Helicobacter suis strain NHP19-4022 plasmid pNHP194022_2, complete sequence.
type: Entry
definition: Helicobacter suis strain NHP19-4022 plasmid pNHP194022_2, complete sequence.
sequence version: NZ_AP023048.1
sequence date: 2022-12-19
sequence: sequence
division: CON
label: NZ_AP023048.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMD00215133
keyword: RefSeq
source: Helicobacter suis
organism: Helicobacter suis
taxonomy: Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae; Helicobacter.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nAP023048.1.\nAnnotated at DFAST https://dfast.nig.ac.jp/\n\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. 0.4.8.0\nGenome Coverage :: 377.3x\nSequencing Technology :: Illumina MiniSeq; ONT MinION R9.4.1\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/19/2022 14:14:17\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) :: 1,763\nCDSs (total) :: 1,714\nGenes (coding) :: 1,652\nCDSs (with protein) :: 1,652\nGenes (RNA) :: 49\nrRNAs :: 3, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 2, 2 (5S, 16S, 23S)\ntRNAs :: 39\nncRNAs :: 3\nPseudo Genes (total) :: 62\nCDSs (without protein) :: 62\nPseudo Genes (ambiguous residues) :: 0 of 62\nPseudo Genes (frameshifted) :: 31 of 62\nPseudo Genes (incomplete) :: 27 of 62\nPseudo Genes (internal stop) :: 14 of 62\nPseudo Genes (multiple problems) :: 10 of 62\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5825
topology: circular
so has quality: SO_0000988
location: 1..5825
location: region:1-5825:1
RO_0002162: 104628

NZ_AP023048
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMD00215133
type: BioSample
SIO_000068: biosample

1
title: Genomic analysis of gastric non-Helicobacter pylori Helicobacters isolated in Japan
author: Suzuki, M.
author: Rimbara, E.
journal: Unpublished

2
title: Direct Submission
author: Suzuki, M.
author: Rimbara, E.
journal: Submitted (10-APR-2020) Contact:Masato Suzuki National Institute of Infectious Diseases, AMR Research Center; 4-2-1 Aobacho, Higashimurayama, Tokyo 189-0002, Japan

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

position:5825:1
position: 5825
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5825:1:source
so part of: sequence
organism: Helicobacter suis
mol type: genomic DNA
strain: NHP19-4022
isolation source: stomach
host: Homo sapiens
plasmid: pNHP194022_2
country: Japan:Fukuoka
collection date: 2019

104628
type: Taxonomy
SIO_000068: taxonomy

HXS61_RS08575
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08575
old locus tag: NHP194022_17270
so part of: sequence
location: 1..582
location: region:1-582:1
so has part: feature:1-582:1:exon
subclass of: SO_0000010

56929571
type: Gene
SIO_000068: ncbigene

position:582:1
position: 582
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-582:1:exon

HXS61_RS08575
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08575
old locus tag: NHP194022_17270
inference: COORDINATES: protein motif:HMM:NF017542.2
GO process: GO:0006260 - DNA replication [Evidence IEA]; GO:0006276 - plasmid maintenance [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication/maintenance protein RepL
translation: MDKPTTTKGRIKGGKIKNAKTTKVQRVEIPGQRVYLQSIKTGEIQESNALICDAIVEKDCNFDKLFTGILFHILGEIGGALLKACIKVIELRDRENAVYITGAKLAKLCDISQLTAQRALKTLIEKNVLQPLTAHGGAYRVNGDMIFKGGYESRRTLVFRFHEREEEIKQEKTAKATTDTKKPKREKKKGDSK
SIO_010081: HXS61_RS08575
subclass of: SO_0000673
so part of: HXS61_RS08575
location: 1..582
location: region:1-582:1
so has part: feature:1-582:1:exon

WP_034377236.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-582:1:exon

HXS61_RS08580
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08580
old locus tag: NHP194022_17280
so part of: sequence
location: 579..932
location: region:579-932:1
so has part: feature:579-932:1:exon
subclass of: SO_0000010

56929572
type: Gene
SIO_000068: ncbigene

position:579:1
position: 579
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:932:1
position: 932
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:579-932:1:exon

HXS61_RS08580
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08580
old locus tag: NHP194022_17280
inference: COORDINATES: protein motif:HMM:NF017542.2
GO process: GO:0006260 - DNA replication [Evidence IEA]; GO:0006276 - plasmid maintenance [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication/maintenance protein RepL
translation: MKHTACELHIPHNSNIDENALLAGFVIHDIIKDGTNDMSITMLKACIKLVELRDRENSVFVTSVKLAKLCGVSLDTAKRALKALVDKKVLQPLTARGGAYRLNTKVVFIHQRAPRES
SIO_010081: HXS61_RS08580
subclass of: SO_0000673
so part of: HXS61_RS08580
location: 579..932
location: region:579-932:1
so has part: feature:579-932:1:exon

WP_034377234.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:579-932:1:exon

HXS61_RS08585
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08585
old locus tag: NHP194022_17290
so part of: sequence
location: 922..2412
location: region:922-2412:1
so has part: feature:922-2412:1:exon
subclass of: SO_0000010

56929573
type: Gene
SIO_000068: ncbigene

position:922:1
position: 922
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2412:1
position: 2412
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:922-2412:1:exon

HXS61_RS08585
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08585
old locus tag: NHP194022_17290
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: MNLSLSICHDNTQYALNQWQVIYNIESLEKLAELALKYDTSPMIFCADKERQKYAKSQRSHANVIGFNNALFFDIDNQENEPYLSVQEAQKILKKHQIFSVIIPSRNYLKIKPKDTRKNIERYRIIIPTQMPISNFFFQEKEAYQILQISIAKALKIYDFVDKSALKDLARFYRKNDPNSPTLLKPIIIEGNRIMNLEFLEQNAIQKFQETREKKIVLQVPRQPVKEVRDKDLKSRGYLTHADMEKILSTDILLLISIFEGIEREYYEGSYHMVKTNKGGKYSLLEDRKVAHDFKTDATFNCLSYLEFQLQTTNLNKIARELEHITGESYIVLNPEVFGVVCHAINEFKNIIKVEQFLKNFYGVKFVKISLEGWVKIADQYIQLLAHSLDIFKSPNTAPQQHPKVSYNQGKKNHPNKEKKMSHTKEQILEILSAIETCEEELYDKEKEVKQLRAKLKGLKVKLQGAINKIGKSKNTTPKKHKTHTNPHTENQPSQN
SIO_010081: HXS61_RS08585
subclass of: SO_0000673
so part of: HXS61_RS08585
location: 922..2412
location: region:922-2412:1
so has part: feature:922-2412:1:exon

WP_176486247.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:922-2412:1:exon

HXS61_RS08590
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
gene: mobC
locus tag: HXS61_RS08590
old locus tag: NHP194022_17300
so part of: sequence
location: 2552..2908
location: region:2552-2908:1
so has part: feature:2552-2908:1:exon
subclass of: SO_0000010

56929574
type: Gene
SIO_000068: ncbigene

position:2552:1
position: 2552
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2908:1
position: 2908
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2552-2908:1:exon

HXS61_RS08590
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
gene: mobC
locus tag: HXS61_RS08590
old locus tag: NHP194022_17300
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001024584.1
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: MNPQRKIKENALITKPITKRLRLSEKEWEIIQFEMQKSHLNFSQFALTSMLKSQPKIPAKKARVLANKDLIIELAKWGNNLNQIAKHLNTQKSMDKISLKMLAEIEKNLEQIRAHFVS
SIO_010081: HXS61_RS08590
subclass of: SO_0000673
so part of: HXS61_RS08590
location: 2552..2908
location: region:2552-2908:1
so has part: feature:2552-2908:1:exon

WP_231630319.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2552-2908:1:exon

HXS61_RS08595
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08595
so part of: sequence
location: 2898..4745
location: region:2898-4745:1
so has part: feature:2898-4745:1:exon
subclass of: SO_0000010

56929575
type: Gene
SIO_000068: ncbigene

position:2898:1
position: 2898
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4745:1
position: 4745
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2898-4745:1:exon

HXS61_RS08595
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08595
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015087711.1
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: MLVKFWGNKKGGSESSIDYLLDERFKAGTARILKGNAELTRNLINTLTQKHKICVGCLSFEESNIEEHLKQEIIENFERALLTEEMQGRYNILWVEHRDKGRLELNFVIPRIDLATKKAFTPYYHRADLTRIDTWKNLVNLEHNFSNPKDLNKVQKIQRCNTKIPQQKKLFKDCQELDDFLHDKVKNNFLDTRQEIIELLEQHGIEVTRQGKDYISVKLPESKKAIRLKGEIYHEQFGNVAKHGSHTDQEKAGERTADTRASQSDHRHTHADSREQTESDRRYDHTERRKEVANLRQKLHELITHKQRYYATTHREGRTRLADDRHTEHQRAQNYSQSNRTTSDHTNTKSREEKQCIDSDHELHIDNAFNASRVSTFYRATPHQRDRGERARNSSDGGRACQADTRAQGSDSRTESQAWQETQSVRAVRGKDFDDDDRDTERIRARIVRRSRELAERSGELARQDRELAERESGLLGAIRAHEESSRGARETITRAHSQIMQFRGSTSARDTKPYSDPIREFESDSERFKAQIRGIVAGGADRARENQSRDAILLQGLREADTARLQYASERARETLQRFRGFVARATSAIRNESEKLRLASLYQPQSRGRGRGR
SIO_010081: HXS61_RS08595
subclass of: SO_0000673
so part of: HXS61_RS08595
location: 2898..4745
location: region:2898-4745:1
so has part: feature:2898-4745:1:exon

WP_176486574.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2898-4745:1:exon

HXS61_RS08600
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08600
old locus tag: NHP194022_17330
so part of: sequence
location: 4742..5137
location: region:4742-5137:1
so has part: feature:4742-5137:1:exon
subclass of: SO_0000010

56929576
type: Gene
SIO_000068: ncbigene

position:4742:1
position: 4742
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

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

urn:…
SIO_000300: 1
SIO_000628: feature:4742-5137:1:exon

HXS61_RS08600
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08600
old locus tag: NHP194022_17330
EC number: 3.1.-.-
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014659979.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system PemK/MazF family toxin
translation: MTERFDSWNEQKKKLDKNPPHKVIVGNIYWICIGQNIGHEVYGKSASFTRPVLVVKLLSNKLFLGVPLSSQIHKKTMPFHHGFKDSNDTEQVALLHQIRVFDTKRRRTKIAQVSDEVLKIIKDRIKSEVID
SIO_010081: HXS61_RS08600
subclass of: SO_0000673
so part of: HXS61_RS08600
location: 4742..5137
location: region:4742-5137:1
so has part: feature:4742-5137:1:exon

WP_006565308.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4742-5137:1:exon