.1 3609403 D 246200 CDS YP_168604.1 56698232 3195101 complement(3609809..3610981) 1 NC_003911.11 identified by match to protein family HMM PF00108; match to protein family HMM PF02803; match to protein family HMM TIGR01930; acetyl-CoA C-acetyltransferase 3610981 3195101 SPO3408 Ruegeria pomeroyi DSS-3 acetyl-CoA C-acetyltransferase YP_168604.1 3609809 R 246200 CDS YP_168605.1 56698233 3194671 3611080..3611418 1 NC_003911.11 identified by match to protein family HMM PF01740; match to protein family HMM TIGR00377; anti-anti-sigma factor 3611418 3194671 SPO3409 Ruegeria pomeroyi DSS-3 anti-anti-sigma factor YP_168605.1 3611080 D 246200 CDS YP_168606.1 56698234 3194055 3611441..3611890 1 NC_003911.11 identified by similarity to SP:P17904; match to protein family HMM PF02518; anti-sigma B factor 3611890 3194055 SPO3410 Ruegeria pomeroyi DSS-3 anti-sigma B factor YP_168606.1 3611441 D 246200 CDS YP_168607.1 56698235 3195917 3612877..3614454 1 NC_003911.11 identified by match to protein family HMM PF01019; gamma-glutamyltranspeptidase 3614454 3195917 SPO3411 Ruegeria pomeroyi DSS-3 gamma-glutamyltranspeptidase YP_168607.1 3612877 D 246200 CDS YP_168608.1 56698734 3196339 complement(3614476..3614808) 1 NC_003911.11 identified by similarity to GB:AAN33763.1; match to protein family HMM TIGR02097; hypothetical protein 3614808 3196339 SPO3412 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168608.1 3614476 R 246200 CDS YP_168609.1 56698236 3195296 3614887..3615768 1 NC_003911.11 identified by match to protein family HMM PF03547; auxin efflux carrier family protein 3615768 3195296 SPO3413 Ruegeria pomeroyi DSS-3 auxin efflux carrier family protein YP_168609.1 3614887 D 246200 CDS YP_168610.1 56698237 3194006 3615830..3616420 1 NC_003911.11 lipoprotein 3616420 3194006 SPO3414 Ruegeria pomeroyi DSS-3 lipoprotein YP_168610.1 3615830 D 246200 CDS YP_168611.1 56698238 3193951 complement(3616443..3617039) 1 NC_003911.11 identified by match to protein family HMM PF03548; outer membrane lipoprotein carrier protein LolA 3617039 3193951 SPO3415 Ruegeria pomeroyi DSS-3 outer membrane lipoprotein carrier protein LolA YP_168611.1 3616443 R 246200 CDS YP_168612.1 56698239 3195414 complement(3617078..3620074) 1 NC_003911.11 identified by match to protein family HMM PF01580; DNA translocase FtsK 3620074 3195414 SPO3416 Ruegeria pomeroyi DSS-3 DNA translocase FtsK YP_168612.1 3617078 R 246200 CDS YP_168613.1 56698240 3194694 complement(3620089..3621270) 1 NC_003911.11 identified by match to protein family HMM PF00155; aminotransferase, classes I and II 3621270 3194694 SPO3417 Ruegeria pomeroyi DSS-3 aminotransferase, classes I and II YP_168613.1 3620089 R 246200 CDS YP_168614.1 56698241 3194471 complement(3621379..3622707) 1 NC_003911.11 identified by match to protein family HMM PF01425; amidase 3622707 3194471 SPO3418 Ruegeria pomeroyi DSS-3 amidase YP_168614.1 3621379 R 246200 CDS YP_168615.1 56698242 3192835 3622756..3624018 1 NC_003911.11 identified by match to protein family HMM PF01360; match to protein family HMM TIGR01988; UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase 3624018 3192835 SPO3419 Ruegeria pomeroyi DSS-3 UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase YP_168615.1 3622756 D 246200 CDS YP_168616.1 56698243 3194192 complement(3624053..3624820) 1 NC_003911.11 identified by similarity to GB:BAB50604.1; hypothetical protein 3624820 3194192 SPO3420 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168616.1 3624053 R 246200 CDS YP_168617.1 56698244 3195132 complement(3624813..3625001) 1 NC_003911.11 identified by similarity to GB:AAK22095.1; match to protein family HMM PF03966; hypothetical protein 3625001 3195132 SPO3421 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168617.1 3624813 R 246200 CDS YP_168618.1 56698245 3195441 complement(3624998..3625639) 1 NC_003911.11 identified by match to protein family HMM PF02190; ATP-dependent protease La 3625639 3195441 SPO3422 Ruegeria pomeroyi DSS-3 ATP-dependent protease La YP_168618.1 3624998 R 246200 CDS YP_168619.1 56698246 3195223 complement(3625670..3626584) 1 NC_003911.11 identified by match to protein family HMM PF00085; thioredoxin 3626584 3195223 SPO3423 Ruegeria pomeroyi DSS-3 thioredoxin YP_168619.1 3625670 R 246200 CDS YP_168620.1 56698247 3194873 complement(3626667..3628337) 1 NC_003911.11 identified by match to protein family HMM PF00560; hypothetical protein 3628337 3194873 SPO3424 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168620.1 3626667 R 246200 CDS YP_168621.1 56698248 3195340 complement(3628506..3629294) 1 NC_003911.11 identified by match to protein family HMM PF03372; match to protein family HMM TIGR00633; exodeoxyribonuclease III 3629294 3195340 SPO3425 Ruegeria pomeroyi DSS-3 exodeoxyribonuclease III YP_168621.1 3628506 R 246200 CDS YP_168622.1 56698249 3195773 complement(3629493..3630179) 1 NC_003911.11 identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator 3630179 3195773 SPO3426 Ruegeria pomeroyi DSS-3 DNA-binding response regulator YP_168622.1 3629493 R 246200 CDS YP_168623.1 56698250 3194516 3630346..3631437 1 NC_003911.11 identified by similarity to SP:P43525; match to protein family HMM PF00925; match to protein family HMM TIGR00505; 3,4-dihydroxy-2-butanone 4-phosphate synthase 3631437 ribBA 3194516 ribBA Ruegeria pomeroyi DSS-3 3,4-dihydroxy-2-butanone 4-phosphate synthase YP_168623.1 3630346 D 246200 CDS YP_168624.1 56698251 3194615 3631434..3631934 1 NC_003911.11 identified by similarity to GB:BAB50941.1; hypothetical protein 3631934 3194615 SPO3428 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168624.1 3631434 D 246200 CDS YP_168625.1 56698252 3195919 complement(3631918..3632616) 1 NC_003911.11 identified by match to protein family HMM PF01168; match to protein family HMM TIGR00044; alanine racemase 3632616 3195919 SPO3429 Ruegeria pomeroyi DSS-3 alanine racemase YP_168625.1 3631918 R 246200 CDS YP_168626.1 56698253 3195739 complement(3632685..3633698) 1 NC_003911.11 identified by similarity to GB:CAA70599.1; porin 3633698 3195739 SPO3430 Ruegeria pomeroyi DSS-3 porin YP_168626.1 3632685 R 246200 CDS YP_168627.1 56698254 3193985 3633976..3634482 1 NC_003911.11 identified by similarity to GB:AAK25710.1; hypothetical protein 3634482 3193985 SPO3431 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168627.1 3633976 D 246200 CDS YP_168628.1 56698255 3192670 3634559..3637117 1 NC_003911.11 leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase; leucyl-tRNA synthetase 3637117 leuS 3192670 leuS Ruegeria pomeroyi DSS-3 leucyl-tRNA synthetase YP_168628.1 3634559 D 246200 CDS YP_168629.1 56698256 3193740 3637104..3637595 1 NC_003911.11 lipoprotein 3637595 3193740 SPO3433 Ruegeria pomeroyi DSS-3 lipoprotein YP_168629.1 3637104 D 246200 CDS YP_168630.1 56698257 3194833 3637592..3638620 1 NC_003911.11 identified by similarity to GB:CAE25733.1; hypothetical protein 3638620 3194833 SPO3434 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168630.1 3637592 D 246200 CDS YP_168631.1 56698258 3195481 3638702..3639295 1 NC_003911.11 identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 3639295 3195481 SPO3435 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_168631.1 3638702 D 246200 CDS YP_168632.1 56698259 3195635 complement(3639265..3640464) 1 NC_003911.11 identified by similarity to GB:CAE27628.1; hypothetical protein 3640464 3195635 SPO3436 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168632.1 3639265 R 246200 CDS YP_168633.1 56698260 3193967 complement(3640461..3641822) 1 NC_003911.11 identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS 3641822 3193967 SPO3437 Ruegeria pomeroyi DSS-3 mechanosensitive ion channel MscS YP_168633.1 3640461 R 246200 CDS YP_168634.1 56698261 3194739 3641837..3642169 1 NC_003911.11 identified by similarity to GB:CAD55640.1; hypothetical protein 3642169 3194739 SPO3438 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168634.1 3641837 D 246200 CDS YP_168635.1 56698262 3195413 complement(3642266..3642874) 1 NC_003911.11 identified by match to protein family HMM PF00378; enoyl-CoA hydratase 3642874 3195413 SPO3439 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_168635.1 3642266 R 246200 CDS YP_168636.1 56698263 3194462 complement(3642871..3643623) 1 NC_003911.11 identified by similarity to SP:P19992; match to protein family HMM PF00106; 20-beta-hydroxysteroid dehydrogenase 3643623 3194462 SPO3440 Ruegeria pomeroyi DSS-3 20-beta-hydroxysteroid dehydrogenase YP_168636.1 3642871 R 246200 CDS YP_168637.1 56698264 3194151 3643755..3645281 1 NC_003911.11 identified by similarity to GB:AAC02256.1; hypothetical protein 3645281 3194151 SPO3441 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168637.1 3643755 D 246200 CDS YP_168638.1 56698265 3195884 3645348..3646754 1 NC_003911.11 identified by similarity to SP:P24231; hypothetical protein 3646754 3195884 SPO3442 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168638.1 3645348 D 246200 CDS YP_168639.1 56698266 3194021 3646741..3647544 1 NC_003911.11 identified by similarity to SP:P22783; match to protein family HMM PF00459; inositol monophosphatase 3647544 3194021 SPO3443 Ruegeria pomeroyi DSS-3 inositol monophosphatase YP_168639.1 3646741 D 246200 CDS YP_168640.1 56698267 3194902 3647712..3648941 1 NC_003911.11 identified by similarity to SP:P23282; 3-deoxy-D-manno-octulosonic-acid transferase 3648941 3194902 SPO3444 Ruegeria pomeroyi DSS-3 3-deoxy-D-manno-octulosonic-acid transferase YP_168640.1 3647712 D 246200 CDS YP_168641.1 56698268 3194962 3648928..3649929 1 NC_003911.11 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate; tetraacyldisaccharide 4'-kinase 3649929 lpxK 3194962 lpxK Ruegeria pomeroyi DSS-3 tetraacyldisaccharide 4'-kinase YP_168641.1 3648928 D 246200 CDS YP_168642.1 56698269 3194983 complement(3649932..3650600) 1 NC_003911.11 identified by match to protein family HMM PF01323; DsbA family thiol:disulfide interchange protein 3650600 3194983 SPO3446 Ruegeria pomeroyi DSS-3 DsbA family thiol:disulfide interchange protein YP_168642.1 3649932 R 246200 CDS YP_168643.1 56698270 3194979 complement(3650615..3651121) 1 NC_003911.11 identified by similarity to GB:CAE29927.1; hypothetical protein 3651121 3194979 SPO3447 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168643.1 3650615 R 246200 CDS YP_168644.1 56698271 3195498 3651203..3652258 1 NC_003911.11 identified by match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01084; A/G-specific adenine glycosylase 3652258 mutY 3195498 mutY Ruegeria pomeroyi DSS-3 A/G-specific adenine glycosylase YP_168644.1 3651203 D 246200 CDS YP_168645.1 56698272 3194577 3652319..3653452 1 NC_003911.11 identified by match to protein family HMM PF00487; fatty acid desaturase 3653452 3194577 SPO3449 Ruegeria pomeroyi DSS-3 fatty acid desaturase YP_168645.1 3652319 D 246200 CDS YP_168646.1 56698273 3194754 complement(3653459..3654835) 1 NC_003911.11 identified by match to protein family HMM PF00211; guanylate cyclase 3654835 3194754 SPO3450 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_168646.1 3653459 R 246200 CDS YP_168647.1 56698274 3195587 complement(3654996..3656099) 1 NC_003911.11 identified by match to protein family HMM PF01555; modification methylase 3656099 3195587 SPO3451 Ruegeria pomeroyi DSS-3 modification methylase YP_168647.1 3654996 R 246200 CDS YP_168648.1 56698275 3195469 complement(3656206..3656910) 1 NC_003911.11 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII 3656910 rnhB 3195469 rnhB Ruegeria pomeroyi DSS-3 ribonuclease HII YP_168648.1 3656206 R 246200 CDS YP_168649.1 56698276 3194667 3657415..3657864 1 NC_003911.11 hypothetical protein 3657864 3194667 SPO3453 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168649.1 3657415 D 246200 CDS YP_168650.1 56698277 3194931 3657836..3658537 1 NC_003911.11 hypothetical protein 3658537 3194931 SPO3454 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168650.1 3657836 D 246200 CDS YP_168651.1 56698278 3192945 3658917..3660494 1 NC_003911.11 identified by match to protein family HMM PF00211; match to protein family HMM PF04248; guanylate cyclase 3660494 3192945 SPO3455 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_168651.1 3658917 D 246200 CDS YP_168652.1 56698279 3194157 complement(3660508..3661305) 1 NC_003911.11 identified by similarity to PIR:AC3648; flagellar protein 3661305 3194157 SPO3456 Ruegeria pomeroyi DSS-3 flagellar protein YP_168652.1 3660508 R 246200 CDS YP_168653.1 56698280 3194488 complement(3661302..3661706) 1 NC_003911.11 post-transcriptional repressor of flagellum biosynthesis; promotes degradation of fljK mRNA: Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella; flagellar biosynthesis repressor FlbT 3661706 flbT 3194488 flbT Ruegeria pomeroyi DSS-3 flagellar biosynthesis repressor FlbT YP_168653.1 3661302 R 246200 CDS YP_168654.1 56698281 3194748 complement(3661703..3662080) 1 NC_003911.11 acts as an activator of flagellin translation and may be required for filament secretion or assembly; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagellum; flagellar biosynthesis regulatory protein FlaF 3662080 flaF 3194748 flaF Ruegeria pomeroyi DSS-3 flagellar biosynthesis regulatory protein FlaF YP_168654.1 3661703 R 246200 CDS YP_168655.1 56698282 3194040 complement(3662147..3663373) 1 NC_003911.11 identified by match to protein family HMM PF00669; match to protein family HMM PF00700; flagellin protein 3663373 3194040 SPO3459 Ruegeria pomeroyi DSS-3 flagellin protein YP_168655.1 3662147 R 246200 CDS YP_168656.1 56698283 3194311 complement(3663584..3663943) 1 NC_003911.11 identified by similarity to PIR:E98268; hypothetical protein 3663943 3194311 SPO3460 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168656.1 3663584 R 246200 CDS YP_168657.1 56698284 3194687 complement(3663933..3664220) 1 NC_003911.11 identified by similarity to SP:P75942; flagellar protein FlgJ 3664220 3194687 SPO3461 Ruegeria pomeroyi DSS-3 flagellar protein FlgJ YP_168657.1 3663933 R 246200 CDS YP_168658.1 56698285 3193348 3664298..3666775 1 NC_003911.11 identified by match to protein family HMM PF02120; flagellar hook-length control protein 3666775 3193348 SPO3462 Ruegeria pomeroyi DSS-3 flagellar hook-length control protein YP_168658.1 3664298 D 246200 CDS YP_168659.1 56698286 3193584 3666779..3667447 1 NC_003911.11 acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of many flagellar genes; the Rhodobacter protein in this cluster is associated with a set of flagellar genes acquired by lateral gene transfer; these genes are not normally expressed; flagellar basal body rod modification protein 3667447 flgD 3193584 flgD Ruegeria pomeroyi DSS-3 flagellar basal body rod modification protein YP_168659.1 3666779 D 246200 CDS YP_168660.1 56698287 3194550 3667512..3668381 1 NC_003911.11 identified by similarity to GB:CAB76068.1; hypothetical protein 3668381 3194550 SPO3464 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168660.1 3667512 D 246200 CDS YP_168661.1 56698288 3195553 complement(3668386..3669690) 1 NC_003911.11 identified by similarity to GB:CAE33186.1; hypothetical protein 3669690 3195553 SPO3465 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168661.1 3668386 R 246200 CDS YP_168662.1 56698289 3194338 complement(3669690..3670505) 1 NC_003911.11 identified by similarity to SP:P31136; match to protein family HMM PF00528; putrescine ABC transporter permease 3670505 potI 3194338 potI Ruegeria pomeroyi DSS-3 putrescine ABC transporter permease YP_168662.1 3669690 R 246200 CDS YP_168663.1 56698290 3195161 complement(3670502..3671419) 1 NC_003911.11 identified by similarity to SP:P31135; match to protein family HMM PF00528; putrescine ABC transporter permease 3671419 potH 3195161 potH Ruegeria pomeroyi DSS-3 putrescine ABC transporter permease YP_168663.1 3670502 R 246200 CDS YP_168664.1 56698291 3195099 complement(3671383..3672510) 1 NC_003911.11 identified by similarity to SP:P31134; match to protein family HMM PF00005; match to protein family HMM PF03459; match to protein family HMM TIGR01187; putrescine ABC transporter ATP-binding protein 3672510 potG 3195099 potG Ruegeria pomeroyi DSS-3 putrescine ABC transporter ATP-binding protein YP_168664.1 3671383 R 246200 CDS YP_168665.1 56698292 3195405 complement(3672592..3673677) 1 NC_003911.11 identified by similarity to SP:P31133; match to protein family HMM PF01547; putrescine ABC transporter periplasmic putrescine-binding protein 3673677 potF 3195405 potF Ruegeria pomeroyi DSS-3 putrescine ABC transporter periplasmic putrescine-binding protein YP_168665.1 3672592 R 246200 CDS YP_168666.1 56698293 3193899 3673824..3674504 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 3674504 3193899 SPO3470 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_168666.1 3673824 D 246200 CDS YP_168667.1 56698294 3192924 3674581..3675975 1 NC_003911.11 identified by similarity to SP:Q53196; match to protein family HMM PF00202; aminotransferase 3675975 3192924 SPO3471 Ruegeria pomeroyi DSS-3 aminotransferase YP_168667.1 3674581 D 246200 CDS YP_168668.1 56698295 3195306 3676162..3677280 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01187; polyamine ABC transporter ATP-binding protein 3677280 3195306 SPO3472 Ruegeria pomeroyi DSS-3 polyamine ABC transporter ATP-binding protein YP_168668.1 3676162 D 246200 CDS YP_168669.1 56698296 3195492 3677396..3678469 1 NC_003911.11 Assignment partly based on membership in polyamine ABC transporter gene cluster.; identified by match to protein family HMM PF01547; polyamine ABC transporter periplasmic polyamine-binding protein 3678469 3195492 SPO3473 Ruegeria pomeroyi DSS-3 polyamine ABC transporter periplasmic polyamine-binding protein YP_168669.1 3677396 D 246200 CDS YP_168670.1 56698297 3195140 3678540..3679823 1 NC_003911.11 Assignment based partly on membership in polyamine ABC transporter gene cluster.; identified by match to protein family HMM PF00528; polyamine ABC transporter permease 3679823 3195140 SPO3474 Ruegeria pomeroyi DSS-3 polyamine ABC transporter permease YP_168670.1 3678540 D 246200 CDS YP_168671.1 56698298 3195437 3679830..3680750 1 NC_003911.11 identified by similarity to SP:P23859; match to protein family HMM PF00528; polyamine ABC transporter permease 3680750 3195437 SPO3475 Ruegeria pomeroyi DSS-3 polyamine ABC transporter permease YP_168671.1 3679830 D 246200 CDS YP_168672.1 56698299 3194985 complement(3680835..3681182) 1 NC_003911.11 hypothetical protein 3681182 3194985 SPO3476 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168672.1 3680835 R 246200 CDS YP_168673.1 56698300 3194520 complement(3681218..3681940) 1 NC_003911.11 identified by similarity to GB:BAB48216.1; hypothetical protein 3681940 3194520 SPO3477 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168673.1 3681218 R 246200 CDS YP_168674.1 56698301 3196032 3682022..3683470 1 NC_003911.11 identified by similarity to SP:P52075; match to protein family HMM PF01565; match to protein family HMM PF02913; glycolate oxidase subunit GlcD 3683470 glcD 3196032 glcD Ruegeria pomeroyi DSS-3 glycolate oxidase subunit GlcD YP_168674.1 3682022 D 246200 CDS YP_168675.1 56698302 3194290 3683536..3684624 1 NC_003911.11 identified by similarity to SP:P52073; match to protein family HMM PF01565; glycolate oxidase subunit GlcE 3684624 glcE 3194290 glcE Ruegeria pomeroyi DSS-3 glycolate oxidase subunit GlcE YP_168675.1 3683536 D 246200 CDS YP_168676.1 56698303 3192951 3684628..3685950 1 NC_003911.11 identified by similarity to SP:P52074; match to protein family HMM PF00037; match to protein family HMM PF02754; glycolate oxidase, iron-sulfur subunit 3685950 glcF 3192951 glcF Ruegeria pomeroyi DSS-3 glycolate oxidase, iron-sulfur subunit YP_168676.1 3684628 D 246200 CDS YP_168677.1 56698304 3195308 complement(3686010..3687212) 1 NC_003911.11 hypothetical protein 3687212 3195308 SPO3481 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168677.1 3686010 R 246200 CDS YP_168678.1 56698305 3196357 3687295..3688200 1 NC_003911.11 identified by match to protein family HMM PF00089; serine protease 3688200 3196357 SPO3482 Ruegeria pomeroyi DSS-3 serine protease YP_168678.1 3687295 D 246200 CDS YP_168679.1 56698306 3194857 3688197..3689015 1 NC_003911.11 identified by similarity to PIR:E85765; hypothetical protein 3689015 3194857 SPO3483 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168679.1 3688197 D 246200 CDS YP_168680.1 56698307 3193438 3689142..3689612 1 NC_003911.11 identified by match to protein family HMM PF00011; heat shock protein 20 3689612 3193438 SPO3484 Ruegeria pomeroyi DSS-3 heat shock protein 20 YP_168680.1 3689142 D 246200 CDS YP_168681.1 56698308 3193289 complement(3689754..3690146) 1 NC_003911.11 identified by similarity to GB:AAN48213.1; hypothetical protein 3690146 3193289 SPO3485 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168681.1 3689754 R 246200 CDS YP_168682.1 56698309 3196291 complement(3690143..3690841) 1 NC_003911.11 identified by similarity to PIR:B83165; hypothetical protein 3690841 3196291 SPO3486 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168682.1 3690143 R 246200 CDS YP_168683.1 56698310 3193332 3690925..3691614 1 NC_003911.11 identified by similarity to PIR:AB3193; hypothetical protein 3691614 3193332 SPO3487 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168683.1 3690925 D 246200 CDS YP_168684.1 56698311 3196369 3691679..3692950 1 NC_003911.11 identified by match to protein family HMM PF01471; peptidoglycan binding domain-containing protein 3692950 3196369 SPO3488 Ruegeria pomeroyi DSS-3 peptidoglycan binding domain-containing protein YP_168684.1 3691679 D 246200 CDS YP_168685.1 56698312 3194649 3693085..3695481 1 NC_003911.11 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily; phenylalanyl-tRNA synthetase subunit beta 3695481 pheT 3194649 pheT Ruegeria pomeroyi DSS-3 phenylalanyl-tRNA synthetase subunit beta YP_168685.1 3693085 D 246200 CDS YP_168686.1 56698313 3194920 complement(3695536..3696420) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; match to protein family HMM TIGR01199; LysR family transcriptional regulator 3696420 3194920 SPO3490 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168686.1 3695536 R 246200 CDS YP_168687.1 56698314 3194089 3696505..3697137 1 NC_003911.11 identified by match to protein family HMM PF01209; UbiE/COQ5 family methlytransferase 3697137 3194089 SPO3491 Ruegeria pomeroyi DSS-3 UbiE/COQ5 family methlytransferase YP_168687.1 3696505 D 246200 CDS YP_168688.1 56698315 3196297 3697148..3697654 1 NC_003911.11 identified by similarity to GB:BAC17897.1; hypothetical protein 3697654 3196297 SPO3492 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168688.1 3697148 D 246200 CDS YP_168689.1 56698316 3194301 3697729..3698886 1 NC_003911.11 transporter 3698886 3194301 SPO3493 Ruegeria pomeroyi DSS-3 transporter YP_168689.1 3697729 D 246200 CDS YP_168690.1 56698317 3196295 complement(3698893..3699594) 1 NC_003911.11 identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 3699594 3196295 SPO3494 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_168690.1 3698893 R 246200 CDS YP_168691.1 56698318 3194704 3699884..3700315 1 NC_003911.11 identified by match to protein family HMM PF01741; match to protein family HMM TIGR00220; large conductance mechanosensitive channel protein 3700315 mscL 3194704 mscL Ruegeria pomeroyi DSS-3 large conductance mechanosensitive channel protein YP_168691.1 3699884 D 246200 CDS YP_168692.1 56698319 3193548 3700403..3701209 1 NC_003911.11 identified by similarity to GB:BAC95620.1; match to protein family HMM PF00924; mechanosensitive ion channel MscS 3701209 3193548 SPO3496 Ruegeria pomeroyi DSS-3 mechanosensitive ion channel MscS YP_168692.1 3700403 D 246200 CDS YP_168693.1 56698320 3195007 complement(3701731..3702906) 1 NC_003911.11 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 3702906 tuf-2 3195007 tuf-2 Ruegeria pomeroyi DSS-3 elongation factor Tu YP_168693.1 3701731 R 246200 CDS YP_168694.1 56698321 3195147 complement(3703463..3705580) 1 NC_003911.11 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 3705580 fusA 3195147 fusA Ruegeria pomeroyi DSS-3 elongation factor G YP_168694.1 3703463 R 246200 CDS YP_168695.1 56698322 3196305 complement(3705599..3706069) 1 NC_003911.11 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 3706069 rpsG 3196305 rpsG Ruegeria pomeroyi DSS-3 30S ribosomal protein S7 YP_168695.1 3705599 R 246200 CDS YP_168696.1 56698323 3193405 complement(3706085..3706456) 1 NC_003911.11 interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance; 30S ribosomal protein S12 3706456 rpsL 3193405 rpsL Ruegeria pomeroyi DSS-3 30S ribosomal protein S12 YP_168696.1 3706085 R 246200 CDS YP_168697.1 56698324 3193494 3706787..3707608 1 NC_003911.11 hypothetical protein 3707608 3193494 SPO3502 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168697.1 3706787 D 246200 CDS YP_168698.1 56698325 3193218 3707611..3708426 1 NC_003911.11 identified by similarity to GB:AAC44076.1; hypothetical protein 3708426 3193218 SPO3503 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168698.1 3707611 D 246200 CDS YP_168699.1 56698326 3195352 complement(3708409..3709344) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 3709344 3195352 SPO3504 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168699.1 3708409 R 246200 CDS YP_168700.1 56698327 3194635 complement(3709396..3710604) 1 NC_003911.11 hypothetical protein 3710604 3194635 SPO3505 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168700.1 3709396 R 246200 CDS YP_168701.1 56698328 3196241 complement(3710608..3711177) 1 NC_003911.11 identified by match to protein family HMM PF01381; DNA-binding protein 3711177 3196241 SPO3506 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_168701.1 3710608 R 246200 CDS YP_168702.1 56698329 3196349 complement(3711273..3715514) 1 NC_003911.11 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit beta' binds to sigma factor allowing it to bind to the -10 region of the promoter; DNA-directed RNA polymerase subunit beta' 3715514 rpoC 3196349 rpoC Ruegeria pomeroyi DSS-3 DNA-directed RNA polymerase subunit beta' YP_168702.1 3711273 R 246200 CDS YP_168703.1 56698330 3196296 complement(3715822..3719958) 1 NC_003911.11 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme; DNA-directed RNA polymerase subunit beta 3719958 rpoB 3196296 rpoB Ruegeria pomeroyi DSS-3 DNA-directed RNA polymerase subunit beta YP_168703.1 3715822 R 246200 CDS YP_168704.1 56698331 3194266 complement(3720252..3720629) 1 NC_003911.11 present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors; 50S ribosomal protein L7/L12 3720629 rplL 3194266 rplL Ruegeria pomeroyi DSS-3 50S ribosomal protein L7/L12 YP_168704.1 3720252 R 246200 CDS YP_168705.2 161598430 3195233 complement(3720709..3721227) 1 NC_003911.11 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 3721227 rplJ 3195233 rplJ Ruegeria pomeroyi DSS-3 50S ribosomal protein L10 YP_168705.2 3720709 R 246200 CDS YP_168706.1 56698333 3195396 complement(3721519..3722445) 1 NC_003911.11 hypothetical protein 3722445 3195396 SPO3511 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168706.1 3721519 R 246200 CDS YP_168707.1 56698334 3196303 3722616..3723467 1 NC_003911.11 hypothetical protein 3723467 3196303 SPO3512 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168707.1 3722616 D 246200 CDS YP_168708.1 56698335 3194818 complement(3723558..3724256) 1 NC_003911.11 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA; 50S ribosomal protein L1 3724256 rplA 3194818 rplA Ruegeria pomeroyi DSS-3 50S ribosomal protein L1 YP_168708.1 3723558 R 246200 CDS YP_168709.1 56698336 3195557 complement(3724258..3724683) 1 NC_003911.11 binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 3724683 rplK 3195557 rplK Ruegeria pomeroyi DSS-3 50S ribosomal protein L11 YP_168709.1 3724258 R 246200 CDS YP_168710.1 56698337 3196340 3724914..3726068 1 NC_003911.11 identified by similarity to GB:AAR38409.1; hypothetical protein 3726068 3196340 SPO3515 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168710.1 3724914 D 246200 CDS YP_168711.1 56698338 3193106 complement(3726043..3726576) 1 NC_003911.11 identified by match to protein family HMM PF00467; match to protein family HMM PF02357; match to protein family HMM TIGR00922; transcription termination/antitermination factor NusG 3726576 nusG 3193106 nusG Ruegeria pomeroyi DSS-3 transcription termination/antitermination factor NusG YP_168711.1 3726043 R 246200 CDS YP_168712.1 56698339 3194975 complement(3726779..3727012) 1 NC_003911.11 forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force; preprotein translocase subunit SecE 3727012 secE 3194975 secE Ruegeria pomeroyi DSS-3 preprotein translocase subunit SecE YP_168712.1 3726779 R 246200 CDS YP_168713.1 56698340 3196320 complement(3727035..3727457) 1 NC_003911.11 identified by similarity to GB:CAE28126.1; hypothetical protein 3727457 3196320 SPO3518 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168713.1 3727035 R 246200 CDS YP_168714.1 56698341 3193658 complement(3727505..3727663) 1 NC_003911.11 identified by match to protein family HMM PF03597; match to protein family HMM TIGR00847; cbb3-type cytochrome oxidase maturation protein 3727663 ccoS 3193658 ccoS Ruegeria pomeroyi DSS-3 cbb3-type cytochrome oxidase maturation protein YP_168714.1 3727505 R 246200 CDS YP_168715.1 56698342 3194618 complement(3727668..3729845) 1 NC_003911.11 identified by match to protein family HMM PF00122; match to protein family HMM PF00403; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01511; match to protein family HMM TIGR01525; copper-translocating P-type ATPase 3729845 3194618 SPO3520 Ruegeria pomeroyi DSS-3 copper-translocating P-type ATPase YP_168715.1 3727668 R 246200 CDS YP_168716.1 56698343 3193180 complement(3729850..3730308) 1 NC_003911.11 identified by similarity to SP:P18397; fixH protein 3730308 3193180 SPO3521 Ruegeria pomeroyi DSS-3 fixH protein YP_168716.1 3729850 R 246200 CDS YP_168717.1 56698344 3194702 complement(3730311..3731738) 1 NC_003911.11 identified by similarity to SP:P18396; match to protein family HMM PF00037; iron-sulfur-binding protein RdxA/RdxB/FixG family 3731738 3194702 SPO3522 Ruegeria pomeroyi DSS-3 iron-sulfur-binding protein RdxA/RdxB/FixG family YP_168717.1 3730311 R 246200 CDS YP_168718.1 56698345 3194654 complement(3732122..3732988) 1 NC_003911.11 identified by similarity to PIR:S77598; match to protein family HMM PF00034; match to protein family HMM TIGR00782; cytochrome c oxidase, cbb3-type subunit III 3732988 ccoP-1 3194654 ccoP-1 Ruegeria pomeroyi DSS-3 cytochrome c oxidase, cbb3-type subunit III YP_168718.1 3732122 R 246200 CDS YP_168719.1 56698346 3196218 complement(3732985..3733221) 1 NC_003911.11 identified by similarity to GB:AAB02558.1; match to protein family HMM PF05545; cytochrome c oxidase, cbb3-type subunit IV 3733221 ccoQ-1 3196218 ccoQ-1 Ruegeria pomeroyi DSS-3 cytochrome c oxidase, cbb3-type subunit IV YP_168719.1 3732985 R 246200 CDS YP_168720.1 56698347 3195203 complement(3733232..3733960) 1 NC_003911.11 CcoO; FixO; cbb3-type cytochrome c oxidase subunit II 3733960 ccoO-1 3195203 ccoO-1 Ruegeria pomeroyi DSS-3 cbb3-type cytochrome c oxidase subunit II YP_168720.1 3733232 R 246200 CDS YP_168721.1 56698348 3196353 complement(3733975..3735582) 1 NC_003911.11 CcoN; FixN; cbb3-type cytochrome c oxidase subunit I 3735582 ccoN-1 3196353 ccoN-1 Ruegeria pomeroyi DSS-3 cbb3-type cytochrome c oxidase subunit I YP_168721.1 3733975 R 246200 CDS YP_168722.1 56698349 3196283 3735771..3736613 1 NC_003911.11 identified by match to protein family HMM PF00582; universal stress protein family protein 3736613 3196283 SPO3527 Ruegeria pomeroyi DSS-3 universal stress protein family protein YP_168722.1 3735771 D 246200 CDS YP_168723.1 56698350 3194973 complement(3736673..3736927) 1 NC_003911.11 identified by similarity to GB:BAB50217.1; match to protein family HMM PF04226; hypothetical protein 3736927 3194973 SPO3528 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168723.1 3736673 R 246200 CDS YP_168724.1 56698351 3192992 complement(3736984..3738279) 1 NC_003911.11 identified by match to protein family HMM PF00464; serine hydroxymethyltransferase 3738279 glyA-3 3192992 glyA-3 Ruegeria pomeroyi DSS-3 serine hydroxymethyltransferase YP_168724.1 3736984 R 246200 CDS YP_168725.1 56698352 3193917 3738405..3739277 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3739277 3193917 SPO3530 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168725.1 3738405 D 246200 CDS YP_168726.1 56698353 3196390 complement(3739351..3740094) 1 NC_003911.11 identified by similarity to SP:P51007; match to protein family HMM PF00027; match to protein family HMM PF00325; transcriptional activator protein FnrL 3740094 fnrL 3196390 fnrL Ruegeria pomeroyi DSS-3 transcriptional activator protein FnrL YP_168726.1 3739351 R 246200 CDS YP_168727.1 56698354 3193999 3740159..3741514 1 NC_003911.11 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 3741514 hemN 3193999 hemN Ruegeria pomeroyi DSS-3 coproporphyrinogen III oxidase YP_168727.1 3740159 D 246200 CDS YP_168728.1 56698355 3195897 3741694..3743700 1 NC_003911.11 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 3743700 3195897 SPO3533 Ruegeria pomeroyi DSS-3 elongation factor G YP_168728.1 3741694 D 246200 CDS YP_168729.1 56698356 3194408 complement(3743775..3745355) 1 NC_003911.11 identified by similarity to SP:P33916; match to protein family HMM PF00005; oligopeptide/dipeptide ABC transporter ATP-binding protein 3745355 yejF 3194408 yejF Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter ATP-binding protein YP_168729.1 3743775 R 246200 CDS YP_168730.1 56698357 3193795 complement(3745352..3746458) 1 NC_003911.11 identified by similarity to SP:P33915; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 3746458 yejE 3193795 yejE Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter permease YP_168730.1 3745352 R 246200 CDS YP_168731.1 56698358 3194738 complement(3746462..3747553) 1 NC_003911.11 identified by match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 3747553 yejB 3194738 yejB Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter permease YP_168731.1 3746462 R 246200 CDS YP_168732.1 56698359 3196277 complement(3747563..3749503) 1 NC_003911.11 identified by match to protein family HMM PF00496; oligopeptide/dipeptide ABC transporter substrate-binding protein 3749503 yejA 3196277 yejA Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter substrate-binding protein YP_168732.1 3747563 R 246200 CDS YP_168733.1 56698360 3195032 complement(3749646..3750152) 1 NC_003911.11 identified by similarity to SP:P54820; match to protein family HMM PF00034; cytochrome c552 3750152 cycM 3195032 cycM Ruegeria pomeroyi DSS-3 cytochrome c552 YP_168733.1 3749646 R 246200 CDS YP_168734.1 56698361 3196270 3750251..3751105 1 NC_003911.11 catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis; prephenate dehydratase 3751105 3196270 SPO3539 Ruegeria pomeroyi DSS-3 prephenate dehydratase YP_168734.1 3750251 D 246200 CDS YP_168735.1 56698362 3193086 3751133..3751360 1 NC_003911.11 hypothetical protein 3751360 3193086 SPO3540 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168735.1 3751133 D 246200 CDS YP_168736.1 56698363 3194000 complement(3751644..3752627) 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX family hydrolase 3752627 3194000 SPO3541 Ruegeria pomeroyi DSS-3 NUDIX family hydrolase YP_168736.1 3751644 R 246200 CDS YP_168737.1 56698364 3193775 3752853..3754724 1 NC_003911.11 identified by similarity to SP:P08331; match to protein family HMM PF00149; match to protein family HMM PF02872; 2`,3`-cyclic-nucleotide 2`-phosphodiesterase 3754724 3193775 SPO3542 Ruegeria pomeroyi DSS-3 2`,3`-cyclic-nucleotide 2`-phosphodiesterase YP_168737.1 3752853 D 246200 CDS YP_168738.1 56698365 3194031 3754990..3755421 1 NC_003911.11 identified by similarity to GB:BAC96093.1; hypothetical protein 3755421 3194031 SPO3543 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168738.1 3754990 D 246200 CDS YP_168739.1 56698366 3195839 complement(3755444..3756304) 1 NC_003911.11 identified by similarity to GB:BAC49042.1; hypothetical protein 3756304 3195839 SPO3544 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168739.1 3755444 R 246200 CDS YP_168740.1 56698367 3193217 3756388..3756945 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 3756945 3193217 SPO3545 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_168740.1 3756388 D 246200 CDS YP_168741.1 56698368 3195385 complement(3756942..3757793) 1 NC_003911.11 identified by match to protein family HMM PF04228; zinc metallopeptidase 3757793 3195385 SPO3546 Ruegeria pomeroyi DSS-3 zinc metallopeptidase YP_168741.1 3756942 R 246200 CDS YP_168742.1 56698369 3195504 3758150..3758593 1 NC_003911.11 hypothetical protein 3758593 3195504 SPO3547 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168742.1 3758150 D 246200 CDS YP_168743.1 56698370 3196215 complement(3758598..3759095) 1 NC_003911.11 identified by similarity to GB:CAE29730.1; hypothetical protein 3759095 3196215 SPO3548 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168743.1 3758598 R 246200 CDS YP_168744.1 56698371 3193557 complement(3759230..3759847) 1 NC_003911.11 identified by similarity to GB:CAD13774.1; hypothetical protein 3759847 3193557 SPO3549 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168744.1 3759230 R 246200 CDS YP_168745.1 56698372 3193201 3759926..3761677 1 NC_003911.11 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA; DNA polymerase III subunits gamma and tau 3761677 dnaX 3193201 dnaX Ruegeria pomeroyi DSS-3 DNA polymerase III subunits gamma and tau YP_168745.1 3759926 D 246200 CDS YP_168746.1 56698373 3193378 complement(3761757..3762230) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3762230 3193378 SPO3551 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168746.1 3761757 R 246200 CDS YP_168747.1 56698374 3193041 complement(3762227..3763270) 1 NC_003911.11 identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding 3763270 3193041 SPO3552 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_168747.1 3762227 R 246200 CDS YP_168748.1 56698375 3193298 3763320..3763985 1 NC_003911.11 identified by similarity to PIR:C75368; match to protein family HMM PF05430; hypothetical protein 3763985 3193298 SPO3553 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168748.1 3763320 D 246200 CDS YP_168749.1 56698376 3196322 3763982..3764878 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 3764878 3196322 SPO3554 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168749.1 3763982 D 246200 CDS YP_168750.1 56698377 3194924 complement(3764834..3766840) 1 NC_003911.11 identified by match to protein family HMM PF01464; Slt family transglycosylase 3766840 3194924 SPO3555 Ruegeria pomeroyi DSS-3 Slt family transglycosylase YP_168750.1 3764834 R 246200 CDS YP_168751.1 56698378 3196309 3766956..3767828 1 NC_003911.11 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase 3767828 dapA 3196309 dapA Ruegeria pomeroyi DSS-3 dihydrodipicolinate synthase YP_168751.1 3766956 D 246200 CDS YP_168752.1 56698379 3193004 complement(3767921..3768793) 1 NC_003911.11 identified by match to protein family HMM PF04976; dimethyl sulfoxide reductase subunit C 3768793 3193004 SPO3557 Ruegeria pomeroyi DSS-3 dimethyl sulfoxide reductase subunit C YP_168752.1 3767921 R 246200 CDS YP_168753.1 56698380 3193404 complement(3768793..3769599) 1 NC_003911.11 identified by match to protein family HMM PF00037; (Fe-S)-binding protein 3769599 3193404 SPO3558 Ruegeria pomeroyi DSS-3 (Fe-S)-binding protein YP_168753.1 3768793 R 246200 CDS YP_168754.1 56698381 3196227 complement(3769625..3772465) 1 NC_003911.11 identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; molybdopterin-binding oxidoreductase 3772465 3196227 SPO3559 Ruegeria pomeroyi DSS-3 molybdopterin-binding oxidoreductase YP_168754.1 3769625 R 246200 CDS YP_168755.1 56698382 3196250 complement(3772593..3773606) 1 NC_003911.11 identified by match to protein family HMM PF01515; match to protein family HMM TIGR00651; phosphate acetyltransferase 3773606 pta 3196250 pta Ruegeria pomeroyi DSS-3 phosphate acetyltransferase YP_168755.1 3772593 R 246200 CDS YP_168756.1 56698383 3196354 complement(3773624..3775414) 1 NC_003911.11 catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 3775414 xsc 3196354 xsc Ruegeria pomeroyi DSS-3 sulfoacetaldehyde acetyltransferase YP_168756.1 3773624 R 246200 CDS YP_168757.1 56698384 3196382 complement(3775524..3776990) 1 NC_003911.11 identified by match to protein family HMM PF00392; taurine transcriptional regulator 3776990 tauR 3196382 tauR Ruegeria pomeroyi DSS-3 taurine transcriptional regulator YP_168757.1 3775524 R 246200 CDS YP_168758.1 56698385 3196024 3777172..3777489 1 NC_003911.11 identified by match to protein family HMM PF01022; ArsR family transcriptional regulator 3777489 3196024 SPO3563 Ruegeria pomeroyi DSS-3 ArsR family transcriptional regulator YP_168758.1 3777172 D 246200 CDS YP_168759.1 56698386 3196042 3777482..3778510 1 NC_003911.11 identified by match to protein family HMM PF03773; permease 3778510 3196042 SPO3564 Ruegeria pomeroyi DSS-3 permease YP_168759.1 3777482 D 246200 CDS YP_168760.1 56698387 3196063 complement(3778516..3778908) 1 NC_003911.11 hypothetical protein 3778908 3196063 SPO3565 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168760.1 3778516 R 246200 CDS YP_168761.1 56698388 3195503 complement(3778959..3779735) 1 NC_003911.11 identified by similarity to GB:CAC47907.1; hypothetical protein 3779735 3195503 SPO3566 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168761.1 3778959 R 246200 CDS YP_168762.1 56698389 3196307 3779864..3780493 1 NC_003911.11 identified by match to protein family HMM PF00445; ribonuclease T2 family protein 3780493 3196307 SPO3567 Ruegeria pomeroyi DSS-3 ribonuclease T2 family protein YP_168762.1 3779864 D 246200 CDS YP_168763.1 56698390 3195616 complement(3780522..3781097) 1 NC_003911.11 identified by similarity to PIR:D95307; hypothetical protein 3781097 3195616 SPO3568 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168763.1 3780522 R 246200 CDS YP_168764.1 56698391 3196401 complement(3781123..3781719) 1 NC_003911.11 involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR 3781719 recR 3196401 recR Ruegeria pomeroyi DSS-3 recombination protein RecR YP_168764.1 3781123 R 246200 CDS YP_168765.1 56698392 3195408 complement(3781794..3782138) 1 NC_003911.11 identified by similarity to PIR:A82247; match to protein family HMM PF02575; match to protein family HMM TIGR00103; hypothetical protein 3782138 3195408 SPO3570 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168765.1 3781794 R 246200 CDS YP_168766.1 56698393 3196214 complement(3782189..3783151) 1 NC_003911.11 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 3783151 3196214 SPO3571 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_168766.1 3782189 R 246200 CDS YP_168767.1 56698394 3196149 3783221..3783766 1 NC_003911.11 identified by match to protein family HMM PF00857; isochorismatase 3783766 3196149 SPO3572 Ruegeria pomeroyi DSS-3 isochorismatase YP_168767.1 3783221 D 246200 CDS YP_168768.1 56698395 3196242 complement(3783768..3784310) 1 NC_003911.11 identified by match to protein family HMM PF03358; NADPH-dependent FMN reductase domain-containing protein 3784310 3196242 SPO3573 Ruegeria pomeroyi DSS-3 NADPH-dependent FMN reductase domain-containing protein YP_168768.1 3783768 R 246200 CDS YP_168769.1 56698396 3196271 complement(3784425..3785024) 1 NC_003911.11 identified by similarity to GB:CAD17119.1; short chain dehydrogenase 3785024 3196271 SPO3574 Ruegeria pomeroyi DSS-3 short chain dehydrogenase YP_168769.1 3784425 R 246200 CDS YP_168770.1 56698397 3195216 complement(3785026..3785382) 1 NC_003911.11 identified by match to protein family HMM PF00376; MerR family transcriptional regulator 3785382 3195216 SPO3575 Ruegeria pomeroyi DSS-3 MerR family transcriptional regulator YP_168770.1 3785026 R 246200 CDS YP_168771.1 56698398 3196348 complement(3785535..3786200) 1 NC_003911.11 identified by match to protein family HMM PF00691; OmpA domain-containing protein 3786200 3196348 SPO3576 Ruegeria pomeroyi DSS-3 OmpA domain-containing protein YP_168771.1 3785535 R 246200 CDS YP_168772.1 56698399 3196100 complement(3786327..3787025) 1 NC_003911.11 identified by similarity to GB:BAB51517.1; hypothetical protein 3787025 3196100 SPO3577 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168772.1 3786327 R 246200 CDS YP_168773.1 56698400 3195031 complement(3787295..3788146) 1 NC_003911.11 identified by similarity to SP:P06134; match to protein family HMM PF00165; match to protein family HMM PF01035; match to protein family HMM TIGR00589; ADA regulatory protein 3788146 3195031 SPO3578 Ruegeria pomeroyi DSS-3 ADA regulatory protein YP_168773.1 3787295 R 246200 CDS YP_168774.1 56698401 3195034 3788268..3788717 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 3788717 3195034 SPO3579 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_168774.1 3788268 D 246200 CDS YP_168775.1 56698402 3195932 3788719..3789363 1 NC_003911.11 identified by match to protein family HMM PF00857; isochorismatase 3789363 3195932 SPO3580 Ruegeria pomeroyi DSS-3 isochorismatase YP_168775.1 3788719 D 246200 CDS YP_168776.1 56698403 3196325 3789415..3790059 1 NC_003911.11 identified by match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01083; endonuclease III 3790059 nth 3196325 nth Ruegeria pomeroyi DSS-3 endonuclease III YP_168776.1 3789415 D 246200 CDS YP_168777.1 56698404 3193718 3790056..3791042 1 NC_003911.11 identified by match to protein family HMM PF00294; PfkB family kinase 3791042 3193718 SPO3582 Ruegeria pomeroyi DSS-3 PfkB family kinase YP_168777.1 3790056 D 246200 CDS YP_168778.1 56698405 3195389 complement(3791148..3791657) 1 NC_003911.11 identified by similarity to SP:P42195; match to protein family HMM PF01047; transcriptional regulator PecS 3791657 pecS 3195389 pecS Ruegeria pomeroyi DSS-3 transcriptional regulator PecS YP_168778.1 3791148 R 246200 CDS YP_168779.1 56698406 3193360 3791729..3792649 1 NC_003911.11 identified by similarity to SP:P42194; match to protein family HMM PF00892; drug/metabolite transporter family membrane protein 3792649 3193360 SPO3584 Ruegeria pomeroyi DSS-3 drug/metabolite transporter family membrane protein YP_168779.1 3791729 D 246200 CDS YP_168780.1 56698407 3195400 complement(3792607..3793092) 1 NC_003911.11 identified by match to protein family HMM PF00293; NUDIX family hydrolase NudH subfamily hydrolase 3793092 3195400 SPO3585 Ruegeria pomeroyi DSS-3 NUDIX family hydrolase NudH subfamily hydrolase YP_168780.1 3792607 R 246200 CDS YP_168781.1 56698408 3194304 3793226..3795253 1 NC_003911.11 identified by similarity to SP:P42593; match to protein family HMM PF00070; match to protein family HMM PF00724; 2,4-dienoyl-CoA reductase 3795253 fadH 3194304 fadH Ruegeria pomeroyi DSS-3 2,4-dienoyl-CoA reductase YP_168781.1 3793226 D 246200 CDS YP_168782.1 56698409 3196128 3795394..3796023 1 NC_003911.11 hypothetical protein 3796023 3196128 SPO3587 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168782.1 3795394 D 246200 CDS YP_168783.1 56698410 3196111 complement(3796089..3796433) 1 NC_003911.11 identified by similarity to GB:BAB51219.1; match to protein family HMM PF03992; hypothetical protein 3796433 3196111 SPO3588 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168783.1 3796089 R 246200 CDS YP_168784.1 56698411 3195996 complement(3796430..3796753) 1 NC_003911.11 identified by similarity to PIR:AH2740; match to protein family HMM PF06499; hypothetical protein 3796753 3195996 SPO3589 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168784.1 3796430 R 246200 CDS YP_168785.1 56698412 3194543 complement(3796832..3797272) 1 NC_003911.11 identified by similarity to PIR:B83607; hypothetical protein 3797272 3194543 SPO3590 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168785.1 3796832 R 246200 CDS YP_168786.1 56698413 3194484 3797417..3798331 1 NC_003911.11 identified by match to protein family HMM PF03547; auxin efflux carrier family protein 3798331 3194484 SPO3591 Ruegeria pomeroyi DSS-3 auxin efflux carrier family protein YP_168786.1 3797417 D 246200 CDS YP_168787.1 56698414 3195976 3798481..3799386 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3799386 3195976 SPO3592 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168787.1 3798481 D 246200 CDS YP_168788.1 56698415 3195684 3799579..3801237 1 NC_003911.11 identified by match to protein family HMM PF00884; sulfatase 3801237 3195684 SPO3593 Ruegeria pomeroyi DSS-3 sulfatase YP_168788.1 3799579 D 246200 CDS YP_168789.1 56698416 3196269 complement(3801673..3802746) 1 NC_003911.11 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily; phenylalanyl-tRNA synthetase subunit alpha 3802746 pheS 3196269 pheS Ruegeria pomeroyi DSS-3 phenylalanyl-tRNA synthetase subunit alpha YP_168789.1 3801673 R 246200 CDS YP_168790.1 56698417 3196230 complement(3802852..3803568) 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF02311; AraC family transcriptional regulator 3803568 3196230 SPO3595 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_168790.1 3802852 R 246200 CDS YP_168791.1 56698418 3196365 3803691..3804293 1 NC_003911.11 identified by match to protein family HMM PF01243; pyridoxamine 5'-phosphate oxidase 3804293 3196365 SPO3596 Ruegeria pomeroyi DSS-3 pyridoxamine 5'-phosphate oxidase YP_168791.1 3803691 D 246200 CDS YP_168792.1 56698419 3196252 3804457..3805806 1 NC_003911.11 identified by match to protein family HMM PF01593; amine oxidase 3805806 3196252 SPO3597 Ruegeria pomeroyi DSS-3 amine oxidase YP_168792.1 3804457 D 246200 CDS YP_168793.1 56698420 3196278 complement(3805961..3806326) 1 NC_003911.11 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 3806326 rplT 3196278 rplT Ruegeria pomeroyi DSS-3 50S ribosomal protein L20 YP_168793.1 3805961 R 246200 CDS YP_168794.1 56698716 3196240 complement(3806342..3806542) 1 NC_003911.11 identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001; 50S ribosomal protein L35 3806542 rpmI 3196240 rpmI Ruegeria pomeroyi DSS-3 50S ribosomal protein L35 YP_168794.1 3806342 R 246200 CDS YP_168795.1 56698421 3196306 complement(3806925..3808370) 1 NC_003911.11 identified by match to protein family HMM PF00224; match to protein family HMM PF02887; match to protein family HMM TIGR01064; pyruvate kinase 3808370 pyk 3196306 pyk Ruegeria pomeroyi DSS-3 pyruvate kinase YP_168795.1 3806925 R 246200 CDS YP_168796.1 56698422 3196364 3808488..3809225 1 NC_003911.11 identified by match to protein family HMM PF05013; N-formylglutamate amidohydrolase 3809225 3196364 SPO3601 Ruegeria pomeroyi DSS-3 N-formylglutamate amidohydrolase YP_168796.1 3808488 D 246200 CDS YP_168797.1 56698423 3196379 3809353..3809667 1 NC_003911.11 hypothetical protein 3809667 3196379 SPO3602 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168797.1 3809353 D 246200 CDS YP_168798.1 56698424 3196375 complement(3809680..3810144) 1 NC_003911.11 identified by match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase 3810144 3196375 SPO3603 Ruegeria pomeroyi DSS-3 thioesterase YP_168798.1 3809680 R 246200 CDS YP_168799.1 56698425 3196236 complement(3810300..3811160) 1 NC_003911.11 identified by similarity to PIR:A31422; match to protein family HMM PF01063; D-amino acid aminotransferase 3811160 3196236 SPO3604 Ruegeria pomeroyi DSS-3 D-amino acid aminotransferase YP_168799.1 3810300 R 246200 CDS YP_168800.1 56698426 3194773 complement(3811211..3812056) 1 NC_003911.11 identified by similarity to PIR:AD1992; hypothetical protein 3812056 3194773 SPO3605 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168800.1 3811211 R 246200 CDS YP_168801.1 56698427 3196384 complement(3812075..3813040) 1 NC_003911.11 identified by match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase 3813040 3196384 SPO3606 Ruegeria pomeroyi DSS-3 mandelate racemase YP_168801.1 3812075 R 246200 CDS YP_168802.1 56698428 3195749 complement(3813133..3814251) 1 NC_003911.11 identified by similarity to GB:AAM01784.1; hypothetical protein 3814251 3195749 SPO3607 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168802.1 3813133 R 246200 CDS YP_168803.1 56698429 3196324 3814431..3815393 1 NC_003911.11 identified by similarity to GB:AAB58884.1; match to protein family HMM TIGR01588; malyl-CoA lyase 3815393 mclA 3196324 mclA Ruegeria pomeroyi DSS-3 malyl-CoA lyase YP_168803.1 3814431 D 246200 CDS YP_168804.1 56698430 3196265 complement(3815439..3816221) 1 NC_003911.11 identified by similarity to SP:P50197; match to protein family HMM PF00106; short chain dehydrogenase 3816221 linC-2 3196265 linC-2 Ruegeria pomeroyi DSS-3 short chain dehydrogenase YP_168804.1 3815439 R 246200 CDS YP_168805.1 56698431 3195086 3816353..3816985 1 NC_003911.11 identified by similarity to GB:BAC74958.1; hypothetical protein 3816985 3195086 SPO3610 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168805.1 3816353 D 246200 CDS YP_168806.1 56698432 3195444 complement(3817034..3817615) 1 NC_003911.11 hypothetical protein 3817615 3195444 SPO3611 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168806.1 3817034 R 246200 CDS YP_168807.1 56698433 3193904 complement(3817745..3818197) 1 NC_003911.11 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 3818197 3193904 SPO3612 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_168807.1 3817745 R 246200 CDS YP_168808.1 56698434 3196383 3818270..3818866 1 NC_003911.11 identified by match to protein family HMM PF01810; amino acid transporter LysE 3818866 3196383 SPO3613 Ruegeria pomeroyi DSS-3 amino acid transporter LysE YP_168808.1 3818270 D 246200 CDS YP_168809.1 56698435 3195416 complement(3818863..3818982) 1 NC_003911.11 hypothetical protein 3818982 3195416 SPO3614 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168809.1 3818863 R 246200 CDS YP_168810.1 56698436 3195030 complement(3819351..3820181) 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM PF06445; AraC family transcriptional regulator 3820181 3195030 SPO3615 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_168810.1 3819351 R 246200 CDS YP_168811.1 56698437 3193834 3820304..3821266 1 NC_003911.11 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein; acetyl-CoA carboxylase carboxyltransferase subunit alpha 3821266 accA 3193834 accA Ruegeria pomeroyi DSS-3 acetyl-CoA carboxylase carboxyltransferase subunit alpha YP_168811.1 3820304 D 246200 CDS YP_168812.1 56698438 3194686 complement(3821354..3822511) 1 NC_003911.11 identified by match to protein family HMM PF01471; peptidoglycan-binding protein 3822511 3194686 SPO3617 Ruegeria pomeroyi DSS-3 peptidoglycan-binding protein YP_168812.1 3821354 R 246200 CDS YP_168813.1 56698439 3195768 complement(3822554..3823342) 1 NC_003911.11 identified by similarity to SP:P75851; similarity to SP:Q47539; match to protein family HMM PF00528; sulfonate ABC transporter permease 3823342 3195768 SPO3618 Ruegeria pomeroyi DSS-3 sulfonate ABC transporter permease YP_168813.1 3822554 R 246200 CDS YP_168814.1 56698440 3196104 complement(3823335..3824102) 1 NC_003911.11 identified by match to protein family HMM PF00005; sulfonate ABC transporter ATP-binding protein 3824102 3196104 SPO3619 Ruegeria pomeroyi DSS-3 sulfonate ABC transporter ATP-binding protein YP_168814.1 3823335 R 246200 CDS YP_168815.1 56698441 3194797 complement(3824109..3825125) 1 NC_003911.11 sulfonate ABC transporter periplamic sulfonate-binding protein 3825125 3194797 SPO3620 Ruegeria pomeroyi DSS-3 sulfonate ABC transporter periplamic sulfonate-binding protein YP_168815.1 3824109 R 246200 CDS YP_168816.1 56698442 3195319 complement(3825195..3825842) 1 NC_003911.11 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 3825842 3195319 SPO3621 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_168816.1 3825195 R 246200 CDS YP_168817.1 56698443 3196085 complement(3825873..3826613) 1 NC_003911.11 identified by similarity to GB:BAC46174.1; match to protein family HMM PF01863; hypothetical protein 3826613 3196085 SPO3622 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168817.1 3825873 R 246200 CDS YP_168818.1 56698444 3195261 3826669..3826995 1 NC_003911.11 identified by similarity to GB:CAE25504.1; hypothetical protein 3826995 3195261 SPO3623 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168818.1 3826669 D 246200 CDS YP_168819.1 56698445 3195668 complement(3827599..3827805) 1 NC_003911.11 identified by similarity to SP:P15277; match to protein family HMM PF00313; cold shock protein CspA 3827805 cspA 3195668 cspA Ruegeria pomeroyi DSS-3 cold shock protein CspA YP_168819.1 3827599 R 246200 CDS YP_168820.1 56698446 3195399 complement(3828329..3829699) 1 NC_003911.11 identified by match to protein family HMM PF04107; match to protein family HMM TIGR01436; glutamate--cysteine ligase 3829699 gshA 3195399 gshA Ruegeria pomeroyi DSS-3 glutamate--cysteine ligase YP_168820.1 3828329 R 246200 CDS YP_168821.1 56698447 3194923 complement(3829840..3830367) 1 NC_003911.11 hypothetical protein 3830367 3194923 SPO3627 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168821.1 3829840 R 246200 CDS YP_168822.1 56698448 3195003 complement(3830364..3831209) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3831209 3195003 SPO3628 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168822.1 3830364 R 246200 CDS YP_168823.1 56698449 3195522 complement(3831203..3831958) 1 NC_003911.11 in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase; 16S ribosomal RNA methyltransferase RsmE 3831958 3195522 SPO3629 Ruegeria pomeroyi DSS-3 16S ribosomal RNA methyltransferase RsmE YP_168823.1 3831203 R 246200 CDS YP_168824.1 56698450 3195348 3831971..3832933 1 NC_003911.11 UbiA prenyltransferase catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin; 4-hydroxybenzoate polyprenyltransferase 3832933 ubiA 3195348 ubiA Ruegeria pomeroyi DSS-3 4-hydroxybenzoate polyprenyltransferase YP_168824.1 3831971 D 246200 CDS YP_168825.1 56698451 3195121 3832996..3834909 1 NC_003911.11 identified by match to protein family HMM PF00691; OmpA domain-containing protein 3834909 3195121 SPO3631 Ruegeria pomeroyi DSS-3 OmpA domain-containing protein YP_168825.1 3832996 D 246200 CDS YP_168826.1 56698452 3193781 3834910..3835221 1 NC_003911.11 identified by similarity to GB:BAC45762.1; hypothetical protein 3835221 3193781 SPO3632 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168826.1 3834910 D 246200 CDS YP_168827.1 56698453 3193568 complement(3835239..3835682) 1 NC_003911.11 identified by similarity to SP:P30749; match to protein family HMM PF02391; molybdopterin converting factor subunit 2 3835682 3193568 SPO3633 Ruegeria pomeroyi DSS-3 molybdopterin converting factor subunit 2 YP_168827.1 3835239 R 246200 CDS YP_168828.1 56698454 3196025 complement(3835688..3835933) 1 NC_003911.11 identified by match to protein family HMM PF02597; match to protein family HMM TIGR01682; molybdopterin converting factor subunit 1 3835933 moaD 3196025 moaD Ruegeria pomeroyi DSS-3 molybdopterin converting factor subunit 1 YP_168828.1 3835688 R 246200 CDS YP_168829.1 56698455 3196000 complement(3835933..3836604) 1 NC_003911.11 identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 3836604 pgsA 3196000 pgsA Ruegeria pomeroyi DSS-3 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase YP_168829.1 3835933 R 246200 CDS YP_168830.1 56698456 3196366 complement(3836662..3837822) 1 NC_003911.11 beta-lactamase 3837822 3196366 SPO3636 Ruegeria pomeroyi DSS-3 beta-lactamase YP_168830.1 3836662 R 246200 CDS YP_168831.1 56698457 3196156 complement(3837874..3839745) 1 NC_003911.11 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision; excinuclease ABC subunit C 3839745 uvrC 3196156 uvrC Ruegeria pomeroyi DSS-3 excinuclease ABC subunit C YP_168831.1 3837874 R 246200 CDS YP_168832.1 56698458 3196048 complement(3840036..3840815) 1 NC_003911.11 identified by match to protein family HMM PF00106; short chain dehydrogenase 3840815 3196048 SPO3638 Ruegeria pomeroyi DSS-3 short chain dehydrogenase YP_168832.1 3840036 R 246200 CDS YP_168833.1 56698459 3195871 complement(3840842..3841801) 1 NC_003911.11 identified by match to protein family HMM PF01699; match to protein family HMM TIGR00367; K+-dependent Na+/Ca+ exchanger-like protein 3841801 3195871 SPO3639 Ruegeria pomeroyi DSS-3 K+-dependent Na+/Ca+ exchanger-like protein YP_168833.1 3840842 R 246200 CDS YP_168834.1 56698460 3195166 complement(3841970..3842815) 1 NC_003911.11 identified by match to protein family HMM PF01343; S49 family peptidase 3842815 3195166 SPO3640 Ruegeria pomeroyi DSS-3 S49 family peptidase YP_168834.1 3841970 R 246200 CDS YP_168835.1 56698461 3196212 complement(3842881..3843642) 1 NC_003911.11 identified by similarity to SP:P36880; ABC transporter permease 3843642 3196212 SPO3641 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_168835.1 3842881 R 246200 CDS YP_168836.1 56698462 3195894 complement(3843639..3844568) 1 NC_003911.11 identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 3844568 3195894 SPO3642 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_168836.1 3843639 R 246200 CDS YP_168837.1 56698722 3196316 complement(3844641..3845153) 1 NC_003911.11 identified by similarity to GB:CAB76249.1; match to protein family HMM PF06240; carbon monoxide dehydrogenase G protein 3845153 3196316 SPO3901 Ruegeria pomeroyi DSS-3 carbon monoxide dehydrogenase G protein YP_168837.1 3844641 R 246200 CDS YP_168838.1 56698463 3194480 3845301..3846281 1 NC_003911.11 identified by similarity to GB:CAE33392.1; match to protein family HMM PF00892; hypothetical protein 3846281 3194480 SPO3643 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168838.1 3845301 D 246200 CDS YP_168839.1 56698464 3192923 complement(3846595..3847509) 1 NC_003911.11 identified by similarity to GB:AAM35804.1; hypothetical protein 3847509 3192923 SPO3644 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168839.1 3846595 R 246200 CDS YP_168840.1 56698465 3193933 3847588..3848028 1 NC_003911.11 identified by match to protein family HMM PF01638; transcriptional regulator 3848028 3193933 SPO3645 Ruegeria pomeroyi DSS-3 transcriptional regulator YP_168840.1 3847588 D 246200 CDS YP_168841.1 56698466 3194778 complement(3848025..3848954) 1 NC_003911.11 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 3848954 3194778 SPO3646 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_168841.1 3848025 R 246200 CDS YP_168842.1 56698467 3194974 3849022..3850116 1 NC_003911.11 identified by match to protein family HMM PF02515; CAIB/BAIF family protein 3850116 3194974 SPO3647 Ruegeria pomeroyi DSS-3 CAIB/BAIF family protein YP_168842.1 3849022 D 246200 CDS YP_168843.1 56698468 3196442 complement(3850181..3851215) 1 NC_003911.11 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase 3851215 hemE 3196442 hemE Ruegeria pomeroyi DSS-3 uroporphyrinogen decarboxylase YP_168843.1 3850181 R 246200 CDS YP_168844.1 56698469 3195060 3851322..3852281 1 NC_003911.11 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase 3852281 hemC 3195060 hemC Ruegeria pomeroyi DSS-3 porphobilinogen deaminase YP_168844.1 3851322 D 246200 CDS YP_168845.1 56698470 3195061 3852371..3854143 1 NC_003911.11 identified by match to protein family HMM PF00211; guanylate cyclase 3854143 3195061 SPO3650 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_168845.1 3852371 D 246200 CDS YP_168846.1 56698471 3195064 3854207..3855151 1 NC_003911.11 identified by match to protein family HMM PF00487; fatty acid desaturase 3855151 3195064 SPO3651 Ruegeria pomeroyi DSS-3 fatty acid desaturase YP_168846.1 3854207 D 246200 CDS YP_168847.1 56698472 3196386 3855136..3855669 1 NC_003911.11 hypothetical protein 3855669 3196386 SPO3652 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168847.1 3855136 D 246200 CDS YP_168848.1 56698473 3193274 complement(3855759..3856643) 1 NC_003911.11 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase 3856643 hemF 3193274 hemF Ruegeria pomeroyi DSS-3 coproporphyrinogen III oxidase YP_168848.1 3855759 R 246200 CDS YP_168849.1 56698474 3194427 complement(3856655..3857455) 1 NC_003911.11 identified by similarity to SP:P25529; match to protein family HMM PF00106; 7-alpha-hydroxysteroid dehydrogenase 3857455 3194427 SPO3654 Ruegeria pomeroyi DSS-3 7-alpha-hydroxysteroid dehydrogenase YP_168849.1 3856655 R 246200 CDS YP_168850.1 56698475 3195139 complement(3857493..3858458) 1 NC_003911.11 identified by match to protein family HMM PF05175; methyltransferase 3858458 3195139 SPO3655 Ruegeria pomeroyi DSS-3 methyltransferase YP_168850.1 3857493 R 246200 CDS YP_168851.1 56698476 3193650 complement(3858504..3858845) 1 NC_003911.11 identified by match to protein family HMM PF02617; ATP-dependent Clp protease, adaptor protein ClpS 3858845 clpS 3193650 clpS Ruegeria pomeroyi DSS-3 ATP-dependent Clp protease, adaptor protein ClpS YP_168851.1 3858504 R 246200 CDS YP_168852.1 56698477 3196402 3858909..3859637 1 NC_003911.11 identified by match to protein family HMM PF00702; HAD superfamily hydrolase 3859637 3196402 SPO3657 Ruegeria pomeroyi DSS-3 HAD superfamily hydrolase YP_168852.1 3858909 D 246200 CDS YP_168853.1 56698478 3193913 3859896..3861329 1 NC_003911.11 identified by match to protein family HMM PF00768; D-alanyl-D-alanine carboxypeptidase 3861329 3193913 SPO3658 Ruegeria pomeroyi DSS-3 D-alanyl-D-alanine carboxypeptidase YP_168853.1 3859896 D 246200 CDS YP_168854.1 56698479 3194258 complement(3861401..3862162) 1 NC_003911.11 identified by match to protein family HMM PF03746; LamB/YcsF family protein 3862162 3194258 SPO3659 Ruegeria pomeroyi DSS-3 LamB/YcsF family protein YP_168854.1 3861401 R 246200 CDS YP_168855.1 56698480 3194264 complement(3862173..3863171) 1 NC_003911.11 urea amidolyase 3863171 3194264 SPO3660 Ruegeria pomeroyi DSS-3 urea amidolyase YP_168855.1 3862173 R 246200 CDS YP_168856.1 56698481 3195969 complement(3863168..3863917) 1 NC_003911.11 identified by match to protein family HMM PF02682; allophanate hydrolase 3863917 3195969 SPO3661 Ruegeria pomeroyi DSS-3 allophanate hydrolase YP_168856.1 3863168 R 246200 CDS YP_168857.1 56698482 3196103 complement(3863904..3864824) 1 NC_003911.11 hypothetical protein 3864824 3196103 SPO3662 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168857.1 3863904 R 246200 CDS YP_168858.1 56698483 3196249 complement(3864852..3866165) 1 NC_003911.11 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM 3866165 3196249 SPO3663 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_168858.1 3864852 R 246200 CDS YP_168859.1 56698484 3195571 complement(3866172..3866705) 1 NC_003911.11 hypothetical protein 3866705 3195571 SPO3664 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168859.1 3866172 R 246200 CDS YP_168860.1 56698485 3193540 complement(3866786..3867760) 1 NC_003911.11 identified by match to protein family HMM PF03480; solute-binding family 7 protein 3867760 3193540 SPO3665 Ruegeria pomeroyi DSS-3 solute-binding family 7 protein YP_168860.1 3866786 R 246200 CDS YP_168861.1 56698486 3195066 complement(3867798..3869063) 1 NC_003911.11 identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding 3869063 3195066 SPO3666 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_168861.1 3867798 R 246200 CDS YP_168862.1 56698487 3194959 complement(3869173..3870303) 1 NC_003911.11 identified by similarity to PIR:T48870; match to protein family HMM PF01188; match to protein family HMM PF02746; muconate cycloisomerase I 3870303 catB 3194959 catB Ruegeria pomeroyi DSS-3 muconate cycloisomerase I YP_168862.1 3869173 R 246200 CDS YP_168863.1 56698488 3193036 3870403..3871320 1 NC_003911.11 identified by similarity to SP:P03030; match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3871320 3193036 SPO3668 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168863.1 3870403 D 246200 CDS YP_168864.1 56698723 3196106 3871988..3872626 1 NC_003911.11 identified by similarity to SP:P02918; match to protein family HMM PF00912; transglycosylase domain-containing protein 3872626 3196106 SPO3902 Ruegeria pomeroyi DSS-3 transglycosylase domain-containing protein YP_168864.1 3871988 D 246200 CDS YP_168865.1 56698489 3194575 complement(3872480..3872593) 1 NC_003911.11 hypothetical protein 3872593 3194575 SPO3670 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168865.1 3872480 R 246200 CDS YP_168866.1 56698490 3193681 3873719..3875380 1 NC_003911.11 identified by match to protein family HMM PF00394; match to protein family HMM TIGR01409; muticopper oxidase domain-containing protein 3875380 3193681 SPO3671 Ruegeria pomeroyi DSS-3 muticopper oxidase domain-containing protein YP_168866.1 3873719 D 246200 CDS YP_168867.1 56698491 3195467 3875377..3875853 1 NC_003911.11 hypothetical protein 3875853 3195467 SPO3672 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168867.1 3875377 D 246200 CDS YP_168868.1 56698492 3193854 complement(3876050..3882544) 1 NC_003911.11 identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 3882544 3193854 SPO3673 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_168868.1 3876050 R 246200 CDS YP_168869.1 56698493 3195496 3883357..3883926 1 NC_003911.11 identified by match to protein family HMM PF01609; ISSpo7, transposase 3883926 3195496 SPO3674 Ruegeria pomeroyi DSS-3 ISSpo7, transposase YP_168869.1 3883357 D 246200 CDS YP_168870.1 56698494 3195718 3884095..3884751 1 NC_003911.11 identified by similarity to PIR:AB0616; hypothetical protein 3884751 3195718 SPO3675 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168870.1 3884095 D 246200 CDS YP_168871.1 56698495 3193430 complement(3885158..3886303) 1 NC_003911.11 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase 3886303 argE-2 3193430 argE-2 Ruegeria pomeroyi DSS-3 acetylornithine deacetylase YP_168871.1 3885158 R 246200 CDS YP_168872.1 56698496 3193521 complement(3886300..3887235) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3887235 3193521 SPO3677 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168872.1 3886300 R 246200 CDS YP_168873.1 56698497 3196039 complement(3887290..3888399) 1 NC_003911.11 identified by match to protein family HMM PF00355; Rieske (2Fe-2S) domain-containing protein 3888399 3196039 SPO3678 Ruegeria pomeroyi DSS-3 Rieske (2Fe-2S) domain-containing protein YP_168873.1 3887290 R 246200 CDS YP_168874.1 56698498 3194074 complement(3888425..3889099) 1 NC_003911.11 identified by similarity to PIR:C82973; match to protein family HMM PF06267; hypothetical protein 3889099 3194074 SPO3679 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168874.1 3888425 R 246200 CDS YP_168875.1 56698499 3195750 complement(3889104..3889520) 1 NC_003911.11 identified by match to protein family HMM PF01042; endoribonuclease L-PSP 3889520 3195750 SPO3680 Ruegeria pomeroyi DSS-3 endoribonuclease L-PSP YP_168875.1 3889104 R 246200 CDS YP_168876.1 56698500 3194623 complement(3889522..3890664) 1 NC_003911.11 identified by match to protein family HMM PF00355; Rieske (2Fe-2S) domain-containing protein 3890664 3194623 SPO3681 Ruegeria pomeroyi DSS-3 Rieske (2Fe-2S) domain-containing protein YP_168876.1 3889522 R 246200 CDS YP_168877.1 56698501 3194826 3890849..3892123 1 NC_003911.11 identified by similarity to GB:CAE35157.1; hypothetical protein 3892123 3194826 SPO3682 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168877.1 3890849 D 246200 CDS YP_168878.1 56698502 3196203 3892715..3893740 1 NC_003911.11 identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcriptional regulator 3893740 3196203 SPO3684 Ruegeria pomeroyi DSS-3 LacI family transcriptional regulator YP_168878.1 3892715 D 246200 CDS YP_168879.1 56698503 3196198 3893745..3894959 1 NC_003911.11 identified by similarity to PIR:H97450; match to protein family HMM PF06224; hypothetical protein 3894959 3196198 SPO3685 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168879.1 3893745 D 246200 CDS YP_168880.1 56698504 3193646 complement(3895050..3895820) 1 NC_003911.11 identified by match to protein family HMM PF03328; HpcH/HpaI aldolase 3895820 3193646 SPO3686 Ruegeria pomeroyi DSS-3 HpcH/HpaI aldolase YP_168880.1 3895050 R 246200 CDS YP_168881.1 56698505 3196210 complement(3895885..3897294) 1 NC_003911.11 identified by match to protein family HMM PF00282; decarboxylase, pyridoxal-dependent 3897294 3196210 SPO3687 Ruegeria pomeroyi DSS-3 decarboxylase, pyridoxal-dependent YP_168881.1 3895885 R 246200 CDS YP_168882.1 56698506 3194557 complement(3897316..3898296) 1 NC_003911.11 identified by match to protein family HMM PF00903; extradiol ring-cleavage dioxygenase 3898296 3194557 SPO3688 Ruegeria pomeroyi DSS-3 extradiol ring-cleavage dioxygenase YP_168882.1 3897316 R 246200 CDS YP_168883.1 56698507 3193640 3898392..3898880 1 NC_003911.11 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 3898880 3193640 SPO3689 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_168883.1 3898392 D 246200 CDS YP_168884.1 56698508 3196199 3899365..3900399 1 NC_003911.11 identified by similarity to GB:CAA12267.1; gentisate 1,2-dioxygenase 3900399 gtdA-1 3196199 gtdA-1 Ruegeria pomeroyi DSS-3 gentisate 1,2-dioxygenase YP_168884.1 3899365 D 246200 CDS YP_168885.1 56698509 3194849 3900396..3901094 1 NC_003911.11 identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase 3901094 3194849 SPO3691 Ruegeria pomeroyi DSS-3 fumarylacetoacetate hydrolase YP_168885.1 3900396 D 246200 CDS YP_168886.1 56698510 3194832 3901098..3902285 1 NC_003911.11 catalyzes the formation of catechol from salicylate; salicylate hydroxylase 3902285 3194832 SPO3692 Ruegeria pomeroyi DSS-3 salicylate hydroxylase YP_168886.1 3901098 D 246200 CDS YP_168887.1 56698511 3193774 3902323..3903423 1 NC_003911.11 identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 3903423 3193774 SPO3693 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctP YP_168887.1 3902323 D 246200 CDS YP_168888.1 56698512 3196177 3903497..3904081 1 NC_003911.11 identified by similarity to GB:AAK03610.1; hypothetical protein 3904081 3196177 SPO3694 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168888.1 3903497 D 246200 CDS YP_168889.1 56698513 3196137 3904078..3905577 1 NC_003911.11 identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM 3905577 3196137 SPO3695 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter subunit DctM YP_168889.1 3904078 D 246200 CDS YP_168890.1 56698514 3192902 3905730..3907436 1 NC_003911.11 catalyzes the conversion of ferulic acid to feruloyl-CoA; feruloyl-CoA synthase 3907436 fcs 3192902 fcs Ruegeria pomeroyi DSS-3 feruloyl-CoA synthase YP_168890.1 3905730 D 246200 CDS YP_168891.1 56698515 3195888 3907583..3909112 1 NC_003911.11 identified by similarity to GB:AAA92151.1; match to protein family HMM PF00501; benzoate-coenzyme A ligase 3909112 badA-1 3195888 badA-1 Ruegeria pomeroyi DSS-3 benzoate-coenzyme A ligase YP_168891.1 3907583 D 246200 CDS YP_168892.1 56698516 3195257 3909116..3909931 1 NC_003911.11 identified by similarity to GB:BAC55927.1; hydrolase 3909931 3195257 SPO3698 Ruegeria pomeroyi DSS-3 hydrolase YP_168892.1 3909116 D 246200 CDS YP_168893.1 56698517 3195506 3909935..3910378 1 NC_003911.11 identified by similarity to GB:BAC46344.1; hypothetical protein 3910378 3195506 SPO3699 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168893.1 3909935 D 246200 CDS YP_168894.1 56698518 3195411 3910527..3912188 1 NC_003911.11 cleaves the ring of 2,3-dihydro-2,3-dihydroxybenzoyl-CoA forming 6-hydroxy-3-hexenoyl-CoA; benzoyl-CoA-dihydrodiol lyase 3912188 3195411 SPO3700 Ruegeria pomeroyi DSS-3 benzoyl-CoA-dihydrodiol lyase YP_168894.1 3910527 D 246200 CDS YP_168895.1 56698519 3196248 3912263..3913714 1 NC_003911.11 identified by similarity to GB:AAN39376.1; benzoyl-CoA oxygenase subunit B 3913714 boxB 3196248 boxB Ruegeria pomeroyi DSS-3 benzoyl-CoA oxygenase subunit B YP_168895.1 3912263 D 246200 CDS YP_168896.1 56698520 3196393 3913770..3914012 1 NC_003911.11 hypothetical protein 3914012 3196393 SPO3702 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168896.1 3913770 D 246200 CDS YP_168897.1 56698521 3196404 3914075..3915193 1 NC_003911.11 identified by similarity to GB:AAN39377.1; match to protein family HMM PF00037; match to protein family HMM PF00175; benzoyl-CoA oxygenase, A subunit 3915193 boxA 3196404 boxA Ruegeria pomeroyi DSS-3 benzoyl-CoA oxygenase, A subunit YP_168897.1 3914075 D 246200 CDS YP_168898.1 56698522 3194289 3915279..3916196 1 NC_003911.11 consists of N-terminal helix-turn-helix domain and C-terminal shikimate kinase-like domain which may bind benzoyl-CoA; controls inducible expression of the bzd catabolic operon that is involved in the anaerobic catabolism of benzoate; anaerobic benzoate catabolism transcriptional regulator 3916196 3194289 SPO3704 Ruegeria pomeroyi DSS-3 anaerobic benzoate catabolism transcriptional regulator YP_168898.1 3915279 D 246200 CDS YP_168899.1 56698523 3193699 3916388..3917563 1 NC_003911.11 identified by similarity to GB:AAP25826.1; match to protein family HMM PF01094; branched-chain amino acid ABC transporter periplasmic branched-chain amino acid-binding protein 3917563 3193699 SPO3705 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter periplasmic branched-chain amino acid-binding protein YP_168899.1 3916388 D 246200 CDS YP_168900.1 56698524 3193008 3917634..3918398 1 NC_003911.11 identified by similarity to GB:CAE29839.1; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 3918398 3193008 SPO3706 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_168900.1 3917634 D 246200 CDS YP_168901.1 56698525 3196405 3918391..3919113 1 NC_003911.11 identified by similarity to SP:P30294; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 3919113 3196405 SPO3707 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter ATP-binding protein YP_168901.1 3918391 D 246200 CDS YP_168902.1 56698526 3194208 3919174..3920205 1 NC_003911.11 identified by similarity to GB:AAP25830.1; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 3920205 3194208 SPO3708 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_168902.1 3919174 D 246200 CDS YP_168903.1 56698527 3194531 3920202..3921254 1 NC_003911.11 identified by similarity to GB:CAE29842.1; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 3921254 3194531 SPO3709 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter permease YP_168903.1 3920202 D 246200 CDS YP_168904.1 56698528 3193554 complement(3921251..3922396) 1 NC_003911.11 identified by similarity to GB:BAC53043.1; hypothetical protein 3922396 3193554 SPO3710 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168904.1 3921251 R 246200 CDS YP_168905.1 56698529 3193301 3922533..3923705 1 NC_003911.11 hypothetical protein 3923705 3193301 SPO3711 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168905.1 3922533 D 246200 CDS YP_168906.1 56698530 3196409 3923789..3924811 1 NC_003911.11 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase 3924811 asd 3196409 asd Ruegeria pomeroyi DSS-3 aspartate-semialdehyde dehydrogenase YP_168906.1 3923789 D 246200 CDS YP_168907.1 56698531 3192844 3925765..3927429 1 NC_003911.11 identified by similarity to GB:CAC38742.1; hypothetical protein 3927429 3192844 SPO3713 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168907.1 3925765 D 246200 CDS YP_168908.1 56698532 3193818 complement(3927398..3927877) 1 NC_003911.11 hypothetical protein 3927877 3193818 SPO3714 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168908.1 3927398 R 246200 CDS YP_168909.1 56698533 3194874 complement(3927921..3928571) 1 NC_003911.11 identified by similarity to SP:P17067; match to protein family HMM PF00484; carbonic anhydrase 3928571 3194874 SPO3715 Ruegeria pomeroyi DSS-3 carbonic anhydrase YP_168909.1 3927921 R 246200 CDS YP_168910.1 56698534 3196411 3928730..3929113 1 NC_003911.11 hypothetical protein 3929113 3196411 SPO3716 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168910.1 3928730 D 246200 CDS YP_168911.1 56698535 3193900 3929171..3930568 1 NC_003911.11 identified by match to protein family HMM PF00883; cytosol aminopeptidase 3930568 3193900 SPO3717 Ruegeria pomeroyi DSS-3 cytosol aminopeptidase YP_168911.1 3929171 D 246200 CDS YP_168912.1 56698536 3196410 3930565..3931314 1 NC_003911.11 identified by match to protein family HMM PF00877; NLP/P60 family protein 3931314 3196410 SPO3718 Ruegeria pomeroyi DSS-3 NLP/P60 family protein YP_168912.1 3930565 D 246200 CDS YP_168913.1 56698537 3196413 3931367..3932221 1 NC_003911.11 identified by similarity to PIR:T52663; match to protein family HMM PF00581; thiosulfate sulfurtransferase 3932221 3196413 SPO3719 Ruegeria pomeroyi DSS-3 thiosulfate sulfurtransferase YP_168913.1 3931367 D 246200 CDS YP_168914.1 56698538 3196414 3932221..3933405 1 NC_003911.11 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate; aromatic amino acid aminotransferase 3933405 tyrB 3196414 tyrB Ruegeria pomeroyi DSS-3 aromatic amino acid aminotransferase YP_168914.1 3932221 D 246200 CDS YP_168915.1 56698539 3193101 complement(3933458..3934099) 1 NC_003911.11 hypothetical protein 3934099 3193101 SPO3721 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168915.1 3933458 R 246200 CDS YP_168916.1 56698540 3196421 complement(3934096..3934614) 1 NC_003911.11 identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738; Rrf2 family protein 3934614 3196421 SPO3722 Ruegeria pomeroyi DSS-3 Rrf2 family protein YP_168916.1 3934096 R 246200 CDS YP_168917.1 56698541 3196423 complement(3934721..3936049) 1 NC_003911.11 identified by match to protein family HMM PF00909; match to protein family HMM TIGR00836; ammonium transporter 3936049 amt-2 3196423 amt-2 Ruegeria pomeroyi DSS-3 ammonium transporter YP_168917.1 3934721 R 246200 CDS YP_168918.1 56698542 3196220 complement(3936085..3936423) 1 NC_003911.11 identified by match to protein family HMM PF00543; nitrogen regulatory protein P-II 3936423 glnB-2 3196220 glnB-2 Ruegeria pomeroyi DSS-3 nitrogen regulatory protein P-II YP_168918.1 3936085 R 246200 CDS YP_168919.1 56698543 3196245 3936457..3938823 1 NC_003911.11 identified by match to protein family HMM PF00905; match to protein family HMM PF00912; match to protein family HMM TIGR02074; 1A family penicillin-binding protein 3938823 3196245 SPO3725 Ruegeria pomeroyi DSS-3 1A family penicillin-binding protein YP_168919.1 3936457 D 246200 CDS YP_168920.1 56698544 3196432 complement(3938846..3939454) 1 NC_003911.11 identified by match to protein family HMM PF05494; match to protein family HMM TIGR01409; toluene tolerance family protein 3939454 3196432 SPO3726 Ruegeria pomeroyi DSS-3 toluene tolerance family protein YP_168920.1 3938846 R 246200 CDS YP_168921.1 56698545 3196437 complement(3939444..3940250) 1 NC_003911.11 identified by similarity to SP:P43262; match to protein family HMM PF04333; VacJ lipoprotein 3940250 3196437 SPO3727 Ruegeria pomeroyi DSS-3 VacJ lipoprotein YP_168921.1 3939444 R 246200 CDS YP_168922.1 56698546 3196436 3940449..3942182 1 NC_003911.11 identified by match to protein family HMM PF00005; match to protein family HMM PF00664; match to protein family HMM TIGR01842; type I secretion system ATPase 3942182 3196436 SPO3728 Ruegeria pomeroyi DSS-3 type I secretion system ATPase YP_168922.1 3940449 D 246200 CDS YP_168923.1 56698547 3196438 3942179..3943480 1 NC_003911.11 identified by match to protein family HMM PF00529; match to protein family HMM TIGR01843; HlyD family type I secretion membrane fusion protein 3943480 3196438 SPO3729 Ruegeria pomeroyi DSS-3 HlyD family type I secretion membrane fusion protein YP_168923.1 3942179 D 246200 CDS YP_168924.1 56698548 3196440 3943553..3944011 1 NC_003911.11 identified by match to protein family HMM PF01042; endoribonuclease L-PSP 3944011 3196440 SPO3730 Ruegeria pomeroyi DSS-3 endoribonuclease L-PSP YP_168924.1 3943553 D 246200 CDS YP_168925.1 56698549 3196444 3944008..3944766 1 NC_003911.11 identified by similarity to SP:P10908; match to protein family HMM PF03009; glycerophosphoryl diester phosphodiesterase 3944766 3196444 SPO3731 Ruegeria pomeroyi DSS-3 glycerophosphoryl diester phosphodiesterase YP_168925.1 3944008 D 246200 CDS YP_168926.1 56698550 3196388 3944810..3945997 1 NC_003911.11 identified by similarity to GB:CAC46070.1; match to protein family HMM PF04339; hypothetical protein 3945997 3196388 SPO3732 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168926.1 3944810 D 246200 CDS YP_168927.1 56698551 3196447 3945994..3946287 1 NC_003911.11 4-alpha-hydroxytetrahydrobiopterin dehydratase activity; catalyzes the formation of (6R)-6-(L-erythro-1,2-dihydroxypropyl)-7, 8-dihydro-6H-pterin from (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7, 8-tetrahydro-4a-hydroxypterin; functions in recycling tetrahydrobiopterin (BH4) in phenylalanine hydroxylase reaction; pterin-4-alpha-carbinolamine dehydratase 3946287 phhB 3196447 phhB Ruegeria pomeroyi DSS-3 pterin-4-alpha-carbinolamine dehydratase YP_168927.1 3945994 D 246200 CDS YP_168928.1 56698552 3196448 complement(3946284..3946706) 1 NC_003911.11 identified by match to protein family HMM PF00376; MerR family transcriptional regulator 3946706 3196448 SPO3734 Ruegeria pomeroyi DSS-3 MerR family transcriptional regulator YP_168928.1 3946284 R 246200 CDS YP_168929.1 56698553 3196449 3946774..3947994 1 NC_003911.11 identified by similarity to SP:P21191; match to protein family HMM PF00083; major facilitator family protein 3947994 3196449 SPO3735 Ruegeria pomeroyi DSS-3 major facilitator family protein YP_168929.1 3946774 D 246200 CDS YP_168930.1 56698554 3196451 complement(3947999..3948484) 1 NC_003911.11 identified by match to protein family HMM PF00578; anti-oxidant AhpCTSA family protein 3948484 3196451 SPO3736 Ruegeria pomeroyi DSS-3 anti-oxidant AhpCTSA family protein YP_168930.1 3947999 R 246200 CDS YP_168931.1 56698555 3193821 3948583..3949794 1 NC_003911.11 identified by match to protein family HMM PF00070; pyridine nucleotide-disulfide oxidoreductase 3949794 3193821 SPO3737 Ruegeria pomeroyi DSS-3 pyridine nucleotide-disulfide oxidoreductase YP_168931.1 3948583 D 246200 CDS YP_168932.1 56698556 3194252 3949791..3950351 1 NC_003911.11 identified by match to protein family HMM PF03602; match to protein family HMM TIGR00095; methyltransferase 3950351 3194252 SPO3738 Ruegeria pomeroyi DSS-3 methyltransferase YP_168932.1 3949791 D 246200 CDS YP_168933.1 56698557 3195777 3950451..3952454 1 NC_003911.11 identified by match to protein family HMM PF01968; match to protein family HMM PF05378; hydantoinase/oxoprolinase 3952454 3195777 SPO3739 Ruegeria pomeroyi DSS-3 hydantoinase/oxoprolinase YP_168933.1 3950451 D 246200 CDS YP_168934.1 56698558 3195621 complement(3952494..3953006) 1 NC_003911.11 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress; methionine sulfoxide reductase A 3953006 msrA-2 3195621 msrA-2 Ruegeria pomeroyi DSS-3 methionine sulfoxide reductase A YP_168934.1 3952494 R 246200 CDS YP_168935.1 56698559 3193237 complement(3953003..3953452) 1 NC_003911.11 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress; methionine sulfoxide reductase B 3953452 msrB 3193237 msrB Ruegeria pomeroyi DSS-3 methionine sulfoxide reductase B YP_168935.1 3953003 R 246200 CDS YP_168936.1 56698560 3193573 3953594..3954115 1 NC_003911.11 identified by match to protein family HMM PF00255; glutathione peroxidase 3954115 3193573 SPO3742 Ruegeria pomeroyi DSS-3 glutathione peroxidase YP_168936.1 3953594 D 246200 CDS YP_168937.1 56698561 3194042 complement(3954112..3954990) 1 NC_003911.11 identified by match to protein family HMM PF00892; hypothetical protein 3954990 3194042 SPO3743 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168937.1 3954112 R 246200 CDS YP_168938.1 56698562 3195809 complement(3955186..3955461) 1 NC_003911.11 identified by match to protein family HMM PF00216; DNA-binding protein HU 3955461 hup 3195809 hup Ruegeria pomeroyi DSS-3 DNA-binding protein HU YP_168938.1 3955186 R 246200 CDS YP_168939.1 56698563 3196458 complement(3955606..3957069) 1 NC_003911.11 Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile; AMP nucleosidase 3957069 amn 3196458 amn Ruegeria pomeroyi DSS-3 AMP nucleosidase YP_168939.1 3955606 R 246200 CDS YP_168940.1 56698564 3195819 complement(3957066..3958844) 1 NC_003911.11 identified by similarity to SP:P39761; match to protein family HMM PF01979; match to protein family HMM TIGR01178; adenine deaminase 3958844 ade 3195819 ade Ruegeria pomeroyi DSS-3 adenine deaminase YP_168940.1 3957066 R 246200 CDS YP_168941.1 56698565 3196465 3958990..3959418 1 NC_003911.11 identified by similarity to GB:AAQ59692.1; hypothetical protein 3959418 3196465 SPO3747 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168941.1 3958990 D 246200 CDS YP_168942.1 56698566 3196467 complement(3959512..3960384) 1 NC_003911.11 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3960384 3196467 SPO3748 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168942.1 3959512 R 246200 CDS YP_168943.1 56698567 3196469 3960505..3961260 1 NC_003911.11 identified by match to protein family HMM PF00596; hypothetical protein 3961260 3196469 SPO3749 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168943.1 3960505 D 246200 CDS YP_168944.1 56698568 3196470 3961309..3962328 1 NC_003911.11 identified by similarity to GB:CAC47108.1; hypothetical protein 3962328 3196470 SPO3750 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168944.1 3961309 D 246200 CDS YP_168945.1 56698569 3195766 3962500..3963192 1 NC_003911.11 identified by match to protein family HMM PF06508; match to protein family HMM TIGR00364; exoenzyme S synthesis protein B 3963192 exsB 3195766 exsB Ruegeria pomeroyi DSS-3 exoenzyme S synthesis protein B YP_168945.1 3962500 D 246200 CDS YP_168946.1 56698724 3195893 3963192..3963548 1 NC_003911.11 identified by match to protein family HMM PF01242; 6-pyruvoyl tetrahydrobiopterin synthase 3963548 3195893 SPO3903 Ruegeria pomeroyi DSS-3 6-pyruvoyl tetrahydrobiopterin synthase YP_168946.1 3963192 D 246200 CDS YP_168947.1 56698570 3194070 3963545..3964264 1 NC_003911.11 identified by match to protein family HMM PF04055; radical SAM domain-containing protein 3964264 3194070 SPO3752 Ruegeria pomeroyi DSS-3 radical SAM domain-containing protein YP_168947.1 3963545 D 246200 CDS YP_168948.1 56698571 3195883 3964286..3964753 1 NC_003911.11 NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis; 7-cyano-7-deazaguanine reductase 3964753 3195883 SPO3753 Ruegeria pomeroyi DSS-3 7-cyano-7-deazaguanine reductase YP_168948.1 3964286 D 246200 CDS YP_168949.1 56698572 3195881 complement(3964764..3965474) 1 NC_003911.11 identified by similarity to GB:BAB51829.1; hypothetical protein 3965474 3195881 SPO3754 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168949.1 3964764 R 246200 CDS YP_168950.1 56698573 3195701 3965485..3966336 1 NC_003911.11 identified by similarity to GB:CAE28643.1; hypothetical protein 3966336 3195701 SPO3755 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168950.1 3965485 D 246200 CDS YP_168951.1 56698574 3196473 complement(3966762..3967676) 1 NC_003911.11 identified by match to protein family HMM PF00691; OmpA domain-containing protein 3967676 3196473 SPO3756 Ruegeria pomeroyi DSS-3 OmpA domain-containing protein YP_168951.1 3966762 R 246200 CDS YP_168952.1 56698575 3195520 complement(3967673..3968245) 1 NC_003911.11 identified by match to protein family HMM TIGR00778; match to protein family HMM TIGR01926; alkylhydroperoxidase 3968245 3195520 SPO3757 Ruegeria pomeroyi DSS-3 alkylhydroperoxidase YP_168952.1 3967673 R 246200 CDS YP_168953.1 56698576 3196475 complement(3968242..3968970) 1 NC_003911.11 identified by match to protein family HMM PF00583; acetyltransferase 3968970 3196475 SPO3758 Ruegeria pomeroyi DSS-3 acetyltransferase YP_168953.1 3968242 R 246200 CDS YP_168954.1 56698577 3195923 complement(3968967..3969689) 1 NC_003911.11 identified by match to protein family HMM PF00994; molybdenum cofactor biosynthesis domain-containing protein 3969689 3195923 SPO3759 Ruegeria pomeroyi DSS-3 molybdenum cofactor biosynthesis domain-containing protein YP_168954.1 3968967 R 246200 CDS YP_168955.1 56698578 3194105 3969739..3970431 1 NC_003911.11 Regulatory factor involved in maltose metabolism; sugar fermentation stimulation protein A 3970431 sfsA 3194105 sfsA Ruegeria pomeroyi DSS-3 sugar fermentation stimulation protein A YP_168955.1 3969739 D 246200 CDS YP_168956.1 56698579 3196476 3970517..3971326 1 NC_003911.11 identified by similarity to SP:P07906; match to protein family HMM PF00557; match to protein family HMM TIGR00500; methionine aminopeptidase 3971326 map 3196476 map Ruegeria pomeroyi DSS-3 methionine aminopeptidase YP_168956.1 3970517 D 246200 CDS YP_168957.1 56698580 3196482 complement(3971437..3972075) 1 NC_003911.11 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01509; match to protein family HMM TIGR01549; HAD family hydrolase 3972075 3196482 SPO3762 Ruegeria pomeroyi DSS-3 HAD family hydrolase YP_168957.1 3971437 R 246200 CDS YP_168958.1 56698581 3196483 complement(3972274..3973314) 1 NC_003911.11 identified by match to protein family HMM PF00037; (Fe-S)-binding protein 3973314 3196483 SPO3763 Ruegeria pomeroyi DSS-3 (Fe-S)-binding protein YP_168958.1 3972274 R 246200 CDS YP_168959.1 56698582 3196487 complement(3973387..3974052) 1 NC_003911.11 identified by match to protein family HMM PF02798; glutathione S-transferase 3974052 3196487 SPO3764 Ruegeria pomeroyi DSS-3 glutathione S-transferase YP_168959.1 3973387 R 246200 CDS YP_168960.1 56698583 3196040 3974236..3974709 1 NC_003911.11 identified by similarity to PIR:D83153; hypothetical protein 3974709 3196040 SPO3765 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168960.1 3974236 D 246200 CDS YP_168961.1 56698584 3196494 complement(3974726..3975454) 1 NC_003911.11 identified by similarity to SP:P46022; match to protein family HMM PF00912; match to protein family HMM TIGR02070; monofunctional biosynthetic peptidoglycan transglycosylase 3975454 mtgA 3196494 mtgA Ruegeria pomeroyi DSS-3 monofunctional biosynthetic peptidoglycan transglycosylase YP_168961.1 3974726 R 246200 CDS YP_168962.1 56698585 3196496 complement(3975508..3976494) 1 NC_003911.11 identified by similarity to PIR:T03518; hypothetical protein 3976494 3196496 SPO3767 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168962.1 3975508 R 246200 CDS YP_168963.1 56698586 3196499 complement(3976670..3981202) 1 NC_003911.11 identified by similarity to SP:Q05755; match to protein family HMM PF01493; match to protein family HMM PF01645; match to protein family HMM PF04897; match to protein family HMM PF04898; glutamate synthase, large subunit 3981202 gltB 3196499 gltB Ruegeria pomeroyi DSS-3 glutamate synthase, large subunit YP_168963.1 3976670 R 246200 CDS YP_168964.1 56698587 3196507 complement(3981199..3981636) 1 NC_003911.11 identified by similarity to PIR:AG2732; match to protein family HMM PF04828; hypothetical protein 3981636 3196507 SPO3769 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168964.1 3981199 R 246200 CDS YP_168965.1 56698588 3196508 complement(3981691..3983124) 1 NC_003911.11 function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase 3983124 gltD 3196508 gltD Ruegeria pomeroyi DSS-3 oxidoreductase YP_168965.1 3981691 R 246200 CDS YP_168966.1 56698589 3196513 3983356..3984159 1 NC_003911.11 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters UDP disphosphate which reduces the pool of lipid carrier available to the cell; UDP pyrophosphate phosphatase 3984159 3196513 SPO3771 Ruegeria pomeroyi DSS-3 UDP pyrophosphate phosphatase YP_168966.1 3983356 D 246200 CDS YP_168967.1 56698590 3196515 complement(3984160..3985143) 1 NC_003911.11 identified by similarity to SP:P34943; NADH ubiquinone oxidoreductase 3985143 3196515 SPO3772 Ruegeria pomeroyi DSS-3 NADH ubiquinone oxidoreductase YP_168967.1 3984160 R 246200 CDS YP_168968.1 56698591 3196520 3985928..3987487 1 NC_003911.11 identified by match to protein family HMM PF00496; oligopeptide/dipeptide ABC transporter substrate-binding protein 3987487 3196520 SPO3774 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter substrate-binding protein YP_168968.1 3985928 D 246200 CDS YP_168969.1 56698592 3196521 3987626..3988606 1 NC_003911.11 identified by similarity to SP:P37316; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 3988606 3196521 SPO3775 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter permease YP_168969.1 3987626 D 246200 CDS YP_168970.1 56698593 3196522 3988603..3989547 1 NC_003911.11 identified by similarity to SP:P37315; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 3989547 3196522 SPO3776 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter permease YP_168970.1 3988603 D 246200 CDS YP_168971.1 56698594 3196526 3989516..3990544 1 NC_003911.11 identified by similarity to SP:P76027; match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide/dipeptide ABC transporter ATP-binding protein 3990544 3196526 SPO3777 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter ATP-binding protein YP_168971.1 3989516 D 246200 CDS YP_168972.1 56698595 3196533 3990541..3991569 1 NC_003911.11 identified by similarity to SP:P42065; match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide/dipeptide ABC transporter ATP-binding protein 3991569 3196533 SPO3778 Ruegeria pomeroyi DSS-3 oligopeptide/dipeptide ABC transporter ATP-binding protein YP_168972.1 3990541 D 246200 CDS YP_168973.1 56698596 3196534 3991600..3992508 1 NC_003911.11 identified by match to protein family HMM PF00126; LysR family transcriptional regulator 3992508 3196534 SPO3779 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_168973.1 3991600 D 246200 CDS YP_168974.1 56698597 3196536 3992604..3993731 1 NC_003911.11 identified by match to protein family HMM PF03739; hypothetical protein 3993731 3196536 SPO3780 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168974.1 3992604 D 246200 CDS YP_168975.1 56698598 3196419 complement(3994583..3994960) 1 NC_003911.11 identified by similarity to PIR:AB1999; match to protein family HMM TIGR02058; hypothetical protein 3994960 3196419 SPO3781 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168975.1 3994583 R 246200 CDS YP_168976.1 56698599 3196535 complement(3994957..3995301) 1 NC_003911.11 identified by similarity to PIR:AI1138; match to protein family HMM TIGR02058; hypothetical protein 3995301 3196535 SPO3782 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168976.1 3994957 R 246200 CDS YP_168977.1 56698600 3193746 complement(3995337..3996398) 1 NC_003911.11 identified by similarity to SP:P10907; match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein 3996398 3193746 SPO3783 Ruegeria pomeroyi DSS-3 sugar ABC transporter ATP-binding protein YP_168977.1 3995337 R 246200 CDS YP_168978.1 56698601 3195513 complement(3996400..3997551) 1 NC_003911.11 identified by similarity to SP:P02914; match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein 3997551 3195513 SPO3784 Ruegeria pomeroyi DSS-3 sugar ABC transporter ATP-binding protein YP_168978.1 3996400 R 246200 CDS YP_168979.1 56698602 3196145 complement(3997508..3998446) 1 NC_003911.11 identified by similarity to PIR:T46751; match to protein family HMM PF00528; sugar ABC transporter permease 3998446 3196145 SPO3785 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_168979.1 3997508 R 246200 CDS YP_168980.1 56698603 3196161 complement(3998443..3999300) 1 NC_003911.11 identified by match to protein family HMM PF00528; sugar ABC transporter permease 3999300 3196161 SPO3786 Ruegeria pomeroyi DSS-3 sugar ABC transporter permease YP_168980.1 3998443 R 246200 CDS YP_168981.1 56698604 3193975 complement(3999366..4001015) 1 NC_003911.11 Assignment partly based on membership in sugar ABC transporter gene cluster.; identified by match to protein family HMM TIGR01409; sugar ABC transporter periplasmic sugar-binding protein 4001015 3193975 SPO3787 Ruegeria pomeroyi DSS-3 sugar ABC transporter periplasmic sugar-binding protein YP_168981.1 3999366 R 246200 CDS YP_168982.1 56698605 3195054 complement(4001094..4002827) 1 NC_003911.11 identified by similarity to SP:P28614; match to protein family HMM PF00158; match to protein family HMM PF01590; acetoin catabolism regulatory protein 4002827 acoR 3195054 acoR Ruegeria pomeroyi DSS-3 acetoin catabolism regulatory protein YP_168982.1 4001094 R 246200 CDS YP_168983.1 56698606 3194182 complement(4003168..4003500) 1 NC_003911.11 identified by match to protein family HMM PF02627; match to protein family HMM TIGR00778; alkylhydroperoxidase 4003500 3194182 SPO3789 Ruegeria pomeroyi DSS-3 alkylhydroperoxidase YP_168983.1 4003168 R 246200 CDS YP_168984.1 56698607 3195409 complement(4003568..4004668) 1 NC_003911.11 Catalyzes the transfer of acetyl from acetyldihydrolipoamide to coenzyme A to form acetyl CoA; branched-chain alpha-keto acid dehydrogenase subunit E2 4004668 acoC 3195409 acoC Ruegeria pomeroyi DSS-3 branched-chain alpha-keto acid dehydrogenase subunit E2 YP_168984.1 4003568 R 246200 CDS YP_168985.1 56698608 3196076 complement(4004673..4005680) 1 NC_003911.11 identified by similarity to SP:O34591; match to protein family HMM PF02779; match to protein family HMM PF02780; acetoin dehydrogenase complex, E1 component subunit beta 4005680 acoB 3196076 acoB Ruegeria pomeroyi DSS-3 acetoin dehydrogenase complex, E1 component subunit beta YP_168985.1 4004673 R 246200 CDS YP_168986.1 56698609 3195710 complement(4005711..4006691) 1 NC_003911.11 identified by similarity to PIR:I40790; match to protein family HMM PF00676; acetoin dehydrogenase complex, E1 component subunit alpha 4006691 acoA 3195710 acoA Ruegeria pomeroyi DSS-3 acetoin dehydrogenase complex, E1 component subunit alpha YP_168986.1 4005711 R 246200 CDS YP_168987.1 56698610 3196126 complement(4006688..4007746) 1 NC_003911.11 identified by similarity to SP:P27748; match to protein family HMM PF01513; acetoin catabolism protein X 4007746 acoX 3196126 acoX Ruegeria pomeroyi DSS-3 acetoin catabolism protein X YP_168987.1 4006688 R 246200 CDS YP_168988.1 56698611 3196175 complement(4007899..4008051) 1 NC_003911.11 identified by similarity to GB:AAM35022.1; hypothetical protein 4008051 3196175 SPO3794 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168988.1 4007899 R 246200 CDS YP_168989.1 56698612 3192852 4008387..4009670 1 NC_003911.11 identified by similarity to SP:P26979; match to protein family HMM PF00309; match to protein family HMM PF04552; match to protein family HMM PF04963; RNA polymerase sigma-54 factor 4009670 rpoN 3192852 rpoN Ruegeria pomeroyi DSS-3 RNA polymerase sigma-54 factor YP_168989.1 4008387 D 246200 CDS YP_168990.1 56698613 3194981 4016785..4017324 1 NC_003911.11 identified by similarity to GB:BAC50760.1; hypothetical protein 4017324 3194981 SPO3802 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168990.1 4016785 D 246200 CDS YP_168991.1 56698614 3195189 complement(4017291..4018322) 1 NC_003911.11 identified by match to protein family HMM PF00165; match to protein family HMM TIGR01199; AraC family transcriptional regulator 4018322 3195189 SPO3803 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_168991.1 4017291 R 246200 CDS YP_168992.1 56698615 3196531 4018439..4020205 1 NC_003911.11 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; 3-methylmercaptopropionyl-CoA dehydrogenase 4020205 dmdC 3196531 dmdC Ruegeria pomeroyi DSS-3 3-methylmercaptopropionyl-CoA dehydrogenase YP_168992.1 4018439 D 246200 CDS YP_168993.1 56698616 3196358 4020265..4021068 1 NC_003911.11 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; methylthioacryloyl-CoA hydratase 4021068 dmdD 3196358 dmdD Ruegeria pomeroyi DSS-3 methylthioacryloyl-CoA hydratase YP_168993.1 4020265 D 246200 CDS YP_168994.1 56698617 3193484 4021134..4021610 1 NC_003911.11 binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation; SsrA-binding protein 4021610 smpB 3193484 smpB Ruegeria pomeroyi DSS-3 SsrA-binding protein YP_168994.1 4021134 D 246200 CDS YP_168995.1 56698618 3193879 complement(4021706..4022056) 1 NC_003911.11 identified by similarity to GB:BAC45729.1; hypothetical protein 4022056 3193879 SPO3807 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168995.1 4021706 R 246200 CDS YP_168996.1 56698619 3192990 complement(4022087..4022590) 1 NC_003911.11 identified by similarity to GB:BAB48348.1; hypothetical protein 4022590 3192990 SPO3808 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168996.1 4022087 R 246200 CDS YP_168997.1 56698620 3193525 complement(4022560..4023255) 1 NC_003911.11 identified by match to protein family HMM PF01022; ArsR family transcriptional regulator 4023255 3193525 SPO3809 Ruegeria pomeroyi DSS-3 ArsR family transcriptional regulator YP_168997.1 4022560 R 246200 CDS YP_168998.1 56698621 3195588 4023983..4025500 1 NC_003911.11 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 4025500 gpmI 3195588 gpmI Ruegeria pomeroyi DSS-3 phosphoglyceromutase YP_168998.1 4023983 D 246200 CDS YP_168999.1 56698622 3194556 4025497..4026633 1 NC_003911.11 identified by similarity to GB:AAK25396.1; hypothetical protein 4026633 3194556 SPO3811 Ruegeria pomeroyi DSS-3 hypothetical protein YP_168999.1 4025497 D 246200 CDS YP_169000.1 56698623 3196132 4026640..4027971 1 NC_003911.11 identified by match to protein family HMM PF00595; match to protein family HMM PF03572; match to protein family HMM TIGR00225; carboxyl-terminal protease 4027971 3196132 SPO3812 Ruegeria pomeroyi DSS-3 carboxyl-terminal protease YP_169000.1 4026640 D 246200 CDS YP_169001.1 56698624 3196020 complement(4028065..4028457) 1 NC_003911.11 hypothetical protein 4028457 3196020 SPO3813 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169001.1 4028065 R 246200 CDS YP_169002.1 56698625 3194947 complement(4028454..4029215) 1 NC_003911.11 hypothetical protein 4029215 3194947 SPO3814 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169002.1 4028454 R 246200 CDS YP_169003.1 56698626 3196115 4029463..4032582 1 NC_003911.11 identified by similarity to GB:BAB50188.1; match to protein family HMM PF00027; match to protein family HMM PF00664; ABC transporter permease 4032582 3196115 SPO3815 Ruegeria pomeroyi DSS-3 ABC transporter permease YP_169003.1 4029463 D 246200 CDS YP_169004.1 56698627 3196180 4032572..4033465 1 NC_003911.11 identified by match to protein family HMM PF02517; CAAX amino terminal protease 4033465 3196180 SPO3816 Ruegeria pomeroyi DSS-3 CAAX amino terminal protease YP_169004.1 4032572 D 246200 CDS YP_169005.1 56698628 3196064 4033524..4034468 1 NC_003911.11 identified by similarity to SP:P08193; match to protein family HMM TIGR00515; acetyl-CoA carboxylase, carboxyl transferase subunit beta 4034468 accD 3196064 accD Ruegeria pomeroyi DSS-3 acetyl-CoA carboxylase, carboxyl transferase subunit beta YP_169005.1 4033524 D 246200 CDS YP_169006.1 56698629 3196060 4034465..4035739 1 NC_003911.11 identified by match to protein family HMM PF01225; match to protein family HMM TIGR01499; folC bifunctional protein 4035739 folC 3196060 folC Ruegeria pomeroyi DSS-3 folC bifunctional protein YP_169006.1 4034465 D 246200 CDS YP_169007.1 56698630 3194847 complement(4035815..4036876) 1 NC_003911.11 identified by match to protein family HMM PF03969; AFG1 family ATPase 4036876 3194847 SPO3819 Ruegeria pomeroyi DSS-3 AFG1 family ATPase YP_169007.1 4035815 R 246200 CDS YP_169008.1 56698631 3194897 4037027..4038262 1 NC_003911.11 major facilitator transporter 4038262 3194897 SPO3820 Ruegeria pomeroyi DSS-3 major facilitator transporter YP_169008.1 4037027 D 246200 CDS YP_169009.1 56698632 3196121 complement(4038279..4039187) 1 NC_003911.11 identified by match to protein family HMM PF02423; ornithine cyclodeaminase/mu-crystallin family protein 4039187 3196121 SPO3821 Ruegeria pomeroyi DSS-3 ornithine cyclodeaminase/mu-crystallin family protein YP_169009.1 4038279 R 246200 CDS YP_169010.1 56698633 3196239 complement(4039184..4039804) 1 NC_003911.11 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01509; HAD-superfamily hydrolase 4039804 3196239 SPO3822 Ruegeria pomeroyi DSS-3 HAD-superfamily hydrolase YP_169010.1 4039184 R 246200 CDS YP_169011.1 56698634 3195995 complement(4039971..4040267) 1 NC_003911.11 binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 4040267 rplW 3195995 rplW Ruegeria pomeroyi DSS-3 50S ribosomal protein L23 YP_169011.1 4039971 R 246200 CDS YP_169012.1 56698635 3195311 complement(4040264..4040881) 1 NC_003911.11 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA; 50S ribosomal protein L4 4040881 rplD 3195311 rplD Ruegeria pomeroyi DSS-3 50S ribosomal protein L4 YP_169012.1 4040264 R 246200 CDS YP_169013.1 56698636 3192891 complement(4040878..4041603) 1 NC_003911.11 binds directly near the 3' end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene confer resistance to tiamulin; 50S ribosomal protein L3 4041603 rplC 3192891 rplC Ruegeria pomeroyi DSS-3 50S ribosomal protein L3 YP_169013.1 4040878 R 246200 CDS YP_169014.1 56698637 3196261 complement(4041620..4041934) 1 NC_003911.11 NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex; 30S ribosomal protein S10 4041934 rpsJ 3196261 rpsJ Ruegeria pomeroyi DSS-3 30S ribosomal protein S10 YP_169014.1 4041620 R 246200 CDS YP_169015.1 56698638 3193877 complement(4042161..4042625) 1 NC_003911.11 identified by match to protein family HMM PF02639; YaiI/YqxD family protein 4042625 3193877 SPO3827 Ruegeria pomeroyi DSS-3 YaiI/YqxD family protein YP_169015.1 4042161 R 246200 CDS YP_169016.1 56698639 3196077 complement(4043006..4044433) 1 NC_003911.11 catalyzes the conversion of NADPH to NADH; soluble pyridine nucleotide transhydrogenase 4044433 sthA 3196077 sthA Ruegeria pomeroyi DSS-3 soluble pyridine nucleotide transhydrogenase YP_169016.1 4043006 R 246200 CDS YP_169017.1 56698640 3193731 complement(4044442..4045296) 1 NC_003911.11 identified by similarity to GB:AAC44554.1; match to protein family HMM PF00756; S-formylglutathione hydrolase 4045296 3193731 SPO3829 Ruegeria pomeroyi DSS-3 S-formylglutathione hydrolase YP_169017.1 4044442 R 246200 CDS YP_169018.1 56698641 3195124 4045449..4046687 1 NC_003911.11 catalyzes the release of the N-terminal amino acid from a tripeptide; peptidase T 4046687 pepT 3195124 pepT Ruegeria pomeroyi DSS-3 peptidase T YP_169018.1 4045449 D 246200 CDS YP_169019.1 56698642 3196081 4046691..4047548 1 NC_003911.11 identified by match to protein family HMM PF00561; alpha/beta hydrolase 4047548 3196081 SPO3831 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_169019.1 4046691 D 246200 CDS YP_169020.1 56698643 3192755 4047545..4048492 1 NC_003911.11 identified by match to protein family HMM PF02423; ornithine cyclodeaminase/mu-crystallin family protein 4048492 3192755 SPO3832 Ruegeria pomeroyi DSS-3 ornithine cyclodeaminase/mu-crystallin family protein YP_169020.1 4047545 D 246200 CDS YP_169021.1 56698644 3196362 4048549..4050678 1 NC_003911.11 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF03880; DEAD/DEAH box helicase 4050678 3196362 SPO3833 Ruegeria pomeroyi DSS-3 DEAD/DEAH box helicase YP_169021.1 4048549 D 246200 CDS YP_169022.1 56698645 3196359 complement(4050682..4051491) 1 NC_003911.11 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase 4051491 dapB 3196359 dapB Ruegeria pomeroyi DSS-3 dihydrodipicolinate reductase YP_169022.1 4050682 R 246200 CDS YP_169023.1 56698646 3196286 4051580..4051975 1 NC_003911.11 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock; ribosome-binding factor A 4051975 rbfA 3196286 rbfA Ruegeria pomeroyi DSS-3 ribosome-binding factor A YP_169023.1 4051580 D 246200 CDS YP_169024.1 56698647 3196083 4051972..4052709 1 NC_003911.11 identified by similarity to GB:CAC46553.1; hypothetical protein 4052709 3196083 SPO3836 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169024.1 4051972 D 246200 CDS YP_169025.1 56698648 3196374 4052835..4053746 1 NC_003911.11 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B 4053746 truB 3196374 truB Ruegeria pomeroyi DSS-3 tRNA pseudouridine synthase B YP_169025.1 4052835 D 246200 CDS YP_169026.1 56698649 3196101 4053792..4054298 1 NC_003911.11 identified by similarity to PIR:E95908; hypothetical protein 4054298 3196101 SPO3838 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169026.1 4053792 D 246200 CDS YP_169027.1 56698650 3196012 4054352..4055428 1 NC_003911.11 identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 4055428 3196012 SPO3839 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_169027.1 4054352 D 246200 CDS YP_169028.1 56698651 3196119 4055583..4055852 1 NC_003911.11 primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence; 30S ribosomal protein S15 4055852 rpsO 3196119 rpsO Ruegeria pomeroyi DSS-3 30S ribosomal protein S15 YP_169028.1 4055583 D 246200 CDS YP_169029.1 56698652 3196254 complement(4055937..4056554) 1 NC_003911.11 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 4056554 3196254 SPO3841 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_169029.1 4055937 R 246200 CDS YP_169030.1 56698653 3196287 4056685..4057659 1 NC_003911.11 identified by similarity to GB:AAN30579.1; match to protein family HMM PF01988; hypothetical protein 4057659 3196287 SPO3842 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169030.1 4056685 D 246200 CDS YP_169031.1 56698654 3196329 4057698..4058627 1 NC_003911.11 identified by similarity to GB:AAC45458.1; match to protein family HMM PF03547; malonate transporter 4058627 3196329 SPO3843 Ruegeria pomeroyi DSS-3 malonate transporter YP_169031.1 4057698 D 246200 CDS YP_169032.1 56698655 3195865 4058742..4061543 1 NC_003911.11 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair; DNA polymerase I 4061543 polA 3195865 polA Ruegeria pomeroyi DSS-3 DNA polymerase I YP_169032.1 4058742 D 246200 CDS YP_169033.1 56698656 3196313 complement(4061599..4061907) 1 NC_003911.11 identified by similarity to GB:AAN56041.1; hypothetical protein 4061907 3196313 SPO3845 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169033.1 4061599 R 246200 CDS YP_169034.1 56698657 3196092 complement(4061964..4062143) 1 NC_003911.11 identified by similarity to GB:AAK22176.1; hypothetical protein 4062143 3196092 SPO3846 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169034.1 4061964 R 246200 CDS YP_169035.1 56698658 3195625 4062235..4063164 1 NC_003911.11 identified by similarity to GB:CAD16663.1; match to protein family HMM PF00005; ABC transporter ATP-binding protein 4063164 3195625 SPO3847 Ruegeria pomeroyi DSS-3 ABC transporter ATP-binding protein YP_169035.1 4062235 D 246200 CDS YP_169036.1 56698659 3196146 complement(4063148..4063930) 1 NC_003911.11 identified by similarity to GB:BAC09469.1; match to protein family HMM PF01598; sterol desaturase 4063930 3196146 SPO3848 Ruegeria pomeroyi DSS-3 sterol desaturase YP_169036.1 4063148 R 246200 CDS YP_169037.1 56698660 3196346 complement(4063991..4064479) 1 NC_003911.11 identified by similarity to GB:BAB47957.1; match to protein family HMM PF06718; hypothetical protein 4064479 3196346 SPO3849 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169037.1 4063991 R 246200 CDS YP_169038.1 56698661 3196155 4064943..4066055 1 NC_003911.11 identified by similarity to SP:P45382; match to protein family HMM PF00107; glutathione-dependent formaldehyde dehydrogenase 4066055 3196155 SPO3850 Ruegeria pomeroyi DSS-3 glutathione-dependent formaldehyde dehydrogenase YP_169038.1 4064943 D 246200 CDS YP_169039.1 56698662 3196268 complement(4066155..4067636) 1 NC_003911.11 identified by match to protein family HMM PF07219; HemY domain-containing protein 4067636 3196268 SPO3851 Ruegeria pomeroyi DSS-3 HemY domain-containing protein YP_169039.1 4066155 R 246200 CDS YP_169040.1 56698663 3196207 complement(4067659..4069017) 1 NC_003911.11 hypothetical protein 4069017 3196207 SPO3852 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169040.1 4067659 R 246200 CDS YP_169041.1 56698664 3196160 complement(4069017..4069730) 1 NC_003911.11 identified by match to protein family HMM PF02602; uroporphyrinogen-III synthase 4069730 3196160 SPO3853 Ruegeria pomeroyi DSS-3 uroporphyrinogen-III synthase YP_169041.1 4069017 R 246200 CDS YP_169042.1 56698665 3196188 4069829..4070926 1 NC_003911.11 in most organisms, only the N-terminal domain is present in a single polypeptide; in some archaea this domain is fused to a kinase domain; this gene is essential for growth in Escherichia coli and Bacillus subtilis; the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins; the Pyrococcus structure shows DNA-binding properties, iron-binding, ATP-binding, and AP endonuclease activity; DNA-binding/iron metalloprotein/AP endonuclease 4070926 3196188 SPO3854 Ruegeria pomeroyi DSS-3 DNA-binding/iron metalloprotein/AP endonuclease YP_169042.1 4069829 D 246200 CDS YP_169043.1 56698666 3196197 4070923..4071885 1 NC_003911.11 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 4071885 gpsA 3196197 gpsA Ruegeria pomeroyi DSS-3 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase YP_169043.1 4070923 D 246200 CDS YP_169044.1 56698667 3196403 4071887..4072156 1 NC_003911.11 unknown function; YciI from Haemophilus influenzae presents crystal structure similarity to a muconolactone isomerase, but does not seem to catalyze any of the predicted reactions based on sequence and structure similarity; hypothetical protein 4072156 3196403 SPO3856 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169044.1 4071887 D 246200 CDS YP_169045.1 56698668 3196192 4072156..4072578 1 NC_003911.11 identified by similarity to GB:BAA34646.1; match to protein family HMM PF04543; hypothetical protein 4072578 3196192 SPO3857 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169045.1 4072156 D 246200 CDS YP_169046.1 56698669 3196190 4072621..4073016 1 NC_003911.11 identified by similarity to GB:BAB50937.1; hypothetical protein 4073016 3196190 SPO3858 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169046.1 4072621 D 246200 CDS YP_169047.1 56698670 3196195 complement(4073261..4073602) 1 NC_003911.11 identified by similarity to GB:BAB48836.1; hypothetical protein 4073602 3196195 SPO3859 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169047.1 4073261 R 246200 CDS YP_169048.1 56698671 3196184 complement(4073760..4074371) 1 NC_003911.11 identified by similarity to PIR:S77132; hypothetical protein 4074371 3196184 SPO3860 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169048.1 4073760 R 246200 CDS YP_169049.1 56698672 3196407 complement(4074441..4075829) 1 NC_003911.11 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine; S-adenosyl-L-homocysteine hydrolase 4075829 ahcY 3196407 ahcY Ruegeria pomeroyi DSS-3 S-adenosyl-L-homocysteine hydrolase YP_169049.1 4074441 R 246200 CDS YP_169050.1 56698674 3196185 complement(4075926..4076258) 1 NC_003911.11 identified by similarity to GB:CAC45660.1; lipoprotein 4076258 3196185 SPO3862 Ruegeria pomeroyi DSS-3 lipoprotein YP_169050.1 4075926 R 246200 CDS YP_169051.1 56698673 3196187 4076448..4077041 1 NC_003911.11 identified by match to protein family HMM PF01966; HD domain-containing protein 4077041 3196187 SPO3863 Ruegeria pomeroyi DSS-3 HD domain-containing protein YP_169051.1 4076448 D 246200 CDS YP_169052.1 56698675 3196201 complement(4077014..4078243) 1 NC_003911.11 identified by similarity to PIR:H84070; hypothetical protein 4078243 3196201 SPO3864 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169052.1 4077014 R 246200 CDS YP_169053.1 56698676 3196380 complement(4078254..4078808) 1 NC_003911.11 identified by similarity to SP:P42508; match to protein family HMM PF00072; match to protein family HMM TIGR01199; photosynthetic apparatus regulatory protein RegA 4078808 regA 3196380 regA Ruegeria pomeroyi DSS-3 photosynthetic apparatus regulatory protein RegA YP_169053.1 4078254 R 246200 CDS YP_169054.1 56698677 3196420 complement(4078895..4079515) 1 NC_003911.11 identified by similarity to SP:Q52720; match to protein family HMM PF02630; regulatory protein SenC 4079515 senC 3196420 senC Ruegeria pomeroyi DSS-3 regulatory protein SenC YP_169054.1 4078895 R 246200 CDS YP_169055.1 56698678 3196179 4079603..4081000 1 NC_003911.11 identified by similarity to GB:BAA31475.1; match to protein family HMM PF00512; match to protein family HMM PF02518; sensor histidine kinase RegB 4081000 regB 3196179 regB Ruegeria pomeroyi DSS-3 sensor histidine kinase RegB YP_169055.1 4079603 D 246200 CDS YP_169056.1 56698679 3196345 4081068..4082570 1 NC_003911.11 identified by similarity to GB:AAM48718.1; hypothetical protein 4082570 3196345 SPO3868 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169056.1 4081068 D 246200 CDS YP_169057.1 56698680 3196377 4082613..4083086 1 NC_003911.11 identified by similarity to GB:AAK25496.1; match to protein family HMM PF02367; match to protein family HMM TIGR00150; hypothetical protein 4083086 3196377 SPO3869 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169057.1 4082613 D 246200 CDS YP_169058.1 56698681 3196302 4083056..4084090 1 NC_003911.11 identified by similarity to GB:AAM48719.1; hypothetical protein 4084090 3196302 SPO3870 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169058.1 4083056 D 246200 CDS YP_169059.1 56698682 3196308 4084087..4084773 1 NC_003911.11 identified by match to protein family HMM PF00483; nucleotidyltransferase 4084773 3196308 SPO3871 Ruegeria pomeroyi DSS-3 nucleotidyltransferase YP_169059.1 4084087 D 246200 CDS YP_169060.1 56698683 3196216 4084766..4087693 1 NC_003911.11 identified by similarity to GB:AAM48721.1; hypothetical protein 4087693 3196216 SPO3872 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169060.1 4084766 D 246200 CDS YP_169061.1 56698684 3196426 4087690..4091046 1 NC_003911.11 identified by match to protein family HMM PF00580; ATP-dependent DNA helicase UvrD 4091046 3196426 SPO3873 Ruegeria pomeroyi DSS-3 ATP-dependent DNA helicase UvrD YP_169061.1 4087690 D 246200 CDS YP_169062.1 56698685 3196264 4091107..4091427 1 NC_003911.11 identified by match to protein family HMM PF00085; match to protein family HMM TIGR01068; thioredoxin 4091427 trx 3196264 trx Ruegeria pomeroyi DSS-3 thioredoxin YP_169062.1 4091107 D 246200 CDS YP_169063.1 56698686 3195091 4091515..4091865 1 NC_003911.11 hypothetical protein 4091865 3195091 SPO3875 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169063.1 4091515 D 246200 CDS YP_169064.1 56698687 3196196 4091862..4092239 1 NC_003911.11 identified by similarity to PIR:AB1999; match to protein family HMM TIGR02058; hypothetical protein 4092239 3196196 SPO3876 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169064.1 4091862 D 246200 CDS YP_169065.1 56698688 3196225 4092256..4093149 1 NC_003911.11 identified by similarity to GB:AAF69239.1; match to protein family HMM PF01022; match to protein family HMM PF01451; transcriptional regulator/arsenate reductase 4093149 3196225 SPO3877 Ruegeria pomeroyi DSS-3 transcriptional regulator/arsenate reductase YP_169065.1 4092256 D 246200 CDS YP_169066.1 56698689 3196231 4093183..4094181 1 NC_003911.11 identified by match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534; glyceraldehyde-3-phosphate dehydrogenase, type I 4094181 gap-4 3196231 gap-4 Ruegeria pomeroyi DSS-3 glyceraldehyde-3-phosphate dehydrogenase, type I YP_169066.1 4093183 D 246200 CDS YP_169067.1 56698690 3196219 4094178..4095452 1 NC_003911.11 hypothetical protein 4095452 3196219 SPO3879 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169067.1 4094178 D 246200 CDS YP_169068.1 56698691 3196290 4095915..4096472 1 NC_003911.11 heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit 4096472 hslV 3196290 hslV Ruegeria pomeroyi DSS-3 ATP-dependent protease peptidase subunit YP_169068.1 4095915 D 246200 CDS YP_169069.1 56698692 3196226 complement(4096634..4097023) 1 NC_003911.11 identified by match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 4097023 3196226 SPO3881 Ruegeria pomeroyi DSS-3 twin-arginine translocation pathway signal sequence domain-containing protein YP_169069.1 4096634 R 246200 CDS YP_169070.1 56698693 3196200 4097215..4098522 1 NC_003911.11 heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU 4098522 hslU 3196200 hslU Ruegeria pomeroyi DSS-3 ATP-dependent protease ATP-binding subunit HslU YP_169070.1 4097215 D 246200 CDS YP_169071.1 56698694 3195833 4098555..4099658 1 NC_003911.11 lipoprotein 4099658 3195833 SPO3883 Ruegeria pomeroyi DSS-3 lipoprotein YP_169071.1 4098555 D 246200 CDS YP_169072.1 56698695 3196391 complement(4099655..4100245) 1 NC_003911.11 identified by similarity to GB:AAM48726.1; match to protein family HMM PF01713; smr domain-containing protein 4100245 3196391 SPO3884 Ruegeria pomeroyi DSS-3 smr domain-containing protein YP_169072.1 4099655 R 246200 CDS YP_169073.1 56698696 3196446 complement(4100245..4101285) 1 NC_003911.11 identified by match to protein family HMM PF03562; match to protein family HMM PF06725; MltA/3D domain-containing protein 4101285 3196446 SPO3885 Ruegeria pomeroyi DSS-3 MltA/3D domain-containing protein YP_169073.1 4100245 R 246200 CDS YP_169074.1 56698697 3196097 complement(4101282..4101938) 1 NC_003911.11 identified by similarity to PIR:AG3508; match to protein family HMM PF04280; Tim44 family protein 4101938 3196097 SPO3886 Ruegeria pomeroyi DSS-3 Tim44 family protein YP_169074.1 4101282 R 246200 CDS YP_169075.1 56698698 3196299 4102048..4102539 1 NC_003911.11 identified by similarity to SP:P37147; match to protein family HMM PF04186; FxsA protein 4102539 fxsA 3196299 fxsA Ruegeria pomeroyi DSS-3 FxsA protein YP_169075.1 4102048 D 246200 CDS YP_169076.1 56698699 3196335 4102594..4103091 1 NC_003911.11 molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA; preprotein translocase subunit SecB 4103091 secB 3196335 secB Ruegeria pomeroyi DSS-3 preprotein translocase subunit SecB YP_169076.1 4102594 D 246200 CDS YP_169077.1 56698700 3196237 complement(4103116..4103841) 1 NC_003911.11 identified by match to protein family HMM PF00929; match to protein family HMM TIGR00573; match to protein family HMM TIGR01406; DNA polymerase III subunit epsilon 4103841 dnaQ 3196237 dnaQ Ruegeria pomeroyi DSS-3 DNA polymerase III subunit epsilon YP_169077.1 4103116 R 246200 CDS YP_169078.1 56698702 3196224 complement(4103834..4104427) 1 NC_003911.11 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis; dephospho-CoA kinase 4104427 coaE 3196224 coaE Ruegeria pomeroyi DSS-3 dephospho-CoA kinase YP_169078.1 4103834 R 246200 CDS YP_169079.1 56698701 3196139 complement(4104424..4105257) 1 NC_003911.11 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase 4105257 aroE 3196139 aroE Ruegeria pomeroyi DSS-3 shikimate 5-dehydrogenase YP_169079.1 4104424 R 246200 CDS YP_169080.1 56698703 3196330 complement(4105254..4105853) 1 NC_003911.11 identified by similarity to SP:Q02169; match to protein family HMM PF02545; match to protein family HMM TIGR00172; hypothetical protein 4105853 maf-1 3196330 maf-1 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169080.1 4105254 R 246200 CDS YP_169081.1 56698704 3196311 4106263..4106715 1 NC_003911.11 identified by match to protein family HMM PF03653; hypothetical protein 4106715 3196311 SPO3893 Ruegeria pomeroyi DSS-3 hypothetical protein YP_169081.1 4106263 D 246200 CDS YP_169082.1 56698705 3196235 4106841..4108112 1 NC_003911.11 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 4108112 rho 3196235 rho Ruegeria pomeroyi DSS-3 transcription termination factor Rho YP_169082.1 4106841 D 246200 CDS YP_169083.1 56698706 3196284 4108144..4109430 1 NC_003911.11 in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, which is found in the wobble position of some tRNAs and affects ribosomal frameshifting; shows potassium-dependent dimerization and GTP hydrolysis; also involved in regulation of glutamate-dependent acid resistance and activation of gadE; tRNA modification GTPase TrmE 4109430 trmE 3196284 trmE Ruegeria pomeroyi DSS-3 tRNA modification GTPase TrmE YP_169083.1 4108144 D 246200 CDS YP_164832.1 56709230 3196707 1..798 1 NC_006569.1 identified by match to protein family HMM PF05721; phytanoyl-CoA dioxygenase 798 3196707 SPOA0449 Ruegeria pomeroyi DSS-3 phytanoyl-CoA dioxygenase YP_164832.1 1 D 246200 CDS YP_164833.1 56708792 3196814 complement(872..1777) 1 NC_006569.1 hypothetical protein 1777 3196814 SPOA0001 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164833.1 872 R 246200 CDS YP_164834.1 56708793 3196777 1804..3192 1 NC_006569.1 catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A); (dimethylallyl)adenosine tRNA methylthiotransferase 3192 miaB 3196777 miaB Ruegeria pomeroyi DSS-3 (dimethylallyl)adenosine tRNA methylthiotransferase YP_164834.1 1804 D 246200 CDS YP_164835.1 56708794 3196635 complement(3205..3774) 1 NC_006569.1 hypothetical protein 3774 3196635 SPOA0003 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164835.1 3205 R 246200 CDS YP_164836.1 56708795 3196638 4026..4568 1 NC_006569.1 identified by match to protein family HMM PF00691; OmpA family protein 4568 3196638 SPOA0004 Ruegeria pomeroyi DSS-3 OmpA family protein YP_164836.1 4026 D 246200 CDS YP_164837.1 56708796 3196660 4579..4872 1 NC_006569.1 lipoprotein 4872 3196660 SPOA0005 Ruegeria pomeroyi DSS-3 lipoprotein YP_164837.1 4579 D 246200 CDS YP_164838.1 56708797 3196622 5010..6020 1 NC_006569.1 identified by match to protein family HMM PF02562; PhoH family protein 6020 3196622 SPOA0006 Ruegeria pomeroyi DSS-3 PhoH family protein YP_164838.1 5010 D 246200 CDS YP_164839.1 56708798 3196604 6034..6411 1 NC_006569.1 hypothetical protein 6411 3196604 SPOA0007 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164839.1 6034 D 246200 CDS YP_164840.1 56708799 3196608 6408..6905 1 NC_006569.1 identified by similarity to SP:Q8YEA4; match to protein family HMM PF02130; match to protein family HMM TIGR00043; hypothetical protein 6905 3196608 SPOA0008 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164840.1 6408 D 246200 CDS YP_164841.1 56708800 3196596 6939..7826 1 NC_006569.1 identified by similarity to GB:AAC62436.1; match to protein family HMM PF00571; match to protein family HMM PF03471; hemolysin 7826 3196596 SPOA0009 Ruegeria pomeroyi DSS-3 hemolysin YP_164841.1 6939 D 246200 CDS YP_164842.1 56708801 3196719 7823..9340 1 NC_006569.1 identified by match to protein family HMM PF00795; match to protein family HMM TIGR00546; apolipoprotein N-acyltransferase 9340 cutE 3196719 cutE Ruegeria pomeroyi DSS-3 apolipoprotein N-acyltransferase YP_164842.1 7823 D 246200 CDS YP_164843.1 56708802 3196866 9429..10610 1 NC_006569.1 methionine adenosyltransferase; catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 10610 metK 3196866 metK Ruegeria pomeroyi DSS-3 S-adenosylmethionine synthetase YP_164843.1 9429 D 246200 CDS YP_164844.1 56708803 3196679 10680..11192 1 NC_006569.1 identified by similarity to PIR:S70846; DNA topology modulation kinase FlaR 11192 3196679 SPOA0012 Ruegeria pomeroyi DSS-3 DNA topology modulation kinase FlaR YP_164844.1 10680 D 246200 CDS YP_164845.1 56708804 3196564 11344..12009 1 NC_006569.1 identified by similarity to PIR:S61210; hypothetical protein 12009 3196564 SPOA0013 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164845.1 11344 D 246200 CDS YP_164846.1 56708805 3196748 12070..12783 1 NC_006569.1 tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine; tRNA (guanine-N(7)-)-methyltransferase 12783 trmB 3196748 trmB Ruegeria pomeroyi DSS-3 tRNA (guanine-N(7)-)-methyltransferase YP_164846.1 12070 D 246200 CDS YP_164847.1 56708806 3196800 12930..14276 1 NC_006569.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase 14276 aroA 3196800 aroA Ruegeria pomeroyi DSS-3 3-phosphoshikimate 1-carboxyvinyltransferase YP_164847.1 12930 D 246200 CDS YP_164848.1 56708807 3196828 14273..14890 1 NC_006569.1 Catalyzes the formation of (d)CDP from ATP and (d)CMP; cytidylate kinase 14890 cmk 3196828 cmk Ruegeria pomeroyi DSS-3 cytidylate kinase YP_164848.1 14273 D 246200 CDS YP_164849.1 56708808 3196727 complement(14942..15421) 1 NC_006569.1 identified by similarity to PIR:E82434; match to protein family HMM PF04945; hypothetical protein 15421 3196727 SPOA0018 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164849.1 14942 R 246200 CDS YP_164850.1 56708809 3196767 complement(15573..16718) 1 NC_006569.1 hypothetical protein 16718 3196767 SPOA0019 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164850.1 15573 R 246200 CDS YP_164851.1 56708810 3196689 complement(16728..17900) 1 NC_006569.1 identified by similarity to GB:BAA31547.1; match to protein family HMM PF01168; alanine racemase 17900 3196689 SPOA0020 Ruegeria pomeroyi DSS-3 alanine racemase YP_164851.1 16728 R 246200 CDS YP_164852.1 56708812 3196950 complement(17893..19326) 1 NC_006569.1 identified by match to protein family HMM PF01565; match to protein family HMM TIGR01409; match to protein family HMM TIGR01679; oxidoreductase, FAD-binding 19326 3196950 SPOA0021 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_164852.1 17893 R 246200 CDS YP_164853.1 56708811 3196815 complement(19323..19700) 1 NC_006569.1 identified by similarity to SP:P11732; match to protein family HMM PF00034; cytochrome c5 19700 3196815 SPOA0022 Ruegeria pomeroyi DSS-3 cytochrome c5 YP_164853.1 19323 R 246200 CDS YP_164854.1 56708813 3196853 complement(19700..20356) 1 NC_006569.1 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 20356 3196853 SPOA0023 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_164854.1 19700 R 246200 CDS YP_164855.1 56708814 3196870 complement(20444..21244) 1 NC_006569.1 identified by similarity to SP:P42270; match to protein family HMM PF01689; 2-oxo-hepta-3-ene-1,7-dioic acid hydratase 21244 3196870 SPOA0024 Ruegeria pomeroyi DSS-3 2-oxo-hepta-3-ene-1,7-dioic acid hydratase YP_164855.1 20444 R 246200 CDS YP_164856.1 56708815 3196817 complement(21241..22092) 1 NC_006569.1 identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase family protein 22092 3196817 SPOA0025 Ruegeria pomeroyi DSS-3 fumarylacetoacetate hydrolase family protein YP_164856.1 21241 R 246200 CDS YP_164857.1 56708816 3196605 complement(22119..22970) 1 NC_006569.1 identified by similarity to SP:Q05353; similarity to GB:CAB65144.1; match to protein family HMM PF02900; 3,4-dihydroxyphenylacetate 2,3-dioxygenase 22970 hpcB 3196605 hpcB Ruegeria pomeroyi DSS-3 3,4-dihydroxyphenylacetate 2,3-dioxygenase YP_164857.1 22119 R 246200 CDS YP_164858.1 56708817 3196851 complement(23017..24525) 1 NC_006569.1 identified by similarity to SP:P42269; match to protein family HMM PF00171; 5-carboxy-2-hydroxymuconate semialdehyde dehydrogenase 24525 hpcC 3196851 hpcC Ruegeria pomeroyi DSS-3 5-carboxy-2-hydroxymuconate semialdehyde dehydrogenase YP_164858.1 23017 R 246200 CDS YP_164859.1 56708818 3196751 24898..26241 1 NC_006569.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit A 26241 nqrA 3196751 nqrA Ruegeria pomeroyi DSS-3 Na(+)-translocating NADH-quinone reductase subunit A YP_164859.1 24898 D 246200 CDS YP_164860.1 56708819 3196730 26246..27454 1 NC_006569.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit B 27454 nqrB 3196730 nqrB Ruegeria pomeroyi DSS-3 Na(+)-translocating NADH-quinone reductase subunit B YP_164860.1 26246 D 246200 CDS YP_164861.1 56708820 3196648 27447..28250 1 NC_006569.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit C 28250 nqrC 3196648 nqrC Ruegeria pomeroyi DSS-3 Na(+)-translocating NADH-quinone reductase subunit C YP_164861.1 27447 D 246200 CDS YP_164862.1 56708821 3196881 28250..28903 1 NC_006569.1 Part of the NQR complex which catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit D 28903 nqrD 3196881 nqrD Ruegeria pomeroyi DSS-3 Na(+)-translocating NADH-quinone reductase subunit D YP_164862.1 28250 D 246200 CDS YP_164863.1 56708822 3196744 28903..29511 1 NC_006569.1 Part of the NQR complex which consists of NqrA, NqrB, NqrC, NqrD, NqrE and NqrF; NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm; NqrE is probably involved in the second step, the conversion of ubisemiquinone to ubiquinol.; Na(+)-translocating NADH-quinone reductase subunit E 29511 nqrE 3196744 nqrE Ruegeria pomeroyi DSS-3 Na(+)-translocating NADH-quinone reductase subunit E YP_164863.1 28903 D 246200 CDS YP_164864.1 56708823 3196865 29524..30744 1 NC_006569.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit F 30744 nqrF 3196865 nqrF Ruegeria pomeroyi DSS-3 Na(+)-translocating NADH-quinone reductase subunit F YP_164864.1 29524 D 246200 CDS YP_164865.1 56708824 3196778 complement(30859..31383) 1 NC_006569.1 identified by match to protein family HMM PF00571; CBS domain-containing protein 31383 3196778 SPOA0034 Ruegeria pomeroyi DSS-3 CBS domain-containing protein YP_164865.1 30859 R 246200 CDS YP_164866.1 56708825 3196684 31290..31679 1 NC_006569.1 hypothetical protein 31679 3196684 SPOA0035 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164866.1 31290 D 246200 CDS YP_164867.1 56708826 3196871 31686..32771 1 NC_006569.1 identified by similarity to SP:P41780; match to protein family HMM PF02424; thiamin biosynthesis lipoprotein ApbE 32771 apbE 3196871 apbE Ruegeria pomeroyi DSS-3 thiamin biosynthesis lipoprotein ApbE YP_164867.1 31686 D 246200 CDS YP_164868.1 56708827 3196598 32792..33028 1 NC_006569.1 identified by similarity to GB:BAC95347.1; hypothetical protein 33028 3196598 SPOA0037 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164868.1 32792 D 246200 CDS YP_164869.1 56708828 3196625 complement(33041..34216) 1 NC_006569.1 identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 34216 3196625 SPOA0038 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_164869.1 33041 R 246200 CDS YP_164870.1 56708829 3196726 34623..36542 1 NC_006569.1 identified by similarity to PIR:A83386; hypothetical protein 36542 3196726 SPOA0039 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164870.1 34623 D 246200 CDS YP_164871.1 56708830 3196789 complement(36767..37060) 1 NC_006569.1 identified by match to protein family HMM PF02537; crcB family protein 37060 3196789 SPOA0040 Ruegeria pomeroyi DSS-3 crcB family protein YP_164871.1 36767 R 246200 CDS YP_164872.1 56708831 3196787 complement(37126..37506) 1 NC_006569.1 identified by match to protein family HMM PF02537; crcB family protein 37506 3196787 SPOA0041 Ruegeria pomeroyi DSS-3 crcB family protein YP_164872.1 37126 R 246200 CDS YP_164873.1 56708832 3196918 complement(37538..38389) 1 NC_006569.1 identified by similarity to GB:AAR21632.1; match to protein family HMM PF05853; hypothetical protein 38389 3196918 SPOA0042 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164873.1 37538 R 246200 CDS YP_164874.1 56708833 3196595 complement(38404..39024) 1 NC_006569.1 identified by similarity to GB:AAR21645.1; match to protein family HMM PF00775; protocatechuate 3,4-dioxygenase alpha subunit 39024 pcaG 3196595 pcaG Ruegeria pomeroyi DSS-3 protocatechuate 3,4-dioxygenase alpha subunit YP_164874.1 38404 R 246200 CDS YP_164875.1 56708834 3196582 complement(39088..39816) 1 NC_006569.1 identified by similarity to GB:AAR21644.1; match to protein family HMM PF00775; protocatechuate 3,4-dioxygenase subunit beta 39816 pcaH 3196582 pcaH Ruegeria pomeroyi DSS-3 protocatechuate 3,4-dioxygenase subunit beta YP_164875.1 39088 R 246200 CDS YP_164876.1 56708835 3196569 complement(39861..40238) 1 NC_006569.1 identified by similarity to SP:P20370; match to protein family HMM PF02627; 4-carboxymuconolactone decarboxylase 40238 pcaC 3196569 pcaC Ruegeria pomeroyi DSS-3 4-carboxymuconolactone decarboxylase YP_164876.1 39861 R 246200 CDS YP_164877.1 56708836 3196949 complement(40261..41430) 1 NC_006569.1 catalyzes the formation of protocatechuate from 4-hydroxybenzoate; 4-hydroxybenzoate 3-monooxygenase 41430 pobA 3196949 pobA Ruegeria pomeroyi DSS-3 4-hydroxybenzoate 3-monooxygenase YP_164877.1 40261 R 246200 CDS YP_164878.1 56708837 3196915 41523..42440 1 NC_006569.1 identified by similarity to GB:AAR21641.1; match to protein family HMM PF00126; match to protein family HMM PF03466; pca operon transcriptional activator PcaQ 42440 pcaQ 3196915 pcaQ Ruegeria pomeroyi DSS-3 pca operon transcriptional activator PcaQ YP_164878.1 41523 D 246200 CDS YP_164879.1 56708838 3196690 42513..42911 1 NC_006569.1 hypothetical protein 42911 3196690 SPOA0048 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164879.1 42513 D 246200 CDS YP_164880.1 56708839 3196718 42905..45076 1 NC_006569.1 identified by similarity to SP:Q00790; match to protein family HMM PF04205; nitrous-oxide reductase transcriptional activator NosR 45076 nosR 3196718 nosR Ruegeria pomeroyi DSS-3 nitrous-oxide reductase transcriptional activator NosR YP_164880.1 42905 D 246200 CDS YP_164881.1 56708840 3196583 45091..46998 1 NC_006569.1 reduces nitrous oxide to nitrogen; nitrous-oxide reductase 46998 nosZ 3196583 nosZ Ruegeria pomeroyi DSS-3 nitrous-oxide reductase YP_164881.1 45091 D 246200 CDS YP_164882.1 56708841 3196929 47002..48258 1 NC_006569.1 identified by similarity to SP:P19843; match to protein family HMM PF05048; nitrous oxide maturation protein NosD 48258 nosD 3196929 nosD Ruegeria pomeroyi DSS-3 nitrous oxide maturation protein NosD YP_164882.1 47002 D 246200 CDS YP_164883.1 56708842 3196607 48248..49141 1 NC_006569.1 identified by similarity to SP:P19844; match to protein family HMM PF00005; match to protein family HMM TIGR01189; ABC transporter, ATP-binding protein NosF 49141 nosF 3196607 nosF Ruegeria pomeroyi DSS-3 ABC transporter, ATP-binding protein NosF YP_164883.1 48248 D 246200 CDS YP_164884.1 56708843 3196785 49138..49959 1 NC_006569.1 identified by similarity to SP:P19845; nitrous oxide maturation protein NosY 49959 nosY 3196785 nosY Ruegeria pomeroyi DSS-3 nitrous oxide maturation protein NosY YP_164884.1 49138 D 246200 CDS YP_164885.1 56708844 3196944 49956..50477 1 NC_006569.1 identified by similarity to GB:AAD43477.1; match to protein family HMM PF05573; nitrous oxide reductase accessory protein 50477 nosL 3196944 nosL Ruegeria pomeroyi DSS-3 nitrous oxide reductase accessory protein YP_164885.1 49956 D 246200 CDS YP_164886.1 56708845 3196611 50513..50890 1 NC_006569.1 identified by match to protein family HMM PF00034; cytochrome c family protein 50890 3196611 SPOA0055 Ruegeria pomeroyi DSS-3 cytochrome c family protein YP_164886.1 50513 D 246200 CDS YP_164887.1 56708846 3196902 complement(50922..51536) 1 NC_006569.1 identified by match to protein family HMM PF01381; DNA-binding protein 51536 3196902 SPOA0056 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_164887.1 50922 R 246200 CDS YP_164888.1 56708847 3196668 51916..53013 1 NC_006569.1 identified by match to protein family HMM PF01571; match to protein family HMM TIGR00528; glycine cleavage system T protein 53013 gcvT 3196668 gcvT Ruegeria pomeroyi DSS-3 glycine cleavage system T protein YP_164888.1 51916 D 246200 CDS YP_164889.1 56708848 3196781 53059..53499 1 NC_006569.1 part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor; glycine cleavage system protein H 53499 gcvH-2 3196781 gcvH-2 Ruegeria pomeroyi DSS-3 glycine cleavage system protein H YP_164889.1 53059 D 246200 CDS YP_164890.1 56708849 3196586 53556..56414 1 NC_006569.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase 56414 gcvP 3196586 gcvP Ruegeria pomeroyi DSS-3 glycine dehydrogenase YP_164890.1 53556 D 246200 CDS YP_164891.1 56708850 3196662 56564..57430 1 NC_006569.1 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 57430 3196662 SPOA0060 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_164891.1 56564 D 246200 CDS YP_164892.1 56708851 3196563 complement(57490..59685) 1 NC_006569.1 identified by match to protein family HMM PF00141; match to protein family HMM TIGR00198; catalase/peroxidase HPI 59685 katG 3196563 katG Ruegeria pomeroyi DSS-3 catalase/peroxidase HPI YP_164892.1 57490 R 246200 CDS YP_164893.1 56708852 3196691 complement(59846..60544) 1 NC_006569.1 identified by similarity to PIR:T08467; match to protein family HMM PF01177; match to protein family HMM TIGR00035; aspartate racemase 60544 3196691 SPOA0062 Ruegeria pomeroyi DSS-3 aspartate racemase YP_164893.1 59846 R 246200 CDS YP_164894.1 56708853 3196774 complement(60657..63092) 1 NC_006569.1 identified by match to protein family HMM PF01266; match to protein family HMM PF01571; FAD-dependent oxidoreductase 63092 3196774 SPOA0063 Ruegeria pomeroyi DSS-3 FAD-dependent oxidoreductase YP_164894.1 60657 R 246200 CDS YP_164895.1 56708854 3196641 complement(63234..64016) 1 NC_006569.1 identified by similarity to SP:O08557; match to protein family HMM PF02274; NG,NG-dimethylarginine dimethylaminohydrolase 64016 3196641 SPOA0064 Ruegeria pomeroyi DSS-3 NG,NG-dimethylarginine dimethylaminohydrolase YP_164895.1 63234 R 246200 CDS YP_164896.1 56708855 3196906 complement(64023..65624) 1 NC_006569.1 identified by match to protein family HMM PF00205; match to protein family HMM PF02776; hypothetical protein 65624 3196906 SPOA0065 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164896.1 64023 R 246200 CDS YP_164897.1 56708856 3196573 complement(65624..66811) 1 NC_006569.1 identified by similarity to SP:P23034; match to protein family HMM PF00155; aspartate aminotransferase 66811 3196573 SPOA0066 Ruegeria pomeroyi DSS-3 aspartate aminotransferase YP_164897.1 65624 R 246200 CDS YP_164898.1 56708857 3196941 complement(66808..67455) 1 NC_006569.1 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 67455 3196941 SPOA0067 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_164898.1 66808 R 246200 CDS YP_164899.1 56708858 3196714 67577..68377 1 NC_006569.1 identified by similarity to SP:P07109; match to protein family HMM PF00005; polar amino acid ABC transporter ATP-binding protein 68377 3196714 SPOA0068 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter ATP-binding protein YP_164899.1 67577 D 246200 CDS YP_164900.1 56708859 3196623 68410..69180 1 NC_006569.1 identified by similarity to SP:P39182; similarity to PIR:T44454; match to protein family HMM PF00497; polar amino acid ABC transporter periplasmic substrate-binding protein 69180 3196623 SPOA0069 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter periplasmic substrate-binding protein YP_164900.1 68410 D 246200 CDS YP_164901.1 56708860 3196701 69190..69942 1 NC_006569.1 identified by similarity to PIR:T44455; match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease 69942 3196701 SPOA0070 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter permease YP_164901.1 69190 D 246200 CDS YP_164902.1 56708861 3196695 69939..70727 1 NC_006569.1 identified by similarity to SP:P35114; similarity to PIR:T44456; match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease 70727 3196695 SPOA0071 Ruegeria pomeroyi DSS-3 polar amino acid ABC transporter permease YP_164902.1 69939 D 246200 CDS YP_164903.1 56708862 3196659 70800..71285 1 NC_006569.1 identified by similarity to SP:Q8YF58; hypothetical protein 71285 3196659 SPOA0072 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164903.1 70800 D 246200 CDS YP_164904.1 56708863 3196649 71286..71747 1 NC_006569.1 identified by similarity to SP:Q01257; match to protein family HMM PF01451; arsenate reductase 71747 arsC-2 3196649 arsC-2 Ruegeria pomeroyi DSS-3 arsenate reductase YP_164904.1 71286 D 246200 CDS YP_164905.1 56709228 3196712 71744..72142 1 NC_006569.1 identified by similarity to PIR:C97388; match to protein family HMM TIGR02096; hypothetical protein 72142 3196712 SPOA0074 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164905.1 71744 D 246200 CDS YP_164906.1 56708864 3196585 72135..72728 1 NC_006569.1 identified by similarity to PIR:B97388; hypothetical protein 72728 3196585 SPOA0075 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164906.1 72135 D 246200 CDS YP_164907.1 56708865 3196934 72753..73649 1 NC_006569.1 identified by match to protein family HMM PF00795; carbon-nitrogen family hydrolase 73649 3196934 SPOA0076 Ruegeria pomeroyi DSS-3 carbon-nitrogen family hydrolase YP_164907.1 72753 D 246200 CDS YP_164908.1 56708866 3196692 73720..73938 1 NC_006569.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 73938 infA 3196692 infA Ruegeria pomeroyi DSS-3 translation initiation factor IF-1 YP_164908.1 73720 D 246200 CDS YP_164909.1 56708867 3196780 73949..74527 1 NC_006569.1 identified by match to protein family HMM PF02545; match to protein family HMM TIGR00172; maf protein 74527 maf-2 3196780 maf-2 Ruegeria pomeroyi DSS-3 maf protein YP_164909.1 73949 D 246200 CDS YP_164910.1 56708868 3196772 74524..75546 1 NC_006569.1 identified by similarity to GB:AAQ00701.1; ribonuclease 75546 3196772 SPOA0079 Ruegeria pomeroyi DSS-3 ribonuclease YP_164910.1 74524 D 246200 CDS YP_164911.1 56709231 3196592 75543..75725 1 NC_006569.1 identified by similarity to SP:Q9A5V7; match to protein family HMM PF03884; hypothetical protein 75725 3196592 SPOA0450 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164911.1 75543 D 246200 CDS YP_164912.1 56708869 3196710 complement(76107..77432) 1 NC_006569.1 hypothetical protein 77432 3196710 SPOA0081 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164912.1 76107 R 246200 CDS YP_164913.1 56708870 3196921 complement(77422..79263) 1 NC_006569.1 identified by similarity to GB:BAC49897.1; hypothetical protein 79263 3196921 SPOA0082 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164913.1 77422 R 246200 CDS YP_164914.1 56708871 3196942 complement(79377..80480) 1 NC_006569.1 hypothetical protein 80480 3196942 SPOA0083 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164914.1 79377 R 246200 CDS YP_164915.1 56708872 3196737 complement(80695..80895) 1 NC_006569.1 hypothetical protein 80895 3196737 SPOA0084 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164915.1 80695 R 246200 CDS YP_164916.1 56708873 3196882 complement(80961..81179) 1 NC_006569.1 identified by match to protein family HMM PF01381; DNA-binding protein 81179 3196882 SPOA0085 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_164916.1 80961 R 246200 CDS YP_164917.1 56708874 3196678 complement(82940..84751) 1 NC_006569.1 hypothetical protein 84751 3196678 SPOA0086 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164917.1 82940 R 246200 CDS YP_164918.1 56708875 3196650 complement(85721..86923) 1 NC_006569.1 identified by match to protein family HMM PF00589; phage integrase family site specific recombinase 86923 3196650 SPOA0087 Ruegeria pomeroyi DSS-3 phage integrase family site specific recombinase YP_164918.1 85721 R 246200 CDS YP_164919.1 56708876 3196574 87709..90012 1 NC_006569.1 hypothetical protein 90012 3196574 SPOA0088 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164919.1 87709 D 246200 CDS YP_164920.1 56708877 3196549 90607..91137 1 NC_006569.1 hypothetical protein 91137 3196549 SPOA0089 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164920.1 90607 D 246200 CDS YP_164921.1 56708878 3196568 91354..91923 1 NC_006569.1 identified by match to protein family HMM PF01609; ISSpo7, transposase 91923 3196568 SPOA0090 Ruegeria pomeroyi DSS-3 ISSpo7, transposase YP_164921.1 91354 D 246200 CDS YP_164922.1 56708879 3196951 complement(92045..92353) 1 NC_006569.1 identified by similarity to GB:AAR36473.1; IS3 family transposase orfA 92353 3196951 SPOA0091 Ruegeria pomeroyi DSS-3 IS3 family transposase orfA YP_164922.1 92045 R 246200 CDS YP_164923.1 56708880 3196873 93195..94682 1 NC_006569.1 identified by match to protein family HMM PF01565; FAD binding domain-containing protein 94682 3196873 SPOA0093 Ruegeria pomeroyi DSS-3 FAD binding domain-containing protein YP_164923.1 93195 D 246200 CDS YP_164924.1 56708881 3196922 94679..95089 1 NC_006569.1 hypothetical protein 95089 3196922 SPOA0094 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164924.1 94679 D 246200 CDS YP_164925.1 56708882 3196614 95089..96138 1 NC_006569.1 identified by similarity to GB:BAB49700.1; hypothetical protein 96138 3196614 SPOA0095 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164925.1 95089 D 246200 CDS YP_164926.1 56708883 3196911 complement(96657..97691) 1 NC_006569.1 identified by match to protein family HMM PF00850; histone deacetylase/AcuC/AphA family protein 97691 3196911 SPOA0096 Ruegeria pomeroyi DSS-3 histone deacetylase/AcuC/AphA family protein YP_164926.1 96657 R 246200 CDS YP_164927.1 56708884 3196847 complement(97765..98703) 1 NC_006569.1 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter, permease protein 98703 3196847 SPOA0097 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, permease protein YP_164927.1 97765 R 246200 CDS YP_164928.1 56708885 3196925 complement(98700..99569) 1 NC_006569.1 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter, permease protein 99569 3196925 SPOA0098 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, permease protein YP_164928.1 98700 R 246200 CDS YP_164929.1 56708886 3196658 complement(99566..100270) 1 NC_006569.1 identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter, ATP-binding protein 100270 3196658 SPOA0099 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, ATP-binding protein YP_164929.1 99566 R 246200 CDS YP_164930.1 56708887 3196750 complement(100267..100980) 1 NC_006569.1 identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter, ATP-binding protein 100980 3196750 SPOA0100 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, ATP-binding protein YP_164930.1 100267 R 246200 CDS YP_164931.1 56708888 3196688 complement(100984..102264) 1 NC_006569.1 identified by similarity to GB:CAE37397.1; match to protein family HMM TIGR01409; branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein 102264 3196688 SPOA0101 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein YP_164931.1 100984 R 246200 CDS YP_164932.1 56708889 3196685 complement(102382..103350) 1 NC_006569.1 identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 103350 3196685 SPOA0102 Ruegeria pomeroyi DSS-3 LuxR family transcriptional regulator YP_164932.1 102382 R 246200 CDS YP_164933.1 56708890 3196791 103368..103862 1 NC_006569.1 identified by similarity to GB:BAB49373.1; hypothetical protein 103862 3196791 SPOA0103 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164933.1 103368 D 246200 CDS YP_164934.1 56708891 3196796 103895..105283 1 NC_006569.1 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 105283 3196796 SPOA0104 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_164934.1 103895 D 246200 CDS YP_164935.1 56708892 3196909 complement(105320..105694) 1 NC_006569.1 identified by match to protein family HMM PF01638; transcriptional regulator 105694 3196909 SPOA0105 Ruegeria pomeroyi DSS-3 transcriptional regulator YP_164935.1 105320 R 246200 CDS YP_164936.1 56708893 3196698 105811..106644 1 NC_006569.1 identified by similarity to PIR:E95217; hypothetical protein 106644 3196698 SPOA0106 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164936.1 105811 D 246200 CDS YP_164937.1 56708894 3196832 complement(107348..108241) 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 108241 3196832 SPOA0107 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_164937.1 107348 R 246200 CDS YP_164938.1 56708895 3196809 108335..109549 1 NC_006569.1 hypothetical protein 109549 3196809 SPOA0108 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164938.1 108335 D 246200 CDS YP_164939.1 56709232 3196639 complement(110630..111106) 1 NC_006569.1 identified by similarity to SP:P55740; match to protein family HMM PF01047; MarR family transcriptional regulator 111106 3196639 SPOA0451 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_164939.1 110630 R 246200 CDS YP_164940.1 56709233 3196734 complement(111099..111572) 1 NC_006569.1 identified by similarity to GB:BAC48674.1; match to protein family HMM PF01047; MarR family transcriptional regulator 111572 3196734 SPOA0452 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_164940.1 111099 R 246200 CDS YP_164941.1 56708896 3196935 complement(111593..112039) 1 NC_006569.1 identified by match to protein family HMM PF03061; match to protein family HMM TIGR00051; hypothetical protein 112039 3196935 SPOA0109 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164941.1 111593 R 246200 CDS YP_164942.1 56708897 3196640 complement(112090..113661) 1 NC_006569.1 Involved in the incorporation of exogenous aryl acids in the biosynthesis of aromatic amino acids: catalysis of the ferredoxin-dependent oxidative decarboxylation of arylpyruvates.; indolepyruvate oxidoreductase subunit B 113661 3196640 SPOA0110 Ruegeria pomeroyi DSS-3 indolepyruvate oxidoreductase subunit B YP_164942.1 112090 R 246200 CDS YP_164943.1 56708898 3196838 complement(113658..115832) 1 NC_006569.1 identified by similarity to SP:O07835; match to protein family HMM PF02775; indolepyruvate oxidoreductase, IorA subunit 115832 3196838 SPOA0111 Ruegeria pomeroyi DSS-3 indolepyruvate oxidoreductase, IorA subunit YP_164943.1 113658 R 246200 CDS YP_164944.1 56708899 3196562 115948..117462 1 NC_006569.1 identified by similarity to SP:P80668; match to protein family HMM PF00171; phenylacetaldehyde dehydrogenase 117462 feaB 3196562 feaB Ruegeria pomeroyi DSS-3 phenylacetaldehyde dehydrogenase YP_164944.1 115948 D 246200 CDS YP_164945.1 56708900 3196657 117468..118856 1 NC_006569.1 identified by match to protein family HMM PF00202; hypothetical protein 118856 3196657 SPOA0113 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164945.1 117468 D 246200 CDS YP_164946.1 56708901 3196627 118859..119893 1 NC_006569.1 identified by match to protein family HMM PF00795; nitrilase family protein 119893 3196627 SPOA0114 Ruegeria pomeroyi DSS-3 nitrilase family protein YP_164946.1 118859 D 246200 CDS YP_164947.1 56708902 3196910 119912..121036 1 NC_006569.1 identified by similarity to GB:CAA12267.1; gentisate 1,2-dioxygenase 121036 gtdA-2 3196910 gtdA-2 Ruegeria pomeroyi DSS-3 gentisate 1,2-dioxygenase YP_164947.1 119912 D 246200 CDS YP_164948.1 56708903 3196603 121054..121971 1 NC_006569.1 identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase family protein 121971 3196603 SPOA0116 Ruegeria pomeroyi DSS-3 fumarylacetoacetate hydrolase family protein YP_164948.1 121054 D 246200 CDS YP_164949.1 56708904 3196724 121973..122749 1 NC_006569.1 identified by match to protein family HMM PF01177; Asp/Glu/hydantoin racemase family protein 122749 3196724 SPOA0117 Ruegeria pomeroyi DSS-3 Asp/Glu/hydantoin racemase family protein YP_164949.1 121973 D 246200 CDS YP_164950.1 56708905 3196618 122787..123326 1 NC_006569.1 hypothetical protein 123326 3196618 SPOA0118 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164950.1 122787 D 246200 CDS YP_164951.1 56708906 3196671 123338..124879 1 NC_006569.1 identified by match to protein family HMM PF01970; hypothetical protein 124879 3196671 SPOA0119 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164951.1 123338 D 246200 CDS YP_164952.1 56708907 3196565 125015..125953 1 NC_006569.1 identified by similarity to GB:BAC94333.1; match to protein family HMM PF03401; hypothetical protein 125953 3196565 SPOA0120 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164952.1 125015 D 246200 CDS YP_164953.1 56708908 3196629 126010..127668 1 NC_006569.1 identified by match to protein family HMM PF00884; sulfatase family protein 127668 3196629 SPOA0121 Ruegeria pomeroyi DSS-3 sulfatase family protein YP_164953.1 126010 D 246200 CDS YP_164954.1 56708909 3196681 complement(128113..129045) 1 NC_006569.1 identified by match to protein family HMM PF01609; ISSpo9, transposase 129045 3196681 SPOA0122 Ruegeria pomeroyi DSS-3 ISSpo9, transposase YP_164954.1 128113 R 246200 CDS YP_164955.1 56708910 3196837 129275..132235 1 NC_006569.1 identified by similarity to GB:AAQ60231.1; hypothetical protein 132235 3196837 SPOA0123 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164955.1 129275 D 246200 CDS YP_164956.1 56708911 3196899 132272..135232 1 NC_006569.1 identified by similarity to PIR:A82083; hypothetical protein 135232 3196899 SPOA0124 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164956.1 132272 D 246200 CDS YP_164957.1 56708912 3196852 135246..136139 1 NC_006569.1 hypothetical protein 136139 3196852 SPOA0125 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164957.1 135246 D 246200 CDS YP_164958.1 56708913 3196762 complement(136399..137124) 1 NC_006569.1 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase family oxidoreductase 137124 3196762 SPOA0126 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase family oxidoreductase YP_164958.1 136399 R 246200 CDS YP_164959.1 56708914 3196636 complement(137121..137912) 1 NC_006569.1 identified by match to protein family HMM PF04199; cyclase 137912 3196636 SPOA0127 Ruegeria pomeroyi DSS-3 cyclase YP_164959.1 137121 R 246200 CDS YP_164960.1 56708915 3196947 complement(137909..139147) 1 NC_006569.1 identified by match to protein family HMM PF00106; match to protein family HMM PF01796; short chain dehydrogenase/reductase family oxidoreductase 139147 3196947 SPOA0128 Ruegeria pomeroyi DSS-3 short chain dehydrogenase/reductase family oxidoreductase YP_164960.1 137909 R 246200 CDS YP_164961.1 56708916 3196928 complement(139144..140319) 1 NC_006569.1 hypothetical protein 140319 3196928 SPOA0129 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164961.1 139144 R 246200 CDS YP_164962.1 56708917 3196889 complement(140319..141938) 1 NC_006569.1 identified by match to protein family HMM PF00501; AMP-binding protein 141938 3196889 SPOA0130 Ruegeria pomeroyi DSS-3 AMP-binding protein YP_164962.1 140319 R 246200 CDS YP_164963.1 56708918 3196891 complement(141940..142413) 1 NC_006569.1 identified by match to protein family HMM PF00866; aromatic 1,2-dioxygenase, beta subunit 142413 3196891 SPOA0131 Ruegeria pomeroyi DSS-3 aromatic 1,2-dioxygenase, beta subunit YP_164963.1 141940 R 246200 CDS YP_164964.1 56708919 3196890 complement(142410..143750) 1 NC_006569.1 identified by match to protein family HMM PF00355; match to protein family HMM PF00848; aromatic 1,2-dioxygenase, alpha subunit 143750 3196890 SPOA0132 Ruegeria pomeroyi DSS-3 aromatic 1,2-dioxygenase, alpha subunit YP_164964.1 142410 R 246200 CDS YP_164965.1 56708920 3196936 complement(143773..144717) 1 NC_006569.1 identified by match to protein family HMM PF00111; match to protein family HMM PF00175; match to protein family HMM PF00970; oxidoreductase 144717 3196936 SPOA0133 Ruegeria pomeroyi DSS-3 oxidoreductase YP_164965.1 143773 R 246200 CDS YP_164966.1 56708921 3196888 145949..146518 1 NC_006569.1 identified by match to protein family HMM PF01609; ISSpo7, transposase 146518 3196888 SPOA0134 Ruegeria pomeroyi DSS-3 ISSpo7, transposase YP_164966.1 145949 D 246200 CDS YP_164967.1 56708922 3196930 147504..147659 1 NC_006569.1 hypothetical protein 147659 3196930 SPOA0136 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164967.1 147504 D 246200 CDS YP_164968.1 56708923 3196760 147666..148931 1 NC_006569.1 adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active; UDP-N-acetylglucosamine 1-carboxyvinyltransferase 148931 murA 3196760 murA Ruegeria pomeroyi DSS-3 UDP-N-acetylglucosamine 1-carboxyvinyltransferase YP_164968.1 147666 D 246200 CDS YP_164969.1 56708924 3196557 148931..149407 1 NC_006569.1 identified by similarity to GB:AAK24320.1; hypothetical protein 149407 3196557 SPOA0138 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164969.1 148931 D 246200 CDS YP_164970.1 56708925 3196725 149467..149946 1 NC_006569.1 identified by match to protein family HMM PF00583; acetyltransferase 149946 3196725 SPOA0139 Ruegeria pomeroyi DSS-3 acetyltransferase YP_164970.1 149467 D 246200 CDS YP_164971.1 56708926 3196567 complement(149971..151794) 1 NC_006569.1 identified by similarity to SP:Q56213; match to protein family HMM PF00310; match to protein family HMM PF01380; match to protein family HMM TIGR01135; glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 151794 glmS 3196567 glmS Ruegeria pomeroyi DSS-3 glucosamine--fructose-6-phosphate aminotransferase (isomerizing) YP_164971.1 149971 R 246200 CDS YP_164972.1 56708927 3196907 152200..152550 1 NC_006569.1 identified by similarity to PIR:C95361; hypothetical protein 152550 3196907 SPOA0141 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164972.1 152200 D 246200 CDS YP_164973.1 56708928 3196676 152550..153062 1 NC_006569.1 identified by similarity to GB:BAB54840.1; hypothetical protein 153062 3196676 SPOA0142 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164973.1 152550 D 246200 CDS YP_164974.1 56708929 3196752 complement(153574..154419) 1 NC_006569.1 identified by match to protein family HMM PF01614; IclR family transcriptional regulator 154419 3196752 SPOA0143 Ruegeria pomeroyi DSS-3 IclR family transcriptional regulator YP_164974.1 153574 R 246200 CDS YP_164975.1 56708930 3196833 154606..155796 1 NC_006569.1 identified by similarity to SP:O08374; match to protein family HMM PF00266; serine--glyoxylate transaminase 155796 3196833 SPOA0144 Ruegeria pomeroyi DSS-3 serine--glyoxylate transaminase YP_164975.1 154606 D 246200 CDS YP_164976.1 56708931 3196610 155809..156762 1 NC_006569.1 identified by match to protein family HMM PF00291; pyridoxal-phosphate dependent enzyme 156762 3196610 SPOA0145 Ruegeria pomeroyi DSS-3 pyridoxal-phosphate dependent enzyme YP_164976.1 155809 D 246200 CDS YP_164977.1 56708932 3196834 156768..157931 1 NC_006569.1 identified by similarity to GB:BAA31547.1; match to protein family HMM PF01168; threonine aldolase 157931 3196834 SPOA0146 Ruegeria pomeroyi DSS-3 threonine aldolase YP_164977.1 156768 D 246200 CDS YP_164978.1 56708933 3196758 158076..158954 1 NC_006569.1 identified by match to protein family HMM PF02423; ornithine cyclodeaminase/mu-crystallin family protein 158954 3196758 SPOA0147 Ruegeria pomeroyi DSS-3 ornithine cyclodeaminase/mu-crystallin family protein YP_164978.1 158076 D 246200 CDS YP_164979.1 56708934 3196682 complement(159056..160213) 1 NC_006569.1 identified by similarity to SP:P43531; major facilitator transporter 160213 3196682 SPOA0148 Ruegeria pomeroyi DSS-3 major facilitator transporter YP_164979.1 159056 R 246200 CDS YP_164980.1 56708935 3196620 160318..161634 1 NC_006569.1 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 161634 3196620 SPOA0149 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_164980.1 160318 D 246200 CDS YP_164981.1 56708936 3196666 complement(161659..162696) 1 NC_006569.1 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 162696 3196666 SPOA0150 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_164981.1 161659 R 246200 CDS YP_164982.1 56708937 3196644 162796..163413 1 NC_006569.1 identified by match to protein family HMM PF00034; cytochrome c family protein 163413 3196644 SPOA0151 Ruegeria pomeroyi DSS-3 cytochrome c family protein YP_164982.1 162796 D 246200 CDS YP_164983.1 56708938 3196708 163457..164533 1 NC_006569.1 identified by match to protein family HMM PF03150; di-haem cytochrome c peroxidase family protein 164533 3196708 SPOA0152 Ruegeria pomeroyi DSS-3 di-haem cytochrome c peroxidase family protein YP_164983.1 163457 D 246200 CDS YP_164984.1 56708939 3196643 164552..165628 1 NC_006569.1 hypothetical protein 165628 3196643 SPOA0153 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164984.1 164552 D 246200 CDS YP_164985.1 56708940 3196572 165646..167022 1 NC_006569.1 hypothetical protein 167022 3196572 SPOA0154 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164985.1 165646 D 246200 CDS YP_164986.1 56708941 3196807 complement(167176..171612) 1 NC_006569.1 identified by match to protein family HMM PF00092; match to protein family HMM PF00353; type I secretion target repeat-containing protein 171612 3196807 SPOA0155 Ruegeria pomeroyi DSS-3 type I secretion target repeat-containing protein YP_164986.1 167176 R 246200 CDS YP_164987.1 56708942 3196913 complement(171697..172530) 1 NC_006569.1 hypothetical protein 172530 3196913 SPOA0156 Ruegeria pomeroyi DSS-3 hypothetical protein YP_164987.1 171697 R 246200 CDS YP_164988.1 56708943 3196878 complement(172937..173923) 1 NC_006569.1 nducibly transcribed; Denger et al. Biochem. J. (2006) 394:657-664; sulfite exporter, CuyZ 173923 3196878 SPOA0157 Ruegeria pomeroyi DSS-3 sulfite exporter, CuyZ YP_164988.1 172937 R 246200 CDS YP_164989.1 56708944 3196642 complement(173964..174983) 1 NC_006569.1 Catalyzes the desulfonation of L-cysteate to sulfite, ammonium ion and pyruvate.; L-cysteate sulfo-lyase 174983 cuyA 3196642 cuyA Ruegeria pomeroyi DSS-3 L-cysteate sulfo-lyase YP_164989.1 173964 R 246200 CDS YP_164990.1 56708945 3196606 175095..175997 1 NC_006569.1 transcriptional regulator, LysR family, presumably for cysteate degradation; identified by match to protein family HMM PF00126; match to protein family HMM PF03466; Denger et al. Biochem. J. (2006) 394:657-664; transcriptional regulator CuyR 175997 cuyR 3196606 cuyR Ruegeria pomeroyi DSS-3 transcriptional regulator CuyR YP_164990.1 175095 D 246200 CDS YP_164991.1 56708946 3196665 complement(176064..177386) 1 NC_006569.1 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter, DctM subunit 177386 3196665 SPOA0160 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctM subunit YP_164991.1 176064 R 246200 CDS YP_164992.1 56708947 3196843 complement(177386..177877) 1 NC_006569.1 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit 177877 3196843 SPOA0161 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctQ subunit YP_164992.1 177386 R 246200 CDS YP_164993.1 56708948 3196844 complement(177943..178977) 1 NC_006569.1 identified by match to protein family HMM PF03480; match to protein family HMM TIGR01409; TRAP dicarboxylate family transporter DctP subunit 178977 3196844 SPOA0162 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate family transporter DctP subunit YP_164993.1 177943 R 246200 CDS YP_164994.1 56708949 3196619 complement(179002..180303) 1 NC_006569.1 identified by similarity to SP:P13702; match to protein family HMM PF00368; match to protein family HMM TIGR00532; hydroxymethylglutaryl-CoA reductase, degradative 180303 mvaA 3196619 mvaA Ruegeria pomeroyi DSS-3 hydroxymethylglutaryl-CoA reductase, degradative YP_164994.1 179002 R 246200 CDS YP_164995.1 56708950 3196634 180424..181809 1 NC_006569.1 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 181809 3196634 SPOA0164 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_164995.1 180424 D 246200 CDS YP_164996.1 56708951 3196587 complement(181865..182800) 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 182800 3196587 SPOA0165 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_164996.1 181865 R 246200 CDS YP_164997.1 56708952 3196761 182941..183951 1 NC_006569.1 identified by similarity to SP:P12920; match to protein family HMM TIGR02122; TRAP transporter solute receptor TAXI family protein 183951 3196761 SPOA0166 Ruegeria pomeroyi DSS-3 TRAP transporter solute receptor TAXI family protein YP_164997.1 182941 D 246200 CDS YP_164998.1 56708953 3196555 184036..186249 1 NC_006569.1 identified by match to protein family HMM PF06808; match to protein family HMM TIGR02123; TRAP transporter, 4TM/12TM fusion protein 186249 3196555 SPOA0167 Ruegeria pomeroyi DSS-3 TRAP transporter, 4TM/12TM fusion protein YP_164998.1 184036 D 246200 CDS YP_164999.1 56708954 3196816 186254..187519 1 NC_006569.1 identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding 187519 3196816 SPOA0168 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_164999.1 186254 D 246200 CDS YP_165000.1 56708955 3196670 complement(187676..188389) 1 NC_006569.1 identified by match to protein family HMM PF03473; MOSC domain-containing protein 188389 3196670 SPOA0169 Ruegeria pomeroyi DSS-3 MOSC domain-containing protein YP_165000.1 187676 R 246200 CDS YP_165001.1 56708956 3196876 complement(188365..188907) 1 NC_006569.1 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 188907 3196876 SPOA0170 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_165001.1 188365 R 246200 CDS YP_165002.1 56708957 3196783 188994..189755 1 NC_006569.1 identified by similarity to GB:BAC91536.1; hypothetical protein 189755 3196783 SPOA0171 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165002.1 188994 D 246200 CDS YP_165003.1 56708958 3196848 189812..190042 1 NC_006569.1 identified by similarity to GB:BAC91595.1; hypothetical protein 190042 3196848 SPOA0172 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165003.1 189812 D 246200 CDS YP_165004.1 56708959 3196581 190045..190572 1 NC_006569.1 identified by similarity to GB:CAD84048.1; hypothetical protein 190572 3196581 SPOA0173 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165004.1 190045 D 246200 CDS YP_165005.1 56708960 3196877 190647..191114 1 NC_006569.1 identified by match to protein family HMM PF03473; MOSC domain-containing protein 191114 3196877 SPOA0174 Ruegeria pomeroyi DSS-3 MOSC domain-containing protein YP_165005.1 190647 D 246200 CDS YP_165006.1 56708961 3196702 191127..192059 1 NC_006569.1 identified by match to protein family HMM PF00111; match to protein family HMM PF00175; match to protein family HMM PF00970; oxidoreductase 192059 3196702 SPOA0175 Ruegeria pomeroyi DSS-3 oxidoreductase YP_165006.1 191127 D 246200 CDS YP_165007.1 56708962 3196561 192016..192447 1 NC_006569.1 identified by similarity to GB:AAM38898.1; hypothetical protein 192447 3196561 SPOA0176 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165007.1 192016 D 246200 CDS YP_165008.1 56708963 3196842 complement(192528..193220) 1 NC_006569.1 identified by similarity to SP:P11721; match to protein family HMM PF00126; match to protein family HMM PF03466; hydrogen peroxide-inducible genes activator 193220 3196842 SPOA0177 Ruegeria pomeroyi DSS-3 hydrogen peroxide-inducible genes activator YP_165008.1 192528 R 246200 CDS YP_165009.1 56708964 3196723 complement(194488..194853) 1 NC_006569.1 identified by match to protein family HMM PF00034; cytochrome c family protein 194853 3196723 SPOA0180 Ruegeria pomeroyi DSS-3 cytochrome c family protein YP_165009.1 194488 R 246200 CDS YP_165010.1 56708965 3196860 complement(194918..195736) 1 NC_006569.1 identified by match to protein family HMM PF01226; FNT family protein 195736 3196860 SPOA0181 Ruegeria pomeroyi DSS-3 FNT family protein YP_165010.1 194918 R 246200 CDS YP_165011.1 56708966 3196943 complement(195733..196302) 1 NC_006569.1 hypothetical protein 196302 3196943 SPOA0182 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165011.1 195733 R 246200 CDS YP_165012.1 56708967 3196655 complement(196299..196898) 1 NC_006569.1 identified by match to protein family HMM PF02630; SCO1/SenC family protein 196898 3196655 SPOA0183 Ruegeria pomeroyi DSS-3 SCO1/SenC family protein YP_165012.1 196299 R 246200 CDS YP_165013.1 56708968 3196673 complement(196898..198328) 1 NC_006569.1 identified by similarity to SP:P33518; match to protein family HMM PF00115; heme-copper respiratory oxidase family 198328 3196673 SPOA0184 Ruegeria pomeroyi DSS-3 heme-copper respiratory oxidase family YP_165013.1 196898 R 246200 CDS YP_165014.1 56708969 3196939 complement(198329..198838) 1 NC_006569.1 identified by similarity to SP:P98052; cytochrome c oxidase,ba3-type, subunit I 198838 3196939 SPOA0185 Ruegeria pomeroyi DSS-3 cytochrome c oxidase,ba3-type, subunit I YP_165014.1 198329 R 246200 CDS YP_165015.1 56708970 3196952 198944..199426 1 NC_006569.1 identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738; Rrf2 family protein 199426 3196952 SPOA0186 Ruegeria pomeroyi DSS-3 Rrf2 family protein YP_165015.1 198944 D 246200 CDS YP_165016.1 56708971 3196575 complement(199725..200597) 1 NC_006569.1 identified by similarity to GB:AAC72074.1; match to protein family HMM PF00034; match to protein family HMM TIGR00782; cytochrome c oxidase, cbb3-type, subunit III 200597 ccoP-2 3196575 ccoP-2 Ruegeria pomeroyi DSS-3 cytochrome c oxidase, cbb3-type, subunit III YP_165016.1 199725 R 246200 CDS YP_165017.1 56708972 3196872 complement(200588..200755) 1 NC_006569.1 identified by similarity to GB:AAM76066.1; match to protein family HMM PF05545; cytochrome c oxidase, cbb3-type, subunit IV 200755 ccoQ-2 3196872 ccoQ-2 Ruegeria pomeroyi DSS-3 cytochrome c oxidase, cbb3-type, subunit IV YP_165017.1 200588 R 246200 CDS YP_165018.1 56708973 3196813 complement(200752..201483) 1 NC_006569.1 identified by match to protein family HMM PF02433; match to protein family HMM TIGR00781; cytochrome c oxidase, cbb3-type, subunit II 201483 ccoO-2 3196813 ccoO-2 Ruegeria pomeroyi DSS-3 cytochrome c oxidase, cbb3-type, subunit II YP_165018.1 200752 R 246200 CDS YP_165019.1 56708974 3196716 complement(201488..203110) 1 NC_006569.1 identified by similarity to SP:P98055; match to protein family HMM PF00115; match to protein family HMM TIGR00780; cytochrome c oxidase, cbb3-type, subunit I 203110 ccoN-2 3196716 ccoN-2 Ruegeria pomeroyi DSS-3 cytochrome c oxidase, cbb3-type, subunit I YP_165019.1 201488 R 246200 CDS YP_165020.1 56708975 3196917 complement(203113..203904) 1 NC_006569.1 hypothetical protein 203904 3196917 SPOA0191 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165020.1 203113 R 246200 CDS YP_165021.1 56708976 3196940 complement(203945..204364) 1 NC_006569.1 hypothetical protein 204364 3196940 SPOA0192 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165021.1 203945 R 246200 CDS YP_165022.1 56708977 3196798 complement(204477..204896) 1 NC_006569.1 CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane; cytochrome c-type biogenesis protein CcmE 204896 cycJ 3196798 cycJ Ruegeria pomeroyi DSS-3 cytochrome c-type biogenesis protein CcmE YP_165022.1 204477 R 246200 CDS YP_165023.1 56708978 3196856 complement(204899..206140) 1 NC_006569.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 206140 hemA-2 3196856 hemA-2 Ruegeria pomeroyi DSS-3 5-aminolevulinate synthase YP_165023.1 204899 R 246200 CDS YP_165024.1 56708979 3196818 complement(206169..207119) 1 NC_006569.1 identified by similarity to GB:AAM30460.1; hypothetical protein 207119 3196818 SPOA0195 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165024.1 206169 R 246200 CDS YP_165025.1 56708980 3196924 complement(207119..207571) 1 NC_006569.1 identified by similarity to SP:P45406; match to protein family HMM PF03918; cytochrome c-type biogenesis protein CycL 207571 cycL 3196924 cycL Ruegeria pomeroyi DSS-3 cytochrome c-type biogenesis protein CycL YP_165025.1 207119 R 246200 CDS YP_165026.1 56708981 3196879 complement(207568..208134) 1 NC_006569.1 identified by similarity to SP:P33926; match to protein family HMM TIGR00385; thiol:disulfide interchange protein DsbE 208134 dsbE 3196879 dsbE Ruegeria pomeroyi DSS-3 thiol:disulfide interchange protein DsbE YP_165026.1 207568 R 246200 CDS YP_165027.1 56708982 3196775 complement(208131..210131) 1 NC_006569.1 identified by similarity to SP:Q00500; match to protein family HMM PF01578; cytochrome c-type biogenesis protein CycK 210131 cycK 3196775 cycK Ruegeria pomeroyi DSS-3 cytochrome c-type biogenesis protein CycK YP_165027.1 208131 R 246200 CDS YP_165028.1 56708983 3196894 complement(210138..211616) 1 NC_006569.1 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 211616 3196894 SPOA0199 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_165028.1 210138 R 246200 CDS YP_165029.1 56708984 3196823 complement(211718..212725) 1 NC_006569.1 identified by similarity to GB:CAD86250.1; hypothetical protein 212725 3196823 SPOA0200 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165029.1 211718 R 246200 CDS YP_165030.1 56708985 3196923 complement(212759..214345) 1 NC_006569.1 identified by similarity to SP:Q50925; hydroxylamine oxidoreductase 214345 3196923 SPOA0201 Ruegeria pomeroyi DSS-3 hydroxylamine oxidoreductase YP_165030.1 212759 R 246200 CDS YP_165031.1 56708986 3196717 214950..216251 1 NC_006569.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 216251 hisD 3196717 hisD Ruegeria pomeroyi DSS-3 histidinol dehydrogenase YP_165031.1 214950 D 246200 CDS YP_165032.1 56708987 3196661 complement(216248..219547) 1 NC_006569.1 hypothetical protein 219547 3196661 SPOA0203 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165032.1 216248 R 246200 CDS YP_165033.1 56708988 3196788 complement(219959..221563) 1 NC_006569.1 hypothetical protein 221563 3196788 SPOA0204 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165033.1 219959 R 246200 CDS YP_165034.1 56708989 3196869 complement(221560..224325) 1 NC_006569.1 identified by match to protein family HMM PF00082; serine protease 224325 3196869 SPOA0205 Ruegeria pomeroyi DSS-3 serine protease YP_165034.1 221560 R 246200 CDS YP_165035.1 56708990 3196825 224583..225284 1 NC_006569.1 identified by match to protein family HMM PF00027; match to protein family HMM PF00325; Crp/Fnr family transcriptional regulator 225284 3196825 SPOA0206 Ruegeria pomeroyi DSS-3 Crp/Fnr family transcriptional regulator YP_165035.1 224583 D 246200 CDS YP_165036.1 56708991 3196703 complement(225279..228305) 1 NC_006569.1 identified by match to protein family HMM PF00211; match to protein family HMM PF00536; match to protein family HMM PF06498; guanylate cyclase 228305 3196703 SPOA0207 Ruegeria pomeroyi DSS-3 guanylate cyclase YP_165036.1 225279 R 246200 CDS YP_165037.1 56708992 3196826 complement(228322..229908) 1 NC_006569.1 identified by similarity to SP:P43485; match to protein family HMM PF01565; oxidoreductase, FAD-binding 229908 3196826 SPOA0208 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_165037.1 228322 R 246200 CDS YP_165038.1 56708993 3196920 complement(230029..231330) 1 NC_006569.1 identified by similarity to GB:AAQ59009.1; match to protein family HMM PF01266; oxidoreductase, FAD-binding 231330 3196920 SPOA0209 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_165038.1 230029 R 246200 CDS YP_165039.1 56708994 3196892 complement(231416..232255) 1 NC_006569.1 identified by similarity to GB:BAC71325.1; match to protein family HMM PF00892; hypothetical protein 232255 3196892 SPOA0210 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165039.1 231416 R 246200 CDS YP_165040.1 56708995 3196558 complement(232257..233939) 1 NC_006569.1 identified by match to protein family HMM PF02690; Na/Pi-cotransporter family protein 233939 3196558 SPOA0211 Ruegeria pomeroyi DSS-3 Na/Pi-cotransporter family protein YP_165040.1 232257 R 246200 CDS YP_165041.1 56708996 3196886 complement(234160..234417) 1 NC_006569.1 nitric oxide reductase F protein 234417 3196886 SPOA0212 Ruegeria pomeroyi DSS-3 nitric oxide reductase F protein YP_165041.1 234160 R 246200 CDS YP_165042.1 56708997 3196594 complement(234422..234925) 1 NC_006569.1 identified by match to protein family HMM PF00510; nitric oxide reductase E protein 234925 3196594 SPOA0213 Ruegeria pomeroyi DSS-3 nitric oxide reductase E protein YP_165042.1 234422 R 246200 CDS YP_165043.1 56708998 3196547 complement(234967..236889) 1 NC_006569.1 identified by similarity to GB:AAC45374.1; nitric oxide reductase D protein 236889 norD 3196547 norD Ruegeria pomeroyi DSS-3 nitric oxide reductase D protein YP_165043.1 234967 R 246200 CDS YP_165044.1 56708999 3196863 complement(236898..237713) 1 NC_006569.1 identified by similarity to SP:Q51664; nitric oxide reductase Q protein 237713 norQ 3196863 norQ Ruegeria pomeroyi DSS-3 nitric oxide reductase Q protein YP_165044.1 236898 R 246200 CDS YP_165045.1 56709000 3196893 complement(237713..239080) 1 NC_006569.1 identified by similarity to GB:AAC45372.1; match to protein family HMM PF00115; nitric oxide reductase, large subunit 239080 norB 3196893 norB Ruegeria pomeroyi DSS-3 nitric oxide reductase, large subunit YP_165045.1 237713 R 246200 CDS YP_165046.1 56709001 3196811 complement(239096..239548) 1 NC_006569.1 identified by similarity to SP:Q51662; match to protein family HMM PF00034; nitric oxide reductase, small subunit 239548 norC 3196811 norC Ruegeria pomeroyi DSS-3 nitric oxide reductase, small subunit YP_165046.1 239096 R 246200 CDS YP_165047.1 56709002 3196884 239774..240742 1 NC_006569.1 identified by match to protein family HMM PF01544; magnesium transporter CorA family protein 240742 3196884 SPOA0218 Ruegeria pomeroyi DSS-3 magnesium transporter CorA family protein YP_165047.1 239774 D 246200 CDS YP_165048.1 56709003 3196836 complement(240753..241925) 1 NC_006569.1 identified by match to protein family HMM PF05940; NnrS 241925 3196836 SPOA0219 Ruegeria pomeroyi DSS-3 NnrS YP_165048.1 240753 R 246200 CDS YP_165049.1 56709004 3196854 242141..243835 1 NC_006569.1 identified by similarity to SP:P24474; match to protein family HMM PF00034; match to protein family HMM PF02239; cytochrome cd1 nitrite reductase 243835 nirS 3196854 nirS Ruegeria pomeroyi DSS-3 cytochrome cd1 nitrite reductase YP_165049.1 242141 D 246200 CDS YP_165050.1 56709005 3196801 243923..244696 1 NC_006569.1 identified by similarity to SP:Q51701; match to protein family HMM PF00590; match to protein family HMM TIGR01469; nitrite reductase heme biosynthesis E protein 244696 nirE 3196801 nirE Ruegeria pomeroyi DSS-3 nitrite reductase heme biosynthesis E protein YP_165050.1 243923 D 246200 CDS YP_165051.1 56709006 3196883 244716..245048 1 NC_006569.1 identified by similarity to SP:Q51702; cytochrome c55X 245048 nirC 3196883 nirC Ruegeria pomeroyi DSS-3 cytochrome c55X YP_165051.1 244716 D 246200 CDS YP_165052.1 56709007 3196829 245045..246190 1 NC_006569.1 identified by similarity to SP:Q51480; match to protein family HMM PF02239; cytochrome cd1 nitrite reductase 246190 nirF 3196829 nirF Ruegeria pomeroyi DSS-3 cytochrome cd1 nitrite reductase YP_165052.1 245045 D 246200 CDS YP_165053.1 56709008 3196958 246196..247188 1 NC_006569.1 appears to be fusion of nirD and nir; Lidentified by similarity to PIR:G83581; match to protein family HMM PF01037; nitrite reductase heme biosynthesis D/L protein 247188 3196958 SPOA0224 Ruegeria pomeroyi DSS-3 nitrite reductase heme biosynthesis D/L protein YP_165053.1 246196 D 246200 CDS YP_165054.1 56709009 3196840 247185..247634 1 NC_006569.1 identified by similarity to SP:Q52524; nitrite reductase heme biosynthesis G protein 247634 nirG 3196840 nirG Ruegeria pomeroyi DSS-3 nitrite reductase heme biosynthesis G protein YP_165054.1 247185 D 246200 CDS YP_165055.1 56709010 3196735 247631..248113 1 NC_006569.1 identified by similarity to SP:Q52525; nitrite reductase heme biosynthesis H protein 248113 nirH 3196735 nirH Ruegeria pomeroyi DSS-3 nitrite reductase heme biosynthesis H protein YP_165055.1 247631 D 246200 CDS YP_165056.1 56709011 3196859 248115..249326 1 NC_006569.1 identified by similarity to PIR:C83581; match to protein family HMM PF04055; nitrite reductase heme biosynthesis J protein 249326 nirJ 3196859 nirJ Ruegeria pomeroyi DSS-3 nitrite reductase heme biosynthesis J protein YP_165056.1 248115 D 246200 CDS YP_165057.1 56709012 3196677 249427..250938 1 NC_006569.1 identified by similarity to GB:BAA12683.1; match to protein family HMM PF00034; match to protein family HMM PF02239; nitrite reductase protein N 250938 nirN 3196677 nirN Ruegeria pomeroyi DSS-3 nitrite reductase protein N YP_165057.1 249427 D 246200 CDS YP_165058.1 56709013 3196908 250979..251170 1 NC_006569.1 hypothetical protein 251170 3196908 SPOA0229 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165058.1 250979 D 246200 CDS YP_165059.1 56709014 3196653 complement(251221..252138) 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 252138 3196653 SPOA0230 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165059.1 251221 R 246200 CDS YP_165060.1 56709015 3196802 252309..253250 1 NC_006569.1 identified by similarity to SP:P14177; match to protein family HMM PF04069; glycine betaine/proline ABC transporter, periplasmic substrate-binding protein 253250 3196802 SPOA0231 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter, periplasmic substrate-binding protein YP_165060.1 252309 D 246200 CDS YP_165061.1 56709016 3196706 253363..254415 1 NC_006569.1 identified by similarity to SP:P46920; match to protein family HMM PF00005; match to protein family HMM TIGR01186; glycine betaine/proline ABC transporter, ATP-binding protein 254415 opuAA 3196706 opuAA Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter, ATP-binding protein YP_165061.1 253363 D 246200 CDS YP_165062.1 56709017 3196782 254412..255986 1 NC_006569.1 identified by similarity to SP:P14176; match to protein family HMM PF00528; glycine betaine/proline ABC transporter, permease protein 255986 3196782 SPOA0233 Ruegeria pomeroyi DSS-3 glycine betaine/proline ABC transporter, permease protein YP_165062.1 254412 D 246200 CDS YP_165063.1 56709018 3196550 256041..257039 1 NC_006569.1 identified by similarity to SP:Q9BSE5; match to protein family HMM PF00491; agmatinase 257039 3196550 SPOA0234 Ruegeria pomeroyi DSS-3 agmatinase YP_165063.1 256041 D 246200 CDS YP_165064.1 56709019 3196895 257036..258022 1 NC_006569.1 identified by similarity to SP:Q9BSE5; match to protein family HMM PF00491; match to protein family HMM TIGR01230; agmatinase 258022 speB-4 3196895 speB-4 Ruegeria pomeroyi DSS-3 agmatinase YP_165064.1 257036 D 246200 CDS YP_165065.1 56709020 3196651 258234..259955 1 NC_006569.1 identified by similarity to SP:P10047; match to protein family HMM PF00512; match to protein family HMM PF02518; C4-dicarboxylate transport sensor protein dctB 259955 dctB 3196651 dctB Ruegeria pomeroyi DSS-3 C4-dicarboxylate transport sensor protein dctB YP_165065.1 258234 D 246200 CDS YP_165066.1 56709021 3196880 259961..261301 1 NC_006569.1 identified by similarity to SP:P13632; match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954; match to protein family HMM TIGR01199; C4-dicarboxylate transport transcriptional regulatory protein DctD 261301 dctD-2 3196880 dctD-2 Ruegeria pomeroyi DSS-3 C4-dicarboxylate transport transcriptional regulatory protein DctD YP_165066.1 259961 D 246200 CDS YP_165067.1 56709022 3196835 261428..262441 1 NC_006569.1 identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter, DctP subunit 262441 3196835 SPOA0238 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctP subunit YP_165067.1 261428 D 246200 CDS YP_165068.1 56709023 3196875 262516..263151 1 NC_006569.1 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit 263151 3196875 SPOA0239 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctQ subunit YP_165068.1 262516 D 246200 CDS YP_165069.1 56709024 3196914 263144..264544 1 NC_006569.1 identified by match to protein family HMM PF06808; TRAP transporter, DctM subunit 264544 3196914 SPOA0240 Ruegeria pomeroyi DSS-3 TRAP transporter, DctM subunit YP_165069.1 263144 D 246200 CDS YP_165070.1 56709025 3196672 complement(264766..265689) 1 NC_006569.1 identified by match to protein family HMM PF03758; gluconolactonase 265689 3196672 SPOA0241 Ruegeria pomeroyi DSS-3 gluconolactonase YP_165070.1 264766 R 246200 CDS YP_165071.1 56709026 3196792 complement(265820..266860) 1 NC_006569.1 identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcription regulator 266860 3196792 SPOA0242 Ruegeria pomeroyi DSS-3 LacI family transcription regulator YP_165071.1 265820 R 246200 CDS YP_165072.1 56709027 3196849 complement(266928..268430) 1 NC_006569.1 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 268430 3196849 SPOA0243 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_165072.1 266928 R 246200 CDS YP_165073.1 56709028 3196720 complement(268432..269346) 1 NC_006569.1 identified by match to protein family HMM PF00701; dihydrodipicolinate synthase family protein 269346 3196720 SPOA0244 Ruegeria pomeroyi DSS-3 dihydrodipicolinate synthase family protein YP_165073.1 268432 R 246200 CDS YP_165074.1 56709029 3196696 complement(269349..270524) 1 NC_006569.1 identified by match to protein family HMM PF01188; match to protein family HMM PF02746; galactonate dehydratase 270524 3196696 SPOA0245 Ruegeria pomeroyi DSS-3 galactonate dehydratase YP_165074.1 269349 R 246200 CDS YP_165075.1 56709030 3196957 complement(270521..271546) 1 NC_006569.1 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate); 4-hydroxythreonine-4-phosphate dehydrogenase 271546 pdxA 3196957 pdxA Ruegeria pomeroyi DSS-3 4-hydroxythreonine-4-phosphate dehydrogenase YP_165075.1 270521 R 246200 CDS YP_165076.1 56709031 3196887 complement(271543..272505) 1 NC_006569.1 identified by similarity to GB:AAM32283.1; hypothetical protein 272505 3196887 SPOA0247 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165076.1 271543 R 246200 CDS YP_165077.1 56709032 3196663 complement(272618..273043) 1 NC_006569.1 identified by similarity to GB:AAD03997.1; hypothetical protein 273043 3196663 SPOA0248 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165077.1 272618 R 246200 CDS YP_165078.1 56709033 3196754 complement(273143..274120) 1 NC_006569.1 identified by match to protein family HMM PF03480; match to protein family HMM TIGR00787; TRAP dicarboxylate transporter, DctP subunit 274120 3196754 SPOA0249 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctP subunit YP_165078.1 273143 R 246200 CDS YP_165079.1 56709034 3196864 complement(274138..275418) 1 NC_006569.1 identified by match to protein family HMM PF00597; match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter, DctM subunit 275418 3196864 SPOA0250 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctM subunit YP_165079.1 274138 R 246200 CDS YP_165080.1 56709035 3196858 complement(275421..275969) 1 NC_006569.1 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit 275969 3196858 SPOA0251 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctQ subunit YP_165080.1 275421 R 246200 CDS YP_165081.1 56709036 3196612 276053..277078 1 NC_006569.1 identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcription regulator 277078 3196612 SPOA0252 Ruegeria pomeroyi DSS-3 LacI family transcription regulator YP_165081.1 276053 D 246200 CDS YP_165082.1 56709037 3196779 complement(277117..278247) 1 NC_006569.1 identified by similarity to SP:P02925; similarity to SP:P54300; ribose ABC transporter, periplasmic ribose-binding protein 278247 3196779 SPOA0253 Ruegeria pomeroyi DSS-3 ribose ABC transporter, periplasmic ribose-binding protein YP_165082.1 277117 R 246200 CDS YP_165083.1 56709038 3196588 complement(278352..279479) 1 NC_006569.1 identified by similarity to SP:P36948; match to protein family HMM PF02653; ribose ABC transporter, permease protein 279479 rbsC-1 3196588 rbsC-1 Ruegeria pomeroyi DSS-3 ribose ABC transporter, permease protein YP_165083.1 278352 R 246200 CDS YP_165084.1 56709039 3196793 complement(279491..280252) 1 NC_006569.1 identified by match to protein family HMM PF00005; sugar ABC transporter, ATP binding protein 280252 3196793 SPOA0255 Ruegeria pomeroyi DSS-3 sugar ABC transporter, ATP binding protein YP_165084.1 279491 R 246200 CDS YP_165085.1 56709040 3196654 complement(280380..281426) 1 NC_006569.1 identified by match to protein family HMM PF00532; ribose ABC transporter, periplasmic ribose-binding protein 281426 3196654 SPOA0256 Ruegeria pomeroyi DSS-3 ribose ABC transporter, periplasmic ribose-binding protein YP_165085.1 280380 R 246200 CDS YP_165086.1 56709041 3196946 complement(281449..282468) 1 NC_006569.1 identified by similarity to SP:P36948; match to protein family HMM PF02653; ribose ABC transporter, permease protein 282468 rbsC-2 3196946 rbsC-2 Ruegeria pomeroyi DSS-3 ribose ABC transporter, permease protein YP_165086.1 281449 R 246200 CDS YP_165087.1 56709042 3196931 complement(282480..283985) 1 NC_006569.1 identified by similarity to SP:P36947; match to protein family HMM PF00005; ribose ABC transporter, ATP-binding protein 283985 rbsA 3196931 rbsA Ruegeria pomeroyi DSS-3 ribose ABC transporter, ATP-binding protein YP_165087.1 282480 R 246200 CDS YP_165088.1 56709043 3196768 284124..285167 1 NC_006569.1 identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcription regulator 285167 3196768 SPOA0259 Ruegeria pomeroyi DSS-3 LacI family transcription regulator YP_165088.1 284124 D 246200 CDS YP_165089.1 56709044 3196786 complement(285382..286890) 1 NC_006569.1 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 286890 3196786 SPOA0260 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_165089.1 285382 R 246200 CDS YP_165090.1 56709045 3196757 complement(286995..287675) 1 NC_006569.1 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 287675 3196757 SPOA0261 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_165090.1 286995 R 246200 CDS YP_165091.1 56709046 3196590 complement(287856..289097) 1 NC_006569.1 identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding 289097 3196590 SPOA0262 Ruegeria pomeroyi DSS-3 oxidoreductase, FAD-binding YP_165091.1 287856 R 246200 CDS YP_165092.1 56709047 3196759 complement(289097..290407) 1 NC_006569.1 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP transporter, DctM subunit 290407 3196759 SPOA0263 Ruegeria pomeroyi DSS-3 TRAP transporter, DctM subunit YP_165092.1 289097 R 246200 CDS YP_165093.1 56709048 3196868 complement(290411..290944) 1 NC_006569.1 identified by match to protein family HMM PF04290; TRAP transporter DctQ family protein 290944 3196868 SPOA0264 Ruegeria pomeroyi DSS-3 TRAP transporter DctQ family protein YP_165093.1 290411 R 246200 CDS YP_165094.1 56709049 3196613 complement(291001..292065) 1 NC_006569.1 identified by match to protein family HMM PF03480; TRAP transporter DctP family protein 292065 3196613 SPOA0265 Ruegeria pomeroyi DSS-3 TRAP transporter DctP family protein YP_165094.1 291001 R 246200 CDS YP_165095.1 56709050 3196810 complement(292150..293091) 1 NC_006569.1 identified by similarity to GB:CAB71312.1; match to protein family HMM PF05544; proline racemase 293091 3196810 SPOA0266 Ruegeria pomeroyi DSS-3 proline racemase YP_165095.1 292150 R 246200 CDS YP_165096.1 56709051 3196900 complement(293082..294038) 1 NC_006569.1 identified by match to protein family HMM PF00701; dihydroxydipicolinate synthase family protein 294038 3196900 SPOA0267 Ruegeria pomeroyi DSS-3 dihydroxydipicolinate synthase family protein YP_165096.1 293082 R 246200 CDS YP_165097.1 56709052 3196576 294459..295271 1 NC_006569.1 identified by match to protein family HMM PF01614; IclR family transcriptional regulator 295271 3196576 SPOA0268 Ruegeria pomeroyi DSS-3 IclR family transcriptional regulator YP_165097.1 294459 D 246200 CDS YP_165098.1 56709053 3196645 295294..296604 1 NC_006569.1 identified by similarity to GB:BAB65016.1; hypothetical protein 296604 3196645 SPOA0269 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165098.1 295294 D 246200 CDS YP_165099.1 56709054 3196831 296672..297382 1 NC_006569.1 identified by similarity to PIR:G81801; hypothetical protein 297382 3196831 SPOA0270 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165099.1 296672 D 246200 CDS YP_165100.1 56709055 3196784 297379..298593 1 NC_006569.1 identified by similarity to SP:Q49128; match to protein family HMM PF03150; methylamine utilization protein MauG 298593 3196784 SPOA0271 Ruegeria pomeroyi DSS-3 methylamine utilization protein MauG YP_165100.1 297379 D 246200 CDS YP_165101.1 56709056 3196593 298624..299736 1 NC_006569.1 identified by similarity to SP:P45382; match to protein family HMM PF00107; glutathione-dependent formaldehyde dehydrogenase 299736 3196593 SPOA0272 Ruegeria pomeroyi DSS-3 glutathione-dependent formaldehyde dehydrogenase YP_165101.1 298624 D 246200 CDS YP_165102.1 56709057 3196850 complement(300585..301151) 1 NC_006569.1 identified by match to protein family HMM PF01381; DNA-binding protein 301151 3196850 SPOA0273 Ruegeria pomeroyi DSS-3 DNA-binding protein YP_165102.1 300585 R 246200 CDS YP_165103.1 56709058 3196857 301297..302574 1 NC_006569.1 catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate; 4-aminobutyrate aminotransferase 302574 gabT 3196857 gabT Ruegeria pomeroyi DSS-3 4-aminobutyrate aminotransferase YP_165103.1 301297 D 246200 CDS YP_165104.1 56709059 3196901 302576..304036 1 NC_006569.1 identified by match to protein family HMM PF00171; match to protein family HMM TIGR01780; succinate-semialdehyde dehydrogenase 304036 gabD-3 3196901 gabD-3 Ruegeria pomeroyi DSS-3 succinate-semialdehyde dehydrogenase YP_165104.1 302576 D 246200 CDS YP_165105.1 56709060 3196746 complement(304052..304993) 1 NC_006569.1 identified by similarity to GB:AAC04474.1; match to protein family HMM PF00294; fructokinase 304993 cscK 3196746 cscK Ruegeria pomeroyi DSS-3 fructokinase YP_165105.1 304052 R 246200 CDS YP_165106.1 56709061 3196571 complement(305059..305817) 1 NC_006569.1 identified by match to protein family HMM PF00561; alpha/beta hydrolase 305817 3196571 SPOA0277 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_165106.1 305059 R 246200 CDS YP_165107.1 56709062 3196845 complement(305817..307118) 1 NC_006569.1 identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter, DctM subunit 307118 3196845 SPOA0278 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctM subunit YP_165107.1 305817 R 246200 CDS YP_165108.1 56709063 3196896 complement(307118..307627) 1 NC_006569.1 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit 307627 3196896 SPOA0279 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctQ subunit YP_165108.1 307118 R 246200 CDS YP_165109.1 56709064 3196903 complement(307702..308697) 1 NC_006569.1 identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter, DctP subunit 308697 3196903 SPOA0280 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctP subunit YP_165109.1 307702 R 246200 CDS YP_165110.1 56709065 3196862 308914..309798 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 309798 3196862 SPOA0281 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165110.1 308914 D 246200 CDS YP_165111.1 56709066 3196904 complement(309822..311339) 1 NC_006569.1 catalyzes the formation of malonyl-CoA from malonate and CoA; malonyl-CoA synthase 311339 3196904 SPOA0282 Ruegeria pomeroyi DSS-3 malonyl-CoA synthase YP_165111.1 309822 R 246200 CDS YP_165112.1 56709067 3196740 complement(311439..313043) 1 NC_006569.1 identified by match to protein family HMM PF00732; match to protein family HMM PF05199; GMC family oxidoreductase 313043 3196740 SPOA0283 Ruegeria pomeroyi DSS-3 GMC family oxidoreductase YP_165112.1 311439 R 246200 CDS YP_165113.1 56709068 3196579 313162..314052 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 314052 3196579 SPOA0284 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165113.1 313162 D 246200 CDS YP_165114.1 56709069 3196711 complement(314098..314883) 1 NC_006569.1 catalyzes the dehydration of L-carnitinyl-CoA to crotonobetainyl-CoA; carnitinyl-CoA dehydratase 314883 caiD-2 3196711 caiD-2 Ruegeria pomeroyi DSS-3 carnitinyl-CoA dehydratase YP_165114.1 314098 R 246200 CDS YP_165115.1 56709070 3196846 complement(314883..315488) 1 NC_006569.1 identified by match to protein family HMM PF01965; ThiJ/PfpI family protein 315488 3196846 SPOA0286 Ruegeria pomeroyi DSS-3 ThiJ/PfpI family protein YP_165115.1 314883 R 246200 CDS YP_165116.1 56709071 3196916 complement(315492..317504) 1 NC_006569.1 identified by similarity to GB:BAB86294.1; similarity to GB:CAA10043.1; match to protein family HMM PF02629; acyl-CoA synthetase 317504 3196916 SPOA0287 Ruegeria pomeroyi DSS-3 acyl-CoA synthetase YP_165116.1 315492 R 246200 CDS YP_165117.1 56709072 3196905 complement(317587..318747) 1 NC_006569.1 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF02771; acyl-CoA dehydrogenase 318747 acdA-3 3196905 acdA-3 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_165117.1 317587 R 246200 CDS YP_165118.1 56709073 3196591 318870..319769 1 NC_006569.1 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 319769 3196591 SPOA0289 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_165118.1 318870 D 246200 CDS YP_165119.1 56709074 3196776 complement(319825..320892) 1 NC_006569.1 hypothetical protein 320892 3196776 SPOA0290 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165119.1 319825 R 246200 CDS YP_165120.1 56709075 3196806 complement(320935..321894) 1 NC_006569.1 identified by similarity to GB:AAO91868.1; match to protein family HMM PF01063; branched-chain amino acid aminotransferase 321894 3196806 SPOA0291 Ruegeria pomeroyi DSS-3 branched-chain amino acid aminotransferase YP_165120.1 320935 R 246200 CDS YP_165121.1 56709076 3196790 322185..322844 1 NC_006569.1 catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine; phosphatidylserine decarboxylase 322844 psd 3196790 psd Ruegeria pomeroyi DSS-3 phosphatidylserine decarboxylase YP_165121.1 322185 D 246200 CDS YP_165122.1 56709077 3196597 322880..323635 1 NC_006569.1 identified by match to protein family HMM PF01066; match to protein family HMM TIGR00473; CDP-diacylglycerol--serine O-phosphatidyltransferase 323635 pssA 3196597 pssA Ruegeria pomeroyi DSS-3 CDP-diacylglycerol--serine O-phosphatidyltransferase YP_165122.1 322880 D 246200 CDS YP_165123.1 56709078 3196945 323640..324260 1 NC_006569.1 identified by similarity to SP:Q05197; phosphatidylethanolamine N-methyltransferase 324260 pmtA 3196945 pmtA Ruegeria pomeroyi DSS-3 phosphatidylethanolamine N-methyltransferase YP_165123.1 323640 D 246200 CDS YP_165124.1 56709079 3196664 complement(324468..325151) 1 NC_006569.1 identified by similarity to SP:Q00924; match to protein family HMM PF01177; hydantoin racemase 325151 3196664 SPOA0295 Ruegeria pomeroyi DSS-3 hydantoin racemase YP_165124.1 324468 R 246200 CDS YP_165125.1 56709080 3196937 complement(325158..325880) 1 NC_006569.1 identified by similarity to SP:P21630; match to protein family HMM PF00005; branched-chain amino acid ABC transporter, ATP-binding protein 325880 livF-2 3196937 livF-2 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, ATP-binding protein YP_165125.1 325158 R 246200 CDS YP_165126.1 56709081 3196553 complement(325884..326666) 1 NC_006569.1 identified by similarity to SP:P22730; match to protein family HMM PF00005; branched-chain amino acid ABC transporter, ATP-binding protein 326666 livG 3196553 livG Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, ATP-binding protein YP_165126.1 325884 R 246200 CDS YP_165127.1 56709082 3196912 complement(326663..327643) 1 NC_006569.1 identified by similarity to SP:P22729; match to protein family HMM PF02653; branched-chain amino acid ABC transporter, permease protein 327643 3196912 SPOA0298 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, permease protein YP_165127.1 326663 R 246200 CDS YP_165128.1 56709083 3196694 complement(327648..328517) 1 NC_006569.1 identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter, permease protein 328517 3196694 SPOA0299 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, permease protein YP_165128.1 327648 R 246200 CDS YP_165129.1 56709084 3196769 complement(328607..329794) 1 NC_006569.1 Assignment partly based on membership in branched-chain amino acide ABC transporter gene cluster; identified by similarity to SP:P02917; similarity to SP:P04816; branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein 329794 3196769 SPOA0300 Ruegeria pomeroyi DSS-3 branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein YP_165129.1 328607 R 246200 CDS YP_165130.1 56709085 3196733 330025..330744 1 NC_006569.1 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 330744 3196733 SPOA0301 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_165130.1 330025 D 246200 CDS YP_165131.1 56709086 3196646 331140..332186 1 NC_006569.1 identified by match to protein family HMM PF00589; phage integrase family site specific recombinase 332186 3196646 SPOA0302 Ruegeria pomeroyi DSS-3 phage integrase family site specific recombinase YP_165131.1 331140 D 246200 CDS YP_165132.1 56709087 3196919 complement(332220..333317) 1 NC_006569.1 identified by similarity to GB:AAN05123.1; match to protein family HMM PF02195; replication protein 333317 3196919 SPOA0303 Ruegeria pomeroyi DSS-3 replication protein YP_165132.1 332220 R 246200 CDS YP_165133.1 56709088 3196795 complement(333314..334621) 1 NC_006569.1 identified by similarity to PIR:AI3232; match to protein family HMM PF00991; replication protein 334621 repA 3196795 repA Ruegeria pomeroyi DSS-3 replication protein YP_165133.1 333314 R 246200 CDS YP_165134.1 56709089 3196839 335100..335789 1 NC_006569.1 hypothetical protein 335789 3196839 SPOA0305 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165134.1 335100 D 246200 CDS YP_165135.1 56709090 3196926 complement(335830..338127) 1 NC_006569.1 identified by similarity to SP:P46837; match to protein family HMM PF00575; S1 RNA-binding domain-containing protein 338127 3196926 SPOA0306 Ruegeria pomeroyi DSS-3 S1 RNA-binding domain-containing protein YP_165135.1 335830 R 246200 CDS YP_165136.1 56709091 3196956 complement(339974..341653) 1 NC_006569.1 identified by similarity to SP:Q84H44; match to protein family HMM PF00205; match to protein family HMM PF02776; sulphoacetaldehyde acetyltransferase 341653 3196956 SPOA0309 Ruegeria pomeroyi DSS-3 sulphoacetaldehyde acetyltransferase YP_165136.1 339974 R 246200 CDS YP_165137.1 56709092 3196699 complement(341657..344068) 1 NC_006569.1 identified by match to protein family HMM PF01571; glycine cleavage system protein T 344068 3196699 SPOA0310 Ruegeria pomeroyi DSS-3 glycine cleavage system protein T YP_165137.1 341657 R 246200 CDS YP_165138.1 56709093 3196955 complement(344068..346467) 1 NC_006569.1 identified by match to protein family HMM PF01266; match to protein family HMM PF01571; FAD-dependent oxidoreductase 346467 3196955 SPOA0311 Ruegeria pomeroyi DSS-3 FAD-dependent oxidoreductase YP_165138.1 344068 R 246200 CDS YP_165139.1 56709094 3196932 complement(346464..347753) 1 NC_006569.1 identified by similarity to SP:P24630; match to protein family HMM PF00202; glutamate-1-semialdehyde 2,1-aminomutase 347753 3196932 SPOA0312 Ruegeria pomeroyi DSS-3 glutamate-1-semialdehyde 2,1-aminomutase YP_165139.1 346464 R 246200 CDS YP_165140.1 56709095 3196938 complement(347750..349294) 1 NC_006569.1 identified by match to protein family HMM PF06253; trimethylamine methyltransferase family protein 349294 3196938 SPOA0313 Ruegeria pomeroyi DSS-3 trimethylamine methyltransferase family protein YP_165140.1 347750 R 246200 CDS YP_165141.1 56709096 3196652 349404..350270 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 350270 3196652 SPOA0314 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165141.1 349404 D 246200 CDS YP_165142.1 56709097 3196885 351557..353770 1 NC_006569.1 identified by similarity to SP:P50216; match to protein family HMM PF03971; match to protein family HMM TIGR00178; isocitrate dehydrogenase, NADP-dependent 353770 icd 3196885 icd Ruegeria pomeroyi DSS-3 isocitrate dehydrogenase, NADP-dependent YP_165142.1 351557 D 246200 CDS YP_165143.1 56709098 3196599 complement(353871..355526) 1 NC_006569.1 identified by match to protein family HMM PF01979; amidohydrolase 355526 3196599 SPOA0316 Ruegeria pomeroyi DSS-3 amidohydrolase YP_165143.1 353871 R 246200 CDS YP_165144.1 56709099 3196556 complement(355845..356303) 1 NC_006569.1 identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 356303 3196556 SPOA0317 Ruegeria pomeroyi DSS-3 AsnC family transcriptional regulator YP_165144.1 355845 R 246200 CDS YP_165145.1 56709100 3196830 356420..357622 1 NC_006569.1 catalyzes the formation of methanethiol and 2-ocobutanoate from L-methionine; methionine gamma-lyase 357622 megL 3196830 megL Ruegeria pomeroyi DSS-3 methionine gamma-lyase YP_165145.1 356420 D 246200 CDS YP_165146.1 56709101 3196927 357789..360179 1 NC_006569.1 identified by match to protein family HMM PF00456; match to protein family HMM PF02779; transketolase 360179 3196927 SPOA0319 Ruegeria pomeroyi DSS-3 transketolase YP_165146.1 357789 D 246200 CDS YP_165147.1 56709102 3196797 360331..360708 1 NC_006569.1 identified by similarity to SP:Q05354; match to protein family HMM PF02962; 5-carboxymethyl-2-hydroxymuconate delta-isomerase 360708 hpcD 3196797 hpcD Ruegeria pomeroyi DSS-3 5-carboxymethyl-2-hydroxymuconate delta-isomerase YP_165147.1 360331 D 246200 CDS YP_165148.1 56709103 3196948 complement(360699..361160) 1 NC_006569.1 identified by match to protein family HMM PF00903; glyoxalase family protein 361160 3196948 SPOA0321 Ruegeria pomeroyi DSS-3 glyoxalase family protein YP_165148.1 360699 R 246200 CDS YP_165149.1 56709104 3196808 361284..362402 1 NC_006569.1 identified by similarity to GB:AAQ61367.1; match to protein family HMM PF01170; hypothetical protein 362402 3196808 SPOA0322 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165149.1 361284 D 246200 CDS YP_165150.1 56709105 3196959 362508..363212 1 NC_006569.1 identified by match to protein family HMM PF00027; cyclic nucleotide-binding protein 363212 3196959 SPOA0323 Ruegeria pomeroyi DSS-3 cyclic nucleotide-binding protein YP_165150.1 362508 D 246200 CDS YP_165151.1 56709106 3196960 363209..363772 1 NC_006569.1 hypothetical protein 363772 3196960 SPOA0324 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165151.1 363209 D 246200 CDS YP_165152.1 56709107 3196961 complement(363781..364857) 1 NC_006569.1 identified by match to protein family HMM PF03060; 2-nitropropane dioxygenase 364857 3196961 SPOA0325 Ruegeria pomeroyi DSS-3 2-nitropropane dioxygenase YP_165152.1 363781 R 246200 CDS YP_165153.1 56709108 3196962 365032..365916 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 365916 3196962 SPOA0326 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165153.1 365032 D 246200 CDS YP_165154.1 56709109 3196963 367716..368282 1 NC_006569.1 identified by similarity to GB:AAF36413.1; rzcC protein 368282 3196963 SPOA0327 Ruegeria pomeroyi DSS-3 rzcC protein YP_165154.1 367716 D 246200 CDS YP_165155.1 56709110 3196964 368322..368957 1 NC_006569.1 identified by similarity to GB:BAB49961.1; hypothetical protein 368957 3196964 SPOA0328 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165155.1 368322 D 246200 CDS YP_165156.1 56709111 3196965 complement(370463..370852) 1 NC_006569.1 catalyzes the formation of methylglyoxal from glycerone phosphate; methylglyoxal synthase 370852 mgsA 3196965 mgsA Ruegeria pomeroyi DSS-3 methylglyoxal synthase YP_165156.1 370463 R 246200 CDS YP_165157.1 56709112 3196966 complement(370846..371505) 1 NC_006569.1 identified by similarity to SP:P10177; match to protein family HMM PF01081; match to protein family HMM TIGR01182; 4-hydroxy-2-oxoglutarate aldolase; 2-dehydro-3-deoxyphosphogluconate aldolase 371505 eda-2 3196966 eda-2 Ruegeria pomeroyi DSS-3 2-dehydro-3-deoxyphosphogluconate aldolase YP_165157.1 370846 R 246200 CDS YP_165158.1 56709113 3196967 complement(371484..372431) 1 NC_006569.1 identified by similarity to SP:P50845; match to protein family HMM PF00294; 2-dehydro-3-deoxygluconokinase 372431 3196967 SPOA0331 Ruegeria pomeroyi DSS-3 2-dehydro-3-deoxygluconokinase YP_165158.1 371484 R 246200 CDS YP_165159.1 56709114 3196745 complement(372441..374237) 1 NC_006569.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase 374237 3196745 SPOA0332 Ruegeria pomeroyi DSS-3 dihydroxy-acid dehydratase YP_165159.1 372441 R 246200 CDS YP_165160.1 56709115 3196969 complement(374238..375503) 1 NC_006569.1 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter, DctM subunit 375503 3196969 SPOA0333 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctM subunit YP_165160.1 374238 R 246200 CDS YP_165161.1 56709116 3196968 complement(375570..376130) 1 NC_006569.1 TRAP dicarboxylate family transporter DctQ subunit 376130 3196968 SPOA0334 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate family transporter DctQ subunit YP_165161.1 375570 R 246200 CDS YP_165162.1 56709117 3196970 complement(376203..377222) 1 NC_006569.1 identified by match to protein family HMM PF03480; TRAP dicarboxylate family transporter DctP subunit 377222 3196970 SPOA0335 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate family transporter DctP subunit YP_165162.1 376203 R 246200 CDS YP_165163.1 56709118 3196971 377348..378382 1 NC_006569.1 identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcription regulator 378382 3196971 SPOA0336 Ruegeria pomeroyi DSS-3 LacI family transcription regulator YP_165163.1 377348 D 246200 CDS YP_165164.1 56709119 3196972 complement(379179..381470) 1 NC_006569.1 hypothetical protein 381470 3196972 SPOA0337 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165164.1 379179 R 246200 CDS YP_165165.1 56709120 3196973 381777..382751 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; match to protein family HMM TIGR01199; LysR family transcriptional regulator 382751 3196973 SPOA0338 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165165.1 381777 D 246200 CDS YP_165166.1 56709121 3196974 complement(383108..383779) 1 NC_006569.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01488; match to protein family HMM TIGR01490; HAD family hydrolase 383779 3196974 SPOA0339 Ruegeria pomeroyi DSS-3 HAD family hydrolase YP_165166.1 383108 R 246200 CDS YP_165167.1 56709122 3196975 complement(383776..384009) 1 NC_006569.1 identified by match to protein family HMM PF01361; tautomerase 384009 3196975 SPOA0340 Ruegeria pomeroyi DSS-3 tautomerase YP_165167.1 383776 R 246200 CDS YP_165168.1 56709123 3196976 complement(384039..384818) 1 NC_006569.1 hypothetical protein 384818 3196976 SPOA0341 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165168.1 384039 R 246200 CDS YP_165169.1 56709124 3196977 complement(384945..385730) 1 NC_006569.1 hypothetical protein 385730 3196977 SPOA0342 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165169.1 384945 R 246200 CDS YP_165170.1 56709125 3196978 complement(385776..386387) 1 NC_006569.1 hypothetical protein 386387 3196978 SPOA0343 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165170.1 385776 R 246200 CDS YP_165171.1 56709126 3196979 complement(386564..387508) 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; match to protein family HMM TIGR01199; LysR family transcriptional regulator 387508 3196979 SPOA0344 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165171.1 386564 R 246200 CDS YP_165172.1 56709127 3196980 387556..388539 1 NC_006569.1 identified by match to protein family HMM PF00248; aldo/keto reductase 388539 3196980 SPOA0345 Ruegeria pomeroyi DSS-3 aldo/keto reductase YP_165172.1 387556 D 246200 CDS YP_165173.1 56709128 3196981 388536..388925 1 NC_006569.1 identified by match to protein family HMM PF02627; carboxymuconolactone decarboxylase family protein 388925 3196981 SPOA0346 Ruegeria pomeroyi DSS-3 carboxymuconolactone decarboxylase family protein YP_165173.1 388536 D 246200 CDS YP_165174.1 56709129 3196982 388947..390134 1 NC_006569.1 hypothetical protein 390134 3196982 SPOA0347 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165174.1 388947 D 246200 CDS YP_165175.1 56709130 3196983 390671..391216 1 NC_006569.1 identified by similarity to GB:AAQ60836.1; hypothetical protein 391216 3196983 SPOA0348 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165175.1 390671 D 246200 CDS YP_165176.1 56709131 3196984 complement(391276..392235) 1 NC_006569.1 identified by match to protein family HMM PF00892; hypothetical protein 392235 3196984 SPOA0349 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165176.1 391276 R 246200 CDS YP_165177.1 56709132 3196985 complement(392232..392450) 1 NC_006569.1 hypothetical protein 392450 3196985 SPOA0350 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165177.1 392232 R 246200 CDS YP_165178.1 56709133 3196986 complement(392392..392625) 1 NC_006569.1 hypothetical protein 392625 3196986 SPOA0351 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165178.1 392392 R 246200 CDS YP_165179.1 56709134 3196749 complement(392691..394046) 1 NC_006569.1 identified by match to protein family HMM PF00202; hypothetical protein 394046 3196749 SPOA0352 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165179.1 392691 R 246200 CDS YP_165180.1 56709135 3196987 394173..395651 1 NC_006569.1 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 395651 3196987 SPOA0353 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_165180.1 394173 D 246200 CDS YP_165181.1 56709136 3196988 395648..396946 1 NC_006569.1 identified by match to protein family HMM PF00202; aminotransferase, class III 396946 3196988 SPOA0354 Ruegeria pomeroyi DSS-3 aminotransferase, class III YP_165181.1 395648 D 246200 CDS YP_165182.1 56709137 3196989 396943..397887 1 NC_006569.1 identified by similarity to GB:AAN34322.1; hypothetical protein 397887 3196989 SPOA0355 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165182.1 396943 D 246200 CDS YP_165183.1 56709138 3196687 397884..399119 1 NC_006569.1 identified by similarity to SP:Q8YDP7; match to protein family HMM PF06792; hypothetical protein 399119 3196687 SPOA0356 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165183.1 397884 D 246200 CDS YP_165184.1 56709139 3196715 399373..400101 1 NC_006569.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator 400101 3196715 SPOA0357 Ruegeria pomeroyi DSS-3 DNA-binding response regulator YP_165184.1 399373 D 246200 CDS YP_165185.1 56709140 3196990 400107..401477 1 NC_006569.1 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase 401477 3196990 SPOA0358 Ruegeria pomeroyi DSS-3 sensor histidine kinase YP_165185.1 400107 D 246200 CDS YP_165186.1 56709141 3196805 401807..402403 1 NC_006569.1 identified by match to protein family HMM PF00034; cytochrome c family protein 402403 3196805 SPOA0359 Ruegeria pomeroyi DSS-3 cytochrome c family protein YP_165186.1 401807 D 246200 CDS YP_165187.1 56709142 3196992 402425..403855 1 NC_006569.1 identified by similarity to GB:AAD24211.1; match to protein family HMM TIGR01409; multicopper oxidase 403855 3196992 SPOA0360 Ruegeria pomeroyi DSS-3 multicopper oxidase YP_165187.1 402425 D 246200 CDS YP_165188.1 56709143 3196993 403852..404352 1 NC_006569.1 identified by match to protein family HMM PF00034; cytochrome c family protein 404352 3196993 SPOA0361 Ruegeria pomeroyi DSS-3 cytochrome c family protein YP_165188.1 403852 D 246200 CDS YP_165189.1 56709144 3196991 404349..405083 1 NC_006569.1 identified by similarity to PIR:A49232; match to protein family HMM PF01323; hypothetical protein 405083 3196991 SPOA0362 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165189.1 404349 D 246200 CDS YP_165190.1 56709145 3196628 405287..406045 1 NC_006569.1 hypothetical protein 406045 3196628 SPOA0363 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165190.1 405287 D 246200 CDS YP_165191.1 56709146 3196753 406161..407222 1 NC_006569.1 identified by similarity to GB:AAM42746.1; hypothetical protein 407222 3196753 SPOA0364 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165191.1 406161 D 246200 CDS YP_165192.1 56709147 3196765 407279..409636 1 NC_006569.1 identified by similarity to SP:P37279; match to protein family HMM PF00122; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01511; match to protein family HMM TIGR01525; copper-translocating P-type ATPase 409636 3196765 SPOA0365 Ruegeria pomeroyi DSS-3 copper-translocating P-type ATPase YP_165192.1 407279 D 246200 CDS YP_165193.1 56709148 3196693 409666..411012 1 NC_006569.1 identified by similarity to SP:P77400; match to protein family HMM PF00324; amino acid permease 411012 3196693 SPOA0366 Ruegeria pomeroyi DSS-3 amino acid permease YP_165193.1 409666 D 246200 CDS YP_165194.1 56709149 3196674 complement(411009..412142) 1 NC_006569.1 identified by match to protein family HMM PF00664; ABC transporter, permease protein 412142 3196674 SPOA0367 Ruegeria pomeroyi DSS-3 ABC transporter, permease protein YP_165194.1 411009 R 246200 CDS YP_165195.1 56709150 3196578 complement(412340..412849) 1 NC_006569.1 identified by similarity to GB:AAF32271.1; hypothetical protein 412849 3196578 SPOA0368 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165195.1 412340 R 246200 CDS YP_165196.1 56709151 3196621 complement(412958..413620) 1 NC_006569.1 identified by similarity to SP:P12375; copper resistance protein B 413620 3196621 SPOA0369 Ruegeria pomeroyi DSS-3 copper resistance protein B YP_165196.1 412958 R 246200 CDS YP_165197.1 56709152 3196763 complement(413692..415635) 1 NC_006569.1 identified by similarity to SP:P12374; match to protein family HMM PF00394; match to protein family HMM TIGR01480; copper resistance protein A 415635 copA 3196763 copA Ruegeria pomeroyi DSS-3 copper resistance protein A YP_165197.1 413692 R 246200 CDS YP_165198.1 56709153 3196615 complement(415806..416144) 1 NC_006569.1 hypothetical protein 416144 3196615 SPOA0371 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165198.1 415806 R 246200 CDS YP_165199.1 56709154 3196577 complement(416293..416856) 1 NC_006569.1 identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit 416856 3196577 SPOA0372 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctQ subunit YP_165199.1 416293 R 246200 CDS YP_165200.1 56709155 3196741 complement(416936..418225) 1 NC_006569.1 identified by match to protein family HMM PF00597; match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter, DctM subunit 418225 3196741 SPOA0373 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctM subunit YP_165200.1 416936 R 246200 CDS YP_165201.1 56709156 3196600 complement(418331..419371) 1 NC_006569.1 identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter, DctP subunit 419371 3196600 SPOA0374 Ruegeria pomeroyi DSS-3 TRAP dicarboxylate transporter, DctP subunit YP_165201.1 418331 R 246200 CDS YP_165202.1 56709157 3196609 419547..421010 1 NC_006569.1 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 421010 3196609 SPOA0375 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_165202.1 419547 D 246200 CDS YP_165203.1 56709158 3196656 421021..422331 1 NC_006569.1 identified by match to protein family HMM PF06441; epoxide hydrolase 422331 3196656 SPOA0376 Ruegeria pomeroyi DSS-3 epoxide hydrolase YP_165203.1 421021 D 246200 CDS YP_165204.1 56709159 3196560 422351..423844 1 NC_006569.1 identified by match to protein family HMM PF00171; aldehyde dehydrogenase 423844 3196560 SPOA0377 Ruegeria pomeroyi DSS-3 aldehyde dehydrogenase YP_165204.1 422351 D 246200 CDS YP_165205.1 56709160 3196713 complement(423926..425029) 1 NC_006569.1 identified by match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase 425029 3196713 SPOA0378 Ruegeria pomeroyi DSS-3 mandelate racemase YP_165205.1 423926 R 246200 CDS YP_165206.1 56709161 3196566 425152..426624 1 NC_006569.1 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 426624 3196566 SPOA0379 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_165206.1 425152 D 246200 CDS YP_165207.1 56709162 3196667 426750..428057 1 NC_006569.1 identified by similarity to GB:CAE41123.1; hypothetical protein 428057 3196667 SPOA0380 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165207.1 426750 D 246200 CDS YP_165208.1 56709163 3196721 428256..429296 1 NC_006569.1 Assignment partly based on membership in spermidine/putrescine ABC transporter gene cluster; identified by match to protein family HMM PF01547; spermidine/putrescine ABC transporter, periplasmic substrate-binding protein 429296 3196721 SPOA0381 Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter, periplasmic substrate-binding protein YP_165208.1 428256 D 246200 CDS YP_165209.1 56709164 3196773 429358..430461 1 NC_006569.1 identified by similarity to SP:P31134; match to protein family HMM PF00005; match to protein family HMM TIGR01187; spermidine/putrescine ABC transporter, ATP-binding protein 430461 3196773 SPOA0382 Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter, ATP-binding protein YP_165209.1 429358 D 246200 CDS YP_165210.1 56709165 3196731 430463..431347 1 NC_006569.1 Assignment partly based on membership in spermidine/putrescine ABC transporter gene cluster; identified by match to protein family HMM PF00528; spermidine/putrescine ABC transporter, permease protein 431347 3196731 SPOA0383 Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter, permease protein YP_165210.1 430463 D 246200 CDS YP_165211.1 56709166 3196738 431347..432174 1 NC_006569.1 identified by match to protein family HMM PF00528; spermidine/putrescine ABC transporter, permease protein 432174 3196738 SPOA0384 Ruegeria pomeroyi DSS-3 spermidine/putrescine ABC transporter, permease protein YP_165211.1 431347 D 246200 CDS YP_165212.1 56709167 3196675 432275..433567 1 NC_006569.1 identified by similarity to GB:CAE33186.1; hypothetical protein 433567 3196675 SPOA0385 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165212.1 432275 D 246200 CDS YP_165213.1 56709168 3196551 433575..435200 1 NC_006569.1 identified by match to protein family HMM PF00732; match to protein family HMM PF05199; GMC family oxidoreductase 435200 3196551 SPOA0386 Ruegeria pomeroyi DSS-3 GMC family oxidoreductase YP_165213.1 433575 D 246200 CDS YP_165214.1 56709169 3196794 435270..436184 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 436184 3196794 SPOA0387 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165214.1 435270 D 246200 CDS YP_165215.1 56709170 3196770 436276..438348 1 NC_006569.1 acetyl-CoA synthetase 438348 3196770 SPOA0388 Ruegeria pomeroyi DSS-3 acetyl-CoA synthetase YP_165215.1 436276 D 246200 CDS YP_165216.1 56709171 3196637 438569..439006 1 NC_006569.1 identified by match to protein family HMM PF00376; MerR family transcriptional regulator 439006 3196637 SPOA0389 Ruegeria pomeroyi DSS-3 MerR family transcriptional regulator YP_165216.1 438569 D 246200 CDS YP_165217.1 56709172 3196617 complement(438997..440526) 1 NC_006569.1 identified by similarity to PIR:T44602; match to protein family HMM PF00884; phosphonate monoester hydrolase 440526 3196617 SPOA0390 Ruegeria pomeroyi DSS-3 phosphonate monoester hydrolase YP_165217.1 438997 R 246200 CDS YP_165218.1 56709173 3196855 440874..441527 1 NC_006569.1 identified by match to protein family HMM PF00027; cyclic nucleotide-binding protein 441527 3196855 SPOA0391 Ruegeria pomeroyi DSS-3 cyclic nucleotide-binding protein YP_165218.1 440874 D 246200 CDS YP_165219.1 56709174 3196680 441633..442271 1 NC_006569.1 identified by match to protein family HMM PF04542; RNA polymerase sigma-70 factor 442271 3196680 SPOA0392 Ruegeria pomeroyi DSS-3 RNA polymerase sigma-70 factor YP_165219.1 441633 D 246200 CDS YP_165220.1 56709175 3196732 442261..442560 1 NC_006569.1 identified by similarity to GB:AAA73405.1; R body protein RebB-like protein 442560 3196732 SPOA0393 Ruegeria pomeroyi DSS-3 R body protein RebB-like protein YP_165220.1 442261 D 246200 CDS YP_165221.1 56709176 3196683 complement(442435..443445) 1 NC_006569.1 hypothetical protein 443445 3196683 SPOA0394 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165221.1 442435 R 246200 CDS YP_165222.1 56709177 3196552 443538..444830 1 NC_006569.1 hypothetical protein 444830 3196552 SPOA0395 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165222.1 443538 D 246200 CDS YP_165223.1 56709178 3196616 444910..445212 1 NC_006569.1 hypothetical protein 445212 3196616 SPOA0396 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165223.1 444910 D 246200 CDS YP_165224.1 56709179 3196841 445209..445832 1 NC_006569.1 identified by similarity to GB:AAQ58401.1; hypothetical protein 445832 3196841 SPOA0397 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165224.1 445209 D 246200 CDS YP_165225.1 56709180 3196874 445902..446225 1 NC_006569.1 identified by similarity to GB:AAA73405.1; R body protein RebB-like protein 446225 3196874 SPOA0398 Ruegeria pomeroyi DSS-3 R body protein RebB-like protein YP_165225.1 445902 D 246200 CDS YP_165226.1 56709181 3196554 446276..446620 1 NC_006569.1 identified by similarity to GB:AAA73405.1; R body protein RebB-like protein 446620 3196554 SPOA0399 Ruegeria pomeroyi DSS-3 R body protein RebB-like protein YP_165226.1 446276 D 246200 CDS YP_165227.1 56709182 3196570 complement(446685..447080) 1 NC_006569.1 identified by match to protein family HMM PF01042; endoribonuclease L-PSP 447080 3196570 SPOA0400 Ruegeria pomeroyi DSS-3 endoribonuclease L-PSP YP_165227.1 446685 R 246200 CDS YP_165228.1 56709183 3196548 complement(447094..448716) 1 NC_006569.1 identified by similarity to GB:AAA92151.1; match to protein family HMM PF00501; benzoate-coenzyme A ligase 448716 badA-2 3196548 badA-2 Ruegeria pomeroyi DSS-3 benzoate-coenzyme A ligase YP_165228.1 447094 R 246200 CDS YP_165229.1 56709184 3196804 complement(448720..449172) 1 NC_006569.1 identified by similarity to SP:P16558; cupin 449172 3196804 SPOA0402 Ruegeria pomeroyi DSS-3 cupin YP_165229.1 448720 R 246200 CDS YP_165230.1 56709185 3196954 complement(449201..450343) 1 NC_006569.1 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 450343 3196954 SPOA0403 Ruegeria pomeroyi DSS-3 acyl-CoA dehydrogenase YP_165230.1 449201 R 246200 CDS YP_165231.1 56709186 3196812 complement(450396..451199) 1 NC_006569.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 451199 3196812 SPOA0404 Ruegeria pomeroyi DSS-3 enoyl-CoA hydratase YP_165231.1 450396 R 246200 CDS YP_165232.1 56709188 3196867 complement(451196..451663) 1 NC_006569.1 identified by match to protein family HMM PF01047; MarR family transcriptional regulator 451663 3196867 SPOA0405 Ruegeria pomeroyi DSS-3 MarR family transcriptional regulator YP_165232.1 451196 R 246200 CDS YP_165233.1 56709187 3196647 complement(451660..452418) 1 NC_006569.1 identified by similarity to SP:O86034; match to protein family HMM PF00106; D-beta-hydroxybutyrate dehydrogenase 452418 3196647 SPOA0406 Ruegeria pomeroyi DSS-3 D-beta-hydroxybutyrate dehydrogenase YP_165233.1 451660 R 246200 CDS YP_165234.1 56709229 3196631 complement(452415..454709) 1 NC_006569.1 catalyzes the conversion of salicylyl-CoA to gentisyl-CoA; salicylyl-CoA 5-hydroxylase 454709 3196631 SPOA0407 Ruegeria pomeroyi DSS-3 salicylyl-CoA 5-hydroxylase YP_165234.1 452415 R 246200 CDS YP_165235.1 56709189 3196861 454843..455619 1 NC_006569.1 identified by similarity to GB:BAC49422.1; hypothetical protein 455619 3196861 SPOA0408 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165235.1 454843 D 246200 CDS YP_165236.1 56709190 3196589 455624..456460 1 NC_006569.1 identified by match to protein family HMM PF03301; tryptophan 2,3-dioxygenase 456460 3196589 SPOA0409 Ruegeria pomeroyi DSS-3 tryptophan 2,3-dioxygenase YP_165236.1 455624 D 246200 CDS YP_165237.1 56709191 3196697 456748..458676 1 NC_006569.1 hypothetical protein 458676 3196697 SPOA0410 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165237.1 456748 D 246200 CDS YP_165238.1 56709192 3196700 complement(457427..458773) 1 NC_006569.1 hypothetical protein 458773 3196700 SPOA0411 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165238.1 457427 R 246200 CDS YP_165239.1 56709193 3196580 459056..459937 1 NC_006569.1 identified by match to protein family HMM PF00941; match to protein family HMM PF03450; xanthine dehydrogenase family protein, medium subunit 459937 3196580 SPOA0412 Ruegeria pomeroyi DSS-3 xanthine dehydrogenase family protein, medium subunit YP_165239.1 459056 D 246200 CDS YP_165240.1 56709194 3196747 459934..460413 1 NC_006569.1 identified by match to protein family HMM PF00111; match to protein family HMM PF01799; xanthine dehydrogenase family protein, small subunit 460413 3196747 SPOA0413 Ruegeria pomeroyi DSS-3 xanthine dehydrogenase family protein, small subunit YP_165240.1 459934 D 246200 CDS YP_165241.1 56709195 3196819 460413..462674 1 NC_006569.1 identified by match to protein family HMM PF01315; match to protein family HMM PF02738; xanthine dehydrogenase family protein, large subunit 462674 3196819 SPOA0414 Ruegeria pomeroyi DSS-3 xanthine dehydrogenase family protein, large subunit YP_165241.1 460413 D 246200 CDS YP_165242.1 56709196 3196756 462667..462912 1 NC_006569.1 identified by similarity to PIR:B95401; hypothetical protein 462912 3196756 SPOA0415 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165242.1 462667 D 246200 CDS YP_165243.1 56709197 3196820 complement(463118..463858) 1 NC_006569.1 identified by similarity to GB:BAC52076.1; hypothetical protein 463858 3196820 SPOA0416 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165243.1 463118 R 246200 CDS YP_165244.1 56709198 3196821 complement(463866..464555) 1 NC_006569.1 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 464555 3196821 SPOA0417 Ruegeria pomeroyi DSS-3 GntR family transcriptional regulator YP_165244.1 463866 R 246200 CDS YP_165245.1 56709199 3196822 464662..466353 1 NC_006569.1 identified by similarity to GB:AAL99356.1; match to protein family HMM PF00205; match to protein family HMM PF02776; acetolactate synthase, large subunit 466353 3196822 SPOA0418 Ruegeria pomeroyi DSS-3 acetolactate synthase, large subunit YP_165245.1 464662 D 246200 CDS YP_165246.1 56709200 3196771 complement(466454..467290) 1 NC_006569.1 identified by match to protein family HMM PF02567; match to protein family HMM TIGR00654; PhzF family phenazine biosynthesis protein 467290 3196771 SPOA0419 Ruegeria pomeroyi DSS-3 PhzF family phenazine biosynthesis protein YP_165246.1 466454 R 246200 CDS YP_165247.1 56709201 3196742 complement(467341..467541) 1 NC_006569.1 hypothetical protein 467541 3196742 SPOA0420 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165247.1 467341 R 246200 CDS YP_165248.1 56709202 3196669 complement(467615..468235) 1 NC_006569.1 identified by match to protein family HMM PF01243; pyridoxamine 5'-phosphate oxidase family protein 468235 3196669 SPOA0421 Ruegeria pomeroyi DSS-3 pyridoxamine 5'-phosphate oxidase family protein YP_165248.1 467615 R 246200 CDS YP_165249.1 56709203 3196824 complement(468250..468714) 1 NC_006569.1 identified by similarity to GB:AAN68558.1; match to protein family HMM PF07080; hypothetical protein 468714 3196824 SPOA0422 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165249.1 468250 R 246200 CDS YP_165250.1 56709204 3196722 469019..469585 1 NC_006569.1 identified by match to protein family HMM PF00440; TetR family transcriptional regulator 469585 3196722 SPOA0423 Ruegeria pomeroyi DSS-3 TetR family transcriptional regulator YP_165250.1 469019 D 246200 CDS YP_165251.1 56709205 3196739 complement(469613..471757) 1 NC_006569.1 identified by similarity to SP:P77399; match to protein family HMM PF00378; match to protein family HMM PF00725; match to protein family HMM PF02737; fatty oxidation complex, alpha subunit 471757 fabJ-2 3196739 fabJ-2 Ruegeria pomeroyi DSS-3 fatty oxidation complex, alpha subunit YP_165251.1 469613 R 246200 CDS YP_165252.1 56709206 3196705 complement(471770..472978) 1 NC_006569.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; acetyl-CoA acetyltransferase 472978 3196705 SPOA0425 Ruegeria pomeroyi DSS-3 acetyl-CoA acetyltransferase YP_165252.1 471770 R 246200 CDS YP_165253.1 56709207 3196602 473076..474071 1 NC_006569.1 identified by match to protein family HMM PF00165; AraC family transcriptional regulator 474071 3196602 SPOA0426 Ruegeria pomeroyi DSS-3 AraC family transcriptional regulator YP_165253.1 473076 D 246200 CDS YP_165254.1 56709208 3196764 complement(474087..474419) 1 NC_006569.1 identified by match to protein family HMM PF01022; ArsR family transcriptional regulator 474419 3196764 SPOA0427 Ruegeria pomeroyi DSS-3 ArsR family transcriptional regulator YP_165254.1 474087 R 246200 CDS YP_165255.1 56709209 3196686 complement(474485..475711) 1 NC_006569.1 identified by match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase 475711 3196686 SPOA0428 Ruegeria pomeroyi DSS-3 mandelate racemase YP_165255.1 474485 R 246200 CDS YP_165256.1 56709210 3196827 475904..477349 1 NC_006569.1 identified by match to protein family HMM PF01546; hypothetical protein 477349 3196827 SPOA0429 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165256.1 475904 D 246200 CDS YP_165257.1 56709211 3196729 complement(477356..478450) 1 NC_006569.1 identified by match to protein family HMM PF00107; zinc-binding dehydrogenase family oxidoreductase 478450 3196729 SPOA0430 Ruegeria pomeroyi DSS-3 zinc-binding dehydrogenase family oxidoreductase YP_165257.1 477356 R 246200 CDS YP_165258.1 56709212 3196633 complement(478537..479736) 1 NC_006569.1 identified by similarity to SP:P02982; tetracycline resistance protein 479736 3196633 SPOA0431 Ruegeria pomeroyi DSS-3 tetracycline resistance protein YP_165258.1 478537 R 246200 CDS YP_165259.1 56709213 3196626 complement(479797..481134) 1 NC_006569.1 identified by similarity to SP:P32427; match to protein family HMM PF00206; 3-carboxy-cis,cis-muconate cycloisomerase 481134 pcaB 3196626 pcaB Ruegeria pomeroyi DSS-3 3-carboxy-cis,cis-muconate cycloisomerase YP_165259.1 479797 R 246200 CDS YP_165260.1 56709214 3196897 complement(481134..481847) 1 NC_006569.1 identified by similarity to GB:AAF66687.1; esterase 481847 3196897 SPOA0433 Ruegeria pomeroyi DSS-3 esterase YP_165260.1 481134 R 246200 CDS YP_165261.1 56709215 3196630 complement(481860..482648) 1 NC_006569.1 identified by similarity to GB:AAL02408.1; match to protein family HMM PF00561; 3-oxoadipate enol-lactone hydrolase 482648 catD 3196630 catD Ruegeria pomeroyi DSS-3 3-oxoadipate enol-lactone hydrolase YP_165261.1 481860 R 246200 CDS YP_165262.1 56709216 3196709 complement(482759..483733) 1 NC_006569.1 identified by match to protein family HMM PF00291; pyridoxal-phosphate dependent enzyme 483733 3196709 SPOA0435 Ruegeria pomeroyi DSS-3 pyridoxal-phosphate dependent enzyme YP_165262.1 482759 R 246200 CDS YP_165263.1 56709217 3196766 complement(483730..484557) 1 NC_006569.1 identified by match to protein family HMM PF00561; alpha/beta hydrolase 484557 3196766 SPOA0436 Ruegeria pomeroyi DSS-3 alpha/beta hydrolase YP_165263.1 483730 R 246200 CDS YP_165264.1 56709218 3196898 complement(484558..485244) 1 NC_006569.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01428; match to protein family HMM TIGR01493; haloacid dehalogenase 485244 dehII 3196898 dehII Ruegeria pomeroyi DSS-3 haloacid dehalogenase YP_165264.1 484558 R 246200 CDS YP_165265.1 56709219 3196933 485378..485806 1 NC_006569.1 identified by match to protein family HMM PF00254; peptidyl-prolyl cis-trans isomerase, FKBP-type 485806 3196933 SPOA0438 Ruegeria pomeroyi DSS-3 peptidyl-prolyl cis-trans isomerase, FKBP-type YP_165265.1 485378 D 246200 CDS YP_165266.1 56709220 3196632 complement(485896..486687) 1 NC_006569.1 identified by similarity to SP:P29132; match to protein family HMM PF00106; enoyl-ACP reductase 486687 fabI-3 3196632 fabI-3 Ruegeria pomeroyi DSS-3 enoyl-ACP reductase YP_165266.1 485896 R 246200 CDS YP_165267.1 56709221 3196704 complement(486694..487923) 1 NC_006569.1 identified by similarity to SP:P14926; match to protein family HMM PF00109; match to protein family HMM PF02801; 3-oxoacyl-ACP synthase 487923 fabB 3196704 fabB Ruegeria pomeroyi DSS-3 3-oxoacyl-ACP synthase YP_165267.1 486694 R 246200 CDS YP_165268.1 56709222 3196559 488138..489025 1 NC_006569.1 identified by similarity to GB:CAE06700.1; hypothetical protein 489025 3196559 SPOA0441 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165268.1 488138 D 246200 CDS YP_165269.1 56709223 3196803 489041..489136 1 NC_006569.1 hypothetical protein 489136 3196803 SPOA0442 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165269.1 489041 D 246200 CDS YP_165270.1 56709224 3196624 489176..489439 1 NC_006569.1 hypothetical protein 489439 3196624 SPOA0443 Ruegeria pomeroyi DSS-3 hypothetical protein YP_165270.1 489176 D 246200 CDS YP_165271.1 56709225 3196601 complement(489506..490015) 1 NC_006569.1 catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-ACP dehydratase 490015 fabA 3196601 fabA Ruegeria pomeroyi DSS-3 3-hydroxydecanoyl-ACP dehydratase YP_165271.1 489506 R 246200 CDS YP_165272.1 56709226 3196743 490204..490623 1 NC_006569.1 identified by match to protein family HMM PF01475; FUR family transcriptional regulator 490623 3196743 SPOA0445 Ruegeria pomeroyi DSS-3 FUR family transcriptional regulator YP_165272.1 490204 D 246200 CDS YP_165273.1 56709227 3196799 complement(490624..491520) 1 NC_006569.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 491520 3196799 SPOA0446 Ruegeria pomeroyi DSS-3 LysR family transcriptional regulator YP_165273.1 490624 R 246200 CDS