Helicobacter suis strain NHP19-4022 plasmid pNHP194022_1, complete sequence.
type: Entry
definition: Helicobacter suis strain NHP19-4022 plasmid pNHP194022_1, complete sequence.
sequence version: NZ_AP023047.1
sequence date: 2022-12-19
sequence: sequence
division: CON
label: NZ_AP023047.1
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\nAP023047.1.\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: 6511
topology: circular
so has quality: SO_0000988
location: 1..6511
location: region:1-6511:1
RO_0002162: 104628

NZ_AP023047
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journal: Unpublished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:6511:1
position: 6511
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6511:1:source
so part of: sequence
organism: Helicobacter suis
mol type: genomic DNA
strain: NHP19-4022
isolation source: stomach
host: Homo sapiens
plasmid: pNHP194022_1
country: Japan:Fukuoka
collection date: 2019

104628
type: Taxonomy
SIO_000068: taxonomy

HXS61_RS08550
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08550
old locus tag: NHP194022_17220
so part of: sequence
location: 1..1812
location: region:1-1812:1
so has part: feature:1-1812:1:exon
subclass of: SO_0000010

56929566
type: Gene
SIO_000068: ncbigene

position:1812:1
position: 1812
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-1812:1:exon

HXS61_RS08550
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08550
old locus tag: NHP194022_17220
inference: COORDINATES: protein motif:HMM:NF013235.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MDIAKQKQLLMEQLSTLQTLINAETDNTFKEMLRQEKADCLKDLKMLVSLMSVLPGDQQDRTENIIQESKTQEHTINKNTIQENTGVNNNIQKNIIANNTIQENTIADNNRQENTIQDIPIEQAKSSQQIQENQVSIPQEAKSIQHQELQGIIPTQQDQNISHPVISEKYIAFHNDVNSVNLGKLSALETNLLFAIFNKLKDRQDELLVFDLDEIETMVHAVKINHSILSGVVKRLWKNIRVANFWILYPRAEENIMLFRKFRINYHDTQKTQVKSMEIQVNMPYFGYLLNFLNANFTSFELLEFQNIRGKYAKTLYRLLKQWKSVGVPPRMEWGKFRELMGILRDYQVGEIEMHILKPAIQELKKLPQFESLCYEKLKTKGMGNRITHIQFYFQPTTKTSKDKEQAKRDLRTIAWKIRSQQVIEQIKRSKKQRAEQAKQEDSVMEILGAAFSKPQDPSIVLVIDSIHPTLKGYNFLAKFYQNGQQIDERSATLANKEILLESFARAGYQRIDLAQQSQQVDQTPQQPPDLNPKDDLTDYIGRNLYMSKNGVPASLKIKDIARLKNGTIQVEVKDVDKPRKSLNPFKFENAAHFKNWFRKFAE
SIO_010081: HXS61_RS08550
subclass of: SO_0000673
so part of: HXS61_RS08550
location: 1..1812
location: region:1-1812:1
so has part: feature:1-1812:1:exon

WP_197942589.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-1812:1:exon

HXS61_RS08555
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08555
old locus tag: NHP194022_17230
so part of: sequence
location: 1953..2636
location: region:1953-2636:1
so has part: feature:1953-2636:1:exon
subclass of: SO_0000010

56929567
type: Gene
SIO_000068: ncbigene

position:1953:1
position: 1953
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2636:1
position: 2636
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1953-2636:1:exon

HXS61_RS08555
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08555
old locus tag: NHP194022_17230
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013882034.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: AAA family ATPase
translation: MIITIANEKGGSGKSTLCINLALQFLAEQKDIVVLDTDPQQSVEVFVNIRSETSLPIFPLFNRTGNITDTLKQMVGKYQIVIIDTKGEHSKESQRAILLSDLVLIPTTPSQLDSAVLLDMLERVQDLQALNEKLKALVLINRIPPIPTLKEKQALVEFIEQNNTNNRVLLLKNHLSERIAFKRSISEGLGVMECGDVKAKREWEQFFNELTSHLPQSMPNKDKSHAL
SIO_010081: HXS61_RS08555
subclass of: SO_0000673
so part of: HXS61_RS08555
location: 1953..2636
location: region:1953-2636:1
so has part: feature:1953-2636:1:exon

WP_073115518.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1953-2636:1:exon

HXS61_RS08560
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08560
old locus tag: NHP194022_17240
so part of: sequence
location: 2927..3181
location: region:2927-3181:1
so has part: feature:2927-3181:1:exon
subclass of: SO_0000010

56929568
type: Gene
SIO_000068: ncbigene

position:2927:1
position: 2927
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3181:1
position: 3181
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2927-3181:1:exon

HXS61_RS08560
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08560
old locus tag: NHP194022_17240
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013882035.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MEIENLESLDAAFEAKNQKNGAKKYYTLFLSQATMSKLEQYLKEFGHFKENKSTFIQEALEEHLKRKREHIKQELSEKLKKLQD
SIO_010081: HXS61_RS08560
subclass of: SO_0000673
so part of: HXS61_RS08560
location: 2927..3181
location: region:2927-3181:1
so has part: feature:2927-3181:1:exon

WP_040499103.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2927-3181:1:exon

HXS61_RS08565
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08565
old locus tag: NHP194022_17250
so part of: sequence
location: 3326..4510
location: region:3326-4510:1
so has part: feature:3326-4510:1:exon
subclass of: SO_0000010

56929569
type: Gene
SIO_000068: ncbigene

position:3326:1
position: 3326
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4510:1
position: 4510
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3326-4510:1:exon

HXS61_RS08565
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08565
old locus tag: NHP194022_17250
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006564015.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system HipA family toxin
translation: MEVYSNTDQVGVLEVYATGRNETYYFTYDANWIQNGFEIDPQLPLQETKVVSKELWGAFCDISPDRWGRLIQKREAKSELTDSEYMLGVSDYFRVGSLRLFKEGLFVSPSTNHPKLANINQLCVSAHRVEQGESLEDDLRKLLAPSGSLGGARPKASVLKEGVLYIAKFPSLKDADKQISRCEKTMLDVAKLAKIQVCKTELLETSKGTVLLVKRFDRKEQERIPFKSAMTLLSARDGEQRSYCDLAKVLDQKNKKELFRRMVFNGLFGNCDDHLRNHGVLYDQENKTWNLSPAFDITPESIVYAKQTHALNFIDLENLPSIELFDRIKHHFSVTETLFKSILKDMWGARERFEILARKNGINRDNLIALKNNYQHVDFEKVQQMFSVNKGIEF
SIO_010081: HXS61_RS08565
subclass of: SO_0000673
so part of: HXS61_RS08565
location: 3326..4510
location: region:3326-4510:1
so has part: feature:3326-4510:1:exon

WP_269150061.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3326-4510:1:exon

HXS61_RS08570
type: Gene
subclass of: SO_0000704
RO_0002162: 104628
locus tag: HXS61_RS08570
old locus tag: NHP194022_17260
so part of: sequence
location: complement(4580..5662)
location: region:4580-5662:-1
so has part: feature:4580-5662:-1:exon
subclass of: SO_0000010

56929570
type: Gene
SIO_000068: ncbigene

position:4580:-1
position: 4580
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5662:-1
position: 5662
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4580-5662:-1:exon

HXS61_RS08570
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 104628
locus tag: HXS61_RS08570
old locus tag: NHP194022_17260
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013889563.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: RNA-guided endonuclease TnpB family protein
translation: MLIAYKQKLYNSSKNKQIDRLLRLYGICYNHCIALHKRYYRLYKKHLNFYTLKKHITKLKRTARFAFLKTLGSQTLQELVGRIDKAYKKFFKKQGRPPRFKKVANYQSFTFSQCGYKIQDNIISFNGYRFKFVKTYDLAGKPKTLTIKRDNLGDYFLCLVCETEDNLKPAGGNSVGLDFGLKTFLTCSNGTQIPSPLFFSKFLPLIRACSRSLSKKKRGSHNRLKARLKLARLHRKVQNLRKDFFYKIANSLAKQYATIFIEDLNLKGMVKLWGRKINDLAFGEFVAILERKTQVVKIDRFYPSSKTCSNCGALKEDLSLKDRFFHCPSCGFSLDRDLNTSINIHRVGASTLGGEAVRPA
SIO_010081: HXS61_RS08570
subclass of: SO_0000673
so part of: HXS61_RS08570
location: complement(4580..5662)
location: region:4580-5662:-1
so has part: feature:4580-5662:-1:exon

WP_176486573.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4580-5662:-1:exon