Database Authors
Pallavi Kaipa1, Peter D Karp1, Tomer Altman1, Ingrid Keseler1, Alex Shearer1, Ron Caspi1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 14-May-2010 by the PathoLogic program [Karp02, Paley02, Karp05, Caspi10] using Pathway Tools software version 14.5 and MetaCyc version 14.1 from the annotated genome of Escherichia coli K-12 substr. W3110 as obtained from the CMR database (version downloaded on March 15th 2010) [Peterson01]. The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

For genomes not sequenced at the J. Craig Venter Institute, CMR contains two alternative annotations; PathoLogic used as its input the annotation created by the sequencing center that sequenced the genome. Please be aware that some genomes in this version of CMR are missing RNA genes. Therefore, this PGDB may be missing RNA genes.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 14,4704,247138854,646,332
Ortholog data available?Yes
Database Contents
Genes4,471
Pathways353
Enzymatic Reactions2,141
Transport Reactions642
Polypeptides4,330
Protein Complexes361
Enzymes1,418
Transporters475
Compounds1,365
Transcription Units2,923
tRNAs87
Protein Features6,149
GO Terms35,136
Database Version29.0
Synonyms Escherichia coli K-12 substr. W3110
Escherichia coli str. K12 substr. W3110
Escherichia coli str. W3110
Escherichia coli strain W3110
Escherichia coli str. K-12 substr. W3110
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Escherichia coli K-12
Escherichia coli K-12 substr. W3110
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0000380
NCBI-Taxonomy316407
Copyright © 2012, 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

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

Karp05: Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N (2005). "Expansion of the BioCyc collection of pathway/genome databases to 160 genomes." Nucleic Acids Research 33(19):6083-6089. PMID: 16246909

Paley02: Paley SM, Karp PD (2002). "Evaluation of computational metabolic-pathway predictions for Helicobacter pylori." Bioinformatics 18:715-24. PMID: 12050068

Peterson01: Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O (2001). "The Comprehensive Microbial Resource." Nucleic Acids Res 29(1);123-5. PMID: 11125067

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