Bacteroides caccae CL03T12C61 plasmid pBcacCL03T12-1, complete sequence.
type: Entry
definition: Bacteroides caccae CL03T12C61 plasmid pBcacCL03T12-1, complete sequence.
sequence version: NZ_CP072259.1
sequence date: 2023-03-20
sequence: sequence
division: CON
label: NZ_CP072259.1
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\nCP072259.1.\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: 7143
topology: circular
so has quality: SO_0000988
location: 1..7143
location: region:1-7143:1
RO_0002162: 997873

NZ_CP072259
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:7143:1
position: 7143
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7143:1:source
so part of: sequence
organism: Bacteroides caccae CL03T12C61
mol type: genomic DNA
strain: CL03T12C61
isolation source: feces
host: Homo sapiens
plasmid: pBcacCL03T12-1
country: USA: Boston
lat lon: 42.3361 N 71.1075 W
collection date: 2009-05

997873
type: Taxonomy
SIO_000068: taxonomy

INE72_RS22805
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22805
old locus tag: INE72_04543
so part of: sequence
location: 1..1023
location: region:1-1023:1
so has part: feature:1-1023:1:exon
subclass of: SO_0000010

75115717
type: Gene
SIO_000068: ncbigene

position:1023:1
position: 1023
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-1023:1:exon

INE72_RS22805
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22805
old locus tag: INE72_04543
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005683039.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MARPIKTQSKDIQQSNYFTTAKYDYTLQEKIILYRVAEQAFEYREANKEWFKEHEGEYIAKDHVSFRLPITHFMTKEQRADGSGKCYDDVVAAFKSLTSKRIEFQTKDAFSFGALLNSADREPGEGIIYFTVHKFVWQSALDFTKGFTKLDLVVAMELKSAYSMRFYEIARRWSDTKIWKISVEDFRDLFGCKEKYPAFNDMKRYIIDNAKEELDRVAPWSFSYEQHKVGRKVESFTFYFYEIPKNKREETERKELLSKYPQAVIRPEVKDWFKNKMGFNTGQIRSNVQLIDELQRIFQNGTIPELEETFQYITKQGFRPQENIGWFIQNLKKKIENAQL
SIO_010081: INE72_RS22805
subclass of: SO_0000673
so part of: INE72_RS22805
location: 1..1023
location: region:1-1023:1
so has part: feature:1-1023:1:exon

WP_005683039.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-1023:1:exon

INE72_RS22810
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22810
old locus tag: INE72_04544
so part of: sequence
location: 1053..1451
location: region:1053-1451:1
so has part: feature:1053-1451:1:exon
subclass of: SO_0000010

75115718
type: Gene
SIO_000068: ncbigene

position:1053:1
position: 1053
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1451:1
position: 1451
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1053-1451:1:exon

INE72_RS22810
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22810
old locus tag: INE72_04544
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005648588.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKPTDYIEWDNLKNIPFFLCQVVEDKENKDIDIYYLGKRVFHDYDHVGHYMRSAIILFRRIKNRTADWVNLQNLWTLRNCIRENYNHGIGVDSLIYGEDFDGENPETLTPLTKKRFDLIVKRIQELDKYATI
SIO_010081: INE72_RS22810
subclass of: SO_0000673
so part of: INE72_RS22810
location: 1053..1451
location: region:1053-1451:1
so has part: feature:1053-1451:1:exon

WP_005683040.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1053-1451:1:exon

INE72_RS22815
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22815
old locus tag: INE72_04545
so part of: sequence
location: 1763..4081
location: region:1763-4081:1
so has part: feature:1763-4081:1:exon
subclass of: SO_0000010

75115719
type: Gene
SIO_000068: ncbigene

position:1763:1
position: 1763
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4081:1
position: 4081
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1763-4081:1:exon

INE72_RS22815
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22815
old locus tag: INE72_04545
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008781630.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: TonB-dependent receptor
translation: MDLNKKHLLYLIVFFLFGNLNAFGQSINISGRILSQGTQDAVEYANIVLFKQDSIFLQGTTSDSIGRFEFMNLSPNDYVLSVSCMGFEPKKILLQNLAETVEIDVFLNESALSLGEVVISASSTISKINQRIVFPTKLQLSHSANGMQLLNTMMLPGININPMANTISSSDGGKVILQINDVNATSEEILTLQPRQIRRVEYSDYAGIRYGEASKIVNYIVTRDDKGGVIGVDLMNSLNILAGGDVFFAKFNKGKSEYALNYTAAFQKINSNNRTRTGSYQFENSPMLQRDEIGEGGDYSYQMHDVTLGYNYQQSDSTFFNAKLKYALTNHPHNDFRSSLKEKGVDVGRIFDGVSQKINTPTVDLYYELGLKNRQKIYTNLVGSYSKVETHRNYIEYDNIDTLFREQFNLVSDKYSLIAEGIYEKSFTHGSLKLGAKHIQSFTQQEVRQNGTFESNLNQAESSVFTEWNHSKDNLSYSLGLRVNRVHLSNSSIDKSYYNLLPKAMFGYRLSENSFIRYDVEMSQTNPTLIELTDTEIRLDPYLAEKGNLSLKPYRNLNNNLFYENKKGLFTLNVNLRHHYKHNPIMESIKRQGDIFLIIPENMKSWSKYNAEMTLKLGMIKNILQFSLTGGYNHFSSQGNNYSHTHSNFYYSANVLAMYKKWMFIGQIQPFEEMLYGETVIKNGNYHYLAVQYNANSFSFGIGAFNPFKNVSRSIMENKNALAPFRRESFSNASQTIVATLTWNFSFGKTHSSSSKSLNNQDADYGVKSSYK
SIO_010081: INE72_RS22815
subclass of: SO_0000673
so part of: INE72_RS22815
location: 1763..4081
location: region:1763-4081:1
so has part: feature:1763-4081:1:exon

WP_224200430.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1763-4081:1:exon

INE72_RS22820
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22820
old locus tag: INE72_04546
so part of: sequence
location: 4090..4308
location: region:4090-4308:1
so has part: feature:4090-4308:1:exon
subclass of: SO_0000010

75115720
type: Gene
SIO_000068: ncbigene

position:4090:1
position: 4090
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4308:1
position: 4308
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4090-4308:1:exon

INE72_RS22820
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22820
old locus tag: INE72_04546
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005683042.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MNKNSLELFSLLSENSHVTDEQMQNAYKSFVEQITTISQSQQSYPEVFRMLNRTRIELDSLESSSLYELEKK
SIO_010081: INE72_RS22820
subclass of: SO_0000673
so part of: INE72_RS22820
location: 4090..4308
location: region:4090-4308:1
so has part: feature:4090-4308:1:exon

WP_005683042.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4090-4308:1:exon

INE72_RS22825
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
gene: mbpC
locus tag: INE72_RS22825
old locus tag: INE72_04547
so part of: sequence
location: complement(4310..4765)
location: region:4310-4765:-1
so has part: feature:4310-4765:-1:exon
subclass of: SO_0000010

75115721
type: Gene
SIO_000068: ncbigene

position:4310:-1
position: 4310
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4765:-1
position: 4765
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4310-4765:-1:exon

INE72_RS22825
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
gene: mbpC
locus tag: INE72_RS22825
old locus tag: INE72_04547
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005683043.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein MbpC
translation: MEKTSYQEKEVSTSNTKRGQYSPRRKDTAPKVNPQLAVELIFQEIKRIEAFTKRIEDATQRKVQIDEKSLENAENSLKSVLSGFEKQSYRMKNGGYVDKRISLWTILCAVFSLLFACLMCYLWVDAAKDRDNYKMYYEYYQKENNPQSRDS
SIO_010081: INE72_RS22825
subclass of: SO_0000673
so part of: INE72_RS22825
location: complement(4310..4765)
location: region:4310-4765:-1
so has part: feature:4310-4765:-1:exon

WP_005683043.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4310-4765:-1:exon

INE72_RS22830
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
gene: mbpB
locus tag: INE72_RS22830
old locus tag: INE72_04548
so part of: sequence
location: complement(4722..5516)
location: region:4722-5516:-1
so has part: feature:4722-5516:-1:exon
subclass of: SO_0000010

75115722
type: Gene
SIO_000068: ncbigene

position:4722:-1
position: 4722
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5516:-1
position: 5516
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4722-5516:-1:exon

INE72_RS22830
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
gene: mbpB
locus tag: INE72_RS22830
old locus tag: INE72_04548
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008675765.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein MbpB
translation: MIAKGKSISHGTAALEYDLSKQIAGKDAATEVCRNGLYGTTGADMVQEMKPYFADFPNVRNNCLRFEVSPSIEESAQYTSEDWRKLADDFLTRMGLQNHQYVVIRHSGTESRKNQAHLHILANRVSMSGELYRDNWIGKRATEAANGMARERNLVQAQDIGKANRQDIKSGMDAVLQKLERFDFGSFKEEMEKAGYPIREARASTGKLNGYYVKAKSGTEYKASEIGKNYTLAHIEKTHFKLHRQTLGQSYGKDIISGKGGLHL
SIO_010081: INE72_RS22830
subclass of: SO_0000673
so part of: INE72_RS22830
location: complement(4722..5516)
location: region:4722-5516:-1
so has part: feature:4722-5516:-1:exon

WP_005683044.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4722-5516:-1:exon

INE72_RS22835
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
gene: mbpA
locus tag: INE72_RS22835
so part of: sequence
location: complement(5513..5809)
location: region:5513-5809:-1
so has part: feature:5513-5809:-1:exon
subclass of: SO_0000010

75115723
type: Gene
SIO_000068: ncbigene

position:5513:-1
position: 5513
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5809:-1
position: 5809
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5513-5809:-1:exon

INE72_RS22835
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
gene: mbpA
locus tag: INE72_RS22835
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: MEVKRTEKITFRCTVLEKAALAEQALRCGLTTSEYCRSLSLGGQPKERYSEEEKALLRDIAKIRGDLQRLNNYFGGRQYREVFEENRVIIEKLKKLLR
SIO_010081: INE72_RS22835
subclass of: SO_0000673
so part of: INE72_RS22835
location: complement(5513..5809)
location: region:5513-5809:-1
so has part: feature:5513-5809:-1:exon

WP_032838721.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5513-5809:-1:exon

INE72_RS22840
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22840
old locus tag: INE72_04549
so part of: sequence
location: complement(6119..6460)
location: region:6119-6460:-1
so has part: feature:6119-6460:-1:exon
subclass of: SO_0000010

75115724
type: Gene
SIO_000068: ncbigene

position:6119:-1
position: 6119
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6460:-1
position: 6460
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6119-6460:-1:exon

INE72_RS22840
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22840
old locus tag: INE72_04549
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005683045.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSFEVKTTPHFEREAKILAKRYKSFKSDLKELVEDLAKDPKIGTELSPGLRKIRLAIVSKGKGKSGGARVITFTICSSESEGRVYLVDVYDKSDYSTVSVPVLKKMIAELDIL
SIO_010081: INE72_RS22840
subclass of: SO_0000673
so part of: INE72_RS22840
location: complement(6119..6460)
location: region:6119-6460:-1
so has part: feature:6119-6460:-1:exon

WP_005683045.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6119-6460:-1:exon

INE72_RS22845
type: Gene
subclass of: SO_0000704
RO_0002162: 997873
locus tag: INE72_RS22845
old locus tag: INE72_04550
so part of: sequence
location: complement(6450..6683)
location: region:6450-6683:-1
so has part: feature:6450-6683:-1:exon
subclass of: SO_0000010

75115725
type: Gene
SIO_000068: ncbigene

position:6450:-1
position: 6450
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6683:-1
position: 6683
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6450-6683:-1:exon

INE72_RS22845
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 997873
locus tag: INE72_RS22845
old locus tag: INE72_04550
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005783253.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MQVVSLSKFRTNQTATLLRAIQGESVFLTSRLGDFKLVPVSAEEKIATRIKEGLNDVKRIESGEIPGKNANAFLDEL
SIO_010081: INE72_RS22845
subclass of: SO_0000673
so part of: INE72_RS22845
location: complement(6450..6683)
location: region:6450-6683:-1
so has part: feature:6450-6683:-1:exon

WP_005683046.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6450-6683:-1:exon