Vibrio chagasii strain LMG 21353 plasmid p2, 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\nAP025468.1.\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: similar to AA sequence:RefSeq:WP_016785901.1
GO:0044423 - virion component [Evidence IEA]
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0016032 - viral process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016736.2
COORDINATES: similar to AA sequence:RefSeq:WP_016785897.1
COORDINATES: similar to AA sequence:RefSeq:WP_016785895.1
COORDINATES: similar to AA sequence:RefSeq:WP_016785893.1
GO:0019068 - virion assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016785892.1
COORDINATES: similar to AA sequence:RefSeq:WP_000002848.1
COORDINATES: protein motif:HMM:NF017192.2
COORDINATES: similar to AA sequence:RefSeq:WP_005424553.1
COORDINATES: similar to AA sequence:RefSeq:WP_012127736.1
COORDINATES: similar to AA sequence:RefSeq:WP_012127735.1
COORDINATES: similar to AA sequence:RefSeq:WP_005376957.1
COORDINATES: similar to AA sequence:RefSeq:WP_010650674.1
COORDINATES: similar to AA sequence:RefSeq:WP_000203897.1
COORDINATES: similar to AA sequence:RefSeq:WP_012127732.1
phage terminase large subunit family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010650678.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016786044.1
COORDINATES: similar to AA sequence:RefSeq:WP_016786043.1
COORDINATES: similar to AA sequence:RefSeq:WP_016786041.1
COORDINATES: protein motif:HMM:NF027406.2
COORDINATES: similar to AA sequence:RefSeq:WP_016786039.1
COORDINATES: similar to AA sequence:RefSeq:WP_001266128.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF003765.0
GO:0000175 - 3'-5'-exoribonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000168322.1
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: similar to AA sequence:RefSeq:WP_000471965.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016281.2
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005424581.1
COORDINATES: similar to AA sequence:RefSeq:WP_008986136.1
COORDINATES: similar to AA sequence:RefSeq:WP_016786025.1
COORDINATES: similar to AA sequence:RefSeq:WP_016786021.1
COORDINATES: protein motif:HMM:NF017673.2
COORDINATES: protein motif:HMM:NF014846.2
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012863.2
COORDINATES: similar to AA sequence:RefSeq:WP_008986183.1
COORDINATES: similar to AA sequence:RefSeq:WP_005424544.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_016786070.1
COORDINATES: similar to AA sequence:RefSeq:WP_016786069.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016786068.1
COORDINATES: similar to AA sequence:RefSeq:WP_016785913.1
contractile injection system protein, VgrG/Pvc8 family
COORDINATES: similar to AA sequence:RefSeq:WP_016785912.1
COORDINATES: similar to AA sequence:RefSeq:WP_016785910.1
COORDINATES: similar to AA sequence:RefSeq:WP_016785909.1
COORDINATES: similar to AA sequence:RefSeq:WP_016785907.1
COORDINATES: similar to AA sequence:RefSeq:WP_000896630.1
COORDINATES: similar to AA sequence:RefSeq:WP_000191479.1
phage tail sheath subtilisin-like domain-containing protein