Helicobacter pylori strain MT5135 plasmid pMT5135, complete sequence.
type: Entry
definition: Helicobacter pylori strain MT5135 plasmid pMT5135, complete sequence.
sequence version: NZ_CP071983.1
sequence date: 2023-02-24
sequence: sequence
division: CON
label: NZ_CP071983.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN18350190
keyword: RefSeq
source: Helicobacter pylori
organism: Helicobacter pylori
taxonomy: Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae; Helicobacter.
reference: 1
references: 33692136
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP071983.1.\nBacteria and source DNA available from James G. Fox.\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 :: HGAP v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 1435.1x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/24/2023 11:38:16\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) :: 1,544\nCDSs (total) :: 1,499\nGenes (coding) :: 1,438\nCDSs (with protein) :: 1,438\nGenes (RNA) :: 45\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 36\nncRNAs :: 3\nPseudo Genes (total) :: 61\nCDSs (without protein) :: 61\nPseudo Genes (ambiguous residues) :: 0 of 61\nPseudo Genes (frameshifted) :: 45 of 61\nPseudo Genes (incomplete) :: 13 of 61\nPseudo Genes (internal stop) :: 10 of 61\nPseudo Genes (multiple problems) :: 5 of 61\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 9259
topology: circular
so has quality: SO_0000988
location: 1..9259
location: region:1-9259:1
RO_0002162: 210

NZ_CP071983
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN18350190
type: BioSample
SIO_000068: biosample

1
title: Helicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk Populations
author: Mannion, A.
author: Dzink-Fox, J.
author: Shen, Z.
author: Piazuelo, M.B.
author: Wilson, K.T.
author: Correa, P.
author: Peek, R.M. Jr.
author: Camargo, M.C.
author: Fox, J.G.
journal: J Clin Microbiol 59 (5), e03203-20 (2021)
pubmed: 33692136
comments: Publication Status: Online-Only

33692136
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Mannion, A.
author: Dzink-Fox, J.
author: Shen, Z.
author: Blanca Piazuelo, M.
author: Wilson, K.T.
author: Correa, P.
author: Peek, R.M. Jr.
author: Constanza Camargo, M.
author: Fox, J.G.
journal: Submitted (18-MAR-2021) Division of Cancer Epidemiology and Genetics, Metabolic Epidemiology Branch, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD 20850, USA

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

position:9259:1
position: 9259
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9259:1:source
so part of: sequence
organism: Helicobacter pylori
mol type: genomic DNA
strain: MT5135
isolation source: Biopsy
host: Homo sapiens
plasmid: pMT5135
country: Colombia
lat lon: 4.5 N 74.29 W
collected by: James G. Fox

210
type: Taxonomy
SIO_000068: taxonomy

J5D21_RS07635
type: Gene
subclass of: SO_0000704
RO_0002162: 210
locus tag: J5D21_RS07635
old locus tag: J5D21_07635
pseudo: true
so part of: sequence
location: complement(<3..200)
location: region:3-200:-1
so has part: feature:3-200:-1:exon
subclass of: SO_0000010

66522783
type: Gene
SIO_000068: ncbigene

position:3:-1
position: 3
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:200:-1
position: 200
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3-200:-1:exon

J5D21_RS07635
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 210
locus tag: J5D21_RS07635
old locus tag: J5D21_07635
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000917061.1
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: 11
product: hypothetical protein
SIO_010081: J5D21_RS07635
subclass of: SO_0000673
so part of: J5D21_RS07635
location: complement(<3..200)
location: region:3-200:-1
so has part: feature:3-200:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:3-200:-1:exon

J5D21_RS07640
type: Gene
subclass of: SO_0000704
RO_0002162: 210
gene: mobC
locus tag: J5D21_RS07640
old locus tag: J5D21_07640
so part of: sequence
location: 358..705
location: region:358-705:1
so has part: feature:358-705:1:exon
subclass of: SO_0000010

66522784
type: Gene
SIO_000068: ncbigene

position:358:1
position: 358
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:705:1
position: 705
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:358-705:1:exon

J5D21_RS07640
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 210
gene: mobC
locus tag: J5D21_RS07640
old locus tag: J5D21_07640
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001925455.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid mobilization relaxosome protein MobC
translation: MREQVDTNKQIIKSLRLSKEQWQTIQNQMQEKNLNFSQLVLNSLLHQNSQTPVKSKKQKAIANKELVIELAKWGNNLNQIAKHLNTNQGVWDRLGLEQLIEISHQLEQIRSKYVG
SIO_010081: J5D21_RS07640
subclass of: SO_0000673
so part of: J5D21_RS07640
location: 358..705
location: region:358-705:1
so has part: feature:358-705:1:exon

WP_209612531.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:358-705:1:exon

J5D21_RS07645
type: Gene
subclass of: SO_0000704
RO_0002162: 210
locus tag: J5D21_RS07645
old locus tag: J5D21_07645
so part of: sequence
location: 695..2632
location: region:695-2632:1
so has part: feature:695-2632:1:exon
subclass of: SO_0000010

66522785
type: Gene
SIO_000068: ncbigene

position:695:1
position: 695
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2632:1
position: 2632
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:695-2632:1:exon

J5D21_RS07645
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 210
locus tag: J5D21_RS07645
old locus tag: J5D21_07645
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001958506.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: relaxase/mobilization nuclease domain-containing protein
translation: MLVKFWSINQGGGDGDGSVNYLLNERVKQGTARVLKGDANLTKSLLLSLTQKHKACVGCLSFEEPDIDENLKHELIESFENALLTEKMQGRYNILWVEHTDKGRLELNFVIPRIDLITQKAFTPYYHSADITRIDIWKDYTNLKHAFTNPKDLEKQNTIQHHNTKTPQGKELLETYEKLDKLIQENLGKLFNSREDIINFLKANQCEVNRQGKDYISVKLPNKPKAKRLKGFYYHETFRTIKDIRNQLSEARQRKSQRERSNPHTTNNNHAELLRELENKLHERVEHKQRYYERLHQTDPRNPRDLKEQPPRARESQQRTQQDYTSEVDRSRETMLQKPNQKILTDALKFSHGVSHNGSNINGGILPHHSALQKQGIRAFTERKFATQTADRSTRQRQSAKILPTNTDQEIRRKNAERLLKQVAERFNQRSRELAERERDFTQRKEQRNREFRERQKRAIEQARESYSRISKTKQRLLEIRDRNLELERELRNAIPNTQHTISQISSLRESRESRIKEFTEQVRTDFTTRITERSNQRSRDFTSSIQRIENTIRDFRNNAQARVRTILHNLYARTRDAINAIKDIYRNAKERIRNFFQRADERLSKRMEQETRELHARTQGLDQGIRKHNQKIDDERSYSRGYGR
SIO_010081: J5D21_RS07645
subclass of: SO_0000673
so part of: J5D21_RS07645
location: 695..2632
location: region:695-2632:1
so has part: feature:695-2632:1:exon

WP_209612533.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:695-2632:1:exon

J5D21_RS07650
type: Gene
subclass of: SO_0000704
RO_0002162: 210
locus tag: J5D21_RS07650
old locus tag: J5D21_07650
so part of: sequence
location: 2910..3962
location: region:2910-3962:1
so has part: feature:2910-3962:1:exon
subclass of: SO_0000010

66522786
type: Gene
SIO_000068: ncbigene

position:2910:1
position: 2910
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3962:1
position: 3962
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2910-3962:1:exon

J5D21_RS07650
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 210
locus tag: J5D21_RS07650
old locus tag: J5D21_07650
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001198810.1
GO function: GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ThiF family adenylyltransferase
translation: MQWYQTSFSACVGQTDTENIIGLGTYQYCVDHNEFEKSLRLLVFLRMKKRMAEIKSFMETSKIEHNIFDKLVANKLITSFILNPNDEQNFKNHLFIDLVSSKPELTINNFKKTIFIIIGCGGIGNFVSYALASFYPKKLILLDKDTVDFSNLNRQFLFDKNYISQYKTSAIKQALSSRFGINIETVDDFASEDNLEEIFSKHKKENLFGIVSGDNPNTVQLATRFFCKCHIPFLNIGYLNDISLIGPFYIPSLSCCPFCHNSFALDDKKDGDKNLDICLINDRMQAPSSFLNNSIASSLAISDIIQFMSNDFNSIKSLNCRFGVDNKTFKTYTLPSSVDHKCAFCSNHNL
SIO_010081: J5D21_RS07650
subclass of: SO_0000673
so part of: J5D21_RS07650
location: 2910..3962
location: region:2910-3962:1
so has part: feature:2910-3962:1:exon

WP_209612535.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2910-3962:1:exon

J5D21_RS07655
type: Gene
subclass of: SO_0000704
RO_0002162: 210
locus tag: J5D21_RS07655
old locus tag: J5D21_07655
so part of: sequence
location: 3974..5137
location: region:3974-5137:1
so has part: feature:3974-5137:1:exon
subclass of: SO_0000010

66522787
type: Gene
SIO_000068: ncbigene

position:3974:1
position: 3974
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5137:1
position: 5137
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3974-5137:1:exon

J5D21_RS07655
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 210
locus tag: J5D21_RS07655
old locus tag: J5D21_07655
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017283504.1
GO function: GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO process: GO:0055085 - transmembrane transport [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MFS transporter
translation: MNKTLKVNILSYYCATILLVIAQSLPHAILTPLLLNKGLSLSQIMIIQATYSLCVLLSEYPSGVLADLINRKMLFIISKLVLVCSFFCVLWLDSFVSMVLAWGIYGLSNALDSGTIDATLITNIKDQKEDLSPFIAKSRQISFIGLIIGSCSGSFLYLKYGVSMYYISVLLTLLCISVIILFFKDDSSHKLEKKRQLQILKQHVRESFRELKDKPLLKNLILLSLILQIFFQSHFQLWQAYLLDKQITENYLFIFYISFQIIGILVHFCNANSYNRYMTITMIFLTGLVSSLLLSMDILLFVSAYILSVALFTYMDFIVSYQFSLYVSKEKISSLTSLKSSVSRVISVIILGITSLELLIFSPTIVIAVHFIATLILTCVFLYKVKI
SIO_010081: J5D21_RS07655
subclass of: SO_0000673
so part of: J5D21_RS07655
location: 3974..5137
location: region:3974-5137:1
so has part: feature:3974-5137:1:exon

WP_209612537.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3974-5137:1:exon

J5D21_RS07660
type: Gene
subclass of: SO_0000704
RO_0002162: 210
locus tag: J5D21_RS07660
old locus tag: J5D21_07660
so part of: sequence
location: complement(5269..5973)
location: region:5269-5973:-1
so has part: feature:5269-5973:-1:exon
subclass of: SO_0000010

66522788
type: Gene
SIO_000068: ncbigene

position:5269:-1
position: 5269
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5973:-1
position: 5973
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5269-5973:-1:exon

J5D21_RS07660
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 210
locus tag: J5D21_RS07660
old locus tag: J5D21_07660
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000956348.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Fic family protein
translation: MLTKLIEKLNHERKNAIKNGIYHLIQIKFSYNSNRIEGSGLTYEQTAHIFDKSVLITEKNTNIKLDDIFETINHFECVNYLLESYQEPLSLEYFKTLHKILKKNCSDEVIGGFKKRPNFVGNSATTRPKLVESELTNLVKNYQRNLEVSLENIIDFHVAFEKIHPFSDGNGRVGRLVMFKECLKNNIMPFIIEDKHKAFYYRGIKEYDNTKGYLKDTILQSQDNFNEMVSYFFS
SIO_010081: J5D21_RS07660
subclass of: SO_0000673
so part of: J5D21_RS07660
location: complement(5269..5973)
location: region:5269-5973:-1
so has part: feature:5269-5973:-1:exon

WP_209612524.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5269-5973:-1:exon

J5D21_RS07665
type: Gene
subclass of: SO_0000704
RO_0002162: 210
locus tag: J5D21_RS07665
old locus tag: J5D21_07665
so part of: sequence
location: complement(5986..7623)
location: region:5986-7623:-1
so has part: feature:5986-7623:-1:exon
subclass of: SO_0000010

66522789
type: Gene
SIO_000068: ncbigene

position:5986:-1
position: 5986
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7623:-1
position: 7623
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5986-7623:-1:exon

J5D21_RS07665
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 210
locus tag: J5D21_RS07665
old locus tag: J5D21_07665
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001132149.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MPMNTNFEQLRKQELELRKLLEELDTLPQTLQIKLQKQKIQTYIDKITPSILSGFNQKFKEITEKLPNEFEKETPKPTPPKEPQTTPTPCKDLVVSTPKDKTYITYHNNANKVNLGKLSEREANLLFAIFQRLKDQGNTLIRFEPQDLKRMIMVKSNLTNRQLLQVLKNLLDNISGANFWIIREHVENGEVYEDHTSYMLFKQFEIRIHKPTQNIEYLDVQLNDSYQYLLNNLGIGGQYTSFKLLEFQRVRGKYAKTLYRLLKQYKSTGILSVEWSQFRELLDIPKDYEMRNIDQKVLTPSIKELHKIYPFEHLSYKKERRSHDKRKVTHIDFYFEQLPEGENKKQKQADKQRAQRDIKLVAWDINNQIAKRSAKATIEARFLELKTLIGYQFRHNDSGIVLQIDNTTFEKNQMFLHVSYPKSKNNPQKFLVSNKTFALELLYVNGYSLKKDMLEIDPPSIHPITNEPIKEFAQYIGKTINITNNNVDQCPEGINNYLKITRIVKLNDNRICVSVQDVDKPDKLLKPFIAKDEKHLKNWFKKYYR
SIO_010081: J5D21_RS07665
subclass of: SO_0000673
so part of: J5D21_RS07665
location: complement(5986..7623)
location: region:5986-7623:-1
so has part: feature:5986-7623:-1:exon

WP_209612526.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5986-7623:-1:exon

J5D21_RS07670
type: Gene
subclass of: SO_0000704
RO_0002162: 210
locus tag: J5D21_RS07670
old locus tag: J5D21_07670
so part of: sequence
location: complement(8773..9042)
location: region:8773-9042:-1
so has part: feature:8773-9042:-1:exon
subclass of: SO_0000010

66522790
type: Gene
SIO_000068: ncbigene

position:8773:-1
position: 8773
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9042:-1
position: 9042
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8773-9042:-1:exon

J5D21_RS07670
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 210
locus tag: J5D21_RS07670
old locus tag: J5D21_07670
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001898867.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
translation: MLEIELKKKFTKDLKKHILNQKIELEVFDLVVENLRNQIPLDKRFKDHALSGTYKGCRERHIKPDVLLVYRVKNNVLTRMLLTPKERMR
SIO_010081: J5D21_RS07670
subclass of: SO_0000673
so part of: J5D21_RS07670
location: complement(8773..9042)
location: region:8773-9042:-1
so has part: feature:8773-9042:-1:exon

WP_209612528.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8773-9042:-1:exon

J5D21_RS07630
type: Gene
subclass of: SO_0000704
RO_0002162: 210
locus tag: J5D21_RS07630
old locus tag: J5D21_07630
so part of: sequence
location: complement(9051..9227)
location: region:9051-9227:-1
so has part: feature:9051-9227:-1:exon
subclass of: SO_0000010

66522782
type: Gene
SIO_000068: ncbigene

position:9051:-1
position: 9051
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9227:-1
position: 9227
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9051-9227:-1:exon

J5D21_RS07630
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 210
locus tag: J5D21_RS07630
old locus tag: J5D21_07630
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKEIKKQYSQAKKDENLASKYIPNDELKKDLLDIDNPNTTENFKPKNASEIWQFALNS
SIO_010081: J5D21_RS07630
subclass of: SO_0000673
so part of: J5D21_RS07630
location: complement(9051..9227)
location: region:9051-9227:-1
so has part: feature:9051-9227:-1:exon

WP_001960584.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:9051-9227:-1:exon