Yersinia ruckeri strain KMM821 plasmid pYRKMM821_2, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Yersinia.
Submitted (12-MAR-2021) Ministry Of Health Of Russia, N.F.Gamaleya National Research Center for Epidemiology and Microbiology, Gamaleya, 18, Moscow 123098, Russia
REFSEQ INFORMATION: The reference sequence is identical to\nCP071804.1.\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 :: CLC Genomics Workbench v. 20; SPAdes v.\n 3.13.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 96.0x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 04:06:26\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) :: 3,536\nCDSs (total) :: 3,420\nGenes (coding) :: 3,334\nCDSs (with protein) :: 3,334\nGenes (RNA) :: 116\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 82\nncRNAs :: 12\nPseudo Genes (total) :: 86\nCDSs (without protein) :: 86\nPseudo Genes (ambiguous residues) :: 0 of 86\nPseudo Genes (frameshifted) :: 40 of 86\nPseudo Genes (incomplete) :: 58 of 86\nPseudo Genes (internal stop) :: 28 of 86\nPseudo Genes (multiple problems) :: 28 of 86\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Russia:Sea of Okhotsk, near Iturup Island
COORDINATES: similar to AA sequence:RefSeq:WP_000678689.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004720845.1
COORDINATES: protein motif:HMM:NF015397.2
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_017891124.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_014695865.1
COORDINATES: similar to AA sequence:RefSeq:WP_010847563.1
COORDINATES: similar to AA sequence:RefSeq:WP_011148113.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011988467.1
COORDINATES: similar to AA sequence:RefSeq:WP_047389784.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003855844.1
COORDINATES: similar to AA sequence:RefSeq:WP_009092747.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612266.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014683018.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611898.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000493398.1
COORDINATES: similar to AA sequence:RefSeq:WP_020316923.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000935451.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_003155746.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_001586233.1
COORDINATES: protein motif:HMM:NF019313.2
COORDINATES: similar to AA sequence:RefSeq:WP_016831339.1
COORDINATES: similar to AA sequence:RefSeq:WP_017788969.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF017020.2
COORDINATES: similar to AA sequence:RefSeq:WP_012548890.1
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_015060658.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000904941.1
COORDINATES: similar to AA sequence:RefSeq:WP_003296370.1
COORDINATES: similar to AA sequence:RefSeq:WP_001493761.1
COORDINATES: similar to AA sequence:RefSeq:WP_017365442.1
putative DNA binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011144772.1
COORDINATES: similar to AA sequence:RefSeq:WP_001653610.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type I restriction endonuclease subunit M
COORDINATES: similar to AA sequence:RefSeq:NP_310935.1
COORDINATES: similar to AA sequence:RefSeq:WP_004144477.1
COORDINATES: similar to AA sequence:RefSeq:WP_015197255.1
COORDINATES: protein motif:HMM:NF033527.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606398.1
COORDINATES: similar to AA sequence:RefSeq:WP_006706936.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006322759.1
COORDINATES: protein motif:HMM:NF020037.2
COORDINATES: similar to AA sequence:RefSeq:WP_000612441.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005082529.1
transcription termination/antitermination NusG family protein
COORDINATES: protein motif:HMM:NF022136.2
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: protein motif:HMM:NF019064.2
COORDINATES: similar to AA sequence:RefSeq:WP_000984842.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]; GO:0009306 - protein secretion [Evidence IEA]
PilN family type IVB pilus formation outer membrane protein
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: similar to AA sequence:RefSeq:WP_017891027.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017891026.1
COORDINATES: similar to AA sequence:RefSeq:WP_017891025.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017891024.1
COORDINATES: similar to AA sequence:RefSeq:WP_017891023.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF013632.2
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017891021.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_004720812.1
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017374630.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873469.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374628.1
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: similar to AA sequence:RefSeq:WP_017374626.1
COORDINATES: similar to AA sequence:RefSeq:WP_017891141.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_017374624.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374622.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374621.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374619.1
COORDINATES: similar to AA sequence:RefSeq:WP_017493161.1
COORDINATES: protein motif:HMM:NF033887.1
COORDINATES: similar to AA sequence:RefSeq:WP_004131796.1
COORDINATES: similar to AA sequence:RefSeq:WP_001595120.1
COORDINATES: protein motif:HMM:NF033891.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: similar to AA sequence:RefSeq:WP_017374614.1
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: similar to AA sequence:RefSeq:WP_004720841.1
F-type conjugative transfer protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_008324931.1