-- dump date 20120504_140927 -- class Genbank::CDS -- table cds -- table main -- field 1 id -- field 2 GI -- field 3 GeneID -- field 4 chrom_position -- field 5 chromosome -- field 6 codon_start -- field 7 contig -- field 8 description -- field 9 end_pos -- field 10 gene -- field 11 gene_id -- field 12 name -- field 13 organism -- field 14 product -- field 15 protein_id -- field 16 start_pos -- field 17 strand -- field 18 taxid -- field 19 type -- header -- id GI GeneID chrom_position chromosome codon_start contig description end_pos gene gene_id name organism product protein_id start_pos strand taxid type YP_903276.1 118602061 4555497 39..1331 1 NC_008610.1 KEGG: cbu:CBU_0001 chromosomal replication initiator protein DnaA; TIGRFAM: chromosomal replication initiator protein DnaA; PFAM: Chromosomal replication initiator, DnaA C-terminal domain; Chromosomal replication initiator, DnaA; SMART: AAA ATPase; chromosomal replication initiator protein DnaA 1331 4555497 Rmag_0001 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) chromosomal replication initiator protein DnaA YP_903276.1 39 D 413404 CDS YP_903277.1 118602062 4555498 1543..2646 1 NC_008610.1 KEGG: mfa:Mfla_0002 DNA polymerase III, beta subunit; TIGRFAM: DNA polymerase III, beta subunit; PFAM: DNA polymerase III, beta chain; DNA polymerase III, beta subunit 2646 4555498 Rmag_0002 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA polymerase III, beta subunit YP_903277.1 1543 D 413404 CDS YP_903278.1 118602063 4555499 2946..5354 1 NC_008610.1 KEGG: tcx:Tcr_0012 DNA gyrase, B subunit; TIGRFAM: DNA gyrase, B subunit; PFAM: DNA gyrase, subunit B domain protein; ATP-binding region, ATPase domain protein domain protein; TOPRIM domain protein; DNA topoisomerase, type IIA, subunit B, region 2 domain protein; SMART: DNA topoisomerase II; DNA gyrase subunit B 5354 4555499 Rmag_0003 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA gyrase subunit B YP_903278.1 2946 D 413404 CDS YP_903279.1 118602064 4555500 5385..6272 1 NC_008610.1 PFAM: phosphoribulokinase/uridine kinase; KEGG: tbd:Tbd_2447 phosphoribulokinase; phosphoribulokinase 6272 4555500 Rmag_0004 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribulokinase YP_903279.1 5385 D 413404 CDS YP_903280.1 118602065 4555501 complement(6904..9354) 1 NC_008610.1 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 9354 leuS 4555501 leuS Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) leucyl-tRNA synthetase YP_903280.1 6904 R 413404 CDS YP_903281.1 118602066 4555333 complement(9387..10325) 1 NC_008610.1 TIGRFAM: dihydroorotate dehydrogenase family protein; PFAM: dihydroorotate dehydrogenase; KEGG: noc:Noc_2822 dihydroorotate dehydrogenase 1; dihydroorotate oxidase B, catalytic subunit 10325 4555333 Rmag_0006 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydroorotate oxidase B, catalytic subunit YP_903281.1 9387 R 413404 CDS YP_903282.1 118602067 4555334 10365..11006 1 NC_008610.1 TIGRFAM: dethiobiotin synthase; KEGG: tcx:Tcr_0261 dethiobiotin synthase; dethiobiotin synthase 11006 4555334 Rmag_0007 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dethiobiotin synthase YP_903282.1 10365 D 413404 CDS YP_903283.1 118602068 4555335 complement(11289..11918) 1 NC_008610.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: hch:HCH_05897 glutathione S-transferase; glutathione S-transferase domain-containing protein 11918 4555335 Rmag_0008 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutathione S-transferase domain-containing protein YP_903283.1 11289 R 413404 CDS YP_903284.1 118602069 4555336 complement(11997..12860) 1 NC_008610.1 KEGG: lpf:lpl2631 ubiquinol-cytochrome c reductase cytochrome c1 subunit; ubiquinol-cytochrome c reductase cytochrome c1 subunit 12860 4555336 Rmag_0009 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ubiquinol-cytochrome c reductase cytochrome c1 subunit YP_903284.1 11997 R 413404 CDS YP_903285.1 118602070 4555337 complement(12864..14087) 1 NC_008610.1 PFAM: Cytochrome b/b6, N-terminal domain; Cytochrome b/b6, C-terminal domain; KEGG: tbd:Tbd_1832 cytochrome b subunit of cytochrome bc1; cytochrome b/b6 domain-containing protein 14087 4555337 Rmag_0010 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome b/b6 domain-containing protein YP_903285.1 12864 R 413404 CDS YP_903286.1 118602071 4555338 complement(14101..14697) 1 NC_008610.1 KEGG: noc:Noc_0299 ubiquinol-cytochrome c reductase, iron-sulfur subunit; TIGRFAM: ubiquinol-cytochrome c reductase, iron-sulfur subunit; PFAM: Rieske [2Fe-2S] domain protein; ubiquinol-cytochrome c reductase, iron-sulfur subunit 14697 4555338 Rmag_0011 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ubiquinol-cytochrome c reductase, iron-sulfur subunit YP_903286.1 14101 R 413404 CDS YP_903287.1 118602072 4555339 complement(14802..15107) 1 NC_008610.1 hypothetical protein 15107 4555339 Rmag_0012 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903287.1 14802 R 413404 CDS YP_903288.1 118602073 4555340 15160..17838 1 NC_008610.1 TIGRFAM: preprotein translocase, SecA subunit; PFAM: helicase domain protein; SEC-C motif domain protein; SecA DEAD domain protein; SecA Wing and Scaffold; SecA preprotein cross-linking region; KEGG: vfi:VF2193 protein translocase subunit SecA; protein translocase subunit secA 17838 4555340 Rmag_0013 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein translocase subunit secA YP_903288.1 15160 D 413404 CDS YP_903289.1 118602074 4555341 17831..18889 1 NC_008610.1 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 18889 anmK 4555341 anmK Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) anhydro-N-acetylmuramic acid kinase YP_903289.1 17831 D 413404 CDS YP_903290.1 118602075 4555342 18879..19913 1 NC_008610.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 19913 4555342 Rmag_0015 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydroorotase YP_903290.1 18879 D 413404 CDS YP_903291.1 118602076 4555343 complement(20251..21153) 1 NC_008610.1 TIGRFAM: riboflavin biosynthesis protein RibF; PFAM: Riboflavin kinase / FAD synthetase; KEGG: son:SO3533 riboflavin biosynthesis protein RibF; FMN adenylyltransferase / riboflavin kinase 21153 4555343 Rmag_0016 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) FMN adenylyltransferase / riboflavin kinase YP_903291.1 20251 R 413404 CDS YP_903292.1 118602077 4555344 complement(22172..23227) 1 NC_008610.1 catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase 23227 4555344 Rmag_0018 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) homoserine O-succinyltransferase YP_903292.1 22172 R 413404 CDS YP_903293.1 118602078 4555345 complement(23227..24063) 1 NC_008610.1 KEGG: noc:Noc_2702 hypothetical protein; hypothetical protein 24063 4555345 Rmag_0019 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903293.1 23227 R 413404 CDS YP_903294.1 118602079 4555346 complement(24091..25278) 1 NC_008610.1 PFAM: aminotransferase, class I and II; KEGG: hch:HCH_01778 aspartate/tyrosine/aromatic aminotransferase; aminotransferase 25278 4555346 Rmag_0020 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aminotransferase YP_903294.1 24091 R 413404 CDS YP_903295.1 118602080 4555347 complement(25334..25639) 1 NC_008610.1 PFAM: peptidylprolyl isomerase, FKBP-type; KEGG: tbd:Tbd_2152 peptidyl-prolyl cis-trans isomerase; peptidylprolyl isomerase, FKBP-type 25639 4555347 Rmag_0021 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidylprolyl isomerase, FKBP-type YP_903295.1 25334 R 413404 CDS YP_903296.1 118602081 4555348 complement(25650..26423) 1 NC_008610.1 KEGG: pha:PSHAa0339 hypothetical protein; hypothetical protein 26423 4555348 Rmag_0022 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903296.1 25650 R 413404 CDS YP_903297.1 118602082 4555349 complement(26456..27334) 1 NC_008610.1 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 27334 4555349 Rmag_0023 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribosylaminoimidazole-succinocarboxamide synthase YP_903297.1 26456 R 413404 CDS YP_903298.1 118602083 4555350 complement(27845..28963) 1 NC_008610.1 PFAM: peptidase M23B; KEGG: pae:PA0667 hypothetical protein; peptidase M23B 28963 4555350 Rmag_0024 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase M23B YP_903298.1 27845 R 413404 CDS YP_903299.1 118602084 4555351 complement(28956..30107) 1 NC_008610.1 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 30107 4555351 Rmag_0025 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 1-deoxy-D-xylulose 5-phosphate reductoisomerase YP_903299.1 28956 R 413404 CDS YP_903300.1 118602085 4555352 complement(30104..30904) 1 NC_008610.1 PFAM: phosphatidate cytidylyltransferase; KEGG: cps:CPS_1558 phosphatidate cytidylyltransferase; phosphatidate cytidylyltransferase 30904 4555352 Rmag_0026 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphatidate cytidylyltransferase YP_903300.1 30104 R 413404 CDS YP_903301.1 118602086 4554914 complement(30898..31644) 1 NC_008610.1 KEGG: vvy:VV2553 undecaprenyl pyrophosphate synthase; TIGRFAM: undecaprenyl diphosphate synthase; PFAM: Di-trans-poly-cis-decaprenylcistransferase; undecaprenyl pyrophosphate synthetase 31644 4554914 Rmag_0027 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) undecaprenyl pyrophosphate synthetase YP_903301.1 30898 R 413404 CDS YP_903302.1 118602087 4554915 34314..35081 1 NC_008610.1 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 35081 4554915 Rmag_0028 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) imidazole glycerol phosphate synthase subunit HisF YP_903302.1 34314 D 413404 CDS YP_903303.1 118602088 4554916 35150..35680 1 NC_008610.1 KEGG: neu:NE1011 putative transmembrane protein; putative transmembrane protein 35680 4554916 Rmag_0029 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative transmembrane protein YP_903303.1 35150 D 413404 CDS YP_903304.1 118602089 4554917 35687..36586 1 NC_008610.1 converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase 36586 4554917 Rmag_0030 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protoheme IX farnesyltransferase YP_903304.1 35687 D 413404 CDS YP_903305.1 118602090 4554918 36587..36778 1 NC_008610.1 hypothetical protein 36778 4554918 Rmag_0031 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903305.1 36587 D 413404 CDS YP_903306.1 118602091 4554919 complement(37140..38111) 1 NC_008610.1 PFAM: cytochrome oxidase assembly; KEGG: noc:Noc_3040 cytochrome oxidase assembly; cytochrome oxidase assembly 38111 4554919 Rmag_0032 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome oxidase assembly YP_903306.1 37140 R 413404 CDS YP_903307.1 118602092 4554920 complement(38205..39029) 1 NC_008610.1 KEGG: cvi:CV3790 hypothetical protein; hypothetical protein 39029 4554920 Rmag_0033 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903307.1 38205 R 413404 CDS YP_903308.1 118602093 4554921 39283..40350 1 NC_008610.1 PFAM: cytochrome c oxidase, subunit II; cytochrome c, class I; cytochrome C oxidase subunit II, transmembrane region; KEGG: pha:PSHAa2872 cytochrome c oxidase, subunit II; cytochrome-c oxidase 40350 4554921 Rmag_0034 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome-c oxidase YP_903308.1 39283 D 413404 CDS YP_903309.1 118602094 4554922 40373..41989 1 NC_008610.1 PFAM: cytochrome c oxidase, subunit I; KEGG: pae:PA0106 cytochrome c oxidase, subunit I; cytochrome-c oxidase 41989 4554922 Rmag_0035 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome-c oxidase YP_903309.1 40373 D 413404 CDS YP_903310.1 118602095 4554923 42080..42613 1 NC_008610.1 PFAM: cytochrome c oxidase assembly protein CtaG/Cox11; KEGG: mca:MCA0882 cytochrome c oxidase assembly protein, putative; cytochrome c oxidase assembly protein CtaG/Cox11 42613 4554923 Rmag_0036 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome c oxidase assembly protein CtaG/Cox11 YP_903310.1 42080 D 413404 CDS YP_903311.1 118602096 4554924 42631..43515 1 NC_008610.1 PFAM: cytochrome c oxidase, subunit III; KEGG: hch:HCH_00049 cytochrome-c oxidase, subnunit III; cytochrome c oxidase, subunit III 43515 4554924 Rmag_0037 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome c oxidase, subunit III YP_903311.1 42631 D 413404 CDS YP_903312.1 118602097 4554925 43758..44504 1 NC_008610.1 KEGG: mca:MCA0131 hypothetical protein; hypothetical protein 44504 4554925 Rmag_0038 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903312.1 43758 D 413404 CDS YP_903313.1 118602098 4554926 44618..46036 1 NC_008610.1 CcoN; FixN; cbb3-type cytochrome c oxidase subunit I 46036 4554926 Rmag_0039 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cbb3-type cytochrome c oxidase subunit I YP_903313.1 44618 D 413404 CDS YP_903314.1 118602099 4554927 46050..46781 1 NC_008610.1 CcoO; FixO; cbb3-type cytochrome c oxidase subunit II 46781 4554927 Rmag_0040 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cbb3-type cytochrome c oxidase subunit II YP_903314.1 46050 D 413404 CDS YP_903315.1 118602100 4554928 46945..47847 1 NC_008610.1 KEGG: tcx:Tcr_1963 cytochrome c oxidase, cbb3-type, subunit III; cytochrome c oxidase, cbb3-type, subunit III 47847 4554928 Rmag_0041 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome c oxidase, cbb3-type, subunit III YP_903315.1 46945 D 413404 CDS YP_903316.1 118602101 4554929 complement(49389..49970) 1 NC_008610.1 PFAM: outer membrane lipoprotein carrier protein LolA; KEGG: pae:PA2614 periplasmic chaperone LolA; outer membrane lipoprotein carrier protein LolA 49970 4554929 Rmag_0042 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) outer membrane lipoprotein carrier protein LolA YP_903316.1 49389 R 413404 CDS YP_903317.1 118602102 4554930 complement(49963..52230) 1 NC_008610.1 PFAM: cell divisionFtsK/SpoIIIE; KEGG: sde:Sde_1693 cell division protein FtsK; DNA translocase FtsK 52230 4554930 Rmag_0043 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA translocase FtsK YP_903317.1 49963 R 413404 CDS YP_903318.1 118602103 4554931 52279..53223 1 NC_008610.1 TIGRFAM: thioredoxin reductase; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: tcx:Tcr_0763 thioredoxin reductase; thioredoxin reductase 53223 4554931 Rmag_0044 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thioredoxin reductase YP_903318.1 52279 D 413404 CDS YP_903319.1 118602104 4554932 complement(54174..55136) 1 NC_008610.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase catalytic subunit 55136 pyrB 4554932 pyrB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aspartate carbamoyltransferase catalytic subunit YP_903319.1 54174 R 413404 CDS YP_903320.1 118602105 4554808 complement(55117..55545) 1 NC_008610.1 PFAM: Holliday junction resolvase YqgF; SMART: Resolvase, RNase H domain protein fold; KEGG: cbu:CBU_2094 putative Holliday junction resolvase; Holliday junction resolvase YqgF 55545 4554808 Rmag_0046 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Holliday junction resolvase YqgF YP_903320.1 55117 R 413404 CDS YP_903321.1 118602106 4554809 complement(55542..56726) 1 NC_008610.1 TIGRFAM: lytic murein transglycosylase; PFAM: Peptidoglycan-binding domain 1 protein; KEGG: sat:SYN_02632 membrane-bound lytic murein transglycosylase B; lytic murein transglycosylase 56726 4554809 Rmag_0047 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lytic murein transglycosylase YP_903321.1 55542 R 413404 CDS YP_903322.1 118602107 4554810 56739..57665 1 NC_008610.1 PFAM: ApbE family lipoprotein; KEGG: sde:Sde_1803 thiamine biosynthesis lipoprotein; ApbE family lipoprotein 57665 4554810 Rmag_0048 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ApbE family lipoprotein YP_903322.1 56739 D 413404 CDS YP_903323.1 118602108 4554811 58950..59342 1 NC_008610.1 TIGRFAM: CrcB protein; PFAM: Camphor resistance CrcB protein; KEGG: lpn:lpg0512 CrcB protein, camphor resistance; camphor resistance protein CrcB 59342 4554811 Rmag_0050 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) camphor resistance protein CrcB YP_903323.1 58950 D 413404 CDS YP_903324.1 118602109 4554812 complement(59339..60301) 1 NC_008610.1 KEGG: tcx:Tcr_1825 glutathione synthetase; TIGRFAM: glutathione synthetase; PFAM: glutathione synthetase domain protein; glutathione synthetase, ATP-binding; RimK domain protein ATP-grasp; glutathione synthase 60301 4554812 Rmag_0051 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutathione synthase YP_903324.1 59339 R 413404 CDS YP_903325.1 118602110 4554813 60518..60982 1 NC_008610.1 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 60982 4554813 Rmag_0052 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903325.1 60518 D 413404 CDS YP_903326.1 118602111 4554814 61014..62489 1 NC_008610.1 KEGG: mca:MCA1316 N utilization substance protein A; TIGRFAM: transcription termination factor NusA; PFAM: RNA binding S1 domain protein; KH, type 1, domain protein; NusA N-terminal domain protein; SMART: KH domain protein; NusA antitermination factor 62489 4554814 Rmag_0053 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NusA antitermination factor YP_903326.1 61014 D 413404 CDS YP_903327.1 118602112 4554815 62546..64993 1 NC_008610.1 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 64993 infB 4554815 infB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) translation initiation factor IF-2 YP_903327.1 62546 D 413404 CDS YP_903328.1 118602113 4554816 65011..65349 1 NC_008610.1 PFAM: ribosome-binding factor A; KEGG: lpp:lpp2819 ribosome-binding factor A; ribosome-binding factor A 65349 4554816 Rmag_0055 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribosome-binding factor A YP_903328.1 65011 D 413404 CDS YP_903329.1 118602114 4554817 65374..66282 1 NC_008610.1 KEGG: pmu:PM0756 tRNA pseudouridine 55 synthase; TIGRFAM: tRNA pseudouridine synthase B; PFAM: pseudouridylate synthase TruB domain protein; tRNA pseudouridine synthase B 66282 4554817 Rmag_0056 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA pseudouridine synthase B YP_903329.1 65374 D 413404 CDS YP_903330.1 118602115 4554818 66845..68116 1 NC_008610.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase 68116 4554818 Rmag_0057 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribosylamine--glycine ligase YP_903330.1 66845 D 413404 CDS YP_903331.1 118602116 4554819 complement(68472..69230) 1 NC_008610.1 KEGG: neu:NE1008 hypothetical protein; periplasmic or secreted lipoprotein-like 69230 4554819 Rmag_0058 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) periplasmic or secreted lipoprotein-like YP_903331.1 68472 R 413404 CDS YP_903332.1 118602117 4554820 69598..70428 1 NC_008610.1 TIGRFAM: Protein of unknown function UPF0011; PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; KEGG: aci:ACIAD1130 putative methyltransferase; hypothetical protein 70428 4554820 Rmag_0059 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903332.1 69598 D 413404 CDS YP_903333.1 118602118 4554821 complement(70723..71328) 1 NC_008610.1 KEGG: cbu:CBU_0152 dephospho-CoA kinase; TIGRFAM: dephospho-CoA kinase; PFAM: Dephospho-CoA kinase; dephospho-CoA kinase 71328 4554821 Rmag_0061 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dephospho-CoA kinase YP_903333.1 70723 R 413404 CDS YP_903334.1 118602119 4554822 71651..73636 1 NC_008610.1 KEGG: tcx:Tcr_0244 transketolase; TIGRFAM: transketolase; PFAM: Transketolase domain protein; Transketolase, central region; transketolase 73636 4554822 Rmag_0062 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) transketolase YP_903334.1 71651 D 413404 CDS YP_903335.1 118602120 4554823 73745..74740 1 NC_008610.1 TIGRFAM: glyceraldehyde-3-phosphate dehydrogenase, type I; PFAM: glyceraldehyde 3-phosphate dehydrogenase; KEGG: tbd:Tbd_0160 glyceraldehyde-3-phosphate dehydrogenase, type I; glyceraldehyde-3-phosphate dehydrogenase 74740 4554823 Rmag_0063 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glyceraldehyde-3-phosphate dehydrogenase YP_903335.1 73745 D 413404 CDS YP_903336.1 118602121 4554824 75162..76337 1 NC_008610.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase 76337 pgk 4554824 pgk Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoglycerate kinase YP_903336.1 75162 D 413404 CDS YP_903337.1 118602122 4554825 76330..77772 1 NC_008610.1 PFAM: pyruvate kinase; KEGG: vpa:VP2039 pyruvate kinase II; pyruvate kinase 77772 4554825 Rmag_0066 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) pyruvate kinase YP_903337.1 76330 D 413404 CDS YP_903338.1 118602123 4554826 77856..78917 1 NC_008610.1 KEGG: noc:Noc_2804 fructose-bisphosphate aldolase, class II, calvin cycle subtype; TIGRFAM: ketose-bisphosphate aldolases; fructose-bisphosphate aldolase, class II, Calvin cycle subtype; PFAM: ketose-bisphosphate aldolase, class-II; fructose-bisphosphate aldolase 78917 4554826 Rmag_0067 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) fructose-bisphosphate aldolase YP_903338.1 77856 D 413404 CDS YP_903339.1 118602124 4554827 78981..80855 1 NC_008610.1 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 enzyme GidA 80855 4554827 Rmag_0068 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA YP_903339.1 78981 D 413404 CDS YP_903340.1 118602125 4554692 80891..81463 1 NC_008610.1 TIGRFAM: methyltransferase GidB; PFAM: glucose inhibited division protein; KEGG: mfa:Mfla_2754 methyltransferase GidB; methyltransferase GidB 81463 4554692 Rmag_0069 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) methyltransferase GidB YP_903340.1 80891 D 413404 CDS YP_903341.1 118602126 4554693 81460..82260 1 NC_008610.1 KEGG: sde:Sde_1913 hypothetical protein; hypothetical protein 82260 4554693 Rmag_0070 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903341.1 81460 D 413404 CDS YP_903342.1 118602127 4554694 82267..83037 1 NC_008610.1 TIGRFAM: hydrolase, TatD family; PFAM: TatD-related deoxyribonuclease; KEGG: rso:RSc1787 putative deoxyribonuclease; TatD family hydrolase 83037 4554694 Rmag_0071 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) TatD family hydrolase YP_903342.1 82267 D 413404 CDS YP_903343.1 118602128 4554695 83034..83945 1 NC_008610.1 TIGRFAM: pseudouridine synthase, RluA family; PFAM: RNA-binding S4 domain protein; pseudouridine synthase; KEGG: pmu:PM0992 ribosomal large subunit pseudouridine synthase C; ribosomal large subunit pseudouridine synthase C 83945 4554695 Rmag_0072 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribosomal large subunit pseudouridine synthase C YP_903343.1 83034 D 413404 CDS YP_903344.1 118602129 4554696 83993..84814 1 NC_008610.1 TIGRFAM: 4-hydroxybenzoate polyprenyl transferase; PFAM: UbiA prenyltransferase; KEGG: vch:VC0094 4-hydroxybenzoate octaprenyltransferase; 4-hydroxybenzoate octaprenyltransferase 84814 4554696 Rmag_0073 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 4-hydroxybenzoate octaprenyltransferase YP_903344.1 83993 D 413404 CDS YP_903345.1 118602130 4554697 complement(85474..86289) 1 NC_008610.1 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 86289 dapD 4554697 dapD Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase YP_903345.1 85474 R 413404 CDS YP_903346.1 118602131 4554698 86449..87843 1 NC_008610.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: tcx:Tcr_1962 4Fe-4S ferredoxin, iron-sulfur binding; 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein 87843 4554698 Rmag_0075 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein YP_903346.1 86449 D 413404 CDS YP_903347.1 118602132 4554699 87843..88322 1 NC_008610.1 KEGG: tcx:Tcr_1961 hypothetical protein; hypothetical protein 88322 4554699 Rmag_0076 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903347.1 87843 D 413404 CDS YP_903348.1 118602133 4554700 complement(90190..90891) 1 NC_008610.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: vfi:VF0829 high-affinity zinc uptake system ATP-binding protein ZnuC; ABC transporter related 90891 4554700 Rmag_0077 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_903348.1 90190 R 413404 CDS YP_903349.1 118602134 4554701 90999..93719 1 NC_008610.1 KEGG: hch:HCH_06350 DNA polymerase I; TIGRFAM: DNA polymerase I; PFAM: DNA-directed DNA polymerase; 5'-3' exonuclease; 3'-5' exonuclease; SMART: Helix-hairpin-helix domain protein, class 2; DNA polymerase I 93719 4554701 Rmag_0078 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA polymerase I YP_903349.1 90999 D 413404 CDS YP_903350.1 118602135 4554702 93735..95438 1 NC_008610.1 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 95438 argS 4554702 argS Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) arginyl-tRNA synthetase YP_903350.1 93735 D 413404 CDS YP_903351.1 118602136 4554703 95435..98596 1 NC_008610.1 PFAM: UvrD/REP helicase; KEGG: cbu:CBU_1230 UvrD/REP helicase family protein; UvrD/REP helicase 98596 4554703 Rmag_0080 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UvrD/REP helicase YP_903351.1 95435 D 413404 CDS YP_903352.1 118602137 4554704 complement(99327..99908) 1 NC_008610.1 PFAM: thiamine monophosphate synthase; KEGG: cvi:CV0150 probable thiamine-phosphate diphosphorylase; thiamine-phosphate diphosphorylase 99908 4554704 Rmag_0082 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thiamine-phosphate diphosphorylase YP_903352.1 99327 R 413404 CDS YP_903353.1 118602138 4554705 99907..100869 1 NC_008610.1 PFAM: protein of unknown function DUF1239; hypothetical protein 100869 4554705 Rmag_0083 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903353.1 99907 D 413404 CDS YP_903354.1 118602139 4554706 100862..101347 1 NC_008610.1 PFAM: OstA family protein; KEGG: noc:Noc_2791 OstA-like protein; OstA family protein 101347 4554706 Rmag_0084 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) OstA family protein YP_903354.1 100862 D 413404 CDS YP_903355.1 118602140 4554707 101492..102700 1 NC_008610.1 ATP sulfurylase; ATPS; converts ATP and sulfate to 5'phosphosulfate and pyrophosphate; in some organisms this enzyme is involved in the incorporation of inorganic sulfate while in others it is involved in the production of ATP in the reverse direction; the enzyme from Thermus thermophilus is dimeric and binds a zinc ion that is coordinated by cysteine and histidine residues that are not found in all related proteins but is found in some thermophilic organisms; sulfate adenylyltransferase 102700 sat 4554707 sat Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sulfate adenylyltransferase YP_903355.1 101492 D 413404 CDS YP_903356.1 118602141 4554708 102897..103766 1 NC_008610.1 KEGG: tbd:Tbd_2284 hypothetical protein; hypothetical protein 103766 4554708 Rmag_0086 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903356.1 102897 D 413404 CDS YP_903357.1 118602142 4554709 103798..104277 1 NC_008610.1 TIGRFAM: adenylylsulfate reductase, beta subunit; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: tbd:Tbd_2283 adenylylsulfate reductase, beta subunit; adenylylsulfate reductase, beta subunit 104277 4554709 Rmag_0087 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) adenylylsulfate reductase, beta subunit YP_903357.1 103798 D 413404 CDS YP_903358.1 118602143 4554710 104277..106160 1 NC_008610.1 catalyzes the reduction of adenosine 5'-phosphosulfate to AMP and sulfite; adenylylsulfate reductase subunit alpha 106160 4554710 Rmag_0088 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) adenylylsulfate reductase subunit alpha YP_903358.1 104277 D 413404 CDS YP_903359.1 118602144 4555313 106231..106581 1 NC_008610.1 KEGG: tbd:Tbd_2281 hypothetical protein; hypothetical protein 106581 4555313 Rmag_0089 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903359.1 106231 D 413404 CDS YP_903360.1 118602145 4555314 106587..107093 1 NC_008610.1 KEGG: tbd:Tbd_2280 putative peptidyl-prolyl cis-trans isomerase; putative peptidyl-prolyl cis-trans isomerase 107093 4555314 Rmag_0090 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative peptidyl-prolyl cis-trans isomerase YP_903360.1 106587 D 413404 CDS YP_903361.1 118602146 4555315 107096..107455 1 NC_008610.1 KEGG: tbd:Tbd_1503 hypothetical protein; hypothetical protein 107455 4555315 Rmag_0091 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903361.1 107096 D 413404 CDS YP_903362.1 118602147 4555316 complement(107558..109558) 1 NC_008610.1 pyrophosphate-energized proton pump; pyrophosphate-energized inorganic pyrophosphatase; H+-PPase; can cleave pyrophosphate to two phosphates; can generate a proton motive force and drive pyrophosphate synthesis when PMF is sufficient; membrane-bound proton-translocating pyrophosphatase 109558 hppA 4555316 hppA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) membrane-bound proton-translocating pyrophosphatase YP_903362.1 107558 R 413404 CDS YP_903363.1 118602148 4555317 complement(110185..110835) 1 NC_008610.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 110835 adk 4555317 adk Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) adenylate kinase YP_903363.1 110185 R 413404 CDS YP_903364.1 118602149 4555318 complement(110906..112150) 1 NC_008610.1 catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis; 6-phosphofructokinase 112150 4555318 Rmag_0094 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 6-phosphofructokinase YP_903364.1 110906 R 413404 CDS YP_903365.1 118602150 4555319 complement(114090..114329) 1 NC_008610.1 KEGG: sdn:Sden_3728 cadherin; hypothetical protein 114329 4555319 Rmag_0095 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903365.1 114090 R 413404 CDS YP_903366.1 118602151 4555320 complement(116484..117872) 1 NC_008610.1 KEGG: mca:MCA0509 cysteinyl-tRNA synthetase; TIGRFAM: cysteinyl-tRNA synthetase; PFAM: cysteinyl-tRNA synthetase, class Ia; cysteinyl-tRNA synthetase 117872 4555320 Rmag_0097 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cysteinyl-tRNA synthetase YP_903366.1 116484 R 413404 CDS YP_903367.1 118602152 4555321 118002..118601 1 NC_008610.1 PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; KEGG: tcx:Tcr_1387 alkyl hydroperoxide reductase/thiol specific antioxidant/Mal allergen; alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen 118601 4555321 Rmag_0098 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen YP_903367.1 118002 D 413404 CDS YP_903368.1 118602153 4555322 118857..119927 1 NC_008610.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase 119927 4555322 Rmag_0099 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-isopropylmalate dehydrogenase YP_903368.1 118857 D 413404 CDS YP_903369.1 118602154 4555323 122225..122770 1 NC_008610.1 ADP-sugar pyrophosphatase; catalyzes the formation of D-ribose 5-phosphate from ADP-ribose; can also act on ADP-mannose and ADP-glucose; ADP-ribose diphosphatase NudE 122770 nudE 4555323 nudE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ADP-ribose diphosphatase NudE YP_903369.1 122225 D 413404 CDS YP_903370.1 118602155 4555324 123511..124758 1 NC_008610.1 TIGRFAM: diaminopimelate decarboxylase; PFAM: Orn/DAP/Arg decarboxylase 2; KEGG: tcx:Tcr_1847 diaminopimelate decarboxylase; diaminopimelate decarboxylase 124758 4555324 Rmag_0103 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) diaminopimelate decarboxylase YP_903370.1 123511 D 413404 CDS YP_903371.1 118602156 4555325 124751..125053 1 NC_008610.1 PFAM: protein of unknown function UPF0044; KEGG: pmu:PM0713 putative RNA-binding protein containing KH domain; hypothetical protein 125053 4555325 Rmag_0104 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903371.1 124751 D 413404 CDS YP_903372.1 118602157 4555326 125019..126146 1 NC_008610.1 KEGG: sde:Sde_2584 lipid-A-disaccharide synthase; TIGRFAM: lipid-A-disaccharide synthase; PFAM: glycosyl transferase, family 19; lipid-A-disaccharide synthase 126146 4555326 Rmag_0105 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lipid-A-disaccharide synthase YP_903372.1 125019 D 413404 CDS YP_903373.1 118602158 4555327 126127..126963 1 NC_008610.1 KEGG: cbu:CBU_0098 nicotinate-nucleotide pyrophosphorylase; TIGRFAM: nicotinate-nucleotide pyrophosphorylase; PFAM: Quinolinate phosphoribosyl transferase; nicotinate-nucleotide pyrophosphorylase [carboxylating] 126963 4555327 Rmag_0106 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) nicotinate-nucleotide pyrophosphorylase [carboxylating] YP_903373.1 126127 D 413404 CDS YP_903374.1 118602159 4555328 complement(126949..127707) 1 NC_008610.1 PFAM: inositol monophosphatase; KEGG: noc:Noc_2419 3(2),5 -bisphosphate nucleotidase; inositol monophosphatase 127707 4555328 Rmag_0107 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) inositol monophosphatase YP_903374.1 126949 R 413404 CDS YP_903375.1 118602160 4555329 complement(127824..129626) 1 NC_008610.1 TIGRFAM: RNA polymerase sigma factor RpoD; PFAM: sigma-70 1.1 domain protein; sigma-70 region 3 domain protein; sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; sigma-70, non-essential domain protein; sigma-70 region 1.2; KEGG: xfa:XF1350 RNA polymerase sigma-70 factor; RNA polymerase, sigma 70 subunit, RpoD 129626 4555329 Rmag_0108 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) RNA polymerase, sigma 70 subunit, RpoD YP_903375.1 127824 R 413404 CDS YP_903376.1 118602161 4555330 complement(129728..130681) 1 NC_008610.1 KEGG: tbd:Tbd_0387 ribose-phosphate pyrophosphokinase; TIGRFAM: ribose-phosphate pyrophosphokinase; PFAM: phosphoribosyltransferase; ribose-phosphate pyrophosphokinase 130681 4555330 Rmag_0109 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribose-phosphate pyrophosphokinase YP_903376.1 129728 R 413404 CDS YP_903377.1 118602162 4555331 complement(130808..131665) 1 NC_008610.1 An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis; 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 131665 ipk 4555331 ipk Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase YP_903377.1 130808 R 413404 CDS YP_903378.1 118602163 4555332 complement(131658..132200) 1 NC_008610.1 3'-5' exoribonuclease specific for small oligoribonuclotides; oligoribonuclease 132200 4555332 Rmag_0111 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) oligoribonuclease YP_903378.1 131658 R 413404 CDS YP_903379.1 118602164 4555519 complement(132215..133234) 1 NC_008610.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate; anthranilate phosphoribosyltransferase 133234 trpD 4555519 trpD Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) anthranilate phosphoribosyltransferase YP_903379.1 132215 R 413404 CDS YP_903380.1 118602165 4555520 complement(133242..134456) 1 NC_008610.1 PFAM: peptidase M24; peptidase M24B, X-Pro dipeptidase/aminopeptidase domain protein; KEGG: aci:ACIAD1126 aminopeptidase P; peptidase M24 134456 4555520 Rmag_0113 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase M24 YP_903380.1 133242 R 413404 CDS YP_903381.1 118602166 4555521 complement(135125..135394) 1 NC_008610.1 hypothetical protein 135394 4555521 Rmag_0114 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903381.1 135125 R 413404 CDS YP_903382.1 118602167 4555522 complement(135363..135722) 1 NC_008610.1 KEGG: tbd:Tbd_2558 hypothetical protein; hypothetical protein 135722 4555522 Rmag_0115 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903382.1 135363 R 413404 CDS YP_903383.1 118602168 4555523 complement(135981..136841) 1 NC_008610.1 KEGG: tcx:Tcr_1837 pyrroline-5-carboxylate reductase; TIGRFAM: pyrroline-5-carboxylate reductase; PFAM: NADP oxidoreductase, coenzyme F420-dependent; NAD-dependent glycerol-3-phosphate dehydrogenase domain protein; pyrroline-5-carboxylate reductase 136841 4555523 Rmag_0116 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) pyrroline-5-carboxylate reductase YP_903383.1 135981 R 413404 CDS YP_903384.1 118602169 4555524 136881..137549 1 NC_008610.1 catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate; phosphoglycolate phosphatase 137549 4555524 Rmag_0117 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoglycolate phosphatase YP_903384.1 136881 D 413404 CDS YP_903385.1 118602170 4555525 137574..138812 1 NC_008610.1 TIGRFAM: adenosylmethionine-8-amino-7-oxononanoate aminotransferase; PFAM: aminotransferase class-III; KEGG: hin:HI1554 adenosylmethionine--8-amino-7-oxononanoate transaminase; aminotransferase 138812 4555525 Rmag_0118 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aminotransferase YP_903385.1 137574 D 413404 CDS YP_903386.1 118602171 4555526 complement(140171..142135) 1 NC_008610.1 TIGRFAM: primosomal protein N'; PFAM: helicase domain protein; type III restriction enzyme, res subunit; DEAD/DEAH box helicase domain protein; KEGG: cbu:CBU_1815 primosomal protein N'; primosomal protein N' 142135 4555526 Rmag_0120 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) primosomal protein N' YP_903386.1 140171 R 413404 CDS YP_903387.1 118602172 4555527 142200..142637 1 NC_008610.1 PFAM: protein of unknown function UPF0054; KEGG: pae:PA3982 conserved hypothetical protein; hypothetical protein 142637 4555527 Rmag_0121 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903387.1 142200 D 413404 CDS YP_903388.1 118602173 4555528 complement(142684..143856) 1 NC_008610.1 TIGRFAM: tRNA(Ile)-lysidine synthetase; tRNA(Ile)-lysidine synthetase-like; PFAM: PP-loop domain protein; KEGG: cbu:CBU_1509 mesJ protein; tRNA(Ile)-lysidine synthetase 143856 4555528 Rmag_0122 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA(Ile)-lysidine synthetase YP_903388.1 142684 R 413404 CDS YP_903389.1 118602174 4555529 complement(143837..144787) 1 NC_008610.1 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 144787 4555529 Rmag_0123 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acetyl-CoA carboxylase carboxyltransferase subunit alpha YP_903389.1 143837 R 413404 CDS YP_903390.1 118602175 4555530 145278..145955 1 NC_008610.1 PFAM: protein of unknown function DUF47; KEGG: pae:PA5208 hypothetical protein; hypothetical protein 145955 4555530 Rmag_0124 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903390.1 145278 D 413404 CDS YP_903391.1 118602176 4555531 145966..147246 1 NC_008610.1 PFAM: phosphate transporter; KEGG: csa:Csal_0712 phosphate transporter; phosphate transporter 147246 4555531 Rmag_0125 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphate transporter YP_903391.1 145966 D 413404 CDS YP_903392.1 118602177 4555532 147250..147480 1 NC_008610.1 PFAM: BolA family protein; KEGG: mca:MCA0260 toluene-tolerance protein, putative; BolA family protein 147480 4555532 Rmag_0126 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) BolA family protein YP_903392.1 147250 D 413404 CDS YP_903393.1 118602178 4555533 147921..149225 1 NC_008610.1 PFAM: helicase domain protein; DEAD/DEAH box helicase domain protein; KEGG: tcx:Tcr_0779 DEAD/DEAH box helicase-like; DEAD/DEAH box helicase domain-containing protein 149225 4555533 Rmag_0127 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DEAD/DEAH box helicase domain-containing protein YP_903393.1 147921 D 413404 CDS YP_903394.1 118602179 4555534 complement(149876..150919) 1 NC_008610.1 KEGG: gme:Gmet_2337 hypothetical protein; hypothetical protein 150919 4555534 Rmag_0128 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903394.1 149876 R 413404 CDS YP_903395.1 118602180 4555535 complement(150928..152394) 1 NC_008610.1 PFAM: membrane bound O-acyl transferase, MBOAT family protein; KEGG: bcz:BCZK0793 alginate O-acetyltransferase; membrane bound O-acyl transferase, MBOAT family protein 152394 4555535 Rmag_0129 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) membrane bound O-acyl transferase, MBOAT family protein YP_903395.1 150928 R 413404 CDS YP_903396.1 118602181 4555536 152860..153246 1 NC_008610.1 hypothetical protein 153246 4555536 Rmag_0130 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903396.1 152860 D 413404 CDS YP_903397.1 118602182 4555537 complement(154782..155966) 1 NC_008610.1 TIGRFAM: tyrosyl-tRNA synthetase; PFAM: aminoacyl-tRNA synthetase, class Ib; RNA-binding S4 domain protein; KEGG: ftl:FTL_0968 tyrosyl-tRNA synthetase; tyrosyl-tRNA synthetase 155966 4555537 Rmag_0132 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tyrosyl-tRNA synthetase YP_903397.1 154782 R 413404 CDS YP_903398.1 118602183 4555381 complement(155972..157231) 1 NC_008610.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase 157231 proA 4555381 proA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) gamma-glutamyl phosphate reductase YP_903398.1 155972 R 413404 CDS YP_903399.1 118602184 4555382 complement(157219..158238) 1 NC_008610.1 KEGG: pfl:PFL_5441 DNA polymerase III, delta subunit; TIGRFAM: DNA polymerase III, delta subunit; PFAM: DNA polymerase III, delta; DNA polymerase III, delta subunit 158238 4555382 Rmag_0134 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA polymerase III, delta subunit YP_903399.1 157219 R 413404 CDS YP_903400.1 118602185 4555383 complement(158228..158680) 1 NC_008610.1 hypothetical protein 158680 4555383 Rmag_0135 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903400.1 158228 R 413404 CDS YP_903401.1 118602186 4555384 158830..160752 1 NC_008610.1 KEGG: mca:MCA1848 cell division protein FtsH; TIGRFAM: ATP-dependent metalloprotease FtsH; PFAM: peptidase M41; AAA ATPase, central domain protein; peptidase M41, FtsH extracellular; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; ATP-dependent metalloprotease FtsH 160752 4555384 Rmag_0136 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP-dependent metalloprotease FtsH YP_903401.1 158830 D 413404 CDS YP_903402.1 118602187 4555385 160794..161594 1 NC_008610.1 KEGG: cps:CPS_3451 dihydropteroate synthase; TIGRFAM: dihydropteroate synthase; PFAM: dihydropteroate synthase, DHPS; dihydropteroate synthase 161594 4555385 Rmag_0137 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydropteroate synthase YP_903402.1 160794 D 413404 CDS YP_903403.1 118602188 4555386 161599..162924 1 NC_008610.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase 162924 glmM 4555386 glmM Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoglucosamine mutase YP_903403.1 161599 D 413404 CDS YP_903404.1 118602189 4555387 165052..165627 1 NC_008610.1 TIGRFAM: electron transport complex, RnfABCDGE type, A subunit; PFAM: RnfA-Nqr electron transport subunit; KEGG: noc:Noc_0970 electron transport complex, RnfABCDGE type, A subunit; electron transport complex, RnfABCDGE type, A subunit 165627 4555387 Rmag_0139 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) electron transport complex, RnfABCDGE type, A subunit YP_903404.1 165052 D 413404 CDS YP_903405.1 118602190 4555388 165614..166153 1 NC_008610.1 TIGRFAM: electron transport complex, RnfABCDGE type, B subunit; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; Fe-S cluster domain protein; KEGG: tbd:Tbd_2016 electron transport complex, RnfABCDGE type, B subunit; electron transport complex, RnfABCDGE type, B subunit 166153 4555388 Rmag_0140 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) electron transport complex, RnfABCDGE type, B subunit YP_903405.1 165614 D 413404 CDS YP_903406.1 118602191 4555389 166146..167639 1 NC_008610.1 TIGRFAM: electron transport complex, RnfABCDGE type, C subunit; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; Respiratory-chain NADH dehydrogenase domain, 51 kDa subunit; KEGG: noc:Noc_1173 electron transport complex protein RnfC; electron transport complex, RnfABCDGE type, C subunit 167639 4555389 Rmag_0141 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) electron transport complex, RnfABCDGE type, C subunit YP_903406.1 166146 D 413404 CDS YP_903407.1 118602192 4555390 167669..168583 1 NC_008610.1 TIGRFAM: electron transport complex, RnfABCDGE type, D subunit; PFAM: NQR2 and RnfD family protein; KEGG: eca:ECA2279 electron transport complex protein; electron transport complex, RnfABCDGE type, D subunit 168583 4555390 Rmag_0142 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) electron transport complex, RnfABCDGE type, D subunit YP_903407.1 167669 D 413404 CDS YP_903408.1 118602193 4555391 168583..169191 1 NC_008610.1 TIGRFAM: electron transport complex, RnfABCDGE type, G subunit; PFAM: FMN-binding domain protein; KEGG: tcx:Tcr_1032 electron transport complex, RnfABCDGE type, G subunit; electron transport complex, RnfABCDGE type, G subunit 169191 4555391 Rmag_0143 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) electron transport complex, RnfABCDGE type, G subunit YP_903408.1 168583 D 413404 CDS YP_903409.1 118602194 4555392 complement(170121..170891) 1 NC_008610.1 KEGG: tcx:Tcr_0902 hypothetical protein; hypothetical protein 170891 4555392 Rmag_0144 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903409.1 170121 R 413404 CDS YP_903410.1 118602195 4555393 complement(170888..171757) 1 NC_008610.1 TIGRFAM: succinyl-CoA synthetase, alpha subunit; PFAM: CoA-binding domain protein; ATP-citrate lyase/succinyl-CoA ligase; KEGG: noc:Noc_0714 succinyl-CoA ligase, alpha subunit; succinyl-CoA synthetase (ADP-forming) alpha subunit 171757 4555393 Rmag_0145 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) succinyl-CoA synthetase (ADP-forming) alpha subunit YP_903410.1 170888 R 413404 CDS YP_903411.1 118602196 4555394 complement(171754..172914) 1 NC_008610.1 catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta 172914 sucC 4555394 sucC Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) succinyl-CoA synthetase subunit beta YP_903411.1 171754 R 413404 CDS YP_903412.1 118602197 4555395 172969..173532 1 NC_008610.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 173532 4555395 Rmag_0147 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) elongation factor P YP_903412.1 172969 D 413404 CDS YP_903413.1 118602198 4555396 173595..174476 1 NC_008610.1 PFAM: tRNA synthetase, class II (D, K and N); KEGG: cps:CPS_4763 conserved hypothetical protein TIGR00462; tRNA synthetase, class II (D, K and N) 174476 4555396 Rmag_0148 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA synthetase, class II (D, K and N) YP_903413.1 173595 D 413404 CDS YP_903414.1 118602199 4555397 174527..175771 1 NC_008610.1 PFAM: Sel1 domain protein repeat-containing protein; KEGG: lpf:lpl1180 hypothetical protein; Sel1 domain-containing protein 175771 4555397 Rmag_0149 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Sel1 domain-containing protein YP_903414.1 174527 D 413404 CDS YP_903415.1 118602200 4555398 176434..177645 1 NC_008610.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase 177645 4555398 Rmag_0151 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) argininosuccinate synthase YP_903415.1 176434 D 413404 CDS YP_903416.1 118602201 4555399 complement(177993..178577) 1 NC_008610.1 TIGRFAM: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; PFAM: CDP-alcohol phosphatidyltransferase; KEGG: aci:ACIAD0342 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (phosphatidylglycerophosphate synthase) (PGP synthase); CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 178577 4555399 Rmag_0152 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase YP_903416.1 177993 R 413404 CDS YP_903417.1 118602202 4555400 complement(178742..179995) 1 NC_008610.1 TIGRFAM: UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase; PFAM: cytoplasmic peptidoglycan synthetase domain protein; cytoplasmic peptidoglycan synthetases domain protein; Mur ligase, middle domain protein; KEGG: par:Psyc_2052 probable UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase; UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase 179995 4555400 Rmag_0153 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase YP_903417.1 178742 R 413404 CDS YP_903418.1 118602203 4554653 complement(180638..182032) 1 NC_008610.1 TIGRFAM: UDP-N-acetylmuramyl-tripeptide synthetases; PFAM: cytoplasmic peptidoglycan synthetase domain protein; cytoplasmic peptidoglycan synthetases domain protein; Mur ligase, middle domain protein; KEGG: lpp:lpp0978 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase 182032 4554653 Rmag_0155 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase YP_903418.1 180638 R 413404 CDS YP_903419.1 118602204 4554654 182253..184142 1 NC_008610.1 TIGRFAM: Twin-arginine translocation pathway signal; PFAM: metallophosphoesterase; 5'-Nucleotidase domain protein; KEGG: tcx:Tcr_1549 sulfate thiol esterase; sulfate thiol esterase SoxB 184142 4554654 Rmag_0156 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sulfate thiol esterase SoxB YP_903419.1 182253 D 413404 CDS YP_903420.1 118602205 4554655 184536..185663 1 NC_008610.1 KEGG: jan:Jann_0120 hypothetical protein; hypothetical protein 185663 4554655 Rmag_0157 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903420.1 184536 D 413404 CDS YP_903421.1 118602206 4554656 complement(185671..186654) 1 NC_008610.1 KEGG: noc:Noc_2788 sugar phosphate isomerase involved in capsule formation, KpsF/GutQ; TIGRFAM: KpsF/GutQ family protein; PFAM: CBS domain containing protein; sugar isomerase (SIS); KpsF/GutQ family protein 186654 4554656 Rmag_0158 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) KpsF/GutQ family protein YP_903421.1 185671 R 413404 CDS YP_903422.1 118602207 4554657 186730..187173 1 NC_008610.1 PFAM: low molecular weight phosphotyrosine protein phosphatase; KEGG: bbr:BB2274 low molecular weight protein-tyrosine-phosphatase; protein tyrosine phosphatase 187173 4554657 Rmag_0159 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein tyrosine phosphatase YP_903422.1 186730 D 413404 CDS YP_903423.1 118602208 4554658 187302..187676 1 NC_008610.1 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 187676 rpsL 4554658 rpsL Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S12 YP_903423.1 187302 D 413404 CDS YP_903424.1 118602209 4554659 187709..188182 1 NC_008610.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 188182 4554659 Rmag_0161 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S7 YP_903424.1 187709 D 413404 CDS YP_903425.1 118602210 4554660 188207..190309 1 NC_008610.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 190309 4554660 Rmag_0162 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) elongation factor G YP_903425.1 188207 D 413404 CDS YP_903426.1 118602211 4554661 190320..191510 1 NC_008610.1 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 191510 4554661 Rmag_0163 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) elongation factor Tu YP_903426.1 190320 D 413404 CDS YP_903427.1 118602212 4554662 191601..191912 1 NC_008610.1 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 191912 rpsJ 4554662 rpsJ Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S10 YP_903427.1 191601 D 413404 CDS YP_903428.1 118602213 4554663 191948..192664 1 NC_008610.1 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 192664 rplC 4554663 rplC Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L3 YP_903428.1 191948 D 413404 CDS YP_903429.1 118602214 4554664 192684..193298 1 NC_008610.1 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 193298 rplD 4554664 rplD Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L4 YP_903429.1 192684 D 413404 CDS YP_903430.1 118602215 4554665 193295..193585 1 NC_008610.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 193585 rplW 4554665 rplW Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L23 YP_903430.1 193295 D 413404 CDS YP_903431.1 118602216 4554666 193596..194426 1 NC_008610.1 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 194426 rplB 4554666 rplB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L2 YP_903431.1 193596 D 413404 CDS YP_903432.1 118602217 4554667 194429..194698 1 NC_008610.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 194698 rpsS 4554667 rpsS Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S19 YP_903432.1 194429 D 413404 CDS YP_903433.1 118602218 4554668 194713..195045 1 NC_008610.1 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 195045 rplV 4554668 rplV Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L22 YP_903433.1 194713 D 413404 CDS YP_903434.1 118602219 4554669 195053..195751 1 NC_008610.1 KEGG: pae:PA4257 30S ribosomal protein S3; TIGRFAM: ribosomal protein S3; PFAM: ribosomal protein S3-C-terminal domain protein; KH, type 2 domain protein; Ribosomal protein S3, N-terminal domain; SMART: KH domain protein; 30S ribosomal protein S3 195751 4554669 Rmag_0171 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S3 YP_903434.1 195053 D 413404 CDS YP_903435.1 118602220 4554670 195764..196174 1 NC_008610.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 196174 rplP 4554670 rplP Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L16 YP_903435.1 195764 D 413404 CDS YP_903436.1 118602221 4554671 196174..196362 1 NC_008610.1 one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 196362 4554671 Rmag_0173 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L29 YP_903436.1 196174 D 413404 CDS YP_903437.1 118602222 4555420 196359..196625 1 NC_008610.1 PFAM: ribosomal protein S17; KEGG: ppu:PP0463 ribosomal protein S17; 30S ribosomal protein S17 196625 4555420 Rmag_0174 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S17 YP_903437.1 196359 D 413404 CDS YP_903438.1 118602223 4555421 196654..197022 1 NC_008610.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 197022 rplN 4555421 rplN Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L14 YP_903438.1 196654 D 413404 CDS YP_903439.1 118602224 4555422 197022..197333 1 NC_008610.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 197333 rplX 4555422 rplX Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L24 YP_903439.1 197022 D 413404 CDS YP_903440.1 118602225 4555423 197356..197895 1 NC_008610.1 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 197895 rplE 4555423 rplE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L5 YP_903440.1 197356 D 413404 CDS YP_903441.1 118602226 4555424 197901..198206 1 NC_008610.1 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 198206 rpsN 4555424 rpsN Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S14 YP_903441.1 197901 D 413404 CDS YP_903442.1 118602227 4555425 198218..198613 1 NC_008610.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 198613 rpsH 4555425 rpsH Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S8 YP_903442.1 198218 D 413404 CDS YP_903443.1 118602228 4555426 198629..199174 1 NC_008610.1 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 199174 rplF 4555426 rplF Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L6 YP_903443.1 198629 D 413404 CDS YP_903444.1 118602229 4555427 199192..199539 1 NC_008610.1 binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 199539 rplR 4555427 rplR Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L18 YP_903444.1 199192 D 413404 CDS YP_903445.1 118602230 4555428 199583..200101 1 NC_008610.1 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 200101 rpsE 4555428 rpsE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S5 YP_903445.1 199583 D 413404 CDS YP_903446.1 118602231 4555429 200101..200421 1 NC_008610.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 200421 rpmD 4555429 rpmD Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L30 YP_903446.1 200101 D 413404 CDS YP_903447.1 118602232 4555430 200426..200869 1 NC_008610.1 late assembly protein; 50S ribosomal protein L15 200869 rplO 4555430 rplO Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L15 YP_903447.1 200426 D 413404 CDS YP_903448.1 118602233 4555431 200873..202171 1 NC_008610.1 TIGRFAM: preprotein translocase, SecY subunit; PFAM: SecY protein; KEGG: noc:Noc_2305 SecY protein; protein translocase subunit secY/sec61 alpha 202171 4555431 Rmag_0185 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein translocase subunit secY/sec61 alpha YP_903448.1 200873 D 413404 CDS YP_903449.1 118602234 4555432 202185..202298 1 NC_008610.1 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 have the motif; 50S ribosomal protein L36 202298 rpmJ 4555432 rpmJ Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L36 YP_903449.1 202185 D 413404 CDS YP_903450.1 118602235 4555433 202454..202807 1 NC_008610.1 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 202807 rpsM 4555433 rpsM Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S13 YP_903450.1 202454 D 413404 CDS YP_903451.1 118602236 4555434 202823..203206 1 NC_008610.1 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 203206 4555434 Rmag_0188 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S11 YP_903451.1 202823 D 413404 CDS YP_903452.1 118602237 4555435 203216..203842 1 NC_008610.1 PFAM: ribosomal protein S4; RNA-binding S4 domain protein; KEGG: sgl:SG2254 30S ribosomal protein S4; 30S ribosomal protein S4 203842 4555435 Rmag_0189 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S4 YP_903452.1 203216 D 413404 CDS YP_903453.1 118602238 4555436 203855..204835 1 NC_008610.1 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 204835 4555436 Rmag_0190 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA-directed RNA polymerase subunit alpha YP_903453.1 203855 D 413404 CDS YP_903454.1 118602239 4555437 204846..205244 1 NC_008610.1 is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 205244 rplQ 4555437 rplQ Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L17 YP_903454.1 204846 D 413404 CDS YP_903455.1 118602240 4555438 205255..205470 1 NC_008610.1 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 205470 rpsU 4555438 rpsU Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S21 YP_903455.1 205255 D 413404 CDS YP_903456.1 118602241 4555439 complement(209161..209529) 1 NC_008610.1 KEGG: noc:Noc_2728 protein-methionine-S-oxide reductase; TIGRFAM: methionine-R-sulfoxide reductase; PFAM: Methionine sulfoxide reductase B; methionine-R-sulfoxide reductase 209529 4555439 Rmag_0196 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) methionine-R-sulfoxide reductase YP_903456.1 209161 R 413404 CDS YP_903457.1 118602242 4555353 209570..210658 1 NC_008610.1 PFAM: Polynucleotide adenylyltransferase region; KEGG: cbu:CBU_1827 tRNA nucleotidyltransferase (CCA-adding enzyme); polynucleotide adenylyltransferase region 210658 4555353 Rmag_0197 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) polynucleotide adenylyltransferase region YP_903457.1 209570 D 413404 CDS YP_903458.1 118602243 4555354 complement(212133..214607) 1 NC_008610.1 KEGG: nmu:Nmul_A0722 hypothetical protein; hypothetical protein 214607 4555354 Rmag_0199 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903458.1 212133 R 413404 CDS YP_903459.1 118602244 4555355 complement(214597..215196) 1 NC_008610.1 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 215196 engB 4555355 engB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribosome biogenesis GTP-binding protein YsxC YP_903459.1 214597 R 413404 CDS YP_903460.1 118602245 4555356 215270..215560 1 NC_008610.1 KEGG: sdn:Sden_1464 cytochrome c, class I; cytochrome c, class I 215560 4555356 Rmag_0201 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome c, class I YP_903460.1 215270 D 413404 CDS YP_903461.1 118602246 4555357 215620..215913 1 NC_008610.1 KEGG: mag:amb3084 cytochrome c4 precursor; cytochrome c4 precursor 215913 4555357 Rmag_0202 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome c4 precursor YP_903461.1 215620 D 413404 CDS YP_903462.1 118602247 4555358 215942..216625 1 NC_008610.1 PFAM: cytochrome c, class I; KEGG: ppr:PBPRA3501 putative cytochrome c4; cytochrome c, class I 216625 4555358 Rmag_0203 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome c, class I YP_903462.1 215942 D 413404 CDS YP_903463.1 118602248 4555359 216740..218029 1 NC_008610.1 TIGRFAM: trigger factor; PFAM: peptidylprolyl isomerase, FKBP-type; trigger factor, C-terminal domain protein; trigger factor, N-terminal domain; KEGG: hch:HCH_02157 trigger factor; trigger factor 218029 4555359 Rmag_0204 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) trigger factor YP_903463.1 216740 D 413404 CDS YP_903464.1 118602249 4555360 218037..218633 1 NC_008610.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit 218633 clpP 4555360 clpP Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP-dependent Clp protease proteolytic subunit YP_903464.1 218037 D 413404 CDS YP_903465.1 118602250 4555361 218638..219903 1 NC_008610.1 binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX 219903 clpX 4555361 clpX Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP-dependent protease ATP-binding subunit ClpX YP_903465.1 218638 D 413404 CDS YP_903466.1 118602251 4555362 219918..221243 1 NC_008610.1 TIGRFAM: small GTP-binding protein; PFAM: GTP-binding protein, HSR1-related; KEGG: eca:ECA3933 putative GTP-binding phage-related protein; small GTP-binding protein 221243 4555362 Rmag_0207 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) small GTP-binding protein YP_903466.1 219918 D 413404 CDS YP_903467.1 118602252 4555363 221207..223543 1 NC_008610.1 KEGG: tbd:Tbd_1675 peptidase S16, ATP-dependent protease La; TIGRFAM: ATP-dependent protease La; PFAM: peptidase S16, lon domain protein; AAA ATPase, central domain protein; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; ATP-dependent protease La 223543 4555363 Rmag_0208 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP-dependent protease La YP_903467.1 221207 D 413404 CDS YP_903468.1 118602253 4555364 complement(224784..226049) 1 NC_008610.1 TIGRFAM: sun protein; PFAM: Fmu (Sun) domain protein; NusB/RsmB/TIM44; KEGG: hin:HI0624 Sun protein; sun protein 226049 4555364 Rmag_0209 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sun protein YP_903468.1 224784 R 413404 CDS YP_903469.1 118602254 4555365 complement(226039..226764) 1 NC_008610.1 KEGG: noc:Noc_2253 thiol-disulfide interchange protein DsbC; thiol-disulfide interchange protein DsbC 226764 4555365 Rmag_0210 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thiol-disulfide interchange protein DsbC YP_903469.1 226039 R 413404 CDS YP_903470.1 118602255 4555366 226850..228271 1 NC_008610.1 PFAM: peptidase M17, leucyl aminopeptidase domain protein; KEGG: noc:Noc_0289 leucyl aminopeptidase; leucyl aminopeptidase 228271 4555366 Rmag_0211 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) leucyl aminopeptidase YP_903470.1 226850 D 413404 CDS YP_903471.1 118602256 4555367 complement(229409..230029) 1 NC_008610.1 KEGG: tcx:Tcr_0450 hypothetical protein; hypothetical protein 230029 4555367 Rmag_0213 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903471.1 229409 R 413404 CDS YP_903472.1 118602257 4555368 complement(230131..230535) 1 NC_008610.1 PFAM: CBS domain containing protein; KEGG: vvy:VV0994 hypothetical protein; signal-transduction protein 230535 4555368 Rmag_0214 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) signal-transduction protein YP_903472.1 230131 R 413404 CDS YP_903473.1 118602258 4555369 complement(230535..230885) 1 NC_008610.1 KEGG: vpa:VP0813 putative nitrogen regulatory protein P-II family protein; putative nitrogen regulatory protein P-II family protein 230885 4555369 Rmag_0215 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative nitrogen regulatory protein P-II family protein YP_903473.1 230535 R 413404 CDS YP_903474.1 118602259 4555370 complement(230894..231634) 1 NC_008610.1 PFAM: protein of unknown function DUF1538; KEGG: vpa:VP0812 hypothetical protein; hypothetical protein 231634 4555370 Rmag_0216 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903474.1 230894 R 413404 CDS YP_903475.1 118602260 4555371 complement(231631..232362) 1 NC_008610.1 PFAM: protein of unknown function DUF1538; KEGG: cps:CPS_1953 hypothetical protein; hypothetical protein 232362 4555371 Rmag_0217 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903475.1 231631 R 413404 CDS YP_903476.1 118602261 4554894 232489..233349 1 NC_008610.1 PFAM: aminotransferase, class IV; KEGG: noc:Noc_1662 aminotransferase, class IV; aminodeoxychorismate lyase apoprotein 233349 4554894 Rmag_0218 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aminodeoxychorismate lyase apoprotein YP_903476.1 232489 D 413404 CDS YP_903477.1 118602262 4554895 233845..234462 1 NC_008610.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP); thymidylate kinase 234462 tmk 4554895 tmk Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thymidylate kinase YP_903477.1 233845 D 413404 CDS YP_903478.1 118602263 4554896 234459..235466 1 NC_008610.1 KEGG: cbu:CBU_0500 DNA polymerase III, delta prime subunit; similar to ATPases involved in DNA replication; DNA polymerase III, delta prime subunit 235466 4554896 Rmag_0221 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA polymerase III, delta prime subunit YP_903478.1 234459 D 413404 CDS YP_903479.1 118602264 4554897 235504..236790 1 NC_008610.1 Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway; glutamate-1-semialdehyde aminotransferase 236790 4554897 Rmag_0222 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutamate-1-semialdehyde aminotransferase YP_903479.1 235504 D 413404 CDS YP_903480.1 118602265 4554898 237349..238002 1 NC_008610.1 TIGRFAM: HAD-superfamily hydrolase, subfamily IB (PSPase-like); HAD-superfamily subfamily IB hydrolase, TIGR01490; KEGG: tcx:Tcr_0999 HAD-superfamily subfamily IB, PSPase-like; HAD family hydrolase 238002 4554898 Rmag_0223 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) HAD family hydrolase YP_903480.1 237349 D 413404 CDS YP_903481.1 118602266 4554899 complement(238031..238546) 1 NC_008610.1 KEGG: tbd:Tbd_0575 hypothetical protein; hypothetical protein 238546 4554899 Rmag_0224 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903481.1 238031 R 413404 CDS YP_903482.1 118602267 4554900 complement(238575..238799) 1 NC_008610.1 PFAM: SirA family protein; KEGG: mag:amb0858 predicted redox protein; SirA family protein 238799 4554900 Rmag_0225 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) SirA family protein YP_903482.1 238575 R 413404 CDS YP_903483.1 118602268 4554901 complement(240174..240845) 1 NC_008610.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway; ribose-5-phosphate isomerase A 240845 4554901 Rmag_0227 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribose-5-phosphate isomerase A YP_903483.1 240174 R 413404 CDS YP_903484.1 118602269 4554902 240887..241492 1 NC_008610.1 TIGRFAM: non-canonical purine NTP pyrophosphatase, rdgB/HAM1 family; PFAM: Ham1 family protein; KEGG: vpa:VP2621 Ham1 protein; RdgB/HAM1 family non-canonical purine NTP pyrophosphatase 241492 4554902 Rmag_0228 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) RdgB/HAM1 family non-canonical purine NTP pyrophosphatase YP_903484.1 240887 D 413404 CDS YP_903485.1 118602270 4554903 244285..245175 1 NC_008610.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase 245175 4554903 Rmag_0232 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acetylglutamate kinase YP_903485.1 244285 D 413404 CDS YP_903486.1 118602271 4554904 245168..246016 1 NC_008610.1 PFAM: oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: noc:Noc_0363 dihydroorotate dehydrogenase electron transfer subunit; dihydroorotate oxidase B, electron transfer subunit 246016 4554904 Rmag_0233 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydroorotate oxidase B, electron transfer subunit YP_903486.1 245168 D 413404 CDS YP_903487.1 118602272 4554905 246013..246651 1 NC_008610.1 TIGRFAM: Protein of unknown function UPF0001; PFAM: alanine racemase domain protein; KEGG: eca:ECA3627 putative alanine racemase; hypothetical protein 246651 4554905 Rmag_0234 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903487.1 246013 D 413404 CDS YP_903488.1 118602273 4554906 248041..250506 1 NC_008610.1 KEGG: lpp:lpp1719 hypothetical protein; membrane protein-like 250506 4554906 Rmag_0235 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) membrane protein-like YP_903488.1 248041 D 413404 CDS YP_903489.1 118602274 4554907 250503..251927 1 NC_008610.1 PFAM: peptidase U62, modulator of DNA gyrase; KEGG: plu:plu4064 tldD protein, suppresses the inhibitory activity of the carbon storage regulator (CSRA); peptidase U62, modulator of DNA gyrase 251927 4554907 Rmag_0236 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase U62, modulator of DNA gyrase YP_903489.1 250503 D 413404 CDS YP_903490.1 118602275 4554908 252028..252384 1 NC_008610.1 PFAM: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; KEGG: tcx:Tcr_0817 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 252384 4554908 Rmag_0237 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 YP_903490.1 252028 D 413404 CDS YP_903491.1 118602276 4554909 252388..252867 1 NC_008610.1 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 252867 4554909 Rmag_0238 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH dehydrogenase subunit B YP_903491.1 252388 D 413404 CDS YP_903492.1 118602277 4554910 252867..253481 1 NC_008610.1 KEGG: lpn:lpg2787 NADH dehydrogenase I, C subunit; TIGRFAM: NADH (or F420H2) dehydrogenase, subunit C; PFAM: NADH dehydrogenase (ubiquinone), 30 kDa subunit; NADH (or F420H2) dehydrogenase, subunit C 253481 4554910 Rmag_0239 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH (or F420H2) dehydrogenase, subunit C YP_903492.1 252867 D 413404 CDS YP_903493.1 118602278 4554911 253483..254736 1 NC_008610.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D 254736 4554911 Rmag_0240 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH dehydrogenase subunit D YP_903493.1 253483 D 413404 CDS YP_903494.1 118602279 4554912 254733..255206 1 NC_008610.1 KEGG: tcx:Tcr_0821 NADH-quinone oxidoreductase, E subunit; TIGRFAM: NADH-quinone oxidoreductase, E subunit; PFAM: NADH dehydrogenase (ubiquinone), 24 kDa subunit; NADH-quinone oxidoreductase, E subunit 255206 4554912 Rmag_0241 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH-quinone oxidoreductase, E subunit YP_903494.1 254733 D 413404 CDS YP_903495.1 118602280 4554913 255203..256471 1 NC_008610.1 KEGG: lpp:lpp2831 NADH dehydrogenase I chain F; TIGRFAM: NADH-quinone oxidoreductase, F subunit; PFAM: Respiratory-chain NADH dehydrogenase domain, 51 kDa subunit; NADH-quinone oxidoreductase, F subunit 256471 4554913 Rmag_0242 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH-quinone oxidoreductase, F subunit YP_903495.1 255203 D 413404 CDS YP_903496.1 118602281 4555645 256476..258737 1 NC_008610.1 TIGRFAM: NADH-quinone oxidoreductase, chain G; PFAM: ferredoxin; molybdopterin oxidoreductase; KEGG: tcx:Tcr_0823 NADH-quinone oxidoreductase, chain G; NADH-quinone oxidoreductase, chain G 258737 4555645 Rmag_0243 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH-quinone oxidoreductase, chain G YP_903496.1 256476 D 413404 CDS YP_903497.1 118602282 4555646 258737..259810 1 NC_008610.1 PFAM: respiratory-chain NADH dehydrogenase, subunit 1; KEGG: tcx:Tcr_0824 respiratory-chain NADH dehydrogenase, subunit 1; respiratory-chain NADH dehydrogenase, subunit 1 259810 4555646 Rmag_0244 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) respiratory-chain NADH dehydrogenase, subunit 1 YP_903497.1 258737 D 413404 CDS YP_903498.1 118602283 4555647 259824..260315 1 NC_008610.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I 260315 4555647 Rmag_0245 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH dehydrogenase subunit I YP_903498.1 259824 D 413404 CDS YP_903499.1 118602284 4555648 260325..260933 1 NC_008610.1 PFAM: NADH-ubiquinone/plastoquinone oxidoreductase, chain 6; KEGG: noc:Noc_2556 NADH-ubiquinone/plastoquinone oxidoreductase, chain 6; NADH-ubiquinone/plastoquinone oxidoreductase, chain 6 260933 4555648 Rmag_0246 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH-ubiquinone/plastoquinone oxidoreductase, chain 6 YP_903499.1 260325 D 413404 CDS YP_903500.1 118602285 4555649 260934..261239 1 NC_008610.1 PFAM: NADH-ubiquinone oxidoreductase, chain 4L; KEGG: rso:RSc2052 probable transmembrane NADH dehydrogenase I (chain K) oxidoreductase protein; NADH-ubiquinone oxidoreductase, chain 4L 261239 4555649 Rmag_0247 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADH-ubiquinone oxidoreductase, chain 4L YP_903500.1 260934 D 413404 CDS YP_903501.1 118602286 4555650 261242..263203 1 NC_008610.1 KEGG: eba:ebA4846 NADH dehydrogenase I, chain L; TIGRFAM: proton-translocating NADH-quinone oxidoreductase, chain L; PFAM: NADH-Ubiquinone oxidoreductase (complex I), chain 5/L domain protein; NADH/Ubiquinone/plastoquinone (complex I); proton-translocating NADH-quinone oxidoreductase, chain L 263203 4555650 Rmag_0248 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) proton-translocating NADH-quinone oxidoreductase, chain L YP_903501.1 261242 D 413404 CDS YP_903502.1 118602287 4555651 263206..264711 1 NC_008610.1 KEGG: tcx:Tcr_0829 proton-translocating NADH-quinone oxidoreductase, chain M; TIGRFAM: proton-translocating NADH-quinone oxidoreductase, chain M; PFAM: NADH/Ubiquinone/plastoquinone (complex I); proton-translocating NADH-quinone oxidoreductase, chain M 264711 4555651 Rmag_0249 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) proton-translocating NADH-quinone oxidoreductase, chain M YP_903502.1 263206 D 413404 CDS YP_903503.1 118602288 4555652 264715..266169 1 NC_008610.1 KEGG: tbd:Tbd_1155 NADH dehydrogenase I chain N; TIGRFAM: proton-translocating NADH-quinone oxidoreductase, chain N; PFAM: NADH/Ubiquinone/plastoquinone (complex I); proton-translocating NADH-quinone oxidoreductase, chain N 266169 4555652 Rmag_0250 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) proton-translocating NADH-quinone oxidoreductase, chain N YP_903503.1 264715 D 413404 CDS YP_903504.1 118602289 4555653 266494..274953 1 NC_008610.1 PFAM: glycosyl hydrolase, BNR repeat-containing protein; KEGG: rso:RS05070 putative hemagglutinin/hemolysin-related protein; BNR repeat-containing glycosyl hydrolase 274953 4555653 Rmag_0251 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) BNR repeat-containing glycosyl hydrolase YP_903504.1 266494 D 413404 CDS YP_903505.1 118602290 4555654 275408..275623 1 NC_008610.1 hypothetical protein 275623 4555654 Rmag_0252 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903505.1 275408 D 413404 CDS YP_903506.1 118602291 4555655 276554..277822 1 NC_008610.1 PFAM: outer membrane efflux protein; KEGG: cvi:CV1734 probable outer membrane protein; outer membrane efflux protein 277822 4555655 Rmag_0253 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) outer membrane efflux protein YP_903506.1 276554 D 413404 CDS YP_903507.1 118602292 4555656 277840..278184 1 NC_008610.1 hypothetical protein 278184 4555656 Rmag_0254 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903507.1 277840 D 413404 CDS YP_903508.1 118602293 4555657 278611..280689 1 NC_008610.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: par:Psyc_1599 ABC drug efflux transporter, fused ATPase and inner mebrane subunits; ABC transporter related 280689 4555657 Rmag_0255 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_903508.1 278611 D 413404 CDS YP_903509.1 118602294 4555658 280701..281870 1 NC_008610.1 PFAM: secretion protein HlyD family protein; KEGG: par:Psyc_1598 HlyD family secretion protein; secretion protein HlyD family protein 281870 4555658 Rmag_0256 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) secretion protein HlyD family protein YP_903509.1 280701 D 413404 CDS YP_903510.1 118602295 4555659 complement(282381..283169) 1 NC_008610.1 TIGRFAM: biotin biosynthesis protein BioC; PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: tcx:Tcr_1981 biotin biosynthesis protein BioC; biotin biosynthesis protein BioC 283169 4555659 Rmag_0257 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) biotin biosynthesis protein BioC YP_903510.1 282381 R 413404 CDS YP_903511.1 118602296 4555660 complement(283157..284008) 1 NC_008610.1 PFAM: periplasmic solute binding protein; KEGG: rty:RT0013 probable zinc/manganese ABC transporter substrate binding protein; periplasmic solute binding protein 284008 4555660 Rmag_0258 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) periplasmic solute binding protein YP_903511.1 283157 R 413404 CDS YP_903512.1 118602297 4555661 complement(284049..285005) 1 NC_008610.1 PFAM: putative methyltransferase; methyltransferase, putative; Methyltransferase type 11; KEGG: vvy:VV2291 hypothetical protein; methyltransferase, putative 285005 4555661 Rmag_0259 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) methyltransferase, putative YP_903512.1 284049 R 413404 CDS YP_903513.1 118602298 4555662 285105..285485 1 NC_008610.1 hypothetical protein 285485 4555662 Rmag_0260 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903513.1 285105 D 413404 CDS YP_903514.1 118602299 4555663 complement(285556..286113) 1 NC_008610.1 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 286113 frr 4555663 frr Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribosome recycling factor YP_903514.1 285556 R 413404 CDS YP_903515.1 118602300 4555157 complement(286117..286836) 1 NC_008610.1 Catalyzes the phosphorylation of UMP to UDP; uridylate kinase 286836 pyrH 4555157 pyrH Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) uridylate kinase YP_903515.1 286117 R 413404 CDS YP_903516.1 118602301 4555158 286912..289728 1 NC_008610.1 TIGRFAM: excinuclease ABC, A subunit; PFAM: ABC transporter related; KEGG: vch:VC0394 excinuclease ABC, subunit A; excinuclease ABC, A subunit 289728 4555158 Rmag_0263 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) excinuclease ABC, A subunit YP_903516.1 286912 D 413404 CDS YP_903517.1 118602302 4555159 complement(289711..290454) 1 NC_008610.1 hypothetical protein 290454 4555159 Rmag_0264 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903517.1 289711 R 413404 CDS YP_903518.1 118602303 4555160 complement(290451..291056) 1 NC_008610.1 TIGRFAM: phosphoribosylglycinamide formyltransferase; PFAM: formyl transferase domain protein; KEGG: pha:PSHAa1948 phosphoribosylglycinamide formyltransferase 1; phosphoribosylglycinamide formyltransferase 291056 4555160 Rmag_0265 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribosylglycinamide formyltransferase YP_903518.1 290451 R 413404 CDS YP_903519.1 118602304 4555161 complement(291071..292072) 1 NC_008610.1 KEGG: eca:ECA1254 phosphoribosylaminoimidazole synthetase; TIGRFAM: phosphoribosylformylglycinamidine cyclo-ligase; PFAM: AIR synthase related protein; AIR synthase related protein domain protein; phosphoribosylformylglycinamidine cyclo-ligase 292072 4555161 Rmag_0266 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribosylformylglycinamidine cyclo-ligase YP_903519.1 291071 R 413404 CDS YP_903520.1 118602305 4555162 292127..292693 1 NC_008610.1 PFAM: CDP-alcohol phosphatidyltransferase; KEGG: noc:Noc_1186 CDP-alcohol phosphatidyltransferase; CDP-alcohol phosphatidyltransferase 292693 4555162 Rmag_0267 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CDP-alcohol phosphatidyltransferase YP_903520.1 292127 D 413404 CDS YP_903521.1 118602306 4555163 292690..293364 1 NC_008610.1 PFAM: Chromosomal replication initiator, DnaA; KEGG: cbu:CBU_1734 chromosomal replication initiator protein DnaA; regulatory inactivation of DnaA Hda protein 293364 4555163 Rmag_0268 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) regulatory inactivation of DnaA Hda protein YP_903521.1 292690 D 413404 CDS YP_903522.1 118602307 4555164 complement(293361..293768) 1 NC_008610.1 hypothetical protein 293768 4555164 Rmag_0269 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903522.1 293361 R 413404 CDS YP_903523.1 118602308 4555165 293865..295283 1 NC_008610.1 TIGRFAM: uroporphyrin-III C-methyltransferase; siroheme synthase; PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; KEGG: mfa:Mfla_0652 uroporphyrin-III C-methyltransferase; uroporphyrinogen-III C-methyltransferase / precorrin-2 dehydrogenase 295283 4555165 Rmag_0270 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) uroporphyrinogen-III C-methyltransferase / precorrin-2 dehydrogenase YP_903523.1 293865 D 413404 CDS YP_903524.1 118602309 4555166 295688..296497 1 NC_008610.1 KEGG: tcx:Tcr_1620 phosphoserine phosphatase SerB; TIGRFAM: phosphoserine phosphatase SerB; HAD-superfamily hydrolase, subfamily IB (PSPase-like); PFAM: Haloacid dehalogenase domain protein hydrolase; phosphoserine phosphatase 296497 4555166 Rmag_0271 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoserine phosphatase YP_903524.1 295688 D 413404 CDS YP_903525.1 118602310 4555167 296552..298456 1 NC_008610.1 TIGRFAM: cytochrome c-type biogenesis protein CcmF; PFAM: cytochrome c assembly protein; KEGG: psp:PSPPH_3309 cytochrome c-type biogenesis protein CcmF; cytochrome c-type biogenesis protein CcmF 298456 4555167 Rmag_0272 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome c-type biogenesis protein CcmF YP_903525.1 296552 D 413404 CDS YP_903526.1 118602311 4555168 298453..299604 1 NC_008610.1 PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: dar:Daro_1405 TPR repeat; TPR repeat-containing protein 299604 4555168 Rmag_0273 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) TPR repeat-containing protein YP_903526.1 298453 D 413404 CDS YP_903527.1 118602312 4555169 299609..300739 1 NC_008610.1 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 300739 4555169 Rmag_0274 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) succinyl-diaminopimelate desuccinylase YP_903527.1 299609 D 413404 CDS YP_903528.1 118602313 4555170 300743..301417 1 NC_008610.1 KEGG: vvy:VV2786 tRNA-(guanine-N1)-methyltransferase; TIGRFAM: tRNA (guanine-N1)-methyltransferase; PFAM: tRNA (guanine-N1-)-methyltransferase; tRNA (Guanine37-N1) methyltransferase 301417 4555170 Rmag_0275 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA (Guanine37-N1) methyltransferase YP_903528.1 300743 D 413404 CDS YP_903529.1 118602314 4555171 301598..301936 1 NC_008610.1 PFAM: nitrogen regulatory protein P-II; KEGG: mca:MCA2137 nitrogen regulatory protein P-II; nitrogen regulatory protein P-II 301936 4555171 Rmag_0276 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) nitrogen regulatory protein P-II YP_903529.1 301598 D 413404 CDS YP_903530.1 118602315 4555172 301983..303221 1 NC_008610.1 TIGRFAM: ammonium transporter; PFAM: Rh family protein/ammonium transporter; KEGG: cps:CPS_3995 ammonium transporter; ammonium transporter 303221 4555172 Rmag_0277 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ammonium transporter YP_903530.1 301983 D 413404 CDS YP_903531.1 118602316 4555173 303496..304386 1 NC_008610.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase 304386 4555173 Rmag_0278 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydrodipicolinate synthase YP_903531.1 303496 D 413404 CDS YP_903532.1 118602317 4555174 304389..305504 1 NC_008610.1 KEGG: dar:Daro_0847 NlpBDapX lipoprotein; NlpBDapX lipoprotein 305504 4555174 Rmag_0279 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NlpBDapX lipoprotein YP_903532.1 304389 D 413404 CDS YP_903533.1 118602318 4555175 305567..307411 1 NC_008610.1 PFAM: NAD-dependent DNA ligase; NAD-dependent DNA ligase, OB-fold; KEGG: dps:DP1006 related to NAD-dependent DNA ligase; DNA ligase (NAD(+)) 307411 4555175 Rmag_0280 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA ligase (NAD(+)) YP_903533.1 305567 D 413404 CDS YP_903534.1 118602319 4555176 307708..308055 1 NC_008610.1 PFAM: nitrogen regulatory protein P-II; KEGG: sde:Sde_0232 nitrogen regulatory protein P-II (GlnB, GlnK); nitrogen regulatory protein P-II 308055 4555176 Rmag_0281 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) nitrogen regulatory protein P-II YP_903534.1 307708 D 413404 CDS YP_903535.1 118602320 4555401 309194..309634 1 NC_008610.1 PFAM: CBS domain containing protein; KEGG: bxe:Bxe_A1873 hypothetical protein; signal-transduction protein 309634 4555401 Rmag_0283 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) signal-transduction protein YP_903535.1 309194 D 413404 CDS YP_903536.1 118602321 4555402 309685..310209 1 NC_008610.1 PFAM: ANTAR domain protein; KEGG: mca:MCA0588 response regulator NasT; response regulator receiver/ANTAR domain-containing protein 310209 4555402 Rmag_0284 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) response regulator receiver/ANTAR domain-containing protein YP_903536.1 309685 D 413404 CDS YP_903537.1 118602322 4555403 complement(310215..311081) 1 NC_008610.1 TIGRFAM: Sec-independent protein translocase, TatC subunit; PFAM: Sec-independent periplasmic protein translocase; KEGG: tcx:Tcr_1974 sec-independent protein translocase TatC; Sec-independent protein translocase, TatC subunit 311081 4555403 Rmag_0285 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Sec-independent protein translocase, TatC subunit YP_903537.1 310215 R 413404 CDS YP_903538.1 118602323 4555404 complement(311081..311362) 1 NC_008610.1 TIGRFAM: twin-arginine translocation protein, TatB subunit; PFAM: sec-independent translocation protein mttA/Hcf106; KEGG: neu:NE0638 mttA/Hcf106 family; twin-arginine translocation protein, TatB subunit 311362 4555404 Rmag_0286 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) twin-arginine translocation protein, TatB subunit YP_903538.1 311081 R 413404 CDS YP_903539.1 118602324 4555405 complement(311374..311577) 1 NC_008610.1 TIGRFAM: twin-arginine translocation protein, TatA/E family subunit; PFAM: sec-independent translocation protein mttA/Hcf106; KEGG: ilo:IL2370 sec-independent protein secretion pathway component, TatA family; twin arginine-targeting protein translocase 311577 4555405 Rmag_0287 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) twin arginine-targeting protein translocase YP_903539.1 311374 R 413404 CDS YP_903540.1 118602325 4555406 complement(311594..311911) 1 NC_008610.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis; phosphoribosyl-ATP pyrophosphatase 311911 hisE 4555406 hisE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribosyl-ATP pyrophosphatase YP_903540.1 311594 R 413404 CDS YP_903541.1 118602326 4555407 complement(311904..312284) 1 NC_008610.1 PR-AMP cyclohydrolase; functions in histidine biosynthesis from PRPP; converts 1-(5-phosphoribosyl)-AMP to 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxyamide during the histidine biosynthesis pathway; binds zinc and magnesium; forms homodimers; phosphoribosyl-AMP cyclohydrolase 312284 hisI 4555407 hisI Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribosyl-AMP cyclohydrolase YP_903541.1 311904 R 413404 CDS YP_903542.1 118602327 4555408 complement(312610..313941) 1 NC_008610.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; pyridine nucleotide-disulphide oxidoreductase dimerisation region; KEGG: tcx:Tcr_0140 glutathione reductase; NADPH-glutathione reductase 313941 4555408 Rmag_0290 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NADPH-glutathione reductase YP_903542.1 312610 R 413404 CDS YP_903543.1 118602328 4555409 complement(315374..316468) 1 NC_008610.1 TIGRFAM: peptide chain release factor 2; PFAM: Class I peptide chain release factor; PCRF domain protein; KEGG: mca:MCA0302 peptide chain release factor 2, programmed frameshift; peptide chain release factor 2 316468 4555409 Rmag_0292 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptide chain release factor 2 YP_903543.1 315374 R 413404 CDS YP_903544.1 118602329 4555410 complement(316527..316787) 1 NC_008610.1 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 316787 rpsO 4555410 rpsO Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S15 YP_903544.1 316527 R 413404 CDS YP_903545.1 118602330 4555411 complement(316850..317746) 1 NC_008610.1 PFAM: lipid A biosynthesis acyltransferase; KEGG: psb:Psyr_1614 lipid A biosynthesis acyltransferase; lipid A biosynthesis acyltransferase 317746 4555411 Rmag_0294 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lipid A biosynthesis acyltransferase YP_903545.1 316850 R 413404 CDS YP_903546.1 118602331 4555412 317787..319568 1 NC_008610.1 KEGG: pfo:Pfl_5148 DNA primase; TIGRFAM: DNA primase; PFAM: zinc finger, CHC2-family protein; TOPRIM domain protein; DNA primase catalytic core, N-terminal domain; SMART: Toprim sub domain protein; DNA primase 319568 4555412 Rmag_0295 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA primase YP_903546.1 317787 D 413404 CDS YP_903547.1 118602332 4555413 complement(319565..321445) 1 NC_008610.1 PFAM: penicillin-binding protein, transpeptidase; Penicillin-binding protein, dimerisation domain; KEGG: tcx:Tcr_0562 peptidoglycan glycosyltransferase; peptidoglycan glycosyltransferase 321445 4555413 Rmag_0296 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidoglycan glycosyltransferase YP_903547.1 319565 R 413404 CDS YP_903548.1 118602333 4555414 complement(321442..321714) 1 NC_008610.1 hypothetical protein 321714 4555414 Rmag_0297 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903548.1 321442 R 413404 CDS YP_903549.1 118602334 4555415 complement(321716..322639) 1 NC_008610.1 TIGRFAM: S-adenosyl-methyltransferase MraW; PFAM: methyltransferase; KEGG: tcx:Tcr_0559 methyltransferase; S-adenosyl-methyltransferase MraW 322639 mraW 4555415 mraW Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) S-adenosyl-methyltransferase MraW YP_903549.1 321716 R 413404 CDS YP_903550.1 118602335 4555416 322947..323222 1 NC_008610.1 hypothetical protein 323222 4555416 Rmag_0299 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903550.1 322947 D 413404 CDS YP_903551.1 118602336 4555417 325602..327839 1 NC_008610.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A 327839 4555417 Rmag_0302 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA topoisomerase IV subunit A YP_903551.1 325602 D 413404 CDS YP_903552.1 118602337 4555418 327941..328318 1 NC_008610.1 PFAM: 6-pyruvoyl tetrahydropterin synthase and hypothetical protein; KEGG: tcx:Tcr_1389 6-pyruvoyl tetrahydropterin synthase and hypothetical protein; putative 6-pyruvoyl tetrahydropterin synthase 328318 4555418 Rmag_0303 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative 6-pyruvoyl tetrahydropterin synthase YP_903552.1 327941 D 413404 CDS YP_903553.1 118602338 4555419 328315..329109 1 NC_008610.1 similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis; putative GTP cyclohydrolase 329109 4555419 Rmag_0304 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative GTP cyclohydrolase YP_903553.1 328315 D 413404 CDS YP_903554.1 118602339 4554868 329103..330197 1 NC_008610.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive; phospho-2-dehydro-3-deoxyheptonate aldolase 330197 4554868 Rmag_0305 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phospho-2-dehydro-3-deoxyheptonate aldolase YP_903554.1 329103 D 413404 CDS YP_903555.1 118602340 4554869 330299..332884 1 NC_008610.1 TIGRFAM: DNA gyrase, A subunit; PFAM: DNA gyrase/topoisomerase IV, subunit A; DNA gyrase C-terminal repeat, beta-propeller; KEGG: mca:MCA1421 DNA gyrase, A subunit; DNA gyrase subunit A 332884 4554869 Rmag_0306 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA gyrase subunit A YP_903555.1 330299 D 413404 CDS YP_903556.1 118602341 4554870 complement(333760..335328) 1 NC_008610.1 TIGRFAM: peptide chain release factor 3; small GTP-binding protein; PFAM: protein synthesis factor, GTP-binding; elongation factor Tu, domain 2 protein; KEGG: lpf:lpl0905 peptide chain release factor 3; peptide chain release factor 3 335328 4554870 Rmag_0307 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptide chain release factor 3 YP_903556.1 333760 R 413404 CDS YP_903557.1 118602342 4554871 complement(335328..335774) 1 NC_008610.1 PFAM: CMP/dCMP deaminase, zinc-binding; KEGG: xcb:XC_0132 deoxycytidylate deaminase; CMP/dCMP deaminase, zinc-binding 335774 4554871 Rmag_0308 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CMP/dCMP deaminase, zinc-binding YP_903557.1 335328 R 413404 CDS YP_903558.1 118602343 4554872 complement(335777..336862) 1 NC_008610.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase 336862 mraY 4554872 mraY Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phospho-N-acetylmuramoyl-pentapeptide- transferase YP_903558.1 335777 R 413404 CDS YP_903559.1 118602344 4554873 complement(336868..337869) 1 NC_008610.1 PFAM: peptidylprolyl isomerase, FKBP-type; peptidyl-prolyl cis-trans isomerase, cyclophilin type; KEGG: tde:TDE2391 peptidyl-prolyl cis-trans isomerase; peptidylprolyl isomerase 337869 4554873 Rmag_0310 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidylprolyl isomerase YP_903559.1 336868 R 413404 CDS YP_903560.1 118602345 4554874 337987..338220 1 NC_008610.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: par:Psyc_0327 putative 4Fe-4S ferredoxin; 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein 338220 4554874 Rmag_0311 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein YP_903560.1 337987 D 413404 CDS YP_903561.1 118602346 4554875 complement(339057..340175) 1 NC_008610.1 PFAM: aminotransferase, class V; KEGG: cps:CPS_2190 aminotransferase, class V; alanine-glyoxylate aminotransferase 340175 4554875 Rmag_0312 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) alanine-glyoxylate aminotransferase YP_903561.1 339057 R 413404 CDS YP_903562.1 118602347 4554876 340995..342425 1 NC_008610.1 PFAM: FAD linked oxidase domain protein; KEGG: psp:PSPPH_3252 glycolate oxidase, GlcD subunit; FAD linked oxidase domain-containing protein 342425 4554876 Rmag_0313 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) FAD linked oxidase domain-containing protein YP_903562.1 340995 D 413404 CDS YP_903563.1 118602348 4554877 342425..342958 1 NC_008610.1 KEGG: eba:ebA4491 FAD linked oxidase; FAD/FMN-containing dehydrogenases-like 342958 4554877 Rmag_0314 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) FAD/FMN-containing dehydrogenases-like YP_903563.1 342425 D 413404 CDS YP_903564.1 118602349 4554878 342958..344082 1 NC_008610.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; protein of unknown function DUF224, cysteine-rich region domain protein; KEGG: neu:NE0673 glycolate oxidase (iron-sulfur subunit) protein; hypothetical protein 344082 4554878 Rmag_0315 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903564.1 342958 D 413404 CDS YP_903565.1 118602350 4554879 344806..345219 1 NC_008610.1 SMART: Rhodanese domain protein; KEGG: pol:Bpro_0171 rhodanese-like; rhodanese domain-containing protein 345219 4554879 Rmag_0316 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) rhodanese domain-containing protein YP_903565.1 344806 D 413404 CDS YP_903566.1 118602351 4554880 345220..346521 1 NC_008610.1 PFAM: major facilitator superfamily MFS_1; KEGG: vvy:VV2596 putative AmpG protein; major facilitator transporter 346521 4554880 Rmag_0317 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) major facilitator transporter YP_903566.1 345220 D 413404 CDS YP_903567.1 118602352 4554881 346518..347501 1 NC_008610.1 PFAM: glycoside hydrolase, family 3 domain protein; KEGG: tbd:Tbd_0727 beta-N-acetylhexosaminidase; Beta-N-acetylhexosaminidase 347501 4554881 Rmag_0318 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Beta-N-acetylhexosaminidase YP_903567.1 346518 D 413404 CDS YP_903568.1 118602353 4554882 347498..347773 1 NC_008610.1 hypothetical protein 347773 4554882 Rmag_0319 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903568.1 347498 D 413404 CDS YP_903569.1 118602354 4554883 complement(347815..349971) 1 NC_008610.1 PFAM: UvrD/REP helicase; KEGG: pha:PSHAa0122 DNA-dependent ATPase I; UvrD/REP helicase 349971 4554883 Rmag_0320 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UvrD/REP helicase YP_903569.1 347815 R 413404 CDS YP_903570.1 118602355 4554884 350089..350274 1 NC_008610.1 hypothetical protein 350274 4554884 Rmag_0321 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903570.1 350089 D 413404 CDS YP_903571.1 118602356 4554885 350332..351279 1 NC_008610.1 TIGRFAM: lysine 2,3-aminomutase YodO family protein; PFAM: Radical SAM domain protein; KEGG: sde:Sde_1081 hypothetical protein; L-lysine 2,3-aminomutase 351279 4554885 Rmag_0322 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) L-lysine 2,3-aminomutase YP_903571.1 350332 D 413404 CDS YP_903572.1 118602357 4554886 complement(351271..351825) 1 NC_008610.1 PFAM: Redoxin domain protein; KEGG: tbd:Tbd_2118 thioredoxin; redoxin domain-containing protein 351825 4554886 Rmag_0323 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) redoxin domain-containing protein YP_903572.1 351271 R 413404 CDS YP_903573.1 118602358 4554887 351838..352185 1 NC_008610.1 TIGRFAM: arsenate reductase; PFAM: arsenate reductase and related; KEGG: sdn:Sden_1646 arsenate reductase; arsenate reductase 352185 4554887 Rmag_0324 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) arsenate reductase YP_903573.1 351838 D 413404 CDS YP_903574.1 118602359 4554615 complement(352211..352870) 1 NC_008610.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: tcx:Tcr_1309 glutathione S-transferase-like; glutathione S-transferase domain-containing protein 352870 4554615 Rmag_0325 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutathione S-transferase domain-containing protein YP_903574.1 352211 R 413404 CDS YP_903575.1 118602360 4554616 complement(353318..353650) 1 NC_008610.1 TIGRFAM: iojap-like protein; PFAM: Iojap-related protein; KEGG: sde:Sde_3343 poly(A) polymerase, PcnB; iojap-like protein 353650 4554616 Rmag_0326 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) iojap-like protein YP_903575.1 353318 R 413404 CDS YP_903576.1 118602361 4554617 complement(353647..354324) 1 NC_008610.1 TIGRFAM: cytidyltransferase-related domain; nicotinate (nicotinamide) nucleotide adenylyltransferase; PFAM: cytidylyltransferase; KEGG: eca:ECA1306 nicotinate-nucleotide adenylyltransferase; nicotinate-nucleotide adenylyltransferase 354324 4554617 Rmag_0327 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) nicotinate-nucleotide adenylyltransferase YP_903576.1 353647 R 413404 CDS YP_903577.1 118602362 4554618 complement(354321..355043) 1 NC_008610.1 PFAM: beta-lactamase domain protein; KEGG: bsu:BG12648 involved in polyketide synthesis; beta-lactamase domain-containing protein 355043 4554618 Rmag_0328 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) beta-lactamase domain-containing protein YP_903577.1 354321 R 413404 CDS YP_903578.1 118602363 4554619 355482..356426 1 NC_008610.1 KEGG: eci:UTI89_C2927 ribosomal large subunit pseudouridine synthase D; TIGRFAM: pseudouridine synthase, RluA family; PFAM: RNA-binding S4 domain protein; pseudouridine synthase; ribosomal large subunit pseudouridine synthase D 356426 4554619 Rmag_0329 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribosomal large subunit pseudouridine synthase D YP_903578.1 355482 D 413404 CDS YP_903579.1 118602364 4554620 complement(357197..357592) 1 NC_008610.1 PFAM: peptidase S24, S26A and S26B; KEGG: tbd:Tbd_1516 hypothetical protein; putative prophage repressor 357592 4554620 Rmag_0331 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative prophage repressor YP_903579.1 357197 R 413404 CDS YP_903580.1 118602365 4554621 complement(357580..358389) 1 NC_008610.1 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 358389 4554621 Rmag_0332 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) formamidopyrimidine-DNA glycosylase YP_903580.1 357580 R 413404 CDS YP_903581.1 118602366 4554622 358468..359055 1 NC_008610.1 KEGG: noc:Noc_1372 hypothetical protein; membrane protein-like 359055 4554622 Rmag_0333 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) membrane protein-like YP_903581.1 358468 D 413404 CDS YP_903582.1 118602367 4554623 359363..360406 1 NC_008610.1 hypothetical protein 360406 4554623 Rmag_0334 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903582.1 359363 D 413404 CDS YP_903583.1 118602368 4554624 361210..362583 1 NC_008610.1 PFAM: Citrate transporter; KEGG: sde:Sde_0065 Na+/H+ antiporter (NhaD family); citrate transporter 362583 4554624 Rmag_0336 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) citrate transporter YP_903583.1 361210 D 413404 CDS YP_903584.1 118602369 4554625 362570..363274 1 NC_008610.1 TIGRFAM: putative transcriptional activator, Baf family; PFAM: Bordetella pertussis Bvg accessory factor; KEGG: cps:CPS_4744 putative transcriptional activator; Baf family transcriptional activator 363274 4554625 Rmag_0337 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Baf family transcriptional activator YP_903584.1 362570 D 413404 CDS YP_903585.1 118602370 4554626 363305..364504 1 NC_008610.1 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 364504 4554626 Rmag_0338 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tryptophanyl-tRNA synthetase YP_903585.1 363305 D 413404 CDS YP_903586.1 118602371 4554627 364507..365235 1 NC_008610.1 TIGRFAM: Pseudouridine synthase, Rsu; PFAM: RNA-binding S4 domain protein; pseudouridine synthase; KEGG: noc:Noc_1041 pseudouridine synthase, Rsu; ribosomal large subunit pseudouridine synthase B 365235 4554627 Rmag_0339 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribosomal large subunit pseudouridine synthase B YP_903586.1 364507 D 413404 CDS YP_903587.1 118602372 4554628 365592..368360 1 NC_008610.1 TIGRFAM: isoleucyl-tRNA synthetase; KEGG: noc:Noc_2277 isoleucyl-tRNA synthetase, class Ia; isoleucyl-tRNA synthetase 368360 4554628 Rmag_0340 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) isoleucyl-tRNA synthetase YP_903587.1 365592 D 413404 CDS YP_903588.1 118602373 4554629 368361..369440 1 NC_008610.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase 369440 aroB 4554629 aroB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-dehydroquinate synthase YP_903588.1 368361 D 413404 CDS YP_903589.1 118602374 4554630 369447..370037 1 NC_008610.1 hypothetical protein 370037 4554630 Rmag_0342 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903589.1 369447 D 413404 CDS YP_903590.1 118602375 4554631 370040..370327 1 NC_008610.1 TIGRFAM: glutamyl-tRNA(Gln) amidotransferase, C subunit; PFAM: Glu-tRNAGln amidotransferase, C subunit; KEGG: neu:NE2071 Glu-tRNAGln amidotransferase C subunit; aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C 370327 4554631 Rmag_0343 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C YP_903590.1 370040 D 413404 CDS YP_903591.1 118602376 4554632 370329..371771 1 NC_008610.1 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 371771 gatA 4554632 gatA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aspartyl/glutamyl-tRNA amidotransferase subunit A YP_903591.1 370329 D 413404 CDS YP_903592.1 118602377 4554633 371773..373203 1 NC_008610.1 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 373203 gatB 4554633 gatB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aspartyl/glutamyl-tRNA amidotransferase subunit B YP_903592.1 371773 D 413404 CDS YP_903593.1 118602378 4554828 373208..374581 1 NC_008610.1 PFAM: protein of unknown function UPF0061; KEGG: vpa:VP0909 hypothetical protein; hypothetical protein 374581 4554828 Rmag_0346 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903593.1 373208 D 413404 CDS YP_903594.1 118602379 4554829 complement(374578..375210) 1 NC_008610.1 PFAM: peptidase M50; KEGG: tcx:Tcr_1229 peptidase M50; peptidase M50 375210 4554829 Rmag_0347 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase M50 YP_903594.1 374578 R 413404 CDS YP_903595.1 118602380 4554830 375246..376925 1 NC_008610.1 TIGRFAM: prolyl-tRNA synthetase; PFAM: tRNA synthetase, class II (G, H, P and S); Anticodon-binding domain protein; YbaK/prolyl-tRNA synthetase associated region; KEGG: hch:HCH_04773 prolyl-tRNA synthetase; prolyl-tRNA synthetase 376925 4554830 Rmag_0348 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) prolyl-tRNA synthetase YP_903595.1 375246 D 413404 CDS YP_903596.1 118602381 4554831 376933..377745 1 NC_008610.1 KEGG: mfa:Mfla_2122 phosphatidylserine decarboxylase; TIGRFAM: phosphatidylserine decarboxylase; PFAM: phosphatidylserine decarboxylase-related; phosphatidylserine decarboxylase 377745 4554831 Rmag_0349 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphatidylserine decarboxylase YP_903596.1 376933 D 413404 CDS YP_903597.1 118602382 4554832 complement(377720..378889) 1 NC_008610.1 PFAM: CBS domain containing protein; protein of unknown function DUF21; transporter-associated region; KEGG: noc:Noc_2263 hypothetical protein; hypothetical protein 378889 4554832 Rmag_0350 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903597.1 377720 R 413404 CDS YP_903598.1 118602383 4554833 complement(379012..380289) 1 NC_008610.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase 380289 eno 4554833 eno Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphopyruvate hydratase YP_903598.1 379012 R 413404 CDS YP_903599.1 118602384 4554834 complement(380307..381401) 1 NC_008610.1 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; chaperone protein DnaJ 381401 4554834 Rmag_0352 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) chaperone protein DnaJ YP_903599.1 380307 R 413404 CDS YP_903600.1 118602385 4554835 complement(381478..383385) 1 NC_008610.1 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 383385 dnaK 4554835 dnaK Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) molecular chaperone DnaK YP_903600.1 381478 R 413404 CDS YP_903601.1 118602386 4554836 complement(383462..383941) 1 NC_008610.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase 383941 coaD 4554836 coaD Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphopantetheine adenylyltransferase YP_903601.1 383462 R 413404 CDS YP_903602.1 118602387 4554837 complement(383962..384540) 1 NC_008610.1 TIGRFAM: putative methyltransferase; PFAM: conserved hypothetical protein 95; KEGG: ilo:IL0225 N6-adenine-specific methylase; putative methyltransferase 384540 4554837 Rmag_0355 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative methyltransferase YP_903602.1 383962 R 413404 CDS YP_903603.1 118602388 4554838 complement(384521..385051) 1 NC_008610.1 PFAM: Inorganic pyrophosphatase; KEGG: ilo:IL2263 inorganic pyrophosphatase; inorganic diphosphatase 385051 4554838 Rmag_0356 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) inorganic diphosphatase YP_903603.1 384521 R 413404 CDS YP_903604.1 118602389 4554839 389644..391806 1 NC_008610.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; KEGG: noc:Noc_3018 signal transduction histidine kinase, NtrY; periplasmic sensor signal transduction histidine kinase 391806 4554839 Rmag_0361 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) periplasmic sensor signal transduction histidine kinase YP_903604.1 389644 D 413404 CDS YP_903605.1 118602390 4554840 391819..392394 1 NC_008610.1 PFAM: response regulator receiver; helix-turn-helix, Fis-type; KEGG: pol:Bpro_4433 two component transcriptional regulator, fis family; response regulator receiver protein 392394 4554840 Rmag_0362 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) response regulator receiver protein YP_903605.1 391819 D 413404 CDS YP_903606.1 118602391 4554841 392401..393774 1 NC_008610.1 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 component 393774 trkA 4554841 trkA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) potassium transporter peripheral membrane component YP_903606.1 392401 D 413404 CDS YP_903607.1 118602392 4554842 393787..395235 1 NC_008610.1 TIGRFAM: potassium uptake protein, TrkH family; PFAM: cation transporter; KEGG: hch:HCH_00025 trk-type K+ transport system, membrane components; TrkH family potassium uptake protein 395235 4554842 Rmag_0364 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) TrkH family potassium uptake protein YP_903607.1 393787 D 413404 CDS YP_903608.1 118602393 4554843 complement(395257..397314) 1 NC_008610.1 helicase involved in DNA repair and perhaps also replication; ATP-dependent DNA helicase DinG 397314 dinG 4554843 dinG Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP-dependent DNA helicase DinG YP_903608.1 395257 R 413404 CDS YP_903609.1 118602394 4554844 complement(397319..398290) 1 NC_008610.1 PFAM: Polyprenyl synthetase; KEGG: ftl:FTL_1041 octaprenyl-diphosphate synthase; dimethylallyltranstransferase 398290 4554844 Rmag_0366 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dimethylallyltranstransferase YP_903609.1 397319 R 413404 CDS YP_903610.1 118602395 4554845 complement(398346..398969) 1 NC_008610.1 PFAM: ribosomal RNA methyltransferase RrmJ/FtsJ; KEGG: sde:Sde_2721 ribosomal RNA methyltransferase RrmJ/FtsJ; ribosomal RNA methyltransferase RrmJ/FtsJ 398969 4554845 Rmag_0367 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribosomal RNA methyltransferase RrmJ/FtsJ YP_903610.1 398346 R 413404 CDS YP_903611.1 118602396 4554846 399040..400857 1 NC_008610.1 TIGRFAM: small GTP-binding protein; GTP-binding protein TypA; PFAM: elongation factor G domain protein; protein synthesis factor, GTP-binding; elongation factor Tu, domain 2 protein; KEGG: sec:SC3900 GTP-binding elongation factor family protein; GTP-binding protein TypA 400857 4554846 Rmag_0368 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GTP-binding protein TypA YP_903611.1 399040 D 413404 CDS YP_903612.1 118602397 4554847 400941..403994 1 NC_008610.1 PFAM: acriflavin resistance protein; KEGG: lil:LA2439 acriflavine resistance protein homolog; acriflavin resistance protein 403994 4554847 Rmag_0369 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acriflavin resistance protein YP_903612.1 400941 D 413404 CDS YP_903613.1 118602398 4554567 complement(408911..409525) 1 NC_008610.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit 409525 leuD 4554567 leuD Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) isopropylmalate isomerase small subunit YP_903613.1 408911 R 413404 CDS YP_903614.1 118602399 4554568 complement(409525..410958) 1 NC_008610.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 410958 4554568 Rmag_0372 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) isopropylmalate isomerase large subunit YP_903614.1 409525 R 413404 CDS YP_903615.1 118602400 4554569 410980..412755 1 NC_008610.1 TIGRFAM: asparagine synthase (glutamine-hydrolyzing); PFAM: glutamine amidotransferase, class-II; asparagine synthase; KEGG: tbd:Tbd_0060 asparagine synthase, glutamine-hydrolyzing; asparagine synthase (glutamine-hydrolyzing) 412755 4554569 Rmag_0373 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) asparagine synthase (glutamine-hydrolyzing) YP_903615.1 410980 D 413404 CDS YP_903616.1 118602401 4554570 412748..413188 1 NC_008610.1 PFAM: ribonuclease H; KEGG: ftl:FTL_0854 ribonuclease H; ribonuclease H 413188 4554570 Rmag_0374 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonuclease H YP_903616.1 412748 D 413404 CDS YP_903617.1 118602402 4554571 414483..415358 1 NC_008610.1 KEGG: tbd:Tbd_2669 hypothetical protein; hypothetical protein 415358 4554571 Rmag_0376 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903617.1 414483 D 413404 CDS YP_903618.1 118602403 4554572 complement(416322..416753) 1 NC_008610.1 PFAM: cyclase/dehydrase; KEGG: vpa:VP0645 hypothetical protein; cyclase/dehydrase 416753 4554572 Rmag_0378 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cyclase/dehydrase YP_903618.1 416322 R 413404 CDS YP_903619.1 118602404 4554573 416752..417249 1 NC_008610.1 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 417249 smpB 4554573 smpB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) SsrA-binding protein YP_903619.1 416752 D 413404 CDS YP_903620.1 118602405 4554574 417438..417713 1 NC_008610.1 PFAM: histone family protein DNA-binding protein; KEGG: mca:MCA0532 DNA-binding protein HU-beta; histone family protein DNA-binding protein 417713 4554574 Rmag_0380 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) histone family protein DNA-binding protein YP_903620.1 417438 D 413404 CDS YP_903621.1 118602406 4554575 417809..418234 1 NC_008610.1 PFAM: nucleoside diphosphate kinase; KEGG: mfa:Mfla_1624 nucleoside-diphosphate kinase; nucleoside diphosphate kinase 418234 4554575 Rmag_0381 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) nucleoside diphosphate kinase YP_903621.1 417809 D 413404 CDS YP_903622.1 118602407 4554576 418283..419353 1 NC_008610.1 TIGRFAM: radical SAM enzyme, Cfr family; PFAM: Radical SAM domain protein; KEGG: lpp:lpp1504 hypothetical protein; radical SAM protein 419353 4554576 Rmag_0382 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) radical SAM protein YP_903622.1 418283 D 413404 CDS YP_903623.1 118602408 4554577 419337..419642 1 NC_008610.1 hypothetical protein 419642 4554577 Rmag_0383 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903623.1 419337 D 413404 CDS YP_903624.1 118602409 4554578 419642..420718 1 NC_008610.1 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 420718 ispG 4554578 ispG Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase YP_903624.1 419642 D 413404 CDS YP_903625.1 118602410 4554579 complement(420705..421199) 1 NC_008610.1 KEGG: cps:CPS_2123 hypothetical protein; hypothetical protein 421199 4554579 Rmag_0385 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903625.1 420705 R 413404 CDS YP_903626.1 118602411 4554580 complement(421196..422998) 1 NC_008610.1 TIGRFAM: deoxyxylulose-5-phosphate synthase; PFAM: Transketolase, central region; Transketolase domain protein; KEGG: mca:MCA0817 1-deoxy-D-xylulose-5-phosphate synthase; 1-deoxy-D-xylulose-5-phosphate synthase 422998 4554580 Rmag_0386 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 1-deoxy-D-xylulose-5-phosphate synthase YP_903626.1 421196 R 413404 CDS YP_903627.1 118602412 4554581 complement(423060..424433) 1 NC_008610.1 PFAM: peptidase U32; KEGG: son:SO1252 peptidase, U32 family; peptidase U32 424433 4554581 Rmag_0387 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase U32 YP_903627.1 423060 R 413404 CDS YP_903628.1 118602413 4554582 424463..425062 1 NC_008610.1 PFAM: methyltransferase small; KEGG: tcx:Tcr_0213 methyltransferase small; methyltransferase small 425062 4554582 Rmag_0388 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) methyltransferase small YP_903628.1 424463 D 413404 CDS YP_903629.1 118602414 4554583 425113..425442 1 NC_008610.1 TIGRFAM: glutaredoxin-like protein; PFAM: glutaredoxin; KEGG: tbd:Tbd_2499 glutaredoxin-related protein; glutaredoxin-like protein 425442 4554583 Rmag_0389 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutaredoxin-like protein YP_903629.1 425113 D 413404 CDS YP_903630.1 118602415 4554584 complement(426387..427046) 1 NC_008610.1 PFAM: protein of unknown function DUF45; KEGG: chy:CHY_0833 hypothetical protein; hypothetical protein 427046 4554584 Rmag_0391 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903630.1 426387 R 413404 CDS YP_903631.1 118602416 4554585 complement(427440..431264) 1 NC_008610.1 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 431264 4554585 Rmag_0392 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribosylformylglycinamidine synthase YP_903631.1 427440 R 413404 CDS YP_903632.1 118602417 4555625 complement(432600..433340) 1 NC_008610.1 PFAM: protein of unknown function DUF28; KEGG: ilo:IL1088 uncharacterized conserved enzyme; hypothetical protein 433340 4555625 Rmag_0394 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903632.1 432600 R 413404 CDS YP_903633.1 118602418 4555626 complement(433379..434329) 1 NC_008610.1 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate; quinolinate synthetase 434329 4555626 Rmag_0395 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) quinolinate synthetase YP_903633.1 433379 R 413404 CDS YP_903634.1 118602419 4555627 complement(434336..436087) 1 NC_008610.1 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 436087 aspS 4555627 aspS Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aspartyl-tRNA synthetase YP_903634.1 434336 R 413404 CDS YP_903635.1 118602420 4555628 complement(436092..436694) 1 NC_008610.1 PFAM: protein of unknown function DUF502; KEGG: mfa:Mfla_2385 protein of unknown function DUF502; hypothetical protein 436694 4555628 Rmag_0397 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903635.1 436092 R 413404 CDS YP_903636.1 118602421 4555629 complement(436749..437525) 1 NC_008610.1 TIGRFAM: methionine aminopeptidase, type I; PFAM: peptidase M24; KEGG: lpp:lpp1684 methionyl aminopeptidase; methionine aminopeptidase, type I 437525 4555629 Rmag_0398 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) methionine aminopeptidase, type I YP_903636.1 436749 R 413404 CDS YP_903637.1 118602422 4555630 complement(437525..438550) 1 NC_008610.1 PFAM: peptidase M48, Ste24p; KEGG: vvy:VVA0973 Zn-dependent protease with chaperone function; peptidase M48, Ste24p 438550 4555630 Rmag_0399 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase M48, Ste24p YP_903637.1 437525 R 413404 CDS YP_903638.1 118602423 4555631 complement(438696..439304) 1 NC_008610.1 PFAM: LemA family protein; KEGG: sde:Sde_3150 divalent cation transporter; LemA family protein 439304 4555631 Rmag_0400 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) LemA family protein YP_903638.1 438696 R 413404 CDS YP_903639.1 118602424 4555632 complement(443731..444399) 1 NC_008610.1 KEGG: lpp:lpp1339 DNA polymerase III epsilon subunit; TIGRFAM: DNA polymerase III, epsilon subunit; PFAM: Exonuclease, RNase T and DNA polymerase III; SMART: Exonuclease; DNA polymerase III, epsilon subunit 444399 4555632 Rmag_0404 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA polymerase III, epsilon subunit YP_903639.1 443731 R 413404 CDS YP_903640.1 118602425 4555633 444470..444709 1 NC_008610.1 TIGRFAM: DNA-directed RNA polymerase, omega subunit; PFAM: RNA polymerase Rpb6; KEGG: psp:PSPPH_0198 DNA-directed RNA polymerase omega chain (RNAP omegasubunit) (transcriptase omega chain) (RNA polymerase omega subunit); DNA-directed RNA polymerase, omega subunit 444709 4555633 Rmag_0405 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA-directed RNA polymerase, omega subunit YP_903640.1 444470 D 413404 CDS YP_903641.1 118602426 4555634 complement(446690..446950) 1 NC_008610.1 hypothetical protein 446950 4555634 Rmag_0408 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903641.1 446690 R 413404 CDS YP_903642.1 118602427 4555635 complement(446938..447924) 1 NC_008610.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase 447924 4555635 Rmag_0409 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) delta-aminolevulinic acid dehydratase YP_903642.1 446938 R 413404 CDS YP_903643.1 118602428 4555636 447965..449833 1 NC_008610.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 449833 4555636 Rmag_0410 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thiamine biosynthesis protein ThiC YP_903643.1 447965 D 413404 CDS YP_903644.1 118602429 4555637 complement(450077..451333) 1 NC_008610.1 PFAM: Three-deoxy-D-manno-octulosonic-acid transferase domain protein; KEGG: plu:plu4854 3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase); 3-deoxy-D-manno-octulosonic-acid transferase domain-containing protein 451333 4555637 Rmag_0411 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-deoxy-D-manno-octulosonic-acid transferase domain-containing protein YP_903644.1 450077 R 413404 CDS YP_903645.1 118602430 4555638 451387..452394 1 NC_008610.1 TIGRFAM: small GTP-binding protein; PFAM: GTP-binding protein, HSR1-related; GTP1/OBG sub domain protein; KEGG: lpp:lpp2702 hypothetical protein; small GTP-binding protein 452394 4555638 Rmag_0412 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) small GTP-binding protein YP_903645.1 451387 D 413404 CDS YP_903646.1 118602431 4555639 452387..453157 1 NC_008610.1 KEGG: tcx:Tcr_0344 glutamate 5-kinase; TIGRFAM: glutamate 5-kinase; PFAM: aspartate/glutamate/uridylate kinase; glutamate 5-kinase 453157 4555639 Rmag_0413 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutamate 5-kinase YP_903646.1 452387 D 413404 CDS YP_903647.1 118602432 4555640 453151..453624 1 NC_008610.1 KEGG: hit:NTHI0077 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase; TIGRFAM: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase; PFAM: 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK; 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase 453624 4555640 Rmag_0414 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase YP_903647.1 453151 D 413404 CDS YP_903648.1 118602433 4555641 453621..454403 1 NC_008610.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate; 3-methyl-2-oxobutanoate hydroxymethyltransferase 454403 panB 4555641 panB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-methyl-2-oxobutanoate hydroxymethyltransferase YP_903648.1 453621 D 413404 CDS YP_903649.1 118602434 4555642 454403..455239 1 NC_008610.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine; pantoate--beta-alanine ligase 455239 panC 4555642 panC Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) pantoate--beta-alanine ligase YP_903649.1 454403 D 413404 CDS YP_903650.1 118602435 4555643 455242..455820 1 NC_008610.1 PFAM: HesB/YadR/YfhF-family protein; nitrogen-fixing NifU domain protein; KEGG: hch:HCH_02543 thioredoxin-like protein; NifU domain-containing protein 455820 4555643 Rmag_0417 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NifU domain-containing protein YP_903650.1 455242 D 413404 CDS YP_903651.1 118602436 4555644 455872..456381 1 NC_008610.1 KEGG: tcx:Tcr_0164 hypothetical protein; hypothetical protein 456381 4555644 Rmag_0418 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903651.1 455872 D 413404 CDS YP_903652.1 118602437 4555216 456381..457310 1 NC_008610.1 TIGRFAM: thiamine-monophosphate kinase; PFAM: AIR synthase related protein domain protein; KEGG: hit:NTHI1618 thiamine-monophosphate kinase; thiamine-monophosphate kinase 457310 4555216 Rmag_0419 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thiamine-monophosphate kinase YP_903652.1 456381 D 413404 CDS YP_903653.1 118602438 4555217 complement(457348..457758) 1 NC_008610.1 TIGRFAM: RNA polymerase-binding protein DksA; PFAM: zinc finger, DksA/TraR C4-type; KEGG: aci:ACIAD0273 DnaK suppressor protein; TraR/DksA family transcriptional regulator 457758 4555217 Rmag_0420 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) TraR/DksA family transcriptional regulator YP_903653.1 457348 R 413404 CDS YP_903654.1 118602439 4555218 457849..458610 1 NC_008610.1 TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: tcx:Tcr_1242 HAD-superfamily hydrolase subfamily IA, variant 3; HAD family hydrolase 458610 4555218 Rmag_0421 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) HAD family hydrolase YP_903654.1 457849 D 413404 CDS YP_903655.1 118602440 4555219 460425..461705 1 NC_008610.1 TIGRFAM: isocitrate dehydrogenase, NADP-dependent; PFAM: isocitrate/isopropylmalate dehydrogenase; KEGG: cbu:CBU_1200 isocitrate dehydrogenase, NADP-dependent; isocitrate dehydrogenase (NADP) 461705 4555219 Rmag_0423 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) isocitrate dehydrogenase (NADP) YP_903655.1 460425 D 413404 CDS YP_903656.1 118602441 4555220 462345..462869 1 NC_008610.1 KEGG: pfa:PF14_0644 hypothetical protein; hypothetical protein 462869 4555220 Rmag_0424 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903656.1 462345 D 413404 CDS YP_903657.1 118602442 4555221 complement(463180..464358) 1 NC_008610.1 PFAM: aminotransferase, class I and II; KEGG: hch:HCH_04972 aspartate/tyrosine/aromatic aminotransferase; aminotransferase 464358 4555221 Rmag_0425 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aminotransferase YP_903657.1 463180 R 413404 CDS YP_903658.1 118602443 4555222 464419..466413 1 NC_008610.1 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 466413 4555222 Rmag_0426 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) excinuclease ABC subunit B YP_903658.1 464419 D 413404 CDS YP_903659.1 118602444 4555223 466410..467051 1 NC_008610.1 PFAM: Radical SAM domain protein; KEGG: mfa:Mfla_2336 radical SAM; radical SAM domain-containing protein 467051 4555223 Rmag_0427 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) radical SAM domain-containing protein YP_903659.1 466410 D 413404 CDS YP_903660.1 118602445 4555224 complement(467052..467540) 1 NC_008610.1 PFAM: heat shock protein Hsp20; KEGG: rfe:RF_1004 small heat shock protein; heat shock protein Hsp20 467540 4555224 Rmag_0428 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) heat shock protein Hsp20 YP_903660.1 467052 R 413404 CDS YP_903661.1 118602446 4555225 complement(468744..469841) 1 NC_008610.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase 469841 4555225 Rmag_0430 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) chorismate synthase YP_903661.1 468744 R 413404 CDS YP_903662.1 118602447 4555226 470704..471399 1 NC_008610.1 KEGG: mca:MCA1094 orotidine 5'-phosphate decarboxylase; TIGRFAM: orotidine 5'-phosphate decarboxylase; PFAM: Orotidine 5'-phosphate decarboxylase; orotidine-5'-phosphate decarboxylase 471399 4555226 Rmag_0432 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) orotidine-5'-phosphate decarboxylase YP_903662.1 470704 D 413404 CDS YP_903663.1 118602448 4555227 472435..473628 1 NC_008610.1 TIGRFAM: Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; PFAM: monooxygenase, FAD-binding; KEGG: ngo:NGO1678 hypothetical protein; hypothetical protein 473628 4555227 Rmag_0433 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903663.1 472435 D 413404 CDS YP_903664.1 118602449 4555228 473628..474266 1 NC_008610.1 KEGG: tcx:Tcr_1992 pyridoxamine 5'-phosphate oxidase; TIGRFAM: pyridoxamine 5'-phosphate oxidase; PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding; pyridoxamine 5'-phosphate oxidase 474266 4555228 Rmag_0434 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) pyridoxamine 5'-phosphate oxidase YP_903664.1 473628 D 413404 CDS YP_903665.1 118602450 4555229 complement(474255..475058) 1 NC_008610.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase 475058 aroE 4555229 aroE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) shikimate 5-dehydrogenase YP_903665.1 474255 R 413404 CDS YP_903666.1 118602451 4555230 complement(475090..476844) 1 NC_008610.1 TIGRFAM: ribonuclease, Rne/Rng family; PFAM: RNA binding S1 domain protein; KEGG: tcx:Tcr_0703 ribonuclease, Rne/Rng family; ribonuclease 476844 4555230 Rmag_0436 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonuclease YP_903666.1 475090 R 413404 CDS YP_903667.1 118602452 4555231 complement(477164..477883) 1 NC_008610.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: nmu:Nmul_A0336 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 477883 4555231 Rmag_0437 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) short-chain dehydrogenase/reductase SDR YP_903667.1 477164 R 413404 CDS YP_903668.1 118602453 4555232 477898..478992 1 NC_008610.1 PFAM: protein of unknown function DUF185; KEGG: noc:Noc_0037 protein of unknown function DUF185; hypothetical protein 478992 4555232 Rmag_0438 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903668.1 477898 D 413404 CDS YP_903669.1 118602454 4555233 479009..479809 1 NC_008610.1 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell; undecaprenyl pyrophosphate phosphatase 479809 4555233 Rmag_0439 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) undecaprenyl pyrophosphate phosphatase YP_903669.1 479009 D 413404 CDS YP_903670.1 118602455 4555234 480525..483062 1 NC_008610.1 TIGRFAM: aminopeptidase N; PFAM: peptidase M1, membrane alanine aminopeptidase; KEGG: noc:Noc_1314 peptidase M, neutral zinc metallopeptidase, zinc-binding site; aminopeptidase N 483062 pepN 4555234 pepN Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aminopeptidase N YP_903670.1 480525 D 413404 CDS YP_903671.1 118602456 4555605 483059..483517 1 NC_008610.1 PFAM: CinA domain protein; KEGG: reu:Reut_A2850 CinA, C-terminal; CinA domain-containing protein 483517 4555605 Rmag_0441 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CinA domain-containing protein YP_903671.1 483059 D 413404 CDS YP_903672.1 118602457 4555606 483504..484472 1 NC_008610.1 TIGRFAM: TIM-barrel protein, yjbN family; PFAM: dihydrouridine synthase, DuS; KEGG: noc:Noc_2960 dihydrouridine synthase TIM-barrel protein YjbN; tRNA-dihydrouridine synthase A 484472 4555606 Rmag_0442 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA-dihydrouridine synthase A YP_903672.1 483504 D 413404 CDS YP_903673.1 118602458 4555607 484462..485682 1 NC_008610.1 PFAM: cell division protein FtsA; KEGG: mca:MCA2424 cell division protein FtsA; cell division protein FtsA 485682 4555607 Rmag_0443 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cell division protein FtsA YP_903673.1 484462 D 413404 CDS YP_903674.1 118602459 4555608 485688..486599 1 NC_008610.1 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 486599 lpxC 4555608 lpxC Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase YP_903674.1 485688 D 413404 CDS YP_903675.1 118602460 4555609 486667..488406 1 NC_008610.1 TIGRFAM: acetolactate synthase, large subunit, biosynthetic type; PFAM: thiamine pyrophosphate enzyme domain protein TPP-binding; thiamine pyrophosphate enzyme, central region; thiamine pyrophosphate enzyme TPP binding domain protein; KEGG: mca:MCA2270 acetolactate synthase, large subunit, biosynthetic type; acetolactate synthase, large subunit 488406 4555609 Rmag_0445 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acetolactate synthase, large subunit YP_903675.1 486667 D 413404 CDS YP_903676.1 118602461 4555610 488403..488879 1 NC_008610.1 TIGRFAM: acetolactate synthase, small subunit; PFAM: amino acid-binding ACT domain protein; KEGG: dar:Daro_3074 acetolactate synthase, small subunit; acetolactate synthase, small subunit 488879 4555610 Rmag_0446 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acetolactate synthase, small subunit YP_903676.1 488403 D 413404 CDS YP_903677.1 118602462 4555611 488924..489928 1 NC_008610.1 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 489928 4555611 Rmag_0447 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ketol-acid reductoisomerase YP_903677.1 488924 D 413404 CDS YP_903678.1 118602463 4555612 489981..490727 1 NC_008610.1 KEGG: tcx:Tcr_0610 CDP-diacylglycerol--serine O-phosphatidyltransferase; TIGRFAM: CDP-diacylglycerol--serine O-phosphatidyltransferase; PFAM: CDP-alcohol phosphatidyltransferase; CDP-diacylglycerol--serine O-phosphatidyltransferase 490727 4555612 Rmag_0448 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CDP-diacylglycerol--serine O-phosphatidyltransferase YP_903678.1 489981 D 413404 CDS YP_903679.1 118602464 4555613 490882..492417 1 NC_008610.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase 492417 4555613 Rmag_0449 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 2-isopropylmalate synthase YP_903679.1 490882 D 413404 CDS YP_903680.1 118602465 4555614 492414..492833 1 NC_008610.1 hypothetical protein 492833 4555614 Rmag_0450 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903680.1 492414 D 413404 CDS YP_903681.1 118602466 4555615 complement(493205..494104) 1 NC_008610.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase 494104 4555615 Rmag_0452 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ornithine carbamoyltransferase YP_903681.1 493205 R 413404 CDS YP_903682.1 118602467 4555616 complement(494117..495262) 1 NC_008610.1 catalyzes the formation of N-acetyl-l-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine; acetylornithine aminotransferase 495262 4555616 Rmag_0453 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acetylornithine aminotransferase YP_903682.1 494117 R 413404 CDS YP_903683.1 118602468 4555617 495702..495998 1 NC_008610.1 TIGRFAM: ribosomal subunit interface protein; PFAM: sigma 54 modulation protein/ribosomal protein S30EA; KEGG: ilo:IL0395 S30EA ribosomal protein; SSU ribosomal protein S30P / sigma 54 modulation protein 495998 4555617 Rmag_0454 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) SSU ribosomal protein S30P / sigma 54 modulation protein YP_903683.1 495702 D 413404 CDS YP_903684.1 118602469 4555618 496056..497408 1 NC_008610.1 TIGRFAM: magnesium transporter; PFAM: CBS domain containing protein; MgtE integral membrane region; MgtE intracellular region; KEGG: hch:HCH_05326 magnesium transporter; magnesium transporter 497408 4555618 Rmag_0455 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) magnesium transporter YP_903684.1 496056 D 413404 CDS YP_903685.1 118602470 4555619 complement(497533..498948) 1 NC_008610.1 PFAM: phosphoglucomutase/phosphomannomutase C terminal; phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I; phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain II; phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain III; KEGG: noc:Noc_2994 phosphomannomutase; phosphomannomutase 498948 4555619 Rmag_0456 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphomannomutase YP_903685.1 497533 R 413404 CDS YP_903686.1 118602471 4555620 498962..499339 1 NC_008610.1 PFAM: Positive regulator of sigma(E), RseC/MucC; KEGG: eca:ECA3281 sigma-E factor regulatory protein; positive regulator of sigma E, RseC/MucC 499339 4555620 Rmag_0457 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) positive regulator of sigma E, RseC/MucC YP_903686.1 498962 D 413404 CDS YP_903687.1 118602472 4555621 499445..502096 1 NC_008610.1 E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC; pyruvate dehydrogenase subunit E1 502096 aceE 4555621 aceE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) pyruvate dehydrogenase subunit E1 YP_903687.1 499445 D 413404 CDS YP_903688.1 118602473 4555622 complement(502426..502749) 1 NC_008610.1 hypothetical protein 502749 4555622 Rmag_0460 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903688.1 502426 R 413404 CDS YP_903689.1 118602474 4555623 complement(503211..505298) 1 NC_008610.1 KEGG: hch:HCH_01244 polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase); PFAM: 3' exoribonuclease; RNA binding S1 domain protein; KH, type 1, domain protein; SMART: KH domain protein; polynucleotide phosphorylase/polyadenylase 505298 4555623 Rmag_0461 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) polynucleotide phosphorylase/polyadenylase YP_903689.1 503211 R 413404 CDS YP_903690.1 118602475 4555624 complement(507070..508530) 1 NC_008610.1 KEGG: mca:MCA0291 inosine-5'-monophosphate dehydrogenase; TIGRFAM: inosine-5'-monophosphate dehydrogenase; PFAM: CBS domain containing protein; IMP dehydrogenase/GMP reductase; 2-nitropropane dioxygenase, NPD; inosine-5'-monophosphate dehydrogenase 508530 4555624 Rmag_0462 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) inosine-5'-monophosphate dehydrogenase YP_903690.1 507070 R 413404 CDS YP_903691.1 118602476 4554789 complement(508530..509180) 1 NC_008610.1 PFAM: SH3, type 3 domain protein; KEGG: tcx:Tcr_1504 SH3-like region; SH3 type 3 domain-containing protein 509180 4554789 Rmag_0463 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) SH3 type 3 domain-containing protein YP_903691.1 508530 R 413404 CDS YP_903692.1 118602477 4554790 complement(509177..511924) 1 NC_008610.1 TIGRFAM: valyl-tRNA synthetase; KEGG: tcx:Tcr_1503 valyl-tRNA synthetase; valyl-tRNA synthetase 511924 4554790 Rmag_0464 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) valyl-tRNA synthetase YP_903692.1 509177 R 413404 CDS YP_903693.1 118602478 4554791 complement(512915..514504) 1 NC_008610.1 KEGG: neu:NE0433 DNA polymerase III (subunits tau and gamma) protein; TIGRFAM: DNA polymerase III, subunits gamma and tau; PFAM: AAA ATPase, central domain protein; SMART: AAA ATPase; DNA polymerase III, subunits gamma and tau 514504 4554791 Rmag_0466 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA polymerase III, subunits gamma and tau YP_903693.1 512915 R 413404 CDS YP_903694.1 118602479 4554792 complement(514646..515320) 1 NC_008610.1 PFAM: Nucleotidyl transferase; KEGG: pha:PSHAa2630 mannose-1-phosphate guanyltransferase-related protein; nucleotidyl transferase 515320 4554792 Rmag_0467 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) nucleotidyl transferase YP_903694.1 514646 R 413404 CDS YP_903695.1 118602480 4554793 complement(515308..516252) 1 NC_008610.1 PFAM: aminoglycoside phosphotransferase; KEGG: neu:NE0191 domain of unknown function DUF227; aminoglycoside phosphotransferase 516252 4554793 Rmag_0468 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aminoglycoside phosphotransferase YP_903695.1 515308 R 413404 CDS YP_903696.1 118602481 4554794 complement(516245..517078) 1 NC_008610.1 PFAM: aminotransferase, class IV; KEGG: noc:Noc_2631 D-alanine transaminase; branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase 517078 4554794 Rmag_0469 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase YP_903696.1 516245 R 413404 CDS YP_903697.1 118602482 4554795 complement(517078..518205) 1 NC_008610.1 PFAM: peptidase S11, D-alanyl-D-alanine carboxypeptidase 1; Penicillin-binding protein 5 domain protein; KEGG: lpf:lpl1517 D-alanyl-D-alanine carboxypeptidase; Serine-type D-Ala-D-Ala carboxypeptidase 518205 4554795 Rmag_0470 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Serine-type D-Ala-D-Ala carboxypeptidase YP_903697.1 517078 R 413404 CDS YP_903698.1 118602483 4554796 complement(519001..520140) 1 NC_008610.1 TIGRFAM: rod shape-determining protein RodA; PFAM: cell cycle protein; KEGG: ppr:PBPRA2891 putative rod shape-determining protein RodA; rod shape-determining protein RodA 520140 4554796 Rmag_0471 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) rod shape-determining protein RodA YP_903698.1 519001 R 413404 CDS YP_903699.1 118602484 4554797 complement(520137..520499) 1 NC_008610.1 PFAM: protein of unknown function DUF498; KEGG: cvi:CV0994 hypothetical protein; hypothetical protein 520499 4554797 Rmag_0472 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903699.1 520137 R 413404 CDS YP_903700.1 118602485 4554798 520579..521028 1 NC_008610.1 PFAM: Sel1 domain protein repeat-containing protein; KEGG: hit:NTHI1567 hypothetical protein; Sel1 domain-containing protein 521028 4554798 Rmag_0473 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Sel1 domain-containing protein YP_903700.1 520579 D 413404 CDS YP_903701.1 118602486 4554799 521034..522398 1 NC_008610.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 522398 gltX 4554799 gltX Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutamyl-tRNA synthetase YP_903701.1 521034 D 413404 CDS YP_903702.1 118602487 4554800 522436..524955 1 NC_008610.1 KEGG: pae:PA3658 protein-PII uridylyltransferase; TIGRFAM: protein-P-II uridylyltransferase; PFAM: amino acid-binding ACT domain protein; DNA polymerase, beta domain protein region; metal-dependent phosphohydrolase, HD sub domain; GlnD PII-uridylyltransferase; SMART: metal-dependent phosphohydrolase, HD region; UTP-GlnB uridylyltransferase, GlnD 524955 4554800 Rmag_0475 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UTP-GlnB uridylyltransferase, GlnD YP_903702.1 522436 D 413404 CDS YP_903703.1 118602488 4554801 525051..525377 1 NC_008610.1 TIGRFAM: thioredoxin; PFAM: Thioredoxin domain; KEGG: ppr:PBPRA3541 putative thioredoxin; thioredoxin 525377 4554801 Rmag_0476 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thioredoxin YP_903703.1 525051 D 413404 CDS YP_903704.1 118602489 4554802 525485..526759 1 NC_008610.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 526759 rho 4554802 rho Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) transcription termination factor Rho YP_903704.1 525485 D 413404 CDS YP_903705.1 118602490 4554803 526972..528087 1 NC_008610.1 PFAM: permease YjgP/YjgQ family protein; KEGG: mfa:Mfla_0221 permease YjgP/YjgQ; permease YjgP/YjgQ family protein 528087 4554803 Rmag_0478 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) permease YjgP/YjgQ family protein YP_903705.1 526972 D 413404 CDS YP_903706.1 118602491 4554804 528138..528524 1 NC_008610.1 NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis; 7-cyano-7-deazaguanine reductase 528524 4554804 Rmag_0479 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 7-cyano-7-deazaguanine reductase YP_903706.1 528138 D 413404 CDS YP_903707.1 118602492 4554805 528545..529684 1 NC_008610.1 TIGRFAM: poly(A) polymerase; PFAM: Polynucleotide adenylyltransferase region; KEGG: tcx:Tcr_1528 poly(A) polymerase; poly(A) polymerase 529684 4554805 Rmag_0480 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) poly(A) polymerase YP_903707.1 528545 D 413404 CDS YP_903708.1 118602493 4554806 530326..530550 1 NC_008610.1 catalyzes the bidirectional exonucleolytic cleavage of DNA; exodeoxyribonuclease VII small subunit 530550 4554806 Rmag_0481 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) exodeoxyribonuclease VII small subunit YP_903708.1 530326 D 413404 CDS YP_903709.1 118602494 4554807 530600..531454 1 NC_008610.1 PFAM: Polyprenyl synthetase; KEGG: pfo:Pfl_5006 polyprenyl synthetase; farnesyl-diphosphate synthase 531454 4554807 Rmag_0482 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) farnesyl-diphosphate synthase YP_903709.1 530600 D 413404 CDS YP_903710.1 118602495 4555108 complement(531451..532395) 1 NC_008610.1 KEGG: nme:NMB1916 3-oxoacyl-(acyl-carrier-protein) synthase III; TIGRFAM: 3-oxoacyl-(acyl-carrier-protein) synthase III; PFAM: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal domain protein; 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III; 3-oxoacyl-[acyl-carrier-protein] synthase III 532395 4555108 Rmag_0483 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-oxoacyl-[acyl-carrier-protein] synthase III YP_903710.1 531451 R 413404 CDS YP_903711.1 118602496 4555109 complement(532388..533407) 1 NC_008610.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY; putative glycerol-3-phosphate acyltransferase PlsX 533407 4555109 Rmag_0484 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative glycerol-3-phosphate acyltransferase PlsX YP_903711.1 532388 R 413404 CDS YP_903712.1 118602497 4555110 complement(533413..533610) 1 NC_008610.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 533610 rpmF 4555110 rpmF Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L32 YP_903712.1 533413 R 413404 CDS YP_903713.1 118602498 4555111 complement(533627..534127) 1 NC_008610.1 PFAM: protein of unknown function DUF177; KEGG: yps:YPTB2476 hypothetical protein; hypothetical protein 534127 4555111 Rmag_0486 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903713.1 533627 R 413404 CDS YP_903714.1 118602499 4555112 complement(534851..535552) 1 NC_008610.1 PFAM: phospholipid/glycerol acyltransferase; KEGG: mfa:Mfla_0642 phospholipid/glycerol acyltransferase; phospholipid/glycerol acyltransferase 535552 4555112 Rmag_0487 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phospholipid/glycerol acyltransferase YP_903714.1 534851 R 413404 CDS YP_903715.1 118602500 4555113 535618..536253 1 NC_008610.1 KEGG: sde:Sde_2151 flagellar FliJ and related; TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; HAD-superfamily hydrolase, subfamily IA, variant 1; PFAM: Haloacid dehalogenase domain protein hydrolase; HAD family hydrolase 536253 4555113 Rmag_0488 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) HAD family hydrolase YP_903715.1 535618 D 413404 CDS YP_903716.1 118602501 4555114 536253..537389 1 NC_008610.1 PFAM: protein of unknown function DUF195; KEGG: wsu:WS1465 hypothetical protein; hypothetical protein 537389 4555114 Rmag_0489 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903716.1 536253 D 413404 CDS YP_903717.1 118602502 4555115 537389..538141 1 NC_008610.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: vfi:VF1039 short chain dehydrogenase; short-chain dehydrogenase/reductase SDR 538141 4555115 Rmag_0490 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) short-chain dehydrogenase/reductase SDR YP_903717.1 537389 D 413404 CDS YP_903718.1 118602503 4555116 complement(538163..538963) 1 NC_008610.1 PFAM: inositol monophosphatase; KEGG: eba:ebA6410 inositol monophosphatase (extragenic suppressor protein); inositol monophosphatase 538963 4555116 Rmag_0491 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) inositol monophosphatase YP_903718.1 538163 R 413404 CDS YP_903719.1 118602504 4555117 538989..539720 1 NC_008610.1 TIGRFAM: RNA methyltransferase, TrmH family, group 1; PFAM: tRNA/rRNA methyltransferase (SpoU); KEGG: tcx:Tcr_0615 RNA methyltransferase TrmH, group 1; RNA methyltransferase 539720 4555117 Rmag_0492 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) RNA methyltransferase YP_903719.1 538989 D 413404 CDS YP_903720.1 118602505 4555118 complement(539762..541612) 1 NC_008610.1 molecular chaperone; heat shock protein 90 541612 4555118 Rmag_0493 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) heat shock protein 90 YP_903720.1 539762 R 413404 CDS YP_903721.1 118602506 4555119 541961..542497 1 NC_008610.1 PFAM: SUA5/yciO/yrdC, N-terminal domain; KEGG: cps:CPS_0027 putative RNA-binding protein; translation factor SUA5 542497 4555119 Rmag_0495 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) translation factor SUA5 YP_903721.1 541961 D 413404 CDS YP_903722.1 118602507 4555120 542494..543402 1 NC_008610.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase 543402 4555120 Rmag_0496 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) coproporphyrinogen III oxidase YP_903722.1 542494 D 413404 CDS YP_903723.1 118602508 4555121 543415..543639 1 NC_008610.1 PFAM: SirA family protein; KEGG: noc:Noc_2653 SirA-like protein; SirA family protein 543639 4555121 Rmag_0497 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) SirA family protein YP_903723.1 543415 D 413404 CDS YP_903724.1 118602509 4555122 543750..545165 1 NC_008610.1 KEGG: mca:MCA1677 glutamine synthetase, type I; TIGRFAM: glutamine synthetase, type I; PFAM: glutamine synthetase, catalytic region; glutamine synthetase, beta-Grasp; L-glutamine synthetase 545165 4555122 Rmag_0498 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) L-glutamine synthetase YP_903724.1 543750 D 413404 CDS YP_903725.1 118602510 4555123 545262..546230 1 NC_008610.1 KEGG: ilo:IL1324 biotin synthase; TIGRFAM: biotin synthase; PFAM: Radical SAM domain protein; biotin and thiamin synthesis associated; SMART: Elongator protein 3/MiaB/NifB; biotin synthase 546230 4555123 Rmag_0499 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) biotin synthase YP_903725.1 545262 D 413404 CDS YP_903726.1 118602511 4555124 complement(546193..547209) 1 NC_008610.1 KEGG: pst:PSPTO4408 UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; TIGRFAM: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; PFAM: glycosyl transferase, family 28; Glycosyltransferase 28, C-terminal domain; UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase 547209 4555124 Rmag_0500 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase YP_903726.1 546193 R 413404 CDS YP_903727.1 118602512 4555125 complement(547202..548335) 1 NC_008610.1 PFAM: cell cycle protein; KEGG: lpp:lpp2668 cell division protein FtsW; cell cycle protein 548335 4555125 Rmag_0501 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cell cycle protein YP_903727.1 547202 R 413404 CDS YP_903728.1 118602513 4555126 548464..550077 1 NC_008610.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: tcx:Tcr_1606 ABC transporter related; ABC transporter related 550077 4555126 Rmag_0502 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_903728.1 548464 D 413404 CDS YP_903729.1 118602514 4555127 551174..551752 1 NC_008610.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha 551752 4555127 Rmag_0504 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) riboflavin synthase subunit alpha YP_903729.1 551174 D 413404 CDS YP_903730.1 118602515 4554634 551762..552835 1 NC_008610.1 PFAM: 3,4-dihydroxy-2-butanone 4-phosphate synthase; GTP cyclohydrolase II; KEGG: tcx:Tcr_1398 3,4-dihydroxy-2-butanone 4-phosphate synthase; GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthase 552835 4554634 Rmag_0505 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthase YP_903730.1 551762 D 413404 CDS YP_903731.1 118602516 4554635 552846..553349 1 NC_008610.1 PFAM: 6,7-dimethyl-8-ribityllumazine synthase; KEGG: fnu:FN1505 6,7-dimethyl-8-ribityllumazine synthase; 6,7-dimethyl-8-ribityllumazine synthase 553349 4554635 Rmag_0506 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 6,7-dimethyl-8-ribityllumazine synthase YP_903731.1 552846 D 413404 CDS YP_903732.1 118602517 4554636 553352..553774 1 NC_008610.1 TIGRFAM: transcription antitermination factor NusB; PFAM: NusB/RsmB/TIM44; KEGG: yps:YPTB0936 transcription termination; L factor; NusB antitermination factor 553774 4554636 Rmag_0507 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NusB antitermination factor YP_903732.1 553352 D 413404 CDS YP_903733.1 118602518 4554637 554198..554566 1 NC_008610.1 hypothetical protein 554566 4554637 Rmag_0508 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903733.1 554198 D 413404 CDS YP_903734.1 118602519 4554638 554952..555344 1 NC_008610.1 PFAM: histidine triad (HIT) protein; KEGG: rfr:Rfer_1209 histidine triad (HIT) protein; histidine triad (HIT) protein 555344 4554638 Rmag_0509 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) histidine triad (HIT) protein YP_903734.1 554952 D 413404 CDS YP_903735.1 118602520 4554639 complement(555356..555847) 1 NC_008610.1 TIGRFAM: single-strand binding protein; PFAM: single-strand binding protein/Primosomal replication protein n; KEGG: stt:t4237 single strand binding protein; single-strand binding protein 555847 4554639 Rmag_0510 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) single-strand binding protein YP_903735.1 555356 R 413404 CDS YP_903736.1 118602521 4554640 complement(555862..557037) 1 NC_008610.1 PFAM: major facilitator superfamily MFS_1; KEGG: tcx:Tcr_0326 major facilitator superfamily MFS_1; major facilitator transporter 557037 4554640 Rmag_0511 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) major facilitator transporter YP_903736.1 555862 R 413404 CDS YP_903737.1 118602522 4554641 complement(557062..557823) 1 NC_008610.1 KEGG: noc:Noc_0716 probable transmembrane protein; putative transmembrane protein 557823 4554641 Rmag_0512 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative transmembrane protein YP_903737.1 557062 R 413404 CDS YP_903738.1 118602523 4554642 557921..560023 1 NC_008610.1 KEGG: tcx:Tcr_2144 (p)ppGpp synthetase I (GTP pyrophosphokinase), SpoT/RelA; TIGRFAM: RelA/SpoT family protein; PFAM: amino acid-binding ACT domain protein; TGS domain protein; metal-dependent phosphohydrolase, HD sub domain; RelA/SpoT domain protein; SMART: metal-dependent phosphohydrolase, HD region; (p)ppGpp synthetase I, SpoT/RelA 560023 4554642 Rmag_0513 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) (p)ppGpp synthetase I, SpoT/RelA YP_903738.1 557921 D 413404 CDS YP_903739.1 118602524 4554643 560102..560296 1 NC_008610.1 PFAM: protein of unknown function DUF528; KEGG: bur:Bcep18194_A5426 protein of unknown function DUF528; hypothetical protein 560296 4554643 Rmag_0514 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903739.1 560102 D 413404 CDS YP_903740.1 118602525 4554644 560293..561567 1 NC_008610.1 PFAM: TolB, N-terminal domain protein; WD40 domain protein beta Propeller; KEGG: noc:Noc_0145 TolB; TolB domain-containing protein 561567 4554644 Rmag_0515 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) TolB domain-containing protein YP_903740.1 560293 D 413404 CDS YP_903741.1 118602526 4554645 561578..562150 1 NC_008610.1 PFAM: OmpA/MotB domain protein; KEGG: noc:Noc_0146 OmpA/MotB; OmpA/MotB domain-containing protein 562150 4554645 Rmag_0516 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) OmpA/MotB domain-containing protein YP_903741.1 561578 D 413404 CDS YP_903742.1 118602527 4554646 562157..562825 1 NC_008610.1 PFAM: Tetratricopeptide TPR_2 repeat protein; KEGG: psp:PSPPH_3765 hypothetical protein; TPR repeat-containing protein 562825 4554646 Rmag_0517 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) TPR repeat-containing protein YP_903742.1 562157 D 413404 CDS YP_903743.1 118602528 4554647 562828..564117 1 NC_008610.1 PFAM: Anthranilate synthase component I and chorismate binding protein; Anthranilate synthase component I domain protein; KEGG: tcx:Tcr_0715 anthranilate synthase; hypothetical protein 564117 4554647 Rmag_0518 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903743.1 562828 D 413404 CDS YP_903744.1 118602529 4554648 complement(564419..565042) 1 NC_008610.1 PFAM: multiple antibiotic resistance (MarC)-related proteins; KEGG: cps:CPS_1844 conserved hypothetical protein TIGR00427; multiple antibiotic resistance (MarC)-related proteins 565042 4554648 Rmag_0519 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) multiple antibiotic resistance (MarC)-related proteins YP_903744.1 564419 R 413404 CDS YP_903745.1 118602530 4554649 complement(565433..567313) 1 NC_008610.1 KEGG: tcx:Tcr_1372 NAD+ synthetase; TIGRFAM: NAD+ synthetase; PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; NAD+ synthase; ExsB family protein; NAD+ synthetase 567313 4554649 Rmag_0520 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NAD+ synthetase YP_903745.1 565433 R 413404 CDS YP_903746.1 118602531 4554650 567633..568058 1 NC_008610.1 KEGG: mhu:Mhun_1900 putative transcriptional regulator; hypothetical protein 568058 4554650 Rmag_0521 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903746.1 567633 D 413404 CDS YP_903747.1 118602532 4554651 568082..569077 1 NC_008610.1 PFAM: ferrochelatase; KEGG: tcx:Tcr_1864 ferrochelatase; ferrochelatase 569077 4554651 Rmag_0522 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ferrochelatase YP_903747.1 568082 D 413404 CDS YP_903748.1 118602533 4554652 569353..571626 1 NC_008610.1 Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 571626 4554652 Rmag_0523 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonucleotide-diphosphate reductase subunit alpha YP_903748.1 569353 D 413404 CDS YP_903749.1 118602534 4555293 571709..572845 1 NC_008610.1 B2 or R2 protein; type 1a enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdA; ribonucleotide-diphosphate reductase subunit beta 572845 nrdB 4555293 nrdB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonucleotide-diphosphate reductase subunit beta YP_903749.1 571709 D 413404 CDS YP_903750.1 118602535 4555294 572854..573117 1 NC_008610.1 PFAM: ferredoxin; KEGG: sgl:SG1586 hypothetical protein; ferredoxin 573117 4555294 Rmag_0525 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ferredoxin YP_903750.1 572854 D 413404 CDS YP_903751.1 118602536 4555295 complement(573467..574141) 1 NC_008610.1 KEGG: tdn:Tmden_0484 putative dUTPase; putative dUTPase 574141 4555295 Rmag_0526 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative dUTPase YP_903751.1 573467 R 413404 CDS YP_903752.1 118602537 4555296 complement(574556..575143) 1 NC_008610.1 Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A); ribonuclease T 575143 4555296 Rmag_0527 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonuclease T YP_903752.1 574556 R 413404 CDS YP_903753.1 118602538 4555297 complement(575133..575555) 1 NC_008610.1 PFAM: GCN5-related N-acetyltransferase; KEGG: reu:Reut_A2066 amino-acid N-acetyltransferase (ArgA); GCN5-related N-acetyltransferase 575555 4555297 Rmag_0528 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GCN5-related N-acetyltransferase YP_903753.1 575133 R 413404 CDS YP_903754.1 118602539 4555298 575616..577295 1 NC_008610.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 577295 4555298 Rmag_0529 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydroxy-acid dehydratase YP_903754.1 575616 D 413404 CDS YP_903755.1 118602540 4555299 complement(577629..579746) 1 NC_008610.1 KEGG: mfa:Mfla_1626 ribonuclease R; TIGRFAM: VacB and RNase II family 3'-5' exoribonucleases; ribonuclease R; PFAM: ribonuclease II; RNA binding S1 domain protein; Ribonuclease B, OB region N-terminal domain; SMART: Cold shock protein; ribonuclease R 579746 4555299 Rmag_0530 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonuclease R YP_903755.1 577629 R 413404 CDS YP_903756.1 118602541 4555300 complement(579751..581067) 1 NC_008610.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase 581067 4555300 Rmag_0531 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) adenylosuccinate synthetase YP_903756.1 579751 R 413404 CDS YP_903757.1 118602542 4555301 complement(581125..582081) 1 NC_008610.1 KEGG: tbd:Tbd_0606 ATP phosphoribosyltransferase regulatory subunit; ATP phosphoribosyltransferase regulatory subunit 582081 4555301 Rmag_0532 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP phosphoribosyltransferase regulatory subunit YP_903757.1 581125 R 413404 CDS YP_903758.1 118602543 4555302 complement(582087..582944) 1 NC_008610.1 TIGRFAM: HflC protein; PFAM: band 7 protein; KEGG: tcx:Tcr_1091 HflC protein; HflC protein 582944 4555302 Rmag_0533 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) HflC protein YP_903758.1 582087 R 413404 CDS YP_903759.1 118602544 4555303 complement(582944..584095) 1 NC_008610.1 TIGRFAM: HflK protein; PFAM: band 7 protein; KEGG: tcx:Tcr_1090 HflK protein; HflK protein 584095 4555303 Rmag_0534 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) HflK protein YP_903759.1 582944 R 413404 CDS YP_903760.1 118602545 4555304 584160..586427 1 NC_008610.1 PFAM: OstA family protein; Organic solvent tolerance protein; KEGG: rso:RSc0515 probable organic solvent tolerance transmembrane protein; organic solvent tolerance protein 586427 4555304 Rmag_0535 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) organic solvent tolerance protein YP_903760.1 584160 D 413404 CDS YP_903761.1 118602546 4555305 586429..587325 1 NC_008610.1 PFAM: PpiC-type peptidyl-prolyl cis-trans isomerase; KEGG: lpn:lpg0298 peptidyl-prolyl cis-trans isomerase D (SurA); PpiC-type peptidyl-prolyl cis-trans isomerase 587325 4555305 Rmag_0536 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) PpiC-type peptidyl-prolyl cis-trans isomerase YP_903761.1 586429 D 413404 CDS YP_903762.1 118602547 4555306 587326..588069 1 NC_008610.1 TIGRFAM: RNA methyltransferase, TrmH family, group 3; PFAM: tRNA/rRNA methyltransferase (SpoU); RNA 2-O ribose methyltransferase, substrate binding; KEGG: eca:ECA3621 probable tRNA/rRNA methyltransferase; RNA methyltransferase 588069 4555306 Rmag_0537 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) RNA methyltransferase YP_903762.1 587326 D 413404 CDS YP_903763.1 118602548 4555307 588492..589796 1 NC_008610.1 TIGRFAM: isocitrate lyase; PFAM: isocitrate lyase and phosphorylmutase; KEGG: son:SO1484 isocitrate lyase; isocitrate lyase 589796 4555307 Rmag_0538 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) isocitrate lyase YP_903763.1 588492 D 413404 CDS YP_903764.1 118602549 4555308 592398..592676 1 NC_008610.1 PFAM: protein of unknown function DUF493; KEGG: neu:NE1487 hypothetical protein; hypothetical protein 592676 4555308 Rmag_0541 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903764.1 592398 D 413404 CDS YP_903765.1 118602550 4555309 592683..593297 1 NC_008610.1 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 593297 lipB 4555309 lipB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lipoate-protein ligase B YP_903765.1 592683 D 413404 CDS YP_903766.1 118602551 4555310 593275..594222 1 NC_008610.1 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 594222 4555310 Rmag_0543 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lipoyl synthase YP_903766.1 593275 D 413404 CDS YP_903767.1 118602552 4555311 complement(594313..597717) 1 NC_008610.1 PFAM: acriflavin resistance protein; KEGG: gme:Gmet_3127 acriflavin resistance protein; acriflavin resistance protein 597717 4555311 Rmag_0544 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acriflavin resistance protein YP_903767.1 594313 R 413404 CDS YP_903768.1 118602553 4555312 complement(597725..598900) 1 NC_008610.1 TIGRFAM: efflux transporter, RND family, MFP subunit; KEGG: pha:PSHAa2832 multidrug efflux system (AcrA/AcrE); RND family efflux transporter MFP subunit 598900 4555312 Rmag_0545 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) RND family efflux transporter MFP subunit YP_903768.1 597725 R 413404 CDS YP_903769.1 118602554 4555070 599097..600095 1 NC_008610.1 KEGG: sde:Sde_0738 4-hydroxythreonine-4-phosphate dehydrogenase; TIGRFAM: 4-hydroxythreonine-4-phosphate dehydrogenase; PFAM: Pyridoxal phosphate biosynthetic protein PdxA; 4-hydroxythreonine-4-phosphate dehydrogenase 600095 4555070 Rmag_0546 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 4-hydroxythreonine-4-phosphate dehydrogenase YP_903769.1 599097 D 413404 CDS YP_903770.1 118602555 4555071 600088..600840 1 NC_008610.1 TIGRFAM: dimethyladenosine transferase; PFAM: ribosomal RNA adenine methylase transferase; KEGG: pfo:Pfl_5135 16S rRNA dimethylase; dimethyladenosine transferase 600840 4555071 Rmag_0547 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dimethyladenosine transferase YP_903770.1 600088 D 413404 CDS YP_903771.1 118602556 4555072 600824..601195 1 NC_008610.1 protein associated with Co2+ and Mg2+ efflux; ApaG 601195 apaG 4555072 apaG Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ApaG YP_903771.1 600824 D 413404 CDS YP_903772.1 118602557 4555073 601195..601992 1 NC_008610.1 hydrolyzes P(1),P(4)-bis(5'-adenosyl) tetraphosphate to form 2 ADP; diadenosine tetraphosphatase 601992 apaH 4555073 apaH Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) diadenosine tetraphosphatase YP_903772.1 601195 D 413404 CDS YP_903773.1 118602558 4555074 complement(601989..602804) 1 NC_008610.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate; diaminopimelate epimerase 602804 dapF 4555074 dapF Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) diaminopimelate epimerase YP_903773.1 601989 R 413404 CDS YP_903774.1 118602559 4555075 602892..603245 1 NC_008610.1 PFAM: protein of unknown function DUF971; KEGG: eba:ebB94 hypothetical protein; hypothetical protein 603245 4555075 Rmag_0551 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903774.1 602892 D 413404 CDS YP_903775.1 118602560 4555076 603252..604589 1 NC_008610.1 TIGRFAM: putative membrane-associated zinc metalloprotease; PFAM: PDZ/DHR/GLGF domain protein; peptidase M50; KEGG: neu:NE1711 membrane-associated Zn-dependent proteases 1; putative membrane-associated zinc metalloprotease 604589 4555076 Rmag_0552 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative membrane-associated zinc metalloprotease YP_903775.1 603252 D 413404 CDS YP_903776.1 118602561 4555077 604593..606881 1 NC_008610.1 PFAM: surface antigen (D15); surface antigen variable number repeat protein; KEGG: eba:ebA5996 probable outer membrane protein/surface antigen; surface antigen (D15) 606881 4555077 Rmag_0553 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) surface antigen (D15) YP_903776.1 604593 D 413404 CDS YP_903777.1 118602562 4555078 606924..607922 1 NC_008610.1 TIGRFAM: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; PFAM: transferase hexapeptide repeat containing protein; UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; KEGG: ftl:FTL_0537 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase 607922 4555078 Rmag_0554 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase YP_903777.1 606924 D 413404 CDS YP_903778.1 118602563 4555079 607924..608367 1 NC_008610.1 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 608367 fabZ 4555079 fabZ Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) (3R)-hydroxymyristoyl-ACP dehydratase YP_903778.1 607924 D 413404 CDS YP_903779.1 118602564 4555080 608391..609182 1 NC_008610.1 TIGRFAM: acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase; KEGG: pae:PA3644 UDP-N-acetylglucosamine acyltransferase; acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase 609182 4555080 Rmag_0556 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase YP_903779.1 608391 D 413404 CDS YP_903780.1 118602565 4555081 609242..610729 1 NC_008610.1 TIGRFAM: integral membrane protein MviN; PFAM: multi antimicrobial extrusion protein MatE; virulence factor MVIN family protein; KEGG: tcx:Tcr_0493 integral membrane protein MviN; integral membrane protein MviN 610729 4555081 Rmag_0557 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) integral membrane protein MviN YP_903780.1 609242 D 413404 CDS YP_903781.1 118602566 4555082 610726..610995 1 NC_008610.1 PFAM: Fe(II) trafficking protein YggX; KEGG: dar:Daro_3583 hypothetical protein; hypothetical protein 610995 4555082 Rmag_0558 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903781.1 610726 D 413404 CDS YP_903782.1 118602567 4555083 610988..611599 1 NC_008610.1 Essential for recycling GMP and indirectly, cGMP; guanylate kinase 611599 gmk 4555083 gmk Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) guanylate kinase YP_903782.1 610988 D 413404 CDS YP_903783.1 118602568 4555084 611648..612490 1 NC_008610.1 TIGRFAM: RNA polymerase sigma factor RpoH; PFAM: sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; KEGG: ilo:IL0229 DNA-directed RNA polymerase sigma 32 subunit; RNA polymerase, sigma 32 subunit, RpoH 612490 4555084 Rmag_0560 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) RNA polymerase, sigma 32 subunit, RpoH YP_903783.1 611648 D 413404 CDS YP_903784.1 118602569 4555085 612560..612847 1 NC_008610.1 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 612847 groES 4555085 groES Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) co-chaperonin GroES YP_903784.1 612560 D 413404 CDS YP_903785.1 118602570 4555086 612860..614494 1 NC_008610.1 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 essential for growth; chaperonin GroEL 614494 groEL 4555086 groEL Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) chaperonin GroEL YP_903785.1 612860 D 413404 CDS YP_903786.1 118602571 4555087 614731..616614 1 NC_008610.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B 616614 4555087 Rmag_0563 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA topoisomerase IV subunit B YP_903786.1 614731 D 413404 CDS YP_903787.1 118602572 4555088 616607..617299 1 NC_008610.1 TIGRFAM: exsB protein; PFAM: ExsB family protein; KEGG: cbu:CBU_2083 ExsB protein; exsB protein 617299 4555088 Rmag_0564 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) exsB protein YP_903787.1 616607 D 413404 CDS YP_903788.1 118602573 4555440 617405..617632 1 NC_008610.1 carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein 617632 acpP 4555440 acpP Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acyl carrier protein YP_903788.1 617405 D 413404 CDS YP_903789.1 118602574 4555441 617710..618948 1 NC_008610.1 PFAM: beta-ketoacyl synthase; KEGG: bxe:Bxe_A1076 3-oxoacyl-(acyl-carrier-protein) synthase II; 3-oxoacyl-[acyl-carrier-protein] synthase II 618948 4555441 Rmag_0566 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-oxoacyl-[acyl-carrier-protein] synthase II YP_903789.1 617710 D 413404 CDS YP_903790.1 118602575 4555442 complement(618998..619201) 1 NC_008610.1 hypothetical protein 619201 4555442 Rmag_0567 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903790.1 618998 R 413404 CDS YP_903791.1 118602576 4555443 complement(619225..621135) 1 NC_008610.1 PFAM: peptidase M3A and M3B, thimet/oligopeptidase F; KEGG: pha:PSHAa0361 oligopeptidase A; oligopeptidase A 621135 4555443 Rmag_0568 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) oligopeptidase A YP_903791.1 619225 R 413404 CDS YP_903792.1 118602577 4555444 complement(621606..623258) 1 NC_008610.1 TIGRFAM: methionyl-tRNA synthetase; KEGG: vfi:VF1754 methionyl-tRNA synthetase; methionyl-tRNA synthetase 623258 4555444 Rmag_0570 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) methionyl-tRNA synthetase YP_903792.1 621606 R 413404 CDS YP_903793.1 118602578 4555445 623343..624425 1 NC_008610.1 PFAM: protein of unknown function DUF59; KEGG: tbd:Tbd_2108 ATP-binding protein involved in chromosome partitioning; hypothetical protein 624425 4555445 Rmag_0571 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903793.1 623343 D 413404 CDS YP_903794.1 118602579 4555446 complement(625471..625809) 1 NC_008610.1 TIGRFAM: ferredoxin, 2Fe-2S type, ISC system; PFAM: ferredoxin; KEGG: reu:Reut_A1064 ferredoxin, 2Fe-2S type; ferredoxin, 2Fe-2S type, ISC system 625809 4555446 Rmag_0572 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ferredoxin, 2Fe-2S type, ISC system YP_903794.1 625471 R 413404 CDS YP_903795.1 118602580 4555447 complement(625833..627677) 1 NC_008610.1 involved in the maturation of iron-sulfur cluster-containing proteins; chaperone protein HscA 627677 hscA 4555447 hscA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) chaperone protein HscA YP_903795.1 625833 R 413404 CDS YP_903796.1 118602581 4555448 complement(627693..628208) 1 NC_008610.1 TIGRFAM: co-chaperone Hsc20; PFAM: heat shock protein DnaJ domain protein; HSCB oligomerisation domain protein; KEGG: sdy:SDY_2723 hypothetical protein; co-chaperone Hsc20 628208 4555448 Rmag_0574 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) co-chaperone Hsc20 YP_903796.1 627693 R 413404 CDS YP_903797.1 118602582 4555449 complement(628221..628544) 1 NC_008610.1 TIGRFAM: iron-sulfur cluster assembly accessory protein; iron-sulfur cluster assembly protein IscA; PFAM: HesB/YadR/YfhF-family protein; KEGG: vvy:VV0757 hypothetical protein; iron-sulfur cluster assembly protein IscA 628544 4555449 Rmag_0575 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) iron-sulfur cluster assembly protein IscA YP_903797.1 628221 R 413404 CDS YP_903798.1 118602583 4555450 complement(628551..628928) 1 NC_008610.1 TIGRFAM: FeS cluster assembly scaffold IscU; PFAM: nitrogen-fixing NifU domain protein; KEGG: par:Psyc_1478 nitrogen-fixing NifU-like; scaffold protein 628928 4555450 Rmag_0576 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) scaffold protein YP_903798.1 628551 R 413404 CDS YP_903799.1 118602584 4555451 complement(628988..630202) 1 NC_008610.1 catalyzes the removal of elemental sulfur from cysteine to produce alanine; involved in NAD biosynthesis; cysteine desulfurase 630202 4555451 Rmag_0577 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cysteine desulfurase YP_903799.1 628988 R 413404 CDS YP_903800.1 118602585 4555452 complement(630205..630624) 1 NC_008610.1 TIGRFAM: putative transcriptional regulator, Rrf2 family; PFAM: protein of unknown function UPF0074; KEGG: tcx:Tcr_0617 transcriptional regulator, BadM/Rrf2 family; BadM/Rrf2 family transcriptional regulator 630624 4555452 Rmag_0578 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) BadM/Rrf2 family transcriptional regulator YP_903800.1 630205 R 413404 CDS YP_903801.1 118602586 4555453 complement(630710..631408) 1 NC_008610.1 TIGRFAM: serine O-acetyltransferase; KEGG: tcx:Tcr_0616 serine O-acetyltransferase; serine O-acetyltransferase 631408 4555453 Rmag_0579 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) serine O-acetyltransferase YP_903801.1 630710 R 413404 CDS YP_903802.1 118602587 4555454 complement(631473..632279) 1 NC_008610.1 PFAM: lipid A biosynthesis acyltransferase; KEGG: tcx:Tcr_0183 lipid A biosynthesis acyltransferase; lipid A biosynthesis acyltransferase 632279 4555454 Rmag_0580 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lipid A biosynthesis acyltransferase YP_903802.1 631473 R 413404 CDS YP_903803.1 118602588 4555455 complement(632305..633096) 1 NC_008610.1 PFAM: PP-loop domain protein; KEGG: tcx:Tcr_0182 PP-loop; PP-loop domain-containing protein 633096 4555455 Rmag_0581 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) PP-loop domain-containing protein YP_903803.1 632305 R 413404 CDS YP_903804.1 118602589 4555456 complement(633947..635338) 1 NC_008610.1 KEGG: bfr:BF4142 outer membrane efflux protein; Outer membrane protein-like 635338 4555456 Rmag_0582 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Outer membrane protein-like YP_903804.1 633947 R 413404 CDS YP_903805.1 118602590 4555457 complement(635335..635856) 1 NC_008610.1 PFAM: shikimate kinase; KEGG: csa:Csal_0613 shikimate kinase; shikimate kinase 635856 4555457 Rmag_0583 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) shikimate kinase YP_903805.1 635335 R 413404 CDS YP_903806.1 118602591 4555458 complement(636053..636982) 1 NC_008610.1 TIGRFAM: branched-chain amino acid aminotransferase; PFAM: aminotransferase, class IV; KEGG: hch:HCH_01045 branched-chain amino acid aminotransferase; branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase / branched chain amino acid aminotransferase 636982 4555458 Rmag_0584 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase / branched chain amino acid aminotransferase YP_903806.1 636053 R 413404 CDS YP_903807.1 118602592 4555459 complement(636985..638208) 1 NC_008610.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.; aspartate kinase 638208 4555459 Rmag_0585 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aspartate kinase YP_903807.1 636985 R 413404 CDS YP_903808.1 118602593 4554952 complement(640785..641027) 1 NC_008610.1 hypothetical protein 641027 4554952 Rmag_0586 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903808.1 640785 R 413404 CDS YP_903809.1 118602594 4554953 641235..642485 1 NC_008610.1 PFAM: peptidase M48, Ste24p; KEGG: neu:NE0076 peptidase family M48; Ste24 endopeptidase 642485 4554953 Rmag_0587 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Ste24 endopeptidase YP_903809.1 641235 D 413404 CDS YP_903810.1 118602595 4554954 642520..642798 1 NC_008610.1 KEGG: dar:Daro_3003 hypothetical protein; hypothetical protein 642798 4554954 Rmag_0588 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903810.1 642520 D 413404 CDS YP_903811.1 118602596 4554955 642817..643773 1 NC_008610.1 TIGRFAM: ribosome small subunit-dependent GTPase A; PFAM: GTPase EngC; KEGG: hch:HCH_05392 predicted GTPase; ribosome small subunit-dependent GTPase A 643773 4554955 Rmag_0589 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribosome small subunit-dependent GTPase A YP_903811.1 642817 D 413404 CDS YP_903812.1 118602597 4554956 complement(644316..644624) 1 NC_008610.1 PFAM: protein of unknown function DUF423; KEGG: oih:OB3027 hypothetical protein; hypothetical protein 644624 4554956 Rmag_0590 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903812.1 644316 R 413404 CDS YP_903813.1 118602598 4554957 complement(645635..645940) 1 NC_008610.1 PFAM: histone family protein DNA-binding protein; KEGG: aba:Acid345_4105 histone-like DNA-binding protein; histone family protein DNA-binding protein 645940 4554957 Rmag_0591 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) histone family protein DNA-binding protein YP_903813.1 645635 R 413404 CDS YP_903814.1 118602599 4554958 complement(645961..647637) 1 NC_008610.1 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 647637 rpsA 4554958 rpsA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S1 YP_903814.1 645961 R 413404 CDS YP_903815.1 118602600 4554959 complement(647733..648410) 1 NC_008610.1 KEGG: hch:HCH_04979 cytidylate kinase; TIGRFAM: cytidylate kinase; PFAM: cytidylate kinase region; cytidylate kinase 648410 4554959 Rmag_0593 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytidylate kinase YP_903815.1 647733 R 413404 CDS YP_903816.1 118602601 4554960 complement(648690..650183) 1 NC_008610.1 TIGRFAM: lysyl-tRNA synthetase; PFAM: tRNA synthetase, class II (D, K and N); nucleic acid binding, OB-fold, tRNA/helicase-type; KEGG: tcx:Tcr_0726 lysyl-tRNA synthetase; lysyl-tRNA synthetase 650183 4554960 Rmag_0594 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lysyl-tRNA synthetase YP_903816.1 648690 R 413404 CDS YP_903817.1 118602602 4554961 complement(650622..651059) 1 NC_008610.1 PFAM: cytochrome C biogenesis protein; KEGG: rme:Rmet_2392 cytochrome c biogenesis protein; cytochrome C biogenesis protein 651059 4554961 Rmag_0595 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome C biogenesis protein YP_903817.1 650622 R 413404 CDS YP_903818.1 118602603 4554962 651095..652942 1 NC_008610.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: vvu:VV12632 ATPase component of ABC transporter with duplicated ATPase domains; ABC transporter related 652942 4554962 Rmag_0596 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_903818.1 651095 D 413404 CDS YP_903819.1 118602604 4554963 652939..653568 1 NC_008610.1 KEGG: bms:BRA0855 hypothetical protein; hypothetical protein 653568 4554963 Rmag_0597 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903819.1 652939 D 413404 CDS YP_903820.1 118602605 4554964 complement(653849..655633) 1 NC_008610.1 TIGRFAM: excinuclease ABC, C subunit; PFAM: Excinuclease ABC, C subunit domain protein; excinuclease ABC, C subunit domain protein; UvrB/UvrC protein; KEGG: plu:plu2027 excinuclease ABC subunit C; excinuclease ABC subunit C 655633 4554964 Rmag_0598 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) excinuclease ABC subunit C YP_903820.1 653849 R 413404 CDS YP_903821.1 118602606 4554965 655761..656345 1 NC_008610.1 PFAM: toluene tolerance family protein; KEGG: neu:NE2381 putative signal peptide protein; toluene tolerance family protein 656345 4554965 Rmag_0599 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) toluene tolerance family protein YP_903821.1 655761 D 413404 CDS YP_903822.1 118602607 4554966 656345..657604 1 NC_008610.1 adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active; UDP-N-acetylglucosamine 1-carboxyvinyltransferase 657604 4554966 Rmag_0600 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-N-acetylglucosamine 1-carboxyvinyltransferase YP_903822.1 656345 D 413404 CDS YP_903823.1 118602608 4554967 657610..658227 1 NC_008610.1 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 catalytic subunit 658227 hisG 4554967 hisG Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP phosphoribosyltransferase catalytic subunit YP_903823.1 657610 D 413404 CDS YP_903824.1 118602609 4554968 658224..659531 1 NC_008610.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 659531 hisD 4554968 hisD Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) histidinol dehydrogenase YP_903824.1 658224 D 413404 CDS YP_903825.1 118602610 4554969 complement(660101..661495) 1 NC_008610.1 KEGG: tcx:Tcr_0998 signal recognition particle protein; TIGRFAM: signal recognition particle protein; PFAM: GTP-binding signal recognition particle SRP54, G- domain; Signal peptide binding (SRP54) M- domain protein; SMART: AAA ATPase; signal recognition particle subunit FFH/SRP54 (srp54) 661495 4554969 Rmag_0604 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) signal recognition particle subunit FFH/SRP54 (srp54) YP_903825.1 660101 R 413404 CDS YP_903826.1 118602611 4554970 661558..662343 1 NC_008610.1 PFAM: cytochrome c assembly protein; KEGG: mca:MCA1337 hypothetical protein; cytochrome c assembly protein 662343 4554970 Rmag_0605 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome c assembly protein YP_903826.1 661558 D 413404 CDS YP_903827.1 118602612 4554848 complement(662388..664175) 1 NC_008610.1 binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA 664175 4554848 Rmag_0606 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GTP-binding protein LepA YP_903827.1 662388 R 413404 CDS YP_903828.1 118602613 4554849 664217..664666 1 NC_008610.1 PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; KEGG: csa:Csal_2817 alkyl hydroperoxide reductase/thiol specific antioxidant/Mal allergen; alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen 664666 4554849 Rmag_0607 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen YP_903828.1 664217 D 413404 CDS YP_903829.1 118602614 4554850 664663..665367 1 NC_008610.1 KEGG: psp:PSPPH_3670 ubiquinone biosynthesis O-methyltransferase; TIGRFAM: ubiquinone biosynthesis O-methyltransferase; PFAM: NodS family protein; Methyltransferase type 11; Methyltransferase type 12; 3-demethylubiquinone-9 3-methyltransferase 665367 4554850 Rmag_0608 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-demethylubiquinone-9 3-methyltransferase YP_903829.1 664663 D 413404 CDS YP_903830.1 118602615 4554851 665379..665687 1 NC_008610.1 hypothetical protein 665687 4554851 Rmag_0609 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903830.1 665379 D 413404 CDS YP_903831.1 118602616 4554852 complement(665684..666067) 1 NC_008610.1 KEGG: mfa:Mfla_1012 phosphopantethiene--protein transferase domain; TIGRFAM: holo-acyl-carrier-protein synthase; Phosphopantethiene-protein transferase; PFAM: 4'-phosphopantetheinyl transferase; holo-acyl-carrier-protein synthase 666067 4554852 Rmag_0610 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) holo-acyl-carrier-protein synthase YP_903831.1 665684 R 413404 CDS YP_903832.1 118602617 4554853 complement(666064..666789) 1 NC_008610.1 involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase 666789 4554853 Rmag_0611 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) pyridoxine 5'-phosphate synthase YP_903832.1 666064 R 413404 CDS YP_903833.1 118602618 4554854 complement(667455..668381) 1 NC_008610.1 TIGRFAM: small GTP-binding protein; GTP-binding; GTP-binding protein Era; PFAM: GTP-binding protein, HSR1-related; KH, type 2 domain protein; Miro domain protein; KEGG: tcx:Tcr_0735 GTP-binding protein Era; GTP-binding protein Era 668381 4554854 Rmag_0613 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GTP-binding protein Era YP_903833.1 667455 R 413404 CDS YP_903834.1 118602619 4554855 complement(668378..669043) 1 NC_008610.1 PFAM: ribonuclease III; double-stranded RNA binding domain protein; KEGG: vfi:VF2087 ribonuclease III; ribonuclease III 669043 4554855 Rmag_0614 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonuclease III YP_903834.1 668378 R 413404 CDS YP_903835.1 118602620 4554856 669120..669782 1 NC_008610.1 KEGG: tbd:Tbd_2487 hypothetical protein; hypothetical protein 669782 4554856 Rmag_0615 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903835.1 669120 D 413404 CDS YP_903836.1 118602621 4554857 complement(670751..671545) 1 NC_008610.1 ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived; thymidylate synthase 671545 thyA 4554857 thyA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thymidylate synthase YP_903836.1 670751 R 413404 CDS YP_903837.1 118602622 4554858 complement(671542..672321) 1 NC_008610.1 PFAM: prolipoprotein diacylglyceryl transferase; KEGG: noc:Noc_0233 prolipoprotein diacylglyceryl transferase; prolipoprotein diacylglyceryl transferase 672321 4554858 Rmag_0617 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) prolipoprotein diacylglyceryl transferase YP_903837.1 671542 R 413404 CDS YP_903838.1 118602623 4554859 complement(672441..672746) 1 NC_008610.1 PFAM: regulatory protein, ArsR; KEGG: tcx:Tcr_1782 transcriptional regulator, ArsR family; ArsR family transcriptional regulator 672746 4554859 Rmag_0618 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ArsR family transcriptional regulator YP_903838.1 672441 R 413404 CDS YP_903839.1 118602624 4554860 complement(672775..673356) 1 NC_008610.1 hypothetical protein 673356 4554860 Rmag_0619 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903839.1 672775 R 413404 CDS YP_903840.1 118602625 4554861 673448..674800 1 NC_008610.1 KEGG: hch:HCH_01350 periplasmic protease; TIGRFAM: carboxyl-terminal protease; PFAM: PDZ/DHR/GLGF domain protein; peptidase S41; carboxyl-terminal protease 674800 4554861 Rmag_0620 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) carboxyl-terminal protease YP_903840.1 673448 D 413404 CDS YP_903841.1 118602626 4554862 complement(675432..676316) 1 NC_008610.1 KEGG: mca:MCA1465 signal peptidase I; TIGRFAM: signal peptidase I; PFAM: peptidase S24, S26A and S26B; signal peptidase I 676316 4554862 Rmag_0621 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) signal peptidase I YP_903841.1 675432 R 413404 CDS YP_903842.1 118602627 4554863 676385..676711 1 NC_008610.1 PFAM: DsrC family protein; KEGG: buc:BU467 putative sulfite reductase; DsrC family protein 676711 4554863 Rmag_0622 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DsrC family protein YP_903842.1 676385 D 413404 CDS YP_903843.1 118602628 4554864 complement(677358..678665) 1 NC_008610.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase 678665 4554864 Rmag_0623 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-phosphoshikimate 1-carboxyvinyltransferase YP_903843.1 677358 R 413404 CDS YP_903844.1 118602629 4554865 complement(678672..679526) 1 NC_008610.1 PFAM: Prephenate dehydrogenase; NAD-dependent glycerol-3-phosphate dehydrogenase domain protein; KEGG: tcx:Tcr_1195 prephenate dehydrogenase; prephenate dehydrogenase 679526 4554865 Rmag_0624 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) prephenate dehydrogenase YP_903844.1 678672 R 413404 CDS YP_903845.1 118602630 4554866 complement(679523..680587) 1 NC_008610.1 TIGRFAM: histidinol-phosphate aminotransferase; PFAM: aminotransferase, class I and II; KEGG: ilo:IL1358 histidinol-phosphate/aromatic aminotransferase; aminotransferase 680587 4554866 Rmag_0625 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aminotransferase YP_903845.1 679523 R 413404 CDS YP_903846.1 118602631 4554867 complement(680691..681770) 1 NC_008610.1 TIGRFAM: chorismate mutase; PFAM: prephenate dehydratase; Chorismate mutase; amino acid-binding ACT domain protein; KEGG: csa:Csal_2166 chorismate mutase; chorismate mutase 681770 4554867 Rmag_0626 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) chorismate mutase YP_903846.1 680691 R 413404 CDS YP_903847.1 118602632 4555197 complement(681781..682938) 1 NC_008610.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: noc:Noc_0173 D-isomer specific 2-hydroxyacid dehydrogenase; D-3-phosphoglycerate dehydrogenase 682938 4555197 Rmag_0627 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) D-3-phosphoglycerate dehydrogenase YP_903847.1 681781 R 413404 CDS YP_903848.1 118602633 4555198 complement(682938..684017) 1 NC_008610.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine; phosphoserine aminotransferase 684017 4555198 Rmag_0628 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoserine aminotransferase YP_903848.1 682938 R 413404 CDS YP_903849.1 118602634 4555199 complement(685451..685900) 1 NC_008610.1 TIGRFAM: Ribonucleotide reductase regulator NrdR-like; PFAM: ATP-cone domain protein; KEGG: cbu:CBU_1418 conserved hypothetical protein TIGR00244; ribonucleotide reductase regulator NrdR-like 685900 4555199 Rmag_0631 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonucleotide reductase regulator NrdR-like YP_903849.1 685451 R 413404 CDS YP_903850.1 118602635 4555200 complement(685912..687165) 1 NC_008610.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 687165 glyA 4555200 glyA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) serine hydroxymethyltransferase YP_903850.1 685912 R 413404 CDS YP_903851.1 118602636 4555201 complement(689034..689780) 1 NC_008610.1 PFAM: UBA/THIF-type NAD/FAD binding protein; MoeZ/MoeB domain protein; KEGG: pfo:Pfl_4746 UBA/ThiF-type NAD/FAD binding fold; UBA/THIF-type NAD/FAD binding protein 689780 4555201 Rmag_0635 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UBA/THIF-type NAD/FAD binding protein YP_903851.1 689034 R 413404 CDS YP_903852.1 118602637 4555202 complement(689777..690268) 1 NC_008610.1 KEGG: pha:PSHAa2274 protein-methionine-S-oxide reductase (peptide Met(O) reductase); TIGRFAM: peptide methionine sulfoxide reductase; PFAM: Methionine sulfoxide reductase A; peptide methionine sulfoxide reductase 690268 4555202 Rmag_0636 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptide methionine sulfoxide reductase YP_903852.1 689777 R 413404 CDS YP_903853.1 118602638 4555203 690310..691014 1 NC_008610.1 KEGG: lpp:plpp0108 hypothetical protein; hypothetical protein 691014 4555203 Rmag_0637 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903853.1 690310 D 413404 CDS YP_903854.1 118602639 4555204 691087..691326 1 NC_008610.1 hypothetical protein 691326 4555204 Rmag_0638 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903854.1 691087 D 413404 CDS YP_903855.1 118602640 4555205 691323..692405 1 NC_008610.1 PFAM: protein of unknown function UPF0118; KEGG: tcx:Tcr_1881 hypothetical protein; hypothetical protein 692405 4555205 Rmag_0639 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903855.1 691323 D 413404 CDS YP_903856.1 118602641 4555206 692472..692942 1 NC_008610.1 hypothetical protein 692942 4555206 Rmag_0640 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903856.1 692472 D 413404 CDS YP_903857.1 118602642 4555207 complement(693042..693329) 1 NC_008610.1 PFAM: histone family protein DNA-binding protein; KEGG: msu:MS1089 bacterial nucleoid DNA-binding protein; histone family protein DNA-binding protein 693329 4555207 Rmag_0641 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) histone family protein DNA-binding protein YP_903857.1 693042 R 413404 CDS YP_903858.1 118602643 4555208 complement(693329..695671) 1 NC_008610.1 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 695671 pheT 4555208 pheT Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phenylalanyl-tRNA synthetase subunit beta YP_903858.1 693329 R 413404 CDS YP_903859.1 118602644 4555209 complement(695668..696687) 1 NC_008610.1 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 696687 pheS 4555209 pheS Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phenylalanyl-tRNA synthetase subunit alpha YP_903859.1 695668 R 413404 CDS YP_903860.1 118602645 4555210 complement(696696..697172) 1 NC_008610.1 KEGG: tbd:Tbd_0170 outer membrane lipoprotein, putative; hypothetical protein 697172 4555210 Rmag_0644 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903860.1 696696 R 413404 CDS YP_903861.1 118602646 4555211 complement(697195..697554) 1 NC_008610.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 697554 rplT 4555211 rplT Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L20 YP_903861.1 697195 R 413404 CDS YP_903862.1 118602647 4555212 complement(697572..697772) 1 NC_008610.1 PFAM: ribosomal protein L35; KEGG: ilo:IL1397 ribosomal protein L35; 50S ribosomal protein L35 697772 rpmI 4555212 rpmI Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L35 YP_903862.1 697572 R 413404 CDS YP_903863.1 118602648 4555213 complement(697812..698279) 1 NC_008610.1 TIGRFAM: translation initiation factor IF-3; PFAM: initiation factor 3; KEGG: ppu:PP2466 translation initiation factor IF-3; translation initiation factor 3 698279 4555213 Rmag_0647 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) translation initiation factor 3 YP_903863.1 697812 R 413404 CDS YP_903864.1 118602649 4555214 complement(698339..700237) 1 NC_008610.1 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 700237 thrS 4555214 thrS Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) threonyl-tRNA synthetase YP_903864.1 698339 R 413404 CDS YP_903865.1 118602650 4555215 complement(700269..701990) 1 NC_008610.1 TIGRFAM: single-stranded-DNA-specific exonuclease RecJ; PFAM: phosphoesterase, RecJ domain protein; phosphoesterase, DHHA1; KEGG: lpn:lpg1461 single stranded DNA specific exonuclease RecJ; single-stranded-DNA-specific exonuclease RecJ 701990 4555215 Rmag_0649 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) single-stranded-DNA-specific exonuclease RecJ YP_903865.1 700269 R 413404 CDS YP_903866.1 118602651 4554586 complement(701980..702531) 1 NC_008610.1 KEGG: hch:HCH_00116 hypothetical protein; hypothetical protein 702531 4554586 Rmag_0650 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903866.1 701980 R 413404 CDS YP_903867.1 118602652 4554587 complement(702524..703510) 1 NC_008610.1 PFAM: FAD dependent oxidoreductase; KEGG: csa:Csal_0494 glycine oxidase ThiO; FAD dependent oxidoreductase 703510 4554587 Rmag_0651 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) FAD dependent oxidoreductase YP_903867.1 702524 R 413404 CDS YP_903868.1 118602653 4554588 complement(703507..703965) 1 NC_008610.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase 703965 lspA 4554588 lspA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lipoprotein signal peptidase YP_903868.1 703507 R 413404 CDS YP_903869.1 118602654 4554589 704850..705632 1 NC_008610.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: noc:Noc_1769 short-chain dehydrogenase/reductase SDR; enoyl-[acyl-carrier-protein] reductase [NADH] 705632 4554589 Rmag_0654 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) enoyl-[acyl-carrier-protein] reductase [NADH] YP_903869.1 704850 D 413404 CDS YP_903870.1 118602655 4554590 complement(705797..706198) 1 NC_008610.1 hypothetical protein 706198 4554590 Rmag_0655 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903870.1 705797 R 413404 CDS YP_903871.1 118602656 4554591 complement(706427..708274) 1 NC_008610.1 PFAM: PpiC-type peptidyl-prolyl cis-trans isomerase; KEGG: tcx:Tcr_1096 PpiC-type peptidyl-prolyl cis-trans isomerase; PpiC-type peptidyl-prolyl cis-trans isomerase 708274 4554591 Rmag_0656 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) PpiC-type peptidyl-prolyl cis-trans isomerase YP_903871.1 706427 R 413404 CDS YP_903872.1 118602657 4554592 complement(709564..709983) 1 NC_008610.1 CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane; cytochrome c-type biogenesis protein CcmE 709983 4554592 Rmag_0659 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cytochrome c-type biogenesis protein CcmE YP_903872.1 709564 R 413404 CDS YP_903873.1 118602658 4554593 complement(709980..710156) 1 NC_008610.1 hypothetical protein 710156 4554593 Rmag_0660 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903873.1 709980 R 413404 CDS YP_903874.1 118602659 4554594 complement(710156..710896) 1 NC_008610.1 TIGRFAM: heme exporter protein CcmC; PFAM: cytochrome c assembly protein; KEGG: noc:Noc_0946 cytochrome c-type biogenesis protein CcmC; heme exporter protein CcmC 710896 4554594 Rmag_0661 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) heme exporter protein CcmC YP_903874.1 710156 R 413404 CDS YP_903875.1 118602660 4554595 complement(710944..711603) 1 NC_008610.1 PFAM: peptidase M22, glycoprotease; KEGG: noc:Noc_0917 peptidase M22, glycoprotease; peptidase M22, glycoprotease 711603 4554595 Rmag_0662 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase M22, glycoprotease YP_903875.1 710944 R 413404 CDS YP_903876.1 118602661 4554596 complement(711608..712195) 1 NC_008610.1 PFAM: glycosyl transferase, family 51; KEGG: cps:CPS_4301 penicillin-binding protein; glycosyl transferase family protein 712195 4554596 Rmag_0663 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycosyl transferase family protein YP_903876.1 711608 R 413404 CDS YP_903877.1 118602662 4554597 712415..712756 1 NC_008610.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 712756 rpsF 4554597 rpsF Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S6 YP_903877.1 712415 D 413404 CDS YP_903878.1 118602663 4554598 712756..713010 1 NC_008610.1 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 713010 rpsR 4554598 rpsR Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S18 YP_903878.1 712756 D 413404 CDS YP_903879.1 118602664 4554599 713020..713472 1 NC_008610.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 713472 rplI 4554599 rplI Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L9 YP_903879.1 713020 D 413404 CDS YP_903880.1 118602665 4554600 713503..714948 1 NC_008610.1 TIGRFAM: replicative DNA helicase; PFAM: DnaB domain protein helicase, N-terminal domain protein; DnaB domain protein helicase, C-terminal domain protein; KEGG: noc:Noc_0223 DnaB helicase; primary replicative DNA helicase 714948 4554600 Rmag_0667 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) primary replicative DNA helicase YP_903880.1 713503 D 413404 CDS YP_903881.1 118602666 4554601 714963..716015 1 NC_008610.1 KEGG: cbu:CBU_0869 alanine racemase; TIGRFAM: alanine racemase; PFAM: alanine racemase domain protein; alanine racemase 716015 4554601 Rmag_0668 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) alanine racemase YP_903881.1 714963 D 413404 CDS YP_903882.1 118602667 4554602 716012..716716 1 NC_008610.1 PFAM: metallophosphoesterase; KEGG: cyb:CYB_0131 icc protein; metallophosphoesterase 716716 4554602 Rmag_0669 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) metallophosphoesterase YP_903882.1 716012 D 413404 CDS YP_903883.1 118602668 4554603 717051..717956 1 NC_008610.1 PFAM: 5-nucleotidase; KEGG: noc:Noc_1810 5-nucleotidase; 5-nucleotidase 717956 4554603 Rmag_0670 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 5-nucleotidase YP_903883.1 717051 D 413404 CDS YP_903884.1 118602669 4554604 719593..720861 1 NC_008610.1 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 720861 hisS 4554604 hisS Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) histidyl-tRNA synthetase YP_903884.1 719593 D 413404 CDS YP_903885.1 118602670 4554605 720858..721466 1 NC_008610.1 KEGG: pha:PSHAb0136 puttive membrane-associated protein with TPR-like domain; TPR-like domain-containing protein 721466 4554605 Rmag_0672 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) TPR-like domain-containing protein YP_903885.1 720858 D 413404 CDS YP_903886.1 118602671 4555274 721472..722869 1 NC_008610.1 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 722869 engA 4555274 engA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GTP-binding protein EngA YP_903886.1 721472 D 413404 CDS YP_903887.2 229576705 4555275 complement(723517..725154) 1 NC_008610.1 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 725154 pyrG 4555275 pyrG Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CTP synthetase YP_903887.2 723517 R 413404 CDS YP_903888.1 118602673 4555276 728199..729926 1 NC_008610.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: tbd:Tbd_2507 lipid A export ATP-binding/permease protein MsbA; ABC transporter related 729926 4555276 Rmag_0676 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_903888.1 728199 D 413404 CDS YP_903889.1 118602674 4555277 complement(731475..732539) 1 NC_008610.1 PFAM: glycosyl transferase, family 3; KEGG: tbd:Tbd_0270 anthranilate phosphoribosyltransferase-like protein; anthranilate phosphoribosyltransferase 732539 4555277 Rmag_0677 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) anthranilate phosphoribosyltransferase YP_903889.1 731475 R 413404 CDS YP_903890.1 118602675 4555278 complement(732544..732861) 1 NC_008610.1 PFAM: Rieske [2Fe-2S] domain protein; KEGG: tbd:Tbd_0271 putative dioxygenase ferredoxin subunit; Rieske (2Fe-2S) domain-containing protein 732861 4555278 Rmag_0678 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Rieske (2Fe-2S) domain-containing protein YP_903890.1 732544 R 413404 CDS YP_903891.1 118602676 4555279 complement(732846..733454) 1 NC_008610.1 PFAM: Lytic transglycosylase, catalytic; KEGG: cps:CPS_4077 putative lipoprotein; lytic transglycosylase, catalytic 733454 4555279 Rmag_0679 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lytic transglycosylase, catalytic YP_903891.1 732846 R 413404 CDS YP_903892.1 118602677 4555280 complement(733451..733765) 1 NC_008610.1 PFAM: Cold-shock protein, DNA-binding; SMART: Cold shock protein; cold-shock DNA-binding domain-containing protein 733765 4555280 Rmag_0680 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cold-shock DNA-binding domain-containing protein YP_903892.1 733451 R 413404 CDS YP_903893.1 118602678 4555281 734378..734860 1 NC_008610.1 KEGG: tcx:Tcr_1759 thioredoxin, putative; thioredoxin, putative 734860 4555281 Rmag_0682 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thioredoxin, putative YP_903893.1 734378 D 413404 CDS YP_903894.1 118602679 4555282 734857..735516 1 NC_008610.1 TIGRFAM: uracil-DNA glycosylase; PFAM: Uracil-DNA glycosylase superfamily; KEGG: bba:Bd3500 uracil-DNA glycosylase; uracil-DNA glycosylase 735516 4555282 Rmag_0683 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) uracil-DNA glycosylase YP_903894.1 734857 D 413404 CDS YP_903895.1 118602680 4555283 735516..736553 1 NC_008610.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: tcx:Tcr_0451 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region 736553 4555283 Rmag_0684 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region YP_903895.1 735516 D 413404 CDS YP_903896.1 118602681 4555284 complement(736550..738007) 1 NC_008610.1 PFAM: molybdopterin oxidoreductase; molybdopterin oxidoreductase Fe4S4 region; KEGG: mca:MCA0590 nitrate reductase; molybdopterin oxidoreductase 738007 4555284 Rmag_0685 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) molybdopterin oxidoreductase YP_903896.1 736550 R 413404 CDS YP_903897.1 118602682 4555285 complement(738017..739717) 1 NC_008610.1 PFAM: protein kinase; protein phosphatase 2C domain protein; SMART: tyrosine protein kinase; serine/threonine protein kinase; KEGG: hch:HCH_05817 serine/threonine protein kinase; serine/threonine protein kinase 739717 4555285 Rmag_0686 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) serine/threonine protein kinase YP_903897.1 738017 R 413404 CDS YP_903898.1 118602683 4555286 complement(739720..741186) 1 NC_008610.1 PFAM: major facilitator superfamily MFS_1; KEGG: sde:Sde_2277 conserved hypothetical nitrate transporter; major facilitator transporter 741186 4555286 Rmag_0687 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) major facilitator transporter YP_903898.1 739720 R 413404 CDS YP_903899.1 118602684 4555287 complement(741202..743577) 1 NC_008610.1 TIGRFAM: nitrite reductase [NAD(P)H], large subunit; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin domain protein; nitrite and sulphite reductase 4Fe-4S region; BFD domain protein [2Fe-2S]-binding domain protein; KEGG: mca:MCA0592 nitrite reductase [NAD(P)H], large subunit; assimilatory nitrite reductase (NAD(P)H) large subunit precursor 743577 4555287 Rmag_0688 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) assimilatory nitrite reductase (NAD(P)H) large subunit precursor YP_903899.1 741202 R 413404 CDS YP_903900.1 118602685 4555288 743944..744306 1 NC_008610.1 PFAM: molybdopterin biosynthesis MoaE; KEGG: vvu:VV13084 molybdenum cofactor biosynthesis protein E; molybdopterin synthase subunit MoaE 744306 4555288 Rmag_0689 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) molybdopterin synthase subunit MoaE YP_903900.1 743944 D 413404 CDS YP_903901.1 118602686 4555289 complement(744312..744896) 1 NC_008610.1 TIGRFAM: molybdopterin-guanine dinucleotide biosynthesis protein A; KEGG: son:SO4722 molybdopterin-guanine dinucleotide biosynthesis protein; molybdenum cofactor guanylyltransferase 744896 4555289 Rmag_0690 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) molybdenum cofactor guanylyltransferase YP_903901.1 744312 R 413404 CDS YP_903902.1 118602687 4555290 744979..746244 1 NC_008610.1 TIGRFAM: molybdenum cofactor synthesis domain; PFAM: molybdopterin binding domain; MoeA domain protein, domain I and II; MoeA domain protein, domain IV; KEGG: tcx:Tcr_0161 molybdopterin binding domain MoeA; molybdopterin molybdochelatase 746244 4555290 Rmag_0691 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) molybdopterin molybdochelatase YP_903902.1 744979 D 413404 CDS YP_903903.1 118602688 4555291 746270..746752 1 NC_008610.1 TIGRFAM: molybdenum cofactor biosynthesis protein C; PFAM: molybdopterin cofactor biosynthesis MoaC region; KEGG: tcx:Tcr_0162 molybdenum cofactor biosynthesis protein C; GTP cyclohydrolase subunit MoaC 746752 4555291 Rmag_0692 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GTP cyclohydrolase subunit MoaC YP_903903.1 746270 D 413404 CDS YP_903904.1 118602689 4555292 746745..747740 1 NC_008610.1 KEGG: tcx:Tcr_0158 molybdenum cofactor synthesis-like; TIGRFAM: molybdenum cofactor biosynthesis protein A; PFAM: Radical SAM domain protein; molybdenum cofactor synthesis domain protein; SMART: Elongator protein 3/MiaB/NifB; GTP cyclohydrolase subunit MoaA 747740 4555292 Rmag_0693 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GTP cyclohydrolase subunit MoaA YP_903904.1 746745 D 413404 CDS YP_903905.1 118602690 4554711 747775..748011 1 NC_008610.1 PFAM: thiamineS protein; KEGG: dar:Daro_1784 molybdopterin converting factor, subunit 1; molybdopterin synthase subunit MoaD 748011 4554711 Rmag_0694 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) molybdopterin synthase subunit MoaD YP_903905.1 747775 D 413404 CDS YP_903906.1 118602691 4554712 749895..750425 1 NC_008610.1 TIGRFAM: molybdenum cofactor synthesis domain; PFAM: molybdopterin binding domain; KEGG: tcx:Tcr_1547 molybdopterin binding domain; molybdopterin adenylyltransferase 750425 4554712 Rmag_0698 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) molybdopterin adenylyltransferase YP_903906.1 749895 D 413404 CDS YP_903907.1 118602692 4554713 complement(750733..752976) 1 NC_008610.1 PFAM: von Willebrand factor, type A; KEGG: tcx:Tcr_0422 von Willebrand factor, type A; von Willebrand factor, type A 752976 4554713 Rmag_0699 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) von Willebrand factor, type A YP_903907.1 750733 R 413404 CDS YP_903908.1 118602693 4554714 complement(752989..753798) 1 NC_008610.1 PFAM: ATPase associated with various cellular activities, AAA_5; CbbQ/NirQ/NorQ C-terminal domain protein; SMART: AAA ATPase; KEGG: tcx:Tcr_0423 ATPase associated with various cellular activities, AAA_5; CbbQ/NirQ/NorQ C-terminal domain-containing protein 753798 4554714 Rmag_0700 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CbbQ/NirQ/NorQ C-terminal domain-containing protein YP_903908.1 752989 R 413404 CDS YP_903909.1 118602694 4554715 complement(753897..755279) 1 NC_008610.1 catalyzes the carboxylation of D-ribulose 1,5-bisphosphate in carbon dioxide fixation; ribulose bisphosphate carboxylase 755279 4554715 Rmag_0701 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribulose bisphosphate carboxylase YP_903909.1 753897 R 413404 CDS YP_903910.1 118602695 4554716 complement(756979..758208) 1 NC_008610.1 KEGG: tcx:Tcr_0590 arginine biosynthesis bifunctional protein ArgJ; TIGRFAM: arginine biosynthesis bifunctional protein ArgJ; PFAM: arginine biosynthesis protein ArgJ; glutamate N-acetyltransferase 758208 4554716 Rmag_0704 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutamate N-acetyltransferase YP_903910.1 756979 R 413404 CDS YP_903911.1 118602696 4554717 complement(758286..759842) 1 NC_008610.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: pst:PSPTO0315 iron ABC transporter, permease protein; binding-protein-dependent transport systems inner membrane component 759842 4554717 Rmag_0705 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) binding-protein-dependent transport systems inner membrane component YP_903911.1 758286 R 413404 CDS YP_903912.1 118602697 4554718 complement(759992..761011) 1 NC_008610.1 PFAM: extracellular solute-binding protein, family 1; KEGG: tbd:Tbd_0990 ABC transporter, iron binding protein; extracellular solute-binding protein 761011 4554718 Rmag_0706 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) extracellular solute-binding protein YP_903912.1 759992 R 413404 CDS YP_903913.1 118602698 4554719 complement(761072..761728) 1 NC_008610.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: eba:ebA4892 probable transport system ATP-binding protein; ABC transporter related 761728 4554719 Rmag_0707 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_903913.1 761072 R 413404 CDS YP_903914.1 118602699 4554720 complement(761791..763488) 1 NC_008610.1 PFAM: multicopper oxidase, type 2; multicopper oxidase, type 3; KEGG: tcx:Tcr_1576 bilirubin oxidase; cell division protein SufI 763488 4554720 Rmag_0708 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cell division protein SufI YP_903914.1 761791 R 413404 CDS YP_903915.1 118602700 4554721 complement(764431..764829) 1 NC_008610.1 hypothetical protein 764829 4554721 Rmag_0710 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903915.1 764431 R 413404 CDS YP_903916.1 118602701 4554722 complement(765115..766482) 1 NC_008610.1 PFAM: protein of unknown function DUF1111; KEGG: pae:PA4371 hypothetical protein; hypothetical protein 766482 4554722 Rmag_0711 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903916.1 765115 R 413404 CDS YP_903917.1 118602702 4554723 complement(766460..767767) 1 NC_008610.1 KEGG: vpa:VP1920 putative iron-regulated protein A; putative iron-regulated protein A 767767 4554723 Rmag_0712 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative iron-regulated protein A YP_903917.1 766460 R 413404 CDS YP_903918.1 118602703 4554724 769769..770923 1 NC_008610.1 TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: lpf:lpl2012 hypothetical protein; cation diffusion facilitator family transporter 770923 4554724 Rmag_0714 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cation diffusion facilitator family transporter YP_903918.1 769769 D 413404 CDS YP_903919.1 118602704 4554725 771437..771790 1 NC_008610.1 TIGRFAM: thioredoxin; PFAM: Thioredoxin domain; KEGG: tcx:Tcr_1385 thioredoxin; thioredoxin 771790 4554725 Rmag_0716 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thioredoxin YP_903919.1 771437 D 413404 CDS YP_903920.1 118602705 4554726 complement(771800..772120) 1 NC_008610.1 TIGRFAM: conserved hypothetical protein; PFAM: arsenate reductase and related; KEGG: pha:PSHAa1332 enzyme with thioredoxin-like domain; hypothetical protein 772120 4554726 Rmag_0717 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903920.1 771800 R 413404 CDS YP_903921.1 118602706 4554727 complement(772126..772755) 1 NC_008610.1 KEGG: tcx:Tcr_0163 hypothetical protein; hypothetical protein 772755 4554727 Rmag_0718 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903921.1 772126 R 413404 CDS YP_903922.1 118602707 4554728 complement(772759..773169) 1 NC_008610.1 hypothetical protein 773169 4554728 Rmag_0719 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903922.1 772759 R 413404 CDS YP_903923.1 118602708 4554729 complement(773533..775569) 1 NC_008610.1 KEGG: cbu:CBU_1914 glycyl-tRNA synthetase, beta subunit; glycine--tRNA ligase 775569 4554729 Rmag_0721 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycine--tRNA ligase YP_903923.1 773533 R 413404 CDS YP_903924.1 118602709 4554730 complement(776085..776477) 1 NC_008610.1 KEGG: noc:Noc_2908 hypothetical protein; hypothetical protein 776477 4554730 Rmag_0722 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903924.1 776085 R 413404 CDS YP_903925.1 118602710 4555586 complement(776477..777358) 1 NC_008610.1 KEGG: tcx:Tcr_0897 TolA; hypothetical protein 777358 4555586 Rmag_0723 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903925.1 776477 R 413404 CDS YP_903926.1 118602711 4555587 complement(777358..777810) 1 NC_008610.1 PFAM: Biopolymer transport protein ExbD/TolR; KEGG: ftl:FTL_0332 TolR protein; biopolymer transport protein ExbD/TolR 777810 4555587 Rmag_0724 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) biopolymer transport protein ExbD/TolR YP_903926.1 777358 R 413404 CDS YP_903927.1 118602712 4555588 complement(777807..778478) 1 NC_008610.1 PFAM: MotA/TolQ/ExbB proton channel; KEGG: ilo:IL1083 TonB system biopolymer transport component; MotA/TolQ/ExbB proton channel 778478 4555588 Rmag_0725 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) MotA/TolQ/ExbB proton channel YP_903927.1 777807 R 413404 CDS YP_903928.1 118602713 4555589 complement(779785..780297) 1 NC_008610.1 hypothetical protein 780297 4555589 Rmag_0729 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903928.1 779785 R 413404 CDS YP_903929.1 118602714 4555590 780375..781625 1 NC_008610.1 catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins; glutamyl-tRNA reductase 781625 hemA 4555590 hemA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutamyl-tRNA reductase YP_903929.1 780375 D 413404 CDS YP_903930.1 118602715 4555591 781625..782716 1 NC_008610.1 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 782716 prfA 4555591 prfA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptide chain release factor 1 YP_903930.1 781625 D 413404 CDS YP_903931.1 118602716 4555592 complement(782708..783496) 1 NC_008610.1 PFAM: ABC-3 protein; KEGG: ppr:PBPRA1053 putative ABC-type Mn2+/Zn2+ transport system, permease component; ABC-3 protein 783496 4555592 Rmag_0732 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC-3 protein YP_903931.1 782708 R 413404 CDS YP_903932.1 118602717 4555593 complement(783502..783909) 1 NC_008610.1 PFAM: ferric-uptake regulator; KEGG: noc:Noc_1194 ferric-uptake regulator; ferric uptake regulator family protein 783909 4555593 Rmag_0733 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ferric uptake regulator family protein YP_903932.1 783502 R 413404 CDS YP_903933.1 118602718 4555594 783965..784423 1 NC_008610.1 PFAM: SmpA/OmlA domain protein; KEGG: nmu:Nmul_A0476 SmpA/OmlA; SmpA/OmlA domain-containing protein 784423 4555594 Rmag_0734 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) SmpA/OmlA domain-containing protein YP_903933.1 783965 D 413404 CDS YP_903934.1 118602719 4555595 complement(784526..785473) 1 NC_008610.1 PFAM: peptidase S49; KEGG: tcx:Tcr_1144 peptidase S49; peptidase S49 785473 4555595 Rmag_0735 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase S49 YP_903934.1 784526 R 413404 CDS YP_903935.1 118602720 4555596 785489..786085 1 NC_008610.1 TIGRFAM: heme exporter protein CcmA; PFAM: ABC transporter related; KEGG: vfi:VF1824 heme exporter protein A; heme exporter protein CcmA 786085 4555596 Rmag_0736 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) heme exporter protein CcmA YP_903935.1 785489 D 413404 CDS YP_903936.1 118602721 4555597 786082..786747 1 NC_008610.1 TIGRFAM: heme exporter protein CcmB; PFAM: cytochrome c-type biogenesis protein CcmB; KEGG: cps:CPS_1033 heme exporter protein CcmB; heme exporter protein CcmB 786747 4555597 Rmag_0737 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) heme exporter protein CcmB YP_903936.1 786082 D 413404 CDS YP_903937.1 118602722 4555598 786901..788034 1 NC_008610.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 788034 4555598 Rmag_0738 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) S-adenosylmethionine synthetase YP_903937.1 786901 D 413404 CDS YP_903938.1 118602723 4555599 788129..789526 1 NC_008610.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine; S-adenosyl-L-homocysteine hydrolase 789526 4555599 Rmag_0739 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) S-adenosyl-L-homocysteine hydrolase YP_903938.1 788129 D 413404 CDS YP_903939.1 118602724 4555600 789614..790537 1 NC_008610.1 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 790537 glyQ 4555600 glyQ Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycyl-tRNA synthetase subunit alpha YP_903939.1 789614 D 413404 CDS YP_903940.1 118602725 4555601 790539..791111 1 NC_008610.1 KEGG: ilo:IL0747 hypothetical protein; hypothetical protein 791111 4555601 Rmag_0741 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903940.1 790539 D 413404 CDS YP_903941.1 118602726 4555602 791598..792623 1 NC_008610.1 PFAM: MscS Mechanosensitive ion channel; KEGG: vfi:VFA0405 mechanosensitive ion channel; MscS mechanosensitive ion channel 792623 4555602 Rmag_0742 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) MscS mechanosensitive ion channel YP_903941.1 791598 D 413404 CDS YP_903942.1 118602727 4555603 792630..793964 1 NC_008610.1 catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A); (dimethylallyl)adenosine tRNA methylthiotransferase 793964 4555603 Rmag_0743 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) (dimethylallyl)adenosine tRNA methylthiotransferase YP_903942.1 792630 D 413404 CDS YP_903943.1 118602728 4555604 complement(794032..794706) 1 NC_008610.1 PFAM: electron transport protein SCO1/SenC; KEGG: rbe:RBE_0699 Sco2 protein precursor; electron transport protein SCO1/SenC 794706 4555604 Rmag_0744 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) electron transport protein SCO1/SenC YP_903943.1 794032 R 413404 CDS YP_903944.1 118602729 4555664 complement(794707..795174) 1 NC_008610.1 PFAM: protein of unknown function DUF461; KEGG: dar:Daro_1578 protein of unknown function DUF461; hypothetical protein 795174 4555664 Rmag_0745 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903944.1 794707 R 413404 CDS YP_903945.1 118602730 4555665 796173..797264 1 NC_008610.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA 797264 mnmA 4555665 mnmA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA-specific 2-thiouridylase MnmA YP_903945.1 796173 D 413404 CDS YP_903946.1 118602731 4555666 797264..797878 1 NC_008610.1 HflD; UPF0274; in Escherichia coli this protein is peripherally associated with the membrane and appears to act with lambda CII protein; in Haemophilus influenzae a knockout of the HI0638 gene affected paracytosis; hypothetical protein 797878 4555666 Rmag_0748 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903946.1 797264 D 413404 CDS YP_903947.1 118602732 4555667 797922..798215 1 NC_008610.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 798215 rpsT 4555667 rpsT Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S20 YP_903947.1 797922 D 413404 CDS YP_903948.1 118602733 4555668 798563..799963 1 NC_008610.1 KEGG: pha:PSHAa0647 exodeoxyribonuclease VII large subunit; TIGRFAM: exodeoxyribonuclease VII, large subunit; PFAM: Exonuclease VII, large subunit; nucleic acid binding, OB-fold, tRNA/helicase-type; exodeoxyribonuclease VII, large subunit 799963 4555668 Rmag_0750 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) exodeoxyribonuclease VII, large subunit YP_903948.1 798563 D 413404 CDS YP_903949.1 118602734 4555669 799920..800771 1 NC_008610.1 PFAM: peptidase M23B; KEGG: psp:PSPPH_1330 peptidase, M23/M37 family; peptidase M23B 800771 4555669 Rmag_0751 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase M23B YP_903949.1 799920 D 413404 CDS YP_903950.1 118602735 4555670 800762..801178 1 NC_008610.1 PFAM: RDD domain containing protein; KEGG: nmu:Nmul_A1054 RDD; RDD domain-containing protein 801178 4555670 Rmag_0752 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) RDD domain-containing protein YP_903950.1 800762 D 413404 CDS YP_903951.1 118602736 4555671 801256..801495 1 NC_008610.1 hypothetical protein 801495 4555671 Rmag_0753 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903951.1 801256 D 413404 CDS YP_903952.1 118602737 4555672 801513..801866 1 NC_008610.1 PFAM: Septum formation initiator; cell division protein FtsB 801866 4555672 Rmag_0754 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cell division protein FtsB YP_903952.1 801513 D 413404 CDS YP_903953.1 118602738 4555673 801885..802604 1 NC_008610.1 TIGRFAM: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; PFAM: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; KEGG: vvy:VV2816 4-diphosphocytidyl-2-methyl-D-erithritol synthase; 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 802604 4555673 Rmag_0755 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase YP_903953.1 801885 D 413404 CDS YP_903954.1 118602739 4555674 802601..803071 1 NC_008610.1 catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 803071 ispF 4555674 ispF Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase YP_903954.1 802601 D 413404 CDS YP_903955.1 118602740 4555675 803071..804480 1 NC_008610.1 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 804480 murC 4555675 murC Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-N-acetylmuramate--L-alanine ligase YP_903955.1 803071 D 413404 CDS YP_903956.1 118602741 4555676 804513..805325 1 NC_008610.1 KEGG: mfa:Mfla_2267 UDP-N-acetylenolpyruvoylglucosamine reductase; TIGRFAM: UDP-N-acetylenolpyruvoylglucosamine reductase; PFAM: FAD linked oxidase domain protein; UDP-N-acetylenolpyruvoylglucosamine reductase domain protein; UDP-N-acetylmuramate dehydrogenase 805325 4555676 Rmag_0758 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-N-acetylmuramate dehydrogenase YP_903956.1 804513 D 413404 CDS YP_903957.1 118602742 4555677 805322..806203 1 NC_008610.1 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 806203 ddl 4555677 ddl Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) D-alanine--D-alanine ligase YP_903957.1 805322 D 413404 CDS YP_903958.1 118602743 4555678 806193..806942 1 NC_008610.1 KEGG: pfo:Pfl_4670 cell division protein FtsQ; hypothetical protein 806942 4555678 Rmag_0760 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903958.1 806193 D 413404 CDS YP_903959.1 118602744 4555679 complement(806948..807625) 1 NC_008610.1 hypothetical protein 807625 4555679 Rmag_0761 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903959.1 806948 R 413404 CDS YP_903960.1 118602745 4555680 complement(807630..809204) 1 NC_008610.1 PFAM: Peptidoglycan-binding LysM; Lytic transglycosylase, catalytic; KEGG: cps:CPS_1998 putative membrane-bound lytic murein transglycosylase; lytic transglycosylase, catalytic 809204 4555680 Rmag_0762 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) lytic transglycosylase, catalytic YP_903960.1 807630 R 413404 CDS YP_903961.1 118602746 4555681 complement(809180..809488) 1 NC_008610.1 PFAM: BolA family protein; KEGG: pha:PSHAa2243 regulator protein; transcriptional regulator BolA 809488 4555681 Rmag_0763 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) transcriptional regulator BolA YP_903961.1 809180 R 413404 CDS YP_903962.1 118602747 4555682 complement(809485..810552) 1 NC_008610.1 PFAM: ferredoxin; oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; Ferric reductase, NAD binding; KEGG: tbd:Tbd_2563 NAD(P)H-flavin reductase; oxidoreductase FAD/NAD(P)-binding subunit 810552 4555682 Rmag_0764 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) oxidoreductase FAD/NAD(P)-binding subunit YP_903962.1 809485 R 413404 CDS YP_903963.1 118602748 4555683 810579..811496 1 NC_008610.1 KEGG: vpa:VP2818 tRNA delta(2)-isopentenylpyrophosphate transferase; TIGRFAM: tRNA delta(2)-isopentenylpyrophosphate transferase; PFAM: tRNA isopentenyltransferase; tRNA delta(2)-isopentenylpyrophosphate transferase 811496 4555683 Rmag_0765 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA delta(2)-isopentenylpyrophosphate transferase YP_903963.1 810579 D 413404 CDS YP_903964.1 118602749 4555128 complement(812554..813855) 1 NC_008610.1 TIGRFAM: UDP-N-acetylmuramoylalanine--D-glutamate ligase; PFAM: cytoplasmic peptidoglycan synthetases domain protein; Mur ligase, middle domain protein; KEGG: noc:Noc_2863 UDP-N-acetylmuramoylalanine-D-glutamate ligase; UDP-N-acetylmuramoylalanine--D-glutamate ligase 813855 4555128 Rmag_0766 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-N-acetylmuramoylalanine--D-glutamate ligase YP_903964.1 812554 R 413404 CDS YP_903965.1 118602750 4555129 813914..814573 1 NC_008610.1 PFAM: protein of unknown function UPF0005; KEGG: tbd:Tbd_0489 hypothetical protein; hypothetical protein 814573 4555129 Rmag_0767 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903965.1 813914 D 413404 CDS YP_903966.1 118602751 4555130 814593..815132 1 NC_008610.1 PFAM: NUDIX hydrolase; KEGG: sdn:Sden_2782 NUDIX hydrolase; NUDIX hydrolase 815132 4555130 Rmag_0768 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NUDIX hydrolase YP_903966.1 814593 D 413404 CDS YP_903967.1 118602752 4555131 815217..816494 1 NC_008610.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase 816494 4555131 Rmag_0769 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) homoserine dehydrogenase YP_903967.1 815217 D 413404 CDS YP_903968.1 118602753 4555132 816505..817569 1 NC_008610.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase 817569 4555132 Rmag_0770 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) threonine synthase YP_903968.1 816505 D 413404 CDS YP_903969.1 118602754 4555133 817605..817829 1 NC_008610.1 KEGG: xoo:XOO4599 hypothetical protein; hypothetical protein 817829 4555133 Rmag_0771 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903969.1 817605 D 413404 CDS YP_903970.1 118602755 4555134 817856..818743 1 NC_008610.1 catalyzes the formation of cysteine from 3-O-acetyl-L-serine and hydrogen sulfide; cysteine synthase B 818743 cysM 4555134 cysM Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cysteine synthase B YP_903970.1 817856 D 413404 CDS YP_903971.1 118602756 4555135 818740..820014 1 NC_008610.1 PFAM: Cl- channel, voltage-gated family protein; KEGG: rpa:RPA3953 putative chloride channel protein; Cl- channel, voltage-gated family protein 820014 4555135 Rmag_0773 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Cl- channel, voltage-gated family protein YP_903971.1 818740 D 413404 CDS YP_903972.1 118602757 4555136 complement(820001..820423) 1 NC_008610.1 PFAM: conserved hypothetical protein 701; KEGG: hch:HCH_06247 predicted membrane protein; hypothetical protein 820423 4555136 Rmag_0774 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903972.1 820001 R 413404 CDS YP_903973.1 118602758 4555137 821283..821576 1 NC_008610.1 hypothetical protein 821576 4555137 Rmag_0775 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903973.1 821283 D 413404 CDS YP_903974.1 118602759 4555138 complement(822013..822348) 1 NC_008610.1 KEGG: bur:Bcep18194_C6923 hypothetical protein; hypothetical protein 822348 4555138 Rmag_0776 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903974.1 822013 R 413404 CDS YP_903975.1 118602760 4555139 complement(822359..823648) 1 NC_008610.1 PFAM: peptidase M16 domain protein; KEGG: tcx:Tcr_1940 peptidase M16-like; peptidase M16 domain-containing protein 823648 4555139 Rmag_0777 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase M16 domain-containing protein YP_903975.1 822359 R 413404 CDS YP_903976.1 118602761 4555140 complement(823645..824970) 1 NC_008610.1 PFAM: peptidase M16 domain protein; KEGG: mca:MCA0063 peptidase, M16 family; peptidase M16 domain-containing protein 824970 4555140 Rmag_0778 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase M16 domain-containing protein YP_903976.1 823645 R 413404 CDS YP_903977.1 118602762 4555141 825783..826739 1 NC_008610.1 KEGG: lpp:lpp2724 signal recognition particle receptor; TIGRFAM: signal recognition particle-docking protein FtsY; PFAM: GTP-binding signal recognition particle SRP54, G- domain; SMART: AAA ATPase; signal recognition particle-docking protein FtsY 826739 4555141 Rmag_0781 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) signal recognition particle-docking protein FtsY YP_903977.1 825783 D 413404 CDS YP_903978.1 118602763 4555142 827882..828088 1 NC_008610.1 hypothetical protein 828088 4555142 Rmag_0782 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903978.1 827882 D 413404 CDS YP_903979.1 118602764 4555143 complement(829347..830261) 1 NC_008610.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase 830261 hemC 4555143 hemC Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) porphobilinogen deaminase YP_903979.1 829347 R 413404 CDS YP_903980.1 118602765 4555144 830726..832168 1 NC_008610.1 catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase 832168 4555144 Rmag_0784 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) argininosuccinate lyase YP_903980.1 830726 D 413404 CDS YP_903981.1 118602766 4555145 832168..833130 1 NC_008610.1 TIGRFAM: methionyl-tRNA formyltransferase; PFAM: formyl transferase domain protein; KEGG: tcx:Tcr_0192 methionyl-tRNA formyltransferase; methionyl-tRNA formyltransferase 833130 4555145 Rmag_0785 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) methionyl-tRNA formyltransferase YP_903981.1 832168 D 413404 CDS YP_903982.1 118602767 4555146 complement(833902..834363) 1 NC_008610.1 PFAM: tRNA/rRNA methyltransferase (SpoU); KEGG: lpp:lpp2563 RNA methyltransferase TrmH family; tRNA/rRNA methyltransferase (SpoU) 834363 4555146 Rmag_0786 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA/rRNA methyltransferase (SpoU) YP_903982.1 833902 R 413404 CDS YP_903983.1 118602768 4554750 834423..837002 1 NC_008610.1 PFAM: AAA ATPase, central domain protein; Clp N terminal domain protein; ATPase associated with various cellular activities, AAA_5; ATPase AAA-2 domain protein; SMART: AAA ATPase; KEGG: tcx:Tcr_0414 AAA ATPase; ATPase 837002 4554750 Rmag_0787 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATPase YP_903983.1 834423 D 413404 CDS YP_903984.1 118602769 4554751 837559..838212 1 NC_008610.1 TIGRFAM: electron transport complex, RnfABCDGE type, E subunit; PFAM: RnfA-Nqr electron transport subunit; KEGG: tcx:Tcr_1031 electron transport complex, RnfABCDGE type, E subunit; electron transport complex, RnfABCDGE type, E subunit 838212 4554751 Rmag_0788 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) electron transport complex, RnfABCDGE type, E subunit YP_903984.1 837559 D 413404 CDS YP_903985.1 118602770 4554752 838715..839500 1 NC_008610.1 TIGRFAM: modification methylase, HemK family; PFAM: methyltransferase small; KEGG: tcx:Tcr_0388 modification methylase, HemK family; HemK family modification methylase 839500 4554752 Rmag_0790 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) HemK family modification methylase YP_903985.1 838715 D 413404 CDS YP_903986.1 118602771 4554753 complement(841083..842573) 1 NC_008610.1 TIGRFAM: hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha subunit; hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta subunit; PFAM: Fe-S type hydro-lyases tartrate/fumarate alpha region; Fe-S type hydro-lyases tartrate/fumarate beta region; KEGG: pha:PSHAa1166 fumarate hydratase, class I; fumarase 842573 4554753 Rmag_0793 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) fumarase YP_903986.1 841083 R 413404 CDS YP_903987.1 118602772 4554754 842653..843684 1 NC_008610.1 functions in MreBCD complex in some organisms; rod shape-determining protein MreB 843684 4554754 Rmag_0794 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) rod shape-determining protein MreB YP_903987.1 842653 D 413404 CDS YP_903988.1 118602773 4554755 843720..844514 1 NC_008610.1 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 844514 4554755 Rmag_0795 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) rod shape-determining protein MreC YP_903988.1 843720 D 413404 CDS YP_903989.1 118602774 4554756 844518..844985 1 NC_008610.1 KEGG: pfo:Pfl_0840 rod shape-determining protein MreD; rod shape-determining protein MreD 844985 4554756 Rmag_0796 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) rod shape-determining protein MreD YP_903989.1 844518 D 413404 CDS YP_903990.1 118602775 4554757 844973..846823 1 NC_008610.1 PFAM: penicillin-binding protein, transpeptidase; Penicillin-binding protein, dimerisation domain; KEGG: pae:PA4003 penicillin-binding protein 2; peptidoglycan glycosyltransferase 846823 4554757 Rmag_0797 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidoglycan glycosyltransferase YP_903990.1 844973 D 413404 CDS YP_903991.1 118602776 4554758 complement(847598..849394) 1 NC_008610.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: rfr:Rfer_3493 ABC transporter related; ABC transporter related 849394 4554758 Rmag_0799 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_903991.1 847598 R 413404 CDS YP_903992.1 118602777 4554759 850241..851290 1 NC_008610.1 KEGG: vpa:VP0679 5-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase; TIGRFAM: riboflavin biosynthesis protein RibD; Riboflavin-specific deaminase-like; PFAM: CMP/dCMP deaminase, zinc-binding; bifunctional deaminase-reductase domain protein; diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase 851290 4554759 Rmag_0800 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase YP_903992.1 850241 D 413404 CDS YP_903993.1 118602778 4554760 851287..852480 1 NC_008610.1 TIGRFAM: phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase; PFAM: flavoprotein; DNA/pantothenate metabolism flavoprotein domain protein; KEGG: ilo:IL0239 phosphopantothenoylcysteine synthetase/decarboxylase; phosphopantothenoylcysteine decarboxylase / phosphopantothenate-cysteine ligase 852480 4554760 Rmag_0801 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphopantothenoylcysteine decarboxylase / phosphopantothenate-cysteine ligase YP_903993.1 851287 D 413404 CDS YP_903994.1 118602779 4554761 854216..854470 1 NC_008610.1 hypothetical protein 854470 4554761 Rmag_0802 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903994.1 854216 D 413404 CDS YP_903995.1 118602780 4554762 complement(854485..857919) 1 NC_008610.1 KEGG: noc:Noc_0846 DNA polymerase III, alpha subunit; TIGRFAM: DNA polymerase III, alpha subunit; PFAM: PHP C-terminal domain protein; nucleic acid binding, OB-fold, tRNA/helicase-type; SMART: phosphoesterase PHP domain protein; DNA polymerase III, alpha subunit 857919 4554762 Rmag_0803 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA polymerase III, alpha subunit YP_903995.1 854485 R 413404 CDS YP_903996.1 118602781 4554763 complement(858081..858401) 1 NC_008610.1 hypothetical protein 858401 4554763 Rmag_0804 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_903996.1 858081 R 413404 CDS YP_903997.1 118602782 4554764 complement(858411..859226) 1 NC_008610.1 KEGG: tcx:Tcr_0601 sulfur oxidation protein SoxA; diheme cytochrome SoxA (sulfur oxidation) 859226 4554764 Rmag_0805 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) diheme cytochrome SoxA (sulfur oxidation) YP_903997.1 858411 R 413404 CDS YP_903998.1 118602783 4554765 complement(859254..859556) 1 NC_008610.1 KEGG: bja:bll1012 sulfur oxidation protein; sulfur oxidation protein 859556 4554765 Rmag_0806 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sulfur oxidation protein YP_903998.1 859254 R 413404 CDS YP_903999.1 118602784 4554766 complement(859589..860032) 1 NC_008610.1 KEGG: tcx:Tcr_0603 sulfur oxidation protein SoxY-like; sulfur oxidation protein SoxY-like 860032 4554766 Rmag_0807 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sulfur oxidation protein SoxY-like YP_903999.1 859589 R 413404 CDS YP_904000.1 118602785 4554767 complement(860043..860390) 1 NC_008610.1 KEGG: tbd:Tbd_0567 sulfur oxidation protein SoxX; hypothetical protein 860390 4554767 Rmag_0808 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904000.1 860043 R 413404 CDS YP_904001.1 118602786 4554768 complement(860706..862160) 1 NC_008610.1 KEGG: noc:Noc_2494 anthranilate synthase component I; TIGRFAM: anthranilate synthase component I; PFAM: Anthranilate synthase component I and chorismate binding protein; Anthranilate synthase component I domain protein; anthranilate synthase, component I 862160 4554768 Rmag_0809 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) anthranilate synthase, component I YP_904001.1 860706 R 413404 CDS YP_904002.1 118602787 4554769 complement(862265..866452) 1 NC_008610.1 KEGG: lpf:lpl0363 RNA polymerase beta' subunit; TIGRFAM: DNA-directed RNA polymerase, beta' subunit; PFAM: RNA polymerase, alpha subunit; RNA polymerase Rpb1, domain 3; RNA polymerase Rpb1, domain 1; RNA polymerase Rpb1, domain 5; RNA polymerase Rpb1, domain 4; SMART: RNA polymerase I subunit A domain protein; DNA-directed RNA polymerase, beta' subunit 866452 4554769 Rmag_0810 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA-directed RNA polymerase, beta' subunit YP_904002.1 862265 R 413404 CDS YP_904003.1 118602788 4554731 complement(866466..870548) 1 NC_008610.1 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 870548 rpoB 4554731 rpoB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA-directed RNA polymerase subunit beta YP_904003.1 866466 R 413404 CDS YP_904004.1 118602789 4554732 complement(870717..871094) 1 NC_008610.1 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 871094 rplL 4554732 rplL Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L7/L12 YP_904004.1 870717 R 413404 CDS YP_904005.1 118602790 4554733 complement(871125..871637) 1 NC_008610.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 871637 rplJ 4554733 rplJ Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L10 YP_904005.1 871125 R 413404 CDS YP_904006.1 118602791 4554734 complement(871827..872522) 1 NC_008610.1 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 872522 rplA 4554734 rplA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L1 YP_904006.1 871827 R 413404 CDS YP_904007.1 118602792 4554735 complement(872527..872955) 1 NC_008610.1 binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 872955 rplK 4554735 rplK Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L11 YP_904007.1 872527 R 413404 CDS YP_904008.1 118602793 4554736 complement(873044..873577) 1 NC_008610.1 KEGG: tcx:Tcr_0283 NusG antitermination factor; TIGRFAM: transcription termination/antitermination factor NusG; PFAM: transcription antitermination protein NusG; SMART: NGN domain protein; transcription antitermination protein nusG 873577 4554736 Rmag_0816 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) transcription antitermination protein nusG YP_904008.1 873044 R 413404 CDS YP_904009.1 118602794 4554737 complement(873588..873959) 1 NC_008610.1 TIGRFAM: preprotein translocase, SecE subunit; PFAM: protein secE/sec61-gamma protein; KEGG: tbd:Tbd_0392 SecE subunit of protein translocation complex; protein translocase subunit secE/sec61 gamma 873959 4554737 Rmag_0817 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein translocase subunit secE/sec61 gamma YP_904009.1 873588 R 413404 CDS YP_904010.1 118602795 4554738 complement(874128..875318) 1 NC_008610.1 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 875318 4554738 Rmag_0818 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) elongation factor Tu YP_904010.1 874128 R 413404 CDS YP_904011.1 118602796 4554739 complement(875718..876938) 1 NC_008610.1 PFAM: malic enzyme domain protein; malic enzyme, NAD-binding; KEGG: hch:HCH_05974 malic enzyme; malate dehydrogenase 876938 4554739 Rmag_0819 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) malate dehydrogenase YP_904011.1 875718 R 413404 CDS YP_904012.1 118602797 4554740 complement(879395..882208) 1 NC_008610.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase 882208 4554740 Rmag_0821 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycine dehydrogenase YP_904012.1 879395 R 413404 CDS YP_904013.1 118602798 4554741 complement(882317..882655) 1 NC_008610.1 PFAM: histidine triad (HIT) protein; KEGG: csa:Csal_0911 histidine triad (HIT) protein; histidine triad (HIT) protein 882655 4554741 Rmag_0822 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) histidine triad (HIT) protein YP_904013.1 882317 R 413404 CDS YP_904014.1 118602799 4554742 complement(883302..884432) 1 NC_008610.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: tcx:Tcr_1381 sulfide-quinone reductase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase 884432 4554742 Rmag_0824 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) FAD-dependent pyridine nucleotide-disulphide oxidoreductase YP_904014.1 883302 R 413404 CDS YP_904015.1 118602800 4554743 884970..885551 1 NC_008610.1 PFAM: nitroreductase; KEGG: reu:Reut_A1045 nitroreductase; hypothetical protein 885551 4554743 Rmag_0825 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904015.1 884970 D 413404 CDS YP_904016.1 118602801 4554744 complement(885977..886687) 1 NC_008610.1 PFAM: beta-lactamase domain protein; KEGG: dre:405865 zgc:85680; beta-lactamase domain-containing protein 886687 4554744 Rmag_0826 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) beta-lactamase domain-containing protein YP_904016.1 885977 R 413404 CDS YP_904017.1 118602802 4554745 complement(887536..888279) 1 NC_008610.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase 888279 4554745 Rmag_0828 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydrodipicolinate reductase YP_904017.1 887536 R 413404 CDS YP_904018.1 118602803 4554746 888615..888953 1 NC_008610.1 hypothetical protein 888953 4554746 Rmag_0829 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904018.1 888615 D 413404 CDS YP_904019.1 118602804 4554747 complement(891032..891865) 1 NC_008610.1 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 891865 4554747 Rmag_0831 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 2-dehydro-3-deoxyphosphooctonate aldolase YP_904019.1 891032 R 413404 CDS YP_904020.1 118602805 4554748 891934..892731 1 NC_008610.1 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 892731 trpC 4554748 trpC Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) indole-3-glycerol-phosphate synthase YP_904020.1 891934 D 413404 CDS YP_904021.1 118602806 4554749 892728..893138 1 NC_008610.1 PFAM: OsmC family protein; KEGG: mfa:Mfla_0380 OsmC-like protein; OsmC family protein 893138 4554749 Rmag_0833 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) OsmC family protein YP_904021.1 892728 D 413404 CDS YP_904022.1 118602807 4554672 893783..894565 1 NC_008610.1 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 894565 thiG 4554672 thiG Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thiazole synthase YP_904022.1 893783 D 413404 CDS YP_904023.1 118602808 4554673 894898..896037 1 NC_008610.1 PFAM: aminotransferase, class I and II; KEGG: pfl:PFL_5692 8-amino-7-oxononanoate synthase; 8-amino-7-oxononanoate synthase 896037 4554673 Rmag_0835 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 8-amino-7-oxononanoate synthase YP_904023.1 894898 D 413404 CDS YP_904024.1 118602809 4554674 896024..896761 1 NC_008610.1 PFAM: alpha/beta hydrolase fold; KEGG: sdn:Sden_3530 BioH protein; alpha/beta hydrolase fold 896761 4554674 Rmag_0836 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) alpha/beta hydrolase fold YP_904024.1 896024 D 413404 CDS YP_904025.1 118602810 4554675 896776..897267 1 NC_008610.1 KEGG: tcx:Tcr_1819 phosphoribosylaminoimidazole carboxylase, catalytic subunit; TIGRFAM: phosphoribosylaminoimidazole carboxylase, catalytic subunit; PFAM: 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR) carboxylase; phosphoribosylaminoimidazole carboxylase, catalytic subunit 897267 4554675 Rmag_0837 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribosylaminoimidazole carboxylase, catalytic subunit YP_904025.1 896776 D 413404 CDS YP_904026.1 118602811 4554676 897264..898355 1 NC_008610.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway; phosphoribosylaminoimidazole carboxylase ATPase subunit 898355 4554676 Rmag_0838 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoribosylaminoimidazole carboxylase ATPase subunit YP_904026.1 897264 D 413404 CDS YP_904027.1 118602812 4554677 complement(898359..898733) 1 NC_008610.1 PFAM: glutaredoxin; KEGG: pha:PSHAa0634 glutaredoxin; glutaredoxin 898733 4554677 Rmag_0839 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutaredoxin YP_904027.1 898359 R 413404 CDS YP_904028.1 118602813 4554678 complement(898730..899563) 1 NC_008610.1 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 899563 4554678 Rmag_0840 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase YP_904028.1 898730 R 413404 CDS YP_904029.1 118602814 4554679 complement(899567..900301) 1 NC_008610.1 KEGG: hdu:HD0334 3-deoxy-manno-octulosonate cytidylyltransferase; TIGRFAM: 3-deoxy-D-manno-octulosonate cytidylyltransferase; PFAM: acylneuraminate cytidylyltransferase; 3-deoxy-D-manno-octulosonate cytidylyltransferase 900301 4554679 Rmag_0841 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-deoxy-D-manno-octulosonate cytidylyltransferase YP_904029.1 899567 R 413404 CDS YP_904030.1 118602815 4554680 complement(900301..900480) 1 NC_008610.1 PFAM: protein of unknown function DUF343; KEGG: tfu:Tfu_2509 hypothetical protein; hypothetical protein 900480 4554680 Rmag_0842 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904030.1 900301 R 413404 CDS YP_904031.1 118602816 4554681 complement(900477..901424) 1 NC_008610.1 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 901424 lpxK 4554681 lpxK Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tetraacyldisaccharide 4'-kinase YP_904031.1 900477 R 413404 CDS YP_904032.1 118602817 4554682 901900..903135 1 NC_008610.1 TIGRFAM: lipoprotein releasing system, transmembrane protein, LolC/E family; PFAM: protein of unknown function DUF214; KEGG: mfa:Mfla_2095 lipoprotein releasing system, transmembrane protein, LolC/E family; LolC/E family lipoprotein releasing system, transmembrane protein 903135 4554682 Rmag_0844 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) LolC/E family lipoprotein releasing system, transmembrane protein YP_904032.1 901900 D 413404 CDS YP_904033.1 118602818 4554683 903128..903808 1 NC_008610.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: neu:NE1056 lipoprotein releasing system ATP-binding ABC transporter; ABC transporter related 903808 4554683 Rmag_0845 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_904033.1 903128 D 413404 CDS YP_904034.1 118602819 4554684 complement(905442..905801) 1 NC_008610.1 Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5); aspartate alpha-decarboxylase 905801 4554684 Rmag_0846 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aspartate alpha-decarboxylase YP_904034.1 905442 R 413404 CDS YP_904035.1 118602820 4554685 complement(905811..906941) 1 NC_008610.1 KEGG: cps:CPS_1050 oxaloacetate decarboxylase, beta subunit; TIGRFAM: sodium ion-translocating decarboxylase, beta subunit; PFAM: Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit; sodium ion-translocating decarboxylase, beta subunit 906941 4554685 Rmag_0847 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sodium ion-translocating decarboxylase, beta subunit YP_904035.1 905811 R 413404 CDS YP_904036.1 118602821 4554686 complement(906957..908786) 1 NC_008610.1 catalyzes the formation of pyruvate from oxaloacetate; oxaloacetate decarboxylase 908786 4554686 Rmag_0848 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) oxaloacetate decarboxylase YP_904036.1 906957 R 413404 CDS YP_904037.1 118602822 4554687 complement(908779..909033) 1 NC_008610.1 TIGRFAM: sodium pump decarboxylases, gamma subunit; PFAM: sodium pump decarboxylase, gamma subunit; sodium pump decarboxylases, gamma subunit 909033 4554687 Rmag_0849 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sodium pump decarboxylases, gamma subunit YP_904037.1 908779 R 413404 CDS YP_904038.1 118602823 4554688 complement(909149..909367) 1 NC_008610.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 909367 infA 4554688 infA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) translation initiation factor IF-1 YP_904038.1 909149 R 413404 CDS YP_904039.1 118602824 4554689 909537..910358 1 NC_008610.1 KEGG: reu:Reut_A0215 5,10-methylenetetrahydrofolate reductase; TIGRFAM: 5,10-methylenetetrahydrofolate reductase; PFAM: methylenetetrahydrofolate reductase; 5,10-methylenetetrahydrofolate reductase 910358 4554689 Rmag_0851 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 5,10-methylenetetrahydrofolate reductase YP_904039.1 909537 D 413404 CDS YP_904040.1 118602825 4554690 complement(910727..911170) 1 NC_008610.1 hypothetical protein 911170 4554690 Rmag_0852 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904040.1 910727 R 413404 CDS YP_904041.1 118602826 4554691 complement(911209..911955) 1 NC_008610.1 PFAM: Uroporphyrinogen III synthase HEM4; KEGG: mca:MCA3061 uroporphyrinogen-III synthase/uroporphyrin-III C-methyltransferase; uroporphyrinogen III synthase HEM4 911955 4554691 Rmag_0853 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) uroporphyrinogen III synthase HEM4 YP_904041.1 911209 R 413404 CDS YP_904042.1 118602827 4555011 complement(911959..912552) 1 NC_008610.1 hypothetical protein 912552 4555011 Rmag_0854 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904042.1 911959 R 413404 CDS YP_904043.1 118602828 4555012 912612..913565 1 NC_008610.1 TIGRFAM: Na+/Ca+ antiporter, CaCA family; PFAM: sodium/calcium exchanger membrane region; KEGG: tcx:Tcr_0977 K+-dependent Na+/Ca+ exchanger related-protein; CaCA family Na(+)/Ca(+) antiporter 913565 4555012 Rmag_0855 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CaCA family Na(+)/Ca(+) antiporter YP_904043.1 912612 D 413404 CDS YP_904044.1 118602829 4555013 913550..914020 1 NC_008610.1 PFAM: protein of unknown function UPF0079; KEGG: msu:MS1514 predicted ATPase or kinase; hypothetical protein 914020 4555013 Rmag_0856 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904044.1 913550 D 413404 CDS YP_904045.1 118602830 4555014 complement(915036..916736) 1 NC_008610.1 TIGRFAM: cobyrinic acid a,c-diamide synthase; PFAM: HesB/YadR/YfhF-family protein; Cobyrinic acid a,c-diamide synthase; CobB/CobQ domain protein glutamine amidotransferase; KEGG: tbd:Tbd_2473 cobyrinic acid a,c-diamide synthase CbiA; hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) / cobyrinate a,c-diamide synthase 916736 4555014 Rmag_0858 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) / cobyrinate a,c-diamide synthase YP_904045.1 915036 R 413404 CDS YP_904046.1 118602831 4555015 complement(916759..917961) 1 NC_008610.1 PFAM: Polysulphide reductase, NrfD; KEGG: tbd:Tbd_2474 molybdopterin oxidoreductase, membrane subunit; polysulphide reductase, NrfD 917961 4555015 Rmag_0859 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) polysulphide reductase, NrfD YP_904046.1 916759 R 413404 CDS YP_904047.1 118602832 4555016 complement(917987..918718) 1 NC_008610.1 TIGRFAM: Twin-arginine translocation pathway signal; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: tbd:Tbd_2475 iron-sulfur cluster protein; twin-arginine translocation pathway signal 918718 4555016 Rmag_0860 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) twin-arginine translocation pathway signal YP_904047.1 917987 R 413404 CDS YP_904048.1 118602833 4555017 complement(918715..919098) 1 NC_008610.1 KEGG: mag:amb3376 Hdr-like menaquinol oxidoreductase cytochrome c subunit; hypothetical protein 919098 4555017 Rmag_0861 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904048.1 918715 R 413404 CDS YP_904049.1 118602834 4555018 complement(919128..921092) 1 NC_008610.1 unknown function; putative glutamate synthase (NADPH) small subunit 921092 4555018 Rmag_0862 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative glutamate synthase (NADPH) small subunit YP_904049.1 919128 R 413404 CDS YP_904050.1 118602835 4555019 complement(921159..922715) 1 NC_008610.1 PFAM: protein of unknown function DUF224, cysteine-rich region domain protein; KEGG: tbd:Tbd_2478 reductase, iron-sulfur binding subunit, putative; hypothetical protein 922715 4555019 Rmag_0863 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904050.1 921159 R 413404 CDS YP_904051.1 118602836 4555020 complement(922717..923490) 1 NC_008610.1 PFAM: Nitrate reductase, gamma subunit; KEGG: tbd:Tbd_2479 putative DsrM protein; nitrate reductase, gamma subunit 923490 4555020 Rmag_0864 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) nitrate reductase, gamma subunit YP_904051.1 922717 R 413404 CDS YP_904052.1 118602837 4555021 complement(923564..923887) 1 NC_008610.1 PFAM: DsrC family protein; KEGG: mag:amb3372 dissimilatory sulfite reductase; DsrC family protein 923887 4555021 Rmag_0865 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DsrC family protein YP_904052.1 923564 R 413404 CDS YP_904053.1 118602838 4555022 complement(923914..924210) 1 NC_008610.1 PFAM: DsrH family protein; KEGG: tbd:Tbd_2481 DsrH protein; DsrH family protein 924210 4555022 Rmag_0866 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DsrH family protein YP_904053.1 923914 R 413404 CDS YP_904054.1 118602839 4555023 complement(924223..924621) 1 NC_008610.1 PFAM: DsrE family protein; KEGG: mag:amb3370 uncharacterized protein involved in the oxidation of intracellular sulfur; DsrE family protein 924621 4555023 Rmag_0867 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DsrE family protein YP_904054.1 924223 R 413404 CDS YP_904055.1 118602840 4555024 complement(924623..925024) 1 NC_008610.1 PFAM: DsrE family protein; KEGG: mag:amb3369 intracellular sulfur oxidation protein DsrE; DsrE family protein 925024 4555024 Rmag_0868 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DsrE family protein YP_904055.1 924623 R 413404 CDS YP_904056.1 118602841 4555025 complement(925037..926110) 1 NC_008610.1 KEGG: tbd:Tbd_2484 sulfite reductase, dissimilatory-type beta subunit; TIGRFAM: sulfite reductase, dissimilatory-type beta subunit; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin domain protein; nitrite and sulphite reductase 4Fe-4S region; sulfite reductase, dissimilatory-type beta subunit 926110 4555025 Rmag_0869 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sulfite reductase, dissimilatory-type beta subunit YP_904056.1 925037 R 413404 CDS YP_904057.1 118602842 4555026 complement(926183..927484) 1 NC_008610.1 KEGG: tbd:Tbd_2485 sulfite reductase, dissimilatory-type alpha subunit; TIGRFAM: sulfite reductase, dissimilatory-type alpha subunit; PFAM: nitrite and sulphite reductase 4Fe-4S region; sulfite reductase, dissimilatory-type alpha subunit 927484 4555026 Rmag_0870 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sulfite reductase, dissimilatory-type alpha subunit YP_904057.1 926183 R 413404 CDS YP_904058.1 118602843 4555027 complement(927703..929136) 1 NC_008610.1 TIGRFAM: glutamate synthases, NADH/NADPH, small subunit; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: rba:RB5653 NADH-glutamate synthase small chain; glutamate synthase (NADH) small subunit 929136 4555027 Rmag_0871 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutamate synthase (NADH) small subunit YP_904058.1 927703 R 413404 CDS YP_904059.1 118602844 4555028 929302..929655 1 NC_008610.1 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 929655 rplS 4555028 rplS Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L19 YP_904059.1 929302 D 413404 CDS YP_904060.1 118602845 4555029 complement(931477..931953) 1 NC_008610.1 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 931953 greA 4555029 greA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) transcription elongation factor GreA YP_904060.1 931477 R 413404 CDS YP_904061.1 118602846 4555030 complement(931953..935162) 1 NC_008610.1 TIGRFAM: carbamoyl-phosphate synthase, large subunit; PFAM: Carbamoyl-phosphate synthase L chain, ATP-binding; Carbamoyl-phosphate synthetase large chain, oligomerisation; Carbamoyl-phosphate synthetase large chain domain protein; MGS domain protein; RimK domain protein ATP-grasp; KEGG: noc:Noc_2572 carbamoyl-phosphate synthase, large subunit, glutamine-dependent; carbamoyl-phosphate synthase large subunit 935162 4555030 Rmag_0875 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) carbamoyl-phosphate synthase large subunit YP_904061.1 931953 R 413404 CDS YP_904062.1 118602847 4555031 complement(935184..935870) 1 NC_008610.1 PFAM: VacJ family lipoprotein; KEGG: noc:Noc_2787 VacJ-like lipoprotein; VacJ family lipoprotein 935870 4555031 Rmag_0876 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) VacJ family lipoprotein YP_904062.1 935184 R 413404 CDS YP_904063.1 118602848 4555032 complement(935867..936988) 1 NC_008610.1 TIGRFAM: carbamoyl-phosphate synthase, small subunit; PFAM: glutamine amidotransferase class-I; Carbamoyl-phosphate synthase, small chain; KEGG: vfi:VF0472 carbamoyl-phosphate synthase small chain; carbamoyl-phosphate synthase small subunit 936988 4555032 Rmag_0877 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) carbamoyl-phosphate synthase small subunit YP_904063.1 935867 R 413404 CDS YP_904064.1 118602849 4555033 937107..937376 1 NC_008610.1 KEGG: tcx:Tcr_0383 heavy metal transport/detoxification protein; heavy metal transport/detoxification protein 937376 4555033 Rmag_0878 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) heavy metal transport/detoxification protein YP_904064.1 937107 D 413404 CDS YP_904065.1 118602850 4555034 937373..937573 1 NC_008610.1 TIGRFAM: thiamine biosynthesis protein ThiS; PFAM: thiamineS protein; KEGG: csa:Csal_3147 thiamine biosynthesis protein ThiS; thiamine biosynthesis protein ThiS 937573 4555034 Rmag_0879 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) thiamine biosynthesis protein ThiS YP_904065.1 937373 D 413404 CDS YP_904066.1 118602851 4555035 complement(937616..938698) 1 NC_008610.1 KEGG: noc:Noc_2654 hypothetical protein; hypothetical protein 938698 4555035 Rmag_0880 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904066.1 937616 R 413404 CDS YP_904067.1 118602852 4555036 939512..939802 1 NC_008610.1 KEGG: vpa:VP1626 sulfite reductase, gamma subunit-related protein; sulfite reductase, gamma subunit-related protein 939802 4555036 Rmag_0881 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sulfite reductase, gamma subunit-related protein YP_904067.1 939512 D 413404 CDS YP_904068.1 118602853 4555037 complement(939811..942408) 1 NC_008610.1 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 942408 alaS 4555037 alaS Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) alanyl-tRNA synthetase YP_904068.1 939811 R 413404 CDS YP_904069.1 118602854 4555038 943128..944975 1 NC_008610.1 TIGRFAM: glucosamine--fructose-6-phosphate aminotransferase, isomerizing; PFAM: glutamine amidotransferase, class-II; sugar isomerase (SIS); KEGG: tcx:Tcr_1692 glucosamine--fructose-6-phosphate aminotransferase, isomerizing; glutamine--fructose-6-phosphate transaminase 944975 4555038 Rmag_0883 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutamine--fructose-6-phosphate transaminase YP_904069.1 943128 D 413404 CDS YP_904070.1 118602855 4555039 944985..946220 1 NC_008610.1 catalyzes the formation of D-fructose 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate isomerase 946220 4555039 Rmag_0884 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glucose-6-phosphate isomerase YP_904070.1 944985 D 413404 CDS YP_904071.1 118602856 4555040 946217..947047 1 NC_008610.1 TIGRFAM: UTP-glucose-1-phosphate uridylyltransferase; PFAM: Nucleotidyl transferase; KEGG: tdn:Tmden_1473 UTP--glucose-1-phosphate uridylyltransferase; UDP-glucose pyrophosphorylase 947047 4555040 Rmag_0885 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-glucose pyrophosphorylase YP_904071.1 946217 D 413404 CDS YP_904072.1 118602857 4555041 complement(947071..948969) 1 NC_008610.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; dTDP-4-dehydrorhamnose reductase; Male sterility C-terminal domain; KEGG: cps:CPS_0594 polysaccharide biosynthesis protein; polysaccharide biosynthesis protein CapD 948969 4555041 Rmag_0886 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) polysaccharide biosynthesis protein CapD YP_904072.1 947071 R 413404 CDS YP_904073.1 118602858 4555042 complement(948984..949544) 1 NC_008610.1 PFAM: sugar transferase; KEGG: dar:Daro_1277 sugar transferase; sugar transferase 949544 4555042 Rmag_0887 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sugar transferase YP_904073.1 948984 R 413404 CDS YP_904074.1 118602859 4555043 complement(950432..951175) 1 NC_008610.1 PFAM: glycosyl transferase, family 2; KEGG: hpy:HP0102 hypothetical protein; glycosyl transferase family protein 951175 4555043 Rmag_0889 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycosyl transferase family protein YP_904074.1 950432 R 413404 CDS YP_904075.1 118602860 4555044 complement(951172..952320) 1 NC_008610.1 PFAM: glycosyl transferase, group 1; KEGG: dge:Dgeo_2669 glycosyl transferase, group 1; glycosyl transferase, group 1 952320 4555044 Rmag_0890 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycosyl transferase, group 1 YP_904075.1 951172 R 413404 CDS YP_904076.1 118602861 4555045 complement(953316..954080) 1 NC_008610.1 PFAM: glycosyl transferase, family 2; KEGG: hpy:HP0102 hypothetical protein; glycosyl transferase family protein 954080 4555045 Rmag_0891 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycosyl transferase family protein YP_904076.1 953316 R 413404 CDS YP_904077.1 118602862 4555046 complement(954598..955236) 1 NC_008610.1 KEGG: cpe:CPE0622 hypothetical protein; hypothetical protein 955236 4555046 Rmag_0892 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904077.1 954598 R 413404 CDS YP_904078.1 118602863 4555047 complement(955226..955681) 1 NC_008610.1 TIGRFAM: cytidyltransferase-related domain; PFAM: Riboflavin kinase / FAD synthetase; cytidylyltransferase; KEGG: msu:MS0658 cytidylyltransferase; glycerol-3-phosphate cytidylyltransferase 955681 4555047 Rmag_0893 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycerol-3-phosphate cytidylyltransferase YP_904078.1 955226 R 413404 CDS YP_904079.1 118602864 4555048 complement(955686..956630) 1 NC_008610.1 KEGG: ava:Ava_1042 methyltransferase FkbM; methyltransferase FkbM 956630 4555048 Rmag_0894 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) methyltransferase FkbM YP_904079.1 955686 R 413404 CDS YP_904080.1 118602865 4555049 complement(956721..957371) 1 NC_008610.1 hypothetical protein 957371 4555049 Rmag_0895 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904080.1 956721 R 413404 CDS YP_904081.1 118602866 4555089 complement(957611..958744) 1 NC_008610.1 KEGG: pub:SAR11_0530 cyclopropane-fatty-acyl-phospholipid synthase (CMAS family); hypothetical protein 958744 4555089 Rmag_0896 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904081.1 957611 R 413404 CDS YP_904082.1 118602867 4555090 complement(958744..960315) 1 NC_008610.1 KEGG: pmi:PMT9312_1328 hypothetical protein; hypothetical protein 960315 4555090 Rmag_0897 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904082.1 958744 R 413404 CDS YP_904083.1 118602868 4555091 complement(960317..960664) 1 NC_008610.1 KEGG: mth:MTH1523 glucose-1-phosphate adenylyltransferase related protein; glucose-1-phosphate adenylyltransferase related protein 960664 4555091 Rmag_0898 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glucose-1-phosphate adenylyltransferase related protein YP_904083.1 960317 R 413404 CDS YP_904084.1 118602869 4555092 complement(960675..961820) 1 NC_008610.1 KEGG: lmf:LMOf2365_0663 hypothetical protein; hypothetical protein 961820 4555092 Rmag_0899 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904084.1 960675 R 413404 CDS YP_904085.1 118602870 4555093 complement(961847..962338) 1 NC_008610.1 KEGG: aae:aq_2171 putative 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase; putative 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase 962338 4555093 Rmag_0900 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase YP_904085.1 961847 R 413404 CDS YP_904086.1 118602871 4555094 complement(962328..963656) 1 NC_008610.1 PFAM: polysaccharide biosynthesis protein; KEGG: cch:Cag_0665 probable polysaccharide biosynthesis protein; polysaccharide biosynthesis protein 963656 4555094 Rmag_0901 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) polysaccharide biosynthesis protein YP_904086.1 962328 R 413404 CDS YP_904087.1 118602872 4555095 complement(963646..964602) 1 NC_008610.1 PFAM: NAD-dependent epimerase/dehydratase; KEGG: dps:DP0023 probable GDP-L-fucose synthetase; NAD-dependent epimerase/dehydratase 964602 4555095 Rmag_0902 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NAD-dependent epimerase/dehydratase YP_904087.1 963646 R 413404 CDS YP_904088.1 118602873 4555096 complement(964613..965704) 1 NC_008610.1 TIGRFAM: GDP-mannose 4,6-dehydratase; PFAM: NAD-dependent epimerase/dehydratase; KEGG: tbd:Tbd_1776 GDP-mannose 4,6-dehydratase; GDP-mannose 4,6-dehydratase 965704 4555096 Rmag_0903 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GDP-mannose 4,6-dehydratase YP_904088.1 964613 R 413404 CDS YP_904089.1 118602874 4555097 complement(965758..967176) 1 NC_008610.1 KEGG: csa:Csal_1692 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; TIGRFAM: mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; PFAM: mannose-6-phosphate isomerase, type II; Nucleotidyl transferase; Cupin 2, conserved barrel domain protein; mannose-1-phosphate guanylyltransferase (GDP) 967176 4555097 Rmag_0904 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) mannose-1-phosphate guanylyltransferase (GDP) YP_904089.1 965758 R 413404 CDS YP_904090.1 118602875 4555098 967571..968275 1 NC_008610.1 KEGG: par:Psyc_1205 hypothetical protein; hypothetical protein 968275 4555098 Rmag_0905 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904090.1 967571 D 413404 CDS YP_904091.1 118602876 4555099 969710..970498 1 NC_008610.1 PFAM: glycosyl transferase, family 25; KEGG: ppr:PBPRA0217 putative Lex2B protein (lipooligosaccharide 5G8 epitope biosynthesis-associated protein); glycosyl transferase family protein 970498 4555099 Rmag_0907 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycosyl transferase family protein YP_904091.1 969710 D 413404 CDS YP_904092.1 118602877 4555100 complement(970509..971744) 1 NC_008610.1 PFAM: O-antigen polymerase; KEGG: hin:HI0874 hypothetical protein; O-antigen polymerase 971744 4555100 Rmag_0908 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) O-antigen polymerase YP_904092.1 970509 R 413404 CDS YP_904093.1 118602878 4555101 971787..973436 1 NC_008610.1 catalyzes a two-step reaction, first charging a glutamine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; glutaminyl-tRNA synthetase 973436 4555101 Rmag_0909 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutaminyl-tRNA synthetase YP_904093.1 971787 D 413404 CDS YP_904094.1 118602879 4555102 complement(974772..975515) 1 NC_008610.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE 975515 surE 4555102 surE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) stationary phase survival protein SurE YP_904094.1 974772 R 413404 CDS YP_904095.1 118602880 4555103 complement(975539..977761) 1 NC_008610.1 PFAM: AAA ATPase, central domain protein; Clp N terminal domain protein; ATPase associated with various cellular activities, AAA_5; ATPase AAA-2 domain protein; SMART: AAA ATPase; KEGG: mca:MCA1789 ATP-dependent Clp protease, ATP-binding subunit ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA 977761 4555103 Rmag_0911 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP-dependent Clp protease ATP-binding subunit ClpA YP_904095.1 975539 R 413404 CDS YP_904096.1 118602881 4555104 complement(977769..978068) 1 NC_008610.1 PFAM: ATP-dependent Clp protease adaptor protein ClpS; KEGG: nha:Nham_2417 ATP-dependent Clp protease adaptor protein ClpS; ATP-dependent Clp protease adaptor protein ClpS 978068 4555104 Rmag_0912 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP-dependent Clp protease adaptor protein ClpS YP_904096.1 977769 R 413404 CDS YP_904097.1 118602882 4555105 complement(978071..979153) 1 NC_008610.1 PFAM: permease YjgP/YjgQ family protein; KEGG: noc:Noc_1909 permease YjgP/YjgQ; permease YjgP/YjgQ family protein 979153 4555105 Rmag_0913 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) permease YjgP/YjgQ family protein YP_904097.1 978071 R 413404 CDS YP_904098.1 118602883 4555106 979196..980761 1 NC_008610.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase 980761 guaA 4555106 guaA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GMP synthase YP_904098.1 979196 D 413404 CDS YP_904099.1 118602884 4555107 980752..981222 1 NC_008610.1 PFAM: CMP/dCMP deaminase, zinc-binding; KEGG: pha:PSHAa2333 tRNA-specific adenosine deaminase; CMP/dCMP deaminase, zinc-binding 981222 4555107 Rmag_0915 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CMP/dCMP deaminase, zinc-binding YP_904099.1 980752 D 413404 CDS YP_904100.1 118602885 4555177 complement(981816..982562) 1 NC_008610.1 TIGRFAM: 3-oxoacyl-(acyl-carrier-protein) reductase; PFAM: short-chain dehydrogenase/reductase SDR; KEGG: tcx:Tcr_0712 3-oxoacyl-(acyl-carrier-protein) reductase; 3-oxoacyl-[acyl-carrier-protein] reductase 982562 4555177 Rmag_0916 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-oxoacyl-[acyl-carrier-protein] reductase YP_904100.1 981816 R 413404 CDS YP_904101.1 118602886 4555178 complement(982559..983491) 1 NC_008610.1 TIGRFAM: malonyl CoA-acyl carrier protein transacylase; KEGG: tcx:Tcr_0711 malonyl CoA-acyl carrier protein transacylase; [Acyl-carrier-protein] S-malonyltransferase 983491 4555178 Rmag_0917 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) [Acyl-carrier-protein] S-malonyltransferase YP_904101.1 982559 R 413404 CDS YP_904102.1 118602887 4555179 complement(983580..983837) 1 NC_008610.1 involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 983837 rpmA 4555179 rpmA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L27 YP_904102.1 983580 R 413404 CDS YP_904103.1 118602888 4555180 complement(983849..984160) 1 NC_008610.1 PFAM: ribosomal protein L21; KEGG: pfo:Pfl_4860 ribosomal protein L21; 50S ribosomal protein L21 984160 rplU 4555180 rplU Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L21 YP_904103.1 983849 R 413404 CDS YP_904104.1 118602889 4555181 984288..984776 1 NC_008610.1 PFAM: peptidyl-prolyl cis-trans isomerase, cyclophilin type; KEGG: ppu:PP2903 peptidyl-prolyl cis-trans isomerase B; peptidyl-prolyl cis-trans isomerase, cyclophilin type 984776 4555181 Rmag_0920 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidyl-prolyl cis-trans isomerase, cyclophilin type YP_904104.1 984288 D 413404 CDS YP_904105.1 118602890 4555182 984776..985495 1 NC_008610.1 TIGRFAM: UDP-2,3-diacylglucosamine hydrolase; PFAM: metallophosphoesterase; KEGG: hdu:HD1938 UDP-2,3 diacylglucosamine hydrolase; UDP-2,3-diacylglucosamine hydrolase 985495 4555182 Rmag_0921 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-2,3-diacylglucosamine hydrolase YP_904105.1 984776 D 413404 CDS YP_904106.1 118602891 4555183 complement(985460..987265) 1 NC_008610.1 PFAM: ribonuclease II; KEGG: ftu:FTT0257 ribonuclease II family protein; ribonuclease II 987265 4555183 Rmag_0922 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonuclease II YP_904106.1 985460 R 413404 CDS YP_904107.1 118602892 4555184 complement(987273..987647) 1 NC_008610.1 part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor; glycine cleavage system protein H 987647 4555184 Rmag_0923 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycine cleavage system protein H YP_904107.1 987273 R 413404 CDS YP_904108.1 118602893 4555185 complement(987691..988767) 1 NC_008610.1 catalyzes the transfer of a methylene carbon from the methylamine-loaded GcvH protein to tetrahydrofolate, causing the release of ammonia and the generation of reduced GcvH protein; glycine cleavage system aminomethyltransferase T 988767 gcvT 4555185 gcvT Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glycine cleavage system aminomethyltransferase T YP_904108.1 987691 R 413404 CDS YP_904109.1 118602894 4555186 complement(988767..989417) 1 NC_008610.1 PFAM: Intracellular septation protein A; KEGG: mca:MCA1646 intracellular septation protein A; intracellular septation protein A 989417 4555186 Rmag_0925 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) intracellular septation protein A YP_904109.1 988767 R 413404 CDS YP_904110.1 118602895 4555187 complement(989421..989666) 1 NC_008610.1 hypothetical protein 989666 4555187 Rmag_0926 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904110.1 989421 R 413404 CDS YP_904111.1 118602896 4555188 990023..990430 1 NC_008610.1 TIGRFAM: putative endoribonuclease L-PSP; PFAM: Endoribonuclease L-PSP; KEGG: sde:Sde_3698 peptidase S1C, Do; putative endoribonuclease L-PSP 990430 4555188 Rmag_0927 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative endoribonuclease L-PSP YP_904111.1 990023 D 413404 CDS YP_904112.1 118602897 4555189 990509..992569 1 NC_008610.1 PFAM: helicase domain protein; nucleic acid binding, OB-fold, tRNA/helicase-type; DEAD/DEAH box helicase domain protein; KEGG: csa:Csal_3245 ATP-dependent DNA helicase RecG; DEAD/DEAH box helicase domain-containing protein 992569 4555189 Rmag_0928 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DEAD/DEAH box helicase domain-containing protein YP_904112.1 990509 D 413404 CDS YP_904113.1 118602898 4555190 992601..993074 1 NC_008610.1 PFAM: Chorismate lyase; KEGG: pha:PSHAa2311 chorismate pyruvate lyase UbiC; chorismate lyase 993074 4555190 Rmag_0929 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) chorismate lyase YP_904113.1 992601 D 413404 CDS YP_904114.1 118602899 4555191 993111..993824 1 NC_008610.1 TIGRFAM: putative methyltransferase; PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: sbo:SBO_1132 hypothetical protein; putative methyltransferase 993824 4555191 Rmag_0930 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative methyltransferase YP_904114.1 993111 D 413404 CDS YP_904115.1 118602900 4555192 993833..994420 1 NC_008610.1 TIGRFAM: glutamine amidotransferase of anthranilate synthase; PFAM: glutamine amidotransferase class-I; KEGG: hch:HCH_06126 anthranilate/para-aminobenzoate synthases component II; anthranilate synthase, component II 994420 4555192 Rmag_0931 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) anthranilate synthase, component II YP_904115.1 993833 D 413404 CDS YP_904116.1 118602901 4555193 994424..994843 1 NC_008610.1 PFAM: Rhodanese domain protein; KEGG: tbd:Tbd_2399 rhodanese-like protein; rhodanese domain-containing protein 994843 4555193 Rmag_0932 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) rhodanese domain-containing protein YP_904116.1 994424 D 413404 CDS YP_904117.1 118602902 4555194 994850..995098 1 NC_008610.1 PFAM: glutaredoxin; KEGG: wol:WD0758 glutaredoxin family protein; glutaredoxin 995098 4555194 Rmag_0933 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutaredoxin YP_904117.1 994850 D 413404 CDS YP_904118.1 118602903 4555195 995101..996069 1 NC_008610.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 996069 gpsA 4555195 gpsA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase YP_904118.1 995101 D 413404 CDS YP_904119.1 118602904 4555196 complement(997190..997585) 1 NC_008610.1 PFAM: ribosomal protein S9; KEGG: cps:CPS_4442 ribosomal protein S9; 30S ribosomal protein S9 997585 4555196 Rmag_0935 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S9 YP_904119.1 997190 R 413404 CDS YP_904120.1 118602905 4554770 complement(997600..998028) 1 NC_008610.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 998028 rplM 4554770 rplM Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L13 YP_904120.1 997600 R 413404 CDS YP_904121.1 118602906 4554771 complement(998144..999739) 1 NC_008610.1 PFAM: sulfatase; protein of unknown function DUF1705; KEGG: pfo:Pfl_3156 hypothetical protein; phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase 999739 4554771 Rmag_0937 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase YP_904121.1 998144 R 413404 CDS YP_904122.1 118602907 4554772 1000436..1000999 1 NC_008610.1 PFAM: Redoxin domain protein; KEGG: tcx:Tcr_0234 hypothetical protein; redoxin domain-containing protein 1000999 4554772 Rmag_0939 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) redoxin domain-containing protein YP_904122.1 1000436 D 413404 CDS YP_904123.1 118602908 4554773 1002704..1004524 1 NC_008610.1 PFAM: helicase domain protein; DbpA, RNA-binding domain protein; DEAD/DEAH box helicase domain protein; KEGG: sde:Sde_3034 ATP-dependent RNA helicase DeaD; DEAD/DEAH box helicase domain-containing protein 1004524 4554773 Rmag_0942 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DEAD/DEAH box helicase domain-containing protein YP_904123.1 1002704 D 413404 CDS YP_904124.1 118602909 4554774 1006158..1006361 1 NC_008610.1 PFAM: Cold-shock protein, DNA-binding; SMART: Cold shock protein; KEGG: bca:BCE5298 cold shock protein CspC; cold-shock DNA-binding protein family protein 1006361 4554774 Rmag_0944 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) cold-shock DNA-binding protein family protein YP_904124.1 1006158 D 413404 CDS YP_904125.1 118602910 4554775 complement(1006765..1007016) 1 NC_008610.1 hypothetical protein 1007016 4554775 Rmag_0945 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904125.1 1006765 R 413404 CDS YP_904126.1 118602911 4554776 1008296..1009711 1 NC_008610.1 KEGG: ppr:PBPRA1693 putative exonuclease I; PFAM: Exonuclease, RNase T and DNA polymerase III; Exonuclease C-terminal domain protein; SMART: Exonuclease; exodeoxyribonuclease I subunit C 1009711 4554776 Rmag_0946 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) exodeoxyribonuclease I subunit C YP_904126.1 1008296 D 413404 CDS YP_904127.1 118602912 4554777 1009779..1010411 1 NC_008610.1 KEGG: tcx:Tcr_1030 endonuclease III; TIGRFAM: endonuclease III; PFAM: helix-hairpin-helix motif; HhH-GPD family protein; SMART: iron-sulfur cluster loop; DNA-(apurinic or apyrimidinic site) lyase / endonuclease III 1010411 4554777 Rmag_0947 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA-(apurinic or apyrimidinic site) lyase / endonuclease III YP_904127.1 1009779 D 413404 CDS YP_904128.1 118602913 4554778 1010778..1011632 1 NC_008610.1 PFAM: aminoglycoside phosphotransferase; fructosamine kinase; KEGG: ath:At3g61080 fructosamine kinase family protein; fructosamine kinase 1011632 4554778 Rmag_0948 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) fructosamine kinase YP_904128.1 1010778 D 413404 CDS YP_904129.1 118602914 4554779 complement(1011849..1012469) 1 NC_008610.1 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 1012469 hisH 4554779 hisH Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) imidazole glycerol phosphate synthase subunit HisH YP_904129.1 1011849 R 413404 CDS YP_904130.1 118602915 4554780 complement(1012476..1013054) 1 NC_008610.1 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 1013054 hisB 4554780 hisB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) imidazoleglycerol-phosphate dehydratase YP_904130.1 1012476 R 413404 CDS YP_904131.1 118602916 4554781 complement(1013293..1014318) 1 NC_008610.1 KEGG: tcx:Tcr_0800 aspartate-semialdehyde dehydrogenase, USG-1 related; TIGRFAM: aspartate-semialdehyde dehydrogenase; PFAM: Semialdehyde dehydrogenase, NAD - binding; Semialdehyde dehydrogenase, dimerisation region; aspartate semialdehyde dehydrogenase 1014318 4554781 Rmag_0951 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) aspartate semialdehyde dehydrogenase YP_904131.1 1013293 R 413404 CDS YP_904132.1 118602917 4554782 complement(1014735..1015475) 1 NC_008610.1 PFAM: protein of unknown function DUF34; KEGG: nmu:Nmul_A0806 protein of unknown function DUF34; hypothetical protein 1015475 4554782 Rmag_0952 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904132.1 1014735 R 413404 CDS YP_904133.1 118602918 4554783 complement(1015462..1016523) 1 NC_008610.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase 1016523 4554783 Rmag_0953 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) histidinol-phosphate aminotransferase YP_904133.1 1015462 R 413404 CDS YP_904134.1 118602919 4554784 complement(1016520..1017272) 1 NC_008610.1 PFAM: Phosphomethylpyrimidine kinase type-1; KEGG: ppu:PP4782 phosphomethylpyrimidine kinase; phosphomethylpyrimidine kinase type-1 1017272 4554784 Rmag_0954 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphomethylpyrimidine kinase type-1 YP_904134.1 1016520 R 413404 CDS YP_904135.1 118602920 4554785 complement(1017265..1017882) 1 NC_008610.1 PFAM: DSBA oxidoreductase; KEGG: mca:MCA2602 thiol:disulfide interchange protein DsbA; DSBA oxidoreductase 1017882 4554785 Rmag_0955 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DSBA oxidoreductase YP_904135.1 1017265 R 413404 CDS YP_904136.1 118602921 4554786 complement(1017885..1018367) 1 NC_008610.1 TIGRFAM: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase; PFAM: 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK; KEGG: noc:Noc_0038 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase, HppK; 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase 1018367 4554786 Rmag_0956 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase YP_904136.1 1017885 R 413404 CDS YP_904137.1 118602922 4554787 complement(1018360..1018719) 1 NC_008610.1 TIGRFAM: dihydroneopterin aldolase; KEGG: mca:MCA2988 dihydroneopterin aldolase; dihydroneopterin aldolase 1018719 4554787 Rmag_0957 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydroneopterin aldolase YP_904137.1 1018360 R 413404 CDS YP_904138.1 118602923 4554788 1018774..1019367 1 NC_008610.1 PFAM: protein of unknown function DUF205; KEGG: tcx:Tcr_1811 protein of unknown function DUF205; acyl-phosphate glycerol-3-phosphate acyltransferase 1019367 4554788 Rmag_0958 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acyl-phosphate glycerol-3-phosphate acyltransferase YP_904138.1 1018774 D 413404 CDS YP_904139.1 118602924 4555050 complement(1020244..1021002) 1 NC_008610.1 PFAM: ABC-2 type transporter; KEGG: ppr:PBPRA3177 putative permease; ABC-2 type transporter 1021002 4555050 Rmag_0960 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC-2 type transporter YP_904139.1 1020244 R 413404 CDS YP_904140.1 118602925 4555051 complement(1021002..1021919) 1 NC_008610.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: ilo:IL2259 ABC-type multidrug transport system, ATPase component; ABC transporter related 1021919 4555051 Rmag_0961 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_904140.1 1021002 R 413404 CDS YP_904141.1 118602926 4555052 1022029..1023537 1 NC_008610.1 PFAM: biotin/lipoyl attachment domain-containing protein; catalytic domain of components of various dehydrogenase complexes; E3 binding domain protein; KEGG: ftl:FTL_0310 pyruvate dehydrogenase, E2 component; dehydrogenase catalytic domain-containing protein 1023537 4555052 Rmag_0962 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dehydrogenase catalytic domain-containing protein YP_904141.1 1022029 D 413404 CDS YP_904142.1 118602927 4555053 1023534..1024949 1 NC_008610.1 TIGRFAM: dihydrolipoamide dehydrogenase; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; glucose-inhibited division protein A; pyridine nucleotide-disulphide oxidoreductase dimerisation region; KEGG: tcx:Tcr_1003 dihydrolipoamide dehydrogenase; dihydrolipoamide dehydrogenase 1024949 4555053 Rmag_0963 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydrolipoamide dehydrogenase YP_904142.1 1023534 D 413404 CDS YP_904143.1 118602928 4555054 1024946..1025599 1 NC_008610.1 PFAM: protein-L-isoaspartate(D-aspartate) O-methyltransferase; Methyltransferase type 11; KEGG: dar:Daro_3924 protein-L-isoaspartate(D-aspartate) O-methyltransferase:O-methyltransferase, family 3; protein-L-isoaspartate(D-aspartate) O-methyltransferase 1025599 4555054 Rmag_0964 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein-L-isoaspartate(D-aspartate) O-methyltransferase YP_904143.1 1024946 D 413404 CDS YP_904144.1 118602929 4555055 1025603..1027984 1 NC_008610.1 KEGG: sde:Sde_3357 putative integral membrane protein; putative integral membrane protein 1027984 4555055 Rmag_0965 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative integral membrane protein YP_904144.1 1025603 D 413404 CDS YP_904145.1 118602930 4555056 1028040..1029623 1 NC_008610.1 KEGG: noc:Noc_2467 L-aspartate oxidase; TIGRFAM: L-aspartate oxidase; PFAM: fumarate reductase/succinate dehydrogenase flavoprotein domain protein; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; L-aspartate oxidase 1029623 4555056 Rmag_0966 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) L-aspartate oxidase YP_904145.1 1028040 D 413404 CDS YP_904146.1 118602931 4555057 1029595..1030152 1 NC_008610.1 KEGG: nma:NMA0164 polypeptide deformylase; TIGRFAM: peptide deformylase; PFAM: formylmethionine deformylase; peptide deformylase 1030152 4555057 Rmag_0967 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptide deformylase YP_904146.1 1029595 D 413404 CDS YP_904147.1 118602932 4555058 1030617..1030847 1 NC_008610.1 PFAM: helix-turn-helix, Fis-type; KEGG: mfa:Mfla_0350 helix-turn-helix, fis-type; helix-turn-helix, Fis-type 1030847 4555058 Rmag_0968 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) helix-turn-helix, Fis-type YP_904147.1 1030617 D 413404 CDS YP_904148.1 118602933 4555059 1030888..1032429 1 NC_008610.1 involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase 1032429 purH 4555059 purH Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase YP_904148.1 1030888 D 413404 CDS YP_904149.1 118602934 4555060 1033738..1034295 1 NC_008610.1 PFAM: 5-formyltetrahydrofolate cyclo-ligase; KEGG: csa:Csal_0021 5-formyltetrahydrofolate cyclo-ligase; 5-formyltetrahydrofolate cyclo-ligase 1034295 4555060 Rmag_0971 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 5-formyltetrahydrofolate cyclo-ligase YP_904149.1 1033738 D 413404 CDS YP_904150.1 118602935 4555061 complement(1034705..1035886) 1 NC_008610.1 TIGRFAM: Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; PFAM: monooxygenase, FAD-binding; KEGG: tcx:Tcr_1557 ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase 1035886 4555061 Rmag_0972 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase YP_904150.1 1034705 R 413404 CDS YP_904151.1 118602936 4555062 complement(1035886..1037205) 1 NC_008610.1 PFAM: peptidase U62, modulator of DNA gyrase; KEGG: mca:MCA0383 PmbA protein; peptidase U62, modulator of DNA gyrase 1037205 4555062 Rmag_0973 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidase U62, modulator of DNA gyrase YP_904151.1 1035886 R 413404 CDS YP_904152.1 118602937 4555063 complement(1037213..1037974) 1 NC_008610.1 KEGG: tcx:Tcr_0203 hypothetical protein; hypothetical protein 1037974 4555063 Rmag_0974 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904152.1 1037213 R 413404 CDS YP_904153.1 118602938 4555064 complement(1037974..1038822) 1 NC_008610.1 PFAM: CBS domain containing protein; transporter-associated region; KEGG: hch:HCH_05351 putative Mg2+ and Co2+ transporter CorC; CBS domain-containing protein 1038822 4555064 Rmag_0975 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CBS domain-containing protein YP_904153.1 1037974 R 413404 CDS YP_904154.1 118602939 4555065 complement(1038861..1039157) 1 NC_008610.1 PFAM: protein of unknown function UPF0125; KEGG: dar:Daro_2340 hypothetical protein; hypothetical protein 1039157 4555065 Rmag_0976 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904154.1 1038861 R 413404 CDS YP_904155.1 118602940 4555066 complement(1039147..1039878) 1 NC_008610.1 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 1039878 4555066 Rmag_0977 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase YP_904155.1 1039147 R 413404 CDS YP_904156.1 118602941 4555067 complement(1040476..1040907) 1 NC_008610.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: ilo:IL1434 lactoylglutathione lyase; glyoxalase/bleomycin resistance protein/dioxygenase 1040907 4555067 Rmag_0978 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glyoxalase/bleomycin resistance protein/dioxygenase YP_904156.1 1040476 R 413404 CDS YP_904157.1 118602942 4555068 complement(1042886..1043956) 1 NC_008610.1 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; putative DNA-binding/iron metalloprotein/AP endonuclease 1043956 4555068 Rmag_0980 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) putative DNA-binding/iron metalloprotein/AP endonuclease YP_904157.1 1042886 R 413404 CDS YP_904158.1 118602943 4555069 complement(1043949..1044674) 1 NC_008610.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: pae:PA4461 probable ATP-binding component of ABC transporter; ABC transporter related 1044674 4555069 Rmag_0981 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ABC transporter related YP_904158.1 1043949 R 413404 CDS YP_904159.1 118602944 4554933 complement(1044987..1045739) 1 NC_008610.1 TIGRFAM: biotin--acetyl-CoA-carboxylase ligase; PFAM: biotin protein ligase domain protein; biotin/lipoate A/B protein ligase; KEGG: cbu:CBU_1002 birA bifunctional protein; biotin--acetyl-CoA-carboxylase ligase 1045739 4554933 Rmag_0982 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) biotin--acetyl-CoA-carboxylase ligase YP_904159.1 1044987 R 413404 CDS YP_904160.1 118602945 4554934 complement(1045718..1046074) 1 NC_008610.1 PFAM: diacylglycerol kinase; KEGG: hdu:HD1253 diacylglycerol kinase; diacylglycerol kinase 1046074 4554934 Rmag_0983 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) diacylglycerol kinase YP_904160.1 1045718 R 413404 CDS YP_904161.1 118602946 4554935 1046122..1046865 1 NC_008610.1 KEGG: pfo:Pfl_1896 pseudouridylate synthase; TIGRFAM: tRNA pseudouridine synthase A; PFAM: tRNA pseudouridine synthase; tRNA pseudouridine synthase A 1046865 4554935 Rmag_0984 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA pseudouridine synthase A YP_904161.1 1046122 D 413404 CDS YP_904162.1 118602947 4554936 complement(1046867..1049143) 1 NC_008610.1 catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine; 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase 1049143 4554936 Rmag_0985 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase YP_904162.1 1046867 R 413404 CDS YP_904163.1 118602948 4554937 1049242..1050135 1 NC_008610.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bur:Bcep18194_B0361 transcriptional regulator, LysR family; LysR family transcriptional regulator 1050135 4554937 Rmag_0986 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) LysR family transcriptional regulator YP_904163.1 1049242 D 413404 CDS YP_904164.1 118602949 4554938 1050238..1052181 1 NC_008610.1 PFAM: Citrate transporter; TrkA-C domain protein; KEGG: sru:SRU_1767 putative sodium-dependent transporter; citrate transporter 1052181 4554938 Rmag_0987 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) citrate transporter YP_904164.1 1050238 D 413404 CDS YP_904165.1 118602950 4554939 1052209..1052814 1 NC_008610.1 PFAM: carbonic anhydrase; KEGG: aci:ACIAD1056 putative carbonic anhydrase; carbonic anhydrase 1052814 4554939 Rmag_0988 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) carbonic anhydrase YP_904165.1 1052209 D 413404 CDS YP_904166.1 118602951 4554940 complement(1052847..1053416) 1 NC_008610.1 TIGRFAM: 16S rRNA processing protein RimM; PFAM: RimM protein; PRC-barrel domain protein; KEGG: noc:Noc_2259 16S rRNA processing protein RimM; 16S rRNA processing protein RimM 1053416 4554940 Rmag_0989 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 16S rRNA processing protein RimM YP_904166.1 1052847 R 413404 CDS YP_904167.1 118602952 4554941 complement(1053394..1053669) 1 NC_008610.1 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 1053669 rpsP 4554941 rpsP Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S16 YP_904167.1 1053394 R 413404 CDS YP_904168.1 118602953 4554942 complement(1053729..1055105) 1 NC_008610.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 1055105 4554942 Rmag_0991 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) adenylosuccinate lyase YP_904168.1 1053729 R 413404 CDS YP_904169.1 118602954 4554943 1055216..1057774 1 NC_008610.1 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 1057774 4554943 Rmag_0992 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase YP_904169.1 1055216 D 413404 CDS YP_904170.1 118602955 4554944 complement(1057827..1057982) 1 NC_008610.1 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 1057982 rpmG 4554944 rpmG Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L33 YP_904170.1 1057827 R 413404 CDS YP_904171.1 118602956 4554945 complement(1057992..1058228) 1 NC_008610.1 required for 70S ribosome assembly; 50S ribosomal protein L28 1058228 rpmB 4554945 rpmB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L28 YP_904171.1 1057992 R 413404 CDS YP_904172.1 118602957 4554946 complement(1058957..1059595) 1 NC_008610.1 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 1059595 pyrE 4554946 pyrE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) orotate phosphoribosyltransferase YP_904172.1 1058957 R 413404 CDS YP_904173.1 118602958 4554947 1059620..1060390 1 NC_008610.1 KEGG: mca:MCA0321 exodeoxyribonuclease III; TIGRFAM: exodeoxyribonuclease III; exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase; exodeoxyribonuclease III 1060390 4554947 Rmag_0996 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) exodeoxyribonuclease III YP_904173.1 1059620 D 413404 CDS YP_904174.1 118602959 4554948 1061233..1061790 1 NC_008610.1 PFAM: putative methyltransferase; KEGG: lpf:lpl0521 S-adenosylmethionine-dependent methyltransferase; tRNA (guanine-N(7)-)-methyltransferase 1061790 4554948 Rmag_0997 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA (guanine-N(7)-)-methyltransferase YP_904174.1 1061233 D 413404 CDS YP_904175.1 118602960 4554949 1061792..1062244 1 NC_008610.1 PFAM: FxsA cytoplasmic membrane protein; KEGG: pha:PSHAa0261 F exclusion suppressor; FxsA cytoplasmic membrane protein 1062244 4554949 Rmag_0998 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) FxsA cytoplasmic membrane protein YP_904175.1 1061792 D 413404 CDS YP_904176.1 118602961 4554950 1062232..1063446 1 NC_008610.1 KEGG: mca:MCA2492 folylpolyglutamate synthase/dihydrofolate synthase; TIGRFAM: FolC bifunctional protein; PFAM: Mur ligase, middle domain protein; FolC bifunctional protein 1063446 4554950 Rmag_0999 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) FolC bifunctional protein YP_904176.1 1062232 D 413404 CDS YP_904177.1 118602962 4554951 1063494..1064342 1 NC_008610.1 KEGG: hch:HCH_02441 uncharacterized membrane protein, required for colicin V production; hypothetical protein 1064342 4554951 Rmag_1000 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904177.1 1063494 D 413404 CDS YP_904178.1 118602963 4554991 1064353..1065870 1 NC_008610.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase 1065870 4554991 Rmag_1001 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) amidophosphoribosyltransferase YP_904178.1 1064353 D 413404 CDS YP_904179.1 118602964 4554992 1068429..1069592 1 NC_008610.1 KEGG: noc:Noc_1151 O-succinylhomoserine sulfhydrylase; TIGRFAM: O-succinylhomoserine sulfhydrylase; PFAM: Cys/Met metabolism pyridoxal-phosphate-dependent enzymes; O-succinylhomoserine sulfhydrylase 1069592 4554992 Rmag_1002 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) O-succinylhomoserine sulfhydrylase YP_904179.1 1068429 D 413404 CDS YP_904180.1 118602965 4554993 1069621..1070130 1 NC_008610.1 catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-(acyl carrier protein) dehydratase 1070130 4554993 Rmag_1003 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-hydroxydecanoyl-(acyl carrier protein) dehydratase YP_904180.1 1069621 D 413404 CDS YP_904181.1 118602966 4554994 1070130..1071347 1 NC_008610.1 PFAM: beta-ketoacyl synthase; KEGG: tcx:Tcr_1945 beta-ketoacyl synthase; 3-oxoacyl-[acyl-carrier-protein] synthase I 1071347 4554994 Rmag_1004 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-oxoacyl-[acyl-carrier-protein] synthase I YP_904181.1 1070130 D 413404 CDS YP_904182.1 118602967 4554995 complement(1071387..1072313) 1 NC_008610.1 TIGRFAM: protein-export membrane protein, SecD/SecF family; protein-export membrane protein SecF; PFAM: SecD/SecF/SecDF export membrane protein; KEGG: noc:Noc_2349 SecF protein; protein translocase subunit secF 1072313 4554995 Rmag_1005 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein translocase subunit secF YP_904182.1 1071387 R 413404 CDS YP_904183.1 118602968 4554996 complement(1072310..1074157) 1 NC_008610.1 TIGRFAM: protein-export membrane protein, SecD/SecF family; protein-export membrane protein SecD; PFAM: SecD/SecF/SecDF export membrane protein; KEGG: tcx:Tcr_1331 protein-export membrane protein SecD; protein-export membrane protein SecD 1074157 4554996 Rmag_1006 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein-export membrane protein SecD YP_904183.1 1072310 R 413404 CDS YP_904184.1 118602969 4554997 complement(1074174..1074515) 1 NC_008610.1 TIGRFAM: preprotein translocase, YajC subunit; PFAM: YajC family protein; KEGG: ftl:FTL_0847 preprotein translocase family protein; protein translocase subunit yajC 1074515 4554997 Rmag_1007 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein translocase subunit yajC YP_904184.1 1074174 R 413404 CDS YP_904185.1 118602970 4554998 complement(1074537..1075826) 1 NC_008610.1 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 1075826 4554998 Rmag_1008 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) seryl-tRNA synthetase YP_904185.1 1074537 R 413404 CDS YP_904186.1 118602971 4554999 1075911..1076198 1 NC_008610.1 PFAM: Rhodanese domain protein; KEGG: vch:VCA0100 phage shock protein E; rhodanese domain-containing protein 1076198 4554999 Rmag_1009 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) rhodanese domain-containing protein YP_904186.1 1075911 D 413404 CDS YP_904187.1 118602972 4555000 1076228..1076860 1 NC_008610.1 KEGG: tbd:Tbd_2490 hypothetical protein; hypothetical protein 1076860 4555000 Rmag_1010 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904187.1 1076228 D 413404 CDS YP_904188.1 118602973 4555001 complement(1083153..1083638) 1 NC_008610.1 PFAM: Rhodanese domain protein; KEGG: plt:Plut_0032 rhodanese-like; rhodanese domain-containing protein 1083638 4555001 Rmag_1011 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) rhodanese domain-containing protein YP_904188.1 1083153 R 413404 CDS YP_904189.1 118602974 4555002 complement(1083644..1084273) 1 NC_008610.1 PFAM: regulatory protein, LuxR; response regulator receiver; KEGG: hch:HCH_04021 response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain; two component LuxR family transcriptional regulator 1084273 4555002 Rmag_1012 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) two component LuxR family transcriptional regulator YP_904189.1 1083644 R 413404 CDS YP_904190.1 118602975 4555003 complement(1084270..1085754) 1 NC_008610.1 PFAM: GAF domain protein; ATP-binding region, ATPase domain protein domain protein; histidine kinase, dimerisation and phosphoacceptor region; KEGG: dar:Daro_0833 GAF:ATP-binding region, ATPase-like:histidine kinase, HAMP region:histidine kinase, dimerization and phosphoacceptor region; signal transduction histidine kinase, nitrate/nitrite-specific, NarQ 1085754 4555003 Rmag_1013 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) signal transduction histidine kinase, nitrate/nitrite-specific, NarQ YP_904190.1 1084270 R 413404 CDS YP_904191.1 118602976 4555004 complement(1085788..1087131) 1 NC_008610.1 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 1087131 trmE 4555004 trmE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tRNA modification GTPase TrmE YP_904191.1 1085788 R 413404 CDS YP_904192.1 118602977 4555005 complement(1087139..1088629) 1 NC_008610.1 TIGRFAM: glutamate--cysteine ligase; KEGG: hch:HCH_06422 glutamate--cysteine ligase; glutamate-cysteine ligase 1088629 4555005 Rmag_1015 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutamate-cysteine ligase YP_904192.1 1087139 R 413404 CDS YP_904193.1 118602978 4555006 1088741..1089664 1 NC_008610.1 TIGRFAM: mutator MutT protein; PFAM: NUDIX hydrolase; thiamine monophosphate synthase; KEGG: noc:Noc_0306 mutator MutT; hypothetical protein 1089664 4555006 Rmag_1016 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904193.1 1088741 D 413404 CDS YP_904194.1 118602979 4555007 1092217..1096716 1 NC_008610.1 PFAM: glutamine amidotransferase, class-II; glutamate synthase, alpha subunit domain protein; ferredoxin-dependent glutamate synthase; glutamate synthase; KEGG: rba:RB5654 glutamate synthase [NADPH] large chain; glutamate synthase (ferredoxin) 1096716 4555007 Rmag_1018 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) glutamate synthase (ferredoxin) YP_904194.1 1092217 D 413404 CDS YP_904195.1 118602980 4555008 complement(1097134..1097625) 1 NC_008610.1 PFAM: dihydrofolate reductase region; KEGG: noc:Noc_0235 dihydrofolate reductase; dihydrofolate reductase 1097625 4555008 Rmag_1019 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) dihydrofolate reductase YP_904195.1 1097134 R 413404 CDS YP_904196.1 118602981 4555009 1097679..1098284 1 NC_008610.1 TIGRFAM: maf protein; PFAM: Maf family protein; KEGG: pha:PSHAa1813 Maf/Ham1 domain; maf protein 1098284 4555009 Rmag_1020 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) maf protein YP_904196.1 1097679 D 413404 CDS YP_904197.1 118602982 4555010 1098290..1101718 1 NC_008610.1 TIGRFAM: transcription-repair coupling factor; PFAM: helicase domain protein; transcription factor CarD; TRCF domain protein; type III restriction enzyme, res subunit; DEAD/DEAH box helicase domain protein; KEGG: noc:Noc_1642 transcription-repair coupling factor; transcription-repair coupling factor 1101718 4555010 Rmag_1021 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) transcription-repair coupling factor YP_904197.1 1098290 D 413404 CDS YP_904198.1 118602983 4555538 complement(1101751..1102692) 1 NC_008610.1 PFAM: PfkB domain protein; KEGG: noc:Noc_2548 carbohydrate kinase, PfkB; ribokinase-like domain-containing protein 1102692 4555538 Rmag_1022 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribokinase-like domain-containing protein YP_904198.1 1101751 R 413404 CDS YP_904199.1 118602984 4555539 complement(1102755..1103675) 1 NC_008610.1 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 1103675 ispH 4555539 ispH Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase YP_904199.1 1102755 R 413404 CDS YP_904200.1 118602985 4555540 complement(1104035..1104883) 1 NC_008610.1 TIGRFAM: acetyl-CoA carboxylase, carboxyl transferase, beta subunit; KEGG: csa:Csal_1263 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha 1104883 4555540 Rmag_1024 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha YP_904200.1 1104035 R 413404 CDS YP_904201.1 118602986 4555541 complement(1104903..1105700) 1 NC_008610.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha 1105700 trpA 4555541 trpA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tryptophan synthase subunit alpha YP_904201.1 1104903 R 413404 CDS YP_904202.1 118602987 4555542 complement(1105707..1106750) 1 NC_008610.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase 1106750 hemE 4555542 hemE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) uroporphyrinogen decarboxylase YP_904202.1 1105707 R 413404 CDS YP_904203.1 118602988 4555543 complement(1106860..1107135) 1 NC_008610.1 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 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 1107135 rpmE 4555543 rpmE Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L31 YP_904203.1 1106860 R 413404 CDS YP_904204.1 118602989 4555544 complement(1107145..1109547) 1 NC_008610.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; copper-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; E1-E2 ATPase-associated domain protein; KEGG: tcx:Tcr_1960 heavy metal translocating P-type ATPase; heavy metal translocating P-type ATPase 1109547 4555544 Rmag_1028 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) heavy metal translocating P-type ATPase YP_904204.1 1107145 R 413404 CDS YP_904205.1 118602990 4555545 1109652..1110413 1 NC_008610.1 hypothetical protein 1110413 4555545 Rmag_1029 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904205.1 1109652 D 413404 CDS YP_904206.1 118602991 4555546 1110422..1111780 1 NC_008610.1 KEGG: sde:Sde_3959 UDP-N-acetylglucosamine diphosphorylase; TIGRFAM: UDP-N-acetylglucosamine pyrophosphorylase; PFAM: transferase hexapeptide repeat containing protein; Nucleotidyl transferase; UDP-N-acetylglucosamine pyrophosphorylase / glucosamine-1-phosphate N-acetyltransferase 1111780 4555546 Rmag_1030 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) UDP-N-acetylglucosamine pyrophosphorylase / glucosamine-1-phosphate N-acetyltransferase YP_904206.1 1110422 D 413404 CDS YP_904207.1 118602992 4555547 complement(1112002..1113207) 1 NC_008610.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 1113207 4555547 Rmag_1031 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) tryptophan synthase subunit beta YP_904207.1 1112002 R 413404 CDS YP_904208.1 118602993 4555548 complement(1113204..1113812) 1 NC_008610.1 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 1113812 4555548 Rmag_1032 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) N-(5'-phosphoribosyl)anthranilate isomerase YP_904208.1 1113204 R 413404 CDS YP_904209.1 118602994 4555549 complement(1113812..1114519) 1 NC_008610.1 hypothetical protein 1114519 4555549 Rmag_1033 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904209.1 1113812 R 413404 CDS YP_904210.1 118602995 4555550 complement(1115413..1117746) 1 NC_008610.1 KEGG: tcx:Tcr_0196 DNA topoisomerase; TIGRFAM: DNA topoisomerase I; PFAM: TOPRIM domain protein; DNA topoisomerase, type IA, central domain protein; SMART: DNA topoisomerase I, ATP-binding; DNA topoisomerase I, DNA-binding; Toprim sub domain protein; DNA topoisomerase I 1117746 4555550 Rmag_1034 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) DNA topoisomerase I YP_904210.1 1115413 R 413404 CDS YP_904211.1 118602996 4555551 complement(1117746..1118237) 1 NC_008610.1 PFAM: protein of unknown function DUF494; KEGG: noc:Noc_3011 protein of unknown function DUF494; hypothetical protein 1118237 4555551 Rmag_1035 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904211.1 1117746 R 413404 CDS YP_904212.1 118602997 4555552 1119415..1119555 1 NC_008610.1 PFAM: ribosomal protein L34; KEGG: vvy:VV0005 ribosomal protein L34; 50S ribosomal protein L34P 1119555 4555552 Rmag_1037 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L34P YP_904212.1 1119415 D 413404 CDS YP_904213.1 118602998 4555553 1119565..1119885 1 NC_008610.1 TIGRFAM: ribonuclease P protein component; PFAM: ribonuclease P protein; KEGG: pha:PSHAa3025 ribonuclease P protein component (RNaseP protein) (RNase P protein) (protein C5); ribonuclease P protein component 1119885 4555553 Rmag_1038 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribonuclease P protein component YP_904213.1 1119565 D 413404 CDS YP_904214.1 118602999 4555554 1119886..1120101 1 NC_008610.1 PFAM: protein of unknown function DUF37; KEGG: tcx:Tcr_1890 protein of unknown function DUF37; hypothetical protein 1120101 4555554 Rmag_1039 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904214.1 1119886 D 413404 CDS YP_904215.1 118603000 4555555 1120130..1121755 1 NC_008610.1 PFAM: 60 kDa inner membrane insertion protein; KEGG: tcx:Tcr_2197 60 kDa inner membrane insertion protein; protein translocase subunit yidC 1121755 4555555 Rmag_1040 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein translocase subunit yidC YP_904215.1 1120130 D 413404 CDS YP_904216.1 118603001 4555556 1121764..1122624 1 NC_008610.1 KEGG: tbd:Tbd_2491 hypothetical protein; hypothetical protein 1122624 4555556 Rmag_1041 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904216.1 1121764 D 413404 CDS YP_904217.1 118603002 4555254 1122640..1123164 1 NC_008610.1 PFAM: N-acetylmuramoyl-L-alanine amidase, family 2; KEGG: aci:ACIAD0063 N-acetyl-anhydromuramyl-L-alanine amidase (regulates ampC); N-acetyl-anhydromuranmyl-L-alanine amidase 1123164 4555254 Rmag_1042 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) N-acetyl-anhydromuranmyl-L-alanine amidase YP_904217.1 1122640 D 413404 CDS YP_904218.1 118603003 4555255 1123151..1123684 1 NC_008610.1 TIGRFAM: hydrolase, HAD-superfamily, subfamily IIIA; 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family; KEGG: noc:Noc_2789 phosphatase KdsC; 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase 1123684 4555255 Rmag_1043 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase YP_904218.1 1123151 D 413404 CDS YP_904219.1 118603004 4555256 complement(1123948..1124364) 1 NC_008610.1 part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane; F0F1 ATP synthase subunit epsilon 1124364 atpC 4555256 atpC Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) F0F1 ATP synthase subunit epsilon YP_904219.1 1123948 R 413404 CDS YP_904220.1 118603005 4555257 complement(1124365..1125744) 1 NC_008610.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit; F0F1 ATP synthase subunit beta 1125744 4555257 Rmag_1045 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) F0F1 ATP synthase subunit beta YP_904220.1 1124365 R 413404 CDS YP_904221.1 118603006 4555258 complement(1125766..1126629) 1 NC_008610.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit; F0F1 ATP synthase subunit gamma 1126629 4555258 Rmag_1046 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) F0F1 ATP synthase subunit gamma YP_904221.1 1125766 R 413404 CDS YP_904222.1 118603007 4555259 complement(1126643..1128184) 1 NC_008610.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit; F0F1 ATP synthase subunit alpha 1128184 4555259 Rmag_1047 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) F0F1 ATP synthase subunit alpha YP_904222.1 1126643 R 413404 CDS YP_904223.1 118603008 4555260 complement(1128212..1128763) 1 NC_008610.1 TIGRFAM: ATP synthase F1, delta subunit; PFAM: H+-transporting two-sector ATPase, delta (OSCP) subunit; KEGG: noc:Noc_3077 H+-transporting two-sector ATPase, delta (OSCP) subunit; ATP synthase F1, delta subunit 1128763 4555260 Rmag_1048 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP synthase F1, delta subunit YP_904223.1 1128212 R 413404 CDS YP_904224.1 118603009 4555261 complement(1128770..1129243) 1 NC_008610.1 TIGRFAM: ATP synthase F0, B subunit; PFAM: H+-transporting two-sector ATPase, B/B' subunit; KEGG: ngo:NGO2146 F-type H+-transporting ATPase b chain; ATP synthase F0, B subunit 1129243 4555261 Rmag_1049 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ATP synthase F0, B subunit YP_904224.1 1128770 R 413404 CDS YP_904225.1 118603010 4555262 complement(1129277..1129510) 1 NC_008610.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0; F0F1 ATP synthase subunit C 1129510 4555262 Rmag_1050 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) F0F1 ATP synthase subunit C YP_904225.1 1129277 R 413404 CDS YP_904226.1 118603011 4555263 complement(1129535..1130389) 1 NC_008610.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0; F0F1 ATP synthase subunit A 1130389 4555263 Rmag_1051 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) F0F1 ATP synthase subunit A YP_904226.1 1129535 R 413404 CDS YP_904227.1 118603012 4555264 complement(1130389..1130736) 1 NC_008610.1 KEGG: tcx:Tcr_2172 ATP synthase protein I; hypothetical protein 1130736 4555264 Rmag_1052 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904227.1 1130389 R 413404 CDS YP_904228.1 118603013 4555265 1130921..1132216 1 NC_008610.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: tcx:Tcr_1170 sulfide-quinone reductase; sulfide-quinone reductase 1132216 4555265 Rmag_1053 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) sulfide-quinone reductase YP_904228.1 1130921 D 413404 CDS YP_904229.1 118603014 4555266 complement(1133403..1134221) 1 NC_008610.1 PFAM: ATP-NAD/AcoX kinase; KEGG: tcx:Tcr_0867 NAD(+) kinase; NAD(+) kinase 1134221 4555266 Rmag_1054 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NAD(+) kinase YP_904229.1 1133403 R 413404 CDS YP_904230.1 118603015 4555267 1134345..1134887 1 NC_008610.1 PFAM: GrpE protein; KEGG: tcx:Tcr_0869 GrpE protein; GrpE protein 1134887 4555267 Rmag_1055 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GrpE protein YP_904230.1 1134345 D 413404 CDS YP_904231.1 118603016 4555268 1137794..1138033 1 NC_008610.1 hypothetical protein 1138033 4555268 Rmag_1056 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904231.1 1137794 D 413404 CDS YP_904232.1 118603017 4555269 1138229..1140454 1 NC_008610.1 PFAM: cytochrome c biogenesis protein, transmembrane region; Thioredoxin domain; KEGG: tcx:Tcr_0446 protein-disulfide reductase; protein-disulfide reductase 1140454 4555269 Rmag_1057 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein-disulfide reductase YP_904232.1 1138229 D 413404 CDS YP_904233.1 118603018 4555270 1140544..1140993 1 NC_008610.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis; 3-dehydroquinate dehydratase 1140993 4555270 Rmag_1058 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 3-dehydroquinate dehydratase YP_904233.1 1140544 D 413404 CDS YP_904234.1 118603019 4555271 1140994..1141401 1 NC_008610.1 TIGRFAM: acetyl-CoA carboxylase, biotin carboxyl carrier protein; PFAM: biotin/lipoyl attachment domain-containing protein; KEGG: vpa:VP2880 acetyl-CoA carboxylase, biotin carboxyl carrier protein; acetyl-CoA carboxylase, biotin carboxyl carrier protein 1141401 4555271 Rmag_1059 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acetyl-CoA carboxylase, biotin carboxyl carrier protein YP_904234.1 1140994 D 413404 CDS YP_904235.1 118603020 4555272 1141398..1142762 1 NC_008610.1 TIGRFAM: acetyl-CoA carboxylase, biotin carboxylase; PFAM: Carbamoyl-phosphate synthase L chain, ATP-binding; Carbamoyl-phosphate synthetase large chain domain protein; biotin carboxylase domain protein; RimK domain protein ATP-grasp; KEGG: hin:HI0972 biotin carboxylase; acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha / biotin carboxylase 1142762 4555272 Rmag_1060 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha / biotin carboxylase YP_904235.1 1141398 D 413404 CDS YP_904236.1 118603021 4555273 1142755..1143777 1 NC_008610.1 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 1143777 argC 4555273 argC Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) N-acetyl-gamma-glutamyl-phosphate reductase YP_904236.1 1142755 D 413404 CDS YP_904237.1 118603022 4555502 1143787..1144140 1 NC_008610.1 essential respiratory protein A; may be involved in the transfer of iron-sulfur clusters; essential for growth using oxygen or alternate electron acceptors; iron-sulfur cluster insertion protein ErpA 1144140 4555502 Rmag_1062 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) iron-sulfur cluster insertion protein ErpA YP_904237.1 1143787 D 413404 CDS YP_904238.1 118603023 4555503 1144144..1145280 1 NC_008610.1 catalyzes the formation of citrate from acetyl-CoA and oxaloacetate; citrate synthase 1145280 4555503 Rmag_1063 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) citrate synthase YP_904238.1 1144144 D 413404 CDS YP_904239.1 118603024 4555504 1145283..1146023 1 NC_008610.1 TIGRFAM: ubiquinone/menaquinone biosynthesis methyltransferases; PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: pha:PSHAa2926 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase / S-adenosylmethionine; ubiquinone/menaquinone biosynthesis methyltransferases 1146023 4555504 Rmag_1064 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ubiquinone/menaquinone biosynthesis methyltransferases YP_904239.1 1145283 D 413404 CDS YP_904240.1 118603025 4555505 1146150..1146470 1 NC_008610.1 hypothetical protein 1146470 4555505 Rmag_1065 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904240.1 1146150 D 413404 CDS YP_904241.1 118603026 4555506 1146473..1148077 1 NC_008610.1 TIGRFAM: 2-polyprenylphenol 6-hydroxylase; PFAM: ABC-1 domain protein; KEGG: tcx:Tcr_0400 2-polyprenylphenol 6-hydroxylase; 2-polyprenylphenol 6-hydroxylase 1148077 4555506 Rmag_1066 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 2-polyprenylphenol 6-hydroxylase YP_904241.1 1146473 D 413404 CDS YP_904242.1 118603027 4555507 1148231..1148899 1 NC_008610.1 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/general stress protein Ctc 1148899 4555507 Rmag_1067 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 50S ribosomal protein L25/general stress protein Ctc YP_904242.1 1148231 D 413404 CDS YP_904243.1 118603028 4555508 1148916..1149491 1 NC_008610.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase 1149491 4555508 Rmag_1068 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) peptidyl-tRNA hydrolase YP_904243.1 1148916 D 413404 CDS YP_904244.1 118603029 4555509 1149515..1150606 1 NC_008610.1 TIGRFAM: GTP-binding protein YchF; PFAM: GTP-binding protein, HSR1-related; Protein of unknown function DUF933; KEGG: vvy:VV0924 predicted GTPase; GTP-binding protein YchF 1150606 4555509 Rmag_1069 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) GTP-binding protein YchF YP_904244.1 1149515 D 413404 CDS YP_904245.1 118603030 4555510 1150638..1152176 1 NC_008610.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 1152176 4555510 Rmag_1070 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) phosphoglyceromutase YP_904245.1 1150638 D 413404 CDS YP_904246.1 118603031 4555511 1152203..1152874 1 NC_008610.1 PFAM: ribulose-phosphate 3-epimerase; KEGG: son:SO0292 ribulose-phosphate 3-epimerase; ribulose-5-phosphate 3-epimerase 1152874 4555511 Rmag_1071 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) ribulose-5-phosphate 3-epimerase YP_904246.1 1152203 D 413404 CDS YP_904247.1 118603032 4555512 1153103..1154041 1 NC_008610.1 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 1154041 rpsB 4555512 rpsB Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) 30S ribosomal protein S2 YP_904247.1 1153103 D 413404 CDS YP_904248.1 118603033 4555513 1154120..1155010 1 NC_008610.1 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 1155010 tsf 4555513 tsf Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) elongation factor Ts YP_904248.1 1154120 D 413404 CDS YP_904249.1 118603034 4555514 complement(1157100..1157624) 1 NC_008610.1 KEGG: bba:Bd2932 hypothetical protein; hypothetical protein 1157624 4555514 Rmag_1074 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) hypothetical protein YP_904249.1 1157100 R 413404 CDS YP_904250.1 118603035 4555515 complement(1159152..1159517) 1 NC_008610.1 TIGRFAM: preprotein translocase, SecG subunit; PFAM: Preprotein translocase SecG subunit; KEGG: lpp:lpp2837 protein-export membrane protein SecG (preprotein translocase subunit); protein translocase subunit secG 1159517 4555515 Rmag_1075 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) protein translocase subunit secG YP_904250.1 1159152 R 413404 CDS YP_904251.1 118603036 4555516 complement(1159520..1160266) 1 NC_008610.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate; triosephosphate isomerase 1160266 tpiA 4555516 tpiA Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) triosephosphate isomerase YP_904251.1 1159520 R 413404 CDS