Ancylobacter polymorphus strain ZM13 plasmid pD, 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\nCP083243.1.\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_017956509.1
GO:0045027 - DNA end binding [Evidence IEA]
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010916162.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993002.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564798.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993004.1
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_018390218.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655055.1
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_011578766.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023696.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023695.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019200141.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913795.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011578771.1
COORDINATES: similar to AA sequence:RefSeq:WP_017979475.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012477327.1
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_008121574.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023669.1
COORDINATES: similar to AA sequence:RefSeq:WP_013651064.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578777.1
COORDINATES: similar to AA sequence:RefSeq:WP_003508813.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_014989435.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_003508816.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523838.1
Ti-type conjugative transfer relaxase TraA
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_020046841.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505204.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF024491.2
phospholipase D-like domain-containing protein
COORDINATES: protein motif:HMM:NF024487.2
COORDINATES: similar to AA sequence:RefSeq:WP_007797226.1
COORDINATES: similar to AA sequence:RefSeq:WP_018493259.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913807.1
COORDINATES: protein motif:HMM:NF020789.2
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003523583.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_012649093.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650736.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_018482029.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501279.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_012649097.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020046777.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_011505221.1
COORDINATES: similar to AA sequence:RefSeq:WP_013984785.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505223.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_018098148.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006205756.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505227.1
COORDINATES: similar to AA sequence:RefSeq:WP_018067137.1
COORDINATES: similar to AA sequence:RefSeq:WP_011992914.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008873506.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008873507.1
COORDINATES: protein motif:HMM:NF018259.2
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: similar to AA sequence:RefSeq:WP_011992920.1
COORDINATES: similar to AA sequence:RefSeq:WP_011992921.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913712.1
COORDINATES: similar to AA sequence:RefSeq:WP_012047434.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018289577.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913723.1
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_006023674.1
GO:0003684 - damaged DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003551728.1
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_003525445.1
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]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015314866.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092589.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431440.1
COORDINATES: similar to AA sequence:RefSeq:WP_006697472.1
COORDINATES: similar to AA sequence:RefSeq:WP_007755274.1
GO:0008853 - exodeoxyribonuclease III activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012385723.1
COORDINATES: similar to AA sequence:RefSeq:WP_017967626.1
COORDINATES: similar to AA sequence:RefSeq:WP_010967223.1