Shigella dysenteriae strain SWHEFF_49 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Shigella.
High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria
Submitted (10-JUN-2020) Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong 000000, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP055056.1.\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 :: \"Other\" v. Unicycler\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 200x\nSequencing Technology :: Illumina; Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/08/2023 23:10:00\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) :: 4,996\nCDSs (total) :: 4,880\nGenes (coding) :: 4,748\nCDSs (with protein) :: 4,748\nGenes (RNA) :: 116\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 88\nncRNAs :: 6\nPseudo Genes (total) :: 132\nCDSs (without protein) :: 132\nPseudo Genes (ambiguous residues) :: 0 of 132\nPseudo Genes (frameshifted) :: 35 of 132\nPseudo Genes (incomplete) :: 90 of 132\nPseudo Genes (internal stop) :: 17 of 132\nPseudo Genes (multiple problems) :: 13 of 132\nPseudo Genes (short protein) :: 4 of 132\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:NP_052630.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:NP_052628.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_958721.1
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_010892530.1
COORDINATES: similar to AA sequence:RefSeq:WP_001193612.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
omptin family outer membrane protease OmpP
COORDINATES: similar to AA sequence:RefSeq:WP_000995793.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015474 - autotransporter activity [Evidence IEA]
GO:0046819 - protein secretion by the type V secretion system [Evidence IEA]
autotransporter outer membrane beta-barrel domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010892528.1
COORDINATES: similar to AA sequence:RefSeq:WP_000286435.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558235.1
frameshifted; internal stop; 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_001604455.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_020219146.1
COORDINATES: similar to AA sequence:RefSeq:WP_020219148.1
COORDINATES: similar to AA sequence:RefSeq:WP_001351581.1
COORDINATES: similar to AA sequence:RefSeq:WP_001351580.1
COORDINATES: similar to AA sequence:RefSeq:WP_001092154.1
COORDINATES: similar to AA sequence:RefSeq:WP_015869530.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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.
GO:0015074 - DNA integration [Evidence IEA]
frameshifted; 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_000627495.1
IS21-like element IS100 family transposase
COORDINATES: similar to AA sequence:RefSeq:NP_858162.1
COORDINATES: similar to AA sequence:RefSeq:NP_052636.1
COORDINATES: similar to AA sequence:RefSeq:NP_052635.1
type II toxin-antitoxin system toxin CcdB
COORDINATES: similar to AA sequence:RefSeq:NP_052634.1
type II toxin-antitoxin system antitoxin CcdA
COORDINATES: similar to AA sequence:RefSeq:WP_003917573.1
COORDINATES: similar to AA sequence:RefSeq:WP_013578371.1
COORDINATES: similar to AA sequence:RefSeq:WP_001553853.1
S-4TM family putative pore-forming effector
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017899886.1
COORDINATES: similar to AA sequence:RefSeq:WP_013023783.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013023782.1
COORDINATES: similar to AA sequence:RefSeq:WP_000921251.1
COORDINATES: similar to AA sequence:RefSeq:WP_000494510.1
COORDINATES: similar to AA sequence:RefSeq:WP_000528931.1
COORDINATES: similar to AA sequence:RefSeq:WP_001523449.1
COORDINATES: similar to AA sequence:RefSeq:WP_001545742.1
COORDINATES: similar to AA sequence:RefSeq:WP_001563283.1
COORDINATES: similar to AA sequence:RefSeq:WP_001402899.1
COORDINATES: similar to AA sequence:RefSeq:WP_001057990.1
COORDINATES: similar to AA sequence:RefSeq:WP_013009346.1
type II toxin-antitoxin system toxin YacB
COORDINATES: similar to AA sequence:RefSeq:WP_015056448.1
type II toxin-antitoxin system antitoxin YacA
COORDINATES: similar to AA sequence:RefSeq:WP_004031751.1
COORDINATES: similar to AA sequence:RefSeq:NP_052675.1
GO:0006276 - plasmid maintenance [Evidence IEA]
incFII family plasmid replication initiator RepA
COORDINATES: similar to AA sequence:RefSeq:WP_001273588.1
COORDINATES: protein motif:HMM:TIGR03475.1
COORDINATES: similar to AA sequence:RefSeq:WP_001410080.1
COORDINATES: similar to AA sequence:RefSeq:WP_001297746.1
COORDINATES: similar to AA sequence:RefSeq:WP_001300273.1
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:NP_858385.1
COORDINATES: similar to AA sequence:RefSeq:NP_858384.1
COORDINATES: similar to AA sequence:RefSeq:NP_052669.1
COORDINATES: similar to AA sequence:RefSeq:NP_490592.1
GO:0003678 - DNA helicase activity [Evidence IEA]
conjugative transfer relaxase/helicase TraI
COORDINATES: similar to AA sequence:RefSeq:WP_001577029.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:NP_490587.1
conjugal transfer complement resistance protein TraT
COORDINATES: similar to AA sequence:RefSeq:WP_003898910.1
TraS, as the term is used in F-like plasmids, is a plasmid entry exclusion protein. It interacts with the F-like plasmid mating stabilization protein TraG; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugal transfer entry exclusion protein TraS
COORDINATES: similar to AA sequence:RefSeq:WP_001007007.1
conjugal transfer mating-pair stabilization protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_001137359.1
conjugal transfer pilus assembly protein TraH
COORDINATES: similar to AA sequence:RefSeq:WP_001677181.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_000052622.1
type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB
COORDINATES: similar to AA sequence:RefSeq:WP_001617873.1
type-F conjugative transfer system pilin chaperone TraQ
COORDINATES: similar to AA sequence:RefSeq:WP_001287890.1
COORDINATES: similar to AA sequence:RefSeq:WP_001030376.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: similar to AA sequence:RefSeq:WP_000864342.1
COORDINATES: similar to AA sequence:RefSeq:WP_001756807.1
type-F conjugative transfer system mating-pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_001553832.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:NP_490576.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:NP_490575.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:NP_490574.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_000069745.1
COORDINATES: similar to AA sequence:RefSeq:WP_000836674.1
COORDINATES: similar to AA sequence:RefSeq:WP_000556747.1
COORDINATES: similar to AA sequence:RefSeq:WP_000549572.1
COORDINATES: similar to AA sequence:RefSeq:WP_000549587.1
COORDINATES: similar to AA sequence:RefSeq:NP_490571.1
COORDINATES: similar to AA sequence:RefSeq:WP_016233168.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_001057305.1
COORDINATES: similar to AA sequence:RefSeq:WP_001528624.1
conjugal transfer pilus-stabilizing protein TraP
COORDINATES: similar to AA sequence:RefSeq:WP_001553749.1
F-type conjugal transfer pilus assembly protein TraB
COORDINATES: similar to AA sequence:RefSeq:WP_001230803.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:NP_490565.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:NP_490564.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_001825183.1
type IV conjugative transfer system pilin TraA
COORDINATES: similar to AA sequence:RefSeq:WP_012006553.1
conjugal transfer relaxosome DNA-bindin protein TraY
COORDINATES: similar to AA sequence:RefSeq:WP_003979562.1
conjugal transfer transcriptional regulator TraJ
COORDINATES: similar to AA sequence:RefSeq:WP_001151541.1
conjugal transfer relaxosome DNA-binding protein TraM
COORDINATES: similar to AA sequence:RefSeq:WP_020246007.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001234456.1
COORDINATES: similar to AA sequence:RefSeq:WP_001825190.1
COORDINATES: similar to AA sequence:RefSeq:WP_000547968.1
COORDINATES: similar to AA sequence:RefSeq:NP_052655.1
COORDINATES: similar to AA sequence:RefSeq:WP_001380705.1
COORDINATES: similar to AA sequence:RefSeq:NP_052660.1
type I toxin-antitoxin system Hok family toxin
COORDINATES: protein motif:HMM:NF010277.0
COORDINATES: similar to AA sequence:RefSeq:WP_001763821.1
COORDINATES: similar to AA sequence:RefSeq:WP_000845953.1
COORDINATES: similar to AA sequence:RefSeq:NP_052657.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:NP_958724.1
COORDINATES: similar to AA sequence:RefSeq:WP_000290791.1
COORDINATES: similar to AA sequence:RefSeq:WP_001366172.1
COORDINATES: similar to AA sequence:RefSeq:WP_001496291.1
COORDINATES: similar to AA sequence:RefSeq:NP_052654.1
COORDINATES: similar to AA sequence:RefSeq:NP_052653.1
COORDINATES: similar to AA sequence:RefSeq:NP_052652.1
COORDINATES: similar to AA sequence:RefSeq:WP_016238862.1
COORDINATES: similar to AA sequence:RefSeq:NP_052650.1
COORDINATES: similar to AA sequence:RefSeq:NP_490551.1
COORDINATES: similar to AA sequence:RefSeq:NP_052647.1
COORDINATES: similar to AA sequence:RefSeq:NP_052646.1
COORDINATES: similar to AA sequence:RefSeq:NP_958723.1
COORDINATES: similar to AA sequence:RefSeq:NP_052645.1
COORDINATES: similar to AA sequence:RefSeq:NP_052644.1
COORDINATES: similar to AA sequence:RefSeq:NP_052643.1
COORDINATES: similar to AA sequence:RefSeq:WP_001697964.1
COORDINATES: similar to AA sequence:RefSeq:WP_001536590.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_001766293.1
COORDINATES: similar to AA sequence:RefSeq:WP_001555635.1
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001505082.1
COORDINATES: similar to AA sequence:RefSeq:WP_000633910.1
COORDINATES: similar to AA sequence:RefSeq:WP_000241708.1
COORDINATES: similar to AA sequence:RefSeq:WP_000016493.1
COORDINATES: similar to AA sequence:RefSeq:WP_001385965.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221000.1
IS6-like element IS26 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001398511.1
COORDINATES: similar to AA sequence:RefSeq:WP_020803592.1
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001567368.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229628.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229629.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:YP_005229630.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:YP_005229631.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229632.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213073.1
VapC toxin family PIN domain ribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_000544830.1
COORDINATES: similar to AA sequence:RefSeq:WP_000952428.1
IS21-like element IS21 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_000990665.1