Note_GeneFunctionalAnnotation – GeneFunctionalAnnotation

Name
WID Note_GeneFunctionalAnnotation
Name GeneFunctionalAnnotation
 
Comments
Comments The specific biochemical function of each gene product was compiled starting with the CMR [PUB_0182], NCBI GenBank [PUB_0576], and UniProt [PUB_0096] M. genitalium annotations. In addition to the primary annotations and the primary literature we compiled gene anotations from several databases: Whole-genome annotation – ASAP [PUB_0582] (E. coli), BioCyc [PUB_0006], FIG [PUB_0583], Proteome Analyst [PUB_0584] Transporters – ABCdb [PUB_0580], ABCISSE [PUB_0581], TransportDB [PUB_0440] Carbohydrate-binding modules – CAZy [PUB_0579] Peptidase – MEROPS [PUB_0578] Restriction enzymes – REBASE [PUB_0577] Small non-coding RNAs - [PUB_0576, PUB_0643]
References
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  2. Bostan B, Greiner R, Szafron D, Lu P. Predicting homologous signaling pathways using machine learning. Bioinformatics 25, 2913-20 (2009). WholeCell: PUB_0584, PubMed: 19736253, URL: http://pa.cs.ualberta.ca:8080/pa/

  3. Bouige P, Laurent D, Piloyan L, Dassa E. Phylogenetic and functional classification of ATP-binding cassette (ABC) systems. Curr Protein Pept Sci 3, 541-59 (2002). WholeCell: PUB_0581, PubMed: 12370001, URL: http://www1.pasteur.fr/recherche/unites/pmtg/abc/database.iphtml

  4. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37, D233-8 (2009). WholeCell: PUB_0579, PubMed: 18838391, URL: http://www.cazy.org/

  5. Glasner JD, Liss P, Plunkett G 3rd, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT. ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31, 147-51 (2003). WholeCell: PUB_0582, PubMed: 12519969, URL: http://www.genome.wisc.edu/tools/asap.htm

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  7. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37, D464-70 (2009). WholeCell: PUB_0006, PubMed: 18974181

  8. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33, 5691-702 (2005). WholeCell: PUB_0583, PubMed: 16214803, URL: http://theseed.uchicago.edu/FIG/index.cgi

  9. Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O. The Comprehensive Microbial Resource. Nucleic Acids Res 29, 123-5 (2001). WholeCell: PUB_0182, PubMed: 11125067, URL: http://cmr.jcvi.org/

  10. Quentin Y, Fichant G. ABCdb: an ABC transporter database. J Mol Microbiol Biotechnol 2, 501-4 (2000). WholeCell: PUB_0580, PubMed: 11075924, URL: http://www-abcdb.biotoul.fr/

  11. Rawlings ND, Barrett AJ, Bateman A. MEROPS: the peptidase database. Nucleic Acids Res 38, D227-33 (2010). WholeCell: PUB_0578, PubMed: 19892822, URL: http://merops.sanger.ac.uk/

  12. Ren Q, Chen K, Paulsen IT. TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res 35, D274-9 (2007). WholeCell: PUB_0440, PubMed: 17135193, URL: http://membranetransport.org/

  13. Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38, D234-6 (2010). WholeCell: PUB_0577, PubMed: 19846593, URL: http://rebase.neb.com/rebase/rebase.html

  14. UniProt Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37, D169-74 (2009). WholeCell: PUB_0096, PubMed: 18836194, URL: http://www.uniprot.org/uniprot/

  15. Ushida C, Izawa D, Muto A. RNase P RNA of Mycoplasma capricolum. Mol Biol Rep 22, 125-9 (1995). WholeCell: PUB_0643, PubMed: 8901498

 
Metadata
Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:57