Database Authors
Pallavi Subhraveti1, Tomer Altman1, Ingrid Keseler1, Alexander Shearer, Ron Caspi1, Quang Ong1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic program [Karp02, Dale10, Caspi10] using Pathway Tools software version 15.5 and MetaCyc version 15.1 on 12-Jul-2011 18:43:19 from the annotated genome of Escherichia coli B str. REL606 as obtained from RefSeq [Sayers09]. The PGDB integrate the biochemical reaction network and metabolic pathways of the organism with its genome.

The PGDB has undergone modest curation focusing primarily on the differences between this organism and Escherichia coli K-12 substr. MG1655. The majority of the information within this database has not been manually reviewed.

Differences between Escherichia coli B str. REL606 and Escherichia coli K-12 substr. MG1655 were manually reviewed by the SRI PortEco group in late 2012. The major differences appear to be a lack of the paa operon genes in Escherichia coli B str. REL606. This operon codes for at least 10 enzymes responsible for phenylethylamine and phenylacetate degradation.

O antigen building block biosynthesis lacks the glf gene and carnitine degradation may also be deficient in this strain, as one of the genes involved in the pathway appears to be a pseudogene.

Development of this database was supported by grant GM088849 from the National Institutes of Health.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 14,3664,203107564,629,812RefSeq:254160123
Ortholog data available?Yes
Database Contents
Genes4,366
Pathways368
Enzymatic Reactions2,129
Transport Reactions638
Polypeptides4,266
Protein Complexes338
Enzymes1,390
Transporters471
Compounds1,582
Transcription Units2,823
tRNAs85
Growth Media383
Protein Features6,090
Phenotype Microarray Datasets1
GO Terms24,294
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Escherichia coli B str. REL606
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0002253
NCBI BioProject58803
NCBI-Taxonomy413997
Copyright © 2011, SRI International. All rights reserved.

References

Caspi10: Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley SM, Popescu L, Pujar A, Shearer A, Zhang P, Karp PD (2010). "The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of pathway/Genome Databases." Nucleic Acids Research 38(Database issue):D473-479. PMID: 19850718

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

Karp02: Karp PD, Paley SM, Romero P (2002). "The Pathway Tools Software." Bioinformatics 18:S225-32. PMID: 12169551

Sayers09: Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). "Database resources of the National Center for Biotechnology Information." Nucleic Acids Res 37(Database issue);D5-15. PMID: 18940862

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC14.