Prevotella scopos JCM 17725 strain W2052 plasmid unnamed1, complete sequence.
type: Entry
definition: Prevotella scopos JCM 17725 strain W2052 plasmid unnamed1, complete sequence.
sequence version: NZ_CP016206.1
sequence date: 2022-10-06
sequence: sequence
division: CON
label: NZ_CP016206.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN03897722
keyword: RefSeq
source: Prevotella scopos JCM 17725
organism: Prevotella scopos JCM 17725
taxonomy: Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella.
reference: 1
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP016206.1.\nDNA isolation: W. G. Wade, Barts and The London School of Medicine\nand Dentistry, Queen Mary University of London, 4 Newark Street,\nLondon E1 2AT United Kingdom.\n Source DNA and bacterial cultures: T. A. Joyce and F. E. Dewhirst\nDirect requests to the Human Oral Microbiome Project, The Forsyth\nInstitute, 245 First Street, Cambridge, MA, 02142, USA.\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 :: SPAdes v. 3.8.0\nAssembly Name :: W2052_Prevotella_scopus\nGenome Coverage :: 65x\nSequencing Technology :: Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/05/2022 14:35:32\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 2,638\nCDSs (total) :: 2,574\nGenes (coding) :: 2,494\nCDSs (with protein) :: 2,494\nGenes (RNA) :: 64\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 3\nPseudo Genes (total) :: 80\nCDSs (without protein) :: 80\nPseudo Genes (ambiguous residues) :: 0 of 80\nPseudo Genes (frameshifted) :: 35 of 80\nPseudo Genes (incomplete) :: 49 of 80\nPseudo Genes (internal stop) :: 13 of 80\nPseudo Genes (multiple problems) :: 15 of 80\nCRISPR Arrays :: 5\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7335
topology: circular
so has quality: SO_0000988
location: 1..7335
location: region:1-7335:1
RO_0002162: 1236518

NZ_CP016206
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN03897722
type: BioSample
SIO_000068: biosample

1
title: Direct Submission
author: Holder, M.E.
author: Ajami, N.J.
author: Petrosino, J.F.
journal: Submitted (21-JUN-2016) Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

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

position:7335:1
position: 7335
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7335:1:source
so part of: sequence
organism: Prevotella scopos JCM 17725
mol type: genomic DNA
strain: W2052
isolation source: Dental implant
host: Homo sapiens
type material: type strain of Prevotella scopos
plasmid: unnamed1
country: United Kingdom: Cardiff
lat lon: 51.48 N 3.18 W
collection date: 1988

1236518
type: Taxonomy
SIO_000068: taxonomy

AXF22_RS13030
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13030
old locus tag: AXF22_13030
so part of: sequence
location: join(6824..7335,1..148)
location: region:1-7335:1
so has part: feature:6824-7335:1:exon
so has part: feature:1-148:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:6824-7335:1:exon

position:6824:1
position: 6824
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-148:1:exon

position:148:1
position: 148
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

AXF22_RS13030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13030
old locus tag: AXF22_13030
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: outer membrane beta-barrel protein
translation: MKKTYIILLFVVLGVVTVNAQGIRYGVTGGINLHTTSGDVDTEGVLVGYYAGVKSIYDFSQNGQGLYLTGTLALSEKAFKTVPIELTPNRPETSTYGKVKTHSVEVPIRMGYKFPIGRTVKLLAEAGPYISIGLWGNYDVYTNGKKVAKYNEAFDKYGIRRCDFGLGMGLGLQYSEHYQLNISYNHGLAQLTHPEKKEKMFSTPSLYNRTFNITISYIF
SIO_010081: AXF22_RS13030
subclass of: SO_0000673
so part of: AXF22_RS13030
location: join(6824..7335,1..148)
location: region:1-7335:1
so has part: feature:6824-7335:1:exon
so has part: feature:1-148:1:exon

WP_065368085.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6824-7335:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-148:1:exon

AXF22_RS13035
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13035
old locus tag: AXF22_13035
so part of: sequence
location: complement(200..1231)
location: region:200-1231:-1
so has part: feature:200-1231:-1:exon
subclass of: SO_0000010

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

position:1231:-1
position: 1231
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:200-1231:-1:exon

AXF22_RS13035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13035
old locus tag: AXF22_13035
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017645576.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MARPVEENKNVIQSYMLTAARYDFSVYEKRILYRLVELAQAELQGKDFVEWIGMKVETNLFGDKDITMPVRCILANEEDKNYVLAKKAFKAMSSRTIEQTKGNVWYLDHMLERVRVNLGTGVAKFRVSPNVWNIVLDFTKGYRKYELKTTMQFKSVYSMRFYELLSGQTNPLKYSIEEFRKMFSLEKKFKAVADIERYVLEVAQKELDESSPYSFSWERQEVSSRGRNGKKVVGYTFYPKYIQKNKDPQLEKKELQAKVGNIAGAYGMLDRAVSDYLLYNLNMTKEEINANKALFLTAQQTLPNLVEHLADLRERAVRSGKGTGWIINGLKGKLKEIKDLEEL
SIO_010081: AXF22_RS13035
subclass of: SO_0000673
so part of: AXF22_RS13035
location: complement(200..1231)
location: region:200-1231:-1
so has part: feature:200-1231:-1:exon

WP_025839937.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:200-1231:-1:exon

AXF22_RS13040
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13040
old locus tag: AXF22_13040
so part of: sequence
location: complement(1244..1438)
location: region:1244-1438:-1
so has part: feature:1244-1438:-1:exon
subclass of: SO_0000010

position:1244:-1
position: 1244
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1438:-1
position: 1438
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1244-1438:-1:exon

AXF22_RS13040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13040
old locus tag: AXF22_13040
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017645928.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MDKRLFDAQLKAAEVQGLLAHIAKNVNYKQDLEEPATRNIDVINATLSEVCQMLEKLNQELTNQ
SIO_010081: AXF22_RS13040
subclass of: SO_0000673
so part of: AXF22_RS13040
location: complement(1244..1438)
location: region:1244-1438:-1
so has part: feature:1244-1438:-1:exon

WP_025839938.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1244-1438:-1:exon

AXF22_RS13045
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13045
old locus tag: AXF22_13045
so part of: sequence
location: 1852..2112
location: region:1852-2112:1
so has part: feature:1852-2112:1:exon
subclass of: SO_0000010

position:1852:1
position: 1852
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2112:1
position: 2112
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1852-2112:1:exon

AXF22_RS13045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13045
old locus tag: AXF22_13045
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004295507.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MAVLNFTSREFRSQQAHVFELADQGEKVIIRRSKKQAYTLVPVSDDDFTITPELQARIDKARAEIKAGECITVRGKEELNAYLTSL
SIO_010081: AXF22_RS13045
subclass of: SO_0000673
so part of: AXF22_RS13045
location: 1852..2112
location: region:1852-2112:1
so has part: feature:1852-2112:1:exon

WP_025839939.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1852-2112:1:exon

AXF22_RS13050
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13050
old locus tag: AXF22_13050
so part of: sequence
location: 2109..2384
location: region:2109-2384:1
so has part: feature:2109-2384:1:exon
subclass of: SO_0000010

position:2109:1
position: 2109
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2384:1
position: 2384
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2109-2384:1:exon

AXF22_RS13050
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13050
old locus tag: AXF22_13050
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004327436.1
GO process: GO:0008219 - cell death [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Txe/YoeB family addiction module toxin
translation: MIYDLRFSSQANKVAKKWKKSNPTAFKKYAKILSELMEHPRSGLGHPEALKGGDDITWSRHITAHDRMIYDIYDDIIEVYVLELEGHYDDK
SIO_010081: AXF22_RS13050
subclass of: SO_0000673
so part of: AXF22_RS13050
location: 2109..2384
location: region:2109-2384:1
so has part: feature:2109-2384:1:exon

WP_025839940.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2109-2384:1:exon

AXF22_RS13055
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13055
old locus tag: AXF22_13055
so part of: sequence
location: complement(2388..3617)
location: region:2388-3617:-1
so has part: feature:2388-3617:-1:exon
subclass of: SO_0000010

position:2388:-1
position: 2388
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3617:-1
position: 3617
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2388-3617:-1:exon

AXF22_RS13055
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13055
old locus tag: AXF22_13055
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000813408.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein
translation: MKIMKQQTSIHVQPVKGGSEQHNKREKELDYIRPELSHLNEYWEKDTQTDRLENIKSRYLKSTGQKMQSKATPIREAVVVIKSETTMEDLKRLSDAYRQRFGIDTFQIAIHKDEGYPKGEWKPNLHAHLVFDWTDQETGKSLKLKRQDMVEMQTITAEVLQMDRGVSSDKQHLTAQQYKSFAEEAKLKQLEEERVRKEKQMKEELERFKVSKARKEAAIETAKTLSEGVKGLFGQSSKDKQIKTLKTQLNTREKEIFNLKAEQIGQLGSATQKIDKAYQEGFNKAYGEVYNLQAQLKKAKELAADAQKYRADIEKFQSIPIIARCINAIRSYVRHINGRFDAEDKRLLSFVMQGDSDAAEKLKDAAYYGCGIIGQYQYGSKWDQAERELRNIANGVREEEQQRNRGLRR
SIO_010081: AXF22_RS13055
subclass of: SO_0000673
so part of: AXF22_RS13055
location: complement(2388..3617)
location: region:2388-3617:-1
so has part: feature:2388-3617:-1:exon

WP_199897354.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2388-3617:-1:exon

AXF22_RS13060
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13060
old locus tag: AXF22_13060
so part of: sequence
location: complement(4102..4380)
location: region:4102-4380:-1
so has part: feature:4102-4380:-1:exon
subclass of: SO_0000010

position:4102:-1
position: 4102
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4380:-1
position: 4380
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4102-4380:-1:exon

AXF22_RS13060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13060
old locus tag: AXF22_13060
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: MLNIKNLYTAATQGTDQFKRNETIRLWVDIAFDHPTDNKTITTTDKIISSDKCDMFFNKCIYYDDQITAGNMTTQHVKNTLRKILRDEFNIK
SIO_010081: AXF22_RS13060
subclass of: SO_0000673
so part of: AXF22_RS13060
location: complement(4102..4380)
location: region:4102-4380:-1
so has part: feature:4102-4380:-1:exon

WP_025839942.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4102-4380:-1:exon

AXF22_RS13065
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13065
old locus tag: AXF22_13065
so part of: sequence
location: complement(4398..4943)
location: region:4398-4943:-1
so has part: feature:4398-4943:-1:exon
subclass of: SO_0000010

position:4398:-1
position: 4398
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4943:-1
position: 4943
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4398-4943:-1:exon

AXF22_RS13065
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13065
old locus tag: AXF22_13065
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009237662.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKRNIILIFLISLVLNSCQISGLTSGYSHLSRQQKTKVIDYKGNIEDITDNTKIYTITVKQVKDYILSHEKVLVYNYTPYCKSQYCCSPNLLVSLCERQGIKVLVIANVYDDIFKRINNGFPLLMINTKPYSKWRWKYTDRFYYDLIGYIGKDIDYASFHYFINGTYIKSFKDFKDIGQES
SIO_010081: AXF22_RS13065
subclass of: SO_0000673
so part of: AXF22_RS13065
location: complement(4398..4943)
location: region:4398-4943:-1
so has part: feature:4398-4943:-1:exon

WP_025839943.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4398-4943:-1:exon

AXF22_RS13070
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13070
old locus tag: AXF22_13070
so part of: sequence
location: complement(4946..5527)
location: region:4946-5527:-1
so has part: feature:4946-5527:-1:exon
subclass of: SO_0000010

position:4946:-1
position: 4946
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5527:-1
position: 5527
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4946-5527:-1:exon

AXF22_RS13070
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13070
old locus tag: AXF22_13070
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: MKRFYLFAITLLSLASCQQEDIATNGMYSDAFMSKLKFNTINVSKTRAFDNGKDAEESIINDNSVKTTNAGVNIGIFSVRIARPSTDCVYGFGFCDFVWFPKQNNEVDFRNNHLYDNSFEVKCDSEGNKFVDMELLEVPKNLDISKLQPLVVEDSLESIRTIDGKEKEVVVPMGTYVFDRTIGKYGGYRIPLK
SIO_010081: AXF22_RS13070
subclass of: SO_0000673
so part of: AXF22_RS13070
location: complement(4946..5527)
location: region:4946-5527:-1
so has part: feature:4946-5527:-1:exon

WP_025839944.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4946-5527:-1:exon

AXF22_RS13075
type: Gene
subclass of: SO_0000704
RO_0002162: 1236518
locus tag: AXF22_RS13075
old locus tag: AXF22_13075
so part of: sequence
location: 5879..6811
location: region:5879-6811:1
so has part: feature:5879-6811:1:exon
subclass of: SO_0000010

position:5879:1
position: 5879
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6811:1
position: 6811
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5879-6811:1:exon

AXF22_RS13075
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1236518
locus tag: AXF22_RS13075
old locus tag: AXF22_13075
inference: COORDINATES: protein motif:HMM:NF027466.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF4848 domain-containing protein
translation: MRNYLTYFTIAILFLSSCNNQDDEIILKKNESFNPLSRVEVVSLSGSSTRAKNEEEKTLRFEDVEHLNKVVEILENRNDRENEDFFRKINFRGIFLRNIEANKAIDDIFDIEDYDTFLNEVKKYKEQYGDLLKGNVSEYDLTPNLQFDDEVIRLLGNKNGEILVGEKVYAPKASLSSFRGLLSGPYAPTFREFPGNPVNIMLREGKYQGSVTLGACRENGDFMVECASQKKKKFWKRRNETDYSGDVYINGAHFFFNVLRKKRQAVFLSPFVNVGQYAGKKITVSISNFKVGCCPSLVGNQTFELDLRNR
SIO_010081: AXF22_RS13075
subclass of: SO_0000673
so part of: AXF22_RS13075
location: 5879..6811
location: region:5879-6811:1
so has part: feature:5879-6811:1:exon

WP_025839946.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5879-6811:1:exon