Xanthobacter dioxanivorans strain YN2 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Xanthobacteraceae; Xanthobacter.
Degradation of 1,4-Dioxane by Xanthobacter sp. YN2
Submitted (23-OCT-2020) Environment, Harbin Institute of Technology, No. 73 Huanghe Road, Harbin, Heilongjiang 150090, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP063363.1.\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. Feb-2018\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 220.97x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 01/04/2023 02:42:34\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 6,351\nCDSs (total) :: 6,292\nGenes (coding) :: 5,987\nCDSs (with protein) :: 5,987\nGenes (RNA) :: 59\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 4\nPseudo Genes (total) :: 305\nCDSs (without protein) :: 305\nPseudo Genes (ambiguous residues) :: 0 of 305\nPseudo Genes (frameshifted) :: 196 of 305\nPseudo Genes (incomplete) :: 144 of 305\nPseudo Genes (internal stop) :: 20 of 305\nPseudo Genes (multiple problems) :: 50 of 305\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Xanthobacter dioxanivorans
COORDINATES: similar to AA sequence:RefSeq:WP_003523837.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF018152.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011505305.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
Ti-type conjugative transfer system protein TraG
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_006832494.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654902.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477327.1
COORDINATES: protein motif:HMM:NF024626.2
COORDINATES: protein motif:HMM:NF012703.2
COORDINATES: similar to AA sequence:RefSeq:WP_010974888.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018238686.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012706353.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018482054.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655024.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505296.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578767.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578766.1
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_012655055.1
COORDINATES: similar to AA sequence:RefSeq:WP_018390218.1
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_011993004.1
COORDINATES: similar to AA sequence:RefSeq:WP_003525125.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993002.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018096562.1
internal stop; 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_013913714.1
COORDINATES: similar to AA sequence:RefSeq:WP_018481377.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011993001.1
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611865.1
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_012483840.1
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_006329629.1
DsbE family thiol:disulfide interchange protein
COORDINATES: similar to AA sequence:RefSeq:WP_002718022.1
COORDINATES: similar to AA sequence:RefSeq:WP_018234700.1
COORDINATES: similar to AA sequence:RefSeq:WP_002718026.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [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_008875183.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012092600.1
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012114889.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092602.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332372.1
COORDINATES: protein motif:HMM:NF028226.2
cation transporter dimerization domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003508794.1
COORDINATES: similar to AA sequence:RefSeq:WP_007539096.1
COORDINATES: similar to AA sequence:RefSeq:WP_010512305.1
COORDINATES: similar to AA sequence:RefSeq:WP_001138082.1
COORDINATES: similar to AA sequence:RefSeq:WP_006178571.1
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019173060.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011579711.1
FAD-linked oxidase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006018763.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione S-transferase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013500414.1
COORDINATES: similar to AA sequence:RefSeq:WP_008834688.1
COORDINATES: similar to AA sequence:RefSeq:WP_002713034.1
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018428191.1
GO:0004362 - glutathione-disulfide reductase (NADPH) activity [Evidence IEA]
GO:0045454 - cell redox homeostasis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019955798.1
COORDINATES: similar to AA sequence:RefSeq:WP_019197712.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006018748.1
COORDINATES: similar to AA sequence:RefSeq:WP_002713038.1
COORDINATES: similar to AA sequence:RefSeq:WP_002713039.1
COORDINATES: similar to AA sequence:RefSeq:WP_002716820.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: similar to AA sequence:RefSeq:WP_019140267.1
CaiB/BaiF CoA-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611229.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611221.1
frameshifted; 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_012562462.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011982795.1
frameshifted; 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_020818539.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982997.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502925.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010399276.1
COORDINATES: similar to AA sequence:RefSeq:WP_011509171.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011390589.1
COORDINATES: similar to AA sequence:RefSeq:WP_011996094.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: similar to AA sequence:RefSeq:WP_011997539.1
IS1380-like element ISPme1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_015840579.1
zinc-dependent alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018331461.1
SMP-30/gluconolactonase/LRE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003568405.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502936.1
COORDINATES: similar to AA sequence:RefSeq:WP_010399291.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_010399294.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502934.1
COORDINATES: similar to AA sequence:RefSeq:WP_014341994.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019200203.1
COORDINATES: similar to AA sequence:RefSeq:WP_010969960.1
COORDINATES: similar to AA sequence:RefSeq:WP_013263588.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502927.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200209.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913713.1
COORDINATES: similar to AA sequence:RefSeq:WP_009338084.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913705.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431405.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611806.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_011505235.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505234.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018448905.1
COORDINATES: similar to AA sequence:RefSeq:WP_008873507.1
COORDINATES: protein motif:HMM:NF012870.2
COORDINATES: protein motif:HMM:NF020606.2
COORDINATES: similar to AA sequence:RefSeq:WP_018391527.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332777.1
COORDINATES: similar to AA sequence:RefSeq:WP_008878427.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011505228.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505227.1
COORDINATES: similar to AA sequence:RefSeq:WP_006205756.1
COORDINATES: similar to AA sequence:RefSeq:WP_018482021.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505223.1
COORDINATES: similar to AA sequence:RefSeq:WP_013984785.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505221.1
COORDINATES: similar to AA sequence:RefSeq:WP_008120552.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_012649097.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010974835.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_018482029.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650736.1
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_012649093.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518529.1
IncP-type conjugal transfer protein TrbI
COORDINATES: protein motif:HMM:NF020789.2
COORDINATES: similar to AA sequence:RefSeq:WP_012112383.1
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_003234665.1
COORDINATES: protein motif:HMM:NF019334.2
COORDINATES: similar to AA sequence:RefSeq:WP_052642793.1
COORDINATES: protein motif:HMM:NF025053.2
protein phosphatase 2C domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003597728.1
COORDINATES: similar to AA sequence:RefSeq:WP_003615680.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505204.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006470243.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046840.1
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_003501350.1