Klebsiella michiganensis strain THO-011 plasmid pTHO-011-1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
complete genome sequences of Klebsiella michiganensis str. THO-011 isolated from a patient
Submitted (03-FEB-2020) Contact:Tsuyoshi Sekizuka National Institute of Infectious Diseases, Pathogen Genomics Center; 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP022548.1.\nAnnotated by DFAST v.1.2.3 (https://dfast.nig.ac.jp).\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 :: flye v. 2.5; minimap v. 0.2-r124; racon v.\n 1.1.0; circlator v. 1.5.3; Pilon v. 1.18;\n SPAdes v. 3.11.1; A5-miseq v. 20140604\nGenome Coverage :: 240x\nSequencing Technology :: Sequel; NextSeq 500\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/08/2022 04:35:29\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;\n repeat_region\nGenes (total) :: 5,676\nCDSs (total) :: 5,561\nGenes (coding) :: 5,482\nCDSs (with protein) :: 5,482\nGenes (RNA) :: 115\nrRNAs :: 9, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 8, 8 (5S, 16S, 23S)\ntRNAs :: 84\nncRNAs :: 6\nPseudo Genes (total) :: 79\nCDSs (without protein) :: 79\nPseudo Genes (ambiguous residues) :: 0 of 79\nPseudo Genes (frameshifted) :: 35 of 79\nPseudo Genes (incomplete) :: 56 of 79\nPseudo Genes (internal stop) :: 13 of 79\nPseudo Genes (multiple problems) :: 22 of 79\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_001054900.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000062602.1
COORDINATES: similar to AA sequence:RefSeq:WP_001480010.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: similar to AA sequence:RefSeq:WP_000698353.1
COORDINATES: similar to AA sequence:RefSeq:WP_001037983.1
IncI1-type conjugal transfer protein TraX
COORDINATES: similar to AA sequence:RefSeq:WP_001387490.1
IncI1-type conjugal transfer protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_000337395.1
IncI1-type conjugal transfer protein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_001024789.1
IncI1-type conjugal transfer protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_001164783.1
IncI1-type conjugal transfer protein TraT
COORDINATES: similar to AA sequence:RefSeq:WP_001277253.1
COORDINATES: similar to AA sequence:RefSeq:WP_000086965.1
IncI1-type conjugal transfer protein TraR
COORDINATES: similar to AA sequence:RefSeq:WP_001055571.1
COORDINATES: similar to AA sequence:RefSeq:WP_000801920.1
IncI1-type conjugal transfer protein TraP
COORDINATES: similar to AA sequence:RefSeq:WP_001272004.1
COORDINATES: similar to AA sequence:RefSeq:WP_001191879.1
IncI1-type conjugal transfer protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_000138553.1
DotI/IcmL family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_001629514.1
COORDINATES: similar to AA sequence:RefSeq:WP_016231897.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001493807.1
COORDINATES: similar to AA sequence:RefSeq:WP_001542523.1
COORDINATES: similar to AA sequence:RefSeq:WP_001480051.1
COORDINATES: similar to AA sequence:RefSeq:WP_000646098.1
IncI1-type conjugal transfer lipoprotein TraI
COORDINATES: similar to AA sequence:RefSeq:WP_001079808.1
IncI1-type conjugal transfer lipoprotein TraH
COORDINATES: similar to AA sequence:RefSeq:WP_001542524.1
COORDINATES: similar to AA sequence:RefSeq:WP_003557916.1
COORDINATES: similar to AA sequence:RefSeq:WP_001238934.1
COORDINATES: similar to AA sequence:RefSeq:WP_001396170.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000080172.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_309365.1
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; 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_001373091.1
COORDINATES: similar to AA sequence:RefSeq:WP_012565250.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_001193550.1
COORDINATES: similar to AA sequence:RefSeq:WP_001774171.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000908226.1
COORDINATES: similar to AA sequence:RefSeq:WP_001722224.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000362204.1
COORDINATES: similar to AA sequence:RefSeq:WP_001247331.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001682966.1
COORDINATES: similar to AA sequence:RefSeq:WP_001744074.1
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: similar to AA sequence:RefSeq:WP_001744073.1
COORDINATES: similar to AA sequence:RefSeq:WP_001360287.1
type IV pilus biogenesis lipoprotein PilL
COORDINATES: similar to AA sequence:RefSeq:WP_086558215.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001136193.1
COORDINATES: similar to AA sequence:RefSeq:WP_000213862.1
COORDINATES: similar to AA sequence:RefSeq:WP_001303319.1
transcription termination/antitermination NusG family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000074849.1
COORDINATES: protein motif:HMM:NF022029.2
COORDINATES: similar to AA sequence:RefSeq:WP_000907860.1
COORDINATES: similar to AA sequence:RefSeq:NP_052676.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:NP_858351.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_001105075.1
COORDINATES: similar to AA sequence:RefSeq:WP_000627831.1
COORDINATES: similar to AA sequence:RefSeq:WP_001582574.1
COORDINATES: similar to AA sequence:RefSeq:WP_001697843.1
COORDINATES: similar to AA sequence:RefSeq:WP_001632353.1
COORDINATES: similar to AA sequence:RefSeq:WP_001610315.1
GO:0019835 - cytolysis [Evidence IEA]; GO:0050829 - defense response to Gram-negative bacterium [Evidence IEA]
colicin Ia central receptor-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000762570.1
GO:0015643 - toxic substance binding [Evidence IEA]
GO:0030153 - bacteriocin immunity [Evidence IEA]
colicin E1 family microcin immunity protein
COORDINATES: similar to AA sequence:RefSeq:WP_001563283.1
COORDINATES: similar to AA sequence:RefSeq:WP_001545742.1
COORDINATES: similar to AA sequence:RefSeq:WP_000343099.1
COORDINATES: similar to AA sequence:RefSeq:WP_001536595.1
COORDINATES: similar to AA sequence:RefSeq:WP_001164196.1
COORDINATES: similar to AA sequence:RefSeq:WP_001144037.1
COORDINATES: similar to AA sequence:RefSeq:WP_000030202.1
COORDINATES: similar to AA sequence:RefSeq:WP_001401593.1
COORDINATES: similar to AA sequence:RefSeq:WP_001278810.1
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001566943.1
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_001743492.1
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_012904571.1
IS66-like element ISCro1 family transposase
COORDINATES: similar to AA sequence:RefSeq:NP_858152.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
IS66-like element accessory protein TnpA
COORDINATES: similar to AA sequence:RefSeq:WP_000457541.1
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:YP_005221000.1
IS6-like element IS26 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001339197.1
IS4-like element ISVsa5 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_032489170.1
extended-spectrum class A beta-lactamase CTX-M-8
COORDINATES: similar to AA sequence:RefSeq:NP_052643.1
COORDINATES: similar to AA sequence:RefSeq:NP_052644.1
COORDINATES: similar to AA sequence:RefSeq:NP_858331.2
COORDINATES: similar to AA sequence:RefSeq:NP_958723.1
COORDINATES: similar to AA sequence:RefSeq:NP_052646.1
COORDINATES: similar to AA sequence:RefSeq:WP_001005031.1
COORDINATES: similar to AA sequence:RefSeq:WP_001198918.1
COORDINATES: similar to AA sequence:RefSeq:NP_052650.1
COORDINATES: similar to AA sequence:RefSeq:WP_016238862.1
COORDINATES: similar to AA sequence:RefSeq:WP_000741240.1
COORDINATES: similar to AA sequence:RefSeq:WP_000005972.1
COORDINATES: similar to AA sequence:RefSeq:NP_052657.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_000845953.1
COORDINATES: similar to AA sequence:RefSeq:WP_001584594.1
COORDINATES: similar to AA sequence:RefSeq:WP_001298859.1
IS21-like element ISEc12 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001514323.1
IS21-like element ISEc12 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_001723065.1
COORDINATES: similar to AA sequence:RefSeq:WP_000942659.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000117633.1
COORDINATES: similar to AA sequence:RefSeq:WP_000218847.1
COORDINATES: similar to AA sequence:RefSeq:WP_001247860.1
COORDINATES: similar to AA sequence:RefSeq:WP_000038340.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_000150325.1
COORDINATES: similar to AA sequence:RefSeq:WP_003980153.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_000544830.1
IS21-like element IS21 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_000952428.1
IS21-like element IS21 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001401764.1
COORDINATES: similar to AA sequence:RefSeq:WP_000157082.1
molybdopterin-guanine dinucleotide biosynthesis protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_001283947.1
IncI1-type relaxosome accessory protein NikA
COORDINATES: similar to AA sequence:RefSeq:WP_001387486.1
COORDINATES: similar to AA sequence:RefSeq:WP_001289278.1
F-type conjugative transfer protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_000151583.1
IncI1-type conjugal transfer protein TrbB
COORDINATES: similar to AA sequence:RefSeq:WP_000121273.1
IncI1-type conjugal transfer protein TrbA
COORDINATES: similar to AA sequence:RefSeq:WP_001618166.1
COORDINATES: similar to AA sequence:RefSeq:WP_001291967.1