Bifidobacterium breve strain BR3 plasmid pBR3, complete sequence.
type: Entry
definition: Bifidobacterium breve strain BR3 plasmid pBR3, complete sequence.
sequence version: NZ_CP010414.1
sequence date: 2023-02-05
sequence: sequence
division: CON
label: NZ_CP010414.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN03271681
keyword: RefSeq
source: Bifidobacterium breve
organism: Bifidobacterium breve
taxonomy: Bacteria; Actinomycetota; Actinomycetes; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP010414.1.\nSource DNA is available from Jihyun F. Kim (jfk1@yonsei.ac.kr);\nSource bacteria available from Jae-Gu Seo (jgseo@cellbiotech.com).\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 :: SMRT pipe v. Aug 2014\nGenome Coverage :: 115.32x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/05/2023 18:13:17\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) :: 2,176\nCDSs (total) :: 2,109\nGenes (coding) :: 2,037\nCDSs (with protein) :: 2,037\nGenes (RNA) :: 67\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 3\nPseudo Genes (total) :: 72\nCDSs (without protein) :: 72\nPseudo Genes (ambiguous residues) :: 0 of 72\nPseudo Genes (frameshifted) :: 27 of 72\nPseudo Genes (incomplete) :: 53 of 72\nPseudo Genes (internal stop) :: 6 of 72\nPseudo Genes (multiple problems) :: 13 of 72\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4891
topology: circular
so has quality: SO_0000988
location: 1..4891
location: region:1-4891:1
RO_0002162: 1685

NZ_CP010414
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN03271681
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of Bifidobacterium breve BR3
author: Kim, J.F.
author: Kwak, M.-J.
journal: Unpublished

2
title: Direct Submission
author: Kim, J.F.
author: Kwak, M.-J.
journal: Submitted (29-DEC-2014) Department of Systems Biology, Yonsei University, Yonsei-ro, Seoul, Seodaemun-gu 120-749, Republic of Korea

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

position:4891:1
position: 4891
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4891:1:source
so part of: sequence
organism: Bifidobacterium breve
mol type: genomic DNA
strain: BR3
isolation source: feces
host: Homo sapiens
plasmid: pBR3
country: Korea
collection date: 2001-08-13

1685
type: Taxonomy
SIO_000068: taxonomy

RY69_RS10530
type: Gene
subclass of: SO_0000704
RO_0002162: 1685
locus tag: RY69_RS10530
old locus tag: RY69_2241
so part of: sequence
location: complement(32..1234)
location: region:32-1234:-1
so has part: feature:32-1234:-1:exon
subclass of: SO_0000010

69566741
type: Gene
SIO_000068: ncbigene

position:32:-1
position: 32
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1234:-1
position: 1234
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:32-1234:-1:exon

RY69_RS10530
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1685
locus tag: RY69_RS10530
old locus tag: RY69_2241
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008783733.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobA/MobL family protein
translation: MAIYSLHVSNVSRAAGSSAVASCSYITSRRMRDERTGEAFNGFGRRERVEHVCTMLPEGAPGEYLDPERLFNAVEMAEKRSDARPAKKIMVALPREFDARERFRALEDFISWNITANGYACTYAIHTDKDGRNPHAHILVANRRIDPKTGRWAAKSRSEFALDANGRRIPVIDPDTGRQKIGARNRKVWKRVNVSNNPLDSKEFLERLRREWADSCNALLPGYAVIDHRSFKARGIERIPTIHEGYASREMEKRGGRGDLCEENRRIQALNRLLDALRAMIGRLSDQAQGILTAVKRRQRPSGAPQAPSSPEPAEKPQERPQARETPPQAPQEPPKPIRTKKALTDRFKTRLDERLAENERKQAEKQAEPDMEETWDLSDPADPLNIGMGWGTGGHGLGL
SIO_010081: RY69_RS10530
subclass of: SO_0000673
so part of: RY69_RS10530
location: complement(32..1234)
location: region:32-1234:-1
so has part: feature:32-1234:-1:exon

WP_080790630.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:32-1234:-1:exon

RY69_RS10535
type: Gene
subclass of: SO_0000704
RO_0002162: 1685
locus tag: RY69_RS10535
old locus tag: RY69_2242
so part of: sequence
location: 1855..2274
location: region:1855-2274:1
so has part: feature:1855-2274:1:exon
subclass of: SO_0000010

69566742
type: Gene
SIO_000068: ncbigene

position:1855:1
position: 1855
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2274:1
position: 2274
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1855-2274:1:exon

RY69_RS10535
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1685
locus tag: RY69_RS10535
old locus tag: RY69_2242
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008783728.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTRSVEEQMADIERRMKQLRARKQRIVARENAKARKRRTHLIIRLGGILSNEGVLGYDEGVWNDEGNRQRLLDMLKAHAAELRAWASDAGVRLPSAESAGELREQVRDLPQEPQIQEQPGYGYQPGFQQPQQWQQQPWN
SIO_010081: RY69_RS10535
subclass of: SO_0000673
so part of: RY69_RS10535
location: 1855..2274
location: region:1855-2274:1
so has part: feature:1855-2274:1:exon

WP_008783728.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1855-2274:1:exon

RY69_RS10540
type: Gene
subclass of: SO_0000704
RO_0002162: 1685
locus tag: RY69_RS10540
old locus tag: RY69_2243
so part of: sequence
location: 2534..3445
location: region:2534-3445:1
so has part: feature:2534-3445:1:exon
subclass of: SO_0000010

69566743
type: Gene
SIO_000068: ncbigene

position:2534:1
position: 2534
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3445:1
position: 3445
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2534-3445:1:exon

RY69_RS10540
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1685
locus tag: RY69_RS10540
old locus tag: RY69_2243
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008783729.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MSDEIVKYSNQFNNQALRKFTALDLDLLMAIASRVRDKGTDEVAFTFEELKRLAGLQRNMTNDEFAKQIANVNRRLLALNFEFQNEEHDIIQFALFAGFVTSPTKRTLTVSVNSRFSFLLNDLTSQFTRFELAEFTALRSSYAKECYRRLKQYRQTGVWKVSLEDFRRLLDVPKSYRPSEINKYVLKPIEEELGPLLNLKVHRKYLKKKPGRGRASLVGFEFEFDPEKVPGGAPAPRVELSGSVVTDEARKSLRDVSKTPVPDLSVPGEGPALDPDTQAFLDAHGGHGFAGAEGYVSDWPSAA
SIO_010081: RY69_RS10540
subclass of: SO_0000673
so part of: RY69_RS10540
location: 2534..3445
location: region:2534-3445:1
so has part: feature:2534-3445:1:exon

WP_008783729.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2534-3445:1:exon

RY69_RS10545
type: Gene
subclass of: SO_0000704
RO_0002162: 1685
locus tag: RY69_RS10545
old locus tag: RY69_2244
so part of: sequence
location: complement(3496..3714)
location: region:3496-3714:-1
so has part: feature:3496-3714:-1:exon
subclass of: SO_0000010

69566744
type: Gene
SIO_000068: ncbigene

position:3496:-1
position: 3496
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3714:-1
position: 3714
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3496-3714:-1:exon

RY69_RS10545
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1685
locus tag: RY69_RS10545
old locus tag: RY69_2244
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008783730.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MAASGHLEWCQTIVGRLIRIQFSPGSFRRKFTALDLDLLMAVIAVCLAPAVHPIAADIILTALAVWAMRNSR
SIO_010081: RY69_RS10545
subclass of: SO_0000673
so part of: RY69_RS10545
location: complement(3496..3714)
location: region:3496-3714:-1
so has part: feature:3496-3714:-1:exon

WP_008783730.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3496-3714:-1:exon

RY69_RS11810
type: Gene
subclass of: SO_0000704
RO_0002162: 1685
locus tag: RY69_RS11810
old locus tag: RY69_2245
so part of: sequence
location: complement(3819..3971)
location: region:3819-3971:-1
so has part: feature:3819-3971:-1:exon
subclass of: SO_0000010

69566850
type: Gene
SIO_000068: ncbigene

position:3819:-1
position: 3819
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3971:-1
position: 3971
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3819-3971:-1:exon

RY69_RS11810
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1685
locus tag: RY69_RS11810
old locus tag: RY69_2245
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008783731.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MRMGNKGPHGRPWIWLMAVIVICLAPVMDPIAADITVTALAVWAMASSRR
SIO_010081: RY69_RS11810
subclass of: SO_0000673
so part of: RY69_RS11810
location: complement(3819..3971)
location: region:3819-3971:-1
so has part: feature:3819-3971:-1:exon

WP_008783731.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3819-3971:-1:exon

RY69_RS10550
type: Gene
subclass of: SO_0000704
RO_0002162: 1685
locus tag: RY69_RS10550
old locus tag: RY69_2246
so part of: sequence
location: 4380..4859
location: region:4380-4859:1
so has part: feature:4380-4859:1:exon
subclass of: SO_0000010

69566745
type: Gene
SIO_000068: ncbigene

position:4380:1
position: 4380
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4859:1
position: 4859
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4380-4859:1:exon

RY69_RS10550
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1685
locus tag: RY69_RS10550
old locus tag: RY69_2246
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007056228.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: memba protein
translation: MAVVPMTLLALLSTAVPVASAQETTDESFYELTTTPSGGDMIVGEPGTTILFDSSNGELVDVLPPSEAEDYSVTVSRGCADSNAGCWAGGNALGDMQFAGTGTATGSWPYRNSYTTGNKSGQITFAINGVTYTPVAAGPWMRIATADGSGVDGVSVTRW
SIO_010081: RY69_RS10550
subclass of: SO_0000673
so part of: RY69_RS10550
location: 4380..4859
location: region:4380-4859:1
so has part: feature:4380-4859:1:exon

WP_230846545.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4380-4859:1:exon