Photobacterium toruni strain WD2103 plasmid unnamed1, 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\nCP101696.1.\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: protein motif:HMM:NF024498.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
thioredoxin fold domain-containing protein
COORDINATES: protein motif:HMM:NF025125.2
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_017190447.1
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF012651.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF017973.2
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:NF023203.2
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF022590.2
COORDINATES: protein motif:HMM:NF015776.2
COORDINATES: protein motif:HMM:TIGR00616.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF016214.2
COORDINATES: similar to AA sequence:RefSeq:WP_011638043.1
COORDINATES: protein motif:HMM:NF015140.2
COORDINATES: protein motif:HMM:NF019237.2
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF017870.2
COORDINATES: protein motif:HMM:NF008729.0
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
GO:0006139 - nucleobase-containing compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001898922.1
COORDINATES: protein motif:HMM:NF012381.2
COORDINATES: protein motif:HMM:NF016296.2
LytTR family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:TIGR00571.1
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
Dam family site-specific DNA-(adenine-N6)-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_005905091.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612096.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_019440458.1
COORDINATES: similar to AA sequence:RefSeq:WP_019440459.1
COORDINATES: similar to AA sequence:RefSeq:WP_019440460.1
COORDINATES: similar to AA sequence:RefSeq:WP_019440461.1
COORDINATES: similar to AA sequence:RefSeq:WP_005477174.1
COORDINATES: similar to AA sequence:RefSeq:WP_011717781.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025388.2
COORDINATES: similar to AA sequence:RefSeq:WP_000343613.1
COORDINATES: similar to AA sequence:RefSeq:WP_005486471.1
COORDINATES: similar to AA sequence:RefSeq:WP_004734912.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF012894.2
COORDINATES: protein motif:HMM:NF017300.2
DNA replication terminus site-binding protein
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:TIGR02740.1
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF019153.2
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.; 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
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:NF021212.2
COORDINATES: similar to AA sequence:RefSeq:WP_017190572.1
COORDINATES: similar to AA sequence:RefSeq:WP_013571434.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007479726.1
COORDINATES: similar to AA sequence:RefSeq:WP_005368167.1
phage integrase N-terminal SAM-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017048576.1
COORDINATES: similar to AA sequence:RefSeq:WP_012197125.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005366055.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025027.2
COORDINATES: similar to AA sequence:RefSeq:WP_013347207.1
COORDINATES: similar to AA sequence:RefSeq:WP_013347204.1
COORDINATES: similar to AA sequence:RefSeq:WP_008844497.1
HipA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001610793.1
COORDINATES: similar to AA sequence:RefSeq:WP_005370446.1
reverse transcriptase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004744686.1
COORDINATES: protein motif:HMM:TIGR02563.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
type I-F CRISPR-associated endoribonuclease Cas6/Csy4
COORDINATES: similar to AA sequence:RefSeq:WP_012588884.1
COORDINATES: protein motif:HMM:NF021154.2
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: protein motif:HMM:NF027421.2
COORDINATES: similar to AA sequence:RefSeq:WP_010606796.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013465407.1
COORDINATES: similar to AA sequence:RefSeq:WP_010388169.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_008133907.1
TnsA endonuclease N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013571433.1
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: protein motif:HMM:NF013555.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
topoisomerase DNA-binding C4 zinc finger domain-containing protein
COORDINATES: protein motif:HMM:NF024996.2
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008910695.1
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF024977.2
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: protein motif:HMM:NF024096.2
PD-(D/E)XK nuclease-like domain-containing protein
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_004747125.1
COORDINATES: similar to AA sequence:RefSeq:WP_012849579.1
COORDINATES: similar to AA sequence:RefSeq:WP_005417965.1
GO:0019239 - deaminase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012142877.1
L-serine ammonia-lyase, iron-sulfur-dependent, subunit alpha
COORDINATES: protein motif:HMM:NF013790.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF013658.2
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: protein motif:HMM:NF025815.2
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_006663469.1
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]