Ruminococcus albus 7 = DSM 20455 plasmid pRUMAL04, complete sequence.
type: Entry
definition: Ruminococcus albus 7 = DSM 20455 plasmid pRUMAL04, complete sequence.
sequence version: NC_014827.1
sequence date: 2023-08-02
sequence: sequence
division: CON
label: NC_014827.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN00016988
keyword: GSC:MIGS:2.1
keyword: RefSeq
source: Ruminococcus albus 7 = DSM 20455
organism: Ruminococcus albus 7 = DSM 20455
taxonomy: Bacteria; Bacillota; Clostridia; Eubacteriales; Oscillospiraceae; Ruminococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP002407.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4085694\nSource DNA and organism available from David Mead\n(dmead@lucigen.com)\nContacts: David Mead (dmead@lucigen.com)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. it is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Ruminococcus albus 7\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Host\nnum_replicons :: 5\nref_biomaterial :: Missing\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Anaerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi07008\nGene Calling Method :: JGI-ORNL pipeline\nCell Shape :: Coccus-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 40C\nGram Staining :: Gram+\nDiseases :: None\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: Newbler v. 2.3\nGenome Coverage :: 30x\nSequencing Technology :: 454, Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI …

sequence
subclass of: SO_0000155
sequence length: 7420
topology: circular
so has quality: SO_0000988
location: 1..7420
location: region:1-7420:1
RO_0002162: 697329

NC_014827
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN00016988
type: BioSample
SIO_000068: biosample

1
title: Complete sequence of plasmid4 of Ruminococcus albus 7
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Cheng, J.-F.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Chertkov, O.
author: Detter, J.C.
author: Han, C.
author: Tapia, R.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Ivanova, N.
author: Ovchinnikova, G.
author: Weimer, P.
author: Mead, D.
author: Woyke, T.
journal: Unpublished

2
title: Direct Submission
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Cheng, J.-F.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Chertkov, O.
author: Detter, J.C.
author: Han, C.
author: Tapia, R.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Ivanova, N.
author: Ovchinnikova, G.
author: Weimer, P.
author: Mead, D.
author: Woyke, T.
journal: Submitted (17-DEC-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA

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

position:7420:1
position: 7420
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7420:1:source
so part of: sequence
organism: Ruminococcus albus 7 = DSM 20455
mol type: genomic DNA
strain: 7
type material: type strain of Ruminococcus albus
plasmid: pRUMAL04

697329
type: Taxonomy
SIO_000068: taxonomy

RUMAL_RS20345
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS20345
old locus tag: Rumal_4008
so part of: sequence
location: 14..376
location: region:14-376:1
so has part: feature:14-376:1:exon
subclass of: SO_0000010

position:14:1
position: 14
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:376:1
position: 376
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:14-376:1:exon

RUMAL_RS20345
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS20345
old locus tag: Rumal_4008
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010245415.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system RelE/ParE family toxin
translation: MQEFEIIFYEKADGTEPAKDFILSLDTKMRAKMFRTVELLQKNGNRLREPESKPIEDGIMELRAKVGSDISRVLYFFVVGHKVVLTNGFIKKTQKTPRSEIERAKQYRADYLSRKENEND
SIO_010081: RUMAL_RS20345
subclass of: SO_0000673
so part of: RUMAL_RS20345
location: 14..376
location: region:14-376:1
so has part: feature:14-376:1:exon

WP_013483965.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:14-376:1:exon

RUMAL_RS20350
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS20350
old locus tag: Rumal_4009
so part of: sequence
location: 369..641
location: region:369-641:1
so has part: feature:369-641:1:exon
subclass of: SO_0000010

position:369:1
position: 369
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:641:1
position: 641
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:369-641:1:exon

RUMAL_RS20350
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS20350
old locus tag: Rumal_4009
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005924206.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix transcriptional regulator
translation: MTNFNELLAEQMKDDEFRREYEALEPEFTIMQAMIDARNSSGLTQKQLSDRSGIAQGDISKLENGNANPSIRTLQRLANAMGKKLRIEFL
SIO_010081: RUMAL_RS20350
subclass of: SO_0000673
so part of: RUMAL_RS20350
location: 369..641
location: region:369-641:1
so has part: feature:369-641:1:exon

WP_013483966.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:369-641:1:exon

RUMAL_RS20355
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS20355
old locus tag: Rumal_4010
so part of: sequence
location: complement(707..991)
location: region:707-991:-1
so has part: feature:707-991:-1:exon
subclass of: SO_0000010

position:707:-1
position: 707
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:991:-1
position: 991
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:707-991:-1:exon

RUMAL_RS20355
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS20355
old locus tag: Rumal_4010
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005337289.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSKSKTYEERIAELQEKQKQLKAQEKKLKAQKSADERKKRTRHLIEIGGAVYSVLGREYADGDIERLVAFLKGQNQRGGFFNKAMNDFPDNKPE
SIO_010081: RUMAL_RS20355
subclass of: SO_0000673
so part of: RUMAL_RS20355
location: complement(707..991)
location: region:707-991:-1
so has part: feature:707-991:-1:exon

WP_013483967.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:707-991:-1:exon

RUMAL_RS20360
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS20360
old locus tag: Rumal_4011
so part of: sequence
location: complement(978..1391)
location: region:978-1391:-1
so has part: feature:978-1391:-1:exon
subclass of: SO_0000010

position:978:-1
position: 978
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1391:-1
position: 1391
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:978-1391:-1:exon

RUMAL_RS20360
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS20360
old locus tag: Rumal_4011
inference: COORDINATES: protein motif:HMM:NF013691.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: GIY-YIG nuclease family protein
translation: MLRDFQLEALKEWYRIKALGLDDIIYEPNCILYDRSPYIYLFYNNNNIVIYVGHTQNIANRMSKHIEESPFWEEVSYIMCAETPNLNSLADYERYYIQKYKPKYNKRGFKKPPYLPDMVALDFIEYKGKEVLNYVKK
SIO_010081: RUMAL_RS20360
subclass of: SO_0000673
so part of: RUMAL_RS20360
location: complement(978..1391)
location: region:978-1391:-1
so has part: feature:978-1391:-1:exon

WP_013483968.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:978-1391:-1:exon

RUMAL_RS21110
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
gene: mobQ
locus tag: RUMAL_RS21110
old locus tag: Rumal_4012
so part of: sequence
location: 1621..3027
location: region:1621-3027:1
so has part: feature:1621-3027:1:exon
subclass of: SO_0000010

position:1621:1
position: 1621
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3027:1
position: 3027
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1621-3027:1:exon

RUMAL_RS21110
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
gene: mobQ
locus tag: RUMAL_RS21110
old locus tag: Rumal_4012
inference: COORDINATES: protein motif:HMM:NF015354.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobQ family relaxase
translation: MAIYHCSIKIGSRANGQSAIAAAAYRAGDNLKDKETGLVSDYSRKGGVVFSEISLCQNAPAEYADRATLWNAVHEIEKAKNSQLWREFEVALPQEFSRAEQIDTVRGFVKGLTKQGMCVDWSLHDKEDGNPHAHIMATMRSITEGGKWAPKSRKVYDLDENGERIFQKVDKSGRKQYKNHKEDYNDWNKKERVEEWRAAWAACCNERLAERDRIDHRSYKRQGIEQEPTIHEGYAARKIAAEGKPSERVRINEEIRERNNMLKQLAEQLHHIEQQLAELIKEKGSAAINAGKQRIADLLARRSRAVDSDDRGLADGERTTESRTERTTATEADRLIRESEAERRAALRNVGLEESGRTAQGNEKKAEHSATRLQPTEQPDTAAIFGAADSLIQDTDTNQEAVRAATADTDSTIRQSETKVTSAAAHRQERELAEQRRAAEERRRAEEAERKARAASERARKTSYDRGR
SIO_010081: RUMAL_RS21110
subclass of: SO_0000673
so part of: RUMAL_RS21110
location: 1621..3027
location: region:1621-3027:1
so has part: feature:1621-3027:1:exon

WP_050793340.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1621-3027:1:exon

RUMAL_RS22645
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS22645
so part of: sequence
location: 2915..3667
location: region:2915-3667:1
so has part: feature:2915-3667:1:exon
subclass of: SO_0000010

position:2915:1
position: 2915
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3667:1
position: 3667
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2915-3667:1:exon

RUMAL_RS22645
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS22645
inference: COORDINATES: protein motif:HMM:NF040306.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF6040 family protein
translation: MQSSDEQLKNAEELKKQSARQEQQAKERERRATIEADRARREAAAAIARAEQKEEAAIIAKNAAEHTKQQQESIIKEKAEALNRQYQVEWNVIGVALIVYSLFATVFTAIKSKRCMSDITAAGKLIVKIAKGIVHVITALASRVGSVGAKIPQPIVSTIVSYLLMALITAICVVVILAPLYLGIKAISNCYTLHCWDEVSPLVALVCLAVLVWGAELMPLNIVLLMILSHAAYIVVRWYIDGWREARGLA
SIO_010081: RUMAL_RS22645
subclass of: SO_0000673
so part of: RUMAL_RS22645
location: 2915..3667
location: region:2915-3667:1
so has part: feature:2915-3667:1:exon

WP_028504453.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2915-3667:1:exon

RUMAL_RS20375
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS20375
old locus tag: Rumal_4013
so part of: sequence
location: 4147..5556
location: region:4147-5556:1
so has part: feature:4147-5556:1:exon
subclass of: SO_0000010

position:4147:1
position: 4147
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5556:1
position: 5556
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4147-5556:1:exon

RUMAL_RS20375
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS20375
old locus tag: Rumal_4013
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015087707.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSDNVLNNFRECYELLSNVYDQVNGEDFYRYIFPDNENSGELSSDFSHPNAIYLYHDEQDEGAKRRLRRRIMLNDTWASDYMDYVEGNGMTLCSGLTYHSRSNKLQYAQTMNALIFDLDGVGRSELEHVLERTTGSGDVYRSIPKPTFIVLSGRGLHLYYVFDEPIALYPNIKLQLKSLKHDLTFRIWEYKGTSQVESIQYQSIGQGFRMVGSTNSKYGNTVTAFKIGGKVSLDFLNSYAIKPENRVDVNRPYRPSKIDRATAAELYPEWYQKVVVEGNKRPNKWNIGYRKKKQVKDYALYEWWKRRVTEIEGGHRYFYLMCLVIYACKCDVPKKQLKVDIQACFEVLRAYKHNNELTQDDVDSAMECYSKDYYNFTIADIEILTDVRIERNKRNYQKQEWHLEDIRSKKANMKRRGQPFRNAEGRPSKQQIVLEWQQLHPMGRKVDCIRDTGLSKPTVLKWWRKEFEA
SIO_010081: RUMAL_RS20375
subclass of: SO_0000673
so part of: RUMAL_RS20375
location: 4147..5556
location: region:4147-5556:1
so has part: feature:4147-5556:1:exon

WP_013483969.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4147-5556:1:exon

RUMAL_RS20380
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS20380
old locus tag: Rumal_4014
so part of: sequence
location: 5553..6104
location: region:5553-6104:1
so has part: feature:5553-6104:1:exon
subclass of: SO_0000010

position:5553:1
position: 5553
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6104:1
position: 6104
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5553-6104:1:exon

RUMAL_RS20380
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS20380
old locus tag: Rumal_4014
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: MarR family transcriptional regulator
translation: MSKTIKQIADELGVSKDRVKYLVKKLPSGWVEKRGNITYINADGERNIYMLEGKKWGKSDEITHIETELDRVISTHLPTEEQKKDMEIERLKARVAELERQLEYERANSEEKQALLKAWNDEQIQQFNRIIEDNKKLLQLIDQEQQLHLRSIESKDKGLAIEEKQPEPKRHWWQRKRKEPTEE
SIO_010081: RUMAL_RS20380
subclass of: SO_0000673
so part of: RUMAL_RS20380
location: 5553..6104
location: region:5553-6104:1
so has part: feature:5553-6104:1:exon

WP_013483970.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5553-6104:1:exon

RUMAL_RS20385
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS20385
old locus tag: Rumal_4015
so part of: sequence
location: 6101..6307
location: region:6101-6307:1
so has part: feature:6101-6307:1:exon
subclass of: SO_0000010

position:6101:1
position: 6101
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6307:1
position: 6307
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6101-6307:1:exon

RUMAL_RS20385
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS20385
old locus tag: Rumal_4015
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: MNEPTKKKKGGARAGAGAKPKYGCKTVTMRVPADMVDEIRAFICKKKHIEPKPEPEQELEGQVSFSDI
SIO_010081: RUMAL_RS20385
subclass of: SO_0000673
so part of: RUMAL_RS20385
location: 6101..6307
location: region:6101-6307:1
so has part: feature:6101-6307:1:exon

WP_013483971.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6101-6307:1:exon

RUMAL_RS20390
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS20390
old locus tag: Rumal_4016
so part of: sequence
location: 6320..6718
location: region:6320-6718:1
so has part: feature:6320-6718:1:exon
subclass of: SO_0000010

position:6320:1
position: 6320
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6718:1
position: 6718
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6320-6718:1:exon

RUMAL_RS20390
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS20390
old locus tag: Rumal_4016
inference: COORDINATES: protein motif:HMM:NF039645.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF6075 family protein
translation: MDIKFYNEEHQKAFYSICKRMKHLDCYHFSLAYLLSLDKVLREHTDEVFDFKEDCIKREGLHKGFQTGTSMKTTRLAFNLWNGCYDDGETYTNKDGYETELPSSYYSPDQIFCCKDYAPYYWQAIRIRFELN
SIO_010081: RUMAL_RS20390
subclass of: SO_0000673
so part of: RUMAL_RS20390
location: 6320..6718
location: region:6320-6718:1
so has part: feature:6320-6718:1:exon

WP_013483972.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6320-6718:1:exon

RUMAL_RS22035
type: Gene
subclass of: SO_0000704
RO_0002162: 697329
locus tag: RUMAL_RS22035
so part of: sequence
location: complement(6991..7233)
location: region:6991-7233:-1
so has part: feature:6991-7233:-1:exon
subclass of: SO_0000010

position:6991:-1
position: 6991
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7233:-1
position: 7233
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6991-7233:-1:exon

RUMAL_RS22035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 697329
locus tag: RUMAL_RS22035
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: MSGTIYCSNTSILKPKSYFSGRIDEYKDLNGRYNKANGSTKSFSIPKNTKKVKVGWKNVYITTIAGGKAYLGNASSTVKL
SIO_010081: RUMAL_RS22035
subclass of: SO_0000673
so part of: RUMAL_RS22035
location: complement(6991..7233)
location: region:6991-7233:-1
so has part: feature:6991-7233:-1:exon

WP_154662904.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6991-7233:-1:exon