Piscirickettsia salmonis strain Psal-070 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Thiotrichales; Piscirickettsiaceae; Piscirickettsia.
Complete genome sequencing of Piscirickettsia salmonis strain Psal-070
Submitted (06-APR-2019) Bioinformatics, Leibniz Institute DSMZ, Inhoffenstr. 7B, Braunschweig 38124, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP039033.1.\nBacteria and source DNA available from Sergio H. Marshall,\nLaboratorio de Genetica e Inmunologia Molecular, Instituto de\nBiologia, Pontificia Universidad Catolica de Valparaiso, Av.\nUniversidad 330 Curauma, Valparaiso, Chile.\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 :: HGAP SMRTPortal v. 2.3.0\nAssembly Name :: PiscirickettsiaPsal-070_HGAP3_1SC\nGenome Coverage :: 225x\nSequencing Technology :: PacBio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/14/2023 01:42:14\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,614\nCDSs (total) :: 3,536\nGenes (coding) :: 3,394\nCDSs (with protein) :: 3,394\nGenes (RNA) :: 78\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 4\nPseudo Genes (total) :: 142\nCDSs (without protein) :: 142\nPseudo Genes (ambiguous residues) :: 0 of 142\nPseudo Genes (frameshifted) :: 25 of 142\nPseudo Genes (incomplete) :: 117 of 142\nPseudo Genes (internal stop) :: 13 of 142\nPseudo Genes (multiple problems) :: 11 of 142\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF013793.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_075273802.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017376171.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
DDE-type integrase/transposase/recombinase
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_076611779.1
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017377586.1
frameshifted; 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_017376303.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF013842.2
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: protein motif:HMM:NF024997.2
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019236582.1
COORDINATES: similar to AA sequence:RefSeq:WP_017375895.1
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF033545.0
COORDINATES: similar to AA sequence:RefSeq:WP_035718769.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017377523.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611371.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012307.2
reverse transcriptase domain-containing protein
COORDINATES: protein motif:HMM:NF016847.2
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013924677.1
COORDINATES: protein motif:HMM:NF033580.1
COORDINATES: protein motif:HMM:NF024736.2
IS6-like element ISPsa2 family transposase
COORDINATES: protein motif:HMM:NF024950.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016211654.1
COORDINATES: protein motif:HMM:NF012305.2
COORDINATES: similar to AA sequence:RefSeq:WP_011879712.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
type II toxin-antitoxin system PemK/MazF family toxin
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017377056.1
COORDINATES: similar to AA sequence:RefSeq:WP_017375855.1
COORDINATES: protein motif:HMM:NF033563.0
COORDINATES: protein motif:HMM:NF024673.2
COORDINATES: similar to AA sequence:RefSeq:WP_017377554.1
COORDINATES: similar to AA sequence:RefSeq:WP_019518979.1
COORDINATES: similar to AA sequence:RefSeq:WP_018062164.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_016212329.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: protein motif:HMM:NF012783.2
GO:0004176 - ATP-dependent peptidase activity [Evidence IEA]; GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
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:NF018691.2
COORDINATES: similar to AA sequence:RefSeq:WP_017378397.1
COORDINATES: similar to AA sequence:RefSeq:WP_009986376.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014550344.1
COORDINATES: protein motif:HMM:NF025063.2
COORDINATES: similar to AA sequence:RefSeq:WP_017273848.1
COORDINATES: similar to AA sequence:RefSeq:WP_009847097.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF023331.2
COORDINATES: similar to AA sequence:RefSeq:WP_006801688.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611921.1
COORDINATES: similar to AA sequence:RefSeq:WP_016209526.1
GO:0000156 - phosphorelay response regulator activity [Evidence IEA]
GO:0006935 - chemotaxis [Evidence IEA]; GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF020360.2
nucleotidyltransferase substrate binding protein
COORDINATES: protein motif:HMM:NF037100.2
nucleotidyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF025677.2
transposase zinc-binding domain-containing protein