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. H 2687 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. H 2687 ECO2687_53, whole genome39138830425,325RefSeq:AETZ01000161
Escherichia coli O157:H- str. H 2687 ECO2687_212, whole genome34333580393,513RefSeq:AETZ01000110
Escherichia coli O157:H- str. H 2687 ECO2687_165, whole genome28527870316,237RefSeq:AETZ01000062
Escherichia coli O157:H- str. H 2687 ECO2687_198, whole genome28027460286,239RefSeq:AETZ01000093
Escherichia coli O157:H- str. H 2687 ECO2687_199, whole genome27026910272,099RefSeq:AETZ01000094
Escherichia coli O157:H- str. H 2687 ECO2687_124, whole genome26726430251,962RefSeq:AETZ01000025
Escherichia coli O157:H- str. H 2687 ECO2687_190, whole genome21721250241,867RefSeq:AETZ01000086
Escherichia coli O157:H- str. H 2687 ECO2687_1, whole genome19819710227,236RefSeq:AETZ01000001
Escherichia coli O157:H- str. H 2687 ECO2687_23, whole genome15515500184,368RefSeq:AETZ01000129
Escherichia coli O157:H- str. H 2687 ECO2687_43, whole genome13512870151,360RefSeq:AETZ01000151
Escherichia coli O157:H- str. H 2687 ECO2687_204, whole genome14013910145,857RefSeq:AETZ01000101
Escherichia coli O157:H- str. H 2687 ECO2687_112, whole genome13913720142,965RefSeq:AETZ01000013
Escherichia coli O157:H- str. H 2687 ECO2687_164, whole genome11411310132,216RefSeq:AETZ01000061
Escherichia coli O157:H- str. H 2687 ECO2687_22, whole genome10810710121,349RefSeq:AETZ01000118
Escherichia coli O157:H- str. H 2687 ECO2687_73, whole genome10910900114,648RefSeq:AETZ01000182
Escherichia coli O157:H- str. H 2687 ECO2687_91, whole genome979700113,801RefSeq:AETZ01000202
Escherichia coli O157:H- str. H 2687 ECO2687_60, whole genome87870093,893RefSeq:AETZ01000168
Escherichia coli O157:H- str. H 2687 ECO2687_206, whole genome92848091,491RefSeq:AETZ01000103
Escherichia coli O157:H- str. H 2687 ECO2687_189, whole genome86824082,350RefSeq:AETZ01000084
Escherichia coli O157:H- str. H 2687 ECO2687_88, whole genome72720079,069RefSeq:AETZ01000198
Escherichia coli O157:H- str. H 2687 ECO2687_188, whole genome75732074,513RefSeq:AETZ01000083
Escherichia coli O157:H- str. H 2687 ECO2687_202, whole genome69681074,281RefSeq:AETZ01000099
Escherichia coli O157:H- str. H 2687 ECO2687_200, whole genome60591067,925RefSeq:AETZ01000097
Escherichia coli O157:H- str. H 2687 ECO2687_207, whole genome52502058,315RefSeq:AETZ01000104
Escherichia coli O157:H- str. H 2687 ECO2687_44, whole genome48480050,393RefSeq:AETZ01000152
Escherichia coli O157:H- str. H 2687 ECO2687_166, whole genome41410045,759RefSeq:AETZ01000063
Escherichia coli O157:H- str. H 2687 ECO2687_209, whole genome39381044,558RefSeq:AETZ01000106
Escherichia coli O157:H- str. H 2687 ECO2687_151, whole genome35350042,220RefSeq:AETZ01000051
Escherichia coli O157:H- str. H 2687 ECO2687_2, whole genome38344038,842RefSeq:AETZ01000095
Escherichia coli O157:H- str. H 2687 ECO2687_61, whole genome47461038,771RefSeq:AETZ01000169
Escherichia coli O157:H- str. H 2687 ECO2687_25, whole genome36351037,122RefSeq:AETZ01000132
Escherichia coli O157:H- str. H 2687 ECO2687_208, whole genome38380034,826RefSeq:AETZ01000105
Escherichia coli O157:H- str. H 2687 ECO2687_211, whole genome29281031,250RefSeq:AETZ01000109
Escherichia coli O157:H- str. H 2687 ECO2687_230, whole genome31310030,970RefSeq:AETZ01000130
Escherichia coli O157:H- str. H 2687 ECO2687_46, whole genome31274028,930RefSeq:AETZ01000154
Escherichia coli O157:H- str. H 2687 ECO2687_144, whole genome23185028,914RefSeq:AETZ01000044
Escherichia coli O157:H- str. H 2687 ECO2687_173, whole genome29272026,491RefSeq:AETZ01000067
Escherichia coli O157:H- str. H 2687 ECO2687_175, whole genome30291026,217RefSeq:AETZ01000069
Escherichia coli O157:H- str. H 2687 ECO2687_48, whole genome29290021,773RefSeq:AETZ01000156
Escherichia coli O157:H- str. H 2687 ECO2687_153, whole genome22220018,705RefSeq:AETZ01000053
Escherichia coli O157:H- str. H 2687 ECO2687_3, whole genome16160015,840RefSeq:AETZ01000137
Escherichia coli O157:H- str. H 2687 ECO2687_4, whole genome16151013,963RefSeq:AETZ01000147
Escherichia coli O157:H- str. H 2687 ECO2687_182, whole genome17170013,248RefSeq:AETZ01000077
Escherichia coli O157:H- str. H 2687 ECO2687_146, whole genome14140011,726RefSeq:AETZ01000046
Escherichia coli O157:H- str. H 2687 ECO2687_118, whole genome17170011,418RefSeq:AETZ01000018
Escherichia coli O157:H- str. H 2687 ECO2687_103, whole genome1515008,262RefSeq:AETZ01000006
Escherichia coli O157:H- str. H 2687 ECO2687_78, whole genome1411307,213RefSeq:AETZ01000187
162 Undisplayed Contigs/Replicons442420220277,904
Total:4,9384,82811005,048,194
Ortholog data available?Yes
Database Contents
Genes4,938
Pathways500
Enzymatic Reactions2,003
Transport Reactions429
Polypeptides4,836
Protein Complexes292
Enzymes1,348
Transporters507
Compounds1,365
Transcription Units3,219
tRNAs87
GO Annotations19,077
Database Version29.6
Synonyms Escherichia coli O157:H- strain H 2687
Escherichia coli O157:H- str. H 2687
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Escherichia coli O157:H-
Escherichia coli O157:H- str. H 2687
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0009843
NCBI-Taxonomy926028
Geographic LocationUnited Kingdom
Collection Date2003
HostHomo sapiens
Human Microbiome Body Sitenot-specified

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

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