Photobacterium toruni strain WD2103 plasmid unnamed2, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Photobacterium.
Photobacterium toruni isolated from olive flounder(Paralichthys olivaceus) in Korea: pathogenicity and completed genome sequences
Submitted (21-JUL-2022) Department of Aqualife Medical Sciences, Chonnam National University, 50, Daehak-ro, Yeosu-si, Yeosu 59626, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP101697.1.\nBacteria and source DNA available from Department of Aqualife\nMedicine, Chonnam National University, Yeosu, Republic of\nKorea-59626.\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 Date :: 25-MAR-2021\nAssembly Method :: Unicycler v. V0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/31/2022 10:22:48\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.2\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,319\nCDSs (total) :: 4,037\nGenes (coding) :: 3,963\nCDSs (with protein) :: 3,963\nGenes (RNA) :: 282\nrRNAs :: 22, 20, 20 (5S, 16S, 23S)\ncomplete rRNAs :: 22, 20, 20 (5S, 16S, 23S)\ntRNAs :: 216\nncRNAs :: 4\nPseudo Genes (total) :: 74\nCDSs (without protein) :: 74\nPseudo Genes (ambiguous residues) :: 0 of 74\nPseudo Genes (frameshifted) :: 18 of 74\nPseudo Genes (incomplete) :: 51 of 74\nPseudo Genes (internal stop) :: 22 of 74\nPseudo Genes (multiple problems) :: 14 of 74\nCRISPR Arrays :: 3\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_016402481.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010385708.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954901.1
COORDINATES: protein motif:HMM:NF016247.2
COORDINATES: similar to AA sequence:RefSeq:WP_008374842.1
COORDINATES: protein motif:HMM:NF015669.2
COORDINATES: similar to AA sequence:RefSeq:WP_000343613.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076612096.1
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_015740484.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611742.1
frameshifted; 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_005536335.1
COORDINATES: similar to AA sequence:RefSeq:WP_005452155.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017101741.1
COORDINATES: similar to AA sequence:RefSeq:WP_017051799.1
COORDINATES: similar to AA sequence:RefSeq:WP_002044001.1
COORDINATES: similar to AA sequence:RefSeq:WP_014727914.1
COORDINATES: protein motif:HMM:NF016408.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612263.1
COORDINATES: protein motif:HMM:NF012245.2
COORDINATES: protein motif:HMM:NF012863.2
COORDINATES: protein motif:HMM:NF024140.2
IS1595-like element ISPma1 family transposase
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611522.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016785054.1
COORDINATES: similar to AA sequence:RefSeq:WP_012976048.1
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_016785056.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000985865.1
chemotaxis response regulator protein-glutamate methylesterase
COORDINATES: similar to AA sequence:RefSeq:WP_005300506.1
protein-glutamate O-methyltransferase CheR
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
frameshifted; 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:NF012894.2
COORDINATES: protein motif:HMM:NF006584.0
MotA/TolQ/ExbB proton channel family protein
COORDINATES: protein motif:HMM:NF014143.2
flagellar hook-basal body complex protein FliE
COORDINATES: protein motif:HMM:NF013236.2
FliM/FliN family flagellar motor C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF012973.2
COORDINATES: protein motif:HMM:TIGR03170.1
GO:0009428 - bacterial-type flagellum basal body, distal rod, P ring [Evidence IEA]
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0001539 - cilium or flagellum-dependent cell motility [Evidence IEA]
flagellar basal body P-ring formation chaperone FlgA
COORDINATES: protein motif:HMM:NF013838.2
FliG C-terminal domain-containing protein
COORDINATES: protein motif:HMM:TIGR00206.1
GO:0009431 - bacterial-type flagellum basal body, MS ring [Evidence IEA]
flagellar basal-body MS-ring/collar protein FliF
COORDINATES: protein motif:HMM:TIGR02937.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF014206.2
flagellar basal body P-ring protein FlgI
COORDINATES: protein motif:HMM:NF014195.2
flagellar basal body L-ring protein FlgH
COORDINATES: protein motif:HMM:TIGR02488.1
GO:0009426 - bacterial-type flagellum basal body, distal rod [Evidence IEA]
GO:0071973 - bacterial-type flagellum-dependent cell motility [Evidence IEA]
COORDINATES: protein motif:HMM:NF018168.2
flagellar basal body rod C-terminal domain-containing protein
COORDINATES: protein motif:HMM:TIGR03506.1
COORDINATES: protein motif:HMM:NF015896.2
flagellar hook capping FlgD N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011636636.1
GO:0009425 - bacterial-type flagellum basal body [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01396.1
GO:0009429 - bacterial-type flagellum basal body, proximal rod [Evidence IEA]
COORDINATES: protein motif:HMM:NF014196.2
COORDINATES: protein motif:HMM:NF016250.2
COORDINATES: similar to AA sequence:RefSeq:WP_014708076.1
The bacterial flagellar biogenesis protein FliP forms a type III secretion system (T3SS)-type pore required for flagellar assembly.; The bacterial flagellar biogenesis protein FliP forms a type III secretion system (T3SS)-type pore required for flagellar assembly; Derived by automated computational analysis using gene prediction method: Protein Homology.
flagellar type III secretion system pore protein FliP
COORDINATES: similar to AA sequence:RefSeq:WP_008955244.1
GO:0009288 - bacterial-type flagellum [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01400.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0044780 - bacterial-type flagellum assembly [Evidence IEA]; GO:0006605 - protein targeting [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00328.1
COORDINATES: protein motif:HMM:NF018852.2
GO:0007155 - cell adhesion [Evidence IEA]
COORDINATES: protein motif:HMM:NF014604.2
COORDINATES: similar to AA sequence:RefSeq:WP_010385676.1
COORDINATES: protein motif:HMM:NF012874.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612230.1
COORDINATES: similar to AA sequence:RefSeq:WP_005366907.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558267.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014144.2