Desulfosporosinus acidiphilus SJ4 plasmid pDESACI.01, complete sequence.
Bacteria; Firmicutes; Clostridia; Eubacteriales; Desulfitobacteriaceae; Desulfosporosinus.
Finished plasmid 1 of genome of Desulfosporosinus acidiphilus SJ4
Submitted (01-JUN-2012) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003640.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4092115\nSource DNA and Organism available from Alexander Loy\n(loy@microbial-ecology.net)\nContacts: Alexander Loy (loy@microbial-ecology.net)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nAnnotation by JGI-ORNL\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 :: Desulfosporosinus acidiphilus SJ4, DSM 22704\ncollection_date :: 2010\nlat_lon :: 45.888783 4.605968\ndepth :: Missing\nalt_elev :: Missing\ncountry :: France\nenvironment :: Acid mine, Fresh water, Mud, Sea water, Soil\nnum_replicons :: 3\nref_biomaterial :: DSM 22704\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Obligate anaerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release), VELVET v.\n 1.0.13, Parallel phrap v. 4.24 SPS\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi08592\nFunding Program :: DOE-CSP 2010\nGene Calling Method :: GenePrimp, Prodigal1.4\nIsolation Site :: Acid mining effluent decantation pond;\n France, Chessy les Mines.\nIsolation Comments :: isolated by Alazard et al.\nCell Shape :: Rod-shaped\nMotility :: Motile\nSporulation :: Sporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 37C\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 (pre-release), VELVET v.\n 1.0.13, Parallel phrap v. 4.24 SPS\nGenome Coverage :: 30x\nSequencing Technology :: 454/Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/01/2022 10:09:09\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.1\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,667\nCDSs (total) :: 4,570\nGenes (coding) :: 4,503\nCDSs (with protein) :: 4,503\nGenes (RNA) :: 97\nrRNAs :: 8, 9, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 9, 8 (5S, 16S, 23S)\ntRNAs :: 66\nncRNAs :: 6\nPseudo Genes (total) :: 67\nCDSs (without protein) :: 67\nPseudo Genes (ambiguous residues) :: 0 of 67\nPseudo Genes (frameshifted) :: 36 of 67\nPseudo Genes (incomplete) :: 34 of 67\nPseudo Genes (internal stop) :: 6 of 67\nPseudo Genes (multiple problems) :: 8 of 67\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Desulfosporosinus acidiphilus
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012652.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013632.2
COORDINATES: protein motif:HMM:NF025442.2
COORDINATES: similar to AA sequence:RefSeq:WP_018211981.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - transcription, DNA-templated [Evidence IEA]
COORDINATES: protein motif:HMM:NF025010.2
SurA N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF016047.2
cell wall-binding repeat-containing protein
COORDINATES: protein motif:HMM:NF012632.2
COORDINATES: protein motif:HMM:NF012320.2
COORDINATES: protein motif:HMM:NF024491.2
phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008908358.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF014505.2
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: protein motif:HMM:NF013252.2
COORDINATES: similar to AA sequence:RefSeq:WP_014472594.1
adenylate/guanylate cyclase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003337593.1
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015594552.1
Cthe_2314 family HEPN domain-containing protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF024139.2
COORDINATES: similar to AA sequence:RefSeq:WP_014794920.1
primase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004355968.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR03831.1
COORDINATES: similar to AA sequence:RefSeq:WP_014017799.1
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:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF020952.2
COORDINATES: protein motif:HMM:NF025186.2
COORDINATES: protein motif:HMM:NF024986.2
ATPase involved in chromosome partitioning
COORDINATES: protein motif:HMM:NF012772.2