Database Authors
Caroline Moore-Kochlacs, SRI International; Peter D. Karp, SRI International
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic program [Karp02, Paley02] on 07-Mar-2005 from the annotated genome of Escherichia coli CFT073 as obtained from the CMR database (version downloaded on Nov-13-2004) [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 TIGR, CMR contains two alternative annotations; PathoLogic used the one created by the sequencing center that sequenced the genome. Please be aware that this version of CMR is missing mRNA genes, which therefore will be missing from this PGDB.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
chromosome5,3795,379005,231,428
Ortholog data available?Yes
Database Contents
Genes5,379
Pathways436
Enzymatic Reactions2,286
Transport Reactions458
Polypeptides5,388
Protein Complexes282
Enzymes1,426
Transporters477
Compounds1,588
Transcription Units3,399
tRNAs4
Growth Media20
Transcriptional Regulation1
Protein Features6,673
GO Annotations29,792
Gene Essentiality Datasets1
Database Version29.6
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Escherichia coli CFT073
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0000663
NCBI-Taxonomy199310
Relationship to Oxygenfacultative
Trophic Levelheterotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
Pathogenicityhuman
Copyright © 2014, SRI International. All rights reserved.

References

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

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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