Vibrio azureus strain LC2-005 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
Submitted (05-DEC-2016) Marine Microbiology, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nCP018618.1.\nMolecules not circularized.\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 :: Newbler v. 2.7\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 55.6x\nSequencing Technology :: 454\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 07:52:38\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) :: 4,319\nCDSs (total) :: 4,170\nGenes (coding) :: 4,102\nCDSs (with protein) :: 4,102\nGenes (RNA) :: 149\nrRNAs :: 11, 10, 10 (5S, 16S, 23S)\ncomplete rRNAs :: 11, 10, 10 (5S, 16S, 23S)\ntRNAs :: 114\nncRNAs :: 4\nPseudo Genes (total) :: 68\nCDSs (without protein) :: 68\nPseudo Genes (ambiguous residues) :: 0 of 68\nPseudo Genes (frameshifted) :: 28 of 68\nPseudo Genes (incomplete) :: 52 of 68\nPseudo Genes (internal stop) :: 16 of 68\nPseudo Genes (multiple problems) :: 24 of 68\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_005372765.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005372767.1
COORDINATES: similar to AA sequence:RefSeq:WP_017052758.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176793.1
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_017002846.1
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF020355.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
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:NF018836.2
GO:0019867 - outer membrane [Evidence IEA]
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:TIGR02747.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: protein motif:HMM:NF041281.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:TIGR02746.1
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_001170921.1
COORDINATES: similar to AA sequence:RefSeq:WP_017134217.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF022337.2
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_017079546.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012128579.1
COORDINATES: protein motif:HMM:NF025047.2
COORDINATES: similar to AA sequence:RefSeq:WP_012127722.1
COORDINATES: protein motif:HMM:NF015377.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]
cysteine peptidase family C39 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_086558335.1
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_005974421.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
protease Lon-related BREX system protein BrxL
COORDINATES: similar to AA sequence:RefSeq:WP_005444588.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005444577.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
BREX-1 system adenine-specific DNA-methyltransferase PglX
COORDINATES: similar to AA sequence:RefSeq:WP_005444576.1
COORDINATES: similar to AA sequence:RefSeq:WP_006071675.1
COORDINATES: similar to AA sequence:RefSeq:WP_006071676.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954222.1
COORDINATES: similar to AA sequence:RefSeq:WP_017822012.1
COORDINATES: similar to AA sequence:RefSeq:WP_016767830.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: similar to AA sequence:RefSeq:WP_017085245.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03033.1
COORDINATES: similar to AA sequence:RefSeq:WP_004729594.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF022433.2
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: similar to AA sequence:RefSeq:WP_004929849.1
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF014044.2
COORDINATES: similar to AA sequence:RefSeq:WP_017789123.1
COORDINATES: protein motif:HMM:NF025789.2
COORDINATES: protein motif:HMM:NF022602.2
COORDINATES: protein motif:HMM:NF024702.2
leucine-rich repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004741866.1
internal stop; 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_016767832.1
COORDINATES: similar to AA sequence:RefSeq:WP_006712091.1
COORDINATES: similar to AA sequence:RefSeq:WP_004522719.1
COORDINATES: similar to AA sequence:RefSeq:WP_010378842.1
COORDINATES: similar to AA sequence:RefSeq:WP_017629982.1
COORDINATES: protein motif:HMM:NF017528.2
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_017010907.1
COORDINATES: protein motif:HMM:NF022019.2
COORDINATES: similar to AA sequence:RefSeq:WP_017085272.1
COORDINATES: similar to AA sequence:RefSeq:WP_010308590.1