Database Authors
Dan Weaver1, Pallavi Subhraveti1, Quang Ong1, Tim Holland1, Anamika Kothari1, Ingrid Keseler1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 10-Aug-2014 by the PathoLogic program [Karp02, Dale10, Karp11, Caspi12] using Pathway Tools software version 18.5 and MetaCyc version 18.5 from the annotated genome of Methanobrevibacter smithii ATCC 35061 as obtained from RefSeq.

The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation for the generation of a metabolic model.

Development of this PGDB was supported by grant GM080746 from the NIH.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_009515 chromosome1,8371,7934401,853,160
Ortholog data available?Yes
Database Contents
Genes1,837
Pathways172
Enzymatic Reactions863
Transport Reactions59
Polypeptides1,794
Protein Complexes49
Enzymes549
Transporters104
Compounds732
Transcription Units1,043
tRNAs36
Protein Features2,067
GO Terms7,151
Database Version29.0
Synonyms Methanobrevibacter smithii str. ATCC 35061
Methanobrevibacter smithii strain ATCC 35061
Methanobrevibacter smithii ATCC 35061
Taxonomic Lineage cellular organisms
Archaea
Euryarchaeota
Methanomada group
Methanobacteria
Methanobacteriales
Methanobacteriaceae
Methanobrevibacter
Methanobrevibacter smithii
Methanobrevibacter smithii ATCC 35061
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLDGp0000134
NCBI BioProjectPRJNA58827
NCBI-Taxonomy420247
NCBI Genome Typerepresentative

References

Caspi12: Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD (2012). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases." Nucleic Acids Res 40(D1);D742-D753. PMID: 22102576

Dale10: Dale JM, Popescu L, Karp PD (2010). "Machine learning methods for metabolic pathway prediction." BMC Bioinformatics 11;15. PMID: 20064214

Karp02: Karp PD, Paley S, Romero P (2002). "The Pathway Tools software." Bioinformatics 18 Suppl 1;S225-32. PMID: 12169551

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

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