Ruminococcus albus 7 = DSM 20455 plasmid pRUMAL01, complete sequence.
Bacteria; Bacillota; Clostridia; Eubacteriales; Oscillospiraceae; Ruminococcus.
Complete sequence of plasmid1 of Ruminococcus albus 7
Submitted (17-DEC-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002404.1.\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 RefSeq\nAnnotation Date :: 02/10/2023 14:27:20\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) :: 4,128\nCDSs (total) :: 4,038\nGenes (coding) :: 3,991\nCDSs (with protein) :: 3,991\nGenes (RNA) :: 90\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 75\nncRNAs :: 3\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 15 of 47\nPseudo Genes (incomplete) :: 26 of 47\nPseudo Genes (internal stop) :: 11 of 47\nPseudo Genes (multiple problems) :: 5 of 47\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF024991.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013601.2
COORDINATES: protein motif:HMM:NF039815.1
COORDINATES: protein motif:HMM:NF013930.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003896 - DNA primase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
CHC2 zinc finger domain-containing protein
COORDINATES: protein motif:HMM:TIGR00594.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF033849.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002847217.1
COORDINATES: protein motif:HMM:NF013632.2
COORDINATES: protein motif:HMM:NF013122.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF017520.2
COORDINATES: similar to AA sequence:RefSeq:WP_005608342.1
COORDINATES: similar to AA sequence:RefSeq:WP_015262159.1
COORDINATES: protein motif:HMM:NF033516.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024412.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF016119.2
COORDINATES: protein motif:HMM:NF013528.2
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: protein motif:HMM:NF025563.2
COORDINATES: protein motif:HMM:NF015958.2
COORDINATES: protein motif:HMM:NF024702.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF023203.2
COORDINATES: protein motif:HMM:NF025973.2
GO:0004525 - ribonuclease III activity [Evidence IEA]
GO:0006396 - RNA processing [Evidence IEA]
ribonuclease III domain-containing protein
COORDINATES: protein motif:HMM:NF013311.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF025053.2
COORDINATES: similar to AA sequence:RefSeq:WP_013483531.1
IS200/IS605 family element transposase accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_013483367.1
COORDINATES: protein motif:HMM:NF016168.2
leucine-rich repeat domain-containing protein
COORDINATES: protein motif:HMM:NF025189.2
COORDINATES: similar to AA sequence:RefSeq:WP_013483391.1
BspA family leucine-rich repeat surface protein
COORDINATES: similar to AA sequence:RefSeq:WP_009984668.1
COORDINATES: similar to AA sequence:RefSeq:WP_006189145.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_009983275.1
COORDINATES: similar to AA sequence:RefSeq:WP_004604173.1
COORDINATES: similar to AA sequence:RefSeq:WP_013483501.1
IS200/IS605 family element RNA-guided endonuclease TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_002851897.1
COORDINATES: protein motif:HMM:NF013921.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009260458.1
COORDINATES: similar to AA sequence:RefSeq:WP_002848423.1
COORDINATES: similar to AA sequence:RefSeq:WP_009986924.1
COORDINATES: protein motif:HMM:NF014427.2
pilus assembly protein N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014793811.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002852505.1
COORDINATES: similar to AA sequence:RefSeq:WP_013483496.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273520.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_013483394.1
COORDINATES: similar to AA sequence:RefSeq:WP_002847210.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024700.2
COORDINATES: similar to AA sequence:RefSeq:WP_009983620.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: protein motif:HMM:NF013540.2
COORDINATES: similar to AA sequence:RefSeq:WP_002849021.1
COORDINATES: similar to AA sequence:RefSeq:WP_002848994.1
redox-sensing transcriptional repressor Rex
COORDINATES: similar to AA sequence:RefSeq:WP_002848936.1
GO:0004022 - alcohol dehydrogenase (NAD+) activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0006066 - alcohol metabolic process [Evidence IEA]; GO:0015976 - carbon utilization [Evidence IEA]
bifunctional acetaldehyde-CoA/alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013483408.1
COORDINATES: similar to AA sequence:RefSeq:WP_015557768.1
(2Fe-2S) ferredoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013483410.1
COORDINATES: similar to AA sequence:RefSeq:WP_002849014.1
[Fe-Fe] hydrogenase large subunit C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002848954.1
GO:0016791 - phosphatase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013483413.1
4Fe-4S dicluster domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006907146.1
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011068386.1
COORDINATES: similar to AA sequence:RefSeq:WP_013483415.1
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_002852308.1
COORDINATES: similar to AA sequence:RefSeq:WP_002852035.1
COORDINATES: similar to AA sequence:RefSeq:WP_019680617.1
COORDINATES: similar to AA sequence:RefSeq:WP_013483421.1
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002586562.1
COORDINATES: protein motif:HMM:NF040112.1
COORDINATES: protein motif:HMM:NF025919.2
COORDINATES: protein motif:HMM:NF025768.2
COORDINATES: similar to AA sequence:RefSeq:WP_009987347.1
COORDINATES: similar to AA sequence:RefSeq:WP_013483431.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_005342978.1
COORDINATES: protein motif:HMM:NF037745.2
COORDINATES: protein motif:HMM:NF025819.2
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011345514.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0003674 - molecular_function [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
protease Lon-related BREX system protein BrxL
COORDINATES: similar to AA sequence:RefSeq:WP_002850180.1
COORDINATES: protein motif:HMM:NF012298.2
COORDINATES: similar to AA sequence:RefSeq:WP_013483442.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_002847213.1
COORDINATES: protein motif:HMM:NF018446.2
GO:0005267 - potassium channel activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009145723.1
COORDINATES: protein motif:HMM:NF012920.2
COORDINATES: similar to AA sequence:RefSeq:WP_002847206.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_013483451.1
COORDINATES: protein motif:HMM:NF012869.2
COORDINATES: protein motif:HMM:NF015557.2
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002848965.1
COORDINATES: similar to AA sequence:RefSeq:WP_002852658.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_015557906.1
COORDINATES: protein motif:HMM:NF016362.2
COORDINATES: protein motif:HMM:NF012464.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016440411.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01051
cyclic di-GMP riboswitch class I; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: protein motif:HMM:NF012700.2
COORDINATES: similar to AA sequence:RefSeq:WP_002847209.1
COORDINATES: protein motif:HMM:NF024993.2
ankyrin repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015557803.1
COORDINATES: protein motif:HMM:NF024637.2
COORDINATES: similar to AA sequence:RefSeq:WP_013965117.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_002593895.1
COORDINATES: similar to AA sequence:RefSeq:WP_013483777.1
COORDINATES: protein motif:HMM:NF037639.2
SpaA isopeptide-forming pilin-related protein
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: similar to AA sequence:RefSeq:WP_008981146.1
COORDINATES: protein motif:HMM:NF015038.2
COORDINATES: protein motif:HMM:NF033517.1
COORDINATES: protein motif:HMM:NF020904.2
COORDINATES: protein motif:HMM:NF019908.2
dockerin type I repeat-containing protein
COORDINATES: protein motif:HMM:NF012731.2
DNA topoisomerase (ATP-hydrolyzing) subunit A
COORDINATES: similar to AA sequence:RefSeq:WP_009985237.1
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF012371.2
serine hydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019680808.1
COORDINATES: similar to AA sequence:RefSeq:WP_009987697.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009988081.1
COORDINATES: protein motif:HMM:NF012622.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0000272 - polysaccharide catabolic process [Evidence IEA]
dockerin type I domain-containing protein
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: protein motif:HMM:NF025562.2
COORDINATES: similar to AA sequence:RefSeq:WP_002851326.1
COORDINATES: similar to AA sequence:RefSeq:WP_011916753.1
COORDINATES: similar to AA sequence:RefSeq:WP_013726328.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002851373.1
COORDINATES: similar to AA sequence:RefSeq:WP_002848907.1
COORDINATES: similar to AA sequence:RefSeq:WP_002852627.1
COORDINATES: similar to AA sequence:RefSeq:WP_002851360.1
COORDINATES: protein motif:HMM:NF024919.2
COORDINATES: similar to AA sequence:RefSeq:WP_013499639.1
COORDINATES: similar to AA sequence:RefSeq:WP_002852602.1
COORDINATES: similar to AA sequence:RefSeq:WP_005355245.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002848905.1
COORDINATES: similar to AA sequence:RefSeq:WP_002848896.1
COORDINATES: similar to AA sequence:RefSeq:WP_013498105.1
COORDINATES: similar to AA sequence:RefSeq:WP_013483574.1
COORDINATES: similar to AA sequence:RefSeq:WP_002849041.1
COORDINATES: similar to AA sequence:RefSeq:WP_002849038.1
COORDINATES: similar to AA sequence:RefSeq:WP_002847202.1
COORDINATES: protein motif:HMM:NF016147.2
COORDINATES: protein motif:HMM:NF017416.2
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_009987320.1
COORDINATES: protein motif:HMM:NF014453.2
COORDINATES: similar to AA sequence:RefSeq:WP_002326282.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014547280.1
COORDINATES: similar to AA sequence:RefSeq:WP_014547279.1
COORDINATES: similar to AA sequence:RefSeq:WP_003508172.1
COORDINATES: similar to AA sequence:RefSeq:WP_002567335.1
GO:0008761 - UDP-N-acetylglucosamine 2-epimerase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF016852.2
COORDINATES: similar to AA sequence:RefSeq:WP_009429702.1
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_004033433.1
adenylyltransferase/cytidyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002847290.1
COORDINATES: similar to AA sequence:RefSeq:WP_002847315.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002847276.1
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: protein motif:HMM:NF016145.2
polysaccharide pyruvyl transferase family protein
COORDINATES: protein motif:HMM:NF014051.2
COORDINATES: similar to AA sequence:RefSeq:WP_009131434.1
GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005794840.1
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: similar to AA sequence:RefSeq:WP_006526723.1
UDP-N-acetylglucosamine pyrophosphorylase
COORDINATES: protein motif:HMM:NF026257.2
COORDINATES: similar to AA sequence:RefSeq:WP_002847194.1
COORDINATES: similar to AA sequence:RefSeq:WP_009987424.1
COORDINATES: similar to AA sequence:RefSeq:WP_002847197.1
COORDINATES: protein motif:HMM:NF013222.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: protein motif:HMM:NF021028.2
COORDINATES: similar to AA sequence:RefSeq:WP_013497279.1
COORDINATES: protein motif:HMM:NF024501.2
COORDINATES: protein motif:HMM:NF020476.2
COORDINATES: protein motif:HMM:NF040103.1
COORDINATES: protein motif:HMM:NF012870.2
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF024793.2
COORDINATES: similar to AA sequence:RefSeq:WP_013483522.1
COORDINATES: similar to AA sequence:RefSeq:WP_013483626.1
COORDINATES: similar to AA sequence:RefSeq:WP_013498631.1
COORDINATES: similar to AA sequence:RefSeq:WP_013498630.1
COORDINATES: similar to AA sequence:RefSeq:WP_013498629.1
COORDINATES: protein motif:HMM:NF012606.2
phosphatidylinositol-specific phospholipase C domain-containing protein
COORDINATES: protein motif:HMM:NF039179.1
COORDINATES: similar to AA sequence:RefSeq:WP_013498626.1
COORDINATES: protein motif:HMM:NF025554.2
COORDINATES: similar to AA sequence:RefSeq:WP_012743503.1
COORDINATES: similar to AA sequence:RefSeq:WP_015569082.1
COORDINATES: protein motif:HMM:TIGR01391.1
GO:0003896 - DNA primase activity [Evidence IEA]
GO:0006269 - DNA replication, synthesis of RNA primer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002847207.1
COORDINATES: similar to AA sequence:RefSeq:WP_003425840.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: protein motif:HMM:TIGR00621.2
COORDINATES: similar to AA sequence:RefSeq:WP_005359458.1
COORDINATES: similar to AA sequence:RefSeq:WP_013497815.1
COORDINATES: similar to AA sequence:RefSeq:WP_013497816.1
COORDINATES: protein motif:HMM:NF017538.2
YqiA/YcfP family alpha/beta fold hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_013497818.1
COORDINATES: similar to AA sequence:RefSeq:WP_013497819.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:TIGR02937.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor