Comamonas antarctica strain 16-35-5 plasmid unnamed2, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Comamonas.
Acidovorax antarctica sp. nov., isolated from Corinth ice sheet soil, Antarctic Fields Peninsula
Submitted (10-JUN-2020) College of Life Science, Wuhan University, Guangba Road, Wuhan, Hubei 430072, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP054842.1.\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 :: HGAP v. 4.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 115.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 06/25/2023 10:17:35\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) :: 4,640\nCDSs (total) :: 4,526\nGenes (coding) :: 4,466\nCDSs (with protein) :: 4,466\nGenes (RNA) :: 114\nrRNAs :: 9, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 9, 9 (5S, 16S, 23S)\ntRNAs :: 84\nncRNAs :: 3\nPseudo Genes (total) :: 60\nCDSs (without protein) :: 60\nPseudo Genes (ambiguous residues) :: 0 of 60\nPseudo Genes (frameshifted) :: 23 of 60\nPseudo Genes (incomplete) :: 45 of 60\nPseudo Genes (internal stop) :: 6 of 60\nPseudo Genes (multiple problems) :: 12 of 60\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF012369.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007974938.1
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_003490875.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_014194529.1
COORDINATES: similar to AA sequence:RefSeq:WP_019303572.1
COORDINATES: similar to AA sequence:RefSeq:WP_015462617.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017167764.1
COORDINATES: similar to AA sequence:RefSeq:WP_019303576.1
COORDINATES: similar to AA sequence:RefSeq:WP_008345286.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_005931779.1
COORDINATES: similar to AA sequence:RefSeq:WP_008343655.1
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_007968770.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008343651.1
COORDINATES: similar to AA sequence:RefSeq:WP_017157753.1
COORDINATES: similar to AA sequence:RefSeq:WP_017164708.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007966864.1
COORDINATES: similar to AA sequence:RefSeq:WP_017172642.1
COORDINATES: similar to AA sequence:RefSeq:WP_014253279.1
COORDINATES: similar to AA sequence:RefSeq:WP_017844373.1
COORDINATES: similar to AA sequence:RefSeq:WP_014619721.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011800684.1
GO:0004803 - transposase activity [Evidence IEA]
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007967235.1
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_011829265.1
COORDINATES: similar to AA sequence:RefSeq:WP_012838635.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - DNA damage response [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012838621.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003069338.1
COORDINATES: similar to AA sequence:RefSeq:WP_019654146.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013168399.1
COORDINATES: similar to AA sequence:RefSeq:WP_013539963.1
COORDINATES: similar to AA sequence:RefSeq:WP_011695115.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
COORDINATES: protein motif:HMM:NF024673.2
COORDINATES: similar to AA sequence:RefSeq:WP_011799846.1
COORDINATES: protein motif:HMM:NF017528.2
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.; 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: similar to AA sequence:RefSeq:WP_015913892.1
COORDINATES: similar to AA sequence:RefSeq:WP_004152397.1
internal stop; 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_008647635.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396494.1
winged helix-turn-helix domain-containing protein
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611775.1
COORDINATES: similar to AA sequence:RefSeq:WP_013594332.1
TonB-dependent receptor plug domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611491.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005792827.1
GO:0042597 - periplasmic space [Evidence IEA]
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013517262.1
COORDINATES: similar to AA sequence:RefSeq:WP_018260533.1
GO:0004061 - arylformamidase activity [Evidence IEA]
GO:0019441 - tryptophan catabolic process to kynurenine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019657276.1
COORDINATES: similar to AA sequence:RefSeq:WP_006385031.1
COORDINATES: similar to AA sequence:RefSeq:WP_019657867.1
COORDINATES: similar to AA sequence:RefSeq:WP_019657273.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611734.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611071.1
COORDINATES: similar to AA sequence:RefSeq:WP_020249149.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611586.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611435.1
COORDINATES: protein motif:HMM:NF023701.2
GSU2403 family nucleotidyltransferase fold protein
COORDINATES: similar to AA sequence:RefSeq:WP_086558246.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_076611352.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003434181.1
glutathione-independent formaldehyde dehydrogenase
COORDINATES: protein motif:HMM:TIGR02605.1
COORDINATES: similar to AA sequence:RefSeq:WP_010961901.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005312113.1
internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type I restriction endonuclease subunit R
COORDINATES: similar to AA sequence:RefSeq:WP_000920559.1
COORDINATES: similar to AA sequence:RefSeq:WP_012218040.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019042300.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611807.1
COORDINATES: similar to AA sequence:RefSeq:WP_019702756.1
COORDINATES: similar to AA sequence:RefSeq:WP_010955146.1
COORDINATES: protein motif:HMM:NF012772.2
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity [Evidence IEA]; GO:0052621 - diguanylate cyclase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
bifunctional diguanylate cyclase/phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_006402480.1
GO:0035550 - urease complex [Evidence IEA]
GO:0043419 - urea catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019511160.1
GO:0016151 - nickel cation binding [Evidence IEA]; GO:0009039 - urease activity [Evidence IEA]
GO:0019627 - urea metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006402478.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016530 - metallochaperone activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013899.2
GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012431170.1
COORDINATES: similar to AA sequence:RefSeq:WP_006470598.1
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF024825.2
transporter substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF015799.2
COORDINATES: similar to AA sequence:RefSeq:WP_013341089.1
COORDINATES: similar to AA sequence:RefSeq:WP_013341090.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0015803 - branched-chain amino acid transport [Evidence IEA]
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_013393342.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013393343.1
COORDINATES: similar to AA sequence:RefSeq:WP_018418399.1
COORDINATES: protein motif:HMM:NF019588.2
COORDINATES: similar to AA sequence:RefSeq:WP_013722127.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722128.1
GO:0000166 - nucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011485291.1
COORDINATES: similar to AA sequence:RefSeq:WP_013518853.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005797418.1
COORDINATES: similar to AA sequence:RefSeq:WP_018006505.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013520966.1
GO:0008784 - alanine racemase activity [Evidence IEA]
GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017393432.1
GO:0008718 - D-amino-acid dehydrogenase activity [Evidence IEA]; GO:0071949 - FAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0055130 - D-alanine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007836101.1
winged helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_017363482.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0003941 - L-serine ammonia-lyase activity [Evidence IEA]
GO:0009063 - amino acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019702651.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015366.2
COORDINATES: similar to AA sequence:RefSeq:WP_009762400.1
COORDINATES: similar to AA sequence:RefSeq:WP_010955165.1
carbon-nitrogen hydrolase family protein
COORDINATES: protein motif:HMM:NF014698.2
GO:0051213 - dioxygenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012202451.1
COORDINATES: similar to AA sequence:RefSeq:WP_009520421.1
COORDINATES: similar to AA sequence:RefSeq:WP_009520422.1
COORDINATES: similar to AA sequence:RefSeq:WP_011870876.1
COORDINATES: similar to AA sequence:RefSeq:WP_009520424.1
COORDINATES: similar to AA sequence:RefSeq:WP_009805270.1
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.
COORDINATES: protein motif:HMM:NF033542.1
COORDINATES: similar to AA sequence:RefSeq:WP_065285158.1
COORDINATES: similar to AA sequence:RefSeq:WP_013587694.1
COORDINATES: protein motif:HMM:NF015658.2
COORDINATES: similar to AA sequence:RefSeq:WP_019018863.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012435813.1
COORDINATES: similar to AA sequence:RefSeq:WP_013341695.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012838517.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012838518.1
COORDINATES: similar to AA sequence:RefSeq:WP_019439190.1
COORDINATES: similar to AA sequence:RefSeq:WP_005795305.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722089.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]; GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019042269.1
heavy metal response regulator transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_015913648.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722281.1
COORDINATES: similar to AA sequence:RefSeq:WP_011805880.1
COORDINATES: similar to AA sequence:RefSeq:WP_011805845.1
COORDINATES: similar to AA sequence:RefSeq:WP_015014704.1
COORDINATES: similar to AA sequence:RefSeq:WP_005793717.1
COORDINATES: similar to AA sequence:RefSeq:WP_013519549.1
COORDINATES: similar to AA sequence:RefSeq:WP_017900682.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016243538.1
COORDINATES: protein motif:HMM:NF023227.2
COORDINATES: similar to AA sequence:RefSeq:WP_019042280.1
COORDINATES: similar to AA sequence:RefSeq:WP_003081407.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016450895.1
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_012838527.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0015105 - arsenite transmembrane transporter activity [Evidence IEA]
GO:0046685 - response to arsenic-containing substance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016445462.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013721968.1
ArsI/CadI family heavy metal resistance metalloenzyme
COORDINATES: similar to AA sequence:RefSeq:WP_016445460.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_000890580.1
COORDINATES: similar to AA sequence:RefSeq:WP_013804400.1
COORDINATES: similar to AA sequence:RefSeq:WP_015012943.1
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015012942.1
COORDINATES: similar to AA sequence:RefSeq:WP_003098961.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015913615.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
Cd(II)/Pb(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015012939.1
GO:0004359 - glutaminase activity [Evidence IEA]; GO:0003952 - NAD+ synthase (glutamine-hydrolyzing) activity [Evidence IEA]; GO:0008795 - NAD+ synthase activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
frameshifted; internal stop; 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_015012936.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003121561.1
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.
COORDINATES: similar to AA sequence:RefSeq:WP_014509628.1
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_004337220.1
COORDINATES: similar to AA sequence:RefSeq:WP_003153636.1
COORDINATES: similar to AA sequence:RefSeq:WP_004538188.1
COORDINATES: similar to AA sequence:RefSeq:WP_005015689.1
type IV toxin-antitoxin system AbiEi family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007162636.1
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003052529.1
COORDINATES: similar to AA sequence:RefSeq:WP_007851356.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]