Afipia carboxidovorans OM5 plasmid pHCG3, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Nitrobacteraceae; Afipia.
Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5
Complete nucleotide sequence of the circular megaplasmid pHCG3 of Oligotropha carboxidovorans: function in the chemolithoautotrophic utilization of CO, H(2) and CO(2)
Sequence analysis, characterization and CO-specific transcription of the cox gene cluster on the megaplasmid pHCG3 of Oligotropha carboxidovorans
Purification and molecular characterization of the H2 uptake membrane-bound NiFe-hydrogenase from the carboxidotrophic bacterium Oligotropha carboxidovorans
Molecular characterization of the gene cluster coxMSL encoding the molybdenum-containing carbon monoxide dehydrogenase of Oligotropha carboxidovorans
Submitted (25-MAY-2011) Goettingen Genomics Laboratory, Georg-August University Goettingen, Institute of Microbiology and Genetics, Grisebachstr. 8, Goettingen, Lower Saxony 37077, Germany
Submitted (01-JUL-1993) Lehrstuhl f. Mikrobiologie, Universitaet Bayreuth, Universitaetsstr. 30, Bayreuth D-95447, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP002827.1.\nDNA or bacteria of O. carboxidovorans OM5 is available from Prof.\nDr. Ortwin Meyer Chair of Microbiology, University of Bayreuth,\nUniversitaetsstrasse 30, 95440 Bayreuth, Germany\n(ortwin.meyer@uni-bayreuth.de).\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/09/2023 09:08:05\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,748\nCDSs (total) :: 3,690\nGenes (coding) :: 3,665\nCDSs (with protein) :: 3,665\nGenes (RNA) :: 58\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 4\nPseudo Genes (total) :: 25\nCDSs (without protein) :: 25\nPseudo Genes (ambiguous residues) :: 0 of 25\nPseudo Genes (frameshifted) :: 9 of 25\nPseudo Genes (incomplete) :: 20 of 25\nPseudo Genes (internal stop) :: 2 of 25\nPseudo Genes (multiple problems) :: 5 of 25\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Oligotropha carboxidovorans
COORDINATES: similar to AA sequence:RefSeq:WP_013913700.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013913701.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913702.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913703.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913704.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913705.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913706.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913707.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913708.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012417.2
COORDINATES: protein motif:HMM:NF012956.2
GO:0030246 - carbohydrate binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF025033.2
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913712.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913713.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913714.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913715.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013913716.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913717.1
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913718.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913719.1
GO:0005509 - calcium ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913720.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913721.1
GO:0030253 - protein secretion by the type I secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913722.1
HlyD family type I secretion periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013913723.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092589.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092590.1
GO:0003824 - catalytic activity [Evidence IEA]
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_013913726.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913727.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913728.1
carbon monoxide dehydrogenase medium subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013913729.1
carbon monoxide dehydrogenase small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013913730.1
aerobic carbon-monoxide dehydrogenase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_019200215.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913732.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913733.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913734.1
COORDINATES: protein motif:HMM:NF015652.2
COORDINATES: similar to AA sequence:RefSeq:WP_013913735.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913736.1
COORDINATES: similar to AA sequence:RefSeq:WP_002717574.1
GO:0005215 - transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913738.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913739.1
GO:0042132 - fructose 1,6-bisphosphate 1-phosphatase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913740.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008974 - phosphoribulokinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913741.1
GO:0004802 - transketolase activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913742.1
GO:0006094 - gluconeogenesis [Evidence IEA]; GO:0019682 - glyceraldehyde-3-phosphate metabolic process [Evidence IEA]; GO:0006096 - glycolytic process [Evidence IEA]
type I glyceraldehyde-3-phosphate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013913743.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004618 - phosphoglycerate kinase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011473339.1
GO:0004332 - fructose-bisphosphate aldolase activity [Evidence IEA]
catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis, and/or gluconeogenesis; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis, and/or gluconeogenesis; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007594836.1
form I ribulose bisphosphate carboxylase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011662800.1
ribulose bisphosphate carboxylase small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013913747.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913748.1
GO:0004750 - D-ribulose-phosphate 3-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913749.1
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913750.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913751.1
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014071526.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
hydrogenase nickel incorporation protein HypB
COORDINATES: similar to AA sequence:RefSeq:WP_013913753.1
GO:0008901 - ferredoxin hydrogenase activity [Evidence IEA]
hydrogenase maturation nickel metallochaperone HypA
COORDINATES: similar to AA sequence:RefSeq:WP_013913754.1
nickel-dependent hydrogenase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013913755.1
[NiFe]-hydrogenase assembly chaperone HybE
COORDINATES: similar to AA sequence:RefSeq:WP_013913756.1
hydrogenase expression/formation protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913757.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913758.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0051082 - unfolded protein binding [Evidence IEA]
GO:0065003 - protein-containing complex assembly [Evidence IEA]
HypC/HybG/HupF family hydrogenase formation chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_013913759.1
HyaD/HybD family hydrogenase maturation endopeptidase
COORDINATES: similar to AA sequence:RefSeq:WP_013913760.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
GO:0022904 - respiratory electron transport chain [Evidence IEA]
Ni/Fe-hydrogenase, b-type cytochrome subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013913761.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913762.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913763.1
GO:0016151 - nickel cation binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913764.1
Ni/Fe-hydrogenase-like protein small subunit HoxB
COORDINATES: similar to AA sequence:RefSeq:WP_013913765.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
histidine kinase dimerization/phospho-acceptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913766.1
GO:0003998 - acylphosphatase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913767.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913768.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913769.1
GO:0016530 - metallochaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913770.1
hydrogenase expression/formation protein HypE
COORDINATES: similar to AA sequence:RefSeq:WP_020176858.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913772.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913773.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]; GO:0010045 - response to nickel cation [Evidence IEA]
nickel-responsive transcriptional regulator NikR
COORDINATES: similar to AA sequence:RefSeq:WP_013913774.1
COORDINATES: similar to AA sequence:RefSeq:WP_002718856.1
GO:0008535 - respiratory chain complex IV assembly [Evidence IEA]
cbb3-type cytochrome oxidase assembly protein CcoS
COORDINATES: similar to AA sequence:RefSeq:WP_013913775.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0015662 - P-type ion transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913776.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913777.1
COORDINATES: similar to AA sequence:RefSeq:WP_019198783.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
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_076611756.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012592079.1
COORDINATES: similar to AA sequence:RefSeq:WP_006328923.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913781.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913782.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913783.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913784.1
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_013913785.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655055.1
COORDINATES: similar to AA sequence:RefSeq:WP_014763243.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913788.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913789.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913790.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913791.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913792.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913793.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913794.1
GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913795.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002719000.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431456.1
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_013913799.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913800.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_013913801.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_013913802.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048127.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_013913804.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_013913805.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913806.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913807.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF017658.2
filamentous hemagglutinin N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913809.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913810.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913811.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_013913812.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913813.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_018482029.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913815.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_013913816.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913817.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_013913818.1
COORDINATES: similar to AA sequence:RefSeq:WP_013984785.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913820.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913822.1