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MMP specifications

Information


Unique identifier OMICS_21569
Name MMP
Alternative name Methanococcus maripaludis S2
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Nitin Baliga
  • person_outline John Leigh

Publication for Methanococcus maripaludis S2

MMP citations

 (7)
library_books

Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes

2015
PLoS One
PMCID: 4529154
PMID: 26252577
DOI: 10.1371/journal.pone.0133990

[…] than average (Z-scores , note Z-score = 0 implies ‘like average’, +1/-1: imply values one standard deviation above/below average) and much higher than the values for their closest taxonomic relative Methanococcus maripaludis S2 [] (Z-scores<-0.5 ) that does not survive in high salt. The same tendency was observed for the other methods and thresholds ( and Tables).The difference in disorder abund […]

call_split

Protein Localization Analysis of Essential Genes in Prokaryotes

2014
Sci Rep
PMCID: 4126397
PMID: 25105358
DOI: 10.1038/srep06001
call_split See protocol

[…] Tb will output the most possible localization site. Because PSORTb 3.0 added the capability of predicting subcellular localizations of archaeal proteins, we can obtain the localization information of Methanococcus maripaludis S2 with this tool. Compared with other localization prediction tools, PSORTb is able to discriminate between Gram-positive and Gram-negative bacteria, which makes it a more s […]

library_books

The structural code of cyanobacterial genomes

2014
Nucleic Acids Res
PMCID: 4132750
PMID: 25056315
DOI: 10.1093/nar/gku641

[…] yanobacterial strains were used, including genomes from a recent sequencing effort (). For comparison we included two enterobacteriaceaeal species (E. coli K-12, Dickeya dadantii 3937), one archaeum (Methanococcus maripaludis S2) and one eukaryote (chromosome IV of Saccharomyces cerevisiae). Only sequences longer than 1 Mb were considered; plasmids and sequences annotated as unfinished were exclud […]

library_books

Comparative Genomics of Gardnerella vaginalis Strains Reveals Substantial Differences in Metabolic and Virulence Potential

2010
PLoS One
PMCID: 2928729
PMID: 20865041
DOI: 10.1371/journal.pone.0012411

[…] within the genome that are orthologous (e-value ≥1×10−5, >70% coverage of the longest gene and >20% sequence ID) to genes that have been shown to be highly expressed in both Escherichia coli K-12 and Methanococcus maripaludis S2 was then constructed in a 59-dimensional plot where each dimension represents each of the synonymous codons, excluding termination codons. Genes found to match any point a […]

call_split

Characterizing the Native Codon Usages of a Genome: An Axis Projection Approach

2010
Mol Biol Evol
PMCID: 3002238
PMID: 20679093
DOI: 10.1093/molbev/msq185
call_split See protocol

[…] n reference genome (or set of diverse reference genomes), all the “high-expression” protein sequences are included in a perl module (our default organisms for this are E. coli K-12 substr. MG1655 and Methanococcus maripaludis S2). The module also includes a list of the identifiers of proteins considered to be highly expressed (see Results). Given the coding sequences of a new genome, we seek the o […]

library_books

Identification and Genomic Analysis of Transcription Factors in Archaeal Genomes Exemplifies Their Functional Architecture and Evolutionary Origin

2010
Mol Biol Evol
PMCID: 2872624
PMID: 20123795
DOI: 10.1093/molbev/msq033

[…] ptions could be observed. The TF repertoire also reflects the main lifestyle of archaea, such as the first cluster that includes mainly methanogenic archaea (such as Methanocaldococcus jannaschii and Methanococcus maripaludis S2 among others). The intermixing of organisms in some clusters might be a consequence of lateral gene transfer events, as has been suggested for archaea included in the four […]

Citations

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MMP institution(s)
Institute for Systems Biology, Seattle, WA, USA; Department of Microbiology, University of Washington, Seattle, WA, USA; Department of Chemical Engineering, University of Washington, Seattle, WA, USA; Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
MMP funding source(s)
Supported by the U.S. Department of Energy, Award Nos. DE-FG02-07ER64327 and DG-FG02-08ER64685; the Office of Science (BER), U.S. Department of Energy, Award No. DE-FG02-08ER64685; and the National Science Foundation MRI, Grant No. 0923536; by the Office of Science, Office of Biological and Environmental Research, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 and by KRIBB and the Korean Ministry of Science, ICT & Future Planning (NRF-2012-C1AAA001-2012M1A2A2026559).

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