Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Summary of Aquifex aeolicus, Strain VF5, version 18.5

Authors: 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 by the PathoLogic program [Karp02, Dale10, Karp11, Caspi12] using Pathway Tools software version 18.5 and MetaCyc version 18.5 on 10-Aug-2014 18:43:19 from the annotated genome of Aquifex aeolicus VF5 as obtained from RefSeq.

This BioCyc Tier 3 PGDB was computationally generated. It has not undergone any manual curation nor manual review, and thus may contain errors. Development of this PGDB was supported by grant GM080746 from the NIH.

Taxonomic lineage: cellular organisms , Bacteria , Aquificae , Aquificae , Aquificales , Aquificaceae , Aquifex , Aquifex aeolicus , Aquifex aeolicus VF5

Unification Links: GOLD:0000776 , NCBI BioProject:PRJNA57765 , NCBI-Taxonomy:224324

RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_000918 chromosome1548149850141,551,335
NC_001880 plasmid29290039,456
Total:1589152750141,590,791

Pathways:171
Enzymatic Reactions:947
Transport Reactions:16
Polypeptides:1529
Protein Complexes:3
Enzymes:494
Transporters:31
Compounds:685
Transcription Units:758
tRNAs:44

Genetic Code Number:
11 -- Bacterial and Plant Plastid (same as Standard, except for alternate initiation codons)

PGDB Unique ID: JBH


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


Report Errors or Provide Feedback
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 28, 2014, biocyc14.