Leigh Lab : Genome
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John Leigh, Ph.D.

Methanococcus maripaludis Genome

Methanococcus maripaludis possesses a small, circular genome of 1.66 Mb in length with no extrachromosomal elements. The genome has a low, 33%, GC content. Open reading frame predictions indicate 1722 orfs. The maripaludis genome is relatively simple with few repeated sequences, though it contains three copies of the 16S and 23S ribosomal genes. Interestingly, while the genome of the closely related Methanocaldococcus jannaschii contains a number of inteins, maripaludis appears to lack inteins entirely, even in orfs that are otherwise highly homologous to their M. jannashii counterparts.

M.Maripaludis genome The complete M. maripaludis genome sequence is available at NCBI, and its accession number is NC_005791. The sequence was obtained at the University of Washington Genome Center under the direction of Maynard Olson. The computational phase of the annotation was carried out at the Oak Ridge National Laboratory under the supervision of Frank Larimer.

We regularly update the M. maripaludis genome annotation, and our latest version (October 6, 2006) can be downloaded here. This file can be read as a text file, or it can be opened for graphical viewing using Artemis. Also, more information can be obtained by reading our genome paper entitled "Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis".

Whether you open the genome file with a text editor or Artemis, you will see the following entries:

Entries under "CDS": Coding sequence (nucleotide interval, and "complement" if coding is on complementary strand)

/locus_tag: the ORF number, MmpXXXX
/gene: the gene designation or the ORF number
/EC_number: Enzyme Commission number
/evidence: not experimental (inferred by informatics) or experimentally verified
/function: explanation of function
/product: identification of protein or enzyme
/note: notes, including literature references used for annotation
/colour: indicates functional category as follows:
    1 (black) = other
    2 (red) = replication and repair
    3 (green) = energy metabolism
    4 (blue) = carbohydrate metabolism
    5 (cyan) = lipid metabolism
    6 (magenta) = transcription
    7 (yellow) = translation
    9 (sky blue) = cellular processes
    10 (orange) = amino acid metabolism
    11 (brown) = unassigned
    12 (pink) = cofactor metabolism
    13 (light grey) = conserved hypothetical protein
    14 (black) = transport
    15 (dull red) = signal transduction
    16 (light red) = nucleotide metabolism
/blastp_match: actually, not blastp match, but special notes made by the annotator, including the TIGR functional category and subcategory
/translation: translation

Entries under "gene": Coding sequence (nucleotide interval, and "complement" if coding is on complementary strand)

/locus_tag: : the ORF number, MmpXXXX
/gene: the gene designation
/colour: indicates functional category as above

Entries under "rRNA", "tRNA", and "misc_RNA"

/evidence: not experimental (inferred by informatics) or experimentally verified
/gene: the gene designation
/product: identification of the RNA
/locus_tag: the RNA number
/colour: 8 (pale green) = RNA

misc_feature: probable trans-membrane helices predicted by TMHMM2.0
sig_peptide: probable signal peptide predicted by SignalP 2.0 HMM

More About Methanococcus maripaludis