Methanocaldococcus fervens AG86 plasmid pMEFER01, complete sequence.
Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales; Methanocaldococcaceae; Methanocaldococcus.
Complete sequence of plasmid of Methanocaldococcus fervens AG86
Submitted (10-AUG-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001697.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4085029\nSource DNA and organism available from William B. Whitman\n(whitman@uga.edu)\nContacts: William B. Whitman (whitman@uga.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\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##Metadata-START##\nOrganism Display Name :: Methanocaldococcus fervens AG86\nCulture Collection ID :: DSM 4213\nGOLD Stamp ID :: Gi02047\nGreengenes ID :: 16\nIsolation Site :: Deep-sea hydrothermal chimney sample\n collected on the East Pacific Rise at a\n depth of 2600m\nDepth :: 2600m\nOxygen Requirement :: Anaerobe\nCell Shape :: Coccus-shaped\nMotility :: Motile\nSporulation :: Nonsporulating\nTemperature Range :: Thermophile\nTemperature Optimum :: 49 - 89C\npH :: 6.5\nGram Staining :: gram-\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Deep sea, Marine\nPhenotypes :: Methanogen, Piezophile\nEnergy Source :: Autotroph, Lithotroph\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/02/2023 01:19:10\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) :: 1,662\nCDSs (total) :: 1,617\nGenes (coding) :: 1,595\nCDSs (with protein) :: 1,595\nGenes (RNA) :: 45\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 37\nncRNAs :: 2\nPseudo Genes (total) :: 22\nCDSs (without protein) :: 22\nPseudo Genes (ambiguous residues) :: 0 of 22\nPseudo Genes (frameshifted) :: 15 of 22\nPseudo Genes (incomplete) :: 6 of 22\nPseudo Genes (internal stop) :: 6 of 22\nPseudo Genes (multiple problems) :: 4 of 22\nCRISPR Arrays :: 7\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Methanocaldococcus fervens
COORDINATES: similar to AA sequence:RefSeq:WP_012980720.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012980721.1
COORDINATES: similar to AA sequence:RefSeq:WP_012980722.1
COORDINATES: similar to AA sequence:RefSeq:WP_012980723.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013798663.1
COORDINATES: similar to AA sequence:RefSeq:WP_012980726.1
COORDINATES: similar to AA sequence:RefSeq:WP_013180903.1
COORDINATES: protein motif:HMM:NF019911.2
COORDINATES: similar to AA sequence:RefSeq:WP_010885284.1
COORDINATES: similar to AA sequence:RefSeq:WP_012980731.1
COORDINATES: similar to AA sequence:RefSeq:WP_010869854.1
COORDINATES: similar to AA sequence:RefSeq:WP_015732841.1
COORDINATES: similar to AA sequence:RefSeq:WP_012980695.1
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_010870057.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013798675.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013798674.1
COORDINATES: similar to AA sequence:RefSeq:WP_012980717.1
COORDINATES: similar to AA sequence:RefSeq:WP_013798670.1
COORDINATES: similar to AA sequence:RefSeq:WP_012980719.1