Vibrio chagasii strain LMG 21353 plasmid p1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach
DOI:10.1007/s00284-021-02725-0 Publication Status: Online-Only
Submitted (05-JAN-2022) Contact:Tomoo Sawabe Hokkaido University, Faculty of Fisheries Sciences; 3-1-1 Minato-cho, Hakodate, Hokkaido 041-8611, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP025467.1.\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 :: Unicycler v. 0.4.8; Flye v. 2.8.3\nGenome Coverage :: 140x\nSequencing Technology :: Illumina MiSeq; Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/29/2022 11:15:21\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 5,112\nCDSs (total) :: 4,928\nGenes (coding) :: 4,803\nCDSs (with protein) :: 4,803\nGenes (RNA) :: 184\nrRNAs :: 15, 14, 14 (5S, 16S, 23S)\ncomplete rRNAs :: 15, 14, 14 (5S, 16S, 23S)\ntRNAs :: 137\nncRNAs :: 4\nPseudo Genes (total) :: 125\nCDSs (without protein) :: 125\nPseudo Genes (ambiguous residues) :: 0 of 125\nPseudo Genes (frameshifted) :: 58 of 125\nPseudo Genes (incomplete) :: 60 of 125\nPseudo Genes (internal stop) :: 35 of 125\nPseudo Genes (multiple problems) :: 25 of 125\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0008236 - serine-type peptidase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024642.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013311.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF024754.2
COORDINATES: protein motif:HMM:NF016855.2
TfoX/Sxy family DNA transformation protein
COORDINATES: protein motif:HMM:NF022835.2
COORDINATES: protein motif:HMM:NF024108.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF023713.2
DotH/IcmK family type IV secretion protein
COORDINATES: protein motif:HMM:NF018028.2
COORDINATES: similar to AA sequence:RefSeq:WP_007583928.1
GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011998875.1
COORDINATES: similar to AA sequence:RefSeq:WP_004744686.1
COORDINATES: similar to AA sequence:RefSeq:WP_016766871.1
HNH endonuclease signature motif containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016788556.1
COORDINATES: similar to AA sequence:RefSeq:WP_016788557.1
Fe3+-citrate ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004637882.1
COORDINATES: similar to AA sequence:RefSeq:WP_016800593.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_011261952.1
COORDINATES: similar to AA sequence:RefSeq:WP_009838282.1
COORDINATES: similar to AA sequence:RefSeq:WP_000929401.1
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010434886.1
COORDINATES: similar to AA sequence:RefSeq:WP_010434885.1
COORDINATES: similar to AA sequence:RefSeq:WP_008760287.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF016160.2
SoxR reducing system RseC family protein
COORDINATES: protein motif:HMM:NF028242.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF012485.2
COORDINATES: protein motif:HMM:NF016281.2
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR04346.1
COORDINATES: protein motif:HMM:NF013878.2
COORDINATES: protein motif:HMM:NF013632.2
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: protein motif:HMM:NF025438.2
COORDINATES: similar to AA sequence:RefSeq:WP_017015861.1
COORDINATES: protein motif:HMM:NF037425.2
COORDINATES: similar to AA sequence:RefSeq:WP_004681960.1
COORDINATES: protein motif:HMM:NF023254.2
COORDINATES: similar to AA sequence:RefSeq:WP_017041248.1
PDDEXK nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015068678.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017016910.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:TIGR02012.1
GO:0008094 - ATP-dependent activity, acting on DNA [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]