Afipia carboxidovorans OM5 plasmid pOC167, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Nitrobacteraceae; Afipia.
Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5
Submitted (25-MAY-2011) Goettingen Genomics Laboratory, Georg-August University Goettingen, Institute of Microbiology and Genetics, Grisebachstr. 8, Goettingen, Lower Saxony 37077, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP002828.1.\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_012564770.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013913427.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505047.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822431.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564766.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013913429.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913430.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913431.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564764.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012564762.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913433.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913434.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011505174.1
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012564757.1
COORDINATES: similar to AA sequence:RefSeq:WP_013912802.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564755.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013912803.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564753.1
COORDINATES: similar to AA sequence:RefSeq:WP_013912805.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564751.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913441.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913442.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564748.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564747.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913443.1
GO:0042597 - periplasmic space [Evidence IEA]
GO:0005507 - copper ion binding [Evidence IEA]
GO:0006825 - copper ion transport [Evidence IEA]
copper homeostasis periplasmic binding protein CopC
COORDINATES: similar to AA sequence:RefSeq:WP_013913444.1
copper homeostasis membrane protein CopD
COORDINATES: similar to AA sequence:RefSeq:WP_013913445.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913446.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611865.1
frameshifted; 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_013913448.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564896.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913449.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913450.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564894.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013913451.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564892.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505154.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_011505152.1
COORDINATES: protein motif:HMM:NF015720.2
COORDINATES: similar to AA sequence:RefSeq:WP_013913456.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564888.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913457.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564885.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:WP_013913458.1
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564884.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011505142.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505141.1
heavy metal-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013913460.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913461.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564879.1
GO:0046872 - metal ion binding [Evidence IEA]
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611908.1
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_013913463.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564876.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_012564875.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409526.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913466.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564872.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564871.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013913467.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564869.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012564868.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564867.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564866.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_013913468.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564864.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564863.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564861.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564860.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564859.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564858.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_013913470.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913471.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564854.1
GO:0035438 - cyclic-di-GMP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564853.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564852.1
COORDINATES: protein motif:HMM:NF013382.2
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913473.1
COORDINATES: similar to AA sequence:RefSeq:WP_011502559.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564848.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564847.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913475.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564845.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564844.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913476.1
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011252263.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012564841.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564840.1
flagellar hook-basal body complex protein
COORDINATES: similar to AA sequence:RefSeq:WP_018251228.1
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_076612037.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564839.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564838.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913479.1
COORDINATES: similar to AA sequence:RefSeq:WP_012041717.1
GO:0015288 - porin activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564832.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913483.1
COORDINATES: similar to AA sequence:RefSeq:WP_004190526.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564828.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564827.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564826.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564825.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564824.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_012564823.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564822.1
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019200173.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564819.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564818.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564817.1
VirB4 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564816.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564815.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564814.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913484.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913485.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564811.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564810.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564809.1
COORDINATES: similar to AA sequence:RefSeq:WP_002719035.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564807.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564806.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564805.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505097.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_012564802.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564801.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913489.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564798.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564797.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564796.1
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_012564795.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564794.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564793.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564792.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564791.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913490.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564790.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913491.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002719000.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564787.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564786.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012564785.1
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012564784.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
Eco57I restriction-modification methylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913493.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564781.1
GO:0004386 - helicase activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564780.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913494.1
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564778.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564777.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564776.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564775.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913495.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564774.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012564773.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015822436.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564771.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]