-- dump date 20120504_160859 -- class Genbank::Feature -- table feature -- table main -- field 1 id -- field 2 type -- field 3 name -- field 4 contig -- field 5 start_pos -- field 6 end_pos -- field 7 strand -- field 8 description -- field 9 chrom_position -- field 10 organism -- field 11 GeneID -- header -- id type name contig start_pos end_pos strand description chrom_position organism GeneID 246200000001 SEQ_END SEQ_END NC_003911.11 4109442 4109442 DR NC_003911.11; contig end 4109442..4109442 Ruegeria pomeroyi DSS-3 246200000002 SEQ_END SEQ_END NC_006569.1 491611 491611 DR NC_006569.1; contig end 491611..491611 Ruegeria pomeroyi DSS-3 YP_165274.1 CDS gidA NC_003911.11 1 1869 D 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 1..1869 Ruegeria pomeroyi DSS-3 3194636 YP_165275.1 CDS gidB NC_003911.11 1866 2480 D identified by match to protein family HMM PF02527; match to protein family HMM TIGR00138; glucose-inhibited division protein B 1866..2480 Ruegeria pomeroyi DSS-3 3194097 YP_165276.1 CDS parA NC_003911.11 2473 3276 D identified by similarity to SP:O05189; match to protein family HMM PF01656; chromosome partitioning protein ParA 2473..3276 Ruegeria pomeroyi DSS-3 3196454 YP_165277.1 CDS parB NC_003911.11 3299 4189 D identified by similarity to SP:O05190; match to protein family HMM PF02195; match to protein family HMM TIGR00180; chromosome partitioning protein parB 3299..4189 Ruegeria pomeroyi DSS-3 3192954 YP_165278.1 CDS SPO0005 NC_003911.11 4179 4532 R identified by similarity to GB:AAN55061.1; match to protein family HMM PF04304; hypothetical protein complement(4179..4532) Ruegeria pomeroyi DSS-3 3196415 YP_165279.1 CDS SPO0006 NC_003911.11 4536 5693 R catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase complement(4536..5693) Ruegeria pomeroyi DSS-3 3196529 YP_165280.1 CDS SPO0007 NC_003911.11 5683 6297 R 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 complement(5683..6297) Ruegeria pomeroyi DSS-3 3196546 YP_165281.1 CDS rph NC_003911.11 6294 7007 R 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 complement(6294..7007) Ruegeria pomeroyi DSS-3 3193125 YP_165282.1 CDS hrcA NC_003911.11 7130 8194 D 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 7130..8194 Ruegeria pomeroyi DSS-3 3195247 YP_165283.1 CDS grpE NC_003911.11 8205 8768 D identified by match to protein family HMM PF01025; co-chaperone GrpE 8205..8768 Ruegeria pomeroyi DSS-3 3195554 YP_165284.1 CDS mutS NC_003911.11 8822 11455 R This protein performs the mismatch recognition step during the DNA repair process; DNA mismatch repair protein MutS complement(8822..11455) Ruegeria pomeroyi DSS-3 3194479 YP_165285.1 CDS maeB NC_003911.11 11598 13853 D NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate; malic enzyme 11598..13853 Ruegeria pomeroyi DSS-3 3194690 YP_165286.1 CDS rbsK NC_003911.11 13857 14729 D identified by similarity to SP:P05054; match to protein family HMM PF00294; ribokinase 13857..14729 Ruegeria pomeroyi DSS-3 3194154 YP_165287.1 CDS msrA-1 NC_003911.11 14726 15388 R identified by similarity to SP:Q93P63; match to protein family HMM PF01625; match to protein family HMM TIGR00401; methionine-S-sulfoxide reductase complement(14726..15388) Ruegeria pomeroyi DSS-3 3196173 YP_165288.1 CDS SPO0015 NC_003911.11 15491 16264 D hypothetical protein 15491..16264 Ruegeria pomeroyi DSS-3 3192837 YP_165289.1 CDS SPO0016 NC_003911.11 16332 16613 R identified by match to protein family HMM PF02036; sterol carrier protein complement(16332..16613) Ruegeria pomeroyi DSS-3 3194043 YP_165290.1 CDS SPO0017 NC_003911.11 16689 17132 R identified by similarity to GB:BAC49462.1; hypothetical protein complement(16689..17132) Ruegeria pomeroyi DSS-3 3194316 YP_165291.1 CDS argG NC_003911.11 17129 18358 R catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase complement(17129..18358) Ruegeria pomeroyi DSS-3 3192922 YP_165292.1 CDS SPO0019 NC_003911.11 18450 19280 D hypothetical protein 18450..19280 Ruegeria pomeroyi DSS-3 3194726 YP_165293.1 CDS ilvA NC_003911.11 19338 20564 D catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic; threonine dehydratase 19338..20564 Ruegeria pomeroyi DSS-3 3193232 YP_165294.1 CDS SPO0021 NC_003911.11 20571 20924 R identified by match to protein family HMM PF01627; Hpt domain-containing protein complement(20571..20924) Ruegeria pomeroyi DSS-3 3196142 YP_165295.1 CDS SPO0022 NC_003911.11 21005 22342 D identified by match to protein family HMM PF00072; match to protein family HMM PF07228; response regulator 21005..22342 Ruegeria pomeroyi DSS-3 3194721 YP_165296.1 CDS SPO0023 NC_003911.11 22329 22781 R identified by match to protein family HMM PF00293; NUDIX family hydrolase complement(22329..22781) Ruegeria pomeroyi DSS-3 3194753 YP_165297.1 CDS hslO NC_003911.11 22858 23838 D identified by similarity to SP:P45803; match to protein family HMM PF01430; chaperonin, 33 kDa 22858..23838 Ruegeria pomeroyi DSS-3 3194665 YP_165298.1 CDS SPO0025 NC_003911.11 23855 24427 D identified by match to protein family HMM PF00293; NUDIX family hydrolase 23855..24427 Ruegeria pomeroyi DSS-3 3193819 YP_165299.1 CDS SPO0026 NC_003911.11 24424 25578 D identified by match to protein family HMM PF01743; poly(A) polymerase 24424..25578 Ruegeria pomeroyi DSS-3 3195220 YP_165300.1 CDS SPO0027 NC_003911.11 25770 27608 D identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter transmembrane ATP-binding protein 25770..27608 Ruegeria pomeroyi DSS-3 3196318 YP_165301.1 CDS SPO0028 NC_003911.11 27605 29437 D 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 27605..29437 Ruegeria pomeroyi DSS-3 3194381 YP_165302.1 CDS rumA NC_003911.11 29456 30709 D identified by similarity to SP:P55135; 23S rRNA (uracil-5-)-methyltransferase RumA 29456..30709 Ruegeria pomeroyi DSS-3 3196355 YP_165303.1 CDS SPO0030 NC_003911.11 30727 31503 D identified by similarity to GB:CAD24429.1; match to protein family HMM PF00520; voltage-gated sodium channel 30727..31503 Ruegeria pomeroyi DSS-3 3195038 YP_165304.1 CDS SPO0031 NC_003911.11 31478 32086 D identified by match to protein family HMM PF03734; ErfK/YbiS/YcfS/YnhG family protein 31478..32086 Ruegeria pomeroyi DSS-3 3194916 YP_165305.1 CDS SPO0032 NC_003911.11 32070 32372 R hypothetical protein complement(32070..32372) Ruegeria pomeroyi DSS-3 3194226 YP_165306.1 CDS SPO0033 NC_003911.11 32458 33366 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 32458..33366 Ruegeria pomeroyi DSS-3 3196462 YP_165307.1 CDS SPO0034 NC_003911.11 33377 34816 R identified by similarity to GB:AAM48703.1; hypothetical protein complement(33377..34816) Ruegeria pomeroyi DSS-3 3193208 YP_165308.1 CDS SPO0035 NC_003911.11 34823 36502 R identified by match to protein family HMM PF02485; core-2/I-branching enzyme family protein complement(34823..36502) Ruegeria pomeroyi DSS-3 3193855 YP_165309.1 CDS SPO0036 NC_003911.11 36520 37542 R identified by similarity to GB:CAC46616.1; hypothetical protein complement(36520..37542) Ruegeria pomeroyi DSS-3 3195595 YP_165310.1 CDS SPO0037 NC_003911.11 37703 38752 R identified by similarity to GB:CAC46616.1; hypothetical protein complement(37703..38752) Ruegeria pomeroyi DSS-3 3195218 YP_165311.1 CDS kdsB NC_003911.11 38766 39566 R 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 complement(38766..39566) Ruegeria pomeroyi DSS-3 3196170 YP_165312.1 CDS cysQ NC_003911.11 39567 40364 R identified by similarity to SP:P22255; match to protein family HMM PF00459; match to protein family HMM TIGR01331; 3'(2'),5'-bisphosphate nucleotidase complement(39567..40364) Ruegeria pomeroyi DSS-3 3194237 YP_165313.1 CDS SPO0040 NC_003911.11 40483 41304 D ABC transporter permease 40483..41304 Ruegeria pomeroyi DSS-3 3195714 YP_165314.1 CDS SPO0041 NC_003911.11 41301 41885 D identified by similarity to PIR:E82361; hypothetical protein 41301..41885 Ruegeria pomeroyi DSS-3 3192766 YP_165315.1 CDS SPO0042 NC_003911.11 41882 42478 R identified by similarity to SP:P05050; match to protein family HMM PF03171; alkylated DNA repair protein complement(41882..42478) Ruegeria pomeroyi DSS-3 3194568 YP_165316.1 CDS dnaK NC_003911.11 42698 44611 D 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 42698..44611 Ruegeria pomeroyi DSS-3 3195579 YP_165317.1 CDS dnaJ NC_003911.11 44687 45832 D 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 44687..45832 Ruegeria pomeroyi DSS-3 3196511 YP_165318.1 CDS thiD NC_003911.11 46122 46925 D identified by similarity to SP:P76422; match to protein family HMM TIGR00097; phosphomethylpyrimidine kinase 46122..46925 Ruegeria pomeroyi DSS-3 3196387 YP_165319.1 CDS SPO0046 NC_003911.11 46922 47899 D identified by match to protein family HMM PF01266; thiamine biosynthesis oxidoreductase ThiO 46922..47899 Ruegeria pomeroyi DSS-3 3194412 YP_165320.1 CDS thiS NC_003911.11 47883 48077 D identified by match to protein family HMM PF02597; match to protein family HMM TIGR01683; thiamine biosynthesis protein ThiS 47883..48077 Ruegeria pomeroyi DSS-3 3196328 YP_165321.1 CDS thiG NC_003911.11 48081 48845 D 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 48081..48845 Ruegeria pomeroyi DSS-3 3195546 YP_165322.1 CDS thiE NC_003911.11 48842 49438 D Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate; thiamine-phosphate pyrophosphorylase 48842..49438 Ruegeria pomeroyi DSS-3 3194380 YP_165323.1 CDS SPO0049 NC_003911.11 49417 50400 D identified by match to protein family HMM PF00899; match to protein family HMM PF05237; thiamine biosynthesis protein ThiF 49417..50400 Ruegeria pomeroyi DSS-3 3194908 YP_165324.1 CDS SPO0050 NC_003911.11 50309 51349 D Assignment based partly on membership in ABC transporter gene cluster.; ABC transporter substrate-binding protein 50309..51349 Ruegeria pomeroyi DSS-3 3192843 YP_165325.1 CDS SPO0051 NC_003911.11 51382 52026 D identified by match to protein family HMM PF03070; TENA/THI-4 family protein 51382..52026 Ruegeria pomeroyi DSS-3 3194303 YP_165326.1 CDS SPO0052 NC_003911.11 51960 52751 D identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 51960..52751 Ruegeria pomeroyi DSS-3 3193579 YP_165327.1 CDS SPO0053 NC_003911.11 52706 53482 D identified by match to protein family HMM PF00528; ABC transporter permease 52706..53482 Ruegeria pomeroyi DSS-3 3196528 YP_165328.1 CDS radC NC_003911.11 53600 54274 D 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 53600..54274 Ruegeria pomeroyi DSS-3 3195576 YP_165329.1 CDS SPO0055 NC_003911.11 54337 55893 R identified by match to protein family HMM PF00691; OmpA domain-containing protein complement(54337..55893) Ruegeria pomeroyi DSS-3 3194535 YP_165330.1 CDS SPO0056 NC_003911.11 55908 56147 D hypothetical protein 55908..56147 Ruegeria pomeroyi DSS-3 3193841 YP_165331.1 CDS secA NC_003911.11 57011 59716 R 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 complement(57011..59716) Ruegeria pomeroyi DSS-3 3194508 YP_165332.1 CDS SPO0058 NC_003911.11 59912 60742 D identified by match to protein family HMM PF00639; peptidyl-prolyl cis-trans isomerase domain-containing protein 59912..60742 Ruegeria pomeroyi DSS-3 3196485 YP_165333.1 CDS argJ NC_003911.11 60750 61976 D 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 60750..61976 Ruegeria pomeroyi DSS-3 3193952 YP_165334.1 CDS mutT NC_003911.11 61973 62371 D identified by match to protein family HMM PF00293; match to protein family HMM TIGR00586; mutator mutT protein 61973..62371 Ruegeria pomeroyi DSS-3 3196202 YP_165335.1 CDS infB NC_003911.11 62848 65355 R 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 complement(62848..65355) Ruegeria pomeroyi DSS-3 3193823 YP_165336.1 CDS SPO0062 NC_003911.11 65364 65987 R identified by similarity to GB:AAK22031.1; match to protein family HMM PF04296; hypothetical protein complement(65364..65987) Ruegeria pomeroyi DSS-3 3194394 YP_165337.1 CDS nusA NC_003911.11 66012 67637 R modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA complement(66012..67637) Ruegeria pomeroyi DSS-3 3196304 YP_165338.1 CDS SPO0064 NC_003911.11 67637 68263 R 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 complement(67637..68263) Ruegeria pomeroyi DSS-3 3194733 YP_165339.1 CDS SPO0065 NC_003911.11 68420 69241 R peptide/opine/nickel uptake ABC transporter substrate-binding protein complement(68420..69241) Ruegeria pomeroyi DSS-3 3192830 YP_165340.1 CDS pip NC_003911.11 69238 70188 R identified by match to protein family HMM PF00561; match to protein family HMM TIGR01249; proline iminopeptidase complement(69238..70188) Ruegeria pomeroyi DSS-3 3193990 YP_165341.1 CDS ubiG NC_003911.11 70268 71014 D Involved in ubiquinone biosynthesis; 3-demethylubiquinone-9 3-methyltransferase 70268..71014 Ruegeria pomeroyi DSS-3 3196541 YP_165342.1 CDS SPO0068 NC_003911.11 71105 71545 R transcriptional regulator complement(71105..71545) Ruegeria pomeroyi DSS-3 3195175 YP_165343.1 CDS SPO0069 NC_003911.11 71558 72388 R identified by match to protein family HMM PF00795; carbon-nitrogen family hydrolase complement(71558..72388) Ruegeria pomeroyi DSS-3 3192744 YP_165344.1 CDS SPO0070 NC_003911.11 72385 72645 R identified by match to protein family HMM PF00462; match to protein family HMM TIGR02181; glutaredoxin complement(72385..72645) Ruegeria pomeroyi DSS-3 3196331 YP_165345.1 CDS SPO0071 NC_003911.11 72738 73466 R identified by similarity to GB:AAK22815.1; competence protein F complement(72738..73466) Ruegeria pomeroyi DSS-3 3194872 YP_165346.1 CDS SPO0072 NC_003911.11 73483 74316 D identified by similarity to GB:CAE26039.1; hypothetical protein 73483..74316 Ruegeria pomeroyi DSS-3 3194699 YP_165347.1 CDS hemH NC_003911.11 74429 75424 D 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 74429..75424 Ruegeria pomeroyi DSS-3 3192903 YP_165348.1 CDS SPO0074 NC_003911.11 75521 75706 R hypothetical protein complement(75521..75706) Ruegeria pomeroyi DSS-3 3194101 YP_165349.1 CDS SPO0075 NC_003911.11 75848 76474 R identified by match to protein family HMM PF03734; ErfK/YbiS/YcfS/YnhG family protein complement(75848..76474) Ruegeria pomeroyi DSS-3 3193322 YP_165350.1 CDS SPO0076 NC_003911.11 76609 77127 D lipoprotein 76609..77127 Ruegeria pomeroyi DSS-3 3195730 YP_165351.1 CDS ptsN NC_003911.11 77195 77659 R identified by match to protein family HMM PF00359; match to protein family HMM TIGR01419; PTS transporter subunit IIA-like nitrogen-regulatory protein PtsN complement(77195..77659) Ruegeria pomeroyi DSS-3 3193872 YP_165352.1 CDS SPO0078 NC_003911.11 77723 78286 R identified by match to protein family HMM PF02482; match to protein family HMM TIGR00741; ribosomal subunit interface protein complement(77723..78286) Ruegeria pomeroyi DSS-3 3194769 YP_165353.1 CDS SPO0079 NC_003911.11 78536 79294 R identified by similarity to GB:AAM48706.1; match to protein family HMM PF00005; ABC transporter ATP-binding protein complement(78536..79294) Ruegeria pomeroyi DSS-3 3196351 YP_165354.1 CDS SPO0080 NC_003911.11 79294 79785 R identified by match to protein family HMM PF03968; hypothetical protein complement(79294..79785) Ruegeria pomeroyi DSS-3 3195158 YP_165355.1 CDS SPO0081 NC_003911.11 79789 80397 R identified by similarity to GB:AAM48708.1; hypothetical protein complement(79789..80397) Ruegeria pomeroyi DSS-3 3195608 YP_165356.1 CDS kdsD NC_003911.11 80401 81369 R 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 complement(80401..81369) Ruegeria pomeroyi DSS-3 3196256 YP_165357.1 CDS SPO0083 NC_003911.11 81366 81980 R identified by match to protein family HMM PF01612; exonuclease complement(81366..81980) Ruegeria pomeroyi DSS-3 3193828 YP_165358.1 CDS betB NC_003911.11 82247 83701 R catalyzes the formation of betaine from betaine aldehyde; betaine aldehyde dehydrogenase complement(82247..83701) Ruegeria pomeroyi DSS-3 3194160 YP_165359.1 CDS SPO0085 NC_003911.11 83874 84212 D identified by similarity to GB:CAE29577.1; hypothetical protein 83874..84212 Ruegeria pomeroyi DSS-3 3192846 YP_165360.1 CDS SPO0086 NC_003911.11 84326 85588 D identified by similarity to GB:CAC41759.1; lipoprotein 84326..85588 Ruegeria pomeroyi DSS-3 3193941 YP_165361.1 CDS SPO0087 NC_003911.11 85616 86671 D hypothetical protein 85616..86671 Ruegeria pomeroyi DSS-3 3195276 YP_165362.1 CDS SPO0088 NC_003911.11 86668 88158 D identified by similarity to GB:BAB51963.1; hypothetical protein 86668..88158 Ruegeria pomeroyi DSS-3 3196530 YP_165363.1 CDS SPO0089 NC_003911.11 88160 89155 D identified by similarity to GB:CAE32220.1; hypothetical protein 88160..89155 Ruegeria pomeroyi DSS-3 3196117 YP_165364.1 CDS SPO0090 NC_003911.11 89159 90235 D identified by similarity to GB:CAE37570.1; hypothetical protein 89159..90235 Ruegeria pomeroyi DSS-3 3196424 YP_165365.1 CDS SPO0091 NC_003911.11 90242 91147 R identified by match to protein family HMM PF00581; rhodanese-like domain-containing protein complement(90242..91147) Ruegeria pomeroyi DSS-3 3195736 YP_165366.1 CDS SPO0092 NC_003911.11 91224 92447 R identified by similarity to SP:P36928; molecular chaperone DnaK complement(91224..92447) Ruegeria pomeroyi DSS-3 3196517 YP_165367.1 CDS pncA NC_003911.11 92595 93185 D identified by similarity to SP:P21369; match to protein family HMM PF00857; pyrazinamidase/nicotinamidase 92595..93185 Ruegeria pomeroyi DSS-3 3195369 YP_165368.1 CDS SPO0094 NC_003911.11 93264 95495 D 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 93264..95495 Ruegeria pomeroyi DSS-3 3196418 YP_165369.1 CDS pncB NC_003911.11 95526 96869 D catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase 95526..96869 Ruegeria pomeroyi DSS-3 3194607 YP_165370.1 CDS SPO0096 NC_003911.11 96926 97840 R identified by match to protein family HMM PF00892; hypothetical protein complement(96926..97840) Ruegeria pomeroyi DSS-3 3194541 YP_165371.1 CDS SPO0097 NC_003911.11 97843 99294 R identified by match to protein family HMM PF00171; aldehyde dehydrogenase complement(97843..99294) Ruegeria pomeroyi DSS-3 3196084 YP_165372.1 CDS SPO0098 NC_003911.11 99759 101357 R identified by match to protein family HMM PF00005; peptide/opine/nickel uptake ABC transporter ATP-binding protein complement(99759..101357) Ruegeria pomeroyi DSS-3 3194676 YP_165373.1 CDS SPO0099 NC_003911.11 101354 102169 R identified by match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease complement(101354..102169) Ruegeria pomeroyi DSS-3 3193770 YP_165374.1 CDS SPO0100 NC_003911.11 102166 103113 R identified by match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease complement(102166..103113) Ruegeria pomeroyi DSS-3 3194346 YP_165375.1 CDS SPO0101 NC_003911.11 103222 104709 R identified by match to protein family HMM PF00496; peptide/opine/nickel uptake ABC transporter substrate-binding protein complement(103222..104709) Ruegeria pomeroyi DSS-3 3196223 YP_165376.1 CDS panB NC_003911.11 104880 105719 D catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate; 3-methyl-2-oxobutanoate hydroxymethyltransferase 104880..105719 Ruegeria pomeroyi DSS-3 3194680 YP_165377.1 CDS panC NC_003911.11 105716 106573 D catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine; pantoate--beta-alanine ligase 105716..106573 Ruegeria pomeroyi DSS-3 3195525 YP_165378.1 CDS glpK NC_003911.11 106644 108122 D identified by match to protein family HMM PF00370; match to protein family HMM PF02782; match to protein family HMM TIGR01311; glycerol kinase 106644..108122 Ruegeria pomeroyi DSS-3 3194950 YP_165379.1 CDS SPO0105 NC_003911.11 108119 109378 R identified by match to protein family HMM PF01360; hypothetical protein complement(108119..109378) Ruegeria pomeroyi DSS-3 3196392 YP_165380.1 CDS SPO0106 NC_003911.11 109440 110210 R identified by similarity to SP:Q9A321; match to protein family HMM PF03883; hypothetical protein complement(109440..110210) Ruegeria pomeroyi DSS-3 3194930 YP_165381.1 CDS recQ NC_003911.11 110244 112283 R 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 complement(110244..112283) Ruegeria pomeroyi DSS-3 3194995 YP_165382.1 CDS SPO0108 NC_003911.11 112680 112952 R identified by similarity to GB:AAR33383.1; transposase, truncation complement(112680..112952) Ruegeria pomeroyi DSS-3 3196275 YP_165383.1 CDS SPO0109 NC_003911.11 113139 114266 R identified by match to protein family HMM PF01061; hypothetical protein complement(113139..114266) Ruegeria pomeroyi DSS-3 3193800 YP_165384.1 CDS SPO0110 NC_003911.11 114268 116994 R identified by match to protein family HMM PF00005; match to protein family HMM PF01061; ABC transporter ATP-binding protein/permease complement(114268..116994) Ruegeria pomeroyi DSS-3 3194511 YP_165385.1 CDS SPO0111 NC_003911.11 116991 118055 R identified by similarity to PIR:H82993; hypothetical protein complement(116991..118055) Ruegeria pomeroyi DSS-3 3194548 YP_165386.1 CDS SPO0112 NC_003911.11 118243 120084 D identified by match to protein family HMM PF07167; poly(3-hydroxyalkanoate) polymerase 118243..120084 Ruegeria pomeroyi DSS-3 3192952 YP_165387.1 CDS fabI-1 NC_003911.11 120115 120879 D Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-ACP reductase 120115..120879 Ruegeria pomeroyi DSS-3 3196492 YP_165388.1 CDS SPO0114 NC_003911.11 120897 121097 D hypothetical protein 120897..121097 Ruegeria pomeroyi DSS-3 3194359 YP_165389.1 CDS SPO0115 NC_003911.11 121130 122524 D Catalyses the synthesis of acetylphosphate from acetyl-CoA and inorganic phosphate; bifunctional enoyl-CoA hydratase/phosphate acetyltransferase 121130..122524 Ruegeria pomeroyi DSS-3 3194439 YP_165390.1 CDS ackA NC_003911.11 122521 123705 D identified by match to protein family HMM PF00871; match to protein family HMM TIGR00016; acetate kinase 122521..123705 Ruegeria pomeroyi DSS-3 3192885 YP_165391.1 CDS SPO0118 NC_003911.11 126237 127478 D hypothetical protein 126237..127478 Ruegeria pomeroyi DSS-3 3196217 YP_165392.1 CDS SPO0119 NC_003911.11 127691 128194 R identified by match to protein family HMM PF01037; AsnC family transcriptional regulator complement(127691..128194) Ruegeria pomeroyi DSS-3 3195575 YP_165393.1 CDS SPO0120 NC_003911.11 128242 129201 D identified by match to protein family HMM PF00892; hypothetical protein 128242..129201 Ruegeria pomeroyi DSS-3 3194375 YP_165394.1 CDS SPO0122 NC_003911.11 130161 130448 R identified by match to protein family HMM PF02325; hypothetical protein complement(130161..130448) Ruegeria pomeroyi DSS-3 3194448 YP_165395.1 CDS SPO0123 NC_003911.11 130602 131966 D identified by match to protein family HMM PF07690; hypothetical protein 130602..131966 Ruegeria pomeroyi DSS-3 3194881 YP_165396.1 CDS mepA NC_003911.11 131966 132847 D D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm; penicillin-insensitive murein endopeptidase 131966..132847 Ruegeria pomeroyi DSS-3 3196344 YP_165397.1 CDS SPO0125 NC_003911.11 132820 133704 D identified by similarity to PIR:F98281; hypothetical protein 132820..133704 Ruegeria pomeroyi DSS-3 3193228 YP_165398.1 CDS SPO0126 NC_003911.11 133714 134445 D identified by match to protein family HMM PF02592; match to protein family HMM TIGR00697; hypothetical protein 133714..134445 Ruegeria pomeroyi DSS-3 3194605 YP_165399.1 CDS SPO0127 NC_003911.11 134704 135123 D identified by similarity to GB:AAM35138.1; match to protein family HMM PF00472; peptidyl-tRNA hydrolase domain-containing protein 134704..135123 Ruegeria pomeroyi DSS-3 3196191 YP_165400.1 CDS fabG NC_003911.11 135168 135923 D Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 135168..135923 Ruegeria pomeroyi DSS-3 3196090 YP_165401.1 CDS SPO0129 NC_003911.11 135951 136958 D identified by match to protein family HMM PF03576; T4 family peptidase 135951..136958 Ruegeria pomeroyi DSS-3 3194709 YP_165402.1 CDS SPO0130 NC_003911.11 137081 137494 D identified by match to protein family HMM PF00034; cytochrome c family protein 137081..137494 Ruegeria pomeroyi DSS-3 3194236 YP_165403.1 CDS SPO0131 NC_003911.11 137668 138210 D identified by similarity to SP:P26173; match to protein family HMM PF00293; match to protein family HMM TIGR02150; isopentyl-diphosphate delta-isomerase 137668..138210 Ruegeria pomeroyi DSS-3 3194796 YP_165404.1 CDS SPO0132 NC_003911.11 138223 140442 R 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 complement(138223..140442) Ruegeria pomeroyi DSS-3 3196450 YP_165405.1 CDS SPO0133 NC_003911.11 140575 146001 D identified by match to protein family HMM PF00024; match to protein family HMM PF01835; match to protein family HMM PF07703; PAN domain-containing protein 140575..146001 Ruegeria pomeroyi DSS-3 3194066 YP_165406.1 CDS SPO0134 NC_003911.11 145998 146564 D identified by similarity to GB:BAB50328.1; hypothetical protein 145998..146564 Ruegeria pomeroyi DSS-3 3196545 YP_165407.1 CDS pbpC NC_003911.11 146554 148593 D 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 146554..148593 Ruegeria pomeroyi DSS-3 3195559 YP_165408.1 CDS SPO0136 NC_003911.11 148600 150645 R identified by similarity to GB:BAC47727.1; hypothetical protein complement(148600..150645) Ruegeria pomeroyi DSS-3 3193811 YP_165409.1 CDS SPO0137 NC_003911.11 150642 153404 R identified by similarity to PIR:D97630; match to protein family HMM TIGR02226; hypothetical protein complement(150642..153404) Ruegeria pomeroyi DSS-3 3192756 YP_165410.1 CDS SPO0138 NC_003911.11 153401 154276 R identified by similarity to GB:AAN30463.1; hypothetical protein complement(153401..154276) Ruegeria pomeroyi DSS-3 3193576 YP_165411.1 CDS SPO0139 NC_003911.11 154273 155280 R MoxR family ATPase complement(154273..155280) Ruegeria pomeroyi DSS-3 3196129 YP_165412.1 CDS SPO0140 NC_003911.11 155346 155927 D identified by similarity to PIR:E83277; match to protein family HMM PF06938; hypothetical protein 155346..155927 Ruegeria pomeroyi DSS-3 3194666 YP_165413.1 CDS SPO0141 NC_003911.11 155946 156515 R identified by match to protein family HMM PF01381; DNA binding protein complement(155946..156515) Ruegeria pomeroyi DSS-3 3196273 YP_165414.1 CDS bktB NC_003911.11 156963 158138 D catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA; beta-ketothiolase 156963..158138 Ruegeria pomeroyi DSS-3 3196131 YP_165415.1 CDS SPO0143 NC_003911.11 158208 159194 R identified by match to protein family HMM PF00037; (Fe-S)-binding protein complement(158208..159194) Ruegeria pomeroyi DSS-3 3193922 YP_165416.1 CDS ubiB NC_003911.11 159233 160762 R identified by similarity to SP:P27854; match to protein family HMM PF03109; match to protein family HMM TIGR01982; 2-polyprenylphenol 6-hydroxylase complement(159233..160762) Ruegeria pomeroyi DSS-3 3194970 YP_165417.1 CDS ubiE NC_003911.11 160766 161539 R identified by similarity to SP:P27851; match to protein family HMM PF01209; match to protein family HMM TIGR01934; ubiquinone/menaquinone biosynthesis methyltransferase UbiE complement(160766..161539) Ruegeria pomeroyi DSS-3 3193275 YP_165418.1 CDS mutM NC_003911.11 161604 162455 D 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 161604..162455 Ruegeria pomeroyi DSS-3 3194954 YP_165419.1 CDS SPO0147 NC_003911.11 162522 163298 D identified by similarity to SP:P14604; match to protein family HMM PF00378; enoyl-CoA hydratase 162522..163298 Ruegeria pomeroyi DSS-3 3193769 YP_165420.1 CDS rpsT NC_003911.11 163518 163781 D binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 163518..163781 Ruegeria pomeroyi DSS-3 3195937 YP_165421.1 CDS dnaA NC_003911.11 164331 165737 D 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 164331..165737 Ruegeria pomeroyi DSS-3 3194668 YP_165422.1 CDS dnaN NC_003911.11 165999 167117 D binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta 165999..167117 Ruegeria pomeroyi DSS-3 3195527 YP_165423.1 CDS recF NC_003911.11 167177 168277 D Required for DNA replication; binds preferentially to single-stranded, linear DNA; recombination protein F 167177..168277 Ruegeria pomeroyi DSS-3 3196176 YP_165424.1 CDS SPO0152 NC_003911.11 168274 168894 D identified by match to protein family HMM PF01810; amino acid transporter LysE 168274..168894 Ruegeria pomeroyi DSS-3 3193950 YP_165425.1 CDS SPO0153 NC_003911.11 168887 169474 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(168887..169474) Ruegeria pomeroyi DSS-3 3194138 YP_165426.1 CDS SPO0154 NC_003911.11 169581 170174 D identified by similarity to SP:P45245; match to protein family HMM PF02525; quinone family NAD(P)H dehydrogenase 169581..170174 Ruegeria pomeroyi DSS-3 3196293 YP_165427.1 CDS gyrB NC_003911.11 170259 172676 D negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B 170259..172676 Ruegeria pomeroyi DSS-3 3194940 YP_165428.1 CDS rtcR NC_003911.11 172724 174295 R identified by similarity to SP:P38035; match to protein family HMM PF00158; transcriptional regulator RtcR complement(172724..174295) Ruegeria pomeroyi DSS-3 3195211 YP_165429.1 CDS SPO0157 NC_003911.11 174344 176026 D identified by match to protein family HMM PF05731; TROVE domain-containing protein 174344..176026 Ruegeria pomeroyi DSS-3 3195479 YP_165430.1 CDS SPO0160 NC_003911.11 177007 178419 D identified by similarity to PIR:D75521; hypothetical protein 177007..178419 Ruegeria pomeroyi DSS-3 3196417 YP_165431.1 CDS SPO0161 NC_003911.11 178533 179147 R identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator complement(178533..179147) Ruegeria pomeroyi DSS-3 3196211 YP_165432.1 CDS SPO0162 NC_003911.11 179479 179967 D identified by similarity to GB:AAQ59886.1; hypothetical protein 179479..179967 Ruegeria pomeroyi DSS-3 3194449 YP_165433.1 CDS SPO0163 NC_003911.11 180023 182494 D 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 180023..182494 Ruegeria pomeroyi DSS-3 3194882 YP_165434.1 CDS SPO0164 NC_003911.11 182491 184470 R identified by match to protein family HMM PF00070; match to protein family HMM PF00724; oxidoreductase, FMN-binding/pyridine nucleotide-disulfide oxidoreductase complement(182491..184470) Ruegeria pomeroyi DSS-3 3194895 YP_165435.1 CDS SPO0165 NC_003911.11 184467 185198 R pyrroline-5-carboxylate reductase complement(184467..185198) Ruegeria pomeroyi DSS-3 3194960 YP_165436.1 CDS SPO0166 NC_003911.11 185200 187245 R identified by similarity to SP:O87278; match to protein family HMM PF00724; N-methylproline demethylase complement(185200..187245) Ruegeria pomeroyi DSS-3 3195336 YP_165437.1 CDS SPO0167 NC_003911.11 187255 188823 R identified by match to protein family HMM PF06253; trimethylamine methyltransferase complement(187255..188823) Ruegeria pomeroyi DSS-3 3195109 YP_165438.1 CDS SPO0168 NC_003911.11 188930 189568 D identified by match to protein family HMM PF00440; TetR family transcriptional regulator 188930..189568 Ruegeria pomeroyi DSS-3 3193023 YP_165439.1 CDS SPO0169 NC_003911.11 189622 190320 D identified by match to protein family HMM PF01464; Slt family transglycosylase 189622..190320 Ruegeria pomeroyi DSS-3 3195096 YP_165440.1 CDS flhA NC_003911.11 190330 192417 D membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA 190330..192417 Ruegeria pomeroyi DSS-3 3193109 YP_165441.1 CDS fliR NC_003911.11 192414 193187 D identified by similarity to SP:P35537; similarity to SP:Q45975; match to protein family HMM PF01311; flagellar biosynthetic protein FliR 192414..193187 Ruegeria pomeroyi DSS-3 3193095 YP_165442.1 CDS flhB NC_003911.11 193184 194272 D membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB 193184..194272 Ruegeria pomeroyi DSS-3 3195100 YP_165443.1 CDS SPO0173 NC_003911.11 194266 194679 D hypothetical protein 194266..194679 Ruegeria pomeroyi DSS-3 3195174 YP_165444.1 CDS SPO0174 NC_003911.11 194774 195310 R hypothetical protein complement(194774..195310) Ruegeria pomeroyi DSS-3 3195169 YP_165445.1 CDS flgH NC_003911.11 195319 196059 R 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 complement(195319..196059) Ruegeria pomeroyi DSS-3 3195762 YP_165446.1 CDS flgA NC_003911.11 196056 196472 R required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA complement(196056..196472) Ruegeria pomeroyi DSS-3 3195181 YP_165447.1 CDS flgG NC_003911.11 196472 197257 R 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 complement(196472..197257) Ruegeria pomeroyi DSS-3 3195735 YP_165448.1 CDS flgF NC_003911.11 197281 197931 R 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 complement(197281..197931) Ruegeria pomeroyi DSS-3 3194052 YP_165449.1 CDS fliQ NC_003911.11 197995 198267 R identified by similarity to SP:P35535; match to protein family HMM PF01313; match to protein family HMM TIGR01402; flagellar biosynthetic protein FliQ complement(197995..198267) Ruegeria pomeroyi DSS-3 3194330 YP_165450.1 CDS fliE NC_003911.11 198271 198561 R 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 complement(198271..198561) Ruegeria pomeroyi DSS-3 3196430 YP_165451.1 CDS flgC NC_003911.11 198574 198981 R with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC complement(198574..198981) Ruegeria pomeroyi DSS-3 3192784 YP_165452.1 CDS flgB NC_003911.11 198978 199394 R with FlgF and C makes up the proximal portion of the flagellar basal body rod; flagellar basal-body rod protein FlgB complement(198978..199394) Ruegeria pomeroyi DSS-3 3192893 YP_165453.1 CDS fliI NC_003911.11 199455 200792 D 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 199455..200792 Ruegeria pomeroyi DSS-3 3195322 YP_165454.1 CDS SPO0184 NC_003911.11 200811 202328 R identified by match to protein family HMM PF01970; hypothetical protein complement(200811..202328) Ruegeria pomeroyi DSS-3 3193797 YP_165455.1 CDS SPO0185 NC_003911.11 202330 202956 R hypothetical protein complement(202330..202956) Ruegeria pomeroyi DSS-3 3194629 YP_165456.1 CDS SPO0186 NC_003911.11 203121 204098 R identified by match to protein family HMM PF03401; hypothetical protein complement(203121..204098) Ruegeria pomeroyi DSS-3 3195491 YP_165457.1 CDS SPO0187 NC_003911.11 204208 204873 D identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator 204208..204873 Ruegeria pomeroyi DSS-3 3193850 YP_165458.1 CDS SPO0188 NC_003911.11 204870 206255 D identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase 204870..206255 Ruegeria pomeroyi DSS-3 3195286 YP_165459.1 CDS SPO0189 NC_003911.11 206225 207250 D identified by similarity to GB:AAM42620.1; hypothetical protein 206225..207250 Ruegeria pomeroyi DSS-3 3195068 YP_165460.1 CDS SPO0190 NC_003911.11 207330 208943 D identified by match to protein family HMM PF00732; match to protein family HMM PF05199; GMC family oxidoreductase 207330..208943 Ruegeria pomeroyi DSS-3 3195583 YP_165461.1 CDS motB NC_003911.11 209006 209863 D identified by similarity to SP:P09349; chemotaxis protein MotB 209006..209863 Ruegeria pomeroyi DSS-3 3194641 YP_165462.1 CDS SPO0192 NC_003911.11 209965 211260 D identified by similarity to SP:O07884; match to protein family HMM PF00460; match to protein family HMM PF06429; flagellar hook protein FlgE 209965..211260 Ruegeria pomeroyi DSS-3 3195683 YP_165463.1 CDS flgK NC_003911.11 211299 212750 D with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK 211299..212750 Ruegeria pomeroyi DSS-3 3195278 YP_165464.1 CDS SPO0194 NC_003911.11 212754 213761 D flagellar hook-associated protein FlgL family protein 212754..213761 Ruegeria pomeroyi DSS-3 3194464 YP_165465.1 CDS flgI NC_003911.11 213758 214858 D 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 213758..214858 Ruegeria pomeroyi DSS-3 3193009 YP_165466.1 CDS fliP NC_003911.11 215016 215759 R FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP complement(215016..215759) Ruegeria pomeroyi DSS-3 3195673 YP_165467.1 CDS fliN NC_003911.11 215756 216085 R identified by similarity to SP:Q03593; match to protein family HMM PF01052; flagellar motor switch protein FliN complement(215756..216085) Ruegeria pomeroyi DSS-3 3196056 YP_165468.1 CDS SPO0198 NC_003911.11 216042 216632 R ABC transporter ATP-binding protein, flagellar complement(216042..216632) Ruegeria pomeroyi DSS-3 3196035 YP_165469.1 CDS fliF NC_003911.11 216632 218236 R 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 complement(216632..218236) Ruegeria pomeroyi DSS-3 3192761 YP_165470.1 CDS fliL NC_003911.11 218355 218861 D identified by similarity to SP:P34008; match to protein family HMM PF03748; flagellar basal body protein FliL 218355..218861 Ruegeria pomeroyi DSS-3 3195727 YP_165471.1 CDS SPO0201 NC_003911.11 218871 219290 D identified by similarity to GB:AAF27716.1; hypothetical protein 218871..219290 Ruegeria pomeroyi DSS-3 3195986 YP_165472.1 CDS SPO0202 NC_003911.11 219287 219877 D identified by similarity to PIR:E83956; hypothetical protein 219287..219877 Ruegeria pomeroyi DSS-3 3194244 YP_165473.1 CDS motA NC_003911.11 219941 220810 D 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 219941..220810 Ruegeria pomeroyi DSS-3 3195632 YP_165474.1 CDS SPO0204 NC_003911.11 220807 223038 D hypothetical protein 220807..223038 Ruegeria pomeroyi DSS-3 3196368 YP_165475.1 CDS SPO0205 NC_003911.11 223341 224723 R identified by similarity to GB:AAO56546.1; match to protein family HMM PF03972; MmgE/PrpD family protein complement(223341..224723) Ruegeria pomeroyi DSS-3 3196222 YP_165476.1 CDS SPO0206 NC_003911.11 224915 225808 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 224915..225808 Ruegeria pomeroyi DSS-3 3194494 YP_165477.1 CDS SPO0207 NC_003911.11 225805 228222 R identified by match to protein family HMM PF01266; match to protein family HMM PF01571; glycine cleavage system protein T complement(225805..228222) Ruegeria pomeroyi DSS-3 3195798 YP_165478.1 CDS SPO0209 NC_003911.11 228804 230498 D identified by match to protein family HMM PF02690; Na/Pi-cotransporter family protein 228804..230498 Ruegeria pomeroyi DSS-3 3192860 YP_165479.1 CDS leuB NC_003911.11 230495 231598 R catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase complement(230495..231598) Ruegeria pomeroyi DSS-3 3195751 YP_165480.1 CDS SPO0211 NC_003911.11 231701 232597 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(231701..232597) Ruegeria pomeroyi DSS-3 3196243 YP_165481.1 CDS SPO0212 NC_003911.11 232647 233597 D identified by similarity to PIR:G97622; hypothetical protein 232647..233597 Ruegeria pomeroyi DSS-3 3194278 YP_165482.1 CDS SPO0213 NC_003911.11 233547 234620 R identified by similarity to GB:AAM40439.1; hypothetical protein complement(233547..234620) Ruegeria pomeroyi DSS-3 3195593 YP_165483.1 CDS SPO0214 NC_003911.11 234617 235450 R hypothetical protein complement(234617..235450) Ruegeria pomeroyi DSS-3 3196489 YP_165484.1 CDS leuD NC_003911.11 235799 236404 R catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit complement(235799..236404) Ruegeria pomeroyi DSS-3 3194679 YP_165485.1 CDS leuC-1 NC_003911.11 236489 237895 R dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit complement(236489..237895) Ruegeria pomeroyi DSS-3 3195137 YP_165486.1 CDS SPO0217 NC_003911.11 237948 238112 R hypothetical protein complement(237948..238112) Ruegeria pomeroyi DSS-3 3196527 YP_165487.1 CDS SPO0218 NC_003911.11 238133 239485 D identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS 238133..239485 Ruegeria pomeroyi DSS-3 3193938 YP_165488.1 CDS SPO0219 NC_003911.11 239625 240011 D identified by match to protein family HMM PF02410; match to protein family HMM TIGR00090; iojap family protein 239625..240011 Ruegeria pomeroyi DSS-3 3195586 YP_165489.1 CDS SPO0220 NC_003911.11 240058 240528 D 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 240058..240528 Ruegeria pomeroyi DSS-3 3196019 YP_165490.1 CDS SPO0221 NC_003911.11 240537 241022 D identified by similarity to GB:CAE38612.1; hypothetical protein 240537..241022 Ruegeria pomeroyi DSS-3 3196497 YP_165491.1 CDS ald NC_003911.11 241109 242224 R 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 complement(241109..242224) Ruegeria pomeroyi DSS-3 3196062 YP_165492.1 CDS SPO0223 NC_003911.11 242364 242822 D identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 242364..242822 Ruegeria pomeroyi DSS-3 3196105 YP_165493.1 CDS SPO0224 NC_003911.11 242986 243903 D identified by similarity to GB:AAN87337.1; match to protein family HMM PF03976; polyphosphate kinase 242986..243903 Ruegeria pomeroyi DSS-3 3196455 YP_165494.1 CDS SPO0225 NC_003911.11 243987 244499 R transcriptional regulator complement(243987..244499) Ruegeria pomeroyi DSS-3 3195104 YP_165495.1 CDS SPO0226 NC_003911.11 244548 245786 D cytochrome P450 family protein 244548..245786 Ruegeria pomeroyi DSS-3 3194470 YP_165496.1 CDS SPO0227 NC_003911.11 245787 247157 R identified by similarity to GB:AAF15370.1; match to protein family HMM PF00353; PaxA complement(245787..247157) Ruegeria pomeroyi DSS-3 3196495 YP_165497.1 CDS SPO0228 NC_003911.11 247265 248473 D identified by match to protein family HMM PF00892; hypothetical protein 247265..248473 Ruegeria pomeroyi DSS-3 3196464 YP_165498.1 CDS rpsU NC_003911.11 248574 248780 R 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 complement(248574..248780) Ruegeria pomeroyi DSS-3 3196118 YP_165499.1 CDS SPO0230 NC_003911.11 248890 249570 D identified by similarity to GB:AAK25258.1; hypothetical protein 248890..249570 Ruegeria pomeroyi DSS-3 3195644 YP_165500.1 CDS SPO0231 NC_003911.11 249647 250630 D identified by match to protein family HMM PF00107; alcohol dehydrogenase 249647..250630 Ruegeria pomeroyi DSS-3 3193028 YP_165501.1 CDS SPO0232 NC_003911.11 250710 251693 D identified by similarity to SP:P40783; match to protein family HMM PF00107; quinone oxidoreductase 250710..251693 Ruegeria pomeroyi DSS-3 3194003 YP_165502.1 CDS SPO0233 NC_003911.11 251746 252174 D identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator 251746..252174 Ruegeria pomeroyi DSS-3 3195984 YP_165503.1 CDS SPO0234 NC_003911.11 252290 253396 D identified by similarity to GB:BAB51119.1; hypothetical protein 252290..253396 Ruegeria pomeroyi DSS-3 3196075 YP_165504.1 CDS SPO0235 NC_003911.11 253400 254914 D identified by match to protein family HMM PF00171; aldehyde dehydrogenase 253400..254914 Ruegeria pomeroyi DSS-3 3196441 YP_165505.1 CDS SPO0236 NC_003911.11 255034 255972 R identified by similarity to SP:P37965; match to protein family HMM PF03009; glycerophosphoryl diester phosphodiesterase complement(255034..255972) Ruegeria pomeroyi DSS-3 3194627 YP_165506.1 CDS ugpC NC_003911.11 255969 257024 R part of the UgpABCE glycerol-3-phosphate uptake system; glycerol-3-phosphate transporter ATP-binding subunit complement(255969..257024) Ruegeria pomeroyi DSS-3 3196148 YP_165507.1 CDS ugpE NC_003911.11 257035 257886 R identified by similarity to SP:P10906; match to protein family HMM PF00528; SN-glycerol-3-phosphate ABC transporter permease complement(257035..257886) Ruegeria pomeroyi DSS-3 3192706 YP_165508.1 CDS ugpA NC_003911.11 257886 258806 R identified by similarity to SP:P10905; match to protein family HMM PF00528; SN-glycerol-3-phosphate ABC transporter permease complement(257886..258806) Ruegeria pomeroyi DSS-3 3195670 YP_165509.1 CDS ugpB NC_003911.11 258851 260236 R identified by similarity to SP:P10904; match to protein family HMM PF01547; SN-glycerol-3-phophate ABC transporter substrate-binding protein complement(258851..260236) Ruegeria pomeroyi DSS-3 3196154 YP_165510.1 CDS SPO0241 NC_003911.11 260302 261231 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 260302..261231 Ruegeria pomeroyi DSS-3 3194549 YP_165511.1 CDS dxs NC_003911.11 267660 269588 R catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase complement(267660..269588) Ruegeria pomeroyi DSS-3 3196253 YP_165512.1 CDS ispA NC_003911.11 269616 270482 R identified by similarity to GB:BAA96458.1; match to protein family HMM PF00348; farnesyl diphosphate synthase complement(269616..270482) Ruegeria pomeroyi DSS-3 3196371 YP_165513.1 CDS xseB NC_003911.11 270485 270703 R identified by match to protein family HMM PF02609; match to protein family HMM TIGR01280; exodeoxyribonuclease VII small subunit complement(270485..270703) Ruegeria pomeroyi DSS-3 3196276 YP_165514.1 CDS SPO0250 NC_003911.11 270724 271650 R identified by match to protein family HMM PF00850; histone deacetylase complement(270724..271650) Ruegeria pomeroyi DSS-3 3196238 YP_165515.1 CDS petR NC_003911.11 271676 272377 R identified by similarity to SP:P31079; match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator PetR complement(271676..272377) Ruegeria pomeroyi DSS-3 3196152 YP_165516.1 CDS petP NC_003911.11 272374 272886 R identified by similarity to SP:P31078; match to protein family HMM PF01047; transcriptional regulator PetP complement(272374..272886) Ruegeria pomeroyi DSS-3 3195959 YP_165517.1 CDS ilvE NC_003911.11 273044 273910 D catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase 273044..273910 Ruegeria pomeroyi DSS-3 3194036 YP_165518.1 CDS ohr NC_003911.11 273966 274406 R identified by similarity to GB:AAC38562.1; match to protein family HMM PF02566; organic hydroperoxide resistance protein complement(273966..274406) Ruegeria pomeroyi DSS-3 3196543 YP_165519.1 CDS SPO0255 NC_003911.11 274505 274942 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 274505..274942 Ruegeria pomeroyi DSS-3 3196321 YP_165520.1 CDS SPO0256 NC_003911.11 274955 275284 R identified by match to protein family HMM PF00127; plastocyanin/azurin family copper binding protein complement(274955..275284) Ruegeria pomeroyi DSS-3 3194099 YP_165521.1 CDS SPO0257 NC_003911.11 275275 275799 R identified by similarity to PIR:A96030; hypothetical protein complement(275275..275799) Ruegeria pomeroyi DSS-3 3195225 YP_165522.1 CDS SPO0258 NC_003911.11 275937 276917 D identified by match to protein family HMM PF00165; AraC family transcriptional regulator 275937..276917 Ruegeria pomeroyi DSS-3 3195966 YP_165523.1 CDS SPO0259 NC_003911.11 276985 277395 D identified by similarity to GB:CAE32384.1; hypothetical protein 276985..277395 Ruegeria pomeroyi DSS-3 3194001 YP_165524.1 CDS SPO0260 NC_003911.11 277569 279137 D identified by similarity to SP:P42251; match to protein family HMM PF00245; match to protein family HMM TIGR01409; alkaline phosphatase 277569..279137 Ruegeria pomeroyi DSS-3 3194912 YP_165525.1 CDS SPO0261 NC_003911.11 279220 280086 R identified by match to protein family HMM PF00892; hypothetical protein complement(279220..280086) Ruegeria pomeroyi DSS-3 3196288 YP_165526.1 CDS cobO NC_003911.11 280092 280691 R identified by match to protein family HMM PF02572; match to protein family HMM TIGR00708; cob(I)alamin adenosyltransferase complement(280092..280691) Ruegeria pomeroyi DSS-3 3196500 YP_165527.1 CDS SPO0263 NC_003911.11 280748 281791 R identified by match to protein family HMM PF00892; hypothetical protein complement(280748..281791) Ruegeria pomeroyi DSS-3 3192897 YP_165528.1 CDS SPO0264 NC_003911.11 281790 283121 D identified by match to protein family HMM PF02515; CaiB/BaiF family protein 281790..283121 Ruegeria pomeroyi DSS-3 3193993 YP_165529.1 CDS SPO0265 NC_003911.11 283122 284063 R identified by similarity to GB:AAA99820.1; match to protein family HMM PF03547; auxin efflux carrier protein complement(283122..284063) Ruegeria pomeroyi DSS-3 3193839 YP_165530.1 CDS SPO0266 NC_003911.11 284060 284764 R identified by match to protein family HMM PF01966; HD domain-containing protein complement(284060..284764) Ruegeria pomeroyi DSS-3 3196435 YP_165531.1 CDS aroC NC_003911.11 284706 285806 R catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase complement(284706..285806) Ruegeria pomeroyi DSS-3 3196504 YP_165532.2 CDS ribH-1 NC_003911.11 285959 286399 R 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 complement(285959..286399) Ruegeria pomeroyi DSS-3 3195724 YP_165533.1 CDS SPO0269 NC_003911.11 286691 287305 D identified by match to protein family HMM PF04299; negative transcriptional regulator 286691..287305 Ruegeria pomeroyi DSS-3 3195962 YP_165534.1 CDS SPO0270 NC_003911.11 287383 287994 D identified by match to protein family HMM PF02798; glutathione S-transferase 287383..287994 Ruegeria pomeroyi DSS-3 3194841 YP_165535.1 CDS petA NC_003911.11 288197 288760 D 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 288197..288760 Ruegeria pomeroyi DSS-3 3196282 YP_165536.1 CDS petB NC_003911.11 288773 290101 D identified by similarity to SP:P05418; match to protein family HMM PF00032; match to protein family HMM PF00033; ubiquinol--cytochrome c reductase, cytochrome B 288773..290101 Ruegeria pomeroyi DSS-3 3195221 YP_165537.1 CDS petC NC_003911.11 290120 290983 D identified by similarity to SP:Q02760; match to protein family HMM PF02167; ubiquinol--cytochrome c reductase, cytochrome c1 290120..290983 Ruegeria pomeroyi DSS-3 3194314 YP_165538.1 CDS SPO0274 NC_003911.11 291065 291460 D identified by similarity to GB:BAC74098.1; hypothetical protein 291065..291460 Ruegeria pomeroyi DSS-3 3196540 YP_165539.1 CDS SPO0275 NC_003911.11 291467 292033 D identified by match to protein family HMM PF01292; cytochrome b 291467..292033 Ruegeria pomeroyi DSS-3 3196491 YP_165540.1 CDS SPO0276 NC_003911.11 292054 292551 D identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 292054..292551 Ruegeria pomeroyi DSS-3 3196434 YP_165541.1 CDS SPO0277 NC_003911.11 292631 293887 R 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 complement(292631..293887) Ruegeria pomeroyi DSS-3 3196395 YP_165542.1 CDS dapF NC_003911.11 293884 294693 R identified by similarity to SP:P08885; match to protein family HMM PF01678; match to protein family HMM TIGR00652; diaminopimelate epimerase complement(293884..294693) Ruegeria pomeroyi DSS-3 3196503 YP_165543.1 CDS SPO0280 NC_003911.11 295170 295337 D identified by similarity to GB:AAC43509.1; transposase, truncation 295170..295337 Ruegeria pomeroyi DSS-3 3196279 YP_165544.1 CDS SPO0281 NC_003911.11 295450 295923 R identified by similarity to GB:BAC93558.1; hypothetical protein complement(295450..295923) Ruegeria pomeroyi DSS-3 3195726 YP_165545.1 CDS SPO0282 NC_003911.11 296104 296379 R hypothetical protein complement(296104..296379) Ruegeria pomeroyi DSS-3 3196323 YP_165546.1 CDS SPO0283 NC_003911.11 296376 296987 R identified by similarity to GB:CAE28560.1; match to protein family HMM PF02660; match to protein family HMM TIGR00023; hypothetical protein complement(296376..296987) Ruegeria pomeroyi DSS-3 3195725 YP_165547.1 CDS SPO0284 NC_003911.11 296987 298276 R identified by similarity to SP:P46538; match to protein family HMM PF01979; match to protein family HMM TIGR00857; dihydroorotase, multifunctional complex type complement(296987..298276) Ruegeria pomeroyi DSS-3 3195702 YP_165548.1 CDS SPO0285 NC_003911.11 298273 298659 R hypothetical protein complement(298273..298659) Ruegeria pomeroyi DSS-3 3193013 YP_165549.1 CDS SPO0286 NC_003911.11 298644 299168 R hypothetical protein complement(298644..299168) Ruegeria pomeroyi DSS-3 3194341 YP_165550.1 CDS pyrB NC_003911.11 299165 300100 R catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase complement(299165..300100) Ruegeria pomeroyi DSS-3 3196460 YP_165551.1 CDS udgA NC_003911.11 300846 301631 D identified by similarity to GB:CAD29336.1; match to protein family HMM PF03167; match to protein family HMM TIGR00758; uracil-DNA glycosylase 300846..301631 Ruegeria pomeroyi DSS-3 3196228 YP_165552.1 CDS SPO0289 NC_003911.11 301631 302230 D identified by match to protein family HMM PF00149; Ser/Thr protein phosphatase 301631..302230 Ruegeria pomeroyi DSS-3 3196135 YP_165553.1 CDS SPO0290 NC_003911.11 302227 302847 D identified by match to protein family HMM PF01810; transmembrane amino acid efflux protein 302227..302847 Ruegeria pomeroyi DSS-3 3195828 YP_165554.1 CDS SPO0291 NC_003911.11 302852 303394 D identified by similarity to SP:P30746; match to protein family HMM PF00994; match to protein family HMM TIGR00177; molybdenum cofactor biosynthesis protein B 302852..303394 Ruegeria pomeroyi DSS-3 3196337 YP_165555.1 CDS SPO0292 NC_003911.11 303491 304948 D identified by match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 303491..304948 Ruegeria pomeroyi DSS-3 3193281 YP_165556.1 CDS SPO0293 NC_003911.11 304955 308356 D identified by match to protein family HMM PF00873; AcrB/AcrD/AcrF family transporter 304955..308356 Ruegeria pomeroyi DSS-3 3194582 YP_165557.1 CDS SPO0294 NC_003911.11 308364 308783 R identified by match to protein family HMM PF00293; NUDIX family hydrolase complement(308364..308783) Ruegeria pomeroyi DSS-3 3196361 YP_165558.1 CDS SPO0295 NC_003911.11 308787 309605 R identified by similarity to GB:BAC46756.1; hypothetical protein complement(308787..309605) Ruegeria pomeroyi DSS-3 3193762 YP_165559.1 CDS SPO0296 NC_003911.11 309710 310294 D identified by similarity to GB:BAC46757.1; match to protein family HMM PF02622; hypothetical protein 309710..310294 Ruegeria pomeroyi DSS-3 3195560 YP_165560.1 CDS SPO0297 NC_003911.11 310446 311396 R 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 complement(310446..311396) Ruegeria pomeroyi DSS-3 3193859 YP_165561.1 CDS SPO0298 NC_003911.11 311525 313228 D identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 311525..313228 Ruegeria pomeroyi DSS-3 3193203 YP_165562.1 CDS SPO0299 NC_003911.11 313225 314274 D identified by match to protein family HMM PF00753; metallo-beta-lactamase 313225..314274 Ruegeria pomeroyi DSS-3 3193047 YP_165563.1 CDS SPO0300 NC_003911.11 314278 314733 D hypothetical protein 314278..314733 Ruegeria pomeroyi DSS-3 3196352 YP_165564.1 CDS SPO0301 NC_003911.11 314804 316648 D identified by match to protein family HMM PF03009; glycerophosphoryl diester phosphodiesterase 314804..316648 Ruegeria pomeroyi DSS-3 3196120 YP_165565.1 CDS SPO0302 NC_003911.11 316617 317195 D identified by similarity to GB:CAE78911.1; hypothetical protein 316617..317195 Ruegeria pomeroyi DSS-3 3194544 YP_165566.1 CDS SPO0303 NC_003911.11 317258 317392 D cytochrome c oxidase subunit IV 317258..317392 Ruegeria pomeroyi DSS-3 3196055 YP_165567.1 CDS SPO0304 NC_003911.11 317412 318029 D lipoprotein 317412..318029 Ruegeria pomeroyi DSS-3 3193909 YP_165568.1 CDS SPO0305 NC_003911.11 318368 319084 R identified by match to protein family HMM PF03591; AzlC family protein complement(318368..319084) Ruegeria pomeroyi DSS-3 3193808 YP_165569.1 CDS fdhD NC_003911.11 319140 320021 D identified by match to protein family HMM PF02634; match to protein family HMM TIGR00129; formate dehydrogenase accessory protein FdhD 319140..320021 Ruegeria pomeroyi DSS-3 3192759 YP_165570.1 CDS mobA NC_003911.11 320619 321254 D 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 320619..321254 Ruegeria pomeroyi DSS-3 3193793 YP_165571.1 CDS mobB NC_003911.11 321251 321742 D identified by similarity to SP:P32125; match to protein family HMM PF03205; match to protein family HMM TIGR00176; molybdopterin-guanine dinucleotide biosynthesis protein B 321251..321742 Ruegeria pomeroyi DSS-3 3193692 YP_165572.1 CDS SPO0309 NC_003911.11 321739 322539 D identified by similarity to GB:AAK23994.1; hypothetical protein 321739..322539 Ruegeria pomeroyi DSS-3 3192816 YP_165573.1 CDS moeA NC_003911.11 322536 323795 D is involved in the formation of active molybdenum cofactor and the chelation of molybdenum; molybdopterin biosynthesis protein MoeA 322536..323795 Ruegeria pomeroyi DSS-3 3194185 YP_165574.1 CDS SPO0311 NC_003911.11 323819 324826 R hypothetical protein complement(323819..324826) Ruegeria pomeroyi DSS-3 3194146 YP_165575.1 CDS greA NC_003911.11 324840 325310 R 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 complement(324840..325310) Ruegeria pomeroyi DSS-3 3194600 YP_165576.1 CDS SPO0313 NC_003911.11 325446 325826 R identified by match to protein family HMM PF00903; glyoxalase complement(325446..325826) Ruegeria pomeroyi DSS-3 3194049 YP_165577.1 CDS soxR NC_003911.11 325911 326366 D identified by match to protein family HMM PF00376; match to protein family HMM TIGR01950; redox-sensitive transcriptional activator SoxR 325911..326366 Ruegeria pomeroyi DSS-3 3194247 YP_165578.1 CDS SPO0315 NC_003911.11 326374 326682 R identified by similarity to GB:AAM41091.1; match to protein family HMM TIGR02118; hypothetical protein complement(326374..326682) Ruegeria pomeroyi DSS-3 3194162 YP_165579.1 CDS SPO0316 NC_003911.11 326914 328560 D identified by similarity to SP:Q16134; match to protein family HMM PF05187; electrotransfer ubiquinone oxidoreductase 326914..328560 Ruegeria pomeroyi DSS-3 3192928 YP_165580.1 CDS SPO0317 NC_003911.11 328606 330441 D identified by similarity to GB:CAE26481.1; match to protein family HMM PF00515; hypothetical protein 328606..330441 Ruegeria pomeroyi DSS-3 3195165 YP_165581.1 CDS ispE NC_003911.11 330431 331270 D identified by match to protein family HMM PF00288; match to protein family HMM TIGR00154; 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 330431..331270 Ruegeria pomeroyi DSS-3 3193014 YP_165582.1 CDS ddsA NC_003911.11 331351 332349 R identified by similarity to GB:CAD24417.1; match to protein family HMM PF00348; decaprenyl diphosphate synthase complement(331351..332349) Ruegeria pomeroyi DSS-3 3194982 YP_165583.1 CDS SPO0320 NC_003911.11 332406 332621 D identified by similarity to GB:CAC45419.1; hypothetical protein 332406..332621 Ruegeria pomeroyi DSS-3 3192970 YP_165584.1 CDS SPO0321 NC_003911.11 332618 333391 D identified by similarity to GB:CAD24416.1; hypothetical protein 332618..333391 Ruegeria pomeroyi DSS-3 3193164 YP_165585.1 CDS SPO0322 NC_003911.11 333505 333669 D identified by similarity to PIR:AE3289; match to protein family HMM PF04325; hypothetical protein 333505..333669 Ruegeria pomeroyi DSS-3 3193178 YP_165586.1 CDS SPO0323 NC_003911.11 333666 334532 R identified by match to protein family HMM PF00892; hypothetical protein complement(333666..334532) Ruegeria pomeroyi DSS-3 3193016 YP_165587.1 CDS SPO0324 NC_003911.11 334529 335476 R 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 complement(334529..335476) Ruegeria pomeroyi DSS-3 3194175 YP_165588.1 CDS phbB NC_003911.11 335827 336549 R identified by similarity to SP:P23238; match to protein family HMM PF00106; match to protein family HMM TIGR01829; acetoacetyl-CoA reductase complement(335827..336549) Ruegeria pomeroyi DSS-3 3193146 YP_165589.1 CDS phbA NC_003911.11 336736 337911 R 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 complement(336736..337911) Ruegeria pomeroyi DSS-3 3194058 YP_165590.1 CDS SPO0327 NC_003911.11 338082 338921 R identified by match to protein family HMM PF00563; diguanylate phosphodiesterase complement(338082..338921) Ruegeria pomeroyi DSS-3 3195449 YP_165591.1 CDS SPO0328 NC_003911.11 339136 340068 R identified by similarity to GB:BAB48523.1; hypothetical protein complement(339136..340068) Ruegeria pomeroyi DSS-3 3192694 YP_165592.1 CDS SPO0329 NC_003911.11 340065 340484 R hypothetical protein complement(340065..340484) Ruegeria pomeroyi DSS-3 3193423 YP_165593.1 CDS ccpA NC_003911.11 340918 341967 D identified by similarity to SP:P14532; match to protein family HMM PF03150; cytochrome c peroxidase 340918..341967 Ruegeria pomeroyi DSS-3 3195929 YP_165594.1 CDS SPO0331 NC_003911.11 342014 342577 R identified by similarity to SP:P43221; thiol:disulfide interchange protein complement(342014..342577) Ruegeria pomeroyi DSS-3 3194061 YP_165595.1 CDS argH NC_003911.11 342602 343993 D catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase 342602..343993 Ruegeria pomeroyi DSS-3 3196544 YP_165596.1 CDS SPO0333 NC_003911.11 343990 344172 D lipoprotein 343990..344172 Ruegeria pomeroyi DSS-3 3196542 YP_165597.1 CDS lysA NC_003911.11 344379 345644 D identified by match to protein family HMM PF00278; match to protein family HMM PF02784; match to protein family HMM TIGR01048; diaminopimelate decarboxylase 344379..345644 Ruegeria pomeroyi DSS-3 3195501 YP_165598.1 CDS SPO0335 NC_003911.11 345684 348242 D hypothetical protein 345684..348242 Ruegeria pomeroyi DSS-3 3196168 YP_165599.1 CDS SPO0336 NC_003911.11 348262 349101 R identified by match to protein family HMM TIGR02098; hypothetical protein complement(348262..349101) Ruegeria pomeroyi DSS-3 3196186 YP_165600.1 CDS ftsE NC_003911.11 349240 349971 D identified by similarity to SP:P10115; match to protein family HMM PF00005; cell division ATP-binding protein FtsE 349240..349971 Ruegeria pomeroyi DSS-3 3196289 YP_165601.1 CDS SPO0338 NC_003911.11 349968 350867 D identified by match to protein family HMM PF02687; cell division permease FtsX 349968..350867 Ruegeria pomeroyi DSS-3 3196209 YP_165602.1 CDS SPO0339 NC_003911.11 350864 351595 D identified by match to protein family HMM PF01553; acyltransferase 350864..351595 Ruegeria pomeroyi DSS-3 3196208 YP_165603.1 CDS lpdA NC_003911.11 351721 353109 R identified by match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM TIGR01350; 2-oxoglutarate dehydrogenase E3 complement(351721..353109) Ruegeria pomeroyi DSS-3 3196204 YP_165604.1 CDS SPO0341 NC_003911.11 353124 353468 D hypothetical protein 353124..353468 Ruegeria pomeroyi DSS-3 3196182 YP_165605.1 CDS SPO0342 NC_003911.11 353181 353450 R hypothetical protein complement(353181..353450) Ruegeria pomeroyi DSS-3 3196194 YP_165606.1 CDS sucB NC_003911.11 353635 354831 R 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 complement(353635..354831) Ruegeria pomeroyi DSS-3 3196189 YP_165607.1 CDS sucA NC_003911.11 355147 358104 R 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 complement(355147..358104) Ruegeria pomeroyi DSS-3 3196406 YP_165608.1 CDS SPO0345 NC_003911.11 358880 359431 R identified by similarity to GB:AAN82305.1; match to protein family HMM PF05656; hypothetical protein complement(358880..359431) Ruegeria pomeroyi DSS-3 3196205 YP_165609.1 CDS sucD NC_003911.11 359481 360365 R 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 complement(359481..360365) Ruegeria pomeroyi DSS-3 3196431 YP_165610.1 CDS sucC NC_003911.11 360913 362106 R catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta complement(360913..362106) Ruegeria pomeroyi DSS-3 3196412 YP_165611.1 CDS SPO0348 NC_003911.11 362383 363507 D hypothetical protein 362383..363507 Ruegeria pomeroyi DSS-3 3196422 YP_165612.1 CDS mdh NC_003911.11 363558 364520 R Catalyzes the reversible oxidation of malate to oxaloacetate; malate dehydrogenase complement(363558..364520) Ruegeria pomeroyi DSS-3 3196445 YP_165613.1 CDS SPO0350 NC_003911.11 364683 365438 D identified by match to protein family HMM PF01925; hypothetical protein 364683..365438 Ruegeria pomeroyi DSS-3 3196429 YP_165614.1 CDS SPO0351 NC_003911.11 365521 365835 R identified by similarity to GB:CAC45660.1; hypothetical protein complement(365521..365835) Ruegeria pomeroyi DSS-3 3196453 YP_165615.1 CDS citE NC_003911.11 366147 367004 D identified by similarity to SP:P77770; citrate lyase subunit beta 366147..367004 Ruegeria pomeroyi DSS-3 3196439 YP_165616.1 CDS SPO0353 NC_003911.11 367011 367565 D identified by match to protein family HMM PF07298; NnrU family protein 367011..367565 Ruegeria pomeroyi DSS-3 3196459 YP_165617.1 CDS SPO0354 NC_003911.11 367576 367782 D identified by similarity to PIR:AE3561; hypothetical protein 367576..367782 Ruegeria pomeroyi DSS-3 3196257 YP_165618.1 CDS SPO0355 NC_003911.11 367782 368810 D identified by similarity to GB:AAK25618.1; hypothetical protein 367782..368810 Ruegeria pomeroyi DSS-3 3196452 YP_165619.1 CDS SPO0356 NC_003911.11 368789 369547 D identified by similarity to GB:BAC61369.1; hypothetical protein 368789..369547 Ruegeria pomeroyi DSS-3 3196463 YP_165620.1 CDS SPO0357 NC_003911.11 369582 370244 D identified by match to protein family HMM PF00092; von Willebrand factor A 369582..370244 Ruegeria pomeroyi DSS-3 3196456 YP_165621.1 CDS sdhC NC_003911.11 370463 370849 D identified by match to protein family HMM PF01127; succinate dehydrogenase, cytochrome b556 subunit 370463..370849 Ruegeria pomeroyi DSS-3 3196468 YP_165622.1 CDS sdhD NC_003911.11 370862 371233 D identified by similarity to GB:AAC17941.1; succinate dehydrogenase, hydrophobic membrane anchor protein 370862..371233 Ruegeria pomeroyi DSS-3 3196461 YP_165623.1 CDS sdhA NC_003911.11 371250 373055 D 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 371250..373055 Ruegeria pomeroyi DSS-3 3196466 YP_165624.1 CDS sdhB NC_003911.11 373340 374119 D 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 373340..374119 Ruegeria pomeroyi DSS-3 3196472 YP_165625.1 CDS SPO0362 NC_003911.11 374164 376323 D identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 374164..376323 Ruegeria pomeroyi DSS-3 3196478 YP_165626.1 CDS SPO0363 NC_003911.11 376576 376791 D hypothetical protein 376576..376791 Ruegeria pomeroyi DSS-3 3196486 YP_165627.1 CDS SPO0364 NC_003911.11 377206 378387 D identified by match to protein family HMM PF00278; match to protein family HMM PF02784; decarboxylase, pyridoxal-dependent 377206..378387 Ruegeria pomeroyi DSS-3 3196498 YP_165628.1 CDS SPO0365 NC_003911.11 378468 379325 D identified by similarity to PIR:G97525; hypothetical protein 378468..379325 Ruegeria pomeroyi DSS-3 3196506 YP_165629.1 CDS deoD NC_003911.11 379410 380120 R catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate; purine nucleoside phosphorylase complement(379410..380120) Ruegeria pomeroyi DSS-3 3196509 YP_165630.1 CDS SPO0367 NC_003911.11 380136 380453 R identified by match to protein family HMM PF00816; H-NS family DNA-binding protein complement(380136..380453) Ruegeria pomeroyi DSS-3 3196512 YP_165631.1 CDS SPO0368 NC_003911.11 380565 382565 R 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 complement(380565..382565) Ruegeria pomeroyi DSS-3 3196514 YP_165632.1 CDS SPO0369 NC_003911.11 382532 384115 D identified by similarity to SP:P00482; match to protein family HMM PF01553; acyltransferase 382532..384115 Ruegeria pomeroyi DSS-3 3196523 YP_165633.1 CDS ccrA NC_003911.11 384226 385512 D identified by match to protein family HMM PF00107; match to protein family HMM TIGR01751; crotonyl-CoA reductase 384226..385512 Ruegeria pomeroyi DSS-3 3196525 YP_165634.1 CDS luxR-1 NC_003911.11 385883 386602 D identified by match to protein family HMM PF00196; match to protein family HMM PF03472; LuxR family transcriptional regulator 385883..386602 Ruegeria pomeroyi DSS-3 3196532 YP_165635.1 CDS SPO0372 NC_003911.11 386685 387323 D identified by match to protein family HMM PF00765; autoinducer synthesis protein 386685..387323 Ruegeria pomeroyi DSS-3 3196537 YP_165636.1 CDS SPO0373 NC_003911.11 387521 388918 D helicase, ATP-dependent 387521..388918 Ruegeria pomeroyi DSS-3 3196397 YP_165637.1 CDS SPO0374 NC_003911.11 389073 389870 R identified by similarity to GB:CAE26256.1; hypothetical protein complement(389073..389870) Ruegeria pomeroyi DSS-3 3196206 YP_165638.1 CDS SPO0375 NC_003911.11 389848 390798 R identified by match to protein family HMM PF01925; hypothetical protein complement(389848..390798) Ruegeria pomeroyi DSS-3 3196372 YP_165639.1 CDS SPO0376 NC_003911.11 390860 391828 R identified by match to protein family HMM PF02653; sugar ABC transporter permease complement(390860..391828) Ruegeria pomeroyi DSS-3 3194229 YP_165640.1 CDS SPO0377 NC_003911.11 391825 392919 R identified by match to protein family HMM PF02653; sugar ABC transporter permease complement(391825..392919) Ruegeria pomeroyi DSS-3 3194004 YP_165641.1 CDS SPO0378 NC_003911.11 392919 394448 R identified by match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein complement(392919..394448) Ruegeria pomeroyi DSS-3 3192747 YP_165642.1 CDS SPO0379 NC_003911.11 394572 395570 R identified by match to protein family HMM PF02608; sugar ABC transporter periplasmic sugar-binding protein complement(394572..395570) Ruegeria pomeroyi DSS-3 3196193 YP_165643.1 CDS SPO0380 NC_003911.11 395729 396142 R identified by similarity to SP:P09453; match to protein family HMM PF00583; ribosomal-protein-alanine acetyltransferase complement(395729..396142) Ruegeria pomeroyi DSS-3 3195351 YP_165644.1 CDS SPO0381 NC_003911.11 396139 396729 R identified by match to protein family HMM PF00814; protease complement(396139..396729) Ruegeria pomeroyi DSS-3 3194018 YP_165645.1 CDS SPO0382 NC_003911.11 396719 397282 R identified by match to protein family HMM PF01106; NifU domain-containing protein complement(396719..397282) Ruegeria pomeroyi DSS-3 3196136 YP_165646.1 CDS SPO0383 NC_003911.11 397406 398020 R identified by similarity to SP:P41407; match to protein family HMM PF02525; ACP phosphodieterase complement(397406..398020) Ruegeria pomeroyi DSS-3 3196394 YP_165647.1 CDS SPO0384 NC_003911.11 398149 398739 D identified by similarity to GB:BAC89223.1; match to protein family HMM PF07336; hypothetical protein 398149..398739 Ruegeria pomeroyi DSS-3 3194611 YP_165648.1 CDS SPO0385 NC_003911.11 398793 399386 R identified by match to protein family HMM PF01323; 2-hydroxychromene-2-carboxylate isomerase complement(398793..399386) Ruegeria pomeroyi DSS-3 3196516 YP_165649.1 CDS SPO0386 NC_003911.11 399394 399864 R identified by match to protein family HMM PF00582; universal stress family protein complement(399394..399864) Ruegeria pomeroyi DSS-3 3196363 YP_165650.1 CDS SPO0387 NC_003911.11 399889 400953 R hypothetical protein complement(399889..400953) Ruegeria pomeroyi DSS-3 3196034 YP_165651.1 CDS SPO0388 NC_003911.11 400950 401813 R catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; aminotransferase complement(400950..401813) Ruegeria pomeroyi DSS-3 3192972 YP_165652.1 CDS SPO0389 NC_003911.11 401873 402334 R identified by match to protein family HMM PF01037; AsnC family transcriptional regulator complement(401873..402334) Ruegeria pomeroyi DSS-3 3196281 YP_165653.1 CDS SPO0390 NC_003911.11 402464 403513 D identified by match to protein family HMM PF00208; match to protein family HMM PF02812; glutamate/leucine/phenylalanine/valine dehydrogenase 402464..403513 Ruegeria pomeroyi DSS-3 3195417 YP_165654.1 CDS bphC3 NC_003911.11 403532 404017 R identified by similarity to SP:P47233; match to protein family HMM PF00903; biphenyl-2,3-diol 1,2-dioxygenase III complement(403532..404017) Ruegeria pomeroyi DSS-3 3196315 YP_165655.1 CDS trpS NC_003911.11 404139 405155 R 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 complement(404139..405155) Ruegeria pomeroyi DSS-3 3196317 YP_165656.1 CDS SPO0393 NC_003911.11 405115 405927 D identified by match to protein family HMM PF01694; rhomboid family protein 405115..405927 Ruegeria pomeroyi DSS-3 3196163 YP_165657.1 CDS SPO0394 NC_003911.11 405948 406139 R identified by similarity to GB:CAE09894.1; hypothetical protein complement(405948..406139) Ruegeria pomeroyi DSS-3 3196232 YP_165658.1 CDS SPO0395 NC_003911.11 406211 406795 R identified by match to protein family HMM PF00027; cyclic nucleotide-binding protein complement(406211..406795) Ruegeria pomeroyi DSS-3 3196147 YP_165659.1 CDS mviN NC_003911.11 406792 408333 R identified by similarity to SP:O05467; match to protein family HMM PF03023; match to protein family HMM TIGR01695; integral membrane protein MviN complement(406792..408333) Ruegeria pomeroyi DSS-3 3193673 YP_165660.1 CDS glnD NC_003911.11 408330 411056 R catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein; PII uridylyl-transferase complement(408330..411056) Ruegeria pomeroyi DSS-3 3195406 YP_165661.1 CDS SPO0398 NC_003911.11 411124 412299 R identified by similarity to GB:BAC45936.1; hypothetical protein complement(411124..412299) Ruegeria pomeroyi DSS-3 3196178 YP_165662.1 CDS SPO0399 NC_003911.11 412384 413241 D identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096; tetrapyrrole methylase 412384..413241 Ruegeria pomeroyi DSS-3 3195371 YP_165663.1 CDS SPO0400 NC_003911.11 413243 413614 D identified by similarity to GB:AAN66948.1; match to protein family HMM PF02021; hypothetical protein 413243..413614 Ruegeria pomeroyi DSS-3 3195920 YP_165664.1 CDS gshB NC_003911.11 413677 414609 D catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione; glutathione synthetase 413677..414609 Ruegeria pomeroyi DSS-3 3196266 YP_165665.1 CDS comM NC_003911.11 414677 416191 R identified by similarity to SP:P45049; match to protein family HMM PF01078; match to protein family HMM TIGR00368; competence protein ComM complement(414677..416191) Ruegeria pomeroyi DSS-3 3196310 YP_165666.1 CDS SPO0403 NC_003911.11 416250 417134 R identified by similarity to GB:CAD13614.1; hypothetical protein complement(416250..417134) Ruegeria pomeroyi DSS-3 3196259 YP_165667.1 CDS SPO0404 NC_003911.11 417186 417764 R identified by match to protein family HMM PF00300; phosphoglycerate mutase complement(417186..417764) Ruegeria pomeroyi DSS-3 3196408 YP_165668.1 CDS SPO0405 NC_003911.11 417761 418285 R identified by match to protein family HMM PF02283; cobinamide kinase/cobinamide phosphate guanyltransferase complement(417761..418285) Ruegeria pomeroyi DSS-3 3196251 YP_165669.1 CDS rpoH2 NC_003911.11 418384 419262 D 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 418384..419262 Ruegeria pomeroyi DSS-3 3196326 YP_165670.1 CDS SPO0407 NC_003911.11 419259 420083 D identified by similarity to PIR:E83058; hypothetical protein 419259..420083 Ruegeria pomeroyi DSS-3 3196229 YP_165671.1 CDS coaBC NC_003911.11 420163 421359 D 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 420163..421359 Ruegeria pomeroyi DSS-3 3196298 YP_165672.1 CDS dut NC_003911.11 421423 421878 D catalyzes the formation of dUMP from dUTP; deoxyuridine 5'-triphosphate nucleotidohydrolase 421423..421878 Ruegeria pomeroyi DSS-3 3196171 YP_165673.1 CDS SPO0410 NC_003911.11 421878 422918 D identified by match to protein family HMM PF00899; match to protein family HMM PF05237; molybdopterin biosynthesis protein MoeB 421878..422918 Ruegeria pomeroyi DSS-3 3196134 YP_165674.1 CDS SPO0411 NC_003911.11 422854 423549 D hypothetical protein 422854..423549 Ruegeria pomeroyi DSS-3 3193668 YP_165675.1 CDS SPO0412 NC_003911.11 423669 424136 R hypothetical protein complement(423669..424136) Ruegeria pomeroyi DSS-3 3196398 YP_165676.1 CDS SPO0413 NC_003911.11 424229 425440 R identified by match to protein family HMM PF01053; Cys/Met metabolism PLP-dependent enzyme family protein complement(424229..425440) Ruegeria pomeroyi DSS-3 3196400 YP_165677.1 CDS SPO0414 NC_003911.11 425562 427577 D identified by similarity to SP:P27236; match to protein family HMM PF01432; peptidyl-dipeptidase 425562..427577 Ruegeria pomeroyi DSS-3 3196255 YP_165678.1 CDS SPO0415 NC_003911.11 427642 428589 R identified by match to protein family HMM PF02826; D-isomer specific 2-hydroxyacid dehydrogenase complement(427642..428589) Ruegeria pomeroyi DSS-3 3196539 YP_165679.1 CDS mreD NC_003911.11 428594 429733 R identified by similarity to SP:P15035; match to protein family HMM PF01098; match to protein family HMM TIGR02210; rod shape-determining protein MreD complement(428594..429733) Ruegeria pomeroyi DSS-3 3195922 YP_165680.1 CDS pbpA NC_003911.11 429730 431676 R identified by similarity to SP:P08150; match to protein family HMM PF00905; match to protein family HMM PF03717; penicillin-binding protein 2 complement(429730..431676) Ruegeria pomeroyi DSS-3 3196071 YP_165681.1 CDS SPO0418 NC_003911.11 431678 432214 R identified by similarity to GB:CAE53834.1; hypothetical protein complement(431678..432214) Ruegeria pomeroyi DSS-3 3196538 YP_165682.1 CDS mreC NC_003911.11 432207 433142 R 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 complement(432207..433142) Ruegeria pomeroyi DSS-3 3194068 YP_165683.1 CDS mreB NC_003911.11 433204 434250 R functions in MreBCD complex in some organisms; rod shape-determining protein MreB complement(433204..434250) Ruegeria pomeroyi DSS-3 3194772 YP_165684.1 CDS SPO0421 NC_003911.11 434416 435201 D hypothetical protein 434416..435201 Ruegeria pomeroyi DSS-3 3192983 YP_165685.1 CDS leuA NC_003911.11 435291 436865 R catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase complement(435291..436865) Ruegeria pomeroyi DSS-3 3193656 YP_165686.1 CDS SPO0423 NC_003911.11 437092 437673 R identified by match to protein family HMM PF01381; DNA-binding protein complement(437092..437673) Ruegeria pomeroyi DSS-3 3192695 YP_165687.1 CDS SPO0424 NC_003911.11 437751 438938 D identified by match to protein family HMM PF07690; hypothetical protein 437751..438938 Ruegeria pomeroyi DSS-3 3192742 YP_165688.1 CDS SPO0425 NC_003911.11 438976 440388 R identified by match to protein family HMM PF02493; MORN repeat-containing protein complement(438976..440388) Ruegeria pomeroyi DSS-3 3192656 YP_165689.1 CDS nadE NC_003911.11 440542 442200 D 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 440542..442200 Ruegeria pomeroyi DSS-3 3192654 YP_165690.1 CDS SPO0427 NC_003911.11 442341 443000 D hypothetical protein 442341..443000 Ruegeria pomeroyi DSS-3 3193641 YP_165691.1 CDS SPO0428 NC_003911.11 443116 444447 D identified by similarity to GB:AAA86752.1; match to protein family HMM PF01266; amino acid deaminase 443116..444447 Ruegeria pomeroyi DSS-3 3192889 YP_165692.1 CDS SPO0429 NC_003911.11 444464 445396 R identified by match to protein family HMM PF00753; match to protein family HMM TIGR01409; metallo-beta-lactamase complement(444464..445396) Ruegeria pomeroyi DSS-3 3193104 YP_165693.1 CDS gltX NC_003911.11 445622 446953 D Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 445622..446953 Ruegeria pomeroyi DSS-3 3192955 YP_165694.1 CDS SPO0431 NC_003911.11 447047 447616 R identified by similarity to PIR:E82090; hypothetical protein complement(447047..447616) Ruegeria pomeroyi DSS-3 3193635 YP_165695.1 CDS SPO0432 NC_003911.11 447721 448167 D identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738; rrf2 family protein 447721..448167 Ruegeria pomeroyi DSS-3 3193691 YP_165696.1 CDS SPO0433 NC_003911.11 448191 450707 R identified by match to protein family HMM PF02687; ABC transporter permease complement(448191..450707) Ruegeria pomeroyi DSS-3 3195618 YP_165697.1 CDS SPO0434 NC_003911.11 450704 451399 R ABC transporter ATP-binding protein complement(450704..451399) Ruegeria pomeroyi DSS-3 3194411 YP_165698.1 CDS SPO0435 NC_003911.11 451448 452083 D identified by similarity to SP:P29679; acyl-CoA thioesterase 451448..452083 Ruegeria pomeroyi DSS-3 3194389 YP_165699.1 CDS SPO0436 NC_003911.11 452085 452702 D identified by similarity to PIR:AC2205; hypothetical protein 452085..452702 Ruegeria pomeroyi DSS-3 3192880 YP_165700.1 CDS SPO0437 NC_003911.11 452742 452948 R cold shock family protein complement(452742..452948) Ruegeria pomeroyi DSS-3 3192720 YP_165701.1 CDS SPO0438 NC_003911.11 453151 453708 R ErfK/YbiS/YcfS/YnhG family protein complement(453151..453708) Ruegeria pomeroyi DSS-3 3192946 YP_165702.1 CDS SPO0439 NC_003911.11 453771 454187 R hypothetical protein complement(453771..454187) Ruegeria pomeroyi DSS-3 3193493 YP_165703.1 CDS SPO0440 NC_003911.11 454260 454676 D thioesterase 454260..454676 Ruegeria pomeroyi DSS-3 3196114 YP_165704.1 CDS SPO0441 NC_003911.11 454811 455152 D hypothetical protein 454811..455152 Ruegeria pomeroyi DSS-3 3192927 YP_165705.1 CDS SPO0442 NC_003911.11 455224 455649 D thioredoxin 455224..455649 Ruegeria pomeroyi DSS-3 3193475 YP_165706.1 CDS SPO0443 NC_003911.11 455724 455942 D identified by similarity to GB:BAC62291.1; hypothetical protein 455724..455942 Ruegeria pomeroyi DSS-3 3193659 YP_165707.1 CDS SPO0444 NC_003911.11 455955 456170 R hypothetical protein complement(455955..456170) Ruegeria pomeroyi DSS-3 3194282 YP_165708.1 CDS SPO0445 NC_003911.11 456283 456858 D identified by similarity to GB:AAQ60337.1; hypothetical protein 456283..456858 Ruegeria pomeroyi DSS-3 3193470 YP_165709.1 CDS SPO0446 NC_003911.11 456890 458665 R ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence; ABC transporter ATP-binding protein complement(456890..458665) Ruegeria pomeroyi DSS-3 3193465 YP_165710.1 CDS SPO0447 NC_003911.11 458806 459792 D hypothetical protein 458806..459792 Ruegeria pomeroyi DSS-3 3193325 YP_165711.1 CDS SPO0448 NC_003911.11 459926 460420 D MOSC domain-containing protein 459926..460420 Ruegeria pomeroyi DSS-3 3192916 YP_165712.1 CDS nadD NC_003911.11 460454 461095 D 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 460454..461095 Ruegeria pomeroyi DSS-3 3193074 YP_165713.1 CDS SPO0450 NC_003911.11 461048 461875 R hypothetical protein complement(461048..461875) Ruegeria pomeroyi DSS-3 3193421 YP_165714.1 CDS dacB NC_003911.11 461960 463450 D identified by match to protein family HMM PF02113; match to protein family HMM TIGR00666; D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase 461960..463450 Ruegeria pomeroyi DSS-3 3193279 YP_165715.1 CDS SPO0452 NC_003911.11 463501 463923 R identified by similarity to PIR:AD3572; hypothetical protein complement(463501..463923) Ruegeria pomeroyi DSS-3 3193518 YP_165716.1 CDS SPO0453 NC_003911.11 464016 464474 R identified by similarity to GB:AAM06297.1; hypothetical protein complement(464016..464474) Ruegeria pomeroyi DSS-3 3192993 YP_165717.1 CDS SPO0454 NC_003911.11 464569 465450 D LysR family transcriptional regulator 464569..465450 Ruegeria pomeroyi DSS-3 3193773 YP_165718.1 CDS lysK NC_003911.11 465480 467126 D 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 465480..467126 Ruegeria pomeroyi DSS-3 3196262 YP_165719.1 CDS SPO0456 NC_003911.11 467225 467545 D hypothetical protein 467225..467545 Ruegeria pomeroyi DSS-3 3193501 YP_165720.1 CDS SPO0457 NC_003911.11 467598 467999 D identified by similarity to GB:BAC47480.1; hypothetical protein 467598..467999 Ruegeria pomeroyi DSS-3 3193703 YP_165721.1 CDS SPO0458 NC_003911.11 467966 470359 R hypothetical protein complement(467966..470359) Ruegeria pomeroyi DSS-3 3193456 YP_165722.1 CDS SPO0459 NC_003911.11 468056 470425 D hypothetical protein 468056..470425 Ruegeria pomeroyi DSS-3 3192963 YP_165723.1 CDS SPO0460 NC_003911.11 470475 471332 R hypothetical protein complement(470475..471332) Ruegeria pomeroyi DSS-3 3193316 YP_165724.1 CDS SPO0461 NC_003911.11 471280 471909 D ParA family protein 471280..471909 Ruegeria pomeroyi DSS-3 3193709 YP_165725.1 CDS SPO0462 NC_003911.11 471959 472285 D antibiotic biosynthesis monooxygenase domain-containing protein 471959..472285 Ruegeria pomeroyi DSS-3 3192854 YP_165726.1 CDS SPO0463 NC_003911.11 472365 472772 D universal stress family protein 472365..472772 Ruegeria pomeroyi DSS-3 3195754 YP_165727.1 CDS SPO0464 NC_003911.11 472839 473417 D hypothetical protein 472839..473417 Ruegeria pomeroyi DSS-3 3195342 YP_165728.1 CDS SPO0465 NC_003911.11 473414 473896 R identified by match to protein family HMM PF01243; pyridoxamine 5'-phosphate oxidase complement(473414..473896) Ruegeria pomeroyi DSS-3 3193344 YP_165729.1 CDS SPO0466 NC_003911.11 473906 474685 R identified by similarity to SP:P21501; formate/nitrate transporter complement(473906..474685) Ruegeria pomeroyi DSS-3 3193634 YP_165730.1 CDS SPO0467 NC_003911.11 474743 475453 R GntR family transcriptional regulator complement(474743..475453) Ruegeria pomeroyi DSS-3 3193960 YP_165731.1 CDS phnG NC_003911.11 475557 476012 D identified by similarity to SP:P16685; alkylphosphonate utilization protein PhnG 475557..476012 Ruegeria pomeroyi DSS-3 3195430 YP_165732.1 CDS phnH NC_003911.11 476009 476587 D identified by similarity to SP:P16686; carbon-phosphorus lyase complex subunit 476009..476587 Ruegeria pomeroyi DSS-3 3193639 YP_165733.1 CDS phnI NC_003911.11 476591 477682 D identified by similarity to SP:P16687; alkylphosphonate utilization protein PhnI 476591..477682 Ruegeria pomeroyi DSS-3 3192943 YP_165734.1 CDS phnJ NC_003911.11 477762 478598 D identified by similarity to SP:P16688; alkylphosphonate utilization protein PhnJ 477762..478598 Ruegeria pomeroyi DSS-3 3193860 YP_165735.1 CDS phnK NC_003911.11 478684 479454 D identified by similarity to SP:P16678; phosphonate C-P lyase system protein PhnK 478684..479454 Ruegeria pomeroyi DSS-3 3193357 YP_165736.1 CDS phnL NC_003911.11 479522 480205 D identified by similarity to SP:P16679; alkylphosphonate utilization protein PhnL 479522..480205 Ruegeria pomeroyi DSS-3 3195983 YP_165737.1 CDS phnN NC_003911.11 480202 480750 D identified by similarity to SP:P16690; alkylphosphonate utilization protein PhnN 480202..480750 Ruegeria pomeroyi DSS-3 3195461 YP_165738.1 CDS SPO0475 NC_003911.11 480732 481415 R identified by similarity to GB:AAN29788.1; hypothetical protein complement(480732..481415) Ruegeria pomeroyi DSS-3 3195260 YP_165739.1 CDS phnM NC_003911.11 481469 482611 D identified by similarity to SP:P16689; alkylphosphonate utilization protein PhnM 481469..482611 Ruegeria pomeroyi DSS-3 3195241 YP_165740.1 CDS SPO0477 NC_003911.11 482616 483182 R hypothetical protein complement(482616..483182) Ruegeria pomeroyi DSS-3 3195249 YP_165741.1 CDS SPO0478 NC_003911.11 483205 483456 D hypothetical protein 483205..483456 Ruegeria pomeroyi DSS-3 3195989 YP_165742.1 CDS SPO0479 NC_003911.11 483607 484674 D identified by similarity to GB:AAF61102.1; ISSpo8, transposase 483607..484674 Ruegeria pomeroyi DSS-3 3195622 YP_165743.1 CDS SPO0481 NC_003911.11 485499 485975 R acetyltransferase complement(485499..485975) Ruegeria pomeroyi DSS-3 3195280 YP_165744.1 CDS SPO0482 NC_003911.11 485983 486294 R NADH-ubiquinone oxidoreductase complement(485983..486294) Ruegeria pomeroyi DSS-3 3195294 YP_165745.1 CDS SPO0483 NC_003911.11 486480 487127 R microcystin dependent protein complement(486480..487127) Ruegeria pomeroyi DSS-3 3195475 YP_165746.1 CDS rplB NC_003911.11 487568 488410 D 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 487568..488410 Ruegeria pomeroyi DSS-3 3195307 YP_165747.1 CDS rpsS NC_003911.11 488414 488692 D protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 488414..488692 Ruegeria pomeroyi DSS-3 3195270 YP_165748.1 CDS rplV NC_003911.11 488696 489076 D 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 488696..489076 Ruegeria pomeroyi DSS-3 3195009 YP_165749.1 CDS rpsC NC_003911.11 489076 489783 D 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 489076..489783 Ruegeria pomeroyi DSS-3 3195573 YP_165750.1 CDS rplP NC_003911.11 489796 490209 D located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 489796..490209 Ruegeria pomeroyi DSS-3 3195318 YP_165751.1 CDS SPO0489 NC_003911.11 491490 492839 R ISSpo2, transposase complement(491490..492839) Ruegeria pomeroyi DSS-3 3193409 YP_165752.1 CDS SPO0490 NC_003911.11 493432 494433 D identified by similarity to GB:AAO08434.1; calcium-binding domain-containing protein 493432..494433 Ruegeria pomeroyi DSS-3 3195633 YP_165753.1 CDS SPO0491 NC_003911.11 494436 495119 D identified by similarity to GB:CAE79871.1; hypothetical protein 494436..495119 Ruegeria pomeroyi DSS-3 3195948 YP_165754.1 CDS SPO0492 NC_003911.11 495649 496491 D identified by similarity to GB:BAC74954.1; cyclic nucleotide-binding protein 495649..496491 Ruegeria pomeroyi DSS-3 3195349 YP_165755.1 CDS rpmC NC_003911.11 496675 496875 D one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 496675..496875 Ruegeria pomeroyi DSS-3 3195500 YP_165756.1 CDS rpsQ NC_003911.11 496888 497118 D primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17 496888..497118 Ruegeria pomeroyi DSS-3 3194784 YP_165757.1 CDS rplN NC_003911.11 497221 497589 D binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 497221..497589 Ruegeria pomeroyi DSS-3 3195401 YP_165758.1 CDS rplX NC_003911.11 497592 497903 D assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 497592..497903 Ruegeria pomeroyi DSS-3 3195436 YP_165759.1 CDS rplE NC_003911.11 497896 498456 D 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 497896..498456 Ruegeria pomeroyi DSS-3 3195440 YP_165760.1 CDS rpsN NC_003911.11 498474 498779 D 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 498474..498779 Ruegeria pomeroyi DSS-3 3196049 YP_165761.1 CDS rpsH NC_003911.11 498792 499184 D binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 498792..499184 Ruegeria pomeroyi DSS-3 3195046 YP_165762.1 CDS rplF NC_003911.11 499197 499730 D 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 499197..499730 Ruegeria pomeroyi DSS-3 3195456 YP_165763.1 CDS rplR NC_003911.11 499742 500101 D binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 499742..500101 Ruegeria pomeroyi DSS-3 3196026 YP_165764.1 CDS rpsE NC_003911.11 500214 500786 D 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 500214..500786 Ruegeria pomeroyi DSS-3 3195459 YP_165765.1 CDS rpmD NC_003911.11 500799 500987 D L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 500799..500987 Ruegeria pomeroyi DSS-3 3195239 YP_165766.1 CDS SPO0504 NC_003911.11 501390 501515 R hypothetical protein complement(501390..501515) Ruegeria pomeroyi DSS-3 3196030 YP_165767.1 CDS rplO NC_003911.11 502782 503432 D identified by similarity to SP:P19946; 50S ribosomal protein L15 502782..503432 Ruegeria pomeroyi DSS-3 3195630 YP_165768.1 CDS secY NC_003911.11 503545 504912 D 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 503545..504912 Ruegeria pomeroyi DSS-3 3194103 YP_165769.1 CDS adk NC_003911.11 504909 505550 D essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 504909..505550 Ruegeria pomeroyi DSS-3 3195636 YP_165770.1 CDS SPO0508 NC_003911.11 505599 506672 D identified by similarity to PIR:AB2876; hypothetical protein 505599..506672 Ruegeria pomeroyi DSS-3 3194553 YP_165771.1 CDS rpsM NC_003911.11 506867 507235 D 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 506867..507235 Ruegeria pomeroyi DSS-3 3195393 YP_165772.1 CDS rpsK NC_003911.11 507251 507643 D 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 507251..507643 Ruegeria pomeroyi DSS-3 3195723 YP_165773.1 CDS rpoA NC_003911.11 507760 508776 D 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 507760..508776 Ruegeria pomeroyi DSS-3 3193120 YP_165774.1 CDS rplQ NC_003911.11 508954 509376 D is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 508954..509376 Ruegeria pomeroyi DSS-3 3195334 YP_165775.1 CDS SPO0513 NC_003911.11 509484 509891 D identified by similarity to GB:BAC52410.1; hypothetical protein 509484..509891 Ruegeria pomeroyi DSS-3 3194712 YP_165776.1 CDS SPO0514 NC_003911.11 509955 511337 D serine protease 509955..511337 Ruegeria pomeroyi DSS-3 3196017 YP_165777.1 CDS SPO0515 NC_003911.11 511341 512657 D recombination factor protein RarA 511341..512657 Ruegeria pomeroyi DSS-3 3194720 YP_165778.1 CDS rluC NC_003911.11 512820 513863 D identified by similarity to SP:P23851; ribosomal large subunit pseudouridine synthase C 512820..513863 Ruegeria pomeroyi DSS-3 3196070 YP_165779.1 CDS SPO0517 NC_003911.11 513860 514531 D HAD family hydrolase 513860..514531 Ruegeria pomeroyi DSS-3 3195802 YP_165780.1 CDS SPO0518 NC_003911.11 514528 515244 D identified by similarity to GB:BAC50629.1; hypothetical protein 514528..515244 Ruegeria pomeroyi DSS-3 3192817 YP_165781.1 CDS SPO0519 NC_003911.11 515315 516457 D glutamate/glutamine/aspartate/asparagine ABC transporter substrate-binding protein 515315..516457 Ruegeria pomeroyi DSS-3 3195297 YP_165782.1 CDS SPO0520 NC_003911.11 516592 517860 D identified by similarity to SP:Q52664; glutamate/glutamine/aspartate/asparagine ABC transporter permease 516592..517860 Ruegeria pomeroyi DSS-3 3194763 YP_165783.1 CDS SPO0521 NC_003911.11 517862 519175 D identified by similarity to SP:Q52665; glutamate/glutamine/aspartate/asparagine ABC transporter permease 517862..519175 Ruegeria pomeroyi DSS-3 3194506 YP_165784.1 CDS SPO0522 NC_003911.11 519186 519977 D identified by similarity to SP:Q52666; glutamate/glutamine/aspartate/asparagine ABC transporter ATP-binding protein 519186..519977 Ruegeria pomeroyi DSS-3 3196183 YP_165785.1 CDS SPO0523 NC_003911.11 520026 520535 R phosphoglycerate mutase complement(520026..520535) Ruegeria pomeroyi DSS-3 3195243 YP_165786.1 CDS SPO0524 NC_003911.11 520532 521167 R identified by similarity to GB:BAB48651.1; hypothetical protein complement(520532..521167) Ruegeria pomeroyi DSS-3 3194837 YP_165787.1 CDS SPO0525 NC_003911.11 521164 521958 R sterol desaturase-like protein complement(521164..521958) Ruegeria pomeroyi DSS-3 3194956 YP_165788.1 CDS argB NC_003911.11 522016 522879 R catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase complement(522016..522879) Ruegeria pomeroyi DSS-3 3195896 YP_165789.1 CDS SPO0527 NC_003911.11 522955 523722 D short chain dehydrogenase/reductase oxidoreductase 522955..523722 Ruegeria pomeroyi DSS-3 3194658 YP_165790.1 CDS SPO0528 NC_003911.11 523761 525158 R hypothetical protein complement(523761..525158) Ruegeria pomeroyi DSS-3 3195914 YP_165791.1 CDS SPO0529 NC_003911.11 525224 525592 R hypothetical protein complement(525224..525592) Ruegeria pomeroyi DSS-3 3196479 YP_165792.1 CDS engB NC_003911.11 525589 526242 R 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 complement(525589..526242) Ruegeria pomeroyi DSS-3 3194815 YP_165793.1 CDS SPO0531 NC_003911.11 526239 526976 R MOSC domain-containing protein complement(526239..526976) Ruegeria pomeroyi DSS-3 3194917 YP_165794.1 CDS SPO0532 NC_003911.11 526973 528802 R 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 complement(526973..528802) Ruegeria pomeroyi DSS-3 3195935 YP_165795.1 CDS SPO0533 NC_003911.11 528927 530468 R diguanylate cyclase complement(528927..530468) Ruegeria pomeroyi DSS-3 3195906 YP_165796.1 CDS SPO0534 NC_003911.11 530541 531425 R TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs; C32 tRNA thiolase complement(530541..531425) Ruegeria pomeroyi DSS-3 3195432 YP_165797.1 CDS SPO0535 NC_003911.11 531470 532399 R K+-dependent Na+/Ca+ exchanger-like protein complement(531470..532399) Ruegeria pomeroyi DSS-3 3195517 YP_165798.1 CDS SPO0536 NC_003911.11 532528 532785 R identified by similarity to GB:CAE35356.1; hypothetical protein complement(532528..532785) Ruegeria pomeroyi DSS-3 3195209 YP_165799.1 CDS SPO0537 NC_003911.11 532846 533271 R ribonuclease P protein component complement(532846..533271) Ruegeria pomeroyi DSS-3 3195555 YP_165800.2 CDS rpmH NC_003911.11 533296 533430 R in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 complement(533296..533430) Ruegeria pomeroyi DSS-3 3195490 YP_165801.1 CDS SPO0539 NC_003911.11 533672 534469 D hypothetical protein 533672..534469 Ruegeria pomeroyi DSS-3 3194861 YP_165802.1 CDS SPO0540 NC_003911.11 534469 535887 D identified by similarity to SP:P17239; mercuric reductase 534469..535887 Ruegeria pomeroyi DSS-3 3195222 YP_165803.1 CDS SPO0541 NC_003911.11 535901 537286 D identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase 535901..537286 Ruegeria pomeroyi DSS-3 3195574 YP_165804.1 CDS SPO0543 NC_003911.11 537802 539055 R identified by similarity to GB:CAD14035.1; hypothetical protein complement(537802..539055) Ruegeria pomeroyi DSS-3 3194211 YP_165805.1 CDS SPO0544 NC_003911.11 539068 541503 R glycine cleavage system protein T complement(539068..541503) Ruegeria pomeroyi DSS-3 3195841 YP_165806.1 CDS uvrB NC_003911.11 541827 544025 D 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 541827..544025 Ruegeria pomeroyi DSS-3 3194622 YP_165807.1 CDS SPO0546 NC_003911.11 544149 544619 D hypothetical protein 544149..544619 Ruegeria pomeroyi DSS-3 3195284 YP_165808.1 CDS SPO0547 NC_003911.11 544720 545253 R identified by similarity to PIR:H83501; hypothetical protein complement(544720..545253) Ruegeria pomeroyi DSS-3 3194705 YP_165809.1 CDS SPO0548 NC_003911.11 545461 545724 D hypothetical protein 545461..545724 Ruegeria pomeroyi DSS-3 3193736 YP_165810.1 CDS SPO0549 NC_003911.11 545732 546238 R identified by similarity to PIR:G97668; hypothetical protein complement(545732..546238) Ruegeria pomeroyi DSS-3 3195285 YP_165811.1 CDS SPO0550 NC_003911.11 546205 546969 R identified by similarity to PIR:E95936; hypothetical protein complement(546205..546969) Ruegeria pomeroyi DSS-3 3195961 YP_165812.1 CDS SPO0551 NC_003911.11 546966 548105 R identified by similarity to PIR:B97670; hypothetical protein complement(546966..548105) Ruegeria pomeroyi DSS-3 3195452 YP_165813.1 CDS SPO0552 NC_003911.11 548102 548686 R phosphoglycerate mutase complement(548102..548686) Ruegeria pomeroyi DSS-3 3193954 YP_165814.1 CDS SPO0553 NC_003911.11 548683 549762 R group 1 family glycosyltransferase complement(548683..549762) Ruegeria pomeroyi DSS-3 3195963 YP_165815.1 CDS SPO0554 NC_003911.11 549765 551009 R glycoside hydrolase complement(549765..551009) Ruegeria pomeroyi DSS-3 3195640 YP_165816.1 CDS SPO0555 NC_003911.11 551006 552220 R identified by similarity to GB:BAB50184.1; hypothetical protein complement(551006..552220) Ruegeria pomeroyi DSS-3 3193898 YP_165817.1 CDS SPO0556 NC_003911.11 552230 553540 R UDP-glucose/GDP-mannose dehydrogenase complement(552230..553540) Ruegeria pomeroyi DSS-3 3195062 YP_165818.1 CDS SPO0557 NC_003911.11 553643 556090 D mechanosensitive ion channel MscS 553643..556090 Ruegeria pomeroyi DSS-3 3193953 YP_165819.1 CDS SPO0558 NC_003911.11 556181 557332 R identified by similarity to SP:P42063; oligopeptide ABC transporter permease complement(556181..557332) Ruegeria pomeroyi DSS-3 3193760 YP_165820.1 CDS SPO0559 NC_003911.11 557329 558357 R identified by similarity to SP:P42062; oligopeptide ABC transporter permease complement(557329..558357) Ruegeria pomeroyi DSS-3 3193982 YP_165821.1 CDS SPO0560 NC_003911.11 558370 560286 R identified by similarity to GB:BAB50197.1; oligopeptide ABC transporter periplasmic oligopeptide-binding protein complement(558370..560286) Ruegeria pomeroyi DSS-3 3193966 YP_165822.1 CDS SPO0562 NC_003911.11 562276 562797 D identified by similarity to GB:BAB50200.1; hypothetical protein 562276..562797 Ruegeria pomeroyi DSS-3 3193858 YP_165823.1 CDS SPO0563 NC_003911.11 562898 563527 D identified by similarity to SP:Q12390; glutathione S-transferase 562898..563527 Ruegeria pomeroyi DSS-3 3193873 YP_165824.1 CDS SPO0564 NC_003911.11 563719 566127 D glycine cleavage system protein T 563719..566127 Ruegeria pomeroyi DSS-3 3193816 YP_165825.1 CDS SPO0565 NC_003911.11 566124 567647 D trimethylamine methyltransferase 566124..567647 Ruegeria pomeroyi DSS-3 3193832 YP_165826.1 CDS SPO0566 NC_003911.11 567710 568333 D TetR family transcriptional regulator 567710..568333 Ruegeria pomeroyi DSS-3 3193829 YP_165827.1 CDS SPO0567 NC_003911.11 568330 569634 D oxidoreductase, FAD-binding 568330..569634 Ruegeria pomeroyi DSS-3 3194259 YP_165828.1 CDS SPO0568 NC_003911.11 569856 573269 R catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; 2-oxoacid ferredoxin oxidoreductase complement(569856..573269) Ruegeria pomeroyi DSS-3 3194242 YP_165829.1 CDS SPO0569 NC_003911.11 573420 573878 D AsnC family transcriptional regulator 573420..573878 Ruegeria pomeroyi DSS-3 3193796 YP_165830.1 CDS SPO0570 NC_003911.11 574060 576396 D identified by similarity to GB:CAD14776.1; hypothetical protein 574060..576396 Ruegeria pomeroyi DSS-3 3193963 YP_165831.1 CDS SPO0571 NC_003911.11 576430 581301 D PKD domain-containing protein 576430..581301 Ruegeria pomeroyi DSS-3 3194013 YP_165832.1 CDS SPO0572 NC_003911.11 581384 583099 D guanylate cyclase 581384..583099 Ruegeria pomeroyi DSS-3 3194243 YP_165833.1 CDS SPO0573 NC_003911.11 583202 583597 R identified by similarity to GB:AAQ87470.1; hypothetical protein complement(583202..583597) Ruegeria pomeroyi DSS-3 3193880 YP_165834.1 CDS SPO0574 NC_003911.11 583707 586805 D ABC transporter transmembrane ATP-binding protein 583707..586805 Ruegeria pomeroyi DSS-3 3193862 YP_165835.1 CDS acdA-1 NC_003911.11 586901 588058 R acyl-CoA dehydrogenase complement(586901..588058) Ruegeria pomeroyi DSS-3 3194165 YP_165836.1 CDS SPO0576 NC_003911.11 588055 588684 R identified by similarity to GB:AAS05297.1; TetR family transcriptional regulator complement(588055..588684) Ruegeria pomeroyi DSS-3 3193916 YP_165837.1 CDS SPO0577 NC_003911.11 588798 590561 D identified by similarity to PIR:D83286; hypothetical protein 588798..590561 Ruegeria pomeroyi DSS-3 3194204 YP_165838.1 CDS SPO0578 NC_003911.11 590574 592193 D identified by similarity to GB:BAB16296.1; acetyl-CoA carboxylase carboxyltransferase 590574..592193 Ruegeria pomeroyi DSS-3 3194171 YP_165839.1 CDS SPO0579 NC_003911.11 592193 594175 D identified by similarity to GB:BAB16297.1; acetyl-CoA carboxylase, biotin carboxylase 592193..594175 Ruegeria pomeroyi DSS-3 3193852 YP_165840.1 CDS SPO0580 NC_003911.11 594172 595302 D 2-nitropropane dioxygenase 594172..595302 Ruegeria pomeroyi DSS-3 3193969 YP_165841.1 CDS SPO0581 NC_003911.11 595305 596096 D identified by similarity to GB:CAB95889.1; hypothetical protein 595305..596096 Ruegeria pomeroyi DSS-3 3192697 YP_165842.1 CDS acdA-2 NC_003911.11 596201 597358 D acyl-CoA dehydrogenase 596201..597358 Ruegeria pomeroyi DSS-3 3194156 YP_165843.1 CDS SPO0583 NC_003911.11 597541 598422 R LysR family transcriptional regulator complement(597541..598422) Ruegeria pomeroyi DSS-3 3194065 YP_165844.1 CDS aspC-1 NC_003911.11 598520 599683 D identified by similarity to SP:Q06191; aspartate aminotransferase 598520..599683 Ruegeria pomeroyi DSS-3 3193806 YP_165845.1 CDS SPO0585 NC_003911.11 599693 601915 D dehydrogenase/transketolase 599693..601915 Ruegeria pomeroyi DSS-3 3194057 YP_165846.1 CDS SPO0586 NC_003911.11 601912 602949 D identified by similarity to PIR:T00580; acyl carrier protein 601912..602949 Ruegeria pomeroyi DSS-3 3193757 YP_165847.1 CDS SPO0587 NC_003911.11 602993 604270 D identified by similarity to GB:CAC46788.1; hypothetical protein 602993..604270 Ruegeria pomeroyi DSS-3 3193649 YP_165848.1 CDS SPO0588 NC_003911.11 604264 605175 R LysR family transcriptional regulator complement(604264..605175) Ruegeria pomeroyi DSS-3 3193919 YP_165849.1 CDS SPO0589 NC_003911.11 605197 608469 D oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein 605197..608469 Ruegeria pomeroyi DSS-3 3192824 YP_165850.1 CDS hpsR NC_003911.11 608479 609507 R LacI family transcriptional regulator complement(608479..609507) Ruegeria pomeroyi DSS-3 3193422 YP_165851.1 CDS hpsK NC_003911.11 609873 611018 D identified by similarity to SP:P37735; dihydroxypropanesulfonateTRAP transporter 609873..611018 Ruegeria pomeroyi DSS-3 3193906 YP_165852.1 CDS hpsL NC_003911.11 611098 611640 D dihydroxypropanesulfonateTRAP transporter 611098..611640 Ruegeria pomeroyi DSS-3 3193787 YP_165853.1 CDS hpsM NC_003911.11 611651 612979 D dihydroxypropanesulfonateTRAP transporter 611651..612979 Ruegeria pomeroyi DSS-3 3195982 YP_165854.1 CDS hpsN NC_003911.11 612992 614299 D catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; dihydroxypropanesulfonate-3-dehydrogenase 612992..614299 Ruegeria pomeroyi DSS-3 3193878 YP_165855.1 CDS hpsO NC_003911.11 614292 615053 D identified by similarity to SP:P50199; R or S-dihydroxypropanesulfonate-2-dehydrogenase 614292..615053 Ruegeria pomeroyi DSS-3 3193226 YP_165856.1 CDS hpsP NC_003911.11 615050 616048 D S or R-dihydroxypropanesulfonate-2-dehydrogenase 615050..616048 Ruegeria pomeroyi DSS-3 3193939 YP_165857.1 CDS hpsQ NC_003911.11 616052 616456 D UspA family stress protein 616052..616456 Ruegeria pomeroyi DSS-3 3193130 YP_165858.1 CDS slcD NC_003911.11 616497 617612 D membrane-bound sulfolactate dehydrogenase 616497..617612 Ruegeria pomeroyi DSS-3 3196027 YP_165859.1 CDS speB-1 NC_003911.11 617619 618467 R agmatinase complement(617619..618467) Ruegeria pomeroyi DSS-3 3192836 YP_165860.1 CDS nspC NC_003911.11 618464 619642 R carboxynorspermidine decarboxylase complement(618464..619642) Ruegeria pomeroyi DSS-3 3193162 YP_165861.1 CDS SPO0601 NC_003911.11 619738 620949 R saccharopine dehydrogenase complement(619738..620949) Ruegeria pomeroyi DSS-3 3193831 YP_165862.1 CDS speA NC_003911.11 620975 622960 R catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis; arginine decarboxylase complement(620975..622960) Ruegeria pomeroyi DSS-3 3193886 YP_165863.1 CDS SPO0603 NC_003911.11 623033 623347 R identified by similarity to PIR:AH0077; hypothetical protein complement(623033..623347) Ruegeria pomeroyi DSS-3 3192733 YP_165864.1 CDS SPO0604 NC_003911.11 623376 623753 R identified by similarity to GB:BAC62948.1; hypothetical protein complement(623376..623753) Ruegeria pomeroyi DSS-3 3192988 YP_165865.1 CDS SPO0605 NC_003911.11 623756 624208 R MarR family transcriptional regulator complement(623756..624208) Ruegeria pomeroyi DSS-3 3193745 YP_165866.1 CDS SPO0606 NC_003911.11 624481 626169 D identified by similarity to PIR:C95874; hypothetical protein 624481..626169 Ruegeria pomeroyi DSS-3 3195886 YP_165867.1 CDS SPO0607 NC_003911.11 626169 627194 D identified by similarity to GB:CAB71312.1; proline racemase 626169..627194 Ruegeria pomeroyi DSS-3 3195347 YP_165868.1 CDS SPO0608 NC_003911.11 627308 629086 D Assignment partly based on location in sugar transporter operon.; sugar ABC transporter periplasmic sugar-binding protein 627308..629086 Ruegeria pomeroyi DSS-3 3195271 YP_165869.1 CDS SPO0609 NC_003911.11 629201 630265 D Assignment partly based on location in sugar transport operon.; sugar ABC transporter ATP-binding protein 629201..630265 Ruegeria pomeroyi DSS-3 3195033 YP_165870.1 CDS SPO0610 NC_003911.11 630273 631358 D Assignment partly based on location in sugar transport operon.; sugar ABC transporter ATP-binding protein 630273..631358 Ruegeria pomeroyi DSS-3 3194437 YP_165871.1 CDS SPO0611 NC_003911.11 631355 632218 D Assignment partly based on location in sugar transport operon.; identified by similarity to PIR:T46751; sugar ABC transporter permease 631355..632218 Ruegeria pomeroyi DSS-3 3195016 YP_165872.1 CDS SPO0612 NC_003911.11 632230 633027 D Assignment partly based on location in sugar transport operon.; sugar ABC transporter permease 632230..633027 Ruegeria pomeroyi DSS-3 3193837 YP_165873.1 CDS SPO0613 NC_003911.11 633027 633305 D identified by similarity to GB:BAB48242.1; hypothetical protein 633027..633305 Ruegeria pomeroyi DSS-3 3195703 YP_165874.1 CDS SPO0614 NC_003911.11 633393 633788 D identified by similarity to SP:P06555; transcriptional regulator 633393..633788 Ruegeria pomeroyi DSS-3 3195955 YP_165875.1 CDS SPO0615 NC_003911.11 633778 634911 D identified by similarity to GB:CAD73596.1; hypothetical protein 633778..634911 Ruegeria pomeroyi DSS-3 3196484 YP_165876.1 CDS SPO0616 NC_003911.11 634997 635989 D zinc-binding dehydrogenase oxidoreductase 634997..635989 Ruegeria pomeroyi DSS-3 3195107 YP_165877.1 CDS SPO0618 NC_003911.11 636308 637354 R AraC family transcriptional regulator complement(636308..637354) Ruegeria pomeroyi DSS-3 3195131 YP_165878.1 CDS SPO0619 NC_003911.11 637522 638718 D sterol desaturase 637522..638718 Ruegeria pomeroyi DSS-3 3194955 YP_165879.1 CDS SPO0620 NC_003911.11 638752 639378 D identified by similarity to GB:BAC91031.1; hypothetical protein 638752..639378 Ruegeria pomeroyi DSS-3 3195691 YP_165880.1 CDS SPO0621 NC_003911.11 639827 641368 D ankyrin repeat-containing protein 639827..641368 Ruegeria pomeroyi DSS-3 3195217 YP_165881.1 CDS SPO0622 NC_003911.11 641833 642891 R ISSpo1, transposase complement(641833..642891) Ruegeria pomeroyi DSS-3 3194020 YP_165882.1 CDS SPO0623 NC_003911.11 642986 643534 R cytochrome c oxidase domain-containing protein complement(642986..643534) Ruegeria pomeroyi DSS-3 3196274 YP_165883.1 CDS SPO0624 NC_003911.11 643541 644167 R identified by similarity to PIR:B75629; hypothetical protein complement(643541..644167) Ruegeria pomeroyi DSS-3 3195267 YP_165884.1 CDS SPO0628 NC_003911.11 648529 649044 R transposase, degenerate complement(648529..649044) Ruegeria pomeroyi DSS-3 3195188 YP_165885.1 CDS SPO0629 NC_003911.11 650052 650945 R identified by similarity to GB:AAN56319.1; ISSpo3, transposase complement(650052..650945) Ruegeria pomeroyi DSS-3 3194515 YP_165886.1 CDS SPO0631 NC_003911.11 652365 652889 R hypothetical protein complement(652365..652889) Ruegeria pomeroyi DSS-3 3194691 YP_165887.1 CDS SPO0632 NC_003911.11 653027 654013 D Involved in the metabolism of aromatic amino acids; 2-hydroxyacid dehydrogenase 653027..654013 Ruegeria pomeroyi DSS-3 3194128 YP_165888.1 CDS ggt NC_003911.11 654249 656042 D identified by similarity to SP:P54422; gamma-glutamyltranspeptidase 654249..656042 Ruegeria pomeroyi DSS-3 3194587 YP_165889.1 CDS SPO0634 NC_003911.11 656146 657543 D oxidoreductase, FAD-binding 656146..657543 Ruegeria pomeroyi DSS-3 3195266 YP_165890.1 CDS SPO0635 NC_003911.11 657754 660261 D glycine cleavage system protein T 657754..660261 Ruegeria pomeroyi DSS-3 3195325 YP_165891.1 CDS SPO0636 NC_003911.11 660314 660850 R EF hand domain-containing protein complement(660314..660850) Ruegeria pomeroyi DSS-3 3195627 YP_165892.1 CDS SPO0637 NC_003911.11 660904 661020 R hypothetical protein complement(660904..661020) Ruegeria pomeroyi DSS-3 3194193 YP_165893.1 CDS SPO0638 NC_003911.11 661053 661670 R identified by similarity to GB:AAO90814.1; hypothetical protein complement(661053..661670) Ruegeria pomeroyi DSS-3 3195719 YP_165894.1 CDS SPO0639 NC_003911.11 661739 662596 D LysR family transcriptional regulator 661739..662596 Ruegeria pomeroyi DSS-3 3194616 YP_165895.1 CDS SPO0640 NC_003911.11 662593 662928 R alkylhydroperoxidase complement(662593..662928) Ruegeria pomeroyi DSS-3 3195051 YP_165896.1 CDS SPO0641 NC_003911.11 662997 663647 R identified by similarity to GB:AAP57703.1; hypothetical protein complement(662997..663647) Ruegeria pomeroyi DSS-3 3195244 YP_165897.1 CDS SPO0642 NC_003911.11 663644 664714 R oxidoreductase, FAD-binding complement(663644..664714) Ruegeria pomeroyi DSS-3 3195488 YP_165898.1 CDS SPO0643 NC_003911.11 664711 665649 R aldo/keto reductase complement(664711..665649) Ruegeria pomeroyi DSS-3 3195705 YP_165899.1 CDS SPO0644 NC_003911.11 665747 666202 D identified by similarity to GB:BAC48747.1; hypothetical protein 665747..666202 Ruegeria pomeroyi DSS-3 3195619 YP_165900.1 CDS SPO0645 NC_003911.11 666206 667444 D identified by similarity to GB:BAC48748.1; multidrug resistance efflux pump 666206..667444 Ruegeria pomeroyi DSS-3 3194633 YP_165901.1 CDS SPO0646 NC_003911.11 667490 667897 R identified by similarity to GB:AAQ61228.1; hypothetical protein complement(667490..667897) Ruegeria pomeroyi DSS-3 3195864 YP_165902.1 CDS SPO0647 NC_003911.11 667894 668199 R hypothetical protein complement(667894..668199) Ruegeria pomeroyi DSS-3 3192754 YP_165903.1 CDS SPO0648 NC_003911.11 668375 669448 R bmp family protein complement(668375..669448) Ruegeria pomeroyi DSS-3 3195807 YP_165904.1 CDS SPO0649 NC_003911.11 669502 670422 R Assignment based partly on membership in sugar ABC transporter operon; sugar ABC transporter permease complement(669502..670422) Ruegeria pomeroyi DSS-3 3195273 YP_165905.1 CDS SPO0650 NC_003911.11 670426 671508 R Assignment based partly on membership in sugar ABC transporter operon; sugar ABC transporter permease complement(670426..671508) Ruegeria pomeroyi DSS-3 3194022 YP_165906.1 CDS SPO0651 NC_003911.11 671563 673080 R sugar ABC transporter ATP-binding protein complement(671563..673080) Ruegeria pomeroyi DSS-3 3195876 YP_165907.1 CDS xdhC NC_003911.11 673077 674045 R identified by similarity to GB:CAB41849.1; xanthine dehydrogenase accessory factor complement(673077..674045) Ruegeria pomeroyi DSS-3 3194591 YP_165908.1 CDS xdhB NC_003911.11 674035 676365 R identified by similarity to GB:CAA04470.2; xanthine dehydrogenase subunit B complement(674035..676365) Ruegeria pomeroyi DSS-3 3194183 YP_165909.1 CDS xdhA NC_003911.11 676362 677747 R identified by similarity to GB:CAA04469.1; xanthine dehydrogenase, A subunit complement(676362..677747) Ruegeria pomeroyi DSS-3 3195620 YP_165910.1 CDS SPO0655 NC_003911.11 678063 678827 R identified by similarity to PIR:D95421; hypothetical protein complement(678063..678827) Ruegeria pomeroyi DSS-3 3195387 YP_165911.1 CDS dnaE NC_003911.11 678963 682526 D 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 678963..682526 Ruegeria pomeroyi DSS-3 3194643 YP_165912.1 CDS naaT NC_003911.11 682533 683429 R metallochaperone complement(682533..683429) Ruegeria pomeroyi DSS-3 3193738 YP_165913.1 CDS naaS NC_003911.11 683429 685072 R N-acetyltaurine amidohydrolas complement(683429..685072) Ruegeria pomeroyi DSS-3 3195737 YP_165914.1 CDS naaR NC_003911.11 685171 686103 D LysR family transcriptional regulator 685171..686103 Ruegeria pomeroyi DSS-3 3193567 YP_165915.1 CDS naaA NC_003911.11 686223 687797 D N-acetyltaurine ABC transporter substrate-binding protein 686223..687797 Ruegeria pomeroyi DSS-3 3194493 YP_165916.1 CDS naaB NC_003911.11 687865 688842 D identified by similarity to SP:P42062; N-acetyltaurine 687865..688842 Ruegeria pomeroyi DSS-3 3195988 YP_165917.1 CDS naaB' NC_003911.11 688839 689726 D identified by similarity to SP:P42063; N-acetyltaurine ABC transporter permease 688839..689726 Ruegeria pomeroyi DSS-3 3194688 YP_165918.1 CDS naaC NC_003911.11 689663 690715 D identified by similarity to SP:P26905; N-acetyltaurine ABC transporter ATP-binding protein 689663..690715 Ruegeria pomeroyi DSS-3 3195712 YP_165919.1 CDS naaC' NC_003911.11 690716 691714 D identified by similarity to SP:P42065; N-acetyltaurine ABC transporter ATP-binding protein 690716..691714 Ruegeria pomeroyi DSS-3 3194255 YP_165920.1 CDS SPO0665 NC_003911.11 691743 691937 R identified by similarity to SP:Q89SJ8; SlyX protein complement(691743..691937) Ruegeria pomeroyi DSS-3 3195981 YP_165921.1 CDS SPO0666 NC_003911.11 692042 692845 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 692042..692845 Ruegeria pomeroyi DSS-3 3195344 YP_165922.1 CDS hisS NC_003911.11 692935 694422 D 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 692935..694422 Ruegeria pomeroyi DSS-3 3192980 YP_165923.1 CDS hisZ NC_003911.11 694419 695507 D May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine; ATP phosphoribosyltransferase 694419..695507 Ruegeria pomeroyi DSS-3 3193863 YP_165924.1 CDS hisG NC_003911.11 695504 696196 D 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 695504..696196 Ruegeria pomeroyi DSS-3 3195758 YP_165925.1 CDS SPO0670 NC_003911.11 696285 699590 R DNA polymerase III subunit alpha complement(696285..699590) Ruegeria pomeroyi DSS-3 3195523 YP_165926.1 CDS SPO0671 NC_003911.11 699587 700960 R identified by similarity to GB:BAB51085.1; hypothetical protein complement(699587..700960) Ruegeria pomeroyi DSS-3 3195816 YP_165927.1 CDS SPO0672 NC_003911.11 700980 701555 R identified by similarity to PIR:AH2953; hypothetical protein complement(700980..701555) Ruegeria pomeroyi DSS-3 3195663 YP_165928.1 CDS tpa NC_003911.11 701701 703098 R identified by similarity to SP:Q9APM5; taurine--pyruvate aminotransferase complement(701701..703098) Ruegeria pomeroyi DSS-3 3195442 YP_165929.1 CDS tauA NC_003911.11 703493 704503 D Assignment partly based on membership in taurine ABC transporter gene cluster.; identified by similarity to SP:Q47537; taurine ABC transporter periplasmic taurine-binding protein 703493..704503 Ruegeria pomeroyi DSS-3 3195870 YP_165930.1 CDS tauB NC_003911.11 704612 705418 D identified by similarity to SP:Q47538; taurine ABC transporter ATP-binding protein 704612..705418 Ruegeria pomeroyi DSS-3 3194041 YP_165931.1 CDS tauC NC_003911.11 705817 706689 D identified by similarity to SP:Q47539; taurine ABC transporter permease 705817..706689 Ruegeria pomeroyi DSS-3 3195375 YP_165932.1 CDS SPO0677 NC_003911.11 706831 708459 D activates fatty acids by binding to coenzyme A; acyl-CoA synthetase 706831..708459 Ruegeria pomeroyi DSS-3 3195740 YP_165933.1 CDS SPO0678 NC_003911.11 708546 709505 R identified by similarity to SP:Q9BSE5; agmatinase complement(708546..709505) Ruegeria pomeroyi DSS-3 3195947 YP_165934.1 CDS hmgC NC_003911.11 709636 710277 R identified by similarity to SP:O43708; maleylacetoacetate isomerase complement(709636..710277) Ruegeria pomeroyi DSS-3 3196015 YP_165935.1 CDS SPO0680 NC_003911.11 710424 710969 R glyoxalase complement(710424..710969) Ruegeria pomeroyi DSS-3 3195869 YP_165936.1 CDS SPO0681 NC_003911.11 710975 711169 R identified by similarity to GB:CAE31393.1; hypothetical protein complement(710975..711169) Ruegeria pomeroyi DSS-3 3195879 YP_165937.1 CDS SPO0682 NC_003911.11 711175 712836 R FAD-dependent oxidoreductase complement(711175..712836) Ruegeria pomeroyi DSS-3 3195775 YP_165938.1 CDS SPO0683 NC_003911.11 713009 713959 R metallo-beta-lactamase complement(713009..713959) Ruegeria pomeroyi DSS-3 3196052 YP_165939.1 CDS SPO0684 NC_003911.11 713963 714322 R glyoxalase complement(713963..714322) Ruegeria pomeroyi DSS-3 3195669 YP_165940.1 CDS hmgB NC_003911.11 714330 715583 R fumarylacetoacetase complement(714330..715583) Ruegeria pomeroyi DSS-3 3194878 YP_165941.1 CDS hmgA NC_003911.11 715657 717012 R 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 complement(715657..717012) Ruegeria pomeroyi DSS-3 3194373 YP_165942.1 CDS SPO0687 NC_003911.11 717071 717523 D MarR family transcriptional regulator 717071..717523 Ruegeria pomeroyi DSS-3 3195872 YP_165943.1 CDS SPO0688 NC_003911.11 717598 718845 D guanylate cyclase 717598..718845 Ruegeria pomeroyi DSS-3 3195979 YP_165944.1 CDS SPO0689 NC_003911.11 718846 719655 R identified by similarity to GB:AAK24136.1; hypothetical protein complement(718846..719655) Ruegeria pomeroyi DSS-3 3194579 YP_165945.1 CDS SPO0690 NC_003911.11 720123 720452 R identified by similarity to GB:BAC48339.1; hypothetical protein complement(720123..720452) Ruegeria pomeroyi DSS-3 3196285 YP_165946.1 CDS era NC_003911.11 720511 721416 R 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 complement(720511..721416) Ruegeria pomeroyi DSS-3 3195765 YP_165947.1 CDS SPO0692 NC_003911.11 721599 722984 D identified by similarity to GB:AAD24211.1; multicopper oxidase 721599..722984 Ruegeria pomeroyi DSS-3 3193482 YP_165948.1 CDS SPO0693 NC_003911.11 723039 724733 R identified by similarity to GB:AAL17673.1; isobutyryl-CoA dehydrogenase complement(723039..724733) Ruegeria pomeroyi DSS-3 3194836 YP_165949.1 CDS SPO0694 NC_003911.11 724858 725421 R hypothetical protein complement(724858..725421) Ruegeria pomeroyi DSS-3 3194169 YP_165950.1 CDS SPO0695 NC_003911.11 725430 725723 R hypothetical protein complement(725430..725723) Ruegeria pomeroyi DSS-3 3194399 YP_165951.1 CDS modC NC_003911.11 726145 727224 R identified by similarity to SP:P09833; molybdate ABC transporter ATP-binding protein complement(726145..727224) Ruegeria pomeroyi DSS-3 3194867 YP_165952.1 CDS modB NC_003911.11 727221 727913 R part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE; molybdate ABC transporter permease complement(727221..727913) Ruegeria pomeroyi DSS-3 3194843 YP_165953.1 CDS modA NC_003911.11 727917 728681 R identified by similarity to SP:P37329; molybdate ABC transporter periplasmic molybdate-binding protein complement(727917..728681) Ruegeria pomeroyi DSS-3 3193763 YP_165954.1 CDS SPO0700 NC_003911.11 728732 729154 R identified by similarity to SP:P46930; molybdenum-binding transcriptional regulator complement(728732..729154) Ruegeria pomeroyi DSS-3 3193318 YP_165955.1 CDS gap-1 NC_003911.11 729188 730213 R glyceraldehyde-3-phosphate dehydrogenase, type I complement(729188..730213) Ruegeria pomeroyi DSS-3 3195539 YP_165956.1 CDS SPO0702 NC_003911.11 730361 731347 R oligopeptide ABC transporter ATP-binding protein complement(730361..731347) Ruegeria pomeroyi DSS-3 3195845 YP_165957.1 CDS SPO0703 NC_003911.11 731344 732339 R oligopeptide ABC transporter ATP-binding protein complement(731344..732339) Ruegeria pomeroyi DSS-3 3195190 YP_165958.1 CDS SPO0704 NC_003911.11 732336 733460 R identified by similarity to SP:P42063; oligopeptide ABC transporter permease complement(732336..733460) Ruegeria pomeroyi DSS-3 3194918 YP_165959.1 CDS SPO0705 NC_003911.11 733465 734469 R Assignment partly based on location in oligopeptide ABC transport gene cluster; oligopeptide ABC transporter permease complement(733465..734469) Ruegeria pomeroyi DSS-3 3195945 YP_165960.1 CDS SPO0706 NC_003911.11 734530 736569 R Assignment partly based on location in oligopeptide ABC transporter gene cluster.; identified by similarity to SP:Q9X4Y1; oligopeptide ABC transporter periplasmic oligopeptide-binding protein complement(734530..736569) Ruegeria pomeroyi DSS-3 3195934 YP_165961.1 CDS SPO0707 NC_003911.11 736566 737441 R DeoR family transcriptional regulator complement(736566..737441) Ruegeria pomeroyi DSS-3 3193428 YP_165962.1 CDS SPO0708 NC_003911.11 737679 739049 D identified by similarity to GB:AAF98391.2; invasion protein IbeA 737679..739049 Ruegeria pomeroyi DSS-3 3195213 YP_165963.1 CDS pckA NC_003911.11 739100 740698 R PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase complement(739100..740698) Ruegeria pomeroyi DSS-3 3195361 YP_165964.1 CDS chvI NC_003911.11 741039 741743 D identified by similarity to SP:P50350; DNA-binding response regulator ChvI 741039..741743 Ruegeria pomeroyi DSS-3 3195446 YP_165965.1 CDS chvG NC_003911.11 741777 743486 D sensor histidine kinase ChvG 741777..743486 Ruegeria pomeroyi DSS-3 3195818 YP_165966.1 CDS SPO0712 NC_003911.11 743434 743952 D identified by similarity to SP:O34483; Hpr serine kinase/phosphatase domain-containing protein 743434..743952 Ruegeria pomeroyi DSS-3 3192731 YP_165967.2 CDS SPO0713 NC_003911.11 743957 744838 D hypothetical protein 743957..744838 Ruegeria pomeroyi DSS-3 3194619 YP_165968.1 CDS SPO0714 NC_003911.11 744835 745227 D PTS system mannose subfamily IIA subunit 744835..745227 Ruegeria pomeroyi DSS-3 3195950 YP_165969.1 CDS SPO0715 NC_003911.11 745244 745513 D phosphocarrier protein HPr 745244..745513 Ruegeria pomeroyi DSS-3 3195949 YP_165970.1 CDS SPO0716 NC_003911.11 745552 746439 D identified by similarity to PIR:D82434; hypothetical protein 745552..746439 Ruegeria pomeroyi DSS-3 3195913 YP_165971.1 CDS bhbD NC_003911.11 746531 747406 R converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase complement(746531..747406) Ruegeria pomeroyi DSS-3 3195358 YP_165972.1 CDS SPO0718 NC_003911.11 747563 748405 D identified by similarity to GB:AAK08138.1; hypothetical protein 747563..748405 Ruegeria pomeroyi DSS-3 3195680 YP_165973.1 CDS etfA NC_003911.11 748465 749394 R identified by similarity to SP:P38974; electron transfer flavoprotein subunit alpha complement(748465..749394) Ruegeria pomeroyi DSS-3 3194972 YP_165974.1 CDS etfB NC_003911.11 749394 750152 R identified by similarity to SP:P38975; electron transfer flavoprotein subunit beta complement(749394..750152) Ruegeria pomeroyi DSS-3 3195524 YP_165975.1 CDS SPO0721 NC_003911.11 750351 750716 D glyoxalase 750351..750716 Ruegeria pomeroyi DSS-3 3195237 YP_165976.1 CDS SPO0722 NC_003911.11 750883 751455 R ATP:cob(I)alamin adenosyltransferase complement(750883..751455) Ruegeria pomeroyi DSS-3 3195264 YP_165977.1 CDS SPO0723 NC_003911.11 751459 751659 R identified by similarity to PIR:C98285; hypothetical protein complement(751459..751659) Ruegeria pomeroyi DSS-3 3195661 YP_165978.1 CDS SPO0724 NC_003911.11 751738 752565 R short chain dehydrogenase/reductase oxidoreductase complement(751738..752565) Ruegeria pomeroyi DSS-3 3195854 YP_165979.1 CDS SPO0725 NC_003911.11 752176 753495 D hypothetical protein 752176..753495 Ruegeria pomeroyi DSS-3 3195493 YP_165980.1 CDS parC NC_003911.11 753492 755840 D decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A 753492..755840 Ruegeria pomeroyi DSS-3 3193734 YP_165981.1 CDS SPO0727 NC_003911.11 755809 756531 D hypothetical protein 755809..756531 Ruegeria pomeroyi DSS-3 3194576 YP_165982.1 CDS tuf-1 NC_003911.11 756639 757814 D 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 756639..757814 Ruegeria pomeroyi DSS-3 3195418 YP_165983.1 CDS SPO0729 NC_003911.11 758046 758747 R identified by similarity to GB:AAK22291.1; hypothetical protein complement(758046..758747) Ruegeria pomeroyi DSS-3 3193804 YP_165984.1 CDS glpR NC_003911.11 759232 760005 D identified by similarity to SP:P09392; match to protein family HMM PF00455; glycerol-3-phosphate regulon repressor 759232..760005 Ruegeria pomeroyi DSS-3 3193942 YP_165985.1 CDS glpD NC_003911.11 759998 761569 D 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 759998..761569 Ruegeria pomeroyi DSS-3 3195024 YP_165986.1 CDS SPO0733 NC_003911.11 761582 762559 R identified by similarity to GB:AAC36352.1; match to protein family HMM PF00561; esterase complement(761582..762559) Ruegeria pomeroyi DSS-3 3195013 YP_165987.1 CDS SPO0734 NC_003911.11 762661 763461 R identified by similarity to SP:P76086; PaaX domain-containing protein complement(762661..763461) Ruegeria pomeroyi DSS-3 3194222 YP_165988.1 CDS paaZ NC_003911.11 763540 765561 R catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA; bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase complement(763540..765561) Ruegeria pomeroyi DSS-3 3194459 YP_165989.1 CDS SPO0736 NC_003911.11 765718 767070 R identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM complement(765718..767070) Ruegeria pomeroyi DSS-3 3194675 YP_165990.1 CDS SPO0737 NC_003911.11 767067 767573 R TRAP dicarboxylate transporter subunit DctQ complement(767067..767573) Ruegeria pomeroyi DSS-3 3194388 YP_165991.1 CDS SPO0738 NC_003911.11 767630 768649 R identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP complement(767630..768649) Ruegeria pomeroyi DSS-3 3194986 YP_165992.1 CDS SPO0739 NC_003911.11 768721 770766 R identified by match to protein family HMM PF00378; match to protein family HMM PF00725; match to protein family HMM PF02737; enoyl-CoA hydratase complement(768721..770766) Ruegeria pomeroyi DSS-3 3193505 YP_165993.1 CDS paaB NC_003911.11 770869 771654 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 770869..771654 Ruegeria pomeroyi DSS-3 3195412 YP_165994.1 CDS paaD NC_003911.11 771657 772085 D identified by similarity to SP:P76084; match to protein family HMM PF03061; match to protein family HMM TIGR00369; phenylacetic acid degradation protein PaaD 771657..772085 Ruegeria pomeroyi DSS-3 3195354 YP_165995.1 CDS paaF NC_003911.11 772101 773411 D identified by similarity to GB:AAF26285.1; match to protein family HMM TIGR02155; phenylacetate-CoA ligase 772101..773411 Ruegeria pomeroyi DSS-3 3195746 YP_165996.1 CDS SPO0743 NC_003911.11 773415 774011 D identified by match to protein family HMM PF00440; TetR family transcriptional regulator 773415..774011 Ruegeria pomeroyi DSS-3 3195010 YP_165997.1 CDS SPO0744 NC_003911.11 774970 776691 R identified by similarity to GB:CAE30152.1; hypothetical protein complement(774970..776691) Ruegeria pomeroyi DSS-3 3194876 YP_165998.1 CDS SPO0745 NC_003911.11 776692 778908 R hypothetical protein complement(776692..778908) Ruegeria pomeroyi DSS-3 3195150 YP_165999.1 CDS SPO0746 NC_003911.11 778868 780238 R identified by similarity to PIR:C83621; hypothetical protein complement(778868..780238) Ruegeria pomeroyi DSS-3 3195844 YP_166000.1 CDS SPO0747 NC_003911.11 780325 782022 D identified by match to protein family HMM PF03098; peroxidase 780325..782022 Ruegeria pomeroyi DSS-3 3195070 YP_166001.1 CDS SPO0748 NC_003911.11 782079 783101 R hypothetical protein complement(782079..783101) Ruegeria pomeroyi DSS-3 3194477 YP_166002.1 CDS SPO0749 NC_003911.11 783082 783651 R identified by similarity to PIR:AE2995; hypothetical protein complement(783082..783651) Ruegeria pomeroyi DSS-3 3194870 YP_166003.1 CDS SPO0750 NC_003911.11 784282 785040 D identified by similarity to GB:CAE14641.1; hypothetical protein 784282..785040 Ruegeria pomeroyi DSS-3 3195197 YP_166004.1 CDS SPO0751 NC_003911.11 785123 786295 R identified by match to protein family HMM PF00211; guanylate cyclase complement(785123..786295) Ruegeria pomeroyi DSS-3 3194759 YP_166005.1 CDS SPO0752 NC_003911.11 786573 787331 R phenylacetic acid degradation protein complement(786573..787331) Ruegeria pomeroyi DSS-3 3194813 YP_166006.1 CDS paaK NC_003911.11 787342 788415 R 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 complement(787342..788415) Ruegeria pomeroyi DSS-3 3195933 YP_166007.1 CDS paaJ NC_003911.11 788426 788887 R identified by similarity to SP:P76080; match to protein family HMM PF01883; match to protein family HMM TIGR02159; phenylacetic acid degradation protein PaaJ complement(788426..788887) Ruegeria pomeroyi DSS-3 3195585 YP_166008.1 CDS paaI NC_003911.11 788892 789653 R identified by similarity to SP:P76079; match to protein family HMM PF05138; match to protein family HMM TIGR02158; phenylacetic acid degradation protein PaaI complement(788892..789653) Ruegeria pomeroyi DSS-3 3195321 YP_166009.1 CDS paaB NC_003911.11 789653 789937 R with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation; phenylacetate-CoA oxygenase subunit PaaB complement(789653..789937) Ruegeria pomeroyi DSS-3 3195639 YP_166010.1 CDS paaA NC_003911.11 790031 791023 R with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; phenylacetate-CoA oxygenase subunit PaaA complement(790031..791023) Ruegeria pomeroyi DSS-3 3195813 YP_166011.1 CDS SPO0758 NC_003911.11 791039 792241 R catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA; beta-ketoadipyl CoA thiolase complement(791039..792241) Ruegeria pomeroyi DSS-3 3195388 YP_166012.1 CDS SPO0759 NC_003911.11 792463 792786 R hypothetical protein complement(792463..792786) Ruegeria pomeroyi DSS-3 3195677 YP_166013.1 CDS SPO0760 NC_003911.11 792824 793219 R identified by match to protein family HMM PF02627; match to protein family HMM TIGR00778; alkylhydroperoxidase complement(792824..793219) Ruegeria pomeroyi DSS-3 3195183 YP_166014.1 CDS SPO0761 NC_003911.11 793223 794041 R identified by match to protein family HMM PF04199; match to protein family HMM TIGR01409; cyclase complement(793223..794041) Ruegeria pomeroyi DSS-3 3193876 YP_166015.1 CDS SPO0762 NC_003911.11 794236 794886 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 794236..794886 Ruegeria pomeroyi DSS-3 3195565 YP_166016.1 CDS SPO0763 NC_003911.11 794968 795681 R identified by match to protein family HMM PF00117; glutamine amidotransferase complement(794968..795681) Ruegeria pomeroyi DSS-3 3195600 YP_166017.1 CDS SPO0764 NC_003911.11 795780 797039 D identified by match to protein family HMM PF00067; cytochrome P450 family protein 795780..797039 Ruegeria pomeroyi DSS-3 3195602 YP_166018.1 CDS SPO0765 NC_003911.11 797079 798368 D identified by match to protein family HMM PF00120; glutamine synthetase 797079..798368 Ruegeria pomeroyi DSS-3 3195087 YP_166019.1 CDS SPO0766 NC_003911.11 798379 798693 D identified by match to protein family HMM PF00111; (Fe-S)-binding protein 798379..798693 Ruegeria pomeroyi DSS-3 3195760 YP_166020.1 CDS SPO0767 NC_003911.11 798878 799570 D identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 798878..799570 Ruegeria pomeroyi DSS-3 3195905 YP_166021.1 CDS SPO0768 NC_003911.11 799573 800346 R identified by match to protein family HMM PF01614; IclR family transcriptional regulator complement(799573..800346) Ruegeria pomeroyi DSS-3 3195953 YP_166022.1 CDS SPO0769 NC_003911.11 800420 801460 D identified by match to protein family HMM PF03401; hypothetical protein 800420..801460 Ruegeria pomeroyi DSS-3 3195678 YP_166023.1 CDS SPO0770 NC_003911.11 801482 802048 D hypothetical protein 801482..802048 Ruegeria pomeroyi DSS-3 3194213 YP_166024.1 CDS SPO0771 NC_003911.11 802048 803667 D identified by match to protein family HMM PF01970; hypothetical protein 802048..803667 Ruegeria pomeroyi DSS-3 3195171 YP_166025.1 CDS SPO0772 NC_003911.11 803809 805905 D identified by match to protein family HMM PF00378; match to protein family HMM PF00725; match to protein family HMM PF02737; enoyl-CoA hydratase 803809..805905 Ruegeria pomeroyi DSS-3 3194899 YP_166026.1 CDS SPO0773 NC_003911.11 805905 807080 D identified by match to protein family HMM PF00108; match to protein family HMM PF02803; match to protein family HMM TIGR01930; acetyl-CoA acyltransferase/thiolase 805905..807080 Ruegeria pomeroyi DSS-3 3192775 YP_166027.1 CDS SPO0774 NC_003911.11 807187 808377 D identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 807187..808377 Ruegeria pomeroyi DSS-3 3195860 YP_166028.1 CDS SPO0775 NC_003911.11 808383 809510 D identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 808383..809510 Ruegeria pomeroyi DSS-3 3193308 YP_166029.1 CDS SPO0776 NC_003911.11 809491 809916 D identified by match to protein family HMM PF03061; match to protein family HMM TIGR00369; hypothetical protein 809491..809916 Ruegeria pomeroyi DSS-3 3195863 YP_166030.1 CDS SPO0777 NC_003911.11 809916 810683 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 809916..810683 Ruegeria pomeroyi DSS-3 3194199 YP_166031.1 CDS SPO0778 NC_003911.11 810706 812196 D identified by similarity to SP:P94547; match to protein family HMM PF00501; long-chain-fatty-acid--CoA ligase 810706..812196 Ruegeria pomeroyi DSS-3 3194774 YP_166032.1 CDS rpe NC_003911.11 812452 813141 R identified by match to protein family HMM PF00834; match to protein family HMM TIGR01163; ribulose-phosphate 3-epimerase complement(812452..813141) Ruegeria pomeroyi DSS-3 3195182 YP_166033.1 CDS phoC NC_003911.11 813316 814137 D identified by similarity to SP:P16677; match to protein family HMM PF00005; phosphonate ABC transporter ATP-binding protein 813316..814137 Ruegeria pomeroyi DSS-3 3195497 YP_166034.1 CDS phnD NC_003911.11 814166 815101 D identified by similarity to SP:P16682; phosphonate ABC transporter periplasmic phosphonate-binding protein 814166..815101 Ruegeria pomeroyi DSS-3 3194026 YP_166035.1 CDS phoE NC_003911.11 815167 816048 D identified by similarity to SP:P16683; match to protein family HMM PF00528; phosphonate ABC transporter permease 815167..816048 Ruegeria pomeroyi DSS-3 3195615 YP_166036.1 CDS phnE NC_003911.11 816045 817415 D identified by similarity to PIR:H95946; match to protein family HMM PF00528; phosphonate ABC transporter permease 816045..817415 Ruegeria pomeroyi DSS-3 3195365 YP_166037.1 CDS SPO0784 NC_003911.11 817437 818051 D identified by similarity to SP:P26838; match to protein family HMM PF00132; chloramphenicol acetyltransferase 817437..818051 Ruegeria pomeroyi DSS-3 3195036 YP_166038.1 CDS SPO0785 NC_003911.11 818129 818983 D 2-dehydro-3-deoxygalactonokinase 818129..818983 Ruegeria pomeroyi DSS-3 3195078 YP_166039.1 CDS SPO0786 NC_003911.11 819040 819444 D identified by match to protein family HMM PF03061; thioesterase 819040..819444 Ruegeria pomeroyi DSS-3 3195875 YP_166040.1 CDS gph-1 NC_003911.11 819426 820082 R catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate; phosphoglycolate phosphatase complement(819426..820082) Ruegeria pomeroyi DSS-3 3194551 YP_166041.1 CDS SPO0788 NC_003911.11 820377 821297 R identified by match to protein family HMM PF00753; match to protein family HMM TIGR01409; metallo-beta-lactamase complement(820377..821297) Ruegeria pomeroyi DSS-3 3195040 YP_166042.1 CDS SPO0789 NC_003911.11 821481 821648 D identified by similarity to GB:AAQ61556.1; hypothetical protein 821481..821648 Ruegeria pomeroyi DSS-3 3195095 YP_166043.1 CDS SPO0790 NC_003911.11 821645 822088 D hypothetical protein 821645..822088 Ruegeria pomeroyi DSS-3 3193737 YP_166044.1 CDS SPO0791 NC_003911.11 822093 825149 R identified by match to protein family HMM PF00202; match to protein family HMM PF01551; hypothetical protein complement(822093..825149) Ruegeria pomeroyi DSS-3 3194770 YP_166045.1 CDS SPO0792 NC_003911.11 825265 826137 R identified by match to protein family HMM PF03446; match to protein family HMM TIGR00872; match to protein family HMM TIGR00873; 6-phosphogluconate dehydrogenase complement(825265..826137) Ruegeria pomeroyi DSS-3 3194481 YP_166046.1 CDS cueR NC_003911.11 826233 826622 R identified by match to protein family HMM PF00376; match to protein family HMM TIGR02044; Cu(I)-responsive transcriptional regulator complement(826233..826622) Ruegeria pomeroyi DSS-3 3194968 YP_166047.1 CDS SPO0794 NC_003911.11 826633 829119 R 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 complement(826633..829119) Ruegeria pomeroyi DSS-3 3193988 YP_166048.1 CDS SPO0795 NC_003911.11 829201 829956 R identified by similarity to PIR:E83152; match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase complement(829201..829956) Ruegeria pomeroyi DSS-3 3195238 YP_166049.1 CDS SPO0796 NC_003911.11 829953 830876 R identified by similarity to GB:BAC72444.1; hypothetical protein complement(829953..830876) Ruegeria pomeroyi DSS-3 3195367 YP_166050.1 CDS SPO0797 NC_003911.11 830873 831775 R identified by match to protein family HMM PF01758; bile acid transporter family protein complement(830873..831775) Ruegeria pomeroyi DSS-3 3194595 YP_166051.1 CDS SPO0798 NC_003911.11 831772 833088 R identified by similarity to GB:AAS47561.1; monooxygenase domain-containing protein complement(831772..833088) Ruegeria pomeroyi DSS-3 3195453 YP_166052.1 CDS SPO0799 NC_003911.11 833156 833818 D identified by match to protein family HMM PF00440; TetR family transcriptional regulator 833156..833818 Ruegeria pomeroyi DSS-3 3195157 YP_166053.1 CDS SPO0800 NC_003911.11 833887 835335 R identified by similarity to GB:AAC13371.1; match to protein family HMM PF00884; choline sulfatase complement(833887..835335) Ruegeria pomeroyi DSS-3 3195931 YP_166054.1 CDS fadD NC_003911.11 835353 836960 R identified by similarity to PIR:T08074; match to protein family HMM PF00501; 4-coumarate--CoA ligase complement(835353..836960) Ruegeria pomeroyi DSS-3 3193580 YP_166055.1 CDS rpsA NC_003911.11 837242 838918 D 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 837242..838918 Ruegeria pomeroyi DSS-3 3195039 YP_166056.1 CDS SPO0803 NC_003911.11 839256 839723 R identified by match to protein family HMM PF00293; NUDIX domain-containing protein complement(839256..839723) Ruegeria pomeroyi DSS-3 3193570 YP_166057.1 CDS ihfB NC_003911.11 840121 840405 D 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 840121..840405 Ruegeria pomeroyi DSS-3 3195204 YP_166058.1 CDS SPO0805 NC_003911.11 840409 840765 D identified by similarity to GB:CAE25511.1; hypothetical protein 840409..840765 Ruegeria pomeroyi DSS-3 3195956 YP_166059.1 CDS trpF NC_003911.11 840774 841424 D 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 840774..841424 Ruegeria pomeroyi DSS-3 3195077 YP_166060.1 CDS SPO0807 NC_003911.11 841540 841719 D hypothetical protein 841540..841719 Ruegeria pomeroyi DSS-3 3195097 YP_166061.1 CDS trpB NC_003911.11 841825 843075 D catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 841825..843075 Ruegeria pomeroyi DSS-3 3193893 YP_166062.1 CDS SPO0809 NC_003911.11 843088 843465 R identified by similarity to GB:AAD29263.1; hypothetical protein complement(843088..843465) Ruegeria pomeroyi DSS-3 3195611 YP_166063.1 CDS SPO0810 NC_003911.11 843475 844638 R identified by similarity to GB:BAA01524.1; match to protein family HMM PF00144; 6-aminohexanoate-dimer hydrolase complement(843475..844638) Ruegeria pomeroyi DSS-3 3193861 YP_166064.1 CDS pth NC_003911.11 844717 845436 R Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase complement(844717..845436) Ruegeria pomeroyi DSS-3 3195572 YP_166065.1 CDS rplY NC_003911.11 845578 846201 R 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 complement(845578..846201) Ruegeria pomeroyi DSS-3 3194994 YP_166066.1 CDS SPO0813 NC_003911.11 846327 847490 R identified by similarity to SP:P46454; match to protein family HMM PF01070; L-lactate dehydrogenase complement(846327..847490) Ruegeria pomeroyi DSS-3 3195125 YP_166067.1 CDS SPO0814 NC_003911.11 847599 848042 D identified by match to protein family HMM PF01575; acyl dehydratase MaoC 847599..848042 Ruegeria pomeroyi DSS-3 3195110 YP_166068.1 CDS trpA NC_003911.11 848046 848837 R catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha complement(848046..848837) Ruegeria pomeroyi DSS-3 3195134 YP_166069.1 CDS SPO0816 NC_003911.11 848916 849404 R identified by similarity to GB:AAN66362.1; hypothetical protein complement(848916..849404) Ruegeria pomeroyi DSS-3 3195164 YP_166070.1 CDS ychF NC_003911.11 849588 850685 D 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 849588..850685 Ruegeria pomeroyi DSS-3 3195076 YP_166071.1 CDS SPO0818 NC_003911.11 850682 851281 R identified by similarity to GB:AAL18255.1; match to protein family HMM PF01124; MAPEG family protein complement(850682..851281) Ruegeria pomeroyi DSS-3 3195152 YP_166072.1 CDS SPO0819 NC_003911.11 851411 852577 D identified by match to protein family HMM PF01979; amidohydrolase 851411..852577 Ruegeria pomeroyi DSS-3 3195939 YP_166073.1 CDS SPO0820 NC_003911.11 852622 853734 D identified by match to protein family HMM PF02515; CAIB/BAIF family protein 852622..853734 Ruegeria pomeroyi DSS-3 3195002 YP_166074.1 CDS SPO0821 NC_003911.11 853729 854166 R identified by match to protein family HMM PF01047; MarR family transcriptional regulator complement(853729..854166) Ruegeria pomeroyi DSS-3 3194566 YP_166075.1 CDS SPO0822 NC_003911.11 854229 854960 R identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein complement(854229..854960) Ruegeria pomeroyi DSS-3 3194996 YP_166076.1 CDS SPO0823 NC_003911.11 854923 855696 R identified by similarity to SP:P22730; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein complement(854923..855696) Ruegeria pomeroyi DSS-3 3194473 YP_166077.1 CDS SPO0824 NC_003911.11 855693 857537 R identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease complement(855693..857537) Ruegeria pomeroyi DSS-3 3195212 YP_166078.1 CDS SPO0825 NC_003911.11 857605 858915 R 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 complement(857605..858915) Ruegeria pomeroyi DSS-3 3195410 YP_166079.1 CDS SPO0826 NC_003911.11 858912 859493 R identified by similarity to GB:AAR38363.1; match to protein family HMM PF06684; hypothetical protein complement(858912..859493) Ruegeria pomeroyi DSS-3 3195398 YP_166080.1 CDS SPO0827 NC_003911.11 859490 860077 R identified by similarity to GB:AAR38364.1; match to protein family HMM PF06684; hypothetical protein complement(859490..860077) Ruegeria pomeroyi DSS-3 3195119 YP_166081.1 CDS SPO0828 NC_003911.11 860064 860933 R identified by similarity to GB:AAR38365.1; hypothetical protein complement(860064..860933) Ruegeria pomeroyi DSS-3 3195052 YP_166082.1 CDS SPO0829 NC_003911.11 860930 862423 R identified by similarity to GB:AAR38366.1; hypothetical protein complement(860930..862423) Ruegeria pomeroyi DSS-3 3195138 YP_166083.1 CDS SPO0830 NC_003911.11 862416 865163 R 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 complement(862416..865163) Ruegeria pomeroyi DSS-3 3195146 YP_166084.1 CDS SPO0831 NC_003911.11 865160 865987 R identified by match to protein family HMM PF00941; xanthine dehydrogenase, medium subunit complement(865160..865987) Ruegeria pomeroyi DSS-3 3195136 YP_166085.1 CDS SPO0832 NC_003911.11 866161 867018 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 866161..867018 Ruegeria pomeroyi DSS-3 3195123 YP_166086.1 CDS SPO0833 NC_003911.11 867103 868806 D identified by similarity to GB:AAN03798.1; match to protein family HMM PF01257; match to protein family HMM PF01512; formate dehydrogenase subunit beta 867103..868806 Ruegeria pomeroyi DSS-3 3195069 YP_166087.1 CDS SPO0834 NC_003911.11 868808 871585 D 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 868808..871585 Ruegeria pomeroyi DSS-3 3194589 YP_166088.1 CDS SPO0835 NC_003911.11 871766 872560 D identified by similarity to GB:AAC38443.1; match to protein family HMM PF04199; cyclase 871766..872560 Ruegeria pomeroyi DSS-3 3195133 YP_166089.1 CDS SPO0836 NC_003911.11 872582 873097 D identified by similarity to GB:BAB48851.1; hypothetical protein 872582..873097 Ruegeria pomeroyi DSS-3 3193050 YP_166090.1 CDS SPO0837 NC_003911.11 873206 874339 D hypothetical protein 873206..874339 Ruegeria pomeroyi DSS-3 3194988 YP_166091.1 CDS SPO0838 NC_003911.11 874894 875658 D identified by match to protein family HMM PF02397; sugar transferase 874894..875658 Ruegeria pomeroyi DSS-3 3195690 YP_166092.1 CDS SPO0839 NC_003911.11 875694 876629 D identified by similarity to SP:Q45409; exopolysaccharide biosynthesis domain-containing protein 875694..876629 Ruegeria pomeroyi DSS-3 3195974 YP_166093.1 CDS SPO0840 NC_003911.11 876722 878005 D identified by match to protein family HMM PF02706; chain length determinant protein 876722..878005 Ruegeria pomeroyi DSS-3 3195379 YP_166094.1 CDS SPO0841 NC_003911.11 878016 879374 R identified by match to protein family HMM PF01943; polysaccharide biosynthesis protein complement(878016..879374) Ruegeria pomeroyi DSS-3 3192809 YP_166095.1 CDS SPO0842 NC_003911.11 879591 880796 D identified by match to protein family HMM PF00534; glycoside hydrolase 879591..880796 Ruegeria pomeroyi DSS-3 3195858 YP_166096.1 CDS SPO0843 NC_003911.11 880836 881681 R identified by match to protein family HMM PF00535; glycosyl transferase family protein complement(880836..881681) Ruegeria pomeroyi DSS-3 3195596 YP_166097.1 CDS SPO0844 NC_003911.11 881678 884215 R hypothetical protein complement(881678..884215) Ruegeria pomeroyi DSS-3 3195861 YP_166098.1 CDS SPO0845 NC_003911.11 884212 885159 R hypothetical protein complement(884212..885159) Ruegeria pomeroyi DSS-3 3194383 YP_166099.1 CDS SPO0846 NC_003911.11 885191 885862 R identified by similarity to GB:AAG43513.1; match to protein family HMM PF01648; phosphopantetheinyl transferase PptA complement(885191..885862) Ruegeria pomeroyi DSS-3 3193236 YP_166100.1 CDS SPO0847 NC_003911.11 885859 890463 R 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 complement(885859..890463) Ruegeria pomeroyi DSS-3 3195891 YP_166101.1 CDS SPO0848 NC_003911.11 890460 891467 R identified by match to protein family HMM PF00535; glycosyl transferase family protein complement(890460..891467) Ruegeria pomeroyi DSS-3 3193835 YP_166102.1 CDS SPO0849 NC_003911.11 891472 897897 R 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 complement(891472..897897) Ruegeria pomeroyi DSS-3 3193890 YP_166103.1 CDS SPO0850 NC_003911.11 898157 899653 R hypothetical protein complement(898157..899653) Ruegeria pomeroyi DSS-3 3195681 YP_166104.1 CDS SPO0851 NC_003911.11 899799 900551 D 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 899799..900551 Ruegeria pomeroyi DSS-3 3193690 YP_166105.1 CDS SPO0852 NC_003911.11 900554 902653 R identified by match to protein family HMM PF01408; Gfo/Idh/MocA family oxidoreductase complement(900554..902653) Ruegeria pomeroyi DSS-3 3195862 YP_166106.1 CDS SPO0853 NC_003911.11 902661 903626 R identified by match to protein family HMM PF00535; glycosyl transferase family protein complement(902661..903626) Ruegeria pomeroyi DSS-3 3195817 YP_166107.1 CDS SPO0854 NC_003911.11 903623 904702 R identified by match to protein family HMM PF00534; glycoside hydrolase complement(903623..904702) Ruegeria pomeroyi DSS-3 3195928 YP_166108.1 CDS xylB NC_003911.11 904917 906365 D 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 904917..906365 Ruegeria pomeroyi DSS-3 3193306 YP_166109.1 CDS xylA NC_003911.11 906362 907666 D catalyzes the interconversion of D-xylose to D-xylulose; xylose isomerase 906362..907666 Ruegeria pomeroyi DSS-3 3195629 YP_166110.1 CDS galM NC_003911.11 907689 908624 D identified by match to protein family HMM PF01263; aldose 1-epimerase 907689..908624 Ruegeria pomeroyi DSS-3 3195652 YP_166111.1 CDS SPO0858 NC_003911.11 908621 909919 D identified by similarity to SP:Q49128; methylamine utilization protein MauG 908621..909919 Ruegeria pomeroyi DSS-3 3194938 YP_166112.1 CDS SPO0859 NC_003911.11 909977 911506 R identified by match to protein family HMM PF01839; hypothetical protein complement(909977..911506) Ruegeria pomeroyi DSS-3 3195384 YP_166113.1 CDS SPO0860 NC_003911.11 911496 912692 R identified by similarity to SP:P16557; match to protein family HMM PF00480; xylose repressor complement(911496..912692) Ruegeria pomeroyi DSS-3 3195885 YP_166114.1 CDS xylF NC_003911.11 912912 913940 D identified by similarity to SP:P37387; match to protein family HMM PF00532; xylose ABC transporter periplasmic xylose-binding protein 912912..913940 Ruegeria pomeroyi DSS-3 3195789 YP_166115.1 CDS xylH NC_003911.11 914007 915305 D identified by similarity to SP:P37389; match to protein family HMM PF02653; xylose ABC transporter permease 914007..915305 Ruegeria pomeroyi DSS-3 3195938 YP_166116.1 CDS xylG NC_003911.11 915302 916072 D identified by match to protein family HMM PF00005; xylose ABC transporter ATP-binding protein 915302..916072 Ruegeria pomeroyi DSS-3 3195820 YP_166117.1 CDS SPO0864 NC_003911.11 916075 916998 D glucokinase 916075..916998 Ruegeria pomeroyi DSS-3 3195769 YP_166118.1 CDS SPO0865 NC_003911.11 916989 917981 D identified by match to protein family HMM PF01408; match to protein family HMM PF02894; Gfo/Idh/MocA family oxidoreductase 916989..917981 Ruegeria pomeroyi DSS-3 3195791 YP_166119.1 CDS SPO0866 NC_003911.11 918039 919829 R identified by match to protein family HMM PF01019; gamma-glutamyltranspeptidase complement(918039..919829) Ruegeria pomeroyi DSS-3 3195728 YP_166120.1 CDS SPO0867 NC_003911.11 919833 923915 R identified by similarity to GB:AAN29006.1; match to protein family HMM PF04357; hypothetical protein complement(919833..923915) Ruegeria pomeroyi DSS-3 3195346 YP_166121.1 CDS SPO0868 NC_003911.11 923915 925720 R identified by match to protein family HMM PF01103; OMP85 family outer membrane protein complement(923915..925720) Ruegeria pomeroyi DSS-3 3195797 YP_166122.1 CDS SPO0869 NC_003911.11 925865 927094 R identified by match to protein family HMM PF00034; match to protein family HMM PF06181; hypothetical protein complement(925865..927094) Ruegeria pomeroyi DSS-3 3194596 YP_166123.1 CDS SPO0870 NC_003911.11 927189 928112 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 927189..928112 Ruegeria pomeroyi DSS-3 3193205 YP_166124.1 CDS SPO0871 NC_003911.11 928331 928687 R identified by match to protein family HMM PF00576; transthyretin family protein complement(928331..928687) Ruegeria pomeroyi DSS-3 3195386 YP_166125.1 CDS SPO0872 NC_003911.11 928972 930387 D polysaccharide deacetylase 928972..930387 Ruegeria pomeroyi DSS-3 3195926 YP_166126.1 CDS allA NC_003911.11 930384 930872 D catalyzes the formation of glyoxylate from (S)-ureidoglycolate; ureidoglycolate hydrolase 930384..930872 Ruegeria pomeroyi DSS-3 3195530 YP_166127.1 CDS SPO0874 NC_003911.11 930939 932351 D identified by match to protein family HMM PF00860; match to protein family HMM TIGR00801; xanthine/uracil permease 930939..932351 Ruegeria pomeroyi DSS-3 3195822 YP_166128.1 CDS gap-2 NC_003911.11 932526 933509 R identified by match to protein family HMM PF00044; match to protein family HMM PF02800; glyceraldehyde-3-phosphate dehydrogenase, type I complement(932526..933509) Ruegeria pomeroyi DSS-3 3195512 YP_166129.1 CDS SPO0876 NC_003911.11 933712 934539 R identified by similarity to GB:BAB51632.1; match to protein family HMM PF06038; hypothetical protein complement(933712..934539) Ruegeria pomeroyi DSS-3 3195641 YP_166130.1 CDS SPO0877 NC_003911.11 934903 936054 D identified by similarity to GB:AAM05262.1; hypothetical protein 934903..936054 Ruegeria pomeroyi DSS-3 3193998 YP_166131.1 CDS gcvH-1 NC_003911.11 936297 936656 D identified by similarity to SP:P23884; match to protein family HMM PF01597; match to protein family HMM TIGR00527; glycine cleavage system H protein 936297..936656 Ruegeria pomeroyi DSS-3 3195867 YP_166132.1 CDS SPO0879 NC_003911.11 936870 938105 D identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 936870..938105 Ruegeria pomeroyi DSS-3 3194469 YP_166133.1 CDS SPO0880 NC_003911.11 938111 938902 D identified by similarity to PIR:T36459; hypothetical protein 938111..938902 Ruegeria pomeroyi DSS-3 3193980 YP_166134.1 CDS SPO0881 NC_003911.11 938910 939143 R hypothetical protein complement(938910..939143) Ruegeria pomeroyi DSS-3 3192876 YP_166135.1 CDS SPO0882 NC_003911.11 939782 940129 D hypothetical protein 939782..940129 Ruegeria pomeroyi DSS-3 3194505 YP_166136.1 CDS SPO0883 NC_003911.11 940268 940918 D identified by similarity to GB:CAE26317.1; hypothetical protein 940268..940918 Ruegeria pomeroyi DSS-3 3194120 YP_166137.1 CDS SPO0884 NC_003911.11 940903 941802 D identified by match to protein family HMM PF03824; hypothetical protein 940903..941802 Ruegeria pomeroyi DSS-3 3195246 YP_166138.1 CDS SPO0885 NC_003911.11 941799 942734 R identified by match to protein family HMM PF00561; alpha/beta hydrolase complement(941799..942734) Ruegeria pomeroyi DSS-3 3195895 YP_166139.1 CDS groES NC_003911.11 942925 943212 D 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 942925..943212 Ruegeria pomeroyi DSS-3 3195778 YP_166140.1 CDS groEL NC_003911.11 943275 944915 D 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 943275..944915 Ruegeria pomeroyi DSS-3 3194998 YP_166141.1 CDS SPO0888 NC_003911.11 945190 945660 D identified by match to protein family HMM PF00583; acetyltransferase 945190..945660 Ruegeria pomeroyi DSS-3 3195231 YP_166142.1 CDS SPO0889 NC_003911.11 945708 946550 D identified by match to protein family HMM PF00892; hypothetical protein 945708..946550 Ruegeria pomeroyi DSS-3 3195642 YP_166143.1 CDS SPO0890 NC_003911.11 946589 947362 D identified by similarity to GB:AAM73853.1; lipase 946589..947362 Ruegeria pomeroyi DSS-3 3193652 YP_166144.1 CDS SPO0891 NC_003911.11 947359 948507 D identified by similarity to SP:P16689; match to protein family HMM PF01979; alkylphosphonate utilization protein PhnM 947359..948507 Ruegeria pomeroyi DSS-3 3195911 YP_166145.1 CDS purK NC_003911.11 948640 949713 R With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway; phosphoribosylaminoimidazole carboxylase ATPase subunit complement(948640..949713) Ruegeria pomeroyi DSS-3 3194564 YP_166146.1 CDS purE NC_003911.11 949706 950194 R identified by similarity to SP:P09028; match to protein family HMM PF00731; match to protein family HMM TIGR01162; phosphoribosylaminoimidazole carboxylase catalytic subunit complement(949706..950194) Ruegeria pomeroyi DSS-3 3195654 YP_166147.1 CDS SPO0894 NC_003911.11 950284 950535 R identified by similarity to GB:BAC52375.1; match to protein family HMM PF04325; hypothetical protein complement(950284..950535) Ruegeria pomeroyi DSS-3 3195333 YP_166148.1 CDS SPO0895 NC_003911.11 950677 951090 D identified by match to protein family HMM PF00011; heat shock protein 20 950677..951090 Ruegeria pomeroyi DSS-3 3195429 YP_166149.1 CDS SPO0896 NC_003911.11 951094 951318 D identified by similarity to GB:AAK25555.1; hypothetical protein 951094..951318 Ruegeria pomeroyi DSS-3 3194196 YP_166150.1 CDS SPO0897 NC_003911.11 951414 952292 D identified by match to protein family HMM PF02567; match to protein family HMM TIGR00654; PhzF family phenazine biosynthesis protein 951414..952292 Ruegeria pomeroyi DSS-3 3195731 YP_166151.1 CDS SPO0898 NC_003911.11 952299 953159 D identified by similarity to PIR:AH1879; hypothetical protein 952299..953159 Ruegeria pomeroyi DSS-3 3195946 YP_166152.1 CDS SPO0899 NC_003911.11 953214 954386 D hypothetical protein 953214..954386 Ruegeria pomeroyi DSS-3 3195994 YP_166153.1 CDS sat NC_003911.11 954455 956164 R 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 complement(954455..956164) Ruegeria pomeroyi DSS-3 3193730 YP_166154.1 CDS SPO0901 NC_003911.11 956356 958053 R identified by match to protein family HMM PF00111; match to protein family HMM PF00211; guanylate cyclase complement(956356..958053) Ruegeria pomeroyi DSS-3 3194090 YP_166155.1 CDS SPO0902 NC_003911.11 958113 958577 R identified by similarity to GB:AAM35160.1; hypothetical protein complement(958113..958577) Ruegeria pomeroyi DSS-3 3195584 YP_166156.1 CDS trxB NC_003911.11 958582 959523 R identified by match to protein family HMM PF00070; match to protein family HMM TIGR01292; thioredoxin-disulfide reductase complement(958582..959523) Ruegeria pomeroyi DSS-3 3195877 YP_166157.1 CDS SPO0904 NC_003911.11 959740 960240 D identified by similarity to SP:P37403; match to protein family HMM PF01037; leucine-responsive regulatory protein 959740..960240 Ruegeria pomeroyi DSS-3 3195548 YP_166158.1 CDS SPO0905 NC_003911.11 960339 961124 R identified by similarity to PIR:T03518; hypothetical protein complement(960339..961124) Ruegeria pomeroyi DSS-3 3194209 YP_166159.1 CDS SPO0906 NC_003911.11 961875 962630 R identified by similarity to GB:CAC46924.1; match to protein family HMM PF02578; match to protein family HMM TIGR00726; hypothetical protein complement(961875..962630) Ruegeria pomeroyi DSS-3 3195910 YP_166160.1 CDS SPO0907 NC_003911.11 962627 963694 R identified by similarity to GB:BAB49749.1; match to protein family HMM PF02636; hypothetical protein complement(962627..963694) Ruegeria pomeroyi DSS-3 3195997 YP_166161.1 CDS lgt NC_003911.11 963691 964578 R transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase complement(963691..964578) Ruegeria pomeroyi DSS-3 3196007 YP_166162.1 CDS SPO0909 NC_003911.11 964675 964923 D identified by similarity to GB:CAC46921.1; match to protein family HMM PF04380; hypothetical protein 964675..964923 Ruegeria pomeroyi DSS-3 3195193 YP_166163.1 CDS SPO0910 NC_003911.11 965251 965751 D identified by similarity to GB:CAE29805.1; hypothetical protein 965251..965751 Ruegeria pomeroyi DSS-3 3193477 YP_166164.1 CDS proC NC_003911.11 965770 966606 D catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase 965770..966606 Ruegeria pomeroyi DSS-3 3193059 YP_166165.1 CDS csaA NC_003911.11 966599 966937 D identified by similarity to SP:P37584; match to protein family HMM PF01588; chaperonin csaA 966599..966937 Ruegeria pomeroyi DSS-3 3196065 YP_166166.1 CDS SPO0913 NC_003911.11 966937 967890 D identified by match to protein family HMM PF00389; match to protein family HMM PF02826; D-isomer specific 2-hydroxyacid dehydrogenase 966937..967890 Ruegeria pomeroyi DSS-3 3196166 YP_166167.1 CDS tdk NC_003911.11 968104 968700 R catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase complement(968104..968700) Ruegeria pomeroyi DSS-3 3195435 YP_166168.1 CDS SPO0915 NC_003911.11 968966 969526 D identified by similarity to PIR:AB2631; hypothetical protein 968966..969526 Ruegeria pomeroyi DSS-3 3196143 YP_166169.1 CDS SPO0916 NC_003911.11 969637 970500 D identified by similarity to GB:AAS41921.1; hypothetical protein 969637..970500 Ruegeria pomeroyi DSS-3 3196080 YP_166170.1 CDS SPO0917 NC_003911.11 970668 971045 D identified by match to protein family HMM PF00903; glyoxalase 970668..971045 Ruegeria pomeroyi DSS-3 3196074 YP_166171.1 CDS fabH-1 NC_003911.11 971105 972232 R 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 complement(971105..972232) Ruegeria pomeroyi DSS-3 3195073 YP_166172.1 CDS SPO0919 NC_003911.11 972396 972869 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 972396..972869 Ruegeria pomeroyi DSS-3 3196050 YP_166173.1 CDS SPO0920 NC_003911.11 972903 973904 D identified by match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 972903..973904 Ruegeria pomeroyi DSS-3 3193025 YP_166174.1 CDS SPO0921 NC_003911.11 973916 976948 D identified by match to protein family HMM PF00873; AcrB/AcrD/AcrF family transporter 973916..976948 Ruegeria pomeroyi DSS-3 3196016 YP_166175.1 CDS SPO0922 NC_003911.11 976963 977373 R identified by similarity to PIR:D83152; match to protein family HMM PF00903; hypothetical protein complement(976963..977373) Ruegeria pomeroyi DSS-3 3195428 YP_166176.1 CDS carB NC_003911.11 977565 980933 R 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 complement(977565..980933) Ruegeria pomeroyi DSS-3 3195282 YP_166177.1 CDS pabB NC_003911.11 981130 982251 D catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine; aminodeoxychorismate synthase 981130..982251 Ruegeria pomeroyi DSS-3 3194612 YP_166178.1 CDS SPO0925 NC_003911.11 982206 982853 D identified by similarity to GB:CAC47377.1; hypothetical protein 982206..982853 Ruegeria pomeroyi DSS-3 3194864 YP_166179.1 CDS aspS NC_003911.11 983055 984836 D 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 983055..984836 Ruegeria pomeroyi DSS-3 3194889 YP_166180.1 CDS SPO0927 NC_003911.11 984839 985012 D hypothetical protein 984839..985012 Ruegeria pomeroyi DSS-3 3194999 YP_166181.1 CDS SPO0928 NC_003911.11 984844 985557 R hypothetical protein complement(984844..985557) Ruegeria pomeroyi DSS-3 3195291 YP_166182.1 CDS SPO0929 NC_003911.11 985559 986191 R Possibly an isoschizomer of M.MboI found in Moraxella bovis.; identified by match to protein family HMM PF05063; type II DNA modification methyltransferase complement(985559..986191) Ruegeria pomeroyi DSS-3 3195463 YP_166183.1 CDS SPO0930 NC_003911.11 986386 986493 R hypothetical protein complement(986386..986493) Ruegeria pomeroyi DSS-3 3196319 YP_166184.1 CDS SPO0931 NC_003911.11 986495 987214 R identified by match to protein family HMM PF00072; response regulator complement(986495..987214) Ruegeria pomeroyi DSS-3 3193727 YP_166185.1 CDS SPO0932 NC_003911.11 987345 987755 D identified by similarity to GB:AAK52053.1; match to protein family HMM PF00903; methylmalonyl-CoA epimerase 987345..987755 Ruegeria pomeroyi DSS-3 3194735 YP_166186.1 CDS SPO0933 NC_003911.11 987789 988064 D identified by similarity to GB:BAB48740.1; hypothetical protein 987789..988064 Ruegeria pomeroyi DSS-3 3195403 YP_166187.1 CDS SPO0934 NC_003911.11 988097 988792 R hypothetical protein complement(988097..988792) Ruegeria pomeroyi DSS-3 3194914 YP_166188.1 CDS SPO0935 NC_003911.11 988789 989367 R identified by match to protein family HMM PF00881; nitroreductase complement(988789..989367) Ruegeria pomeroyi DSS-3 3195763 YP_166189.1 CDS SPO0936 NC_003911.11 989512 989697 D hypothetical protein 989512..989697 Ruegeria pomeroyi DSS-3 3196043 YP_166190.1 CDS SPO0937 NC_003911.11 989745 990023 D identified by similarity to SP:Q9Z854; match to protein family HMM PF02594; hypothetical protein 989745..990023 Ruegeria pomeroyi DSS-3 3194129 YP_166191.1 CDS SPO0938 NC_003911.11 990027 990296 R hypothetical protein complement(990027..990296) Ruegeria pomeroyi DSS-3 3195799 YP_166192.1 CDS SPO0939 NC_003911.11 990386 991102 D identified by match to protein family HMM PF01435; M48 family peptidase 990386..991102 Ruegeria pomeroyi DSS-3 3195502 YP_166193.1 CDS SPO0940 NC_003911.11 991099 991467 D identified by similarity to PIR:T27104; match to protein family HMM PF01205; hypothetical protein 991099..991467 Ruegeria pomeroyi DSS-3 3196047 YP_166194.1 CDS SPO0941 NC_003911.11 991539 991790 D hypothetical protein 991539..991790 Ruegeria pomeroyi DSS-3 3195366 YP_166195.1 CDS SPO0942 NC_003911.11 991821 992078 D hypothetical protein 991821..992078 Ruegeria pomeroyi DSS-3 3194871 YP_166196.1 CDS SPO0943 NC_003911.11 992079 992321 R identified by similarity to GB:AAO38330.1; hypothetical protein complement(992079..992321) Ruegeria pomeroyi DSS-3 3194179 YP_166197.1 CDS rimO NC_003911.11 993168 994568 R catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; ribosomal protein S12 methylthiotransferase complement(993168..994568) Ruegeria pomeroyi DSS-3 3196011 YP_166198.1 CDS SPO0945 NC_003911.11 994657 996594 D identified by match to protein family HMM PF05170; AsmA family protein 994657..996594 Ruegeria pomeroyi DSS-3 3194777 YP_166199.1 CDS algC NC_003911.11 996822 998261 R 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 complement(996822..998261) Ruegeria pomeroyi DSS-3 3195637 YP_166200.1 CDS kdsA NC_003911.11 998339 999172 R 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 complement(998339..999172) Ruegeria pomeroyi DSS-3 3195476 YP_166201.1 CDS kpsE NC_003911.11 999177 1000355 R capsule polysaccharide exporter complement(999177..1000355) Ruegeria pomeroyi DSS-3 3193114 YP_166202.1 CDS kpsT NC_003911.11 1000873 1001586 R identified by similarity to SP:P10640; match to protein family HMM PF00005; capsular polysaccharide export ATP-binding protein complement(1000873..1001586) Ruegeria pomeroyi DSS-3 3193970 YP_166203.1 CDS SPO0950 NC_003911.11 1001795 1002421 D identified by similarity to GB:CAD29336.1; match to protein family HMM PF03167; uracil-DNA glycosylase 1001795..1002421 Ruegeria pomeroyi DSS-3 3193379 YP_166204.1 CDS SPO0951 NC_003911.11 1002390 1003178 D hypothetical protein 1002390..1003178 Ruegeria pomeroyi DSS-3 3195105 YP_166205.1 CDS SPO0952 NC_003911.11 1003206 1004636 D hypothetical protein 1003206..1004636 Ruegeria pomeroyi DSS-3 3195207 YP_166206.1 CDS SPO0953 NC_003911.11 1004465 1005343 R YghU; B2989; one of eight glutathione transferases from E. coli; glutathione S-transferase complement(1004465..1005343) Ruegeria pomeroyi DSS-3 3195255 YP_166207.1 CDS SPO0954 NC_003911.11 1005566 1006090 D identified by similarity to PIR:E82434; hypothetical protein 1005566..1006090 Ruegeria pomeroyi DSS-3 3195543 YP_166208.1 CDS SPO0955 NC_003911.11 1006275 1008170 D identified by match to protein family HMM PF01979; amidohydrolase 1006275..1008170 Ruegeria pomeroyi DSS-3 3194212 YP_166209.1 CDS SPO0956 NC_003911.11 1008222 1008818 R identified by similarity to PIR:AI3454; hypothetical protein complement(1008222..1008818) Ruegeria pomeroyi DSS-3 3195214 YP_166210.1 CDS SPO0957 NC_003911.11 1008968 1009759 D identified by match to protein family HMM PF01061; ABC transporter permease 1008968..1009759 Ruegeria pomeroyi DSS-3 3195509 YP_166211.1 CDS SPO0958 NC_003911.11 1009820 1011052 R hypothetical protein complement(1009820..1011052) Ruegeria pomeroyi DSS-3 3192875 YP_166212.1 CDS SPO0959 NC_003911.11 1011250 1012266 R identified by match to protein family HMM PF00892; hypothetical protein complement(1011250..1012266) Ruegeria pomeroyi DSS-3 3195638 YP_166213.1 CDS SPO0960 NC_003911.11 1012299 1012664 R identified by match to protein family HMM PF00376; MerR family transcriptional regulator complement(1012299..1012664) Ruegeria pomeroyi DSS-3 3195781 YP_166214.1 CDS SPO0961 NC_003911.11 1012748 1013005 D identified by similarity to PIR:B86741; hypothetical protein 1012748..1013005 Ruegeria pomeroyi DSS-3 3194644 YP_166215.1 CDS argD NC_003911.11 1013246 1014421 D 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 1013246..1014421 Ruegeria pomeroyi DSS-3 3194580 YP_166216.1 CDS argF NC_003911.11 1014510 1015436 D catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase 1014510..1015436 Ruegeria pomeroyi DSS-3 3195160 YP_166217.1 CDS argC-1 NC_003911.11 1015554 1016471 D 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 1015554..1016471 Ruegeria pomeroyi DSS-3 3194685 YP_166218.1 CDS SPO0965 NC_003911.11 1016468 1017358 D identified by match to protein family HMM PF00583; acetyltransferase 1016468..1017358 Ruegeria pomeroyi DSS-3 3196036 YP_166219.1 CDS panE-1 NC_003911.11 1017416 1018411 D catalyzes the formation of 2-dehydropantoate from (R)-pantoate; 2-dehydropantoate 2-reductase 1017416..1018411 Ruegeria pomeroyi DSS-3 3194571 YP_166220.1 CDS SPO0967 NC_003911.11 1018497 1019975 R identified by match to protein family HMM PF01384; phosphate transporter family protein complement(1018497..1019975) Ruegeria pomeroyi DSS-3 3196041 YP_166221.1 CDS SPO0968 NC_003911.11 1020068 1020526 R identified by match to protein family HMM PF00293; NUDIX family hydrolase complement(1020068..1020526) Ruegeria pomeroyi DSS-3 3195155 YP_166222.1 CDS apqZ NC_003911.11 1021580 1022275 D porin involved in osmoregulation allowing water to move into and out of the cell in response to osmotic pressure; aquaporin Z 1021580..1022275 Ruegeria pomeroyi DSS-3 3195594 YP_166223.1 CDS SPO0971 NC_003911.11 1022390 1023994 D identified by match to protein family HMM PF00732; match to protein family HMM PF05199; GMC family oxidoreductase 1022390..1023994 Ruegeria pomeroyi DSS-3 3195473 YP_166224.1 CDS hrpB NC_003911.11 1024037 1026487 R identified by match to protein family HMM PF00271; match to protein family HMM PF04408; match to protein family HMM TIGR01970; ATP-dependent helicase HrpB complement(1024037..1026487) Ruegeria pomeroyi DSS-3 3192888 YP_166225.1 CDS SPO0973 NC_003911.11 1026711 1027688 D 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 1026711..1027688 Ruegeria pomeroyi DSS-3 3194801 YP_166226.1 CDS rpmB NC_003911.11 1027916 1028203 D required for 70S ribosome assembly; 50S ribosomal protein L28 1027916..1028203 Ruegeria pomeroyi DSS-3 3194737 YP_166227.1 CDS SPO0975 NC_003911.11 1028308 1028754 D hypothetical protein 1028308..1028754 Ruegeria pomeroyi DSS-3 3195494 YP_166228.1 CDS SPO0976 NC_003911.11 1028800 1029279 D identified by match to protein family HMM PF04314; hypothetical protein 1028800..1029279 Ruegeria pomeroyi DSS-3 3195975 YP_166229.1 CDS SPO0977 NC_003911.11 1029330 1030364 R identified by match to protein family HMM PF02423; ornithine cyclodeaminase/mu-crystallin family protein complement(1029330..1030364) Ruegeria pomeroyi DSS-3 3195980 YP_166230.1 CDS SPO0978 NC_003911.11 1030331 1031029 R Modulates the activities of several enzymes which are inactive in their acetylated form; NAD-dependent deacetylase complement(1030331..1031029) Ruegeria pomeroyi DSS-3 3195581 YP_166231.1 CDS SPO0979 NC_003911.11 1031074 1031535 D identified by similarity to SP:P53433; match to protein family HMM PF01451; low molecular weight phosphotyrosine protein phosphatase 1031074..1031535 Ruegeria pomeroyi DSS-3 3195056 YP_166232.1 CDS SPO0980 NC_003911.11 1031810 1032769 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(1031810..1032769) Ruegeria pomeroyi DSS-3 3193747 YP_166233.1 CDS hisD NC_003911.11 1032853 1034154 D catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 1032853..1034154 Ruegeria pomeroyi DSS-3 3193830 YP_166234.1 CDS SPO0982 NC_003911.11 1034805 1036106 R hypothetical protein complement(1034805..1036106) Ruegeria pomeroyi DSS-3 3195259 YP_166235.1 CDS lepA NC_003911.11 1036159 1037958 D binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA 1036159..1037958 Ruegeria pomeroyi DSS-3 3194387 YP_166236.1 CDS znuB NC_003911.11 1038962 1039759 R identified by similarity to SP:P39832; match to protein family HMM PF00950; zinc ABC transporter permease complement(1038962..1039759) Ruegeria pomeroyi DSS-3 3194603 YP_166237.1 CDS znuC NC_003911.11 1039756 1040526 R identified by similarity to SP:P52648; match to protein family HMM PF00005; zinc ABC transporter ATP-binding protein complement(1039756..1040526) Ruegeria pomeroyi DSS-3 3195402 YP_166238.1 CDS zur NC_003911.11 1040523 1041002 R Part of a zinc ABC transporter gene cluster.; identified by similarity to SP:P32692; zinc uptake regulation protein complement(1040523..1041002) Ruegeria pomeroyi DSS-3 3195534 YP_166239.1 CDS znuA NC_003911.11 1041090 1042058 D identified by similarity to SP:P39172; match to protein family HMM PF01297; zinc ABC transporter periplasmic zinc-binding protein 1041090..1042058 Ruegeria pomeroyi DSS-3 3194922 YP_166240.1 CDS SPO0988 NC_003911.11 1042071 1043129 R identified by similarity to SP:P33015; match to protein family HMM PF04143; hypothetical protein complement(1042071..1043129) Ruegeria pomeroyi DSS-3 3196004 YP_166241.1 CDS SPO0989 NC_003911.11 1043193 1043579 R identified by match to protein family HMM PF01022; transcriptional regulator SoxR complement(1043193..1043579) Ruegeria pomeroyi DSS-3 3195455 YP_166242.1 CDS soxS NC_003911.11 1043673 1044050 R identified by similarity to GB:AAO11779.1; regulatory protein SoxS complement(1043673..1044050) Ruegeria pomeroyi DSS-3 3195943 YP_166243.1 CDS soxV NC_003911.11 1044146 1044883 D identified by similarity to GB:AAF99429.1; match to protein family HMM PF02683; sulfur oxidation V protein 1044146..1044883 Ruegeria pomeroyi DSS-3 3193615 YP_166244.1 CDS soxW NC_003911.11 1044911 1045486 D identified by similarity to GB:CAB94378.1; thioredoxin 1044911..1045486 Ruegeria pomeroyi DSS-3 3194811 YP_166245.1 CDS soxX NC_003911.11 1045605 1046090 D identified by similarity to GB:CAB94379.1; match to protein family HMM PF00034; monoheme cytochrome c SoxX 1045605..1046090 Ruegeria pomeroyi DSS-3 3195339 YP_166246.1 CDS soxY NC_003911.11 1046133 1046549 D with SoxZ catalyzes the oxidation of sulfur compounds; sulfur oxidation protein SoxY 1046133..1046549 Ruegeria pomeroyi DSS-3 3194856 YP_166247.1 CDS soxZ NC_003911.11 1046583 1046912 D identified by similarity to GB:CAB94381.1; sulfur oxidation Z protein 1046583..1046912 Ruegeria pomeroyi DSS-3 3195930 YP_166248.1 CDS soxA NC_003911.11 1046990 1047841 D identified by similarity to GB:AAF99434.1; diheme cytochrome c SoxA 1046990..1047841 Ruegeria pomeroyi DSS-3 3194976 YP_166249.1 CDS soxB NC_003911.11 1047943 1049646 D 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 1047943..1049646 Ruegeria pomeroyi DSS-3 3194111 YP_166250.1 CDS soxC NC_003911.11 1049725 1051008 D 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 1049725..1051008 Ruegeria pomeroyi DSS-3 3195075 YP_166251.1 CDS soxD NC_003911.11 1050992 1052035 D identified by similarity to PIR:T46966; match to protein family HMM PF00034; diheme cytochrome c SoxD 1050992..1052035 Ruegeria pomeroyi DSS-3 3195695 YP_166252.1 CDS soxE NC_003911.11 1052039 1052749 D identified by match to protein family HMM PF00034; diheme cytochrome c SoxE 1052039..1052749 Ruegeria pomeroyi DSS-3 3194630 YP_166253.1 CDS soxF NC_003911.11 1052788 1054050 D identified by similarity to GB:CAA55826.2; sulfur oxidation F protein 1052788..1054050 Ruegeria pomeroyi DSS-3 3194648 YP_166254.1 CDS SPO1002 NC_003911.11 1054075 1055079 R identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator complement(1054075..1055079) Ruegeria pomeroyi DSS-3 3195743 YP_166255.1 CDS clpP NC_003911.11 1055324 1055953 D hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit 1055324..1055953 Ruegeria pomeroyi DSS-3 3193881 YP_166256.1 CDS clpX NC_003911.11 1056087 1057361 D binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX 1056087..1057361 Ruegeria pomeroyi DSS-3 3195507 YP_166257.1 CDS SPO1005 NC_003911.11 1057373 1057888 D identified by match to protein family HMM PF01042; endoribonuclease L-PSP 1057373..1057888 Ruegeria pomeroyi DSS-3 3194692 YP_166258.1 CDS SPO1006 NC_003911.11 1057980 1058363 D 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 1057980..1058363 Ruegeria pomeroyi DSS-3 3196053 YP_166259.1 CDS SPO1007 NC_003911.11 1058374 1058829 D identified by match to protein family HMM PF02470; hypothetical protein 1058374..1058829 Ruegeria pomeroyi DSS-3 3195753 YP_166260.1 CDS SPO1008 NC_003911.11 1058826 1059185 D identified by similarity to GB:AAN29832.1; hypothetical protein 1058826..1059185 Ruegeria pomeroyi DSS-3 3194292 YP_166261.1 CDS aat NC_003911.11 1059149 1059781 R 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 complement(1059149..1059781) Ruegeria pomeroyi DSS-3 3194540 YP_166262.1 CDS accC NC_003911.11 1059833 1061182 R 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 complement(1059833..1061182) Ruegeria pomeroyi DSS-3 3195480 YP_166263.1 CDS accB NC_003911.11 1061193 1061687 R identified by match to protein family HMM PF00364; match to protein family HMM TIGR00531; acetyl-CoA carboxylase, biotin carboxyl carrier protein complement(1061193..1061687) Ruegeria pomeroyi DSS-3 3195545 YP_166264.1 CDS SPO1012 NC_003911.11 1061835 1062371 R identified by match to protein family HMM PF00196; LuxR family transcriptional regulator complement(1061835..1062371) Ruegeria pomeroyi DSS-3 3194617 YP_166265.1 CDS SPO1013 NC_003911.11 1062462 1063622 D 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 1062462..1063622 Ruegeria pomeroyi DSS-3 3195826 YP_166266.1 CDS SPO1014 NC_003911.11 1063619 1065127 D identified by match to protein family HMM PF00501; AMP-binding protein 1063619..1065127 Ruegeria pomeroyi DSS-3 3195103 YP_166267.1 CDS SPO1015 NC_003911.11 1065124 1065927 D identified by similarity to SP:O86034; match to protein family HMM PF00106; 3-hydroxybutyrate dehydrogenase 1065124..1065927 Ruegeria pomeroyi DSS-3 3193768 YP_166268.1 CDS SPO1016 NC_003911.11 1065929 1066909 R hypothetical protein complement(1065929..1066909) Ruegeria pomeroyi DSS-3 3194536 YP_166269.1 CDS SPO1017 NC_003911.11 1066986 1067741 R 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 complement(1066986..1067741) Ruegeria pomeroyi DSS-3 3195692 YP_166270.1 CDS SPO1018 NC_003911.11 1067811 1068566 R identified by similarity to SP:P22730; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein complement(1067811..1068566) Ruegeria pomeroyi DSS-3 3195795 YP_166271.1 CDS SPO1019 NC_003911.11 1068579 1069781 R identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease complement(1068579..1069781) Ruegeria pomeroyi DSS-3 3195228 YP_166272.1 CDS SPO1020 NC_003911.11 1069785 1070825 R identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease complement(1069785..1070825) Ruegeria pomeroyi DSS-3 3195954 YP_166273.1 CDS SPO1021 NC_003911.11 1070921 1072273 R 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 complement(1070921..1072273) Ruegeria pomeroyi DSS-3 3195562 YP_166274.1 CDS SPO1022 NC_003911.11 1072502 1073800 D identified by match to protein family HMM PF01381; transcriptional regulator 1072502..1073800 Ruegeria pomeroyi DSS-3 3193733 YP_166275.1 CDS SPO1023 NC_003911.11 1073886 1074266 D identified by match to protein family HMM PF00072; response regulator 1073886..1074266 Ruegeria pomeroyi DSS-3 3195651 YP_166276.1 CDS SPO1024 NC_003911.11 1074263 1074568 D hypothetical protein 1074263..1074568 Ruegeria pomeroyi DSS-3 3195598 YP_166277.1 CDS SPO1025 NC_003911.11 1074565 1077243 D identified by match to protein family HMM PF00512; match to protein family HMM PF02518; sensor histidine kinase 1074565..1077243 Ruegeria pomeroyi DSS-3 3194941 YP_166278.1 CDS SPO1026 NC_003911.11 1077322 1078488 D hypothetical protein 1077322..1078488 Ruegeria pomeroyi DSS-3 3196067 YP_166279.1 CDS SPO1027 NC_003911.11 1078508 1078939 R identified by similarity to PIR:T10511; match to protein family HMM PF04273; match to protein family HMM TIGR01244; hypothetical protein complement(1078508..1078939) Ruegeria pomeroyi DSS-3 3195967 YP_166280.1 CDS SPO1028 NC_003911.11 1078949 1079380 R identified by match to protein family HMM PF04143; hypothetical protein complement(1078949..1079380) Ruegeria pomeroyi DSS-3 3194527 YP_166281.1 CDS SPO1029 NC_003911.11 1079380 1079808 R identified by match to protein family HMM PF04143; hypothetical protein complement(1079380..1079808) Ruegeria pomeroyi DSS-3 3195195 YP_166282.1 CDS SPO1030 NC_003911.11 1079849 1080766 R identified by match to protein family HMM PF00753; metallo-beta-lactamase complement(1079849..1080766) Ruegeria pomeroyi DSS-3 3194430 YP_166283.1 CDS SPO1031 NC_003911.11 1080814 1081185 D hypothetical protein 1080814..1081185 Ruegeria pomeroyi DSS-3 3195824 YP_166284.1 CDS SPO1032 NC_003911.11 1081210 1081431 R hypothetical protein complement(1081210..1081431) Ruegeria pomeroyi DSS-3 3195849 YP_166285.1 CDS SPO1033 NC_003911.11 1081578 1081838 D identified by similarity to GB:BAB50739.1; hypothetical protein 1081578..1081838 Ruegeria pomeroyi DSS-3 3194604 YP_166286.1 CDS SPO1034 NC_003911.11 1081875 1082750 R hypothetical protein complement(1081875..1082750) Ruegeria pomeroyi DSS-3 3195486 YP_166287.1 CDS SPO1036 NC_003911.11 1083132 1084376 D identified by match to protein family HMM PF00589; phage integrase site specific recombinase 1083132..1084376 Ruegeria pomeroyi DSS-3 3195462 YP_166288.1 CDS SPO1037 NC_003911.11 1084691 1086001 D hypothetical protein 1084691..1086001 Ruegeria pomeroyi DSS-3 3195599 YP_166289.1 CDS SPO1038 NC_003911.11 1085995 1086156 R hypothetical protein complement(1085995..1086156) Ruegeria pomeroyi DSS-3 3195978 YP_166290.1 CDS SPO1039 NC_003911.11 1087398 1088780 D identified by similarity to GB:CAE33998.1; hypothetical protein 1087398..1088780 Ruegeria pomeroyi DSS-3 3194771 YP_166291.1 CDS SPO1040 NC_003911.11 1088777 1089391 D hypothetical protein 1088777..1089391 Ruegeria pomeroyi DSS-3 3195173 YP_166292.1 CDS SPO1041 NC_003911.11 1089461 1089865 D hypothetical protein 1089461..1089865 Ruegeria pomeroyi DSS-3 3195335 YP_166293.1 CDS SPO1042 NC_003911.11 1089858 1090526 D hypothetical protein 1089858..1090526 Ruegeria pomeroyi DSS-3 3196006 YP_166294.1 CDS SPO1043 NC_003911.11 1090717 1090953 D hypothetical protein 1090717..1090953 Ruegeria pomeroyi DSS-3 3193491 YP_166295.1 CDS SPO1044 NC_003911.11 1091162 1092196 D identified by similarity to GB:BAC45394.1; hypothetical protein 1091162..1092196 Ruegeria pomeroyi DSS-3 3193542 YP_166296.1 CDS SPO1045 NC_003911.11 1092791 1093339 D hypothetical protein 1092791..1093339 Ruegeria pomeroyi DSS-3 3196334 YP_166297.1 CDS SPO1046 NC_003911.11 1093332 1094060 D hypothetical protein 1093332..1094060 Ruegeria pomeroyi DSS-3 3196181 YP_166298.1 CDS SPO1047 NC_003911.11 1094205 1095173 D identified by match to protein family HMM PF00078; RNA-dependent DNA polymerase 1094205..1095173 Ruegeria pomeroyi DSS-3 3196332 YP_166299.1 CDS SPO1048 NC_003911.11 1095296 1096321 D hypothetical protein 1095296..1096321 Ruegeria pomeroyi DSS-3 3194608 YP_166300.1 CDS SPO1049 NC_003911.11 1096391 1097512 D identified by match to protein family HMM PF00145; match to protein family HMM TIGR00675; C-5 cytosine-specific family DNA methylase 1096391..1097512 Ruegeria pomeroyi DSS-3 3194254 YP_166301.1 CDS SPO1050 NC_003911.11 1098451 1099539 D identified by match to protein family HMM PF00589; phage integrase site specific recombinase 1098451..1099539 Ruegeria pomeroyi DSS-3 3194594 YP_166302.1 CDS SPO1051 NC_003911.11 1100582 1101598 R hypothetical protein complement(1100582..1101598) Ruegeria pomeroyi DSS-3 3195200 YP_166303.1 CDS SPO1052 NC_003911.11 1102078 1102485 R hypothetical protein complement(1102078..1102485) Ruegeria pomeroyi DSS-3 3194086 YP_166304.1 CDS SPO1053 NC_003911.11 1105457 1105987 R identified by similarity to PIR:H75269; hypothetical protein complement(1105457..1105987) Ruegeria pomeroyi DSS-3 3195709 YP_166305.1 CDS SPO1054 NC_003911.11 1106015 1106524 R identified by similarity to PIR:AB1950; hypothetical protein complement(1106015..1106524) Ruegeria pomeroyi DSS-3 3193822 YP_166306.1 CDS SPO1055 NC_003911.11 1106581 1107015 R hypothetical protein complement(1106581..1107015) Ruegeria pomeroyi DSS-3 3195744 YP_166307.1 CDS SPO1056 NC_003911.11 1107039 1107866 R identified by similarity to GB:BAB50720.1; hypothetical protein complement(1107039..1107866) Ruegeria pomeroyi DSS-3 3195606 YP_166308.1 CDS SPO1057 NC_003911.11 1108042 1109040 D identified by match to protein family HMM PF00165; match to protein family HMM TIGR01199; AraC family transcriptional regulator 1108042..1109040 Ruegeria pomeroyi DSS-3 3195397 YP_166309.1 CDS SPO1058 NC_003911.11 1109195 1110070 R identified by similarity to GB:CAA74897.1; match to protein family HMM PF03279; acyltransferase complement(1109195..1110070) Ruegeria pomeroyi DSS-3 3195055 YP_166310.1 CDS SPO1059 NC_003911.11 1110768 1112879 D identified by match to protein family HMM PF00069; serine/threonine protein kinase 1110768..1112879 Ruegeria pomeroyi DSS-3 3195072 YP_166311.1 CDS SPO1060 NC_003911.11 1112983 1114359 D hypothetical protein 1112983..1114359 Ruegeria pomeroyi DSS-3 3195704 YP_166312.1 CDS SPO1061 NC_003911.11 1114443 1115543 D identified by match to protein family HMM PF01476; LysM domain-containing protein 1114443..1115543 Ruegeria pomeroyi DSS-3 3196002 YP_166313.1 CDS SPO1062 NC_003911.11 1115805 1116899 D identified by match to protein family HMM PF01476; LysM domain-containing protein 1115805..1116899 Ruegeria pomeroyi DSS-3 3195421 YP_166314.1 CDS SPO1063 NC_003911.11 1117059 1117895 D identified by similarity to GB:AAS02340.1; hypothetical protein 1117059..1117895 Ruegeria pomeroyi DSS-3 3195805 YP_166315.1 CDS SPO1064 NC_003911.11 1117879 1118835 D serine/threonine protein phosphatase 1117879..1118835 Ruegeria pomeroyi DSS-3 3194190 YP_166316.1 CDS SPO1065 NC_003911.11 1118838 1120214 D hypothetical protein 1118838..1120214 Ruegeria pomeroyi DSS-3 3195532 YP_166317.1 CDS SPO1066 NC_003911.11 1120242 1121030 R hypothetical protein complement(1120242..1121030) Ruegeria pomeroyi DSS-3 3192819 YP_166318.1 CDS SPO1067 NC_003911.11 1121069 1121482 R hypothetical protein complement(1121069..1121482) Ruegeria pomeroyi DSS-3 3194131 YP_166319.1 CDS SPO1068 NC_003911.11 1121522 1122424 R identified by similarity to GB:CAE10435.1; hypothetical protein complement(1121522..1122424) Ruegeria pomeroyi DSS-3 3195556 YP_166320.1 CDS SPO1069 NC_003911.11 1122421 1124523 R hypothetical protein complement(1122421..1124523) Ruegeria pomeroyi DSS-3 3194725 YP_166321.1 CDS SPO1070 NC_003911.11 1125279 1126940 R proposed role in polysaccahride synthesis; FAD-binding dehydrogenase complement(1125279..1126940) Ruegeria pomeroyi DSS-3 3194756 YP_166322.1 CDS SPO1071 NC_003911.11 1127009 1127743 R Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group; glutamine amidotransferase complement(1127009..1127743) Ruegeria pomeroyi DSS-3 3195404 YP_166323.1 CDS SPO1072 NC_003911.11 1127946 1128686 R identified by similarity to PIR:AC3292; match to protein family HMM PF01709; match to protein family HMM TIGR01033; hypothetical protein complement(1127946..1128686) Ruegeria pomeroyi DSS-3 3195080 YP_166324.1 CDS SPO1073 NC_003911.11 1128890 1129834 D identified by match to protein family HMM PF03401; hypothetical protein 1128890..1129834 Ruegeria pomeroyi DSS-3 3195338 YP_166325.1 CDS SPO1074 NC_003911.11 1129842 1130273 D hypothetical protein 1129842..1130273 Ruegeria pomeroyi DSS-3 3195168 YP_166326.1 CDS SPO1075 NC_003911.11 1130297 1131802 D identified by match to protein family HMM PF01970; hypothetical protein 1130297..1131802 Ruegeria pomeroyi DSS-3 3194391 YP_166327.1 CDS SPO1076 NC_003911.11 1131862 1133637 D identified by match to protein family HMM PF02080; TrkA domain-containing protein 1131862..1133637 Ruegeria pomeroyi DSS-3 3192906 YP_166328.1 CDS SPO1077 NC_003911.11 1133708 1134400 R identified by match to protein family HMM PF00881; nitroreductase complement(1133708..1134400) Ruegeria pomeroyi DSS-3 3195236 YP_166329.1 CDS SPO1078 NC_003911.11 1134438 1135322 R 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 complement(1134438..1135322) Ruegeria pomeroyi DSS-3 3194722 YP_166330.1 CDS SPO1079 NC_003911.11 1135414 1136025 D identified by similarity to SP:P94633; match to protein family HMM PF01810; L-lysine exporter 1135414..1136025 Ruegeria pomeroyi DSS-3 3193931 YP_166331.1 CDS SPO1080 NC_003911.11 1136078 1137004 D identified by match to protein family HMM PF00892; hypothetical protein 1136078..1137004 Ruegeria pomeroyi DSS-3 3195295 YP_166332.1 CDS SPO1081 NC_003911.11 1137018 1137476 D identified by similarity to GB:AAM82654.1; hypothetical protein 1137018..1137476 Ruegeria pomeroyi DSS-3 3194677 YP_166333.1 CDS betI NC_003911.11 1137532 1138110 D HTH-type; bet1; Repressor involved in choline regulation of the bet genes; transcriptional regulator BetI 1137532..1138110 Ruegeria pomeroyi DSS-3 3195688 YP_166334.1 CDS betC-1 NC_003911.11 1138107 1139615 D identified by similarity to SP:O69787; match to protein family HMM PF00884; choline sulfatase 1138107..1139615 Ruegeria pomeroyi DSS-3 3195014 YP_166335.1 CDS SPO1084 NC_003911.11 1139766 1140125 D identified by similarity to GB:CAC41724.1; hypothetical protein 1139766..1140125 Ruegeria pomeroyi DSS-3 3194664 YP_166336.1 CDS SPO1085 NC_003911.11 1140146 1140952 R identified by similarity to GB:CAE29266.1; hypothetical protein complement(1140146..1140952) Ruegeria pomeroyi DSS-3 3195172 YP_166337.1 CDS SPO1086 NC_003911.11 1141118 1141699 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(1141118..1141699) Ruegeria pomeroyi DSS-3 3193964 YP_166338.1 CDS SPO1087 NC_003911.11 1141865 1143067 D hypothetical protein 1141865..1143067 Ruegeria pomeroyi DSS-3 3195815 YP_166339.1 CDS betA NC_003911.11 1143150 1144808 D catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine; choline dehydrogenase 1143150..1144808 Ruegeria pomeroyi DSS-3 3195720 YP_166340.1 CDS SPO1089 NC_003911.11 1144931 1145170 D identified by similarity to GB:AAN33382.1; match to protein family HMM PF04325; hypothetical protein 1144931..1145170 Ruegeria pomeroyi DSS-3 3193441 YP_166341.1 CDS SPO1090 NC_003911.11 1145243 1146640 R identified by match to protein family HMM PF01381; match to protein family HMM PF06114; DNA-binding protein complement(1145243..1146640) Ruegeria pomeroyi DSS-3 3195215 YP_166342.1 CDS SPO1091 NC_003911.11 1146710 1146997 R identified by similarity to GB:AAG42024.1; match to protein family HMM PF03795; hypothetical protein complement(1146710..1146997) Ruegeria pomeroyi DSS-3 3193826 YP_166343.1 CDS SPO1092 NC_003911.11 1147095 1147997 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1147095..1147997 Ruegeria pomeroyi DSS-3 3194862 YP_166344.1 CDS SPO1093 NC_003911.11 1147941 1149146 R identified by match to protein family HMM TIGR00710; Bcr/CflA subfamily drug resistance transporter complement(1147941..1149146) Ruegeria pomeroyi DSS-3 3194409 YP_166345.1 CDS pccB NC_003911.11 1149329 1150861 D identified by similarity to PIR:T42208; match to protein family HMM PF01039; propionyl-CoA carboxylase subunit beta 1149329..1150861 Ruegeria pomeroyi DSS-3 3195272 YP_166346.1 CDS SPO1095 NC_003911.11 1151639 1152133 D identified by similarity to GB:BAC50887.1; hypothetical protein 1151639..1152133 Ruegeria pomeroyi DSS-3 3195281 YP_166347.1 CDS SPO1096 NC_003911.11 1152824 1152961 D lipoprotein 1152824..1152961 Ruegeria pomeroyi DSS-3 3194202 YP_166348.1 CDS SPO1097 NC_003911.11 1153031 1153390 D identified by similarity to PIR:C98286; hypothetical protein 1153031..1153390 Ruegeria pomeroyi DSS-3 3195852 YP_166349.1 CDS SPO1098 NC_003911.11 1153471 1154610 R identified by similarity to GB:AAM43280.1; hypothetical protein complement(1153471..1154610) Ruegeria pomeroyi DSS-3 3194937 YP_166350.1 CDS SPO1099 NC_003911.11 1155083 1155205 D hypothetical protein 1155083..1155205 Ruegeria pomeroyi DSS-3 3194396 YP_166351.1 CDS SPO1100 NC_003911.11 1155270 1155473 D lipoprotein 1155270..1155473 Ruegeria pomeroyi DSS-3 3195626 YP_166352.1 CDS pccA NC_003911.11 1155594 1157639 D 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 1155594..1157639 Ruegeria pomeroyi DSS-3 3193848 YP_166353.1 CDS SPO1102 NC_003911.11 1157644 1158165 D lipoprotein 1157644..1158165 Ruegeria pomeroyi DSS-3 3194810 YP_166354.1 CDS SPO1103 NC_003911.11 1158182 1158766 R hypothetical protein complement(1158182..1158766) Ruegeria pomeroyi DSS-3 3195337 YP_166355.1 CDS SPO1104 NC_003911.11 1158731 1159732 D hypothetical protein 1158731..1159732 Ruegeria pomeroyi DSS-3 3195234 YP_166356.1 CDS SPO1105 NC_003911.11 1159698 1161827 D MDM; functions in conversion of succinate to propionate; methylmalonyl-CoA mutase 1159698..1161827 Ruegeria pomeroyi DSS-3 3196172 YP_166357.1 CDS SPO1106 NC_003911.11 1161906 1162559 D identified by similarity to PIR:B75327; hypothetical protein 1161906..1162559 Ruegeria pomeroyi DSS-3 3194681 YP_166358.1 CDS SPO1107 NC_003911.11 1162556 1163050 D identified by similarity to SP:P21861; match to protein family HMM PF00583; phosphinothricin N-acetyltransferase 1162556..1163050 Ruegeria pomeroyi DSS-3 3196164 YP_166359.1 CDS SPO1108 NC_003911.11 1163091 1163771 D identified by similarity to SP:P31680; match to protein family HMM PF00226; DnaJ-like protein DjlA 1163091..1163771 Ruegeria pomeroyi DSS-3 3195067 YP_166360.1 CDS SPO1109 NC_003911.11 1163776 1164789 D identified by match to protein family HMM PF03372; hypothetical protein 1163776..1164789 Ruegeria pomeroyi DSS-3 3195812 YP_166361.1 CDS SPO1110 NC_003911.11 1165314 1166216 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1165314..1166216 Ruegeria pomeroyi DSS-3 3196144 YP_166362.1 CDS SPO1111 NC_003911.11 1166294 1167121 D identified by similarity to GB:CAE33489.1; match to protein family HMM PF07286; hypothetical protein 1166294..1167121 Ruegeria pomeroyi DSS-3 3195111 YP_166363.1 CDS SPO1112 NC_003911.11 1167143 1168180 D identified by match to protein family HMM PF03480; TRAP transporter, periplasmic protein 1167143..1168180 Ruegeria pomeroyi DSS-3 3195696 YP_166364.1 CDS SPO1113 NC_003911.11 1168219 1168752 D Assignment based partly on membership in a TRAP-T gene trio.; identified by similarity to GB:CAE33493.1; TRAP transporter, transmembrane protein 1168219..1168752 Ruegeria pomeroyi DSS-3 3195613 YP_166365.1 CDS SPO1114 NC_003911.11 1168749 1170035 D identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM 1168749..1170035 Ruegeria pomeroyi DSS-3 3193589 YP_166366.1 CDS SPO1115 NC_003911.11 1170039 1170692 D identified by similarity to GB:CAE33491.1; hypothetical protein 1170039..1170692 Ruegeria pomeroyi DSS-3 3193929 YP_166367.1 CDS SPO1116 NC_003911.11 1170850 1172775 R hypothetical protein complement(1170850..1172775) Ruegeria pomeroyi DSS-3 3195847 YP_166368.1 CDS SPO1117 NC_003911.11 1173336 1174880 R identified by match to protein family HMM PF02541; Ppx/GppA phosphatase complement(1173336..1174880) Ruegeria pomeroyi DSS-3 3195224 YP_166369.1 CDS SPO1118 NC_003911.11 1174942 1175619 R identified by similarity to GB:BAC49388.1; hypothetical protein complement(1174942..1175619) Ruegeria pomeroyi DSS-3 3196130 YP_166370.1 CDS SPO1119 NC_003911.11 1175620 1176687 R identified by match to protein family HMM PF01594; hypothetical protein complement(1175620..1176687) Ruegeria pomeroyi DSS-3 3192989 YP_166371.1 CDS SPO1120 NC_003911.11 1176927 1177682 D identified by similarity to PIR:T10512; hypothetical protein 1176927..1177682 Ruegeria pomeroyi DSS-3 3193090 YP_166372.1 CDS proS NC_003911.11 1177999 1179393 D catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase 1177999..1179393 Ruegeria pomeroyi DSS-3 3195540 YP_166373.1 CDS SPO1122 NC_003911.11 1179398 1179763 R hypothetical protein complement(1179398..1179763) Ruegeria pomeroyi DSS-3 3193001 YP_166374.1 CDS lolE NC_003911.11 1179969 1181312 D identified by similarity to SP:P75956; match to protein family HMM PF02687; lipoprotein releasing system transmembrane protein LolE 1179969..1181312 Ruegeria pomeroyi DSS-3 3196122 YP_166375.1 CDS lolD NC_003911.11 1181305 1181991 D identified by similarity to SP:P75957; match to protein family HMM PF00005; lipoprotein releasing system ATP-binding protein 1181305..1181991 Ruegeria pomeroyi DSS-3 3195423 YP_166376.1 CDS SPO1125 NC_003911.11 1182006 1182461 D hypothetical protein 1182006..1182461 Ruegeria pomeroyi DSS-3 3196116 YP_166377.1 CDS SPO1126 NC_003911.11 1182487 1182879 D cytochrome c family protein 1182487..1182879 Ruegeria pomeroyi DSS-3 3195907 YP_166378.1 CDS SPO1127 NC_003911.11 1182895 1183302 D identified by match to protein family HMM PF00034; cytochrome c family protein 1182895..1183302 Ruegeria pomeroyi DSS-3 3193945 YP_166379.1 CDS SPO1128 NC_003911.11 1183370 1184170 R hypothetical protein complement(1183370..1184170) Ruegeria pomeroyi DSS-3 3195112 YP_166380.1 CDS SPO1129 NC_003911.11 1184211 1184873 R identified by similarity to PIR:D83497; hypothetical protein complement(1184211..1184873) Ruegeria pomeroyi DSS-3 3196109 YP_166381.1 CDS SPO1130 NC_003911.11 1184936 1185343 R identified by match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase complement(1184936..1185343) Ruegeria pomeroyi DSS-3 3196096 YP_166382.1 CDS SPO1131 NC_003911.11 1185539 1186549 D identified by match to protein family HMM PF04069; glycine betaine/proline ABC transporter substrate-binding protein 1185539..1186549 Ruegeria pomeroyi DSS-3 3196089 YP_166383.1 CDS SPO1132 NC_003911.11 1186559 1187611 D identified by similarity to SP:P46920; match to protein family HMM PF00005; glycine betaine/proline ABC transporter ATP-binding protein 1186559..1187611 Ruegeria pomeroyi DSS-3 3196091 YP_166384.1 CDS SPO1133 NC_003911.11 1187608 1189671 D identified by similarity to SP:P14176; match to protein family HMM PF00528; glycine betaine/proline ABC transporter permease 1187608..1189671 Ruegeria pomeroyi DSS-3 3196072 YP_166385.1 CDS SPO1134 NC_003911.11 1189756 1190424 D identified by match to protein family HMM PF07298; NnrU family protein 1189756..1190424 Ruegeria pomeroyi DSS-3 3195924 YP_166386.1 CDS SPO1135 NC_003911.11 1190456 1191007 D identified by similarity to PIR:AB3629; hypothetical protein 1190456..1191007 Ruegeria pomeroyi DSS-3 3193578 YP_166387.1 CDS SPO1136 NC_003911.11 1191289 1192662 R identified by match to protein family HMM PF00202; hypothetical protein complement(1191289..1192662) Ruegeria pomeroyi DSS-3 3195074 YP_166388.1 CDS gabD-1 NC_003911.11 1192817 1194292 R identified by similarity to SP:P25526; match to protein family HMM PF00171; match to protein family HMM TIGR01780; succinate-semialdehyde dehydrogenase complement(1192817..1194292) Ruegeria pomeroyi DSS-3 3194046 YP_166389.1 CDS asnC NC_003911.11 1194420 1194899 R identified by match to protein family HMM PF01037; amino acid metabolism regulator complement(1194420..1194899) Ruegeria pomeroyi DSS-3 3193874 YP_166390.1 CDS SPO1139 NC_003911.11 1194911 1195903 R identified by match to protein family HMM PF04952; ectoine utilization protein EutE complement(1194911..1195903) Ruegeria pomeroyi DSS-3 3195186 YP_166391.1 CDS SPO1140 NC_003911.11 1195907 1197094 R identified by similarity to SP:P55667; ectoine utilization protein EutD complement(1195907..1197094) Ruegeria pomeroyi DSS-3 3195544 YP_166392.1 CDS SPO1141 NC_003911.11 1197114 1198148 R cyclodeaminase; ectoine utilization protein EutC complement(1197114..1198148) Ruegeria pomeroyi DSS-3 3195478 YP_166393.1 CDS eutB NC_003911.11 1198099 1199106 R catalyzes the formation of 2-oxobutanoate from L-threonine; involved in ectoine utilization; threonine dehydratase complement(1198099..1199106) Ruegeria pomeroyi DSS-3 3193370 YP_166394.1 CDS SPO1143 NC_003911.11 1199124 1199888 R identified by match to protein family HMM PF01177; ectoine utilization protein EutA complement(1199124..1199888) Ruegeria pomeroyi DSS-3 3194757 YP_166395.1 CDS SPO1144 NC_003911.11 1199897 1200334 R identified by match to protein family HMM PF00582; universal stress protein family protein complement(1199897..1200334) Ruegeria pomeroyi DSS-3 3192648 YP_166396.1 CDS uehC NC_003911.11 1200347 1201633 R 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 complement(1200347..1201633) Ruegeria pomeroyi DSS-3 3195851 YP_166397.1 CDS uehB NC_003911.11 1201644 1202210 R identified by match to protein family HMM PF04290; ectoin/5-hydroxyectoin TRAP transporter small integral membrane protein complement(1201644..1202210) Ruegeria pomeroyi DSS-3 3195006 YP_166398.1 CDS uehA NC_003911.11 1202280 1203299 R identified by similarity to SP:P37735; match to protein family HMM PF03480; ectoin/5-hydroxyectoin TRAP transporter large integral membrane protein complement(1202280..1203299) Ruegeria pomeroyi DSS-3 3195242 YP_166399.1 CDS gntR NC_003911.11 1203397 1204791 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(1203397..1204791) Ruegeria pomeroyi DSS-3 3195381 YP_166400.1 CDS SPO1150 NC_003911.11 1205883 1206656 D identified by match to protein family HMM PF00588; match to protein family HMM TIGR00186; RNA methyltransferase 1205883..1206656 Ruegeria pomeroyi DSS-3 3195708 YP_166401.1 CDS SPO1151 NC_003911.11 1206671 1206976 D hypothetical protein 1206671..1206976 Ruegeria pomeroyi DSS-3 3194323 YP_166402.1 CDS SPO1152 NC_003911.11 1207067 1207525 D identified by similarity to PIR:E82434; match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1207067..1207525 Ruegeria pomeroyi DSS-3 3195020 YP_166403.1 CDS SPO1153 NC_003911.11 1207721 1208197 D identified by match to protein family HMM PF02629; CoA-binding domain-containing protein 1207721..1208197 Ruegeria pomeroyi DSS-3 3193315 YP_166404.1 CDS SPO1154 NC_003911.11 1208194 1208754 R lipoprotein complement(1208194..1208754) Ruegeria pomeroyi DSS-3 3194032 YP_166405.1 CDS hisE NC_003911.11 1208815 1209132 R catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis; phosphoribosyl-ATP pyrophosphatase complement(1208815..1209132) Ruegeria pomeroyi DSS-3 3194083 YP_166406.1 CDS hisF NC_003911.11 1209129 1209890 R 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 complement(1209129..1209890) Ruegeria pomeroyi DSS-3 3195843 YP_166407.1 CDS SPO1157 NC_003911.11 1209924 1210418 R identified by similarity to GB:BAC46085.1; hypothetical protein complement(1209924..1210418) Ruegeria pomeroyi DSS-3 3195045 YP_166408.1 CDS hisA NC_003911.11 1210495 1211217 R 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 complement(1210495..1211217) Ruegeria pomeroyi DSS-3 3195806 YP_166409.1 CDS SPO1159 NC_003911.11 1211350 1211748 D identified by similarity to GB:AAN29556.1; hypothetical protein 1211350..1211748 Ruegeria pomeroyi DSS-3 3194740 YP_166410.1 CDS SPO1160 NC_003911.11 1211792 1212328 R identified by similarity to GB:AAM73219.1; hypothetical protein complement(1211792..1212328) Ruegeria pomeroyi DSS-3 3193244 YP_166411.1 CDS SPO1161 NC_003911.11 1212347 1213138 D identified by match to protein family HMM PF00165; AraC family transcriptional regulator 1212347..1213138 Ruegeria pomeroyi DSS-3 3193382 YP_166412.1 CDS hisH NC_003911.11 1213227 1213865 R 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 complement(1213227..1213865) Ruegeria pomeroyi DSS-3 3195662 YP_166413.1 CDS hisB NC_003911.11 1213865 1214452 R 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 complement(1213865..1214452) Ruegeria pomeroyi DSS-3 3195098 YP_166414.1 CDS SPO1164 NC_003911.11 1214565 1214852 D identified by similarity to PIR:A97666; hypothetical protein 1214565..1214852 Ruegeria pomeroyi DSS-3 3194632 YP_166415.1 CDS SPO1165 NC_003911.11 1214839 1215612 R identified by similarity to GB:BAB52792.1; hypothetical protein complement(1214839..1215612) Ruegeria pomeroyi DSS-3 3195889 YP_166416.1 CDS SPO1166 NC_003911.11 1215666 1217018 R identified by match to protein family HMM PF00202; aminotransferase complement(1215666..1217018) Ruegeria pomeroyi DSS-3 3195918 YP_166417.1 CDS SPO1168 NC_003911.11 1217387 1217911 D identified by similarity to PIR:D95307; hypothetical protein 1217387..1217911 Ruegeria pomeroyi DSS-3 3194788 YP_166418.1 CDS pyc NC_003911.11 1218331 1221768 R biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate; pyruvate carboxylase complement(1218331..1221768) Ruegeria pomeroyi DSS-3 3195551 YP_166419.1 CDS SPO1172 NC_003911.11 1221906 1223021 R identified by match to protein family HMM PF01070; FMN-dependent alpha-hydroxy acid dehydrogenase complement(1221906..1223021) Ruegeria pomeroyi DSS-3 3194219 YP_166420.1 CDS SPO1173 NC_003911.11 1223161 1224957 R identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254; diguanylate cyclase complement(1223161..1224957) Ruegeria pomeroyi DSS-3 3195229 YP_166421.1 CDS SPO1174 NC_003911.11 1225205 1227544 D identified by match to protein family HMM PF00580; DNA helicase II 1225205..1227544 Ruegeria pomeroyi DSS-3 3195921 YP_166422.1 CDS SPO1175 NC_003911.11 1227563 1228426 R hypothetical protein complement(1227563..1228426) Ruegeria pomeroyi DSS-3 3192965 YP_166423.1 CDS SPO1176 NC_003911.11 1228427 1229203 R identified by match to protein family HMM PF00149; Ser/Thr protein phosphatase complement(1228427..1229203) Ruegeria pomeroyi DSS-3 3195151 YP_166424.1 CDS SPO1177 NC_003911.11 1229631 1229855 R identified by similarity to GB:BAB50586.1; match to protein family HMM PF06568; hypothetical protein complement(1229631..1229855) Ruegeria pomeroyi DSS-3 3194542 YP_166425.1 CDS SPO1178 NC_003911.11 1230789 1231292 D MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ 1230789..1231292 Ruegeria pomeroyi DSS-3 3193765 YP_166426.1 CDS mraW NC_003911.11 1231297 1232292 D identified by similarity to SP:P60391; match to protein family HMM PF01795; match to protein family HMM TIGR00006; S-adenosyl-methyltransferase MraW 1231297..1232292 Ruegeria pomeroyi DSS-3 3193020 YP_166427.1 CDS SPO1180 NC_003911.11 1232289 1232657 D identified by similarity to GB:BAB48908.1; hypothetical protein 1232289..1232657 Ruegeria pomeroyi DSS-3 3194791 YP_166428.1 CDS SPO1181 NC_003911.11 1232654 1234441 D identified by similarity to SP:P11882; match to protein family HMM PF00905; match to protein family HMM PF03717; penicillin-binding protein 1232654..1234441 Ruegeria pomeroyi DSS-3 3195148 YP_166429.1 CDS murE NC_003911.11 1234460 1235941 D 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 1234460..1235941 Ruegeria pomeroyi DSS-3 3194562 YP_166430.1 CDS murF NC_003911.11 1235938 1237332 D 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 1235938..1237332 Ruegeria pomeroyi DSS-3 3193363 YP_166431.1 CDS mraY NC_003911.11 1237348 1238430 D First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase 1237348..1238430 Ruegeria pomeroyi DSS-3 3194606 YP_166432.1 CDS SPO1185 NC_003911.11 1238573 1239373 D hypothetical protein 1238573..1239373 Ruegeria pomeroyi DSS-3 3194062 YP_166433.1 CDS SPO1186 NC_003911.11 1239345 1240469 D identified by similarity to PIR:AG2285; match to protein family HMM PF00515; hypothetical protein 1239345..1240469 Ruegeria pomeroyi DSS-3 3195360 YP_166434.1 CDS murD NC_003911.11 1240536 1241936 D 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 1240536..1241936 Ruegeria pomeroyi DSS-3 3195454 YP_166435.1 CDS SPO1188 NC_003911.11 1242072 1243292 R identified by similarity to PIR:E97432; match to protein family HMM PF03486; match to protein family HMM TIGR00275; hypothetical protein complement(1242072..1243292) Ruegeria pomeroyi DSS-3 3194363 YP_166436.1 CDS SPO1189 NC_003911.11 1243312 1244196 R identified by match to protein family HMM PF00892; hypothetical protein complement(1243312..1244196) Ruegeria pomeroyi DSS-3 3194007 YP_166437.1 CDS SPO1190 NC_003911.11 1244296 1244658 R identified by match to protein family HMM PF01638; transcriptional regulator family protein complement(1244296..1244658) Ruegeria pomeroyi DSS-3 3193777 YP_166438.1 CDS gst NC_003911.11 1244786 1245400 D identified by similarity to SP:P39100; match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 1244786..1245400 Ruegeria pomeroyi DSS-3 3193256 YP_166439.1 CDS SPO1192 NC_003911.11 1245397 1245783 D identified by similarity to GB:AAK24936.1; hypothetical protein 1245397..1245783 Ruegeria pomeroyi DSS-3 3194240 YP_166440.1 CDS SPO1193 NC_003911.11 1245844 1246050 D identified by match to protein family HMM PF01361; match to protein family HMM TIGR00013; 4-oxalocrotonate tautomerase 1245844..1246050 Ruegeria pomeroyi DSS-3 3194260 YP_166441.1 CDS SPO1194 NC_003911.11 1246139 1247380 D identified by similarity to SP:P16457; match to protein family HMM PF01098; cell division protein FtsW 1246139..1247380 Ruegeria pomeroyi DSS-3 3193181 YP_166442.1 CDS murG NC_003911.11 1247394 1248491 D 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 1247394..1248491 Ruegeria pomeroyi DSS-3 3193006 YP_166443.1 CDS murC NC_003911.11 1248488 1249885 D 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 1248488..1249885 Ruegeria pomeroyi DSS-3 3192978 YP_166444.1 CDS SPO1197 NC_003911.11 1249978 1251186 D identified by match to protein family HMM PF00324; amino acid permease 1249978..1251186 Ruegeria pomeroyi DSS-3 3193190 YP_166445.1 CDS SPO1198 NC_003911.11 1251431 1251676 D identified by similarity to GB:BAC67841.1; hypothetical protein 1251431..1251676 Ruegeria pomeroyi DSS-3 3194119 YP_166446.1 CDS SPO1199 NC_003911.11 1251913 1252227 D hypothetical protein 1251913..1252227 Ruegeria pomeroyi DSS-3 3192865 YP_166447.1 CDS murB NC_003911.11 1252296 1253222 D catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase 1252296..1253222 Ruegeria pomeroyi DSS-3 3193384 YP_166448.1 CDS ddl NC_003911.11 1253322 1254242 D 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 1253322..1254242 Ruegeria pomeroyi DSS-3 3192915 YP_166449.1 CDS SPO1202 NC_003911.11 1254230 1255237 D identified by match to protein family HMM PF03799; cell division protein FtsQ 1254230..1255237 Ruegeria pomeroyi DSS-3 3193369 YP_166450.1 CDS ftsA NC_003911.11 1255243 1256580 D identified by match to protein family HMM PF02491; match to protein family HMM TIGR01174; cell division protein FtsA 1255243..1256580 Ruegeria pomeroyi DSS-3 3193675 YP_166451.1 CDS ftsZ NC_003911.11 1256978 1258606 D 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 1256978..1258606 Ruegeria pomeroyi DSS-3 3193425 YP_166452.1 CDS lpxC NC_003911.11 1258819 1259739 D 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 1258819..1259739 Ruegeria pomeroyi DSS-3 3193410 YP_166453.1 CDS SPO1206 NC_003911.11 1259890 1260744 D identified by similarity to SP:Q50985; match to protein family HMM PF03696; competence lipoprotein ComL 1259890..1260744 Ruegeria pomeroyi DSS-3 3192904 YP_166454.1 CDS recN NC_003911.11 1260784 1262433 D identified by match to protein family HMM TIGR00634; DNA repair protein RecN 1260784..1262433 Ruegeria pomeroyi DSS-3 3192969 YP_166455.1 CDS SPO1208 NC_003911.11 1262479 1264224 D identified by match to protein family HMM PF00654; voltage-gated chloride channel family protein 1262479..1264224 Ruegeria pomeroyi DSS-3 3192751 YP_166456.1 CDS SPO1209 NC_003911.11 1264368 1265816 D identified by match to protein family HMM PF07171; match to protein family HMM PF07364; MlrC domain-containing protein 1264368..1265816 Ruegeria pomeroyi DSS-3 3193817 YP_166457.1 CDS SPO1210 NC_003911.11 1265972 1267567 D identified by similarity to SP:P75797; match to protein family HMM PF00496; oligopeptide ABC transporter periplasmic oligopeptide-binding protein 1265972..1267567 Ruegeria pomeroyi DSS-3 3192737 YP_166458.1 CDS SPO1211 NC_003911.11 1267642 1268583 D identified by match to protein family HMM PF00528; oligopeptide ABC transporter permease 1267642..1268583 Ruegeria pomeroyi DSS-3 3193723 YP_166459.1 CDS SPO1212 NC_003911.11 1268583 1269485 D identified by similarity to SP:P42063; match to protein family HMM PF00528; oligopeptide ABC transporter permease 1268583..1269485 Ruegeria pomeroyi DSS-3 3193116 YP_166460.1 CDS SPO1213 NC_003911.11 1269469 1271139 D 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 1269469..1271139 Ruegeria pomeroyi DSS-3 3193925 YP_166461.1 CDS SPO1214 NC_003911.11 1271143 1272312 D identified by similarity to PIR:I40762; match to protein family HMM PF01546; match to protein family HMM TIGR01891; hippurate hydrolase 1271143..1272312 Ruegeria pomeroyi DSS-3 3193697 YP_166462.1 CDS SPO1215 NC_003911.11 1272318 1273448 D catalyzes the release of C-terminal glutamate residues from N-acylating moieties; carboxypeptidase 1272318..1273448 Ruegeria pomeroyi DSS-3 3193545 YP_166463.1 CDS SPO1216 NC_003911.11 1274319 1275038 R hypothetical protein complement(1274319..1275038) Ruegeria pomeroyi DSS-3 3192714 YP_166464.1 CDS SPO1217 NC_003911.11 1275144 1275398 D identified by match to protein family HMM PF01381; DNA-binding protein 1275144..1275398 Ruegeria pomeroyi DSS-3 3193779 YP_166465.1 CDS SPO1218 NC_003911.11 1277271 1278860 R identified by match to protein family HMM PF00589; phage integrase site specific recombinase complement(1277271..1278860) Ruegeria pomeroyi DSS-3 3193761 YP_166466.1 CDS SPO1219 NC_003911.11 1279111 1280238 D identified by match to protein family HMM PF00589; phage integrase site specific recombinase 1279111..1280238 Ruegeria pomeroyi DSS-3 3196333 YP_166467.1 CDS SPO1220 NC_003911.11 1280321 1280677 R hypothetical protein complement(1280321..1280677) Ruegeria pomeroyi DSS-3 3193935 YP_166468.1 CDS SPO1221 NC_003911.11 1280672 1282654 D hypothetical protein 1280672..1282654 Ruegeria pomeroyi DSS-3 3193786 YP_166469.1 CDS SPO1222 NC_003911.11 1283506 1284990 R identified by match to protein family HMM PF00239; match to protein family HMM PF07508; resolvase site-specific recombinase complement(1283506..1284990) Ruegeria pomeroyi DSS-3 3193810 YP_166470.1 CDS SPO1223 NC_003911.11 1285246 1286073 R hypothetical protein complement(1285246..1286073) Ruegeria pomeroyi DSS-3 3193168 YP_166471.1 CDS SPO1224 NC_003911.11 1286092 1287255 R identified by similarity to GB:BAB66386.1; hypothetical protein complement(1286092..1287255) Ruegeria pomeroyi DSS-3 3192942 YP_166472.1 CDS SPO1225 NC_003911.11 1287409 1287987 D identified by similarity to GB:AAQ58890.1; hypothetical protein 1287409..1287987 Ruegeria pomeroyi DSS-3 3193780 YP_166473.1 CDS SPO1226 NC_003911.11 1288109 1289455 D lipoprotein 1288109..1289455 Ruegeria pomeroyi DSS-3 3193968 YP_166474.1 CDS SPO1227 NC_003911.11 1290725 1291075 D identified by similarity to GB:AAQ58888.1; hypothetical protein 1290725..1291075 Ruegeria pomeroyi DSS-3 3193891 YP_166475.1 CDS SPO1228 NC_003911.11 1291062 1291544 D hypothetical protein 1291062..1291544 Ruegeria pomeroyi DSS-3 3194108 YP_166476.1 CDS SPO1229 NC_003911.11 1292517 1292876 D hypothetical protein 1292517..1292876 Ruegeria pomeroyi DSS-3 3193870 YP_166477.1 CDS SPO1230 NC_003911.11 1292876 1295182 D identified by similarity to PIR:T31014; hypothetical protein 1292876..1295182 Ruegeria pomeroyi DSS-3 3194728 YP_166478.1 CDS SPO1231 NC_003911.11 1295431 1296327 D hypothetical protein 1295431..1296327 Ruegeria pomeroyi DSS-3 3193972 YP_166479.1 CDS SPO1232 NC_003911.11 1296349 1296696 R identified by similarity to SP:P42505; match to protein family HMM PF00816; H-NS family DNA-binding protein complement(1296349..1296696) Ruegeria pomeroyi DSS-3 3193871 YP_166480.1 CDS SPO1233 NC_003911.11 1297126 1300509 D hypothetical protein 1297126..1300509 Ruegeria pomeroyi DSS-3 3194015 YP_166481.1 CDS SPO1234 NC_003911.11 1300861 1301811 D identified by similarity to GB:AAO28025.1; hypothetical protein 1300861..1301811 Ruegeria pomeroyi DSS-3 3196336 YP_166482.1 CDS SPO1235 NC_003911.11 1302040 1303836 D identified by similarity to GB:CAE15648.1; hypothetical protein 1302040..1303836 Ruegeria pomeroyi DSS-3 3192647 YP_166483.1 CDS SPO1236 NC_003911.11 1303933 1305291 D hypothetical protein 1303933..1305291 Ruegeria pomeroyi DSS-3 3193015 YP_166484.1 CDS SPO1237 NC_003911.11 1305533 1306843 R hypothetical protein complement(1305533..1306843) Ruegeria pomeroyi DSS-3 3194555 YP_166485.1 CDS pcm-1 NC_003911.11 1307788 1308441 D identified by match to protein family HMM PF01135; protein-L-isoaspartate O-methyltransferase 1307788..1308441 Ruegeria pomeroyi DSS-3 3193027 YP_166486.1 CDS SPO1240 NC_003911.11 1308540 1309958 D identified by match to protein family HMM PF02321; match to protein family HMM TIGR01844; TolC family type I secretion outer membrane protein 1308540..1309958 Ruegeria pomeroyi DSS-3 3195283 YP_166487.1 CDS SPO1241 NC_003911.11 1310034 1310963 D identified by similarity to GB:AAK23300.1; hypothetical protein 1310034..1310963 Ruegeria pomeroyi DSS-3 3193017 YP_166488.1 CDS cobQ NC_003911.11 1310964 1312421 R 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 complement(1310964..1312421) Ruegeria pomeroyi DSS-3 3193022 YP_166489.1 CDS SPO1243 NC_003911.11 1312625 1313164 R identified by similarity to GB:AAR38391.1; hypothetical protein complement(1312625..1313164) Ruegeria pomeroyi DSS-3 3194786 YP_166490.1 CDS efp NC_003911.11 1313163 1313726 D Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 1313163..1313726 Ruegeria pomeroyi DSS-3 3193034 YP_166491.1 CDS SPO1245 NC_003911.11 1313798 1314730 R identified by match to protein family HMM PF00664; ABC transporter permease complement(1313798..1314730) Ruegeria pomeroyi DSS-3 3193048 YP_166492.1 CDS SPO1246 NC_003911.11 1314759 1315493 R identified by match to protein family HMM PF01571; glycine cleavage system protein T complement(1314759..1315493) Ruegeria pomeroyi DSS-3 3193070 YP_166493.1 CDS SPO1247 NC_003911.11 1315573 1316253 D identified by match to protein family HMM PF00535; glycosyl transferase family protein 1315573..1316253 Ruegeria pomeroyi DSS-3 3193977 YP_166494.1 CDS SPO1249 NC_003911.11 1317572 1319986 D identified by similarity to SP:P43671; paraquat-inducible protein 1317572..1319986 Ruegeria pomeroyi DSS-3 3192675 YP_166495.1 CDS SPO1250 NC_003911.11 1319990 1320547 D identified by similarity to GB:AAQ60217.1; match to protein family HMM PF03886; lipoprotein 1319990..1320547 Ruegeria pomeroyi DSS-3 3193790 YP_166496.1 CDS SPO1251 NC_003911.11 1320544 1321305 R hypothetical protein complement(1320544..1321305) Ruegeria pomeroyi DSS-3 3193140 YP_166497.1 CDS SPO1252 NC_003911.11 1321425 1321550 R hypothetical protein complement(1321425..1321550) Ruegeria pomeroyi DSS-3 3193815 YP_166498.1 CDS parE NC_003911.11 1322648 1324606 R decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B complement(1322648..1324606) Ruegeria pomeroyi DSS-3 3192730 YP_166499.1 CDS SPO1254 NC_003911.11 1324740 1325333 R hypothetical protein complement(1324740..1325333) Ruegeria pomeroyi DSS-3 3194147 YP_166500.1 CDS SPO1255 NC_003911.11 1325382 1326056 D identified by match to protein family HMM TIGR01926; alkylhydroperoxidase 1325382..1326056 Ruegeria pomeroyi DSS-3 3193846 YP_166501.1 CDS ppk2 NC_003911.11 1326265 1327299 D identified by similarity to GB:AAN87337.1; match to protein family HMM PF03976; polyphosphate kinase 1326265..1327299 Ruegeria pomeroyi DSS-3 3194096 YP_166502.1 CDS SPO1257 NC_003911.11 1327302 1327913 R identified by match to protein family HMM PF02798; glutathione S-transferase complement(1327302..1327913) Ruegeria pomeroyi DSS-3 3194291 YP_166503.1 CDS SPO1258 NC_003911.11 1327910 1328809 R identified by match to protein family HMM PF00561; alpha/beta hydrolase complement(1327910..1328809) Ruegeria pomeroyi DSS-3 3193923 YP_166504.1 CDS SPO1259 NC_003911.11 1328806 1329441 R identified by similarity to GB:AAN30332.1; hypothetical protein complement(1328806..1329441) Ruegeria pomeroyi DSS-3 3192687 YP_166505.1 CDS SPO1260 NC_003911.11 1329564 1330904 D identified by similarity to SP:P37340; match to protein family HMM PF01554; match to protein family HMM TIGR00797; MATE efflux family protein 1329564..1330904 Ruegeria pomeroyi DSS-3 3194224 YP_166506.1 CDS SPO1261 NC_003911.11 1331077 1331619 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1331077..1331619 Ruegeria pomeroyi DSS-3 3194465 YP_166507.1 CDS SPO1262 NC_003911.11 1331616 1332515 D identified by match to protein family HMM PF00892; hypothetical protein 1331616..1332515 Ruegeria pomeroyi DSS-3 3192911 YP_166508.1 CDS SPO1263 NC_003911.11 1332653 1333054 R hypothetical protein complement(1332653..1333054) Ruegeria pomeroyi DSS-3 3194023 YP_166509.1 CDS aspC-2 NC_003911.11 1333071 1334273 R catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase complement(1333071..1334273) Ruegeria pomeroyi DSS-3 3194016 YP_166510.1 CDS SPO1265 NC_003911.11 1334366 1334758 D identified by match to protein family HMM PF01381; DNA-binding protein 1334366..1334758 Ruegeria pomeroyi DSS-3 3194460 YP_166511.1 CDS SPO1266 NC_003911.11 1334755 1335012 D identified by match to protein family HMM PF03937; hypothetical protein 1334755..1335012 Ruegeria pomeroyi DSS-3 3194734 YP_166512.1 CDS SPO1267 NC_003911.11 1335135 1335587 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1335135..1335587 Ruegeria pomeroyi DSS-3 3192807 YP_166513.1 CDS SPO1268 NC_003911.11 1335581 1336345 R lipoprotein complement(1335581..1336345) Ruegeria pomeroyi DSS-3 3192996 YP_166514.1 CDS SPO1269 NC_003911.11 1336342 1337037 R identified by similarity to GB:BAB50411.1; hypothetical protein complement(1336342..1337037) Ruegeria pomeroyi DSS-3 3193381 YP_166515.1 CDS SPO1270 NC_003911.11 1337034 1337462 R identified by match to protein family HMM PF00903; lactoylglutathione lyase complement(1337034..1337462) Ruegeria pomeroyi DSS-3 3193319 YP_166516.1 CDS SPO1271 NC_003911.11 1337529 1338932 R hypothetical protein complement(1337529..1338932) Ruegeria pomeroyi DSS-3 3193752 YP_166517.1 CDS SPO1272 NC_003911.11 1338938 1340065 R hypothetical protein complement(1338938..1340065) Ruegeria pomeroyi DSS-3 3194028 YP_166518.1 CDS thyX NC_003911.11 1340119 1341096 D 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 1340119..1341096 Ruegeria pomeroyi DSS-3 3194823 YP_166519.1 CDS SPO1274 NC_003911.11 1341164 1342057 D hypothetical protein 1341164..1342057 Ruegeria pomeroyi DSS-3 3193771 YP_166520.1 CDS SPO1275 NC_003911.11 1342151 1342357 R identified by match to protein family HMM PF00313; cold shock family protein complement(1342151..1342357) Ruegeria pomeroyi DSS-3 3194159 YP_166521.1 CDS SPO1276 NC_003911.11 1342577 1342894 D identified by match to protein family HMM PF03960; ArsC family protein 1342577..1342894 Ruegeria pomeroyi DSS-3 3193983 YP_166522.1 CDS SPO1277 NC_003911.11 1342943 1343311 D hypothetical protein 1342943..1343311 Ruegeria pomeroyi DSS-3 3193038 YP_166523.1 CDS SPO1278 NC_003911.11 1343352 1343915 R identified by similarity to GB:AAK25219.1; hypothetical protein complement(1343352..1343915) Ruegeria pomeroyi DSS-3 3194345 YP_166524.1 CDS SPO1279 NC_003911.11 1343890 1344672 R identified by similarity to GB:CAE43198.1; hypothetical protein complement(1343890..1344672) Ruegeria pomeroyi DSS-3 3194144 YP_166525.1 CDS SPO1280 NC_003911.11 1344669 1345547 R identified by similarity to SP:Q92W37; match to protein family HMM PF05114; hypothetical protein complement(1344669..1345547) Ruegeria pomeroyi DSS-3 3194268 YP_166526.1 CDS SPO1281 NC_003911.11 1345624 1345935 R identified by similarity to GB:CAE31790.1; hypothetical protein complement(1345624..1345935) Ruegeria pomeroyi DSS-3 3194277 YP_166527.1 CDS thrS NC_003911.11 1346148 1348094 R 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 complement(1346148..1348094) Ruegeria pomeroyi DSS-3 3194092 YP_166528.1 CDS SPO1283 NC_003911.11 1348253 1348666 R identified by similarity to GB:BAC49624.1; hypothetical protein complement(1348253..1348666) Ruegeria pomeroyi DSS-3 3194775 YP_166529.1 CDS SPO1284 NC_003911.11 1348663 1349406 R identified by match to protein family HMM PF01022; match to protein family HMM PF05146; ArsR family transcriptional regulator complement(1348663..1349406) Ruegeria pomeroyi DSS-3 3194238 YP_166530.1 CDS SPO1285 NC_003911.11 1349522 1350265 D identified by similarity to GB:CAE25485.1; hypothetical protein 1349522..1350265 Ruegeria pomeroyi DSS-3 3194274 YP_166531.1 CDS SPO1286 NC_003911.11 1350265 1351257 D identified by similarity to GB:BAB47950.1; hypothetical protein 1350265..1351257 Ruegeria pomeroyi DSS-3 3193324 YP_166532.1 CDS SPO1287 NC_003911.11 1351257 1351685 D identified by match to protein family HMM PF00903; glyoxalase 1351257..1351685 Ruegeria pomeroyi DSS-3 3192997 YP_166533.1 CDS SPO1288 NC_003911.11 1351685 1352317 D identified by similarity to GB:CAC41730.1; hypothetical protein 1351685..1352317 Ruegeria pomeroyi DSS-3 3194302 YP_166534.1 CDS SPO1289 NC_003911.11 1352390 1353094 D identified by match to protein family HMM PF00561; alpha/beta hydrolase 1352390..1353094 Ruegeria pomeroyi DSS-3 3193667 YP_166535.1 CDS SPO1290 NC_003911.11 1353085 1353669 R identified by similarity to PIR:D83123; hypothetical protein complement(1353085..1353669) Ruegeria pomeroyi DSS-3 3192655 YP_166536.1 CDS phaZ NC_003911.11 1353672 1354946 R identified by similarity to GB:BAA33394.1; match to protein family HMM PF06850; match to protein family HMM TIGR01849; polyhydroxyalkanoate depolymerase complement(1353672..1354946) Ruegeria pomeroyi DSS-3 3193958 YP_166537.1 CDS phaC NC_003911.11 1355058 1356860 D identified by match to protein family HMM PF07167; match to protein family HMM TIGR01838; poly(3-hydroxyalkanoate) polymerase 1355058..1356860 Ruegeria pomeroyi DSS-3 3194012 YP_166538.1 CDS phaP NC_003911.11 1356992 1357438 D identified by similarity to GB:BAA77258.1; phasin, PhaP 1356992..1357438 Ruegeria pomeroyi DSS-3 3193788 YP_166539.1 CDS SPO1294 NC_003911.11 1357700 1358257 D identified by match to protein family HMM TIGR01848; polyhydroxyalkanoate synthesis repressor PhaR 1357700..1358257 Ruegeria pomeroyi DSS-3 3194014 YP_166540.1 CDS SPO1295 NC_003911.11 1358270 1359562 R identified by match to protein family HMM PF01041; aminotransferase complement(1358270..1359562) Ruegeria pomeroyi DSS-3 3193776 YP_166541.1 CDS SPO1298 NC_003911.11 1362412 1363401 R identified by match to protein family HMM PF00248; oxidoreductase, aldo/keto reductase complement(1362412..1363401) Ruegeria pomeroyi DSS-3 3193820 YP_166542.1 CDS SPO1299 NC_003911.11 1363484 1364311 D identified by match to protein family HMM PF00126; LysR family transcriptional regulator 1363484..1364311 Ruegeria pomeroyi DSS-3 3196258 YP_166543.1 CDS SPO1300 NC_003911.11 1364561 1365919 R identified by match to protein family HMM PF00120; glutamine synthetase complement(1364561..1365919) Ruegeria pomeroyi DSS-3 3193789 YP_166544.1 CDS SPO1301 NC_003911.11 1365921 1366601 R identified by match to protein family HMM PF00117; glutamine amidotransferase complement(1365921..1366601) Ruegeria pomeroyi DSS-3 3194907 YP_166545.1 CDS SPO1302 NC_003911.11 1366663 1368003 R identified by match to protein family HMM PF00120; glutamine synthetase complement(1366663..1368003) Ruegeria pomeroyi DSS-3 3193944 YP_166546.1 CDS SPO1303 NC_003911.11 1368111 1369169 R identified by similarity to GB:BAB91123.1; match to protein family HMM PF01266; fructosyl-amino acid oxidase complement(1368111..1369169) Ruegeria pomeroyi DSS-3 3193802 YP_166547.1 CDS SPO1304 NC_003911.11 1369179 1369988 R 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 complement(1369179..1369988) Ruegeria pomeroyi DSS-3 3193749 YP_166548.1 CDS SPO1305 NC_003911.11 1369985 1370872 R identified by similarity to PIR:T44455; match to protein family HMM PF00528; ABC transporter permease complement(1369985..1370872) Ruegeria pomeroyi DSS-3 3193894 YP_166549.1 CDS SPO1306 NC_003911.11 1370957 1371769 R 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 complement(1370957..1371769) Ruegeria pomeroyi DSS-3 3194724 YP_166550.1 CDS SPO1307 NC_003911.11 1371711 1372487 R identified by similarity to SP:P07109; match to protein family HMM PF00005; His/Glu/Gln/Arg/opine family ABC transporter ATP-binding protein complement(1371711..1372487) Ruegeria pomeroyi DSS-3 3193924 YP_166551.1 CDS SPO1308 NC_003911.11 1372597 1373349 R identified by similarity to PIR:F83007; hypothetical protein complement(1372597..1373349) Ruegeria pomeroyi DSS-3 3193748 YP_166552.1 CDS SPO1309 NC_003911.11 1373346 1373783 R identified by similarity to GB:CAC47662.1; match to protein family HMM PF07049; hypothetical protein complement(1373346..1373783) Ruegeria pomeroyi DSS-3 3193754 YP_166553.1 CDS SPO1310 NC_003911.11 1373810 1374253 R identified by similarity to GB:BAB50927.1; match to protein family HMM PF07049; hypothetical protein complement(1373810..1374253) Ruegeria pomeroyi DSS-3 3192770 YP_166554.1 CDS SPO1311 NC_003911.11 1374686 1375726 D identified by match to protein family HMM PF01244; renal dipeptidase 1374686..1375726 Ruegeria pomeroyi DSS-3 3193783 YP_166555.1 CDS pyrG NC_003911.11 1375919 1377562 R 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 complement(1375919..1377562) Ruegeria pomeroyi DSS-3 3193759 YP_166556.1 CDS secG NC_003911.11 1377725 1378090 R identified by match to protein family HMM PF03840; match to protein family HMM TIGR00810; preprotein translocase subunit SecG complement(1377725..1378090) Ruegeria pomeroyi DSS-3 3193914 YP_166557.1 CDS nthA NC_003911.11 1378242 1378856 D identified by similarity to SP:P97051; match to protein family HMM PF02979; match to protein family HMM TIGR01323; nitrile hydratase subunit alpha 1378242..1378856 Ruegeria pomeroyi DSS-3 3193903 YP_166558.1 CDS nthB NC_003911.11 1378853 1379527 D identified by similarity to SP:P97052; nitrile hydratase subunit beta 1378853..1379527 Ruegeria pomeroyi DSS-3 3195537 YP_166559.1 CDS SPO1316 NC_003911.11 1379524 1379856 D identified by similarity to GB:BAC49761.1; hypothetical protein 1379524..1379856 Ruegeria pomeroyi DSS-3 3194498 YP_166560.1 CDS SPO1317 NC_003911.11 1379867 1380100 R identified by similarity to PIR:H81075; hypothetical protein complement(1379867..1380100) Ruegeria pomeroyi DSS-3 3192887 YP_166561.1 CDS purA NC_003911.11 1380100 1381392 R catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase complement(1380100..1381392) Ruegeria pomeroyi DSS-3 3193892 YP_166562.1 CDS SPO1319 NC_003911.11 1381548 1381943 D hypothetical protein 1381548..1381943 Ruegeria pomeroyi DSS-3 3193961 YP_166563.1 CDS SPO1320 NC_003911.11 1382017 1384080 R lipoprotein complement(1382017..1384080) Ruegeria pomeroyi DSS-3 3193947 YP_166564.1 CDS SPO1321 NC_003911.11 1384220 1384912 D identified by match to protein family HMM PF04263; thiamine pyrophosphokinase 1384220..1384912 Ruegeria pomeroyi DSS-3 3192704 YP_166565.1 CDS SPO1322 NC_003911.11 1384857 1385771 R identified by match to protein family HMM PF00892; hypothetical protein complement(1384857..1385771) Ruegeria pomeroyi DSS-3 3193946 YP_166566.1 CDS sdaA NC_003911.11 1385906 1387279 R 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 complement(1385906..1387279) Ruegeria pomeroyi DSS-3 3193948 YP_166567.1 CDS SPO1324 NC_003911.11 1387281 1387982 R identified by match to protein family HMM PF02798; glutathione S-transferase complement(1387281..1387982) Ruegeria pomeroyi DSS-3 3193987 YP_166568.1 CDS SPO1325 NC_003911.11 1388090 1388536 R lipoprotein complement(1388090..1388536) Ruegeria pomeroyi DSS-3 3193716 YP_166569.1 CDS SPO1326 NC_003911.11 1388612 1389043 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1388612..1389043 Ruegeria pomeroyi DSS-3 3193949 YP_166570.1 CDS rpiA NC_003911.11 1389138 1389926 D Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway; ribose-5-phosphate isomerase A 1389138..1389926 Ruegeria pomeroyi DSS-3 3193647 YP_166571.1 CDS gor NC_003911.11 1390068 1391426 D identified by match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM TIGR01424; glutathione-disulfide reductase 1390068..1391426 Ruegeria pomeroyi DSS-3 3193528 YP_166572.1 CDS SPO1329 NC_003911.11 1391501 1392652 D identified by similarity to SP:P25662; match to protein family HMM PF01145; match to protein family HMM TIGR01933; HflK protein 1391501..1392652 Ruegeria pomeroyi DSS-3 3193619 YP_166573.1 CDS hflC NC_003911.11 1392652 1393527 D identified by match to protein family HMM PF01145; match to protein family HMM TIGR01932; HflC protein 1392652..1393527 Ruegeria pomeroyi DSS-3 3193971 YP_166574.1 CDS SPO1331 NC_003911.11 1393603 1394889 D hypothetical protein 1393603..1394889 Ruegeria pomeroyi DSS-3 3194009 YP_166575.1 CDS SPO1332 NC_003911.11 1394886 1395083 D identified by similarity to GB:BAB48824.1; hypothetical protein 1394886..1395083 Ruegeria pomeroyi DSS-3 3193426 YP_166576.1 CDS SPO1333 NC_003911.11 1395279 1396736 D identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037; serine protease 1395279..1396736 Ruegeria pomeroyi DSS-3 3194011 YP_166577.1 CDS SPO1334 NC_003911.11 1396733 1397173 D hypothetical protein 1396733..1397173 Ruegeria pomeroyi DSS-3 3193721 YP_166578.1 CDS SPO1335 NC_003911.11 1397382 1398050 R identified by match to protein family HMM PF00027; match to protein family HMM PF00325; Crp/Fnr family transcriptional regulator complement(1397382..1398050) Ruegeria pomeroyi DSS-3 3193756 YP_166579.1 CDS ispZ NC_003911.11 1398127 1398738 R identified by match to protein family HMM PF04279; intracellular septation protein A complement(1398127..1398738) Ruegeria pomeroyi DSS-3 3195515 YP_166580.1 CDS SPO1337 NC_003911.11 1398756 1399658 R identified by match to protein family HMM PF00892; hypothetical protein complement(1398756..1399658) Ruegeria pomeroyi DSS-3 3193439 YP_166581.1 CDS ftsY NC_003911.11 1400200 1401372 R 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 complement(1400200..1401372) Ruegeria pomeroyi DSS-3 3192959 YP_166582.1 CDS SPO1340 NC_003911.11 1401434 1402072 R hypothetical protein complement(1401434..1402072) Ruegeria pomeroyi DSS-3 3192917 YP_166583.1 CDS SPO1341 NC_003911.11 1402098 1403183 D identified by match to protein family HMM PF00487; alkane-1 monooxygenase 1402098..1403183 Ruegeria pomeroyi DSS-3 3194344 YP_166584.1 CDS SPO1342 NC_003911.11 1403217 1403609 D hypothetical protein 1403217..1403609 Ruegeria pomeroyi DSS-3 3193677 YP_166585.1 CDS SPO1343 NC_003911.11 1403684 1404325 R identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase complement(1403684..1404325) Ruegeria pomeroyi DSS-3 3192776 YP_166586.1 CDS xseA NC_003911.11 1404325 1405773 R bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides; exodeoxyribonuclease VII large subunit complement(1404325..1405773) Ruegeria pomeroyi DSS-3 3193062 YP_166587.1 CDS purD NC_003911.11 1405900 1407162 D catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase 1405900..1407162 Ruegeria pomeroyi DSS-3 3192964 YP_166588.1 CDS SPO1346 NC_003911.11 1407319 1407933 D identified by match to protein family HMM PF00196; match to protein family HMM TIGR00229; LuxR family transcriptional regulator 1407319..1407933 Ruegeria pomeroyi DSS-3 3192660 YP_166589.1 CDS SPO1347 NC_003911.11 1407941 1408873 R hypothetical protein complement(1407941..1408873) Ruegeria pomeroyi DSS-3 3193670 YP_166590.1 CDS SPO1348 NC_003911.11 1408873 1409196 R identified by match to protein family HMM PF00111; (Fe-S)-binding protein complement(1408873..1409196) Ruegeria pomeroyi DSS-3 3195755 YP_166591.1 CDS SPO1349 NC_003911.11 1409382 1409909 D lipoprotein 1409382..1409909 Ruegeria pomeroyi DSS-3 3193126 YP_166592.1 CDS SPO1350 NC_003911.11 1409922 1410035 R hypothetical protein complement(1409922..1410035) Ruegeria pomeroyi DSS-3 3193698 YP_166593.1 CDS metZ NC_003911.11 1410221 1411411 D identified by match to protein family HMM PF01053; match to protein family HMM TIGR01325; O-succinylhomoserine sulfhydrylase 1410221..1411411 Ruegeria pomeroyi DSS-3 3193007 YP_166594.1 CDS SPO1352 NC_003911.11 1411589 1412692 D 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 1411589..1412692 Ruegeria pomeroyi DSS-3 3193416 YP_166595.1 CDS trkH-1 NC_003911.11 1413474 1414922 D identified by similarity to GB:BAA31229.1; match to protein family HMM PF02386; Trk system potassium uptake protein TrkH 1413474..1414922 Ruegeria pomeroyi DSS-3 3192781 YP_166596.1 CDS SPO1354 NC_003911.11 1415023 1416942 R identified by match to protein family HMM PF01471; peptidoglycan binding domain-containing protein complement(1415023..1416942) Ruegeria pomeroyi DSS-3 3192792 YP_166597.1 CDS glyQ NC_003911.11 1416986 1417921 D 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 1416986..1417921 Ruegeria pomeroyi DSS-3 3194795 YP_166598.1 CDS SPO1356 NC_003911.11 1417947 1418633 D identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 1417947..1418633 Ruegeria pomeroyi DSS-3 3194785 YP_166599.1 CDS gltS NC_003911.11 1419209 1420420 D identified by similarity to SP:P19933; match to protein family HMM PF03616; match to protein family HMM TIGR00210; sodium/glutamate symporter 1419209..1420420 Ruegeria pomeroyi DSS-3 3192724 YP_166600.1 CDS glyS NC_003911.11 1420430 1422637 D 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 1420430..1422637 Ruegeria pomeroyi DSS-3 3194984 YP_166601.1 CDS ppdK NC_003911.11 1422758 1425382 D catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate phosphate dikinase 1422758..1425382 Ruegeria pomeroyi DSS-3 3193323 YP_166602.1 CDS SPO1360 NC_003911.11 1425556 1426200 D identified by similarity to SP:P50739; hypothetical protein 1425556..1426200 Ruegeria pomeroyi DSS-3 3193026 YP_166603.1 CDS SPO1361 NC_003911.11 1426278 1427654 D identified by match to protein family HMM PF00394; multicopper oxidase domain-containing protein 1426278..1427654 Ruegeria pomeroyi DSS-3 3193079 YP_166604.1 CDS SPO1362 NC_003911.11 1427754 1428674 D identified by match to protein family HMM TIGR00526; dihydroneopterin aldolase 1427754..1428674 Ruegeria pomeroyi DSS-3 3193448 YP_166605.1 CDS folP NC_003911.11 1428875 1429669 D identified by match to protein family HMM PF00809; match to protein family HMM TIGR01496; dihydropteroate synthase 1428875..1429669 Ruegeria pomeroyi DSS-3 3194284 YP_166606.1 CDS glmM NC_003911.11 1429708 1431054 D catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase 1429708..1431054 Ruegeria pomeroyi DSS-3 3195909 YP_166607.1 CDS SPO1365 NC_003911.11 1431592 1432512 R identified by match to protein family HMM PF00892; hypothetical protein complement(1431592..1432512) Ruegeria pomeroyi DSS-3 3193269 YP_166608.1 CDS ilvC NC_003911.11 1432639 1433661 R 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 complement(1432639..1433661) Ruegeria pomeroyi DSS-3 3193655 YP_166609.1 CDS SPO1367 NC_003911.11 1433793 1434248 D identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 1433793..1434248 Ruegeria pomeroyi DSS-3 3193388 YP_166610.1 CDS SPO1368 NC_003911.11 1434245 1434703 D identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator 1434245..1434703 Ruegeria pomeroyi DSS-3 3193664 YP_166611.1 CDS SPO1369 NC_003911.11 1434700 1435401 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(1434700..1435401) Ruegeria pomeroyi DSS-3 3193707 YP_166612.1 CDS SPO1370 NC_003911.11 1435912 1437039 D identified by match to protein family HMM PF00266; aminotransferase 1435912..1437039 Ruegeria pomeroyi DSS-3 3193653 YP_166613.1 CDS SPO1371 NC_003911.11 1437104 1438300 R identified by similarity to SP:P25534; match to protein family HMM PF01360; match to protein family HMM TIGR01988; 2-octaprenyl-6-methoxyphenyl hydroxylase complement(1437104..1438300) Ruegeria pomeroyi DSS-3 3193144 YP_166614.1 CDS SPO1372 NC_003911.11 1438378 1438626 R hypothetical protein complement(1438378..1438626) Ruegeria pomeroyi DSS-3 3193040 YP_166615.1 CDS SPO1373 NC_003911.11 1438825 1440393 D identified by similarity to GB:BAB81303.1; hypothetical protein 1438825..1440393 Ruegeria pomeroyi DSS-3 3192938 YP_166616.1 CDS SPO1374 NC_003911.11 1440400 1441044 R identified by match to protein family HMM PF00702; match to protein family HMM TIGR01509; match to protein family HMM TIGR01993; pyrimidine 5'-nucleotidase complement(1440400..1441044) Ruegeria pomeroyi DSS-3 3194368 YP_166617.1 CDS SPO1375 NC_003911.11 1441145 1441795 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1441145..1441795 Ruegeria pomeroyi DSS-3 3192851 YP_166618.1 CDS SPO1376 NC_003911.11 1441842 1443794 R identified by match to protein family HMM PF00535; match to protein family HMM PF05157; glycosyl transferase family protein complement(1441842..1443794) Ruegeria pomeroyi DSS-3 3193431 YP_166619.1 CDS carA NC_003911.11 1443878 1445044 R 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 complement(1443878..1445044) Ruegeria pomeroyi DSS-3 3193092 YP_166620.1 CDS SPO1378 NC_003911.11 1445233 1445712 D identified by match to protein family HMM PF02637; GatB/YqeY domain-containing protein 1445233..1445712 Ruegeria pomeroyi DSS-3 3192721 YP_166621.1 CDS SPO1379 NC_003911.11 1446295 1447089 R identified by match to protein family HMM PF02153; prephenate dehydrogenase complement(1446295..1447089) Ruegeria pomeroyi DSS-3 3193212 YP_166622.1 CDS SPO1380 NC_003911.11 1447210 1447707 R identified by similarity to GB:BAB50627.1; hypothetical protein complement(1447210..1447707) Ruegeria pomeroyi DSS-3 3193075 YP_166623.1 CDS SPO1381 NC_003911.11 1447722 1448198 R identified by similarity to PIR:E98182; hypothetical protein complement(1447722..1448198) Ruegeria pomeroyi DSS-3 3195114 YP_166624.1 CDS SPO1382 NC_003911.11 1448269 1449195 R hypothetical protein complement(1448269..1449195) Ruegeria pomeroyi DSS-3 3193704 YP_166625.1 CDS ctaD NC_003911.11 1449390 1451048 R identified by similarity to SP:P33517; match to protein family HMM PF00115; cytochrome c oxidase, aa3-type, subunit I complement(1449390..1451048) Ruegeria pomeroyi DSS-3 3192919 YP_166626.1 CDS SPO1384 NC_003911.11 1451287 1451748 R identified by match to protein family HMM PF01047; MarR family transcriptional regulator complement(1451287..1451748) Ruegeria pomeroyi DSS-3 3194561 YP_166627.1 CDS SPO1385 NC_003911.11 1451745 1452893 R identified by match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein complement(1451745..1452893) Ruegeria pomeroyi DSS-3 3194033 YP_166628.1 CDS SPO1386 NC_003911.11 1453104 1453526 D identified by match to protein family HMM PF01230; HIT family protein 1453104..1453526 Ruegeria pomeroyi DSS-3 3193526 YP_166629.1 CDS SPO1387 NC_003911.11 1453606 1454568 D identified by similarity to SP:P13512; match to protein family HMM PF01545; match to protein family HMM TIGR01297; cation efflux system protein 1453606..1454568 Ruegeria pomeroyi DSS-3 3192909 YP_166630.1 CDS SPO1388 NC_003911.11 1454801 1456573 D identified by similarity to GB:BAC51348.1; match to protein family HMM PF00196; match to protein family HMM PF00561; LuxR family transcriptional regulator 1454801..1456573 Ruegeria pomeroyi DSS-3 3193520 YP_166631.1 CDS lipB NC_003911.11 1456579 1457229 R 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 complement(1456579..1457229) Ruegeria pomeroyi DSS-3 3195079 YP_166632.1 CDS SPO1390 NC_003911.11 1457276 1457935 R identified by match to protein family HMM PF01323; thioredoxin complement(1457276..1457935) Ruegeria pomeroyi DSS-3 3193424 YP_166633.1 CDS SPO1392 NC_003911.11 1458355 1458801 R identified by match to protein family HMM PF02627; match to protein family HMM TIGR00778; alkylhydroperoxidase complement(1458355..1458801) Ruegeria pomeroyi DSS-3 3192953 YP_166634.1 CDS SPO1393 NC_003911.11 1458889 1459383 D identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738; Rrf2 family protein 1458889..1459383 Ruegeria pomeroyi DSS-3 3194989 YP_166635.1 CDS SPO1394 NC_003911.11 1459532 1461655 D identified by match to protein family HMM PF00144; match to protein family HMM PF00353; beta-lactamase 1459532..1461655 Ruegeria pomeroyi DSS-3 3193523 YP_166636.1 CDS SPO1395 NC_003911.11 1461711 1462940 D identified by match to protein family HMM PF00165; AraC family transcriptional regulator 1461711..1462940 Ruegeria pomeroyi DSS-3 3193084 YP_166637.1 CDS SPO1396 NC_003911.11 1462852 1464129 R identified by similarity to GB:AAK38164.1; transporter complement(1462852..1464129) Ruegeria pomeroyi DSS-3 3193516 YP_166638.1 CDS SPO1397 NC_003911.11 1464160 1467288 R identified by match to protein family HMM PF00873; match to protein family HMM TIGR00915; hydrophobe/amphiphile efflux-1 family protein complement(1464160..1467288) Ruegeria pomeroyi DSS-3 3193043 YP_166639.1 CDS SPO1398 NC_003911.11 1467292 1468551 R identified by match to protein family HMM PF00529; match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit complement(1467292..1468551) Ruegeria pomeroyi DSS-3 3193300 YP_166640.1 CDS SPO1399 NC_003911.11 1468642 1469613 D identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 1468642..1469613 Ruegeria pomeroyi DSS-3 3193694 YP_166641.1 CDS SPO1400 NC_003911.11 1469684 1470442 D identified by match to protein family HMM PF05853; hypothetical protein 1469684..1470442 Ruegeria pomeroyi DSS-3 3193317 YP_166642.1 CDS SPO1401 NC_003911.11 1470439 1471761 D identified by match to protein family HMM PF00202; hypothetical protein 1470439..1471761 Ruegeria pomeroyi DSS-3 3193648 YP_166643.1 CDS SPO1402 NC_003911.11 1471842 1472129 D hypothetical protein 1471842..1472129 Ruegeria pomeroyi DSS-3 3193633 YP_166644.1 CDS metG NC_003911.11 1472241 1473959 R 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 complement(1472241..1473959) Ruegeria pomeroyi DSS-3 3193132 YP_166645.1 CDS SPO1404 NC_003911.11 1474041 1475267 R identified by similarity to GB:BAB53930.1; hypothetical protein complement(1474041..1475267) Ruegeria pomeroyi DSS-3 3193534 YP_166646.1 CDS SPO1405 NC_003911.11 1475741 1477204 D identified by match to protein family HMM PF00264; tyrosinase domain-containing protein 1475741..1477204 Ruegeria pomeroyi DSS-3 3194620 YP_166647.1 CDS SPO1406 NC_003911.11 1477201 1478067 D hypothetical protein 1477201..1478067 Ruegeria pomeroyi DSS-3 3193446 YP_166648.1 CDS SPO1407 NC_003911.11 1478180 1478482 R identified by similarity to GB:BAD02216.1; hypothetical protein complement(1478180..1478482) Ruegeria pomeroyi DSS-3 3193443 YP_166649.1 CDS rluD NC_003911.11 1478481 1479509 D 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 1478481..1479509 Ruegeria pomeroyi DSS-3 3193242 YP_166650.1 CDS rpoH-2 NC_003911.11 1479660 1480556 D 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 1479660..1480556 Ruegeria pomeroyi DSS-3 3195142 YP_166651.1 CDS SPO1410 NC_003911.11 1480689 1481867 R identified by match to protein family HMM PF01244; renal dipeptidase complement(1480689..1481867) Ruegeria pomeroyi DSS-3 3195128 YP_166652.1 CDS SPO1411 NC_003911.11 1482007 1482276 D identified by match to protein family HMM PF01258; hypothetical protein 1482007..1482276 Ruegeria pomeroyi DSS-3 3193724 YP_166653.1 CDS SPO1412 NC_003911.11 1482323 1482505 D DNA modification methyltransferase domain-containing protein 1482323..1482505 Ruegeria pomeroyi DSS-3 3193196 YP_166654.1 CDS pepF NC_003911.11 1483569 1485389 R identified by match to protein family HMM PF01432; oligoendopeptidase F complement(1483569..1485389) Ruegeria pomeroyi DSS-3 3193066 YP_166655.1 CDS SPO1414 NC_003911.11 1485525 1486487 R identified by match to protein family HMM PF00561; alpha/beta hydrolase complement(1485525..1486487) Ruegeria pomeroyi DSS-3 3193148 YP_166656.1 CDS SPO1415 NC_003911.11 1486487 1486777 R identified by match to protein family HMM PF02036; sterol carrier family protein complement(1486487..1486777) Ruegeria pomeroyi DSS-3 3192760 YP_166657.1 CDS SPO1416 NC_003911.11 1486857 1487426 D identified by match to protein family HMM PF00515; hypothetical protein 1486857..1487426 Ruegeria pomeroyi DSS-3 3193065 YP_166658.1 CDS SPO1417 NC_003911.11 1487460 1490339 D identified by match to protein family HMM PF00271; helicase 1487460..1490339 Ruegeria pomeroyi DSS-3 3192722 YP_166659.1 CDS SPO1418 NC_003911.11 1490346 1490648 D identified by match to protein family HMM PF01479; S4 domain-containing protein 1490346..1490648 Ruegeria pomeroyi DSS-3 3192801 YP_166660.1 CDS SPO1419 NC_003911.11 1490784 1491122 D identified by match to protein family HMM PF00037; (Fe-S)-binding protein 1490784..1491122 Ruegeria pomeroyi DSS-3 3192740 YP_166661.1 CDS SPO1420 NC_003911.11 1491414 1491923 D identified by match to protein family HMM PF02559; CarD family transcriptional regulator 1491414..1491923 Ruegeria pomeroyi DSS-3 3192823 YP_166662.1 CDS SPO1421 NC_003911.11 1492040 1492813 D identified by match to protein family HMM PF00520; cation channel family protein 1492040..1492813 Ruegeria pomeroyi DSS-3 3192796 YP_166663.1 CDS SPO1422 NC_003911.11 1492825 1493589 R identified by match to protein family HMM PF02654; match to protein family HMM TIGR00317; cobalamin 5'-phosphate synthase complement(1492825..1493589) Ruegeria pomeroyi DSS-3 3193304 YP_166664.1 CDS cobT NC_003911.11 1493668 1494678 D catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 1493668..1494678 Ruegeria pomeroyi DSS-3 3195790 YP_166665.1 CDS SPO1424 NC_003911.11 1494719 1496599 R identified by similarity to SP:P03819; match to protein family HMM PF02254; match to protein family HMM TIGR00932; glutathione-regulated potassium-efflux system protein complement(1494719..1496599) Ruegeria pomeroyi DSS-3 3193373 YP_166666.1 CDS SPO1425 NC_003911.11 1496619 1497074 R identified by match to protein family HMM PF01037; AsnC family transcriptional regulator complement(1496619..1497074) Ruegeria pomeroyi DSS-3 3194790 YP_166667.1 CDS hppD NC_003911.11 1497219 1498319 D identified by similarity to SP:P80064; match to protein family HMM PF00903; match to protein family HMM TIGR01263; 4-hydroxyphenylpyruvate dioxygenase 1497219..1498319 Ruegeria pomeroyi DSS-3 3193684 YP_166668.1 CDS SPO1427 NC_003911.11 1498437 1500689 R hypothetical protein complement(1498437..1500689) Ruegeria pomeroyi DSS-3 3195589 YP_166669.1 CDS SPO1428 NC_003911.11 1499940 1500860 D hypothetical protein 1499940..1500860 Ruegeria pomeroyi DSS-3 3193489 YP_166670.1 CDS omp28 NC_003911.11 1500857 1501555 D identified by similarity to SP:Q57099; match to protein family HMM PF04402; outer membrane protein, 28Kda 1500857..1501555 Ruegeria pomeroyi DSS-3 3194723 YP_166671.1 CDS SPO1430 NC_003911.11 1501651 1502868 D identified by similarity to GB:AAB84282.1; antibiotic efflux protein 1501651..1502868 Ruegeria pomeroyi DSS-3 3195017 YP_166672.1 CDS SPO1431 NC_003911.11 1502903 1504195 R identified by similarity to GB:BAB68505.1; match to protein family HMM PF01053; match to protein family HMM TIGR01326; O-acetylhomoserine aminocarboxypropyltransferase complement(1502903..1504195) Ruegeria pomeroyi DSS-3 3193072 YP_166673.1 CDS SPO1432 NC_003911.11 1504401 1504799 R identified by match to protein family HMM PF00581; rhodanese domain-containing protein complement(1504401..1504799) Ruegeria pomeroyi DSS-3 3192727 YP_166674.1 CDS SPO1433 NC_003911.11 1504914 1505960 D identified by match to protein family HMM PF00248; aldo/keto reductase 1504914..1505960 Ruegeria pomeroyi DSS-3 3194752 YP_166675.1 CDS SPO1434 NC_003911.11 1506043 1507032 R identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator complement(1506043..1507032) Ruegeria pomeroyi DSS-3 3195356 YP_166676.1 CDS SPO1435 NC_003911.11 1507175 1508080 D identified by match to protein family HMM PF05853; hypothetical protein 1507175..1508080 Ruegeria pomeroyi DSS-3 3194678 YP_166677.1 CDS SPO1436 NC_003911.11 1508173 1509636 D Converts (S)-3-hydroxyacyl-CoA to 3-oxyacyl-CoA; may also act as a thioesterase; bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase 1508173..1509636 Ruegeria pomeroyi DSS-3 3193457 YP_166678.1 CDS fabG NC_003911.11 1509633 1510394 D Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 1509633..1510394 Ruegeria pomeroyi DSS-3 3193485 YP_166679.1 CDS SPO1438 NC_003911.11 1510501 1510770 R identified by similarity to GB:BAC50099.1; hypothetical protein complement(1510501..1510770) Ruegeria pomeroyi DSS-3 3195373 YP_166680.1 CDS SPO1439 NC_003911.11 1510771 1511622 R identified by match to protein family HMM PF01381; DNA binding protein complement(1510771..1511622) Ruegeria pomeroyi DSS-3 3194906 YP_166681.1 CDS SPO1440 NC_003911.11 1511739 1511942 D identified by similarity to PIR:E84256; hypothetical protein 1511739..1511942 Ruegeria pomeroyi DSS-3 3193463 YP_166682.1 CDS SPO1441 NC_003911.11 1511935 1512837 D identified by match to protein family HMM PF00487; fatty acid desaturase 1511935..1512837 Ruegeria pomeroyi DSS-3 3194121 YP_166683.1 CDS SPO1442 NC_003911.11 1512858 1513760 D identified by match to protein family HMM PF00892; hypothetical protein 1512858..1513760 Ruegeria pomeroyi DSS-3 3193660 YP_166684.1 CDS rhlE NC_003911.11 1513975 1515390 R identified by similarity to SP:P25888; match to protein family HMM PF00270; match to protein family HMM PF00271; ATP-dependent RNA helicase RhlE complement(1513975..1515390) Ruegeria pomeroyi DSS-3 3193638 YP_166685.1 CDS SPO1444 NC_003911.11 1515581 1516549 R hypothetical protein complement(1515581..1516549) Ruegeria pomeroyi DSS-3 3194035 YP_166686.1 CDS SPO1445 NC_003911.11 1516571 1517293 R identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase complement(1516571..1517293) Ruegeria pomeroyi DSS-3 3193229 YP_166687.1 CDS SPO1446 NC_003911.11 1517290 1518066 R identified by match to protein family HMM PF04199; cyclase complement(1517290..1518066) Ruegeria pomeroyi DSS-3 3193476 YP_166688.1 CDS SPO1447 NC_003911.11 1518063 1519358 R identified by match to protein family HMM PF00106; match to protein family HMM PF01796; short chain dehydrogenase/reductase oxidoreductase complement(1518063..1519358) Ruegeria pomeroyi DSS-3 3193167 YP_166689.1 CDS SPO1448 NC_003911.11 1519316 1520494 R identified by similarity to GB:BAC48694.1; hypothetical protein complement(1519316..1520494) Ruegeria pomeroyi DSS-3 3193455 YP_166690.1 CDS SPO1449 NC_003911.11 1520491 1522140 R identified by match to protein family HMM PF00501; AMP-binding protein complement(1520491..1522140) Ruegeria pomeroyi DSS-3 3192939 YP_166691.1 CDS SPO1450 NC_003911.11 1522101 1522577 R identified by match to protein family HMM PF00866; aromatic 1,2-dioxygenase subunit beta complement(1522101..1522577) Ruegeria pomeroyi DSS-3 3194761 YP_166692.1 CDS SPO1451 NC_003911.11 1522595 1523920 R identified by match to protein family HMM PF00355; match to protein family HMM PF00848; aromatic 1,2-dioxygenase subunit alpha complement(1522595..1523920) Ruegeria pomeroyi DSS-3 3192871 YP_166693.1 CDS SPO1452 NC_003911.11 1523932 1524858 R identified by match to protein family HMM PF00111; match to protein family HMM PF00175; oxidoreductase complement(1523932..1524858) Ruegeria pomeroyi DSS-3 3193179 YP_166694.1 CDS SPO1453 NC_003911.11 1524926 1525384 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1524926..1525384 Ruegeria pomeroyi DSS-3 3192646 YP_166695.1 CDS SPO1454 NC_003911.11 1525447 1526514 D identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 1525447..1526514 Ruegeria pomeroyi DSS-3 3195742 YP_166696.1 CDS SPO1455 NC_003911.11 1526568 1527065 D TRAP dicarboxylate transporter subunit DctQ 1526568..1527065 Ruegeria pomeroyi DSS-3 3193986 YP_166697.1 CDS SPO1456 NC_003911.11 1527062 1528375 D identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP C4-dicarboxylate transport system permease DctM 1527062..1528375 Ruegeria pomeroyi DSS-3 3193613 YP_166698.1 CDS SPO1457 NC_003911.11 1528378 1528809 R identified by match to protein family HMM PF03061; thioesterase complement(1528378..1528809) Ruegeria pomeroyi DSS-3 3195591 YP_166699.1 CDS SPO1458 NC_003911.11 1528988 1529467 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 1528988..1529467 Ruegeria pomeroyi DSS-3 3193389 YP_166700.1 CDS SPO1459 NC_003911.11 1529475 1531622 D identified by similarity to SP:O07835; match to protein family HMM PF02775; indolepyruvate oxidoreductase, IorA subunit 1529475..1531622 Ruegeria pomeroyi DSS-3 3192907 YP_166701.1 CDS SPO1460 NC_003911.11 1531619 1533172 D 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 1531619..1533172 Ruegeria pomeroyi DSS-3 3193712 YP_166702.1 CDS SPO1461 NC_003911.11 1533243 1534046 D identified by similarity to GB:BAC48692.1; hypothetical protein 1533243..1534046 Ruegeria pomeroyi DSS-3 3193221 YP_166703.1 CDS SPO1462 NC_003911.11 1534089 1535336 D identified by match to protein family HMM PF00691; OmpA family protein 1534089..1535336 Ruegeria pomeroyi DSS-3 3193387 YP_166704.1 CDS SPO1463 NC_003911.11 1535349 1536686 R identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM complement(1535349..1536686) Ruegeria pomeroyi DSS-3 3195607 YP_166705.1 CDS SPO1464 NC_003911.11 1536714 1537217 R TRAP dicarboxylate transporter subunit DctQ complement(1536714..1537217) Ruegeria pomeroyi DSS-3 3193586 YP_166706.1 CDS SPO1465 NC_003911.11 1537282 1538310 R identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP complement(1537282..1538310) Ruegeria pomeroyi DSS-3 3193271 YP_166707.1 CDS SPO1466 NC_003911.11 1538519 1539598 D identified by similarity to SP:Q44297; opine dehydrogenase 1538519..1539598 Ruegeria pomeroyi DSS-3 3193032 YP_166708.1 CDS SPO1467 NC_003911.11 1539600 1540583 D converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase 1539600..1540583 Ruegeria pomeroyi DSS-3 3193135 YP_166709.1 CDS SPO1468 NC_003911.11 1540668 1541756 R identified by match to protein family HMM PF00155; aminotransferase complement(1540668..1541756) Ruegeria pomeroyi DSS-3 3193376 YP_166710.1 CDS SPO1469 NC_003911.11 1541807 1543195 R identified by similarity to GB:AAF19054.1; match to protein family HMM PF00890; 3-ketosteroid dehydrogenase complement(1541807..1543195) Ruegeria pomeroyi DSS-3 3194803 YP_166711.1 CDS SPO1470 NC_003911.11 1543179 1544042 R identified by similarity to SP:Q56062; isocitrate lyase complement(1543179..1544042) Ruegeria pomeroyi DSS-3 3195000 YP_166712.1 CDS SPO1471 NC_003911.11 1544039 1544659 R identified by match to protein family HMM PF00857; isochorismatase complement(1544039..1544659) Ruegeria pomeroyi DSS-3 3195693 YP_166713.1 CDS hyuA NC_003911.11 1544656 1546722 R identified by similarity to SP:Q01262; match to protein family HMM PF01968; match to protein family HMM PF05378; hydantoin utilization protein A complement(1544656..1546722) Ruegeria pomeroyi DSS-3 3194486 YP_166714.1 CDS SPO1473 NC_003911.11 1546719 1548413 R identified by similarity to SP:Q01263; match to protein family HMM PF02538; hydantoin utilization protein B complement(1546719..1548413) Ruegeria pomeroyi DSS-3 3192767 YP_166715.1 CDS SPO1474 NC_003911.11 1548410 1548976 R tautomerase complement(1548410..1548976) Ruegeria pomeroyi DSS-3 3193108 YP_166716.1 CDS SPO1475 NC_003911.11 1549109 1549888 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1549109..1549888 Ruegeria pomeroyi DSS-3 3195561 YP_166717.1 CDS leuC-2 NC_003911.11 1549934 1551292 D dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 1549934..1551292 Ruegeria pomeroyi DSS-3 3192795 YP_166718.1 CDS leuD-2 NC_003911.11 1551292 1551903 D identified by similarity to SP:P30126; match to protein family HMM PF00694; match to protein family HMM TIGR00171; 3-isopropylmalate dehydratase small subunit 1551292..1551903 Ruegeria pomeroyi DSS-3 3193666 YP_166719.1 CDS SPO1478 NC_003911.11 1552129 1552764 D 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 1552129..1552764 Ruegeria pomeroyi DSS-3 3192773 YP_166720.1 CDS SPO1479 NC_003911.11 1552761 1553396 D identified by similarity to SP:P40685; transcriptional activator 1552761..1553396 Ruegeria pomeroyi DSS-3 3192763 YP_166721.1 CDS SPO1480 NC_003911.11 1553536 1554261 R identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase complement(1553536..1554261) Ruegeria pomeroyi DSS-3 3192762 YP_166722.1 CDS SPO1481 NC_003911.11 1554258 1555130 R identified by similarity to GB:AAQ64061.1; hypothetical protein complement(1554258..1555130) Ruegeria pomeroyi DSS-3 3194384 YP_166723.1 CDS SPO1482 NC_003911.11 1555154 1556497 D identified by similarity to PIR:F97597; hypothetical protein 1555154..1556497 Ruegeria pomeroyi DSS-3 3195829 YP_166724.1 CDS SPO1483 NC_003911.11 1556436 1557593 D identified by similarity to SP:P30010; match to protein family HMM PF02353; cyclopropane-fatty-acyl-phospholipid synthase 1556436..1557593 Ruegeria pomeroyi DSS-3 3193601 YP_166725.1 CDS SPO1484 NC_003911.11 1557586 1558080 D identified by similarity to GB:AAO56021.1; hypothetical protein 1557586..1558080 Ruegeria pomeroyi DSS-3 3195081 YP_166726.1 CDS SPO1485 NC_003911.11 1558077 1559306 D identified by similarity to SP:P96792; sodium:galactoside symporter family protein 1558077..1559306 Ruegeria pomeroyi DSS-3 3192937 YP_166727.1 CDS SPO1486 NC_003911.11 1559303 1559863 D identified by similarity to GB:AAN56374.1; hypothetical protein 1559303..1559863 Ruegeria pomeroyi DSS-3 3195706 YP_166728.1 CDS SPO1487 NC_003911.11 1559898 1560632 D hypothetical protein 1559898..1560632 Ruegeria pomeroyi DSS-3 3192691 YP_166729.1 CDS SPO1488 NC_003911.11 1560881 1561597 D identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 1560881..1561597 Ruegeria pomeroyi DSS-3 3193437 YP_166730.1 CDS SPO1489 NC_003911.11 1561657 1563036 D catalyzes the formation of indole-3-acetic acid from indole-3-acetamide; indole acetimide hydrolase 1561657..1563036 Ruegeria pomeroyi DSS-3 3194684 YP_166731.1 CDS SPO1490 NC_003911.11 1563063 1564214 D identified by similarity to GB:BAA11039.1; regulatory protein 1563063..1564214 Ruegeria pomeroyi DSS-3 3192765 YP_166732.1 CDS SPO1491 NC_003911.11 1564225 1565073 D identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1564225..1565073 Ruegeria pomeroyi DSS-3 3192820 YP_166733.1 CDS SPO1492 NC_003911.11 1565048 1566796 D identified by match to protein family HMM PF00005; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease/ATP-binding protein 1565048..1566796 Ruegeria pomeroyi DSS-3 3192679 YP_166734.1 CDS SPO1493 NC_003911.11 1566793 1567476 D 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 1566793..1567476 Ruegeria pomeroyi DSS-3 3194547 YP_166735.1 CDS SPO1494 NC_003911.11 1567665 1569029 D 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 1567665..1569029 Ruegeria pomeroyi DSS-3 3193598 YP_166736.1 CDS SPO1495 NC_003911.11 1569268 1569975 D identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 1569268..1569975 Ruegeria pomeroyi DSS-3 3195004 YP_166737.1 CDS SPO1496 NC_003911.11 1569983 1572346 D identified by match to protein family HMM PF02687; ABC transporter permease 1569983..1572346 Ruegeria pomeroyi DSS-3 3193089 YP_166738.1 CDS SPO1497 NC_003911.11 1572343 1573593 D identified by match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 1572343..1573593 Ruegeria pomeroyi DSS-3 3192753 YP_166739.1 CDS SPO1498 NC_003911.11 1573629 1575137 R 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 complement(1573629..1575137) Ruegeria pomeroyi DSS-3 3195115 YP_166740.1 CDS SPO1499 NC_003911.11 1575373 1576266 D identified by match to protein family HMM PF00561; alpha/beta hydrolase 1575373..1576266 Ruegeria pomeroyi DSS-3 3192676 YP_166741.1 CDS pqqE NC_003911.11 1576263 1577387 R identified by similarity to SP:P27507; match to protein family HMM PF04055; match to protein family HMM TIGR02109; pyrroloquinoline quinone biosynthesis protein PqqE complement(1576263..1577387) Ruegeria pomeroyi DSS-3 3195721 YP_166742.1 CDS pqqD NC_003911.11 1577452 1577739 R identified by similarity to SP:P27506; match to protein family HMM PF05402; coenzyme PQQ synthesis protein D complement(1577452..1577739) Ruegeria pomeroyi DSS-3 3193984 YP_166743.1 CDS pqqC NC_003911.11 1577736 1578461 R Required in the synthesis of PPQ, but its exact function is unknown; pyrroloquinoline quinone biosynthesis protein PqqC complement(1577736..1578461) Ruegeria pomeroyi DSS-3 3194751 YP_166744.1 CDS pqqB NC_003911.11 1578458 1579345 R possibly involved in transport of pyrroloquinoline quinone transport; pyrroloquinoline quinone biosynthesis protein PqqB complement(1578458..1579345) Ruegeria pomeroyi DSS-3 3192929 YP_166745.1 CDS pqqA NC_003911.11 1579373 1579480 R identified by match to protein family HMM TIGR02107; coenzyme PQQ biosynthesis protein A complement(1579373..1579480) Ruegeria pomeroyi DSS-3 3193989 YP_166746.1 CDS SPO1505 NC_003911.11 1579566 1581779 R 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 complement(1579566..1581779) Ruegeria pomeroyi DSS-3 3194858 YP_166747.1 CDS SPO1506 NC_003911.11 1581786 1582955 R identified by similarity to GB:AAL30776.1; GfdT protein complement(1581786..1582955) Ruegeria pomeroyi DSS-3 3195065 YP_166748.1 CDS SPO1507 NC_003911.11 1582986 1583690 R identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator complement(1582986..1583690) Ruegeria pomeroyi DSS-3 3193082 YP_166749.1 CDS SPO1508 NC_003911.11 1583913 1585733 R identified by similarity to SP:Q9Z4J7; match to protein family HMM PF01011; quinoprotein ethanol dehydrogenase complement(1583913..1585733) Ruegeria pomeroyi DSS-3 3193500 YP_166750.1 CDS SPO1509 NC_003911.11 1585981 1586388 R identified by match to protein family HMM PF00034; cytochrome c family protein complement(1585981..1586388) Ruegeria pomeroyi DSS-3 3193361 YP_166751.1 CDS SPO1510 NC_003911.11 1586503 1587294 R identified by match to protein family HMM PF01061; ABC transporter permease complement(1586503..1587294) Ruegeria pomeroyi DSS-3 3193955 YP_166752.1 CDS SPO1511 NC_003911.11 1587291 1588022 R identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein complement(1587291..1588022) Ruegeria pomeroyi DSS-3 3192674 YP_166753.1 CDS SPO1512 NC_003911.11 1588019 1588465 R identified by similarity to PIR:D95864; hypothetical protein complement(1588019..1588465) Ruegeria pomeroyi DSS-3 3193981 YP_166754.1 CDS SPO1513 NC_003911.11 1588479 1589435 R identified by similarity to GB:AAM77056.1; hypothetical protein complement(1588479..1589435) Ruegeria pomeroyi DSS-3 3193418 YP_166755.1 CDS SPO1514 NC_003911.11 1589441 1590622 R identified by similarity to PIR:B95864; hypothetical protein complement(1589441..1590622) Ruegeria pomeroyi DSS-3 3193537 YP_166756.1 CDS SPO1515 NC_003911.11 1590779 1591453 D identified by similarity to GB:AAC79658.1; cytochrome c550 1590779..1591453 Ruegeria pomeroyi DSS-3 3194727 YP_166757.1 CDS SPO1516 NC_003911.11 1591450 1592364 D amino acid ABC transporter substrate-binding protein 1591450..1592364 Ruegeria pomeroyi DSS-3 3193614 YP_166758.1 CDS coxG NC_003911.11 1592481 1593005 D identified by similarity to GB:CAB76249.1; match to protein family HMM PF06240; carbon monoxide dehydrogenase operon G protein 1592481..1593005 Ruegeria pomeroyi DSS-3 3193185 YP_166759.1 CDS coxS-1 NC_003911.11 1593042 1593527 D identified by similarity to SP:P19921; match to protein family HMM PF00111; match to protein family HMM PF01799; carbon-monoxide dehydrogenase, small subunit 1593042..1593527 Ruegeria pomeroyi DSS-3 3193851 YP_166760.1 CDS coxL-1 NC_003911.11 1593624 1595990 D identified by similarity to SP:P19913; match to protein family HMM PF01315; match to protein family HMM PF02738; carbon monoxide dehydrogenase, large subunit 1593624..1595990 Ruegeria pomeroyi DSS-3 3193481 YP_166761.1 CDS SPO1520 NC_003911.11 1596090 1596872 D identified by similarity to SP:P19920; match to protein family HMM PF00941; carbon monoxide dehydrogenase, medium subunit 1596090..1596872 Ruegeria pomeroyi DSS-3 3195391 YP_166762.1 CDS SPO1521 NC_003911.11 1596963 1599032 R identified by similarity to SP:Q00790; regulatory protein complement(1596963..1599032) Ruegeria pomeroyi DSS-3 3193080 YP_166763.1 CDS SPO1522 NC_003911.11 1599214 1599801 D identified by similarity to GB:BAC51459.1; hypothetical protein 1599214..1599801 Ruegeria pomeroyi DSS-3 3195687 YP_166764.1 CDS SPO1523 NC_003911.11 1599809 1600765 R identified by match to protein family HMM PF00753; match to protein family HMM TIGR01409; metallo-beta-lactamase complement(1599809..1600765) Ruegeria pomeroyi DSS-3 3192986 YP_166765.1 CDS SPO1524 NC_003911.11 1600765 1601547 R identified by similarity to GB:AAN68285.1; hypothetical protein complement(1600765..1601547) Ruegeria pomeroyi DSS-3 3192789 YP_166766.1 CDS SPO1525 NC_003911.11 1601623 1604829 R identified by match to protein family HMM PF00873; AcrB/AcrD/AcrF family transporter complement(1601623..1604829) Ruegeria pomeroyi DSS-3 3195090 YP_166767.1 CDS SPO1526 NC_003911.11 1604822 1605802 R identified by similarity to SP:P75830; match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit complement(1604822..1605802) Ruegeria pomeroyi DSS-3 3193490 YP_166768.1 CDS SPO1527 NC_003911.11 1605949 1606545 R identified by similarity to GB:CAF18626.1; hypothetical protein complement(1605949..1606545) Ruegeria pomeroyi DSS-3 3193219 YP_166769.1 CDS SPO1528 NC_003911.11 1606542 1608782 R identified by similarity to GB:AAQ00309.1; hypothetical protein complement(1606542..1608782) Ruegeria pomeroyi DSS-3 3193688 YP_166770.1 CDS SPO1529 NC_003911.11 1608788 1609501 R identified by similarity to GB:BAC14468.1; hypothetical protein complement(1608788..1609501) Ruegeria pomeroyi DSS-3 3193414 YP_166771.1 CDS SPO1530 NC_003911.11 1609667 1611196 R integral membrane protein MviN complement(1609667..1611196) Ruegeria pomeroyi DSS-3 3193864 YP_166772.1 CDS SPO1531 NC_003911.11 1611310 1612476 D identified by similarity to GB:BAC73064.1; hypothetical protein 1611310..1612476 Ruegeria pomeroyi DSS-3 3193060 YP_166773.1 CDS SPO1532 NC_003911.11 1613519 1614226 R hypothetical protein complement(1613519..1614226) Ruegeria pomeroyi DSS-3 3193644 YP_166774.1 CDS SPO1533 NC_003911.11 1614257 1615399 R identified by match to protein family HMM PF00534; glycoside hydrolase complement(1614257..1615399) Ruegeria pomeroyi DSS-3 3194817 YP_166775.1 CDS SPO1534 NC_003911.11 1615633 1616832 D identified by match to protein family HMM PF02397; sugar transferase 1615633..1616832 Ruegeria pomeroyi DSS-3 3193330 YP_166776.1 CDS SPO1535 NC_003911.11 1616839 1618122 D identified by match to protein family HMM PF01522; polysaccharide deacetylase 1616839..1618122 Ruegeria pomeroyi DSS-3 3193462 YP_166777.1 CDS SPO1536 NC_003911.11 1618119 1619354 D identified by match to protein family HMM PF00534; group 1 family glycosyltransferase 1618119..1619354 Ruegeria pomeroyi DSS-3 3192728 YP_166778.1 CDS SPO1537 NC_003911.11 1619351 1620322 D identified by match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1619351..1620322 Ruegeria pomeroyi DSS-3 3193358 YP_166779.1 CDS SPO1538 NC_003911.11 1620325 1622094 D identified by match to protein family HMM PF02706; chain length determinant protein 1620325..1622094 Ruegeria pomeroyi DSS-3 3193413 YP_166780.1 CDS SPO1539 NC_003911.11 1622091 1623488 D identified by match to protein family HMM PF04932; O-antigen polymerase 1622091..1623488 Ruegeria pomeroyi DSS-3 3193345 YP_166781.1 CDS SPO1540 NC_003911.11 1623485 1624627 D identified by match to protein family HMM PF00535; glycosyl transferase family protein 1623485..1624627 Ruegeria pomeroyi DSS-3 3192699 YP_166782.1 CDS SPO1541 NC_003911.11 1624752 1625663 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(1624752..1625663) Ruegeria pomeroyi DSS-3 3192693 YP_166783.1 CDS SPO1542 NC_003911.11 1625777 1626835 D identified by match to protein family HMM PF01244; renal dipeptidase 1625777..1626835 Ruegeria pomeroyi DSS-3 3195063 YP_166784.1 CDS SPO1543 NC_003911.11 1626885 1628489 D identified by match to protein family HMM PF00496; peptide/opine/nickel uptake ABC transporter substrate-binding protein 1626885..1628489 Ruegeria pomeroyi DSS-3 3193888 YP_166785.1 CDS SPO1544 NC_003911.11 1628490 1629548 D identified by similarity to SP:P37316; match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease 1628490..1629548 Ruegeria pomeroyi DSS-3 3192711 YP_166786.1 CDS SPO1545 NC_003911.11 1629545 1630459 D identified by similarity to SP:P37315; match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease 1629545..1630459 Ruegeria pomeroyi DSS-3 3192782 YP_166787.1 CDS SPO1546 NC_003911.11 1630456 1631310 D identified by similarity to SP:P24136; match to protein family HMM PF00005; peptide/opine/nickel uptake ABC transporter ATP-binding protein 1630456..1631310 Ruegeria pomeroyi DSS-3 3194487 YP_166788.1 CDS SPO1547 NC_003911.11 1631307 1632071 D identified by match to protein family HMM PF00005; peptide/opine/nickel uptake ABC transporter ATP-binding protein 1631307..1632071 Ruegeria pomeroyi DSS-3 3192874 YP_166789.1 CDS SPO1548 NC_003911.11 1632385 1633386 D identified by match to protein family HMM PF04069; glycine betaine/proline ABC transporter substrate-binding protein 1632385..1633386 Ruegeria pomeroyi DSS-3 3193272 YP_166790.1 CDS SPO1549 NC_003911.11 1633461 1634483 D identified by similarity to SP:P46920; match to protein family HMM PF00005; glycine betaine/proline ABC transporter ATP-binding protein 1633461..1634483 Ruegeria pomeroyi DSS-3 3193478 YP_166791.1 CDS SPO1550 NC_003911.11 1634483 1636459 D identified by similarity to SP:P46921; match to protein family HMM PF00528; glycine betaine/proline ABC transporter permease 1634483..1636459 Ruegeria pomeroyi DSS-3 3193160 YP_166792.1 CDS SPO1551 NC_003911.11 1636630 1637982 R identified by similarity to PIR:JC7986; flavin-containing monooxygenase complement(1636630..1637982) Ruegeria pomeroyi DSS-3 3193211 YP_166793.1 CDS SPO1552 NC_003911.11 1638115 1639449 D ABC transporter substrate-binding protein 1638115..1639449 Ruegeria pomeroyi DSS-3 3192999 YP_166794.1 CDS SPO1553 NC_003911.11 1639494 1640213 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(1639494..1640213) Ruegeria pomeroyi DSS-3 3193827 YP_166795.1 CDS SPO1554 NC_003911.11 1640347 1642062 R identified by match to protein family HMM PF00909; ammonium transporter complement(1640347..1642062) Ruegeria pomeroyi DSS-3 3195092 YP_166796.1 CDS SPO1555 NC_003911.11 1642162 1643844 D identified by similarity to GB:AAN03798.1; match to protein family HMM PF01257; match to protein family HMM PF01512; formate dehydrogenase subunit beta 1642162..1643844 Ruegeria pomeroyi DSS-3 3194780 YP_166797.1 CDS SPO1556 NC_003911.11 1643846 1646626 D 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 1643846..1646626 Ruegeria pomeroyi DSS-3 3193002 YP_166798.1 CDS fhs-1 NC_003911.11 1646655 1648331 D catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase 1646655..1648331 Ruegeria pomeroyi DSS-3 3194762 YP_166799.1 CDS SPO1558 NC_003911.11 1648391 1648696 D identified by match to protein family HMM PF01817; match to protein family HMM TIGR01803; chorismate mutase 1648391..1648696 Ruegeria pomeroyi DSS-3 3193429 YP_166800.1 CDS SPO1559 NC_003911.11 1648760 1649650 D 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 1648760..1649650 Ruegeria pomeroyi DSS-3 3194901 YP_166801.1 CDS folD NC_003911.11 1649647 1650525 D identified by match to protein family HMM PF00763; match to protein family HMM PF02882; folD bifunctional protein 1649647..1650525 Ruegeria pomeroyi DSS-3 3193492 YP_166802.1 CDS SPO1561 NC_003911.11 1650542 1651387 R identified by match to protein family HMM PF00892; hypothetical protein complement(1650542..1651387) Ruegeria pomeroyi DSS-3 3193188 YP_166803.1 CDS SPO1562 NC_003911.11 1652735 1653880 D identified by match to protein family HMM PF01571; glycine cleavage system T protein 1652735..1653880 Ruegeria pomeroyi DSS-3 3192949 YP_166804.1 CDS SPO1563 NC_003911.11 1653926 1654378 D identified by match to protein family HMM PF01152; hypothetical protein 1653926..1654378 Ruegeria pomeroyi DSS-3 3193408 YP_166805.1 CDS SPO1564 NC_003911.11 1654384 1655658 R identified by match to protein family HMM PF05161; MOFRL domain-containing protein complement(1654384..1655658) Ruegeria pomeroyi DSS-3 3192931 YP_166806.1 CDS SPO1565 NC_003911.11 1655645 1656622 R identified by similarity to SP:O53078; citrate lyase complement(1655645..1656622) Ruegeria pomeroyi DSS-3 3193772 YP_166807.1 CDS SPO1566 NC_003911.11 1656751 1657365 R identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator complement(1656751..1657365) Ruegeria pomeroyi DSS-3 3193657 YP_166808.1 CDS SPO1567 NC_003911.11 1657594 1658841 D aminotransferase 1657594..1658841 Ruegeria pomeroyi DSS-3 3192808 YP_166809.1 CDS sucC NC_003911.11 1658883 1660082 D catalyzes the formation of malyl-CoA from malate and CoA; malate--CoA ligase subunit beta 1658883..1660082 Ruegeria pomeroyi DSS-3 3193005 YP_166810.1 CDS SPO1569 NC_003911.11 1660079 1660969 D Catalyzes the only substrate-level phosphorylation in the TCA cycle; succinyl-CoA synthetase subunit alpha 1660079..1660969 Ruegeria pomeroyi DSS-3 3193138 YP_166811.1 CDS SPO1570 NC_003911.11 1660969 1661961 D Involved in the metabolism of aromatic amino acids; 2-hydroxyacid dehydrogenase 1660969..1661961 Ruegeria pomeroyi DSS-3 3192973 YP_166812.1 CDS ppc NC_003911.11 1661961 1664600 D identified by match to protein family HMM PF00311; phosphoenolpyruvate carboxylase 1661961..1664600 Ruegeria pomeroyi DSS-3 3192821 YP_166813.1 CDS glyA NC_003911.11 1664626 1665921 D catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 1664626..1665921 Ruegeria pomeroyi DSS-3 3194742 YP_166814.1 CDS glnT NC_003911.11 1665986 1667314 R identified by similarity to SP:P31592; match to protein family HMM PF00120; match to protein family HMM PF03951; glutamine synthetase complement(1665986..1667314) Ruegeria pomeroyi DSS-3 3192810 YP_166815.1 CDS SPO1574 NC_003911.11 1667388 1668740 R identified by match to protein family HMM PF01645; glutamate synthase complement(1667388..1668740) Ruegeria pomeroyi DSS-3 3193151 YP_166816.1 CDS SPO1575 NC_003911.11 1668748 1669425 R identified by match to protein family HMM PF01493; FwdC/FmdC family protein complement(1668748..1669425) Ruegeria pomeroyi DSS-3 3195021 YP_166817.1 CDS SPO1576 NC_003911.11 1669426 1670355 R identified by match to protein family HMM PF00310; glutamine amidotransferase complement(1669426..1670355) Ruegeria pomeroyi DSS-3 3195025 YP_166818.1 CDS SPO1577 NC_003911.11 1670500 1670718 R hypothetical protein complement(1670500..1670718) Ruegeria pomeroyi DSS-3 3193726 YP_166819.1 CDS SPO1578 NC_003911.11 1670731 1672104 R identified by match to protein family HMM PF00909; ammonium transporter complement(1670731..1672104) Ruegeria pomeroyi DSS-3 3193288 YP_166820.1 CDS SPO1579 NC_003911.11 1672349 1673494 D identified by match to protein family HMM PF01571; glycine cleavage system protein T 1672349..1673494 Ruegeria pomeroyi DSS-3 3192995 YP_166821.1 CDS SPO1580 NC_003911.11 1673539 1674180 D identified by similarity to GB:BAB53453.1; hypothetical protein 1673539..1674180 Ruegeria pomeroyi DSS-3 3193265 YP_166822.1 CDS SPO1581 NC_003911.11 1674177 1675163 D identified by match to protein family HMM PF00111; match to protein family HMM PF00175; oxidoreductase 1674177..1675163 Ruegeria pomeroyi DSS-3 3193252 YP_166823.1 CDS SPO1582 NC_003911.11 1675175 1676242 D identified by similarity to GB:BAB53455.1; hypothetical protein 1675175..1676242 Ruegeria pomeroyi DSS-3 3193341 YP_166824.1 CDS SPO1583 NC_003911.11 1676294 1676947 R identified by match to protein family HMM PF01381; DNA-binding protein complement(1676294..1676947) Ruegeria pomeroyi DSS-3 3193299 YP_166825.1 CDS SPO1584 NC_003911.11 1677085 1678074 D identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 1677085..1678074 Ruegeria pomeroyi DSS-3 3192827 YP_166826.1 CDS SPO1585 NC_003911.11 1678075 1678635 R identified by match to protein family HMM PF04268; match to protein family HMM TIGR01375; sarcosine oxidase subunit gamma complement(1678075..1678635) Ruegeria pomeroyi DSS-3 3192866 YP_166827.1 CDS SPO1586 NC_003911.11 1678628 1681579 R identified by similarity to SP:Q46337; match to protein family HMM PF01571; match to protein family HMM TIGR01372; sarcosine oxidase subunit alpha complement(1678628..1681579) Ruegeria pomeroyi DSS-3 3192653 YP_166828.1 CDS SPO1587 NC_003911.11 1681576 1681863 R identified by similarity to SP:Q46336; match to protein family HMM PF04267; sarcosine oxidase subunit delta complement(1681576..1681863) Ruegeria pomeroyi DSS-3 3193198 YP_166829.1 CDS SPO1588 NC_003911.11 1681877 1683127 R identified by similarity to SP:P40875; match to protein family HMM TIGR01373; sarcosine oxidase subunit beta complement(1681877..1683127) Ruegeria pomeroyi DSS-3 3192812 YP_166830.1 CDS SPO1589 NC_003911.11 1683246 1683629 R identified by match to protein family HMM PF02627; carboxymuconolactone decarboxylase complement(1683246..1683629) Ruegeria pomeroyi DSS-3 3195047 YP_166831.1 CDS SPO1590 NC_003911.11 1683694 1684785 R identified by match to protein family HMM PF00355; Rieske (2Fe-2S) domain-containing protein complement(1683694..1684785) Ruegeria pomeroyi DSS-3 3193705 YP_166832.1 CDS SPO1591 NC_003911.11 1684791 1685678 R identified by match to protein family HMM PF01380; SIS domain-containing protein complement(1684791..1685678) Ruegeria pomeroyi DSS-3 3193142 YP_166833.1 CDS SPO1592 NC_003911.11 1685750 1688206 D identified by match to protein family HMM PF01571; glycine cleavage system protein T 1685750..1688206 Ruegeria pomeroyi DSS-3 3193241 YP_166834.1 CDS SPO1593 NC_003911.11 1688221 1689285 D identified by match to protein family HMM PF00107; alcohol dehydrogenase 1688221..1689285 Ruegeria pomeroyi DSS-3 3193186 YP_166835.1 CDS SPO1594 NC_003911.11 1689282 1690388 D identified by similarity to SP:P27099; match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase 1689282..1690388 Ruegeria pomeroyi DSS-3 3193978 YP_166836.1 CDS SPO1595 NC_003911.11 1690385 1691488 D identified by similarity to SP:P95608; match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase 1690385..1691488 Ruegeria pomeroyi DSS-3 3192788 YP_166837.1 CDS SPO1596 NC_003911.11 1691493 1692098 D identified by similarity to GB:CAE27785.1; hypothetical protein 1691493..1692098 Ruegeria pomeroyi DSS-3 3193536 YP_166838.1 CDS hemL NC_003911.11 1692095 1693369 D identified by similarity to SP:P48247; match to protein family HMM PF00202; glutamate-1-semialdehyde 2,1-aminomutase 1692095..1693369 Ruegeria pomeroyi DSS-3 3195552 YP_166839.1 CDS SPO1598 NC_003911.11 1693554 1694387 R identified by similarity to GB:CAE31122.1; hypothetical protein complement(1693554..1694387) Ruegeria pomeroyi DSS-3 3194840 YP_166840.1 CDS SPO1599 NC_003911.11 1694413 1695750 R identified by match to protein family HMM PF03972; MmgE/PrpD family protein complement(1694413..1695750) Ruegeria pomeroyi DSS-3 3193606 YP_166841.1 CDS SPO1600 NC_003911.11 1695747 1696592 R identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase complement(1695747..1696592) Ruegeria pomeroyi DSS-3 3193497 YP_166842.1 CDS panE-2 NC_003911.11 1696589 1697524 R identified by match to protein family HMM PF02558; match to protein family HMM TIGR00745; 2-dehydropantoate 2-reductase complement(1696589..1697524) Ruegeria pomeroyi DSS-3 3193337 YP_166843.1 CDS SPO1602 NC_003911.11 1697521 1699029 R identified by match to protein family HMM PF06253; trimethylamine methyltransferase complement(1697521..1699029) Ruegeria pomeroyi DSS-3 3195011 YP_166844.1 CDS SPO1603 NC_003911.11 1699026 1700078 R identified by match to protein family HMM PF02615; malate/L-lactate dehydrogenase complement(1699026..1700078) Ruegeria pomeroyi DSS-3 3193995 YP_166845.1 CDS SPO1604 NC_003911.11 1700190 1701119 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1700190..1701119 Ruegeria pomeroyi DSS-3 3195655 YP_166846.1 CDS SPO1605 NC_003911.11 1701082 1702764 R identified by similarity to GB:BAB49910.1; hypothetical protein complement(1701082..1702764) Ruegeria pomeroyi DSS-3 3194695 YP_166847.1 CDS potD NC_003911.11 1702821 1703840 R identified by similarity to SP:P23861; match to protein family HMM PF01547; spermidine/putrescine ABC transporter substrate-binding protein complement(1702821..1703840) Ruegeria pomeroyi DSS-3 3192957 YP_166848.1 CDS SPO1607 NC_003911.11 1703859 1704662 R identified by similarity to SP:P31136; match to protein family HMM PF00528; spermidine/putrescine ABC transporter permease complement(1703859..1704662) Ruegeria pomeroyi DSS-3 3192984 YP_166849.1 CDS potB NC_003911.11 1704655 1705566 R identified by similarity to SP:P23860; match to protein family HMM PF00528; spermidine/putrescine ABC transporter permease complement(1704655..1705566) Ruegeria pomeroyi DSS-3 3192873 YP_166850.1 CDS potA NC_003911.11 1705570 1706670 R 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 complement(1705570..1706670) Ruegeria pomeroyi DSS-3 3193682 YP_166851.1 CDS SPO1610 NC_003911.11 1706791 1707582 D identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 1706791..1707582 Ruegeria pomeroyi DSS-3 3193663 YP_166852.1 CDS SPO1611 NC_003911.11 1707651 1708880 D identified by similarity to GB:CAE10095.1; hypothetical protein 1707651..1708880 Ruegeria pomeroyi DSS-3 3192661 YP_166853.1 CDS SPO1612 NC_003911.11 1708920 1710209 D identified by similarity to GB:AAK03561.1; match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1708920..1710209 Ruegeria pomeroyi DSS-3 3193599 YP_166854.1 CDS SPO1613 NC_003911.11 1710222 1710596 D identified by similarity to SP:Q9CKX3; hypothetical protein 1710222..1710596 Ruegeria pomeroyi DSS-3 3193396 YP_166855.1 CDS SPO1614 NC_003911.11 1710770 1711204 D identified by similarity to GB:AAM72242.1; hypothetical protein 1710770..1711204 Ruegeria pomeroyi DSS-3 3193631 YP_166856.1 CDS SPO1615 NC_003911.11 1711334 1712008 D identified by match to protein family HMM PF00027; cyclic nucleotide-binding protein 1711334..1712008 Ruegeria pomeroyi DSS-3 3192905 YP_166857.1 CDS SPO1616 NC_003911.11 1712041 1712931 R identified by match to protein family HMM PF04397; transcriptional regulator complement(1712041..1712931) Ruegeria pomeroyi DSS-3 3193134 YP_166858.1 CDS SPO1617 NC_003911.11 1713363 1716374 D identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 1713363..1716374 Ruegeria pomeroyi DSS-3 3193097 YP_166859.1 CDS SPO1618 NC_003911.11 1716368 1716964 D hypothetical protein 1716368..1716964 Ruegeria pomeroyi DSS-3 3192800 YP_166860.1 CDS SPO1619 NC_003911.11 1716958 1717341 D identified by similarity to GB:CAE07324.1; hypothetical protein 1716958..1717341 Ruegeria pomeroyi DSS-3 3192920 YP_166861.1 CDS SPO1620 NC_003911.11 1717383 1717970 R identified by match to protein family HMM PF00903; glyoxalase complement(1717383..1717970) Ruegeria pomeroyi DSS-3 3193719 YP_166862.1 CDS SPO1621 NC_003911.11 1718117 1718467 R TfoX domain-containing protein complement(1718117..1718467) Ruegeria pomeroyi DSS-3 3193406 YP_166863.1 CDS SPO1622 NC_003911.11 1718611 1719903 D identified by match to protein family HMM PF00067; cytochrome P450 family protein 1718611..1719903 Ruegeria pomeroyi DSS-3 3192858 YP_166864.1 CDS SPO1623 NC_003911.11 1719919 1721289 R identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase complement(1719919..1721289) Ruegeria pomeroyi DSS-3 3194307 YP_166865.1 CDS SPO1624 NC_003911.11 1721282 1721962 R identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator complement(1721282..1721962) Ruegeria pomeroyi DSS-3 3193367 YP_166866.1 CDS SPO1625 NC_003911.11 1722127 1723563 R identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037; serine protease complement(1722127..1723563) Ruegeria pomeroyi DSS-3 3192705 YP_166867.1 CDS SPO1626 NC_003911.11 1724415 1728230 D identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 1724415..1728230 Ruegeria pomeroyi DSS-3 3193076 YP_166868.1 CDS SPO1627 NC_003911.11 1728320 1728916 R hypothetical protein complement(1728320..1728916) Ruegeria pomeroyi DSS-3 3193486 YP_166869.1 CDS SPO1628 NC_003911.11 1728948 1731356 R identified by match to protein family HMM PF01266; match to protein family HMM PF01571; glycine cleavage system protein T complement(1728948..1731356) Ruegeria pomeroyi DSS-3 3193115 YP_166870.1 CDS SPO1629 NC_003911.11 1731481 1732731 D identified by similarity to GB:AAN68935.1; hypothetical protein 1731481..1732731 Ruegeria pomeroyi DSS-3 3192834 YP_166871.1 CDS SPO1630 NC_003911.11 1732715 1734346 R hypothetical protein complement(1732715..1734346) Ruegeria pomeroyi DSS-3 3193364 YP_166872.1 CDS SPO1631 NC_003911.11 1734343 1735650 R identified by match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471; hypothetical protein complement(1734343..1735650) Ruegeria pomeroyi DSS-3 3193722 YP_166873.1 CDS xerD NC_003911.11 1735714 1736673 R identified by similarity to SP:P21891; match to protein family HMM PF00589; match to protein family HMM PF02899; tyrosine recombinase XerD complement(1735714..1736673) Ruegeria pomeroyi DSS-3 3193328 YP_166874.1 CDS SPO1633 NC_003911.11 1737148 1738335 D hypothetical protein 1737148..1738335 Ruegeria pomeroyi DSS-3 3193010 YP_166875.1 CDS aroK NC_003911.11 1738445 1739032 D catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis; shikimate kinase 1738445..1739032 Ruegeria pomeroyi DSS-3 3194890 YP_166876.1 CDS aroB NC_003911.11 1739034 1740146 D catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase 1739034..1740146 Ruegeria pomeroyi DSS-3 3192771 YP_166877.1 CDS SPO1636 NC_003911.11 1740157 1741227 R identified by match to protein family HMM PF00571; match to protein family HMM PF02163; SREBP protease complement(1740157..1741227) Ruegeria pomeroyi DSS-3 3192829 YP_166878.1 CDS ssb NC_003911.11 1741243 1741785 R identified by similarity to SP:P02339; match to protein family HMM PF00436; match to protein family HMM TIGR00621; single-strand binding protein complement(1741243..1741785) Ruegeria pomeroyi DSS-3 3193067 YP_166879.1 CDS SPO1638 NC_003911.11 1741995 1742573 D identified by match to protein family HMM PF01464; transglycosylase 1741995..1742573 Ruegeria pomeroyi DSS-3 3193449 YP_166880.1 CDS SPO1639 NC_003911.11 1742777 1743238 D identified by similarity to GB:AAK18170.1; FadB domain-containing protein 1742777..1743238 Ruegeria pomeroyi DSS-3 3193174 YP_166881.1 CDS SPO1640 NC_003911.11 1743226 1744155 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(1743226..1744155) Ruegeria pomeroyi DSS-3 3194706 YP_166882.1 CDS SPO1641 NC_003911.11 1744264 1745460 D identified by match to protein family HMM PF00144; beta-lactamase 1744264..1745460 Ruegeria pomeroyi DSS-3 3192663 YP_166883.1 CDS SPO1642 NC_003911.11 1745477 1746055 R hypothetical protein complement(1745477..1746055) Ruegeria pomeroyi DSS-3 3193291 YP_166884.1 CDS SPO1643 NC_003911.11 1746137 1747537 R identified by match to protein family HMM PF05694; selenium-binding protein complement(1746137..1747537) Ruegeria pomeroyi DSS-3 3193350 YP_166885.1 CDS SPO1644 NC_003911.11 1747689 1749470 R identified by match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide/dipeptide ABC transporter ATP-binding protein complement(1747689..1749470) Ruegeria pomeroyi DSS-3 3195301 YP_166886.1 CDS SPO1645 NC_003911.11 1749467 1750342 R identified by similarity to SP:P37315; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease complement(1749467..1750342) Ruegeria pomeroyi DSS-3 3193177 YP_166887.1 CDS SPO1646 NC_003911.11 1750339 1751286 R identified by match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease complement(1750339..1751286) Ruegeria pomeroyi DSS-3 3193053 YP_166888.1 CDS SPO1647 NC_003911.11 1751479 1753137 D identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; oligopeptide/dipeptide ABC transporter substrate-binding protein 1751479..1753137 Ruegeria pomeroyi DSS-3 3193305 YP_166889.1 CDS SPO1648 NC_003911.11 1753243 1754346 D identified by match to protein family HMM PF01571; glycine cleavage system protein T 1753243..1754346 Ruegeria pomeroyi DSS-3 3193889 YP_166890.1 CDS SPO1649 NC_003911.11 1754354 1755715 D identified by similarity to GB:AAF98391.2; invasion protein IbeA 1754354..1755715 Ruegeria pomeroyi DSS-3 3193403 YP_166891.1 CDS SPO1650 NC_003911.11 1755718 1755828 D hypothetical protein 1755718..1755828 Ruegeria pomeroyi DSS-3 3193112 YP_166892.1 CDS SPO1651 NC_003911.11 1755968 1756324 D hypothetical protein 1755968..1756324 Ruegeria pomeroyi DSS-3 3192673 YP_166893.1 CDS SPO1652 NC_003911.11 1756358 1756930 D identified by similarity to GB:CAF32821.1; transposase, truncation 1756358..1756930 Ruegeria pomeroyi DSS-3 3192868 YP_166894.1 CDS SPO1655 NC_003911.11 1761171 1761857 D hypothetical protein 1761171..1761857 Ruegeria pomeroyi DSS-3 3192994 YP_166895.1 CDS SPO1656 NC_003911.11 1761894 1764113 R identified by match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide/dipeptide ABC transporter ATP-binding protein complement(1761894..1764113) Ruegeria pomeroyi DSS-3 3192700 YP_166896.1 CDS SPO1657 NC_003911.11 1764115 1765317 R identified by match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease complement(1764115..1765317) Ruegeria pomeroyi DSS-3 3192684 YP_166897.1 CDS SPO1658 NC_003911.11 1765332 1766378 R identified by similarity to SP:P42062; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease complement(1765332..1766378) Ruegeria pomeroyi DSS-3 3195345 YP_166898.1 CDS SPO1659 NC_003911.11 1766522 1768348 R identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; oligopeptide/dipeptide ABC transporter substrate-binding protein complement(1766522..1768348) Ruegeria pomeroyi DSS-3 3193539 YP_166899.1 CDS SPO1660 NC_003911.11 1768418 1769224 R identified by match to protein family HMM PF00165; AraC family transcriptional regulator complement(1768418..1769224) Ruegeria pomeroyi DSS-3 3193230 YP_166900.1 CDS miaA NC_003911.11 1769266 1770141 R 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 complement(1769266..1770141) Ruegeria pomeroyi DSS-3 3192726 YP_166901.1 CDS pyrH NC_003911.11 1770258 1771013 D Catalyzes the phosphorylation of UMP to UDP; uridylate kinase 1770258..1771013 Ruegeria pomeroyi DSS-3 3192709 YP_166902.1 CDS SPO1663 NC_003911.11 1771076 1771771 D hypothetical protein 1771076..1771771 Ruegeria pomeroyi DSS-3 3192678 YP_166903.1 CDS frr NC_003911.11 1771943 1772506 D 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 1771943..1772506 Ruegeria pomeroyi DSS-3 3193529 YP_166904.1 CDS uppS NC_003911.11 1772517 1773248 D identified by match to protein family HMM PF01255; match to protein family HMM TIGR00055; UDP diphosphate synthase 1772517..1773248 Ruegeria pomeroyi DSS-3 3194281 YP_166905.1 CDS cdsA NC_003911.11 1773245 1774027 D identified by similarity to SP:P06466; match to protein family HMM PF01148; phosphatidate cytidylyltransferase 1773245..1774027 Ruegeria pomeroyi DSS-3 3193513 YP_166906.1 CDS dxr NC_003911.11 1774027 1775214 D 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 1774027..1775214 Ruegeria pomeroyi DSS-3 3194834 YP_166907.1 CDS SPO1668 NC_003911.11 1775219 1776589 D identified by match to protein family HMM PF00595; match to protein family HMM PF02163; match to protein family HMM TIGR00054; zinc metalloprotease 1775219..1776589 Ruegeria pomeroyi DSS-3 3195245 YP_166908.1 CDS SPO1669 NC_003911.11 1776689 1776814 D hypothetical protein 1776689..1776814 Ruegeria pomeroyi DSS-3 3193515 YP_166909.1 CDS SPO1670 NC_003911.11 1776944 1779307 D identified by match to protein family HMM PF01103; match to protein family HMM PF07244; OMP85 family outer membrane protein 1776944..1779307 Ruegeria pomeroyi DSS-3 3193626 YP_166910.1 CDS SPO1671 NC_003911.11 1779315 1779887 D hypothetical protein 1779315..1779887 Ruegeria pomeroyi DSS-3 3195422 YP_166911.1 CDS fabZ NC_003911.11 1779981 1780454 D 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 1779981..1780454 Ruegeria pomeroyi DSS-3 3192982 YP_166912.1 CDS lpxA NC_003911.11 1780451 1781236 D catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase 1780451..1781236 Ruegeria pomeroyi DSS-3 3193293 YP_166913.1 CDS SPO1674 NC_003911.11 1781238 1782032 D identified by similarity to GB:CAE28351.1; hypothetical protein 1781238..1782032 Ruegeria pomeroyi DSS-3 3194991 YP_166914.1 CDS lpxB NC_003911.11 1781984 1783189 D identified by similarity to SP:P10441; match to protein family HMM PF02684; match to protein family HMM TIGR00215; lipid-A-disaccharide synthase 1781984..1783189 Ruegeria pomeroyi DSS-3 3194064 YP_166915.1 CDS SPO1676 NC_003911.11 1783186 1783698 R identified by match to protein family HMM PF00583; acetyltransferase complement(1783186..1783698) Ruegeria pomeroyi DSS-3 3192948 YP_166916.1 CDS mnmA NC_003911.11 1783688 1784815 R catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA complement(1783688..1784815) Ruegeria pomeroyi DSS-3 3192677 YP_166917.1 CDS SPO1678 NC_003911.11 1784961 1785242 D identified by similarity to PIR:AE3305; hypothetical protein 1784961..1785242 Ruegeria pomeroyi DSS-3 3192768 YP_166918.1 CDS ctrA NC_003911.11 1785341 1786057 D identified by similarity to SP:Q45994; match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator CtrA 1785341..1786057 Ruegeria pomeroyi DSS-3 3194546 YP_166919.1 CDS ligA NC_003911.11 1786196 1788415 D 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 1786196..1788415 Ruegeria pomeroyi DSS-3 3192682 YP_166920.1 CDS recG NC_003911.11 1788412 1790502 D catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG 1788412..1790502 Ruegeria pomeroyi DSS-3 3193560 YP_166921.1 CDS SPO1682 NC_003911.11 1790617 1790739 D hypothetical protein 1790617..1790739 Ruegeria pomeroyi DSS-3 3192900 YP_166922.1 CDS SPO1683 NC_003911.11 1790995 1791447 R identified by similarity to GB:AAK22449.1; hypothetical protein complement(1790995..1791447) Ruegeria pomeroyi DSS-3 3193123 YP_166923.1 CDS hisI NC_003911.11 1791515 1791874 D identified by match to protein family HMM PF01502; phosphoribosyl-AMP cyclohydrolase 1791515..1791874 Ruegeria pomeroyi DSS-3 3195450 YP_166924.1 CDS SPO1685 NC_003911.11 1791878 1792717 R identified by match to protein family HMM PF00749; tRNA synthetase, class I family protein complement(1791878..1792717) Ruegeria pomeroyi DSS-3 3192785 YP_166925.1 CDS gid NC_003911.11 1792746 1794095 R 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 complement(1792746..1794095) Ruegeria pomeroyi DSS-3 3193555 YP_166926.1 CDS SPO1687 NC_003911.11 1794417 1795202 R Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase complement(1794417..1795202) Ruegeria pomeroyi DSS-3 3193602 YP_166927.1 CDS SPO1688 NC_003911.11 1795261 1795704 D identified by similarity to GB:AAN29721.1; match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase 1795261..1795704 Ruegeria pomeroyi DSS-3 3193708 YP_166928.1 CDS SPO1689 NC_003911.11 1795773 1796000 R identified by similarity to PIR:AE2803; hypothetical protein complement(1795773..1796000) Ruegeria pomeroyi DSS-3 3193559 YP_166929.1 CDS SPO1690 NC_003911.11 1796102 1797505 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1796102..1797505 Ruegeria pomeroyi DSS-3 3194963 YP_166930.1 CDS rplM NC_003911.11 1797669 1798127 D in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 1797669..1798127 Ruegeria pomeroyi DSS-3 3193556 YP_166931.1 CDS rpsI NC_003911.11 1798133 1798615 D forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 1798133..1798615 Ruegeria pomeroyi DSS-3 3193551 YP_166932.1 CDS SPO1693 NC_003911.11 1799149 1800744 D identified by similarity to GB:AAR33500.1; hypothetical protein 1799149..1800744 Ruegeria pomeroyi DSS-3 3194945 YP_166933.1 CDS SPO1694 NC_003911.11 1802181 1803143 D identified by match to protein family HMM PF00294; carbohydrate kinase 1802181..1803143 Ruegeria pomeroyi DSS-3 3196343 YP_166934.1 CDS SPO1695 NC_003911.11 1804224 1806323 D identified by similarity to SP:Q01262; match to protein family HMM PF01968; match to protein family HMM PF05378; hydantoin utilization protein 1804224..1806323 Ruegeria pomeroyi DSS-3 3192787 YP_166935.1 CDS SPO1696 NC_003911.11 1806320 1807969 D identified by match to protein family HMM PF02538; hydantoinase/oxoprolinase 1806320..1807969 Ruegeria pomeroyi DSS-3 3195350 YP_166936.1 CDS SPO1697 NC_003911.11 1807966 1809048 D identified by match to protein family HMM PF00155; aminotransferase, classes I and II 1807966..1809048 Ruegeria pomeroyi DSS-3 3193553 YP_166937.1 CDS SPO1698 NC_003911.11 1809064 1809789 D identified by match to protein family HMM PF01177; Asp/Glu/Hydantoin racemase 1809064..1809789 Ruegeria pomeroyi DSS-3 3193468 YP_166938.1 CDS SPO1699 NC_003911.11 1809786 1811132 D identified by match to protein family HMM PF03972; MmgE/PrpD family protein 1809786..1811132 Ruegeria pomeroyi DSS-3 3193547 YP_166939.1 CDS SPO1700 NC_003911.11 1811125 1812093 D identified by match to protein family HMM PF02826; D-isomer specific 2-hydroxyacid dehydrogenase 1811125..1812093 Ruegeria pomeroyi DSS-3 3193595 YP_166940.1 CDS SPO1701 NC_003911.11 1812104 1812997 D identified by match to protein family HMM PF00701; dihydrodipicolinate synthase 1812104..1812997 Ruegeria pomeroyi DSS-3 3193676 YP_166941.1 CDS SPO1702 NC_003911.11 1813320 1814963 R identified by similarity to GB:BAC48815.1; hypothetical protein complement(1813320..1814963) Ruegeria pomeroyi DSS-3 3194828 YP_166942.1 CDS SPO1703 NC_003911.11 1814968 1817448 R identified by match to protein family HMM PF02515; CaiB/BaiF family protein complement(1814968..1817448) Ruegeria pomeroyi DSS-3 3193546 YP_166943.1 CDS SPO1704 NC_003911.11 1817549 1818472 D identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 1817549..1818472 Ruegeria pomeroyi DSS-3 3193594 YP_166944.1 CDS SPO1705 NC_003911.11 1819114 1820538 D phage head morphogenesis domain-containing protein 1819114..1820538 Ruegeria pomeroyi DSS-3 3193591 YP_166945.1 CDS SPO1707 NC_003911.11 1823098 1823793 R identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein complement(1823098..1823793) Ruegeria pomeroyi DSS-3 3195008 YP_166946.1 CDS SPOA0447 NC_003911.11 1823797 1824537 R identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein complement(1823797..1824537) Ruegeria pomeroyi DSS-3 3196350 YP_166947.1 CDS SPO1708 NC_003911.11 1824534 1825763 R identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease complement(1824534..1825763) Ruegeria pomeroyi DSS-3 3193583 YP_166948.1 CDS SPO1709 NC_003911.11 1825767 1827722 R identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease complement(1825767..1827722) Ruegeria pomeroyi DSS-3 3195518 YP_166949.1 CDS SPO1710 NC_003911.11 1827788 1829122 R Assignment based partly on membership in branched-chain amino acid ABC transporter gene cluster; branched-chain amino acid ABC transporter substrate-binding protein complement(1827788..1829122) Ruegeria pomeroyi DSS-3 3193581 YP_166950.1 CDS ureD NC_003911.11 1829519 1830292 D identified by match to protein family HMM PF01774; urease accessory protein UreD 1829519..1830292 Ruegeria pomeroyi DSS-3 3193571 YP_166951.1 CDS ureA NC_003911.11 1830294 1830596 D identified by match to protein family HMM PF00547; match to protein family HMM TIGR00193; urease subunit gamma 1830294..1830596 Ruegeria pomeroyi DSS-3 3193563 YP_166952.1 CDS ureB NC_003911.11 1830773 1831078 D identified by similarity to GB:BAB21066.1; match to protein family HMM PF00699; match to protein family HMM TIGR00192; urease subunit beta 1830773..1831078 Ruegeria pomeroyi DSS-3 3196338 YP_166953.1 CDS ureC NC_003911.11 1831078 1832787 D 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 1831078..1832787 Ruegeria pomeroyi DSS-3 3192899 YP_166954.1 CDS ureE NC_003911.11 1832799 1833248 D identified by similarity to SP:P18317; match to protein family HMM PF02814; match to protein family HMM PF05194; urease accessory protein ureE 1832799..1833248 Ruegeria pomeroyi DSS-3 3193558 YP_166955.1 CDS ureF NC_003911.11 1833232 1833885 D identified by match to protein family HMM PF01730; urease accessory protein UreF 1833232..1833885 Ruegeria pomeroyi DSS-3 3192879 YP_166956.1 CDS ureG NC_003911.11 1833882 1834529 D identified by match to protein family HMM PF01495; match to protein family HMM TIGR00101; urease accessory protein UreG 1833882..1834529 Ruegeria pomeroyi DSS-3 3193533 YP_166957.1 CDS SPO1718 NC_003911.11 1834693 1835868 R hypothetical protein complement(1834693..1835868) Ruegeria pomeroyi DSS-3 3194250 YP_166958.1 CDS SPO3897 NC_003911.11 1837668 1837859 R identified by similarity to SP:P39140; match to protein family HMM PF02796; resolvase site-specific recombinase complement(1837668..1837859) Ruegeria pomeroyi DSS-3 3196272 YP_166959.1 CDS SPO1719 NC_003911.11 1838069 1839346 R 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 complement(1838069..1839346) Ruegeria pomeroyi DSS-3 3193582 YP_166960.1 CDS SPO1720 NC_003911.11 1839351 1839851 R identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ complement(1839351..1839851) Ruegeria pomeroyi DSS-3 3193024 YP_166961.1 CDS SPO1721 NC_003911.11 1839928 1840950 R identified by match to protein family HMM PF03480; match to protein family HMM TIGR00787; TRAP dicarboxylate transporter subunit DctP complement(1839928..1840950) Ruegeria pomeroyi DSS-3 3193550 YP_166962.1 CDS SPO1722 NC_003911.11 1840901 1841641 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(1840901..1841641) Ruegeria pomeroyi DSS-3 3193054 YP_166963.1 CDS uxuA NC_003911.11 1841740 1842951 D catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate; mannonate dehydratase 1841740..1842951 Ruegeria pomeroyi DSS-3 3193519 YP_166964.1 CDS uxuB NC_003911.11 1842948 1844432 D identified by similarity to SP:P39160; match to protein family HMM PF01232; D-mannonate oxidoreductase 1842948..1844432 Ruegeria pomeroyi DSS-3 3193566 YP_166965.1 CDS SPO1725 NC_003911.11 1845036 1845779 R identified by similarity to GB:CAD15199.1; hypothetical protein complement(1845036..1845779) Ruegeria pomeroyi DSS-3 3195564 YP_166966.1 CDS SPO3896 NC_003911.11 1845847 1846458 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(1845847..1846458) Ruegeria pomeroyi DSS-3 3193527 YP_166967.1 CDS SPO1727 NC_003911.11 1846451 1847356 R identified by similarity to GB:AAN87337.1; match to protein family HMM PF03976; polyphosphate kinase complement(1846451..1847356) Ruegeria pomeroyi DSS-3 3193544 YP_166968.1 CDS SPO1728 NC_003911.11 1847375 1848322 R identified by similarity to GB:AAC36352.1; match to protein family HMM PF00561; esterase complement(1847375..1848322) Ruegeria pomeroyi DSS-3 3193393 YP_166969.1 CDS metA NC_003911.11 1848329 1849267 R catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase complement(1848329..1849267) Ruegeria pomeroyi DSS-3 3194898 YP_166970.1 CDS recJ NC_003911.11 1849853 1851508 R 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 complement(1849853..1851508) Ruegeria pomeroyi DSS-3 3192707 YP_166971.1 CDS glpX NC_003911.11 1851701 1852654 R type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese; fructose 1,6-bisphosphatase II complement(1851701..1852654) Ruegeria pomeroyi DSS-3 3193511 YP_166972.1 CDS hom NC_003911.11 1852754 1854040 R catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase complement(1852754..1854040) Ruegeria pomeroyi DSS-3 3193343 YP_166973.1 CDS SPO1735 NC_003911.11 1854142 1854477 R hypothetical protein complement(1854142..1854477) Ruegeria pomeroyi DSS-3 3195711 YP_166974.1 CDS SPO1736 NC_003911.11 1854520 1855104 D identified by match to protein family HMM PF00440; TetR family transcriptional regulator 1854520..1855104 Ruegeria pomeroyi DSS-3 3193150 YP_166975.1 CDS SPO1737 NC_003911.11 1855180 1856091 R identified by match to protein family HMM PF02678; match to protein family HMM PF05726; pirin complement(1855180..1856091) Ruegeria pomeroyi DSS-3 3193290 YP_166976.1 CDS SPO1738 NC_003911.11 1856210 1857394 R identified by similarity to GB:AAO60101.1; match to protein family HMM PF00037; match to protein family HMM PF03860; dehalogenase complement(1856210..1857394) Ruegeria pomeroyi DSS-3 3192799 YP_166977.1 CDS SPO1739 NC_003911.11 1857384 1857971 D hypothetical protein 1857384..1857971 Ruegeria pomeroyi DSS-3 3193165 YP_166978.1 CDS SPO1740 NC_003911.11 1857975 1858550 R identified by similarity to PIR:F97376; hypothetical protein complement(1857975..1858550) Ruegeria pomeroyi DSS-3 3193469 YP_166979.1 CDS SPO1741 NC_003911.11 1858531 1859064 R identified by similarity to GB:CAE29115.1; hypothetical protein complement(1858531..1859064) Ruegeria pomeroyi DSS-3 3193390 YP_166980.1 CDS SPO1742 NC_003911.11 1859061 1860737 R identified by similarity to GB:BAB54226.1; hypothetical protein complement(1859061..1860737) Ruegeria pomeroyi DSS-3 3193561 YP_166981.1 CDS SPO1743 NC_003911.11 1861061 1862491 D identified by similarity to SP:P96110; match to protein family HMM PF00208; match to protein family HMM PF02812; glutamate dehydrogenase 1861061..1862491 Ruegeria pomeroyi DSS-3 3192979 YP_166982.1 CDS SPO1744 NC_003911.11 1862691 1863944 D identified by similarity to SP:P40875; match to protein family HMM PF01266; match to protein family HMM TIGR01373; sarcosine oxidase subunit beta 1862691..1863944 Ruegeria pomeroyi DSS-3 3193224 YP_166983.1 CDS SPO1745 NC_003911.11 1864000 1864263 D identified by similarity to SP:Q46336; match to protein family HMM PF04267; sarcosine oxidase subunit delta 1864000..1864263 Ruegeria pomeroyi DSS-3 3192833 YP_166984.1 CDS SPO1746 NC_003911.11 1864260 1867193 D identified by similarity to SP:Q46337; match to protein family HMM PF01571; match to protein family HMM TIGR01372; sarcosine oxidase subunit alpha 1864260..1867193 Ruegeria pomeroyi DSS-3 3193191 YP_166985.1 CDS SPO1747 NC_003911.11 1867162 1867731 D identified by match to protein family HMM PF04268; sarcosine oxidase subunit gamma 1867162..1867731 Ruegeria pomeroyi DSS-3 3193268 YP_166986.1 CDS SPO1748 NC_003911.11 1867767 1868063 D hypothetical protein 1867767..1868063 Ruegeria pomeroyi DSS-3 3196013 YP_166987.1 CDS dnaG NC_003911.11 1868156 1870105 D synthesizes RNA primers at the replication forks; DNA primase 1868156..1870105 Ruegeria pomeroyi DSS-3 3195570 YP_166988.1 CDS rpoD NC_003911.11 1870217 1872199 D 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 1870217..1872199 Ruegeria pomeroyi DSS-3 3193502 YP_166989.1 CDS SPO1751 NC_003911.11 1872471 1872884 D hypothetical protein 1872471..1872884 Ruegeria pomeroyi DSS-3 3192777 YP_166990.1 CDS SPO1752 NC_003911.11 1872904 1873314 D identified by similarity to PIR:D97619; match to protein family HMM PF01894; match to protein family HMM TIGR00149; hypothetical protein 1872904..1873314 Ruegeria pomeroyi DSS-3 3193331 YP_166991.1 CDS nrdR NC_003911.11 1873443 1873913 D identified by similarity to GB:BAC44848.1; match to protein family HMM PF03477; match to protein family HMM TIGR00244; transcriptional regulator NrdR 1873443..1873913 Ruegeria pomeroyi DSS-3 3192977 YP_166992.1 CDS ribD NC_003911.11 1873910 1875004 D 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 1873910..1875004 Ruegeria pomeroyi DSS-3 3193058 YP_166993.1 CDS kpsC NC_003911.11 1875208 1877211 R identified by similarity to SP:P42217; match to protein family HMM PF05159; capsular polysaccharide export protein KpsC complement(1875208..1877211) Ruegeria pomeroyi DSS-3 3192840 YP_166994.1 CDS SPO1756 NC_003911.11 1877215 1878348 R identified by match to protein family HMM PF02563; polysaccharide biosynthesis/export protein complement(1877215..1878348) Ruegeria pomeroyi DSS-3 3192729 YP_166995.1 CDS kpsS NC_003911.11 1878444 1879736 R identified by similarity to SP:P42218; match to protein family HMM PF05159; capsular polysaccharide export protein KpsS complement(1878444..1879736) Ruegeria pomeroyi DSS-3 3193254 YP_166996.1 CDS SPO1758 NC_003911.11 1879735 1879902 D hypothetical protein 1879735..1879902 Ruegeria pomeroyi DSS-3 3193450 YP_166997.1 CDS ribE NC_003911.11 1879908 1880495 D catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha 1879908..1880495 Ruegeria pomeroyi DSS-3 3193407 YP_166998.1 CDS SPO1760 NC_003911.11 1880499 1881071 D hypothetical protein 1880499..1881071 Ruegeria pomeroyi DSS-3 3192748 YP_166999.1 CDS SPO1761 NC_003911.11 1881259 1882380 D 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 1881259..1882380 Ruegeria pomeroyi DSS-3 3193366 YP_167000.1 CDS ribH NC_003911.11 1882382 1882933 D 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 1882382..1882933 Ruegeria pomeroyi DSS-3 3192913 YP_167001.1 CDS nusB NC_003911.11 1882930 1883412 D identified by similarity to SP:P04381; match to protein family HMM PF01029; match to protein family HMM TIGR01951; transcription antitermination factor NusB 1882930..1883412 Ruegeria pomeroyi DSS-3 3193374 YP_167002.1 CDS SPO1764 NC_003911.11 1883585 1884361 R identified by match to protein family HMM PF00196; LuxR family transcriptional regulator complement(1883585..1884361) Ruegeria pomeroyi DSS-3 3195163 YP_167003.1 CDS SPO1765 NC_003911.11 1884458 1884763 D identified by similarity to GB:CAE26745.1; hypothetical protein 1884458..1884763 Ruegeria pomeroyi DSS-3 3193385 YP_167004.1 CDS SPO1766 NC_003911.11 1885036 1885488 D identified by similarity to GB:CAA06860.1; hypothetical protein 1885036..1885488 Ruegeria pomeroyi DSS-3 3194650 YP_167005.1 CDS SPO1767 NC_003911.11 1885835 1886317 D identified by match to protein family HMM PF00583; acetyltransferase 1885835..1886317 Ruegeria pomeroyi DSS-3 3193625 YP_167006.1 CDS SPO1769 NC_003911.11 1886497 1887588 R hypothetical protein complement(1886497..1887588) Ruegeria pomeroyi DSS-3 3194626 YP_167007.1 CDS SPO1770 NC_003911.11 1887615 1888205 D hypothetical protein 1887615..1888205 Ruegeria pomeroyi DSS-3 3193295 YP_167008.1 CDS SPO1771 NC_003911.11 1888276 1889535 R 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 complement(1888276..1889535) Ruegeria pomeroyi DSS-3 3194565 YP_167009.1 CDS SPO1772 NC_003911.11 1889532 1890110 R TRAP dicarboxylate transporter subunit DctQ complement(1889532..1890110) Ruegeria pomeroyi DSS-3 3195263 YP_167010.1 CDS SPO1773 NC_003911.11 1890141 1891124 R identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP complement(1890141..1891124) Ruegeria pomeroyi DSS-3 3192797 YP_167011.1 CDS SPO1774 NC_003911.11 1891175 1891717 R 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 complement(1891175..1891717) Ruegeria pomeroyi DSS-3 3192877 YP_167012.1 CDS SPO1775 NC_003911.11 1891953 1892672 D identified by similarity to GB:CAE42879.1; hypothetical protein 1891953..1892672 Ruegeria pomeroyi DSS-3 3195305 YP_167013.1 CDS SPO1776 NC_003911.11 1892849 1894186 D function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase 1892849..1894186 Ruegeria pomeroyi DSS-3 3193113 YP_167014.1 CDS SPO1777 NC_003911.11 1894229 1895533 D catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines; dihydropyrimidine dehydrogenase 1894229..1895533 Ruegeria pomeroyi DSS-3 3193314 YP_167015.1 CDS SPO1778 NC_003911.11 1895588 1895818 R hypothetical protein complement(1895588..1895818) Ruegeria pomeroyi DSS-3 3193235 YP_167016.1 CDS SPO1779 NC_003911.11 1895936 1897216 D major facilitator transporter 1895936..1897216 Ruegeria pomeroyi DSS-3 3193122 YP_167017.1 CDS SPO1780 NC_003911.11 1897197 1897814 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(1897197..1897814) Ruegeria pomeroyi DSS-3 3194887 YP_167018.1 CDS SPO1781 NC_003911.11 1897978 1899228 D 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 1897978..1899228 Ruegeria pomeroyi DSS-3 3193623 YP_167019.1 CDS SPO1782 NC_003911.11 1899283 1899600 D hypothetical protein 1899283..1899600 Ruegeria pomeroyi DSS-3 3193696 YP_167020.1 CDS hydA NC_003911.11 1899626 1901080 D catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase 1899626..1901080 Ruegeria pomeroyi DSS-3 3192976 YP_167021.1 CDS SPO1784 NC_003911.11 1901086 1901499 R identified by similarity to GB:BAB48956.1; hypothetical protein complement(1901086..1901499) Ruegeria pomeroyi DSS-3 3193645 YP_167022.1 CDS SPO1785 NC_003911.11 1901532 1902335 D identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 1901532..1902335 Ruegeria pomeroyi DSS-3 3193055 YP_167023.1 CDS SPO1786 NC_003911.11 1902369 1903361 D identified by match to protein family HMM PF00528; ABC transporter permease 1902369..1903361 Ruegeria pomeroyi DSS-3 3193336 YP_167024.1 CDS SPO1787 NC_003911.11 1903423 1904301 D identified by match to protein family HMM PF00528; ABC transporter permease 1903423..1904301 Ruegeria pomeroyi DSS-3 3192738 YP_167025.1 CDS SPO1788 NC_003911.11 1904267 1905361 D ABC transporter substrate-binding protein 1904267..1905361 Ruegeria pomeroyi DSS-3 3192831 YP_167026.1 CDS SPO1789 NC_003911.11 1905532 1906245 D identified by similarity to GB:CAC40783.1; match to protein family HMM PF00528; sulfate/tungstate ABC transporter permease 1905532..1906245 Ruegeria pomeroyi DSS-3 3193479 YP_167027.1 CDS SPO1790 NC_003911.11 1906238 1906972 D identified by similarity to GB:CAC40784.1; match to protein family HMM PF00005; sulfate/tungstate ABC transporter ATP-binding protein 1906238..1906972 Ruegeria pomeroyi DSS-3 3196221 YP_167028.1 CDS SPO1791 NC_003911.11 1906992 1907807 D identified by similarity to GB:CAC40782.1; match to protein family HMM PF01547; sulfate/tungstate ABC transporter substrate-binding protein 1906992..1907807 Ruegeria pomeroyi DSS-3 3195511 YP_167029.1 CDS SPO1792 NC_003911.11 1907919 1908791 R identified by match to protein family HMM TIGR01764; excisionase complement(1907919..1908791) Ruegeria pomeroyi DSS-3 3193420 YP_167030.1 CDS SPO1793 NC_003911.11 1908914 1910263 R identified by match to protein family HMM PF00034; match to protein family HMM PF00400; hypothetical protein complement(1908914..1910263) Ruegeria pomeroyi DSS-3 3193683 YP_167031.1 CDS SPO1794 NC_003911.11 1910179 1911360 R identified by match to protein family HMM TIGR01583; formate dehydrogenase subunit gamma complement(1910179..1911360) Ruegeria pomeroyi DSS-3 3193031 YP_167032.1 CDS SPO1795 NC_003911.11 1911485 1912078 R identified by similarity to SP:P27273; match to protein family HMM PF00037; formate dehydrogenase, iron-sulfur subunit complement(1911485..1912078) Ruegeria pomeroyi DSS-3 3193506 YP_167033.1 CDS SPO1796 NC_003911.11 1912091 1914985 R 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 complement(1912091..1914985) Ruegeria pomeroyi DSS-3 3193356 YP_167034.1 CDS SPO1797 NC_003911.11 1915092 1915283 R identified by match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein complement(1915092..1915283) Ruegeria pomeroyi DSS-3 3192921 YP_167035.1 CDS SPO1798 NC_003911.11 1915351 1915962 R identified by match to protein family HMM PF06192; chaperone TorD complement(1915351..1915962) Ruegeria pomeroyi DSS-3 3193220 YP_167036.1 CDS SPO1799 NC_003911.11 1915966 1916595 R hypothetical protein complement(1915966..1916595) Ruegeria pomeroyi DSS-3 3193349 YP_167037.1 CDS SPO1800 NC_003911.11 1917429 1919378 D identified by match to protein family HMM PF00037; (Fe-S)-binding protein 1917429..1919378 Ruegeria pomeroyi DSS-3 3193680 YP_167038.1 CDS SPO1801 NC_003911.11 1919486 1920214 R identified by similarity to SP:P24059; hypothetical protein complement(1919486..1920214) Ruegeria pomeroyi DSS-3 3195510 YP_167039.1 CDS SPO1802 NC_003911.11 1920259 1920480 D identified by similarity to PIR:H95364; hypothetical protein 1920259..1920480 Ruegeria pomeroyi DSS-3 3193608 YP_167040.1 CDS SPO1803 NC_003911.11 1920477 1921538 D Mrp/NBP35 family protein 1920477..1921538 Ruegeria pomeroyi DSS-3 3192975 YP_167041.1 CDS SPO1804 NC_003911.11 1921535 1922242 D identified by similarity to GB:BAC50748.1; hypothetical protein 1921535..1922242 Ruegeria pomeroyi DSS-3 3193128 YP_167042.1 CDS SPO1805 NC_003911.11 1922239 1922718 D hypothetical protein 1922239..1922718 Ruegeria pomeroyi DSS-3 3193110 YP_167043.1 CDS SPO1806 NC_003911.11 1922858 1923358 R identified by match to protein family HMM PF01613; flavin reductase domain-containing protein complement(1922858..1923358) Ruegeria pomeroyi DSS-3 3192890 YP_167044.1 CDS SPO1807 NC_003911.11 1923541 1924953 R identified by match to protein family HMM PF00929; match to protein family HMM TIGR00573; DNA polymerase III subunit epsilon complement(1923541..1924953) Ruegeria pomeroyi DSS-3 3193715 YP_167045.1 CDS SPO1808 NC_003911.11 1924955 1925506 R identified by similarity to GB:AAD22393.1; hypothetical protein complement(1924955..1925506) Ruegeria pomeroyi DSS-3 3194750 YP_167046.1 CDS SPO1809 NC_003911.11 1925559 1927382 R 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 complement(1925559..1927382) Ruegeria pomeroyi DSS-3 3193042 YP_167047.1 CDS SPO1810 NC_003911.11 1927492 1929276 R identified by match to protein family HMM PF00474; sodium/solute symporter family protein complement(1927492..1929276) Ruegeria pomeroyi DSS-3 3192878 YP_167048.1 CDS SPO1811 NC_003911.11 1929283 1929567 R identified by similarity to GB:CAE09733.1; hypothetical protein complement(1929283..1929567) Ruegeria pomeroyi DSS-3 3194297 YP_167049.1 CDS adk-2 NC_003911.11 1929739 1930407 R 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 complement(1929739..1930407) Ruegeria pomeroyi DSS-3 3193471 YP_167050.1 CDS acs NC_003911.11 1930433 1932397 R identified by similarity to SP:P27550; match to protein family HMM PF00501; acetyl-coenzyme A synthetase complement(1930433..1932397) Ruegeria pomeroyi DSS-3 3192793 YP_167051.1 CDS SPO1814 NC_003911.11 1932854 1933870 D identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 1932854..1933870 Ruegeria pomeroyi DSS-3 3193194 YP_167052.1 CDS SPO1815 NC_003911.11 1933945 1934580 D identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ 1933945..1934580 Ruegeria pomeroyi DSS-3 3193096 YP_167053.1 CDS SPO1816 NC_003911.11 1934567 1935976 D identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM 1934567..1935976 Ruegeria pomeroyi DSS-3 3192985 YP_167054.1 CDS SPO1817 NC_003911.11 1936040 1936789 D identified by match to protein family HMM PF01925; hypothetical protein 1936040..1936789 Ruegeria pomeroyi DSS-3 3195314 YP_167055.1 CDS SPO1818 NC_003911.11 1936854 1937642 D identified by match to protein family HMM PF01925; hypothetical protein 1936854..1937642 Ruegeria pomeroyi DSS-3 3193672 YP_167056.1 CDS SPO1819 NC_003911.11 1937847 1938674 R identified by similarity to GB:AAN52089.1; match to protein family HMM PF00149; phosphodiesterase complement(1937847..1938674) Ruegeria pomeroyi DSS-3 3195317 YP_167057.1 CDS SPO1820 NC_003911.11 1938786 1940033 R identified by similarity to SP:P10904; match to protein family HMM PF01547; sugar ABC transporter periplasmic sugar-binding protein complement(1938786..1940033) Ruegeria pomeroyi DSS-3 3193496 YP_167058.1 CDS SPO1821 NC_003911.11 1940135 1940815 R identified by match to protein family HMM PF00528; sugar ABC transporter permease complement(1940135..1940815) Ruegeria pomeroyi DSS-3 3192715 YP_167059.1 CDS SPO1822 NC_003911.11 1941094 1942035 R identified by match to protein family HMM PF00528; sugar ABC transporter permease complement(1941094..1942035) Ruegeria pomeroyi DSS-3 3194949 YP_167060.1 CDS SPO1823 NC_003911.11 1942037 1943194 R identified by match to protein family HMM PF00005; match to protein family HMM PF03459; sugar ABC transporter ATP-binding protein complement(1942037..1943194) Ruegeria pomeroyi DSS-3 3194693 YP_167061.1 CDS SPO1824 NC_003911.11 1943307 1944179 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 1943307..1944179 Ruegeria pomeroyi DSS-3 3193604 YP_167062.1 CDS SPO1825 NC_003911.11 1944190 1945491 R glutamine synthetase complement(1944190..1945491) Ruegeria pomeroyi DSS-3 3194357 YP_167063.1 CDS SPO1826 NC_003911.11 1945493 1946335 R identified by match to protein family HMM PF01380; match to protein family HMM PF01418; RpiR family transcriptional regulator complement(1945493..1946335) Ruegeria pomeroyi DSS-3 3194888 YP_167064.1 CDS SPO1827 NC_003911.11 1946349 1947188 D identified by match to protein family HMM PF05013; N-formylglutamate amidohydrolase 1946349..1947188 Ruegeria pomeroyi DSS-3 3192701 YP_167065.1 CDS SPO1828 NC_003911.11 1947185 1947826 D identified by match to protein family HMM PF00857; isochorismatase 1947185..1947826 Ruegeria pomeroyi DSS-3 3193702 YP_167066.1 CDS SPO1829 NC_003911.11 1947819 1948544 D identified by similarity to SP:P21629; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1947819..1948544 Ruegeria pomeroyi DSS-3 3192665 YP_167067.1 CDS SPO1830 NC_003911.11 1948576 1949730 D 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 1948576..1949730 Ruegeria pomeroyi DSS-3 3193071 YP_167068.1 CDS livF-1 NC_003911.11 1949792 1950490 D identified by similarity to SP:P22731; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 1949792..1950490 Ruegeria pomeroyi DSS-3 3192764 YP_167069.1 CDS SPO1832 NC_003911.11 1950492 1951388 D identified by similarity to SP:P08340; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1950492..1951388 Ruegeria pomeroyi DSS-3 3192828 YP_167070.1 CDS SPO1833 NC_003911.11 1951385 1952404 D identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 1951385..1952404 Ruegeria pomeroyi DSS-3 3194492 YP_167071.1 CDS SPO1834 NC_003911.11 1952414 1953352 D identified by match to protein family HMM PF03069; acetamidase/formamidase 1952414..1953352 Ruegeria pomeroyi DSS-3 3193637 YP_167072.1 CDS SPO1835 NC_003911.11 1953388 1954389 R identified by similarity to GB:AAC04471.1; match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein complement(1953388..1954389) Ruegeria pomeroyi DSS-3 3194807 YP_167073.1 CDS SPO1836 NC_003911.11 1954391 1955419 R identified by match to protein family HMM PF01408; Gfo/Idh/MocA family oxidoreductase complement(1954391..1955419) Ruegeria pomeroyi DSS-3 3193706 YP_167074.1 CDS SPO1837 NC_003911.11 1955416 1956255 R identified by match to protein family HMM PF00528; sugar ABC transporter permease complement(1955416..1956255) Ruegeria pomeroyi DSS-3 3193145 YP_167075.1 CDS SPO1838 NC_003911.11 1956268 1957182 R identified by similarity to SP:P29823; match to protein family HMM PF00528; sugar ABC transporter permease complement(1956268..1957182) Ruegeria pomeroyi DSS-3 3193662 YP_167076.1 CDS SPO1839 NC_003911.11 1957239 1958489 R identified by similarity to SP:Q00749; match to protein family HMM PF01547; sugar ABC transporter periplasmic sugar-binding protein complement(1957239..1958489) Ruegeria pomeroyi DSS-3 3193267 YP_167077.1 CDS murQ NC_003911.11 1958486 1959394 R 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 complement(1958486..1959394) Ruegeria pomeroyi DSS-3 3192849 YP_167078.1 CDS SPO1841 NC_003911.11 1959554 1960444 D identified by match to protein family HMM PF01869; BadF/BadG/BcrA/BcrD ATPase 1959554..1960444 Ruegeria pomeroyi DSS-3 3194707 YP_167079.1 CDS SPO1842 NC_003911.11 1960441 1961217 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 1960441..1961217 Ruegeria pomeroyi DSS-3 3195848 YP_167080.1 CDS SPO1843 NC_003911.11 1961226 1962257 D identified by match to protein family HMM PF01380; SIS domain-containing protein 1961226..1962257 Ruegeria pomeroyi DSS-3 3193173 YP_167081.1 CDS nagA NC_003911.11 1962254 1963399 D identified by similarity to SP:P15300; match to protein family HMM PF01979; match to protein family HMM TIGR00221; N-acetylglucosamine-6-phosphate deacetylase 1962254..1963399 Ruegeria pomeroyi DSS-3 3192869 YP_167082.1 CDS SPO1845 NC_003911.11 1963574 1965676 R identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; molybdopterin-binding oxidoreductase complement(1963574..1965676) Ruegeria pomeroyi DSS-3 3193400 YP_167083.1 CDS SPO1846 NC_003911.11 1965749 1966909 R 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 complement(1965749..1966909) Ruegeria pomeroyi DSS-3 3193624 YP_167084.1 CDS SPO1847 NC_003911.11 1966939 1968825 R identified by match to protein family HMM PF00501; AMP-binding protein complement(1966939..1968825) Ruegeria pomeroyi DSS-3 3193687 YP_167085.1 CDS SPO1848 NC_003911.11 1968843 1969616 R 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 complement(1968843..1969616) Ruegeria pomeroyi DSS-3 3194806 YP_167086.1 CDS SPO1849 NC_003911.11 1969613 1970377 R 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 complement(1969613..1970377) Ruegeria pomeroyi DSS-3 3193037 YP_167087.1 CDS SPO1850 NC_003911.11 1970374 1971471 R 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 complement(1970374..1971471) Ruegeria pomeroyi DSS-3 3192662 YP_167088.1 CDS SPO1851 NC_003911.11 1971476 1972351 R 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 complement(1971476..1972351) Ruegeria pomeroyi DSS-3 3193102 YP_167089.1 CDS SPO1852 NC_003911.11 1972430 1973458 R identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase complement(1972430..1973458) Ruegeria pomeroyi DSS-3 3192686 YP_167090.1 CDS SPO1853 NC_003911.11 1973477 1974118 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(1973477..1974118) Ruegeria pomeroyi DSS-3 3193248 YP_167091.1 CDS SPO1854 NC_003911.11 1974322 1974792 D identified by similarity to GB:CAD18588.1; hypothetical protein 1974322..1974792 Ruegeria pomeroyi DSS-3 3193286 YP_167092.1 CDS SPO1855 NC_003911.11 1974867 1975550 R hypothetical protein complement(1974867..1975550) Ruegeria pomeroyi DSS-3 3193099 YP_167093.1 CDS SPO1856 NC_003911.11 1975957 1976811 D identified by match to protein family HMM PF03631; match to protein family HMM TIGR00765; ribonuclease BN 1975957..1976811 Ruegeria pomeroyi DSS-3 3195275 YP_167094.1 CDS SPO1857 NC_003911.11 1976918 1977220 D hypothetical protein 1976918..1977220 Ruegeria pomeroyi DSS-3 3193189 YP_167095.1 CDS rrmJ NC_003911.11 1977167 1977868 R identified by match to protein family HMM PF01728; ribosomal RNA large subunit methyltransferase J complement(1977167..1977868) Ruegeria pomeroyi DSS-3 3195971 YP_167096.1 CDS SPO1859 NC_003911.11 1977989 1979101 R identified by match to protein family HMM PF02541; Ppx/GppA phosphatase complement(1977989..1979101) Ruegeria pomeroyi DSS-3 3195288 YP_167097.1 CDS SPO1860 NC_003911.11 1979284 1981167 D identified by match to protein family HMM PF05787; match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein 1979284..1981167 Ruegeria pomeroyi DSS-3 3195716 YP_167098.1 CDS SPO1861 NC_003911.11 1981420 1981716 D identified by similarity to GB:BAB48658.1; hypothetical protein 1981420..1981716 Ruegeria pomeroyi DSS-3 3193225 YP_167099.1 CDS SPO1862 NC_003911.11 1981743 1982672 D identified by similarity to PIR:B97532; MetF-like protein 1981743..1982672 Ruegeria pomeroyi DSS-3 3192752 YP_167100.1 CDS SPO1863 NC_003911.11 1982683 1983744 D 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 1982683..1983744 Ruegeria pomeroyi DSS-3 3192958 YP_167101.1 CDS SPO1864 NC_003911.11 1983863 1984102 R hypothetical protein complement(1983863..1984102) Ruegeria pomeroyi DSS-3 3193210 YP_167102.1 CDS tkt NC_003911.11 1984235 1986256 R 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 complement(1984235..1986256) Ruegeria pomeroyi DSS-3 3192774 YP_167103.1 CDS SPO1866 NC_003911.11 1986524 1987405 D hypothetical protein 1986524..1987405 Ruegeria pomeroyi DSS-3 3193238 YP_167104.1 CDS SPO1867 NC_003911.11 1987405 1987800 D identified by similarity to GB:AAK25209.1; hypothetical protein 1987405..1987800 Ruegeria pomeroyi DSS-3 3193472 YP_167105.1 CDS SPO1868 NC_003911.11 1987932 1988294 R identified by match to protein family HMM TIGR00365; glutaredoxin-like protein complement(1987932..1988294) Ruegeria pomeroyi DSS-3 3192918 YP_167106.1 CDS SPO1869 NC_003911.11 1988361 1988597 R identified by match to protein family HMM PF01722; BolA family protein complement(1988361..1988597) Ruegeria pomeroyi DSS-3 3192908 YP_167107.1 CDS purL NC_003911.11 1988722 1990881 R 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 complement(1988722..1990881) Ruegeria pomeroyi DSS-3 3194711 YP_167108.1 CDS SPO1871 NC_003911.11 1991015 1993288 R identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS complement(1991015..1993288) Ruegeria pomeroyi DSS-3 3193943 YP_167109.1 CDS SPO1872 NC_003911.11 1993553 1994488 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(1993553..1994488) Ruegeria pomeroyi DSS-3 3195605 YP_167110.1 CDS SPO1873 NC_003911.11 1994630 1998049 D Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; indolepyruvate ferredoxin oxidoreductase 1994630..1998049 Ruegeria pomeroyi DSS-3 3192932 YP_167111.1 CDS SPO1874 NC_003911.11 1998130 1999008 D identified by match to protein family HMM PF01553; acyltransferase domain-containing protein 1998130..1999008 Ruegeria pomeroyi DSS-3 3193459 YP_167112.1 CDS murI NC_003911.11 1999017 1999826 D identified by similarity to SP:P48797; match to protein family HMM PF01177; match to protein family HMM TIGR00067; glutamate racemase 1999017..1999826 Ruegeria pomeroyi DSS-3 3193464 YP_167113.1 CDS argC NC_003911.11 1999917 2000945 D 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 1999917..2000945 Ruegeria pomeroyi DSS-3 3193483 YP_167114.1 CDS ccmE NC_003911.11 2000953 2001396 D 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 2000953..2001396 Ruegeria pomeroyi DSS-3 3192772 YP_167115.1 CDS SPO1878 NC_003911.11 2001542 2002153 D identified by similarity to GB:AAF26222.1; match to protein family HMM PF05838; hypothetical protein 2001542..2002153 Ruegeria pomeroyi DSS-3 3193467 YP_167116.1 CDS SPO1879 NC_003911.11 2002126 2002818 R hypothetical protein complement(2002126..2002818) Ruegeria pomeroyi DSS-3 3193253 YP_167117.1 CDS ccmF NC_003911.11 2002798 2004762 D identified by similarity to SP:Q00500; match to protein family HMM PF01578; match to protein family HMM TIGR00353; cytochrome c-type biogenesis protein CcmF 2002798..2004762 Ruegeria pomeroyi DSS-3 3192786 YP_167118.1 CDS SPO1881 NC_003911.11 2004759 2005211 D identified by match to protein family HMM PF03918; cytochrome c biogenesis family protein 2004759..2005211 Ruegeria pomeroyi DSS-3 3193434 YP_167119.1 CDS SPO1882 NC_003911.11 2005288 2006064 D identified by match to protein family HMM PF00378; enoyl-CoA hydratase 2005288..2006064 Ruegeria pomeroyi DSS-3 3193419 YP_167120.1 CDS SPO1883 NC_003911.11 2006114 2007667 D identified by similarity to SP:O43464; hypothetical protein 2006114..2007667 Ruegeria pomeroyi DSS-3 3193204 YP_167121.1 CDS SPO1884 NC_003911.11 2007677 2008696 R catalyzes the formation of methionine from L-homocysteine and S-adenosyl-L-methionine; methionine synthase I complement(2007677..2008696) Ruegeria pomeroyi DSS-3 3193239 YP_167122.1 CDS SPO1885 NC_003911.11 2008757 2010664 R hypothetical protein complement(2008757..2010664) Ruegeria pomeroyi DSS-3 3192659 YP_167123.1 CDS SPO1886 NC_003911.11 2010734 2011051 R identified by similarity to GB:CAC46350.1; match to protein family HMM PF07345; hypothetical protein complement(2010734..2011051) Ruegeria pomeroyi DSS-3 3193466 YP_167124.1 CDS purC NC_003911.11 2011211 2011966 D 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 2011211..2011966 Ruegeria pomeroyi DSS-3 3193415 YP_167125.1 CDS purS NC_003911.11 2012153 2012383 D identified by match to protein family HMM PF02700; match to protein family HMM TIGR00302; phosphoribosylformylglycinamidine synthase, PurS protein 2012153..2012383 Ruegeria pomeroyi DSS-3 3193488 YP_167126.1 CDS SPO1889 NC_003911.11 2012387 2013430 D identified by match to protein family HMM PF00107; alcohol dehydrogenase 2012387..2013430 Ruegeria pomeroyi DSS-3 3192783 YP_167127.1 CDS purQ NC_003911.11 2013443 2014111 D 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 2013443..2014111 Ruegeria pomeroyi DSS-3 3193087 YP_167128.1 CDS SPO1891 NC_003911.11 2014148 2015917 D identified by similarity to SP:P13633; match to protein family HMM PF00512; match to protein family HMM PF02518; C4-dicarboxylate transport sensor protein DctB 2014148..2015917 Ruegeria pomeroyi DSS-3 3192652 YP_167129.1 CDS dctD-1 NC_003911.11 2015932 2017266 D 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 2015932..2017266 Ruegeria pomeroyi DSS-3 3193394 YP_167130.1 CDS SPO1893 NC_003911.11 2017824 2020805 D identified by match to protein family HMM TIGR00757; ribonuclease 2017824..2020805 Ruegeria pomeroyi DSS-3 3192750 YP_167131.1 CDS SPO1895 NC_003911.11 2020838 2021071 R identified by similarity to SP:P37618; match to protein family HMM PF01206; SirA family protein complement(2020838..2021071) Ruegeria pomeroyi DSS-3 3194393 YP_167132.1 CDS ccdA NC_003911.11 2021197 2021949 D identified by similarity to GB:AAF26218.1; match to protein family HMM PF02683; cytochrome c-type biogenesis protein CcdA 2021197..2021949 Ruegeria pomeroyi DSS-3 3195230 YP_167133.1 CDS SPO1897 NC_003911.11 2022105 2023337 D identified by similarity to PIR:AF3633; hypothetical protein 2022105..2023337 Ruegeria pomeroyi DSS-3 3192857 YP_167134.1 CDS SPO1898 NC_003911.11 2023334 2024686 D identified by match to protein family HMM PF00067; cytochrome P450 family protein 2023334..2024686 Ruegeria pomeroyi DSS-3 3193352 YP_167135.1 CDS fda NC_003911.11 2024755 2025636 D catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis; fructose-1,6-bisphosphate aldolase 2024755..2025636 Ruegeria pomeroyi DSS-3 3193495 YP_167136.1 CDS tag NC_003911.11 2025682 2026290 R identified by similarity to SP:P05100; match to protein family HMM PF03352; DNA-3-methyladenine glycosylase I complement(2025682..2026290) Ruegeria pomeroyi DSS-3 3195713 YP_167137.1 CDS SPO1901 NC_003911.11 2026287 2026586 R identified by similarity to GB:AAQ61811.1; hypothetical protein complement(2026287..2026586) Ruegeria pomeroyi DSS-3 3193100 YP_167138.1 CDS SPO1902 NC_003911.11 2026599 2027174 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(2026599..2027174) Ruegeria pomeroyi DSS-3 3193487 YP_167139.1 CDS SPO1903 NC_003911.11 2027240 2027461 R identified by similarity to GB:CAC46714.1; hypothetical protein complement(2027240..2027461) Ruegeria pomeroyi DSS-3 3195550 YP_167140.1 CDS SPO1904 NC_003911.11 2027458 2027634 R identified by similarity to GB:AAK23509.1; hypothetical protein complement(2027458..2027634) Ruegeria pomeroyi DSS-3 3193630 YP_167141.1 CDS fumC NC_003911.11 2027634 2028983 R 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 complement(2027634..2028983) Ruegeria pomeroyi DSS-3 3193215 YP_167142.1 CDS SPO1906 NC_003911.11 2029197 2029748 D hypothetical protein 2029197..2029748 Ruegeria pomeroyi DSS-3 3192841 YP_167143.1 CDS SPO1907 NC_003911.11 2029818 2030273 R identified by similarity to GB:AAK24073.1; hypothetical protein complement(2029818..2030273) Ruegeria pomeroyi DSS-3 3193447 YP_167144.1 CDS SPO1908 NC_003911.11 2030354 2031724 R identified by similarity to SP:P17551; match to protein family HMM PF02417; chromate transporter complement(2030354..2031724) Ruegeria pomeroyi DSS-3 3195788 YP_167145.1 CDS SPO1909 NC_003911.11 2031767 2032222 R identified by similarity to PIR:AB2272; hypothetical protein complement(2031767..2032222) Ruegeria pomeroyi DSS-3 3192894 YP_167146.1 CDS SPO1911 NC_003911.11 2032765 2033016 R hypothetical protein complement(2032765..2033016) Ruegeria pomeroyi DSS-3 3193353 YP_167147.1 CDS SPO1912 NC_003911.11 2033030 2033761 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(2033030..2033761) Ruegeria pomeroyi DSS-3 3192669 YP_167148.1 CDS dmdA NC_003911.11 2033984 2035078 D 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 2033984..2035078 Ruegeria pomeroyi DSS-3 3192947 YP_167149.1 CDS SPO1914 NC_003911.11 2035156 2036148 D identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase 2035156..2036148 Ruegeria pomeroyi DSS-3 3192712 YP_167150.1 CDS SPO1915 NC_003911.11 2036201 2036584 R identified by match to protein family HMM PF00903; glyoxalase complement(2036201..2036584) Ruegeria pomeroyi DSS-3 3193227 YP_167151.1 CDS SPO1916 NC_003911.11 2036724 2037947 D identified by match to protein family HMM PF00266; class V aminotransferase 2036724..2037947 Ruegeria pomeroyi DSS-3 3192708 YP_167152.1 CDS phrB NC_003911.11 2037997 2039442 D identified by similarity to SP:P00914; match to protein family HMM PF00875; match to protein family HMM PF03441; deoxyribodipyrimidine photolyase 2037997..2039442 Ruegeria pomeroyi DSS-3 3192692 YP_167153.1 CDS cfa NC_003911.11 2039492 2040706 D identified by match to protein family HMM PF02353; cyclopropane-fatty-acyl-phospholipid synthase 2039492..2040706 Ruegeria pomeroyi DSS-3 3195566 YP_167154.1 CDS trgA NC_003911.11 2040718 2041158 D identified by similarity to GB:AAB95446.1; tellurite resistance protein 2040718..2041158 Ruegeria pomeroyi DSS-3 3193833 YP_167155.1 CDS trgB NC_003911.11 2041159 2042304 D identified by similarity to GB:AAB95442.1; match to protein family HMM PF00293; match to protein family HMM TIGR00052; tellurite resistance protein 2041159..2042304 Ruegeria pomeroyi DSS-3 3195180 YP_167156.1 CDS SPO1921 NC_003911.11 2042389 2043423 D CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis; cysteine synthase A 2042389..2043423 Ruegeria pomeroyi DSS-3 3194670 YP_167157.1 CDS SPO1922 NC_003911.11 2043404 2045836 D identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS 2043404..2045836 Ruegeria pomeroyi DSS-3 3193175 YP_167158.1 CDS SPO1923 NC_003911.11 2045826 2046548 D identified by similarity to GB:CAC46199.1; hypothetical protein 2045826..2046548 Ruegeria pomeroyi DSS-3 3193618 YP_167159.1 CDS SPO1925 NC_003911.11 2047083 2047958 R hypothetical protein complement(2047083..2047958) Ruegeria pomeroyi DSS-3 3193453 YP_167160.1 CDS SPO1926 NC_003911.11 2047955 2050852 R identified by similarity to GB:AAK22811.1; hypothetical protein complement(2047955..2050852) Ruegeria pomeroyi DSS-3 3193163 YP_167161.1 CDS SPO3898 NC_003911.11 2052890 2053081 R identified by similarity to SP:P12552; match to protein family HMM PF05930; DNA-binding protein complement(2052890..2053081) Ruegeria pomeroyi DSS-3 3196263 YP_167162.1 CDS SPO1927 NC_003911.11 2053837 2055057 R identified by match to protein family HMM PF00589; phage integrase site specific recombinase complement(2053837..2055057) Ruegeria pomeroyi DSS-3 3194586 YP_167163.1 CDS SPO1928 NC_003911.11 2055392 2055997 R identified by match to protein family HMM PF05951; match to protein family HMM TIGR01409; Tat pathway signal sequence domain-containing protein complement(2055392..2055997) Ruegeria pomeroyi DSS-3 3192805 YP_167164.1 CDS SPO1929 NC_003911.11 2056316 2057929 D identified by match to protein family HMM PF01471; peptidoglycan binding protein 2056316..2057929 Ruegeria pomeroyi DSS-3 3193273 YP_167165.1 CDS lpxD NC_003911.11 2057964 2059055 D 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 2057964..2059055 Ruegeria pomeroyi DSS-3 3192672 YP_167166.1 CDS SPO1931 NC_003911.11 2059087 2059344 D identified by similarity to SP:P20804; match to protein family HMM PF00550; acyl carrier protein 2059087..2059344 Ruegeria pomeroyi DSS-3 3193176 YP_167167.1 CDS SPO1932 NC_003911.11 2059353 2060561 D identified by match to protein family HMM PF00109; match to protein family HMM PF02801; beta-ketoacyl synthase 2059353..2060561 Ruegeria pomeroyi DSS-3 3193139 YP_167168.1 CDS SPO1933 NC_003911.11 2060640 2061314 R identified by match to protein family HMM PF06776; invasion associated family protein complement(2060640..2061314) Ruegeria pomeroyi DSS-3 3193077 YP_167169.1 CDS SPO1934 NC_003911.11 2061709 2063262 D identified by similarity to PIR:B97464; match to protein family HMM PF05872; hypothetical protein 2061709..2063262 Ruegeria pomeroyi DSS-3 3192689 YP_167170.1 CDS SPO1935 NC_003911.11 2063401 2064705 R identified by similarity to SP:P22729; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease complement(2063401..2064705) Ruegeria pomeroyi DSS-3 3193517 YP_167171.1 CDS SPO1936 NC_003911.11 2064702 2065712 R identified by similarity to SP:P08340; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease complement(2064702..2065712) Ruegeria pomeroyi DSS-3 3192832 YP_167172.1 CDS SPO1937 NC_003911.11 2065716 2066546 R identified by similarity to SP:P22731; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein complement(2065716..2066546) Ruegeria pomeroyi DSS-3 3193285 YP_167173.1 CDS SPO1938 NC_003911.11 2066543 2067433 R 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 complement(2066543..2067433) Ruegeria pomeroyi DSS-3 3193021 YP_167174.1 CDS SPO1939 NC_003911.11 2067471 2068664 R 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 complement(2067471..2068664) Ruegeria pomeroyi DSS-3 3193383 YP_167175.1 CDS SPO1940 NC_003911.11 2068824 2069936 D identified by similarity to GB:CAC46907.1; hypothetical protein 2068824..2069936 Ruegeria pomeroyi DSS-3 3193184 YP_167176.1 CDS SPO1941 NC_003911.11 2070049 2071026 R identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator complement(2070049..2071026) Ruegeria pomeroyi DSS-3 3193292 YP_167177.1 CDS SPO1942 NC_003911.11 2071198 2072595 D identified by match to protein family HMM PF01474; match to protein family HMM TIGR01358; 3-deoxy-7-phosphoheptulonate synthase 2071198..2072595 Ruegeria pomeroyi DSS-3 3193118 YP_167178.1 CDS SPO1943 NC_003911.11 2072666 2073358 R identified by similarity to PIR:C97571; hypothetical protein complement(2072666..2073358) Ruegeria pomeroyi DSS-3 3192872 YP_167179.1 CDS SPO1944 NC_003911.11 2073600 2074490 D identified by match to protein family HMM PF03755; match to protein family HMM TIGR00255; hypothetical protein 2073600..2074490 Ruegeria pomeroyi DSS-3 3193035 YP_167180.1 CDS gmk NC_003911.11 2074509 2075150 D Essential for recycling GMP and indirectly, cGMP; guanylate kinase 2074509..2075150 Ruegeria pomeroyi DSS-3 3193183 YP_167181.1 CDS SPO1946 NC_003911.11 2075147 2075671 D identified by match to protein family HMM PF00132; transferase 2075147..2075671 Ruegeria pomeroyi DSS-3 3193643 YP_167182.1 CDS SPO1947 NC_003911.11 2075688 2076734 D identified by similarity to SP:P23621; match to protein family HMM PF00512; match to protein family HMM PF02518; phosphate regulon sensor histidine kinase 2075688..2076734 Ruegeria pomeroyi DSS-3 3193213 YP_167183.1 CDS pstS NC_003911.11 2076961 2078001 D phosphate ABC transporter substrate-binding protein 2076961..2078001 Ruegeria pomeroyi DSS-3 3194730 YP_167184.1 CDS pstC NC_003911.11 2078079 2079554 D identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138; phosphate ABC transporter permease 2078079..2079554 Ruegeria pomeroyi DSS-3 3193326 YP_167185.1 CDS pstA NC_003911.11 2079551 2080903 D identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974; phosphate ABC transporter permease 2079551..2080903 Ruegeria pomeroyi DSS-3 3192719 YP_167186.1 CDS pstB NC_003911.11 2080887 2081714 D 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 2080887..2081714 Ruegeria pomeroyi DSS-3 3195194 YP_167187.1 CDS phoU NC_003911.11 2081732 2082433 D identified by match to protein family HMM PF01895; match to protein family HMM TIGR02135; phosphate transport system regulatory protein PhoU 2081732..2082433 Ruegeria pomeroyi DSS-3 3192941 YP_167188.1 CDS phoB NC_003911.11 2082449 2083138 D identified by similarity to SP:P08402; match to protein family HMM PF00072; match to protein family HMM PF00486; phosphate regulon transcriptional regulatory protein PhoB 2082449..2083138 Ruegeria pomeroyi DSS-3 3193549 YP_167189.1 CDS SPO1954 NC_003911.11 2083157 2084068 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(2083157..2084068) Ruegeria pomeroyi DSS-3 3192743 YP_167190.1 CDS gcdH NC_003911.11 2084084 2085394 D 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 2084084..2085394 Ruegeria pomeroyi DSS-3 3192934 YP_167191.1 CDS sulP NC_003911.11 2085537 2087285 D identified by match to protein family HMM PF00916; match to protein family HMM PF01740; match to protein family HMM TIGR00815; sulfate permease 2085537..2087285 Ruegeria pomeroyi DSS-3 3193371 YP_167192.1 CDS SPO1957 NC_003911.11 2087518 2088288 D identified by similarity to GB:AAR05249.1; match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2087518..2088288 Ruegeria pomeroyi DSS-3 3192968 YP_167193.1 CDS SPO1958 NC_003911.11 2088285 2089154 R identified by similarity to SP:P23911; match to protein family HMM PF02551; match to protein family HMM TIGR00189; acyl-CoA thioesterase complement(2088285..2089154) Ruegeria pomeroyi DSS-3 3192914 YP_167194.1 CDS SPO1959 NC_003911.11 2089171 2091132 R AcsA; in Sinorhizobium meliloti this enzyme is required for acetoacetate activation; similar to acetyl-CoA synthase; acetoacetyl-CoA synthetase complement(2089171..2091132) Ruegeria pomeroyi DSS-3 3193701 YP_167195.1 CDS SPO1960 NC_003911.11 2091123 2092358 R identified by match to protein family HMM PF00144; beta-lactamase complement(2091123..2092358) Ruegeria pomeroyi DSS-3 3193532 YP_167196.1 CDS SPO1961 NC_003911.11 2092464 2093234 R identified by match to protein family HMM PF01614; IclR family transcriptional regulator complement(2092464..2093234) Ruegeria pomeroyi DSS-3 3193069 YP_167197.1 CDS SPO1962 NC_003911.11 2093261 2094289 R identified by match to protein family HMM PF01636; phosphotransferase complement(2093261..2094289) Ruegeria pomeroyi DSS-3 3193362 YP_167198.1 CDS SPO1963 NC_003911.11 2094300 2094950 R identified by match to protein family HMM PF00300; phosphoglycerate mutase complement(2094300..2094950) Ruegeria pomeroyi DSS-3 3194758 YP_167199.1 CDS SPO1964 NC_003911.11 2094954 2095955 R identified by similarity to GB:AAL02322.2; hypothetical protein complement(2094954..2095955) Ruegeria pomeroyi DSS-3 3192749 YP_167200.1 CDS SPO1965 NC_003911.11 2095969 2096898 R identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase complement(2095969..2096898) Ruegeria pomeroyi DSS-3 3193695 YP_167201.1 CDS SPO1966 NC_003911.11 2096909 2097727 R identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase complement(2096909..2097727) Ruegeria pomeroyi DSS-3 3192838 YP_167202.1 CDS SPO1967 NC_003911.11 2097737 2098852 R identified by match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF02771; acyl-CoA dehydrogenase complement(2097737..2098852) Ruegeria pomeroyi DSS-3 3192803 YP_167203.1 CDS SPO1968 NC_003911.11 2098858 2100015 R identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase complement(2098858..2100015) Ruegeria pomeroyi DSS-3 3192936 YP_167204.1 CDS SPO1969 NC_003911.11 2100154 2101146 D identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase 2100154..2101146 Ruegeria pomeroyi DSS-3 3193674 YP_167205.1 CDS SPO1970 NC_003911.11 2101153 2101809 R identified by match to protein family HMM PF00300; phosphoglycerate mutase complement(2101153..2101809) Ruegeria pomeroyi DSS-3 3193170 YP_167206.1 CDS SPO1971 NC_003911.11 2101866 2102690 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 2101866..2102690 Ruegeria pomeroyi DSS-3 3193616 YP_167207.1 CDS SPO1972 NC_003911.11 2102697 2103203 D identified by similarity to SP:P25200; match to protein family HMM PF01575; nodulation protein N 2102697..2103203 Ruegeria pomeroyi DSS-3 3193445 YP_167208.1 CDS aroQ NC_003911.11 2103300 2103752 D catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis; 3-dehydroquinate dehydratase 2103300..2103752 Ruegeria pomeroyi DSS-3 3193440 YP_167209.1 CDS SPO1974 NC_003911.11 2103755 2104504 D identified by match to protein family HMM PF00196; match to protein family HMM PF03472; LuxR family transcriptional regulator 2103755..2104504 Ruegeria pomeroyi DSS-3 3193044 YP_167210.1 CDS tsf NC_003911.11 2104998 2105873 R 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 complement(2104998..2105873) Ruegeria pomeroyi DSS-3 3192723 YP_167211.1 CDS rpsB NC_003911.11 2105951 2106724 R 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 complement(2105951..2106724) Ruegeria pomeroyi DSS-3 3192960 YP_167212.1 CDS SPO1977 NC_003911.11 2107034 2108089 D hypothetical protein 2107034..2108089 Ruegeria pomeroyi DSS-3 3192745 YP_167213.1 CDS SPO1978 NC_003911.11 2108083 2109255 D hypothetical protein 2108083..2109255 Ruegeria pomeroyi DSS-3 3195265 YP_167214.1 CDS SPO1979 NC_003911.11 2109260 2110093 R identified by match to protein family HMM PF01553; acyltransferase complement(2109260..2110093) Ruegeria pomeroyi DSS-3 3193119 YP_167215.1 CDS SPO1980 NC_003911.11 2110096 2110851 R identified by similarity to PIR:AB3477; hypothetical protein complement(2110096..2110851) Ruegeria pomeroyi DSS-3 3193154 YP_167216.1 CDS SPO1981 NC_003911.11 2110844 2110963 R hypothetical protein complement(2110844..2110963) Ruegeria pomeroyi DSS-3 3194789 YP_167217.1 CDS SPO1982 NC_003911.11 2110960 2111199 R hypothetical protein complement(2110960..2111199) Ruegeria pomeroyi DSS-3 3194201 YP_167218.1 CDS SPO1983 NC_003911.11 2111191 2111787 D identified by similarity to PIR:AB3305; hypothetical protein 2111191..2111787 Ruegeria pomeroyi DSS-3 3193572 YP_167219.1 CDS proA NC_003911.11 2111788 2113041 R Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase complement(2111788..2113041) Ruegeria pomeroyi DSS-3 3193622 YP_167220.1 CDS proB NC_003911.11 2113096 2114202 R catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase complement(2113096..2114202) Ruegeria pomeroyi DSS-3 3193117 YP_167221.1 CDS obgE NC_003911.11 2114190 2115224 R essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE complement(2114190..2115224) Ruegeria pomeroyi DSS-3 3193499 YP_167222.1 CDS SPO1987 NC_003911.11 2115261 2115797 R identified by match to protein family HMM PF00583; acetyltransferase complement(2115261..2115797) Ruegeria pomeroyi DSS-3 3193182 YP_167223.1 CDS SPO1988 NC_003911.11 2115794 2116474 R identified by match to protein family HMM PF01810; amino acid transporter LysE complement(2115794..2116474) Ruegeria pomeroyi DSS-3 3192898 YP_167224.1 CDS rpmA NC_003911.11 2116505 2116774 R involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 complement(2116505..2116774) Ruegeria pomeroyi DSS-3 3195614 YP_167225.1 CDS rplU NC_003911.11 2116786 2117367 R fusion of ribosomal protein L21 and COG3743; 50S ribosomal protein L21 complement(2116786..2117367) Ruegeria pomeroyi DSS-3 3193713 YP_167226.1 CDS SPO1991 NC_003911.11 2117632 2118438 R hypothetical protein complement(2117632..2118438) Ruegeria pomeroyi DSS-3 3195563 YP_167227.1 CDS SPO1992 NC_003911.11 2118435 2119274 R hypothetical protein complement(2118435..2119274) Ruegeria pomeroyi DSS-3 3192966 YP_167228.1 CDS SPO1994 NC_003911.11 2119882 2121195 R identified by match to protein family HMM PF00529; match to protein family HMM TIGR01843; HlyD family type I secretion membrane fusion protein complement(2119882..2121195) Ruegeria pomeroyi DSS-3 3194056 YP_167229.1 CDS SPO1995 NC_003911.11 2121199 2123004 R identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter ATP-binding protein/permease complement(2121199..2123004) Ruegeria pomeroyi DSS-3 3192680 YP_167230.1 CDS SPO1996 NC_003911.11 2123136 2123981 R identified by similarity to GB:CAE79871.1; hypothetical protein complement(2123136..2123981) Ruegeria pomeroyi DSS-3 3194745 YP_167231.1 CDS SPO1997 NC_003911.11 2123980 2124903 D hypothetical protein 2123980..2124903 Ruegeria pomeroyi DSS-3 3193524 YP_167232.1 CDS SPO1998 NC_003911.11 2124900 2125643 D hypothetical protein 2124900..2125643 Ruegeria pomeroyi DSS-3 3195734 YP_167233.1 CDS SPO1999 NC_003911.11 2125795 2128956 R hypothetical protein complement(2125795..2128956) Ruegeria pomeroyi DSS-3 3193334 YP_167234.1 CDS SPO2000 NC_003911.11 2129470 2129823 R identified by match to protein family HMM PF01042; endoribonuclease L-PSP complement(2129470..2129823) Ruegeria pomeroyi DSS-3 3193577 YP_167235.1 CDS SPO2001 NC_003911.11 2129839 2130939 R identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding complement(2129839..2130939) Ruegeria pomeroyi DSS-3 3193574 YP_167236.1 CDS SPO2002 NC_003911.11 2130936 2131961 R identified by similarity to SP:Q48935; match to protein family HMM PF00850; acetylpolyamine aminohydrolase complement(2130936..2131961) Ruegeria pomeroyi DSS-3 3192741 YP_167237.1 CDS SPO2003 NC_003911.11 2131958 2132437 R identified by match to protein family HMM PF00583; acetyltransferase complement(2131958..2132437) Ruegeria pomeroyi DSS-3 3193588 YP_167238.1 CDS SPO2004 NC_003911.11 2132437 2133363 R identified by similarity to GB:BAB47761.1; match to protein family HMM PF05853; hypothetical protein complement(2132437..2133363) Ruegeria pomeroyi DSS-3 3193552 YP_167239.1 CDS SPO2005 NC_003911.11 2133365 2134696 R identified by match to protein family HMM PF00202; class III aminotransferase complement(2133365..2134696) Ruegeria pomeroyi DSS-3 3192725 YP_167240.1 CDS SPO2006 NC_003911.11 2134698 2135774 R identified by match to protein family HMM PF00005; match to protein family HMM TIGR01187; spermidine/putrescine ABC transporter ATP-binding protein complement(2134698..2135774) Ruegeria pomeroyi DSS-3 3195227 YP_167241.1 CDS SPO2007 NC_003911.11 2135835 2136986 R identified by match to protein family HMM PF01547; match to protein family HMM TIGR01409; spermidine/putrescine ABC transporter substrate-binding protein complement(2135835..2136986) Ruegeria pomeroyi DSS-3 3192716 YP_167242.1 CDS SPO2008 NC_003911.11 2137028 2137813 R identified by similarity to SP:P23859; match to protein family HMM PF00528; spermidine/putrescine ABC transporter permease complement(2137028..2137813) Ruegeria pomeroyi DSS-3 3192658 YP_167243.1 CDS SPO2009 NC_003911.11 2137813 2138730 R 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 complement(2137813..2138730) Ruegeria pomeroyi DSS-3 3193121 YP_167244.1 CDS SPO2010 NC_003911.11 2138773 2139741 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2138773..2139741 Ruegeria pomeroyi DSS-3 3193266 YP_167245.1 CDS SPO2013 NC_003911.11 2140917 2142413 D hypothetical protein 2140917..2142413 Ruegeria pomeroyi DSS-3 3193590 YP_167246.1 CDS sufS NC_003911.11 2142515 2143735 R identified by match to protein family HMM PF00266; match to protein family HMM TIGR01979; cysteine desulfurase complement(2142515..2143735) Ruegeria pomeroyi DSS-3 3193329 YP_167247.1 CDS SPO2015 NC_003911.11 2143728 2144315 R hypothetical protein complement(2143728..2144315) Ruegeria pomeroyi DSS-3 3194782 YP_167248.1 CDS SPO2016 NC_003911.11 2144312 2144797 R hypothetical protein complement(2144312..2144797) Ruegeria pomeroyi DSS-3 3193019 YP_167249.1 CDS SPO2017 NC_003911.11 2144797 2146077 R identified by match to protein family HMM PF01458; match to protein family HMM TIGR01981; FeS assembly protein SufD complement(2144797..2146077) Ruegeria pomeroyi DSS-3 3193302 YP_167250.1 CDS sufC NC_003911.11 2146077 2146832 R identified by match to protein family HMM PF00005; match to protein family HMM TIGR01978; FeS assembly ATPase SufC complement(2146077..2146832) Ruegeria pomeroyi DSS-3 3193375 YP_167251.1 CDS SPO2019 NC_003911.11 2146845 2147681 R identified by similarity to GB:AAA16052.1; exoV domain-containing protein complement(2146845..2147681) Ruegeria pomeroyi DSS-3 3193133 YP_167252.1 CDS SPO2020 NC_003911.11 2147683 2148612 R identified by match to protein family HMM TIGR01444; FkbM family methyltransferase complement(2147683..2148612) Ruegeria pomeroyi DSS-3 3192886 YP_167253.1 CDS SPO2021 NC_003911.11 2148629 2148943 R identified by similarity to SP:Q8D461; match to protein family HMM PF01906; hypothetical protein complement(2148629..2148943) Ruegeria pomeroyi DSS-3 3193078 YP_167254.1 CDS SPO2022 NC_003911.11 2148971 2149576 R hypothetical protein complement(2148971..2149576) Ruegeria pomeroyi DSS-3 3192961 YP_167255.1 CDS sufB NC_003911.11 2149615 2151135 R with SufCD activates cysteine desulfurase SufS; cysteine desulfurase complement(2149615..2151135) Ruegeria pomeroyi DSS-3 3193051 YP_167256.1 CDS SPO2025 NC_003911.11 2152297 2152755 R 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 complement(2152297..2152755) Ruegeria pomeroyi DSS-3 3193530 YP_167257.1 CDS SPO2026 NC_003911.11 2152941 2153594 D identified by similarity to GB:BAB47692.1; hypothetical protein 2152941..2153594 Ruegeria pomeroyi DSS-3 3193991 YP_167258.1 CDS SPO2027 NC_003911.11 2153594 2153833 D hypothetical protein 2153594..2153833 Ruegeria pomeroyi DSS-3 3194779 YP_167259.1 CDS SPO2028 NC_003911.11 2153830 2154990 D identified by match to protein family HMM PF01966; HD domain-containing protein 2153830..2154990 Ruegeria pomeroyi DSS-3 3193187 YP_167260.1 CDS SPO2029 NC_003911.11 2155218 2156012 R identified by match to protein family HMM PF00310; glutamine amidotransferase complement(2155218..2156012) Ruegeria pomeroyi DSS-3 3193636 YP_167261.1 CDS SPO2030 NC_003911.11 2156239 2156574 D identified by similarity to SP:P23895; match to protein family HMM PF00893; SMR family multidrug efflux pump 2156239..2156574 Ruegeria pomeroyi DSS-3 3193155 YP_167262.1 CDS typA NC_003911.11 2156688 2158508 D 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 2156688..2158508 Ruegeria pomeroyi DSS-3 3193107 YP_167263.1 CDS SPO2032 NC_003911.11 2158606 2158893 R identified by similarity to GB:CAC41768.1; match to protein family HMM PF07045; hypothetical protein complement(2158606..2158893) Ruegeria pomeroyi DSS-3 3192791 YP_167264.1 CDS alaS NC_003911.11 2158898 2161570 R 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 complement(2158898..2161570) Ruegeria pomeroyi DSS-3 3195191 YP_167265.1 CDS recA NC_003911.11 2161731 2162774 R 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 complement(2161731..2162774) Ruegeria pomeroyi DSS-3 3193665 YP_167266.1 CDS SPO2035 NC_003911.11 2162985 2163578 D hypothetical protein 2162985..2163578 Ruegeria pomeroyi DSS-3 3193654 YP_167267.1 CDS SPO2036 NC_003911.11 2163585 2165891 R 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 complement(2163585..2165891) Ruegeria pomeroyi DSS-3 3193689 YP_167268.1 CDS SPO2037 NC_003911.11 2165997 2167172 R identified by match to protein family HMM PF01189; NOL1/NOP2/sun family protein complement(2165997..2167172) Ruegeria pomeroyi DSS-3 3193597 YP_167269.1 CDS SPO2038 NC_003911.11 2167176 2167961 R identified by match to protein family HMM PF00753; metallo-beta-lactamase complement(2167176..2167961) Ruegeria pomeroyi DSS-3 3195226 YP_167270.1 CDS guaB NC_003911.11 2167961 2169409 R identified by match to protein family HMM PF00478; match to protein family HMM PF00571; match to protein family HMM TIGR01302; inosine-5'-monophosphate dehydrogenase complement(2167961..2169409) Ruegeria pomeroyi DSS-3 3195341 YP_167271.1 CDS SPO2040 NC_003911.11 2169594 2170751 D identified by match to protein family HMM PF02515; CaiB/BaiF family protein 2169594..2170751 Ruegeria pomeroyi DSS-3 3193159 YP_167272.1 CDS SPO2041 NC_003911.11 2170882 2172921 D identified by match to protein family HMM PF00111; (Fe-S)-binding protein 2170882..2172921 Ruegeria pomeroyi DSS-3 3192814 YP_167273.1 CDS SPO2042 NC_003911.11 2172943 2173800 D identified by match to protein family HMM PF01209; UbiE/COQ5 family methlytransferase 2172943..2173800 Ruegeria pomeroyi DSS-3 3193585 YP_167274.1 CDS SPO2044 NC_003911.11 2174023 2174442 D lipoprotein 2174023..2174442 Ruegeria pomeroyi DSS-3 3193611 YP_167275.1 CDS dmdB NC_003911.11 2174589 2176208 R identified by similarity to SP:Q00594; 3-methylmercaptopropionyl-CoA ligase complement(2174589..2176208) Ruegeria pomeroyi DSS-3 3195206 YP_167276.1 CDS pgi NC_003911.11 2176372 2177991 R 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 complement(2176372..2177991) Ruegeria pomeroyi DSS-3 3195577 YP_167277.1 CDS pgl NC_003911.11 2178001 2178672 R identified by match to protein family HMM TIGR01198; 6-phosphogluconolactonase complement(2178001..2178672) Ruegeria pomeroyi DSS-3 3194880 YP_167278.1 CDS zwf-1 NC_003911.11 2178669 2180126 R catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase complement(2178669..2180126) Ruegeria pomeroyi DSS-3 3193693 YP_167279.1 CDS SPO2049 NC_003911.11 2180180 2181238 D identified by match to protein family HMM PF04055; radical SAM domain-containing protein 2180180..2181238 Ruegeria pomeroyi DSS-3 3195256 YP_167280.1 CDS SPO2050 NC_003911.11 2181311 2181580 R identified by similarity to SP:P12288; match to protein family HMM PF06233; Usg complement(2181311..2181580) Ruegeria pomeroyi DSS-3 3192804 YP_167281.1 CDS gyrA NC_003911.11 2181848 2184523 D negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A 2181848..2184523 Ruegeria pomeroyi DSS-3 3193149 YP_167282.1 CDS SPO2052 NC_003911.11 2184627 2184977 D hypothetical protein 2184627..2184977 Ruegeria pomeroyi DSS-3 3194951 YP_167283.1 CDS SPO2053 NC_003911.11 2185071 2186540 R identified by match to protein family HMM PF02074; thermostable carboxypeptidase complement(2185071..2186540) Ruegeria pomeroyi DSS-3 3193386 YP_167284.1 CDS SPO2054 NC_003911.11 2186547 2187620 R identified by match to protein family HMM PF02628; cytochrome c oxidase assembly protein complement(2186547..2187620) Ruegeria pomeroyi DSS-3 3193327 YP_167285.1 CDS SPO2055 NC_003911.11 2187757 2188503 R identified by match to protein family HMM PF00588; match to protein family HMM TIGR00050; RNA methyltransferase complement(2187757..2188503) Ruegeria pomeroyi DSS-3 3193313 YP_167286.1 CDS SPO2056 NC_003911.11 2188790 2189410 D identified by similarity to SP:P39594; thiamine-phosphate pyrophosphorylase 2188790..2189410 Ruegeria pomeroyi DSS-3 3194714 YP_167287.1 CDS SPO2057 NC_003911.11 2189419 2190591 R hypothetical protein complement(2189419..2190591) Ruegeria pomeroyi DSS-3 3193029 YP_167288.1 CDS SPO2058 NC_003911.11 2190590 2191357 D identified by similarity to GB:BAC89701.1; hypothetical protein 2190590..2191357 Ruegeria pomeroyi DSS-3 3193461 YP_167289.1 CDS SPO2059 NC_003911.11 2191417 2192259 D identified by match to protein family HMM PF02798; glutathione S-transferase 2191417..2192259 Ruegeria pomeroyi DSS-3 3193538 YP_167290.1 CDS SPO2060 NC_003911.11 2192314 2193207 D identified by match to protein family HMM PF00294; PfkB family kinase 2192314..2193207 Ruegeria pomeroyi DSS-3 3194812 YP_167291.1 CDS SPO2061 NC_003911.11 2193204 2194118 D identified by match to protein family HMM PF04227; indigoidine synthase A family protein 2193204..2194118 Ruegeria pomeroyi DSS-3 3193592 YP_167292.1 CDS SPO2062 NC_003911.11 2194196 2194870 D identified by similarity to GB:AAQ61403.1; match to protein family HMM PF04367; hypothetical protein 2194196..2194870 Ruegeria pomeroyi DSS-3 3193433 YP_167293.1 CDS SPO2063 NC_003911.11 2194867 2195373 D identified by match to protein family HMM PF00583; acetyltransferase 2194867..2195373 Ruegeria pomeroyi DSS-3 3193283 YP_167294.1 CDS SPO2064 NC_003911.11 2195370 2196401 R identified by match to protein family HMM PF01734; patatin family phospholipase complement(2195370..2196401) Ruegeria pomeroyi DSS-3 3193098 YP_167295.1 CDS bdh-1 NC_003911.11 2196494 2197267 R identified by similarity to SP:O86034; match to protein family HMM PF00106; match to protein family HMM TIGR01963; D-beta-hydroxybutyrate dehydrogenase complement(2196494..2197267) Ruegeria pomeroyi DSS-3 3193339 YP_167296.1 CDS SPO2066 NC_003911.11 2197677 2199491 D identified by match to protein family HMM PF00496; ABC transporter substrate-binding protein 2197677..2199491 Ruegeria pomeroyi DSS-3 3193685 YP_167297.1 CDS SPO2067 NC_003911.11 2199640 2199864 D identified by similarity to GB:BAC46738.1; hypothetical protein 2199640..2199864 Ruegeria pomeroyi DSS-3 3193845 YP_167298.1 CDS SPO2068 NC_003911.11 2199868 2200491 R identified by match to protein family HMM PF01381; DNA-binding protein complement(2199868..2200491) Ruegeria pomeroyi DSS-3 3193401 YP_167299.1 CDS SPO2069 NC_003911.11 2200556 2202073 D identified by similarity to GB:AAA92151.1; match to protein family HMM PF00501; benzoate-coenzyme A ligase 2200556..2202073 Ruegeria pomeroyi DSS-3 3193610 YP_167300.1 CDS SPO2070 NC_003911.11 2202070 2202726 D identified by match to protein family HMM PF01323; DSBA-like thioredoxin family protein 2202070..2202726 Ruegeria pomeroyi DSS-3 3193085 YP_167301.1 CDS SPO2071 NC_003911.11 2202805 2204013 D identified by similarity to SP:P28246; match to protein family HMM PF00083; match to protein family HMM TIGR00710; Bcr/CflA subfamily drug resistance transporter 2202805..2204013 Ruegeria pomeroyi DSS-3 3193264 YP_167302.1 CDS SPO2072 NC_003911.11 2204065 2205738 D identified by match to protein family HMM PF00515; hypothetical protein 2204065..2205738 Ruegeria pomeroyi DSS-3 3193603 YP_167303.1 CDS SPO2073 NC_003911.11 2205699 2206394 D hypothetical protein 2205699..2206394 Ruegeria pomeroyi DSS-3 3193157 YP_167304.1 CDS mfd NC_003911.11 2206464 2209892 R 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 complement(2206464..2209892) Ruegeria pomeroyi DSS-3 3193158 YP_167305.1 CDS SPO2075 NC_003911.11 2209947 2210471 R identified by similarity to GB:AAL26882.1; hypothetical protein complement(2209947..2210471) Ruegeria pomeroyi DSS-3 3194746 YP_167306.1 CDS hemB NC_003911.11 2210595 2211593 D catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase 2210595..2211593 Ruegeria pomeroyi DSS-3 3193195 YP_167307.1 CDS SPO2077 NC_003911.11 2211735 2212307 D twin-arginine translocation pathway signal sequence domain-containing protein 2211735..2212307 Ruegeria pomeroyi DSS-3 3193725 YP_167308.1 CDS SPO2078 NC_003911.11 2212452 2214920 D identified by similarity to SP:P07941; match to protein family HMM PF01804; penicillin amidase 2212452..2214920 Ruegeria pomeroyi DSS-3 3192839 YP_167309.1 CDS SPO2079 NC_003911.11 2214924 2216108 D Na(+)/H(+) antiporter-like protein 2214924..2216108 Ruegeria pomeroyi DSS-3 3193397 YP_167310.1 CDS hflX NC_003911.11 2216093 2217367 R identified by similarity to SP:P25519; match to protein family HMM TIGR00231; GTP-binding protein HflX complement(2216093..2217367) Ruegeria pomeroyi DSS-3 3195610 YP_167311.1 CDS hfq NC_003911.11 2217364 2217603 R Stimulates the elongation of poly(A) tails; RNA-binding protein Hfq complement(2217364..2217603) Ruegeria pomeroyi DSS-3 3193311 YP_167312.1 CDS trkH-2 NC_003911.11 2217741 2219276 R identified by similarity to SP:P21166; match to protein family HMM PF02386; Trk system potassium uptake protein TrkH complement(2217741..2219276) Ruegeria pomeroyi DSS-3 3193259 YP_167313.1 CDS trkA NC_003911.11 2219276 2220652 R 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 complement(2219276..2220652) Ruegeria pomeroyi DSS-3 3192863 YP_167314.1 CDS SPO2084 NC_003911.11 2220715 2221230 D hypothetical protein 2220715..2221230 Ruegeria pomeroyi DSS-3 3192956 YP_167315.1 CDS ntrX NC_003911.11 2221246 2222658 R 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 complement(2221246..2222658) Ruegeria pomeroyi DSS-3 3192664 YP_167316.1 CDS ntrY NC_003911.11 2222655 2224940 R 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 complement(2222655..2224940) Ruegeria pomeroyi DSS-3 3192681 YP_167317.1 CDS ntrC NC_003911.11 2225040 2226413 R 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 complement(2225040..2226413) Ruegeria pomeroyi DSS-3 3195357 YP_167318.1 CDS ntrB NC_003911.11 2226413 2227492 R identified by similarity to SP:P09431; match to protein family HMM PF00512; match to protein family HMM PF02518; nitrogen regulation protein NtrB complement(2226413..2227492) Ruegeria pomeroyi DSS-3 3193223 YP_167319.1 CDS SPO2089 NC_003911.11 2227489 2228472 R identified by similarity to SP:Q08111; match to protein family HMM PF01207; match to protein family HMM TIGR00737; tRNA-dihydrouridine synthase complement(2227489..2228472) Ruegeria pomeroyi DSS-3 3193240 YP_167320.1 CDS ispDF NC_003911.11 2228508 2229800 D 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 2228508..2229800 Ruegeria pomeroyi DSS-3 3193402 YP_167321.1 CDS SPO2091 NC_003911.11 2229797 2230294 D identified by similarity to SP:P18200; match to protein family HMM PF04608; phosphatidylglycerophosphatase 2229797..2230294 Ruegeria pomeroyi DSS-3 3192901 YP_167322.1 CDS SPO2092 NC_003911.11 2230291 2230770 D identified by match to protein family HMM PF02464; match to protein family HMM TIGR00199; competence/damage inducible protein CinA 2230291..2230770 Ruegeria pomeroyi DSS-3 3193111 YP_167323.1 CDS amt-1 NC_003911.11 2230811 2232106 D identified by match to protein family HMM PF00909; match to protein family HMM TIGR00836; ammonium transporter 2230811..2232106 Ruegeria pomeroyi DSS-3 3194760 YP_167324.1 CDS SPO2094 NC_003911.11 2232174 2232686 R identified by similarity to GB:AAK38651.1; ACT domain-containing protein complement(2232174..2232686) Ruegeria pomeroyi DSS-3 3193351 YP_167325.1 CDS SPO2095 NC_003911.11 2232782 2234077 R identified by match to protein family HMM PF03972; MmgE/PrpD family protein complement(2232782..2234077) Ruegeria pomeroyi DSS-3 3193629 YP_167326.1 CDS SPO2096 NC_003911.11 2234124 2234570 R identified by match to protein family HMM PF03654; aromatic-rich family protein complement(2234124..2234570) Ruegeria pomeroyi DSS-3 3193710 YP_167327.1 CDS hpt NC_003911.11 2234645 2235187 D identified by similarity to SP:P37171; match to protein family HMM PF00156; match to protein family HMM TIGR01203; hypoxanthine phosphoribosyltransferase 2234645..2235187 Ruegeria pomeroyi DSS-3 3194848 YP_167328.1 CDS SPO2098 NC_003911.11 2235249 2236100 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(2235249..2236100) Ruegeria pomeroyi DSS-3 3192912 YP_167329.1 CDS cycF NC_003911.11 2236210 2236686 D identified by similarity to SP:Q53142; match to protein family HMM PF01322; cytochrome c-554 2236210..2236686 Ruegeria pomeroyi DSS-3 3192870 YP_167330.1 CDS cycG NC_003911.11 2236745 2237629 D identified by similarity to SP:Q53143; match to protein family HMM PF00034; diheme cytochrome c-type 2236745..2237629 Ruegeria pomeroyi DSS-3 3193411 YP_167331.1 CDS SPO2101 NC_003911.11 2237607 2238779 R identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase complement(2237607..2238779) Ruegeria pomeroyi DSS-3 3192825 YP_167332.1 CDS lipA NC_003911.11 2238776 2239726 R 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 complement(2238776..2239726) Ruegeria pomeroyi DSS-3 3193172 YP_167333.1 CDS SPO2103 NC_003911.11 2239931 2240479 D identified by similarity to PIR:S39907; match to protein family HMM PF00578; anti-oxidant AhpCTSA family protein 2239931..2240479 Ruegeria pomeroyi DSS-3 3193320 YP_167334.1 CDS SPO2104 NC_003911.11 2240640 2241104 D identified by similarity to GB:AAK22261.1; hypothetical protein 2240640..2241104 Ruegeria pomeroyi DSS-3 3192864 YP_167335.1 CDS SPO2105 NC_003911.11 2241182 2242147 R identified by similarity to SP:P52677; match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(2241182..2242147) Ruegeria pomeroyi DSS-3 3193609 YP_167336.1 CDS SPO2106 NC_003911.11 2242171 2243325 R identified by similarity to GB:CAE27296.1; hypothetical protein complement(2242171..2243325) Ruegeria pomeroyi DSS-3 3193011 YP_167337.1 CDS SPO2107 NC_003911.11 2243536 2243877 D hypothetical protein 2243536..2243877 Ruegeria pomeroyi DSS-3 3192855 YP_167338.1 CDS SPO2108 NC_003911.11 2243870 2245414 R identified by match to protein family HMM PF06253; trimethylamine methyltransferase complement(2243870..2245414) Ruegeria pomeroyi DSS-3 3195647 YP_167339.1 CDS guaA NC_003911.11 2245651 2247210 D contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase 2245651..2247210 Ruegeria pomeroyi DSS-3 3193064 YP_167340.1 CDS SPO2110 NC_003911.11 2247244 2248110 D identified by match to protein family HMM PF00892; hypothetical protein 2247244..2248110 Ruegeria pomeroyi DSS-3 3193391 YP_167341.1 CDS SPO2111 NC_003911.11 2248223 2249362 D identified by match to protein family HMM PF03349; OmpP1/FadL/TodX family outer membrane transporter 2248223..2249362 Ruegeria pomeroyi DSS-3 3193347 YP_167342.1 CDS SPO2112 NC_003911.11 2249417 2250316 D identified by match to protein family HMM PF00892; transmembrane drug/metabolite transporter family protein 2249417..2250316 Ruegeria pomeroyi DSS-3 3193460 YP_167343.1 CDS SPO2113 NC_003911.11 2250313 2251236 D hypothetical protein 2250313..2251236 Ruegeria pomeroyi DSS-3 3192971 YP_167344.1 CDS SPO2116 NC_003911.11 2251862 2252440 D identified by match to protein family HMM PF00597; DedA family protein 2251862..2252440 Ruegeria pomeroyi DSS-3 3193260 YP_167345.1 CDS SPO2117 NC_003911.11 2252440 2252901 D identified by match to protein family HMM PF02600; DsbB family disulfide bond formation protein 2252440..2252901 Ruegeria pomeroyi DSS-3 3195631 YP_167346.1 CDS SPO2118 NC_003911.11 2253001 2253426 R identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator complement(2253001..2253426) Ruegeria pomeroyi DSS-3 3195643 YP_167347.1 CDS rocF NC_003911.11 2253447 2254460 D identified by similarity to SP:Q59174; match to protein family HMM PF00491; match to protein family HMM TIGR01229; arginase 2253447..2254460 Ruegeria pomeroyi DSS-3 3193436 YP_167348.1 CDS SPO2120 NC_003911.11 2254457 2255386 D identified by match to protein family HMM PF02274; amidinotransferase 2254457..2255386 Ruegeria pomeroyi DSS-3 3194700 YP_167349.1 CDS arcB NC_003911.11 2255383 2256447 D catalyzes the formation of L-proline from L-ornithine; ornithine cyclodeaminase 2255383..2256447 Ruegeria pomeroyi DSS-3 3192981 YP_167350.1 CDS phnA NC_003911.11 2256609 2256944 D identified by match to protein family HMM PF03831; match to protein family HMM TIGR00686; alkylphosphonate utilization protein PhnA 2256609..2256944 Ruegeria pomeroyi DSS-3 3192690 YP_167351.1 CDS SPO2123 NC_003911.11 2256948 2257532 R identified by match to protein family HMM PF01844; HNH endonuclease complement(2256948..2257532) Ruegeria pomeroyi DSS-3 3193103 YP_167352.1 CDS SPO2124 NC_003911.11 2257748 2258350 D identified by match to protein family HMM PF00849; match to protein family HMM TIGR00093; RNA pseudouridylate synthase 2257748..2258350 Ruegeria pomeroyi DSS-3 3192861 YP_167353.1 CDS SPO2125 NC_003911.11 2258355 2258852 R identified by match to protein family HMM PF00583; acetyltransferase complement(2258355..2258852) Ruegeria pomeroyi DSS-3 3193458 YP_167354.1 CDS SPO2126 NC_003911.11 2258849 2259514 R identified by match to protein family HMM PF02230; phospholipase/carboxylesterase complement(2258849..2259514) Ruegeria pomeroyi DSS-3 3195484 YP_167355.1 CDS SPO2127 NC_003911.11 2259511 2260143 R identified by match to protein family HMM PF00730; DNA-3-methyladenine glycosylase II complement(2259511..2260143) Ruegeria pomeroyi DSS-3 3193412 YP_167356.1 CDS SPO2128 NC_003911.11 2260247 2261464 D identified by similarity to GB:CAE30241.1; transporter 2260247..2261464 Ruegeria pomeroyi DSS-3 3193805 YP_167357.1 CDS SPO2129 NC_003911.11 2261595 2262377 R identified by similarity to PIR:F87495; hypothetical protein complement(2261595..2262377) Ruegeria pomeroyi DSS-3 3194891 YP_167358.1 CDS SPO2130 NC_003911.11 2262374 2264008 R catalyzes the formation of 2-isopropylmalate from 1-methyl-2-oxobutanoate and acetyl-CoA; alpha-isopropylmalate synthase complement(2262374..2264008) Ruegeria pomeroyi DSS-3 3192780 YP_167359.1 CDS cysS NC_003911.11 2264124 2265521 R identified by similarity to SP:P21888; match to protein family HMM PF01406; match to protein family HMM TIGR00435; cysteinyl-tRNA synthetase complement(2264124..2265521) Ruegeria pomeroyi DSS-3 3193717 YP_167360.1 CDS aspC-3 NC_003911.11 2265779 2266966 D identified by similarity to SP:Q56232; match to protein family HMM PF00155; aspartate aminotransferase 2265779..2266966 Ruegeria pomeroyi DSS-3 3192683 YP_167361.1 CDS SPO2133 NC_003911.11 2267010 2267546 R identified by similarity to GB:AAL60203.1; hypothetical protein complement(2267010..2267546) Ruegeria pomeroyi DSS-3 3193812 YP_167362.1 CDS SPO2134 NC_003911.11 2267949 2269493 D identified by match to protein family HMM PF06253; trimethylamine methyltransferase 2267949..2269493 Ruegeria pomeroyi DSS-3 3193504 YP_167363.1 CDS SPO2135 NC_003911.11 2269551 2269796 R identified by similarity to GB:BAC50222.1; hypothetical protein complement(2269551..2269796) Ruegeria pomeroyi DSS-3 3193454 YP_167364.1 CDS nrdJ NC_003911.11 2270351 2273995 R Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha complement(2270351..2273995) Ruegeria pomeroyi DSS-3 3192806 YP_167365.1 CDS SPO2137 NC_003911.11 2274542 2274985 D lipoprotein 2274542..2274985 Ruegeria pomeroyi DSS-3 3195477 YP_167366.1 CDS SPO2139 NC_003911.11 2275116 2275583 R identified by similarity to GB:CAE27967.1; match to protein family HMM PF02643; hypothetical protein complement(2275116..2275583) Ruegeria pomeroyi DSS-3 3194744 YP_167367.1 CDS SPO2140 NC_003911.11 2275594 2276121 R identified by similarity to SP:P32081; similarity to SP:P36997; match to protein family HMM PF00313; cold shock DNA-binding domain-containing protein complement(2275594..2276121) Ruegeria pomeroyi DSS-3 3193503 YP_167368.1 CDS SPO2141 NC_003911.11 2276242 2276871 R identified by match to protein family HMM PF01243; pyridoxamine 5''-phosphate oxidase complement(2276242..2276871) Ruegeria pomeroyi DSS-3 3193231 YP_167369.1 CDS fabI-2 NC_003911.11 2276982 2277788 D Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-ACP reductase 2276982..2277788 Ruegeria pomeroyi DSS-3 3192884 YP_167370.1 CDS gpt NC_003911.11 2277802 2278317 D catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively; xanthine-guanine phosphoribosyltransferase 2277802..2278317 Ruegeria pomeroyi DSS-3 3192842 YP_167371.1 CDS SPO2144 NC_003911.11 2278388 2279563 D identified by match to protein family HMM PF00155; hypothetical protein 2278388..2279563 Ruegeria pomeroyi DSS-3 3193068 YP_167372.1 CDS SPO2145 NC_003911.11 2279655 2281499 D identified by similarity to PIR:T46851; hypothetical protein 2279655..2281499 Ruegeria pomeroyi DSS-3 3192930 YP_167373.1 CDS trpE NC_003911.11 2281509 2283020 D with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine; anthranilate synthase component I 2281509..2283020 Ruegeria pomeroyi DSS-3 3192794 YP_167374.1 CDS SPO2147 NC_003911.11 2283020 2283544 D identified by similarity to GB:CAC47284.1; match to protein family HMM PF05962; hypothetical protein 2283020..2283544 Ruegeria pomeroyi DSS-3 3193480 YP_167375.1 CDS SPO2148 NC_003911.11 2283631 2285076 R hypothetical protein complement(2283631..2285076) Ruegeria pomeroyi DSS-3 3192649 YP_167376.1 CDS trpG NC_003911.11 2285237 2285818 D TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity; anthranilate synthase component II 2285237..2285818 Ruegeria pomeroyi DSS-3 3192657 YP_167377.1 CDS trpD NC_003911.11 2285815 2286834 D Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate; anthranilate phosphoribosyltransferase 2285815..2286834 Ruegeria pomeroyi DSS-3 3192757 YP_167378.1 CDS trpC NC_003911.11 2286831 2287643 D 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 2286831..2287643 Ruegeria pomeroyi DSS-3 3194776 YP_167379.1 CDS moaC NC_003911.11 2287643 2288116 D 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 2287643..2288116 Ruegeria pomeroyi DSS-3 3192710 YP_167380.1 CDS moaA NC_003911.11 2288113 2289282 D 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 2288113..2289282 Ruegeria pomeroyi DSS-3 3195433 YP_167381.1 CDS lexA NC_003911.11 2289362 2290057 D Represses a number of genes involved in the response to DNA damage; LexA repressor 2289362..2290057 Ruegeria pomeroyi DSS-3 3193214 YP_167382.1 CDS SPO2155 NC_003911.11 2290065 2292095 R competence protein complement(2290065..2292095) Ruegeria pomeroyi DSS-3 3193627 YP_167383.1 CDS gltX NC_003911.11 2292177 2293583 D Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 2292177..2293583 Ruegeria pomeroyi DSS-3 3192862 YP_167384.1 CDS gltA NC_003911.11 2293707 2295002 D identified by similarity to SP:P00891; match to protein family HMM PF00285; match to protein family HMM TIGR01798; citrate synthase I 2293707..2295002 Ruegeria pomeroyi DSS-3 3193605 YP_167385.1 CDS SPO2158 NC_003911.11 2295317 2296498 D hypothetical protein 2295317..2296498 Ruegeria pomeroyi DSS-3 3196471 YP_167386.1 CDS SPO2159 NC_003911.11 2296512 2297696 R identified by similarity to PIR:B97447; match to protein family HMM PF04055; radical SAM domain-containing protein complement(2296512..2297696) Ruegeria pomeroyi DSS-3 3193372 YP_167387.1 CDS SPO2160 NC_003911.11 2297868 2298566 D identified by similarity to SP:O93657; match to protein family HMM PF02310; match to protein family HMM PF02607; corrinoid methyltransferase 2297868..2298566 Ruegeria pomeroyi DSS-3 3193365 YP_167388.1 CDS SPO2161 NC_003911.11 2298744 2299784 D identified by similarity to PIR:T03518; hypothetical protein 2298744..2299784 Ruegeria pomeroyi DSS-3 3192967 YP_167389.1 CDS SPO2162 NC_003911.11 2299870 2300532 D identified by similarity to GB:BAB48654.1; hypothetical protein 2299870..2300532 Ruegeria pomeroyi DSS-3 3193686 YP_167390.1 CDS SPO2163 NC_003911.11 2300559 2301188 R identified by similarity to PIR:AC3193; hypothetical protein complement(2300559..2301188) Ruegeria pomeroyi DSS-3 3193243 YP_167391.1 CDS SPO2164 NC_003911.11 2301282 2301992 D identified by similarity to PIR:AB3193; hypothetical protein 2301282..2301992 Ruegeria pomeroyi DSS-3 3193342 YP_167392.1 CDS SPO2165 NC_003911.11 2301997 2302407 R identified by match to protein family HMM PF02657; Fe-S metabolism associated family protein complement(2301997..2302407) Ruegeria pomeroyi DSS-3 3195531 YP_167393.1 CDS SPO2166 NC_003911.11 2302553 2303077 D lipoprotein 2302553..2303077 Ruegeria pomeroyi DSS-3 3192718 YP_167394.1 CDS rnd NC_003911.11 2303155 2304312 R identified by match to protein family HMM PF01612; match to protein family HMM TIGR01388; ribonuclease D complement(2303155..2304312) Ruegeria pomeroyi DSS-3 3193200 YP_167395.1 CDS purN NC_003911.11 2304432 2305028 R identified by similarity to SP:P08179; match to protein family HMM PF00551; match to protein family HMM TIGR00639; phosphoribosylglycinamide formyltransferase complement(2304432..2305028) Ruegeria pomeroyi DSS-3 3193498 YP_167396.1 CDS purM NC_003911.11 2305025 2306071 R catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase complement(2305025..2306071) Ruegeria pomeroyi DSS-3 3193262 YP_167397.1 CDS SPO2170 NC_003911.11 2306176 2307150 R identified by similarity to GB:AAR21562.1; match to protein family HMM PF00753; match to protein family HMM TIGR01409; metallo-beta-lactamase complement(2306176..2307150) Ruegeria pomeroyi DSS-3 3194651 YP_167398.1 CDS SPO2171 NC_003911.11 2307258 2308181 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2307258..2308181 Ruegeria pomeroyi DSS-3 3193209 YP_167399.1 CDS SPO2173 NC_003911.11 2308313 2309638 R identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase complement(2308313..2309638) Ruegeria pomeroyi DSS-3 3192848 YP_167400.1 CDS SPO2174 NC_003911.11 2309680 2310597 D identified by match to protein family HMM PF00753; metallo-beta-lactamase 2309680..2310597 Ruegeria pomeroyi DSS-3 3193247 YP_167401.1 CDS SPO2176 NC_003911.11 2311560 2312672 D identified by similarity to SP:P77535; match to protein family HMM PF01594; hypothetical protein 2311560..2312672 Ruegeria pomeroyi DSS-3 3195312 YP_167402.1 CDS acuC NC_003911.11 2312693 2313799 D identified by similarity to SP:P39067; match to protein family HMM PF00850; acetoin utilization protein AcuC 2312693..2313799 Ruegeria pomeroyi DSS-3 3193192 YP_167403.1 CDS cls NC_003911.11 2313848 2315260 D catalyzes the transfer of a phosphatidyl group to phosphodidylglycerol to form cardiolipin (diphosphatidylglycerol); cardiolipin synthetase 2313848..2315260 Ruegeria pomeroyi DSS-3 3194660 YP_167404.1 CDS SPO2179 NC_003911.11 2315271 2315705 R identified by similarity to GB:BAB52889.1; hypothetical protein complement(2315271..2315705) Ruegeria pomeroyi DSS-3 3193617 YP_167405.1 CDS SPO2180 NC_003911.11 2315802 2316107 R hypothetical protein complement(2315802..2316107) Ruegeria pomeroyi DSS-3 3193435 YP_167406.1 CDS SPO2181 NC_003911.11 2316132 2316920 D identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 2316132..2316920 Ruegeria pomeroyi DSS-3 3194674 YP_167407.1 CDS SPO2182 NC_003911.11 2316917 2319331 D identified by match to protein family HMM PF02687; permease 2316917..2319331 Ruegeria pomeroyi DSS-3 3192736 YP_167408.1 CDS SPO2183 NC_003911.11 2319315 2320364 D identified by similarity to GB:AAK90829.1; hypothetical protein 2319315..2320364 Ruegeria pomeroyi DSS-3 3193399 YP_167409.1 CDS SPO2184 NC_003911.11 2320417 2321469 R identified by similarity to SP:P55495; hypothetical protein complement(2320417..2321469) Ruegeria pomeroyi DSS-3 3192671 YP_167410.1 CDS SPO2185 NC_003911.11 2321564 2322001 R identified by match to protein family HMM PF00582; universal stress protein family protein complement(2321564..2322001) Ruegeria pomeroyi DSS-3 3193417 YP_167411.1 CDS SPO2186 NC_003911.11 2321998 2324607 R identified by match to protein family HMM PF06808; match to protein family HMM TIGR02123; TRAP transporter, 4TM/12TM fusion protein complement(2321998..2324607) Ruegeria pomeroyi DSS-3 3193091 YP_167412.1 CDS SPO2187 NC_003911.11 2324731 2325732 R identified by similarity to SP:P12920; match to protein family HMM TIGR02122; TRAP transporter solute receptor TAXI family protein complement(2324731..2325732) Ruegeria pomeroyi DSS-3 3192688 YP_167413.1 CDS SPO2188 NC_003911.11 2325957 2326376 R identified by match to protein family HMM PF00583; acetyltransferase complement(2325957..2326376) Ruegeria pomeroyi DSS-3 3194655 YP_167414.1 CDS SPO2189 NC_003911.11 2326570 2327034 R identified by match to protein family HMM PF01037; AsnC family transcriptional regulator complement(2326570..2327034) Ruegeria pomeroyi DSS-3 3193169 YP_167415.1 CDS hutC NC_003911.11 2327119 2327820 R identified by match to protein family HMM PF00392; histidine utilization repressor complement(2327119..2327820) Ruegeria pomeroyi DSS-3 3193905 YP_167416.1 CDS hutI NC_003911.11 2327900 2329207 D catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway; imidazolonepropionase 2327900..2329207 Ruegeria pomeroyi DSS-3 3193081 YP_167417.1 CDS hutH NC_003911.11 2329204 2330742 D catalyzes the degradation of histidine to urocanate and ammmonia; histidine ammonia-lyase 2329204..2330742 Ruegeria pomeroyi DSS-3 3192758 YP_167418.1 CDS hutG NC_003911.11 2330739 2331554 D identified by match to protein family HMM PF05013; match to protein family HMM TIGR02017; N-formylglutamate amidohydrolase 2330739..2331554 Ruegeria pomeroyi DSS-3 3196342 YP_167419.1 CDS hutU NC_003911.11 2331557 2333239 D catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism; urocanate hydratase 2331557..2333239 Ruegeria pomeroyi DSS-3 3194783 YP_167420.1 CDS hutF NC_003911.11 2333251 2334612 D catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate; N-formimino-L-glutamate deiminase 2333251..2334612 Ruegeria pomeroyi DSS-3 3192698 YP_167421.1 CDS SPO2195 NC_003911.11 2334740 2335882 D identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase 2334740..2335882 Ruegeria pomeroyi DSS-3 3194647 YP_167422.1 CDS SPO2196 NC_003911.11 2335885 2337078 D catalyzes the formation of pyruvate from 2,3-diaminopropionate; diaminopropionate ammonia-lyase 2335885..2337078 Ruegeria pomeroyi DSS-3 3192935 YP_167423.1 CDS SPO2197 NC_003911.11 2337097 2338077 R identified by similarity to PIR:H75411; match to protein family HMM PF05661; hypothetical protein complement(2337097..2338077) Ruegeria pomeroyi DSS-3 3192867 YP_167424.1 CDS gap-3 NC_003911.11 2338261 2339262 D 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 2338261..2339262 Ruegeria pomeroyi DSS-3 3192734 YP_167425.1 CDS SPO2199 NC_003911.11 2339278 2339481 D hypothetical protein 2339278..2339481 Ruegeria pomeroyi DSS-3 3194935 YP_167426.1 CDS coaD NC_003911.11 2339581 2340078 R Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase complement(2339581..2340078) Ruegeria pomeroyi DSS-3 3193063 YP_167427.1 CDS SPO2201 NC_003911.11 2340172 2340606 R identified by match to protein family HMM PF00571; hypothetical protein complement(2340172..2340606) Ruegeria pomeroyi DSS-3 3192666 YP_167428.1 CDS SPO2202 NC_003911.11 2340667 2341569 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(2340667..2341569) Ruegeria pomeroyi DSS-3 3194869 YP_167429.1 CDS mmsA NC_003911.11 2341675 2343174 D identified by similarity to SP:P28810; match to protein family HMM PF00171; match to protein family HMM TIGR01722; methylmalonate-semialdehyde dehydrogenase 2341675..2343174 Ruegeria pomeroyi DSS-3 3194905 YP_167430.1 CDS SPO2204 NC_003911.11 2343235 2343735 R identified by similarity to GB:AAM72242.1; hypothetical protein complement(2343235..2343735) Ruegeria pomeroyi DSS-3 3195192 YP_167431.1 CDS SPO2205 NC_003911.11 2343876 2344526 D identified by match to protein family HMM PF03734; ErfK/YbiS/YcfS/YnhG family protein 2343876..2344526 Ruegeria pomeroyi DSS-3 3194713 YP_167432.1 CDS SPO2206 NC_003911.11 2344523 2344993 R hypothetical protein complement(2344523..2344993) Ruegeria pomeroyi DSS-3 3194915 YP_167433.1 CDS SPO2207 NC_003911.11 2345034 2345492 R hypothetical protein complement(2345034..2345492) Ruegeria pomeroyi DSS-3 3194879 YP_167434.1 CDS SPO2208 NC_003911.11 2345609 2346454 R identified by similarity to GB:BAB53466.1; hypothetical protein complement(2345609..2346454) Ruegeria pomeroyi DSS-3 3194896 YP_167435.1 CDS SPO2209 NC_003911.11 2346548 2347702 D ATP-dependent carboxylate-amine ligase; carboxylate-amine ligase 2346548..2347702 Ruegeria pomeroyi DSS-3 3194886 YP_167436.1 CDS SPO2210 NC_003911.11 2347766 2349916 R identified by match to protein family HMM PF02012; BNR/Asp-box repeat-containing protein complement(2347766..2349916) Ruegeria pomeroyi DSS-3 3194855 YP_167437.1 CDS SPO2211 NC_003911.11 2350328 2351470 D 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 2350328..2351470 Ruegeria pomeroyi DSS-3 3194875 YP_167438.1 CDS SPO2212 NC_003911.11 2351478 2352524 D identified by match to protein family HMM PF00378; enoyl-CoA hydratase 2351478..2352524 Ruegeria pomeroyi DSS-3 3195378 YP_167439.1 CDS mmsB-1 NC_003911.11 2352521 2353393 D identified by similarity to SP:P28811; match to protein family HMM PF03446; match to protein family HMM TIGR01692; 3-hydroxyisobutyrate dehydrogenase 2352521..2353393 Ruegeria pomeroyi DSS-3 3192822 YP_167440.1 CDS betC-2 NC_003911.11 2353972 2355468 R identified by similarity to SP:O69787; match to protein family HMM PF00884; choline sulfatase complement(2353972..2355468) Ruegeria pomeroyi DSS-3 3194829 YP_167441.1 CDS SPO2215 NC_003911.11 2355531 2356112 R identified by match to protein family HMM PF00903; glyoxalase complement(2355531..2356112) Ruegeria pomeroyi DSS-3 3194851 YP_167442.1 CDS SPO2216 NC_003911.11 2356164 2356949 R identified by match to protein family HMM PF01381; DNA-binding protein complement(2356164..2356949) Ruegeria pomeroyi DSS-3 3193962 YP_167443.1 CDS SPO2217 NC_003911.11 2357103 2357516 R hypothetical protein complement(2357103..2357516) Ruegeria pomeroyi DSS-3 3195603 YP_167444.1 CDS uvrA NC_003911.11 2357532 2360447 R 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 complement(2357532..2360447) Ruegeria pomeroyi DSS-3 3194701 YP_167445.1 CDS SPO2219 NC_003911.11 2360617 2360976 D identified by match to protein family HMM PF00581; rhodanese-like domain-containing protein 2360617..2360976 Ruegeria pomeroyi DSS-3 3194768 YP_167446.1 CDS SPO2220 NC_003911.11 2360983 2361633 R identified by similarity to GB:BAB53751.1; hypothetical protein complement(2360983..2361633) Ruegeria pomeroyi DSS-3 3194845 YP_167447.1 CDS SPO2221 NC_003911.11 2361733 2363430 D identified by match to protein family HMM PF00092; von Willebrand factor A 2361733..2363430 Ruegeria pomeroyi DSS-3 3194696 YP_167448.1 CDS SPO2222 NC_003911.11 2363490 2364884 R E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase complement(2363490..2364884) Ruegeria pomeroyi DSS-3 3194814 YP_167449.1 CDS SPO2223 NC_003911.11 2365060 2365491 D hypothetical protein 2365060..2365491 Ruegeria pomeroyi DSS-3 3194747 YP_167450.1 CDS SPO2224 NC_003911.11 2365502 2366083 R identified by similarity to GB:BAC46583.1; match to protein family HMM PF06041; hypothetical protein complement(2365502..2366083) Ruegeria pomeroyi DSS-3 3194710 YP_167451.1 CDS SPO2225 NC_003911.11 2366199 2367461 R hypothetical protein complement(2366199..2367461) Ruegeria pomeroyi DSS-3 3194883 YP_167452.1 CDS queA NC_003911.11 2367563 2368612 R Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine--tRNA ribosyltransferase-isomerase complement(2367563..2368612) Ruegeria pomeroyi DSS-3 3194698 YP_167453.1 CDS SPO2227 NC_003911.11 2368682 2372104 R identified by similarity to GB:BAC49590.1; hypothetical protein complement(2368682..2372104) Ruegeria pomeroyi DSS-3 3194005 YP_167454.1 CDS SPO2228 NC_003911.11 2372166 2372627 D identified by match to protein family HMM PF00578; AhpC/TSA family protein 2372166..2372627 Ruegeria pomeroyi DSS-3 3194741 YP_167455.1 CDS SPO2229 NC_003911.11 2372624 2373460 D identified by similarity to PIR:G97580; match to protein family HMM PF04305; hypothetical protein 2372624..2373460 Ruegeria pomeroyi DSS-3 3194288 YP_167456.1 CDS SPO2230 NC_003911.11 2373484 2374977 D identified by match to protein family HMM PF01551; M24/M37 family peptidase 2373484..2374977 Ruegeria pomeroyi DSS-3 3194885 YP_167457.1 CDS SPO2231 NC_003911.11 2374967 2375482 D identified by match to protein family HMM PF04519; hypothetical protein 2374967..2375482 Ruegeria pomeroyi DSS-3 3194027 YP_167458.1 CDS SPO2232 NC_003911.11 2375617 2376603 R hypothetical protein complement(2375617..2376603) Ruegeria pomeroyi DSS-3 3194697 YP_167459.1 CDS SPO2233 NC_003911.11 2376704 2377249 R identified by match to protein family HMM PF00160; cyclophilin type peptidyl-prolyl cis-trans isomerase complement(2376704..2377249) Ruegeria pomeroyi DSS-3 3194792 YP_167460.1 CDS SPO2234 NC_003911.11 2377242 2377748 R identified by match to protein family HMM PF00160; cyclophilin type peptidyl-prolyl cis-trans isomerase complement(2377242..2377748) Ruegeria pomeroyi DSS-3 3194048 YP_167461.1 CDS pgk NC_003911.11 2377881 2379077 D Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase 2377881..2379077 Ruegeria pomeroyi DSS-3 3194419 YP_167462.1 CDS SPO2236 NC_003911.11 2379090 2379257 R hypothetical protein complement(2379090..2379257) Ruegeria pomeroyi DSS-3 3194717 YP_167463.1 CDS SPO2237 NC_003911.11 2379254 2379514 R hypothetical protein complement(2379254..2379514) Ruegeria pomeroyi DSS-3 3194597 YP_167464.1 CDS SPO2238 NC_003911.11 2379647 2380579 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2379647..2380579 Ruegeria pomeroyi DSS-3 3193222 YP_167465.1 CDS SPO2239 NC_003911.11 2380704 2381003 D identified by similarity to GB:AAN30050.1; hypothetical protein 2380704..2381003 Ruegeria pomeroyi DSS-3 3195489 YP_167466.1 CDS pdhA NC_003911.11 2381179 2382171 D identified by similarity to SP:Q9R9N5; match to protein family HMM PF00676; pyruvate dehydrogenase complex, E1 component subunit alpha 2381179..2382171 Ruegeria pomeroyi DSS-3 3192883 YP_167467.1 CDS pdhB NC_003911.11 2382186 2383565 D 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 2382186..2383565 Ruegeria pomeroyi DSS-3 3194559 YP_167468.1 CDS pdhC NC_003911.11 2383578 2384891 D 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 2383578..2384891 Ruegeria pomeroyi DSS-3 3194537 YP_167469.1 CDS SPO2243 NC_003911.11 2385038 2386612 R hypothetical protein complement(2385038..2386612) Ruegeria pomeroyi DSS-3 3194045 YP_167470.1 CDS SPO2244 NC_003911.11 2386575 2388632 R hypothetical protein complement(2386575..2388632) Ruegeria pomeroyi DSS-3 3193794 YP_167471.1 CDS SPO2245 NC_003911.11 2389149 2390372 D identified by similarity to GB:BAB53127.1; hypothetical protein 2389149..2390372 Ruegeria pomeroyi DSS-3 3194943 YP_167472.1 CDS cysK NC_003911.11 2390631 2391695 R 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 complement(2390631..2391695) Ruegeria pomeroyi DSS-3 3194926 YP_167473.1 CDS cysE NC_003911.11 2391975 2392787 R 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 complement(2391975..2392787) Ruegeria pomeroyi DSS-3 3193744 YP_167474.1 CDS SPO2248 NC_003911.11 2392851 2393210 D identified by similarity to SP:P18274; dnaK suppressor protein 2392851..2393210 Ruegeria pomeroyi DSS-3 3192739 YP_167475.1 CDS SPO2249 NC_003911.11 2393191 2393487 R hypothetical protein complement(2393191..2393487) Ruegeria pomeroyi DSS-3 3194468 YP_167476.1 CDS SPO2250 NC_003911.11 2393491 2397417 R identified by similarity to PIR:G97477; hypothetical protein complement(2393491..2397417) Ruegeria pomeroyi DSS-3 3194538 YP_167477.1 CDS SPO2251 NC_003911.11 2397417 2397863 R identified by similarity to PIR:F97477; hypothetical protein complement(2397417..2397863) Ruegeria pomeroyi DSS-3 3194932 YP_167478.1 CDS SPO2252 NC_003911.11 2397860 2398747 R identified by similarity to GB:CAE27346.1; hypothetical protein complement(2397860..2398747) Ruegeria pomeroyi DSS-3 3194927 YP_167479.1 CDS SPO2253 NC_003911.11 2398747 2399379 R identified by similarity to PIR:D97477; hypothetical protein complement(2398747..2399379) Ruegeria pomeroyi DSS-3 3193321 YP_167480.1 CDS SPO2255 NC_003911.11 2400044 2400253 R identified by similarity to GB:CAE27342.1; hypothetical protein complement(2400044..2400253) Ruegeria pomeroyi DSS-3 3193867 YP_167481.1 CDS SPO2256 NC_003911.11 2400250 2400570 R hypothetical protein complement(2400250..2400570) Ruegeria pomeroyi DSS-3 3194276 YP_167482.1 CDS SPO2257 NC_003911.11 2400573 2400986 R identified by match to protein family HMM TIGR02126; TP901-1 family major tail protein complement(2400573..2400986) Ruegeria pomeroyi DSS-3 3193233 YP_167483.1 CDS SPO2258 NC_003911.11 2401011 2401424 R identified by similarity to GB:AAN29524.1; hypothetical protein complement(2401011..2401424) Ruegeria pomeroyi DSS-3 3193956 YP_167484.1 CDS SPO2259 NC_003911.11 2401421 2401759 R identified by match to protein family HMM TIGR01563; head-tail adaptor complement(2401421..2401759) Ruegeria pomeroyi DSS-3 3194085 YP_167485.1 CDS SPO2260 NC_003911.11 2401756 2402370 R identified by similarity to GB:AAN29521.1; match to protein family HMM TIGR02215; hypothetical protein complement(2401756..2402370) Ruegeria pomeroyi DSS-3 3193896 YP_167486.1 CDS SPO2261 NC_003911.11 2402520 2403698 R identified by match to protein family HMM PF05065; match to protein family HMM TIGR01554; HK97 family major capsid protein complement(2402520..2403698) Ruegeria pomeroyi DSS-3 3192998 YP_167487.1 CDS SPO2262 NC_003911.11 2403732 2404289 R identified by match to protein family HMM PF04586; match to protein family HMM TIGR01543; HK97 family phage prohead protease complement(2403732..2404289) Ruegeria pomeroyi DSS-3 3195355 YP_167488.1 CDS SPO2263 NC_003911.11 2404318 2404548 R hypothetical protein complement(2404318..2404548) Ruegeria pomeroyi DSS-3 3193792 YP_167489.1 CDS SPO2264 NC_003911.11 2404535 2405707 R identified by match to protein family HMM PF04860; match to protein family HMM TIGR01537; HK97 family portal protein complement(2404535..2405707) Ruegeria pomeroyi DSS-3 3193535 YP_167490.1 CDS SPO2266 NC_003911.11 2405833 2407059 R identified by similarity to GB:AAF13179.1; terminase large subunit complement(2405833..2407059) Ruegeria pomeroyi DSS-3 3194781 YP_167491.1 CDS SPO2267 NC_003911.11 2407112 2407837 R hypothetical protein complement(2407112..2407837) Ruegeria pomeroyi DSS-3 3193057 YP_167492.1 CDS SPO2268 NC_003911.11 2407713 2408099 D identified by similarity to GB:AAK25445.1; hypothetical protein 2407713..2408099 Ruegeria pomeroyi DSS-3 3192769 YP_167493.1 CDS SPO2269 NC_003911.11 2408460 2408984 R identified by similarity to GB:BAB49728.1; hypothetical protein complement(2408460..2408984) Ruegeria pomeroyi DSS-3 3193651 YP_167494.1 CDS SPO2270 NC_003911.11 2409460 2410614 R identified by similarity to GB:AAK23657.1; match to protein family HMM PF02618; match to protein family HMM TIGR00247; hypothetical protein complement(2409460..2410614) Ruegeria pomeroyi DSS-3 3194329 YP_167495.1 CDS fabF NC_003911.11 2410614 2411879 R 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 complement(2410614..2411879) Ruegeria pomeroyi DSS-3 3194842 YP_167496.1 CDS SPO2272 NC_003911.11 2412015 2412758 R identified by similarity to SP:P26720; match to protein family HMM PF00977; phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase complement(2412015..2412758) Ruegeria pomeroyi DSS-3 3193857 YP_167497.1 CDS SPO2273 NC_003911.11 2412853 2413392 R identified by match to protein family HMM PF00583; acetyltransferase complement(2412853..2413392) Ruegeria pomeroyi DSS-3 3193882 YP_167498.1 CDS acpP NC_003911.11 2413533 2413766 R carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein complement(2413533..2413766) Ruegeria pomeroyi DSS-3 3193338 YP_167499.1 CDS fabG NC_003911.11 2413979 2414716 R identified by match to protein family HMM PF00106; match to protein family HMM TIGR01830; 3-oxoacyl-ACP reductase complement(2413979..2414716) Ruegeria pomeroyi DSS-3 3194395 YP_167500.1 CDS fabD NC_003911.11 2414774 2415712 R identified by similarity to SP:P71019; match to protein family HMM PF00698; match to protein family HMM TIGR00128; ACP S-malonyltransferase complement(2414774..2415712) Ruegeria pomeroyi DSS-3 3194285 YP_167501.1 CDS SPO2277 NC_003911.11 2415874 2417091 D identified by match to protein family HMM PF01292; match to protein family HMM PF04264; cytochrome 2415874..2417091 Ruegeria pomeroyi DSS-3 3194621 YP_167502.1 CDS SPO2278 NC_003911.11 2417264 2418736 R hypothetical protein complement(2417264..2418736) Ruegeria pomeroyi DSS-3 3194495 YP_167503.1 CDS SPO2279 NC_003911.11 2418954 2419532 R identified by similarity to GB:AAQ60940.1; match to protein family HMM PF04264; hypothetical protein complement(2418954..2419532) Ruegeria pomeroyi DSS-3 3192651 YP_167504.1 CDS SPO2280 NC_003911.11 2419670 2420395 R hypothetical protein complement(2419670..2420395) Ruegeria pomeroyi DSS-3 3193206 YP_167505.1 CDS rpsF NC_003911.11 2420491 2420844 D binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 2420491..2420844 Ruegeria pomeroyi DSS-3 3194317 YP_167506.1 CDS rpsR NC_003911.11 2420872 2421099 D 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 2420872..2421099 Ruegeria pomeroyi DSS-3 3193473 YP_167507.1 CDS rplI NC_003911.11 2421112 2421714 D in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 2421112..2421714 Ruegeria pomeroyi DSS-3 3192811 YP_167508.1 CDS SPO2284 NC_003911.11 2421897 2422370 D identified by match to protein family HMM PF01464; transglycosylase 2421897..2422370 Ruegeria pomeroyi DSS-3 3194230 YP_167509.1 CDS SPO2285 NC_003911.11 2422764 2423168 D identified by match to protein family HMM PF01381; DNA-binding protein 2422764..2423168 Ruegeria pomeroyi DSS-3 3194528 YP_167510.1 CDS luxR-2 NC_003911.11 2423208 2423909 D identified by match to protein family HMM PF00196; match to protein family HMM PF03472; LuxR family transcriptional regulator 2423208..2423909 Ruegeria pomeroyi DSS-3 3194844 YP_167511.1 CDS SPO2287 NC_003911.11 2424015 2424875 D identified by match to protein family HMM PF00765; autoinducer synthesis protein 2424015..2424875 Ruegeria pomeroyi DSS-3 3193562 YP_167512.1 CDS tig NC_003911.11 2424967 2426298 R Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor complement(2424967..2426298) Ruegeria pomeroyi DSS-3 3194965 YP_167513.1 CDS SPO2289 NC_003911.11 2426489 2427751 R identified by similarity to PIR:E82389; hypothetical protein complement(2426489..2427751) Ruegeria pomeroyi DSS-3 3194334 YP_167514.1 CDS SPO2290 NC_003911.11 2427851 2429167 D hypothetical protein 2427851..2429167 Ruegeria pomeroyi DSS-3 3193920 YP_167515.1 CDS SPO2292 NC_003911.11 2429724 2430233 D identified by similarity to GB:AAR38409.1; hypothetical protein 2429724..2430233 Ruegeria pomeroyi DSS-3 3193936 YP_167516.1 CDS SPO2293 NC_003911.11 2430230 2431900 R 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 complement(2430230..2431900) Ruegeria pomeroyi DSS-3 3194194 YP_167517.1 CDS glnB-1 NC_003911.11 2432038 2432376 D identified by match to protein family HMM PF00543; nitrogen regulatory protein P-II 2432038..2432376 Ruegeria pomeroyi DSS-3 3196300 YP_167518.1 CDS glnA NC_003911.11 2432409 2433815 D 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 2432409..2433815 Ruegeria pomeroyi DSS-3 3194467 YP_167519.1 CDS SPO2296 NC_003911.11 2433950 2434792 D hypothetical protein 2433950..2434792 Ruegeria pomeroyi DSS-3 3195415 YP_167520.1 CDS SPO2297 NC_003911.11 2434985 2435911 D hypothetical protein 2434985..2435911 Ruegeria pomeroyi DSS-3 3195519 YP_167521.1 CDS SPO2298 NC_003911.11 2435967 2436704 R identified by similarity to GB:BAC90287.1; hypothetical protein complement(2435967..2436704) Ruegeria pomeroyi DSS-3 3193282 YP_167522.1 CDS SPO2299 NC_003911.11 2436996 2438177 D identified by match to protein family HMM PF00557; M24 family metallopeptidase 2436996..2438177 Ruegeria pomeroyi DSS-3 3193310 YP_167523.1 CDS SPO2300 NC_003911.11 2438202 2438393 R hypothetical protein complement(2438202..2438393) Ruegeria pomeroyi DSS-3 3193061 YP_167524.1 CDS SPO2301 NC_003911.11 2438618 2439838 D identified by match to protein family HMM PF02566; osmC-like family protein 2438618..2439838 Ruegeria pomeroyi DSS-3 3194936 YP_167525.1 CDS SPO2302 NC_003911.11 2439904 2440491 R identified by match to protein family HMM PF02632; bioY family protein complement(2439904..2440491) Ruegeria pomeroyi DSS-3 3195485 YP_167526.1 CDS SPO2303 NC_003911.11 2440568 2440990 R identified by similarity to PIR:T36819; hypothetical protein complement(2440568..2440990) Ruegeria pomeroyi DSS-3 3193368 YP_167527.1 CDS SPO2304 NC_003911.11 2440987 2441385 R hypothetical protein complement(2440987..2441385) Ruegeria pomeroyi DSS-3 3194293 YP_167528.1 CDS purB NC_003911.11 2441408 2442712 D Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 2441408..2442712 Ruegeria pomeroyi DSS-3 3195293 YP_167529.1 CDS SPO2306 NC_003911.11 2442758 2442979 D hypothetical protein 2442758..2442979 Ruegeria pomeroyi DSS-3 3193297 YP_167530.1 CDS SPO2307 NC_003911.11 2443074 2443628 D identified by similarity to GB:BAB49208.1; hypothetical protein 2443074..2443628 Ruegeria pomeroyi DSS-3 3194491 YP_167531.1 CDS fliG NC_003911.11 2443771 2444820 D identified by similarity to SP:P23448; match to protein family HMM PF01706; flagellar motor switch protein FliG 2443771..2444820 Ruegeria pomeroyi DSS-3 3194628 YP_167532.1 CDS SPO2309 NC_003911.11 2444866 2445849 D identified by match to protein family HMM PF00892; hypothetical protein 2444866..2445849 Ruegeria pomeroyi DSS-3 3194267 YP_167533.1 CDS SPO2310 NC_003911.11 2445859 2446785 D identified by similarity to SP:P24187; match to protein family HMM PF03279; lipid A biosynthesis lauroyl acyltransferase 2445859..2446785 Ruegeria pomeroyi DSS-3 3193277 YP_167534.1 CDS SPO2311 NC_003911.11 2446786 2447670 R identified by similarity to GB:CAC47807.1; match to protein family HMM PF06764; hypothetical protein complement(2446786..2447670) Ruegeria pomeroyi DSS-3 3194732 YP_167535.1 CDS acnA NC_003911.11 2447736 2450426 D Catalyzes the conversion of citrate to isocitrate; aconitate hydratase 2447736..2450426 Ruegeria pomeroyi DSS-3 3193296 YP_167536.1 CDS SPO2313 NC_003911.11 2450606 2450923 D hypothetical protein 2450606..2450923 Ruegeria pomeroyi DSS-3 3194102 YP_167537.1 CDS SPO2314 NC_003911.11 2450992 2451531 R identified by match to protein family HMM TIGR00385; DsbE subfamily periplasmic protein thiol:disulfide oxidoreductase complement(2450992..2451531) Ruegeria pomeroyi DSS-3 3194354 YP_167538.1 CDS ccmC NC_003911.11 2451679 2452452 R identified by similarity to SP:P33929; match to protein family HMM PF01578; match to protein family HMM TIGR01191; heme exporter protein CcmC complement(2451679..2452452) Ruegeria pomeroyi DSS-3 3195309 YP_167539.1 CDS ccmB NC_003911.11 2452498 2453154 R identified by similarity to SP:P33930; match to protein family HMM PF03379; match to protein family HMM TIGR01190; heme exporter protein CcmB complement(2452498..2453154) Ruegeria pomeroyi DSS-3 3193255 YP_167540.1 CDS ccmA NC_003911.11 2453151 2453765 R ATP-binding protein; required for proper cytochrome c maturation; cytochrome c biogenesis protein CcmA complement(2453151..2453765) Ruegeria pomeroyi DSS-3 3194563 YP_167541.1 CDS SPO2318 NC_003911.11 2453905 2454258 R identified by similarity to GB:AAB61905.1; match to protein family HMM PF04635; hypothetical protein complement(2453905..2454258) Ruegeria pomeroyi DSS-3 3194592 YP_167542.1 CDS SPO2319 NC_003911.11 2454260 2455015 R identified by similarity to GB:BAC45969.1; match to protein family HMM PF01925; hypothetical protein complement(2454260..2455015) Ruegeria pomeroyi DSS-3 3193261 YP_167543.1 CDS secF NC_003911.11 2455085 2456053 R 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 complement(2455085..2456053) Ruegeria pomeroyi DSS-3 3193136 YP_167544.1 CDS secD NC_003911.11 2456055 2457716 R 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 complement(2456055..2457716) Ruegeria pomeroyi DSS-3 3194904 YP_167545.1 CDS yajC NC_003911.11 2457745 2458110 R identified by match to protein family HMM PF02699; match to protein family HMM TIGR00739; preprotein translocase subunit YajC complement(2457745..2458110) Ruegeria pomeroyi DSS-3 3194318 YP_167546.1 CDS SPO2323 NC_003911.11 2458194 2459810 D identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS 2458194..2459810 Ruegeria pomeroyi DSS-3 3194610 YP_167547.1 CDS SPO2324 NC_003911.11 2459957 2460373 D identified by similarity to GB:BAB50081.1; hypothetical protein 2459957..2460373 Ruegeria pomeroyi DSS-3 3194625 YP_167548.1 CDS serS NC_003911.11 2460515 2461807 D 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 2460515..2461807 Ruegeria pomeroyi DSS-3 3194584 YP_167549.1 CDS SPO2326 NC_003911.11 2461847 2462536 R hypothetical protein complement(2461847..2462536) Ruegeria pomeroyi DSS-3 3194602 YP_167550.1 CDS SPO2327 NC_003911.11 2462563 2463546 R identified by match to protein family HMM PF00487; fatty acid desaturase complement(2462563..2463546) Ruegeria pomeroyi DSS-3 3192895 YP_167551.1 CDS engA NC_003911.11 2463747 2465210 R 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 complement(2463747..2465210) Ruegeria pomeroyi DSS-3 3194590 YP_167552.1 CDS SPO2329 NC_003911.11 2465260 2466537 R identified by match to protein family HMM PF01011; PQQ repeat-containing protein complement(2465260..2466537) Ruegeria pomeroyi DSS-3 3193836 YP_167553.1 CDS SPO2330 NC_003911.11 2466641 2467417 R hypothetical protein complement(2466641..2467417) Ruegeria pomeroyi DSS-3 3194583 YP_167554.1 CDS SPO2331 NC_003911.11 2467487 2468791 D identified by match to protein family HMM TIGR01730; RND family efflux transporter MFP subunit 2467487..2468791 Ruegeria pomeroyi DSS-3 3193452 YP_167555.1 CDS SPO2332 NC_003911.11 2468788 2472567 D AcrB/AcrD/AcrF family transporter 2468788..2472567 Ruegeria pomeroyi DSS-3 3194573 YP_167556.1 CDS SPO2333 NC_003911.11 2472669 2473028 D hypothetical protein 2472669..2473028 Ruegeria pomeroyi DSS-3 3194552 YP_167557.1 CDS SPO2334 NC_003911.11 2473038 2474666 R identified by match to protein family HMM PF02517; CAAX amino terminal protease complement(2473038..2474666) Ruegeria pomeroyi DSS-3 3194054 YP_167558.1 CDS SPO2335 NC_003911.11 2474742 2476571 R identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter ATP-binding protein/permease complement(2474742..2476571) Ruegeria pomeroyi DSS-3 3192746 YP_167559.1 CDS SPO2336 NC_003911.11 2476640 2478298 R identified by match to protein family HMM PF01476; lysM domain-containing protein complement(2476640..2478298) Ruegeria pomeroyi DSS-3 3194558 YP_167560.1 CDS SPO2337 NC_003911.11 2478424 2478975 D identified by match to protein family HMM PF03641; match to protein family HMM TIGR00730; decarboxylase 2478424..2478975 Ruegeria pomeroyi DSS-3 3194047 YP_167561.1 CDS rarD-1 NC_003911.11 2478912 2479832 R identified by similarity to SP:P27844; match to protein family HMM PF00892; match to protein family HMM TIGR00688; protein RarD complement(2478912..2479832) Ruegeria pomeroyi DSS-3 3194765 YP_167562.1 CDS SPO2339 NC_003911.11 2479902 2480672 R identified by match to protein family HMM PF00378; enoyl-CoA hydratase complement(2479902..2480672) Ruegeria pomeroyi DSS-3 3194933 YP_167563.1 CDS sodB NC_003911.11 2480854 2481453 R identified by similarity to SP:P09157; superoxide dismutase, Fe complement(2480854..2481453) Ruegeria pomeroyi DSS-3 3194900 YP_167564.1 CDS SPO2341 NC_003911.11 2481555 2482307 D identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 2481555..2482307 Ruegeria pomeroyi DSS-3 3194072 YP_167565.1 CDS SPO2342 NC_003911.11 2482748 2483182 R hypothetical protein complement(2482748..2483182) Ruegeria pomeroyi DSS-3 3194186 YP_167566.1 CDS SPO2343 NC_003911.11 2483207 2483656 R hypothetical protein complement(2483207..2483656) Ruegeria pomeroyi DSS-3 3195568 YP_167567.1 CDS SPO2344 NC_003911.11 2484213 2484779 R identified by similarity to SP:Q46338; match to protein family HMM PF04268; sarcosine oxidase subunit gamma complement(2484213..2484779) Ruegeria pomeroyi DSS-3 3194262 YP_167568.1 CDS SPO2345 NC_003911.11 2484772 2487804 R identified by similarity to SP:Q46337; match to protein family HMM PF01571; match to protein family HMM TIGR01372; sarcosine oxidase subunit alpha complement(2484772..2487804) Ruegeria pomeroyi DSS-3 3193813 YP_167569.1 CDS SPO2346 NC_003911.11 2487850 2488179 R identified by similarity to SP:Q46336; match to protein family HMM PF04267; sarcosine oxidase subunit delta complement(2487850..2488179) Ruegeria pomeroyi DSS-3 3193543 YP_167570.1 CDS SPO2347 NC_003911.11 2488757 2489149 R identified by similarity to GB:BAB54267.1; hypothetical protein complement(2488757..2489149) Ruegeria pomeroyi DSS-3 3193514 YP_167571.1 CDS SPO2348 NC_003911.11 2489175 2490476 R identified by similarity to SP:P40875; match to protein family HMM PF01266; match to protein family HMM TIGR01373; sarcosine oxidase subunit beta complement(2489175..2490476) Ruegeria pomeroyi DSS-3 3193974 YP_167572.1 CDS cycH NC_003911.11 2490597 2491832 D identified by similarity to SP:P45400; cytochrome c-type biogenesis protein CycH 2490597..2491832 Ruegeria pomeroyi DSS-3 3195443 YP_167573.1 CDS SPO2350 NC_003911.11 2491829 2492293 D similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function; Holliday junction resolvase-like protein 2491829..2492293 Ruegeria pomeroyi DSS-3 3194839 YP_167574.1 CDS SPO2351 NC_003911.11 2492307 2492540 D identified by similarity to GB:BAB48126.1; match to protein family HMM PF06945; hypothetical protein 2492307..2492540 Ruegeria pomeroyi DSS-3 3193565 YP_167575.1 CDS SPO2352 NC_003911.11 2492612 2494006 R identified by similarity to SP:P55127; match to protein family HMM PF00353; type I secretion target repeat-containing protein complement(2492612..2494006) Ruegeria pomeroyi DSS-3 3194059 YP_167576.1 CDS SPO2353 NC_003911.11 2494151 2494936 R hypothetical protein complement(2494151..2494936) Ruegeria pomeroyi DSS-3 3196490 YP_167577.1 CDS SPO2354 NC_003911.11 2494930 2495754 R identified by match to protein family HMM PF01925; hypothetical protein complement(2494930..2495754) Ruegeria pomeroyi DSS-3 3194755 YP_167578.1 CDS iseR NC_003911.11 2495995 2496801 R identified by match to protein family HMM PF01614; isethionate dissimilation regulator complement(2495995..2496801) Ruegeria pomeroyi DSS-3 3194809 YP_167579.1 CDS iseM NC_003911.11 2496837 2498198 R identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; isethionate TRAP transporter complement(2496837..2498198) Ruegeria pomeroyi DSS-3 3194820 YP_167580.1 CDS iseL NC_003911.11 2498209 2498763 R identified by match to protein family HMM PF04290; isethionate TRAP transporter complement(2498209..2498763) Ruegeria pomeroyi DSS-3 3194893 YP_167581.1 CDS iseK NC_003911.11 2498972 2500204 R identified by match to protein family HMM PF03480; match to protein family HMM TIGR01409; isethionate TRAP transporter complement(2498972..2500204) Ruegeria pomeroyi DSS-3 3194653 YP_167582.1 CDS iseJ NC_003911.11 2500332 2501939 D identified by match to protein family HMM PF00732; match to protein family HMM PF05199; isethionate dehydrogenase 2500332..2501939 Ruegeria pomeroyi DSS-3 3192668 YP_167583.1 CDS SPO2361 NC_003911.11 2503503 2505671 R 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 complement(2503503..2505671) Ruegeria pomeroyi DSS-3 3194743 YP_167584.1 CDS SPO2362 NC_003911.11 2505668 2506669 R identified by similarity to SP:Q52663; amino acid ABC transporter substrate-binding protein complement(2505668..2506669) Ruegeria pomeroyi DSS-3 3194657 YP_167585.1 CDS serB-1 NC_003911.11 2506666 2507559 R identified by match to protein family HMM PF00702; match to protein family HMM TIGR00338; match to protein family HMM TIGR01488; phosphoserine phosphatase complement(2506666..2507559) Ruegeria pomeroyi DSS-3 3194824 YP_167586.1 CDS SPO2364 NC_003911.11 2507889 2508902 D identified by similarity to SP:Q52663; amino acid ABC transporter substrate-binding protein 2507889..2508902 Ruegeria pomeroyi DSS-3 3192845 YP_167587.1 CDS SPO2365 NC_003911.11 2508969 2510141 D identified by similarity to SP:Q52664; match to protein family HMM PF00528; match to protein family HMM TIGR01726; amino acid ABC transporter permease 2508969..2510141 Ruegeria pomeroyi DSS-3 3194682 YP_167588.1 CDS SPO2366 NC_003911.11 2510119 2511246 D identified by similarity to SP:Q52665; match to protein family HMM PF00528; match to protein family HMM TIGR01726; amino acid ABC transporter permease 2510119..2511246 Ruegeria pomeroyi DSS-3 3193628 YP_167589.1 CDS SPO2367 NC_003911.11 2511266 2512036 D identified by similarity to SP:Q52666; match to protein family HMM PF00005; amino acid ABC transporter ATP-binding protein 2511266..2512036 Ruegeria pomeroyi DSS-3 3193012 YP_167590.1 CDS SPO2368 NC_003911.11 2512088 2513695 D identified by match to protein family HMM PF02690; Na/Pi-cotransporter family protein 2512088..2513695 Ruegeria pomeroyi DSS-3 3195298 YP_167591.1 CDS SPO2369 NC_003911.11 2513756 2514418 D identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator 2513756..2514418 Ruegeria pomeroyi DSS-3 3194639 YP_167592.1 CDS SPO2370 NC_003911.11 2514751 2516337 R identified by similarity to SP:P30144; match to protein family HMM PF01235; match to protein family HMM TIGR00835; sodium:alanine symporter family protein complement(2514751..2516337) Ruegeria pomeroyi DSS-3 3193444 YP_167593.1 CDS SPO2371 NC_003911.11 2516319 2516753 R identified by match to protein family HMM PF00582; universal stress protein family protein complement(2516319..2516753) Ruegeria pomeroyi DSS-3 3194860 YP_167594.1 CDS SPO2372 NC_003911.11 2516900 2517355 D identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 2516900..2517355 Ruegeria pomeroyi DSS-3 3193856 YP_167595.1 CDS SPO2373 NC_003911.11 2517367 2517783 R identified by similarity to PIR:B98206; match to protein family HMM PF00903; hypothetical protein complement(2517367..2517783) Ruegeria pomeroyi DSS-3 3192850 YP_167596.1 CDS SPO2374 NC_003911.11 2517869 2518903 R identified by similarity to SP:Q8X5V6; match to protein family HMM PF01207; match to protein family HMM TIGR00742; tRNA-dihydrouridine synthase A complement(2517869..2518903) Ruegeria pomeroyi DSS-3 3194172 YP_167597.1 CDS SPO2376 NC_003911.11 2520538 2521002 R identified by match to protein family HMM PF02629; CoA-binding domain-containing protein complement(2520538..2521002) Ruegeria pomeroyi DSS-3 3192717 YP_167598.1 CDS SPO2377 NC_003911.11 2521006 2521404 R identified by match to protein family HMM PF00111; ferredoxin complement(2521006..2521404) Ruegeria pomeroyi DSS-3 3193359 YP_167599.1 CDS SPO2378 NC_003911.11 2521401 2522750 R identified by match to protein family HMM PF05694; selenium-binding protein complement(2521401..2522750) Ruegeria pomeroyi DSS-3 3194894 YP_167600.1 CDS SPO2380 NC_003911.11 2523564 2524730 R identified by match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF02771; acyl-CoA dehydrogenase complement(2523564..2524730) Ruegeria pomeroyi DSS-3 3195664 YP_167601.1 CDS SPO2381 NC_003911.11 2524849 2525784 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(2524849..2525784) Ruegeria pomeroyi DSS-3 3192856 YP_167602.1 CDS SPO2382 NC_003911.11 2526033 2526986 D identified by similarity to GB:CAE42344.1; match to protein family HMM PF03401; tricarboxylate transporter family protein 2526033..2526986 Ruegeria pomeroyi DSS-3 3192847 YP_167603.1 CDS SPO2383 NC_003911.11 2527016 2527504 D hypothetical protein 2527016..2527504 Ruegeria pomeroyi DSS-3 3193046 YP_167604.1 CDS SPO2384 NC_003911.11 2527492 2529066 D identified by match to protein family HMM PF01970; tricarboxylate transporter family protein 2527492..2529066 Ruegeria pomeroyi DSS-3 3192798 YP_167605.1 CDS SPO2385 NC_003911.11 2529082 2530812 D identified by similarity to SP:P51853; match to protein family HMM PF00205; match to protein family HMM PF02776; benzaldehyde lyase 2529082..2530812 Ruegeria pomeroyi DSS-3 3192974 YP_167606.1 CDS SPO2386 NC_003911.11 2530812 2531141 D identified by similarity to GB:AAM35187.1; hypothetical protein 2530812..2531141 Ruegeria pomeroyi DSS-3 3194640 YP_167607.1 CDS SPO2387 NC_003911.11 2531150 2532556 D identified by match to protein family HMM PF01565; match to protein family HMM PF02913; oxidoreductase, FAD-binding 2531150..2532556 Ruegeria pomeroyi DSS-3 3193395 YP_167608.1 CDS SPO2388 NC_003911.11 2532582 2533223 D identified by similarity to SP:P27847; match to protein family HMM PF01810; LysE family translocator protein 2532582..2533223 Ruegeria pomeroyi DSS-3 3194440 YP_167609.1 CDS SPO2389 NC_003911.11 2533224 2535506 D identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM TIGR00509; molybdopterin-binding oxidoreductase 2533224..2535506 Ruegeria pomeroyi DSS-3 3194863 YP_167610.1 CDS SPO2390 NC_003911.11 2537527 2538186 D identified by match to protein family HMM PF00589; phage integrase site specific recombinase 2537527..2538186 Ruegeria pomeroyi DSS-3 3194646 YP_167611.1 CDS SPO2392 NC_003911.11 2538865 2538969 R hypothetical protein complement(2538865..2538969) Ruegeria pomeroyi DSS-3 3194637 YP_167612.1 CDS SPO2393 NC_003911.11 2539789 2540241 R identified by similarity to GB:CAB76249.1; match to protein family HMM PF06240; carbon monoxide dehydrogenase G protein complement(2539789..2540241) Ruegeria pomeroyi DSS-3 3194846 YP_167613.1 CDS coxF NC_003911.11 2540453 2541235 R identified by similarity to GB:CAB76248.1; match to protein family HMM PF02625; carbon monoxide dehydrogenase F protein complement(2540453..2541235) Ruegeria pomeroyi DSS-3 3193728 YP_167614.1 CDS coxE NC_003911.11 2541232 2542413 R identified by similarity to GB:CAB76247.1; match to protein family HMM PF05762; carbon monoxide dehydrogenase E protein complement(2541232..2542413) Ruegeria pomeroyi DSS-3 3194529 YP_167615.1 CDS coxD NC_003911.11 2542410 2543312 R identified by similarity to GB:CAA57830.1; carbon monoxide dehydrogenase D protein complement(2542410..2543312) Ruegeria pomeroyi DSS-3 3192987 YP_167616.1 CDS coxL-2 NC_003911.11 2543344 2545773 R identified by similarity to SP:P19919; match to protein family HMM PF01315; match to protein family HMM PF02738; carbon monoxide dehydrogenase, large subunit complement(2543344..2545773) Ruegeria pomeroyi DSS-3 3194835 YP_167617.1 CDS coxS-2 NC_003911.11 2545770 2546264 R identified by similarity to SP:P19921; match to protein family HMM PF00111; match to protein family HMM PF01799; carbon monoxide dehydrogenase, small subunit complement(2545770..2546264) Ruegeria pomeroyi DSS-3 3194614 YP_167618.1 CDS coxM NC_003911.11 2546278 2547132 R identified by similarity to SP:P19920; match to protein family HMM PF00941; match to protein family HMM PF03450; carbon monoxide dehydrogenase, medium subunit complement(2546278..2547132) Ruegeria pomeroyi DSS-3 3194034 YP_167619.1 CDS coxC NC_003911.11 2547244 2548365 R identified by similarity to GB:CAB76246.1; match to protein family HMM PF03707; carbon monoxide dehydrogenase operon C protein complement(2547244..2548365) Ruegeria pomeroyi DSS-3 3193853 YP_167620.1 CDS SPO2401 NC_003911.11 2548868 2552137 R identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein complement(2548868..2552137) Ruegeria pomeroyi DSS-3 3193807 YP_167621.1 CDS SPO2403 NC_003911.11 2554589 2554693 D hypothetical protein 2554589..2554693 Ruegeria pomeroyi DSS-3 3193564 YP_167622.1 CDS SPO2405 NC_003911.11 2555372 2556031 R identified by match to protein family HMM PF00589; phage integrase site specific recombinase complement(2555372..2556031) Ruegeria pomeroyi DSS-3 3194572 YP_167623.1 CDS SPO2406 NC_003911.11 2556700 2557140 D identified by similarity to PIR:F95919; ISSpo6, transposase orf A 2556700..2557140 Ruegeria pomeroyi DSS-3 3196314 YP_167624.1 CDS SPO2407 NC_003911.11 2557085 2557660 D identified by similarity to GB:CAC47676.1; ISSpo6, transposase orfB 2557085..2557660 Ruegeria pomeroyi DSS-3 3193340 YP_167625.1 CDS SPO2408 NC_003911.11 2559208 2559843 R hypothetical protein complement(2559208..2559843) Ruegeria pomeroyi DSS-3 3194825 YP_167626.1 CDS SPO2409 NC_003911.11 2560699 2561466 R identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase complement(2560699..2561466) Ruegeria pomeroyi DSS-3 3192703 YP_167627.1 CDS SPO2410 NC_003911.11 2561463 2563244 R catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase complement(2561463..2563244) Ruegeria pomeroyi DSS-3 3192713 YP_167628.1 CDS SPO2411 NC_003911.11 2563267 2563821 D hypothetical protein 2563267..2563821 Ruegeria pomeroyi DSS-3 3194822 YP_167629.1 CDS SPO2412 NC_003911.11 2563843 2564538 D identified by similarity to GB:BAB21456.3; aldolase 2563843..2564538 Ruegeria pomeroyi DSS-3 3192853 YP_167630.1 CDS SPO2413 NC_003911.11 2564548 2565300 D identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2564548..2565300 Ruegeria pomeroyi DSS-3 3194827 YP_167631.1 CDS SPO2414 NC_003911.11 2565441 2566610 R identified by match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase complement(2565441..2566610) Ruegeria pomeroyi DSS-3 3194010 YP_167632.1 CDS SPO2415 NC_003911.11 2566607 2567521 R identified by match to protein family HMM PF05721; phytanoyl-CoA dioxygenase complement(2566607..2567521) Ruegeria pomeroyi DSS-3 3193600 YP_167633.1 CDS SPO2416 NC_003911.11 2567541 2568452 R identified by similarity to SP:P23523; 3-hydroxyisobutyrate dehydrogenase complement(2567541..2568452) Ruegeria pomeroyi DSS-3 3194997 YP_167634.1 CDS idnO NC_003911.11 2568543 2569304 R catalyzes the formation of 5-dehydro-D-gluconate from D-gluconate; gluconate 5-dehydrogenase complement(2568543..2569304) Ruegeria pomeroyi DSS-3 3192778 YP_167635.1 CDS SPO2418 NC_003911.11 2569503 2570105 D identified by match to protein family HMM PF01810; amino acid transporter LysE 2569503..2570105 Ruegeria pomeroyi DSS-3 3194808 YP_167636.1 CDS SPO2419 NC_003911.11 2570166 2571317 D identified by similarity to GB:CAB55723.1; hypothetical protein 2570166..2571317 Ruegeria pomeroyi DSS-3 3195201 YP_167637.1 CDS kdgK NC_003911.11 2571466 2572380 D identified by similarity to SP:P37647; match to protein family HMM PF00294; 2-dehydro-3-deoxygluconokinase 2571466..2572380 Ruegeria pomeroyi DSS-3 3194444 YP_167638.1 CDS SPO2421 NC_003911.11 2572377 2573345 D identified by similarity to PIR:B96013; hypothetical protein 2572377..2573345 Ruegeria pomeroyi DSS-3 3193263 YP_167639.1 CDS SPO2422 NC_003911.11 2573459 2574400 R identified by match to protein family HMM PF00389; match to protein family HMM PF02826; D-isomer specific 2-hydroxyacid dehydrogenase complement(2573459..2574400) Ruegeria pomeroyi DSS-3 3194503 YP_167640.1 CDS SPO2423 NC_003911.11 2574536 2574799 D identified by similarity to SP:O58489; hypothetical protein 2574536..2574799 Ruegeria pomeroyi DSS-3 3194787 YP_167641.1 CDS idnD NC_003911.11 2574813 2575862 D identified by similarity to SP:P39346; match to protein family HMM PF00107; L-idonate 5-dehydrogenase 2574813..2575862 Ruegeria pomeroyi DSS-3 3193193 YP_167642.1 CDS aroE NC_003911.11 2575872 2576699 D AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase 2575872..2576699 Ruegeria pomeroyi DSS-3 3193039 YP_167643.1 CDS SPO2426 NC_003911.11 2576701 2577588 R identified by match to protein family HMM PF00892; hypothetical protein complement(2576701..2577588) Ruegeria pomeroyi DSS-3 3194474 YP_167644.1 CDS SPO2427 NC_003911.11 2577596 2578318 R identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase complement(2577596..2578318) Ruegeria pomeroyi DSS-3 3193137 YP_167645.1 CDS SPO2428 NC_003911.11 2578315 2579223 R identified by match to protein family HMM PF03446; 6-phosphogluconate dehydrogenase complement(2578315..2579223) Ruegeria pomeroyi DSS-3 3194447 YP_167646.1 CDS SPO2429 NC_003911.11 2579220 2580284 R identified by match to protein family HMM PF01408; match to protein family HMM PF02894; Gfo/Idh/MocA family oxidoreductase complement(2579220..2580284) Ruegeria pomeroyi DSS-3 3194475 YP_167647.1 CDS SPO2430 NC_003911.11 2580281 2581774 R identified by match to protein family HMM PF04292; match to protein family HMM PF04295; UxaA family hydrolase complement(2580281..2581774) Ruegeria pomeroyi DSS-3 3195425 YP_167648.1 CDS SPO2431 NC_003911.11 2581865 2583493 R identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM complement(2581865..2583493) Ruegeria pomeroyi DSS-3 3193883 YP_167649.1 CDS SPO2432 NC_003911.11 2583495 2584103 R identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ complement(2583495..2584103) Ruegeria pomeroyi DSS-3 3194673 YP_167650.1 CDS SPO2433 NC_003911.11 2584432 2585604 R identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP complement(2584432..2585604) Ruegeria pomeroyi DSS-3 3195176 YP_167651.1 CDS SPO2434 NC_003911.11 2585641 2586348 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 2585641..2586348 Ruegeria pomeroyi DSS-3 3193671 YP_167652.1 CDS SPO2435 NC_003911.11 2586391 2587236 D identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase 2586391..2587236 Ruegeria pomeroyi DSS-3 3194708 YP_167653.1 CDS SPO2436 NC_003911.11 2587546 2589984 R identified by match to protein family HMM PF01266; match to protein family HMM PF01571; FAD-dependent oxidoreductase complement(2587546..2589984) Ruegeria pomeroyi DSS-3 3194123 YP_167654.1 CDS SPO2437 NC_003911.11 2590024 2590806 R identified by match to protein family HMM PF01177; Asp/Glu/Hydantoin racemase complement(2590024..2590806) Ruegeria pomeroyi DSS-3 3194574 YP_167655.1 CDS SPO2438 NC_003911.11 2590809 2591696 R identified by match to protein family HMM PF05721; phytanoyl-CoA dioxygenase complement(2590809..2591696) Ruegeria pomeroyi DSS-3 3194661 YP_167656.1 CDS SPO2439 NC_003911.11 2591937 2592704 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 2591937..2592704 Ruegeria pomeroyi DSS-3 3194570 YP_167657.1 CDS SPO2440 NC_003911.11 2592712 2593866 D identified by match to protein family HMM PF00557; M24 family metallopeptidase 2592712..2593866 Ruegeria pomeroyi DSS-3 3195873 YP_167658.1 CDS SPO2441 NC_003911.11 2594080 2595054 D identified by similarity to GB:AAF78097.1; match to protein family HMM PF04069; glycine betaine/L-proline ABC transporter substrate-binding protein 2594080..2595054 Ruegeria pomeroyi DSS-3 3192732 YP_167659.1 CDS SPO2442 NC_003911.11 2595168 2596199 D identified by similarity to SP:P14176; match to protein family HMM PF00528; glycine betaine/proline ABC transporter permease 2595168..2596199 Ruegeria pomeroyi DSS-3 3195170 YP_167660.1 CDS SPO2443 NC_003911.11 2596211 2597272 D identified by similarity to SP:P46920; match to protein family HMM PF00005; glycine betaine/proline ABC transporter ATP-binding protein 2596211..2597272 Ruegeria pomeroyi DSS-3 3194609 YP_167661.1 CDS ndk NC_003911.11 2597384 2597806 R catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase complement(2597384..2597806) Ruegeria pomeroyi DSS-3 3194414 YP_167662.1 CDS SPO2445 NC_003911.11 2597933 2599198 R identified by match to protein family HMM TIGR00710; Bcr/CflA subfamily drug resistance transporter complement(2597933..2599198) Ruegeria pomeroyi DSS-3 3195902 YP_167663.1 CDS SPO2446 NC_003911.11 2599240 2601090 D identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 2599240..2601090 Ruegeria pomeroyi DSS-3 3194578 YP_167664.1 CDS SPO2447 NC_003911.11 2601045 2601569 D identified by match to protein family HMM PF00583; acetyltransferase 2601045..2601569 Ruegeria pomeroyi DSS-3 3195776 YP_167665.1 CDS SPO2448 NC_003911.11 2601566 2602186 D identified by match to protein family HMM PF01914; match to protein family HMM TIGR00427; multiple antibiotic resistance protein MarC 2601566..2602186 Ruegeria pomeroyi DSS-3 3194075 YP_167666.1 CDS SPO2449 NC_003911.11 2602226 2602807 D hypothetical protein 2602226..2602807 Ruegeria pomeroyi DSS-3 3194569 YP_167667.1 CDS SPO2450 NC_003911.11 2602907 2603659 D identified by match to protein family HMM PF01177; Asp/Glu/Hydantoin racemase 2602907..2603659 Ruegeria pomeroyi DSS-3 3194002 YP_167668.1 CDS SPO2451 NC_003911.11 2603669 2604433 R identified by match to protein family HMM PF01553; acyltransferase complement(2603669..2604433) Ruegeria pomeroyi DSS-3 3194053 YP_167669.1 CDS SPO2452 NC_003911.11 2604620 2605084 R 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 complement(2604620..2605084) Ruegeria pomeroyi DSS-3 3192881 YP_167670.1 CDS pepA NC_003911.11 2605089 2606570 R catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase complement(2605089..2606570) Ruegeria pomeroyi DSS-3 3192926 YP_167671.1 CDS SPO2454 NC_003911.11 2606803 2607900 D identified by match to protein family HMM PF03739; YjgP/YjgQ family permease 2606803..2607900 Ruegeria pomeroyi DSS-3 3194435 YP_167672.1 CDS SPO2455 NC_003911.11 2607900 2610056 D identified by similarity to SP:P31554; organic solvent tolerance protein 2607900..2610056 Ruegeria pomeroyi DSS-3 3193355 YP_167673.1 CDS SPO2456 NC_003911.11 2610041 2611279 D peptidyl-prolyl cis-trans isomerase domain-containing protein 2610041..2611279 Ruegeria pomeroyi DSS-3 3194958 YP_167674.1 CDS pdxA NC_003911.11 2611284 2612243 D 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 2611284..2612243 Ruegeria pomeroyi DSS-3 3195279 YP_167675.1 CDS ksgA NC_003911.11 2612325 2613164 D 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 2612325..2613164 Ruegeria pomeroyi DSS-3 3192940 YP_167676.1 CDS SPO2459 NC_003911.11 2613332 2614042 R identified by similarity to PIR:H98216; hypothetical protein complement(2613332..2614042) Ruegeria pomeroyi DSS-3 3194624 YP_167677.1 CDS SPO2460 NC_003911.11 2614200 2615015 R identified by match to protein family HMM TIGR00536; HemK family modification methylase complement(2614200..2615015) Ruegeria pomeroyi DSS-3 3193801 YP_167678.1 CDS prfA NC_003911.11 2615039 2616094 R 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 complement(2615039..2616094) Ruegeria pomeroyi DSS-3 3194030 YP_167679.1 CDS SPO2462 NC_003911.11 2616122 2616451 D identified by similarity to GB:CAC45916.1; hypothetical protein 2616122..2616451 Ruegeria pomeroyi DSS-3 3193596 YP_167680.1 CDS SPO2463 NC_003911.11 2616392 2616796 R identified by similarity to GB:CAE21209.1; hypothetical protein complement(2616392..2616796) Ruegeria pomeroyi DSS-3 3193346 YP_167681.1 CDS speB-2 NC_003911.11 2616800 2617747 R identified by similarity to SP:Q9BSE5; match to protein family HMM PF00491; match to protein family HMM TIGR01230; agmatinase complement(2616800..2617747) Ruegeria pomeroyi DSS-3 3194037 YP_167682.1 CDS SPO2465 NC_003911.11 2617832 2618371 R identified by similarity to GB:AAO54462.1; hypothetical protein complement(2617832..2618371) Ruegeria pomeroyi DSS-3 3194567 YP_167683.1 CDS SPO2466 NC_003911.11 2618411 2618788 D identified by similarity to GB:AAN68182.1; match to protein family HMM PF00903; glyoxalase 2618411..2618788 Ruegeria pomeroyi DSS-3 3192696 YP_167684.1 CDS speB-3 NC_003911.11 2618829 2619812 R catalyzes the formation of putrescine from agmatine; agmatinase complement(2618829..2619812) Ruegeria pomeroyi DSS-3 3193270 YP_167685.1 CDS SPO2468 NC_003911.11 2619858 2621021 R identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase complement(2619858..2621021) Ruegeria pomeroyi DSS-3 3193766 YP_167686.1 CDS mazG NC_003911.11 2621087 2621908 D 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 2621087..2621908 Ruegeria pomeroyi DSS-3 3194456 YP_167687.1 CDS iunH NC_003911.11 2622032 2622973 D identified by match to protein family HMM PF01156; inosine-uridine preferring nucleoside hydrolase 2622032..2622973 Ruegeria pomeroyi DSS-3 3193287 YP_167688.1 CDS SPO2471 NC_003911.11 2622970 2623419 D identified by match to protein family HMM PF00583; acetyltransferase 2622970..2623419 Ruegeria pomeroyi DSS-3 3194164 YP_167689.1 CDS SPO2472 NC_003911.11 2623477 2623791 R identified by similarity to GB:BAC45440.1; hypothetical protein complement(2623477..2623791) Ruegeria pomeroyi DSS-3 3194051 YP_167690.1 CDS SPO2473 NC_003911.11 2623763 2624524 R identified by match to protein family HMM PF00702; match to protein family HMM TIGR01428; match to protein family HMM TIGR01493; haloacid dehalogenase complement(2623763..2624524) Ruegeria pomeroyi DSS-3 3194523 YP_167691.1 CDS eno NC_003911.11 2624682 2625959 R enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase complement(2624682..2625959) Ruegeria pomeroyi DSS-3 3193003 YP_167692.1 CDS SPO2475 NC_003911.11 2626109 2627044 R identified by match to protein family HMM PF00892; hypothetical protein complement(2626109..2627044) Ruegeria pomeroyi DSS-3 3194446 YP_167693.1 CDS SPO2476 NC_003911.11 2627224 2627541 D lipoprotein 2627224..2627541 Ruegeria pomeroyi DSS-3 3194512 YP_167694.1 CDS SPO2477 NC_003911.11 2627656 2628069 R identified by match to protein family HMM PF01475; FUR family transcriptional regulator complement(2627656..2628069) Ruegeria pomeroyi DSS-3 3194017 YP_167695.1 CDS SPO2479 NC_003911.11 2629710 2630141 R identified by similarity to PIR:E87313; match to protein family HMM PF06172; hypothetical protein complement(2629710..2630141) Ruegeria pomeroyi DSS-3 3194429 YP_167696.1 CDS SPO2480 NC_003911.11 2630167 2631612 D identified by similarity to SP:Q89MQ0; match to protein family HMM PF02696; hypothetical protein 2630167..2631612 Ruegeria pomeroyi DSS-3 3193161 YP_167697.1 CDS SPO2481 NC_003911.11 2631700 2632605 R identified by match to protein family HMM PF00892; drug/metabolite exporter family protein complement(2631700..2632605) Ruegeria pomeroyi DSS-3 3194428 YP_167698.1 CDS SPO2482 NC_003911.11 2632691 2633392 D identified by match to protein family HMM PF03372; hypothetical protein 2632691..2633392 Ruegeria pomeroyi DSS-3 3194431 YP_167699.1 CDS anmK NC_003911.11 2633490 2634572 R 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 complement(2633490..2634572) Ruegeria pomeroyi DSS-3 3193994 YP_167700.1 CDS tyrS NC_003911.11 2634665 2635912 D identified by similarity to SP:P00951; match to protein family HMM PF00579; match to protein family HMM TIGR00234; tyrosyl-tRNA synthetase 2634665..2635912 Ruegeria pomeroyi DSS-3 3194517 YP_167701.1 CDS SPO2485 NC_003911.11 2636011 2636133 R hypothetical protein complement(2636011..2636133) Ruegeria pomeroyi DSS-3 3194526 YP_167702.1 CDS SPO2486 NC_003911.11 2636180 2637082 D identified by similarity to GB:AAL49478.1; hypothetical protein 2636180..2637082 Ruegeria pomeroyi DSS-3 3196341 YP_167703.1 CDS SPO2487 NC_003911.11 2637110 2637865 D identified by similarity to SP:O02691; match to protein family HMM PF00106; 3-hydroxyacyl-CoA dehydrogenase 2637110..2637865 Ruegeria pomeroyi DSS-3 3194504 YP_167704.1 CDS SPO2488 NC_003911.11 2637887 2639695 R identified by similarity to SP:P43672; match to protein family HMM PF00005; ABC transporter ATP-binding protein complement(2637887..2639695) Ruegeria pomeroyi DSS-3 3194472 YP_167705.1 CDS SPO2489 NC_003911.11 2639748 2640539 R identified by similarity to GB:BAC75021.1; hypothetical protein complement(2639748..2640539) Ruegeria pomeroyi DSS-3 3194454 YP_167706.1 CDS SPO2490 NC_003911.11 2640575 2641042 R identified by match to protein family HMM PF04355; SmpA/OmlA family lipoprotein complement(2640575..2641042) Ruegeria pomeroyi DSS-3 3195382 YP_167707.1 CDS SPO2491 NC_003911.11 2641058 2641666 D identified by similarity to GB:BAB54306.1; hypothetical protein 2641058..2641666 Ruegeria pomeroyi DSS-3 3194514 YP_167708.1 CDS rpmF NC_003911.11 2641875 2642081 D some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 2641875..2642081 Ruegeria pomeroyi DSS-3 3196294 YP_167709.1 CDS plsX NC_003911.11 2642106 2643221 D 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 2642106..2643221 Ruegeria pomeroyi DSS-3 3194463 YP_167710.1 CDS fabH-2 NC_003911.11 2643227 2644198 D identified by similarity to SP:P24249; match to protein family HMM TIGR00747; 3-oxoacyl-ACP synthase 2643227..2644198 Ruegeria pomeroyi DSS-3 3194497 YP_167711.1 CDS ihfA NC_003911.11 2644283 2644585 D 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 2644283..2644585 Ruegeria pomeroyi DSS-3 3194426 YP_167712.1 CDS SPO2496 NC_003911.11 2644604 2645335 D identified by match to protein family HMM PF00376; MerR family transcriptional regulator 2644604..2645335 Ruegeria pomeroyi DSS-3 3194501 YP_167713.1 CDS SPO2498 NC_003911.11 2645535 2646614 D Catalyzes the deamination of dCTP to form dUTP; 2'-deoxycytidine 5'-triphosphate deaminase 2645535..2646614 Ruegeria pomeroyi DSS-3 3194232 YP_167714.1 CDS SPO2499 NC_003911.11 2646625 2646882 R hypothetical protein complement(2646625..2646882) Ruegeria pomeroyi DSS-3 3194235 YP_167715.1 CDS scpB NC_003911.11 2646909 2647565 R identified by match to protein family HMM PF04079; match to protein family HMM TIGR00281; segregation and condensation protein B complement(2646909..2647565) Ruegeria pomeroyi DSS-3 3194127 YP_167716.1 CDS scpA NC_003911.11 2647562 2648407 R identified by match to protein family HMM PF02616; segregation and condensation protein A complement(2647562..2648407) Ruegeria pomeroyi DSS-3 3194256 YP_167717.1 CDS SPO2502 NC_003911.11 2648343 2649350 R identified by similarity to SP:P75949; match to protein family HMM PF00933; beta-N-acetylhexosaminidase complement(2648343..2649350) Ruegeria pomeroyi DSS-3 3194406 YP_167718.1 CDS SPO2503 NC_003911.11 2649347 2650573 R hypothetical protein complement(2649347..2650573) Ruegeria pomeroyi DSS-3 3195472 YP_167719.1 CDS argS NC_003911.11 2650533 2652278 R 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 complement(2650533..2652278) Ruegeria pomeroyi DSS-3 3193911 YP_167720.1 CDS SPO2505 NC_003911.11 2652350 2653507 R identified by match to protein family HMM PF01966; match to protein family HMM TIGR01353; deoxyguanosinetriphosphate triphosphohydrolase complement(2652350..2653507) Ruegeria pomeroyi DSS-3 3194081 YP_167721.1 CDS SPO2506 NC_003911.11 2653583 2653906 D identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049; Iron-sulfur cluster assembly family protein 2653583..2653906 Ruegeria pomeroyi DSS-3 3194098 YP_167722.1 CDS SPO2507 NC_003911.11 2653910 2654803 R identified by match to protein family HMM PF00892; hypothetical protein complement(2653910..2654803) Ruegeria pomeroyi DSS-3 3194507 YP_167723.1 CDS SPO2508 NC_003911.11 2655936 2656421 R identified by similarity to GB:AAQ93629.1; hypothetical protein complement(2655936..2656421) Ruegeria pomeroyi DSS-3 3195529 YP_167724.1 CDS xth NC_003911.11 2656690 2657496 D identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633; exodeoxyribonuclease III 2656690..2657496 Ruegeria pomeroyi DSS-3 3194499 YP_167725.1 CDS nahG NC_003911.11 2657585 2658751 R identified by similarity to SP:P23262; match to protein family HMM PF01360; salicylate hydroxylase complement(2657585..2658751) Ruegeria pomeroyi DSS-3 3194349 YP_167726.1 CDS SPO2511 NC_003911.11 2658830 2659306 R identified by similarity to SP:P18274; match to protein family HMM PF01258; dnaK suppressor protein complement(2658830..2659306) Ruegeria pomeroyi DSS-3 3194221 YP_167727.1 CDS SPO2512 NC_003911.11 2659642 2660487 D identified by similarity to GB:CAA57830.1; match to protein family HMM PF00004; ATPase AAA 2659642..2660487 Ruegeria pomeroyi DSS-3 3194308 YP_167728.1 CDS SPO2513 NC_003911.11 2660655 2662100 D identified by similarity to GB:CAE27057.1; hypothetical protein 2660655..2662100 Ruegeria pomeroyi DSS-3 3194524 YP_167729.1 CDS SPO2514 NC_003911.11 2662116 2662283 D hypothetical protein 2662116..2662283 Ruegeria pomeroyi DSS-3 3195383 YP_167730.1 CDS SPO2515 NC_003911.11 2662288 2663472 D identified by similarity to GB:BAB50733.1; hypothetical protein 2662288..2663472 Ruegeria pomeroyi DSS-3 3194071 YP_167731.1 CDS SPO2516 NC_003911.11 2663517 2663708 R hypothetical protein complement(2663517..2663708) Ruegeria pomeroyi DSS-3 3194413 YP_167732.1 CDS SPO2517 NC_003911.11 2663950 2664636 D identified by match to protein family HMM PF01435; M48 family peptidase 2663950..2664636 Ruegeria pomeroyi DSS-3 3194332 YP_167733.1 CDS SPO2518 NC_003911.11 2664633 2665637 D identified by match to protein family HMM PF00296; luciferase 2664633..2665637 Ruegeria pomeroyi DSS-3 3194432 YP_167734.1 CDS SPO2519 NC_003911.11 2665629 2666183 R identified by similarity to GB:CAE41104.1; hypothetical protein complement(2665629..2666183) Ruegeria pomeroyi DSS-3 3194275 YP_167735.1 CDS SPO2520 NC_003911.11 2666180 2667391 R identified by similarity to PIR:D83601; hypothetical protein complement(2666180..2667391) Ruegeria pomeroyi DSS-3 3194087 YP_167736.1 CDS SPO2521 NC_003911.11 2667431 2668207 R lipoprotein complement(2667431..2668207) Ruegeria pomeroyi DSS-3 3194418 YP_167737.1 CDS SPO2522 NC_003911.11 2668336 2668611 R hypothetical protein complement(2668336..2668611) Ruegeria pomeroyi DSS-3 3194522 YP_167738.1 CDS glnE NC_003911.11 2668595 2671396 R identified by match to protein family HMM PF03710; glutamate-ammonia ligase adenylyltransferase complement(2668595..2671396) Ruegeria pomeroyi DSS-3 3194476 YP_167739.1 CDS SPO2524 NC_003911.11 2671479 2671952 D identified by match to protein family HMM PF04073; prolyl-tRNA synthetase 2671479..2671952 Ruegeria pomeroyi DSS-3 3194170 YP_167740.1 CDS SPO2525 NC_003911.11 2671962 2672108 R hypothetical protein complement(2671962..2672108) Ruegeria pomeroyi DSS-3 3194335 YP_167741.1 CDS SPO2526 NC_003911.11 2672618 2672830 R hypothetical protein complement(2672618..2672830) Ruegeria pomeroyi DSS-3 3195899 YP_167742.1 CDS nylA NC_003911.11 2675136 2676575 R identified by similarity to SP:P13397; match to protein family HMM PF01425; 6-aminohexanoate-cyclic-dimer hydrolase complement(2675136..2676575) Ruegeria pomeroyi DSS-3 3194246 YP_167743.1 CDS SPO2528 NC_003911.11 2676621 2678336 R activates fatty acids by binding to coenzyme A; AMP-binding protein complement(2676621..2678336) Ruegeria pomeroyi DSS-3 3194385 YP_167744.1 CDS SPO2529 NC_003911.11 2678340 2680004 R identified by similarity to GB:BAB49910.1; hypothetical protein complement(2678340..2680004) Ruegeria pomeroyi DSS-3 3195465 YP_167745.1 CDS SPO2530 NC_003911.11 2680001 2681023 R identified by similarity to SP:P22729; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease complement(2680001..2681023) Ruegeria pomeroyi DSS-3 3194189 YP_167746.1 CDS SPO2531 NC_003911.11 2681020 2681898 R identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease complement(2681020..2681898) Ruegeria pomeroyi DSS-3 3194466 YP_167747.1 CDS SPO2532 NC_003911.11 2681902 2682618 R identified by similarity to SP:P22731; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein complement(2681902..2682618) Ruegeria pomeroyi DSS-3 3194978 YP_167748.1 CDS SPO2533 NC_003911.11 2682615 2683382 R identified by similarity to SP:P21629; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein complement(2682615..2683382) Ruegeria pomeroyi DSS-3 3193897 YP_167749.1 CDS SPO2534 NC_003911.11 2683390 2684709 R 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 complement(2683390..2684709) Ruegeria pomeroyi DSS-3 3194352 YP_167750.1 CDS SPO2535 NC_003911.11 2684729 2685844 R identified by match to protein family HMM PF00850; histone deacetylase/AcuC/AphA family protein complement(2684729..2685844) Ruegeria pomeroyi DSS-3 3194445 YP_167751.1 CDS SPO2536 NC_003911.11 2686001 2686738 D identified by match to protein family HMM PF00196; LuxR family transcriptional regulator 2686001..2686738 Ruegeria pomeroyi DSS-3 3194231 YP_167752.1 CDS SPO2537 NC_003911.11 2687189 2687308 R hypothetical protein complement(2687189..2687308) Ruegeria pomeroyi DSS-3 3194453 YP_167753.1 CDS SPO2538 NC_003911.11 2687395 2688636 R identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase complement(2687395..2688636) Ruegeria pomeroyi DSS-3 3194069 YP_167754.1 CDS SPO2539 NC_003911.11 2688666 2690213 R identified by match to protein family HMM PF00501; AMP-binding protein complement(2688666..2690213) Ruegeria pomeroyi DSS-3 3194407 YP_167755.1 CDS SPO2540 NC_003911.11 2690237 2691607 R identified by match to protein family HMM PF00289; match to protein family HMM PF02785; match to protein family HMM PF02786; carbamoyl-phosphate synthase complement(2690237..2691607) Ruegeria pomeroyi DSS-3 3194166 YP_167756.1 CDS SPO2541 NC_003911.11 2691615 2693171 R identified by similarity to GB:AAD28194.1; match to protein family HMM PF01039; propionyl-CoA carboxylase complement(2691615..2693171) Ruegeria pomeroyi DSS-3 3194433 YP_167757.1 CDS SPO2542 NC_003911.11 2693316 2693543 D identified by match to protein family HMM PF00364; biotin/lipoate binding domain-containing protein 2693316..2693543 Ruegeria pomeroyi DSS-3 3194425 YP_167758.1 CDS SPO2543 NC_003911.11 2693584 2694333 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 2693584..2694333 Ruegeria pomeroyi DSS-3 3195990 YP_167759.1 CDS SPO2544 NC_003911.11 2694321 2695226 R identified by match to protein family HMM PF04909; amidohydrolase complement(2694321..2695226) Ruegeria pomeroyi DSS-3 3194450 YP_167760.1 CDS SPO2545 NC_003911.11 2695285 2696328 R identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP complement(2695285..2696328) Ruegeria pomeroyi DSS-3 3194296 YP_167761.1 CDS SPO2546 NC_003911.11 2696374 2696886 R identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ complement(2696374..2696886) Ruegeria pomeroyi DSS-3 3194374 YP_167762.1 CDS SPO2547 NC_003911.11 2696888 2698201 R identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM complement(2696888..2698201) Ruegeria pomeroyi DSS-3 3194452 YP_167763.1 CDS SPO2548 NC_003911.11 2698322 2699314 D identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase 2698322..2699314 Ruegeria pomeroyi DSS-3 3194298 YP_167764.1 CDS SPO2549 NC_003911.11 2699321 2700352 D identified by match to protein family HMM PF01636; phosphotransferase 2699321..2700352 Ruegeria pomeroyi DSS-3 3194116 YP_167765.1 CDS SPO2550 NC_003911.11 2700409 2701122 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(2700409..2701122) Ruegeria pomeroyi DSS-3 3194265 YP_167766.1 CDS SPO2551 NC_003911.11 2701142 2702098 R 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 complement(2701142..2702098) Ruegeria pomeroyi DSS-3 3194153 YP_167767.1 CDS SPO2552 NC_003911.11 2702098 2703963 R 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 complement(2702098..2703963) Ruegeria pomeroyi DSS-3 3193129 YP_167768.1 CDS SPO2553 NC_003911.11 2703960 2704907 R identified by similarity to SP:P37316; match to protein family HMM PF00528; peptide/opine/nickel uptake ABC transporter permease complement(2703960..2704907) Ruegeria pomeroyi DSS-3 3194148 YP_167769.1 CDS SPO2554 NC_003911.11 2704968 2706599 R identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; peptide/opine/nickel uptake ABC transporter substrate-binding protein complement(2704968..2706599) Ruegeria pomeroyi DSS-3 3195667 YP_167770.1 CDS SPO2555 NC_003911.11 2706647 2707312 D identified by similarity to GB:CAE35155.1; hypothetical protein 2706647..2707312 Ruegeria pomeroyi DSS-3 3194095 YP_167771.1 CDS SPO2556 NC_003911.11 2707305 2708534 D 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 2707305..2708534 Ruegeria pomeroyi DSS-3 3194325 YP_167772.1 CDS gnl NC_003911.11 2710773 2711729 D identified by similarity to SP:Q01578; match to protein family HMM PF03758; gluconolactonase 2710773..2711729 Ruegeria pomeroyi DSS-3 3194423 YP_167773.1 CDS garR NC_003911.11 2711726 2712625 D identified by similarity to SP:P23523; match to protein family HMM PF03446; 2-hydroxy-3-oxopropionate reductase 2711726..2712625 Ruegeria pomeroyi DSS-3 3194136 YP_167774.1 CDS SPO2561 NC_003911.11 2712622 2713854 D identified by match to protein family HMM PF07005; hypothetical protein 2712622..2713854 Ruegeria pomeroyi DSS-3 3194091 YP_167775.1 CDS fucA NC_003911.11 2713851 2714498 D identified by similarity to SP:P11550; match to protein family HMM PF00596; aldolase 2713851..2714498 Ruegeria pomeroyi DSS-3 3194080 YP_167776.1 CDS SPO2563 NC_003911.11 2714495 2715250 D identified by similarity to SP:P30147; hydroxypyruvate isomerase 2714495..2715250 Ruegeria pomeroyi DSS-3 3194109 YP_167777.1 CDS SPO2564 NC_003911.11 2715970 2716074 D hypothetical protein 2715970..2716074 Ruegeria pomeroyi DSS-3 3194642 YP_167778.1 CDS SPO2565 NC_003911.11 2716361 2717443 D 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 2716361..2717443 Ruegeria pomeroyi DSS-3 3194286 YP_167779.1 CDS SPO2566 NC_003911.11 2717430 2718215 D identified by match to protein family HMM PF00903; glyoxalase 2717430..2718215 Ruegeria pomeroyi DSS-3 3194139 YP_167780.1 CDS SPO2567 NC_003911.11 2719098 2719547 D identified by similarity to GB:CAE26557.1; hypothetical protein 2719098..2719547 Ruegeria pomeroyi DSS-3 3194104 YP_167781.1 CDS SPO2568 NC_003911.11 2719605 2720042 D identified by match to protein family HMM PF06271; RDD family protein 2719605..2720042 Ruegeria pomeroyi DSS-3 3194509 YP_167782.2 CDS ate NC_003911.11 2720118 2720939 D Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate; arginyl-tRNA-protein transferase 2720118..2720939 Ruegeria pomeroyi DSS-3 3194485 YP_167783.1 CDS SPO2570 NC_003911.11 2720944 2721324 D identified by match to protein family HMM PF00903; glyoxalase 2720944..2721324 Ruegeria pomeroyi DSS-3 3194518 YP_167784.1 CDS SPO2571 NC_003911.11 2721521 2723875 R identified by match to protein family HMM PF06808; TRAP C4-dicarboxylate transport system permease DctM complement(2721521..2723875) Ruegeria pomeroyi DSS-3 3194458 YP_167785.1 CDS SPO2572 NC_003911.11 2723893 2724588 R hypothetical protein complement(2723893..2724588) Ruegeria pomeroyi DSS-3 3194417 YP_167786.1 CDS SPO2573 NC_003911.11 2724935 2726020 R identified by match to protein family HMM PF03480; match to protein family HMM TIGR01409; solute-binding family 7 protein complement(2724935..2726020) Ruegeria pomeroyi DSS-3 3194455 YP_167787.1 CDS SPO2574 NC_003911.11 2726110 2727714 D identified by similarity to SP:P13799; match to protein family HMM PF02518; sensor histidine kinase 2726110..2727714 Ruegeria pomeroyi DSS-3 3194482 YP_167788.1 CDS SPO2575 NC_003911.11 2727711 2728361 D identified by match to protein family HMM PF00072; match to protein family HMM PF00196; LuxR family transcriptional regulator 2727711..2728361 Ruegeria pomeroyi DSS-3 3194300 YP_167789.1 CDS SPO2576 NC_003911.11 2728313 2728930 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(2728313..2728930) Ruegeria pomeroyi DSS-3 3194063 YP_167790.1 CDS SPO2577 NC_003911.11 2729048 2730136 D hypothetical protein 2729048..2730136 Ruegeria pomeroyi DSS-3 3194451 YP_167791.1 CDS ilvB NC_003911.11 2730491 2732242 D catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; acetolactate synthase 3 catalytic subunit 2730491..2732242 Ruegeria pomeroyi DSS-3 3194403 YP_167792.1 CDS ilvH NC_003911.11 2732312 2732872 D 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 2732312..2732872 Ruegeria pomeroyi DSS-3 3194513 YP_167793.1 CDS SPO2580 NC_003911.11 2732884 2733252 R hypothetical protein complement(2732884..2733252) Ruegeria pomeroyi DSS-3 3194294 YP_167794.1 CDS SPO2581 NC_003911.11 2733470 2734267 D identified by match to protein family HMM PF01381; DNA-binding protein 2733470..2734267 Ruegeria pomeroyi DSS-3 3194420 YP_167795.1 CDS SPO2582 NC_003911.11 2734309 2735088 R hypothetical protein complement(2734309..2735088) Ruegeria pomeroyi DSS-3 3194434 YP_167796.1 CDS SPO2583 NC_003911.11 2735120 2736523 R catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia; amidase complement(2735120..2736523) Ruegeria pomeroyi DSS-3 3194443 YP_167797.1 CDS SPO2584 NC_003911.11 2736658 2737089 D identified by match to protein family HMM PF00903; glyoxalase 2736658..2737089 Ruegeria pomeroyi DSS-3 3194489 YP_167798.1 CDS prfB NC_003911.11 2737185 2738312 R 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 complement(2737185..2738312) Ruegeria pomeroyi DSS-3 3194310 YP_167799.1 CDS SPO2586 NC_003911.11 2738544 2740535 D identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 2738544..2740535 Ruegeria pomeroyi DSS-3 3194270 YP_167800.1 CDS mrca NC_003911.11 2740529 2743015 R identified by match to protein family HMM PF00905; match to protein family HMM PF00912; match to protein family HMM TIGR02074; penicillin-binding protein 1A complement(2740529..2743015) Ruegeria pomeroyi DSS-3 3194379 YP_167801.1 CDS SPO2588 NC_003911.11 2743172 2744389 R identified by match to protein family HMM PF01520; N-acetylmuramoyl-L-alanine amidase complement(2743172..2744389) Ruegeria pomeroyi DSS-3 3194149 YP_167802.1 CDS SPO2589 NC_003911.11 2744451 2745620 R identified by match to protein family HMM PF00155; aminotransferase, classes I and II complement(2744451..2745620) Ruegeria pomeroyi DSS-3 3194336 YP_167803.1 CDS SPO2590 NC_003911.11 2745619 2746968 D identified by match to protein family HMM PF01435; M48 family peptidase 2745619..2746968 Ruegeria pomeroyi DSS-3 3194322 YP_167804.1 CDS SPO2591 NC_003911.11 2746965 2747723 D identified by similarity to PIR:A49232; match to protein family HMM PF01323; hypothetical protein 2746965..2747723 Ruegeria pomeroyi DSS-3 3194331 YP_167805.1 CDS SPO2592 NC_003911.11 2747794 2748582 R identified by similarity to SP:P14489; beta-lactamase complement(2747794..2748582) Ruegeria pomeroyi DSS-3 3194333 YP_167806.1 CDS SPO2593 NC_003911.11 2748813 2749073 D hypothetical protein 2748813..2749073 Ruegeria pomeroyi DSS-3 3194319 YP_167807.1 CDS ispG NC_003911.11 2749081 2750208 R 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 complement(2749081..2750208) Ruegeria pomeroyi DSS-3 3194269 YP_167808.1 CDS SPO2595 NC_003911.11 2750263 2751501 D hypothetical protein 2750263..2751501 Ruegeria pomeroyi DSS-3 3194312 YP_167809.1 CDS hemA-1 NC_003911.11 2751613 2752836 R catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase complement(2751613..2752836) Ruegeria pomeroyi DSS-3 3194287 YP_167810.1 CDS SPO2597 NC_003911.11 2753156 2754544 D identified by match to protein family HMM PF01546; hypothetical protein 2753156..2754544 Ruegeria pomeroyi DSS-3 3194364 YP_167811.1 CDS SPO2598 NC_003911.11 2754573 2755532 R hypothetical protein complement(2754573..2755532) Ruegeria pomeroyi DSS-3 3193249 YP_167812.1 CDS SPO2601 NC_003911.11 2755967 2756905 R identified by match to protein family HMM PF02678; match to protein family HMM PF05726; pirin complement(2755967..2756905) Ruegeria pomeroyi DSS-3 3194283 YP_167813.1 CDS SPO2602 NC_003911.11 2757005 2757877 R identified by match to protein family HMM PF01380; match to protein family HMM PF01418; RpiR family transcriptional regulator complement(2757005..2757877) Ruegeria pomeroyi DSS-3 3194348 YP_167814.1 CDS SPO2603 NC_003911.11 2757973 2758767 D identified by match to protein family HMM PF05013; N-formylglutamate amidohydrolase 2757973..2758767 Ruegeria pomeroyi DSS-3 3194115 YP_167815.1 CDS SPO2604 NC_003911.11 2758784 2759320 D identified by similarity to GB:BAB51666.1; hypothetical protein 2758784..2759320 Ruegeria pomeroyi DSS-3 3194271 YP_167816.1 CDS SPO2605 NC_003911.11 2759322 2760647 D identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM 2759322..2760647 Ruegeria pomeroyi DSS-3 3194272 YP_167817.1 CDS SPO2606 NC_003911.11 2760702 2761736 D identified by match to protein family HMM PF03480; match to protein family HMM TIGR01409; solute-binding family 7 protein 2760702..2761736 Ruegeria pomeroyi DSS-3 3194261 YP_167818.1 CDS SPO2607 NC_003911.11 2761834 2763189 D identified by similarity to GB:CAC81335.1; match to protein family HMM PF00120; gamma-glutamylisopropylamide synthetase 2761834..2763189 Ruegeria pomeroyi DSS-3 3194398 YP_167819.1 CDS SPO2608 NC_003911.11 2763260 2764669 D identified by similarity to GB:CAC81341.1; match to protein family HMM PF00171; aldehyde dehydrogenase 2763260..2764669 Ruegeria pomeroyi DSS-3 3194203 YP_167820.1 CDS SPO2609 NC_003911.11 2764675 2765820 D identified by match to protein family HMM PF00465; alcohol dehydrogenase 2764675..2765820 Ruegeria pomeroyi DSS-3 3194197 YP_167821.1 CDS SPO2610 NC_003911.11 2765921 2766709 D identified by similarity to GB:CAD17488.1; hypothetical protein 2765921..2766709 Ruegeria pomeroyi DSS-3 3194415 YP_167822.1 CDS SPO2612 NC_003911.11 2766944 2767219 R DNA-binding protein HU complement(2766944..2767219) Ruegeria pomeroyi DSS-3 3194174 YP_167823.1 CDS lon NC_003911.11 2767583 2769994 R 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 complement(2767583..2769994) Ruegeria pomeroyi DSS-3 3194158 YP_167824.1 CDS SPO2614 NC_003911.11 2770257 2770940 R hypothetical protein complement(2770257..2770940) Ruegeria pomeroyi DSS-3 3194143 YP_167825.1 CDS SPO2615 NC_003911.11 2770956 2772032 R identified by match to protein family HMM PF00724; Oye family NADH-dependent flavin oxidoreductase complement(2770956..2772032) Ruegeria pomeroyi DSS-3 3194140 YP_167826.1 CDS tgt NC_003911.11 2772306 2773436 R Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr); queuine tRNA-ribosyltransferase complement(2772306..2773436) Ruegeria pomeroyi DSS-3 3193294 YP_167827.1 CDS SPO2617 NC_003911.11 2773612 2774502 D identified by match to protein family HMM PF01145; hypothetical protein 2773612..2774502 Ruegeria pomeroyi DSS-3 3194402 YP_167828.1 CDS SPO2618 NC_003911.11 2774502 2774774 D identified by similarity to PIR:C75311; hypothetical protein 2774502..2774774 Ruegeria pomeroyi DSS-3 3194133 YP_167829.1 CDS SPO2619 NC_003911.11 2774919 2775281 D identified by similarity to GB:AAK23834.1; match to protein family HMM PF01883; hypothetical protein 2774919..2775281 Ruegeria pomeroyi DSS-3 3194220 YP_167830.1 CDS SPO2620 NC_003911.11 2775573 2775947 D identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049; iron-sulfur cluster assembly accessory protein 2775573..2775947 Ruegeria pomeroyi DSS-3 3195353 YP_167831.1 CDS tpiA NC_003911.11 2776049 2776804 D identified by match to protein family HMM PF00121; match to protein family HMM TIGR00419; triosephosphate isomerase 2776049..2776804 Ruegeria pomeroyi DSS-3 3194114 YP_167832.1 CDS SPO2622 NC_003911.11 2776814 2777329 D identified by match to protein family HMM PF00583; acetyltransferase 2776814..2777329 Ruegeria pomeroyi DSS-3 3194167 YP_167833.1 CDS SPO2623 NC_003911.11 2777347 2777964 R identified by match to protein family HMM PF01810; amino acid transporter LysE complement(2777347..2777964) Ruegeria pomeroyi DSS-3 3194124 YP_167834.1 CDS SPO2624 NC_003911.11 2778084 2778539 D identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator 2778084..2778539 Ruegeria pomeroyi DSS-3 3194355 YP_167835.1 CDS SPO2625 NC_003911.11 2778591 2779244 D identified by similarity to GB:AAM40972.1; hypothetical protein 2778591..2779244 Ruegeria pomeroyi DSS-3 3194100 YP_167836.1 CDS SPO2626 NC_003911.11 2779290 2780687 R 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 complement(2779290..2780687) Ruegeria pomeroyi DSS-3 3194079 YP_167837.1 CDS SPO2627 NC_003911.11 2780687 2781358 R identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter subunit DctQ complement(2780687..2781358) Ruegeria pomeroyi DSS-3 3194181 YP_167838.1 CDS SPO2628 NC_003911.11 2781431 2782432 R 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 complement(2781431..2782432) Ruegeria pomeroyi DSS-3 3194093 YP_167839.1 CDS SPO2629 NC_003911.11 2782760 2783989 R 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 complement(2782760..2783989) Ruegeria pomeroyi DSS-3 3194353 YP_167840.1 CDS SPO2630 NC_003911.11 2783986 2785722 R identified by similarity to SP:P13633; match to protein family HMM PF00512; match to protein family HMM PF02518; C4-dicarboxylate transport sensor protein complement(2783986..2785722) Ruegeria pomeroyi DSS-3 3194082 YP_167841.1 CDS SPO2631 NC_003911.11 2785776 2786237 R identified by match to protein family HMM PF01037; match to protein family HMM TIGR01199; AsnC family transcriptional regulator complement(2785776..2786237) Ruegeria pomeroyi DSS-3 3193957 YP_167842.1 CDS cobA-1 NC_003911.11 2786378 2787154 D identified by match to protein family HMM PF00590; match to protein family HMM TIGR01469; uroporphyrin-III C-methyltransferase 2786378..2787154 Ruegeria pomeroyi DSS-3 3194076 YP_167843.1 CDS SPO2633 NC_003911.11 2787154 2787468 D identified by similarity to GB:CAE29655.1; hypothetical protein 2787154..2787468 Ruegeria pomeroyi DSS-3 3194478 YP_167844.1 CDS SPO2634 NC_003911.11 2787532 2789196 D identified by match to protein family HMM PF01077; match to protein family HMM PF03460; sulfite reductase 2787532..2789196 Ruegeria pomeroyi DSS-3 3195199 YP_167845.1 CDS cysH NC_003911.11 2789186 2789947 D catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite; phosphoadenosine phosphosulfate reductase 2789186..2789947 Ruegeria pomeroyi DSS-3 3194868 YP_167846.1 CDS SPO2636 NC_003911.11 2789944 2790351 D identified by similarity to PIR:AF3472; hypothetical protein 2789944..2790351 Ruegeria pomeroyi DSS-3 3194525 YP_167847.1 CDS SPO2637 NC_003911.11 2790466 2791299 D identified by similarity to SP:Q44532; match to protein family HMM PF00970; ferredoxin-NADP reductase 2790466..2791299 Ruegeria pomeroyi DSS-3 3194521 YP_167848.1 CDS infC NC_003911.11 2791446 2791994 D 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 2791446..2791994 Ruegeria pomeroyi DSS-3 3195359 YP_167849.1 CDS SPO2639 NC_003911.11 2792216 2793256 R identified by match to protein family HMM PF00994; molybdopterin biosynthesis protein complement(2792216..2793256) Ruegeria pomeroyi DSS-3 3194500 YP_167850.1 CDS SPO2640 NC_003911.11 2793253 2794233 R identified by match to protein family HMM PF02625; XdhC/CoxI family protein complement(2793253..2794233) Ruegeria pomeroyi DSS-3 3194410 YP_167851.1 CDS SPO2641 NC_003911.11 2794401 2794994 R hypothetical protein complement(2794401..2794994) Ruegeria pomeroyi DSS-3 3194490 YP_167852.1 CDS SPO2642 NC_003911.11 2794998 2795582 R identified by similarity to GB:BAC48787.1; match to protein family HMM PF04143; hypothetical protein complement(2794998..2795582) Ruegeria pomeroyi DSS-3 3194132 YP_167853.1 CDS SPO2643 NC_003911.11 2795667 2796755 R hypothetical protein complement(2795667..2796755) Ruegeria pomeroyi DSS-3 3194422 YP_167854.1 CDS SPO2644 NC_003911.11 2796752 2798014 R identified by match to protein family HMM PF05762; von Willebrand factor A complement(2796752..2798014) Ruegeria pomeroyi DSS-3 3194184 YP_167855.1 CDS SPO2645 NC_003911.11 2798051 2799034 D identified by similarity to SP:P39790; S2 family protease 2798051..2799034 Ruegeria pomeroyi DSS-3 3194400 YP_167856.1 CDS SPO2646 NC_003911.11 2799128 2800036 R identified by similarity to GB:CAE29242.1; hypothetical protein complement(2799128..2800036) Ruegeria pomeroyi DSS-3 3194401 YP_167857.1 CDS SPO2647 NC_003911.11 2800112 2801329 D identified by similarity to PIR:F95909; hypothetical protein 2800112..2801329 Ruegeria pomeroyi DSS-3 3194214 YP_167858.1 CDS SPO2648 NC_003911.11 2801326 2802015 D hypothetical protein 2801326..2802015 Ruegeria pomeroyi DSS-3 3194320 YP_167859.1 CDS SPO2649 NC_003911.11 2802015 2804396 D identified by similarity to GB:CAB52234.1; hypothetical protein 2802015..2804396 Ruegeria pomeroyi DSS-3 3194366 YP_167860.1 CDS SPO2650 NC_003911.11 2804400 2805098 D identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 2804400..2805098 Ruegeria pomeroyi DSS-3 3194280 YP_167861.1 CDS SPO2651 NC_003911.11 2805105 2806184 D identified by match to protein family HMM PF00535; glycosyl transferase family protein 2805105..2806184 Ruegeria pomeroyi DSS-3 3195392 YP_167862.1 CDS SPO2652 NC_003911.11 2806270 2807229 D hypothetical protein 2806270..2807229 Ruegeria pomeroyi DSS-3 3194078 YP_167863.1 CDS SPO2653 NC_003911.11 2807766 2808806 D catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 2807766..2808806 Ruegeria pomeroyi DSS-3 3194392 YP_167864.1 CDS pyrE NC_003911.11 2808884 2809561 D 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 2808884..2809561 Ruegeria pomeroyi DSS-3 3194223 YP_167865.1 CDS dnaB NC_003911.11 2809757 2811247 D unwinds double stranded DNA; replicative DNA helicase 2809757..2811247 Ruegeria pomeroyi DSS-3 3194228 YP_167866.1 CDS SPO2656 NC_003911.11 2811257 2812147 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(2811257..2812147) Ruegeria pomeroyi DSS-3 3194313 YP_167867.2 CDS SPO2657 NC_003911.11 2812318 2813325 D catalyzes the formation of pyruvate from D-cysteine; D-cysteine desulfhydrase 2812318..2813325 Ruegeria pomeroyi DSS-3 3194361 YP_167868.1 CDS gltI NC_003911.11 2813357 2814220 D 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 2813357..2814220 Ruegeria pomeroyi DSS-3 3194326 YP_167869.1 CDS gltJ NC_003911.11 2814287 2815003 D 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 2814287..2815003 Ruegeria pomeroyi DSS-3 3194077 YP_167870.1 CDS gltK NC_003911.11 2815007 2815663 D identified by similarity to SP:P41075; match to protein family HMM PF00528; match to protein family HMM TIGR01726; glutamate/aspartate ABC transporter permease 2815007..2815663 Ruegeria pomeroyi DSS-3 3195471 YP_167871.1 CDS gltL NC_003911.11 2815660 2816388 D identified by similarity to SP:P41076; match to protein family HMM PF00005; glutamate/aspartate ABC transporter ATP-binding protein 2815660..2816388 Ruegeria pomeroyi DSS-3 3194378 YP_167872.1 CDS SPO2662 NC_003911.11 2816520 2817977 R 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 complement(2816520..2817977) Ruegeria pomeroyi DSS-3 3194173 YP_167873.1 CDS aspA NC_003911.11 2817974 2819344 R catalyzes the formation of fumarate from aspartate; aspartate ammonia-lyase complement(2817974..2819344) Ruegeria pomeroyi DSS-3 3194328 YP_167874.1 CDS SPO2664 NC_003911.11 2819355 2820122 R identified by similarity to SP:P27675; match to protein family HMM PF00005; polar amino acid ABC transporter ATP-binding protein complement(2819355..2820122) Ruegeria pomeroyi DSS-3 3194234 YP_167875.1 CDS SPO2665 NC_003911.11 2820124 2820918 R 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 complement(2820124..2820918) Ruegeria pomeroyi DSS-3 3193105 YP_167876.1 CDS SPO2666 NC_003911.11 2820995 2821798 R identified by similarity to SP:P41074; match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease complement(2820995..2821798) Ruegeria pomeroyi DSS-3 3194168 YP_167877.1 CDS SPO2667 NC_003911.11 2821816 2822649 R 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 complement(2821816..2822649) Ruegeria pomeroyi DSS-3 3193739 YP_167878.1 CDS SPO2668 NC_003911.11 2822841 2823734 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 2822841..2823734 Ruegeria pomeroyi DSS-3 3194134 YP_167879.1 CDS SPO2669 NC_003911.11 2823920 2824873 D identified by match to protein family HMM PF03171; 2OG-Fe(II) oxygenase 2823920..2824873 Ruegeria pomeroyi DSS-3 3193427 YP_167880.1 CDS alr NC_003911.11 2824893 2826026 D 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 2824893..2826026 Ruegeria pomeroyi DSS-3 3193741 YP_167881.1 CDS SPO2671 NC_003911.11 2826023 2826805 D identified by similarity to GB:AAD17958.1; match to protein family HMM PF02405; match to protein family HMM TIGR00056; hypothetical protein 2826023..2826805 Ruegeria pomeroyi DSS-3 3194118 YP_167882.1 CDS SPO2672 NC_003911.11 2826802 2827551 D identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 2826802..2827551 Ruegeria pomeroyi DSS-3 3194342 YP_167883.1 CDS SPO2673 NC_003911.11 2827548 2828051 D identified by match to protein family HMM PF04403; paraquat-inducible protein A 2827548..2828051 Ruegeria pomeroyi DSS-3 3193927 YP_167884.1 CDS radA NC_003911.11 2828263 2829624 D 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 2828263..2829624 Ruegeria pomeroyi DSS-3 3193849 YP_167885.1 CDS SPO2675 NC_003911.11 2829667 2830221 D identified by similarity to SP:P08550; match to protein family HMM PF02674; colicin V production protein CvpA 2829667..2830221 Ruegeria pomeroyi DSS-3 3195324 YP_167886.1 CDS SPO2676 NC_003911.11 2830468 2831040 D hypothetical protein 2830468..2831040 Ruegeria pomeroyi DSS-3 3194306 YP_167887.1 CDS purF NC_003911.11 2831183 2832655 D Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase 2831183..2832655 Ruegeria pomeroyi DSS-3 3194339 YP_167888.1 CDS SPO2678 NC_003911.11 2832800 2833048 D hypothetical protein 2832800..2833048 Ruegeria pomeroyi DSS-3 3193758 YP_167889.1 CDS SPO2679 NC_003911.11 2833090 2833734 D identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 2833090..2833734 Ruegeria pomeroyi DSS-3 3194315 YP_167890.1 CDS SPO2680 NC_003911.11 2833789 2834631 R identified by similarity to GB:BAB48529.1; match to protein family HMM PF05673; hypothetical protein complement(2833789..2834631) Ruegeria pomeroyi DSS-3 3193735 YP_167891.1 CDS tatC NC_003911.11 2834750 2835688 R identified by match to protein family HMM PF00902; match to protein family HMM TIGR00945; twin-arginine translocation protein TatC complement(2834750..2835688) Ruegeria pomeroyi DSS-3 3194249 YP_167892.1 CDS tatB NC_003911.11 2835685 2836143 R identified by match to protein family HMM PF02416; match to protein family HMM TIGR01410; twin-arginine translocation protein TatB complement(2835685..2836143) Ruegeria pomeroyi DSS-3 3194245 YP_167893.1 CDS SPO2683 NC_003911.11 2836150 2836365 R identified by match to protein family HMM PF02416; twin arginine-targeting protein translocase complement(2836150..2836365) Ruegeria pomeroyi DSS-3 3195048 YP_167894.1 CDS SPO2684 NC_003911.11 2836590 2836889 D identified by similarity to GB:BAC96491.1; hypothetical protein 2836590..2836889 Ruegeria pomeroyi DSS-3 3194241 YP_167895.1 CDS SPO2685 NC_003911.11 2836955 2837620 D hypothetical protein 2836955..2837620 Ruegeria pomeroyi DSS-3 3193908 YP_167896.1 CDS SPO2686 NC_003911.11 2837760 2838950 R identified by match to protein family HMM PF01476; match to protein family HMM PF01551; LysM/M23/M37 peptidase complement(2837760..2838950) Ruegeria pomeroyi DSS-3 3195390 YP_167897.1 CDS pcm-2 NC_003911.11 2839029 2839676 R identified by match to protein family HMM PF01135; match to protein family HMM TIGR00080; protein-L-isoaspartate O-methyltransferase complement(2839029..2839676) Ruegeria pomeroyi DSS-3 3193932 YP_167898.1 CDS surE NC_003911.11 2839673 2840455 R catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE complement(2839673..2840455) Ruegeria pomeroyi DSS-3 3194205 YP_167899.1 CDS SPO2689 NC_003911.11 2840667 2841764 R identified by similarity to SP:P21410; match to protein family HMM PF00005; iron ABC transporter ATP-binding protein complement(2840667..2841764) Ruegeria pomeroyi DSS-3 3194206 YP_167900.1 CDS SPO2690 NC_003911.11 2841855 2842910 R identified by similarity to GB:CAB61860.1; hypothetical protein complement(2841855..2842910) Ruegeria pomeroyi DSS-3 3194178 YP_167901.1 CDS SPO2691 NC_003911.11 2843069 2844175 R identified by similarity to GB:CAD72185.1; hypothetical protein complement(2843069..2844175) Ruegeria pomeroyi DSS-3 3195053 YP_167902.1 CDS SPO2692 NC_003911.11 2844179 2844958 R identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase complement(2844179..2844958) Ruegeria pomeroyi DSS-3 3194152 YP_167903.1 CDS SPO2693 NC_003911.11 2845138 2846148 D identified by similarity to GB:AAN33954.1; hypothetical protein 2845138..2846148 Ruegeria pomeroyi DSS-3 3193843 YP_167904.1 CDS SPO2694 NC_003911.11 2846275 2846718 D identified by match to protein family HMM PF01322; cytochrome c' 2846275..2846718 Ruegeria pomeroyi DSS-3 3194273 YP_167905.1 CDS SPO2695 NC_003911.11 2846764 2848371 D 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 2846764..2848371 Ruegeria pomeroyi DSS-3 3194161 YP_167906.1 CDS SPO2696 NC_003911.11 2848417 2849544 R identified by match to protein family HMM PF00144; beta-lactamase complement(2848417..2849544) Ruegeria pomeroyi DSS-3 3194125 YP_167907.1 CDS SPO2697 NC_003911.11 2849547 2851640 R identified by similarity to GB:AAN69320.1; similarity to GB:BAC79255.1; match to protein family HMM PF02629; acyl-CoA synthetase complement(2849547..2851640) Ruegeria pomeroyi DSS-3 3194122 YP_167908.1 CDS SPO2698 NC_003911.11 2851637 2852797 R identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase complement(2851637..2852797) Ruegeria pomeroyi DSS-3 3193764 YP_167909.1 CDS SPO2699 NC_003911.11 2852811 2853608 R identified by match to protein family HMM PF00528; opine/polyamine ABC transporter permease complement(2852811..2853608) Ruegeria pomeroyi DSS-3 3194110 YP_167910.1 CDS SPO2700 NC_003911.11 2853605 2854483 R identified by match to protein family HMM PF00528; opine/polyamine ABC transporter permease complement(2853605..2854483) Ruegeria pomeroyi DSS-3 3194367 YP_167911.1 CDS SPO2701 NC_003911.11 2854509 2855618 R identified by match to protein family HMM TIGR01409; opine/polyamine ABC transporter substrate-binding protein complement(2854509..2855618) Ruegeria pomeroyi DSS-3 3194107 YP_167912.1 CDS SPO2702 NC_003911.11 2855698 2856699 R identified by match to protein family HMM PF00005; opine/polyamine ABC transporter ATP-binding protein complement(2855698..2856699) Ruegeria pomeroyi DSS-3 3194356 YP_167913.1 CDS SPO2703 NC_003911.11 2856700 2857590 R identified by similarity to PIR:G82972; match to protein family HMM PF05853; hypothetical protein complement(2856700..2857590) Ruegeria pomeroyi DSS-3 3194386 YP_167914.1 CDS SPO2704 NC_003911.11 2857726 2858811 D identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 2857726..2858811 Ruegeria pomeroyi DSS-3 3194351 YP_167915.1 CDS SPO2705 NC_003911.11 2858777 2859730 R identified by match to protein family HMM PF00725; match to protein family HMM PF02737; 3-hydroxyacyl-CoA dehydrogenase complement(2858777..2859730) Ruegeria pomeroyi DSS-3 3194362 YP_167916.1 CDS caiD-1 NC_003911.11 2859727 2860548 R catalyzes the dehydration of L-carnitinyl-CoA to crotonobetainyl-CoA; carnitinyl-CoA dehydratase complement(2859727..2860548) Ruegeria pomeroyi DSS-3 3193838 YP_167917.1 CDS SPO2707 NC_003911.11 2860545 2861579 R identified by match to protein family HMM PF00296; luciferase complement(2860545..2861579) Ruegeria pomeroyi DSS-3 3194309 YP_167918.1 CDS SPO2708 NC_003911.11 2861607 2863088 R identified by match to protein family HMM PF00171; aldehyde dehydrogenase complement(2861607..2863088) Ruegeria pomeroyi DSS-3 3194155 YP_167919.1 CDS SPO2709 NC_003911.11 2863232 2863636 D endoribonuclease L-PSP 2863232..2863636 Ruegeria pomeroyi DSS-3 3194321 YP_167920.1 CDS SPO2710 NC_003911.11 2863636 2864442 D identified by similarity to GB:AAR21628.1; match to protein family HMM PF00561; 3-oxoadipate enol-lactonase 2863636..2864442 Ruegeria pomeroyi DSS-3 3194382 YP_167921.1 CDS SPO2711 NC_003911.11 2864439 2866550 D identified by match to protein family HMM PF01613; match to protein family HMM PF02515; CaiB/BaiF family protein 2864439..2866550 Ruegeria pomeroyi DSS-3 3194295 YP_167922.1 CDS SPO2712 NC_003911.11 2866564 2867178 D identified by similarity to PIR:C95315; match to protein family HMM PF06684; hypothetical protein 2866564..2867178 Ruegeria pomeroyi DSS-3 3194347 YP_167923.1 CDS secA NC_003911.11 2867244 2869202 R 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 complement(2867244..2869202) Ruegeria pomeroyi DSS-3 3194324 YP_167924.1 CDS SPO2714 NC_003911.11 2869195 2871342 R identified by similarity to GB:CAD78905.1; match to protein family HMM PF02163; M50 family peptidase complement(2869195..2871342) Ruegeria pomeroyi DSS-3 3194299 YP_167925.1 CDS SPO2715 NC_003911.11 2871339 2873192 R identified by match to protein family HMM PF01590; GAF domain-containing protein complement(2871339..2873192) Ruegeria pomeroyi DSS-3 3194305 YP_167926.1 CDS SPO2716 NC_003911.11 2873400 2897681 R 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 complement(2873400..2897681) Ruegeria pomeroyi DSS-3 3194248 YP_167927.1 CDS SPO2717 NC_003911.11 2897729 2898511 D identified by similarity to GB:AAC97196.1; match to protein family HMM PF07277; protein SapC protein 2897729..2898511 Ruegeria pomeroyi DSS-3 3194210 YP_167928.1 CDS SPO2718 NC_003911.11 2898520 2899335 D identified by similarity to GB:CAD84993.1; hypothetical protein 2898520..2899335 Ruegeria pomeroyi DSS-3 3196028 YP_167929.1 CDS SPO2719 NC_003911.11 2899435 2900271 R identified by similarity to GB:AAN87700.1; hypothetical protein complement(2899435..2900271) Ruegeria pomeroyi DSS-3 3194253 YP_167930.1 CDS SPO2720 NC_003911.11 2901443 2902948 R hypothetical protein complement(2901443..2902948) Ruegeria pomeroyi DSS-3 3194216 YP_167931.1 CDS SPO2721 NC_003911.11 2903106 2903702 D hypothetical protein 2903106..2903702 Ruegeria pomeroyi DSS-3 3194239 YP_167932.1 CDS SPO2722 NC_003911.11 2903699 2904058 D hypothetical protein 2903699..2904058 Ruegeria pomeroyi DSS-3 3194251 YP_167933.1 CDS SPO2723 NC_003911.11 2904055 2905611 D hypothetical protein 2904055..2905611 Ruegeria pomeroyi DSS-3 3194207 YP_167934.1 CDS SPO2724 NC_003911.11 2906229 2910770 D hypothetical protein 2906229..2910770 Ruegeria pomeroyi DSS-3 3194200 YP_167935.1 CDS SPO2725 NC_003911.11 2911529 2911627 R hypothetical protein complement(2911529..2911627) Ruegeria pomeroyi DSS-3 3194187 YP_167936.1 CDS SPO2726 NC_003911.11 2912002 2913927 R hypothetical protein complement(2912002..2913927) Ruegeria pomeroyi DSS-3 3194195 YP_167937.1 CDS SPO2729 NC_003911.11 2917912 2918346 R identified by similarity to PIR:F97477; hypothetical protein complement(2917912..2918346) Ruegeria pomeroyi DSS-3 3195694 YP_167938.1 CDS SPO2730 NC_003911.11 2918343 2918549 R identified by similarity to PIR:H97795; hypothetical protein complement(2918343..2918549) Ruegeria pomeroyi DSS-3 3193875 YP_167939.1 CDS SPO2731 NC_003911.11 2918831 2919400 D identified by match to protein family HMM PF01609; ISSpo7, transposase 2918831..2919400 Ruegeria pomeroyi DSS-3 3194188 YP_167940.1 CDS hsdM NC_003911.11 2920543 2923245 D 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 2920543..2923245 Ruegeria pomeroyi DSS-3 3194088 YP_167941.1 CDS hsdS NC_003911.11 2923238 2924542 D identified by similarity to SP:P05719; match to protein family HMM PF01420; type I restriction-modification system subunit S 2923238..2924542 Ruegeria pomeroyi DSS-3 3194163 YP_167942.1 CDS hsdR NC_003911.11 2924539 2927922 D identified by match to protein family HMM PF04313; match to protein family HMM TIGR00348; type I restriction-modification system, R subunit 2924539..2927922 Ruegeria pomeroyi DSS-3 3194130 YP_167943.1 CDS SPO3899 NC_003911.11 2927919 2928632 D identified by similarity to GB:BAD02160.1; match to protein family HMM PF01863; hypothetical protein 2927919..2928632 Ruegeria pomeroyi DSS-3 3196260 YP_167944.1 CDS SPO2736 NC_003911.11 2928710 2929648 D identified by similarity to GB:CAD79234.1; hypothetical protein 2928710..2929648 Ruegeria pomeroyi DSS-3 3194141 YP_167945.1 CDS SPO2738 NC_003911.11 2930229 2931110 D lipoprotein 2930229..2931110 Ruegeria pomeroyi DSS-3 3194126 YP_167946.1 CDS SPO2739 NC_003911.11 2931128 2932294 D identified by similarity to SP:P08506; match to protein family HMM PF00768; D-alanyl-D-alanine carboxypeptidase 2931128..2932294 Ruegeria pomeroyi DSS-3 3194117 YP_167947.1 CDS tmk NC_003911.11 2932291 2932926 D identified by match to protein family HMM PF02223; match to protein family HMM TIGR00041; thymidylate kinase 2932291..2932926 Ruegeria pomeroyi DSS-3 3194112 YP_167948.1 CDS SPO2741 NC_003911.11 2932923 2934044 D 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' 2932923..2934044 Ruegeria pomeroyi DSS-3 3194106 YP_167949.1 CDS SPO2742 NC_003911.11 2934041 2934856 D identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010; TatD family hydrolase 2934041..2934856 Ruegeria pomeroyi DSS-3 3194150 YP_167950.1 CDS SPO2743 NC_003911.11 2934853 2935653 D identified by similarity to GB:AAK23796.1; hypothetical protein 2934853..2935653 Ruegeria pomeroyi DSS-3 3194145 YP_167951.1 CDS SPO2744 NC_003911.11 2935709 2936641 D identified by similarity to GB:AAC45458.1; match to protein family HMM PF03547; malonate transporter 2935709..2936641 Ruegeria pomeroyi DSS-3 3194137 YP_167952.1 CDS SPO2745 NC_003911.11 2936614 2937381 D identified by similarity to GB:AAS06255.1; hypothetical protein 2936614..2937381 Ruegeria pomeroyi DSS-3 3195380 YP_167953.1 CDS SPO2746 NC_003911.11 2937384 2938670 R hypothetical protein complement(2937384..2938670) Ruegeria pomeroyi DSS-3 3194135 YP_167954.1 CDS SPO2747 NC_003911.11 2938818 2939885 R identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254; diguanylate cyclase complement(2938818..2939885) Ruegeria pomeroyi DSS-3 3194094 YP_167955.1 CDS SPO2748 NC_003911.11 2939891 2940478 R identified by similarity to PIR:AG2090; hypothetical protein complement(2939891..2940478) Ruegeria pomeroyi DSS-3 3193937 YP_167956.1 CDS SPO2749 NC_003911.11 2940566 2942341 R identified by similarity to GB:AAQ58806.1; hypothetical protein complement(2940566..2942341) Ruegeria pomeroyi DSS-3 3195145 YP_167957.1 CDS SPO2750 NC_003911.11 2942424 2943983 R identified by match to protein family HMM PF06253; trimethylamine methyltransferase complement(2942424..2943983) Ruegeria pomeroyi DSS-3 3194084 YP_167958.1 CDS SPO2751 NC_003911.11 2944100 2944789 R identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549; HAD-superfamily hydrolase complement(2944100..2944789) Ruegeria pomeroyi DSS-3 3194073 YP_167959.1 CDS SPO2752 NC_003911.11 2944829 2945110 R identified by similarity to GB:AAN33802.1; hypothetical protein complement(2944829..2945110) Ruegeria pomeroyi DSS-3 3194067 YP_167960.1 CDS SPO2753 NC_003911.11 2945206 2946594 D identified by match to protein family HMM PF00072; match to protein family HMM PF00990; match to protein family HMM TIGR00254; diguanylate cyclase, /response regulator 2945206..2946594 Ruegeria pomeroyi DSS-3 3193997 YP_167961.1 CDS SPO2754 NC_003911.11 2946591 2947061 R identified by similarity to GB:AAK24713.1; hypothetical protein complement(2946591..2947061) Ruegeria pomeroyi DSS-3 3193992 YP_167962.1 CDS SPO2755 NC_003911.11 2947062 2947430 R hypothetical protein complement(2947062..2947430) Ruegeria pomeroyi DSS-3 3193866 YP_167963.1 CDS SPO2756 NC_003911.11 2947414 2948016 R 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 complement(2947414..2948016) Ruegeria pomeroyi DSS-3 3193973 YP_167964.1 CDS SPO2757 NC_003911.11 2948022 2948501 R identified by match to protein family HMM PF00036; EF hand domain-containing protein complement(2948022..2948501) Ruegeria pomeroyi DSS-3 3195800 YP_167965.1 CDS SPO2758 NC_003911.11 2948736 2949128 D identified by similarity to GB:CAE28567.1; hypothetical protein 2948736..2949128 Ruegeria pomeroyi DSS-3 3193844 YP_167966.1 CDS SPO2759 NC_003911.11 2949152 2949859 D identified by match to protein family HMM PF00293; NUDIX family hydrolase 2949152..2949859 Ruegeria pomeroyi DSS-3 3193778 YP_167967.1 CDS SPO2760 NC_003911.11 2949942 2951609 R identified by match to protein family HMM PF00753; match to protein family HMM PF07521; metallo-beta-lactamase complement(2949942..2951609) Ruegeria pomeroyi DSS-3 3193750 YP_167968.1 CDS SPO2761 NC_003911.11 2951606 2952385 R 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 complement(2951606..2952385) Ruegeria pomeroyi DSS-3 3194372 YP_167969.1 CDS SPO2762 NC_003911.11 2952399 2953148 R 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 complement(2952399..2953148) Ruegeria pomeroyi DSS-3 3193847 YP_167970.1 CDS nuoN NC_003911.11 2953207 2954649 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit N complement(2953207..2954649) Ruegeria pomeroyi DSS-3 3194358 YP_167971.1 CDS nuoM NC_003911.11 2954665 2956206 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit M complement(2954665..2956206) Ruegeria pomeroyi DSS-3 3193979 YP_167972.1 CDS nuoL NC_003911.11 2956206 2958350 R Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L complement(2956206..2958350) Ruegeria pomeroyi DSS-3 3195784 YP_167973.1 CDS nuoK NC_003911.11 2958357 2958662 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit K complement(2958357..2958662) Ruegeria pomeroyi DSS-3 3193895 YP_167974.1 CDS nuoJ NC_003911.11 2958741 2959343 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J complement(2958741..2959343) Ruegeria pomeroyi DSS-3 3193743 YP_167975.1 CDS SPO2768 NC_003911.11 2959340 2959759 R identified by match to protein family HMM PF02627; 4-carboxymuconolactone decarboxylase complement(2959340..2959759) Ruegeria pomeroyi DSS-3 3193751 YP_167976.1 CDS SPO2769 NC_003911.11 2959756 2960625 R identified by similarity to GB:AAN30033.1; hypothetical protein complement(2959756..2960625) Ruegeria pomeroyi DSS-3 3193996 YP_167977.1 CDS nuoI NC_003911.11 2960622 2961116 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I complement(2960622..2961116) Ruegeria pomeroyi DSS-3 3193825 YP_167978.1 CDS SPO2771 NC_003911.11 2961113 2961328 R hypothetical protein complement(2961113..2961328) Ruegeria pomeroyi DSS-3 3193632 YP_167979.1 CDS nuoH NC_003911.11 2961330 2962367 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H complement(2961330..2962367) Ruegeria pomeroyi DSS-3 3193930 YP_167980.1 CDS SPO2773 NC_003911.11 2962374 2962760 R lipoprotein complement(2962374..2962760) Ruegeria pomeroyi DSS-3 3194961 YP_167981.1 CDS nuoG NC_003911.11 2962757 2964781 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit G complement(2962757..2964781) Ruegeria pomeroyi DSS-3 3193753 YP_167982.1 CDS SPO2775 NC_003911.11 2964785 2965291 R identified by similarity to SP:P29909; hypothetical protein complement(2964785..2965291) Ruegeria pomeroyi DSS-3 3193661 YP_167983.1 CDS SPO2776 NC_003911.11 2965288 2965671 R hypothetical protein complement(2965288..2965671) Ruegeria pomeroyi DSS-3 3193620 YP_167984.1 CDS nuoF NC_003911.11 2965668 2966966 R 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 complement(2965668..2966966) Ruegeria pomeroyi DSS-3 3193143 YP_167985.1 CDS SPO2778 NC_003911.11 2966976 2967221 R identified by similarity to SP:P29907; hypothetical protein complement(2966976..2967221) Ruegeria pomeroyi DSS-3 3193276 YP_167986.1 CDS SPO2779 NC_003911.11 2967225 2967671 R hypothetical protein complement(2967225..2967671) Ruegeria pomeroyi DSS-3 3193333 YP_167987.1 CDS nuoE NC_003911.11 2967694 2968938 R catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit E complement(2967694..2968938) Ruegeria pomeroyi DSS-3 3193152 YP_167988.1 CDS SPO2781 NC_003911.11 2968964 2969275 R lipoprotein complement(2968964..2969275) Ruegeria pomeroyi DSS-3 3192802 YP_167989.1 CDS nuoD NC_003911.11 2969272 2970489 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D complement(2969272..2970489) Ruegeria pomeroyi DSS-3 3193679 YP_167990.1 CDS SPO2783 NC_003911.11 2970565 2970702 R hypothetical protein complement(2970565..2970702) Ruegeria pomeroyi DSS-3 3195925 YP_167991.1 CDS nuoC NC_003911.11 2970881 2971483 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit C complement(2970881..2971483) Ruegeria pomeroyi DSS-3 3193202 YP_167992.1 CDS nuoB NC_003911.11 2971496 2972050 R 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 complement(2971496..2972050) Ruegeria pomeroyi DSS-3 3193700 YP_167993.1 CDS nuoA NC_003911.11 2972020 2972385 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit A complement(2972020..2972385) Ruegeria pomeroyi DSS-3 3193166 YP_167994.1 CDS SPO2787 NC_003911.11 2972571 2973359 R Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase complement(2972571..2973359) Ruegeria pomeroyi DSS-3 3193392 YP_167995.1 CDS mvaB NC_003911.11 2973426 2974280 R catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA; hydroxymethylglutaryl-CoA lyase complement(2973426..2974280) Ruegeria pomeroyi DSS-3 3193250 YP_167996.1 CDS mccA NC_003911.11 2974346 2976283 R 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 complement(2974346..2976283) Ruegeria pomeroyi DSS-3 3193216 YP_167997.1 CDS SPO3900 NC_003911.11 2976302 2976868 R identified by match to protein family HMM PF00565; thermonuclease complement(2976302..2976868) Ruegeria pomeroyi DSS-3 3196312 YP_167998.1 CDS mccB NC_003911.11 2976955 2978559 R identified by similarity to SP:Q9HCC0; match to protein family HMM PF01039; methylcrotonyl-CoA carboxylase subunit beta complement(2976955..2978559) Ruegeria pomeroyi DSS-3 3192650 YP_167999.1 CDS acsA NC_003911.11 2978556 2980088 R identified by similarity to SP:P39062; match to protein family HMM PF00501; acetyl-coenzyme A synthetase complement(2978556..2980088) Ruegeria pomeroyi DSS-3 3193312 YP_168000.1 CDS ompW NC_003911.11 2980256 2980861 D identified by similarity to SP:P17266; match to protein family HMM PF03922; outer membrane protein OmpW 2980256..2980861 Ruegeria pomeroyi DSS-3 3193377 YP_168001.1 CDS ivD NC_003911.11 2980923 2982086 R 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 complement(2980923..2982086) Ruegeria pomeroyi DSS-3 3193199 YP_168002.1 CDS SPO2794 NC_003911.11 2982120 2982236 R hypothetical protein complement(2982120..2982236) Ruegeria pomeroyi DSS-3 3194799 YP_168003.1 CDS SPO2795 NC_003911.11 2982241 2983431 R identified by match to protein family HMM PF01041; aminotransferase complement(2982241..2983431) Ruegeria pomeroyi DSS-3 3193246 YP_168004.1 CDS gph-2 NC_003911.11 2983505 2984167 R 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 complement(2983505..2984167) Ruegeria pomeroyi DSS-3 3194599 YP_168005.1 CDS glmU NC_003911.11 2984286 2985638 D 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 2984286..2985638 Ruegeria pomeroyi DSS-3 3193284 YP_168006.1 CDS SPO2798 NC_003911.11 2985719 2986405 D identified by similarity to PIR:AG1725; hypothetical protein 2985719..2986405 Ruegeria pomeroyi DSS-3 3193124 YP_168007.1 CDS moaA NC_003911.11 2986945 2987952 D together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A 2986945..2987952 Ruegeria pomeroyi DSS-3 3196169 YP_168008.1 CDS kdtA NC_003911.11 2987956 2989254 D identified by similarity to SP:P23282; match to protein family HMM PF04413; 3-deoxy-D-manno-octulosonic acid transferase 2987956..2989254 Ruegeria pomeroyi DSS-3 3195810 YP_168009.1 CDS lpcC NC_003911.11 2989254 2990309 D identified by similarity to SP:O68547; match to protein family HMM PF00534; lipopolysaccharide core biosynthesis mannosyltransferase 2989254..2990309 Ruegeria pomeroyi DSS-3 3193131 YP_168010.1 CDS SPO2802 NC_003911.11 2990371 2991426 D identified by match to protein family HMM PF02608; bmp family protein 2990371..2991426 Ruegeria pomeroyi DSS-3 3196174 YP_168011.1 CDS SPO2803 NC_003911.11 2991469 2992986 D identified by match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein 2991469..2992986 Ruegeria pomeroyi DSS-3 3193000 YP_168012.1 CDS SPO2804 NC_003911.11 2992983 2994056 D identified by match to protein family HMM PF02653; sugar ABC transporter permease 2992983..2994056 Ruegeria pomeroyi DSS-3 3196167 YP_168013.1 CDS SPO2805 NC_003911.11 2994053 2994997 D identified by match to protein family HMM PF02653; sugar ABC transporter permease 2994053..2994997 Ruegeria pomeroyi DSS-3 3195022 YP_168014.1 CDS SPO2806 NC_003911.11 2995007 2996299 D Catalyzes the deamination of cytosine to uracil and ammonia; cytosine deaminase 2995007..2996299 Ruegeria pomeroyi DSS-3 3196165 YP_168015.1 CDS SPO2807 NC_003911.11 2996358 2996996 D identified by similarity to GB:AAQ87176.1; hypothetical protein 2996358..2996996 Ruegeria pomeroyi DSS-3 3196159 YP_168016.1 CDS SPO2808 NC_003911.11 2997045 2998208 R identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase complement(2997045..2998208) Ruegeria pomeroyi DSS-3 3194441 YP_168017.1 CDS SPO2809 NC_003911.11 2998230 2999399 R identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase complement(2998230..2999399) Ruegeria pomeroyi DSS-3 3193033 YP_168018.1 CDS SPO2810 NC_003911.11 2999414 3000577 R identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase complement(2999414..3000577) Ruegeria pomeroyi DSS-3 3193307 YP_168019.1 CDS SPO2811 NC_003911.11 3000608 3001774 R identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891; amidohydrolase complement(3000608..3001774) Ruegeria pomeroyi DSS-3 3196157 YP_168020.1 CDS argE-1 NC_003911.11 3001939 3003105 R catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase complement(3001939..3003105) Ruegeria pomeroyi DSS-3 3196162 YP_168021.1 CDS SPO2813 NC_003911.11 3003109 3004974 R identified by match to protein family HMM PF00005; peptide/nickel/opine uptake ABC transporter ATP-binding protein complement(3003109..3004974) Ruegeria pomeroyi DSS-3 3194980 YP_168022.1 CDS SPO2814 NC_003911.11 3005240 3006961 D identified by similarity to SP:P42061; match to protein family HMM PF00496; peptide/opine/nickel uptake ABC transporter substrate-binding protein 3005240..3006961 Ruegeria pomeroyi DSS-3 3196158 YP_168023.1 CDS SPO2815 NC_003911.11 3007058 3008065 D identified by similarity to SP:P42062; match to protein family HMM PF00528; peptide/nickel/opine uptake ABC transporter permease 3007058..3008065 Ruegeria pomeroyi DSS-3 3195376 YP_168024.1 CDS SPO2816 NC_003911.11 3008040 3008969 D identified by similarity to SP:P42063; match to protein family HMM PF00528; peptide/nickel/opine uptake ABC transporter permease 3008040..3008969 Ruegeria pomeroyi DSS-3 3196150 YP_168025.1 CDS SPO2817 NC_003911.11 3009179 3010252 D identified by similarity to GB:CAE29903.1; match to protein family HMM PF04143; hypothetical protein 3009179..3010252 Ruegeria pomeroyi DSS-3 3196153 YP_168026.1 CDS SPO2818 NC_003911.11 3010188 3011468 R identified by similarity to GB:CAE26946.1; hypothetical protein complement(3010188..3011468) Ruegeria pomeroyi DSS-3 3196140 YP_168027.1 CDS pntB NC_003911.11 3011655 3013088 R identified by match to protein family HMM PF02233; NAD(P) transhydrogenase subunit beta complement(3011655..3013088) Ruegeria pomeroyi DSS-3 3196151 YP_168028.1 CDS pntA NC_003911.11 3013102 3014673 R 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 complement(3013102..3014673) Ruegeria pomeroyi DSS-3 3193432 YP_168029.1 CDS SPO2821 NC_003911.11 3014804 3015253 R identified by match to protein family HMM PF04140; isoprenylcysteine carboxyl methyltransferase complement(3014804..3015253) Ruegeria pomeroyi DSS-3 3195154 YP_168030.1 CDS SPO2822 NC_003911.11 3015442 3016389 R identified by similarity to GB:CAD33969.1; soxH protein-like protein complement(3015442..3016389) Ruegeria pomeroyi DSS-3 3196141 YP_168031.1 CDS bdh-2 NC_003911.11 3016510 3017262 D identified by similarity to SP:O86034; match to protein family HMM PF00106; D-beta-hydroxybutyrate dehydrogenase 3016510..3017262 Ruegeria pomeroyi DSS-3 3195434 YP_168032.1 CDS kynU NC_003911.11 3017478 3018683 D identified by similarity to SP:Q16719; match to protein family HMM TIGR01814; kynureninase 3017478..3018683 Ruegeria pomeroyi DSS-3 3196138 YP_168033.1 CDS SPO2825 NC_003911.11 3018691 3019269 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(3018691..3019269) Ruegeria pomeroyi DSS-3 3196133 YP_168034.1 CDS iorA NC_003911.11 3019391 3019855 D identified by similarity to SP:Q51697; match to protein family HMM PF00111; match to protein family HMM PF01799; isoquinoline 1-oxidoreductase subunit alpha 3019391..3019855 Ruegeria pomeroyi DSS-3 3195329 YP_168035.1 CDS SPO2827 NC_003911.11 3019859 3022099 D identified by similarity to SP:Q51698; match to protein family HMM PF02738; match to protein family HMM TIGR01409; isoquinoline 1-oxidoreductase subunit beta 3019859..3022099 Ruegeria pomeroyi DSS-3 3196127 YP_168036.1 CDS SPO2828 NC_003911.11 3022301 3024379 D identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 3022301..3024379 Ruegeria pomeroyi DSS-3 3196124 YP_168037.1 CDS SPO2829 NC_003911.11 3024665 3026080 R identified by similarity to SP:O85304; match to protein family HMM PF03577; dipeptidase domain-containing protein complement(3024665..3026080) Ruegeria pomeroyi DSS-3 3196125 YP_168038.1 CDS SPO2830 NC_003911.11 3026077 3027693 R identified by similarity to GB:AAN53028.1; hypothetical protein complement(3026077..3027693) Ruegeria pomeroyi DSS-3 3196123 YP_168039.1 CDS SPO2831 NC_003911.11 3027690 3028676 R identified by similarity to SP:P42065; match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide ABC transporter ATP-binding protein complement(3027690..3028676) Ruegeria pomeroyi DSS-3 3196112 YP_168040.1 CDS SPO2832 NC_003911.11 3028673 3029647 R 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 complement(3028673..3029647) Ruegeria pomeroyi DSS-3 3193803 YP_168041.1 CDS SPO2833 NC_003911.11 3029644 3030522 R identified by match to protein family HMM PF00528; dipeptide ABC transporter permease complement(3029644..3030522) Ruegeria pomeroyi DSS-3 3196113 YP_168042.1 CDS SPO2834 NC_003911.11 3030533 3031477 R 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 complement(3030533..3031477) Ruegeria pomeroyi DSS-3 3196110 YP_168043.1 CDS SPO2835 NC_003911.11 3031553 3033121 R 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 complement(3031553..3033121) Ruegeria pomeroyi DSS-3 3196108 YP_168044.1 CDS SPO2836 NC_003911.11 3033296 3034087 D identified by match to protein family HMM PF01381; DNA-binding protein 3033296..3034087 Ruegeria pomeroyi DSS-3 3196095 YP_168045.1 CDS SPO2837 NC_003911.11 3034345 3035124 R identified by similarity to GB:BAB51661.1; hypothetical protein complement(3034345..3035124) Ruegeria pomeroyi DSS-3 3196107 YP_168046.1 CDS SPO2838 NC_003911.11 3035247 3035672 R identified by similarity to GB:BAB50596.1; match to protein family HMM PF03928; hypothetical protein complement(3035247..3035672) Ruegeria pomeroyi DSS-3 3196102 YP_168047.1 CDS glcB NC_003911.11 3035758 3037905 R catalyzes the formation of malate from glyoxylate and acetyl-CoA; malate synthase G complement(3035758..3037905) Ruegeria pomeroyi DSS-3 3196099 YP_168048.1 CDS SPO2840 NC_003911.11 3038169 3038918 D identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254; diguanylate cyclase 3038169..3038918 Ruegeria pomeroyi DSS-3 3196098 YP_168049.1 CDS pepN NC_003911.11 3039024 3041576 D identified by similarity to SP:P37893; match to protein family HMM PF01433; aminopeptidase 3039024..3041576 Ruegeria pomeroyi DSS-3 3196093 YP_168050.1 CDS SPO2842 NC_003911.11 3041580 3042320 D identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase 3041580..3042320 Ruegeria pomeroyi DSS-3 3193251 YP_168051.1 CDS SPO2843 NC_003911.11 3042280 3042759 D hypothetical protein 3042280..3042759 Ruegeria pomeroyi DSS-3 3194263 YP_168052.1 CDS SPO2844 NC_003911.11 3042304 3043290 R hypothetical protein complement(3042304..3043290) Ruegeria pomeroyi DSS-3 3196086 YP_168053.1 CDS SPO2845 NC_003911.11 3042731 3044167 D hypothetical protein 3042731..3044167 Ruegeria pomeroyi DSS-3 3193510 YP_168054.1 CDS SPO2846 NC_003911.11 3044170 3045012 R identified by similarity to GB:BAC88423.1; hypothetical protein complement(3044170..3045012) Ruegeria pomeroyi DSS-3 3192933 YP_168055.1 CDS gatB NC_003911.11 3045154 3046665 D 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 3045154..3046665 Ruegeria pomeroyi DSS-3 3196088 YP_168056.1 CDS SPO2848 NC_003911.11 3046930 3047457 D identified by similarity to SP:P51702; hypothetical protein 3046930..3047457 Ruegeria pomeroyi DSS-3 3195451 YP_168057.1 CDS SPO2849 NC_003911.11 3047454 3047708 R identified by similarity to SP:P15298; match to protein family HMM PF01722; BolA protein, truncation complement(3047454..3047708) Ruegeria pomeroyi DSS-3 3196082 YP_168058.1 CDS SPO2850 NC_003911.11 3047852 3048472 D identified by match to protein family HMM PF00226; DnaJ domain-containing protein 3047852..3048472 Ruegeria pomeroyi DSS-3 3193976 YP_168059.1 CDS SPO2851 NC_003911.11 3048465 3049628 R identified by similarity to PIR:T03518; hypothetical protein complement(3048465..3049628) Ruegeria pomeroyi DSS-3 3194180 YP_168060.1 CDS SPO2852 NC_003911.11 3049641 3050243 D identified by similarity to SP:P94139; CzcN domain-containing protein 3049641..3050243 Ruegeria pomeroyi DSS-3 3196079 YP_168061.1 CDS SPO2853 NC_003911.11 3050260 3051369 D identified by match to protein family HMM PF06383; match to protein family HMM TIGR01650; cobalt chelatase, CobS subunit 3050260..3051369 Ruegeria pomeroyi DSS-3 3196078 YP_168062.1 CDS nucH NC_003911.11 3051366 3051809 D identified by similarity to SP:P43270; match to protein family HMM PF00565; thermonuclease 3051366..3051809 Ruegeria pomeroyi DSS-3 3195120 YP_168063.1 CDS SPO2855 NC_003911.11 3051930 3053807 D identified by similarity to SP:P29934; match to protein family HMM TIGR01651; cobalt chelatase large subunit 3051930..3053807 Ruegeria pomeroyi DSS-3 3193907 YP_168064.1 CDS SPO2856 NC_003911.11 3053979 3054365 R hypothetical protein complement(3053979..3054365) Ruegeria pomeroyi DSS-3 3196073 YP_168065.1 CDS SPO2857 NC_003911.11 3054457 3056247 D identified by match to protein family HMM PF00557; M24 family metallopeptidase 3054457..3056247 Ruegeria pomeroyi DSS-3 3193785 YP_168066.1 CDS SPO2858 NC_003911.11 3056331 3056675 D identified by similarity to GB:BAC50981.1; match to protein family HMM PF04248; hypothetical protein 3056331..3056675 Ruegeria pomeroyi DSS-3 3196044 YP_168067.1 CDS SPO2859 NC_003911.11 3056743 3057705 R identified by similarity to SP:P23523; 3-hydroxyisobutyrate dehydrogenase complement(3056743..3057705) Ruegeria pomeroyi DSS-3 3195745 YP_168068.1 CDS SPO2860 NC_003911.11 3057925 3058809 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3057925..3058809 Ruegeria pomeroyi DSS-3 3196029 YP_168069.1 CDS SPO2861 NC_003911.11 3059175 3059573 D identified by similarity to PIR:AE2921; hypothetical protein 3059175..3059573 Ruegeria pomeroyi DSS-3 3195757 YP_168070.1 CDS SPO2862 NC_003911.11 3059577 3060632 D identified by similarity to SP:P29937; match to protein family HMM PF02492; match to protein family HMM PF07683; CobW 3059577..3060632 Ruegeria pomeroyi DSS-3 3195686 YP_168071.1 CDS cobN NC_003911.11 3060642 3063935 D 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 3060642..3063935 Ruegeria pomeroyi DSS-3 3193474 YP_168072.1 CDS SPO2864 NC_003911.11 3063932 3065059 D identified by similarity to SP:P21637; match to protein family HMM PF03460; CobG 3063932..3065059 Ruegeria pomeroyi DSS-3 3195892 YP_168073.1 CDS cobH NC_003911.11 3065059 3065688 D catalyzes the interconversion of precorrin-8X and hydrogenobyrinate; precorrin-8X methylmutase 3065059..3065688 Ruegeria pomeroyi DSS-3 3195717 YP_168074.1 CDS cobI NC_003911.11 3065685 3066413 D identified by match to protein family HMM PF00590; match to protein family HMM TIGR01467; precorrin-2 C(20)-methyltransferase 3065685..3066413 Ruegeria pomeroyi DSS-3 3196061 YP_168075.1 CDS cobJ NC_003911.11 3066410 3067162 D identified by match to protein family HMM PF00590; match to protein family HMM TIGR01466; precorrin-3B C(17)-methyltransferase 3066410..3067162 Ruegeria pomeroyi DSS-3 3195887 YP_168076.1 CDS cobK NC_003911.11 3067135 3067887 R 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 complement(3067135..3067887) Ruegeria pomeroyi DSS-3 3193607 YP_168077.1 CDS cobL NC_003911.11 3067886 3069085 D identified by match to protein family HMM PF00590; match to protein family HMM TIGR01468; precorrin-6Y C5,15-methyltransferase 3067886..3069085 Ruegeria pomeroyi DSS-3 3195658 YP_168078.1 CDS SPO2870 NC_003911.11 3069082 3069450 D cobalamin biosynthesis domain-containing protein 3069082..3069450 Ruegeria pomeroyi DSS-3 3193799 YP_168079.1 CDS cobM NC_003911.11 3069447 3070241 D identified by match to protein family HMM PF00590; match to protein family HMM TIGR01465; precorrin-4 C(11)-methyltransferase 3069447..3070241 Ruegeria pomeroyi DSS-3 3195679 YP_168080.1 CDS cobB NC_003911.11 3070255 3071550 D responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid; cobyrinic acid a,c-diamide synthase 3070255..3071550 Ruegeria pomeroyi DSS-3 3195029 YP_168081.1 CDS cobA-2 NC_003911.11 3071547 3072275 D 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 3071547..3072275 Ruegeria pomeroyi DSS-3 3195129 YP_168082.1 CDS cobF NC_003911.11 3072268 3073011 D catalyzes the formation of precorrin 6x from precorrin 5; precorrin 6A synthase 3072268..3073011 Ruegeria pomeroyi DSS-3 3195028 YP_168083.1 CDS SPO2875 NC_003911.11 3073278 3073472 D identified by similarity to GB:AAO56638.1; hypothetical protein 3073278..3073472 Ruegeria pomeroyi DSS-3 3195277 YP_168084.1 CDS SPO2876 NC_003911.11 3073476 3074174 D hypothetical protein 3073476..3074174 Ruegeria pomeroyi DSS-3 3196051 YP_168085.1 CDS SPO2877 NC_003911.11 3074238 3074732 D identified by similarity to PIR:T36736; hypothetical protein 3074238..3074732 Ruegeria pomeroyi DSS-3 3195965 YP_168086.1 CDS SPO2878 NC_003911.11 3074720 3075112 R identified by similarity to GB:BAC48526.1; hypothetical protein complement(3074720..3075112) Ruegeria pomeroyi DSS-3 3194483 YP_168087.1 CDS SPO2879 NC_003911.11 3075132 3076049 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(3075132..3076049) Ruegeria pomeroyi DSS-3 3196058 YP_168088.1 CDS SPO2880 NC_003911.11 3076116 3076943 R catalyzes the formation of L-aspartate to iminoaspartate in NAD(+) biosynthesis; L-aspartate dehydrogenase complement(3076116..3076943) Ruegeria pomeroyi DSS-3 3195767 YP_168089.1 CDS SPO2881 NC_003911.11 3076961 3079156 D identified by match to protein family HMM PF01315; match to protein family HMM PF02738; xanthine dehydrogenase, large subunit 3076961..3079156 Ruegeria pomeroyi DSS-3 3195830 YP_168090.1 CDS SPO2882 NC_003911.11 3079198 3080106 D identified by match to protein family HMM PF00701; dihydrodipicolinate synthase 3079198..3080106 Ruegeria pomeroyi DSS-3 3195005 YP_168091.1 CDS SPO2883 NC_003911.11 3080178 3081728 R thiamine-pyrophosphate requiring enzyme; hypothetical protein complement(3080178..3081728) Ruegeria pomeroyi DSS-3 3195043 YP_168092.1 CDS SPO2884 NC_003911.11 3081815 3082330 D hypothetical protein 3081815..3082330 Ruegeria pomeroyi DSS-3 3195617 YP_168093.1 CDS SPO2885 NC_003911.11 3082404 3084023 D identified by similarity to SP:P27696; match to protein family HMM PF00205; match to protein family HMM PF02776; acetolactate synthase, catabolic 3082404..3084023 Ruegeria pomeroyi DSS-3 3194852 YP_168094.1 CDS SPO2886 NC_003911.11 3084010 3085203 D identified by match to protein family HMM PF02515; CAIB/BAIF family protein 3084010..3085203 Ruegeria pomeroyi DSS-3 3195912 YP_168095.1 CDS SPO2887 NC_003911.11 3085381 3086751 D identified by similarity to GB:CAE31162.1; hypothetical protein 3085381..3086751 Ruegeria pomeroyi DSS-3 3195942 YP_168096.1 CDS SPO2888 NC_003911.11 3086755 3088005 D hypothetical protein 3086755..3088005 Ruegeria pomeroyi DSS-3 3195018 YP_168097.1 CDS mdoG NC_003911.11 3088002 3089501 D involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan; glucan biosynthesis protein G 3088002..3089501 Ruegeria pomeroyi DSS-3 3195856 YP_168098.1 CDS SPO2890 NC_003911.11 3089489 3091372 D necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 3089489..3091372 Ruegeria pomeroyi DSS-3 3195836 YP_168099.1 CDS SPO2891 NC_003911.11 3091377 3092195 R identified by similarity to GB:AAA85939.1; hypothetical protein complement(3091377..3092195) Ruegeria pomeroyi DSS-3 3193257 YP_168100.1 CDS SPO2892 NC_003911.11 3092192 3092674 R identified by similarity to GB:AAM38343.1; hypothetical protein complement(3092192..3092674) Ruegeria pomeroyi DSS-3 3195135 YP_168101.1 CDS phaA NC_003911.11 3092895 3095804 D 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 3092895..3095804 Ruegeria pomeroyi DSS-3 3195927 YP_168102.1 CDS SPO2894 NC_003911.11 3095806 3096165 D subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; monovalent cation/H+ antiporter subunit C 3095806..3096165 Ruegeria pomeroyi DSS-3 3195466 YP_168103.1 CDS phaD NC_003911.11 3096162 3097709 D 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 3096162..3097709 Ruegeria pomeroyi DSS-3 3195796 YP_168104.1 CDS phaE NC_003911.11 3097706 3098203 D 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 3097706..3098203 Ruegeria pomeroyi DSS-3 3194369 YP_168105.1 CDS phaF NC_003911.11 3098200 3098472 D 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 3098200..3098472 Ruegeria pomeroyi DSS-3 3196005 YP_168106.1 CDS phaG NC_003911.11 3098480 3098866 D 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 3098480..3098866 Ruegeria pomeroyi DSS-3 3196008 YP_168107.1 CDS SPO2899 NC_003911.11 3098871 3101030 D identified by match to protein family HMM PF00070; match to protein family HMM PF02769; selenide,water dikinase 3098871..3101030 Ruegeria pomeroyi DSS-3 3196021 YP_168108.1 CDS SPO2900 NC_003911.11 3101186 3102238 R 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 complement(3101186..3102238) Ruegeria pomeroyi DSS-3 3195834 YP_168109.1 CDS SPO2901 NC_003911.11 3102276 3102941 R identified by similarity to GB:AAR33375.1; match to protein family HMM PF02586; hypothetical protein complement(3102276..3102941) Ruegeria pomeroyi DSS-3 3195289 YP_168110.1 CDS SPO2902 NC_003911.11 3102951 3103580 R identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase complement(3102951..3103580) Ruegeria pomeroyi DSS-3 3194613 YP_168111.1 CDS SPO2903 NC_003911.11 3103734 3105482 D identified by match to protein family HMM PF00515; match to protein family HMM PF00685; TPR/sulfotransferase domain-containing protein 3103734..3105482 Ruegeria pomeroyi DSS-3 3193569 YP_168112.1 CDS SPO2904 NC_003911.11 3105486 3107060 R identified by match to protein family HMM PF00149; match to protein family HMM PF02872; Ser/Thr protein phosphatase/nucleotidase complement(3105486..3107060) Ruegeria pomeroyi DSS-3 3195528 YP_168113.1 CDS SPO2905 NC_003911.11 3107178 3107516 D identified by similarity to GB:CAC45122.1; match to protein family HMM PF06108; hypothetical protein 3107178..3107516 Ruegeria pomeroyi DSS-3 3193245 YP_168114.1 CDS SPO2906 NC_003911.11 3107513 3107944 D identified by similarity to GB:CAE26026.1; hypothetical protein 3107513..3107944 Ruegeria pomeroyi DSS-3 3193030 YP_168115.1 CDS pyrD NC_003911.11 3107947 3108999 D 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 3107947..3108999 Ruegeria pomeroyi DSS-3 3195368 YP_168116.1 CDS arsC-1 NC_003911.11 3108996 3109340 D identified by match to protein family HMM PF03960; match to protein family HMM TIGR00014; arsenate reductase 3108996..3109340 Ruegeria pomeroyi DSS-3 3194113 YP_168117.1 CDS dinF NC_003911.11 3109324 3110649 R identified by similarity to SP:P28303; match to protein family HMM PF01554; match to protein family HMM TIGR00797; DNA-damage-inducible protein F complement(3109324..3110649) Ruegeria pomeroyi DSS-3 3193509 YP_168118.1 CDS SPO2910 NC_003911.11 3110657 3111175 R identified by match to protein family HMM PF03061; thioesterase complement(3110657..3111175) Ruegeria pomeroyi DSS-3 3195853 YP_168119.1 CDS SPO2911 NC_003911.11 3111177 3111647 R identified by match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase complement(3111177..3111647) Ruegeria pomeroyi DSS-3 3196069 YP_168120.1 CDS SPO2912 NC_003911.11 3111714 3112082 D identified by match to protein family HMM PF00376; MerR family transcriptional regulator 3111714..3112082 Ruegeria pomeroyi DSS-3 3195835 YP_168121.1 CDS SPO2913 NC_003911.11 3112203 3112397 D hypothetical protein 3112203..3112397 Ruegeria pomeroyi DSS-3 3196022 YP_168122.1 CDS SPO2914 NC_003911.11 3112617 3113018 D identified by match to protein family HMM PF00376; MerR family transcriptional regulator 3112617..3113018 Ruegeria pomeroyi DSS-3 3194350 YP_168123.1 CDS SPO2915 NC_003911.11 3113063 3114844 D identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase 3113063..3114844 Ruegeria pomeroyi DSS-3 3194663 YP_168124.1 CDS SPO2916 NC_003911.11 3114899 3115111 D hypothetical protein 3114899..3115111 Ruegeria pomeroyi DSS-3 3194645 YP_168125.1 CDS SPO2917 NC_003911.11 3115377 3116018 D identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 3115377..3116018 Ruegeria pomeroyi DSS-3 3195269 YP_168126.1 CDS SPO2918 NC_003911.11 3116029 3117240 D 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 3116029..3117240 Ruegeria pomeroyi DSS-3 3195219 YP_168127.1 CDS SPO2919 NC_003911.11 3117240 3117728 D identified by similarity to GB:BAC49273.1; hypothetical protein 3117240..3117728 Ruegeria pomeroyi DSS-3 3195612 YP_168128.1 CDS fabJ-1 NC_003911.11 3117721 3119922 D 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 3117721..3119922 Ruegeria pomeroyi DSS-3 3193840 YP_168129.1 CDS SPO2921 NC_003911.11 3119991 3120725 R identified by similarity to GB:AAA70414.1; hypothetical protein complement(3119991..3120725) Ruegeria pomeroyi DSS-3 3194656 YP_168130.1 CDS SPO2922 NC_003911.11 3120897 3121544 R identified by similarity to PIR:B95911; hypothetical protein complement(3120897..3121544) Ruegeria pomeroyi DSS-3 3194198 YP_168131.1 CDS SPO2923 NC_003911.11 3121576 3122484 R identified by match to protein family HMM PF00892; hypothetical protein complement(3121576..3122484) Ruegeria pomeroyi DSS-3 3194176 YP_168132.1 CDS SPO2924 NC_003911.11 3122519 3123658 D identified by similarity to GB:BAC52505.1; hypothetical protein 3122519..3123658 Ruegeria pomeroyi DSS-3 3194377 YP_168133.1 CDS SPO2925 NC_003911.11 3123695 3124933 D hypothetical protein 3123695..3124933 Ruegeria pomeroyi DSS-3 3195162 YP_168134.1 CDS upp NC_003911.11 3124964 3125596 R Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase complement(3124964..3125596) Ruegeria pomeroyi DSS-3 3193814 YP_168135.1 CDS add NC_003911.11 3125593 3126594 R catalyzes the formation of inosine from adenosine; adenosine deaminase complement(3125593..3126594) Ruegeria pomeroyi DSS-3 3195857 YP_168136.1 CDS deoB NC_003911.11 3126591 3127802 R catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose; phosphopentomutase complement(3126591..3127802) Ruegeria pomeroyi DSS-3 3194718 YP_168137.1 CDS deoA NC_003911.11 3127799 3129109 R Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate; thymidine phosphorylase complement(3127799..3129109) Ruegeria pomeroyi DSS-3 3195037 YP_168138.1 CDS cdd NC_003911.11 3129113 3129505 R identified by similarity to SP:P19079; match to protein family HMM PF00383; match to protein family HMM TIGR01354; cytidine deaminase complement(3129113..3129505) Ruegeria pomeroyi DSS-3 3194421 YP_168139.1 CDS SPO2931 NC_003911.11 3129647 3130831 R identified by similarity to GB:BAC50887.1; hypothetical protein complement(3129647..3130831) Ruegeria pomeroyi DSS-3 3195901 YP_168140.1 CDS SPO2932 NC_003911.11 3130877 3133150 D NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate; malic enzyme 3130877..3133150 Ruegeria pomeroyi DSS-3 3193912 YP_168141.1 CDS SPO2933 NC_003911.11 3133193 3133582 D identified by similarity to GB:BAB50467.1; match to protein family HMM PF04828; hypothetical protein 3133193..3133582 Ruegeria pomeroyi DSS-3 3195759 YP_168142.1 CDS prpE NC_003911.11 3133807 3135696 D identified by similarity to SP:P77495; match to protein family HMM PF00501; propionate--CoA ligase 3133807..3135696 Ruegeria pomeroyi DSS-3 3194703 YP_168143.1 CDS SPO2936 NC_003911.11 3135853 3136878 D hypothetical protein 3135853..3136878 Ruegeria pomeroyi DSS-3 3192991 YP_168144.1 CDS SPO2935 NC_003911.11 3135866 3136321 D hypothetical protein 3135866..3136321 Ruegeria pomeroyi DSS-3 3195292 YP_168145.1 CDS SPO2937 NC_003911.11 3136878 3137450 D identified by match to protein family HMM PF02630; SCO1/SenC family protein 3136878..3137450 Ruegeria pomeroyi DSS-3 3194060 YP_168146.1 CDS SPO2938 NC_003911.11 3137529 3138959 D catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia; amidase 3137529..3138959 Ruegeria pomeroyi DSS-3 3192685 YP_168147.1 CDS ppnK NC_003911.11 3139264 3140025 R catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase complement(3139264..3140025) Ruegeria pomeroyi DSS-3 3196038 YP_168148.1 CDS glyA NC_003911.11 3140194 3141489 D catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 3140194..3141489 Ruegeria pomeroyi DSS-3 3193885 YP_168149.1 CDS SPO2941 NC_003911.11 3141625 3142434 D hypothetical protein 3141625..3142434 Ruegeria pomeroyi DSS-3 3194532 YP_168150.1 CDS SPO2942 NC_003911.11 3142503 3143000 R hypothetical protein complement(3142503..3143000) Ruegeria pomeroyi DSS-3 3193921 YP_168151.1 CDS SPO2943 NC_003911.11 3142980 3143738 D identified by match to protein family HMM PF00561; alpha/beta hydrolase 3142980..3143738 Ruegeria pomeroyi DSS-3 3194598 YP_168152.1 CDS SPO2944 NC_003911.11 3143883 3144107 R hypothetical protein complement(3143883..3144107) Ruegeria pomeroyi DSS-3 3195495 YP_168153.1 CDS SPO2945 NC_003911.11 3144147 3144530 R identified by match to protein family HMM PF00581; rhodanese-like domain-containing protein complement(3144147..3144530) Ruegeria pomeroyi DSS-3 3193049 YP_168154.1 CDS SPO2946 NC_003911.11 3144632 3146119 R identified by similarity to GB:AAB50013.1; monooxygenase domain-containing protein complement(3144632..3146119) Ruegeria pomeroyi DSS-3 3193335 YP_168155.1 CDS SPO2947 NC_003911.11 3146135 3146596 R identified by match to protein family HMM PF00190; cupin complement(3146135..3146596) Ruegeria pomeroyi DSS-3 3195198 YP_168156.1 CDS SPO2948 NC_003911.11 3146698 3147744 D identified by match to protein family HMM PF00165; AraC family transcriptional regulator 3146698..3147744 Ruegeria pomeroyi DSS-3 3194866 YP_168157.1 CDS SPO2949 NC_003911.11 3147750 3148094 R identified by match to protein family HMM PF01042; endoribonuclease L-PSP complement(3147750..3148094) Ruegeria pomeroyi DSS-3 3195985 YP_168158.1 CDS SPO2950 NC_003911.11 3148164 3149345 R identified by similarity to GB:AAQ65571.1; match to protein family HMM PF04536; hypothetical protein complement(3148164..3149345) Ruegeria pomeroyi DSS-3 3192735 YP_168159.1 CDS SPO2951 NC_003911.11 3149400 3150179 R identified by similarity to PIR:G97655; match to protein family HMM PF03724; hypothetical protein complement(3149400..3150179) Ruegeria pomeroyi DSS-3 3195747 YP_168160.1 CDS SPO2952 NC_003911.11 3150256 3152034 R identified by match to protein family HMM PF02080; TrkA domain-containing protein complement(3150256..3152034) Ruegeria pomeroyi DSS-3 3194539 YP_168161.1 CDS SPO2953 NC_003911.11 3152142 3152954 R identified by match to protein family HMM PF00149; Ser/Thr protein phosphatase complement(3152142..3152954) Ruegeria pomeroyi DSS-3 3194948 YP_168162.1 CDS SPO2954 NC_003911.11 3153136 3153693 R identified by match to protein family HMM PF01812; 5-formyltetrahydrofolate cyclo-ligase complement(3153136..3153693) Ruegeria pomeroyi DSS-3 3194884 YP_168163.1 CDS mgtE NC_003911.11 3153702 3155093 R 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 complement(3153702..3155093) Ruegeria pomeroyi DSS-3 3193018 YP_168164.1 CDS SPO2956 NC_003911.11 3155229 3156512 D Catalyzes the deamination of guanine; guanine deaminase 3155229..3156512 Ruegeria pomeroyi DSS-3 3193915 YP_168165.1 CDS SPO2957 NC_003911.11 3156593 3157927 R catalyzes the transformation of hydroxyatrazine to N-isopropylammelide and ethylamine in the atrazine degradation pathway.; hydroxydechloroatrazine ethylaminohydrolase complement(3156593..3157927) Ruegeria pomeroyi DSS-3 3194390 YP_168166.1 CDS SPO2958 NC_003911.11 3158044 3158835 R identified by match to protein family HMM PF00459; match to protein family HMM TIGR02067; inositol monophosphatase complement(3158044..3158835) Ruegeria pomeroyi DSS-3 3192910 YP_168167.1 CDS SPO2959 NC_003911.11 3158885 3159256 R identified by match to protein family HMM PF01381; DNA-binding protein complement(3158885..3159256) Ruegeria pomeroyi DSS-3 3193965 YP_168168.1 CDS SPO2960 NC_003911.11 3159607 3160563 D identified by match to protein family HMM PF00107; zinc-binding dehydrogenase oxidoreductase 3159607..3160563 Ruegeria pomeroyi DSS-3 3192815 YP_168169.1 CDS SPO2961 NC_003911.11 3160726 3161604 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(3160726..3161604) Ruegeria pomeroyi DSS-3 3195732 YP_168170.1 CDS SPO2962 NC_003911.11 3161684 3161935 D identified by similarity to GB:AAO55291.1; hypothetical protein 3161684..3161935 Ruegeria pomeroyi DSS-3 3195533 YP_168171.1 CDS SPO2963 NC_003911.11 3162085 3162894 D identified by match to protein family HMM PF01027; hypothetical protein 3162085..3162894 Ruegeria pomeroyi DSS-3 3195811 YP_168172.1 CDS SPO2964 NC_003911.11 3162966 3163616 R hypothetical protein complement(3162966..3163616) Ruegeria pomeroyi DSS-3 3194953 YP_168173.1 CDS rpmG NC_003911.11 3163621 3163788 R 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 complement(3163621..3163788) Ruegeria pomeroyi DSS-3 3195427 YP_168174.1 CDS SPO2967 NC_003911.11 3164377 3165051 R identified by match to protein family HMM PF01510; N-acetylmuramoyl-L-alanine amidase complement(3164377..3165051) Ruegeria pomeroyi DSS-3 3194805 YP_168175.1 CDS SPO2968 NC_003911.11 3165058 3165969 R hypothetical protein complement(3165058..3165969) Ruegeria pomeroyi DSS-3 3194533 YP_168176.1 CDS gatA NC_003911.11 3165885 3167375 R 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 complement(3165885..3167375) Ruegeria pomeroyi DSS-3 3194340 YP_168177.1 CDS gatC NC_003911.11 3167379 3167666 R 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 complement(3167379..3167666) Ruegeria pomeroyi DSS-3 3194892 YP_168178.1 CDS SPO2971 NC_003911.11 3167743 3168894 R identified by match to protein family HMM TIGR01409; hypothetical protein complement(3167743..3168894) Ruegeria pomeroyi DSS-3 3195761 YP_168179.1 CDS SPO2972 NC_003911.11 3169010 3169492 R hypothetical protein complement(3169010..3169492) Ruegeria pomeroyi DSS-3 3194601 YP_168180.1 CDS SPO2974 NC_003911.11 3171756 3173042 R identified by similarity to GB:CAE27781.1; hypothetical protein complement(3171756..3173042) Ruegeria pomeroyi DSS-3 3194830 YP_168181.1 CDS SPO2975 NC_003911.11 3173116 3173763 R identified by similarity to GB:BAB51018.1; hypothetical protein complement(3173116..3173763) Ruegeria pomeroyi DSS-3 3195343 YP_168182.1 CDS SPO2976 NC_003911.11 3173821 3174513 D identified by match to protein family HMM PF00753; metallo-beta-lactamase 3173821..3174513 Ruegeria pomeroyi DSS-3 3195253 YP_168183.1 CDS SPO2977 NC_003911.11 3174604 3175593 D identified by match to protein family HMM PF00211; guanylate cyclase 3174604..3175593 Ruegeria pomeroyi DSS-3 3195656 YP_168184.1 CDS SPO2978 NC_003911.11 3175590 3176549 D identified by match to protein family HMM PF00211; guanylate cyclase 3175590..3176549 Ruegeria pomeroyi DSS-3 3193901 YP_168185.1 CDS SPO2979 NC_003911.11 3176649 3177098 R hypothetical protein complement(3176649..3177098) Ruegeria pomeroyi DSS-3 3194461 YP_168186.1 CDS SPO2980 NC_003911.11 3177095 3178111 R identified by match to protein family HMM PF04371; peptidyl-arginine deiminase complement(3177095..3178111) Ruegeria pomeroyi DSS-3 3195665 YP_168187.1 CDS SPO2981 NC_003911.11 3178253 3180013 R identified by similarity to GB:CAC67530.1; hypothetical protein complement(3178253..3180013) Ruegeria pomeroyi DSS-3 3195363 YP_168188.1 CDS SPO2982 NC_003911.11 3180077 3180550 R identified by match to protein family HMM PF01980; match to protein family HMM TIGR00104; hypothetical protein complement(3180077..3180550) Ruegeria pomeroyi DSS-3 3195084 YP_168189.1 CDS SPO2983 NC_003911.11 3180552 3181031 R identified by match to protein family HMM PF00383; cytidine and deoxycytidylate deaminase complement(3180552..3181031) Ruegeria pomeroyi DSS-3 3195951 YP_168190.1 CDS SPO2984 NC_003911.11 3181093 3182256 D identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093; RNA pseudouridylate synthase 3181093..3182256 Ruegeria pomeroyi DSS-3 3195842 YP_168191.1 CDS SPO2985 NC_003911.11 3182433 3183332 D hypothetical protein 3182433..3183332 Ruegeria pomeroyi DSS-3 3195187 YP_168192.1 CDS SPO2986 NC_003911.11 3183358 3184548 D identified by similarity to GB:AAB93480.1; tellurite resistance protein 3183358..3184548 Ruegeria pomeroyi DSS-3 3195536 YP_168193.1 CDS SPO2987 NC_003911.11 3184553 3185515 D identified by similarity to GB:AAB93481.1; lipoprotein 3184553..3185515 Ruegeria pomeroyi DSS-3 3195941 YP_168194.1 CDS SPO2988 NC_003911.11 3185543 3186658 D identified by similarity to GB:CAD18447.1; hypothetical protein 3185543..3186658 Ruegeria pomeroyi DSS-3 3194853 YP_168195.1 CDS SPO2989 NC_003911.11 3186722 3187210 D identified by similarity to SP:P16670; match to protein family HMM PF01292; cytochrome b562 3186722..3187210 Ruegeria pomeroyi DSS-3 3195445 YP_168196.1 CDS SPO2990 NC_003911.11 3187214 3188341 D identified by similarity to PIR:F83875; hypothetical protein 3187214..3188341 Ruegeria pomeroyi DSS-3 3195624 YP_168197.1 CDS SPO2991 NC_003911.11 3188990 3189685 D identified by match to protein family HMM PF00881; nitroreductase 3188990..3189685 Ruegeria pomeroyi DSS-3 3195936 YP_168198.1 CDS dtd NC_003911.11 3189696 3190133 D 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 3189696..3190133 Ruegeria pomeroyi DSS-3 3195426 YP_168199.1 CDS SPO2993 NC_003911.11 3190130 3191236 D identified by match to protein family HMM PF05161; MOFRL family protein 3190130..3191236 Ruegeria pomeroyi DSS-3 3195514 YP_168200.1 CDS SPO2994 NC_003911.11 3191281 3193281 D identified by similarity to PIR:I40217; match to protein family HMM PF02129; match to protein family HMM TIGR00976; X-Pro dipeptidyl-peptidase 3191281..3193281 Ruegeria pomeroyi DSS-3 3195156 YP_168201.1 CDS SPO2995 NC_003911.11 3193314 3194990 D identified by match to protein family HMM PF00496; match to protein family HMM TIGR01409; peptide/nickel/opine uptake ABC transporter substrate-binding protein 3193314..3194990 Ruegeria pomeroyi DSS-3 3195604 YP_168202.1 CDS SPO2996 NC_003911.11 3195010 3195966 D identified by match to protein family HMM PF00528; peptide/nickel/opine uptake ABC transporter permease 3195010..3195966 Ruegeria pomeroyi DSS-3 3194971 YP_168203.1 CDS SPO2997 NC_003911.11 3195963 3196778 D identified by similarity to SP:P37315; match to protein family HMM PF00528; peptide/nickel/opine uptake ABC transporter permease 3195963..3196778 Ruegeria pomeroyi DSS-3 3194534 YP_168204.1 CDS SPO2998 NC_003911.11 3196775 3198412 D identified by match to protein family HMM PF00005; peptide/nickel/opine uptake ABC transporter ATP-binding protein 3196775..3198412 Ruegeria pomeroyi DSS-3 3195482 YP_168205.1 CDS SPO2999 NC_003911.11 3198458 3199708 R hypothetical protein complement(3198458..3199708) Ruegeria pomeroyi DSS-3 3195973 YP_168206.1 CDS SPO3000 NC_003911.11 3199824 3200759 D identified by similarity to GB:BAB51623.1; hypothetical protein 3199824..3200759 Ruegeria pomeroyi DSS-3 3195085 YP_168207.1 CDS SPO3001 NC_003911.11 3200818 3201375 D hypothetical protein 3200818..3201375 Ruegeria pomeroyi DSS-3 3195083 YP_168208.1 CDS SPO3002 NC_003911.11 3201378 3202301 R identified by similarity to GB:AAC38151.1; lipase complement(3201378..3202301) Ruegeria pomeroyi DSS-3 3192925 YP_168209.1 CDS SPO3003 NC_003911.11 3202319 3204244 R activates fatty acids by binding to coenzyme A; AMP-binding protein complement(3202319..3204244) Ruegeria pomeroyi DSS-3 3194560 YP_168210.1 CDS SPO3004 NC_003911.11 3204434 3204862 R identified by match to protein family HMM PF01476; match to protein family HMM PF04972; LysM domain/BON superfamily protein complement(3204434..3204862) Ruegeria pomeroyi DSS-3 3195316 YP_168211.1 CDS SPO3005 NC_003911.11 3204929 3206860 R identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter ATP-binding protein/permease complement(3204929..3206860) Ruegeria pomeroyi DSS-3 3195372 YP_168212.1 CDS SPO3008 NC_003911.11 3207376 3207954 R identified by match to protein family HMM PF00515; hypothetical protein complement(3207376..3207954) Ruegeria pomeroyi DSS-3 3194987 YP_168213.1 CDS putR NC_003911.11 3207967 3208455 R identified by similarity to SP:Q52710; match to protein family HMM PF01037; match to protein family HMM TIGR01199; proline dehydrogenase complement(3207967..3208455) Ruegeria pomeroyi DSS-3 3194689 YP_168214.1 CDS putA NC_003911.11 3208560 3211964 D 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 3208560..3211964 Ruegeria pomeroyi DSS-3 3193507 YP_168215.1 CDS SPO3011 NC_003911.11 3212088 3212831 D identified by match to protein family HMM PF01694; rhomboid family protein 3212088..3212831 Ruegeria pomeroyi DSS-3 3195499 YP_168216.1 CDS SPO3012 NC_003911.11 3212902 3213687 R identified by similarity to SP:P22783; match to protein family HMM PF00459; inositol monophosphatase complement(3212902..3213687) Ruegeria pomeroyi DSS-3 3192702 YP_168217.1 CDS SPO3013 NC_003911.11 3213862 3214902 D identified by match to protein family HMM PF00107; L4BD family NADP-dependent oxidoreductase 3213862..3214902 Ruegeria pomeroyi DSS-3 3194024 YP_168218.1 CDS SPO3014 NC_003911.11 3215138 3215497 D hypothetical protein 3215138..3215497 Ruegeria pomeroyi DSS-3 3194800 YP_168219.1 CDS metR NC_003911.11 3215540 3216445 R identified by similarity to SP:P19797; match to protein family HMM PF00126; match to protein family HMM PF03466; transcriptional regulator MetR complement(3215540..3216445) Ruegeria pomeroyi DSS-3 3193156 YP_168220.1 CDS metF NC_003911.11 3216495 3217418 D identified by similarity to SP:P00394; match to protein family HMM PF02219; match to protein family HMM TIGR00676; 5,10-methylenetetrahydrofolate reductase 3216495..3217418 Ruegeria pomeroyi DSS-3 3193512 YP_168221.1 CDS SPO3017 NC_003911.11 3217480 3217965 D identified by similarity to SP:P76084; match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase 3217480..3217965 Ruegeria pomeroyi DSS-3 3193926 YP_168222.1 CDS SPO3018 NC_003911.11 3218169 3219248 R identified by similarity to GB:AAK24661.1; hypothetical protein complement(3218169..3219248) Ruegeria pomeroyi DSS-3 3194044 YP_168223.1 CDS SPO3019 NC_003911.11 3219223 3221514 R identified by match to protein family HMM PF01315; match to protein family HMM PF02738; xanthine dehydrogenase, large subunit complement(3219223..3221514) Ruegeria pomeroyi DSS-3 3195542 YP_168224.1 CDS SPO3020 NC_003911.11 3221652 3223289 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(3221652..3223289) Ruegeria pomeroyi DSS-3 3195801 YP_168225.1 CDS SPO3021 NC_003911.11 3223313 3224281 D identified by match to protein family HMM PF05721; phytanoyl-CoA dioxygenase 3223313..3224281 Ruegeria pomeroyi DSS-3 3193928 YP_168226.1 CDS valS NC_003911.11 3224640 3227702 D 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 3224640..3227702 Ruegeria pomeroyi DSS-3 3194327 YP_168227.1 CDS SPO3023 NC_003911.11 3227728 3228114 D identified by similarity to PIR:C83757; hypothetical protein 3227728..3228114 Ruegeria pomeroyi DSS-3 3194397 YP_168228.1 CDS SPO3024 NC_003911.11 3228187 3229584 D identified by match to protein family HMM PF00211; match to protein family HMM PF00561; adenylate cyclase 3228187..3229584 Ruegeria pomeroyi DSS-3 3192818 YP_168229.1 CDS SPO3025 NC_003911.11 3229758 3230540 R Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase complement(3229758..3230540) Ruegeria pomeroyi DSS-3 3195331 YP_168230.1 CDS SPO3026 NC_003911.11 3230614 3231789 R identified by match to protein family HMM PF03088; strictosidine synthase complement(3230614..3231789) Ruegeria pomeroyi DSS-3 3194929 YP_168231.1 CDS SPO3027 NC_003911.11 3231741 3232883 D catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate; histidinol-phosphate aminotransferase 3231741..3232883 Ruegeria pomeroyi DSS-3 3195868 YP_168232.1 CDS SPO3028 NC_003911.11 3232907 3233113 D hypothetical protein 3232907..3233113 Ruegeria pomeroyi DSS-3 3195179 YP_168233.1 CDS SPO3029 NC_003911.11 3233121 3234329 R identified by similarity to SP:O08374; match to protein family HMM PF00266; serine--glyoxylate transaminase complement(3233121..3234329) Ruegeria pomeroyi DSS-3 3193073 YP_168234.1 CDS SPO3030 NC_003911.11 3234424 3236394 D identified by match to protein family HMM PF00005; match to protein family HMM PF00664; efflux ABC transporter transmembrane ATP-binding protein 3234424..3236394 Ruegeria pomeroyi DSS-3 3193541 YP_168235.1 CDS eda-1 NC_003911.11 3236472 3237104 R identified by similarity to SP:P10177; match to protein family HMM PF01081; match to protein family HMM TIGR01182; 2-dehydro-3-deoxyphosphooctonate aldolase complement(3236472..3237104) Ruegeria pomeroyi DSS-3 3195167 YP_168236.1 CDS edd NC_003911.11 3237108 3238913 R catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate; phosphogluconate dehydratase complement(3237108..3238913) Ruegeria pomeroyi DSS-3 3193093 YP_168237.1 CDS zwf-2 NC_003911.11 3238916 3240367 R catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase complement(3238916..3240367) Ruegeria pomeroyi DSS-3 3194581 YP_168238.1 CDS SPO3034 NC_003911.11 3241134 3243377 R 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 complement(3241134..3243377) Ruegeria pomeroyi DSS-3 3194964 YP_168239.1 CDS SPO3035 NC_003911.11 3243425 3244663 R 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 complement(3243425..3244663) Ruegeria pomeroyi DSS-3 3194877 YP_168240.1 CDS SPO3036 NC_003911.11 3245171 3247231 R identified by match to protein family HMM PF00753; metallo-beta-lactamase complement(3245171..3247231) Ruegeria pomeroyi DSS-3 3193678 YP_168241.1 CDS SPO3037 NC_003911.11 3247808 3248617 D identified by match to protein family HMM PF00072; match to protein family HMM PF00126; LysR family transcriptional regulator 3247808..3248617 Ruegeria pomeroyi DSS-3 3195987 YP_168242.1 CDS SPO3038 NC_003911.11 3248605 3251301 R 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 complement(3248605..3251301) Ruegeria pomeroyi DSS-3 3195648 YP_168243.1 CDS SPO3039 NC_003911.11 3251298 3252041 R polar amino acid ABC transporter substrate-binding protein complement(3251298..3252041) Ruegeria pomeroyi DSS-3 3195535 YP_168244.1 CDS SPO3040 NC_003911.11 3252210 3253043 D identified by match to protein family HMM PF00497; polar amino acid ABC transporter substrate-binding protein 3252210..3253043 Ruegeria pomeroyi DSS-3 3194731 YP_168245.1 CDS SPO3041 NC_003911.11 3253047 3253826 D identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease 3253047..3253826 Ruegeria pomeroyi DSS-3 3194370 YP_168246.1 CDS SPO3042 NC_003911.11 3253816 3254703 D identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease 3253816..3254703 Ruegeria pomeroyi DSS-3 3195792 YP_168247.1 CDS glnQ NC_003911.11 3254716 3255465 D identified by similarity to SP:P27675; match to protein family HMM PF00005; glutamine ABC transporter ATP-binding protein 3254716..3255465 Ruegeria pomeroyi DSS-3 3193767 YP_168248.1 CDS SPO3044 NC_003911.11 3255584 3256588 D identified by match to protein family HMM PF00126; LysR family transcriptional regulator 3255584..3256588 Ruegeria pomeroyi DSS-3 3195235 YP_168249.1 CDS SPO3045 NC_003911.11 3256591 3257394 R identified by match to protein family HMM PF00117; glutamine amidotransferase complement(3256591..3257394) Ruegeria pomeroyi DSS-3 3195044 YP_168250.1 CDS SPO3046 NC_003911.11 3257440 3259527 R identified by match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide ABC transporter ATP-binding protein complement(3257440..3259527) Ruegeria pomeroyi DSS-3 3196059 YP_168251.1 CDS SPO3047 NC_003911.11 3259539 3260744 R identified by similarity to SP:P37315; match to protein family HMM PF00528; dipeptide ABC transporter permease complement(3259539..3260744) Ruegeria pomeroyi DSS-3 3194946 YP_168252.1 CDS SPO3048 NC_003911.11 3260757 3261896 R Assignment partly based on membership in dipeptide ABC transporter gene cluster.; identified by match to protein family HMM PF00528; dipeptide ABC transporter permease complement(3260757..3261896) Ruegeria pomeroyi DSS-3 3195850 YP_168253.1 CDS SPO3049 NC_003911.11 3261914 3263584 R 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 complement(3261914..3263584) Ruegeria pomeroyi DSS-3 3194967 YP_168254.1 CDS SPO3050 NC_003911.11 3263848 3263940 R hypothetical protein complement(3263848..3263940) Ruegeria pomeroyi DSS-3 3195202 YP_168255.1 CDS SPO3051 NC_003911.11 3264047 3264685 R identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase oxidoreductase complement(3264047..3264685) Ruegeria pomeroyi DSS-3 3195567 YP_168256.1 CDS SPO3052 NC_003911.11 3264687 3265112 R identified by similarity to GB:AAK22812.1; match to protein family HMM PF06676; hypothetical protein complement(3264687..3265112) Ruegeria pomeroyi DSS-3 3194919 YP_168257.1 CDS SPO3053 NC_003911.11 3265164 3265664 R identified by match to protein family HMM PF00293; NUDIX domain-containing protein complement(3265164..3265664) Ruegeria pomeroyi DSS-3 3195185 YP_168258.1 CDS SPO3054 NC_003911.11 3265729 3266490 R identified by similarity to GB:CAD71689.1; hypothetical protein complement(3265729..3266490) Ruegeria pomeroyi DSS-3 3195102 YP_168259.1 CDS SPO3055 NC_003911.11 3266540 3267028 R identified by match to protein family HMM PF00583; acetyltransferase complement(3266540..3267028) Ruegeria pomeroyi DSS-3 3195050 YP_168260.1 CDS SPO3056 NC_003911.11 3267112 3267717 D identified by similarity to GB:AAN29988.1; hypothetical protein 3267112..3267717 Ruegeria pomeroyi DSS-3 3194911 YP_168261.1 CDS SPO3057 NC_003911.11 3267717 3268355 D identified by similarity to GB:AAN77593.1; match to protein family HMM PF00132; streptogramin acetyltransferase 3267717..3268355 Ruegeria pomeroyi DSS-3 3194767 YP_168262.1 CDS SPO3058 NC_003911.11 3268484 3270118 R identified by match to protein family HMM PF00916; match to protein family HMM PF01740; sulfate transporter family protein complement(3268484..3270118) Ruegeria pomeroyi DSS-3 3195722 YP_168263.1 CDS SPO3059 NC_003911.11 3270279 3270860 D hypothetical protein 3270279..3270860 Ruegeria pomeroyi DSS-3 3195041 YP_168264.1 CDS mtaP NC_003911.11 3270937 3271809 D Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate; 5'-methylthioadenosine phosphorylase 3270937..3271809 Ruegeria pomeroyi DSS-3 3195483 YP_168265.1 CDS SPO3062 NC_003911.11 3273089 3273562 D identified by similarity to PIR:H95891; hypothetical protein 3273089..3273562 Ruegeria pomeroyi DSS-3 3195315 YP_168266.1 CDS SPO3063 NC_003911.11 3273593 3274252 D identified by similarity to SP:P27847; match to protein family HMM PF01810; transmembrane efflux protein 3273593..3274252 Ruegeria pomeroyi DSS-3 3194819 YP_168267.1 CDS SPO3064 NC_003911.11 3274249 3274482 R identified by similarity to GB:AAM37286.1; hypothetical protein complement(3274249..3274482) Ruegeria pomeroyi DSS-3 3193784 YP_168268.1 CDS SPO3065 NC_003911.11 3274481 3274648 D hypothetical protein 3274481..3274648 Ruegeria pomeroyi DSS-3 3194279 YP_168269.1 CDS apt NC_003911.11 3274764 3275303 D catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 3274764..3275303 Ruegeria pomeroyi DSS-3 3195689 YP_168270.1 CDS SPO3067 NC_003911.11 3275373 3276785 R identified by match to protein family HMM PF01565; match to protein family HMM PF02913; oxidoreductase, FAD-binding complement(3275373..3276785) Ruegeria pomeroyi DSS-3 3193056 YP_168271.1 CDS SPO3068 NC_003911.11 3276824 3277672 R identified by similarity to GB:CAC47333.1; hypothetical protein complement(3276824..3277672) Ruegeria pomeroyi DSS-3 3193522 YP_168272.1 CDS SPO3069 NC_003911.11 3277751 3278335 R identified by similarity to SP:P09454; match to protein family HMM PF00583; ribosomal-protein-alanine acetyltransferase complement(3277751..3278335) Ruegeria pomeroyi DSS-3 3195952 YP_168273.1 CDS SPO3070 NC_003911.11 3278335 3279597 R identified by match to protein family HMM PF00675; match to protein family HMM PF05193; M16 family peptidase complement(3278335..3279597) Ruegeria pomeroyi DSS-3 3196066 YP_168274.1 CDS thrC NC_003911.11 3279594 3280985 R catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase complement(3279594..3280985) Ruegeria pomeroyi DSS-3 3196057 YP_168275.1 CDS SPO3072 NC_003911.11 3280991 3281662 R SURF1 family protein complement(3280991..3281662) Ruegeria pomeroyi DSS-3 3196001 YP_168276.1 CDS ctaE NC_003911.11 3281848 3282663 R identified by match to protein family HMM PF00510; cytochrome c oxidase subunit III complement(3281848..3282663) Ruegeria pomeroyi DSS-3 3195972 YP_168277.1 CDS ctaG NC_003911.11 3282686 3283261 R involved in the insertion of copper into subunit I of cytochrome C oxidase; cytochrome C oxidase assembly protein complement(3282686..3283261) Ruegeria pomeroyi DSS-3 3195127 YP_168278.1 CDS cyoE NC_003911.11 3283425 3284381 R converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase complement(3283425..3284381) Ruegeria pomeroyi DSS-3 3196009 YP_168279.1 CDS ctaC NC_003911.11 3284469 3285305 R identified by similarity to SP:P08306; match to protein family HMM PF00116; match to protein family HMM PF02790; cytochrome c oxidase subunit II complement(3284469..3285305) Ruegeria pomeroyi DSS-3 3196014 YP_168280.1 CDS SPO3077 NC_003911.11 3285483 3286904 D identified by similarity to SP:P46473; match to protein family HMM PF01523; TldD/PmbA family protein 3285483..3286904 Ruegeria pomeroyi DSS-3 3195320 YP_168281.1 CDS SPO3078 NC_003911.11 3287129 3288277 D identified by match to protein family HMM PF02481; match to protein family HMM TIGR00732; DNA processing protein DprA 3287129..3288277 Ruegeria pomeroyi DSS-3 3195908 YP_168282.1 CDS topA NC_003911.11 3288441 3291083 D catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I 3288441..3291083 Ruegeria pomeroyi DSS-3 3196046 YP_168283.1 CDS SPO3080 NC_003911.11 3291105 3291686 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(3291105..3291686) Ruegeria pomeroyi DSS-3 3196045 YP_168284.1 CDS SPO3081 NC_003911.11 3291754 3292179 D identified by match to protein family HMM PF00903; glyoxalase 3291754..3292179 Ruegeria pomeroyi DSS-3 3196033 YP_168285.1 CDS dxnG NC_003911.11 3292312 3293016 D identified by similarity to GB:CAA51372.1; match to protein family HMM PF01144; 3-oxoadipate CoA-succinyl transferase subunit alpha 3292312..3293016 Ruegeria pomeroyi DSS-3 3195964 YP_168286.1 CDS dxnH NC_003911.11 3293020 3293646 D identified by similarity to GB:CAA51373.1; match to protein family HMM PF01144; 3-oxoadipate CoA-succinyl transferase subunit beta 3293020..3293646 Ruegeria pomeroyi DSS-3 3195832 YP_168287.1 CDS SPO3084 NC_003911.11 3293700 3294638 R identified by match to protein family HMM PF01464; Slt family transglycosylase complement(3293700..3294638) Ruegeria pomeroyi DSS-3 3194944 YP_168288.1 CDS SPO3085 NC_003911.11 3294900 3295088 D hypothetical protein 3294900..3295088 Ruegeria pomeroyi DSS-3 3194217 YP_168289.1 CDS SPO3086 NC_003911.11 3295503 3296420 D identified by match to protein family HMM PF06981; CpaB family protein 3295503..3296420 Ruegeria pomeroyi DSS-3 3195786 YP_168290.1 CDS SPO3087 NC_003911.11 3296595 3298022 D identified by match to protein family HMM PF00263; type II/III secretion system protein 3296595..3298022 Ruegeria pomeroyi DSS-3 3195838 YP_168291.1 CDS SPO3088 NC_003911.11 3298030 3298665 D identified by match to protein family HMM PF00691; OmpA family protein 3298030..3298665 Ruegeria pomeroyi DSS-3 3195419 YP_168292.1 CDS SPO3089 NC_003911.11 3298759 3300087 D ATPase 3298759..3300087 Ruegeria pomeroyi DSS-3 3195468 YP_168293.1 CDS SPO3090 NC_003911.11 3300112 3301551 D identified by similarity to GB:AAN75211.1; match to protein family HMM PF00437; type II/IV secretion system protein 3300112..3301551 Ruegeria pomeroyi DSS-3 3195634 YP_168294.1 CDS SPO3091 NC_003911.11 3301563 3302531 D identified by match to protein family HMM PF00482; TadC family type II/IV secretion system protein 3301563..3302531 Ruegeria pomeroyi DSS-3 3195470 YP_168295.1 CDS SPO3092 NC_003911.11 3302542 3303522 D identified by match to protein family HMM PF00482; TadC family type II/IV secretion system protein 3302542..3303522 Ruegeria pomeroyi DSS-3 3193575 YP_168296.1 CDS SPO3093 NC_003911.11 3303527 3304117 D identified by similarity to GB:CAE29125.1; match to protein family HMM PF00515; hypothetical protein 3303527..3304117 Ruegeria pomeroyi DSS-3 3194457 YP_168297.1 CDS SPO3094 NC_003911.11 3304147 3304995 D lipoprotein 3304147..3304995 Ruegeria pomeroyi DSS-3 3193127 YP_168298.1 CDS SPO3095 NC_003911.11 3305000 3305545 D hypothetical protein 3305000..3305545 Ruegeria pomeroyi DSS-3 3194502 YP_168299.1 CDS SPO3096 NC_003911.11 3305583 3306971 D identified by similarity to GB:BAC95426.1; hypothetical protein 3305583..3306971 Ruegeria pomeroyi DSS-3 3192896 YP_168300.1 CDS mmsB-2 NC_003911.11 3306968 3307777 D identified by similarity to GB:AAA50312.1; 3-hydroxyisobutyrate dehydrogenase 3306968..3307777 Ruegeria pomeroyi DSS-3 3195882 YP_168301.1 CDS SPO3098 NC_003911.11 3307859 3310267 D identified by match to protein family HMM PF00270; match to protein family HMM PF00271; DEAD/DEAH box helicase 3307859..3310267 Ruegeria pomeroyi DSS-3 3195597 YP_168302.1 CDS SPO3099 NC_003911.11 3310309 3310971 D identified by similarity to GB:BAC46414.1; hypothetical protein 3310309..3310971 Ruegeria pomeroyi DSS-3 3195840 YP_168303.1 CDS SPO3100 NC_003911.11 3310968 3311711 R identified by similarity to GB:AAN30398.1; hypothetical protein complement(3310968..3311711) Ruegeria pomeroyi DSS-3 3194942 YP_168304.1 CDS SPO3101 NC_003911.11 3311973 3312863 R 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 complement(3311973..3312863) Ruegeria pomeroyi DSS-3 3193798 YP_168305.1 CDS SPO3102 NC_003911.11 3312927 3313232 R identified by match to protein family HMM PF01817; match to protein family HMM TIGR01803; chorismate mutase complement(3312927..3313232) Ruegeria pomeroyi DSS-3 3193669 YP_168306.1 CDS fhs-2 NC_003911.11 3313292 3314968 R catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase complement(3313292..3314968) Ruegeria pomeroyi DSS-3 3195304 YP_168307.1 CDS SPO3104 NC_003911.11 3315135 3315713 R identified by match to protein family HMM PF03473; MOSC domain-containing protein complement(3315135..3315713) Ruegeria pomeroyi DSS-3 3193714 YP_168308.1 CDS ftsH NC_003911.11 3315827 3317746 R 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 complement(3315827..3317746) Ruegeria pomeroyi DSS-3 3195808 YP_168309.1 CDS SPO3106 NC_003911.11 3317819 3319078 R identified by match to protein family HMM PF01171; PP-loop family protein complement(3317819..3319078) Ruegeria pomeroyi DSS-3 3194218 YP_168310.1 CDS SPO3107 NC_003911.11 3319069 3319884 R identified by similarity to GB:AAO57429.1; hypothetical protein complement(3319069..3319884) Ruegeria pomeroyi DSS-3 3193940 YP_168311.1 CDS pal NC_003911.11 3319889 3320434 R identified by similarity to SP:P07176; match to protein family HMM PF00691; peptidoglycan-associated lipoprotein complement(3319889..3320434) Ruegeria pomeroyi DSS-3 3194177 YP_168312.1 CDS tolB NC_003911.11 3320487 3321806 R 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 complement(3320487..3321806) Ruegeria pomeroyi DSS-3 3193729 YP_168313.1 CDS SPO3110 NC_003911.11 3321803 3322945 R TonB domain-containing protein complement(3321803..3322945) Ruegeria pomeroyi DSS-3 3193280 YP_168314.1 CDS SPO3111 NC_003911.11 3322955 3323434 R identified by match to protein family HMM PF02472; biopolymer ExbD/TolR family transporter complement(3322955..3323434) Ruegeria pomeroyi DSS-3 3193621 YP_168315.1 CDS tolQ NC_003911.11 3323438 3324133 R identified by similarity to SP:P05828; match to protein family HMM PF01618; proton transporter TolQ complement(3323438..3324133) Ruegeria pomeroyi DSS-3 3194798 YP_168316.1 CDS SPO3113 NC_003911.11 3324241 3324624 R identified by match to protein family HMM PF03061; match to protein family HMM TIGR00051; hypothetical protein complement(3324241..3324624) Ruegeria pomeroyi DSS-3 3195232 YP_168317.1 CDS SPO3114 NC_003911.11 3324621 3325418 R hypothetical protein complement(3324621..3325418) Ruegeria pomeroyi DSS-3 3195659 YP_168318.1 CDS ruvB NC_003911.11 3325427 3326452 R 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 complement(3325427..3326452) Ruegeria pomeroyi DSS-3 3194519 YP_168319.1 CDS ruvA NC_003911.11 3326499 3327173 R plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA complement(3326499..3327173) Ruegeria pomeroyi DSS-3 3193593 YP_168320.1 CDS ruvC NC_003911.11 3327170 3327667 R 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 complement(3327170..3327667) Ruegeria pomeroyi DSS-3 3195558 YP_168321.1 CDS SPO3118 NC_003911.11 3327999 3328217 D identified by similarity to GB:CAC46124.1; match to protein family HMM PF06568; hypothetical protein 3327999..3328217 Ruegeria pomeroyi DSS-3 3195407 YP_168322.1 CDS SPO3119 NC_003911.11 3328300 3328656 R hypothetical protein complement(3328300..3328656) Ruegeria pomeroyi DSS-3 3195431 YP_168323.1 CDS SPO3120 NC_003911.11 3328744 3329622 R identified by similarity to SP:P28637; match to protein family HMM PF06325; 50S ribosomal protein L11 methyltransferase complement(3328744..3329622) Ruegeria pomeroyi DSS-3 3195458 YP_168324.1 CDS SPO3121 NC_003911.11 3329622 3331016 R identified by match to protein family HMM PF01554; MATE efflux family protein complement(3329622..3331016) Ruegeria pomeroyi DSS-3 3195252 YP_168325.1 CDS SPO3122 NC_003911.11 3331021 3332253 R identified by similarity to GB:BAC62827.1; hypothetical protein complement(3331021..3332253) Ruegeria pomeroyi DSS-3 3194442 YP_168326.1 CDS SPO3123 NC_003911.11 3332423 3333487 D identified by similarity to SP:P33015; match to protein family HMM PF04143; hypothetical protein 3332423..3333487 Ruegeria pomeroyi DSS-3 3195313 YP_168327.1 CDS SPO3124 NC_003911.11 3333559 3333978 D identified by similarity to GB:CAC46680.1; match to protein family HMM PF03640; hypothetical protein 3333559..3333978 Ruegeria pomeroyi DSS-3 3195035 YP_168328.1 CDS SPO3125 NC_003911.11 3333994 3334512 D 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 3333994..3334512 Ruegeria pomeroyi DSS-3 3196068 YP_168329.1 CDS SPO3126 NC_003911.11 3334509 3335255 D identified by similarity to GB:AAF81073.1; sigma factor regulator PrtR 3334509..3335255 Ruegeria pomeroyi DSS-3 3196054 YP_168330.1 CDS priA NC_003911.11 3335405 3337615 R binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA complement(3335405..3337615) Ruegeria pomeroyi DSS-3 3196031 YP_168331.1 CDS fsaB NC_003911.11 3337734 3338387 D similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity; translaldolase 3337734..3338387 Ruegeria pomeroyi DSS-3 3196037 YP_168332.1 CDS SPO3129 NC_003911.11 3338609 3339316 D identified by similarity to GB:AAK22332.1; hypothetical protein 3338609..3339316 Ruegeria pomeroyi DSS-3 3196018 YP_168333.1 CDS xerC NC_003911.11 3339313 3340233 D 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 3339313..3340233 Ruegeria pomeroyi DSS-3 3196023 YP_168334.1 CDS pcs NC_003911.11 3340305 3341012 D identified by similarity to SP:Q9KJY8; match to protein family HMM PF01066; phosphatidylcholine synthase 3340305..3341012 Ruegeria pomeroyi DSS-3 3196010 YP_168335.1 CDS SPO3132 NC_003911.11 3340978 3341601 R identified by similarity to GB:AAQ87450.1; hypothetical protein complement(3340978..3341601) Ruegeria pomeroyi DSS-3 3196003 YP_168336.1 CDS SPO3133 NC_003911.11 3341598 3342056 R hypothetical protein complement(3341598..3342056) Ruegeria pomeroyi DSS-3 3195623 YP_168337.1 CDS ogt NC_003911.11 3342125 3342577 R identified by similarity to SP:P11742; match to protein family HMM PF01035; match to protein family HMM TIGR00589; methylated-DNA--protein-cysteine methyltransferase complement(3342125..3342577) Ruegeria pomeroyi DSS-3 3195793 YP_168338.1 CDS SPO3135 NC_003911.11 3342717 3343679 R identified by match to protein family HMM PF03576; T4 family peptidase complement(3342717..3343679) Ruegeria pomeroyi DSS-3 3195001 YP_168339.1 CDS ileS NC_003911.11 3343681 3346593 R 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 complement(3343681..3346593) Ruegeria pomeroyi DSS-3 3193197 YP_168340.1 CDS SPO3137 NC_003911.11 3346819 3347406 D hypothetical protein 3346819..3347406 Ruegeria pomeroyi DSS-3 3193732 YP_168341.1 CDS SPO3138 NC_003911.11 3347426 3348136 R identified by similarity to GB:BAC19465.1; match to protein family HMM PF01988; hypothetical protein complement(3347426..3348136) Ruegeria pomeroyi DSS-3 3194008 YP_168342.1 CDS SPO3139 NC_003911.11 3348262 3348669 D hypothetical protein 3348262..3348669 Ruegeria pomeroyi DSS-3 3195521 YP_168343.1 CDS SPO3140 NC_003911.11 3348764 3349774 R identified by similarity to GB:BAB48295.1; match to protein family HMM TIGR01620; hypothetical protein complement(3348764..3349774) Ruegeria pomeroyi DSS-3 3195685 YP_168344.1 CDS SPO3141 NC_003911.11 3349759 3350199 R identified by match to protein family HMM PF00583; acetyltransferase complement(3349759..3350199) Ruegeria pomeroyi DSS-3 3195890 YP_168345.1 CDS SPO3142 NC_003911.11 3350196 3351611 R identified by similarity to GB:CAC46385.1; hypothetical protein complement(3350196..3351611) Ruegeria pomeroyi DSS-3 3194588 YP_168346.1 CDS truA NC_003911.11 3351843 3352631 D mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A 3351843..3352631 Ruegeria pomeroyi DSS-3 3193303 YP_168347.1 CDS SPO3144 NC_003911.11 3352586 3353293 R identified by similarity to GB:BAB48071.1; hypothetical protein complement(3352586..3353293) Ruegeria pomeroyi DSS-3 3195898 YP_168348.1 CDS SPO3145 NC_003911.11 3353376 3354392 D identified by similarity to PIR:AD2899; match to protein family HMM PF07446; GumN family protein 3353376..3354392 Ruegeria pomeroyi DSS-3 3195420 YP_168349.1 CDS SPO3146 NC_003911.11 3354395 3355390 D identified by match to protein family HMM PF07446; GumN family protein 3354395..3355390 Ruegeria pomeroyi DSS-3 3195676 YP_168350.1 CDS ppaC NC_003911.11 3355493 3356413 D catalyzes the hydrolysis of pyrophosphate to phosphate; manganese-dependent inorganic pyrophosphatase 3355493..3356413 Ruegeria pomeroyi DSS-3 3195814 YP_168351.1 CDS SPO3148 NC_003911.11 3356468 3357163 R hypothetical protein complement(3356468..3357163) Ruegeria pomeroyi DSS-3 3195248 YP_168352.1 CDS SPO3149 NC_003911.11 3357283 3357741 R identified by similarity to GB:CAE31907.1; match to protein family HMM PF04828; hypothetical protein complement(3357283..3357741) Ruegeria pomeroyi DSS-3 3194850 YP_168353.1 CDS SPO3150 NC_003911.11 3357794 3358711 D identified by match to protein family HMM PF00165; match to protein family HMM PF01965; AraC family transcriptional regulator 3357794..3358711 Ruegeria pomeroyi DSS-3 3195903 YP_168354.1 CDS SPO3151 NC_003911.11 3358735 3359667 D identified by match to protein family HMM PF00702; match to protein family HMM TIGR01459; match to protein family HMM TIGR01460; HAD family hydrolase 3358735..3359667 Ruegeria pomeroyi DSS-3 3194029 YP_168355.1 CDS SPO3152 NC_003911.11 3359719 3360213 D identified by match to protein family HMM PF01575; acyl dehydratase MaoC 3359719..3360213 Ruegeria pomeroyi DSS-3 3194659 YP_168356.1 CDS SPO3153 NC_003911.11 3360454 3362145 D identified by similarity to GB:BAA61829.1; match to protein family HMM PF00173; match to protein family HMM PF01360; monooxygenase 3360454..3362145 Ruegeria pomeroyi DSS-3 3195915 YP_168357.1 CDS ribF NC_003911.11 3362242 3363174 D 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 3362242..3363174 Ruegeria pomeroyi DSS-3 3195108 YP_168358.1 CDS SPO3155 NC_003911.11 3363171 3363641 D identified by similarity to SP:O68068; match to protein family HMM PF05779; hypothetical protein 3363171..3363641 Ruegeria pomeroyi DSS-3 3193398 YP_168359.1 CDS SPO3156 NC_003911.11 3363641 3364678 D identified by similarity to SP:O50584; L-threonine aldolase 3363641..3364678 Ruegeria pomeroyi DSS-3 3195878 YP_168360.1 CDS SPO3157 NC_003911.11 3364767 3365585 R identified by match to protein family HMM PF00561; alpha/beta hydrolase complement(3364767..3365585) Ruegeria pomeroyi DSS-3 3195998 YP_168361.1 CDS nahD NC_003911.11 3365582 3366184 R identified by similarity to SP:Q51948; match to protein family HMM PF01323; 2-hydroxychromene-2-carboxylate isomerase complement(3365582..3366184) Ruegeria pomeroyi DSS-3 3195660 YP_168362.1 CDS prs NC_003911.11 3366292 3367311 D identified by match to protein family HMM PF00156; match to protein family HMM TIGR01251; ribose-phosphate pyrophosphokinase 3366292..3367311 Ruegeria pomeroyi DSS-3 3193207 YP_168363.1 CDS SPO3160 NC_003911.11 3367394 3367762 R identified by similarity to GB:CAA67912.1; hypothetical protein complement(3367394..3367762) Ruegeria pomeroyi DSS-3 3195764 YP_168364.1 CDS atpC NC_003911.11 3367873 3368283 R 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 complement(3367873..3368283) Ruegeria pomeroyi DSS-3 3195323 YP_168365.1 CDS atpD NC_003911.11 3368296 3369720 R 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 complement(3368296..3369720) Ruegeria pomeroyi DSS-3 3194225 YP_168366.1 CDS atpG NC_003911.11 3369740 3370615 R 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 complement(3369740..3370615) Ruegeria pomeroyi DSS-3 3195916 YP_168367.1 CDS atpA NC_003911.11 3370628 3372166 R 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 complement(3370628..3372166) Ruegeria pomeroyi DSS-3 3195837 YP_168368.1 CDS atpH NC_003911.11 3372167 3372727 R identified by similarity to SP:P05437; match to protein family HMM PF00213; match to protein family HMM TIGR01145; ATP synthase subunit delta complement(3372167..3372727) Ruegeria pomeroyi DSS-3 3195251 YP_168369.1 CDS SPO3166 NC_003911.11 3373134 3374081 D hypothetical protein 3373134..3374081 Ruegeria pomeroyi DSS-3 3195825 YP_168370.1 CDS SPO3167 NC_003911.11 3374090 3374842 R identified by similarity to PIR:AC3001; hypothetical protein complement(3374090..3374842) Ruegeria pomeroyi DSS-3 3192859 YP_168371.1 CDS SPO3168 NC_003911.11 3374903 3375670 D identified by match to protein family HMM PF00753; hydroxyacylglutathione hydrolase 3374903..3375670 Ruegeria pomeroyi DSS-3 3195448 YP_168372.1 CDS clpA NC_003911.11 3375845 3378172 D 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 3375845..3378172 Ruegeria pomeroyi DSS-3 3195159 YP_168373.1 CDS SPO3170 NC_003911.11 3378391 3379131 D identified by match to protein family HMM PF01551; M24/M37 family peptidase 3378391..3379131 Ruegeria pomeroyi DSS-3 3195302 YP_168374.1 CDS SPO3171 NC_003911.11 3379134 3381434 R identified by match to protein family HMM PF00691; hypothetical protein complement(3379134..3381434) Ruegeria pomeroyi DSS-3 3195866 YP_168375.1 CDS SPO3172 NC_003911.11 3381438 3382619 R identified by similarity to GB:BAC46776.1; hypothetical protein complement(3381438..3382619) Ruegeria pomeroyi DSS-3 3195210 YP_168376.1 CDS SPO3173 NC_003911.11 3382690 3383223 R identified by similarity to SP:P39163; match to protein family HMM PF04752; cation transport protein ChaC complement(3382690..3383223) Ruegeria pomeroyi DSS-3 3195821 YP_168377.1 CDS SPO3174 NC_003911.11 3383232 3384287 D identified by similarity to GB:AAK24192.1; hypothetical protein 3383232..3384287 Ruegeria pomeroyi DSS-3 3195803 YP_168378.1 CDS SPO3175 NC_003911.11 3384303 3385163 R identified by similarity to GB:AAO55033.1; hypothetical protein complement(3384303..3385163) Ruegeria pomeroyi DSS-3 3195827 YP_168379.1 CDS SPO3176 NC_003911.11 3385160 3386083 R dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate; cyclohexadienyl dehydrogenase complement(3385160..3386083) Ruegeria pomeroyi DSS-3 3195700 YP_168380.1 CDS hisC NC_003911.11 3386080 3387195 R catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase complement(3386080..3387195) Ruegeria pomeroyi DSS-3 3195649 YP_168381.1 CDS SPO3178 NC_003911.11 3387232 3388647 R hypothetical protein complement(3387232..3388647) Ruegeria pomeroyi DSS-3 3194038 YP_168382.1 CDS SPO3179 NC_003911.11 3388753 3389211 D identified by match to protein family HMM PF01037; AsnC family transcriptional regulator 3388753..3389211 Ruegeria pomeroyi DSS-3 3195646 YP_168383.1 CDS rpiB NC_003911.11 3389208 3389657 R 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 complement(3389208..3389657) Ruegeria pomeroyi DSS-3 3195196 YP_168384.1 CDS rpsD NC_003911.11 3389785 3390405 R 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 complement(3389785..3390405) Ruegeria pomeroyi DSS-3 3195804 YP_168385.1 CDS SPO3182 NC_003911.11 3390607 3391671 R identified by similarity to PIR:T03518; hypothetical protein complement(3390607..3391671) Ruegeria pomeroyi DSS-3 3195015 YP_168386.1 CDS SPO3183 NC_003911.11 3391910 3393943 D identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; molybdopterin-binding oxidoreductase 3391910..3393943 Ruegeria pomeroyi DSS-3 3195771 YP_168387.1 CDS SPO3184 NC_003911.11 3393940 3394647 R identified by match to protein family HMM PF00583; acetyltransferase complement(3393940..3394647) Ruegeria pomeroyi DSS-3 3195787 YP_168388.1 CDS SPO3185 NC_003911.11 3394736 3396139 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 3394736..3396139 Ruegeria pomeroyi DSS-3 3195733 YP_168389.1 CDS opuD NC_003911.11 3396229 3398064 R identified by similarity to SP:P54417; match to protein family HMM PF02028; glycine betaine transporter complement(3396229..3398064) Ruegeria pomeroyi DSS-3 3195144 YP_168390.1 CDS comC NC_003911.11 3398172 3399185 R identified by match to protein family HMM PF02615; (2R)-3-sulfolactate dehydrogenase complement(3398172..3399185) Ruegeria pomeroyi DSS-3 3195794 YP_168391.1 CDS SPO3188 NC_003911.11 3399198 3399830 R identified by similarity to GB:AAN68298.1; hypothetical protein complement(3399198..3399830) Ruegeria pomeroyi DSS-3 3194729 YP_168392.1 CDS SPO3189 NC_003911.11 3399827 3401515 R identified by similarity to GB:AAN68299.1; hypothetical protein complement(3399827..3401515) Ruegeria pomeroyi DSS-3 3193083 YP_168393.1 CDS SPO3190 NC_003911.11 3401521 3402501 R identified by match to protein family HMM PF01244; renal dipeptidase complement(3401521..3402501) Ruegeria pomeroyi DSS-3 3195752 YP_168394.1 CDS SPO3191 NC_003911.11 3402498 3403949 R identified by match to protein family HMM PF00171; aldehyde dehydrogenase complement(3402498..3403949) Ruegeria pomeroyi DSS-3 3194957 YP_168395.1 CDS SPO3192 NC_003911.11 3404052 3404924 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3404052..3404924 Ruegeria pomeroyi DSS-3 3195508 YP_168396.1 CDS SPO3193 NC_003911.11 3404928 3405359 R identified by similarity to GB:BAB48214.1; hypothetical protein complement(3404928..3405359) Ruegeria pomeroyi DSS-3 3195823 YP_168397.1 CDS SPO3194 NC_003911.11 3405491 3407773 D identified by match to protein family HMM PF02867; ribonucleoside-diphosphate reductase 3405491..3407773 Ruegeria pomeroyi DSS-3 3192944 YP_168398.1 CDS SPO3195 NC_003911.11 3408049 3409143 D identified by match to protein family HMM PF00850; histone deacetylase 3408049..3409143 Ruegeria pomeroyi DSS-3 3195671 YP_168399.1 CDS recO NC_003911.11 3409228 3409953 D 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 3409228..3409953 Ruegeria pomeroyi DSS-3 3195505 YP_168400.1 CDS SPO3197 NC_003911.11 3409937 3410332 R identified by similarity to GB:BAB54274.1; hypothetical protein complement(3409937..3410332) Ruegeria pomeroyi DSS-3 3194966 YP_168401.1 CDS rnc NC_003911.11 3410341 3411018 R identified by similarity to SP:P05797; match to protein family HMM PF00035; match to protein family HMM PF00636; ribonuclease III complement(3410341..3411018) Ruegeria pomeroyi DSS-3 3195258 YP_168402.1 CDS lepB NC_003911.11 3411015 3411854 R identified by match to protein family HMM PF00717; match to protein family HMM TIGR02227; signal peptidase I complement(3411015..3411854) Ruegeria pomeroyi DSS-3 3194337 YP_168403.1 CDS acpS NC_003911.11 3411888 3412334 R 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 complement(3411888..3412334) Ruegeria pomeroyi DSS-3 3195332 YP_168404.1 CDS pdxJ NC_003911.11 3412399 3413145 R involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase complement(3412399..3413145) Ruegeria pomeroyi DSS-3 3195698 YP_168405.1 CDS SPO3202 NC_003911.11 3413181 3413837 R identified by similarity to PIR:G97485; hypothetical protein complement(3413181..3413837) Ruegeria pomeroyi DSS-3 3194593 YP_168406.1 CDS SPO3203 NC_003911.11 3413869 3416061 R 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 complement(3413869..3416061) Ruegeria pomeroyi DSS-3 3193258 YP_168407.1 CDS rpoZ NC_003911.11 3416030 3416383 R 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 complement(3416030..3416383) Ruegeria pomeroyi DSS-3 3195699 YP_168408.1 CDS folK NC_003911.11 3416475 3417041 R identified by match to protein family HMM PF01288; match to protein family HMM TIGR01498; 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase complement(3416475..3417041) Ruegeria pomeroyi DSS-3 3195424 YP_168409.1 CDS SPO3206 NC_003911.11 3417180 3417752 D identified by similarity to GB:AAK23529.1; match to protein family HMM PF01936; hypothetical protein 3417180..3417752 Ruegeria pomeroyi DSS-3 3195756 YP_168410.1 CDS ispH NC_003911.11 3417945 3418895 D 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 3417945..3418895 Ruegeria pomeroyi DSS-3 3195859 YP_168411.1 CDS SPO3208 NC_003911.11 3418892 3419521 D identified by match to protein family HMM PF00043; glutathione S-transferase 3418892..3419521 Ruegeria pomeroyi DSS-3 3195682 YP_168412.1 CDS SPO3209 NC_003911.11 3419588 3420202 D identified by match to protein family HMM PF01810; amino acid transporter LysE 3419588..3420202 Ruegeria pomeroyi DSS-3 3195674 YP_168413.1 CDS SPO3210 NC_003911.11 3420199 3420651 D identified by similarity to GB:AAK24940.1; hypothetical protein 3420199..3420651 Ruegeria pomeroyi DSS-3 3195113 YP_168414.1 CDS SPO3211 NC_003911.11 3420624 3421241 D identified by similarity to GB:AAK23900.1; hypothetical protein 3420624..3421241 Ruegeria pomeroyi DSS-3 3195855 YP_168415.1 CDS rnhA NC_003911.11 3421234 3421701 D An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H 3421234..3421701 Ruegeria pomeroyi DSS-3 3195666 YP_168416.1 CDS SPO3213 NC_003911.11 3421698 3422327 D identified by similarity to PIR:F97377; match to protein family HMM PF03458; hypothetical protein 3421698..3422327 Ruegeria pomeroyi DSS-3 3195578 YP_168417.1 CDS SPO3214 NC_003911.11 3422394 3422633 R hypothetical protein complement(3422394..3422633) Ruegeria pomeroyi DSS-3 3194436 YP_168418.1 CDS SPO3215 NC_003911.11 3422635 3422877 R hypothetical protein complement(3422635..3422877) Ruegeria pomeroyi DSS-3 3195122 YP_168419.1 CDS fmt NC_003911.11 3422885 3423790 R 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 complement(3422885..3423790) Ruegeria pomeroyi DSS-3 3195992 YP_168420.1 CDS def-1 NC_003911.11 3423795 3424292 R identified by match to protein family HMM PF01327; match to protein family HMM TIGR00079; peptide deformylase complement(3423795..3424292) Ruegeria pomeroyi DSS-3 3194969 YP_168421.1 CDS def-2 NC_003911.11 3424289 3424786 R identified by match to protein family HMM PF01327; match to protein family HMM TIGR00079; peptide deformylase complement(3424289..3424786) Ruegeria pomeroyi DSS-3 3195601 YP_168422.1 CDS def-3 NC_003911.11 3424783 3425301 R identified by match to protein family HMM PF01327; match to protein family HMM TIGR00079; peptide deformylase complement(3424783..3425301) Ruegeria pomeroyi DSS-3 3193782 YP_168423.1 CDS SPO3220 NC_003911.11 3425383 3426573 D identified by match to protein family HMM PF00155; aminotransferase, classes I and II 3425383..3426573 Ruegeria pomeroyi DSS-3 3195058 YP_168424.1 CDS SPO3221 NC_003911.11 3426645 3426995 R hypothetical protein complement(3426645..3426995) Ruegeria pomeroyi DSS-3 3193910 YP_168425.1 CDS SPO3222 NC_003911.11 3427198 3428187 D identified by similarity to PIR:T45023; hypothetical protein 3427198..3428187 Ruegeria pomeroyi DSS-3 3195783 YP_168426.1 CDS SPO3223 NC_003911.11 3428169 3428531 R identified by match to protein family HMM PF00072; response regulator complement(3428169..3428531) Ruegeria pomeroyi DSS-3 3195254 YP_168427.1 CDS cobC NC_003911.11 3428717 3429706 D identified by similarity to SP:P21633; cobalamin biosynthetic protein CobC 3428717..3429706 Ruegeria pomeroyi DSS-3 3195395 YP_168428.1 CDS cobD NC_003911.11 3429703 3430623 D CobD; CbiD in Salmonella; converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group; cobalamin biosynthesis protein 3429703..3430623 Ruegeria pomeroyi DSS-3 3195582 YP_168429.1 CDS SPO3226 NC_003911.11 3430655 3431818 D identified by similarity to PIR:D97614; hypothetical protein 3430655..3431818 Ruegeria pomeroyi DSS-3 3195541 YP_168430.1 CDS SPO3227 NC_003911.11 3431828 3432190 R hypothetical protein complement(3431828..3432190) Ruegeria pomeroyi DSS-3 3195290 YP_168431.1 CDS SPO3228 NC_003911.11 3432247 3435702 R 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 complement(3432247..3435702) Ruegeria pomeroyi DSS-3 3194939 YP_168432.1 CDS SPO3229 NC_003911.11 3435831 3436247 R lipoprotein complement(3435831..3436247) Ruegeria pomeroyi DSS-3 3194343 YP_168433.1 CDS SPO3230 NC_003911.11 3436267 3437475 R identified by match to protein family HMM PF00155; aminotransferase, classes I and II complement(3436267..3437475) Ruegeria pomeroyi DSS-3 3192779 YP_168434.1 CDS pdhR NC_003911.11 3437629 3438399 D identified by similarity to SP:P06957; match to protein family HMM PF00392; pyruvate dehydrogenase complex repressor 3437629..3438399 Ruegeria pomeroyi DSS-3 3194672 YP_168435.1 CDS SPO3232 NC_003911.11 3438399 3438887 D hypothetical protein 3438399..3438887 Ruegeria pomeroyi DSS-3 3195968 YP_168436.1 CDS atpF NC_003911.11 3438997 3439569 R 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 complement(3438997..3439569) Ruegeria pomeroyi DSS-3 3194903 YP_168437.1 CDS SPO3234 NC_003911.11 3439575 3440120 R 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' complement(3439575..3440120) Ruegeria pomeroyi DSS-3 3195208 YP_168438.1 CDS atpE NC_003911.11 3440207 3440431 R 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 complement(3440207..3440431) Ruegeria pomeroyi DSS-3 3195970 YP_168439.1 CDS atpB NC_003911.11 3440508 3441278 R 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 complement(3440508..3441278) Ruegeria pomeroyi DSS-3 3195250 YP_168440.1 CDS atpI NC_003911.11 3441281 3441634 R identified by similarity to GB:CAA72980.1; ATP synthase F0 subunit I complement(3441281..3441634) Ruegeria pomeroyi DSS-3 3195738 YP_168441.1 CDS SPO3238 NC_003911.11 3441856 3442197 D identified by match to protein family HMM PF01022; ArsR family transcriptional regulator 3441856..3442197 Ruegeria pomeroyi DSS-3 3194039 YP_168442.1 CDS SPO3239 NC_003911.11 3442207 3443106 R identified by similarity to GB:CAE09829.1; match to protein family HMM PF00892; hypothetical protein complement(3442207..3443106) Ruegeria pomeroyi DSS-3 3194921 YP_168443.1 CDS SPO3240 NC_003911.11 3443094 3443972 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(3443094..3443972) Ruegeria pomeroyi DSS-3 3195785 YP_168444.1 CDS SPO3241 NC_003911.11 3444135 3444881 D Asp/Glu/Hydantoin racemase 3444135..3444881 Ruegeria pomeroyi DSS-3 3194669 YP_168445.1 CDS SPO3242 NC_003911.11 3444931 3445494 R identified by similarity to GB:CAC47762.1; match to protein family HMM PF04073; prolyl-tRNA synthetase complement(3444931..3445494) Ruegeria pomeroyi DSS-3 3195370 YP_168446.1 CDS nadA NC_003911.11 3445790 3446842 D 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate; quinolinate synthetase 3445790..3446842 Ruegeria pomeroyi DSS-3 3193531 YP_168447.1 CDS SPO3244 NC_003911.11 3446850 3448400 D catalyzes the formation of oxaloacetate from L-aspartate; L-aspartate oxidase 3446850..3448400 Ruegeria pomeroyi DSS-3 3195460 YP_168448.1 CDS nadC NC_003911.11 3448397 3449263 D 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 3448397..3449263 Ruegeria pomeroyi DSS-3 3195118 YP_168449.1 CDS ffh NC_003911.11 3449530 3451062 D 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 3449530..3451062 Ruegeria pomeroyi DSS-3 3195205 YP_168450.1 CDS SPO3247 NC_003911.11 3451064 3451606 D identified by match to protein family HMM PF00583; acetyltransferase 3451064..3451606 Ruegeria pomeroyi DSS-3 3193451 YP_168451.1 CDS SPO3248 NC_003911.11 3451603 3452139 D identified by match to protein family HMM PF00583; acetyltransferase 3451603..3452139 Ruegeria pomeroyi DSS-3 3195240 YP_168452.1 CDS SPO3249 NC_003911.11 3452136 3452645 D identified by match to protein family HMM PF00583; acetyltransferase 3452136..3452645 Ruegeria pomeroyi DSS-3 3195057 YP_168453.1 CDS SPO3250 NC_003911.11 3452642 3453160 D identified by match to protein family HMM PF00583; acetyltransferase 3452642..3453160 Ruegeria pomeroyi DSS-3 3194854 YP_168454.1 CDS SPO3251 NC_003911.11 3453157 3453759 D identified by similarity to PIR:B97652; hypothetical protein 3453157..3453759 Ruegeria pomeroyi DSS-3 3195657 YP_168455.1 CDS SPO3252 NC_003911.11 3453764 3454060 D catalyzes the interconversion of chorismate to prephenate; chorismate mutase 3453764..3454060 Ruegeria pomeroyi DSS-3 3195299 YP_168456.1 CDS rpsP NC_003911.11 3454125 3454490 D 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 3454125..3454490 Ruegeria pomeroyi DSS-3 3195394 YP_168457.1 CDS bluB NC_003911.11 3454502 3455137 D identified by similarity to PIR:S52225; match to protein family HMM PF00881; cobalamin biosynthesis protein BluB 3454502..3455137 Ruegeria pomeroyi DSS-3 3195300 YP_168458.1 CDS rimM NC_003911.11 3455284 3455787 D Essential for efficient processing of 16S rRNA; 16S rRNA-processing protein RimM 3455284..3455787 Ruegeria pomeroyi DSS-3 3194913 YP_168459.1 CDS rpmE NC_003911.11 3456324 3456545 R 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 complement(3456324..3456545) Ruegeria pomeroyi DSS-3 3193045 YP_168460.1 CDS rplS NC_003911.11 3456557 3456940 R 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 complement(3456557..3456940) Ruegeria pomeroyi DSS-3 3195464 YP_168461.1 CDS SPO3258 NC_003911.11 3457342 3458151 D identified by match to protein family HMM PF01183; glycosyl hydrolase 3457342..3458151 Ruegeria pomeroyi DSS-3 3193153 YP_168462.1 CDS trmD NC_003911.11 3458262 3458993 D methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA; tRNA (guanine-N(1)-)-methyltransferase 3458262..3458993 Ruegeria pomeroyi DSS-3 3195328 YP_168463.1 CDS SPO3260 NC_003911.11 3459026 3459808 D identified by similarity to GB:AAD44211.1; methyltransferase-like protein 3459026..3459808 Ruegeria pomeroyi DSS-3 3195779 YP_168464.1 CDS SPO3261 NC_003911.11 3459931 3460599 R identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase complement(3459931..3460599) Ruegeria pomeroyi DSS-3 3194736 YP_168465.1 CDS SPO3262 NC_003911.11 3460699 3461157 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 3460699..3461157 Ruegeria pomeroyi DSS-3 3193711 YP_168466.1 CDS SPO3263 NC_003911.11 3461163 3461615 D hypothetical protein 3461163..3461615 Ruegeria pomeroyi DSS-3 3195377 YP_168467.1 CDS SPO3270 NC_003911.11 3468359 3468955 R 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 complement(3468359..3468955) Ruegeria pomeroyi DSS-3 3195303 YP_168468.1 CDS SPO3271 NC_003911.11 3468959 3469858 R 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 complement(3468959..3469858) Ruegeria pomeroyi DSS-3 3195130 YP_168469.1 CDS SPO3272 NC_003911.11 3469965 3471551 R identified by match to protein family HMM PF01645; glutamate synthase complement(3469965..3471551) Ruegeria pomeroyi DSS-3 3193642 YP_168470.1 CDS SPO3273 NC_003911.11 3471517 3472068 D hypothetical protein 3471517..3472068 Ruegeria pomeroyi DSS-3 3194952 YP_168471.1 CDS SPO3274 NC_003911.11 3472122 3472562 D hypothetical protein 3472122..3472562 Ruegeria pomeroyi DSS-3 3195991 YP_168472.1 CDS SPO3275 NC_003911.11 3472566 3473261 R identified by similarity to GB:CAE20608.1; hypothetical protein complement(3472566..3473261) Ruegeria pomeroyi DSS-3 3195960 YP_168473.1 CDS clpB NC_003911.11 3473444 3476062 R 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 complement(3473444..3476062) Ruegeria pomeroyi DSS-3 3195262 YP_168474.1 CDS SPO3277 NC_003911.11 3476266 3476538 D identified by similarity to GB:AAN69029.1; hypothetical protein 3476266..3476538 Ruegeria pomeroyi DSS-3 3195438 YP_168475.1 CDS pyrF NC_003911.11 3476646 3477380 D 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 3476646..3477380 Ruegeria pomeroyi DSS-3 3195326 YP_168476.1 CDS SPO3279 NC_003911.11 3477706 3478155 R identified by match to protein family HMM PF00293; NUDIX domain-containing protein complement(3477706..3478155) Ruegeria pomeroyi DSS-3 3194631 YP_168477.1 CDS SPO3280 NC_003911.11 3478224 3479486 D 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 3478224..3479486 Ruegeria pomeroyi DSS-3 3193147 YP_168478.1 CDS SPO3281 NC_003911.11 3479535 3480032 D identified by similarity to SP:Q02886; match to protein family HMM PF05163; DinB family protein 3479535..3480032 Ruegeria pomeroyi DSS-3 3195088 YP_168479.1 CDS SPO3282 NC_003911.11 3480049 3480909 R identified by match to protein family HMM PF05013; N-formylglutamate amidohydrolase complement(3480049..3480909) Ruegeria pomeroyi DSS-3 3195780 YP_168480.2 CDS rpmJ NC_003911.11 3481212 3481337 D 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 3481212..3481337 Ruegeria pomeroyi DSS-3 3196292 YP_168481.1 CDS SPO3285 NC_003911.11 3481443 3483047 D hypothetical protein 3481443..3483047 Ruegeria pomeroyi DSS-3 3194928 YP_168482.1 CDS atsA NC_003911.11 3483233 3484840 D identified by similarity to SP:P51691; match to protein family HMM PF00884; arylsulfatase 3483233..3484840 Ruegeria pomeroyi DSS-3 3193868 YP_168483.1 CDS SPO3287 NC_003911.11 3484905 3485954 D identified by match to protein family HMM PF01547; ferric iron ABC transporter periplasmic ferric iron-binding protein 3484905..3485954 Ruegeria pomeroyi DSS-3 3195059 YP_168484.1 CDS SPO3288 NC_003911.11 3486032 3487729 R identified by match to protein family HMM PF00528; ferric iron ABC transporter permease complement(3486032..3487729) Ruegeria pomeroyi DSS-3 3195715 YP_168485.1 CDS SPO3289 NC_003911.11 3487873 3489090 R identified by similarity to GB:AAF26285.1; phenylacetate-CoA ligase complement(3487873..3489090) Ruegeria pomeroyi DSS-3 3195940 YP_168486.1 CDS SPO3290 NC_003911.11 3489105 3489941 R 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 complement(3489105..3489941) Ruegeria pomeroyi DSS-3 3194371 YP_168487.1 CDS SPO3291 NC_003911.11 3490052 3491335 R 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 complement(3490052..3491335) Ruegeria pomeroyi DSS-3 3195772 YP_168488.1 CDS SPO3292 NC_003911.11 3491418 3492494 R 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 complement(3491418..3492494) Ruegeria pomeroyi DSS-3 3195143 YP_168489.1 CDS SPO3293 NC_003911.11 3492498 3492755 R identified by similarity to GB:AAM36995.1; hypothetical protein complement(3492498..3492755) Ruegeria pomeroyi DSS-3 3194019 YP_168490.1 CDS SPO3294 NC_003911.11 3492834 3493820 R 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 complement(3492834..3493820) Ruegeria pomeroyi DSS-3 3195900 YP_168491.1 CDS SPO3295 NC_003911.11 3493862 3494746 R 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 complement(3493862..3494746) Ruegeria pomeroyi DSS-3 3195184 YP_168492.1 CDS SPO3296 NC_003911.11 3494774 3496747 R identified by match to protein family HMM PF00501; AMP-binding protein complement(3494774..3496747) Ruegeria pomeroyi DSS-3 3195178 YP_168493.1 CDS SPO3297 NC_003911.11 3497068 3498966 D 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 3497068..3498966 Ruegeria pomeroyi DSS-3 3193612 YP_168494.1 CDS SPO3298 NC_003911.11 3498963 3499670 D identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator 3498963..3499670 Ruegeria pomeroyi DSS-3 3195116 YP_168495.1 CDS SPO3299 NC_003911.11 3499657 3500241 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(3499657..3500241) Ruegeria pomeroyi DSS-3 3195569 YP_168496.1 CDS SPO3300 NC_003911.11 3500355 3500747 D identified by similarity to PIR:AD0744; hypothetical protein 3500355..3500747 Ruegeria pomeroyi DSS-3 3193720 YP_168497.1 CDS SPO3301 NC_003911.11 3500757 3501623 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(3500757..3501623) Ruegeria pomeroyi DSS-3 3195650 YP_168498.1 CDS SPO3302 NC_003911.11 3501641 3502009 D identified by similarity to GB:BAC50637.1; hypothetical protein 3501641..3502009 Ruegeria pomeroyi DSS-3 3193380 YP_168499.1 CDS SPO3303 NC_003911.11 3502019 3502714 R identified by match to protein family HMM PF00657; GDSL-like lipase/acylhydrolase complement(3502019..3502714) Ruegeria pomeroyi DSS-3 3195538 YP_168500.1 CDS SPO3304 NC_003911.11 3502814 3503998 R 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 complement(3502814..3503998) Ruegeria pomeroyi DSS-3 3194634 YP_168501.1 CDS SPO3305 NC_003911.11 3504162 3504812 D identified by match to protein family HMM PF00300; phosphoglycerate mutase 3504162..3504812 Ruegeria pomeroyi DSS-3 3193278 YP_168502.1 CDS SPO3306 NC_003911.11 3504822 3505436 D identified by similarity to GB:AAC44159.1; match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 3504822..3505436 Ruegeria pomeroyi DSS-3 3195327 YP_168503.1 CDS SPO3307 NC_003911.11 3505451 3506503 D identified by similarity to SP:P43065; match to protein family HMM PF01262; match to protein family HMM PF05222; saccharopine dehydrogenase 3505451..3506503 Ruegeria pomeroyi DSS-3 3194227 YP_168504.1 CDS SPO3308 NC_003911.11 3506500 3506751 D identified by similarity to GB:BAC51725.1; hypothetical protein 3506500..3506751 Ruegeria pomeroyi DSS-3 3193887 YP_168505.1 CDS SPO3309 NC_003911.11 3506765 3507907 D identified by similarity to SP:Q9P4R4; match to protein family HMM PF03435; saccharopine dehydrogenase 3506765..3507907 Ruegeria pomeroyi DSS-3 3195590 YP_168506.1 CDS SPO3310 NC_003911.11 3508018 3508335 R identified by similarity to GB:BAC53154.1; hypothetical protein complement(3508018..3508335) Ruegeria pomeroyi DSS-3 3195089 YP_168507.1 CDS SPO3311 NC_003911.11 3508498 3509571 D 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 3508498..3509571 Ruegeria pomeroyi DSS-3 3195580 YP_168508.1 CDS SPO3312 NC_003911.11 3509568 3510335 D identified by similarity to GB:CAC41875.1; hypothetical protein 3509568..3510335 Ruegeria pomeroyi DSS-3 3195447 YP_168509.1 CDS SPO3313 NC_003911.11 3510359 3510928 R identified by match to protein family HMM PF01381; DNA-binding protein complement(3510359..3510928) Ruegeria pomeroyi DSS-3 3194719 YP_168510.1 CDS ilvD NC_003911.11 3511107 3512939 D catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 3511107..3512939 Ruegeria pomeroyi DSS-3 3195012 YP_168511.1 CDS SPO3315 NC_003911.11 3513089 3514018 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(3513089..3514018) Ruegeria pomeroyi DSS-3 3195904 YP_168512.1 CDS SPO3316 NC_003911.11 3514119 3515087 D hypothetical protein 3514119..3515087 Ruegeria pomeroyi DSS-3 3195094 YP_168513.1 CDS SPO3317 NC_003911.11 3515662 3516219 D transcriptional regulator 3515662..3516219 Ruegeria pomeroyi DSS-3 3195977 YP_168514.1 CDS SPO3318 NC_003911.11 3516235 3517053 R identified by similarity to GB:AAH10441.1; hypothetical protein complement(3516235..3517053) Ruegeria pomeroyi DSS-3 3195149 YP_168515.1 CDS SPO3319 NC_003911.11 3517201 3518778 D identified by similarity to GB:AAC44018.1; match to protein family HMM PF02485; EpsK domain-containing protein 3517201..3518778 Ruegeria pomeroyi DSS-3 3192790 YP_168516.1 CDS SPO3320 NC_003911.11 3518860 3519504 R identified by similarity to GB:AAO54466.1; hypothetical protein complement(3518860..3519504) Ruegeria pomeroyi DSS-3 3195071 YP_168517.1 CDS SPO3321 NC_003911.11 3519515 3519781 R hypothetical protein complement(3519515..3519781) Ruegeria pomeroyi DSS-3 3193442 YP_168518.1 CDS SPO3322 NC_003911.11 3519783 3521132 R identified by similarity to GB:CAC46971.1; hypothetical protein complement(3519783..3521132) Ruegeria pomeroyi DSS-3 3193809 YP_168519.1 CDS SPO3323 NC_003911.11 3521993 3523930 R identified by similarity to GB:CAC46974.1; hypothetical protein complement(3521993..3523930) Ruegeria pomeroyi DSS-3 3195782 YP_168520.1 CDS SPO3324 NC_003911.11 3523998 3525119 R identified by similarity to GB:CAC46975.1; hypothetical protein complement(3523998..3525119) Ruegeria pomeroyi DSS-3 3192826 YP_168521.1 CDS SPO3325 NC_003911.11 3525534 3526613 R identified by similarity to GB:BAB49806.1; hypothetical protein complement(3525534..3526613) Ruegeria pomeroyi DSS-3 3195126 YP_168522.1 CDS SPO3326 NC_003911.11 3526803 3527144 D identified by similarity to GB:BAB54345.1; match to protein family HMM PF05899; hypothetical protein 3526803..3527144 Ruegeria pomeroyi DSS-3 3195082 YP_168523.1 CDS SPO3327 NC_003911.11 3527205 3528422 R identified by similarity to SP:P38488; match to protein family HMM PF00557; match to protein family HMM PF01321; creatinase complement(3527205..3528422) Ruegeria pomeroyi DSS-3 3195993 YP_168524.1 CDS gabD-2 NC_003911.11 3528642 3530153 D identified by similarity to SP:P25526; match to protein family HMM PF00171; match to protein family HMM TIGR01780; succinate-semialdehyde dehydrogenase 3528642..3530153 Ruegeria pomeroyi DSS-3 3194993 YP_168525.1 CDS SPO3329 NC_003911.11 3530160 3530561 R identified by match to protein family HMM PF00042; globin domain-containing protein complement(3530160..3530561) Ruegeria pomeroyi DSS-3 3194838 YP_168526.1 CDS rnr NC_003911.11 3530661 3532919 R 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 complement(3530661..3532919) Ruegeria pomeroyi DSS-3 3193934 YP_168527.1 CDS SPO3331 NC_003911.11 3532951 3533562 R identified by similarity to GB:AAN40802.1; match to protein family HMM PF05143; hypothetical protein complement(3532951..3533562) Ruegeria pomeroyi DSS-3 3193508 YP_168528.1 CDS dapE NC_003911.11 3533572 3534714 R 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 complement(3533572..3534714) Ruegeria pomeroyi DSS-3 3192962 YP_168529.1 CDS SPO3333 NC_003911.11 3535008 3536594 D identified by similarity to GB:AAR38409.1; hypothetical protein 3535008..3536594 Ruegeria pomeroyi DSS-3 3193884 YP_168530.1 CDS SPO3334 NC_003911.11 3536521 3537690 D hypothetical protein 3536521..3537690 Ruegeria pomeroyi DSS-3 3194360 YP_168531.1 CDS SPO3335 NC_003911.11 3537829 3538914 D identified by similarity to SP:P10344; match to protein family HMM PF00497; glutamine ABC transporter periplasmic glutamine-binding protein 3537829..3538914 Ruegeria pomeroyi DSS-3 3194025 YP_168532.1 CDS SPO3336 NC_003911.11 3538921 3539262 R hypothetical protein complement(3538921..3539262) Ruegeria pomeroyi DSS-3 3195748 YP_168533.1 CDS dapD NC_003911.11 3539336 3540163 R 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 complement(3539336..3540163) Ruegeria pomeroyi DSS-3 3195457 YP_168534.1 CDS bioB NC_003911.11 3540260 3541216 R identified by match to protein family HMM PF04055; match to protein family HMM PF06968; match to protein family HMM TIGR00433; biotin synthase complement(3540260..3541216) Ruegeria pomeroyi DSS-3 3195697 YP_168535.1 CDS SPO3339 NC_003911.11 3541209 3541796 R identified by match to protein family HMM PF02632; bioY family protein complement(3541209..3541796) Ruegeria pomeroyi DSS-3 3195106 YP_168536.1 CDS SPO3340 NC_003911.11 3541920 3542519 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(3541920..3542519) Ruegeria pomeroyi DSS-3 3194992 YP_168537.1 CDS SPO3341 NC_003911.11 3542565 3543485 R catalyzes the formation of 2-oxobutanoate from L-threonine; threonine dehydratase complement(3542565..3543485) Ruegeria pomeroyi DSS-3 3195019 YP_168538.1 CDS SPO3342 NC_003911.11 3543541 3544416 D identified by match to protein family HMM PF03641; match to protein family HMM TIGR00730; decarboxylase 3543541..3544416 Ruegeria pomeroyi DSS-3 3195439 YP_168539.1 CDS SPO3343 NC_003911.11 3544432 3544704 R hypothetical protein complement(3544432..3544704) Ruegeria pomeroyi DSS-3 3194050 YP_168540.1 CDS SPO3344 NC_003911.11 3544879 3545994 D catalyzes the formation of cysteine and 2-oxobutanoate from cystathionine; cystathionine gamma-lyase 3544879..3545994 Ruegeria pomeroyi DSS-3 3195049 YP_168541.1 CDS SPO3345 NC_003911.11 3545997 3546422 R hypothetical protein complement(3545997..3546422) Ruegeria pomeroyi DSS-3 3192667 YP_168542.1 CDS SPO3346 NC_003911.11 3546460 3547641 R identified by match to protein family HMM PF04055; match to protein family HMM TIGR00048; radical SAM protein complement(3546460..3547641) Ruegeria pomeroyi DSS-3 3195026 YP_168543.1 CDS SPO3347 NC_003911.11 3547811 3548197 R identified by similarity to SP:P42879; hypothetical protein complement(3547811..3548197) Ruegeria pomeroyi DSS-3 3194376 YP_168544.1 CDS SPO3348 NC_003911.11 3548233 3548772 R identified by similarity to GB:CAD85590.1; hypothetical protein complement(3548233..3548772) Ruegeria pomeroyi DSS-3 3193088 YP_168545.1 CDS SPO3349 NC_003911.11 3548954 3549952 D identified by similarity to GB:AAF00929.1; match to protein family HMM PF06089; L-asparaginase 3548954..3549952 Ruegeria pomeroyi DSS-3 3195547 YP_168546.1 CDS SPO3350 NC_003911.11 3549959 3550273 R identified by similarity to GB:BAB50844.1; hypothetical protein complement(3549959..3550273) Ruegeria pomeroyi DSS-3 3194831 YP_168547.1 CDS SPO3351 NC_003911.11 3550310 3550744 R identified by similarity to PIR:G96031; match to protein family HMM PF05146; Aha1 domain-containing protein complement(3550310..3550744) Ruegeria pomeroyi DSS-3 3193865 YP_168548.1 CDS SPO3352 NC_003911.11 3550732 3551079 R identified by match to protein family HMM PF01022; ArsR family transcriptional regulator complement(3550732..3551079) Ruegeria pomeroyi DSS-3 3194804 YP_168549.1 CDS serB-2 NC_003911.11 3551105 3552013 R identified by match to protein family HMM PF00702; match to protein family HMM TIGR00338; match to protein family HMM TIGR01488; phosphoserine phosphatase complement(3551105..3552013) Ruegeria pomeroyi DSS-3 3195675 YP_168550.1 CDS SPO3354 NC_003911.11 3552346 3553527 D catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; phosphoserine aminotransferase 3552346..3553527 Ruegeria pomeroyi DSS-3 3195374 YP_168551.1 CDS serA NC_003911.11 3553615 3555210 D 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 3553615..3555210 Ruegeria pomeroyi DSS-3 3194715 YP_168552.1 CDS SPO3356 NC_003911.11 3555263 3555646 R identified by similarity to GB:BAB50697.1; hypothetical protein complement(3555263..3555646) Ruegeria pomeroyi DSS-3 3195330 YP_168553.1 CDS SPO3357 NC_003911.11 3555752 3556747 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3555752..3556747 Ruegeria pomeroyi DSS-3 3194934 YP_168554.1 CDS SPO3358 NC_003911.11 3556744 3557478 D identified by similarity to GB:AAC46052.1; match to protein family HMM PF00149; serine/threonine protein phosphatase 3556744..3557478 Ruegeria pomeroyi DSS-3 3194865 YP_168555.1 CDS tdh NC_003911.11 3557551 3558594 R converts threonine and NAD to 1,2-amino-3-oxobutanoate and NADH; functions in threonine catabolism; L-threonine 3-dehydrogenase complement(3557551..3558594) Ruegeria pomeroyi DSS-3 3195944 YP_168556.1 CDS kbl NC_003911.11 3558594 3559778 R catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine; 2-amino-3-ketobutyrate CoA ligase complement(3558594..3559778) Ruegeria pomeroyi DSS-3 3195774 YP_168557.1 CDS SPO3361 NC_003911.11 3559874 3561112 R identified by similarity to GB:BAB51420.1; match to protein family HMM PF02646; RmuC domain-containing protein complement(3559874..3561112) Ruegeria pomeroyi DSS-3 3195177 YP_168558.1 CDS mutL NC_003911.11 3561170 3563035 R 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 complement(3561170..3563035) Ruegeria pomeroyi DSS-3 3194545 YP_168559.1 CDS SPO3363 NC_003911.11 3563304 3564233 R identified by similarity to GB:AAK33470.1; match to protein family HMM PF00950; zinc/manganese/iron ABC transporter permease complement(3563304..3564233) Ruegeria pomeroyi DSS-3 3195117 YP_168560.1 CDS SPO3364 NC_003911.11 3564230 3565435 R identified by similarity to GB:AAS11742.1; match to protein family HMM PF00950; zinc/manganese/iron ABC transporter permease complement(3564230..3565435) Ruegeria pomeroyi DSS-3 3193234 YP_168561.1 CDS SPO3365 NC_003911.11 3565440 3566243 R identified by similarity to SP:P96117; match to protein family HMM PF00005; zinc/manganese/iron ABC transporter ATP-binding protein complement(3565440..3566243) Ruegeria pomeroyi DSS-3 3193094 YP_168562.1 CDS SPO3366 NC_003911.11 3566247 3567200 R identified by similarity to SP:P96116; match to protein family HMM PF01297; zinc/manganese/iron ABC transporter periplasmic zinc/manganese/iron-binding protein complement(3566247..3567200) Ruegeria pomeroyi DSS-3 3194816 YP_168563.1 CDS deoC NC_003911.11 3567556 3568389 D identified by match to protein family HMM PF01791; match to protein family HMM TIGR00126; deoxyribose-phosphate aldolase 3567556..3568389 Ruegeria pomeroyi DSS-3 3195831 YP_168564.1 CDS SPO3368 NC_003911.11 3568476 3570809 D identified by match to protein family HMM PF00171; aldehyde dehydrogenase 3568476..3570809 Ruegeria pomeroyi DSS-3 3194554 YP_168565.1 CDS SPO3369 NC_003911.11 3570837 3571649 D identified by match to protein family HMM PF00106; short chain dehydrogenase 3570837..3571649 Ruegeria pomeroyi DSS-3 3194749 YP_168566.1 CDS SPO3370 NC_003911.11 3571747 3573057 R identified by match to protein family HMM PF00675; match to protein family HMM PF05193; M16 family peptidase complement(3571747..3573057) Ruegeria pomeroyi DSS-3 3195880 YP_168567.1 CDS SPO3371 NC_003911.11 3573054 3574403 R identified by match to protein family HMM PF00675; match to protein family HMM PF05193; M16 family peptidase complement(3573054..3574403) Ruegeria pomeroyi DSS-3 3195729 YP_168568.1 CDS SPO3372 NC_003911.11 3574476 3575048 R hypothetical protein complement(3574476..3575048) Ruegeria pomeroyi DSS-3 3193171 YP_168569.1 CDS lspA NC_003911.11 3575045 3575518 R lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase complement(3575045..3575518) Ruegeria pomeroyi DSS-3 3195474 YP_168570.1 CDS purH NC_003911.11 3575518 3577107 R involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase complement(3575518..3577107) Ruegeria pomeroyi DSS-3 3195268 YP_168571.1 CDS SPO3375 NC_003911.11 3577130 3578851 R identified by similarity to GB:BAB50839.1; hypothetical protein complement(3577130..3578851) Ruegeria pomeroyi DSS-3 3195874 YP_168572.1 CDS SPO3376 NC_003911.11 3578939 3580210 R identified by similarity to SP:P36929; match to protein family HMM PF01029; match to protein family HMM PF01189; ribosomal RNA small subunit methyltransferase B complement(3578939..3580210) Ruegeria pomeroyi DSS-3 3195741 YP_168573.1 CDS SPO3377 NC_003911.11 3580305 3580487 D identified by similarity to GB:AAN30707.1; hypothetical protein 3580305..3580487 Ruegeria pomeroyi DSS-3 3195362 YP_168574.1 CDS SPO3378 NC_003911.11 3580575 3581747 D identified by match to protein family HMM PF03594; match to protein family HMM TIGR00843; benzoate transporter 3580575..3581747 Ruegeria pomeroyi DSS-3 3195628 YP_168575.1 CDS SPO3379 NC_003911.11 3581744 3582586 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(3581744..3582586) Ruegeria pomeroyi DSS-3 3195027 YP_168576.1 CDS SPO3380 NC_003911.11 3582708 3583844 D identified by similarity to SP:P80193; match to protein family HMM PF03322; gamma-butyrobetaine hydroxylase 3582708..3583844 Ruegeria pomeroyi DSS-3 3194530 YP_168577.1 CDS SPO3381 NC_003911.11 3583841 3584431 D identified by similarity to GB:BAB48813.1; hypothetical protein 3583841..3584431 Ruegeria pomeroyi DSS-3 3195957 YP_168578.1 CDS SPO3382 NC_003911.11 3584584 3586023 R identified by match to protein family HMM PF00171; aldehyde dehydrogenase complement(3584584..3586023) Ruegeria pomeroyi DSS-3 3194405 YP_168579.1 CDS SPO3383 NC_003911.11 3586245 3586898 D identified by similarity to GB:BAC00970.1; match to protein family HMM PF00578; thiol-specific antioxidant protein 3586245..3586898 Ruegeria pomeroyi DSS-3 3195770 YP_168580.1 CDS SPO3384 NC_003911.11 3586953 3587609 D identified by match to protein family HMM TIGR01444; FkbM family methyltransferase 3586953..3587609 Ruegeria pomeroyi DSS-3 3195846 YP_168581.1 CDS SPO3385 NC_003911.11 3587617 3588438 R identified by match to protein family HMM PF01755; glycosyl transferase family protein complement(3587617..3588438) Ruegeria pomeroyi DSS-3 3195653 YP_168582.1 CDS SPO3386 NC_003911.11 3588477 3588959 R hypothetical protein complement(3588477..3588959) Ruegeria pomeroyi DSS-3 3195287 YP_168583.1 CDS SPO3387 NC_003911.11 3588946 3590337 R identified by similarity to GB:AAK01513.1; hypothetical protein complement(3588946..3590337) Ruegeria pomeroyi DSS-3 3194424 YP_168584.1 CDS SPO3388 NC_003911.11 3590395 3591018 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(3590395..3591018) Ruegeria pomeroyi DSS-3 3194977 YP_168585.1 CDS pnp NC_003911.11 3591258 3593402 R 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 complement(3591258..3593402) Ruegeria pomeroyi DSS-3 3195958 YP_168586.1 CDS SPO3390 NC_003911.11 3593615 3594139 R identified by similarity to PIR:AH2948; hypothetical protein complement(3593615..3594139) Ruegeria pomeroyi DSS-3 3193902 YP_168587.1 CDS SPO3391 NC_003911.11 3594307 3595152 D identified by similarity to GB:AAC99764.1; match to protein family HMM PF01531; alpha-1,2-fucosyltransferase 3594307..3595152 Ruegeria pomeroyi DSS-3 3195274 YP_168588.1 CDS rluA NC_003911.11 3595235 3595882 R identified by similarity to SP:P39219; match to protein family HMM PF00849; ribosomal large subunit pseudouridine synthase A complement(3595235..3595882) Ruegeria pomeroyi DSS-3 3194821 YP_168589.1 CDS SPO3393 NC_003911.11 3595986 3596396 D identified by similarity to GB:BAC68979.1; hypothetical protein 3595986..3596396 Ruegeria pomeroyi DSS-3 3195153 YP_168590.1 CDS SPO3394 NC_003911.11 3596429 3597130 D identified by match to protein family HMM PF00657; GDSL-like lipase/acylhydrolase 3596429..3597130 Ruegeria pomeroyi DSS-3 3194404 YP_168591.1 CDS rarD-2 NC_003911.11 3597088 3597987 R identified by similarity to SP:P27844; match to protein family HMM PF00892; match to protein family HMM TIGR00688; protein RarD complement(3597088..3597987) Ruegeria pomeroyi DSS-3 3194510 YP_168592.1 CDS SPO3396 NC_003911.11 3598191 3600641 R identified by match to protein family HMM PF01266; match to protein family HMM PF01571; FAD-dependent oxidoreductase complement(3598191..3600641) Ruegeria pomeroyi DSS-3 3195707 YP_168593.1 CDS SPO3397 NC_003911.11 3600729 3601697 R identified by match to protein family HMM PF00165; AraC family transcriptional regulator complement(3600729..3601697) Ruegeria pomeroyi DSS-3 3194496 YP_168594.1 CDS SPO3398 NC_003911.11 3601725 3602621 R identified by match to protein family HMM PF02574; homocysteine S-methyltransferase complement(3601725..3602621) Ruegeria pomeroyi DSS-3 3195042 YP_168595.1 CDS SPO3399 NC_003911.11 3602618 3603685 R identified by match to protein family HMM PF00107; alcohol dehydrogenase complement(3602618..3603685) Ruegeria pomeroyi DSS-3 3195141 YP_168596.1 CDS SPO3400 NC_003911.11 3603682 3606129 R identified by match to protein family HMM PF01571; glycine cleavage system protein T complement(3603682..3606129) Ruegeria pomeroyi DSS-3 3193141 YP_168597.1 CDS SPO3401 NC_003911.11 3606139 3606510 R identified by similarity to GB:BAB48331.1; match to protein family HMM PF04828; hypothetical protein complement(3606139..3606510) Ruegeria pomeroyi DSS-3 3195023 YP_168598.1 CDS SPO3402 NC_003911.11 3606514 3607137 R identified by similarity to SP:P27847; match to protein family HMM PF01810; amino acid transporter LysE complement(3606514..3607137) Ruegeria pomeroyi DSS-3 3195516 YP_168599.1 CDS SPO3403 NC_003911.11 3607148 3607717 R identified by match to protein family HMM PF01381; DNA-binding protein complement(3607148..3607717) Ruegeria pomeroyi DSS-3 3195093 YP_168600.1 CDS SPO3404 NC_003911.11 3607935 3608207 D identified by similarity to GB:AAQ58177.1; match to protein family HMM PF06961; hypothetical protein 3607935..3608207 Ruegeria pomeroyi DSS-3 3195592 YP_168601.1 CDS SPO3405 NC_003911.11 3608184 3608636 R identified by similarity to GB:AAM38460.1; hypothetical protein complement(3608184..3608636) Ruegeria pomeroyi DSS-3 3195526 YP_168602.1 CDS SPO3406 NC_003911.11 3608707 3609303 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(3608707..3609303) Ruegeria pomeroyi DSS-3 3195364 YP_168603.1 CDS SPO3407 NC_003911.11 3609403 3609768 D hypothetical protein 3609403..3609768 Ruegeria pomeroyi DSS-3 3194638 YP_168604.1 CDS SPO3408 NC_003911.11 3609809 3610981 R identified by match to protein family HMM PF00108; match to protein family HMM PF02803; match to protein family HMM TIGR01930; acetyl-CoA C-acetyltransferase complement(3609809..3610981) Ruegeria pomeroyi DSS-3 3195101 YP_168605.1 CDS SPO3409 NC_003911.11 3611080 3611418 D identified by match to protein family HMM PF01740; match to protein family HMM TIGR00377; anti-anti-sigma factor 3611080..3611418 Ruegeria pomeroyi DSS-3 3194671 YP_168606.1 CDS SPO3410 NC_003911.11 3611441 3611890 D identified by similarity to SP:P17904; match to protein family HMM PF02518; anti-sigma B factor 3611441..3611890 Ruegeria pomeroyi DSS-3 3194055 YP_168607.1 CDS SPO3411 NC_003911.11 3612877 3614454 D identified by match to protein family HMM PF01019; gamma-glutamyltranspeptidase 3612877..3614454 Ruegeria pomeroyi DSS-3 3195917 YP_168608.1 CDS SPO3412 NC_003911.11 3614476 3614808 R identified by similarity to GB:AAN33763.1; match to protein family HMM TIGR02097; hypothetical protein complement(3614476..3614808) Ruegeria pomeroyi DSS-3 3196339 YP_168609.1 CDS SPO3413 NC_003911.11 3614887 3615768 D identified by match to protein family HMM PF03547; auxin efflux carrier family protein 3614887..3615768 Ruegeria pomeroyi DSS-3 3195296 YP_168610.1 CDS SPO3414 NC_003911.11 3615830 3616420 D lipoprotein 3615830..3616420 Ruegeria pomeroyi DSS-3 3194006 YP_168611.1 CDS SPO3415 NC_003911.11 3616443 3617039 R identified by match to protein family HMM PF03548; outer membrane lipoprotein carrier protein LolA complement(3616443..3617039) Ruegeria pomeroyi DSS-3 3193951 YP_168612.1 CDS SPO3416 NC_003911.11 3617078 3620074 R identified by match to protein family HMM PF01580; DNA translocase FtsK complement(3617078..3620074) Ruegeria pomeroyi DSS-3 3195414 YP_168613.1 CDS SPO3417 NC_003911.11 3620089 3621270 R identified by match to protein family HMM PF00155; aminotransferase, classes I and II complement(3620089..3621270) Ruegeria pomeroyi DSS-3 3194694 YP_168614.1 CDS SPO3418 NC_003911.11 3621379 3622707 R identified by match to protein family HMM PF01425; amidase complement(3621379..3622707) Ruegeria pomeroyi DSS-3 3194471 YP_168615.1 CDS SPO3419 NC_003911.11 3622756 3624018 D identified by match to protein family HMM PF01360; match to protein family HMM TIGR01988; UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase 3622756..3624018 Ruegeria pomeroyi DSS-3 3192835 YP_168616.1 CDS SPO3420 NC_003911.11 3624053 3624820 R identified by similarity to GB:BAB50604.1; hypothetical protein complement(3624053..3624820) Ruegeria pomeroyi DSS-3 3194192 YP_168617.1 CDS SPO3421 NC_003911.11 3624813 3625001 R identified by similarity to GB:AAK22095.1; match to protein family HMM PF03966; hypothetical protein complement(3624813..3625001) Ruegeria pomeroyi DSS-3 3195132 YP_168618.1 CDS SPO3422 NC_003911.11 3624998 3625639 R identified by match to protein family HMM PF02190; ATP-dependent protease La complement(3624998..3625639) Ruegeria pomeroyi DSS-3 3195441 YP_168619.1 CDS SPO3423 NC_003911.11 3625670 3626584 R identified by match to protein family HMM PF00085; thioredoxin complement(3625670..3626584) Ruegeria pomeroyi DSS-3 3195223 YP_168620.1 CDS SPO3424 NC_003911.11 3626667 3628337 R identified by match to protein family HMM PF00560; hypothetical protein complement(3626667..3628337) Ruegeria pomeroyi DSS-3 3194873 YP_168621.1 CDS SPO3425 NC_003911.11 3628506 3629294 R identified by match to protein family HMM PF03372; match to protein family HMM TIGR00633; exodeoxyribonuclease III complement(3628506..3629294) Ruegeria pomeroyi DSS-3 3195340 YP_168622.1 CDS SPO3426 NC_003911.11 3629493 3630179 R identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator complement(3629493..3630179) Ruegeria pomeroyi DSS-3 3195773 YP_168623.1 CDS ribBA NC_003911.11 3630346 3631437 D 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 3630346..3631437 Ruegeria pomeroyi DSS-3 3194516 YP_168624.1 CDS SPO3428 NC_003911.11 3631434 3631934 D identified by similarity to GB:BAB50941.1; hypothetical protein 3631434..3631934 Ruegeria pomeroyi DSS-3 3194615 YP_168625.1 CDS SPO3429 NC_003911.11 3631918 3632616 R identified by match to protein family HMM PF01168; match to protein family HMM TIGR00044; alanine racemase complement(3631918..3632616) Ruegeria pomeroyi DSS-3 3195919 YP_168626.1 CDS SPO3430 NC_003911.11 3632685 3633698 R identified by similarity to GB:CAA70599.1; porin complement(3632685..3633698) Ruegeria pomeroyi DSS-3 3195739 YP_168627.1 CDS SPO3431 NC_003911.11 3633976 3634482 D identified by similarity to GB:AAK25710.1; hypothetical protein 3633976..3634482 Ruegeria pomeroyi DSS-3 3193985 YP_168628.1 CDS leuS NC_003911.11 3634559 3637117 D 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 3634559..3637117 Ruegeria pomeroyi DSS-3 3192670 YP_168629.1 CDS SPO3433 NC_003911.11 3637104 3637595 D lipoprotein 3637104..3637595 Ruegeria pomeroyi DSS-3 3193740 YP_168630.1 CDS SPO3434 NC_003911.11 3637592 3638620 D identified by similarity to GB:CAE25733.1; hypothetical protein 3637592..3638620 Ruegeria pomeroyi DSS-3 3194833 YP_168631.1 CDS SPO3435 NC_003911.11 3638702 3639295 D identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase 3638702..3639295 Ruegeria pomeroyi DSS-3 3195481 YP_168632.1 CDS SPO3436 NC_003911.11 3639265 3640464 R identified by similarity to GB:CAE27628.1; hypothetical protein complement(3639265..3640464) Ruegeria pomeroyi DSS-3 3195635 YP_168633.1 CDS SPO3437 NC_003911.11 3640461 3641822 R identified by match to protein family HMM PF00924; mechanosensitive ion channel MscS complement(3640461..3641822) Ruegeria pomeroyi DSS-3 3193967 YP_168634.1 CDS SPO3438 NC_003911.11 3641837 3642169 D identified by similarity to GB:CAD55640.1; hypothetical protein 3641837..3642169 Ruegeria pomeroyi DSS-3 3194739 YP_168635.1 CDS SPO3439 NC_003911.11 3642266 3642874 R identified by match to protein family HMM PF00378; enoyl-CoA hydratase complement(3642266..3642874) Ruegeria pomeroyi DSS-3 3195413 YP_168636.1 CDS SPO3440 NC_003911.11 3642871 3643623 R identified by similarity to SP:P19992; match to protein family HMM PF00106; 20-beta-hydroxysteroid dehydrogenase complement(3642871..3643623) Ruegeria pomeroyi DSS-3 3194462 YP_168637.1 CDS SPO3441 NC_003911.11 3643755 3645281 D identified by similarity to GB:AAC02256.1; hypothetical protein 3643755..3645281 Ruegeria pomeroyi DSS-3 3194151 YP_168638.1 CDS SPO3442 NC_003911.11 3645348 3646754 D identified by similarity to SP:P24231; hypothetical protein 3645348..3646754 Ruegeria pomeroyi DSS-3 3195884 YP_168639.1 CDS SPO3443 NC_003911.11 3646741 3647544 D identified by similarity to SP:P22783; match to protein family HMM PF00459; inositol monophosphatase 3646741..3647544 Ruegeria pomeroyi DSS-3 3194021 YP_168640.1 CDS SPO3444 NC_003911.11 3647712 3648941 D identified by similarity to SP:P23282; 3-deoxy-D-manno-octulosonic-acid transferase 3647712..3648941 Ruegeria pomeroyi DSS-3 3194902 YP_168641.1 CDS lpxK NC_003911.11 3648928 3649929 D 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 3648928..3649929 Ruegeria pomeroyi DSS-3 3194962 YP_168642.1 CDS SPO3446 NC_003911.11 3649932 3650600 R identified by match to protein family HMM PF01323; DsbA family thiol:disulfide interchange protein complement(3649932..3650600) Ruegeria pomeroyi DSS-3 3194983 YP_168643.1 CDS SPO3447 NC_003911.11 3650615 3651121 R identified by similarity to GB:CAE29927.1; hypothetical protein complement(3650615..3651121) Ruegeria pomeroyi DSS-3 3194979 YP_168644.1 CDS mutY NC_003911.11 3651203 3652258 D 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 3651203..3652258 Ruegeria pomeroyi DSS-3 3195498 YP_168645.1 CDS SPO3449 NC_003911.11 3652319 3653452 D identified by match to protein family HMM PF00487; fatty acid desaturase 3652319..3653452 Ruegeria pomeroyi DSS-3 3194577 YP_168646.1 CDS SPO3450 NC_003911.11 3653459 3654835 R identified by match to protein family HMM PF00211; guanylate cyclase complement(3653459..3654835) Ruegeria pomeroyi DSS-3 3194754 YP_168647.1 CDS SPO3451 NC_003911.11 3654996 3656099 R identified by match to protein family HMM PF01555; modification methylase complement(3654996..3656099) Ruegeria pomeroyi DSS-3 3195587 YP_168648.1 CDS rnhB NC_003911.11 3656206 3656910 R RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII complement(3656206..3656910) Ruegeria pomeroyi DSS-3 3195469 YP_168649.1 CDS SPO3453 NC_003911.11 3657415 3657864 D hypothetical protein 3657415..3657864 Ruegeria pomeroyi DSS-3 3194667 YP_168650.1 CDS SPO3454 NC_003911.11 3657836 3658537 D hypothetical protein 3657836..3658537 Ruegeria pomeroyi DSS-3 3194931 YP_168651.1 CDS SPO3455 NC_003911.11 3658917 3660494 D identified by match to protein family HMM PF00211; match to protein family HMM PF04248; guanylate cyclase 3658917..3660494 Ruegeria pomeroyi DSS-3 3192945 YP_168652.1 CDS SPO3456 NC_003911.11 3660508 3661305 R identified by similarity to PIR:AC3648; flagellar protein complement(3660508..3661305) Ruegeria pomeroyi DSS-3 3194157 YP_168653.1 CDS flbT NC_003911.11 3661302 3661706 R 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 complement(3661302..3661706) Ruegeria pomeroyi DSS-3 3194488 YP_168654.1 CDS flaF NC_003911.11 3661703 3662080 R 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 complement(3661703..3662080) Ruegeria pomeroyi DSS-3 3194748 YP_168655.1 CDS SPO3459 NC_003911.11 3662147 3663373 R identified by match to protein family HMM PF00669; match to protein family HMM PF00700; flagellin protein complement(3662147..3663373) Ruegeria pomeroyi DSS-3 3194040 YP_168656.1 CDS SPO3460 NC_003911.11 3663584 3663943 R identified by similarity to PIR:E98268; hypothetical protein complement(3663584..3663943) Ruegeria pomeroyi DSS-3 3194311 YP_168657.1 CDS SPO3461 NC_003911.11 3663933 3664220 R identified by similarity to SP:P75942; flagellar protein FlgJ complement(3663933..3664220) Ruegeria pomeroyi DSS-3 3194687 YP_168658.1 CDS SPO3462 NC_003911.11 3664298 3666775 D identified by match to protein family HMM PF02120; flagellar hook-length control protein 3664298..3666775 Ruegeria pomeroyi DSS-3 3193348 YP_168659.1 CDS flgD NC_003911.11 3666779 3667447 D 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 3666779..3667447 Ruegeria pomeroyi DSS-3 3193584 YP_168660.1 CDS SPO3464 NC_003911.11 3667512 3668381 D identified by similarity to GB:CAB76068.1; hypothetical protein 3667512..3668381 Ruegeria pomeroyi DSS-3 3194550 YP_168661.1 CDS SPO3465 NC_003911.11 3668386 3669690 R identified by similarity to GB:CAE33186.1; hypothetical protein complement(3668386..3669690) Ruegeria pomeroyi DSS-3 3195553 YP_168662.1 CDS potI NC_003911.11 3669690 3670505 R identified by similarity to SP:P31136; match to protein family HMM PF00528; putrescine ABC transporter permease complement(3669690..3670505) Ruegeria pomeroyi DSS-3 3194338 YP_168663.1 CDS potH NC_003911.11 3670502 3671419 R identified by similarity to SP:P31135; match to protein family HMM PF00528; putrescine ABC transporter permease complement(3670502..3671419) Ruegeria pomeroyi DSS-3 3195161 YP_168664.1 CDS potG NC_003911.11 3671383 3672510 R 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 complement(3671383..3672510) Ruegeria pomeroyi DSS-3 3195099 YP_168665.1 CDS potF NC_003911.11 3672592 3673677 R identified by similarity to SP:P31133; match to protein family HMM PF01547; putrescine ABC transporter periplasmic putrescine-binding protein complement(3672592..3673677) Ruegeria pomeroyi DSS-3 3195405 YP_168666.1 CDS SPO3470 NC_003911.11 3673824 3674504 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 3673824..3674504 Ruegeria pomeroyi DSS-3 3193899 YP_168667.1 CDS SPO3471 NC_003911.11 3674581 3675975 D identified by similarity to SP:Q53196; match to protein family HMM PF00202; aminotransferase 3674581..3675975 Ruegeria pomeroyi DSS-3 3192924 YP_168668.1 CDS SPO3472 NC_003911.11 3676162 3677280 D identified by match to protein family HMM PF00005; match to protein family HMM TIGR01187; polyamine ABC transporter ATP-binding protein 3676162..3677280 Ruegeria pomeroyi DSS-3 3195306 YP_168669.1 CDS SPO3473 NC_003911.11 3677396 3678469 D 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 3677396..3678469 Ruegeria pomeroyi DSS-3 3195492 YP_168670.1 CDS SPO3474 NC_003911.11 3678540 3679823 D Assignment based partly on membership in polyamine ABC transporter gene cluster.; identified by match to protein family HMM PF00528; polyamine ABC transporter permease 3678540..3679823 Ruegeria pomeroyi DSS-3 3195140 YP_168671.1 CDS SPO3475 NC_003911.11 3679830 3680750 D identified by similarity to SP:P23859; match to protein family HMM PF00528; polyamine ABC transporter permease 3679830..3680750 Ruegeria pomeroyi DSS-3 3195437 YP_168672.1 CDS SPO3476 NC_003911.11 3680835 3681182 R hypothetical protein complement(3680835..3681182) Ruegeria pomeroyi DSS-3 3194985 YP_168673.1 CDS SPO3477 NC_003911.11 3681218 3681940 R identified by similarity to GB:BAB48216.1; hypothetical protein complement(3681218..3681940) Ruegeria pomeroyi DSS-3 3194520 YP_168674.1 CDS glcD NC_003911.11 3682022 3683470 D identified by similarity to SP:P52075; match to protein family HMM PF01565; match to protein family HMM PF02913; glycolate oxidase subunit GlcD 3682022..3683470 Ruegeria pomeroyi DSS-3 3196032 YP_168675.1 CDS glcE NC_003911.11 3683536 3684624 D identified by similarity to SP:P52073; match to protein family HMM PF01565; glycolate oxidase subunit GlcE 3683536..3684624 Ruegeria pomeroyi DSS-3 3194290 YP_168676.1 CDS glcF NC_003911.11 3684628 3685950 D identified by similarity to SP:P52074; match to protein family HMM PF00037; match to protein family HMM PF02754; glycolate oxidase, iron-sulfur subunit 3684628..3685950 Ruegeria pomeroyi DSS-3 3192951 YP_168677.1 CDS SPO3481 NC_003911.11 3686010 3687212 R hypothetical protein complement(3686010..3687212) Ruegeria pomeroyi DSS-3 3195308 YP_168678.1 CDS SPO3482 NC_003911.11 3687295 3688200 D identified by match to protein family HMM PF00089; serine protease 3687295..3688200 Ruegeria pomeroyi DSS-3 3196357 YP_168679.1 CDS SPO3483 NC_003911.11 3688197 3689015 D identified by similarity to PIR:E85765; hypothetical protein 3688197..3689015 Ruegeria pomeroyi DSS-3 3194857 YP_168680.1 CDS SPO3484 NC_003911.11 3689142 3689612 D identified by match to protein family HMM PF00011; heat shock protein 20 3689142..3689612 Ruegeria pomeroyi DSS-3 3193438 YP_168681.1 CDS SPO3485 NC_003911.11 3689754 3690146 R identified by similarity to GB:AAN48213.1; hypothetical protein complement(3689754..3690146) Ruegeria pomeroyi DSS-3 3193289 YP_168682.1 CDS SPO3486 NC_003911.11 3690143 3690841 R identified by similarity to PIR:B83165; hypothetical protein complement(3690143..3690841) Ruegeria pomeroyi DSS-3 3196291 YP_168683.1 CDS SPO3487 NC_003911.11 3690925 3691614 D identified by similarity to PIR:AB3193; hypothetical protein 3690925..3691614 Ruegeria pomeroyi DSS-3 3193332 YP_168684.1 CDS SPO3488 NC_003911.11 3691679 3692950 D identified by match to protein family HMM PF01471; peptidoglycan binding domain-containing protein 3691679..3692950 Ruegeria pomeroyi DSS-3 3196369 YP_168685.1 CDS pheT NC_003911.11 3693085 3695481 D 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 3693085..3695481 Ruegeria pomeroyi DSS-3 3194649 YP_168686.1 CDS SPO3490 NC_003911.11 3695536 3696420 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; match to protein family HMM TIGR01199; LysR family transcriptional regulator complement(3695536..3696420) Ruegeria pomeroyi DSS-3 3194920 YP_168687.1 CDS SPO3491 NC_003911.11 3696505 3697137 D identified by match to protein family HMM PF01209; UbiE/COQ5 family methlytransferase 3696505..3697137 Ruegeria pomeroyi DSS-3 3194089 YP_168688.1 CDS SPO3492 NC_003911.11 3697148 3697654 D identified by similarity to GB:BAC17897.1; hypothetical protein 3697148..3697654 Ruegeria pomeroyi DSS-3 3196297 YP_168689.1 CDS SPO3493 NC_003911.11 3697729 3698886 D transporter 3697729..3698886 Ruegeria pomeroyi DSS-3 3194301 YP_168690.1 CDS SPO3494 NC_003911.11 3698893 3699594 R identified by match to protein family HMM PF00043; match to protein family HMM PF02798; glutathione S-transferase complement(3698893..3699594) Ruegeria pomeroyi DSS-3 3196295 YP_168691.1 CDS mscL NC_003911.11 3699884 3700315 D identified by match to protein family HMM PF01741; match to protein family HMM TIGR00220; large conductance mechanosensitive channel protein 3699884..3700315 Ruegeria pomeroyi DSS-3 3194704 YP_168692.1 CDS SPO3496 NC_003911.11 3700403 3701209 D identified by similarity to GB:BAC95620.1; match to protein family HMM PF00924; mechanosensitive ion channel MscS 3700403..3701209 Ruegeria pomeroyi DSS-3 3193548 YP_168693.1 CDS tuf-2 NC_003911.11 3701731 3702906 R 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 complement(3701731..3702906) Ruegeria pomeroyi DSS-3 3195007 YP_168694.1 CDS fusA NC_003911.11 3703463 3705580 R EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G complement(3703463..3705580) Ruegeria pomeroyi DSS-3 3195147 YP_168695.1 CDS rpsG NC_003911.11 3705599 3706069 R binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 complement(3705599..3706069) Ruegeria pomeroyi DSS-3 3196305 YP_168696.1 CDS rpsL NC_003911.11 3706085 3706456 R 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 complement(3706085..3706456) Ruegeria pomeroyi DSS-3 3193405 YP_168697.1 CDS SPO3502 NC_003911.11 3706787 3707608 D hypothetical protein 3706787..3707608 Ruegeria pomeroyi DSS-3 3193494 YP_168698.1 CDS SPO3503 NC_003911.11 3707611 3708426 D identified by similarity to GB:AAC44076.1; hypothetical protein 3707611..3708426 Ruegeria pomeroyi DSS-3 3193218 YP_168699.1 CDS SPO3504 NC_003911.11 3708409 3709344 R identified by match to protein family HMM PF00892; hypothetical protein complement(3708409..3709344) Ruegeria pomeroyi DSS-3 3195352 YP_168700.1 CDS SPO3505 NC_003911.11 3709396 3710604 R hypothetical protein complement(3709396..3710604) Ruegeria pomeroyi DSS-3 3194635 YP_168701.1 CDS SPO3506 NC_003911.11 3710608 3711177 R identified by match to protein family HMM PF01381; DNA-binding protein complement(3710608..3711177) Ruegeria pomeroyi DSS-3 3196241 YP_168702.1 CDS rpoC NC_003911.11 3711273 3715514 R 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' complement(3711273..3715514) Ruegeria pomeroyi DSS-3 3196349 YP_168703.1 CDS rpoB NC_003911.11 3715822 3719958 R 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 complement(3715822..3719958) Ruegeria pomeroyi DSS-3 3196296 YP_168704.1 CDS rplL NC_003911.11 3720252 3720629 R 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 complement(3720252..3720629) Ruegeria pomeroyi DSS-3 3194266 YP_168705.2 CDS rplJ NC_003911.11 3720709 3721227 R binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 complement(3720709..3721227) Ruegeria pomeroyi DSS-3 3195233 YP_168706.1 CDS SPO3511 NC_003911.11 3721519 3722445 R hypothetical protein complement(3721519..3722445) Ruegeria pomeroyi DSS-3 3195396 YP_168707.1 CDS SPO3512 NC_003911.11 3722616 3723467 D hypothetical protein 3722616..3723467 Ruegeria pomeroyi DSS-3 3196303 YP_168708.1 CDS rplA NC_003911.11 3723558 3724256 R 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 complement(3723558..3724256) Ruegeria pomeroyi DSS-3 3194818 YP_168709.1 CDS rplK NC_003911.11 3724258 3724683 R binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 complement(3724258..3724683) Ruegeria pomeroyi DSS-3 3195557 YP_168710.1 CDS SPO3515 NC_003911.11 3724914 3726068 D identified by similarity to GB:AAR38409.1; hypothetical protein 3724914..3726068 Ruegeria pomeroyi DSS-3 3196340 YP_168711.1 CDS nusG NC_003911.11 3726043 3726576 R 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 complement(3726043..3726576) Ruegeria pomeroyi DSS-3 3193106 YP_168712.1 CDS secE NC_003911.11 3726779 3727012 R 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 complement(3726779..3727012) Ruegeria pomeroyi DSS-3 3194975 YP_168713.1 CDS SPO3518 NC_003911.11 3727035 3727457 R identified by similarity to GB:CAE28126.1; hypothetical protein complement(3727035..3727457) Ruegeria pomeroyi DSS-3 3196320 YP_168714.1 CDS ccoS NC_003911.11 3727505 3727663 R identified by match to protein family HMM PF03597; match to protein family HMM TIGR00847; cbb3-type cytochrome oxidase maturation protein complement(3727505..3727663) Ruegeria pomeroyi DSS-3 3193658 YP_168715.1 CDS SPO3520 NC_003911.11 3727668 3729845 R 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 complement(3727668..3729845) Ruegeria pomeroyi DSS-3 3194618 YP_168716.1 CDS SPO3521 NC_003911.11 3729850 3730308 R identified by similarity to SP:P18397; fixH protein complement(3729850..3730308) Ruegeria pomeroyi DSS-3 3193180 YP_168717.1 CDS SPO3522 NC_003911.11 3730311 3731738 R identified by similarity to SP:P18396; match to protein family HMM PF00037; iron-sulfur-binding protein RdxA/RdxB/FixG family complement(3730311..3731738) Ruegeria pomeroyi DSS-3 3194702 YP_168718.1 CDS ccoP-1 NC_003911.11 3732122 3732988 R 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 complement(3732122..3732988) Ruegeria pomeroyi DSS-3 3194654 YP_168719.1 CDS ccoQ-1 NC_003911.11 3732985 3733221 R identified by similarity to GB:AAB02558.1; match to protein family HMM PF05545; cytochrome c oxidase, cbb3-type subunit IV complement(3732985..3733221) Ruegeria pomeroyi DSS-3 3196218 YP_168720.1 CDS ccoO-1 NC_003911.11 3733232 3733960 R CcoO; FixO; cbb3-type cytochrome c oxidase subunit II complement(3733232..3733960) Ruegeria pomeroyi DSS-3 3195203 YP_168721.1 CDS ccoN-1 NC_003911.11 3733975 3735582 R CcoN; FixN; cbb3-type cytochrome c oxidase subunit I complement(3733975..3735582) Ruegeria pomeroyi DSS-3 3196353 YP_168722.1 CDS SPO3527 NC_003911.11 3735771 3736613 D identified by match to protein family HMM PF00582; universal stress protein family protein 3735771..3736613 Ruegeria pomeroyi DSS-3 3196283 YP_168723.1 CDS SPO3528 NC_003911.11 3736673 3736927 R identified by similarity to GB:BAB50217.1; match to protein family HMM PF04226; hypothetical protein complement(3736673..3736927) Ruegeria pomeroyi DSS-3 3194973 YP_168724.1 CDS glyA-3 NC_003911.11 3736984 3738279 R identified by match to protein family HMM PF00464; serine hydroxymethyltransferase complement(3736984..3738279) Ruegeria pomeroyi DSS-3 3192992 YP_168725.1 CDS SPO3530 NC_003911.11 3738405 3739277 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3738405..3739277 Ruegeria pomeroyi DSS-3 3193917 YP_168726.1 CDS fnrL NC_003911.11 3739351 3740094 R identified by similarity to SP:P51007; match to protein family HMM PF00027; match to protein family HMM PF00325; transcriptional activator protein FnrL complement(3739351..3740094) Ruegeria pomeroyi DSS-3 3196390 YP_168727.1 CDS hemN NC_003911.11 3740159 3741514 D catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 3740159..3741514 Ruegeria pomeroyi DSS-3 3193999 YP_168728.1 CDS SPO3533 NC_003911.11 3741694 3743700 D EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 3741694..3743700 Ruegeria pomeroyi DSS-3 3195897 YP_168729.1 CDS yejF NC_003911.11 3743775 3745355 R identified by similarity to SP:P33916; match to protein family HMM PF00005; oligopeptide/dipeptide ABC transporter ATP-binding protein complement(3743775..3745355) Ruegeria pomeroyi DSS-3 3194408 YP_168730.1 CDS yejE NC_003911.11 3745352 3746458 R identified by similarity to SP:P33915; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease complement(3745352..3746458) Ruegeria pomeroyi DSS-3 3193795 YP_168731.1 CDS yejB NC_003911.11 3746462 3747553 R identified by match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease complement(3746462..3747553) Ruegeria pomeroyi DSS-3 3194738 YP_168732.1 CDS yejA NC_003911.11 3747563 3749503 R identified by match to protein family HMM PF00496; oligopeptide/dipeptide ABC transporter substrate-binding protein complement(3747563..3749503) Ruegeria pomeroyi DSS-3 3196277 YP_168733.1 CDS cycM NC_003911.11 3749646 3750152 R identified by similarity to SP:P54820; match to protein family HMM PF00034; cytochrome c552 complement(3749646..3750152) Ruegeria pomeroyi DSS-3 3195032 YP_168734.1 CDS SPO3539 NC_003911.11 3750251 3751105 D catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis; prephenate dehydratase 3750251..3751105 Ruegeria pomeroyi DSS-3 3196270 YP_168735.1 CDS SPO3540 NC_003911.11 3751133 3751360 D hypothetical protein 3751133..3751360 Ruegeria pomeroyi DSS-3 3193086 YP_168736.1 CDS SPO3541 NC_003911.11 3751644 3752627 R identified by match to protein family HMM PF00293; NUDIX family hydrolase complement(3751644..3752627) Ruegeria pomeroyi DSS-3 3194000 YP_168737.1 CDS SPO3542 NC_003911.11 3752853 3754724 D identified by similarity to SP:P08331; match to protein family HMM PF00149; match to protein family HMM PF02872; 2`,3`-cyclic-nucleotide 2`-phosphodiesterase 3752853..3754724 Ruegeria pomeroyi DSS-3 3193775 YP_168738.1 CDS SPO3543 NC_003911.11 3754990 3755421 D identified by similarity to GB:BAC96093.1; hypothetical protein 3754990..3755421 Ruegeria pomeroyi DSS-3 3194031 YP_168739.1 CDS SPO3544 NC_003911.11 3755444 3756304 R identified by similarity to GB:BAC49042.1; hypothetical protein complement(3755444..3756304) Ruegeria pomeroyi DSS-3 3195839 YP_168740.1 CDS SPO3545 NC_003911.11 3756388 3756945 D identified by match to protein family HMM PF00440; TetR family transcriptional regulator 3756388..3756945 Ruegeria pomeroyi DSS-3 3193217 YP_168741.1 CDS SPO3546 NC_003911.11 3756942 3757793 R identified by match to protein family HMM PF04228; zinc metallopeptidase complement(3756942..3757793) Ruegeria pomeroyi DSS-3 3195385 YP_168742.1 CDS SPO3547 NC_003911.11 3758150 3758593 D hypothetical protein 3758150..3758593 Ruegeria pomeroyi DSS-3 3195504 YP_168743.1 CDS SPO3548 NC_003911.11 3758598 3759095 R identified by similarity to GB:CAE29730.1; hypothetical protein complement(3758598..3759095) Ruegeria pomeroyi DSS-3 3196215 YP_168744.1 CDS SPO3549 NC_003911.11 3759230 3759847 R identified by similarity to GB:CAD13774.1; hypothetical protein complement(3759230..3759847) Ruegeria pomeroyi DSS-3 3193557 YP_168745.1 CDS dnaX NC_003911.11 3759926 3761677 D 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 3759926..3761677 Ruegeria pomeroyi DSS-3 3193201 YP_168746.1 CDS SPO3551 NC_003911.11 3761757 3762230 R identified by match to protein family HMM PF00583; acetyltransferase complement(3761757..3762230) Ruegeria pomeroyi DSS-3 3193378 YP_168747.1 CDS SPO3552 NC_003911.11 3762227 3763270 R identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding complement(3762227..3763270) Ruegeria pomeroyi DSS-3 3193041 YP_168748.1 CDS SPO3553 NC_003911.11 3763320 3763985 D identified by similarity to PIR:C75368; match to protein family HMM PF05430; hypothetical protein 3763320..3763985 Ruegeria pomeroyi DSS-3 3193298 YP_168749.1 CDS SPO3554 NC_003911.11 3763982 3764878 D identified by match to protein family HMM PF00892; hypothetical protein 3763982..3764878 Ruegeria pomeroyi DSS-3 3196322 YP_168750.1 CDS SPO3555 NC_003911.11 3764834 3766840 R identified by match to protein family HMM PF01464; Slt family transglycosylase complement(3764834..3766840) Ruegeria pomeroyi DSS-3 3194924 YP_168751.1 CDS dapA NC_003911.11 3766956 3767828 D catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase 3766956..3767828 Ruegeria pomeroyi DSS-3 3196309 YP_168752.1 CDS SPO3557 NC_003911.11 3767921 3768793 R identified by match to protein family HMM PF04976; dimethyl sulfoxide reductase subunit C complement(3767921..3768793) Ruegeria pomeroyi DSS-3 3193004 YP_168753.1 CDS SPO3558 NC_003911.11 3768793 3769599 R identified by match to protein family HMM PF00037; (Fe-S)-binding protein complement(3768793..3769599) Ruegeria pomeroyi DSS-3 3193404 YP_168754.1 CDS SPO3559 NC_003911.11 3769625 3772465 R identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; molybdopterin-binding oxidoreductase complement(3769625..3772465) Ruegeria pomeroyi DSS-3 3196227 YP_168755.1 CDS pta NC_003911.11 3772593 3773606 R identified by match to protein family HMM PF01515; match to protein family HMM TIGR00651; phosphate acetyltransferase complement(3772593..3773606) Ruegeria pomeroyi DSS-3 3196250 YP_168756.1 CDS xsc NC_003911.11 3773624 3775414 R catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase complement(3773624..3775414) Ruegeria pomeroyi DSS-3 3196354 YP_168757.1 CDS tauR NC_003911.11 3775524 3776990 R identified by match to protein family HMM PF00392; taurine transcriptional regulator complement(3775524..3776990) Ruegeria pomeroyi DSS-3 3196382 YP_168758.1 CDS SPO3563 NC_003911.11 3777172 3777489 D identified by match to protein family HMM PF01022; ArsR family transcriptional regulator 3777172..3777489 Ruegeria pomeroyi DSS-3 3196024 YP_168759.1 CDS SPO3564 NC_003911.11 3777482 3778510 D identified by match to protein family HMM PF03773; permease 3777482..3778510 Ruegeria pomeroyi DSS-3 3196042 YP_168760.1 CDS SPO3565 NC_003911.11 3778516 3778908 R hypothetical protein complement(3778516..3778908) Ruegeria pomeroyi DSS-3 3196063 YP_168761.1 CDS SPO3566 NC_003911.11 3778959 3779735 R identified by similarity to GB:CAC47907.1; hypothetical protein complement(3778959..3779735) Ruegeria pomeroyi DSS-3 3195503 YP_168762.1 CDS SPO3567 NC_003911.11 3779864 3780493 D identified by match to protein family HMM PF00445; ribonuclease T2 family protein 3779864..3780493 Ruegeria pomeroyi DSS-3 3196307 YP_168763.1 CDS SPO3568 NC_003911.11 3780522 3781097 R identified by similarity to PIR:D95307; hypothetical protein complement(3780522..3781097) Ruegeria pomeroyi DSS-3 3195616 YP_168764.1 CDS recR NC_003911.11 3781123 3781719 R involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR complement(3781123..3781719) Ruegeria pomeroyi DSS-3 3196401 YP_168765.1 CDS SPO3570 NC_003911.11 3781794 3782138 R identified by similarity to PIR:A82247; match to protein family HMM PF02575; match to protein family HMM TIGR00103; hypothetical protein complement(3781794..3782138) Ruegeria pomeroyi DSS-3 3195408 YP_168766.1 CDS SPO3571 NC_003911.11 3782189 3783151 R identified by match to protein family HMM PF00165; AraC family transcriptional regulator complement(3782189..3783151) Ruegeria pomeroyi DSS-3 3196214 YP_168767.1 CDS SPO3572 NC_003911.11 3783221 3783766 D identified by match to protein family HMM PF00857; isochorismatase 3783221..3783766 Ruegeria pomeroyi DSS-3 3196149 YP_168768.1 CDS SPO3573 NC_003911.11 3783768 3784310 R identified by match to protein family HMM PF03358; NADPH-dependent FMN reductase domain-containing protein complement(3783768..3784310) Ruegeria pomeroyi DSS-3 3196242 YP_168769.1 CDS SPO3574 NC_003911.11 3784425 3785024 R identified by similarity to GB:CAD17119.1; short chain dehydrogenase complement(3784425..3785024) Ruegeria pomeroyi DSS-3 3196271 YP_168770.1 CDS SPO3575 NC_003911.11 3785026 3785382 R identified by match to protein family HMM PF00376; MerR family transcriptional regulator complement(3785026..3785382) Ruegeria pomeroyi DSS-3 3195216 YP_168771.1 CDS SPO3576 NC_003911.11 3785535 3786200 R identified by match to protein family HMM PF00691; OmpA domain-containing protein complement(3785535..3786200) Ruegeria pomeroyi DSS-3 3196348 YP_168772.1 CDS SPO3577 NC_003911.11 3786327 3787025 R identified by similarity to GB:BAB51517.1; hypothetical protein complement(3786327..3787025) Ruegeria pomeroyi DSS-3 3196100 YP_168773.1 CDS SPO3578 NC_003911.11 3787295 3788146 R 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 complement(3787295..3788146) Ruegeria pomeroyi DSS-3 3195031 YP_168774.1 CDS SPO3579 NC_003911.11 3788268 3788717 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 3788268..3788717 Ruegeria pomeroyi DSS-3 3195034 YP_168775.1 CDS SPO3580 NC_003911.11 3788719 3789363 D identified by match to protein family HMM PF00857; isochorismatase 3788719..3789363 Ruegeria pomeroyi DSS-3 3195932 YP_168776.1 CDS nth NC_003911.11 3789415 3790059 D identified by match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01083; endonuclease III 3789415..3790059 Ruegeria pomeroyi DSS-3 3196325 YP_168777.1 CDS SPO3582 NC_003911.11 3790056 3791042 D identified by match to protein family HMM PF00294; PfkB family kinase 3790056..3791042 Ruegeria pomeroyi DSS-3 3193718 YP_168778.1 CDS pecS NC_003911.11 3791148 3791657 R identified by similarity to SP:P42195; match to protein family HMM PF01047; transcriptional regulator PecS complement(3791148..3791657) Ruegeria pomeroyi DSS-3 3195389 YP_168779.1 CDS SPO3584 NC_003911.11 3791729 3792649 D identified by similarity to SP:P42194; match to protein family HMM PF00892; drug/metabolite transporter family membrane protein 3791729..3792649 Ruegeria pomeroyi DSS-3 3193360 YP_168780.1 CDS SPO3585 NC_003911.11 3792607 3793092 R identified by match to protein family HMM PF00293; NUDIX family hydrolase NudH subfamily hydrolase complement(3792607..3793092) Ruegeria pomeroyi DSS-3 3195400 YP_168781.1 CDS fadH NC_003911.11 3793226 3795253 D identified by similarity to SP:P42593; match to protein family HMM PF00070; match to protein family HMM PF00724; 2,4-dienoyl-CoA reductase 3793226..3795253 Ruegeria pomeroyi DSS-3 3194304 YP_168782.1 CDS SPO3587 NC_003911.11 3795394 3796023 D hypothetical protein 3795394..3796023 Ruegeria pomeroyi DSS-3 3196128 YP_168783.1 CDS SPO3588 NC_003911.11 3796089 3796433 R identified by similarity to GB:BAB51219.1; match to protein family HMM PF03992; hypothetical protein complement(3796089..3796433) Ruegeria pomeroyi DSS-3 3196111 YP_168784.1 CDS SPO3589 NC_003911.11 3796430 3796753 R identified by similarity to PIR:AH2740; match to protein family HMM PF06499; hypothetical protein complement(3796430..3796753) Ruegeria pomeroyi DSS-3 3195996 YP_168785.1 CDS SPO3590 NC_003911.11 3796832 3797272 R identified by similarity to PIR:B83607; hypothetical protein complement(3796832..3797272) Ruegeria pomeroyi DSS-3 3194543 YP_168786.1 CDS SPO3591 NC_003911.11 3797417 3798331 D identified by match to protein family HMM PF03547; auxin efflux carrier family protein 3797417..3798331 Ruegeria pomeroyi DSS-3 3194484 YP_168787.1 CDS SPO3592 NC_003911.11 3798481 3799386 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3798481..3799386 Ruegeria pomeroyi DSS-3 3195976 YP_168788.1 CDS SPO3593 NC_003911.11 3799579 3801237 D identified by match to protein family HMM PF00884; sulfatase 3799579..3801237 Ruegeria pomeroyi DSS-3 3195684 YP_168789.1 CDS pheS NC_003911.11 3801673 3802746 R 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 complement(3801673..3802746) Ruegeria pomeroyi DSS-3 3196269 YP_168790.1 CDS SPO3595 NC_003911.11 3802852 3803568 R identified by match to protein family HMM PF00165; match to protein family HMM PF02311; AraC family transcriptional regulator complement(3802852..3803568) Ruegeria pomeroyi DSS-3 3196230 YP_168791.1 CDS SPO3596 NC_003911.11 3803691 3804293 D identified by match to protein family HMM PF01243; pyridoxamine 5'-phosphate oxidase 3803691..3804293 Ruegeria pomeroyi DSS-3 3196365 YP_168792.1 CDS SPO3597 NC_003911.11 3804457 3805806 D identified by match to protein family HMM PF01593; amine oxidase 3804457..3805806 Ruegeria pomeroyi DSS-3 3196252 YP_168793.1 CDS rplT NC_003911.11 3805961 3806326 R binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 complement(3805961..3806326) Ruegeria pomeroyi DSS-3 3196278 YP_168794.1 CDS rpmI NC_003911.11 3806342 3806542 R identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001; 50S ribosomal protein L35 complement(3806342..3806542) Ruegeria pomeroyi DSS-3 3196240 YP_168795.1 CDS pyk NC_003911.11 3806925 3808370 R identified by match to protein family HMM PF00224; match to protein family HMM PF02887; match to protein family HMM TIGR01064; pyruvate kinase complement(3806925..3808370) Ruegeria pomeroyi DSS-3 3196306 YP_168796.1 CDS SPO3601 NC_003911.11 3808488 3809225 D identified by match to protein family HMM PF05013; N-formylglutamate amidohydrolase 3808488..3809225 Ruegeria pomeroyi DSS-3 3196364 YP_168797.1 CDS SPO3602 NC_003911.11 3809353 3809667 D hypothetical protein 3809353..3809667 Ruegeria pomeroyi DSS-3 3196379 YP_168798.1 CDS SPO3603 NC_003911.11 3809680 3810144 R identified by match to protein family HMM PF03061; match to protein family HMM TIGR00369; thioesterase complement(3809680..3810144) Ruegeria pomeroyi DSS-3 3196375 YP_168799.1 CDS SPO3604 NC_003911.11 3810300 3811160 R identified by similarity to PIR:A31422; match to protein family HMM PF01063; D-amino acid aminotransferase complement(3810300..3811160) Ruegeria pomeroyi DSS-3 3196236 YP_168800.1 CDS SPO3605 NC_003911.11 3811211 3812056 R identified by similarity to PIR:AD1992; hypothetical protein complement(3811211..3812056) Ruegeria pomeroyi DSS-3 3194773 YP_168801.1 CDS SPO3606 NC_003911.11 3812075 3813040 R identified by match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase complement(3812075..3813040) Ruegeria pomeroyi DSS-3 3196384 YP_168802.1 CDS SPO3607 NC_003911.11 3813133 3814251 R identified by similarity to GB:AAM01784.1; hypothetical protein complement(3813133..3814251) Ruegeria pomeroyi DSS-3 3195749 YP_168803.1 CDS mclA NC_003911.11 3814431 3815393 D identified by similarity to GB:AAB58884.1; match to protein family HMM TIGR01588; malyl-CoA lyase 3814431..3815393 Ruegeria pomeroyi DSS-3 3196324 YP_168804.1 CDS linC-2 NC_003911.11 3815439 3816221 R identified by similarity to SP:P50197; match to protein family HMM PF00106; short chain dehydrogenase complement(3815439..3816221) Ruegeria pomeroyi DSS-3 3196265 YP_168805.1 CDS SPO3610 NC_003911.11 3816353 3816985 D identified by similarity to GB:BAC74958.1; hypothetical protein 3816353..3816985 Ruegeria pomeroyi DSS-3 3195086 YP_168806.1 CDS SPO3611 NC_003911.11 3817034 3817615 R hypothetical protein complement(3817034..3817615) Ruegeria pomeroyi DSS-3 3195444 YP_168807.1 CDS SPO3612 NC_003911.11 3817745 3818197 R identified by match to protein family HMM PF01037; AsnC family transcriptional regulator complement(3817745..3818197) Ruegeria pomeroyi DSS-3 3193904 YP_168808.1 CDS SPO3613 NC_003911.11 3818270 3818866 D identified by match to protein family HMM PF01810; amino acid transporter LysE 3818270..3818866 Ruegeria pomeroyi DSS-3 3196383 YP_168809.1 CDS SPO3614 NC_003911.11 3818863 3818982 R hypothetical protein complement(3818863..3818982) Ruegeria pomeroyi DSS-3 3195416 YP_168810.1 CDS SPO3615 NC_003911.11 3819351 3820181 R identified by match to protein family HMM PF00165; match to protein family HMM PF06445; AraC family transcriptional regulator complement(3819351..3820181) Ruegeria pomeroyi DSS-3 3195030 YP_168811.1 CDS accA NC_003911.11 3820304 3821266 D 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 3820304..3821266 Ruegeria pomeroyi DSS-3 3193834 YP_168812.1 CDS SPO3617 NC_003911.11 3821354 3822511 R identified by match to protein family HMM PF01471; peptidoglycan-binding protein complement(3821354..3822511) Ruegeria pomeroyi DSS-3 3194686 YP_168813.1 CDS SPO3618 NC_003911.11 3822554 3823342 R identified by similarity to SP:P75851; similarity to SP:Q47539; match to protein family HMM PF00528; sulfonate ABC transporter permease complement(3822554..3823342) Ruegeria pomeroyi DSS-3 3195768 YP_168814.1 CDS SPO3619 NC_003911.11 3823335 3824102 R identified by match to protein family HMM PF00005; sulfonate ABC transporter ATP-binding protein complement(3823335..3824102) Ruegeria pomeroyi DSS-3 3196104 YP_168815.1 CDS SPO3620 NC_003911.11 3824109 3825125 R sulfonate ABC transporter periplamic sulfonate-binding protein complement(3824109..3825125) Ruegeria pomeroyi DSS-3 3194797 YP_168816.1 CDS SPO3621 NC_003911.11 3825195 3825842 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(3825195..3825842) Ruegeria pomeroyi DSS-3 3195319 YP_168817.1 CDS SPO3622 NC_003911.11 3825873 3826613 R identified by similarity to GB:BAC46174.1; match to protein family HMM PF01863; hypothetical protein complement(3825873..3826613) Ruegeria pomeroyi DSS-3 3196085 YP_168818.1 CDS SPO3623 NC_003911.11 3826669 3826995 D identified by similarity to GB:CAE25504.1; hypothetical protein 3826669..3826995 Ruegeria pomeroyi DSS-3 3195261 YP_168819.1 CDS cspA NC_003911.11 3827599 3827805 R identified by similarity to SP:P15277; match to protein family HMM PF00313; cold shock protein CspA complement(3827599..3827805) Ruegeria pomeroyi DSS-3 3195668 YP_168820.1 CDS gshA NC_003911.11 3828329 3829699 R identified by match to protein family HMM PF04107; match to protein family HMM TIGR01436; glutamate--cysteine ligase complement(3828329..3829699) Ruegeria pomeroyi DSS-3 3195399 YP_168821.1 CDS SPO3627 NC_003911.11 3829840 3830367 R hypothetical protein complement(3829840..3830367) Ruegeria pomeroyi DSS-3 3194923 YP_168822.1 CDS SPO3628 NC_003911.11 3830364 3831209 R identified by match to protein family HMM PF00583; acetyltransferase complement(3830364..3831209) Ruegeria pomeroyi DSS-3 3195003 YP_168823.1 CDS SPO3629 NC_003911.11 3831203 3831958 R 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 complement(3831203..3831958) Ruegeria pomeroyi DSS-3 3195522 YP_168824.1 CDS ubiA NC_003911.11 3831971 3832933 D 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 3831971..3832933 Ruegeria pomeroyi DSS-3 3195348 YP_168825.1 CDS SPO3631 NC_003911.11 3832996 3834909 D identified by match to protein family HMM PF00691; OmpA domain-containing protein 3832996..3834909 Ruegeria pomeroyi DSS-3 3195121 YP_168826.1 CDS SPO3632 NC_003911.11 3834910 3835221 D identified by similarity to GB:BAC45762.1; hypothetical protein 3834910..3835221 Ruegeria pomeroyi DSS-3 3193781 YP_168827.1 CDS SPO3633 NC_003911.11 3835239 3835682 R identified by similarity to SP:P30749; match to protein family HMM PF02391; molybdopterin converting factor subunit 2 complement(3835239..3835682) Ruegeria pomeroyi DSS-3 3193568 YP_168828.1 CDS moaD NC_003911.11 3835688 3835933 R identified by match to protein family HMM PF02597; match to protein family HMM TIGR01682; molybdopterin converting factor subunit 1 complement(3835688..3835933) Ruegeria pomeroyi DSS-3 3196025 YP_168829.1 CDS pgsA NC_003911.11 3835933 3836604 R identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase complement(3835933..3836604) Ruegeria pomeroyi DSS-3 3196000 YP_168830.1 CDS SPO3636 NC_003911.11 3836662 3837822 R beta-lactamase complement(3836662..3837822) Ruegeria pomeroyi DSS-3 3196366 YP_168831.1 CDS uvrC NC_003911.11 3837874 3839745 R 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 complement(3837874..3839745) Ruegeria pomeroyi DSS-3 3196156 YP_168832.1 CDS SPO3638 NC_003911.11 3840036 3840815 R identified by match to protein family HMM PF00106; short chain dehydrogenase complement(3840036..3840815) Ruegeria pomeroyi DSS-3 3196048 YP_168833.1 CDS SPO3639 NC_003911.11 3840842 3841801 R identified by match to protein family HMM PF01699; match to protein family HMM TIGR00367; K+-dependent Na+/Ca+ exchanger-like protein complement(3840842..3841801) Ruegeria pomeroyi DSS-3 3195871 YP_168834.1 CDS SPO3640 NC_003911.11 3841970 3842815 R identified by match to protein family HMM PF01343; S49 family peptidase complement(3841970..3842815) Ruegeria pomeroyi DSS-3 3195166 YP_168835.1 CDS SPO3641 NC_003911.11 3842881 3843642 R identified by similarity to SP:P36880; ABC transporter permease complement(3842881..3843642) Ruegeria pomeroyi DSS-3 3196212 YP_168836.1 CDS SPO3642 NC_003911.11 3843639 3844568 R identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein complement(3843639..3844568) Ruegeria pomeroyi DSS-3 3195894 YP_168837.1 CDS SPO3901 NC_003911.11 3844641 3845153 R identified by similarity to GB:CAB76249.1; match to protein family HMM PF06240; carbon monoxide dehydrogenase G protein complement(3844641..3845153) Ruegeria pomeroyi DSS-3 3196316 YP_168838.1 CDS SPO3643 NC_003911.11 3845301 3846281 D identified by similarity to GB:CAE33392.1; match to protein family HMM PF00892; hypothetical protein 3845301..3846281 Ruegeria pomeroyi DSS-3 3194480 YP_168839.1 CDS SPO3644 NC_003911.11 3846595 3847509 R identified by similarity to GB:AAM35804.1; hypothetical protein complement(3846595..3847509) Ruegeria pomeroyi DSS-3 3192923 YP_168840.1 CDS SPO3645 NC_003911.11 3847588 3848028 D identified by match to protein family HMM PF01638; transcriptional regulator 3847588..3848028 Ruegeria pomeroyi DSS-3 3193933 YP_168841.1 CDS SPO3646 NC_003911.11 3848025 3848954 R Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase complement(3848025..3848954) Ruegeria pomeroyi DSS-3 3194778 YP_168842.1 CDS SPO3647 NC_003911.11 3849022 3850116 D identified by match to protein family HMM PF02515; CAIB/BAIF family protein 3849022..3850116 Ruegeria pomeroyi DSS-3 3194974 YP_168843.1 CDS hemE NC_003911.11 3850181 3851215 R catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase complement(3850181..3851215) Ruegeria pomeroyi DSS-3 3196442 YP_168844.1 CDS hemC NC_003911.11 3851322 3852281 D transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase 3851322..3852281 Ruegeria pomeroyi DSS-3 3195060 YP_168845.1 CDS SPO3650 NC_003911.11 3852371 3854143 D identified by match to protein family HMM PF00211; guanylate cyclase 3852371..3854143 Ruegeria pomeroyi DSS-3 3195061 YP_168846.1 CDS SPO3651 NC_003911.11 3854207 3855151 D identified by match to protein family HMM PF00487; fatty acid desaturase 3854207..3855151 Ruegeria pomeroyi DSS-3 3195064 YP_168847.1 CDS SPO3652 NC_003911.11 3855136 3855669 D hypothetical protein 3855136..3855669 Ruegeria pomeroyi DSS-3 3196386 YP_168848.1 CDS hemF NC_003911.11 3855759 3856643 R catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase complement(3855759..3856643) Ruegeria pomeroyi DSS-3 3193274 YP_168849.1 CDS SPO3654 NC_003911.11 3856655 3857455 R identified by similarity to SP:P25529; match to protein family HMM PF00106; 7-alpha-hydroxysteroid dehydrogenase complement(3856655..3857455) Ruegeria pomeroyi DSS-3 3194427 YP_168850.1 CDS SPO3655 NC_003911.11 3857493 3858458 R identified by match to protein family HMM PF05175; methyltransferase complement(3857493..3858458) Ruegeria pomeroyi DSS-3 3195139 YP_168851.1 CDS clpS NC_003911.11 3858504 3858845 R identified by match to protein family HMM PF02617; ATP-dependent Clp protease, adaptor protein ClpS complement(3858504..3858845) Ruegeria pomeroyi DSS-3 3193650 YP_168852.1 CDS SPO3657 NC_003911.11 3858909 3859637 D identified by match to protein family HMM PF00702; HAD superfamily hydrolase 3858909..3859637 Ruegeria pomeroyi DSS-3 3196402 YP_168853.1 CDS SPO3658 NC_003911.11 3859896 3861329 D identified by match to protein family HMM PF00768; D-alanyl-D-alanine carboxypeptidase 3859896..3861329 Ruegeria pomeroyi DSS-3 3193913 YP_168854.1 CDS SPO3659 NC_003911.11 3861401 3862162 R identified by match to protein family HMM PF03746; LamB/YcsF family protein complement(3861401..3862162) Ruegeria pomeroyi DSS-3 3194258 YP_168855.1 CDS SPO3660 NC_003911.11 3862173 3863171 R urea amidolyase complement(3862173..3863171) Ruegeria pomeroyi DSS-3 3194264 YP_168856.1 CDS SPO3661 NC_003911.11 3863168 3863917 R identified by match to protein family HMM PF02682; allophanate hydrolase complement(3863168..3863917) Ruegeria pomeroyi DSS-3 3195969 YP_168857.1 CDS SPO3662 NC_003911.11 3863904 3864824 R hypothetical protein complement(3863904..3864824) Ruegeria pomeroyi DSS-3 3196103 YP_168858.1 CDS SPO3663 NC_003911.11 3864852 3866165 R identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter subunit DctM complement(3864852..3866165) Ruegeria pomeroyi DSS-3 3196249 YP_168859.1 CDS SPO3664 NC_003911.11 3866172 3866705 R hypothetical protein complement(3866172..3866705) Ruegeria pomeroyi DSS-3 3195571 YP_168860.1 CDS SPO3665 NC_003911.11 3866786 3867760 R identified by match to protein family HMM PF03480; solute-binding family 7 protein complement(3866786..3867760) Ruegeria pomeroyi DSS-3 3193540 YP_168861.1 CDS SPO3666 NC_003911.11 3867798 3869063 R identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding complement(3867798..3869063) Ruegeria pomeroyi DSS-3 3195066 YP_168862.1 CDS catB NC_003911.11 3869173 3870303 R identified by similarity to PIR:T48870; match to protein family HMM PF01188; match to protein family HMM PF02746; muconate cycloisomerase I complement(3869173..3870303) Ruegeria pomeroyi DSS-3 3194959 YP_168863.1 CDS SPO3668 NC_003911.11 3870403 3871320 D identified by similarity to SP:P03030; match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 3870403..3871320 Ruegeria pomeroyi DSS-3 3193036 YP_168864.1 CDS SPO3902 NC_003911.11 3871988 3872626 D identified by similarity to SP:P02918; match to protein family HMM PF00912; transglycosylase domain-containing protein 3871988..3872626 Ruegeria pomeroyi DSS-3 3196106 YP_168865.1 CDS SPO3670 NC_003911.11 3872480 3872593 R hypothetical protein complement(3872480..3872593) Ruegeria pomeroyi DSS-3 3194575 YP_168866.1 CDS SPO3671 NC_003911.11 3873719 3875380 D identified by match to protein family HMM PF00394; match to protein family HMM TIGR01409; muticopper oxidase domain-containing protein 3873719..3875380 Ruegeria pomeroyi DSS-3 3193681 YP_168867.1 CDS SPO3672 NC_003911.11 3875377 3875853 D hypothetical protein 3875377..3875853 Ruegeria pomeroyi DSS-3 3195467 YP_168868.1 CDS SPO3673 NC_003911.11 3876050 3882544 R identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein complement(3876050..3882544) Ruegeria pomeroyi DSS-3 3193854 YP_168869.1 CDS SPO3674 NC_003911.11 3883357 3883926 D identified by match to protein family HMM PF01609; ISSpo7, transposase 3883357..3883926 Ruegeria pomeroyi DSS-3 3195496 YP_168870.1 CDS SPO3675 NC_003911.11 3884095 3884751 D identified by similarity to PIR:AB0616; hypothetical protein 3884095..3884751 Ruegeria pomeroyi DSS-3 3195718 YP_168871.1 CDS argE-2 NC_003911.11 3885158 3886303 R catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase complement(3885158..3886303) Ruegeria pomeroyi DSS-3 3193430 YP_168872.1 CDS SPO3677 NC_003911.11 3886300 3887235 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(3886300..3887235) Ruegeria pomeroyi DSS-3 3193521 YP_168873.1 CDS SPO3678 NC_003911.11 3887290 3888399 R identified by match to protein family HMM PF00355; Rieske (2Fe-2S) domain-containing protein complement(3887290..3888399) Ruegeria pomeroyi DSS-3 3196039 YP_168874.1 CDS SPO3679 NC_003911.11 3888425 3889099 R identified by similarity to PIR:C82973; match to protein family HMM PF06267; hypothetical protein complement(3888425..3889099) Ruegeria pomeroyi DSS-3 3194074 YP_168875.1 CDS SPO3680 NC_003911.11 3889104 3889520 R identified by match to protein family HMM PF01042; endoribonuclease L-PSP complement(3889104..3889520) Ruegeria pomeroyi DSS-3 3195750 YP_168876.1 CDS SPO3681 NC_003911.11 3889522 3890664 R identified by match to protein family HMM PF00355; Rieske (2Fe-2S) domain-containing protein complement(3889522..3890664) Ruegeria pomeroyi DSS-3 3194623 YP_168877.1 CDS SPO3682 NC_003911.11 3890849 3892123 D identified by similarity to GB:CAE35157.1; hypothetical protein 3890849..3892123 Ruegeria pomeroyi DSS-3 3194826 YP_168878.1 CDS SPO3684 NC_003911.11 3892715 3893740 D identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcriptional regulator 3892715..3893740 Ruegeria pomeroyi DSS-3 3196203 YP_168879.1 CDS SPO3685 NC_003911.11 3893745 3894959 D identified by similarity to PIR:H97450; match to protein family HMM PF06224; hypothetical protein 3893745..3894959 Ruegeria pomeroyi DSS-3 3196198 YP_168880.1 CDS SPO3686 NC_003911.11 3895050 3895820 R identified by match to protein family HMM PF03328; HpcH/HpaI aldolase complement(3895050..3895820) Ruegeria pomeroyi DSS-3 3193646 YP_168881.1 CDS SPO3687 NC_003911.11 3895885 3897294 R identified by match to protein family HMM PF00282; decarboxylase, pyridoxal-dependent complement(3895885..3897294) Ruegeria pomeroyi DSS-3 3196210 YP_168882.1 CDS SPO3688 NC_003911.11 3897316 3898296 R identified by match to protein family HMM PF00903; extradiol ring-cleavage dioxygenase complement(3897316..3898296) Ruegeria pomeroyi DSS-3 3194557 YP_168883.1 CDS SPO3689 NC_003911.11 3898392 3898880 D identified by match to protein family HMM PF01047; MarR family transcriptional regulator 3898392..3898880 Ruegeria pomeroyi DSS-3 3193640 YP_168884.1 CDS gtdA-1 NC_003911.11 3899365 3900399 D identified by similarity to GB:CAA12267.1; gentisate 1,2-dioxygenase 3899365..3900399 Ruegeria pomeroyi DSS-3 3196199 YP_168885.1 CDS SPO3691 NC_003911.11 3900396 3901094 D identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase 3900396..3901094 Ruegeria pomeroyi DSS-3 3194849 YP_168886.1 CDS SPO3692 NC_003911.11 3901098 3902285 D catalyzes the formation of catechol from salicylate; salicylate hydroxylase 3901098..3902285 Ruegeria pomeroyi DSS-3 3194832 YP_168887.1 CDS SPO3693 NC_003911.11 3902323 3903423 D identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter subunit DctP 3902323..3903423 Ruegeria pomeroyi DSS-3 3193774 YP_168888.1 CDS SPO3694 NC_003911.11 3903497 3904081 D identified by similarity to GB:AAK03610.1; hypothetical protein 3903497..3904081 Ruegeria pomeroyi DSS-3 3196177 YP_168889.1 CDS SPO3695 NC_003911.11 3904078 3905577 D identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter subunit DctM 3904078..3905577 Ruegeria pomeroyi DSS-3 3196137 YP_168890.1 CDS fcs NC_003911.11 3905730 3907436 D catalyzes the conversion of ferulic acid to feruloyl-CoA; feruloyl-CoA synthase 3905730..3907436 Ruegeria pomeroyi DSS-3 3192902 YP_168891.1 CDS badA-1 NC_003911.11 3907583 3909112 D identified by similarity to GB:AAA92151.1; match to protein family HMM PF00501; benzoate-coenzyme A ligase 3907583..3909112 Ruegeria pomeroyi DSS-3 3195888 YP_168892.1 CDS SPO3698 NC_003911.11 3909116 3909931 D identified by similarity to GB:BAC55927.1; hydrolase 3909116..3909931 Ruegeria pomeroyi DSS-3 3195257 YP_168893.1 CDS SPO3699 NC_003911.11 3909935 3910378 D identified by similarity to GB:BAC46344.1; hypothetical protein 3909935..3910378 Ruegeria pomeroyi DSS-3 3195506 YP_168894.1 CDS SPO3700 NC_003911.11 3910527 3912188 D cleaves the ring of 2,3-dihydro-2,3-dihydroxybenzoyl-CoA forming 6-hydroxy-3-hexenoyl-CoA; benzoyl-CoA-dihydrodiol lyase 3910527..3912188 Ruegeria pomeroyi DSS-3 3195411 YP_168895.1 CDS boxB NC_003911.11 3912263 3913714 D identified by similarity to GB:AAN39376.1; benzoyl-CoA oxygenase subunit B 3912263..3913714 Ruegeria pomeroyi DSS-3 3196248 YP_168896.1 CDS SPO3702 NC_003911.11 3913770 3914012 D hypothetical protein 3913770..3914012 Ruegeria pomeroyi DSS-3 3196393 YP_168897.1 CDS boxA NC_003911.11 3914075 3915193 D identified by similarity to GB:AAN39377.1; match to protein family HMM PF00037; match to protein family HMM PF00175; benzoyl-CoA oxygenase, A subunit 3914075..3915193 Ruegeria pomeroyi DSS-3 3196404 YP_168898.1 CDS SPO3704 NC_003911.11 3915279 3916196 D 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 3915279..3916196 Ruegeria pomeroyi DSS-3 3194289 YP_168899.1 CDS SPO3705 NC_003911.11 3916388 3917563 D 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 3916388..3917563 Ruegeria pomeroyi DSS-3 3193699 YP_168900.1 CDS SPO3706 NC_003911.11 3917634 3918398 D identified by similarity to GB:CAE29839.1; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 3917634..3918398 Ruegeria pomeroyi DSS-3 3193008 YP_168901.1 CDS SPO3707 NC_003911.11 3918391 3919113 D identified by similarity to SP:P30294; match to protein family HMM PF00005; branched-chain amino acid ABC transporter ATP-binding protein 3918391..3919113 Ruegeria pomeroyi DSS-3 3196405 YP_168902.1 CDS SPO3708 NC_003911.11 3919174 3920205 D identified by similarity to GB:AAP25830.1; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 3919174..3920205 Ruegeria pomeroyi DSS-3 3194208 YP_168903.1 CDS SPO3709 NC_003911.11 3920202 3921254 D identified by similarity to GB:CAE29842.1; match to protein family HMM PF02653; branched-chain amino acid ABC transporter permease 3920202..3921254 Ruegeria pomeroyi DSS-3 3194531 YP_168904.1 CDS SPO3710 NC_003911.11 3921251 3922396 R identified by similarity to GB:BAC53043.1; hypothetical protein complement(3921251..3922396) Ruegeria pomeroyi DSS-3 3193554 YP_168905.1 CDS SPO3711 NC_003911.11 3922533 3923705 D hypothetical protein 3922533..3923705 Ruegeria pomeroyi DSS-3 3193301 YP_168906.1 CDS asd NC_003911.11 3923789 3924811 D catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase 3923789..3924811 Ruegeria pomeroyi DSS-3 3196409 YP_168907.1 CDS SPO3713 NC_003911.11 3925765 3927429 D identified by similarity to GB:CAC38742.1; hypothetical protein 3925765..3927429 Ruegeria pomeroyi DSS-3 3192844 YP_168908.1 CDS SPO3714 NC_003911.11 3927398 3927877 R hypothetical protein complement(3927398..3927877) Ruegeria pomeroyi DSS-3 3193818 YP_168909.1 CDS SPO3715 NC_003911.11 3927921 3928571 R identified by similarity to SP:P17067; match to protein family HMM PF00484; carbonic anhydrase complement(3927921..3928571) Ruegeria pomeroyi DSS-3 3194874 YP_168910.1 CDS SPO3716 NC_003911.11 3928730 3929113 D hypothetical protein 3928730..3929113 Ruegeria pomeroyi DSS-3 3196411 YP_168911.1 CDS SPO3717 NC_003911.11 3929171 3930568 D identified by match to protein family HMM PF00883; cytosol aminopeptidase 3929171..3930568 Ruegeria pomeroyi DSS-3 3193900 YP_168912.1 CDS SPO3718 NC_003911.11 3930565 3931314 D identified by match to protein family HMM PF00877; NLP/P60 family protein 3930565..3931314 Ruegeria pomeroyi DSS-3 3196410 YP_168913.1 CDS SPO3719 NC_003911.11 3931367 3932221 D identified by similarity to PIR:T52663; match to protein family HMM PF00581; thiosulfate sulfurtransferase 3931367..3932221 Ruegeria pomeroyi DSS-3 3196413 YP_168914.1 CDS tyrB NC_003911.11 3932221 3933405 D catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate; aromatic amino acid aminotransferase 3932221..3933405 Ruegeria pomeroyi DSS-3 3196414 YP_168915.1 CDS SPO3721 NC_003911.11 3933458 3934099 R hypothetical protein complement(3933458..3934099) Ruegeria pomeroyi DSS-3 3193101 YP_168916.1 CDS SPO3722 NC_003911.11 3934096 3934614 R identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738; Rrf2 family protein complement(3934096..3934614) Ruegeria pomeroyi DSS-3 3196421 YP_168917.1 CDS amt-2 NC_003911.11 3934721 3936049 R identified by match to protein family HMM PF00909; match to protein family HMM TIGR00836; ammonium transporter complement(3934721..3936049) Ruegeria pomeroyi DSS-3 3196423 YP_168918.1 CDS glnB-2 NC_003911.11 3936085 3936423 R identified by match to protein family HMM PF00543; nitrogen regulatory protein P-II complement(3936085..3936423) Ruegeria pomeroyi DSS-3 3196220 YP_168919.1 CDS SPO3725 NC_003911.11 3936457 3938823 D 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 3936457..3938823 Ruegeria pomeroyi DSS-3 3196245 YP_168920.1 CDS SPO3726 NC_003911.11 3938846 3939454 R identified by match to protein family HMM PF05494; match to protein family HMM TIGR01409; toluene tolerance family protein complement(3938846..3939454) Ruegeria pomeroyi DSS-3 3196432 YP_168921.1 CDS SPO3727 NC_003911.11 3939444 3940250 R identified by similarity to SP:P43262; match to protein family HMM PF04333; VacJ lipoprotein complement(3939444..3940250) Ruegeria pomeroyi DSS-3 3196437 YP_168922.1 CDS SPO3728 NC_003911.11 3940449 3942182 D 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 3940449..3942182 Ruegeria pomeroyi DSS-3 3196436 YP_168923.1 CDS SPO3729 NC_003911.11 3942179 3943480 D identified by match to protein family HMM PF00529; match to protein family HMM TIGR01843; HlyD family type I secretion membrane fusion protein 3942179..3943480 Ruegeria pomeroyi DSS-3 3196438 YP_168924.1 CDS SPO3730 NC_003911.11 3943553 3944011 D identified by match to protein family HMM PF01042; endoribonuclease L-PSP 3943553..3944011 Ruegeria pomeroyi DSS-3 3196440 YP_168925.1 CDS SPO3731 NC_003911.11 3944008 3944766 D identified by similarity to SP:P10908; match to protein family HMM PF03009; glycerophosphoryl diester phosphodiesterase 3944008..3944766 Ruegeria pomeroyi DSS-3 3196444 YP_168926.1 CDS SPO3732 NC_003911.11 3944810 3945997 D identified by similarity to GB:CAC46070.1; match to protein family HMM PF04339; hypothetical protein 3944810..3945997 Ruegeria pomeroyi DSS-3 3196388 YP_168927.1 CDS phhB NC_003911.11 3945994 3946287 D 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 3945994..3946287 Ruegeria pomeroyi DSS-3 3196447 YP_168928.1 CDS SPO3734 NC_003911.11 3946284 3946706 R identified by match to protein family HMM PF00376; MerR family transcriptional regulator complement(3946284..3946706) Ruegeria pomeroyi DSS-3 3196448 YP_168929.1 CDS SPO3735 NC_003911.11 3946774 3947994 D identified by similarity to SP:P21191; match to protein family HMM PF00083; major facilitator family protein 3946774..3947994 Ruegeria pomeroyi DSS-3 3196449 YP_168930.1 CDS SPO3736 NC_003911.11 3947999 3948484 R identified by match to protein family HMM PF00578; anti-oxidant AhpCTSA family protein complement(3947999..3948484) Ruegeria pomeroyi DSS-3 3196451 YP_168931.1 CDS SPO3737 NC_003911.11 3948583 3949794 D identified by match to protein family HMM PF00070; pyridine nucleotide-disulfide oxidoreductase 3948583..3949794 Ruegeria pomeroyi DSS-3 3193821 YP_168932.1 CDS SPO3738 NC_003911.11 3949791 3950351 D identified by match to protein family HMM PF03602; match to protein family HMM TIGR00095; methyltransferase 3949791..3950351 Ruegeria pomeroyi DSS-3 3194252 YP_168933.1 CDS SPO3739 NC_003911.11 3950451 3952454 D identified by match to protein family HMM PF01968; match to protein family HMM PF05378; hydantoinase/oxoprolinase 3950451..3952454 Ruegeria pomeroyi DSS-3 3195777 YP_168934.1 CDS msrA-2 NC_003911.11 3952494 3953006 R 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 complement(3952494..3953006) Ruegeria pomeroyi DSS-3 3195621 YP_168935.1 CDS msrB NC_003911.11 3953003 3953452 R 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 complement(3953003..3953452) Ruegeria pomeroyi DSS-3 3193237 YP_168936.1 CDS SPO3742 NC_003911.11 3953594 3954115 D identified by match to protein family HMM PF00255; glutathione peroxidase 3953594..3954115 Ruegeria pomeroyi DSS-3 3193573 YP_168937.1 CDS SPO3743 NC_003911.11 3954112 3954990 R identified by match to protein family HMM PF00892; hypothetical protein complement(3954112..3954990) Ruegeria pomeroyi DSS-3 3194042 YP_168938.1 CDS hup NC_003911.11 3955186 3955461 R identified by match to protein family HMM PF00216; DNA-binding protein HU complement(3955186..3955461) Ruegeria pomeroyi DSS-3 3195809 YP_168939.1 CDS amn NC_003911.11 3955606 3957069 R Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile; AMP nucleosidase complement(3955606..3957069) Ruegeria pomeroyi DSS-3 3196458 YP_168940.1 CDS ade NC_003911.11 3957066 3958844 R identified by similarity to SP:P39761; match to protein family HMM PF01979; match to protein family HMM TIGR01178; adenine deaminase complement(3957066..3958844) Ruegeria pomeroyi DSS-3 3195819 YP_168941.1 CDS SPO3747 NC_003911.11 3958990 3959418 D identified by similarity to GB:AAQ59692.1; hypothetical protein 3958990..3959418 Ruegeria pomeroyi DSS-3 3196465 YP_168942.1 CDS SPO3748 NC_003911.11 3959512 3960384 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(3959512..3960384) Ruegeria pomeroyi DSS-3 3196467 YP_168943.1 CDS SPO3749 NC_003911.11 3960505 3961260 D identified by match to protein family HMM PF00596; hypothetical protein 3960505..3961260 Ruegeria pomeroyi DSS-3 3196469 YP_168944.1 CDS SPO3750 NC_003911.11 3961309 3962328 D identified by similarity to GB:CAC47108.1; hypothetical protein 3961309..3962328 Ruegeria pomeroyi DSS-3 3196470 YP_168945.1 CDS exsB NC_003911.11 3962500 3963192 D identified by match to protein family HMM PF06508; match to protein family HMM TIGR00364; exoenzyme S synthesis protein B 3962500..3963192 Ruegeria pomeroyi DSS-3 3195766 YP_168946.1 CDS SPO3903 NC_003911.11 3963192 3963548 D identified by match to protein family HMM PF01242; 6-pyruvoyl tetrahydrobiopterin synthase 3963192..3963548 Ruegeria pomeroyi DSS-3 3195893 YP_168947.1 CDS SPO3752 NC_003911.11 3963545 3964264 D identified by match to protein family HMM PF04055; radical SAM domain-containing protein 3963545..3964264 Ruegeria pomeroyi DSS-3 3194070 YP_168948.1 CDS SPO3753 NC_003911.11 3964286 3964753 D NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis; 7-cyano-7-deazaguanine reductase 3964286..3964753 Ruegeria pomeroyi DSS-3 3195883 YP_168949.1 CDS SPO3754 NC_003911.11 3964764 3965474 R identified by similarity to GB:BAB51829.1; hypothetical protein complement(3964764..3965474) Ruegeria pomeroyi DSS-3 3195881 YP_168950.1 CDS SPO3755 NC_003911.11 3965485 3966336 D identified by similarity to GB:CAE28643.1; hypothetical protein 3965485..3966336 Ruegeria pomeroyi DSS-3 3195701 YP_168951.1 CDS SPO3756 NC_003911.11 3966762 3967676 R identified by match to protein family HMM PF00691; OmpA domain-containing protein complement(3966762..3967676) Ruegeria pomeroyi DSS-3 3196473 YP_168952.1 CDS SPO3757 NC_003911.11 3967673 3968245 R identified by match to protein family HMM TIGR00778; match to protein family HMM TIGR01926; alkylhydroperoxidase complement(3967673..3968245) Ruegeria pomeroyi DSS-3 3195520 YP_168953.1 CDS SPO3758 NC_003911.11 3968242 3968970 R identified by match to protein family HMM PF00583; acetyltransferase complement(3968242..3968970) Ruegeria pomeroyi DSS-3 3196475 YP_168954.1 CDS SPO3759 NC_003911.11 3968967 3969689 R identified by match to protein family HMM PF00994; molybdenum cofactor biosynthesis domain-containing protein complement(3968967..3969689) Ruegeria pomeroyi DSS-3 3195923 YP_168955.1 CDS sfsA NC_003911.11 3969739 3970431 D Regulatory factor involved in maltose metabolism; sugar fermentation stimulation protein A 3969739..3970431 Ruegeria pomeroyi DSS-3 3194105 YP_168956.1 CDS map NC_003911.11 3970517 3971326 D identified by similarity to SP:P07906; match to protein family HMM PF00557; match to protein family HMM TIGR00500; methionine aminopeptidase 3970517..3971326 Ruegeria pomeroyi DSS-3 3196476 YP_168957.1 CDS SPO3762 NC_003911.11 3971437 3972075 R identified by match to protein family HMM PF00702; match to protein family HMM TIGR01509; match to protein family HMM TIGR01549; HAD family hydrolase complement(3971437..3972075) Ruegeria pomeroyi DSS-3 3196482 YP_168958.1 CDS SPO3763 NC_003911.11 3972274 3973314 R identified by match to protein family HMM PF00037; (Fe-S)-binding protein complement(3972274..3973314) Ruegeria pomeroyi DSS-3 3196483 YP_168959.1 CDS SPO3764 NC_003911.11 3973387 3974052 R identified by match to protein family HMM PF02798; glutathione S-transferase complement(3973387..3974052) Ruegeria pomeroyi DSS-3 3196487 YP_168960.1 CDS SPO3765 NC_003911.11 3974236 3974709 D identified by similarity to PIR:D83153; hypothetical protein 3974236..3974709 Ruegeria pomeroyi DSS-3 3196040 YP_168961.1 CDS mtgA NC_003911.11 3974726 3975454 R identified by similarity to SP:P46022; match to protein family HMM PF00912; match to protein family HMM TIGR02070; monofunctional biosynthetic peptidoglycan transglycosylase complement(3974726..3975454) Ruegeria pomeroyi DSS-3 3196494 YP_168962.1 CDS SPO3767 NC_003911.11 3975508 3976494 R identified by similarity to PIR:T03518; hypothetical protein complement(3975508..3976494) Ruegeria pomeroyi DSS-3 3196496 YP_168963.1 CDS gltB NC_003911.11 3976670 3981202 R 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 complement(3976670..3981202) Ruegeria pomeroyi DSS-3 3196499 YP_168964.1 CDS SPO3769 NC_003911.11 3981199 3981636 R identified by similarity to PIR:AG2732; match to protein family HMM PF04828; hypothetical protein complement(3981199..3981636) Ruegeria pomeroyi DSS-3 3196507 YP_168965.1 CDS gltD NC_003911.11 3981691 3983124 R function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase complement(3981691..3983124) Ruegeria pomeroyi DSS-3 3196508 YP_168966.1 CDS SPO3771 NC_003911.11 3983356 3984159 D 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 3983356..3984159 Ruegeria pomeroyi DSS-3 3196513 YP_168967.1 CDS SPO3772 NC_003911.11 3984160 3985143 R identified by similarity to SP:P34943; NADH ubiquinone oxidoreductase complement(3984160..3985143) Ruegeria pomeroyi DSS-3 3196515 YP_168968.1 CDS SPO3774 NC_003911.11 3985928 3987487 D identified by match to protein family HMM PF00496; oligopeptide/dipeptide ABC transporter substrate-binding protein 3985928..3987487 Ruegeria pomeroyi DSS-3 3196520 YP_168969.1 CDS SPO3775 NC_003911.11 3987626 3988606 D identified by similarity to SP:P37316; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 3987626..3988606 Ruegeria pomeroyi DSS-3 3196521 YP_168970.1 CDS SPO3776 NC_003911.11 3988603 3989547 D identified by similarity to SP:P37315; match to protein family HMM PF00528; oligopeptide/dipeptide ABC transporter permease 3988603..3989547 Ruegeria pomeroyi DSS-3 3196522 YP_168971.1 CDS SPO3777 NC_003911.11 3989516 3990544 D 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 3989516..3990544 Ruegeria pomeroyi DSS-3 3196526 YP_168972.1 CDS SPO3778 NC_003911.11 3990541 3991569 D 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 3990541..3991569 Ruegeria pomeroyi DSS-3 3196533 YP_168973.1 CDS SPO3779 NC_003911.11 3991600 3992508 D identified by match to protein family HMM PF00126; LysR family transcriptional regulator 3991600..3992508 Ruegeria pomeroyi DSS-3 3196534 YP_168974.1 CDS SPO3780 NC_003911.11 3992604 3993731 D identified by match to protein family HMM PF03739; hypothetical protein 3992604..3993731 Ruegeria pomeroyi DSS-3 3196536 YP_168975.1 CDS SPO3781 NC_003911.11 3994583 3994960 R identified by similarity to PIR:AB1999; match to protein family HMM TIGR02058; hypothetical protein complement(3994583..3994960) Ruegeria pomeroyi DSS-3 3196419 YP_168976.1 CDS SPO3782 NC_003911.11 3994957 3995301 R identified by similarity to PIR:AI1138; match to protein family HMM TIGR02058; hypothetical protein complement(3994957..3995301) Ruegeria pomeroyi DSS-3 3196535 YP_168977.1 CDS SPO3783 NC_003911.11 3995337 3996398 R identified by similarity to SP:P10907; match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein complement(3995337..3996398) Ruegeria pomeroyi DSS-3 3193746 YP_168978.1 CDS SPO3784 NC_003911.11 3996400 3997551 R identified by similarity to SP:P02914; match to protein family HMM PF00005; sugar ABC transporter ATP-binding protein complement(3996400..3997551) Ruegeria pomeroyi DSS-3 3195513 YP_168979.1 CDS SPO3785 NC_003911.11 3997508 3998446 R identified by similarity to PIR:T46751; match to protein family HMM PF00528; sugar ABC transporter permease complement(3997508..3998446) Ruegeria pomeroyi DSS-3 3196145 YP_168980.1 CDS SPO3786 NC_003911.11 3998443 3999300 R identified by match to protein family HMM PF00528; sugar ABC transporter permease complement(3998443..3999300) Ruegeria pomeroyi DSS-3 3196161 YP_168981.1 CDS SPO3787 NC_003911.11 3999366 4001015 R 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 complement(3999366..4001015) Ruegeria pomeroyi DSS-3 3193975 YP_168982.1 CDS acoR NC_003911.11 4001094 4002827 R identified by similarity to SP:P28614; match to protein family HMM PF00158; match to protein family HMM PF01590; acetoin catabolism regulatory protein complement(4001094..4002827) Ruegeria pomeroyi DSS-3 3195054 YP_168983.1 CDS SPO3789 NC_003911.11 4003168 4003500 R identified by match to protein family HMM PF02627; match to protein family HMM TIGR00778; alkylhydroperoxidase complement(4003168..4003500) Ruegeria pomeroyi DSS-3 3194182 YP_168984.1 CDS acoC NC_003911.11 4003568 4004668 R Catalyzes the transfer of acetyl from acetyldihydrolipoamide to coenzyme A to form acetyl CoA; branched-chain alpha-keto acid dehydrogenase subunit E2 complement(4003568..4004668) Ruegeria pomeroyi DSS-3 3195409 YP_168985.1 CDS acoB NC_003911.11 4004673 4005680 R 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 complement(4004673..4005680) Ruegeria pomeroyi DSS-3 3196076 YP_168986.1 CDS acoA NC_003911.11 4005711 4006691 R identified by similarity to PIR:I40790; match to protein family HMM PF00676; acetoin dehydrogenase complex, E1 component subunit alpha complement(4005711..4006691) Ruegeria pomeroyi DSS-3 3195710 YP_168987.1 CDS acoX NC_003911.11 4006688 4007746 R identified by similarity to SP:P27748; match to protein family HMM PF01513; acetoin catabolism protein X complement(4006688..4007746) Ruegeria pomeroyi DSS-3 3196126 YP_168988.1 CDS SPO3794 NC_003911.11 4007899 4008051 R identified by similarity to GB:AAM35022.1; hypothetical protein complement(4007899..4008051) Ruegeria pomeroyi DSS-3 3196175 YP_168989.1 CDS rpoN NC_003911.11 4008387 4009670 D 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 4008387..4009670 Ruegeria pomeroyi DSS-3 3192852 YP_168990.1 CDS SPO3802 NC_003911.11 4016785 4017324 D identified by similarity to GB:BAC50760.1; hypothetical protein 4016785..4017324 Ruegeria pomeroyi DSS-3 3194981 YP_168991.1 CDS SPO3803 NC_003911.11 4017291 4018322 R identified by match to protein family HMM PF00165; match to protein family HMM TIGR01199; AraC family transcriptional regulator complement(4017291..4018322) Ruegeria pomeroyi DSS-3 3195189 YP_168992.1 CDS dmdC NC_003911.11 4018439 4020205 D identified by match to protein family HMM PF00441; match to protein family HMM PF02770; 3-methylmercaptopropionyl-CoA dehydrogenase 4018439..4020205 Ruegeria pomeroyi DSS-3 3196531 YP_168993.1 CDS dmdD NC_003911.11 4020265 4021068 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; methylthioacryloyl-CoA hydratase 4020265..4021068 Ruegeria pomeroyi DSS-3 3196358 YP_168994.1 CDS smpB NC_003911.11 4021134 4021610 D 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 4021134..4021610 Ruegeria pomeroyi DSS-3 3193484 YP_168995.1 CDS SPO3807 NC_003911.11 4021706 4022056 R identified by similarity to GB:BAC45729.1; hypothetical protein complement(4021706..4022056) Ruegeria pomeroyi DSS-3 3193879 YP_168996.1 CDS SPO3808 NC_003911.11 4022087 4022590 R identified by similarity to GB:BAB48348.1; hypothetical protein complement(4022087..4022590) Ruegeria pomeroyi DSS-3 3192990 YP_168997.1 CDS SPO3809 NC_003911.11 4022560 4023255 R identified by match to protein family HMM PF01022; ArsR family transcriptional regulator complement(4022560..4023255) Ruegeria pomeroyi DSS-3 3193525 YP_168998.1 CDS gpmI NC_003911.11 4023983 4025500 D catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 4023983..4025500 Ruegeria pomeroyi DSS-3 3195588 YP_168999.1 CDS SPO3811 NC_003911.11 4025497 4026633 D identified by similarity to GB:AAK25396.1; hypothetical protein 4025497..4026633 Ruegeria pomeroyi DSS-3 3194556 YP_169000.1 CDS SPO3812 NC_003911.11 4026640 4027971 D identified by match to protein family HMM PF00595; match to protein family HMM PF03572; match to protein family HMM TIGR00225; carboxyl-terminal protease 4026640..4027971 Ruegeria pomeroyi DSS-3 3196132 YP_169001.1 CDS SPO3813 NC_003911.11 4028065 4028457 R hypothetical protein complement(4028065..4028457) Ruegeria pomeroyi DSS-3 3196020 YP_169002.1 CDS SPO3814 NC_003911.11 4028454 4029215 R hypothetical protein complement(4028454..4029215) Ruegeria pomeroyi DSS-3 3194947 YP_169003.1 CDS SPO3815 NC_003911.11 4029463 4032582 D identified by similarity to GB:BAB50188.1; match to protein family HMM PF00027; match to protein family HMM PF00664; ABC transporter permease 4029463..4032582 Ruegeria pomeroyi DSS-3 3196115 YP_169004.1 CDS SPO3816 NC_003911.11 4032572 4033465 D identified by match to protein family HMM PF02517; CAAX amino terminal protease 4032572..4033465 Ruegeria pomeroyi DSS-3 3196180 YP_169005.1 CDS accD NC_003911.11 4033524 4034468 D identified by similarity to SP:P08193; match to protein family HMM TIGR00515; acetyl-CoA carboxylase, carboxyl transferase subunit beta 4033524..4034468 Ruegeria pomeroyi DSS-3 3196064 YP_169006.1 CDS folC NC_003911.11 4034465 4035739 D identified by match to protein family HMM PF01225; match to protein family HMM TIGR01499; folC bifunctional protein 4034465..4035739 Ruegeria pomeroyi DSS-3 3196060 YP_169007.1 CDS SPO3819 NC_003911.11 4035815 4036876 R identified by match to protein family HMM PF03969; AFG1 family ATPase complement(4035815..4036876) Ruegeria pomeroyi DSS-3 3194847 YP_169008.1 CDS SPO3820 NC_003911.11 4037027 4038262 D major facilitator transporter 4037027..4038262 Ruegeria pomeroyi DSS-3 3194897 YP_169009.1 CDS SPO3821 NC_003911.11 4038279 4039187 R identified by match to protein family HMM PF02423; ornithine cyclodeaminase/mu-crystallin family protein complement(4038279..4039187) Ruegeria pomeroyi DSS-3 3196121 YP_169010.1 CDS SPO3822 NC_003911.11 4039184 4039804 R identified by match to protein family HMM PF00702; match to protein family HMM TIGR01509; HAD-superfamily hydrolase complement(4039184..4039804) Ruegeria pomeroyi DSS-3 3196239 YP_169011.1 CDS rplW NC_003911.11 4039971 4040267 R binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 complement(4039971..4040267) Ruegeria pomeroyi DSS-3 3195995 YP_169012.1 CDS rplD NC_003911.11 4040264 4040881 R 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 complement(4040264..4040881) Ruegeria pomeroyi DSS-3 3195311 YP_169013.1 CDS rplC NC_003911.11 4040878 4041603 R 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 complement(4040878..4041603) Ruegeria pomeroyi DSS-3 3192891 YP_169014.1 CDS rpsJ NC_003911.11 4041620 4041934 R 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 complement(4041620..4041934) Ruegeria pomeroyi DSS-3 3196261 YP_169015.1 CDS SPO3827 NC_003911.11 4042161 4042625 R identified by match to protein family HMM PF02639; YaiI/YqxD family protein complement(4042161..4042625) Ruegeria pomeroyi DSS-3 3193877 YP_169016.1 CDS sthA NC_003911.11 4043006 4044433 R catalyzes the conversion of NADPH to NADH; soluble pyridine nucleotide transhydrogenase complement(4043006..4044433) Ruegeria pomeroyi DSS-3 3196077 YP_169017.1 CDS SPO3829 NC_003911.11 4044442 4045296 R identified by similarity to GB:AAC44554.1; match to protein family HMM PF00756; S-formylglutathione hydrolase complement(4044442..4045296) Ruegeria pomeroyi DSS-3 3193731 YP_169018.1 CDS pepT NC_003911.11 4045449 4046687 D catalyzes the release of the N-terminal amino acid from a tripeptide; peptidase T 4045449..4046687 Ruegeria pomeroyi DSS-3 3195124 YP_169019.1 CDS SPO3831 NC_003911.11 4046691 4047548 D identified by match to protein family HMM PF00561; alpha/beta hydrolase 4046691..4047548 Ruegeria pomeroyi DSS-3 3196081 YP_169020.1 CDS SPO3832 NC_003911.11 4047545 4048492 D identified by match to protein family HMM PF02423; ornithine cyclodeaminase/mu-crystallin family protein 4047545..4048492 Ruegeria pomeroyi DSS-3 3192755 YP_169021.1 CDS SPO3833 NC_003911.11 4048549 4050678 D identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF03880; DEAD/DEAH box helicase 4048549..4050678 Ruegeria pomeroyi DSS-3 3196362 YP_169022.1 CDS dapB NC_003911.11 4050682 4051491 R catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase complement(4050682..4051491) Ruegeria pomeroyi DSS-3 3196359 YP_169023.1 CDS rbfA NC_003911.11 4051580 4051975 D 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 4051580..4051975 Ruegeria pomeroyi DSS-3 3196286 YP_169024.1 CDS SPO3836 NC_003911.11 4051972 4052709 D identified by similarity to GB:CAC46553.1; hypothetical protein 4051972..4052709 Ruegeria pomeroyi DSS-3 3196083 YP_169025.1 CDS truB NC_003911.11 4052835 4053746 D catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B 4052835..4053746 Ruegeria pomeroyi DSS-3 3196374 YP_169026.1 CDS SPO3838 NC_003911.11 4053792 4054298 D identified by similarity to PIR:E95908; hypothetical protein 4053792..4054298 Ruegeria pomeroyi DSS-3 3196101 YP_169027.1 CDS SPO3839 NC_003911.11 4054352 4055428 D identified by match to protein family HMM PF00353; type I secretion target repeat-containing protein 4054352..4055428 Ruegeria pomeroyi DSS-3 3196012 YP_169028.1 CDS rpsO NC_003911.11 4055583 4055852 D 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 4055583..4055852 Ruegeria pomeroyi DSS-3 3196119 YP_169029.1 CDS SPO3841 NC_003911.11 4055937 4056554 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(4055937..4056554) Ruegeria pomeroyi DSS-3 3196254 YP_169030.1 CDS SPO3842 NC_003911.11 4056685 4057659 D identified by similarity to GB:AAN30579.1; match to protein family HMM PF01988; hypothetical protein 4056685..4057659 Ruegeria pomeroyi DSS-3 3196287 YP_169031.1 CDS SPO3843 NC_003911.11 4057698 4058627 D identified by similarity to GB:AAC45458.1; match to protein family HMM PF03547; malonate transporter 4057698..4058627 Ruegeria pomeroyi DSS-3 3196329 YP_169032.1 CDS polA NC_003911.11 4058742 4061543 D 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 4058742..4061543 Ruegeria pomeroyi DSS-3 3195865 YP_169033.1 CDS SPO3845 NC_003911.11 4061599 4061907 R identified by similarity to GB:AAN56041.1; hypothetical protein complement(4061599..4061907) Ruegeria pomeroyi DSS-3 3196313 YP_169034.1 CDS SPO3846 NC_003911.11 4061964 4062143 R identified by similarity to GB:AAK22176.1; hypothetical protein complement(4061964..4062143) Ruegeria pomeroyi DSS-3 3196092 YP_169035.1 CDS SPO3847 NC_003911.11 4062235 4063164 D identified by similarity to GB:CAD16663.1; match to protein family HMM PF00005; ABC transporter ATP-binding protein 4062235..4063164 Ruegeria pomeroyi DSS-3 3195625 YP_169036.1 CDS SPO3848 NC_003911.11 4063148 4063930 R identified by similarity to GB:BAC09469.1; match to protein family HMM PF01598; sterol desaturase complement(4063148..4063930) Ruegeria pomeroyi DSS-3 3196146 YP_169037.1 CDS SPO3849 NC_003911.11 4063991 4064479 R identified by similarity to GB:BAB47957.1; match to protein family HMM PF06718; hypothetical protein complement(4063991..4064479) Ruegeria pomeroyi DSS-3 3196346 YP_169038.1 CDS SPO3850 NC_003911.11 4064943 4066055 D identified by similarity to SP:P45382; match to protein family HMM PF00107; glutathione-dependent formaldehyde dehydrogenase 4064943..4066055 Ruegeria pomeroyi DSS-3 3196155 YP_169039.1 CDS SPO3851 NC_003911.11 4066155 4067636 R identified by match to protein family HMM PF07219; HemY domain-containing protein complement(4066155..4067636) Ruegeria pomeroyi DSS-3 3196268 YP_169040.1 CDS SPO3852 NC_003911.11 4067659 4069017 R hypothetical protein complement(4067659..4069017) Ruegeria pomeroyi DSS-3 3196207 YP_169041.1 CDS SPO3853 NC_003911.11 4069017 4069730 R identified by match to protein family HMM PF02602; uroporphyrinogen-III synthase complement(4069017..4069730) Ruegeria pomeroyi DSS-3 3196160 YP_169042.1 CDS SPO3854 NC_003911.11 4069829 4070926 D 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 4069829..4070926 Ruegeria pomeroyi DSS-3 3196188 YP_169043.1 CDS gpsA NC_003911.11 4070923 4071885 D catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 4070923..4071885 Ruegeria pomeroyi DSS-3 3196197 YP_169044.1 CDS SPO3856 NC_003911.11 4071887 4072156 D 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 4071887..4072156 Ruegeria pomeroyi DSS-3 3196403 YP_169045.1 CDS SPO3857 NC_003911.11 4072156 4072578 D identified by similarity to GB:BAA34646.1; match to protein family HMM PF04543; hypothetical protein 4072156..4072578 Ruegeria pomeroyi DSS-3 3196192 YP_169046.1 CDS SPO3858 NC_003911.11 4072621 4073016 D identified by similarity to GB:BAB50937.1; hypothetical protein 4072621..4073016 Ruegeria pomeroyi DSS-3 3196190 YP_169047.1 CDS SPO3859 NC_003911.11 4073261 4073602 R identified by similarity to GB:BAB48836.1; hypothetical protein complement(4073261..4073602) Ruegeria pomeroyi DSS-3 3196195 YP_169048.1 CDS SPO3860 NC_003911.11 4073760 4074371 R identified by similarity to PIR:S77132; hypothetical protein complement(4073760..4074371) Ruegeria pomeroyi DSS-3 3196184 YP_169049.1 CDS ahcY NC_003911.11 4074441 4075829 R catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine; S-adenosyl-L-homocysteine hydrolase complement(4074441..4075829) Ruegeria pomeroyi DSS-3 3196407 YP_169050.1 CDS SPO3862 NC_003911.11 4075926 4076258 R identified by similarity to GB:CAC45660.1; lipoprotein complement(4075926..4076258) Ruegeria pomeroyi DSS-3 3196185 YP_169051.1 CDS SPO3863 NC_003911.11 4076448 4077041 D identified by match to protein family HMM PF01966; HD domain-containing protein 4076448..4077041 Ruegeria pomeroyi DSS-3 3196187 YP_169052.1 CDS SPO3864 NC_003911.11 4077014 4078243 R identified by similarity to PIR:H84070; hypothetical protein complement(4077014..4078243) Ruegeria pomeroyi DSS-3 3196201 YP_169053.1 CDS regA NC_003911.11 4078254 4078808 R identified by similarity to SP:P42508; match to protein family HMM PF00072; match to protein family HMM TIGR01199; photosynthetic apparatus regulatory protein RegA complement(4078254..4078808) Ruegeria pomeroyi DSS-3 3196380 YP_169054.1 CDS senC NC_003911.11 4078895 4079515 R identified by similarity to SP:Q52720; match to protein family HMM PF02630; regulatory protein SenC complement(4078895..4079515) Ruegeria pomeroyi DSS-3 3196420 YP_169055.1 CDS regB NC_003911.11 4079603 4081000 D identified by similarity to GB:BAA31475.1; match to protein family HMM PF00512; match to protein family HMM PF02518; sensor histidine kinase RegB 4079603..4081000 Ruegeria pomeroyi DSS-3 3196179 YP_169056.1 CDS SPO3868 NC_003911.11 4081068 4082570 D identified by similarity to GB:AAM48718.1; hypothetical protein 4081068..4082570 Ruegeria pomeroyi DSS-3 3196345 YP_169057.1 CDS SPO3869 NC_003911.11 4082613 4083086 D identified by similarity to GB:AAK25496.1; match to protein family HMM PF02367; match to protein family HMM TIGR00150; hypothetical protein 4082613..4083086 Ruegeria pomeroyi DSS-3 3196377 YP_169058.1 CDS SPO3870 NC_003911.11 4083056 4084090 D identified by similarity to GB:AAM48719.1; hypothetical protein 4083056..4084090 Ruegeria pomeroyi DSS-3 3196302 YP_169059.1 CDS SPO3871 NC_003911.11 4084087 4084773 D identified by match to protein family HMM PF00483; nucleotidyltransferase 4084087..4084773 Ruegeria pomeroyi DSS-3 3196308 YP_169060.1 CDS SPO3872 NC_003911.11 4084766 4087693 D identified by similarity to GB:AAM48721.1; hypothetical protein 4084766..4087693 Ruegeria pomeroyi DSS-3 3196216 YP_169061.1 CDS SPO3873 NC_003911.11 4087690 4091046 D identified by match to protein family HMM PF00580; ATP-dependent DNA helicase UvrD 4087690..4091046 Ruegeria pomeroyi DSS-3 3196426 YP_169062.1 CDS trx NC_003911.11 4091107 4091427 D identified by match to protein family HMM PF00085; match to protein family HMM TIGR01068; thioredoxin 4091107..4091427 Ruegeria pomeroyi DSS-3 3196264 YP_169063.1 CDS SPO3875 NC_003911.11 4091515 4091865 D hypothetical protein 4091515..4091865 Ruegeria pomeroyi DSS-3 3195091 YP_169064.1 CDS SPO3876 NC_003911.11 4091862 4092239 D identified by similarity to PIR:AB1999; match to protein family HMM TIGR02058; hypothetical protein 4091862..4092239 Ruegeria pomeroyi DSS-3 3196196 YP_169065.1 CDS SPO3877 NC_003911.11 4092256 4093149 D identified by similarity to GB:AAF69239.1; match to protein family HMM PF01022; match to protein family HMM PF01451; transcriptional regulator/arsenate reductase 4092256..4093149 Ruegeria pomeroyi DSS-3 3196225 YP_169066.1 CDS gap-4 NC_003911.11 4093183 4094181 D 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 4093183..4094181 Ruegeria pomeroyi DSS-3 3196231 YP_169067.1 CDS SPO3879 NC_003911.11 4094178 4095452 D hypothetical protein 4094178..4095452 Ruegeria pomeroyi DSS-3 3196219 YP_169068.1 CDS hslV NC_003911.11 4095915 4096472 D heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit 4095915..4096472 Ruegeria pomeroyi DSS-3 3196290 YP_169069.1 CDS SPO3881 NC_003911.11 4096634 4097023 R identified by match to protein family HMM TIGR01409; twin-arginine translocation pathway signal sequence domain-containing protein complement(4096634..4097023) Ruegeria pomeroyi DSS-3 3196226 YP_169070.1 CDS hslU NC_003911.11 4097215 4098522 D heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU 4097215..4098522 Ruegeria pomeroyi DSS-3 3196200 YP_169071.1 CDS SPO3883 NC_003911.11 4098555 4099658 D lipoprotein 4098555..4099658 Ruegeria pomeroyi DSS-3 3195833 YP_169072.1 CDS SPO3884 NC_003911.11 4099655 4100245 R identified by similarity to GB:AAM48726.1; match to protein family HMM PF01713; smr domain-containing protein complement(4099655..4100245) Ruegeria pomeroyi DSS-3 3196391 YP_169073.1 CDS SPO3885 NC_003911.11 4100245 4101285 R identified by match to protein family HMM PF03562; match to protein family HMM PF06725; MltA/3D domain-containing protein complement(4100245..4101285) Ruegeria pomeroyi DSS-3 3196446 YP_169074.1 CDS SPO3886 NC_003911.11 4101282 4101938 R identified by similarity to PIR:AG3508; match to protein family HMM PF04280; Tim44 family protein complement(4101282..4101938) Ruegeria pomeroyi DSS-3 3196097 YP_169075.1 CDS fxsA NC_003911.11 4102048 4102539 D identified by similarity to SP:P37147; match to protein family HMM PF04186; FxsA protein 4102048..4102539 Ruegeria pomeroyi DSS-3 3196299 YP_169076.1 CDS secB NC_003911.11 4102594 4103091 D 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 4102594..4103091 Ruegeria pomeroyi DSS-3 3196335 YP_169077.1 CDS dnaQ NC_003911.11 4103116 4103841 R 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 complement(4103116..4103841) Ruegeria pomeroyi DSS-3 3196237 YP_169078.1 CDS coaE NC_003911.11 4103834 4104427 R catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis; dephospho-CoA kinase complement(4103834..4104427) Ruegeria pomeroyi DSS-3 3196224 YP_169079.1 CDS aroE NC_003911.11 4104424 4105257 R AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase complement(4104424..4105257) Ruegeria pomeroyi DSS-3 3196139 YP_169080.1 CDS maf-1 NC_003911.11 4105254 4105853 R identified by similarity to SP:Q02169; match to protein family HMM PF02545; match to protein family HMM TIGR00172; hypothetical protein complement(4105254..4105853) Ruegeria pomeroyi DSS-3 3196330 YP_169081.1 CDS SPO3893 NC_003911.11 4106263 4106715 D identified by match to protein family HMM PF03653; hypothetical protein 4106263..4106715 Ruegeria pomeroyi DSS-3 3196311 YP_169082.1 CDS rho NC_003911.11 4106841 4108112 D An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 4106841..4108112 Ruegeria pomeroyi DSS-3 3196235 YP_169083.1 CDS trmE NC_003911.11 4108144 4109430 D 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 4108144..4109430 Ruegeria pomeroyi DSS-3 3196284 YP_164832.1 CDS SPOA0449 NC_006569.1 1 798 D identified by match to protein family HMM PF05721; phytanoyl-CoA dioxygenase 1..798 Ruegeria pomeroyi DSS-3 3196707 YP_164833.1 CDS SPOA0001 NC_006569.1 872 1777 R hypothetical protein complement(872..1777) Ruegeria pomeroyi DSS-3 3196814 YP_164834.1 CDS miaB NC_006569.1 1804 3192 D 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 1804..3192 Ruegeria pomeroyi DSS-3 3196777 YP_164835.1 CDS SPOA0003 NC_006569.1 3205 3774 R hypothetical protein complement(3205..3774) Ruegeria pomeroyi DSS-3 3196635 YP_164836.1 CDS SPOA0004 NC_006569.1 4026 4568 D identified by match to protein family HMM PF00691; OmpA family protein 4026..4568 Ruegeria pomeroyi DSS-3 3196638 YP_164837.1 CDS SPOA0005 NC_006569.1 4579 4872 D lipoprotein 4579..4872 Ruegeria pomeroyi DSS-3 3196660 YP_164838.1 CDS SPOA0006 NC_006569.1 5010 6020 D identified by match to protein family HMM PF02562; PhoH family protein 5010..6020 Ruegeria pomeroyi DSS-3 3196622 YP_164839.1 CDS SPOA0007 NC_006569.1 6034 6411 D hypothetical protein 6034..6411 Ruegeria pomeroyi DSS-3 3196604 YP_164840.1 CDS SPOA0008 NC_006569.1 6408 6905 D identified by similarity to SP:Q8YEA4; match to protein family HMM PF02130; match to protein family HMM TIGR00043; hypothetical protein 6408..6905 Ruegeria pomeroyi DSS-3 3196608 YP_164841.1 CDS SPOA0009 NC_006569.1 6939 7826 D identified by similarity to GB:AAC62436.1; match to protein family HMM PF00571; match to protein family HMM PF03471; hemolysin 6939..7826 Ruegeria pomeroyi DSS-3 3196596 YP_164842.1 CDS cutE NC_006569.1 7823 9340 D identified by match to protein family HMM PF00795; match to protein family HMM TIGR00546; apolipoprotein N-acyltransferase 7823..9340 Ruegeria pomeroyi DSS-3 3196719 YP_164843.1 CDS metK NC_006569.1 9429 10610 D methionine adenosyltransferase; catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 9429..10610 Ruegeria pomeroyi DSS-3 3196866 YP_164844.1 CDS SPOA0012 NC_006569.1 10680 11192 D identified by similarity to PIR:S70846; DNA topology modulation kinase FlaR 10680..11192 Ruegeria pomeroyi DSS-3 3196679 YP_164845.1 CDS SPOA0013 NC_006569.1 11344 12009 D identified by similarity to PIR:S61210; hypothetical protein 11344..12009 Ruegeria pomeroyi DSS-3 3196564 YP_164846.1 CDS trmB NC_006569.1 12070 12783 D 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 12070..12783 Ruegeria pomeroyi DSS-3 3196748 YP_164847.1 CDS aroA NC_006569.1 12930 14276 D catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase 12930..14276 Ruegeria pomeroyi DSS-3 3196800 YP_164848.1 CDS cmk NC_006569.1 14273 14890 D Catalyzes the formation of (d)CDP from ATP and (d)CMP; cytidylate kinase 14273..14890 Ruegeria pomeroyi DSS-3 3196828 YP_164849.1 CDS SPOA0018 NC_006569.1 14942 15421 R identified by similarity to PIR:E82434; match to protein family HMM PF04945; hypothetical protein complement(14942..15421) Ruegeria pomeroyi DSS-3 3196727 YP_164850.1 CDS SPOA0019 NC_006569.1 15573 16718 R hypothetical protein complement(15573..16718) Ruegeria pomeroyi DSS-3 3196767 YP_164851.1 CDS SPOA0020 NC_006569.1 16728 17900 R identified by similarity to GB:BAA31547.1; match to protein family HMM PF01168; alanine racemase complement(16728..17900) Ruegeria pomeroyi DSS-3 3196689 YP_164852.1 CDS SPOA0021 NC_006569.1 17893 19326 R identified by match to protein family HMM PF01565; match to protein family HMM TIGR01409; match to protein family HMM TIGR01679; oxidoreductase, FAD-binding complement(17893..19326) Ruegeria pomeroyi DSS-3 3196950 YP_164853.1 CDS SPOA0022 NC_006569.1 19323 19700 R identified by similarity to SP:P11732; match to protein family HMM PF00034; cytochrome c5 complement(19323..19700) Ruegeria pomeroyi DSS-3 3196815 YP_164854.1 CDS SPOA0023 NC_006569.1 19700 20356 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(19700..20356) Ruegeria pomeroyi DSS-3 3196853 YP_164855.1 CDS SPOA0024 NC_006569.1 20444 21244 R identified by similarity to SP:P42270; match to protein family HMM PF01689; 2-oxo-hepta-3-ene-1,7-dioic acid hydratase complement(20444..21244) Ruegeria pomeroyi DSS-3 3196870 YP_164856.1 CDS SPOA0025 NC_006569.1 21241 22092 R identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase family protein complement(21241..22092) Ruegeria pomeroyi DSS-3 3196817 YP_164857.1 CDS hpcB NC_006569.1 22119 22970 R identified by similarity to SP:Q05353; similarity to GB:CAB65144.1; match to protein family HMM PF02900; 3,4-dihydroxyphenylacetate 2,3-dioxygenase complement(22119..22970) Ruegeria pomeroyi DSS-3 3196605 YP_164858.1 CDS hpcC NC_006569.1 23017 24525 R identified by similarity to SP:P42269; match to protein family HMM PF00171; 5-carboxy-2-hydroxymuconate semialdehyde dehydrogenase complement(23017..24525) Ruegeria pomeroyi DSS-3 3196851 YP_164859.1 CDS nqrA NC_006569.1 24898 26241 D 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 24898..26241 Ruegeria pomeroyi DSS-3 3196751 YP_164860.1 CDS nqrB NC_006569.1 26246 27454 D 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 26246..27454 Ruegeria pomeroyi DSS-3 3196730 YP_164861.1 CDS nqrC NC_006569.1 27447 28250 D 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 27447..28250 Ruegeria pomeroyi DSS-3 3196648 YP_164862.1 CDS nqrD NC_006569.1 28250 28903 D 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 28250..28903 Ruegeria pomeroyi DSS-3 3196881 YP_164863.1 CDS nqrE NC_006569.1 28903 29511 D 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 28903..29511 Ruegeria pomeroyi DSS-3 3196744 YP_164864.1 CDS nqrF NC_006569.1 29524 30744 D 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 29524..30744 Ruegeria pomeroyi DSS-3 3196865 YP_164865.1 CDS SPOA0034 NC_006569.1 30859 31383 R identified by match to protein family HMM PF00571; CBS domain-containing protein complement(30859..31383) Ruegeria pomeroyi DSS-3 3196778 YP_164866.1 CDS SPOA0035 NC_006569.1 31290 31679 D hypothetical protein 31290..31679 Ruegeria pomeroyi DSS-3 3196684 YP_164867.1 CDS apbE NC_006569.1 31686 32771 D identified by similarity to SP:P41780; match to protein family HMM PF02424; thiamin biosynthesis lipoprotein ApbE 31686..32771 Ruegeria pomeroyi DSS-3 3196871 YP_164868.1 CDS SPOA0037 NC_006569.1 32792 33028 D identified by similarity to GB:BAC95347.1; hypothetical protein 32792..33028 Ruegeria pomeroyi DSS-3 3196598 YP_164869.1 CDS SPOA0038 NC_006569.1 33041 34216 R identified by match to protein family HMM PF00196; LuxR family transcriptional regulator complement(33041..34216) Ruegeria pomeroyi DSS-3 3196625 YP_164870.1 CDS SPOA0039 NC_006569.1 34623 36542 D identified by similarity to PIR:A83386; hypothetical protein 34623..36542 Ruegeria pomeroyi DSS-3 3196726 YP_164871.1 CDS SPOA0040 NC_006569.1 36767 37060 R identified by match to protein family HMM PF02537; crcB family protein complement(36767..37060) Ruegeria pomeroyi DSS-3 3196789 YP_164872.1 CDS SPOA0041 NC_006569.1 37126 37506 R identified by match to protein family HMM PF02537; crcB family protein complement(37126..37506) Ruegeria pomeroyi DSS-3 3196787 YP_164873.1 CDS SPOA0042 NC_006569.1 37538 38389 R identified by similarity to GB:AAR21632.1; match to protein family HMM PF05853; hypothetical protein complement(37538..38389) Ruegeria pomeroyi DSS-3 3196918 YP_164874.1 CDS pcaG NC_006569.1 38404 39024 R identified by similarity to GB:AAR21645.1; match to protein family HMM PF00775; protocatechuate 3,4-dioxygenase alpha subunit complement(38404..39024) Ruegeria pomeroyi DSS-3 3196595 YP_164875.1 CDS pcaH NC_006569.1 39088 39816 R identified by similarity to GB:AAR21644.1; match to protein family HMM PF00775; protocatechuate 3,4-dioxygenase subunit beta complement(39088..39816) Ruegeria pomeroyi DSS-3 3196582 YP_164876.1 CDS pcaC NC_006569.1 39861 40238 R identified by similarity to SP:P20370; match to protein family HMM PF02627; 4-carboxymuconolactone decarboxylase complement(39861..40238) Ruegeria pomeroyi DSS-3 3196569 YP_164877.1 CDS pobA NC_006569.1 40261 41430 R catalyzes the formation of protocatechuate from 4-hydroxybenzoate; 4-hydroxybenzoate 3-monooxygenase complement(40261..41430) Ruegeria pomeroyi DSS-3 3196949 YP_164878.1 CDS pcaQ NC_006569.1 41523 42440 D identified by similarity to GB:AAR21641.1; match to protein family HMM PF00126; match to protein family HMM PF03466; pca operon transcriptional activator PcaQ 41523..42440 Ruegeria pomeroyi DSS-3 3196915 YP_164879.1 CDS SPOA0048 NC_006569.1 42513 42911 D hypothetical protein 42513..42911 Ruegeria pomeroyi DSS-3 3196690 YP_164880.1 CDS nosR NC_006569.1 42905 45076 D identified by similarity to SP:Q00790; match to protein family HMM PF04205; nitrous-oxide reductase transcriptional activator NosR 42905..45076 Ruegeria pomeroyi DSS-3 3196718 YP_164881.1 CDS nosZ NC_006569.1 45091 46998 D reduces nitrous oxide to nitrogen; nitrous-oxide reductase 45091..46998 Ruegeria pomeroyi DSS-3 3196583 YP_164882.1 CDS nosD NC_006569.1 47002 48258 D identified by similarity to SP:P19843; match to protein family HMM PF05048; nitrous oxide maturation protein NosD 47002..48258 Ruegeria pomeroyi DSS-3 3196929 YP_164883.1 CDS nosF NC_006569.1 48248 49141 D identified by similarity to SP:P19844; match to protein family HMM PF00005; match to protein family HMM TIGR01189; ABC transporter, ATP-binding protein NosF 48248..49141 Ruegeria pomeroyi DSS-3 3196607 YP_164884.1 CDS nosY NC_006569.1 49138 49959 D identified by similarity to SP:P19845; nitrous oxide maturation protein NosY 49138..49959 Ruegeria pomeroyi DSS-3 3196785 YP_164885.1 CDS nosL NC_006569.1 49956 50477 D identified by similarity to GB:AAD43477.1; match to protein family HMM PF05573; nitrous oxide reductase accessory protein 49956..50477 Ruegeria pomeroyi DSS-3 3196944 YP_164886.1 CDS SPOA0055 NC_006569.1 50513 50890 D identified by match to protein family HMM PF00034; cytochrome c family protein 50513..50890 Ruegeria pomeroyi DSS-3 3196611 YP_164887.1 CDS SPOA0056 NC_006569.1 50922 51536 R identified by match to protein family HMM PF01381; DNA-binding protein complement(50922..51536) Ruegeria pomeroyi DSS-3 3196902 YP_164888.1 CDS gcvT NC_006569.1 51916 53013 D identified by match to protein family HMM PF01571; match to protein family HMM TIGR00528; glycine cleavage system T protein 51916..53013 Ruegeria pomeroyi DSS-3 3196668 YP_164889.1 CDS gcvH-2 NC_006569.1 53059 53499 D 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 53059..53499 Ruegeria pomeroyi DSS-3 3196781 YP_164890.1 CDS gcvP NC_006569.1 53556 56414 D acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase 53556..56414 Ruegeria pomeroyi DSS-3 3196586 YP_164891.1 CDS SPOA0060 NC_006569.1 56564 57430 D identified by match to protein family HMM PF00165; AraC family transcriptional regulator 56564..57430 Ruegeria pomeroyi DSS-3 3196662 YP_164892.1 CDS katG NC_006569.1 57490 59685 R identified by match to protein family HMM PF00141; match to protein family HMM TIGR00198; catalase/peroxidase HPI complement(57490..59685) Ruegeria pomeroyi DSS-3 3196563 YP_164893.1 CDS SPOA0062 NC_006569.1 59846 60544 R identified by similarity to PIR:T08467; match to protein family HMM PF01177; match to protein family HMM TIGR00035; aspartate racemase complement(59846..60544) Ruegeria pomeroyi DSS-3 3196691 YP_164894.1 CDS SPOA0063 NC_006569.1 60657 63092 R identified by match to protein family HMM PF01266; match to protein family HMM PF01571; FAD-dependent oxidoreductase complement(60657..63092) Ruegeria pomeroyi DSS-3 3196774 YP_164895.1 CDS SPOA0064 NC_006569.1 63234 64016 R identified by similarity to SP:O08557; match to protein family HMM PF02274; NG,NG-dimethylarginine dimethylaminohydrolase complement(63234..64016) Ruegeria pomeroyi DSS-3 3196641 YP_164896.1 CDS SPOA0065 NC_006569.1 64023 65624 R identified by match to protein family HMM PF00205; match to protein family HMM PF02776; hypothetical protein complement(64023..65624) Ruegeria pomeroyi DSS-3 3196906 YP_164897.1 CDS SPOA0066 NC_006569.1 65624 66811 R identified by similarity to SP:P23034; match to protein family HMM PF00155; aspartate aminotransferase complement(65624..66811) Ruegeria pomeroyi DSS-3 3196573 YP_164898.1 CDS SPOA0067 NC_006569.1 66808 67455 R identified by match to protein family HMM PF00440; TetR family transcriptional regulator complement(66808..67455) Ruegeria pomeroyi DSS-3 3196941 YP_164899.1 CDS SPOA0068 NC_006569.1 67577 68377 D identified by similarity to SP:P07109; match to protein family HMM PF00005; polar amino acid ABC transporter ATP-binding protein 67577..68377 Ruegeria pomeroyi DSS-3 3196714 YP_164900.1 CDS SPOA0069 NC_006569.1 68410 69180 D 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 68410..69180 Ruegeria pomeroyi DSS-3 3196623 YP_164901.1 CDS SPOA0070 NC_006569.1 69190 69942 D identified by similarity to PIR:T44455; match to protein family HMM PF00528; match to protein family HMM TIGR01726; polar amino acid ABC transporter permease 69190..69942 Ruegeria pomeroyi DSS-3 3196701 YP_164902.1 CDS SPOA0071 NC_006569.1 69939 70727 D 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 69939..70727 Ruegeria pomeroyi DSS-3 3196695 YP_164903.1 CDS SPOA0072 NC_006569.1 70800 71285 D identified by similarity to SP:Q8YF58; hypothetical protein 70800..71285 Ruegeria pomeroyi DSS-3 3196659 YP_164904.1 CDS arsC-2 NC_006569.1 71286 71747 D identified by similarity to SP:Q01257; match to protein family HMM PF01451; arsenate reductase 71286..71747 Ruegeria pomeroyi DSS-3 3196649 YP_164905.1 CDS SPOA0074 NC_006569.1 71744 72142 D identified by similarity to PIR:C97388; match to protein family HMM TIGR02096; hypothetical protein 71744..72142 Ruegeria pomeroyi DSS-3 3196712 YP_164906.1 CDS SPOA0075 NC_006569.1 72135 72728 D identified by similarity to PIR:B97388; hypothetical protein 72135..72728 Ruegeria pomeroyi DSS-3 3196585 YP_164907.1 CDS SPOA0076 NC_006569.1 72753 73649 D identified by match to protein family HMM PF00795; carbon-nitrogen family hydrolase 72753..73649 Ruegeria pomeroyi DSS-3 3196934 YP_164908.1 CDS infA NC_006569.1 73720 73938 D stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 73720..73938 Ruegeria pomeroyi DSS-3 3196692 YP_164909.1 CDS maf-2 NC_006569.1 73949 74527 D identified by match to protein family HMM PF02545; match to protein family HMM TIGR00172; maf protein 73949..74527 Ruegeria pomeroyi DSS-3 3196780 YP_164910.1 CDS SPOA0079 NC_006569.1 74524 75546 D identified by similarity to GB:AAQ00701.1; ribonuclease 74524..75546 Ruegeria pomeroyi DSS-3 3196772 YP_164911.1 CDS SPOA0450 NC_006569.1 75543 75725 D identified by similarity to SP:Q9A5V7; match to protein family HMM PF03884; hypothetical protein 75543..75725 Ruegeria pomeroyi DSS-3 3196592 YP_164912.1 CDS SPOA0081 NC_006569.1 76107 77432 R hypothetical protein complement(76107..77432) Ruegeria pomeroyi DSS-3 3196710 YP_164913.1 CDS SPOA0082 NC_006569.1 77422 79263 R identified by similarity to GB:BAC49897.1; hypothetical protein complement(77422..79263) Ruegeria pomeroyi DSS-3 3196921 YP_164914.1 CDS SPOA0083 NC_006569.1 79377 80480 R hypothetical protein complement(79377..80480) Ruegeria pomeroyi DSS-3 3196942 YP_164915.1 CDS SPOA0084 NC_006569.1 80695 80895 R hypothetical protein complement(80695..80895) Ruegeria pomeroyi DSS-3 3196737 YP_164916.1 CDS SPOA0085 NC_006569.1 80961 81179 R identified by match to protein family HMM PF01381; DNA-binding protein complement(80961..81179) Ruegeria pomeroyi DSS-3 3196882 YP_164917.1 CDS SPOA0086 NC_006569.1 82940 84751 R hypothetical protein complement(82940..84751) Ruegeria pomeroyi DSS-3 3196678 YP_164918.1 CDS SPOA0087 NC_006569.1 85721 86923 R identified by match to protein family HMM PF00589; phage integrase family site specific recombinase complement(85721..86923) Ruegeria pomeroyi DSS-3 3196650 YP_164919.1 CDS SPOA0088 NC_006569.1 87709 90012 D hypothetical protein 87709..90012 Ruegeria pomeroyi DSS-3 3196574 YP_164920.1 CDS SPOA0089 NC_006569.1 90607 91137 D hypothetical protein 90607..91137 Ruegeria pomeroyi DSS-3 3196549 YP_164921.1 CDS SPOA0090 NC_006569.1 91354 91923 D identified by match to protein family HMM PF01609; ISSpo7, transposase 91354..91923 Ruegeria pomeroyi DSS-3 3196568 YP_164922.1 CDS SPOA0091 NC_006569.1 92045 92353 R identified by similarity to GB:AAR36473.1; IS3 family transposase orfA complement(92045..92353) Ruegeria pomeroyi DSS-3 3196951 YP_164923.1 CDS SPOA0093 NC_006569.1 93195 94682 D identified by match to protein family HMM PF01565; FAD binding domain-containing protein 93195..94682 Ruegeria pomeroyi DSS-3 3196873 YP_164924.1 CDS SPOA0094 NC_006569.1 94679 95089 D hypothetical protein 94679..95089 Ruegeria pomeroyi DSS-3 3196922 YP_164925.1 CDS SPOA0095 NC_006569.1 95089 96138 D identified by similarity to GB:BAB49700.1; hypothetical protein 95089..96138 Ruegeria pomeroyi DSS-3 3196614 YP_164926.1 CDS SPOA0096 NC_006569.1 96657 97691 R identified by match to protein family HMM PF00850; histone deacetylase/AcuC/AphA family protein complement(96657..97691) Ruegeria pomeroyi DSS-3 3196911 YP_164927.1 CDS SPOA0097 NC_006569.1 97765 98703 R identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter, permease protein complement(97765..98703) Ruegeria pomeroyi DSS-3 3196847 YP_164928.1 CDS SPOA0098 NC_006569.1 98700 99569 R identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter, permease protein complement(98700..99569) Ruegeria pomeroyi DSS-3 3196925 YP_164929.1 CDS SPOA0099 NC_006569.1 99566 100270 R identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter, ATP-binding protein complement(99566..100270) Ruegeria pomeroyi DSS-3 3196658 YP_164930.1 CDS SPOA0100 NC_006569.1 100267 100980 R identified by match to protein family HMM PF00005; branched-chain amino acid ABC transporter, ATP-binding protein complement(100267..100980) Ruegeria pomeroyi DSS-3 3196750 YP_164931.1 CDS SPOA0101 NC_006569.1 100984 102264 R 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 complement(100984..102264) Ruegeria pomeroyi DSS-3 3196688 YP_164932.1 CDS SPOA0102 NC_006569.1 102382 103350 R identified by match to protein family HMM PF00196; LuxR family transcriptional regulator complement(102382..103350) Ruegeria pomeroyi DSS-3 3196685 YP_164933.1 CDS SPOA0103 NC_006569.1 103368 103862 D identified by similarity to GB:BAB49373.1; hypothetical protein 103368..103862 Ruegeria pomeroyi DSS-3 3196791 YP_164934.1 CDS SPOA0104 NC_006569.1 103895 105283 D identified by match to protein family HMM PF00171; aldehyde dehydrogenase 103895..105283 Ruegeria pomeroyi DSS-3 3196796 YP_164935.1 CDS SPOA0105 NC_006569.1 105320 105694 R identified by match to protein family HMM PF01638; transcriptional regulator complement(105320..105694) Ruegeria pomeroyi DSS-3 3196909 YP_164936.1 CDS SPOA0106 NC_006569.1 105811 106644 D identified by similarity to PIR:E95217; hypothetical protein 105811..106644 Ruegeria pomeroyi DSS-3 3196698 YP_164937.1 CDS SPOA0107 NC_006569.1 107348 108241 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(107348..108241) Ruegeria pomeroyi DSS-3 3196832 YP_164938.1 CDS SPOA0108 NC_006569.1 108335 109549 D hypothetical protein 108335..109549 Ruegeria pomeroyi DSS-3 3196809 YP_164939.1 CDS SPOA0451 NC_006569.1 110630 111106 R identified by similarity to SP:P55740; match to protein family HMM PF01047; MarR family transcriptional regulator complement(110630..111106) Ruegeria pomeroyi DSS-3 3196639 YP_164940.1 CDS SPOA0452 NC_006569.1 111099 111572 R identified by similarity to GB:BAC48674.1; match to protein family HMM PF01047; MarR family transcriptional regulator complement(111099..111572) Ruegeria pomeroyi DSS-3 3196734 YP_164941.1 CDS SPOA0109 NC_006569.1 111593 112039 R identified by match to protein family HMM PF03061; match to protein family HMM TIGR00051; hypothetical protein complement(111593..112039) Ruegeria pomeroyi DSS-3 3196935 YP_164942.1 CDS SPOA0110 NC_006569.1 112090 113661 R 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 complement(112090..113661) Ruegeria pomeroyi DSS-3 3196640 YP_164943.1 CDS SPOA0111 NC_006569.1 113658 115832 R identified by similarity to SP:O07835; match to protein family HMM PF02775; indolepyruvate oxidoreductase, IorA subunit complement(113658..115832) Ruegeria pomeroyi DSS-3 3196838 YP_164944.1 CDS feaB NC_006569.1 115948 117462 D identified by similarity to SP:P80668; match to protein family HMM PF00171; phenylacetaldehyde dehydrogenase 115948..117462 Ruegeria pomeroyi DSS-3 3196562 YP_164945.1 CDS SPOA0113 NC_006569.1 117468 118856 D identified by match to protein family HMM PF00202; hypothetical protein 117468..118856 Ruegeria pomeroyi DSS-3 3196657 YP_164946.1 CDS SPOA0114 NC_006569.1 118859 119893 D identified by match to protein family HMM PF00795; nitrilase family protein 118859..119893 Ruegeria pomeroyi DSS-3 3196627 YP_164947.1 CDS gtdA-2 NC_006569.1 119912 121036 D identified by similarity to GB:CAA12267.1; gentisate 1,2-dioxygenase 119912..121036 Ruegeria pomeroyi DSS-3 3196910 YP_164948.1 CDS SPOA0116 NC_006569.1 121054 121971 D identified by match to protein family HMM PF01557; fumarylacetoacetate hydrolase family protein 121054..121971 Ruegeria pomeroyi DSS-3 3196603 YP_164949.1 CDS SPOA0117 NC_006569.1 121973 122749 D identified by match to protein family HMM PF01177; Asp/Glu/hydantoin racemase family protein 121973..122749 Ruegeria pomeroyi DSS-3 3196724 YP_164950.1 CDS SPOA0118 NC_006569.1 122787 123326 D hypothetical protein 122787..123326 Ruegeria pomeroyi DSS-3 3196618 YP_164951.1 CDS SPOA0119 NC_006569.1 123338 124879 D identified by match to protein family HMM PF01970; hypothetical protein 123338..124879 Ruegeria pomeroyi DSS-3 3196671 YP_164952.1 CDS SPOA0120 NC_006569.1 125015 125953 D identified by similarity to GB:BAC94333.1; match to protein family HMM PF03401; hypothetical protein 125015..125953 Ruegeria pomeroyi DSS-3 3196565 YP_164953.1 CDS SPOA0121 NC_006569.1 126010 127668 D identified by match to protein family HMM PF00884; sulfatase family protein 126010..127668 Ruegeria pomeroyi DSS-3 3196629 YP_164954.1 CDS SPOA0122 NC_006569.1 128113 129045 R identified by match to protein family HMM PF01609; ISSpo9, transposase complement(128113..129045) Ruegeria pomeroyi DSS-3 3196681 YP_164955.1 CDS SPOA0123 NC_006569.1 129275 132235 D identified by similarity to GB:AAQ60231.1; hypothetical protein 129275..132235 Ruegeria pomeroyi DSS-3 3196837 YP_164956.1 CDS SPOA0124 NC_006569.1 132272 135232 D identified by similarity to PIR:A82083; hypothetical protein 132272..135232 Ruegeria pomeroyi DSS-3 3196899 YP_164957.1 CDS SPOA0125 NC_006569.1 135246 136139 D hypothetical protein 135246..136139 Ruegeria pomeroyi DSS-3 3196852 YP_164958.1 CDS SPOA0126 NC_006569.1 136399 137124 R identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase family oxidoreductase complement(136399..137124) Ruegeria pomeroyi DSS-3 3196762 YP_164959.1 CDS SPOA0127 NC_006569.1 137121 137912 R identified by match to protein family HMM PF04199; cyclase complement(137121..137912) Ruegeria pomeroyi DSS-3 3196636 YP_164960.1 CDS SPOA0128 NC_006569.1 137909 139147 R identified by match to protein family HMM PF00106; match to protein family HMM PF01796; short chain dehydrogenase/reductase family oxidoreductase complement(137909..139147) Ruegeria pomeroyi DSS-3 3196947 YP_164961.1 CDS SPOA0129 NC_006569.1 139144 140319 R hypothetical protein complement(139144..140319) Ruegeria pomeroyi DSS-3 3196928 YP_164962.1 CDS SPOA0130 NC_006569.1 140319 141938 R identified by match to protein family HMM PF00501; AMP-binding protein complement(140319..141938) Ruegeria pomeroyi DSS-3 3196889 YP_164963.1 CDS SPOA0131 NC_006569.1 141940 142413 R identified by match to protein family HMM PF00866; aromatic 1,2-dioxygenase, beta subunit complement(141940..142413) Ruegeria pomeroyi DSS-3 3196891 YP_164964.1 CDS SPOA0132 NC_006569.1 142410 143750 R identified by match to protein family HMM PF00355; match to protein family HMM PF00848; aromatic 1,2-dioxygenase, alpha subunit complement(142410..143750) Ruegeria pomeroyi DSS-3 3196890 YP_164965.1 CDS SPOA0133 NC_006569.1 143773 144717 R identified by match to protein family HMM PF00111; match to protein family HMM PF00175; match to protein family HMM PF00970; oxidoreductase complement(143773..144717) Ruegeria pomeroyi DSS-3 3196936 YP_164966.1 CDS SPOA0134 NC_006569.1 145949 146518 D identified by match to protein family HMM PF01609; ISSpo7, transposase 145949..146518 Ruegeria pomeroyi DSS-3 3196888 YP_164967.1 CDS SPOA0136 NC_006569.1 147504 147659 D hypothetical protein 147504..147659 Ruegeria pomeroyi DSS-3 3196930 YP_164968.1 CDS murA NC_006569.1 147666 148931 D 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 147666..148931 Ruegeria pomeroyi DSS-3 3196760 YP_164969.1 CDS SPOA0138 NC_006569.1 148931 149407 D identified by similarity to GB:AAK24320.1; hypothetical protein 148931..149407 Ruegeria pomeroyi DSS-3 3196557 YP_164970.1 CDS SPOA0139 NC_006569.1 149467 149946 D identified by match to protein family HMM PF00583; acetyltransferase 149467..149946 Ruegeria pomeroyi DSS-3 3196725 YP_164971.1 CDS glmS NC_006569.1 149971 151794 R 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) complement(149971..151794) Ruegeria pomeroyi DSS-3 3196567 YP_164972.1 CDS SPOA0141 NC_006569.1 152200 152550 D identified by similarity to PIR:C95361; hypothetical protein 152200..152550 Ruegeria pomeroyi DSS-3 3196907 YP_164973.1 CDS SPOA0142 NC_006569.1 152550 153062 D identified by similarity to GB:BAB54840.1; hypothetical protein 152550..153062 Ruegeria pomeroyi DSS-3 3196676 YP_164974.1 CDS SPOA0143 NC_006569.1 153574 154419 R identified by match to protein family HMM PF01614; IclR family transcriptional regulator complement(153574..154419) Ruegeria pomeroyi DSS-3 3196752 YP_164975.1 CDS SPOA0144 NC_006569.1 154606 155796 D identified by similarity to SP:O08374; match to protein family HMM PF00266; serine--glyoxylate transaminase 154606..155796 Ruegeria pomeroyi DSS-3 3196833 YP_164976.1 CDS SPOA0145 NC_006569.1 155809 156762 D identified by match to protein family HMM PF00291; pyridoxal-phosphate dependent enzyme 155809..156762 Ruegeria pomeroyi DSS-3 3196610 YP_164977.1 CDS SPOA0146 NC_006569.1 156768 157931 D identified by similarity to GB:BAA31547.1; match to protein family HMM PF01168; threonine aldolase 156768..157931 Ruegeria pomeroyi DSS-3 3196834 YP_164978.1 CDS SPOA0147 NC_006569.1 158076 158954 D identified by match to protein family HMM PF02423; ornithine cyclodeaminase/mu-crystallin family protein 158076..158954 Ruegeria pomeroyi DSS-3 3196758 YP_164979.1 CDS SPOA0148 NC_006569.1 159056 160213 R identified by similarity to SP:P43531; major facilitator transporter complement(159056..160213) Ruegeria pomeroyi DSS-3 3196682 YP_164980.1 CDS SPOA0149 NC_006569.1 160318 161634 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 160318..161634 Ruegeria pomeroyi DSS-3 3196620 YP_164981.1 CDS SPOA0150 NC_006569.1 161659 162696 R identified by match to protein family HMM PF00165; AraC family transcriptional regulator complement(161659..162696) Ruegeria pomeroyi DSS-3 3196666 YP_164982.1 CDS SPOA0151 NC_006569.1 162796 163413 D identified by match to protein family HMM PF00034; cytochrome c family protein 162796..163413 Ruegeria pomeroyi DSS-3 3196644 YP_164983.1 CDS SPOA0152 NC_006569.1 163457 164533 D identified by match to protein family HMM PF03150; di-haem cytochrome c peroxidase family protein 163457..164533 Ruegeria pomeroyi DSS-3 3196708 YP_164984.1 CDS SPOA0153 NC_006569.1 164552 165628 D hypothetical protein 164552..165628 Ruegeria pomeroyi DSS-3 3196643 YP_164985.1 CDS SPOA0154 NC_006569.1 165646 167022 D hypothetical protein 165646..167022 Ruegeria pomeroyi DSS-3 3196572 YP_164986.1 CDS SPOA0155 NC_006569.1 167176 171612 R identified by match to protein family HMM PF00092; match to protein family HMM PF00353; type I secretion target repeat-containing protein complement(167176..171612) Ruegeria pomeroyi DSS-3 3196807 YP_164987.1 CDS SPOA0156 NC_006569.1 171697 172530 R hypothetical protein complement(171697..172530) Ruegeria pomeroyi DSS-3 3196913 YP_164988.1 CDS SPOA0157 NC_006569.1 172937 173923 R nducibly transcribed; Denger et al. Biochem. J. (2006) 394:657-664; sulfite exporter, CuyZ complement(172937..173923) Ruegeria pomeroyi DSS-3 3196878 YP_164989.1 CDS cuyA NC_006569.1 173964 174983 R Catalyzes the desulfonation of L-cysteate to sulfite, ammonium ion and pyruvate.; L-cysteate sulfo-lyase complement(173964..174983) Ruegeria pomeroyi DSS-3 3196642 YP_164990.1 CDS cuyR NC_006569.1 175095 175997 D 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 175095..175997 Ruegeria pomeroyi DSS-3 3196606 YP_164991.1 CDS SPOA0160 NC_006569.1 176064 177386 R identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter, DctM subunit complement(176064..177386) Ruegeria pomeroyi DSS-3 3196665 YP_164992.1 CDS SPOA0161 NC_006569.1 177386 177877 R identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit complement(177386..177877) Ruegeria pomeroyi DSS-3 3196843 YP_164993.1 CDS SPOA0162 NC_006569.1 177943 178977 R identified by match to protein family HMM PF03480; match to protein family HMM TIGR01409; TRAP dicarboxylate family transporter DctP subunit complement(177943..178977) Ruegeria pomeroyi DSS-3 3196844 YP_164994.1 CDS mvaA NC_006569.1 179002 180303 R identified by similarity to SP:P13702; match to protein family HMM PF00368; match to protein family HMM TIGR00532; hydroxymethylglutaryl-CoA reductase, degradative complement(179002..180303) Ruegeria pomeroyi DSS-3 3196619 YP_164995.1 CDS SPOA0164 NC_006569.1 180424 181809 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 180424..181809 Ruegeria pomeroyi DSS-3 3196634 YP_164996.1 CDS SPOA0165 NC_006569.1 181865 182800 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(181865..182800) Ruegeria pomeroyi DSS-3 3196587 YP_164997.1 CDS SPOA0166 NC_006569.1 182941 183951 D identified by similarity to SP:P12920; match to protein family HMM TIGR02122; TRAP transporter solute receptor TAXI family protein 182941..183951 Ruegeria pomeroyi DSS-3 3196761 YP_164998.1 CDS SPOA0167 NC_006569.1 184036 186249 D identified by match to protein family HMM PF06808; match to protein family HMM TIGR02123; TRAP transporter, 4TM/12TM fusion protein 184036..186249 Ruegeria pomeroyi DSS-3 3196555 YP_164999.1 CDS SPOA0168 NC_006569.1 186254 187519 D identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding 186254..187519 Ruegeria pomeroyi DSS-3 3196816 YP_165000.1 CDS SPOA0169 NC_006569.1 187676 188389 R identified by match to protein family HMM PF03473; MOSC domain-containing protein complement(187676..188389) Ruegeria pomeroyi DSS-3 3196670 YP_165001.1 CDS SPOA0170 NC_006569.1 188365 188907 R identified by match to protein family HMM PF01047; MarR family transcriptional regulator complement(188365..188907) Ruegeria pomeroyi DSS-3 3196876 YP_165002.1 CDS SPOA0171 NC_006569.1 188994 189755 D identified by similarity to GB:BAC91536.1; hypothetical protein 188994..189755 Ruegeria pomeroyi DSS-3 3196783 YP_165003.1 CDS SPOA0172 NC_006569.1 189812 190042 D identified by similarity to GB:BAC91595.1; hypothetical protein 189812..190042 Ruegeria pomeroyi DSS-3 3196848 YP_165004.1 CDS SPOA0173 NC_006569.1 190045 190572 D identified by similarity to GB:CAD84048.1; hypothetical protein 190045..190572 Ruegeria pomeroyi DSS-3 3196581 YP_165005.1 CDS SPOA0174 NC_006569.1 190647 191114 D identified by match to protein family HMM PF03473; MOSC domain-containing protein 190647..191114 Ruegeria pomeroyi DSS-3 3196877 YP_165006.1 CDS SPOA0175 NC_006569.1 191127 192059 D identified by match to protein family HMM PF00111; match to protein family HMM PF00175; match to protein family HMM PF00970; oxidoreductase 191127..192059 Ruegeria pomeroyi DSS-3 3196702 YP_165007.1 CDS SPOA0176 NC_006569.1 192016 192447 D identified by similarity to GB:AAM38898.1; hypothetical protein 192016..192447 Ruegeria pomeroyi DSS-3 3196561 YP_165008.1 CDS SPOA0177 NC_006569.1 192528 193220 R identified by similarity to SP:P11721; match to protein family HMM PF00126; match to protein family HMM PF03466; hydrogen peroxide-inducible genes activator complement(192528..193220) Ruegeria pomeroyi DSS-3 3196842 YP_165009.1 CDS SPOA0180 NC_006569.1 194488 194853 R identified by match to protein family HMM PF00034; cytochrome c family protein complement(194488..194853) Ruegeria pomeroyi DSS-3 3196723 YP_165010.1 CDS SPOA0181 NC_006569.1 194918 195736 R identified by match to protein family HMM PF01226; FNT family protein complement(194918..195736) Ruegeria pomeroyi DSS-3 3196860 YP_165011.1 CDS SPOA0182 NC_006569.1 195733 196302 R hypothetical protein complement(195733..196302) Ruegeria pomeroyi DSS-3 3196943 YP_165012.1 CDS SPOA0183 NC_006569.1 196299 196898 R identified by match to protein family HMM PF02630; SCO1/SenC family protein complement(196299..196898) Ruegeria pomeroyi DSS-3 3196655 YP_165013.1 CDS SPOA0184 NC_006569.1 196898 198328 R identified by similarity to SP:P33518; match to protein family HMM PF00115; heme-copper respiratory oxidase family complement(196898..198328) Ruegeria pomeroyi DSS-3 3196673 YP_165014.1 CDS SPOA0185 NC_006569.1 198329 198838 R identified by similarity to SP:P98052; cytochrome c oxidase,ba3-type, subunit I complement(198329..198838) Ruegeria pomeroyi DSS-3 3196939 YP_165015.1 CDS SPOA0186 NC_006569.1 198944 199426 D identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738; Rrf2 family protein 198944..199426 Ruegeria pomeroyi DSS-3 3196952 YP_165016.1 CDS ccoP-2 NC_006569.1 199725 200597 R 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 complement(199725..200597) Ruegeria pomeroyi DSS-3 3196575 YP_165017.1 CDS ccoQ-2 NC_006569.1 200588 200755 R identified by similarity to GB:AAM76066.1; match to protein family HMM PF05545; cytochrome c oxidase, cbb3-type, subunit IV complement(200588..200755) Ruegeria pomeroyi DSS-3 3196872 YP_165018.1 CDS ccoO-2 NC_006569.1 200752 201483 R identified by match to protein family HMM PF02433; match to protein family HMM TIGR00781; cytochrome c oxidase, cbb3-type, subunit II complement(200752..201483) Ruegeria pomeroyi DSS-3 3196813 YP_165019.1 CDS ccoN-2 NC_006569.1 201488 203110 R 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 complement(201488..203110) Ruegeria pomeroyi DSS-3 3196716 YP_165020.1 CDS SPOA0191 NC_006569.1 203113 203904 R hypothetical protein complement(203113..203904) Ruegeria pomeroyi DSS-3 3196917 YP_165021.1 CDS SPOA0192 NC_006569.1 203945 204364 R hypothetical protein complement(203945..204364) Ruegeria pomeroyi DSS-3 3196940 YP_165022.1 CDS cycJ NC_006569.1 204477 204896 R 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 complement(204477..204896) Ruegeria pomeroyi DSS-3 3196798 YP_165023.1 CDS hemA-2 NC_006569.1 204899 206140 R catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase complement(204899..206140) Ruegeria pomeroyi DSS-3 3196856 YP_165024.1 CDS SPOA0195 NC_006569.1 206169 207119 R identified by similarity to GB:AAM30460.1; hypothetical protein complement(206169..207119) Ruegeria pomeroyi DSS-3 3196818 YP_165025.1 CDS cycL NC_006569.1 207119 207571 R identified by similarity to SP:P45406; match to protein family HMM PF03918; cytochrome c-type biogenesis protein CycL complement(207119..207571) Ruegeria pomeroyi DSS-3 3196924 YP_165026.1 CDS dsbE NC_006569.1 207568 208134 R identified by similarity to SP:P33926; match to protein family HMM TIGR00385; thiol:disulfide interchange protein DsbE complement(207568..208134) Ruegeria pomeroyi DSS-3 3196879 YP_165027.1 CDS cycK NC_006569.1 208131 210131 R identified by similarity to SP:Q00500; match to protein family HMM PF01578; cytochrome c-type biogenesis protein CycK complement(208131..210131) Ruegeria pomeroyi DSS-3 3196775 YP_165028.1 CDS SPOA0199 NC_006569.1 210138 211616 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(210138..211616) Ruegeria pomeroyi DSS-3 3196894 YP_165029.1 CDS SPOA0200 NC_006569.1 211718 212725 R identified by similarity to GB:CAD86250.1; hypothetical protein complement(211718..212725) Ruegeria pomeroyi DSS-3 3196823 YP_165030.1 CDS SPOA0201 NC_006569.1 212759 214345 R identified by similarity to SP:Q50925; hydroxylamine oxidoreductase complement(212759..214345) Ruegeria pomeroyi DSS-3 3196923 YP_165031.1 CDS hisD NC_006569.1 214950 216251 D catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 214950..216251 Ruegeria pomeroyi DSS-3 3196717 YP_165032.1 CDS SPOA0203 NC_006569.1 216248 219547 R hypothetical protein complement(216248..219547) Ruegeria pomeroyi DSS-3 3196661 YP_165033.1 CDS SPOA0204 NC_006569.1 219959 221563 R hypothetical protein complement(219959..221563) Ruegeria pomeroyi DSS-3 3196788 YP_165034.1 CDS SPOA0205 NC_006569.1 221560 224325 R identified by match to protein family HMM PF00082; serine protease complement(221560..224325) Ruegeria pomeroyi DSS-3 3196869 YP_165035.1 CDS SPOA0206 NC_006569.1 224583 225284 D identified by match to protein family HMM PF00027; match to protein family HMM PF00325; Crp/Fnr family transcriptional regulator 224583..225284 Ruegeria pomeroyi DSS-3 3196825 YP_165036.1 CDS SPOA0207 NC_006569.1 225279 228305 R identified by match to protein family HMM PF00211; match to protein family HMM PF00536; match to protein family HMM PF06498; guanylate cyclase complement(225279..228305) Ruegeria pomeroyi DSS-3 3196703 YP_165037.1 CDS SPOA0208 NC_006569.1 228322 229908 R identified by similarity to SP:P43485; match to protein family HMM PF01565; oxidoreductase, FAD-binding complement(228322..229908) Ruegeria pomeroyi DSS-3 3196826 YP_165038.1 CDS SPOA0209 NC_006569.1 230029 231330 R identified by similarity to GB:AAQ59009.1; match to protein family HMM PF01266; oxidoreductase, FAD-binding complement(230029..231330) Ruegeria pomeroyi DSS-3 3196920 YP_165039.1 CDS SPOA0210 NC_006569.1 231416 232255 R identified by similarity to GB:BAC71325.1; match to protein family HMM PF00892; hypothetical protein complement(231416..232255) Ruegeria pomeroyi DSS-3 3196892 YP_165040.1 CDS SPOA0211 NC_006569.1 232257 233939 R identified by match to protein family HMM PF02690; Na/Pi-cotransporter family protein complement(232257..233939) Ruegeria pomeroyi DSS-3 3196558 YP_165041.1 CDS SPOA0212 NC_006569.1 234160 234417 R nitric oxide reductase F protein complement(234160..234417) Ruegeria pomeroyi DSS-3 3196886 YP_165042.1 CDS SPOA0213 NC_006569.1 234422 234925 R identified by match to protein family HMM PF00510; nitric oxide reductase E protein complement(234422..234925) Ruegeria pomeroyi DSS-3 3196594 YP_165043.1 CDS norD NC_006569.1 234967 236889 R identified by similarity to GB:AAC45374.1; nitric oxide reductase D protein complement(234967..236889) Ruegeria pomeroyi DSS-3 3196547 YP_165044.1 CDS norQ NC_006569.1 236898 237713 R identified by similarity to SP:Q51664; nitric oxide reductase Q protein complement(236898..237713) Ruegeria pomeroyi DSS-3 3196863 YP_165045.1 CDS norB NC_006569.1 237713 239080 R identified by similarity to GB:AAC45372.1; match to protein family HMM PF00115; nitric oxide reductase, large subunit complement(237713..239080) Ruegeria pomeroyi DSS-3 3196893 YP_165046.1 CDS norC NC_006569.1 239096 239548 R identified by similarity to SP:Q51662; match to protein family HMM PF00034; nitric oxide reductase, small subunit complement(239096..239548) Ruegeria pomeroyi DSS-3 3196811 YP_165047.1 CDS SPOA0218 NC_006569.1 239774 240742 D identified by match to protein family HMM PF01544; magnesium transporter CorA family protein 239774..240742 Ruegeria pomeroyi DSS-3 3196884 YP_165048.1 CDS SPOA0219 NC_006569.1 240753 241925 R identified by match to protein family HMM PF05940; NnrS complement(240753..241925) Ruegeria pomeroyi DSS-3 3196836 YP_165049.1 CDS nirS NC_006569.1 242141 243835 D identified by similarity to SP:P24474; match to protein family HMM PF00034; match to protein family HMM PF02239; cytochrome cd1 nitrite reductase 242141..243835 Ruegeria pomeroyi DSS-3 3196854 YP_165050.1 CDS nirE NC_006569.1 243923 244696 D identified by similarity to SP:Q51701; match to protein family HMM PF00590; match to protein family HMM TIGR01469; nitrite reductase heme biosynthesis E protein 243923..244696 Ruegeria pomeroyi DSS-3 3196801 YP_165051.1 CDS nirC NC_006569.1 244716 245048 D identified by similarity to SP:Q51702; cytochrome c55X 244716..245048 Ruegeria pomeroyi DSS-3 3196883 YP_165052.1 CDS nirF NC_006569.1 245045 246190 D identified by similarity to SP:Q51480; match to protein family HMM PF02239; cytochrome cd1 nitrite reductase 245045..246190 Ruegeria pomeroyi DSS-3 3196829 YP_165053.1 CDS SPOA0224 NC_006569.1 246196 247188 D 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 246196..247188 Ruegeria pomeroyi DSS-3 3196958 YP_165054.1 CDS nirG NC_006569.1 247185 247634 D identified by similarity to SP:Q52524; nitrite reductase heme biosynthesis G protein 247185..247634 Ruegeria pomeroyi DSS-3 3196840 YP_165055.1 CDS nirH NC_006569.1 247631 248113 D identified by similarity to SP:Q52525; nitrite reductase heme biosynthesis H protein 247631..248113 Ruegeria pomeroyi DSS-3 3196735 YP_165056.1 CDS nirJ NC_006569.1 248115 249326 D identified by similarity to PIR:C83581; match to protein family HMM PF04055; nitrite reductase heme biosynthesis J protein 248115..249326 Ruegeria pomeroyi DSS-3 3196859 YP_165057.1 CDS nirN NC_006569.1 249427 250938 D identified by similarity to GB:BAA12683.1; match to protein family HMM PF00034; match to protein family HMM PF02239; nitrite reductase protein N 249427..250938 Ruegeria pomeroyi DSS-3 3196677 YP_165058.1 CDS SPOA0229 NC_006569.1 250979 251170 D hypothetical protein 250979..251170 Ruegeria pomeroyi DSS-3 3196908 YP_165059.1 CDS SPOA0230 NC_006569.1 251221 252138 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(251221..252138) Ruegeria pomeroyi DSS-3 3196653 YP_165060.1 CDS SPOA0231 NC_006569.1 252309 253250 D identified by similarity to SP:P14177; match to protein family HMM PF04069; glycine betaine/proline ABC transporter, periplasmic substrate-binding protein 252309..253250 Ruegeria pomeroyi DSS-3 3196802 YP_165061.1 CDS opuAA NC_006569.1 253363 254415 D 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 253363..254415 Ruegeria pomeroyi DSS-3 3196706 YP_165062.1 CDS SPOA0233 NC_006569.1 254412 255986 D identified by similarity to SP:P14176; match to protein family HMM PF00528; glycine betaine/proline ABC transporter, permease protein 254412..255986 Ruegeria pomeroyi DSS-3 3196782 YP_165063.1 CDS SPOA0234 NC_006569.1 256041 257039 D identified by similarity to SP:Q9BSE5; match to protein family HMM PF00491; agmatinase 256041..257039 Ruegeria pomeroyi DSS-3 3196550 YP_165064.1 CDS speB-4 NC_006569.1 257036 258022 D identified by similarity to SP:Q9BSE5; match to protein family HMM PF00491; match to protein family HMM TIGR01230; agmatinase 257036..258022 Ruegeria pomeroyi DSS-3 3196895 YP_165065.1 CDS dctB NC_006569.1 258234 259955 D identified by similarity to SP:P10047; match to protein family HMM PF00512; match to protein family HMM PF02518; C4-dicarboxylate transport sensor protein dctB 258234..259955 Ruegeria pomeroyi DSS-3 3196651 YP_165066.1 CDS dctD-2 NC_006569.1 259961 261301 D 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 259961..261301 Ruegeria pomeroyi DSS-3 3196880 YP_165067.1 CDS SPOA0238 NC_006569.1 261428 262441 D identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter, DctP subunit 261428..262441 Ruegeria pomeroyi DSS-3 3196835 YP_165068.1 CDS SPOA0239 NC_006569.1 262516 263151 D identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit 262516..263151 Ruegeria pomeroyi DSS-3 3196875 YP_165069.1 CDS SPOA0240 NC_006569.1 263144 264544 D identified by match to protein family HMM PF06808; TRAP transporter, DctM subunit 263144..264544 Ruegeria pomeroyi DSS-3 3196914 YP_165070.1 CDS SPOA0241 NC_006569.1 264766 265689 R identified by match to protein family HMM PF03758; gluconolactonase complement(264766..265689) Ruegeria pomeroyi DSS-3 3196672 YP_165071.1 CDS SPOA0242 NC_006569.1 265820 266860 R identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcription regulator complement(265820..266860) Ruegeria pomeroyi DSS-3 3196792 YP_165072.1 CDS SPOA0243 NC_006569.1 266928 268430 R identified by match to protein family HMM PF00171; aldehyde dehydrogenase complement(266928..268430) Ruegeria pomeroyi DSS-3 3196849 YP_165073.1 CDS SPOA0244 NC_006569.1 268432 269346 R identified by match to protein family HMM PF00701; dihydrodipicolinate synthase family protein complement(268432..269346) Ruegeria pomeroyi DSS-3 3196720 YP_165074.1 CDS SPOA0245 NC_006569.1 269349 270524 R identified by match to protein family HMM PF01188; match to protein family HMM PF02746; galactonate dehydratase complement(269349..270524) Ruegeria pomeroyi DSS-3 3196696 YP_165075.1 CDS pdxA NC_006569.1 270521 271546 R 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 complement(270521..271546) Ruegeria pomeroyi DSS-3 3196957 YP_165076.1 CDS SPOA0247 NC_006569.1 271543 272505 R identified by similarity to GB:AAM32283.1; hypothetical protein complement(271543..272505) Ruegeria pomeroyi DSS-3 3196887 YP_165077.1 CDS SPOA0248 NC_006569.1 272618 273043 R identified by similarity to GB:AAD03997.1; hypothetical protein complement(272618..273043) Ruegeria pomeroyi DSS-3 3196663 YP_165078.1 CDS SPOA0249 NC_006569.1 273143 274120 R identified by match to protein family HMM PF03480; match to protein family HMM TIGR00787; TRAP dicarboxylate transporter, DctP subunit complement(273143..274120) Ruegeria pomeroyi DSS-3 3196754 YP_165079.1 CDS SPOA0250 NC_006569.1 274138 275418 R 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 complement(274138..275418) Ruegeria pomeroyi DSS-3 3196864 YP_165080.1 CDS SPOA0251 NC_006569.1 275421 275969 R identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit complement(275421..275969) Ruegeria pomeroyi DSS-3 3196858 YP_165081.1 CDS SPOA0252 NC_006569.1 276053 277078 D identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcription regulator 276053..277078 Ruegeria pomeroyi DSS-3 3196612 YP_165082.1 CDS SPOA0253 NC_006569.1 277117 278247 R identified by similarity to SP:P02925; similarity to SP:P54300; ribose ABC transporter, periplasmic ribose-binding protein complement(277117..278247) Ruegeria pomeroyi DSS-3 3196779 YP_165083.1 CDS rbsC-1 NC_006569.1 278352 279479 R identified by similarity to SP:P36948; match to protein family HMM PF02653; ribose ABC transporter, permease protein complement(278352..279479) Ruegeria pomeroyi DSS-3 3196588 YP_165084.1 CDS SPOA0255 NC_006569.1 279491 280252 R identified by match to protein family HMM PF00005; sugar ABC transporter, ATP binding protein complement(279491..280252) Ruegeria pomeroyi DSS-3 3196793 YP_165085.1 CDS SPOA0256 NC_006569.1 280380 281426 R identified by match to protein family HMM PF00532; ribose ABC transporter, periplasmic ribose-binding protein complement(280380..281426) Ruegeria pomeroyi DSS-3 3196654 YP_165086.1 CDS rbsC-2 NC_006569.1 281449 282468 R identified by similarity to SP:P36948; match to protein family HMM PF02653; ribose ABC transporter, permease protein complement(281449..282468) Ruegeria pomeroyi DSS-3 3196946 YP_165087.1 CDS rbsA NC_006569.1 282480 283985 R identified by similarity to SP:P36947; match to protein family HMM PF00005; ribose ABC transporter, ATP-binding protein complement(282480..283985) Ruegeria pomeroyi DSS-3 3196931 YP_165088.1 CDS SPOA0259 NC_006569.1 284124 285167 D identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcription regulator 284124..285167 Ruegeria pomeroyi DSS-3 3196768 YP_165089.1 CDS SPOA0260 NC_006569.1 285382 286890 R identified by match to protein family HMM PF00171; aldehyde dehydrogenase complement(285382..286890) Ruegeria pomeroyi DSS-3 3196786 YP_165090.1 CDS SPOA0261 NC_006569.1 286995 287675 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(286995..287675) Ruegeria pomeroyi DSS-3 3196757 YP_165091.1 CDS SPOA0262 NC_006569.1 287856 289097 R identified by match to protein family HMM PF01266; oxidoreductase, FAD-binding complement(287856..289097) Ruegeria pomeroyi DSS-3 3196590 YP_165092.1 CDS SPOA0263 NC_006569.1 289097 290407 R identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP transporter, DctM subunit complement(289097..290407) Ruegeria pomeroyi DSS-3 3196759 YP_165093.1 CDS SPOA0264 NC_006569.1 290411 290944 R identified by match to protein family HMM PF04290; TRAP transporter DctQ family protein complement(290411..290944) Ruegeria pomeroyi DSS-3 3196868 YP_165094.1 CDS SPOA0265 NC_006569.1 291001 292065 R identified by match to protein family HMM PF03480; TRAP transporter DctP family protein complement(291001..292065) Ruegeria pomeroyi DSS-3 3196613 YP_165095.1 CDS SPOA0266 NC_006569.1 292150 293091 R identified by similarity to GB:CAB71312.1; match to protein family HMM PF05544; proline racemase complement(292150..293091) Ruegeria pomeroyi DSS-3 3196810 YP_165096.1 CDS SPOA0267 NC_006569.1 293082 294038 R identified by match to protein family HMM PF00701; dihydroxydipicolinate synthase family protein complement(293082..294038) Ruegeria pomeroyi DSS-3 3196900 YP_165097.1 CDS SPOA0268 NC_006569.1 294459 295271 D identified by match to protein family HMM PF01614; IclR family transcriptional regulator 294459..295271 Ruegeria pomeroyi DSS-3 3196576 YP_165098.1 CDS SPOA0269 NC_006569.1 295294 296604 D identified by similarity to GB:BAB65016.1; hypothetical protein 295294..296604 Ruegeria pomeroyi DSS-3 3196645 YP_165099.1 CDS SPOA0270 NC_006569.1 296672 297382 D identified by similarity to PIR:G81801; hypothetical protein 296672..297382 Ruegeria pomeroyi DSS-3 3196831 YP_165100.1 CDS SPOA0271 NC_006569.1 297379 298593 D identified by similarity to SP:Q49128; match to protein family HMM PF03150; methylamine utilization protein MauG 297379..298593 Ruegeria pomeroyi DSS-3 3196784 YP_165101.1 CDS SPOA0272 NC_006569.1 298624 299736 D identified by similarity to SP:P45382; match to protein family HMM PF00107; glutathione-dependent formaldehyde dehydrogenase 298624..299736 Ruegeria pomeroyi DSS-3 3196593 YP_165102.1 CDS SPOA0273 NC_006569.1 300585 301151 R identified by match to protein family HMM PF01381; DNA-binding protein complement(300585..301151) Ruegeria pomeroyi DSS-3 3196850 YP_165103.1 CDS gabT NC_006569.1 301297 302574 D catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate; 4-aminobutyrate aminotransferase 301297..302574 Ruegeria pomeroyi DSS-3 3196857 YP_165104.1 CDS gabD-3 NC_006569.1 302576 304036 D identified by match to protein family HMM PF00171; match to protein family HMM TIGR01780; succinate-semialdehyde dehydrogenase 302576..304036 Ruegeria pomeroyi DSS-3 3196901 YP_165105.1 CDS cscK NC_006569.1 304052 304993 R identified by similarity to GB:AAC04474.1; match to protein family HMM PF00294; fructokinase complement(304052..304993) Ruegeria pomeroyi DSS-3 3196746 YP_165106.1 CDS SPOA0277 NC_006569.1 305059 305817 R identified by match to protein family HMM PF00561; alpha/beta hydrolase complement(305059..305817) Ruegeria pomeroyi DSS-3 3196571 YP_165107.1 CDS SPOA0278 NC_006569.1 305817 307118 R identified by match to protein family HMM PF06808; TRAP dicarboxylate transporter, DctM subunit complement(305817..307118) Ruegeria pomeroyi DSS-3 3196845 YP_165108.1 CDS SPOA0279 NC_006569.1 307118 307627 R identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit complement(307118..307627) Ruegeria pomeroyi DSS-3 3196896 YP_165109.1 CDS SPOA0280 NC_006569.1 307702 308697 R identified by match to protein family HMM PF03480; TRAP dicarboxylate transporter, DctP subunit complement(307702..308697) Ruegeria pomeroyi DSS-3 3196903 YP_165110.1 CDS SPOA0281 NC_006569.1 308914 309798 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 308914..309798 Ruegeria pomeroyi DSS-3 3196862 YP_165111.1 CDS SPOA0282 NC_006569.1 309822 311339 R catalyzes the formation of malonyl-CoA from malonate and CoA; malonyl-CoA synthase complement(309822..311339) Ruegeria pomeroyi DSS-3 3196904 YP_165112.1 CDS SPOA0283 NC_006569.1 311439 313043 R identified by match to protein family HMM PF00732; match to protein family HMM PF05199; GMC family oxidoreductase complement(311439..313043) Ruegeria pomeroyi DSS-3 3196740 YP_165113.1 CDS SPOA0284 NC_006569.1 313162 314052 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 313162..314052 Ruegeria pomeroyi DSS-3 3196579 YP_165114.1 CDS caiD-2 NC_006569.1 314098 314883 R catalyzes the dehydration of L-carnitinyl-CoA to crotonobetainyl-CoA; carnitinyl-CoA dehydratase complement(314098..314883) Ruegeria pomeroyi DSS-3 3196711 YP_165115.1 CDS SPOA0286 NC_006569.1 314883 315488 R identified by match to protein family HMM PF01965; ThiJ/PfpI family protein complement(314883..315488) Ruegeria pomeroyi DSS-3 3196846 YP_165116.1 CDS SPOA0287 NC_006569.1 315492 317504 R identified by similarity to GB:BAB86294.1; similarity to GB:CAA10043.1; match to protein family HMM PF02629; acyl-CoA synthetase complement(315492..317504) Ruegeria pomeroyi DSS-3 3196916 YP_165117.1 CDS acdA-3 NC_006569.1 317587 318747 R identified by match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF02771; acyl-CoA dehydrogenase complement(317587..318747) Ruegeria pomeroyi DSS-3 3196905 YP_165118.1 CDS SPOA0289 NC_006569.1 318870 319769 D identified by match to protein family HMM PF00165; AraC family transcriptional regulator 318870..319769 Ruegeria pomeroyi DSS-3 3196591 YP_165119.1 CDS SPOA0290 NC_006569.1 319825 320892 R hypothetical protein complement(319825..320892) Ruegeria pomeroyi DSS-3 3196776 YP_165120.1 CDS SPOA0291 NC_006569.1 320935 321894 R identified by similarity to GB:AAO91868.1; match to protein family HMM PF01063; branched-chain amino acid aminotransferase complement(320935..321894) Ruegeria pomeroyi DSS-3 3196806 YP_165121.1 CDS psd NC_006569.1 322185 322844 D catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine; phosphatidylserine decarboxylase 322185..322844 Ruegeria pomeroyi DSS-3 3196790 YP_165122.1 CDS pssA NC_006569.1 322880 323635 D identified by match to protein family HMM PF01066; match to protein family HMM TIGR00473; CDP-diacylglycerol--serine O-phosphatidyltransferase 322880..323635 Ruegeria pomeroyi DSS-3 3196597 YP_165123.1 CDS pmtA NC_006569.1 323640 324260 D identified by similarity to SP:Q05197; phosphatidylethanolamine N-methyltransferase 323640..324260 Ruegeria pomeroyi DSS-3 3196945 YP_165124.1 CDS SPOA0295 NC_006569.1 324468 325151 R identified by similarity to SP:Q00924; match to protein family HMM PF01177; hydantoin racemase complement(324468..325151) Ruegeria pomeroyi DSS-3 3196664 YP_165125.1 CDS livF-2 NC_006569.1 325158 325880 R identified by similarity to SP:P21630; match to protein family HMM PF00005; branched-chain amino acid ABC transporter, ATP-binding protein complement(325158..325880) Ruegeria pomeroyi DSS-3 3196937 YP_165126.1 CDS livG NC_006569.1 325884 326666 R identified by similarity to SP:P22730; match to protein family HMM PF00005; branched-chain amino acid ABC transporter, ATP-binding protein complement(325884..326666) Ruegeria pomeroyi DSS-3 3196553 YP_165127.1 CDS SPOA0298 NC_006569.1 326663 327643 R identified by similarity to SP:P22729; match to protein family HMM PF02653; branched-chain amino acid ABC transporter, permease protein complement(326663..327643) Ruegeria pomeroyi DSS-3 3196912 YP_165128.1 CDS SPOA0299 NC_006569.1 327648 328517 R identified by match to protein family HMM PF02653; branched-chain amino acid ABC transporter, permease protein complement(327648..328517) Ruegeria pomeroyi DSS-3 3196694 YP_165129.1 CDS SPOA0300 NC_006569.1 328607 329794 R 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 complement(328607..329794) Ruegeria pomeroyi DSS-3 3196769 YP_165130.1 CDS SPOA0301 NC_006569.1 330025 330744 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 330025..330744 Ruegeria pomeroyi DSS-3 3196733 YP_165131.1 CDS SPOA0302 NC_006569.1 331140 332186 D identified by match to protein family HMM PF00589; phage integrase family site specific recombinase 331140..332186 Ruegeria pomeroyi DSS-3 3196646 YP_165132.1 CDS SPOA0303 NC_006569.1 332220 333317 R identified by similarity to GB:AAN05123.1; match to protein family HMM PF02195; replication protein complement(332220..333317) Ruegeria pomeroyi DSS-3 3196919 YP_165133.1 CDS repA NC_006569.1 333314 334621 R identified by similarity to PIR:AI3232; match to protein family HMM PF00991; replication protein complement(333314..334621) Ruegeria pomeroyi DSS-3 3196795 YP_165134.1 CDS SPOA0305 NC_006569.1 335100 335789 D hypothetical protein 335100..335789 Ruegeria pomeroyi DSS-3 3196839 YP_165135.1 CDS SPOA0306 NC_006569.1 335830 338127 R identified by similarity to SP:P46837; match to protein family HMM PF00575; S1 RNA-binding domain-containing protein complement(335830..338127) Ruegeria pomeroyi DSS-3 3196926 YP_165136.1 CDS SPOA0309 NC_006569.1 339974 341653 R identified by similarity to SP:Q84H44; match to protein family HMM PF00205; match to protein family HMM PF02776; sulphoacetaldehyde acetyltransferase complement(339974..341653) Ruegeria pomeroyi DSS-3 3196956 YP_165137.1 CDS SPOA0310 NC_006569.1 341657 344068 R identified by match to protein family HMM PF01571; glycine cleavage system protein T complement(341657..344068) Ruegeria pomeroyi DSS-3 3196699 YP_165138.1 CDS SPOA0311 NC_006569.1 344068 346467 R identified by match to protein family HMM PF01266; match to protein family HMM PF01571; FAD-dependent oxidoreductase complement(344068..346467) Ruegeria pomeroyi DSS-3 3196955 YP_165139.1 CDS SPOA0312 NC_006569.1 346464 347753 R identified by similarity to SP:P24630; match to protein family HMM PF00202; glutamate-1-semialdehyde 2,1-aminomutase complement(346464..347753) Ruegeria pomeroyi DSS-3 3196932 YP_165140.1 CDS SPOA0313 NC_006569.1 347750 349294 R identified by match to protein family HMM PF06253; trimethylamine methyltransferase family protein complement(347750..349294) Ruegeria pomeroyi DSS-3 3196938 YP_165141.1 CDS SPOA0314 NC_006569.1 349404 350270 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 349404..350270 Ruegeria pomeroyi DSS-3 3196652 YP_165142.1 CDS icd NC_006569.1 351557 353770 D identified by similarity to SP:P50216; match to protein family HMM PF03971; match to protein family HMM TIGR00178; isocitrate dehydrogenase, NADP-dependent 351557..353770 Ruegeria pomeroyi DSS-3 3196885 YP_165143.1 CDS SPOA0316 NC_006569.1 353871 355526 R identified by match to protein family HMM PF01979; amidohydrolase complement(353871..355526) Ruegeria pomeroyi DSS-3 3196599 YP_165144.1 CDS SPOA0317 NC_006569.1 355845 356303 R identified by match to protein family HMM PF01037; AsnC family transcriptional regulator complement(355845..356303) Ruegeria pomeroyi DSS-3 3196556 YP_165145.1 CDS megL NC_006569.1 356420 357622 D catalyzes the formation of methanethiol and 2-ocobutanoate from L-methionine; methionine gamma-lyase 356420..357622 Ruegeria pomeroyi DSS-3 3196830 YP_165146.1 CDS SPOA0319 NC_006569.1 357789 360179 D identified by match to protein family HMM PF00456; match to protein family HMM PF02779; transketolase 357789..360179 Ruegeria pomeroyi DSS-3 3196927 YP_165147.1 CDS hpcD NC_006569.1 360331 360708 D identified by similarity to SP:Q05354; match to protein family HMM PF02962; 5-carboxymethyl-2-hydroxymuconate delta-isomerase 360331..360708 Ruegeria pomeroyi DSS-3 3196797 YP_165148.1 CDS SPOA0321 NC_006569.1 360699 361160 R identified by match to protein family HMM PF00903; glyoxalase family protein complement(360699..361160) Ruegeria pomeroyi DSS-3 3196948 YP_165149.1 CDS SPOA0322 NC_006569.1 361284 362402 D identified by similarity to GB:AAQ61367.1; match to protein family HMM PF01170; hypothetical protein 361284..362402 Ruegeria pomeroyi DSS-3 3196808 YP_165150.1 CDS SPOA0323 NC_006569.1 362508 363212 D identified by match to protein family HMM PF00027; cyclic nucleotide-binding protein 362508..363212 Ruegeria pomeroyi DSS-3 3196959 YP_165151.1 CDS SPOA0324 NC_006569.1 363209 363772 D hypothetical protein 363209..363772 Ruegeria pomeroyi DSS-3 3196960 YP_165152.1 CDS SPOA0325 NC_006569.1 363781 364857 R identified by match to protein family HMM PF03060; 2-nitropropane dioxygenase complement(363781..364857) Ruegeria pomeroyi DSS-3 3196961 YP_165153.1 CDS SPOA0326 NC_006569.1 365032 365916 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 365032..365916 Ruegeria pomeroyi DSS-3 3196962 YP_165154.1 CDS SPOA0327 NC_006569.1 367716 368282 D identified by similarity to GB:AAF36413.1; rzcC protein 367716..368282 Ruegeria pomeroyi DSS-3 3196963 YP_165155.1 CDS SPOA0328 NC_006569.1 368322 368957 D identified by similarity to GB:BAB49961.1; hypothetical protein 368322..368957 Ruegeria pomeroyi DSS-3 3196964 YP_165156.1 CDS mgsA NC_006569.1 370463 370852 R catalyzes the formation of methylglyoxal from glycerone phosphate; methylglyoxal synthase complement(370463..370852) Ruegeria pomeroyi DSS-3 3196965 YP_165157.1 CDS eda-2 NC_006569.1 370846 371505 R 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 complement(370846..371505) Ruegeria pomeroyi DSS-3 3196966 YP_165158.1 CDS SPOA0331 NC_006569.1 371484 372431 R identified by similarity to SP:P50845; match to protein family HMM PF00294; 2-dehydro-3-deoxygluconokinase complement(371484..372431) Ruegeria pomeroyi DSS-3 3196967 YP_165159.1 CDS SPOA0332 NC_006569.1 372441 374237 R catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase complement(372441..374237) Ruegeria pomeroyi DSS-3 3196745 YP_165160.1 CDS SPOA0333 NC_006569.1 374238 375503 R identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786; TRAP dicarboxylate transporter, DctM subunit complement(374238..375503) Ruegeria pomeroyi DSS-3 3196969 YP_165161.1 CDS SPOA0334 NC_006569.1 375570 376130 R TRAP dicarboxylate family transporter DctQ subunit complement(375570..376130) Ruegeria pomeroyi DSS-3 3196968 YP_165162.1 CDS SPOA0335 NC_006569.1 376203 377222 R identified by match to protein family HMM PF03480; TRAP dicarboxylate family transporter DctP subunit complement(376203..377222) Ruegeria pomeroyi DSS-3 3196970 YP_165163.1 CDS SPOA0336 NC_006569.1 377348 378382 D identified by match to protein family HMM PF00356; match to protein family HMM PF00532; LacI family transcription regulator 377348..378382 Ruegeria pomeroyi DSS-3 3196971 YP_165164.1 CDS SPOA0337 NC_006569.1 379179 381470 R hypothetical protein complement(379179..381470) Ruegeria pomeroyi DSS-3 3196972 YP_165165.1 CDS SPOA0338 NC_006569.1 381777 382751 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; match to protein family HMM TIGR01199; LysR family transcriptional regulator 381777..382751 Ruegeria pomeroyi DSS-3 3196973 YP_165166.1 CDS SPOA0339 NC_006569.1 383108 383779 R identified by match to protein family HMM PF00702; match to protein family HMM TIGR01488; match to protein family HMM TIGR01490; HAD family hydrolase complement(383108..383779) Ruegeria pomeroyi DSS-3 3196974 YP_165167.1 CDS SPOA0340 NC_006569.1 383776 384009 R identified by match to protein family HMM PF01361; tautomerase complement(383776..384009) Ruegeria pomeroyi DSS-3 3196975 YP_165168.1 CDS SPOA0341 NC_006569.1 384039 384818 R hypothetical protein complement(384039..384818) Ruegeria pomeroyi DSS-3 3196976 YP_165169.1 CDS SPOA0342 NC_006569.1 384945 385730 R hypothetical protein complement(384945..385730) Ruegeria pomeroyi DSS-3 3196977 YP_165170.1 CDS SPOA0343 NC_006569.1 385776 386387 R hypothetical protein complement(385776..386387) Ruegeria pomeroyi DSS-3 3196978 YP_165171.1 CDS SPOA0344 NC_006569.1 386564 387508 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; match to protein family HMM TIGR01199; LysR family transcriptional regulator complement(386564..387508) Ruegeria pomeroyi DSS-3 3196979 YP_165172.1 CDS SPOA0345 NC_006569.1 387556 388539 D identified by match to protein family HMM PF00248; aldo/keto reductase 387556..388539 Ruegeria pomeroyi DSS-3 3196980 YP_165173.1 CDS SPOA0346 NC_006569.1 388536 388925 D identified by match to protein family HMM PF02627; carboxymuconolactone decarboxylase family protein 388536..388925 Ruegeria pomeroyi DSS-3 3196981 YP_165174.1 CDS SPOA0347 NC_006569.1 388947 390134 D hypothetical protein 388947..390134 Ruegeria pomeroyi DSS-3 3196982 YP_165175.1 CDS SPOA0348 NC_006569.1 390671 391216 D identified by similarity to GB:AAQ60836.1; hypothetical protein 390671..391216 Ruegeria pomeroyi DSS-3 3196983 YP_165176.1 CDS SPOA0349 NC_006569.1 391276 392235 R identified by match to protein family HMM PF00892; hypothetical protein complement(391276..392235) Ruegeria pomeroyi DSS-3 3196984 YP_165177.1 CDS SPOA0350 NC_006569.1 392232 392450 R hypothetical protein complement(392232..392450) Ruegeria pomeroyi DSS-3 3196985 YP_165178.1 CDS SPOA0351 NC_006569.1 392392 392625 R hypothetical protein complement(392392..392625) Ruegeria pomeroyi DSS-3 3196986 YP_165179.1 CDS SPOA0352 NC_006569.1 392691 394046 R identified by match to protein family HMM PF00202; hypothetical protein complement(392691..394046) Ruegeria pomeroyi DSS-3 3196749 YP_165180.1 CDS SPOA0353 NC_006569.1 394173 395651 D identified by match to protein family HMM PF00171; aldehyde dehydrogenase 394173..395651 Ruegeria pomeroyi DSS-3 3196987 YP_165181.1 CDS SPOA0354 NC_006569.1 395648 396946 D identified by match to protein family HMM PF00202; aminotransferase, class III 395648..396946 Ruegeria pomeroyi DSS-3 3196988 YP_165182.1 CDS SPOA0355 NC_006569.1 396943 397887 D identified by similarity to GB:AAN34322.1; hypothetical protein 396943..397887 Ruegeria pomeroyi DSS-3 3196989 YP_165183.1 CDS SPOA0356 NC_006569.1 397884 399119 D identified by similarity to SP:Q8YDP7; match to protein family HMM PF06792; hypothetical protein 397884..399119 Ruegeria pomeroyi DSS-3 3196687 YP_165184.1 CDS SPOA0357 NC_006569.1 399373 400101 D identified by match to protein family HMM PF00072; match to protein family HMM PF00486; DNA-binding response regulator 399373..400101 Ruegeria pomeroyi DSS-3 3196715 YP_165185.1 CDS SPOA0358 NC_006569.1 400107 401477 D identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518; sensor histidine kinase 400107..401477 Ruegeria pomeroyi DSS-3 3196990 YP_165186.1 CDS SPOA0359 NC_006569.1 401807 402403 D identified by match to protein family HMM PF00034; cytochrome c family protein 401807..402403 Ruegeria pomeroyi DSS-3 3196805 YP_165187.1 CDS SPOA0360 NC_006569.1 402425 403855 D identified by similarity to GB:AAD24211.1; match to protein family HMM TIGR01409; multicopper oxidase 402425..403855 Ruegeria pomeroyi DSS-3 3196992 YP_165188.1 CDS SPOA0361 NC_006569.1 403852 404352 D identified by match to protein family HMM PF00034; cytochrome c family protein 403852..404352 Ruegeria pomeroyi DSS-3 3196993 YP_165189.1 CDS SPOA0362 NC_006569.1 404349 405083 D identified by similarity to PIR:A49232; match to protein family HMM PF01323; hypothetical protein 404349..405083 Ruegeria pomeroyi DSS-3 3196991 YP_165190.1 CDS SPOA0363 NC_006569.1 405287 406045 D hypothetical protein 405287..406045 Ruegeria pomeroyi DSS-3 3196628 YP_165191.1 CDS SPOA0364 NC_006569.1 406161 407222 D identified by similarity to GB:AAM42746.1; hypothetical protein 406161..407222 Ruegeria pomeroyi DSS-3 3196753 YP_165192.1 CDS SPOA0365 NC_006569.1 407279 409636 D 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 407279..409636 Ruegeria pomeroyi DSS-3 3196765 YP_165193.1 CDS SPOA0366 NC_006569.1 409666 411012 D identified by similarity to SP:P77400; match to protein family HMM PF00324; amino acid permease 409666..411012 Ruegeria pomeroyi DSS-3 3196693 YP_165194.1 CDS SPOA0367 NC_006569.1 411009 412142 R identified by match to protein family HMM PF00664; ABC transporter, permease protein complement(411009..412142) Ruegeria pomeroyi DSS-3 3196674 YP_165195.1 CDS SPOA0368 NC_006569.1 412340 412849 R identified by similarity to GB:AAF32271.1; hypothetical protein complement(412340..412849) Ruegeria pomeroyi DSS-3 3196578 YP_165196.1 CDS SPOA0369 NC_006569.1 412958 413620 R identified by similarity to SP:P12375; copper resistance protein B complement(412958..413620) Ruegeria pomeroyi DSS-3 3196621 YP_165197.1 CDS copA NC_006569.1 413692 415635 R identified by similarity to SP:P12374; match to protein family HMM PF00394; match to protein family HMM TIGR01480; copper resistance protein A complement(413692..415635) Ruegeria pomeroyi DSS-3 3196763 YP_165198.1 CDS SPOA0371 NC_006569.1 415806 416144 R hypothetical protein complement(415806..416144) Ruegeria pomeroyi DSS-3 3196615 YP_165199.1 CDS SPOA0372 NC_006569.1 416293 416856 R identified by match to protein family HMM PF04290; TRAP dicarboxylate transporter, DctQ subunit complement(416293..416856) Ruegeria pomeroyi DSS-3 3196577 YP_165200.1 CDS SPOA0373 NC_006569.1 416936 418225 R 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 complement(416936..418225) Ruegeria pomeroyi DSS-3 3196741 YP_165201.1 CDS SPOA0374 NC_006569.1 418331 419371 R identified by similarity to SP:P37735; match to protein family HMM PF03480; TRAP dicarboxylate transporter, DctP subunit complement(418331..419371) Ruegeria pomeroyi DSS-3 3196600 YP_165202.1 CDS SPOA0375 NC_006569.1 419547 421010 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 419547..421010 Ruegeria pomeroyi DSS-3 3196609 YP_165203.1 CDS SPOA0376 NC_006569.1 421021 422331 D identified by match to protein family HMM PF06441; epoxide hydrolase 421021..422331 Ruegeria pomeroyi DSS-3 3196656 YP_165204.1 CDS SPOA0377 NC_006569.1 422351 423844 D identified by match to protein family HMM PF00171; aldehyde dehydrogenase 422351..423844 Ruegeria pomeroyi DSS-3 3196560 YP_165205.1 CDS SPOA0378 NC_006569.1 423926 425029 R identified by match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase complement(423926..425029) Ruegeria pomeroyi DSS-3 3196713 YP_165206.1 CDS SPOA0379 NC_006569.1 425152 426624 D identified by match to protein family HMM PF00392; GntR family transcriptional regulator 425152..426624 Ruegeria pomeroyi DSS-3 3196566 YP_165207.1 CDS SPOA0380 NC_006569.1 426750 428057 D identified by similarity to GB:CAE41123.1; hypothetical protein 426750..428057 Ruegeria pomeroyi DSS-3 3196667 YP_165208.1 CDS SPOA0381 NC_006569.1 428256 429296 D 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 428256..429296 Ruegeria pomeroyi DSS-3 3196721 YP_165209.1 CDS SPOA0382 NC_006569.1 429358 430461 D 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 429358..430461 Ruegeria pomeroyi DSS-3 3196773 YP_165210.1 CDS SPOA0383 NC_006569.1 430463 431347 D 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 430463..431347 Ruegeria pomeroyi DSS-3 3196731 YP_165211.1 CDS SPOA0384 NC_006569.1 431347 432174 D identified by match to protein family HMM PF00528; spermidine/putrescine ABC transporter, permease protein 431347..432174 Ruegeria pomeroyi DSS-3 3196738 YP_165212.1 CDS SPOA0385 NC_006569.1 432275 433567 D identified by similarity to GB:CAE33186.1; hypothetical protein 432275..433567 Ruegeria pomeroyi DSS-3 3196675 YP_165213.1 CDS SPOA0386 NC_006569.1 433575 435200 D identified by match to protein family HMM PF00732; match to protein family HMM PF05199; GMC family oxidoreductase 433575..435200 Ruegeria pomeroyi DSS-3 3196551 YP_165214.1 CDS SPOA0387 NC_006569.1 435270 436184 D identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator 435270..436184 Ruegeria pomeroyi DSS-3 3196794 YP_165215.1 CDS SPOA0388 NC_006569.1 436276 438348 D acetyl-CoA synthetase 436276..438348 Ruegeria pomeroyi DSS-3 3196770 YP_165216.1 CDS SPOA0389 NC_006569.1 438569 439006 D identified by match to protein family HMM PF00376; MerR family transcriptional regulator 438569..439006 Ruegeria pomeroyi DSS-3 3196637 YP_165217.1 CDS SPOA0390 NC_006569.1 438997 440526 R identified by similarity to PIR:T44602; match to protein family HMM PF00884; phosphonate monoester hydrolase complement(438997..440526) Ruegeria pomeroyi DSS-3 3196617 YP_165218.1 CDS SPOA0391 NC_006569.1 440874 441527 D identified by match to protein family HMM PF00027; cyclic nucleotide-binding protein 440874..441527 Ruegeria pomeroyi DSS-3 3196855 YP_165219.1 CDS SPOA0392 NC_006569.1 441633 442271 D identified by match to protein family HMM PF04542; RNA polymerase sigma-70 factor 441633..442271 Ruegeria pomeroyi DSS-3 3196680 YP_165220.1 CDS SPOA0393 NC_006569.1 442261 442560 D identified by similarity to GB:AAA73405.1; R body protein RebB-like protein 442261..442560 Ruegeria pomeroyi DSS-3 3196732 YP_165221.1 CDS SPOA0394 NC_006569.1 442435 443445 R hypothetical protein complement(442435..443445) Ruegeria pomeroyi DSS-3 3196683 YP_165222.1 CDS SPOA0395 NC_006569.1 443538 444830 D hypothetical protein 443538..444830 Ruegeria pomeroyi DSS-3 3196552 YP_165223.1 CDS SPOA0396 NC_006569.1 444910 445212 D hypothetical protein 444910..445212 Ruegeria pomeroyi DSS-3 3196616 YP_165224.1 CDS SPOA0397 NC_006569.1 445209 445832 D identified by similarity to GB:AAQ58401.1; hypothetical protein 445209..445832 Ruegeria pomeroyi DSS-3 3196841 YP_165225.1 CDS SPOA0398 NC_006569.1 445902 446225 D identified by similarity to GB:AAA73405.1; R body protein RebB-like protein 445902..446225 Ruegeria pomeroyi DSS-3 3196874 YP_165226.1 CDS SPOA0399 NC_006569.1 446276 446620 D identified by similarity to GB:AAA73405.1; R body protein RebB-like protein 446276..446620 Ruegeria pomeroyi DSS-3 3196554 YP_165227.1 CDS SPOA0400 NC_006569.1 446685 447080 R identified by match to protein family HMM PF01042; endoribonuclease L-PSP complement(446685..447080) Ruegeria pomeroyi DSS-3 3196570 YP_165228.1 CDS badA-2 NC_006569.1 447094 448716 R identified by similarity to GB:AAA92151.1; match to protein family HMM PF00501; benzoate-coenzyme A ligase complement(447094..448716) Ruegeria pomeroyi DSS-3 3196548 YP_165229.1 CDS SPOA0402 NC_006569.1 448720 449172 R identified by similarity to SP:P16558; cupin complement(448720..449172) Ruegeria pomeroyi DSS-3 3196804 YP_165230.1 CDS SPOA0403 NC_006569.1 449201 450343 R identified by match to protein family HMM PF00441; match to protein family HMM PF02770; acyl-CoA dehydrogenase complement(449201..450343) Ruegeria pomeroyi DSS-3 3196954 YP_165231.1 CDS SPOA0404 NC_006569.1 450396 451199 R Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase complement(450396..451199) Ruegeria pomeroyi DSS-3 3196812 YP_165232.1 CDS SPOA0405 NC_006569.1 451196 451663 R identified by match to protein family HMM PF01047; MarR family transcriptional regulator complement(451196..451663) Ruegeria pomeroyi DSS-3 3196867 YP_165233.1 CDS SPOA0406 NC_006569.1 451660 452418 R identified by similarity to SP:O86034; match to protein family HMM PF00106; D-beta-hydroxybutyrate dehydrogenase complement(451660..452418) Ruegeria pomeroyi DSS-3 3196647 YP_165234.1 CDS SPOA0407 NC_006569.1 452415 454709 R catalyzes the conversion of salicylyl-CoA to gentisyl-CoA; salicylyl-CoA 5-hydroxylase complement(452415..454709) Ruegeria pomeroyi DSS-3 3196631 YP_165235.1 CDS SPOA0408 NC_006569.1 454843 455619 D identified by similarity to GB:BAC49422.1; hypothetical protein 454843..455619 Ruegeria pomeroyi DSS-3 3196861 YP_165236.1 CDS SPOA0409 NC_006569.1 455624 456460 D identified by match to protein family HMM PF03301; tryptophan 2,3-dioxygenase 455624..456460 Ruegeria pomeroyi DSS-3 3196589 YP_165237.1 CDS SPOA0410 NC_006569.1 456748 458676 D hypothetical protein 456748..458676 Ruegeria pomeroyi DSS-3 3196697 YP_165238.1 CDS SPOA0411 NC_006569.1 457427 458773 R hypothetical protein complement(457427..458773) Ruegeria pomeroyi DSS-3 3196700 YP_165239.1 CDS SPOA0412 NC_006569.1 459056 459937 D identified by match to protein family HMM PF00941; match to protein family HMM PF03450; xanthine dehydrogenase family protein, medium subunit 459056..459937 Ruegeria pomeroyi DSS-3 3196580 YP_165240.1 CDS SPOA0413 NC_006569.1 459934 460413 D identified by match to protein family HMM PF00111; match to protein family HMM PF01799; xanthine dehydrogenase family protein, small subunit 459934..460413 Ruegeria pomeroyi DSS-3 3196747 YP_165241.1 CDS SPOA0414 NC_006569.1 460413 462674 D identified by match to protein family HMM PF01315; match to protein family HMM PF02738; xanthine dehydrogenase family protein, large subunit 460413..462674 Ruegeria pomeroyi DSS-3 3196819 YP_165242.1 CDS SPOA0415 NC_006569.1 462667 462912 D identified by similarity to PIR:B95401; hypothetical protein 462667..462912 Ruegeria pomeroyi DSS-3 3196756 YP_165243.1 CDS SPOA0416 NC_006569.1 463118 463858 R identified by similarity to GB:BAC52076.1; hypothetical protein complement(463118..463858) Ruegeria pomeroyi DSS-3 3196820 YP_165244.1 CDS SPOA0417 NC_006569.1 463866 464555 R identified by match to protein family HMM PF00392; GntR family transcriptional regulator complement(463866..464555) Ruegeria pomeroyi DSS-3 3196821 YP_165245.1 CDS SPOA0418 NC_006569.1 464662 466353 D identified by similarity to GB:AAL99356.1; match to protein family HMM PF00205; match to protein family HMM PF02776; acetolactate synthase, large subunit 464662..466353 Ruegeria pomeroyi DSS-3 3196822 YP_165246.1 CDS SPOA0419 NC_006569.1 466454 467290 R identified by match to protein family HMM PF02567; match to protein family HMM TIGR00654; PhzF family phenazine biosynthesis protein complement(466454..467290) Ruegeria pomeroyi DSS-3 3196771 YP_165247.1 CDS SPOA0420 NC_006569.1 467341 467541 R hypothetical protein complement(467341..467541) Ruegeria pomeroyi DSS-3 3196742 YP_165248.1 CDS SPOA0421 NC_006569.1 467615 468235 R identified by match to protein family HMM PF01243; pyridoxamine 5'-phosphate oxidase family protein complement(467615..468235) Ruegeria pomeroyi DSS-3 3196669 YP_165249.1 CDS SPOA0422 NC_006569.1 468250 468714 R identified by similarity to GB:AAN68558.1; match to protein family HMM PF07080; hypothetical protein complement(468250..468714) Ruegeria pomeroyi DSS-3 3196824 YP_165250.1 CDS SPOA0423 NC_006569.1 469019 469585 D identified by match to protein family HMM PF00440; TetR family transcriptional regulator 469019..469585 Ruegeria pomeroyi DSS-3 3196722 YP_165251.1 CDS fabJ-2 NC_006569.1 469613 471757 R 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 complement(469613..471757) Ruegeria pomeroyi DSS-3 3196739 YP_165252.1 CDS SPOA0425 NC_006569.1 471770 472978 R 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 complement(471770..472978) Ruegeria pomeroyi DSS-3 3196705 YP_165253.1 CDS SPOA0426 NC_006569.1 473076 474071 D identified by match to protein family HMM PF00165; AraC family transcriptional regulator 473076..474071 Ruegeria pomeroyi DSS-3 3196602 YP_165254.1 CDS SPOA0427 NC_006569.1 474087 474419 R identified by match to protein family HMM PF01022; ArsR family transcriptional regulator complement(474087..474419) Ruegeria pomeroyi DSS-3 3196764 YP_165255.1 CDS SPOA0428 NC_006569.1 474485 475711 R identified by match to protein family HMM PF01188; match to protein family HMM PF02746; mandelate racemase complement(474485..475711) Ruegeria pomeroyi DSS-3 3196686 YP_165256.1 CDS SPOA0429 NC_006569.1 475904 477349 D identified by match to protein family HMM PF01546; hypothetical protein 475904..477349 Ruegeria pomeroyi DSS-3 3196827 YP_165257.1 CDS SPOA0430 NC_006569.1 477356 478450 R identified by match to protein family HMM PF00107; zinc-binding dehydrogenase family oxidoreductase complement(477356..478450) Ruegeria pomeroyi DSS-3 3196729 YP_165258.1 CDS SPOA0431 NC_006569.1 478537 479736 R identified by similarity to SP:P02982; tetracycline resistance protein complement(478537..479736) Ruegeria pomeroyi DSS-3 3196633 YP_165259.1 CDS pcaB NC_006569.1 479797 481134 R identified by similarity to SP:P32427; match to protein family HMM PF00206; 3-carboxy-cis,cis-muconate cycloisomerase complement(479797..481134) Ruegeria pomeroyi DSS-3 3196626 YP_165260.1 CDS SPOA0433 NC_006569.1 481134 481847 R identified by similarity to GB:AAF66687.1; esterase complement(481134..481847) Ruegeria pomeroyi DSS-3 3196897 YP_165261.1 CDS catD NC_006569.1 481860 482648 R identified by similarity to GB:AAL02408.1; match to protein family HMM PF00561; 3-oxoadipate enol-lactone hydrolase complement(481860..482648) Ruegeria pomeroyi DSS-3 3196630 YP_165262.1 CDS SPOA0435 NC_006569.1 482759 483733 R identified by match to protein family HMM PF00291; pyridoxal-phosphate dependent enzyme complement(482759..483733) Ruegeria pomeroyi DSS-3 3196709 YP_165263.1 CDS SPOA0436 NC_006569.1 483730 484557 R identified by match to protein family HMM PF00561; alpha/beta hydrolase complement(483730..484557) Ruegeria pomeroyi DSS-3 3196766 YP_165264.1 CDS dehII NC_006569.1 484558 485244 R identified by match to protein family HMM PF00702; match to protein family HMM TIGR01428; match to protein family HMM TIGR01493; haloacid dehalogenase complement(484558..485244) Ruegeria pomeroyi DSS-3 3196898 YP_165265.1 CDS SPOA0438 NC_006569.1 485378 485806 D identified by match to protein family HMM PF00254; peptidyl-prolyl cis-trans isomerase, FKBP-type 485378..485806 Ruegeria pomeroyi DSS-3 3196933 YP_165266.1 CDS fabI-3 NC_006569.1 485896 486687 R identified by similarity to SP:P29132; match to protein family HMM PF00106; enoyl-ACP reductase complement(485896..486687) Ruegeria pomeroyi DSS-3 3196632 YP_165267.1 CDS fabB NC_006569.1 486694 487923 R identified by similarity to SP:P14926; match to protein family HMM PF00109; match to protein family HMM PF02801; 3-oxoacyl-ACP synthase complement(486694..487923) Ruegeria pomeroyi DSS-3 3196704 YP_165268.1 CDS SPOA0441 NC_006569.1 488138 489025 D identified by similarity to GB:CAE06700.1; hypothetical protein 488138..489025 Ruegeria pomeroyi DSS-3 3196559 YP_165269.1 CDS SPOA0442 NC_006569.1 489041 489136 D hypothetical protein 489041..489136 Ruegeria pomeroyi DSS-3 3196803 YP_165270.1 CDS SPOA0443 NC_006569.1 489176 489439 D hypothetical protein 489176..489439 Ruegeria pomeroyi DSS-3 3196624 YP_165271.1 CDS fabA NC_006569.1 489506 490015 R catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-ACP dehydratase complement(489506..490015) Ruegeria pomeroyi DSS-3 3196601 YP_165272.1 CDS SPOA0445 NC_006569.1 490204 490623 D identified by match to protein family HMM PF01475; FUR family transcriptional regulator 490204..490623 Ruegeria pomeroyi DSS-3 3196743 YP_165273.1 CDS SPOA0446 NC_006569.1 490624 491520 R identified by match to protein family HMM PF00126; match to protein family HMM PF03466; LysR family transcriptional regulator complement(490624..491520) Ruegeria pomeroyi DSS-3 3196799 SPO_tRNA-Gln-1 tRNA SPO_tRNA-Gln-1 NC_003911.11 176231 176306 D tRNA-Gln 176231..176306 Ruegeria pomeroyi DSS-3 3196480 SPO_tRNA-Pro-2 tRNA SPO_tRNA-Pro-2 NC_003911.11 176312 176389 D tRNA-Pro 176312..176389 Ruegeria pomeroyi DSS-3 3196280 SPO_tRNA-Pro-3 tRNA SPO_tRNA-Pro-3 NC_003911.11 228692 228768 R tRNA-Pro complement(228692..228768) Ruegeria pomeroyi DSS-3 3193869 SPO_tRNA-Ile-1 tRNA SPO_tRNA-Ile-1 NC_003911.11 263580 263656 D tRNA-Ile 263580..263656 Ruegeria pomeroyi DSS-3 3196399 SPO_tRNA-Ala-1 tRNA SPO_tRNA-Ala-1 NC_003911.11 263730 263805 D tRNA-Ala 263730..263805 Ruegeria pomeroyi DSS-3 3195549 SPO_tRNA-Lys-2 tRNA SPO_tRNA-Lys-2 NC_003911.11 294934 295009 D tRNA-Lys 294934..295009 Ruegeria pomeroyi DSS-3 3196416 SPO_tRNA-Arg-2 tRNA SPO_tRNA-Arg-2 NC_003911.11 485387 485463 R tRNA-Arg complement(485387..485463) Ruegeria pomeroyi DSS-3 3195999 SPO_tRNA-Arg-3 tRNA SPO_tRNA-Arg-3 NC_003911.11 537350 537426 D tRNA-Arg 537350..537426 Ruegeria pomeroyi DSS-3 3196427 SPO_tRNA-Gln-2 tRNA SPO_tRNA-Gln-2 NC_003911.11 636094 636168 D tRNA-Gln 636094..636168 Ruegeria pomeroyi DSS-3 3196488 SPO_tRNA-Val-2 tRNA SPO_tRNA-Val-2 NC_003911.11 726006 726081 R tRNA-Val complement(726006..726081) Ruegeria pomeroyi DSS-3 3196493 SPO_tRNA-Trp-2 tRNA SPO_tRNA-Trp-2 NC_003911.11 758890 758965 D tRNA-Trp 758890..758965 Ruegeria pomeroyi DSS-3 3194683 SPO_tRNA-Thr-2 tRNA SPO_tRNA-Thr-2 NC_003911.11 1082915 1082990 D tRNA-Thr 1082915..1082990 Ruegeria pomeroyi DSS-3 3196481 SPO_tRNA-Pseudo-2 tRNA SPO_tRNA-Pseudo-2 NC_003911.11 1205683 1205766 R tRNA-OTHER complement(1205683..1205766) Ruegeria pomeroyi DSS-3 3194716 SPO_tRNA-Gly-2 tRNA SPO_tRNA-Gly-2 NC_003911.11 1217181 1217255 R tRNA-Gly complement(1217181..1217255) Ruegeria pomeroyi DSS-3 3196505 SPO_tRNA-Gly-3 tRNA SPO_tRNA-Gly-3 NC_003911.11 1217973 1218047 R tRNA-Gly complement(1217973..1218047) Ruegeria pomeroyi DSS-3 3196094 SPO_tRNA-Gly-4 tRNA SPO_tRNA-Gly-4 NC_003911.11 1218081 1218155 R tRNA-Gly complement(1218081..1218155) Ruegeria pomeroyi DSS-3 3196087 SPO_tRNA-Cys-2 tRNA SPO_tRNA-Cys-2 NC_003911.11 1307509 1307582 R tRNA-Cys complement(1307509..1307582) Ruegeria pomeroyi DSS-3 3196477 SPO_tRNA-Leu-2 tRNA SPO_tRNA-Leu-2 NC_003911.11 1458077 1458163 D tRNA-Leu 1458077..1458163 Ruegeria pomeroyi DSS-3 3194766 SPO_tRNA-Glu-2 tRNA SPO_tRNA-Glu-2 NC_003911.11 1849403 1849477 R tRNA-Glu complement(1849403..1849477) Ruegeria pomeroyi DSS-3 3196356 SPO_tRNA-Glu-3 tRNA SPO_tRNA-Glu-3 NC_003911.11 1849667 1849741 R tRNA-Glu complement(1849667..1849741) Ruegeria pomeroyi DSS-3 3196501 SPO_tRNA-His-1 tRNA SPO_tRNA-His-1 NC_003911.11 1886364 1886440 D tRNA-His 1886364..1886440 Ruegeria pomeroyi DSS-3 3196389 SPO_tRNA-Ser-2 tRNA SPO_tRNA-Ser-2 NC_003911.11 2046619 2046708 D tRNA-Ser 2046619..2046708 Ruegeria pomeroyi DSS-3 3196244 SPO_tRNA-Ser-3 tRNA SPO_tRNA-Ser-3 NC_003911.11 2119397 2119486 D tRNA-Ser 2119397..2119486 Ruegeria pomeroyi DSS-3 3193842 SPO_tRNA-Thr-3 tRNA SPO_tRNA-Thr-3 NC_003911.11 2140232 2140307 R tRNA-Thr complement(2140232..2140307) Ruegeria pomeroyi DSS-3 3193052 SPO_tRNA-Arg-4 tRNA SPO_tRNA-Arg-4 NC_003911.11 2140752 2140828 R tRNA-Arg complement(2140752..2140828) Ruegeria pomeroyi DSS-3 3196428 SPO_tRNA-Gly-5 tRNA SPO_tRNA-Gly-5 NC_003911.11 2173838 2173911 D tRNA-Gly 2173838..2173911 Ruegeria pomeroyi DSS-3 3196381 SPO_tRNA-Asn-1 tRNA SPO_tRNA-Asn-1 NC_003911.11 2251315 2251389 D tRNA-Asn 2251315..2251389 Ruegeria pomeroyi DSS-3 3196213 SPO_tRNA-Leu-3 tRNA SPO_tRNA-Leu-3 NC_003911.11 2251642 2251727 R tRNA-Leu complement(2251642..2251727) Ruegeria pomeroyi DSS-3 3192892 SPO_tRNA-Pro-4 tRNA SPO_tRNA-Pro-4 NC_003911.11 2274996 2275072 R tRNA-Pro complement(2274996..2275072) Ruegeria pomeroyi DSS-3 3194365 SPO_tRNA-Met-2 tRNA SPO_tRNA-Met-2 NC_003911.11 2308217 2308292 D tRNA-Met 2308217..2308292 Ruegeria pomeroyi DSS-3 3193918 SPO_tRNA-Asn-2 tRNA SPO_tRNA-Asn-2 NC_003911.11 2310677 2310751 D tRNA-Asn 2310677..2310751 Ruegeria pomeroyi DSS-3 3196443 SPO_tRNA-Leu-4 tRNA SPO_tRNA-Leu-4 NC_003911.11 2429430 2429513 R tRNA-Leu complement(2429430..2429513) Ruegeria pomeroyi DSS-3 3192882 SPO_tRNA-Pro-5 tRNA SPO_tRNA-Pro-5 NC_003911.11 2645397 2645473 D tRNA-Pro 2645397..2645473 Ruegeria pomeroyi DSS-3 3196267 SPO_tRNA-Asp-1 tRNA SPO_tRNA-Asp-1 NC_003911.11 2755575 2755651 R tRNA-Asp complement(2755575..2755651) Ruegeria pomeroyi DSS-3 3196457 SPO_tRNA-Asp-2 tRNA SPO_tRNA-Asp-2 NC_003911.11 2755704 2755780 R tRNA-Asp complement(2755704..2755780) Ruegeria pomeroyi DSS-3 3196474 SPO_tRNA-Val-3 tRNA SPO_tRNA-Val-3 NC_003911.11 2766850 2766924 R tRNA-Val complement(2766850..2766924) Ruegeria pomeroyi DSS-3 3194794 SPO_tRNA-Ser-4 tRNA SPO_tRNA-Ser-4 NC_003911.11 2929931 2930020 R tRNA-Ser complement(2929931..2930020) Ruegeria pomeroyi DSS-3 3194142 SPO_tRNA-Gly-6 tRNA SPO_tRNA-Gly-6 NC_003911.11 3206889 3206963 R tRNA-Gly complement(3206889..3206963) Ruegeria pomeroyi DSS-3 3196519 SPO_tRNA-Leu-5 tRNA SPO_tRNA-Leu-5 NC_003911.11 3207063 3207149 R tRNA-Leu complement(3207063..3207149) Ruegeria pomeroyi DSS-3 3194764 SPO_tRNA-Met-3 tRNA SPO_tRNA-Met-3 NC_003911.11 3461953 3462029 R tRNA-Met complement(3461953..3462029) Ruegeria pomeroyi DSS-3 3196233 SPO_tRNA-Ala-2 tRNA SPO_tRNA-Ala-2 NC_003911.11 3465737 3465812 R tRNA-Ala complement(3465737..3465812) Ruegeria pomeroyi DSS-3 3196378 SPO_tRNA-Ile-2 tRNA SPO_tRNA-Ile-2 NC_003911.11 3465886 3465962 R tRNA-Ile complement(3465886..3465962) Ruegeria pomeroyi DSS-3 3196524 SPO_tRNA-Val-4 tRNA SPO_tRNA-Val-4 NC_003911.11 3481060 3481134 D tRNA-Val 3481060..3481134 Ruegeria pomeroyi DSS-3 3194585 SPO_tRNA-Met-4 tRNA SPO_tRNA-Met-4 NC_003911.11 3701370 3701446 D tRNA-Met 3701370..3701446 Ruegeria pomeroyi DSS-3 3193742 SPO_tRNA-Ala-3 tRNA SPO_tRNA-Ala-3 NC_003911.11 3827177 3827252 D tRNA-Ala 3827177..3827252 Ruegeria pomeroyi DSS-3 3196234 SPO_tRNA-Ser-5 tRNA SPO_tRNA-Ser-5 NC_003911.11 3871397 3871486 D tRNA-Ser 3871397..3871486 Ruegeria pomeroyi DSS-3 3194910 SPO_tRNA-Arg-5 tRNA SPO_tRNA-Arg-5 NC_003911.11 3892522 3892598 R tRNA-Arg complement(3892522..3892598) Ruegeria pomeroyi DSS-3 3196433 SPO_tRNA-Leu-6 tRNA SPO_tRNA-Leu-6 NC_003911.11 3985347 3985433 D tRNA-Leu 3985347..3985433 Ruegeria pomeroyi DSS-3 3193309 SPO_tRNA-Met-5 tRNA SPO_tRNA-Met-5 NC_003911.11 4010290 4010366 R tRNA-Met complement(4010290..4010366) Ruegeria pomeroyi DSS-3 3196425 SPO_tRNA-Ala-4 tRNA SPO_tRNA-Ala-4 NC_003911.11 4014074 4014149 R tRNA-Ala complement(4014074..4014149) Ruegeria pomeroyi DSS-3 3196396 SPO_tRNA-Ile-3 tRNA SPO_tRNA-Ile-3 NC_003911.11 4014223 4014299 R tRNA-Ile complement(4014223..4014299) Ruegeria pomeroyi DSS-3 3195645 SPOA_tRNA-Phe-1 tRNA SPOA_tRNA-Phe-1 NC_006569.1 75805 75879 D tRNA-Phe 75805..75879 Ruegeria pomeroyi DSS-3 3196736 SPOA_tRNA-Thr-1 tRNA SPOA_tRNA-Thr-1 NC_006569.1 147302 147376 R tRNA-Thr complement(147302..147376) Ruegeria pomeroyi DSS-3 3196728 SPO_Sp16SA rRNA rrsA NC_003911.11 261910 263364 D 16S ribosomal RNA 261910..263364 Ruegeria pomeroyi DSS-3 3196347 SPO_Sp23SA rRNA rrlA NC_003911.11 264255 267149 D 23S ribosomal RNA 264255..267149 Ruegeria pomeroyi DSS-3 3194652 SPO_Sp5SD rRNA rrfD NC_003911.11 267353 267470 D 5S ribosomal RNA 267353..267470 Ruegeria pomeroyi DSS-3 3196376 SPO_Sp5SE rRNA rrfE NC_003911.11 3462072 3462189 R 5S ribosomal RNA complement(3462072..3462189) Ruegeria pomeroyi DSS-3 3196518 SPO_Sp23SB rRNA rrlB NC_003911.11 3462393 3465287 R 23S ribosomal RNA complement(3462393..3465287) Ruegeria pomeroyi DSS-3 3196510 SPO_Sp16SB rRNA rrsB NC_003911.11 3466178 3467632 R 16S ribosomal RNA complement(3466178..3467632) Ruegeria pomeroyi DSS-3 3196502 SPO_Sp5SF rRNA rrfF NC_003911.11 4010409 4010526 R 5S ribosomal RNA complement(4010409..4010526) Ruegeria pomeroyi DSS-3 3196247 SPO_Sp23SC rRNA rrlC NC_003911.11 4010730 4013624 R 23S ribosomal RNA complement(4010730..4013624) Ruegeria pomeroyi DSS-3 3196360 SPO_Sp16SC rRNA rrsC NC_003911.11 4014515 4015969 R 16S ribosomal RNA complement(4014515..4015969) Ruegeria pomeroyi DSS-3 3196367