Ancylobacter pratisalsi strain DSM 102029 plasmid pLGM, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Xanthobacteraceae; Ancylobacter.
Submitted (06-FEB-2020) School of Agriculture and Biology, Key Laboratory of Southwest Rice biology and Genetic Breeding, Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences, Deyang, Sichuan 618000, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP048631.1.\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\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 80.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 01:51:19\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) :: 4,494\nCDSs (total) :: 4,435\nGenes (coding) :: 4,373\nCDSs (with protein) :: 4,373\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) :: 62\nCDSs (without protein) :: 62\nPseudo Genes (ambiguous residues) :: 0 of 62\nPseudo Genes (frameshifted) :: 26 of 62\nPseudo Genes (incomplete) :: 46 of 62\nPseudo Genes (internal stop) :: 11 of 62\nPseudo Genes (multiple problems) :: 19 of 62\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
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]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017484572.1
COORDINATES: similar to AA sequence:RefSeq:WP_017484571.1
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_017484569.1
COORDINATES: similar to AA sequence:RefSeq:WP_017484568.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015823736.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611875.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_009665395.1
GO:0047789 - creatininase activity [Evidence IEA]
GO:0046449 - creatinine metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018387334.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018387333.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018387332.1
COORDINATES: similar to AA sequence:RefSeq:WP_018387331.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]; GO:0019808 - polyamine binding [Evidence IEA]
GO:0015846 - polyamine transport [Evidence IEA]
spermidine/putrescine ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018387330.1
GO:0052717 - tRNA-specific adenosine-34 deaminase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007256169.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013960722.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001030.1
COORDINATES: protein motif:HMM:NF015431.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018387328.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018387327.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018387326.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_018387325.1
GO:0047689 - aspartate racemase activity [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018387324.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015411 - ABC-type taurine transporter transporter activity [Evidence IEA]; GO:0030977 - taurine binding [Evidence IEA]
GO:0015734 - taurine transport [Evidence IEA]
taurine ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018387323.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018387322.1
COORDINATES: similar to AA sequence:RefSeq:WP_013167740.1
GO:0004399 - histidinol dehydrogenase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004180535.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012813213.1
COORDINATES: similar to AA sequence:RefSeq:WP_015499506.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018391663.1
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_018391662.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391661.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_012489489.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_018391658.1
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018391657.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489487.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391655.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_018391653.1
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015003006.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391651.1
COORDINATES: protein motif:HMM:NF010396.0
COORDINATES: protein motif:HMM:NF024487.2
COORDINATES: similar to AA sequence:RefSeq:WP_002719016.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391519.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505047.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391523.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018391524.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018391525.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018391526.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391527.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431405.1
COORDINATES: similar to AA sequence:RefSeq:WP_013525335.1
COORDINATES: similar to AA sequence:RefSeq:WP_005800888.1
COORDINATES: similar to AA sequence:RefSeq:WP_032491591.1
GO:0004803 - transposase activity [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_076611806.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_032490240.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013570627.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003590977.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009113614.1
COORDINATES: similar to AA sequence:RefSeq:WP_008850161.1
COORDINATES: similar to AA sequence:RefSeq:WP_012702315.1
COORDINATES: protein motif:HMM:NF021496.2
COORDINATES: similar to AA sequence:RefSeq:WP_013377824.1
COORDINATES: similar to AA sequence:RefSeq:WP_001515802.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018633972.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014857744.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611858.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819389.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020819388.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018389160.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF016648.2
COORDINATES: similar to AA sequence:RefSeq:WP_011578677.1
COORDINATES: similar to AA sequence:RefSeq:WP_014857716.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469622.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF025091.2
isocitrate lyase/PEP mutase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003898277.1
aconitase/3-isopropylmalate dehydratase large subunit family protein
COORDINATES: protein motif:HMM:TIGR02087.1
COORDINATES: similar to AA sequence:RefSeq:WP_019998818.1
COORDINATES: similar to AA sequence:RefSeq:WP_019998816.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688875.1
GO:0015109 - chromate transmembrane transporter activity [Evidence IEA]
GO:0015703 - chromate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008872370.1
sulfurtransferase/chromate resistance protein
COORDINATES: similar to AA sequence:RefSeq:WP_008535597.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018390380.1
GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018390381.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018390382.1
GO:0015099 - nickel cation transmembrane transporter activity [Evidence IEA]
GO:0035444 - nickel cation transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018390383.1
COORDINATES: similar to AA sequence:RefSeq:WP_014871052.1
COORDINATES: similar to AA sequence:RefSeq:WP_015313468.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611960.1
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_019013976.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018391622.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391621.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018391619.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018391618.1
TadE/TadG family type IV pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_018964219.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391616.1
pilus assembly protein N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018391615.1
COORDINATES: similar to AA sequence:RefSeq:WP_018964220.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391613.1
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03177.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391611.1
type II and III secretion system protein family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018391610.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391608.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391607.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018391606.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391605.1
pilus assembly protein TadG-related protein
COORDINATES: protein motif:HMM:NF024821.2
COORDINATES: similar to AA sequence:RefSeq:WP_007604855.1
COORDINATES: similar to AA sequence:RefSeq:WP_013165444.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_018391600.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_018391599.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391598.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391595.1
COORDINATES: similar to AA sequence:RefSeq:WP_018964227.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391694.1
COORDINATES: protein motif:HMM:TIGR00621.2
COORDINATES: protein motif:HMM:NF017934.2
COORDINATES: similar to AA sequence:RefSeq:WP_018391690.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391688.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_018391687.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993105.1
COORDINATES: protein motif:HMM:TIGR02768.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: protein motif:HMM:NF037136.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611359.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_019561987.1
COORDINATES: protein motif:HMM:TIGR01725.1
COORDINATES: similar to AA sequence:RefSeq:WP_010218926.1
COORDINATES: protein motif:HMM:NF016923.2
GO:0044423 - virion component [Evidence IEA]
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0019068 - virion assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011510872.1
phage regulatory protein/antirepressor Ant
COORDINATES: similar to AA sequence:RefSeq:WP_006613889.1
COORDINATES: similar to AA sequence:RefSeq:WP_015823724.1
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_018388831.1
COORDINATES: similar to AA sequence:RefSeq:WP_018388830.1
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_015823729.1
GO:0016151 - nickel cation binding [Evidence IEA]; GO:0009039 - urease activity [Evidence IEA]