Yersinia pseudotuberculosis IP 32953 strain IP32953 plasmid pYAC_1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Yersinia.
Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica
Submitted (22-OCT-2014) Bioscience, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP009711.1.\nThe DNA was obtained from USAMRIID.\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 :: 16-OCT-2014\nAssembly Method :: Newbler v. 2.6; Velvet v. 1.2.08; Allpaths\n v. 44837; Phrap v. SPS - 4.24; HGAP v.\n 2.2.0\nGenome Coverage :: 465x\nSequencing Technology :: Illumina; PacBio; 454\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/12/2022 19:34:57\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,343\nCDSs (total) :: 4,226\nGenes (coding) :: 4,084\nCDSs (with protein) :: 4,084\nGenes (RNA) :: 117\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 84\nncRNAs :: 11\nPseudo Genes (total) :: 142\nCDSs (without protein) :: 142\nPseudo Genes (ambiguous residues) :: 0 of 142\nPseudo Genes (frameshifted) :: 51 of 142\nPseudo Genes (incomplete) :: 113 of 142\nPseudo Genes (internal stop) :: 26 of 142\nPseudo Genes (multiple problems) :: 38 of 142\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011117631.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
type III secretion system translocon subunit YopD
COORDINATES: similar to AA sequence:RefSeq:WP_012548890.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; 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_012414153.1
COORDINATES: similar to AA sequence:RefSeq:WP_005054087.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_086558335.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_002393889.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002213004.1
type III secretion system chaperone SycT
COORDINATES: similar to AA sequence:RefSeq:WP_002213006.1
COORDINATES: similar to AA sequence:RefSeq:WP_002213007.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611491.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001485398.1
GO:0019867 - outer membrane [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_086558235.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612308.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010891239.1
COORDINATES: similar to AA sequence:RefSeq:WP_002213354.1
ParB/RepB/Spo0J family plasmid partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011171998.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606398.1
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_002224342.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_002213360.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_002229754.1
type III secretion system effector GTPase activator YopE
COORDINATES: similar to AA sequence:RefSeq:WP_002213403.1
type III secretion system chaperone SycE/YerA
COORDINATES: similar to AA sequence:RefSeq:WP_076611475.1
COORDINATES: similar to AA sequence:RefSeq:WP_000952428.1
COORDINATES: similar to AA sequence:RefSeq:WP_000544830.1
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_002213267.1
type III secretion system chaperone SycH
COORDINATES: similar to AA sequence:RefSeq:WP_076611505.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS3-like element ISYps8 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_002229829.1
COORDINATES: similar to AA sequence:RefSeq:WP_012414143.1
COORDINATES: similar to AA sequence:RefSeq:WP_012228742.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611787.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611501.1
COORDINATES: similar to AA sequence:RefSeq:WP_011191362.1
COORDINATES: protein motif:HMM:NF013088.2
COORDINATES: similar to AA sequence:RefSeq:WP_002213246.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001194258.1
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002229817.1
COORDINATES: similar to AA sequence:RefSeq:WP_012615301.1
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.
COORDINATES: protein motif:HMM:TIGR03475.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0006276 - plasmid maintenance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002213292.1
incFII family plasmid replication initiator RepA
COORDINATES: similar to AA sequence:RefSeq:WP_012414139.1
COORDINATES: similar to AA sequence:RefSeq:WP_000957248.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase.; frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_002229809.1
COORDINATES: similar to AA sequence:RefSeq:WP_011191359.1
type III secretion system effector protein kinase YopO/YpkA
COORDINATES: similar to AA sequence:RefSeq:WP_002225474.1
type III secretion system effector acetyltransferase YopJ
COORDINATES: similar to AA sequence:RefSeq:WP_000513068.1
COORDINATES: similar to AA sequence:RefSeq:WP_002213278.1
T3SS effector protein-tyrosine-phosphatase YopH
COORDINATES: similar to AA sequence:RefSeq:WP_000343613.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611456.1
COORDINATES: similar to AA sequence:RefSeq:WP_002212907.1
GO:0006470 - protein dephosphorylation [Evidence IEA]
type III secretion system exported negative regulator LcrQ/YscM1
COORDINATES: similar to AA sequence:RefSeq:WP_010981371.1
SctL family type III secretion system stator protein YscL
COORDINATES: similar to AA sequence:RefSeq:WP_002361471.1
SctK family type III secretion system sorting platform protein YscK
COORDINATES: similar to AA sequence:RefSeq:WP_002212912.1
SctJ family type III secretion inner membrane ring lipoprotein YscJ
COORDINATES: similar to AA sequence:RefSeq:WP_002212914.1
SctI family type III secretion system inner rod subunit LcrO
COORDINATES: similar to AA sequence:RefSeq:WP_002212915.1
T3SS polymerization control protein YopR
COORDINATES: similar to AA sequence:RefSeq:WP_002229801.1
type III secretion system chaperone YscG
COORDINATES: similar to AA sequence:RefSeq:WP_002212916.1
type III secretion system needle filament protein YscF
COORDINATES: similar to AA sequence:RefSeq:WP_002212917.1
type III secretion system co-chaperone YscE
COORDINATES: similar to AA sequence:RefSeq:WP_002212919.1
SctD family type III secretion system inner membrane ring subunit YscD
COORDINATES: similar to AA sequence:RefSeq:WP_002212923.1
SctC family type III secretion system outer membrane ring subunit YscC
COORDINATES: similar to AA sequence:RefSeq:WP_002212925.1
type III secretion system chaperone YscB
COORDINATES: similar to AA sequence:RefSeq:WP_002229797.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891222.1
virulence regulon transcriptional activator VirF
COORDINATES: similar to AA sequence:RefSeq:WP_002222527.1
COORDINATES: similar to AA sequence:RefSeq:WP_002212936.1
type III secretion system export apparatus switch protein YscU
COORDINATES: similar to AA sequence:RefSeq:WP_002212938.1
SctT family type III secretion system export apparatus subunit YscT
COORDINATES: similar to AA sequence:RefSeq:NP_250383.1
SctS family type III secretion system export apparatus subunit YscS
COORDINATES: similar to AA sequence:RefSeq:NP_250384.1
SctR family type III secretion system export apparatus subunit YscR
COORDINATES: similar to AA sequence:RefSeq:WP_002212948.1
SctQ family type III secretion system cytoplasmic ring protein YscQ
COORDINATES: similar to AA sequence:RefSeq:WP_002212950.1
type III secretion system needle length determinant YscP
COORDINATES: similar to AA sequence:RefSeq:WP_005176819.1
type III secretion system central stalk protein YscO
COORDINATES: similar to AA sequence:RefSeq:WP_002212955.1
SctN family type III secretion system ATPase YscN
COORDINATES: similar to AA sequence:RefSeq:WP_011191384.1
SctW family type III secretion system gatekeeper subunit YopN
COORDINATES: similar to AA sequence:RefSeq:WP_002212965.1
type III secretion system gatekeeper subunit TyeA
COORDINATES: similar to AA sequence:RefSeq:WP_002229794.1
COORDINATES: similar to AA sequence:RefSeq:WP_002212969.1
COORDINATES: similar to AA sequence:RefSeq:WP_002229791.1
type III secretion system chaperone YscY
COORDINATES: similar to AA sequence:RefSeq:WP_002212971.1
SctV family type III secretion system export apparatus subunit LcrD
COORDINATES: similar to AA sequence:RefSeq:WP_002220918.1
type III secretion system chaperone LcrR
COORDINATES: similar to AA sequence:RefSeq:WP_002212973.1
type III secretion system chaperone LcrG
COORDINATES: similar to AA sequence:RefSeq:WP_002212981.1
type III secretion system needle tip protein LcrV
COORDINATES: similar to AA sequence:RefSeq:WP_011117633.1
type III secretion system chaperone SycD/LcrH
COORDINATES: similar to AA sequence:RefSeq:WP_011117632.1
type III secretion system translocon subunit YopB