Piscirickettsia salmonis strain Psal-070 plasmid unnamed2, 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\nCP039034.1.\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: similar to AA sequence:RefSeq:WP_018299668.1
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: protein motif:HMM:NF012305.2
COORDINATES: similar to AA sequence:RefSeq:WP_016211378.1
COORDINATES: similar to AA sequence:RefSeq:WP_017375930.1
COORDINATES: similar to AA sequence:RefSeq:WP_016211382.1
COORDINATES: protein motif:HMM:NF033545.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013842.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611371.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_075273802.1
IS6-like element ISPsa2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_012848820.1
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_017377505.1
COORDINATES: similar to AA sequence:RefSeq:WP_017377658.1
COORDINATES: similar to AA sequence:RefSeq:WP_013965593.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: similar to AA sequence:RefSeq:WP_017376688.1
COORDINATES: protein motif:HMM:NF025669.2
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016211440.1
COORDINATES: protein motif:HMM:NF018926.2
COORDINATES: similar to AA sequence:RefSeq:WP_017376171.1
COORDINATES: similar to AA sequence:RefSeq:WP_017375932.1
COORDINATES: similar to AA sequence:RefSeq:WP_016211676.1
COORDINATES: protein motif:HMM:NF033538.1
COORDINATES: protein motif:HMM:NF033563.0
COORDINATES: protein motif:HMM:NF013050.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF019013.2
GO:0030638 - polyketide metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024880.2
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016211079.1
COORDINATES: similar to AA sequence:RefSeq:WP_016211070.1
COORDINATES: similar to AA sequence:RefSeq:WP_016212113.1
COORDINATES: similar to AA sequence:RefSeq:WP_016212111.1
COORDINATES: similar to AA sequence:RefSeq:WP_016212109.1
COORDINATES: similar to AA sequence:RefSeq:WP_016212114.1
COORDINATES: similar to AA sequence:RefSeq:WP_016212110.1
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_017375958.1
COORDINATES: protein motif:HMM:NF040493.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000639719.1
GO:0004540 - ribonuclease activity [Evidence IEA]
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018298445.1
COORDINATES: similar to AA sequence:RefSeq:WP_016211775.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF016975.2
P27 family phage terminase small subunit
COORDINATES: protein motif:HMM:NF015321.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR01537.1
GO:0044423 - virion component [Evidence IEA]
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0019068 - virion assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF012783.2
GO:0004176 - ATP-dependent peptidase activity [Evidence IEA]; GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01554.2
COORDINATES: similar to AA sequence:RefSeq:WP_016211131.1
COORDINATES: similar to AA sequence:RefSeq:WP_016210663.1
GO:0016032 - viral process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016210667.1
COORDINATES: similar to AA sequence:RefSeq:WP_016210658.1
COORDINATES: similar to AA sequence:RefSeq:WP_016210651.1
COORDINATES: similar to AA sequence:RefSeq:WP_016211141.1
COORDINATES: similar to AA sequence:RefSeq:WP_016211138.1
COORDINATES: similar to AA sequence:RefSeq:WP_017375784.1
COORDINATES: similar to AA sequence:RefSeq:WP_016210660.1
COORDINATES: similar to AA sequence:RefSeq:WP_017375786.1
COORDINATES: similar to AA sequence:RefSeq:WP_017375787.1
COORDINATES: similar to AA sequence:RefSeq:WP_017375788.1
COORDINATES: similar to AA sequence:RefSeq:WP_017375789.1
COORDINATES: similar to AA sequence:RefSeq:WP_006880104.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF014643.2
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: protein motif:HMM:NF024939.2
COORDINATES: similar to AA sequence:RefSeq:WP_017378397.1
COORDINATES: similar to AA sequence:RefSeq:WP_016211671.1
COORDINATES: similar to AA sequence:RefSeq:WP_016211673.1
COORDINATES: similar to AA sequence:RefSeq:WP_016212424.1
COORDINATES: protein motif:HMM:NF024835.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006801688.1
COORDINATES: protein motif:HMM:NF025842.2
COORDINATES: protein motif:HMM:NF014631.2
COORDINATES: protein motif:HMM:NF033516.0
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]
COORDINATES: protein motif:HMM:NF024673.2
COORDINATES: protein motif:HMM:NF016847.2
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: similar to AA sequence:RefSeq:WP_013924677.1
COORDINATES: similar to AA sequence:RefSeq:WP_017377554.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF025107.2