Phocaeicola vulgatus strain MG01-10 plasmid pMG01-10_2, complete sequence.
type: Entry
definition: Phocaeicola vulgatus strain MG01-10 plasmid pMG01-10_2, complete sequence.
sequence version: NZ_AP025242.1
sequence date: 2023-03-26
sequence: sequence
division: CON
label: NZ_AP025242.1
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\nAP025242.1.\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: 5594
topology: circular
so has quality: SO_0000988
location: 1..5594
location: region:1-5594:1
RO_0002162: 821

NZ_AP025242
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:5594:1
position: 5594
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5594:1:source
so part of: sequence
organism: Phocaeicola vulgatus
mol type: genomic DNA
strain: MG01-10
isolation source: feces
host: Homo sapiens
plasmid: pMG01-10_2
country: Japan
lat lon: 35.4234 N 136.7606 E
collection date: 2020-09-20

821
type: Taxonomy
SIO_000068: taxonomy

GAIMETA21_RS20650
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20650
old locus tag: GAIMETA21S10_39850
so part of: sequence
location: 277..1527
location: region:277-1527:1
so has part: feature:277-1527:1:exon
subclass of: SO_0000010

69842477
type: Gene
SIO_000068: ncbigene

position:277:1
position: 277
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1527:1
position: 1527
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:277-1527:1:exon

GAIMETA21_RS20650
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20650
old locus tag: GAIMETA21S10_39850
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005799237.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: NBU/pMV158-type mobilization protein
translation: MAKTCIRVEACNIGSSERHNLRSKELDYIRPELTHRNEQWVECSIAEVHRDITEKYKEATGQGLQKKATPIREGVIVISEETTIQQLQDLAEKLEERFGVHAFQIYTHKDEGANVWDGKEEAWKPNYHAHMIFDWTDGHTGKTVKLNRHDMAEMQTITAECLNMERGVSSDKKHLSAMQYKNKMETEKAEQLQKDIEQLNRAYTAGTEKITTVQKELSTAQKELNSMKTDIHINEAKEAAAKAGKTVFNAVTSVFNVGEVKRQAKEIETLKKENYNLSFKNQNLEGQLRTNNIEMRRVQETTDRQIKAEASKLKPITNLFPEMENAQENIEELQTMGIQNKDIRQLLIGKEIYYTGNLYDKDKRKSYQVKNVKIDISKSQNGITTIWLNNIHFKNFLKELWNTLQKTLDNGNWLHR
SIO_010081: GAIMETA21_RS20650
subclass of: SO_0000673
so part of: GAIMETA21_RS20650
location: 277..1527
location: region:277-1527:1
so has part: feature:277-1527:1:exon

WP_005799237.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:277-1527:1:exon

GAIMETA21_RS20655
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20655
old locus tag: GAIMETA21S10_39860
so part of: sequence
location: complement(1597..2367)
location: region:1597-2367:-1
so has part: feature:1597-2367:-1:exon
subclass of: SO_0000010

69842478
type: Gene
SIO_000068: ncbigene

position:1597:-1
position: 1597
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2367:-1
position: 2367
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1597-2367:-1:exon

GAIMETA21_RS20655
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20655
old locus tag: GAIMETA21S10_39860
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016274503.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKKVMFMFISLLTVLGVCSCNDNEVIEPVVSDSVSDMEVLSRFVDVNEITNEYYFNENKKTRALSYVTGSDWQDLEKVSPLSIEKYKNNLQVLNAQVASAISNPNTAYVVFSVNGKTLVKKVKEDANFDFSVFRDVVTETRAVLPSLSINGGSQSTTGVFYDSSRTLKMQVDLNASIQNNYYFFEVLNPNAKPSPDDNITTPESVAFSGTGPLWSNTFTWTSYWDANVPGQGFKWEFKGKGTTPSFGFIANCTFSR
SIO_010081: GAIMETA21_RS20655
subclass of: SO_0000673
so part of: GAIMETA21_RS20655
location: complement(1597..2367)
location: region:1597-2367:-1
so has part: feature:1597-2367:-1:exon

WP_005799241.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1597-2367:-1:exon

GAIMETA21_RS20660
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20660
old locus tag: GAIMETA21S10_39870
so part of: sequence
location: 2459..2920
location: region:2459-2920:1
so has part: feature:2459-2920:1:exon
subclass of: SO_0000010

69842479
type: Gene
SIO_000068: ncbigene

position:2459:1
position: 2459
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2920:1
position: 2920
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2459-2920:1:exon

GAIMETA21_RS20660
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20660
old locus tag: GAIMETA21S10_39870
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005812785.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MNRIIHISLLISTVSLFLISNTGCVEKQGYYNHGEESIISLICDITWAGKKTTDENGSVWQGTYKFNKNGTYTRTNIEIDKQGNKKEANIYGQWSFGDPSFSTIYFGGEHYWDIDELTKNKFSFYDRSGKFGDPFMNREYIELTPYQENNTTN
SIO_010081: GAIMETA21_RS20660
subclass of: SO_0000673
so part of: GAIMETA21_RS20660
location: 2459..2920
location: region:2459-2920:1
so has part: feature:2459-2920:1:exon

WP_005812785.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2459-2920:1:exon

GAIMETA21_RS20665
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20665
old locus tag: GAIMETA21S10_39880
so part of: sequence
location: complement(2924..3826)
location: region:2924-3826:-1
so has part: feature:2924-3826:-1:exon
subclass of: SO_0000010

69842480
type: Gene
SIO_000068: ncbigene

position:2924:-1
position: 2924
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3826:-1
position: 3826
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2924-3826:-1:exon

GAIMETA21_RS20665
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20665
old locus tag: GAIMETA21S10_39880
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005799258.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: protein rep
translation: MKAYMDAHVCSNVYTVQGGKAHSHYCHRAFCPICQRIQTAQNVKKFLPVMKYLASEGREFYFVTLTLQNCVTDDARVLRDFMRRCNRMWADGIRTKHKFRSLGISGVIKKECTYHVVKKDLFSFHYHFHIIVDSLEAAKYVVAQWKKLHGSTVADARFQKYKKIEDFENAAIEVFKYASKASVSKSKGRDGKKKIQINYKALDMIYTAMHGMQRMSSFGQFRTMIGDEALNDFRDEDLVLNIEGLNVEDGCYTWYMSVKDKVADWYNMETGEALCCYKVTRKDELLQDIYLDEDIFPNSG
SIO_010081: GAIMETA21_RS20665
subclass of: SO_0000673
so part of: GAIMETA21_RS20665
location: complement(2924..3826)
location: region:2924-3826:-1
so has part: feature:2924-3826:-1:exon

WP_225538865.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2924-3826:-1:exon

GAIMETA21_RS20670
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20670
old locus tag: GAIMETA21S10_39890
so part of: sequence
location: complement(4468..4866)
location: region:4468-4866:-1
so has part: feature:4468-4866:-1:exon
subclass of: SO_0000010

69842481
type: Gene
SIO_000068: ncbigene

position:4468:-1
position: 4468
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4866:-1
position: 4866
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4468-4866:-1:exon

GAIMETA21_RS20670
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20670
old locus tag: GAIMETA21S10_39890
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005799260.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKPTDYIEWDNLKDIPFFLCQVVEDREKQDLDIYYLGKRVLHDYDHVGHYLRTAVILFRRVKSRTADWVNLRNLWTLRNCVRENYNHGIGMNDLIFGENFDGDNLDTLTPLTKKRFDFLCKRIKELDPYATI
SIO_010081: GAIMETA21_RS20670
subclass of: SO_0000673
so part of: GAIMETA21_RS20670
location: complement(4468..4866)
location: region:4468-4866:-1
so has part: feature:4468-4866:-1:exon

WP_005799260.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4468-4866:-1:exon

GAIMETA21_RS20675
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20675
old locus tag: GAIMETA21S10_39900
so part of: sequence
location: complement(4903..5223)
location: region:4903-5223:-1
so has part: feature:4903-5223:-1:exon
subclass of: SO_0000010

69842482
type: Gene
SIO_000068: ncbigene

position:4903:-1
position: 4903
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5223:-1
position: 5223
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4903-5223:-1:exon

GAIMETA21_RS20675
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20675
old locus tag: GAIMETA21S10_39900
EC number: 3.1.-.-
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005799262.1
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: MVEQYEVYWVELDPTRGGEMAKTRPCVVVTPSDLNMYLTTVVIVPITSTIRNYPYRVLCSVAGREGEIATDQIRTVDKSRLKRKIGDLNFSEIKRLREVFQQMFCE
SIO_010081: GAIMETA21_RS20675
subclass of: SO_0000673
so part of: GAIMETA21_RS20675
location: complement(4903..5223)
location: region:4903-5223:-1
so has part: feature:4903-5223:-1:exon

WP_005799262.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4903-5223:-1:exon

GAIMETA21_RS20680
type: Gene
subclass of: SO_0000704
RO_0002162: 821
locus tag: GAIMETA21_RS20680
old locus tag: GAIMETA21S10_39910
so part of: sequence
location: complement(5217..5465)
location: region:5217-5465:-1
so has part: feature:5217-5465:-1:exon
subclass of: SO_0000010

69842483
type: Gene
SIO_000068: ncbigene

position:5217:-1
position: 5217
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5465:-1
position: 5465
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5217-5465:-1:exon

GAIMETA21_RS20680
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 821
locus tag: GAIMETA21_RS20680
old locus tag: GAIMETA21S10_39910
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008771457.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MVTNIIQIGNSKGIILPSEVLKQLRLSLKSAVSISLDGNNIVIKAQPRQGWAEAAKRAHENGDDELLIPDVFEDEKFEDWTW
SIO_010081: GAIMETA21_RS20680
subclass of: SO_0000673
so part of: GAIMETA21_RS20680
location: complement(5217..5465)
location: region:5217-5465:-1
so has part: feature:5217-5465:-1:exon

WP_005812783.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5217-5465:-1:exon