Butyrivibrio hungatei strain MB2003 plasmid pNP6, complete sequence.
type: Entry
definition: Butyrivibrio hungatei strain MB2003 plasmid pNP6, complete sequence.
sequence version: NZ_CP017833.1
sequence date: 2023-03-13
sequence: sequence
division: CON
label: NZ_CP017833.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN05928573
keyword: RefSeq
source: Butyrivibrio hungatei
organism: Butyrivibrio hungatei
taxonomy: Bacteria; Bacillota; Clostridia; Eubacteriales; Lachnospiraceae; Butyrivibrio.
reference: 1
references: 35124176
reference: 2
references: 31653790
reference: 3
references: 30478228
reference: 4
references: 29553575
reference: 5
references: 29225728
reference: 6
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP017833.1.\nBacteria and source DNA available from AgResearch, Rumen\nMicrobiology, Animal Nutrition and Health, Grasslands Research\nCentre, Tennent Drive, Private Bag 11008, Palmerston North, New\nZealand.\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 :: Newbler v. version 2.3\nGenome Coverage :: 234.0x\nSequencing Technology :: 454 GS FLX Titanium\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/13/2023 01:38:46\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) :: 3,094\nCDSs (total) :: 3,030\nGenes (coding) :: 3,015\nCDSs (with protein) :: 3,015\nGenes (RNA) :: 64\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 4\nPseudo Genes (total) :: 15\nCDSs (without protein) :: 15\nPseudo Genes (ambiguous residues) :: 0 of 15\nPseudo Genes (frameshifted) :: 5 of 15\nPseudo Genes (incomplete) :: 10 of 15\nPseudo Genes (internal stop) :: 0 of 15\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 6284
topology: circular
so has quality: SO_0000988
location: 1..6284
location: region:1-6284:1
RO_0002162: 185008

NZ_CP017833
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN05928573
type: BioSample
SIO_000068: biosample

1
title: Genomic architecture of three newly isolated unclassified Butyrivibrio species elucidate their potential role in the rumen ecosystem
author: Sengupta, K.
author: Hivarkar, S.S.
author: Palevich, N.
author: Chaudhary, P.P.
author: Dhakephalkar, P.K.
author: Dagar, S.S.
journal: Genomics 114 (2), 110281 (2022)
pubmed: 35124176

35124176
type: PubMed
SIO_000068: pubmed

2
title: Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities
author: Palevich, N.
author: Kelly, W.J.
author: Leahy, S.C.
author: Denman, S.
author: Altermann, E.
author: Rakonjac, J.
author: Attwood, G.T.
journal: Appl Environ Microbiol 86 (1), e01993-19 (2019)
pubmed: 31653790
comments: Publication Status: Online-Only

31653790
type: PubMed
SIO_000068: pubmed

3
title: Butyrivibrio hungatei MB2003 Competes Effectively for Soluble Sugars Released by Butyrivibrio proteoclasticus B316T during Growth on Xylan or Pectin
author: Palevich, N.
author: Kelly, W.J.
author: Ganesh, S.
author: Rakonjac, J.
author: Attwood, G.T.
journal: Appl Environ Microbiol 85 (3), e02056-18 (2019)
pubmed: 30478228
comments: Publication Status: Online-Only

30478228
type: PubMed
SIO_000068: pubmed

4
title: Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
author: Seshadri, R.
author: Leahy, S.C.
author: Attwood, G.T.
author: Teh, K.H.
author: Lambie, S.C.
author: Cookson, A.L.
author: Eloe-Fadrosh, E.A.
author: Pavlopoulos, G.A.
author: Hadjithomas, M.
author: Varghese, N.J.
author: Paez-Espino, D.
author: Perry, R.
author: Henderson, G.
author: Creevey, C.J.
author: Terrapon, N.
author: Lapebie, P.
author: Drula, E.
author: Lombard, V.
author: Rubin, E.
author: Kyrpides, N.C.
author: Henrissat, B.
author: Woyke, T.
author: Ivanova, N.N.
author: Kelly, W.J.
journal: Nat Biotechnol
volume: 36
issue: 4
pages: 359-367
year: 2018
pubmed: 29553575

29553575
type: PubMed
SIO_000068: pubmed

5
title: The complete genome sequence of the rumen bacterium Butyrivibrio hungatei MB2003
author: Palevich, N.
author: Kelly, W.J.
author: Leahy, S.C.
author: Altermann, E.
author: Rakonjac, J.
author: Attwood, G.T.
journal: Stand Genomic Sci 12, 72 (2017)
pubmed: 29225728
comments: Publication Status: Online-Only

29225728
type: PubMed
SIO_000068: pubmed

6
title: Direct Submission
author: Palevich, N.
author: Kelly, W.J.
author: Leahy, S.C.
author: Altermann, E.
author: Rakonjac, J.
author: Attwood, G.T.
journal: Submitted (25-OCT-2016) Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, Manawatu 4442, New Zealand

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

position:6284:1
position: 6284
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6284:1:source
so part of: sequence
organism: Butyrivibrio hungatei
mol type: genomic DNA
strain: MB2003
isolation source: Bovine rumen
host: Bovine
lab host: Bos taurus
plasmid: pNP6
country: New Zealand: Ruakura, Hamilton
lat lon: 37.77 S 175.30999999 E
altitude: 40 m
collection date: 2009-05
collected by: AgResearch Limited

185008
type: Taxonomy
SIO_000068: taxonomy

bhn_RS15295
type: Gene
subclass of: SO_0000704
RO_0002162: 185008
locus tag: bhn_RS15295
so part of: sequence
location: complement(join(6043..6284,1..493))
location: region:1-6284:-1
so has part: feature:1-493:-1:exon
so has part: feature:6043-6284:-1:exon
subclass of: SO_0000010

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

position:6284:-1
position: 6284
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-493:-1:exon

position:493:-1
position: 493
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:6043-6284:-1:exon

position:6043:-1
position: 6043
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

bhn_RS15295
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 185008
locus tag: bhn_RS15295
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: replication initiation protein
translation: MKTYEINPKHKYAQKNTMITASFDHALTTHEQKLLRIAIASIDTVKENEFIETKVPLSTLQKLIPENKFKNTYRDIEKACRVLVKTTIEIIEPRKKATFYPLFSKIEYNYGEGCFTFQFNPHMNEYLLNLKNSFTQIPLEDILNMNHKYSMKVYELIRSKLKNNPGTENRYPQIKEFKHRVLYPALEDIAKFETARIHCNVTDIKENRRIIAFKLDCWSINGWDYIQRQKGQIEGQIDMFQLGL
SIO_010081: bhn_RS15295
subclass of: SO_0000673
so part of: bhn_RS15295
location: complement(join(6043..6284,1..493))
location: region:1-6284:-1
so has part: feature:1-493:-1:exon
so has part: feature:6043-6284:-1:exon

WP_193399774.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-493:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:6043-6284:-1:exon

bhn_RS15300
type: Gene
subclass of: SO_0000704
RO_0002162: 185008
gene: mobV
locus tag: bhn_RS15300
old locus tag: bhn_IV001
so part of: sequence
location: 835..1503
location: region:835-1503:1
so has part: feature:835-1503:1:exon
subclass of: SO_0000010

position:835:1
position: 835
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1503:1
position: 1503
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:835-1503:1:exon

bhn_RS15300
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 185008
gene: mobV
locus tag: bhn_RS15300
old locus tag: bhn_IV001
inference: COORDINATES: protein motif:HMM:NF041497.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006310 - DNA recombination [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobV family relaxase
translation: MANFEKIDDPIGICHHNNRTALEAVTDHKINIDPTRTHLNEDWTPQRTDEKGKALTKRQYYNQRLKEVPHLNRKNVRTAVSWVVTLPKDIPAGSTKDREFFRASYDFLSAKYGADNIISVNIHRDEAQPHMHFVFMPVDARGRISCKNLMNKAELSGFHPQLQSFMQSRGIDCNVNSGITRAQGGNRTIAELKKGEHQHEEKHKITRIKRQHDHEHSPNRIR
SIO_010081: bhn_RS15300
subclass of: SO_0000673
so part of: bhn_RS15300
location: 835..1503
location: region:835-1503:1
so has part: feature:835-1503:1:exon

WP_071177707.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:835-1503:1:exon

bhn_RS15305
type: Gene
subclass of: SO_0000704
RO_0002162: 185008
locus tag: bhn_RS15305
old locus tag: bhn_IV002
so part of: sequence
location: 1430..1906
location: region:1430-1906:1
so has part: feature:1430-1906:1:exon
subclass of: SO_0000010

position:1430:1
position: 1430
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1906:1
position: 1906
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1430-1906:1:exon

bhn_RS15305
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 185008
locus tag: bhn_RS15305
old locus tag: bhn_IV002
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: MKKNIKSLVSSDNMTMNIAQIEYADWLIFGAIEKLGLEYAPDQVLSANKVMIKCLYISDKAELQQDNTILGRFKRWKERNEPTNLFEEVNQNQDCTQLAEDICNDLMRFYEMTPRIYYVWLLRNWGIFDNAIVEKAKRWKANDCNYQDDIEPSWYEKY
SIO_010081: bhn_RS15305
subclass of: SO_0000673
so part of: bhn_RS15305
location: 1430..1906
location: region:1430-1906:1
so has part: feature:1430-1906:1:exon

WP_148661988.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1430-1906:1:exon

bhn_RS15310
type: Gene
subclass of: SO_0000704
RO_0002162: 185008
locus tag: bhn_RS15310
old locus tag: bhn_IV003
so part of: sequence
location: 1916..3598
location: region:1916-3598:1
so has part: feature:1916-3598:1:exon
subclass of: SO_0000010

position:1916:1
position: 1916
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3598:1
position: 3598
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1916-3598:1:exon

bhn_RS15310
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 185008
locus tag: bhn_RS15310
old locus tag: bhn_IV003
inference: COORDINATES: protein motif:HMM:NF014581.2
GO component: GO:0016020 - membrane [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type IV secretory system conjugative DNA transfer family protein
translation: MKKIINFWQYHLILWFLLLQVCIFAGNNIFPWLVLQNEIYLIICRYFPFMVYLPKFALLSVLFIFWWIYTLSIFYRHKTGRKWLIDRWNYRRTYLDLINKLNVKHSDPQRLLEDDLEYMQPWECDGVPFGMLGSFLAYRKTADKGHILIFGGSGRGKTQVYAIPTVLQFGKRKPAHIFCIDVKGDILEHVGDKRHVKKFIPHDPEKSCCFDAFRVVRSQDEDSQIEYFTNLSLMLVEDDPHSSQYFVKGGRDMLISACLYALKENKNATLYDIAVLLRQNDFDSLAQLIADAGNETAYNFIRQYENQKDSDVQGCYSHAVDATKIFAQKRMKKLLACDSGYEKMSDIQANSLEEYNNLVPMSLDDFENGYDIFLEIRENDLKQLAPLVSLVVDSVSLEILSRFDGVEGSNTPILMLLDEFASFNRMPNVLELEAKGRSKSCTCMILCQSFDQLFMHYSEHEVQTIVDNSPYIAVLSASGKTAKYFSDMAGNVKTLTTSVNDSQGETSRKTKGSTEKEEPFIAPSALANLHENGEVLLFFDGKHARAKLKPYYKWPDSQKH
SIO_010081: bhn_RS15310
subclass of: SO_0000673
so part of: bhn_RS15310
location: 1916..3598
location: region:1916-3598:1
so has part: feature:1916-3598:1:exon

WP_071177709.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1916-3598:1:exon

bhn_RS15315
type: Gene
subclass of: SO_0000704
RO_0002162: 185008
locus tag: bhn_RS15315
old locus tag: bhn_IV004
so part of: sequence
location: 3920..4675
location: region:3920-4675:1
so has part: feature:3920-4675:1:exon
subclass of: SO_0000010

position:3920:1
position: 3920
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4675:1
position: 4675
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3920-4675:1:exon

bhn_RS15315
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 185008
locus tag: bhn_RS15315
old locus tag: bhn_IV004
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: MGYAGKSERKKYAKAKLQNNVKQCKANINFHQGEKMKISAEFMKDIPSCGYRYLNFRETIVNWYQWEYTHYMFYGDYKRYKYINSKYFDTFKMIYQGFKKEFEEHQKILPCCYRGIVAYSNDFNILMDKTLADIKKGQIGFNRYYSGSLSKEVSQRYIDVYIDDLKKQREEYRFFNDELIAVSVLFEIHNATVYDLTEYNTDNYFVLDDEIILAPSSYKVLDRKLEFVKIDNALMAQNYVVLKALDPKQNH
SIO_010081: bhn_RS15315
subclass of: SO_0000673
so part of: bhn_RS15315
location: 3920..4675
location: region:3920-4675:1
so has part: feature:3920-4675:1:exon

WP_071177710.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3920-4675:1:exon

bhn_RS15320
type: Gene
subclass of: SO_0000704
RO_0002162: 185008
locus tag: bhn_RS15320
old locus tag: bhn_IV005
so part of: sequence
location: complement(5134..5664)
location: region:5134-5664:-1
so has part: feature:5134-5664:-1:exon
subclass of: SO_0000010

position:5134:-1
position: 5134
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5664:-1
position: 5664
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5134-5664:-1:exon

bhn_RS15320
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 185008
locus tag: bhn_RS15320
old locus tag: bhn_IV005
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: MNLTEFAQSHNIEMQVISKHIKAHADEYKGKIKENGKSKELSDEAVMILEKYYPTPKPIQVINGVPEEEHRKKLEELENAQKDLITAKDMIISLKDQLTDYQLKLKDAENEQLRIEEKGKIKDTLIEKLEKSAEEQKNKSAEQELKLSDLQTENEKLKAELETEKNKSWLAKLLRK
SIO_010081: bhn_RS15320
subclass of: SO_0000673
so part of: bhn_RS15320
location: complement(5134..5664)
location: region:5134-5664:-1
so has part: feature:5134-5664:-1:exon

WP_071177711.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5134-5664:-1:exon