Bacteroides caccae CL03T12C61 plasmid pBcacCL03T12-2, complete sequence.
type: Entry
definition: Bacteroides caccae CL03T12C61 plasmid pBcacCL03T12-2, complete sequence.
sequence version: NZ_CP072260.1
sequence date: 2023-03-20
sequence: sequence
division: CON
label: NZ_CP072260.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN16451178
keyword: RefSeq
source: Bacteroides caccae CL03T12C61
organism: Bacteroides caccae CL03T12C61
taxonomy: Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides.
reference: 1
references: 33901198
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP072260.1.\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.\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 :: BcacCL03T12C61_pbv2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 164x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 03:42:25\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) :: 4,595\nCDSs (total) :: 4,505\nGenes (coding) :: 4,391\nCDSs (with protein) :: 4,391\nGenes (RNA) :: 90\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 72\nncRNAs :: 3\nPseudo Genes (total) :: 114\nCDSs (without protein) :: 114\nPseudo Genes (ambiguous residues) :: 0 of 114\nPseudo Genes (frameshifted) :: 36 of 114\nPseudo Genes (incomplete) :: 73 of 114\nPseudo Genes (internal stop) :: 33 of 114\nPseudo Genes (multiple problems) :: 24 of 114\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: 997873

NZ_CP072260
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN16451178
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 caccae CL03T12C61
mol type: genomic DNA
strain: CL03T12C61
isolation source: feces
host: Homo sapiens
plasmid: pBcacCL03T12-2
country: USA: Boston
lat lon: 42.3361 N 71.1075 W
collection date: 2009-05

997873
type: Taxonomy
SIO_000068: taxonomy

INE72_RS22850
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22850
old locus tag: INE72_04551
so part of: sequence
location: 1..1026
location: region:1-1026:1
so has part: feature:1-1026:1:exon
subclass of: SO_0000010

75115726
type: Gene
SIO_000068: ncbigene

position:1026:1
position: 1026
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-1026:1:exon

INE72_RS22850
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22850
old locus tag: INE72_04551
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: MKKKLPITKNKDVVVSWVYTWSKQQDMSIHEQRIVLRILEACQAELKGVKLKDYAGTKRKFEHGLWDVDAQMHVSDVIFSGRDYNEIIAALDSLAGRFFTYEDDEEWWKCGFISNPKYKKHTGIITFRVSNDLWDVFTKFAKGYREFELNKALALPTGYSLRFYMLMSGQVYPLDISLDNLKDRLGIPADKYKDKNGKDRIDNFEERVLKPAKAALDESCPYTFNYVKVRENPNNKRSKVTGFRFYPVYQPQFRDEELEGKELQAKVTARYQIDSHVYEYLRYSCGFTSEEINRNKETFITAQEKITDLIGELALLNGKSREKNNPKGWIINALKGKIKDK
SIO_010081: INE72_RS22850
subclass of: SO_0000673
so part of: INE72_RS22850
location: 1..1026
location: region:1-1026:1
so has part: feature:1-1026:1:exon

WP_005683051.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-1026:1:exon

INE72_RS22855
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22855
old locus tag: INE72_04552
so part of: sequence
location: complement(1063..1293)
location: region:1063-1293:-1
so has part: feature:1063-1293:-1:exon
subclass of: SO_0000010

75115727
type: Gene
SIO_000068: ncbigene

position:1063:-1
position: 1063
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1293:-1
position: 1293
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1063-1293:-1:exon

INE72_RS22855
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22855
old locus tag: INE72_04552
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: MGTTEHEEPRFFFILNKGAKSGGEITHAVLNGSIVSKPAGWDAFHGLALAKEKLSSEEIQQQMKELGVEMEIVPLI
SIO_010081: INE72_RS22855
subclass of: SO_0000673
so part of: INE72_RS22855
location: complement(1063..1293)
location: region:1063-1293:-1
so has part: feature:1063-1293:-1:exon

WP_005683050.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1063-1293:-1:exon

INE72_RS22860
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
gene: mbpC
locus tag: INE72_RS22860
old locus tag: INE72_04553
so part of: sequence
location: complement(1312..1764)
location: region:1312-1764:-1
so has part: feature:1312-1764:-1:exon
subclass of: SO_0000010

75115728
type: Gene
SIO_000068: ncbigene

position:1312:-1
position: 1312
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1764:-1
position: 1764
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1312-1764:-1:exon

INE72_RS22860
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
gene: mbpC
locus tag: INE72_RS22860
old locus tag: INE72_04553
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: METNSHPEAAASTVKQGQYSPRKRKDTAPKVNPQLAIELFFQEMGRIEAYTKRIEDATSRKVQIDGKSLESAENRLKNVLSDFERQGYRMKNGGYVDKRISFYSILCAVISLLFACFMCYLWTDAAKDRDNYKQYYEYFQEQAREQKGNK
SIO_010081: INE72_RS22860
subclass of: SO_0000673
so part of: INE72_RS22860
location: complement(1312..1764)
location: region:1312-1764:-1
so has part: feature:1312-1764:-1:exon

WP_005683049.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1312-1764:-1:exon

INE72_RS22865
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
gene: mbpB
locus tag: INE72_RS22865
old locus tag: INE72_04554
so part of: sequence
location: complement(1721..2515)
location: region:1721-2515:-1
so has part: feature:1721-2515:-1:exon
subclass of: SO_0000010

75115729
type: Gene
SIO_000068: ncbigene

position:1721:-1
position: 1721
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2515:-1
position: 2515
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1721-2515:-1:exon

INE72_RS22865
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
gene: mbpB
locus tag: INE72_RS22865
old locus tag: INE72_04554
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: MIGKGKSISHGTAALEYDLAKEIDGQTAAIEIARHELYGCTGAEMVQEMKPYHADFPNVKNNCLRFEVSPSIEESATFTDADWAELGNDFMQRMGLANHQYIIIRHSGTESKKEQAHLHILANRVSLSGELYRDNWIGKKATEAANAIAKERNFVQSQDIGKANKAEIKEAMDDVLKKMQGFDLTKFKEELGRRGFKVREARASTGKLNGYYVTARSGTEYKASEIGKGYTLAHIERTQSKLKYNSMNISHGNKLTPGSGSFHR
SIO_010081: INE72_RS22865
subclass of: SO_0000673
so part of: INE72_RS22865
location: complement(1721..2515)
location: region:1721-2515:-1
so has part: feature:1721-2515:-1:exon

WP_005683056.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1721-2515:-1:exon

INE72_RS22870
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
gene: mbpA
locus tag: INE72_RS22870
old locus tag: INE72_04555
so part of: sequence
location: complement(2512..2811)
location: region:2512-2811:-1
so has part: feature:2512-2811:-1:exon
subclass of: SO_0000010

75115730
type: Gene
SIO_000068: ncbigene

position:2512:-1
position: 2512
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2811:-1
position: 2811
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2512-2811:-1:exon

INE72_RS22870
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
gene: mbpA
locus tag: INE72_RS22870
old locus tag: INE72_04555
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004327437.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein MbpA
translation: MEVRRNEKITFRCTRYEKLALAEQAARCSMSTSEYCRSLSLGGRPRERYTEEERQLLRDIAQLKGTLQRLNNYFGGRQYREVFEENQALITELKKILSR
SIO_010081: INE72_RS22870
subclass of: SO_0000673
so part of: INE72_RS22870
location: complement(2512..2811)
location: region:2512-2811:-1
so has part: feature:2512-2811:-1:exon

WP_005683055.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2512-2811:-1:exon

INE72_RS22875
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22875
old locus tag: INE72_04556
so part of: sequence
location: complement(3005..3202)
location: region:3005-3202:-1
so has part: feature:3005-3202:-1:exon
subclass of: SO_0000010

75115731
type: Gene
SIO_000068: ncbigene

position:3005:-1
position: 3005
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3202:-1
position: 3202
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3005-3202:-1:exon

INE72_RS22875
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22875
old locus tag: INE72_04556
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: MVEYCVYWLENGEPMHEVFSNLAAAEMYSCAIRGKENVEWVEVSEEEAIDLDELEDMFPDDFCGV
SIO_010081: INE72_RS22875
subclass of: SO_0000673
so part of: INE72_RS22875
location: complement(3005..3202)
location: region:3005-3202:-1
so has part: feature:3005-3202:-1:exon

WP_005683054.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3005-3202:-1:exon

INE72_RS22880
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22880
old locus tag: INE72_04557
so part of: sequence
location: complement(3213..3488)
location: region:3213-3488:-1
so has part: feature:3213-3488:-1:exon
subclass of: SO_0000010

75115732
type: Gene
SIO_000068: ncbigene

position:3213:-1
position: 3213
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3488:-1
position: 3488
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3213-3488:-1:exon

INE72_RS22880
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22880
old locus tag: INE72_04557
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: INE72_RS22880
subclass of: SO_0000673
so part of: INE72_RS22880
location: complement(3213..3488)
location: region:3213-3488:-1
so has part: feature:3213-3488:-1:exon

WP_004327436.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3213-3488:-1:exon

INE72_RS22885
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22885
old locus tag: INE72_04558
so part of: sequence
location: complement(3485..3736)
location: region:3485-3736:-1
so has part: feature:3485-3736:-1:exon
subclass of: SO_0000010

75115733
type: Gene
SIO_000068: ncbigene

position:3485:-1
position: 3485
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3736:-1
position: 3736
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3485-3736:-1:exon

INE72_RS22885
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22885
old locus tag: INE72_04558
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: INE72_RS22885
subclass of: SO_0000673
so part of: INE72_RS22885
location: complement(3485..3736)
location: region:3485-3736:-1
so has part: feature:3485-3736:-1:exon

WP_004295507.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3485-3736:-1:exon