Neisseria gonorrhoeae strain TUM19854 plasmid pMTY19854, complete sequence.
type: Entry
definition: Neisseria gonorrhoeae strain TUM19854 plasmid pMTY19854, complete sequence.
sequence version: NZ_AP023070.1
sequence date: 2023-04-28
sequence: sequence
division: CON
label: NZ_AP023070.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMD00217348
keyword: RefSeq
source: Neisseria gonorrhoeae
organism: Neisseria gonorrhoeae
taxonomy: Bacteria; Pseudomonadota; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria.
reference: 1
references: 33930160
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nAP023070.1.\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-beta\nGenome Coverage :: 94x\nSequencing Technology :: ONT MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 03:59:22\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) :: 2,299\nCDSs (total) :: 2,228\nGenes (coding) :: 2,002\nCDSs (with protein) :: 2,002\nGenes (RNA) :: 71\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 4\nPseudo Genes (total) :: 226\nCDSs (without protein) :: 226\nPseudo Genes (ambiguous residues) :: 0 of 226\nPseudo Genes (frameshifted) :: 115 of 226\nPseudo Genes (incomplete) :: 132 of 226\nPseudo Genes (internal stop) :: 38 of 226\nPseudo Genes (multiple problems) :: 57 of 226\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4153
topology: circular
so has quality: SO_0000988
location: 1..4153
location: region:1-4153:1
RO_0002162: 485

NZ_AP023070
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMD00217348
type: BioSample
SIO_000068: biosample

1
title: Molecular characterization of Neisseria gonorrhoeae isolates collected through a national surveillance programme in Japan, 2013: evidence of the emergence of a ceftriaxone-resistant strain from a ceftriaxone-susceptible lineage
author: Hanao, M.
author: Aoki, K.
author: Ishii, Y.
author: Shimuta, K.
author: Ohnishi, M.
author: Tateda, K.
journal: J Antimicrob Chemother
volume: 76
issue: 7
pages: 1769-1775
year: 2021
pubmed: 33930160
comments: DOI:10.1093/jac/dkab104

33930160
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Hanao, M.
author: Aoki, K.
author: Ishii, Y.
author: Tateda, K.
journal: Submitted (01-MAY-2020) Contact:Mami Hanao Toho University; 5-21-16 Omori-nish, Ota-ku, Tokyo 143-8540, Japan

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

position:4153:1
position: 4153
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4153:1:source
so part of: sequence
organism: Neisseria gonorrhoeae
mol type: genomic DNA
strain: TUM19854
plasmid: pMTY19854

485
type: Taxonomy
SIO_000068: taxonomy

HT085_RS11990
type: Gene
subclass of: SO_0000704
RO_0002162: 485
locus tag: HT085_RS11990
so part of: sequence
location: complement(join(4109..4153,1..336))
location: region:1-4153:-1
so has part: feature:1-336:-1:exon
so has part: feature:4109-4153:-1:exon
subclass of: SO_0000010

71771649
type: Gene
SIO_000068: ncbigene

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

position:4153:-1
position: 4153
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-336:-1:exon

position:336:-1
position: 336
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:4109-4153:-1:exon

position:4109:-1
position: 4109
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

HT085_RS11990
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 485
locus tag: HT085_RS11990
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: MobC family plasmid mobilization relaxosome protein
translation: MTGSSAAEKRTKQLIIRVSPTEFETLTRQKTHPNLARYIRERVLEDGKASDKKTVKFQFPPEVVRVLAGMGNNLNQIAKALNTAAKVGTLGNVEALKATTELAALERSLNSLRDFLAKEKNGWQSQ
SIO_010081: HT085_RS11990
subclass of: SO_0000673
so part of: HT085_RS11990
location: complement(join(4109..4153,1..336))
location: region:1-4153:-1
so has part: feature:1-336:-1:exon
so has part: feature:4109-4153:-1:exon

WP_014580441.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-336:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:4109-4153:-1:exon

HT085_RS11445
type: Gene
subclass of: SO_0000704
RO_0002162: 485
locus tag: HT085_RS11445
old locus tag: TUM19854C_21600
so part of: sequence
location: 722..1591
location: region:722-1591:1
so has part: feature:722-1591:1:exon
subclass of: SO_0000010

66754511
type: Gene
SIO_000068: ncbigene

position:722:1
position: 722
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1591:1
position: 1591
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:722-1591:1:exon

HT085_RS11445
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 485
locus tag: HT085_RS11445
old locus tag: TUM19854C_21600
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003690219.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MSQLYTQPDLFLQERIPHKPYCKDFKEAPMLVRSYAAAIKRRYIQVNPPHLRVFMLFDLDYEGAGLAWEDNNLPMPAWAAINRENGGAHLAYALSAPVLTAEYGGRQKALRYLAALEAAYKAKLRGDVGFVSLITKNPEHPHWLTLRGVPDAIRGYDLEYLADFVDLDKFKPYIGRSNVEAVGLSRNCTVFNLVSRWAHKNVLAFKQQGYTVQGWLKEVHYQCMRVNGDFPVPMWEKEVKCISKSIANWVWYKFDIAASNRRFSELQAHRNSLRKTTINAGRTKIITEL
SIO_010081: HT085_RS11445
subclass of: SO_0000673
so part of: HT085_RS11445
location: 722..1591
location: region:722-1591:1
so has part: feature:722-1591:1:exon

WP_003690219.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:722-1591:1:exon

HT085_RS11450
type: Gene
subclass of: SO_0000704
RO_0002162: 485
locus tag: HT085_RS11450
old locus tag: TUM19854C_21610
so part of: sequence
location: 1595..1837
location: region:1595-1837:1
so has part: feature:1595-1837:1:exon
subclass of: SO_0000010

66754512
type: Gene
SIO_000068: ncbigene

position:1595:1
position: 1595
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1837:1
position: 1837
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1595-1837:1:exon

HT085_RS11450
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 485
locus tag: HT085_RS11450
old locus tag: TUM19854C_21610
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003690220.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: HTH domain-containing protein
translation: MAYPKLKTTKRDVTAKELAKRFGCSTRTVFRAWSQSRADYLAENSISRDKPWEHFGISRATWYRRGKPMPSETDNQSETA
SIO_010081: HT085_RS11450
subclass of: SO_0000673
so part of: HT085_RS11450
location: 1595..1837
location: region:1595-1837:1
so has part: feature:1595-1837:1:exon

WP_003690220.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1595-1837:1:exon

HT085_RS11455
type: Gene
subclass of: SO_0000704
RO_0002162: 485
locus tag: HT085_RS11455
so part of: sequence
location: 1834..2079
location: region:1834-2079:1
so has part: feature:1834-2079:1:exon
subclass of: SO_0000010

66754513
type: Gene
SIO_000068: ncbigene

position:1834:1
position: 1834
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2079:1
position: 2079
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1834-2079:1:exon

HT085_RS11455
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 485
locus tag: HT085_RS11455
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003690221.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTRYAINRDALYSAFKDFLYSEINANPALKSATVDDLADIVLAKKWRIFLPDGIKRTTAEKAAQRVLYMTNQPENQTQQEN
SIO_010081: HT085_RS11455
subclass of: SO_0000673
so part of: HT085_RS11455
location: 1834..2079
location: region:1834-2079:1
so has part: feature:1834-2079:1:exon

WP_003690221.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1834-2079:1:exon

HT085_RS11460
type: Gene
subclass of: SO_0000704
RO_0002162: 485
locus tag: HT085_RS11460
old locus tag: TUM19854C_21620
so part of: sequence
location: 2082..2267
location: region:2082-2267:1
so has part: feature:2082-2267:1:exon
subclass of: SO_0000010

66754514
type: Gene
SIO_000068: ncbigene

position:2082:1
position: 2082
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2267:1
position: 2267
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2082-2267:1:exon

HT085_RS11460
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 485
locus tag: HT085_RS11460
old locus tag: TUM19854C_21620
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003690223.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF5397 family protein
translation: MQTTIPTGSIRTFGDYGVMYIVGTPAEQLPDGDWLVNIELPESGEHTQYKLSHIVQDPKAA
SIO_010081: HT085_RS11460
subclass of: SO_0000673
so part of: HT085_RS11460
location: 2082..2267
location: region:2082-2267:1
so has part: feature:2082-2267:1:exon

WP_003690223.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2082-2267:1:exon

HT085_RS11465
type: Gene
subclass of: SO_0000704
RO_0002162: 485
locus tag: HT085_RS11465
old locus tag: TUM19854C_21630
so part of: sequence
location: 2267..2545
location: region:2267-2545:1
so has part: feature:2267-2545:1:exon
subclass of: SO_0000010

66754515
type: Gene
SIO_000068: ncbigene

position:2545:1
position: 2545
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2267-2545:1:exon

HT085_RS11465
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 485
locus tag: HT085_RS11465
old locus tag: TUM19854C_21630
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013448818.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: endoribonuclease VapD
translation: MYAISFDLVVADTAQNHPKGISQAYADIGYTLRKFGFTRIQGSLYTCQNEDMANLFSAINELKALPWFPSSVRDIRAFRIEQWSDFTSLVKS
SIO_010081: HT085_RS11465
subclass of: SO_0000673
so part of: HT085_RS11465
location: 2267..2545
location: region:2267-2545:1
so has part: feature:2267-2545:1:exon

WP_003690225.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2267-2545:1:exon

HT085_RS11470
type: Gene
subclass of: SO_0000704
RO_0002162: 485
locus tag: HT085_RS11470
old locus tag: TUM19854C_21640
so part of: sequence
location: complement(2523..2777)
location: region:2523-2777:-1
so has part: feature:2523-2777:-1:exon
subclass of: SO_0000010

66754516
type: Gene
SIO_000068: ncbigene

position:2523:-1
position: 2523
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2777:-1
position: 2777
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2523-2777:-1:exon

HT085_RS11470
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 485
locus tag: HT085_RS11470
old locus tag: TUM19854C_21640
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003690227.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Cryptic plasmid protein A
translation: MITENERDRRTAAWLIETYGAEAVAEAETRIAGARKPYPSNIAKVLGASLPEALKRTENAAARQKLAGLRRMLDGKAVKTSQDL
SIO_010081: HT085_RS11470
subclass of: SO_0000673
so part of: HT085_RS11470
location: complement(2523..2777)
location: region:2523-2777:-1
so has part: feature:2523-2777:-1:exon

WP_003690227.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2523-2777:-1:exon

HT085_RS11475
type: Gene
subclass of: SO_0000704
RO_0002162: 485
locus tag: HT085_RS11475
old locus tag: TUM19854C_21650
so part of: sequence
location: complement(2824..3411)
location: region:2824-3411:-1
so has part: feature:2824-3411:-1:exon
subclass of: SO_0000010

66754517
type: Gene
SIO_000068: ncbigene

position:2824:-1
position: 2824
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3411:-1
position: 3411
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2824-3411:-1:exon

HT085_RS11475
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 485
locus tag: HT085_RS11475
old locus tag: TUM19854C_21650
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003690229.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MbeB family mobilization protein
translation: MSKISDLAKTFEQTSRTEAASIEQQTKADLETLRKNINEALKQSEQKITADINARQLRMSKAVFKPYLWSLLGISAAGLIVIAGLFIAIWSVKNELDDLKQQRAEAERTLDLLETKTKGLTLENCPVENSKATRVCVATEKRMMKALTHLGERLAELEQENTSLAQQLASLAAELERQSEIQQRQSEILNQLAKR
SIO_010081: HT085_RS11475
subclass of: SO_0000673
so part of: HT085_RS11475
location: complement(2824..3411)
location: region:2824-3411:-1
so has part: feature:2824-3411:-1:exon

WP_003692168.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2824-3411:-1:exon

HT085_RS11480
type: Gene
subclass of: SO_0000704
RO_0002162: 485
locus tag: HT085_RS11480
old locus tag: TUM19854C_21660
so part of: sequence
location: complement(3495..4124)
location: region:3495-4124:-1
so has part: feature:3495-4124:-1:exon
subclass of: SO_0000010

66754518
type: Gene
SIO_000068: ncbigene

position:3495:-1
position: 3495
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4124:-1
position: 4124
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3495-4124:-1:exon

HT085_RS11480
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 485
locus tag: HT085_RS11480
old locus tag: TUM19854C_21660
inference: COORDINATES: protein motif:HMM:NF015397.2
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: MAVPMIVQFFNRGKGGGSGPIDYLLGKDRDREEARLLRGDPEETAALINSSDYAKKYTAGCLSFEESNIPAEQKHALMDSFEECIFAGLDKDQYNCLWVEHRDKGRLELNFVIPNIELLSGKRLQPYYYAADRGRVDAWRTMQNLTHGYSDPDDPAKRQSMTQAKDLPRNTQEAAQSITEHHRRLRSPSPIRQAKKPRRRAGNAGKGRF
SIO_010081: HT085_RS11480
subclass of: SO_0000673
so part of: HT085_RS11480
location: complement(3495..4124)
location: region:3495-4124:-1
so has part: feature:3495-4124:-1:exon

WP_003696452.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3495-4124:-1:exon