Xanthobacter dioxanivorans strain YN2 plasmid unnamed2, 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\nCP063364.1.\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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
2Fe-2S iron-sulfur cluster binding domain-containing protein
COORDINATES: protein motif:HMM:NF012464.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007606984.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017701651.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011930687.1
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015933876.1
COORDINATES: similar to AA sequence:RefSeq:WP_011503753.1
ribbon-helix-helix domain-containing protein
COORDINATES: protein motif:HMM:NF016843.2
COORDINATES: similar to AA sequence:RefSeq:WP_012112998.1
GO:0018784 - (S)-2-haloacid dehalogenase activity [Evidence IEA]
GO:0006805 - xenobiotic metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012427024.1
COORDINATES: protein motif:HMM:NF016244.2
COORDINATES: protein motif:HMM:NF025885.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma 54-interacting transcriptional regulator
COORDINATES: protein motif:HMM:NF014763.2
sensor domain-containing diguanylate cyclase
COORDINATES: protein motif:HMM:NF015431.2
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF013752.2
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_004446686.1
COORDINATES: similar to AA sequence:RefSeq:WP_012115315.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009490546.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012115404.1
COORDINATES: similar to AA sequence:RefSeq:WP_004357770.1
COORDINATES: protein motif:HMM:NF025840.2
COORDINATES: similar to AA sequence:RefSeq:WP_020177422.1
COORDINATES: similar to AA sequence:RefSeq:WP_013169253.1
COORDINATES: similar to AA sequence:RefSeq:WP_014075685.1
class I SAM-dependent DNA methyltransferase
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF016362.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004446714.1
COORDINATES: similar to AA sequence:RefSeq:WP_003598721.1
COORDINATES: similar to AA sequence:RefSeq:WP_020173739.1
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: protein motif:HMM:NF016908.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF023713.2
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_012778853.1
DotI/IcmL family type IV secretion protein
COORDINATES: protein motif:HMM:NF017277.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013700.2
COORDINATES: similar to AA sequence:RefSeq:WP_012634251.1
COORDINATES: protein motif:HMM:TIGR01051.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]; GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF019903.2
COORDINATES: similar to AA sequence:RefSeq:WP_013041597.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018114451.1
COORDINATES: protein motif:HMM:NF025577.2
COORDINATES: protein motif:HMM:NF019324.2
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: protein motif:HMM:NF016921.2
COORDINATES: protein motif:HMM:NF024895.2
COORDINATES: protein motif:HMM:NF019416.2
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: protein motif:HMM:NF028242.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF017736.2
COORDINATES: protein motif:HMM:NF017026.2
COORDINATES: protein motif:HMM:NF025241.2
COORDINATES: similar to AA sequence:RefSeq:WP_019405863.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009796418.1
COORDINATES: similar to AA sequence:RefSeq:WP_003802960.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008141141.1
COORDINATES: protein motif:HMM:TIGR04346.1
COORDINATES: protein motif:HMM:NF020419.2
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012113861.1
COORDINATES: protein motif:HMM:NF021873.2
COORDINATES: similar to AA sequence:RefSeq:WP_005800888.1
COORDINATES: similar to AA sequence:RefSeq:WP_011255179.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016733547.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165276.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549957.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828772.1
COORDINATES: similar to AA sequence:RefSeq:WP_007600568.1
COORDINATES: protein motif:HMM:NF018568.2
COORDINATES: similar to AA sequence:RefSeq:WP_009818125.1
COORDINATES: similar to AA sequence:RefSeq:WP_009570211.1
COORDINATES: protein motif:HMM:NF015857.2
COORDINATES: similar to AA sequence:RefSeq:WP_006614272.1
COORDINATES: similar to AA sequence:RefSeq:WP_013076037.1
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009030992.1