Phocaeicola vulgatus strain MG01-10 plasmid pMG01-10_3, complete sequence.
type: Entry
definition: Phocaeicola vulgatus strain MG01-10 plasmid pMG01-10_3, complete sequence.
sequence version: NZ_AP025243.1
sequence date: 2023-03-26
sequence: sequence
division: CON
label: NZ_AP025243.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMD00405045
keyword: RefSeq
source: Phocaeicola vulgatus
organism: Phocaeicola vulgatus
taxonomy: Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae; Phocaeicola.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nAP025243.1.\nAnnotated by DFAST https://dfast.ddbj.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\nGenome Coverage :: 100x\nSequencing Technology :: Illumina Miseq; Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/26/2023 07:44:36\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) :: 4,159\nCDSs (total) :: 4,049\nGenes (coding) :: 3,964\nCDSs (with protein) :: 3,964\nGenes (RNA) :: 110\nrRNAs :: 7, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 7, 7 (5S, 16S, 23S)\ntRNAs :: 87\nncRNAs :: 2\nPseudo Genes (total) :: 85\nCDSs (without protein) :: 85\nPseudo Genes (ambiguous residues) :: 0 of 85\nPseudo Genes (frameshifted) :: 30 of 85\nPseudo Genes (incomplete) :: 61 of 85\nPseudo Genes (internal stop) :: 22 of 85\nPseudo Genes (multiple problems) :: 21 of 85\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4306
topology: circular
so has quality: SO_0000988
location: 1..4306
location: region:1-4306:1
RO_0002162: 821

NZ_AP025243
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMD00405045
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequences of three Phocaeicola vulgatus isolated from a healthy Japanese individual
author: Tanaka, K.
author: Noguchi, H.
author: Vu, H.
author: Muto, Y.
author: Hayashi, M.
author: Yamamoto, Y.
journal: Unpublished

2
title: Direct Submission
author: Tanaka, K.
author: Noguchi, H.
author: Vu, H.
author: Muto, Y.
author: Hayashi, M.
author: Yamamoto, Y.
journal: Submitted (29-OCT-2021) Contact:Kaori Tanaka Gifu University; Yanagido, Gifu 501-1194, Japan

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

position:4306:1
position: 4306
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4306:1:source
so part of: sequence
organism: Phocaeicola vulgatus
mol type: genomic DNA
strain: MG01-10
isolation source: feces
host: Homo sapiens
plasmid: pMG01-10_3
country: Japan
lat lon: 35.4234 N 136.7606 E
collection date: 2020-09-20

821
type: Taxonomy
SIO_000068: taxonomy

GAIMETA21_RS20685
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20685
so part of: sequence
location: join(4171..4306,1..50)
location: region:1-4306:1
so has part: feature:4171-4306:1:exon
so has part: feature:1-50:1:exon
subclass of: SO_0000010

69842484
type: Gene
SIO_000068: ncbigene

urn:…
SIO_000300: 1
SIO_000628: feature:4171-4306:1:exon

position:4171:1
position: 4171
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-50:1:exon

position:50:1
position: 50
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

GAIMETA21_RS20685
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20685
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007560600.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKKIIVHFKKEEFERVKNAISILAKFSEIYAPHIDKANSILSFRVDDENETTEEQQCNSRQ
SIO_010081: GAIMETA21_RS20685
subclass of: SO_0000673
so part of: GAIMETA21_RS20685
location: join(4171..4306,1..50)
location: region:1-4306:1
so has part: feature:4171-4306:1:exon
so has part: feature:1-50:1:exon

WP_007560600.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4171-4306:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-50:1:exon

GAIMETA21_RS20690
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20690
old locus tag: GAIMETA21S10_39920
so part of: sequence
location: 73..1005
location: region:73-1005:1
so has part: feature:73-1005:1:exon
subclass of: SO_0000010

69842485
type: Gene
SIO_000068: ncbigene

position:73:1
position: 73
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1005:1
position: 1005
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:73-1005:1:exon

GAIMETA21_RS20690
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20690
old locus tag: GAIMETA21S10_39920
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005812759.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MTTAKYDFSVYEKRILYRIVEMAQGELQGVRFATDCKKIEHTLFDTVHITMPIASLLNGESDENYTRVKQALLSLQKKIFTYEDEKEWISISIIALPKIKKRSSVVSFQIDSHIWDCCLDFSKGFRKYELATAMKFKSVYSMRFYELLSGQKTKLIYPLEQLKEMFKVQDKYAKTNDFVRKVIEPAKNELDELSPYTFEWSANKEGKKIVSFNFYPIFKPEHRDAELYKKELQKQTGLSWDLGRQVISYLKTSLEFSDKEIKNNRDLFVTAQMELPDIMTELAILRGKSRTKTNPKGWIINALKGKIKDK
SIO_010081: GAIMETA21_RS20690
subclass of: SO_0000673
so part of: GAIMETA21_RS20690
location: 73..1005
location: region:73-1005:1
so has part: feature:73-1005:1:exon

WP_229509212.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:73-1005:1:exon

GAIMETA21_RS20695
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20695
old locus tag: GAIMETA21S10_39930
so part of: sequence
location: complement(1044..1274)
location: region:1044-1274:-1
so has part: feature:1044-1274:-1:exon
subclass of: SO_0000010

69842486
type: Gene
SIO_000068: ncbigene

position:1044:-1
position: 1044
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1274:-1
position: 1274
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1044-1274:-1:exon

GAIMETA21_RS20695
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20695
old locus tag: GAIMETA21S10_39930
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005683050.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MGTAEHEEPRFFFILNKGAKSGGEITHAVLNGSIVSKPAGWDAFHGLVLAKEKLSSEEIQRQMKELGVEMEIVPLI
SIO_010081: GAIMETA21_RS20695
subclass of: SO_0000673
so part of: GAIMETA21_RS20695
location: complement(1044..1274)
location: region:1044-1274:-1
so has part: feature:1044-1274:-1:exon

WP_007560596.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1044-1274:-1:exon

GAIMETA21_RS20700
type: Gene
subclass of: SO_0000704
RO_0002162: 821
gene: mbpC
locus tag: GAIMETA21_RS20700
old locus tag: GAIMETA21S10_39940
so part of: sequence
location: complement(1294..1746)
location: region:1294-1746:-1
so has part: feature:1294-1746:-1:exon
subclass of: SO_0000010

69842487
type: Gene
SIO_000068: ncbigene

position:1294:-1
position: 1294
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1746:-1
position: 1746
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1294-1746:-1:exon

GAIMETA21_RS20700
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
gene: mbpC
locus tag: GAIMETA21_RS20700
old locus tag: GAIMETA21S10_39940
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004295511.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein MbpC
translation: METNSHPEAAASNVKQGQYSPRKRKDTTPRVNPQLAVELVYQELKRVEVYTKRIEDATARKVQIDGKSLESAENRLKNVLADFERQGYRMKNGGYVDKRISFYSILCAVISLLFACFMCYLWTDAAKDRDNYKQYYEYYQEQAREQKGNK
SIO_010081: GAIMETA21_RS20700
subclass of: SO_0000673
so part of: GAIMETA21_RS20700
location: complement(1294..1746)
location: region:1294-1746:-1
so has part: feature:1294-1746:-1:exon

WP_004295511.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1294-1746:-1:exon

GAIMETA21_RS20705
type: Gene
subclass of: SO_0000704
RO_0002162: 821
gene: mbpB
locus tag: GAIMETA21_RS20705
old locus tag: GAIMETA21S10_39950
so part of: sequence
location: complement(1703..2497)
location: region:1703-2497:-1
so has part: feature:1703-2497:-1:exon
subclass of: SO_0000010

69842488
type: Gene
SIO_000068: ncbigene

position:1703:-1
position: 1703
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2497:-1
position: 2497
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1703-2497:-1:exon

GAIMETA21_RS20705
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
gene: mbpB
locus tag: GAIMETA21_RS20705
old locus tag: GAIMETA21S10_39950
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007560590.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein MbpB
translation: MIGKGKSISHGVAALEYDLAKEINGQAVATEIARHELYGCTGAEMVQEMKPYHIDFPNVKNNCLRFEVSPSIEESATFTDADWAELGNDFMQRMGLANHQYIIIRHSGTESKKEQAHLHILANRVSLSGELYRDNWIGKKATEAANAIAKERNFVQSQDIGKVNKAEIKEAMDGVLKKMQGFDFTKFKEELGKRGFKVREARASTGKLNGYYVTARSGTEYKASEIGKGYTLAHIERTQSKLKCNSMNISHGNKLTPGSGSFQR
SIO_010081: GAIMETA21_RS20705
subclass of: SO_0000673
so part of: GAIMETA21_RS20705
location: complement(1703..2497)
location: region:1703-2497:-1
so has part: feature:1703-2497:-1:exon

WP_007560590.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1703-2497:-1:exon

GAIMETA21_RS20825
type: Gene
subclass of: SO_0000704
RO_0002162: 821
gene: mbpA
locus tag: GAIMETA21_RS20825
so part of: sequence
location: complement(2494..2793)
location: region:2494-2793:-1
so has part: feature:2494-2793:-1:exon
subclass of: SO_0000010

79412471
type: Gene
SIO_000068: ncbigene

position:2494:-1
position: 2494
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2793:-1
position: 2793
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2494-2793:-1:exon

GAIMETA21_RS20825
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
gene: mbpA
locus tag: GAIMETA21_RS20825
inference: COORDINATES: protein motif:HMM:NF041418.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein MbpA
translation: MELRRNEKITFRCTELEKDALAEQAARCSLSVSEYCRSLSLGGRPRERYTEEERQLLRDIAQLKGTLQRLNNYFGGRQYREVFEENRALITELKKILSR
SIO_010081: GAIMETA21_RS20825
subclass of: SO_0000673
so part of: GAIMETA21_RS20825
location: complement(2494..2793)
location: region:2494-2793:-1
so has part: feature:2494-2793:-1:exon

WP_004327437.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2494-2793:-1:exon

GAIMETA21_RS20710
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20710
old locus tag: GAIMETA21S10_39960
so part of: sequence
location: complement(2975..3172)
location: region:2975-3172:-1
so has part: feature:2975-3172:-1:exon
subclass of: SO_0000010

69842489
type: Gene
SIO_000068: ncbigene

position:2975:-1
position: 2975
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3172:-1
position: 3172
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2975-3172:-1:exon

GAIMETA21_RS20710
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20710
old locus tag: GAIMETA21S10_39960
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007209655.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MVEYCVYWLENGEPMHEVFSNLAAAEMYSCAIRGKENVEWVEVSEEEAIDLDELKDMFPDDFCGV
SIO_010081: GAIMETA21_RS20710
subclass of: SO_0000673
so part of: GAIMETA21_RS20710
location: complement(2975..3172)
location: region:2975-3172:-1
so has part: feature:2975-3172:-1:exon

WP_007209655.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2975-3172:-1:exon

GAIMETA21_RS20715
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20715
old locus tag: GAIMETA21S10_39970
so part of: sequence
location: complement(3183..3458)
location: region:3183-3458:-1
so has part: feature:3183-3458:-1:exon
subclass of: SO_0000010

69842490
type: Gene
SIO_000068: ncbigene

position:3183:-1
position: 3183
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3458:-1
position: 3458
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3183-3458:-1:exon

GAIMETA21_RS20715
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20715
old locus tag: GAIMETA21S10_39970
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004327436.1
GO function: GO:0004519 - endonuclease activity [Evidence IEA]
GO process: GO:0006401 - RNA catabolic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system YoeB family toxin
translation: MMYTIRVSDGVDKVIAKWKKSNPNLFKKYKKIYKELLEHPKTGLGHPEALRGGGDITWSRHITAHDRIIYDIYEEVVEVYILEVEGHYNDK
SIO_010081: GAIMETA21_RS20715
subclass of: SO_0000673
so part of: GAIMETA21_RS20715
location: complement(3183..3458)
location: region:3183-3458:-1
so has part: feature:3183-3458:-1:exon

WP_004327436.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3183-3458:-1:exon

GAIMETA21_RS20720
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20720
old locus tag: GAIMETA21S10_39980
so part of: sequence
location: complement(3455..3706)
location: region:3455-3706:-1
so has part: feature:3455-3706:-1:exon
subclass of: SO_0000010

69842491
type: Gene
SIO_000068: ncbigene

position:3455:-1
position: 3455
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3706:-1
position: 3706
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3455-3706:-1:exon

GAIMETA21_RS20720
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20720
old locus tag: GAIMETA21S10_39980
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: MEALSVREYRNNLAASFTKADNGEQVLIRRKNEIYALVKVGREDLMITPELQARIDKAREEIKSGKCVTLKSSEDIDAYFDSL
SIO_010081: GAIMETA21_RS20720
subclass of: SO_0000673
so part of: GAIMETA21_RS20720
location: complement(3455..3706)
location: region:3455-3706:-1
so has part: feature:3455-3706:-1:exon

WP_004295507.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3455-3706:-1:exon