LOCUS NC_013409 4704 bp DNA circular CON 02-MAY-2023
DEFINITION Methanocaldococcus vulcanius M7 plasmid pMETVU02, complete
sequence.
ACCESSION NC_013409 NZ_ACUW01000000 NZ_ACUW01000001 NZ_ACUW01000002
NZ_ACUW01000003 NZ_ACUW01000004 NZ_ACUW01000005 NZ_ACUW01000006
VERSION NC_013409.1
DBLINK BioProject: PRJNA224116
BioSample: SAMN02598493
Assembly: GCF_000024625.1
KEYWORDS RefSeq.
SOURCE Methanocaldococcus vulcanius M7
ORGANISM Methanocaldococcus vulcanius M7
Archaea; Euryarchaeota; Methanomada group; Methanococci;
Methanococcales; Methanocaldococcaceae; Methanocaldococcus.
REFERENCE 1 (bases 1 to 4704)
AUTHORS Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E.,
Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Lcollab,F.I.,
Brettin,T., Detter,J.C., Han,C., Tapia,R., Kuske,C.R., Schmutz,J.,
Larimer,F., Land,M., Hauser,L., Kyrpides,N., Ovchinikova,G.,
Sieprawska-Lupa,M., Whitman,W.B. and Woyke,T.
CONSRTM US DOE Joint Genome Institute
TITLE Complete sequence of plasmid2 of Methanocaldococcus vulcanius M7
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 4704)
AUTHORS Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Tice,H.,
Bruce,D., Goodwin,L., Pitluck,S., Davenport,K., Detter,J.C.,
Han,C., Tapia,R., Larimer,F., Land,M., Hauser,L., Kyrpides,N.,
Ovchinikova,G., Sieprawska-Lupa,M., Whitman,W.B. and Woyke,T.
CONSRTM US DOE Joint Genome Institute
TITLE Direct Submission
JOURNAL Submitted (06-OCT-2009) US DOE Joint Genome Institute, 2800
Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
COMMENT REFSEQ INFORMATION: The reference sequence is identical to
CP001789.1.
URL -- http://www.jgi.doe.gov
JGI Project ID: 4085125
Source DNA and bacteria available from William B. Whitman
(whitman@uga.edu)
Contacts: William B. Whitman (whitman@uga.edu)
David Bruce (microbe@cuba.jgi-psf.org)
Annotation done by JGI-ORNL and JGI-PGF
Finishing done by JGI-LANL
Finished microbial genomes have been curated to close all gaps with
greater than 98% coverage of at least two independent clones. Each
base pair has a minimum q (quality) value of 30 and the total error
rate is less than one per 50000.
The JGI and collaborators endorse the principles for the
distribution and use of large scale sequencing data adopted by the
larger genome sequencing community and urge users of this data to
follow them. it is our intention to publish the work of this
project in a timely fashion and we welcome collaborative
interaction on the project and analysis.
(http://www.genome.gov/page.cfm?pageID=10506376).
The annotation was added by the NCBI Prokaryotic Genome Annotation
Pipeline (PGAP). Information about PGAP can be found here:
https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
##Metadata-START##
Organism Display Name :: Methanocaldococcus vulcanius M7, DSM 12094
Culture Collection ID :: ATCC 700851, DSM 12094
GOLD Stamp ID :: Gi02049
Greengenes ID :: 17
Isolation Site :: Deep-sea hydrothermal chimney sample
collected on the East Pacific Rise at a
depth of 2600m
Depth :: 2600 meters
Oxygen Requirement :: Anaerobe
Cell Shape :: Coccus-shaped
Motility :: Motile
Sporulation :: Nonsporulating
Temperature Range :: Thermophile
Temperature Optimum :: 49 - 89C
pH :: 6.5
Gram Staining :: gram-
Biotic Relationship :: Free living
Diseases :: None
Habitat :: Deep sea, Marine
Phenotypes :: Piezophile
Energy Source :: Autotroph
##Metadata-END##
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI RefSeq
Annotation Date :: 05/02/2023 01:23:24
Annotation Pipeline :: NCBI Prokaryotic Genome
Annotation Pipeline (PGAP)
Annotation Method :: Best-placed reference protein
set; GeneMarkS-2+
Annotation Software revision :: 6.5
Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA
Genes (total) :: 1,783
CDSs (total) :: 1,738
Genes (coding) :: 1,725
CDSs (with protein) :: 1,725
Genes (RNA) :: 45
rRNAs :: 2, 2, 2 (5S, 16S, 23S)
complete rRNAs :: 2, 2, 2 (5S, 16S, 23S)
tRNAs :: 37
ncRNAs :: 2
Pseudo Genes (total) :: 13
CDSs (without protein) :: 13
Pseudo Genes (ambiguous residues) :: 0 of 13
Pseudo Genes (frameshifted) :: 1 of 13
Pseudo Genes (incomplete) :: 11 of 13
Pseudo Genes (internal stop) :: 1 of 13
CRISPR Arrays :: 17
##Genome-Annotation-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..4704
/organism="Methanocaldococcus vulcanius M7"
/mol_type="genomic DNA"
/strain="M7"
/culture_collection="ATCC:700851"
/type_material="type strain of Methanocaldococcus
vulcanius"
/db_xref="taxon:579137"
/plasmid="pMETVU02"
gene 487..942
/locus_tag="METVU_RS08790"
/old_locus_tag="Metvu_1764"
/db_xref="GeneID:8514137"
CDS 487..942
/locus_tag="METVU_RS08790"
/old_locus_tag="Metvu_1764"
/inference="COORDINATES: ab initio
prediction:GeneMarkS-2+"
/note="Derived by automated computational analysis using
gene prediction method: GeneMarkS-2+."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_012819844.1"
/db_xref="GeneID:8514137"
/translation="MDDNPIVKKLDAITKTLFTIIRSLGIVFITIMIDAIISPSYYSG
FIALTLGVLSFVPILGMVFYGLIDSCLCNLQYEDRIKGLYNFFLEIFQTIIQFGIVGI
GLFLINAYKSNISPKISLAFITTYIVITLLSAVITLLQINKYYEMLKKH"
gene complement(1651..4497)
/locus_tag="METVU_RS08795"
/old_locus_tag="Metvu_1765"
/db_xref="GeneID:8514136"
CDS complement(1651..4497)
/locus_tag="METVU_RS08795"
/old_locus_tag="Metvu_1765"
/inference="COORDINATES: protein motif:HMM:NF012704.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="minichromosome maintenance protein MCM"
/protein_id="WP_012819845.1"
/db_xref="GeneID:8514136"
/translation="MDNYVDSSINNLSNNSDEFEHLNIKIDTIFKQDVKALLGFLKAK
VSNSKDLDRERKFAHNRGLLDDNDFPTKKAINILEILFKLFPDIDFTNIDTIKLIDIT
EIVDKINQIMENNNQIINTELTCINSESENGNSINSDKEVLTCINSESENGNSINSDK
EVLTCINSELIQVNNINNMDKIKSSLNKIKEDIRKLCNELLKKEGVNKSSMPKDAFYD
CINWLLNSSLDFRYIEENIKDLNASLSAYKVTISYLKKIQWIYEDTTGLYKLNVDKFL
SDLNRSGLLKKVEYEKKIATNDYDEETRDRMAGAYEKLVRGFHVDDSGVFRFEFGDGS
LDQYYVSSYLLNNTWHVIDRLQRNYFLNWRKEHVSAIECNNTVLFPLLKCHFTNIPMT
AKEYIQYPDPSKVGKLIVVEAEVLETSPIKNIVICAEYGEEDNPHIEYFDLNTKKIPE
VIKIGSGEDKRELKLIRKYIHTVQEFLLQQPIDELNPKEEPKPIKAVWVGAEGLFDVG
AKVRVVGILDIDKSDRPISPYLIRILSIEEIEEFSHGLSEEDIKIAKDYYNSKKGDLF
RIADDLFPNIVDNELLKVAVLLQLCNVESEPRDGFNWNIHILMVGDPSTGKSRVLKRV
YTLFPNNQYVDLTNATQAGLVGAIEKIKGYLGEVYSFRRGAIPKANGAVLCLDEKNKD
TYKYFNTSMEDGFTKVNKVGRDIHLKTNCAYLWGCNPKREKFDLDRTLTEQIDIPDSI
LSRFDLIFALFNNVKEKEDIKQIVRAIKGGNEKGYVDEDVLKRYILYARTFNPVISDE
IDDFIVDYYYELQGKSEMIDARVIKSLLKLVRAIAKAHLRNEVKKEDFELAKQIYQKY
LDTILYDPESGVYDFGKLGKATKSERDKMDKLIEIIKELSELRDDNLAPQVDIEERAK
ELLGIEGHEVERLLNKLKGEGEVYNPRAGMWGLT"
CONTIG join(CP001789.1:1..4704)
//
