Bifidobacterium pseudocatenulatum strain YIT11953 plasmid unnamed, complete sequence.
type: Entry
definition: Bifidobacterium pseudocatenulatum strain YIT11953 plasmid unnamed, complete sequence.
sequence version: NZ_CP079234.1
sequence date: 2022-10-29
sequence: sequence
division: CON
label: NZ_CP079234.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN20132665
keyword: RefSeq
source: Bifidobacterium pseudocatenulatum
organism: Bifidobacterium pseudocatenulatum
taxonomy: Bacteria; Actinomycetota; Actinomycetes; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP079234.1.\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 v. 0.4.7\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 196.8223093598884x\nSequencing Technology :: Illumina MiSeq + PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/29/2022 05:28:15\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 1,864\nCDSs (total) :: 1,789\nGenes (coding) :: 1,762\nCDSs (with protein) :: 1,762\nGenes (RNA) :: 75\nrRNAs :: 6, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 5, 5 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 3\nPseudo Genes (total) :: 27\nCDSs (without protein) :: 27\nPseudo Genes (ambiguous residues) :: 0 of 27\nPseudo Genes (frameshifted) :: 10 of 27\nPseudo Genes (incomplete) :: 21 of 27\nPseudo Genes (internal stop) :: 2 of 27\nPseudo Genes (multiple problems) :: 5 of 27\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4776
topology: circular
so has quality: SO_0000988
location: 1..4776
location: region:1-4776:1
RO_0002162: 28026

NZ_CP079234
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN20132665
type: BioSample
SIO_000068: biosample

1
title: Xylan utilisation by Bifidobacterium pseudocatenulatum
author: Watanabe, Y.
journal: Unpublished

2
title: Direct Submission
author: Watanabe, Y.
journal: Submitted (09-JUL-2021) Basic Research Department, Yakult Central Institute, 5-11, Kunitachi-shi, Tokyo 1868650, Japan

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

position:4776:1
position: 4776
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4776:1:source
so part of: sequence
organism: Bifidobacterium pseudocatenulatum
mol type: genomic DNA
strain: YIT11953
isolation source: fecal material [ENVO:00002003]
host: Homo sapiens
plasmid: unnamed
country: Japan

28026
type: Taxonomy
SIO_000068: taxonomy

KYE74_RS09245
type: Gene
subclass of: SO_0000704
RO_0002162: 28026
locus tag: KYE74_RS09245
old locus tag: KYE74_09215
so part of: sequence
location: join(4698..4776,1..359)
location: region:1-4776:1
so has part: feature:4698-4776:1:exon
so has part: feature:1-359:1:exon
subclass of: SO_0000010

69564740
type: Gene
SIO_000068: ncbigene

urn:…
SIO_000300: 1
SIO_000628: feature:4698-4776:1:exon

position:4698:1
position: 4698
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-359:1:exon

position:359:1
position: 359
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

KYE74_RS09245
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28026
locus tag: KYE74_RS09245
old locus tag: KYE74_09215
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MVKAPENDEKQGDWSVKMRVRNIDQDPDSLHQRIIADDDLGFTQAIIAQRQGCAQSTVSQVLAAERLRRLRAELGKDADGSNGPETSVRAVHAAEQVREALAYVRAVEKRLMAVQRLLMADAAADSRKQFRKLSKTTFRNMKTTR
SIO_010081: KYE74_RS09245
subclass of: SO_0000673
so part of: KYE74_RS09245
location: join(4698..4776,1..359)
location: region:1-4776:1
so has part: feature:4698-4776:1:exon
so has part: feature:1-359:1:exon

WP_226857233.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4698-4776:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-359:1:exon

KYE74_RS09250
type: Gene
subclass of: SO_0000704
RO_0002162: 28026
locus tag: KYE74_RS09250
old locus tag: KYE74_09220
so part of: sequence
location: 1044..1997
location: region:1044-1997:1
so has part: feature:1044-1997:1:exon
subclass of: SO_0000010

69564741
type: Gene
SIO_000068: ncbigene

position:1044:1
position: 1044
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1997:1
position: 1997
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1044-1997:1:exon

KYE74_RS09250
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28026
locus tag: KYE74_RS09250
old locus tag: KYE74_09220
inference: COORDINATES: protein motif:HMM:NF013235.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MGRKDIVRYDNELNQISFRNWSGLEQELFFAVMAKMQGKGLDTVTFSTDDLRDFIDFAGKNGKRWSDVLTNVGRKVAQLVYVDSTPEEIRIMALFQTFVINLNERTITVKVSENYEYVINKLQAKFTQFELEEFGQLRSTYAKTMYRLLKQWRLTGRREFSIEEFRANLGVPKSYDGRKITQKALRPIMAELPAYFDGLALETKHGRGRGHPITGYVFTWKAEKSGGRQWTEGQYAVVEAKKAASRPTSAPPAYRPQEQEKPAVTVYGRRTMASEGIGQADIDAHLNGTVAVDSCPVCKHDPRNRANHGANQPTLFG
SIO_010081: KYE74_RS09250
subclass of: SO_0000673
so part of: KYE74_RS09250
location: 1044..1997
location: region:1044-1997:1
so has part: feature:1044-1997:1:exon

WP_226857234.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1044-1997:1:exon

KYE74_RS09255
type: Gene
subclass of: SO_0000704
RO_0002162: 28026
locus tag: KYE74_RS09255
old locus tag: KYE74_09225
so part of: sequence
location: complement(2043..2258)
location: region:2043-2258:-1
so has part: feature:2043-2258:-1:exon
subclass of: SO_0000010

69564742
type: Gene
SIO_000068: ncbigene

position:2043:-1
position: 2043
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2258:-1
position: 2258
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2043-2258:-1:exon

KYE74_RS09255
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28026
locus tag: KYE74_RS09255
old locus tag: KYE74_09225
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MEIVFRIIANLAQVLQTPIDADTICGLLVTEALRSAAKAGWDGLARIAELVWGLATDLIHRRRHPARHKKR
SIO_010081: KYE74_RS09255
subclass of: SO_0000673
so part of: KYE74_RS09255
location: complement(2043..2258)
location: region:2043-2258:-1
so has part: feature:2043-2258:-1:exon

WP_226857235.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2043-2258:-1:exon

KYE74_RS09260
type: Gene
subclass of: SO_0000704
RO_0002162: 28026
locus tag: KYE74_RS09260
old locus tag: KYE74_09230
so part of: sequence
location: 2605..2754
location: region:2605-2754:1
so has part: feature:2605-2754:1:exon
subclass of: SO_0000010

69564743
type: Gene
SIO_000068: ncbigene

position:2605:1
position: 2605
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2754:1
position: 2754
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2605-2754:1:exon

KYE74_RS09260
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28026
locus tag: KYE74_RS09260
old locus tag: KYE74_09230
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007056229.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MRDSGKGPRGGPIIWLMAVIAVCLAPAVHPIAADVILTALAVWAMRNGR
SIO_010081: KYE74_RS09260
subclass of: SO_0000673
so part of: KYE74_RS09260
location: 2605..2754
location: region:2605-2754:1
so has part: feature:2605-2754:1:exon

WP_176703058.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2605-2754:1:exon

KYE74_RS09265
type: Gene
subclass of: SO_0000704
RO_0002162: 28026
locus tag: KYE74_RS09265
old locus tag: KYE74_09235
so part of: sequence
location: complement(2808..3128)
location: region:2808-3128:-1
so has part: feature:2808-3128:-1:exon
subclass of: SO_0000010

69564744
type: Gene
SIO_000068: ncbigene

position:2808:-1
position: 2808
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3128:-1
position: 3128
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2808-3128:-1:exon

KYE74_RS09265
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28026
locus tag: KYE74_RS09265
old locus tag: KYE74_09235
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MEIRHADLQIEVEDAEDGGVLLTIIDSARLSLLLPRKTATELLDAIDACMKTGERQTTDSVDVWRTADDLPLFGMHVGIDGASWTCGAVRSRDVDGLADGLEALLA
SIO_010081: KYE74_RS09265
subclass of: SO_0000673
so part of: KYE74_RS09265
location: complement(2808..3128)
location: region:2808-3128:-1
so has part: feature:2808-3128:-1:exon

WP_226857231.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2808-3128:-1:exon

KYE74_RS09270
type: Gene
subclass of: SO_0000704
RO_0002162: 28026
locus tag: KYE74_RS09270
old locus tag: KYE74_09240
so part of: sequence
location: complement(3176..4132)
location: region:3176-4132:-1
so has part: feature:3176-4132:-1:exon
subclass of: SO_0000010

69564745
type: Gene
SIO_000068: ncbigene

position:3176:-1
position: 3176
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4132:-1
position: 4132
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3176-4132:-1:exon

KYE74_RS09270
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28026
locus tag: KYE74_RS09270
old locus tag: KYE74_09240
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007056227.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MSNEIVKYSNQFNAQALRKFTALDLDLLMAIAARVRDQEIDEVTFTFEELRRLAHVKKNLTDKELAARIVEVNDRLLACRFKFQDDSRTVQFTLFSGFETDWKTRKLLVAVNPRFSFLLNDLTSQFTRFELAEFTALKSSYAKETYRRLKQYRQTGVWKVSIEEFRRLLDVPESYQTCDLNKRVLKPIQDELGPLLNLVVHKKFRKGAGRGRRSLAGFEFEFDPERVPGGKGAPRVDLSRSVREDTARRSLESVSPHLVEVRGWGEVWWTGDFDVAAARGHLDGSLPAERCMACRMDARNVAGHGSASNSLVDVPLFD
SIO_010081: KYE74_RS09270
subclass of: SO_0000673
so part of: KYE74_RS09270
location: complement(3176..4132)
location: region:3176-4132:-1
so has part: feature:3176-4132:-1:exon

WP_226857232.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3176-4132:-1:exon