Ancylobacter polymorphus strain ZM13 plasmid pC, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Xanthobacteraceae; Ancylobacter.
Network and meta-omics reveal the key degrader and cooperation patterns in an efficient 1,4-dioxane-degrading microbial community
Submitted (03-SEP-2021) College of Life Sciences, Zhejiang University, Yuhangtang Rode, Hangzhou, Zhejaing 310058, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP083242.1.\nBacteria and source DNA available from Zhenmei Lu, Ph.D, MOE\nLaboratory of Biosystem Homeostasis and Protection, College of Life\nSciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.\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 Date :: AUG-2020\nAssembly Method :: GS De Novo Assembler v. 2.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 99.0x\nSequencing Technology :: Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/21/2023 06:05:36\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) :: 4,980\nCDSs (total) :: 4,919\nGenes (coding) :: 4,834\nCDSs (with protein) :: 4,834\nGenes (RNA) :: 61\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 4\nPseudo Genes (total) :: 85\nCDSs (without protein) :: 85\nPseudo Genes (ambiguous residues) :: 0 of 85\nPseudo Genes (frameshifted) :: 33 of 85\nPseudo Genes (incomplete) :: 72 of 85\nPseudo Genes (internal stop) :: 12 of 85\nPseudo Genes (multiple problems) :: 22 of 85\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_032490240.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011583195.1
COORDINATES: similar to AA sequence:RefSeq:WP_011805390.1
COORDINATES: protein motif:HMM:NF012780.2
COORDINATES: similar to AA sequence:RefSeq:WP_008383496.1
COORDINATES: protein motif:HMM:NF022603.2
COORDINATES: similar to AA sequence:RefSeq:WP_011583199.1
COORDINATES: similar to AA sequence:RefSeq:WP_011583200.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012564647.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015500471.1
GO:0046872 - metal ion binding [Evidence IEA]
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006470251.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653051.1
COORDINATES: similar to AA sequence:RefSeq:WP_005800888.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611490.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012187038.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013913489.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019014756.1
COORDINATES: similar to AA sequence:RefSeq:WP_003525125.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200150.1
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
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011931092.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578767.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501400.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200141.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516741.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011578771.1
COORDINATES: similar to AA sequence:RefSeq:WP_009492047.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015522.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011931089.1
COORDINATES: similar to AA sequence:RefSeq:WP_014248238.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654735.1
COORDINATES: similar to AA sequence:RefSeq:WP_003167764.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092589.1
COORDINATES: similar to AA sequence:RefSeq:WP_017997531.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_011970904.1
COORDINATES: similar to AA sequence:RefSeq:WP_003551142.1
COORDINATES: protein motif:HMM:NF016107.2
COORDINATES: similar to AA sequence:RefSeq:WP_018065860.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065859.1
GO:0031966 - mitochondrial membrane [Evidence IEA]
GO:0033617 - mitochondrial cytochrome c oxidase assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018065858.1
GO:0016531 - copper chaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015599749.1
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_011316288.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009209126.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009209125.1
GO:0005886 - plasma membrane [Evidence IEA]
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_012092647.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013654509.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]; GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_009209121.1
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_007627851.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011428456.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023674.1
GO:0003684 - damaged DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_006023673.1
COORDINATES: similar to AA sequence:RefSeq:WP_015933439.1
COORDINATES: similar to AA sequence:RefSeq:WP_003551577.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930898.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564787.1
COORDINATES: similar to AA sequence:RefSeq:WP_011084500.1
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_007600311.1
COORDINATES: similar to AA sequence:RefSeq:WP_011428412.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016736793.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982997.1
COORDINATES: similar to AA sequence:RefSeq:WP_015823736.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017484568.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017484569.1
COORDINATES: similar to AA sequence:RefSeq:WP_017484570.1
GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017484571.1
COORDINATES: similar to AA sequence:RefSeq:WP_017484572.1
COORDINATES: similar to AA sequence:RefSeq:WP_017484573.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016530 - metallochaperone activity [Evidence IEA]
GO:0019627 - urea metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015823729.1
GO:0016151 - nickel cation binding [Evidence IEA]; GO:0009039 - urease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017484575.1
GO:0035550 - urease complex [Evidence IEA]
GO:0043419 - urea catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018388830.1
COORDINATES: similar to AA sequence:RefSeq:WP_018388831.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018388832.1
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_015823724.1
COORDINATES: similar to AA sequence:RefSeq:WP_006613889.1
COORDINATES: similar to AA sequence:RefSeq:WP_018390857.1
COORDINATES: similar to AA sequence:RefSeq:WP_013167464.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017967252.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611975.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019170255.1
COORDINATES: similar to AA sequence:RefSeq:WP_018387818.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013167960.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
ribosome-associated ATPase/putative transporter RbbA
COORDINATES: similar to AA sequence:RefSeq:WP_013167959.1
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012251879.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391637.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391638.1
COORDINATES: similar to AA sequence:RefSeq:WP_008873509.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_008873507.1
COORDINATES: similar to AA sequence:RefSeq:WP_008873506.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011505053.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505052.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_019200230.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200229.1
COORDINATES: similar to AA sequence:RefSeq:WP_008120987.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200227.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505047.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822431.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015822429.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505044.1
COORDINATES: similar to AA sequence:RefSeq:WP_002719023.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822426.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822425.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023639.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023638.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013912794.1
COORDINATES: similar to AA sequence:RefSeq:WP_012561209.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012561208.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_011664819.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649615.1
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_011578828.1
COORDINATES: protein motif:HMM:NF019283.2
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF019542.2
COORDINATES: similar to AA sequence:RefSeq:WP_006021155.1
COORDINATES: similar to AA sequence:RefSeq:WP_012116574.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993014.1
COORDINATES: similar to AA sequence:RefSeq:WP_018272267.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012631104.1
COORDINATES: protein motif:HMM:NF012257.2
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009209118.1
COORDINATES: similar to AA sequence:RefSeq:WP_019404152.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023727.1
autoinducer binding domain-containing protein
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_006023723.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_006023722.1
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_011505120.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023719.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564818.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023717.1
VirB4 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_006023716.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564815.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023714.1
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_006023712.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564811.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023710.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023709.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023708.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023707.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505106.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564805.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505097.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008282897.1
COORDINATES: similar to AA sequence:RefSeq:WP_013123423.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0008976 - polyphosphate kinase activity [Evidence IEA]
GO:0006793 - phosphorus metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011583173.1
COORDINATES: similar to AA sequence:RefSeq:WP_011583177.1
COORDINATES: similar to AA sequence:RefSeq:WP_018271661.1
GO:0008168 - methyltransferase activity [Evidence IEA]
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015318510.1
GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]; GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA]
cyclopropane-fatty-acyl-phospholipid synthase family protein
COORDINATES: protein motif:HMM:NF018264.2
COORDINATES: similar to AA sequence:RefSeq:WP_008837457.1
COORDINATES: similar to AA sequence:RefSeq:WP_011583182.1
GO:0008804 - carbamate kinase activity [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011995264.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019200253.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039108.1
COORDINATES: similar to AA sequence:RefSeq:WP_011992964.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011992960.1