Runella slithyformis DSM 19594 plasmid pRUNSL02, 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 2 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\nCP002861.1.\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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019990976.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024961.2
COORDINATES: similar to AA sequence:RefSeq:WP_019990981.1
COORDINATES: similar to AA sequence:RefSeq:WP_015056736.1
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:NF019478.2
COORDINATES: similar to AA sequence:RefSeq:WP_019990986.1
COORDINATES: protein motif:HMM:NF023922.2
COORDINATES: similar to AA sequence:RefSeq:WP_015056729.1
COORDINATES: similar to AA sequence:RefSeq:WP_019990990.1
COORDINATES: similar to AA sequence:RefSeq:WP_012925459.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012473532.1
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_013621941.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002679706.1
COORDINATES: similar to AA sequence:RefSeq:WP_018910657.1
HipA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007897914.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: similar to AA sequence:RefSeq:WP_013925937.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013925938.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014114348.1
SprT family zinc-dependent metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_014114349.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014114351.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_015808498.1
COORDINATES: similar to AA sequence:RefSeq:WP_013927380.1
COORDINATES: similar to AA sequence:RefSeq:WP_002985109.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018344002.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_015752956.1
GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]; GO:0043682 - P-type divalent copper transporter activity [Evidence IEA]
GO:0006825 - copper ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015056769.1
COORDINATES: similar to AA sequence:RefSeq:WP_008610789.1
nuclear transport factor 2 family protein
COORDINATES: protein motif:HMM:NF023255.2
COORDINATES: similar to AA sequence:RefSeq:WP_008130145.1
COORDINATES: similar to AA sequence:RefSeq:WP_002996045.1
GDCCVxC domain-containing (seleno)protein
COORDINATES: similar to AA sequence:RefSeq:WP_013768913.1
COORDINATES: similar to AA sequence:RefSeq:WP_012158942.1
COORDINATES: protein motif:HMM:NF022588.2
COORDINATES: similar to AA sequence:RefSeq:WP_013868941.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931245.1
COORDINATES: protein motif:HMM:TIGR01730.1
COORDINATES: protein motif:HMM:NF027890.2
COORDINATES: protein motif:HMM:NF014385.2
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018343261.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018622797.1
COORDINATES: similar to AA sequence:RefSeq:WP_013928916.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931295.1
GO:0005507 - copper ion binding [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004917545.1
COORDINATES: similar to AA sequence:RefSeq:WP_013921609.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012924787.1
COORDINATES: similar to AA sequence:RefSeq:WP_020598441.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF033545.0
COORDINATES: similar to AA sequence:RefSeq:WP_015026383.1
COORDINATES: protein motif:HMM:NF037736.2
COORDINATES: protein motif:HMM:NF041078.1
COORDINATES: protein motif:HMM:NF041079.1
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: protein motif:HMM:NF016724.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF020558.2
COORDINATES: similar to AA sequence:RefSeq:WP_015056713.1
COORDINATES: similar to AA sequence:RefSeq:WP_015056712.1
COORDINATES: similar to AA sequence:RefSeq:WP_019991008.1
COORDINATES: similar to AA sequence:RefSeq:WP_019976171.1
COORDINATES: similar to AA sequence:RefSeq:WP_020527108.1
COORDINATES: similar to AA sequence:RefSeq:WP_013764287.1
COORDINATES: similar to AA sequence:RefSeq:WP_015056709.1