Bacteroides xylanisolvens strain CL11T00C03 plasmid pBxylCL11T00C03-2, complete sequence.
type: Entry
definition: Bacteroides xylanisolvens strain CL11T00C03 plasmid pBxylCL11T00C03-2, complete sequence.
sequence version: NZ_CP072218.1
sequence date: 2023-03-20
sequence: sequence
division: CON
label: NZ_CP072218.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN16451198
keyword: RefSeq
source: Bacteroides xylanisolvens
organism: Bacteroides xylanisolvens
taxonomy: Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides.
reference: 1
references: 33901198
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP072218.1.\nSequencing by the Institute for Genome Sciences, Genomics Resource\nCenter, School of Medicine, University of Maryland, 801 W.\nBaltimore Street, Baltimore, MD 21201, USA. Gene calling method:\nProdigal version 2.6.3. Annotated using a custom modification of\nProkka version 1.14.6.\nBacteria available from Dr. Laurie Comstock, Brigham & Women's\nHospital, 181 Longwood Avenue, Boston, MA 02115 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 Date :: 20-OCT-2020\nAssembly Method :: FALCON-Unzip v. 1.2.0\nAssembly Name :: BxylCL11T00C03_pbv2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 287x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 04:04:28\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) :: 5,388\nCDSs (total) :: 5,299\nGenes (coding) :: 5,193\nCDSs (with protein) :: 5,193\nGenes (RNA) :: 89\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 72\nncRNAs :: 2\nPseudo Genes (total) :: 106\nCDSs (without protein) :: 106\nPseudo Genes (ambiguous residues) :: 0 of 106\nPseudo Genes (frameshifted) :: 24 of 106\nPseudo Genes (incomplete) :: 72 of 106\nPseudo Genes (internal stop) :: 22 of 106\nPseudo Genes (multiple problems) :: 10 of 106\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4148
topology: circular
so has quality: SO_0000988
location: 1..4148
location: region:1-4148:1
RO_0002162: 371601

NZ_CP072218
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN16451198
type: BioSample
SIO_000068: biosample

1
title: Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering
author: Garcia-Bayona, L.
author: Coyne, M.J.
author: Comstock, L.E.
journal: PLoS Genet 17 (4), e1009541 (2021)
pubmed: 33901198
comments: Publication Status: Online-Only

33901198
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Coyne, M.J.
journal: Submitted (25-JAN-2021) Department of Medicine/Division of Infectious Diseases, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, USA

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

position:4148:1
position: 4148
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4148:1:source
so part of: sequence
organism: Bacteroides xylanisolvens
mol type: genomic DNA
strain: CL11T00C03
isolation source: feces
host: Homo sapiens
plasmid: pBxylCL11T00C03-2
country: USA: Boston
lat lon: 42.3361 N 71.1075 W
collection date: 2009-05

371601
type: Taxonomy
SIO_000068: taxonomy

INE92_RS26185
type: Gene
subclass of: SO_0000704
RO_0002162: 371601
locus tag: INE92_RS26185
old locus tag: INE92_05222
so part of: sequence
location: 40..1065
location: region:40-1065:1
so has part: feature:40-1065:1:exon
subclass of: SO_0000010

69483913
type: Gene
SIO_000068: ncbigene

position:40:1
position: 40
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1065:1
position: 1065
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:40-1065:1:exon

INE92_RS26185
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 371601
locus tag: INE92_RS26185
old locus tag: INE92_05222
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008657007.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MKKKLPITKNKDVVVSWVYTWSKQQDMSIHEQRIVLRILEACQAELKGVKLKDYAGTKRKFEHGLWDVDAQMHVSDVIFSGRDYNEIIAALDSLAGRFFTYEDDEEWWKCGFISNPKYKKRTGIITFRVSNDLWDVFTKFAKGYREFELNKALALPTGYSLRFYMLMSGQVYPLDISLENLKDRLGIPADKYKDKNGKDRIDHFEERVLKPAKAALDESCPYTFNYVKVRENPNNKRSKVTGFRFYPVYQPQFRDEELEGKELQAKVTARYQIDSHVYEYLRYSCGFTSEEINRNKETFITAQEKITDLIGELALLNGKSREKNNPKGWIINALKGKIKDK
SIO_010081: INE92_RS26185
subclass of: SO_0000673
so part of: INE92_RS26185
location: 40..1065
location: region:40-1065:1
so has part: feature:40-1065:1:exon

WP_004295509.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:40-1065:1:exon

INE92_RS26190
type: Gene
subclass of: SO_0000704
RO_0002162: 371601
locus tag: INE92_RS26190
old locus tag: INE92_05223
so part of: sequence
location: complement(1102..1332)
location: region:1102-1332:-1
so has part: feature:1102-1332:-1:exon
subclass of: SO_0000010

69483914
type: Gene
SIO_000068: ncbigene

position:1102:-1
position: 1102
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1332:-1
position: 1332
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1102-1332:-1:exon

INE92_RS26190
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 371601
locus tag: INE92_RS26190
old locus tag: INE92_05223
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: MGTTEHEEPRFFFILNKGAKSGGEITHAVLNGSIVSKPAGWDAFHGLALAREKLSSEEIQQQMKELGVEMEIVPLI
SIO_010081: INE92_RS26190
subclass of: SO_0000673
so part of: INE92_RS26190
location: complement(1102..1332)
location: region:1102-1332:-1
so has part: feature:1102-1332:-1:exon

WP_004295510.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1102-1332:-1:exon

INE92_RS26195
type: Gene
subclass of: SO_0000704
RO_0002162: 371601
gene: mbpC
locus tag: INE92_RS26195
old locus tag: INE92_05224
so part of: sequence
location: complement(1352..1804)
location: region:1352-1804:-1
so has part: feature:1352-1804:-1:exon
subclass of: SO_0000010

69483915
type: Gene
SIO_000068: ncbigene

position:1352:-1
position: 1352
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1804:-1
position: 1804
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1352-1804:-1:exon

INE92_RS26195
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 371601
gene: mbpC
locus tag: INE92_RS26195
old locus tag: INE92_05224
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: INE92_RS26195
subclass of: SO_0000673
so part of: INE92_RS26195
location: complement(1352..1804)
location: region:1352-1804:-1
so has part: feature:1352-1804:-1:exon

WP_004295511.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1352-1804:-1:exon

INE92_RS26200
type: Gene
subclass of: SO_0000704
RO_0002162: 371601
gene: mbpB
locus tag: INE92_RS26200
old locus tag: INE92_05225
so part of: sequence
location: complement(1761..2555)
location: region:1761-2555:-1
so has part: feature:1761-2555:-1:exon
subclass of: SO_0000010

69483916
type: Gene
SIO_000068: ncbigene

position:1761:-1
position: 1761
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2555:-1
position: 2555
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1761-2555:-1:exon

INE92_RS26200
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 371601
gene: mbpB
locus tag: INE92_RS26200
old locus tag: INE92_05225
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: INE92_RS26200
subclass of: SO_0000673
so part of: INE92_RS26200
location: complement(1761..2555)
location: region:1761-2555:-1
so has part: feature:1761-2555:-1:exon

WP_007560590.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1761-2555:-1:exon

INE92_RS27140
type: Gene
subclass of: SO_0000704
RO_0002162: 371601
gene: mbpA
locus tag: INE92_RS27140
old locus tag: INE92_05226
so part of: sequence
location: complement(2552..2851)
location: region:2552-2851:-1
so has part: feature:2552-2851:-1:exon
subclass of: SO_0000010

79236272
type: Gene
SIO_000068: ncbigene

position:2552:-1
position: 2552
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2851:-1
position: 2851
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2552-2851:-1:exon

INE92_RS27140
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 371601
gene: mbpA
locus tag: INE92_RS27140
old locus tag: INE92_05226
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: INE92_RS27140
subclass of: SO_0000673
so part of: INE92_RS27140
location: complement(2552..2851)
location: region:2552-2851:-1
so has part: feature:2552-2851:-1:exon

WP_004327437.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2552-2851:-1:exon

INE92_RS26205
type: Gene
subclass of: SO_0000704
RO_0002162: 371601
locus tag: INE92_RS26205
old locus tag: INE92_05227
so part of: sequence
location: complement(3044..3241)
location: region:3044-3241:-1
so has part: feature:3044-3241:-1:exon
subclass of: SO_0000010

69483917
type: Gene
SIO_000068: ncbigene

position:3044:-1
position: 3044
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3241:-1
position: 3241
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3044-3241:-1:exon

INE92_RS26205
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 371601
locus tag: INE92_RS26205
old locus tag: INE92_05227
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: MVEYCVYWLENGEPMHEVFSSLAAAEMYSCAIRGKENIEWVEVSEEETIDLDELEDMFPDDFCGV
SIO_010081: INE92_RS26205
subclass of: SO_0000673
so part of: INE92_RS26205
location: complement(3044..3241)
location: region:3044-3241:-1
so has part: feature:3044-3241:-1:exon

WP_004295503.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3044-3241:-1:exon

INE92_RS26210
type: Gene
subclass of: SO_0000704
RO_0002162: 371601
locus tag: INE92_RS26210
old locus tag: INE92_05228
so part of: sequence
location: complement(3252..3527)
location: region:3252-3527:-1
so has part: feature:3252-3527:-1:exon
subclass of: SO_0000010

69483918
type: Gene
SIO_000068: ncbigene

position:3252:-1
position: 3252
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3527:-1
position: 3527
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3252-3527:-1:exon

INE92_RS26210
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 371601
locus tag: INE92_RS26210
old locus tag: INE92_05228
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: INE92_RS26210
subclass of: SO_0000673
so part of: INE92_RS26210
location: complement(3252..3527)
location: region:3252-3527:-1
so has part: feature:3252-3527:-1:exon

WP_004327436.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3252-3527:-1:exon

INE92_RS26215
type: Gene
subclass of: SO_0000704
RO_0002162: 371601
locus tag: INE92_RS26215
old locus tag: INE92_05229
so part of: sequence
location: complement(3524..3775)
location: region:3524-3775:-1
so has part: feature:3524-3775:-1:exon
subclass of: SO_0000010

69483919
type: Gene
SIO_000068: ncbigene

position:3524:-1
position: 3524
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3775:-1
position: 3775
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3524-3775:-1:exon

INE92_RS26215
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 371601
locus tag: INE92_RS26215
old locus tag: INE92_05229
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: INE92_RS26215
subclass of: SO_0000673
so part of: INE92_RS26215
location: complement(3524..3775)
location: region:3524-3775:-1
so has part: feature:3524-3775:-1:exon

WP_004295507.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3524-3775:-1:exon