Sulfuricurvum kujiense DSM 16994 plasmid pSULKU03, complete sequence.
Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Sulfurimonadaceae; Sulfuricurvum.
Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T))
Submitted (22-NOV-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002358.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4087653\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 :: Sulfuricurvum kujiense YK-1, DSM 16994\ncollection_date :: Missing\nlat_lon :: 40.190524 141.775583\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Japan\nenvironment :: Missing\nnum_replicons :: 5\nref_biomaterial :: DSM 16994, ATCC BAA-921\nbiotic_relationship :: Free living\ntrophic_level :: Chemolithoautotroph\nrel_to_oxygen :: Anaerobe\nisol_growth_condt :: 15545474\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi05071\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2009\nIsolation Site :: Drain water from an underground crude-oil\n storage cavity; Japan, Kuji, Iwate\nCell Shape :: Rod-shaped\nMotility :: Motile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 25C\npH :: 7.0\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 :: 05/02/2023 01:48:21\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,871\nCDSs (total) :: 2,809\nGenes (coding) :: 2,799\nCDSs (with protein) :: 2,799\nGenes (RNA) :: 62\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 4\nPseudo Genes (total) :: 10\nCDSs (without protein) :: 10\nPseudo Genes (ambiguous residues) :: 0 of 10\nPseudo Genes (frameshifted) :: 3 of 10\nPseudo Genes (incomplete) :: 7 of 10\nPseudo Genes (internal stop) :: 1 of 10\nPseudo Genes (multiple problems) :: 1 of 10\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
drain water from underground crude oil storage cavity
COORDINATES: protein motif:HMM:NF013793.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
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_013460166.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
GO:0006281 - DNA repair [Evidence IEA]; GO:0006261 - DNA-templated DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013450019.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449849.1
COORDINATES: similar to AA sequence:RefSeq:WP_013450022.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449851.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449939.1
COORDINATES: similar to AA sequence:RefSeq:WP_004282113.1
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
type I restriction-modification system subunit M/S
COORDINATES: similar to AA sequence:RefSeq:WP_019030056.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
class I SAM-dependent DNA methyltransferase
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003380313.1
COORDINATES: similar to AA sequence:RefSeq:WP_014449557.1
COORDINATES: similar to AA sequence:RefSeq:WP_013175304.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
type I restriction endonuclease subunit R
COORDINATES: protein motif:HMM:NF024668.2
COORDINATES: protein motif:HMM:NF016362.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013450000.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF013676.2
GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011735407.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015547831.1
COORDINATES: similar to AA sequence:RefSeq:WP_011711650.1
COORDINATES: protein motif:HMM:NF013188.2
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015413926.1
COORDINATES: similar to AA sequence:RefSeq:WP_011864796.1
COORDINATES: similar to AA sequence:RefSeq:WP_018925563.1
putative addiction module antidote protein
COORDINATES: similar to AA sequence:RefSeq:WP_014402455.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008339762.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449972.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF013970.2
type II toxin-antitoxin system VapC family toxin
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013449970.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_013449962.1
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_013449959.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449958.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449957.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449956.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449955.1
COORDINATES: similar to AA sequence:RefSeq:WP_013450066.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449953.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449952.1
COORDINATES: protein motif:HMM:NF024872.2