Xanthomonas vesicatoria ATCC 35937 strain LMG911 plasmid pLMG911.1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas.
Complete genome sequences of four Solanaceae pathogen copper-resistant Xanthomonas: X. gardneri, X. euvesicatoria, X. vesicatoria and X. perforans
Submitted (12-DEC-2016) BIOS, CIRAD, 7 ch. de l'IRAT, Saint-Pierre 97410, Reunion
REFSEQ INFORMATION: The reference sequence is identical to\nCP018726.1.\nBacteria and source DNA available from Source DNA is available from\nthe CIRAD research center collection: 7 ch. de IRAT, 97410\nSaint-Pierre, Reunion.\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 :: 2016\nAssembly Method :: SMRT Analysis HGAP protocol v. 2.3\nGenome Coverage :: 151.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/23/2023 02:14:58\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) :: 4,604\nCDSs (total) :: 4,496\nGenes (coding) :: 4,374\nCDSs (with protein) :: 4,374\nGenes (RNA) :: 108\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 46\nPseudo Genes (total) :: 122\nCDSs (without protein) :: 122\nPseudo Genes (ambiguous residues) :: 0 of 122\nPseudo Genes (frameshifted) :: 78 of 122\nPseudo Genes (incomplete) :: 49 of 122\nPseudo Genes (internal stop) :: 19 of 122\nPseudo Genes (multiple problems) :: 21 of 122\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF022580.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:TIGR02762.1
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: protein motif:HMM:NF037161.2
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF013506.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025900.2
COORDINATES: protein motif:HMM:NF037909.2
COORDINATES: similar to AA sequence:RefSeq:WP_014076249.1
COORDINATES: similar to AA sequence:RefSeq:WP_006809794.1
GO:0003824 - catalytic activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF024977.2
COORDINATES: similar to AA sequence:RefSeq:WP_007973427.1
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]
GO:0006139 - nucleobase-containing compound metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012301.2
GO:0000156 - phosphorelay response regulator activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: protein motif:HMM:NF015506.2
GO:0031992 - energy transducer activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024621.2
COORDINATES: similar to AA sequence:RefSeq:WP_019337415.1
GO:0004040 - amidase activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
glucosaminidase domain-containing protein
COORDINATES: protein motif:HMM:NF012442.2
COORDINATES: protein motif:HMM:NF013528.2
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF001464.0
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: protein motif:HMM:NF024578.2
COORDINATES: protein motif:HMM:NF012403.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0140658 - ATP-dependent chromatin remodeler activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014787.2
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03734.1
COORDINATES: protein motif:HMM:TIGR03741.1
COORDINATES: protein motif:HMM:NF025810.2
COORDINATES: protein motif:HMM:TIGR03737.1
COORDINATES: protein motif:HMM:TIGR03735.1
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: protein motif:HMM:NF019843.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF041494.1
COORDINATES: protein motif:HMM:TIGR03743.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: protein motif:HMM:NF024642.2
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: protein motif:HMM:NF012651.2
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF022853.2
protein-disulfide reductase DsbD N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_017154826.1
COORDINATES: similar to AA sequence:RefSeq:WP_011052193.1
COORDINATES: similar to AA sequence:RefSeq:WP_007964591.1
COORDINATES: similar to AA sequence:RefSeq:WP_017163983.1
COORDINATES: similar to AA sequence:RefSeq:WP_014159602.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005413373.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019184740.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005413376.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014159618.1
COORDINATES: similar to AA sequence:RefSeq:WP_012480227.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005413378.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_005996619.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_014159622.1
COORDINATES: similar to AA sequence:RefSeq:WP_005996621.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0015105 - arsenite transmembrane transporter activity [Evidence IEA]
GO:0046685 - response to arsenic-containing substance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012444891.1
COORDINATES: similar to AA sequence:RefSeq:WP_012444890.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014159626.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014159627.1
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_014159628.1
COORDINATES: similar to AA sequence:RefSeq:WP_005996627.1
COORDINATES: similar to AA sequence:RefSeq:WP_012480222.1
COORDINATES: similar to AA sequence:RefSeq:WP_019184732.1
COORDINATES: similar to AA sequence:RefSeq:WP_017354987.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_046934798.1
COORDINATES: similar to AA sequence:RefSeq:WP_005996637.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]
GO:0006825 - copper ion transport [Evidence IEA]
copper resistance system multicopper oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_019184729.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0005507 - copper ion binding [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017354983.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012480215.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012480214.1
COORDINATES: similar to AA sequence:RefSeq:WP_012480213.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005413416.1
GO:0042597 - periplasmic space [Evidence IEA]
copper homeostasis periplasmic binding protein CopC
COORDINATES: similar to AA sequence:RefSeq:WP_017354978.1
copper homeostasis membrane protein CopD
COORDINATES: similar to AA sequence:RefSeq:WP_012480211.1
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_005413412.1
COORDINATES: similar to AA sequence:RefSeq:WP_005995733.1
COORDINATES: similar to AA sequence:RefSeq:WP_016935436.1
GO:0046872 - metal ion binding [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_005995736.1
COORDINATES: similar to AA sequence:RefSeq:WP_012480210.1
COORDINATES: similar to AA sequence:RefSeq:WP_005995740.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447285.1
heavy metal-binding domain-containing protein
COORDINATES: protein motif:HMM:NF027890.2
COORDINATES: similar to AA sequence:RefSeq:WP_005995744.1
COORDINATES: similar to AA sequence:RefSeq:WP_012480207.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_014159632.1
COORDINATES: similar to AA sequence:RefSeq:WP_011345712.1
COORDINATES: similar to AA sequence:RefSeq:WP_011345714.1
COORDINATES: similar to AA sequence:RefSeq:WP_011345715.1
COORDINATES: similar to AA sequence:RefSeq:WP_011345718.1
COORDINATES: similar to AA sequence:RefSeq:WP_011345719.1
COORDINATES: similar to AA sequence:RefSeq:WP_011345720.1
COORDINATES: similar to AA sequence:RefSeq:WP_010486176.1
COORDINATES: similar to AA sequence:RefSeq:WP_017117945.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: protein motif:HMM:NF040044.1
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF018536.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF021981.2