Runella slithyformis DSM 19594 plasmid pRUNSL03, complete sequence.
Bacteria; Bacteroidota; Cytophagia; Cytophagales; Spirosomaceae; Runella.
Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T))
The complete genome of plasmid 3 of Runella slithyformis DSM 19594
Submitted (08-JUN-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002862.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4087357\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\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 :: Runella slithyformis LSU4, DSM 19594\ncollection_date :: Missing\nlat_lon :: 30.46788 -91.129604\ndepth :: Missing\nalt_elev :: Missing\ncountry :: USA\nenvironment :: Fresh water, Host\nnum_replicons :: 6\nref_biomaterial :: DSM 19594, ATCC 29530, LMG 11500, NCIMB\n 11436\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Missing\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi04364\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: Fresh water lake; USA, Louisiana, Baton\n Rouge\nIsolation Comments :: isolated by JM Larkin for Louisiana State\n Univ\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nTemperature Range :: Psychrophile\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 :: 10/05/2022 10:21:24\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) :: 5,864\nCDSs (total) :: 5,813\nGenes (coding) :: 5,779\nCDSs (with protein) :: 5,779\nGenes (RNA) :: 51\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 43\nncRNAs :: 2\nPseudo Genes (total) :: 34\nCDSs (without protein) :: 34\nPseudo Genes (ambiguous residues) :: 0 of 34\nPseudo Genes (frameshifted) :: 16 of 34\nPseudo Genes (incomplete) :: 20 of 34\nPseudo Genes (internal stop) :: 6 of 34\nPseudo Genes (multiple problems) :: 7 of 34\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF018691.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019940771.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009283698.1
COORDINATES: protein motif:HMM:NF013700.2
COORDINATES: protein motif:HMM:NF013395.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF024961.2
COORDINATES: protein motif:HMM:NF024960.2
COORDINATES: protein motif:HMM:TIGR03783.1
GO:0032991 - protein-containing complex [Evidence IEA]
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
GO:0032196 - transposition [Evidence IEA]
TraG family conjugative transposon ATPase
COORDINATES: protein motif:HMM:NF016491.2
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013931215.1
COORDINATES: protein motif:HMM:NF023922.2
COORDINATES: protein motif:HMM:TIGR03780.1
COORDINATES: protein motif:HMM:NF022093.2
COORDINATES: protein motif:HMM:NF022769.2
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: protein motif:HMM:NF039676.1
COORDINATES: similar to AA sequence:RefSeq:WP_008991724.1
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008991723.1
MvaI/BcnI family restriction endonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_018618331.1
COORDINATES: similar to AA sequence:RefSeq:WP_012251330.1
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: protein motif:HMM:NF014825.2
COORDINATES: similar to AA sequence:RefSeq:WP_020607017.1
COORDINATES: similar to AA sequence:RefSeq:WP_008463776.1
COORDINATES: similar to AA sequence:RefSeq:WP_003012767.1
COORDINATES: similar to AA sequence:RefSeq:WP_006255544.1
multiubiquitin domain-containing protein
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: similar to AA sequence:RefSeq:WP_011308721.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF026925.2
COORDINATES: protein motif:HMM:NF039454.1
DUF4097 family beta strand repeat-containing protein
COORDINATES: protein motif:HMM:NF013964.2
COORDINATES: protein motif:HMM:NF019997.2
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019949660.1