Paracoccus aminophilus JCM 7686 plasmid pAMI8, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Paracoccus.
Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids
Submitted (02-AUG-2013) Department of Bacterial Genetics, University of Warsaw, Faculty of Biology, Institute of Microbiology, Miecznikowa 1, Warsaw 02-096, Poland
REFSEQ INFORMATION: The reference sequence is identical to\nCP006655.1.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: Newbler de novo assembler software\n (Roche) v. 2.6\nReference-guided Assembly :: partially based on Paracoccus\n denitrificans PD1222\nGenome Coverage :: 30-50X\nSequencing Technology :: 454\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/14/2022 12:16:24\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,704\nCDSs (total) :: 4,629\nGenes (coding) :: 4,565\nCDSs (with protein) :: 4,565\nGenes (RNA) :: 75\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 60\nncRNAs :: 3\nPseudo Genes (total) :: 64\nCDSs (without protein) :: 64\nPseudo Genes (ambiguous residues) :: 0 of 64\nPseudo Genes (frameshifted) :: 24 of 64\nPseudo Genes (incomplete) :: 49 of 64\nPseudo Genes (internal stop) :: 18 of 64\nPseudo Genes (multiple problems) :: 21 of 64\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF040974.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR03454.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120631.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391525.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009807576.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008888448.1
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011505237.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341784.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065928.1
COORDINATES: protein motif:HMM:NF012493.2
C-terminal helicase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004129019.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020952554.1
GO:0004803 - transposase activity [Evidence IEA]
IS5-like element ISPam2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011540540.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008027660.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010396468.1
GO:0009331 - glycerol-3-phosphate dehydrogenase complex [Evidence IEA]
GO:0004368 - glycerol-3-phosphate dehydrogenase (quinone) activity [Evidence IEA]
GO:0006072 - glycerol-3-phosphate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015920434.1
COORDINATES: similar to AA sequence:RefSeq:WP_002719817.1
COORDINATES: similar to AA sequence:RefSeq:WP_008279276.1
COORDINATES: similar to AA sequence:RefSeq:WP_011337643.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328677.1
COORDINATES: similar to AA sequence:RefSeq:WP_019965034.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011748898.1
GO:0004370 - glycerol kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007813372.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611562.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF033550.5
COORDINATES: similar to AA sequence:RefSeq:WP_007813144.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008336115.1
COORDINATES: similar to AA sequence:RefSeq:WP_010398642.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120685.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187165.1
COORDINATES: similar to AA sequence:RefSeq:WP_014880577.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009574150.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_005859622.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_005859624.1
COORDINATES: similar to AA sequence:RefSeq:WP_014880583.1
COORDINATES: similar to AA sequence:RefSeq:WP_010139194.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065941.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009803686.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065938.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574169.1
COORDINATES: protein motif:HMM:NF012651.2
COORDINATES: similar to AA sequence:RefSeq:WP_013428845.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010812292.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_002718002.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014330237.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014330236.1
COORDINATES: similar to AA sequence:RefSeq:WP_018601397.1
COORDINATES: similar to AA sequence:RefSeq:WP_007197079.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008548899.1
COORDINATES: protein motif:HMM:TIGR02971.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011665935.1
GO:0009055 - electron transfer activity [Evidence IEA]
cytochrome b/b6 domain-containing protein
COORDINATES: protein motif:HMM:NF024600.2
GO:0005509 - calcium ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR04141.1
TIGR04141 family sporadically distributed protein
COORDINATES: similar to AA sequence:RefSeq:WP_011583104.1
COORDINATES: similar to AA sequence:RefSeq:WP_011602053.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859685.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803321.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018065932.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_007803318.1
COORDINATES: protein motif:HMM:NF015437.2
COORDINATES: similar to AA sequence:RefSeq:WP_010336143.1
COORDINATES: similar to AA sequence:RefSeq:WP_011581570.1
COORDINATES: similar to AA sequence:RefSeq:WP_018245369.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003613224.1
COORDINATES: protein motif:HMM:NF015642.2
COORDINATES: similar to AA sequence:RefSeq:WP_009573761.1
COORDINATES: similar to AA sequence:RefSeq:WP_012112737.1
COORDINATES: similar to AA sequence:RefSeq:WP_017140411.1
COORDINATES: similar to AA sequence:RefSeq:WP_011339486.1
COORDINATES: similar to AA sequence:RefSeq:WP_015740136.1
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008877989.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408889.1
COORDINATES: similar to AA sequence:RefSeq:WP_008877992.1
COORDINATES: similar to AA sequence:RefSeq:WP_007424858.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018429574.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828565.1
GO:0015109 - chromate transmembrane transporter activity [Evidence IEA]
GO:0015703 - chromate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611153.1
COORDINATES: similar to AA sequence:RefSeq:WP_011579027.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820102.1
COORDINATES: similar to AA sequence:RefSeq:WP_009450564.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023696.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820093.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065909.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092608.1
COORDINATES: similar to AA sequence:RefSeq:WP_002718979.1
COORDINATES: similar to AA sequence:RefSeq:WP_007749161.1
COORDINATES: similar to AA sequence:RefSeq:WP_007348452.1
COORDINATES: similar to AA sequence:RefSeq:WP_020042524.1
COORDINATES: similar to AA sequence:RefSeq:WP_011473488.1
COORDINATES: similar to AA sequence:RefSeq:WP_015886906.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010660167.1
COORDINATES: similar to AA sequence:RefSeq:WP_015318843.1
COORDINATES: similar to AA sequence:RefSeq:WP_009563849.1
COORDINATES: similar to AA sequence:RefSeq:WP_003610625.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0004076 - biotin synthase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0009102 - biotin biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020818539.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012643403.1
COORDINATES: similar to AA sequence:RefSeq:WP_009564096.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982965.1
COORDINATES: similar to AA sequence:RefSeq:WP_019408203.1
ClbS/DfsB family four-helix bundle protein
COORDINATES: similar to AA sequence:RefSeq:WP_018065906.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827208.1
COORDINATES: similar to AA sequence:RefSeq:WP_020044985.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747863.1
COORDINATES: similar to AA sequence:RefSeq:WP_011713016.1
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00229.1
PAS domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_019589512.1
COORDINATES: similar to AA sequence:RefSeq:WP_008595373.1
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: protein motif:HMM:NF013499.2
GO:0003676 - nucleic acid binding [Evidence IEA]
OB-fold nucleic acid binding domain-containing protein
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: similar to AA sequence:RefSeq:WP_010400404.1
COORDINATES: protein motif:HMM:NF020123.2
COORDINATES: similar to AA sequence:RefSeq:WP_020485875.1
GO:0047134 - protein-disulfide reductase (NAD(P)) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010394293.1
COORDINATES: similar to AA sequence:RefSeq:WP_019965473.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019965472.1
COORDINATES: similar to AA sequence:RefSeq:WP_019965460.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750914.1
COORDINATES: protein motif:HMM:NF014608.2
COORDINATES: similar to AA sequence:RefSeq:WP_020204501.1
COORDINATES: similar to AA sequence:RefSeq:WP_011047352.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013268147.1
COORDINATES: similar to AA sequence:RefSeq:WP_010142174.1
COORDINATES: similar to AA sequence:RefSeq:WP_019400587.1
COORDINATES: similar to AA sequence:RefSeq:WP_010398566.1
COORDINATES: protein motif:HMM:TIGR01244.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010398570.1
GO:0015116 - sulfate transmembrane transporter activity [Evidence IEA]
GO:0008272 - sulfate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010398584.1
GO:0055051 - ATP-binding cassette (ABC) transporter complex, integrated substrate binding [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0033230 - ABC-type cysteine transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0033228 - cysteine export across plasma membrane [Evidence IEA]
thiol reductant ABC exporter subunit CydD
COORDINATES: similar to AA sequence:RefSeq:WP_010398587.1
amino acid ABC transporter ATP-binding/permease protein
COORDINATES: similar to AA sequence:RefSeq:WP_009756543.1
GO:0070069 - cytochrome complex [Evidence IEA]
GO:0019646 - aerobic electron transport chain [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016554609.1
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor [Evidence IEA]
cytochrome d ubiquinol oxidase subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_009756545.1
COORDINATES: similar to AA sequence:RefSeq:WP_013804400.1
COORDINATES: similar to AA sequence:RefSeq:WP_006478784.1
winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_076612142.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611917.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396319.1
COORDINATES: similar to AA sequence:RefSeq:WP_015596585.1
GO:0005384 - manganese ion transmembrane transporter activity [Evidence IEA]
GO:0030026 - cellular manganese ion homeostasis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008032797.1
COORDINATES: protein motif:HMM:NF017689.2
Na+-transporting NADH:ubiquinone oxidoreductase subunit A
COORDINATES: protein motif:HMM:NF015100.2
RnfABCDGE type electron transport complex subunit D
COORDINATES: similar to AA sequence:RefSeq:WP_007198976.1
COORDINATES: similar to AA sequence:RefSeq:WP_008878338.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612398.1
COORDINATES: similar to AA sequence:RefSeq:WP_020952385.1
IS5-like element ISPam1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_009804789.1
COORDINATES: similar to AA sequence:RefSeq:WP_019956125.1
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013077.2
COORDINATES: similar to AA sequence:RefSeq:WP_009450480.1
COORDINATES: protein motif:HMM:NF016299.2
COORDINATES: protein motif:HMM:NF014477.2
GO:0017013 - protein flavinylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009450482.1
GO:0016655 - oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor [Evidence IEA]
GO:0006814 - sodium ion transport [Evidence IEA]
NADH:ubiquinone reductase (Na(+)-transporting) subunit F
COORDINATES: similar to AA sequence:RefSeq:WP_007117501.1
NADH:ubiquinone reductase (Na(+)-transporting) subunit E
COORDINATES: similar to AA sequence:RefSeq:WP_007198975.1
NADH:ubiquinone reductase (Na(+)-transporting) subunit D
COORDINATES: protein motif:HMM:NF015573.2
COORDINATES: similar to AA sequence:RefSeq:WP_012562033.1
GO:0004318 - enoyl-[acyl-carrier-protein] reductase (NADH) activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011853765.1
COORDINATES: similar to AA sequence:RefSeq:WP_011493239.1
bifunctional enoyl-CoA hydratase/phosphate acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_020186172.1
COORDINATES: protein motif:HMM:NF017773.2
COORDINATES: similar to AA sequence:RefSeq:WP_006174421.1
COORDINATES: similar to AA sequence:RefSeq:WP_020186169.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
ribosome-associated ATPase/putative transporter RbbA
COORDINATES: similar to AA sequence:RefSeq:WP_006467159.1
COORDINATES: similar to AA sequence:RefSeq:WP_020087088.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_076611367.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611656.1
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009488349.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_008386986.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187343.1
nucleotidyltransferase/DNA polymerase involved in DNA repair
COORDINATES: similar to AA sequence:RefSeq:WP_009808718.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187345.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]