Runella slithyformis DSM 19594 plasmid pRUNSL04, 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 4 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\nCP002863.1.\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: similar to AA sequence:RefSeq:WP_013930358.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009579784.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012385.2
sigma-54 factor interaction domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019990976.1
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF017935.2
COORDINATES: similar to AA sequence:RefSeq:WP_009284343.1
YeeE/YedE thiosulfate transporter family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015029969.1
COORDINATES: similar to AA sequence:RefSeq:WP_015029968.1
COORDINATES: similar to AA sequence:RefSeq:WP_015029967.1
bifunctional metallophosphatase/5'-nucleotidase
COORDINATES: similar to AA sequence:RefSeq:WP_015029966.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931370.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015027252.1
COORDINATES: similar to AA sequence:RefSeq:WP_013305007.1
COORDINATES: similar to AA sequence:RefSeq:WP_015029964.1
COORDINATES: similar to AA sequence:RefSeq:WP_020597655.1
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009183243.1
COORDINATES: similar to AA sequence:RefSeq:WP_008637793.1
COORDINATES: similar to AA sequence:RefSeq:WP_020604924.1
COORDINATES: similar to AA sequence:RefSeq:WP_015029959.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009284348.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF024751.2
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: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013666971.1
COORDINATES: protein motif:HMM:NF013069.2
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: protein motif:HMM:NF014385.2
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: similar to AA sequence:RefSeq:WP_007808742.1
LytTR family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF018305.2
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF012371.2
serine hydrolase domain-containing protein
COORDINATES: protein motif:HMM:NF012961.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015026390.1