Providencia huaxiensis strain WCHPr000369 plasmid p2_000369, complete sequence.
type: Entry
definition: Providencia huaxiensis strain WCHPr000369 plasmid p2_000369, complete sequence.
sequence version: NZ_CP031119.1
sequence date: 2023-05-14
sequence: sequence
division: CON
label: NZ_CP031119.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN07508212
keyword: RefSeq
source: Providencia huaxiensis
organism: Providencia huaxiensis
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Morganellaceae; Providencia.
reference: 1
references: 32176782
reference: 2
references: 31162027
reference: 3
reference: 4
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP031119.1.\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 :: Unicycler v. 0.4.6\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 200.0x\nSequencing Technology :: Illumina HiSeq; MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/14/2023 09:56:16\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,506\nCDSs (total) :: 4,403\nGenes (coding) :: 4,290\nCDSs (with protein) :: 4,290\nGenes (RNA) :: 103\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 77\nncRNAs :: 4\nPseudo Genes (total) :: 113\nCDSs (without protein) :: 113\nPseudo Genes (ambiguous residues) :: 0 of 113\nPseudo Genes (frameshifted) :: 23 of 113\nPseudo Genes (incomplete) :: 88 of 113\nPseudo Genes (internal stop) :: 8 of 113\nPseudo Genes (multiple problems) :: 5 of 113\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7592
topology: circular
so has quality: SO_0000988
location: 1..7592
location: region:1-7592:1
RO_0002162: 2027290

NZ_CP031119
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN07508212
type: BioSample
SIO_000068: biosample

1
title: A Pandrug-Resistant Providencia Carrying Two blaIMP Carbapenemase-Encoding Genes Including blaIMP-69, a New blaIMP Variant, on a Newly Identified Worldwide-Distributed IncC Plasmid
author: Zhang, X.
author: Wang, C.
author: Feng, Y.
author: Long, H.
author: Zong, Z.
journal: J Infect Dis 221 (Suppl 2), S253-S256 (2020)
pubmed: 32176782

32176782
type: PubMed
SIO_000068: pubmed

2
title: Providencia huaxiensis sp. nov., recovered from a human rectal swab
author: Hu, Y.
author: Feng, Y.
author: Zhang, X.
author: Zong, Z.
journal: Int J Syst Evol Microbiol
volume: 69
issue: 9
pages: 2638-2643
year: 2019
pubmed: 31162027

31162027
type: PubMed
SIO_000068: pubmed

3
title: Direct Submission
author: Zhang, X.
author: Hu, Y.
author: Long, H.
author: Feng, Y.
author: Zong, Z.
journal: Submitted (17-JUL-2018) Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan 610041, China

4
title: Direct Submission
author: Zhang, X.
author: Feng, Y.
author: Zong, Z.
journal: Submitted (17-AUG-2017) Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan 610041, China

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7592:1
position: 7592
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7592:1:source
so part of: sequence
organism: Providencia huaxiensis
mol type: genomic DNA
strain: WCHPr000369
host: Homo sapiens
type material: type strain of Providencia huaxiensis
plasmid: p2_000369
country: China: Sichuan, Chengdu
collection date: 2015

2027290
type: Taxonomy
SIO_000068: taxonomy

CYG50_RS00215
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
locus tag: CYG50_RS00215
old locus tag: CYG50_00215
so part of: sequence
location: 1..840
location: region:1-840:1
so has part: feature:1-840:1:exon
subclass of: SO_0000010

position:840:1
position: 840
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-840:1:exon

CYG50_RS00215
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
locus tag: CYG50_RS00215
old locus tag: CYG50_00215
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001517559.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: helicase RepA family protein
translation: MATHKPINILEAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHASKGAAMMGAGDQQQASRGSSVLVDNIRWQSYLSSMTSAEAEEWGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPAVLERQRKSKGVPRGEA
SIO_010081: CYG50_RS00215
subclass of: SO_0000673
so part of: CYG50_RS00215
location: 1..840
location: region:1-840:1
so has part: feature:1-840:1:exon

WP_000190708.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-840:1:exon

CYG50_RS00220
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
gene: repC
locus tag: CYG50_RS00220
old locus tag: CYG50_00220
so part of: sequence
location: 827..1699
location: region:827-1699:1
so has part: feature:827-1699:1:exon
subclass of: SO_0000010

position:827:1
position: 827
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1699:1
position: 1699
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:827-1699:1:exon

CYG50_RS00220
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
gene: repC
locus tag: CYG50_RS00220
old locus tag: CYG50_00220
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019939540.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: replication protein C, IncQ-type
translation: MVKPKNKHSLSHVRHDPAHCLAPGLFRALKRGERKRSKLDVTYDYGDGKRIEFSGPEPLGADDLRILQGLVAMAGPNGLVLGPEPKTEGGRQLRLFLEPKWEAVTADAMVVKGSYRALAKEIGAEVDSGGALKHIQDCIERLWKVSIIAQNGRKRQGFRLLSEYASDEADGRLYVALNPLIAQAVMGGGQHVRISMDEVRALDSETARLLHQRLCGWIDPGKTGKASIDTLCGYVWPSEASGSTMRKRRQRVREALPELVALGWTVTEFAAGKYDITRPKAAGWPPPTLL
SIO_010081: CYG50_RS00220
subclass of: SO_0000673
so part of: CYG50_RS00220
location: 827..1699
location: region:827-1699:1
so has part: feature:827-1699:1:exon

WP_282559460.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:827-1699:1:exon

CYG50_RS00230
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
locus tag: CYG50_RS00230
old locus tag: CYG50_00235
pseudo: true
so part of: sequence
location: 1987..>2271
location: region:1987-2271:1
so has part: feature:1987-2271:1:exon
subclass of: SO_0000010

position:1987:1
position: 1987
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2271:1
position: 2271
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1987-2271:1:exon

CYG50_RS00230
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
locus tag: CYG50_RS00230
old locus tag: CYG50_00235
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001043260.1
note: incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 4
product: dihydropteroate synthase
SIO_010081: CYG50_RS00230
subclass of: SO_0000673
so part of: CYG50_RS00230
location: 1987..>2271
location: region:1987-2271:1
so has part: feature:1987-2271:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1987-2271:1:exon

CYG50_RS00235
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
gene: bla
locus tag: CYG50_RS00235
old locus tag: CYG50_00240
so part of: sequence
location: 2742..3605
location: region:2742-3605:1
so has part: feature:2742-3605:1:exon
subclass of: SO_0000010

position:2742:1
position: 2742
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3605:1
position: 3605
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2742-3605:1:exon

CYG50_RS00235
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
gene: bla
locus tag: CYG50_RS00235
old locus tag: CYG50_00240
EC number: 3.5.2.6
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019612892.1
GO function: GO:0008800 - beta-lactamase activity [Evidence IEA]
GO process: GO:0030655 - beta-lactam antibiotic catabolic process [Evidence IEA]; GO:0046677 - response to antibiotic [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: class A beta-lactamase
translation: MYSKFVVFVSLLSSLTLSIPANSSPDLIVNSIKEVEQNLGAKVGVSIYSVSDGYLWHYNGDSRFPLMSTFKPLACAKLLHDVETAKLSIDRSVKIEEQDLITWSPITEKLVGESFSLKQACTAALVMSDNTAANIVLDGISGPSELTLFMKELGDEVTRLDRIEPHLNEARSGDERDTTTPNAIVKSLGKLLYGEKLSSGSKEQLIEWMAGNKVSDSLLRSVLPEGWSIADRSGAGGFGSRGITAAIWSNEQQPLIVAIYLTQTEASFDERNKAIAKIGREIFASYN
SIO_010081: CYG50_RS00235
subclass of: SO_0000673
so part of: CYG50_RS00235
location: 2742..3605
location: region:2742-3605:1
so has part: feature:2742-3605:1:exon

WP_102139633.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2742-3605:1:exon

CYG50_RS00240
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
locus tag: CYG50_RS00240
old locus tag: CYG50_00245
pseudo: true
so part of: sequence
location: complement(<3686..3916)
location: region:3686-3916:-1
so has part: feature:3686-3916:-1:exon
subclass of: SO_0000010

position:3686:-1
position: 3686
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:3916:-1
position: 3916
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3686-3916:-1:exon

CYG50_RS00240
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
locus tag: CYG50_RS00240
old locus tag: CYG50_00245
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001120888.1
note: incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 4
product: IS91 family transposase
SIO_010081: CYG50_RS00240
subclass of: SO_0000673
so part of: CYG50_RS00240
location: complement(<3686..3916)
location: region:3686-3916:-1
so has part: feature:3686-3916:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:3686-3916:-1:exon

CYG50_RS00245
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
locus tag: CYG50_RS00245
old locus tag: CYG50_00250
so part of: sequence
location: complement(4413..4754)
location: region:4413-4754:-1
so has part: feature:4413-4754:-1:exon
subclass of: SO_0000010

position:4413:-1
position: 4413
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4754:-1
position: 4754
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4413-4754:-1:exon

CYG50_RS00245
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
locus tag: CYG50_RS00245
old locus tag: CYG50_00250
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001517562.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: mobilization protein
translation: MVKGSNKAADRLAKLEEQRARINAEIQRVRAREQQQERKNETRRKVLVGAMILAKVNSSEWPEDRLMAAMDAYLERDHDRALFGLPPRQKDEPGWMIDRDRPCGAAHAPPPFG
SIO_010081: CYG50_RS00245
subclass of: SO_0000673
so part of: CYG50_RS00245
location: complement(4413..4754)
location: region:4413-4754:-1
so has part: feature:4413-4754:-1:exon

WP_282559459.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4413-4754:-1:exon

CYG50_RS22985
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
locus tag: CYG50_RS22985
pseudo: true
so part of: sequence
location: 5058..>5591
location: region:5058-5591:1
so has part: feature:5058-5591:1:exon
subclass of: SO_0000010

position:5058:1
position: 5058
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5591:1
position: 5591
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5058-5591:1:exon

CYG50_RS22985
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
locus tag: CYG50_RS22985
inference: COORDINATES: protein motif:HMM:NF015354.2
note: incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 4
product: MobA/MobL family protein
SIO_010081: CYG50_RS22985
subclass of: SO_0000673
so part of: CYG50_RS22985
location: 5058..>5591
location: region:5058-5591:1
so has part: feature:5058-5591:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:5058-5591:1:exon

CYG50_RS22990
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
locus tag: CYG50_RS22990
so part of: sequence
location: 5701..6141
location: region:5701-6141:1
so has part: feature:5701-6141:1:exon
subclass of: SO_0000010

position:5701:1
position: 5701
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6141:1
position: 6141
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5701-6141:1:exon

CYG50_RS22990
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
locus tag: CYG50_RS22990
inference: COORDINATES: protein motif:HMM:NF036929.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: IncQ-type mobilization protein MobB
translation: MNAIDRVKKSRGINELAEQIEPLAQSMATLADEARQVMSQTQQASEAQAAEWLKAQRQTGAAWVELAKELREVAAEVSSAAQSARSASRGWHWKLWLTVMLASMMPTVVLLIASLLLLDLTPLTTEDGSIWLRLVARWRTTGLCRP
SIO_010081: CYG50_RS22990
subclass of: SO_0000673
so part of: CYG50_RS22990
location: 5701..6141
location: region:5701-6141:1
so has part: feature:5701-6141:1:exon

WP_282559461.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5701-6141:1:exon

CYG50_RS22995
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
locus tag: CYG50_RS22995
so part of: sequence
location: 6159..7082
location: region:6159-7082:1
so has part: feature:6159-7082:1:exon
subclass of: SO_0000010

position:6159:1
position: 6159
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7082:1
position: 7082
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6159-7082:1:exon

CYG50_RS22995
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
locus tag: CYG50_RS22995
inference: COORDINATES: protein motif:HMM:NF028103.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: DNA-primase RepB domain-containing protein
translation: MGCERFDIGVRDATTGQMMNREWSAAEVLQNTPWLKRMNAQGNDVYIRPAEQERHGLVLVDDLSEFDLDDMKAEGREPALVVETSPKNYQAWVKVADAAGGELRGQIARTLASEYDADPASADSRHYGRLAGFTNRKDKHTTRAGYQPWVLLRESKGKTATAGPALVQQAGQQIEQAQRQQEKARRLASLELPERQLSRHRRTALDEYRSEMAGLVKRFGDDLSKCDFIAAQKLASRGRSAEEIGKAMAEASPALAERKPGHEADYIERTVSKVMGLPSVQLARAELARAPAPRQRGMDRGGPDFSM
SIO_010081: CYG50_RS22995
subclass of: SO_0000673
so part of: CYG50_RS22995
location: 6159..7082
location: region:6159-7082:1
so has part: feature:6159-7082:1:exon

WP_014344452.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6159-7082:1:exon

CYG50_RS00260
type: Gene
subclass of: SO_0000704
RO_0002162: 2027290
gene: urfF
locus tag: CYG50_RS00260
old locus tag: CYG50_00265
so part of: sequence
location: 7357..7563
location: region:7357-7563:1
so has part: feature:7357-7563:1:exon
subclass of: SO_0000010

position:7357:1
position: 7357
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7563:1
position: 7563
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7357-7563:1:exon

CYG50_RS00260
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2027290
gene: urfF
locus tag: CYG50_RS00260
old locus tag: CYG50_00265
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007857788.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: plasmid repression protein F
translation: MKDQKDKQTGDLLASPDAVRQARYAERMKAKGMRQRKFWLTDDEYEALRECLEELRAAQGGGSDPASA
SIO_010081: CYG50_RS00260
subclass of: SO_0000673
so part of: CYG50_RS00260
location: 7357..7563
location: region:7357-7563:1
so has part: feature:7357-7563:1:exon

WP_007857788.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7357-7563:1:exon