Vibrio chagasii strain LMG 21353 plasmid p3, 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\nAP025469.1.\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+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF016232.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016767832.1
COORDINATES: similar to AA sequence:RefSeq:WP_008219613.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF014950.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017106702.1
COORDINATES: similar to AA sequence:RefSeq:WP_017818867.1
COORDINATES: similar to AA sequence:RefSeq:WP_004745260.1
COORDINATES: similar to AA sequence:RefSeq:WP_017098244.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017098243.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017107327.1
COORDINATES: similar to AA sequence:RefSeq:WP_017107123.1
COORDINATES: protein motif:HMM:NF012920.2
COORDINATES: protein motif:HMM:NF017333.2
COORDINATES: similar to AA sequence:RefSeq:WP_016799708.1
type IV conjugative transfer system pilin TraA
COORDINATES: similar to AA sequence:RefSeq:WP_017087952.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_017106246.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_004744180.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_016790711.1
COORDINATES: similar to AA sequence:RefSeq:WP_016787044.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_017106250.1
COORDINATES: protein motif:HMM:TIGR02744.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_016790715.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_017108470.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_017108471.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_017082647.1
type-F conjugative transfer system mating-pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_017818166.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: similar to AA sequence:RefSeq:WP_016768055.1
type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB
COORDINATES: similar to AA sequence:RefSeq:WP_017108476.1
COORDINATES: similar to AA sequence:RefSeq:WP_017085686.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017085687.1
COORDINATES: similar to AA sequence:RefSeq:WP_017106855.1
COORDINATES: similar to AA sequence:RefSeq:WP_016799657.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_017085511.1
conjugative transfer relaxase/helicase TraI
COORDINATES: similar to AA sequence:RefSeq:WP_017085512.1
COORDINATES: similar to AA sequence:RefSeq:WP_017060513.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF012451.2
COORDINATES: protein motif:HMM:NF025438.2
COORDINATES: similar to AA sequence:RefSeq:WP_012548964.1
COORDINATES: similar to AA sequence:RefSeq:WP_019826172.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_016768695.1
COORDINATES: similar to AA sequence:RefSeq:WP_017097181.1
COORDINATES: similar to AA sequence:RefSeq:WP_016788557.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004738054.1
COORDINATES: similar to AA sequence:RefSeq:WP_017104697.1