Xanthomonas oryzae pv. oryzicola strain GX01 plasmid pXOCgx01, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas.
Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola
Submitted (07-APR-2015) College of Life Science and Technology, Guangxi University, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Daxue East Road NO.100, Nanning, Guangxi 530004, China
REFSEQ INFORMATION: The reference sequence is identical to\nKR071788.1.\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##Assembly-Data-START##\nAssembly Method :: SOAPdenovo v. 2.0; Sequencher v. 5.1\nCoverage :: 1179X\nSequencing Technology :: Whole genome shotgun sequencing by Solexa\n and subclone library sequencing by ABI\n 3730, gaps finished by PCR\nGene Prediction :: Glimmer 3.02; GeneMarkS\n##Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/19/2023 14:58:42\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,420\nCDSs (total) :: 4,197\nGenes (coding) :: 3,698\nCDSs (with protein) :: 3,698\nGenes (RNA) :: 223\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 54\nncRNAs :: 163\nPseudo Genes (total) :: 499\nCDSs (without protein) :: 499\nPseudo Genes (ambiguous residues) :: 0 of 499\nPseudo Genes (frameshifted) :: 235 of 499\nPseudo Genes (incomplete) :: 297 of 499\nPseudo Genes (internal stop) :: 139 of 499\nPseudo Genes (multiple problems) :: 157 of 499\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
College of Life Science and Technology, Guangxi University
COORDINATES: similar to AA sequence:RefSeq:WP_017154765.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017113458.1
COORDINATES: similar to AA sequence:RefSeq:WP_008576026.1
COORDINATES: similar to AA sequence:RefSeq:WP_019238176.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008575014.1
COORDINATES: similar to AA sequence:RefSeq:WP_017113447.1
COORDINATES: similar to AA sequence:RefSeq:WP_017154897.1
COORDINATES: similar to AA sequence:RefSeq:WP_017172642.1
COORDINATES: similar to AA sequence:RefSeq:WP_011052937.1
COORDINATES: similar to AA sequence:RefSeq:WP_007966864.1
COORDINATES: similar to AA sequence:RefSeq:WP_017164708.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017157753.1
COORDINATES: similar to AA sequence:RefSeq:WP_019303585.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017158763.1
COORDINATES: similar to AA sequence:RefSeq:WP_011052981.1
COORDINATES: similar to AA sequence:RefSeq:WP_007968770.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008343655.1
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_005931779.1
COORDINATES: similar to AA sequence:RefSeq:WP_011345603.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_019303576.1
COORDINATES: similar to AA sequence:RefSeq:WP_017160491.1
COORDINATES: similar to AA sequence:RefSeq:WP_011345606.1
COORDINATES: similar to AA sequence:RefSeq:WP_015462617.1
COORDINATES: similar to AA sequence:RefSeq:WP_017161282.1
COORDINATES: similar to AA sequence:RefSeq:WP_005931796.1
COORDINATES: similar to AA sequence:RefSeq:WP_003490875.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_017164441.1
COORDINATES: similar to AA sequence:RefSeq:WP_003490957.1
COORDINATES: similar to AA sequence:RefSeq:WP_017113410.1
COORDINATES: similar to AA sequence:RefSeq:WP_017113411.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF025358.2
COORDINATES: similar to AA sequence:RefSeq:WP_005933813.1
COORDINATES: similar to AA sequence:RefSeq:WP_016851366.1
COORDINATES: similar to AA sequence:RefSeq:WP_017163983.1
COORDINATES: similar to AA sequence:RefSeq:WP_008264696.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005411763.1
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_014236233.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_003138995.1
COORDINATES: similar to AA sequence:RefSeq:WP_017355543.1
COORDINATES: similar to AA sequence:RefSeq:WP_005414985.1
COORDINATES: similar to AA sequence:RefSeq:WP_004210815.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_014159631.1
COORDINATES: similar to AA sequence:RefSeq:WP_014159630.1
COORDINATES: similar to AA sequence:RefSeq:WP_005996627.1
COORDINATES: similar to AA sequence:RefSeq:WP_014159628.1
COORDINATES: similar to AA sequence:RefSeq:WP_007971051.1
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_076611205.1
GO:0004803 - transposase activity [Evidence IEA]
Tn3-like element TnXo19 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_017113439.1
COORDINATES: similar to AA sequence:RefSeq:WP_017113441.1
COORDINATES: similar to AA sequence:RefSeq:WP_017164699.1
COORDINATES: similar to AA sequence:RefSeq:WP_017164628.1
COORDINATES: similar to AA sequence:RefSeq:WP_017113443.1