Citrobacter arsenatis strain LY-1 plasmid unnamed2, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Citrobacter.
Complete genome sequence of an arsenate-respiring bacteria, Citrobacter sp. LY-1
Submitted (07-MAR-2019) School of Environmental Science, Hubei Polytechnic University, Guilin North Street, Huangshi, Hubei 435003, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP037863.1.\nBacteria and source DNA available from Jiexun Huang.\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 :: SOAPdenovo v. 2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 12.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/05/2023 02:56:38\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) :: 5,135\nCDSs (total) :: 5,019\nGenes (coding) :: 4,949\nCDSs (with protein) :: 4,949\nGenes (RNA) :: 116\nrRNAs :: 9, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 8, 8 (5S, 16S, 23S)\ntRNAs :: 83\nncRNAs :: 8\nPseudo Genes (total) :: 70\nCDSs (without protein) :: 70\nPseudo Genes (ambiguous residues) :: 0 of 70\nPseudo Genes (frameshifted) :: 26 of 70\nPseudo Genes (incomplete) :: 44 of 70\nPseudo Genes (internal stop) :: 19 of 70\nPseudo Genes (multiple problems) :: 15 of 70\nPseudo Genes (short protein) :: 1 of 70\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:NP_490553.1
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:YP_005229757.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008322852.1
COORDINATES: similar to AA sequence:RefSeq:WP_000274531.1
COORDINATES: similar to AA sequence:RefSeq:WP_001198918.1
COORDINATES: similar to AA sequence:RefSeq:WP_017694197.1
COORDINATES: similar to AA sequence:RefSeq:WP_001568043.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229763.1
COORDINATES: similar to AA sequence:RefSeq:NP_490548.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322842.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322841.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322839.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322837.1
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004146678.1
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_490545.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:NP_490544.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008322834.1
COORDINATES: similar to AA sequence:RefSeq:WP_020314634.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_008322830.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322828.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001575478.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_004213077.1
COORDINATES: similar to AA sequence:RefSeq:WP_000990619.1
COORDINATES: similar to AA sequence:RefSeq:WP_012540156.1
frameshifted; internal stop; 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_000105383.1
COORDINATES: similar to AA sequence:RefSeq:WP_005286570.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005294177.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
dual specificity protein phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011911478.1
GO:0016311 - dephosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF012602.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005494631.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
4Fe-4S dicluster domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004206664.1
COORDINATES: similar to AA sequence:RefSeq:WP_000855179.1
arsenite efflux transporter metallochaperone ArsD
COORDINATES: similar to AA sequence:RefSeq:WP_131199602.1
arsenite efflux transporter ATPase subunit ArsA
COORDINATES: similar to AA sequence:RefSeq:WP_012540054.1
arsenite efflux transporter membrane subunit ArsB
COORDINATES: similar to AA sequence:RefSeq:NP_417960.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
glutaredoxin-dependent arsenate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_008785735.1
COORDINATES: similar to AA sequence:RefSeq:WP_000100193.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000799343.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001057013.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0015446 - ATPase-coupled arsenite transmembrane transporter activity [Evidence IEA]
GO:0071722 - detoxification of arsenic-containing substance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000034287.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
arsenic metallochaperone ArsD family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001286342.1
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: similar to AA sequence:RefSeq:WP_013095191.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001175593.1
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_001089730.1
GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001374687.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002425201.1
COORDINATES: similar to AA sequence:RefSeq:WP_007778984.1
COORDINATES: similar to AA sequence:RefSeq:WP_019843121.1
COORDINATES: similar to AA sequence:RefSeq:WP_000099160.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004966400.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
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: similar to AA sequence:RefSeq:WP_004388333.1
COORDINATES: similar to AA sequence:RefSeq:WP_001480786.1
COORDINATES: similar to AA sequence:RefSeq:WP_001378118.1
copper resistance outer membrane transporter PcoB
COORDINATES: similar to AA sequence:RefSeq:WP_004098941.1
copper resistance system metallochaperone PcoC
COORDINATES: similar to AA sequence:RefSeq:WP_004098940.1
copper resistance inner membrane protein PcoD
COORDINATES: similar to AA sequence:RefSeq:WP_020239536.1
copper response regulator transcription factor PcoR
COORDINATES: similar to AA sequence:RefSeq:WP_001211179.1
copper resistance membrane spanning protein PcoS
COORDINATES: similar to AA sequence:RefSeq:WP_000723069.1
COORDINATES: similar to AA sequence:RefSeq:WP_004152086.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004118348.1
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]
COORDINATES: similar to AA sequence:RefSeq:WP_011906492.1
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_001568530.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000647571.1
COORDINATES: similar to AA sequence:RefSeq:WP_000790485.1
COORDINATES: similar to AA sequence:RefSeq:WP_004385431.1
copper/silver sensor histidine kinase SilS
COORDINATES: similar to AA sequence:RefSeq:WP_001572351.1
copper/silver response regulator transcription factor SilR
COORDINATES: similar to AA sequence:RefSeq:WP_001572989.1
Cu(+)/Ag(+) efflux RND transporter outer membrane channel SilC
COORDINATES: similar to AA sequence:RefSeq:WP_009654303.1
COORDINATES: similar to AA sequence:RefSeq:WP_017146627.1
Cu(+)/Ag(+) efflux RND transporter periplasmic adaptor subunit SilB
COORDINATES: similar to AA sequence:RefSeq:WP_011711636.1
Cu(+)/Ag(+) efflux RND transporter permease subunit SilA
COORDINATES: similar to AA sequence:RefSeq:WP_002436620.1
COORDINATES: similar to AA sequence:RefSeq:WP_032489447.1
COORDINATES: similar to AA sequence:RefSeq:WP_000843499.1
COORDINATES: similar to AA sequence:RefSeq:WP_002436617.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001721177.1
COORDINATES: similar to AA sequence:RefSeq:WP_001403295.1
COORDINATES: similar to AA sequence:RefSeq:WP_001670144.1
GO:0006276 - plasmid maintenance [Evidence IEA]
incFII family plasmid replication initiator RepA
COORDINATES: similar to AA sequence:RefSeq:WP_011906583.1
COORDINATES: similar to AA sequence:RefSeq:WP_008324884.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
conjugative transfer relaxase/helicase TraI
COORDINATES: similar to AA sequence:RefSeq:WP_008324886.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_008324889.1
type II toxin-antitoxin system CcdA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_008324890.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003018683.1
conjugal transfer complement resistance protein TraT
COORDINATES: similar to AA sequence:RefSeq:WP_007853387.1
conjugal transfer mating-pair stabilization protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_019843239.1
conjugal transfer pilus assembly protein TraH
COORDINATES: similar to AA sequence:RefSeq:WP_008324897.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087217.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: similar to AA sequence:RefSeq:WP_019843233.1
type-F conjugative transfer system mating-pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_019843232.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_007853415.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_008325099.1
COORDINATES: similar to AA sequence:RefSeq:WP_008325098.1
COORDINATES: similar to AA sequence:RefSeq:WP_008325090.1
COORDINATES: similar to AA sequence:RefSeq:WP_008325089.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_008325088.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_008325087.1
COORDINATES: similar to AA sequence:RefSeq:WP_008325086.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_013087198.1
F-type conjugal transfer pilus assembly protein TraB
COORDINATES: similar to AA sequence:RefSeq:WP_008324955.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_008324957.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_008324958.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_008324959.1
GO:0005576 - extracellular region [Evidence IEA]
type IV conjugative transfer system pilin TraA
COORDINATES: similar to AA sequence:RefSeq:WP_008324960.1
COORDINATES: similar to AA sequence:RefSeq:WP_008324961.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512865.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013087187.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906551.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229741.1
type I toxin-antitoxin system Hok family toxin
COORDINATES: protein motif:HMM:NF036604.2
COORDINATES: similar to AA sequence:RefSeq:NP_490554.1
COORDINATES: similar to AA sequence:RefSeq:WP_001311849.1
COORDINATES: similar to AA sequence:RefSeq:WP_014063861.1
COORDINATES: similar to AA sequence:RefSeq:WP_001825190.1
COORDINATES: similar to AA sequence:RefSeq:WP_019843213.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229743.1
COORDINATES: similar to AA sequence:RefSeq:WP_004194229.1
COORDINATES: similar to AA sequence:RefSeq:WP_015572066.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087156.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_016495618.1
COORDINATES: similar to AA sequence:RefSeq:WP_007853467.1
COORDINATES: similar to AA sequence:RefSeq:WP_000555355.1
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_008322857.1
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_000218652.1
COORDINATES: similar to AA sequence:RefSeq:WP_001148822.1