Shewanella khirikhana strain TH2012 plasmid pSTH1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella.
Full genome sequence of a non-lethal Shewanella isolate that potentiates virulence of Vibio parahaemolyticus causing acute hepatopancreatic necrosis disease (AHPND) in shrimp
Submitted (17-MAR-2017) Shrimp-Virus Interaction Laboratory, Animal Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology, 113 Paholyothin Road, Tambon Khlong 1, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
REFSEQ INFORMATION: The reference sequence is identical to\nCP020374.1.\nBacteria and source DNA available from Dr. Kallaya\nSritunyalucksana, National Center for Genetic Engineering and\nBiotechnology (BIOTEC), National Science and Technology.\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 :: 27-APR-2016\nAssembly Method :: HGAP3 v. HGAP3\nAssembly Name :: STH1.0\nGenome Coverage :: 258.24x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 09:26:40\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) :: 4,288\nCDSs (total) :: 4,159\nGenes (coding) :: 4,118\nCDSs (with protein) :: 4,118\nGenes (RNA) :: 129\nrRNAs :: 9, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 8, 8 (5S, 16S, 23S)\ntRNAs :: 100\nncRNAs :: 4\nPseudo Genes (total) :: 41\nCDSs (without protein) :: 41\nPseudo Genes (ambiguous residues) :: 0 of 41\nPseudo Genes (frameshifted) :: 20 of 41\nPseudo Genes (incomplete) :: 27 of 41\nPseudo Genes (internal stop) :: 10 of 41\nPseudo Genes (multiple problems) :: 14 of 41\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Penaeus (Litopenaeus) vannamei (whiteleg shrimp)
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012652.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014610906.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014610905.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012198027.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015885378.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198032.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_014610936.1
COORDINATES: similar to AA sequence:RefSeq:WP_010320053.1
type II toxin-antitoxin system HigB family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012198033.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012198034.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013646172.1
COORDINATES: similar to AA sequence:RefSeq:WP_012197988.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017108479.1
COORDINATES: similar to AA sequence:RefSeq:WP_012197991.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012197992.1
conjugal transfer transcriptional regulator TraJ
COORDINATES: protein motif:HMM:NF036299.2
COORDINATES: similar to AA sequence:RefSeq:WP_011304098.1
COORDINATES: protein motif:HMM:NF023087.2
COORDINATES: similar to AA sequence:RefSeq:WP_012197997.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
PapB/FocB family fimbrial expression transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011716472.1
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_010107508.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010676177.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198005.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198006.1
COORDINATES: similar to AA sequence:RefSeq:WP_015296894.1
COORDINATES: similar to AA sequence:RefSeq:WP_010210453.1
COORDINATES: similar to AA sequence:RefSeq:WP_020308233.1
COORDINATES: similar to AA sequence:RefSeq:WP_011839974.1
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: protein motif:HMM:NF020037.2
COORDINATES: similar to AA sequence:RefSeq:WP_012198008.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198009.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505222.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198010.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198011.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_012198012.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_012198013.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198014.1
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_012198015.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198016.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198017.1