Database 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 Escherichia coli O157:H- str. 493-89 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.

Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Escherichia coli O157:H- str. 493-89 ECO9389_50, whole genome49248930528,573RefSeq:AETY01000156
Escherichia coli O157:H- str. 493-89 ECO9389_207, whole genome34433680393,568RefSeq:AETY01000104
Escherichia coli O157:H- str. 493-89 ECO9389_192, whole genome28427770286,459RefSeq:AETY01000087
Escherichia coli O157:H- str. 493-89 ECO9389_193, whole genome27026910272,104RefSeq:AETY01000088
Escherichia coli O157:H- str. 493-89 ECO9389_115, whole genome26426130251,979RefSeq:AETY01000017
Escherichia coli O157:H- str. 493-89 ECO9389_183, whole genome21821350241,866RefSeq:AETY01000078
Escherichia coli O157:H- str. 493-89 ECO9389_23, whole genome15415400184,975RefSeq:AETY01000126
Escherichia coli O157:H- str. 493-89 ECO9389_157, whole genome15315120170,397RefSeq:AETY01000055
Escherichia coli O157:H- str. 493-89 ECO9389_1, whole genome14614600168,853RefSeq:AETY01000001
Escherichia coli O157:H- str. 493-89 ECO9389_40, whole genome13612970151,411RefSeq:AETY01000145
Escherichia coli O157:H- str. 493-89 ECO9389_198, whole genome13813800145,655RefSeq:AETY01000093
Escherichia coli O157:H- str. 493-89 ECO9389_104, whole genome13713520144,145RefSeq:AETY01000006
Escherichia coli O157:H- str. 493-89 ECO9389_21, whole genome10710610121,314RefSeq:AETY01000107
Escherichia coli O157:H- str. 493-89 ECO9389_63, whole genome11111100114,636RefSeq:AETY01000169
Escherichia coli O157:H- str. 493-89 ECO9389_80, whole genome969600113,861RefSeq:AETY01000188
Escherichia coli O157:H- str. 493-89 ECO9389_155, whole genome87870098,969RefSeq:AETY01000053
Escherichia coli O157:H- str. 493-89 ECO9389_153, whole genome80791096,480RefSeq:AETY01000051
Escherichia coli O157:H- str. 493-89 ECO9389_156, whole genome87825092,580RefSeq:AETY01000054
Escherichia coli O157:H- str. 493-89 ECO9389_200, whole genome93849091,806RefSeq:AETY01000097
Escherichia coli O157:H- str. 493-89 ECO9389_182, whole genome85823082,229RefSeq:AETY01000077
Escherichia coli O157:H- str. 493-89 ECO9389_79, whole genome71710079,007RefSeq:AETY01000186
Escherichia coli O157:H- str. 493-89 ECO9389_181, whole genome75732074,502RefSeq:AETY01000076
Escherichia coli O157:H- str. 493-89 ECO9389_196, whole genome69681074,257RefSeq:AETY01000091
Escherichia coli O157:H- str. 493-89 ECO9389_194, whole genome60591067,876RefSeq:AETY01000089
Escherichia coli O157:H- str. 493-89 ECO9389_201, whole genome52502058,351RefSeq:AETY01000098
Escherichia coli O157:H- str. 493-89 ECO9389_2, whole genome53521058,350RefSeq:AETY01000095
Escherichia coli O157:H- str. 493-89 ECO9389_42, whole genome50491050,248RefSeq:AETY01000147
Escherichia coli O157:H- str. 493-89 ECO9389_204, whole genome39381044,515RefSeq:AETY01000101
Escherichia coli O157:H- str. 493-89 ECO9389_140, whole genome35350042,220RefSeq:AETY01000040
Escherichia coli O157:H- str. 493-89 ECO9389_3, whole genome38344038,866RefSeq:AETY01000133
Escherichia coli O157:H- str. 493-89 ECO9389_51, whole genome45441038,796RefSeq:AETY01000157
Escherichia coli O157:H- str. 493-89 ECO9389_24, whole genome38371037,179RefSeq:AETY01000127
Escherichia coli O157:H- str. 493-89 ECO9389_154, whole genome32320035,729RefSeq:AETY01000052
Escherichia coli O157:H- str. 493-89 ECO9389_202, whole genome38380034,808RefSeq:AETY01000099
Escherichia coli O157:H- str. 493-89 ECO9389_206, whole genome29281031,536RefSeq:AETY01000103
Escherichia coli O157:H- str. 493-89 ECO9389_227, whole genome31310031,006RefSeq:AETY01000125
Escherichia coli O157:H- str. 493-89 ECO9389_133, whole genome23185028,883RefSeq:AETY01000033
Escherichia coli O157:H- str. 493-89 ECO9389_44, whole genome28271028,562RefSeq:AETY01000149
Escherichia coli O157:H- str. 493-89 ECO9389_167, whole genome32311027,955RefSeq:AETY01000061
Escherichia coli O157:H- str. 493-89 ECO9389_165, whole genome29281026,384RefSeq:AETY01000059
Escherichia coli O157:H- str. 493-89 ECO9389_46, whole genome29290021,718RefSeq:AETY01000151
Escherichia coli O157:H- str. 493-89 ECO9389_142, whole genome22220018,729RefSeq:AETY01000042
Escherichia coli O157:H- str. 493-89 ECO9389_4, whole genome15150015,851RefSeq:AETY01000144
Escherichia coli O157:H- str. 493-89 ECO9389_5, whole genome16151013,938RefSeq:AETY01000155
Escherichia coli O157:H- str. 493-89 ECO9389_135, whole genome14140011,659RefSeq:AETY01000035
Escherichia coli O157:H- str. 493-89 ECO9389_109, whole genome17170011,436RefSeq:AETY01000010
Escherichia coli O157:H- str. 493-89 ECO9389_95, whole genome1313007,488RefSeq:AETY01000201
157 Undisplayed Contigs/Replicons471445260293,115
Total:4,9464,83810805,054,824
Ortholog data available?Yes
Database Contents
Genes4,946
Pathways500
Enzymatic Reactions2,009
Transport Reactions429
Polypeptides4,846
Protein Complexes290
Enzymes1,353
Transporters508
Compounds1,366
Transcription Units3,226
tRNAs85
GO Terms19,130
Database Version29.1
Synonyms Escherichia coli O157:H- str. 493/89
Escherichia coli O157:H- strain 493-89
Escherichia coli O157:H- str. 493-89
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Escherichia coli O157:H-
Escherichia coli O157:H- str. 493-89
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI-Taxonomy926027

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(Database issue);D742-53. 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 Pathway Tools version 29.0 (software by SRI International) on Fri Oct 31, 2025, BIOCYC18A.