Calditerrivibrio nitroreducens DSM 19672 plasmid pCALNI01, complete sequence.
Calditerrivibrio nitroreducens DSM 19672
Bacteria; Deferribacteres; Deferribacterales; Calditerrivibrionaceae.
Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1)
The complete genome of plasmid of Calditerrivibrio nitroreducens DSM 19672
Submitted (18-NOV-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002348.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4087656\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 :: Calditerrivibrio nitroreducens Yu37-1, DSM\n 19672\ncollection_date :: Missing\nlat_lon :: 36.829513 138.217163\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Japan\nenvironment :: Host\nnum_replicons :: 2\nref_biomaterial :: DSM 19672, NBRC 101217\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Anaerobe\nisol_growth_condt :: 18599715\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi04007\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: Terrestrial hot spring; Japan, Nagano,\n Yumata\nCell Shape :: Vibrio-shaped\nMotility :: Motile\nSporulation :: Nonsporulating\nTemperature Range :: Thermophile\nTemperature Optimum :: 55C\npH :: 7.0 - 7.5\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 :: Illumina, 454\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/22/2022 10:23:30\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) :: 2,185\nCDSs (total) :: 2,134\nGenes (coding) :: 2,114\nCDSs (with protein) :: 2,114\nGenes (RNA) :: 51\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 41\nncRNAs :: 4\nPseudo Genes (total) :: 20\nCDSs (without protein) :: 20\nPseudo Genes (ambiguous residues) :: 0 of 20\nPseudo Genes (frameshifted) :: 4 of 20\nPseudo Genes (incomplete) :: 16 of 20\nPseudo Genes (internal stop) :: 3 of 20\nPseudo Genes (multiple problems) :: 2 of 20\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Calditerrivibrio nitroreducens
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF015927.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024627.2
right-handed parallel beta-helix repeat-containing protein
COORDINATES: protein motif:HMM:NF012570.2
COORDINATES: similar to AA sequence:RefSeq:WP_013638242.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015954950.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011963633.1
COORDINATES: similar to AA sequence:RefSeq:WP_013447272.1
COORDINATES: protein motif:HMM:NF016906.2
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013452131.1
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:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012675491.1
COORDINATES: similar to AA sequence:RefSeq:WP_009295176.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF012529.2
COORDINATES: similar to AA sequence:RefSeq:WP_012003439.1
COORDINATES: similar to AA sequence:RefSeq:WP_015419284.1
COORDINATES: similar to AA sequence:RefSeq:WP_013447288.1
IS256-like element ISCni1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_020251215.1
COORDINATES: similar to AA sequence:RefSeq:WP_020251214.1
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: similar to AA sequence:RefSeq:WP_013447298.1
COORDINATES: similar to AA sequence:RefSeq:WP_013447299.1
COORDINATES: similar to AA sequence:RefSeq:WP_013008756.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_013008755.1
GO:0042242 - cobyrinic acid a,c-diamide synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013008754.1
COORDINATES: similar to AA sequence:RefSeq:WP_013008753.1
COORDINATES: similar to AA sequence:RefSeq:WP_013008752.1
COORDINATES: similar to AA sequence:RefSeq:WP_013008751.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013008750.1
GO:0004851 - uroporphyrin-III C-methyltransferase activity [Evidence IEA]
GO:0019354 - siroheme biosynthetic process [Evidence IEA]
uroporphyrinogen-III C-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_013008749.1
GO:0030788 - precorrin-2 C20-methyltransferase activity [Evidence IEA]
GO:0009236 - cobalamin biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013008748.1
COORDINATES: similar to AA sequence:RefSeq:WP_013008747.1
GO:0016994 - precorrin-6A reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013008742.1
histidinol-phosphate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013008741.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013008740.1
GO:0016880 - acid-ammonia (or amide) ligase activity [Evidence IEA]
adenosylcobinamide-phosphate synthase CbiB
COORDINATES: similar to AA sequence:RefSeq:WP_013008739.1
bifunctional precorrin-2 dehydrogenase/sirohydrochlorin ferrochelatase
COORDINATES: similar to AA sequence:RefSeq:WP_013447314.1
cobalt-precorrin-5B (C(1))-methyltransferase CbiD
COORDINATES: similar to AA sequence:RefSeq:WP_013008737.1
GO:0046025 - precorrin-6Y C5,15-methyltransferase (decarboxylating) activity [Evidence IEA]
GO:0046140 - corrin biosynthetic process [Evidence IEA]
precorrin-6y C5,15-methyltransferase (decarboxylating) subunit CbiE
COORDINATES: similar to AA sequence:RefSeq:WP_013008736.1
GO:0046026 - precorrin-4 C11-methyltransferase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013008735.1
COORDINATES: similar to AA sequence:RefSeq:WP_017752760.1
GO:0030789 - precorrin-3B C17-methyltransferase activity [Evidence IEA]