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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.

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EcoCyc Update History

This document summarizes the history of updates to EcoCyc.

EcoCyc KB Statistics by Year
  2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 Description
Pathways 328 320 300 281 276 246 237 225 205 187 Metabolic plus signaling pathways. Excludes super-pathways.
Reactions 2361 2284 2120 1991 1907 1800 1714 1661 4956 4260 Includes metabolic reactions, transport reactions; as of 2007, excludes reactions for binding of transcription factors to DNA.
Enzymes 1533 1505 1485 1470 1451 1425 1397 1357 1307 1222 Number of enzymes that catalyze biochemical reactions.
Transporters 277 269 264 257 254 247 241 226 211 206 Number of transporters.
Gene product summaries 3804 3751 3706 3710 3676 3612 3532 3438 3332 2830 Number of gene products containing summaries.
Genes 4501 4501 4499 4503 4490 4495 4472 4470 4465 4480 Number of genes, including some that have not been pinned to the DNA sequence.
Transcription Units 3538 4510 4490 4463 3412 3370 3359 3199 3133 1232 Number of transcription units -- includes operons and single-gene transcription-units.
Citations 27,887 25,406 23,909 22,039 20,890 19,156 17,258 15,883 14,951 12,026 Number of distinct references cited within EcoCyc.

The statistics for each year pertain to the last EcoCyc version released in that year.

These release notes omit the many small updates that occur in each release.


Release Notes for EcoCyc Version 18.5

Released on November 07, 2014.

Highlights of Website Improvements

EcoCyc Database Improvements

The text contained within the mini-review summaries for EcoCyc gene and pathway pages is the equivalent of 2,600 textbook pages. This information was curated from 28,000 publications.


Release Notes for EcoCyc Version 18.1

Released on June 23, 2014.

EcoCyc KB Statistics
Pathways 323
Reactions 2342
Enzymes 1524
Transporters 277
Genes 4501
Transcription Units 3528
Citations 26,870

  • A new two component signal transduction pathway, YehUT, has been added. YehUT is involved in a carbon control network that functions when nutrients are limited.

  • Although the chemistry of DNA charge transfer has been well described, the role it plays within the cell (if any) has remained enigmatic. A recent report (Grodick et al.) suggests that the DNA repair proteins DinG and Endonuclease III use DNA charge transfer to communicate over distance and redistribute to sites of DNA damage.

  • New functions have been described for the inner membrane proteins LapA and LapB (formerly YciS and YciM) characterised by Klein et al. as heat shock proteins with a role in lipopolysaccharide assembly, and for CysZ, reported to be a sulfate:proton symporter with a role during cysteine synthesis.

  • MraZ was identified by Eraso et al. as a transcriptional repressor involved in the control of cell division and cell wall genes. It binds to a region of DNA containing three successive TGGGN direct repeats that are separated by two consecutive 5-nt spacers close to the mraZp promoter.

Release Notes for EcoCyc Version 18.0

Released on March 24, 2014.

EcoCyc KB Statistics
Pathways 322
Reactions 2318
Enzymes 1518
Transporters 273
Genes 4499
Transcription Units 4522
Citations 26,275

  • Highlights of Website Improvements

    • RouteSearch: Search for lowest-cost paths through the metabolic network of the selected organism. Or, design lowest-cost pathways to novel compounds by adding reactions from MetaCyc.

    • Sequence pattern searches: You can now search a genome for exact or degenerate short patterns of nucleotides or amino acids.

    • You can now obtain multiple sequence alignments among E. coli genes and proteins, and to other genes/proteins in BioCyc

    • Groups have been renamed to SmartTables

    • Full Pathway Tools release notes: http://brg.ai.sri.com/ptools/release-notes.shtml

  • EcoCyc Database Improvements:

    • We have added one new metabolic pathway, sulfoglycolysis. Denger et al. describe the degradation of sulfoquinovose, which is a major component of organo-sulfur compounds in nature and can be utilized as the sole source of carbon and energy by E. coli K-12.

    • Curation of transport proteins includes the addition of 5 new functions. The 3 inner membrane proteins GhxP, GhxQ and AdeQ (formerly YjcD, YgfQ and YicO) have been characterised by Papakostas et al. as purine transporters: GhxP and GhxQ are high affinity permeases specific for guanine and hypoxanthine while AdeQ and the previously characterised PurP transporter are specific for adenine. New transport functions were added for the inner membrane proteins SatP (formerly YaaH) reported by Sa-Pessoa et al. to be an acetate:proton symporter active at the exponential growth stage and YihO which was implicated in the transport of sulfoquinovose.

    • The characterisation of an E. coli inner membrane glycolipid with enzyme-like activity that is essential for membrane protein integration was first reported by Nishiyama et al. in 2012. More recently Moser et al. have shown that this membrane protein integrase (MPIase) is a novel chaperone that drives protein integration into membranes by modulating the dimer orientation of SecYEG translocase.

    • E. coli K-12 contains eight members of the highly conserved DedA family of membrane proteins which are collectively essential but whose function remains obscure. A recent report by Kumar and Doerrler suggests that two of these proteins (YghB and YqjA) are membrane transporters required for PMF-dependent drug efflux in E. coli K-12.

    • RclR (formerly YkgD) has been experimentally determined to be a redox-sensitive transcriptional activator of essential genes for survival under reactive chlorine stress by Parker et al..

    • Park et al. showed that ArcA utilizes its diverse binding site architecture for global control of carbon oxidation pathways.

Release Notes for EcoCyc Version 17.5

Released on October 11, 2013.

EcoCyc KB Statistics
Pathways 320
Reactions 2284
Enzymes 1505
Transporters 269
Genes 4501
Transcription Units 4510
Citations 25,406

  • Highlights of Website Improvements

    • New Right-Sidebar Menu: The previous object-specific menus have been replaced by a right-sidebar menu of operations that changes depending on what type of page the user is visiting. For example, the menu of operations differs for pathway pages versus metabolite pages. Some operations previously accessible by buttons (e.g., retrieving a protein sequence) are now accessible through this new right menu in gene pages. If you do not see the menu, please reload the page in your web browser while holding down the "Shift" key.

    • Web Cellular Overview and Omics Viewer: This tool has undergone a major overhaul including
      • It runs much faster and many bug fixes have been made
      • Gene expression data to be displayed on the Cellular Overview can now be retrieved from PortEco, from GEO, and from Web Groups
      • Pop-up improvements
      • Many new search commands are available
      • Labels for pathway groups are now included in the diagram

    • Groups Enhancements: A number of enhancements have been made to both Web Groups including:
      • Groups can now be published. Once published a group is publically readable, and the group cannot be deleted, even by its owner. The idea is to encourage scientists to refer to published groups in their scientific publications.
      • Users can now create temporary groups without creating a BioCyc account to facilitate experimentation with Groups.
      • Database identifiers in database links can be added as groups columns, e.g., KEGG IDs for BioCyc compounds.
      • A group of objects can be created via text entry.
      • New row selection operations are available.
      • The star in the heading of the first column allows the user to toggle between viewing object names and object identifiers.

    • Full Pathway Tools release notes: http://brg.ai.sri.com/ptools/release-notes.shtml

  • EcoCyc Database Improvements:

    • We have added three new metabolic pathways: In addition, the colanic acid building blocks biosynthesis pathway has been turned into a superpathway consisting of five component pathways.

    • New transport reactions have been added for pyruvate uptake and export. Although specific transport protein(s) have not been identified, experimental work by Kreth et al. suggests that E. coli K-12 contains both inducible and constitutive systems for the import of pyruvate plus an additional system for pyruvate efflux.

    • A new function has been added to the multidrug resistance protein MdtM, which was reported to be a low-affinity cation:H+ antiporter with a role in alkaline pH homeostasis.

    • VanOrsdel et al. have reported that the small membrane protein CydX (formerly YbgT) is a subunit of cytochrome bd-1 and is required for terminal oxidase activity.

    • We have added the tetrameric conformation for the transcriptional regulator LsrR. Wu et al. reported that in the presence of phosphorylated autoinducer 2 (AI-2), the tetramer dissociates into dimers, and the interaction of LsrR with DNA is greatly reduced. Therefore, we also added its inactive conformation, LsrR-AI-2.

    • Two new conformations, MetJ-MTA and MetJ-adenine for the protein MetJ were recently added. Marti-Arbona et al. reported that the metabolites 5´-deoxy-5´-(methylthio) adenosine (MTA) and adenine (Ade) bind with high affinity to MetJ, but the biological effects of this binding are not known.

Release Notes for EcoCyc Version 17.1

Released on June 11, 2013.

EcoCyc KB Statistics
Pathways 314
Reactions 2232
Enzymes 1500
Transporters 268
Genes 4501
Transcription Units 4509
Citations 24,870

  • 1,4-dihydroxy-2-naphthoyl-CoA thioesterase, EC 3.1.2.28, is an enzyme of the menaquinone biosynthesis pathway. It had long been an orphan activity: the gene encoding the enzyme had been unknown. Recently, Chen et al. showed that ydiI encodes this enzyme and renamed the gene menI.

  • New functions have been added to three membrane proteins. DauA was reported to be an aerobic succinate transporter active at acidic pH by Karinou et al.. WaaH and EptC were shown by Klein et al. to catalyse glucuronic acid and phosphoethanolamine modification to E. coli LPS under low phosphate conditions.

  • Curation of the nitrogen phosphoenolpyruvate-dependent phosphotransferase system (PTSNtr), consisting of the three cytoplasmic proteins PtsP, PtsO and PtsN, has been updated for this release.

  • As part of our curation on transcriptional regulation, we have added literature references to the experimental evidence codes for 225 promoters in which they were missing.

  • We have corrected and relocated the transcription factor binding sites of PuuR. The binding sites of PuuR identified by Nemoto et al. consist of 15 nucleotides, with the following recognition sequence: AAAATATAATGAACA (Nemoto et al. (2012)). Analysis done by the curator on the experimental assays and the sequences identified by Nemoto et al. showed that the binding sites of PuuR may have a length of 20 nucleotides with an inverted repeat symmetry: ATGGaCAATATATTGaCCAT (The consensus sequence identified by Nemoto et al. is included in this proposed consensus sequence, and the nucleotides conserved between the two sequences are underlined.)

  • We have made several revisions to improve agreement between Biolog Phenotype MicroArray activity and flux-balance analysis (FBA) predictions, including fixes to incorrectly reversible reactions and addition of new transport reactions.

Release Notes for EcoCyc Version 17.0

Released on March 28, 2013.

EcoCyc KB Statistics
Pathways 312
Reactions 2175
Enzymes 1497
Transporters 268
Genes 4499
Transcription Units 4506
Citations 24,391

  • We have added a new signaling pathway and two new metabolic pathways to EcoCyc: In addition, pyrimidine nucleotide biosynthesis pathways have been extensively rearranged, resulting in smaller base pathways and new superpathways.

  • Curation of the lipopolysaccharide transport system, comprising seven Lpt proteins in E. coli K-12, has been updated for this release.

  • New functions have been added for the membrane proteins Spr, YdhO and YebA recently characterised by Singh et al. as murein hydrolases. The three D-D endopeptidases are redundantly essential for peptidoglycan incorporation and cell growth.

  • The role of the inner membrane proteins PgaC and PgaD in biofilm formation has been further described and a novel mechanism of cyclic-di-GMP mediated exopolysaccharide control elucidated. Steiner et al. have shown that the second messenger molecule c-di-GMP binds specifically to a PgaCD complex, mediating a productive interaction that results in the formation of an active glycosyltransferase complex.

  • Three newly identified transcription factors have been curated:
    • PgrR is a repressor of the expression of genes related to peptidoglycan degradation (Shimada et al. (2013)).
    • RcdA is involved in the regulation of a number of stress response genes, biofilm formation and of transcription regulator genes (Shimada et al. (2012)).
    • YdfH belongs to the GntR transcription factor family and is a repressor of the rspAB operon (Sakihama et al. (2012)).

Release Notes for EcoCyc Version 16.5

Released on Nov 14, 2012.

EcoCyc KB Statistics
Pathways 300
Reactions 2120
Enzymes 1485
Transporters 264
Genes 4499
Transcription Units 4490
Citations 23,909

  • We have added a new electron transport pathway to EcoCyc: In addition, a number of pathways have been added to EcoCyc based on information in MetaCyc:

  • With the discovery of RlmJ as the enzyme responsible for methylation of A2030 in 23S ribosomal RNA by Golovina et al., the set of methyltransferases that modify E. coli ribosomal RNAs is now complete.

  • New functions have been added for the inner membrane protein UacT (formerly YgfU), characterized as a urate transporter in E. coli K-12, and the outer membrane protein LoiP (formerly YggG) reported to be a metalloprotease.

  • Selkrig et al. have reported the characterization of a novel "translocation and assembly module" that spans the inner and outer membranes of E. coli K-12 and is responsible for the efficient secretion of adhesin protein. This newly described complex comprises the inner membrane protein TamB (YtfO) and the outer membrane protein TamA (YtfM).

  • The release of solutes through mechanosensitive ion channels functions to protect bacterial cells against hypo-osmotic shock. Edwards et al. have recently reported experimental characterization of two mechanosensitive channels encoded by the genes ynaI and ybiO. This latest report brings the total number of known mechanosensitive channels in E. coli K-12 to seven, experimental evidence from Edwards et al. suggests that this represents the full complement.

  • EcoCyc now includes consensus sequences of binding sites for 130 transcription factors (TFs). 70% of the sites have inverted repeat symmetry, 22% are asymmetric binding sites, and 8% have direct repeat symmetry. 49 regulators are local transcription factors that have three or less binding sites and 81 regulators have four or more binding sites in the database.

  • We have also annotated 35 predictions for TF binding sites of 13 regulators. The matrices used for these predictions were constructed by the RegulonDB database (Medina-Rivera et al. (2010)). Four TFs (ArgR, AscG, Cra, and Rob) have regulatory interactions with weak evidence and interactions for eight regulators (CRP, EvgA, ExuR, FIS, LexA, NtrC, PhoP, TorR, and UxuR) have strong evidence.

  • We have completed adding references and evidence codes to 85 transcriptional regulatory interactions. Now every manually curated regulatory interaction has a reference and an evidence code associated with it.

  • We have added a fifth dataset measuring respiration under aerobic conditions using the Biolog platform to our growth media page. This data was published by Yoon et al..

  • The all-growth-media page has been enhanced to enable better visualization and comparison between the five datasets. Some disagreements between the datasets have been resolved by a curator using data from the experimental literature, or by disregarding single outlier results.

  • Previously, there were three different (and on occasion inconsistent) ways to represent protein cellular location: via GO terms, via MultiFun terms, and via our own cellular component ontology. We have combined the data from all three representations, and resolved the inconsistencies. We now store only GO terms, and compute the value of the protein location field from the stored GO terms. We have eliminated the use of MultiFun terms to represent cellular location.

Release Notes for EcoCyc Version 16.1

Released on July 05, 2012.

EcoCyc KB Statistics
Pathways 293
Reactions 2074
Enzymes 1474
Transporters 258
Genes 4500
Transcription Units 4477
Citations 23,382

  • We have reviewed and standardised the naming of membrane transport proteins within EcoCyc. Our aim was to use names that are indicative of both transporter substrate and energetics (e.g. "serine/threonine:Na+ symporter" replaces "SssT DAACS transporter") and to ensure that this was extended to include the individual subunits of transport protein complexes, which until now have often been identified by gene name alone (e.g. "arabinose ABC transporter - ATP binding subunit" replaces "AraG"). Approximately 450 proteins were renamed as part of this project.

  • We have added more Phenotype Microarray (PM) growth data to EcoCyc. Data are available from four PM studies under aerobic conditions, and from one PM study under anaerobic conditions. Significant differences were found. Growth data can be accessed from the All Growth Media page. For details on how to access these data, see the "Conditions of E. coli Growth and Non-Growth" section of the Guide to EcoCyc.

  • For information about the four existing large-scale gene essentiality datasets within EcoCyc, see the "Essential Gene Information" section of the Guide to EcoCyc.

  • Two groups, Thomason et al. and Jørgensen et al., independently discovered that the small RNA McaS regulates the expression of curli as well as flagellar motility and biofilm formation.

  • FliZ is a repressor that contains an α-helix which is similar to helix 3.0 of σS and that represses genes involved in the regulation of motility system and curli expression. Pesavento et al. 2012 determined that this regulator binds to σS-dependent promoters, can recognize alternative σS promoter-like sequences and can also discriminate vegetative promoters.

  • Two new transcription factors have been identified, MatA and YjiE.
    • MatA is a transcriptional dual regulator in the meningitis isolate strain IHE 3034 and it interferes with bacterial motility and flagellar synthesis in E. coli K-12 (Lehti et al. 2012). Given the high similarity between the two strains, we have added this information to E. coli K-12.
    • The YjiE transcription factor regulates genes involved in cysteine, methionine biosynthesis, sulfur metabolism, iron acquisition and homeostasis (Gebendorfer et al. 2012). It was formerly named "QseD", but it does not appear to be directly involved in quorum sensing and was thus renamed to its original name.

  • A new function was identified for OxyR, controlling genes under nitrosative stress during anaerobic respiration (Seth et al. 2012).

  • We have included new consensus binding sequences for 17 transcription factors: AgaR, AraC, ArcA, AscG, CaiF, DnaA, FhlDC, IclR, KdpE, LeuO, MalT, MelR, NanR, PrpR, PutA, RhaS, XylR.


Release Notes for EcoCyc Version 16.0

Released on February 17, 2012.

EcoCyc KB Statistics
Pathways 293
Reactions 2037
Enzymes 1475
Transporters 259
Genes 4502
Transcription Units 4472
Citations 22,895

  • We have added a number of new metabolic pathways to EcoCyc. Three new pathways show reactions in the biosynthesis of molybdenum cofactors: Other pathways have been recently described in the literature, including:

  • Additional knock-out datasets are available in this release of EcoCyc. To list all growth media and their associated knock-outs use command Tools → Summary Statistics, then click on "Growth Media" at the bottom of the table. Knock-out data are also available in a table on most gene pages.

  • A new function was assigned to the inner membrane protein MntP (formerly YebN), characterized by Waters et al. as a manganese transporter.

  • The long running controversy over the structure of the multidrug transporter EmrE may be drawing to a close with a report in the journal Nature providing further evidence for the asymmetric, antiparallel arrangement of monomers within the dimer.

  • Curation of cytochrome bdII oxidase has been updated to include the report by Borisov et al. who have shown that this terminal oxidase does contribute to the generation of proton motive force in E. coli K-12.

  • We have reviewed the reactions included in the new E. coli metabolic model of Orth et al. and updated EcoCyc if necessary.

  • We continue with the effort to update and assign the correct lengths and positions of transcription factor (TF) binding sites. In this release, we added consensus sequences, lengths, and binding site symmetries for 10 TFs. We updated the binding sites for four TFs that belong to the LysR family (ArgP, IlvY, MetR, and NhaR) and three two-component system response regulators (BaeR, CitB, and CpxR), as well as DinJ (part of a toxin/antitoxin system), PurR (regulates genes involved in purine/pyrimidine biosynthesis), and PdhR (involved in central metabolic fluxes, the utilization of glycolate, and cell division).

    In these cases we used different strategies to identify the characteristics of the TFBSs. We performed alignments of the sequences upstream of genes regulated by these proteins and compared orthologous intergenic regions, and we also used other databases, such as RegPrecise (Novichkov et al. 2010). In addition, the binding sites of the regulator MetR were corrected based on comparisons with homologous sequences reported for Salmonella typhimurium. In all cases we also analyzed the available experimental evidence that corresponded to each regulatory interaction.

  • We are continuing to annotate allosteric regulation of RNA polymerase by ppGpp and DksA. In this sense we have expanded the summaries for GreB, GreA and DksA and for transcriptions factors including AidB, ArgP, AtoC, DcuS, DpiB, Fur, HNS, LacI, MalT, MntR, PaaX, PhoB, PutA and SoxS.


Release Notes for EcoCyc Version 15.5

Released on October 21, 2011.

EcoCyc KB Statistics
Pathways 281
Reactions 1991
Enzymes 1470
Transporters 257
Genes 4503
Transcription Units 4463
Citations 22,039

  • All articles from the EcoSal collection are now available for full-text searching from the EcoCyc website (see Search → Search Full-text Articles). Those 131 EcoSal articles are part of a collection of 40,000 indexed articles at EcoCyc; for 27,000 of those articles, the full text is searchable. Note you must have a subscription from EcoSal and other content providers to view many of the full articles.

  • We have begun a new effort to capture conditions of E. coli growth and non-growth within EcoCyc. EcoCyc now contains 406 such growth conditions. You can access information on growth conditions in two ways through the EcoCyc website:
    • To find growth media according to criteria such as name and components of the media, use command Search → Growth Media
    • To list all growth media use command Tools → Summary Statistics, then click on "Growth Media" at the bottom of the table

    Example growth medium page: MOPS medium with 0.4% glucose

    To suggest additional growth media for inclusion, please contact .

  • We have begun a new effort to capture E. coli essential gene information within EcoCyc. When conditions of gene essentiality or non-essentiality for gene G are known, that information will be presented within a table within the gene page for G, located just below the table of Gene Ontology terms.

    Example gene page with essentiality data: fbaA

  • BioCyc.org now contains 130 E. coli genomes. To access them, click "select organism database" under the quick-search box at the top-right of EcoCyc web pages, and select the genome you wish to explore.

  • EcoCyc now includes a functional steady-state metabolic flux model for E. coli produced using the method of flux-balance analysis. Data files describing the model and its computed fluxes can be accessed in the fba subdirectory of the EcoCyc datafile distribution. You can run the model using the downloadable version of EcoCyc plus the Pathway Tools software to explore growth predictions under different nutrient conditions and under different gene and reaction knock-outs.

  • The function of the inner membrane protein RseP has been expanded. Formerly characterised for its role in the activation of the sigmaE stress response, Saito et al. have reported that it is also involved in the degradation of remnant signal proteins left in the inner membrane (a function previously ascribed to the SppA protein of E. coli).

  • New functions have been added to the periplasmic protein RcnB (formerly YohN) - implicated in the maintenance of intracellular levels of nickel and cobalt, and the membrane-associated protein YidD - required for the efficient insertion and maturation of YidC-dependent inner membrane proteins.

  • The curation of a number of inner membrane proteins in EcoCyc has been updated for this release. Updated text summaries for the inner membrane proteins D-lactate dehydrogenase, HPr, PtsI and the protein complexes PntAB and RuvABC have resulted in the addition of 94 new literature citations to EcoCyc.

  • We have curated mechanisms of regulation affecting allosterically the RNA polymerase at transcription initiation. ppGpp is a nucleotide that binds the RNA polymerase alone or forming a complex with DksA, affecting transcription in either a positive or negative manner. Genes involved in response to nutrient limitation as well as amino acid biosynthesis were positively affected by ppGpp and DksA. On the other hand, genes related to rRNA promoters and to the stringent response were negatively controlled by both regulators. Currently, 67 promoter interactions regulated by ppGpp, as well as some of them including regulation by DksA were curated.


Release Notes for EcoCyc Version 15.1

Released on June 8, 2011.

EcoCyc KB Statistics
Pathways 281
Reactions 1945
Enzymes 1467
Transporters 258
Genes 4490
Transcription Units 3433
Citations 21,448

  • We have added three new metabolic pathways to EcoCyc:

  • New functions have been added for three previously uncharacterized inner membrane proteins. PlaP (formerly YeeF) was reported to be a low affinity putrescine symporter; AlaE (formerly YgaW) was characterized as an inducible L-alanine exporter and YjbB was reported to be involved in the export of inorganic phosphate.

  • Biochemical characterization and a crystal structure of the periplasmic protein, Spy, has been recently reported by Quan et al.. Spy is a periplasmic chaperone with a unique cradle structure and it is strongly induced by conditions that induce protein unfolding. Spy acts to prevent protein aggregation; it also supports protein refolding in the absence of an energy cofactor - exactly how this is achieved remains a question for further research.

  • We have analyzed consensus binding sequences for 20 transcription factors (TFs) and as a result we have corrected and generated new regulatory interactions, updated their consensus sequences, length and symmetry of the transcription factor binding sites (TFBSs).

  • We corrected and relocated the TFBSs of seven response regulators of the two component systems: DcuR, EvgA, NtrC, OmpR, PhoB, PhoP and RstA. We have updated the sites of 5 TFs involved in the Acid Resistance System: BglJ, GadE, GadX, GadW, RcsB. We added new consensus sequences for four local transcription factors: SoxR, YqhC, YqjI and CspA.

  • The experimentally characterized TFBSs for the transcriptional regulator components of the HipBA, MqsAR, RelBE and YefM-YoeB toxin/antitoxin systems have been updated.


Release Notes for EcoCyc Version 15.0

Released on March 18, 2011.

EcoCyc KB Statistics
Pathways 277
Reactions 1922
Enzymes 1458
Transporters 254
Genes 4489
Transcription Units 3422
Citations 21,110

  • We have added one new metabolic pathway to EcoCyc:

  • The curation of all the histidine kinase proteins involved in two-component regulatory systems has been updated. EcoCyc includes information on 27 experimentally characterized histidine kinases plus 3 proteins (YedV, YedU and YpdA) with predicted histidine kinase function.

  • The set of full-text E. coli scientific articles available for searching has been updated; 29,000 articles are available for searching, and an additional 7,000 abstracts are available for searching. See website command Search → Search Full-text Articles.

  • As the target of the β-lactam class of antibiotics, the peptidoglycan synthesizing enzymes are always of great interest. Two groups of researchers recently reported the characterization of the outer membrane lipoproteins LpoA (formerly YraM) and LpoB (formerly YcfM), showing that they form complexes with and regulate the activity of, the peptidoglycan synthetases, PBP1A and PBP1B.

  • A new function was added to the inner membrane protein PgpC, characterized by Lu et al. as a phosphatidylglycerophosphatase with a role in phospholipid biosynthesis.

  • A new transcription factor, YqjI, has been identified. The local regulator YqjI was reported to act as a repressor of the synthesis of an NADPH-dependent ferric reductase and its autorepression. Wang et al. determined that this regulator maintains iron homeostasis during high levels of nickel.

  • We have included new consensus sequences for 45 local transcription factors that have three or less binding sites in the database. In these cases we performed alignments of the sequences upstream of genes regulated by these proteins and evaluated the lengths and symmetries of the consensus sequences. Most of these regulators bind to small sequence motifs (11 to 24 nucleotides) with different symmetries and these are arranged as inverted repeats (39), direct repeats (2) or asymmetrical sequences (4). In general, the sequences of unique binding sites are highly conserved and their length and symmetry are evident.
    • Transcription Factors with inverted repeat symmetry: AcrR, AllR, ArsR, AtoC, BaeR, BirA, BetI, CueR, CusR, EnvR, FabR, GlrR, HcaR, HyfR, KdgR IdnR, ilvY, LacI, LldR, MalI, MarR, MhpR, MntR, MurR, NadR, NemR, NikR, NorR, PrpR, RbsR, RcnR, TdcA, TreR, UhpA, UidR, YiaJ, YoeB-YefM, ZntR, Zur.
    • Transcription Factors with direct repeat symmetry: CreB, MngR.
    • Transcription Factors with asymmetric binding sites: ChbR, RhaR, XapR, ZraR.


Release Notes for EcoCyc Version 14.6

Released on December 3, 2010.

EcoCyc KB Statistics
Pathways 276
Reactions 1907
Enzymes 1451
Transporters 254
Genes 4490
Transcription Units 3412
Citations 20,890

  • We have added one new metabolic pathway and one new signalling pathway to EcoCyc: In addition, several purine nucleoside/nucleotide degradation and salvage pathways have been re-arranged into smaller component pathways.

  • All two-component signal transduction pathways in EcoCyc have now been updated. A new aerotactic signalling pathway was added, thus bringing the total number of two-component pathways represented in EcoCyc to 27.

  • A new function was assigned to the periplasmic PliG protein (formerly YcgK), recently reported to be an inhibitor of g-type lysozyme activity.

  • The crystal structures of several transport proteins have been recently solved. EcoCyc provides links to the new Protein Data Bank entries for the membrane transporters CaiT, CusA and FucP and the periplasmic binding protein XylF.

  • Curation of transcription factors (TFs) included updates to the summaries for MalT, UlaR, ArgR, MlrA, McbR, TreR, and YqhC. In addition, GO terms were updated for different TFs. The names of TFs were revised, adding "DNA-binding".


Release Notes for EcoCyc Version 14.5

Released on October 1, 2010.

EcoCyc KB Statistics
Pathways 260
Reactions 1884
Enzymes 1450
Transporters 252
Genes 4489
Transcription Units 3409
Citations 20,284

  • New Regulation Summary Diagram: Gene pages now contain a diagram that summarizes all regulatory influences on the gene as described in the PGDB. For example, the EcoCyc gene page for bglG shows the influences of transcription factors, attenuation, and post-translational modification of the gene product.

  • New Web Services: EcoCyc now supports an array of Web services that enable Web-based retrieval of EcoCyc data such as data for a gene or pathway. [Details]

  • New Monoisotopic Mass Search to Support Metabolomics: The Search → Compounds page now contains a filter for searching for compounds by monoisotopic molecular weight, which is useful for analyzing mass spectroscopy data.

  • Faster Web Cellular Overview: The recent re-implementation of the Web Cellular Overview has been reworked to significantly increase its speed. The Cellular Omics Viewer speed has been increased, and the dialog for invoking the Omics Viewer has been simplified. Tooltips for this diagram have been improved -- these pop-up windows can be moved, and kept, and multiple such windows can be opened simultaneously.

  • Omics Viewer available for Web Regulatory Overview: The Omics viewer is now available for the Web Regulatory Overview, and the speed of the Web Regulatory Overview has been increased significantly.

  • We have added three new metabolic pathways to EcoCyc:

  • Updates have been made to 21 of the 26 two-component pathways currently included in EcoCyc. The pathways now show correct localisation of components plus an intuitive depiction of the phosphotransfer (including multistep phosphorelay) reactions. Text summaries have also been added. Some examples of updated pathways include:

  • Many RNases have been updated so that their associated reactions are more accurate and more comprehensible. EcoCyc also features a new tRNA processing pathway that captures the complex interplay of ribonucleolytic reactions that converts tRNA precursors into the final tRNA that is ready for modification and charging with an amino acid.

  • New functions were assigned for the inner membrane proteins YfgF, reported to be a cyclic di-GMP phosphodiesterase and YbdG, characterised as a low abundance mechanosensitive channel of miniconductance.

  • We are continuing the analysis of binding sites of different transcription factors, resulting in corrected and relocated binding sites for FhlA, YiaJ, NhaR, Ada, and CaiF. This work is based on evidence supporting the identification of overrepresented motifs in the regulatory regions analyzed, using computational tools and the expertise of the curators.

    Initially, the FhlA-binding sites were represented by large regions of 40 bp, but in 2000 Leonhartsberger et al. proposed that FhlA binds to inverted repeat sequences of 16 bp (CATTTCGTACGAAATG) (Leonhartsberger et al. (2000)). However, sequence alignments showed that this sequence is less conserved in the upstream regulated regions. We showed a new overrepresented sequence (TGTCGnnnnTGACA) that overlaps with the sequence proposed by Leonhartsberger and colleagues. We have therefore relocated, reassigned, and corrected all FhlA binding sites in EcoCyc. In addition, the binding sites of the regulators YiaJ and NhaR were corrected, based on comparisons with homologous sequences reported for Klebsiella pneumoniae (Campos et al. (2008)) and in the RegPrecise database (Novichkov et al. (2010)), respectively. We also have corrected the binding sites of two other transcription factors, Ada and CaiF.


Release Notes for EcoCyc Version 14.1

Released on June 16, 2010.

EcoCyc KB Statistics
Pathways 253
Reactions 1829
Enzymes 1445
Transporters 252
Genes 4490
Transcription Units 3397
Citations 20,123

  • We have added three new metabolic pathways and two new signal transduction pathways to EcoCyc:

  • The characterisation of several chaperone-usher fimbrial operons (sfmACDHF, ycbQRSTUVF, yraHIJK, yadCKLMhtrEecpDyadN, yehABCD, and yfcOPQRSTUV) in E.coli K-12 was recently reported by Korea et al. (PMID 20345943). These operons are cryptic under normal laboratory conditions, but induced expression in strains lacking the normal type I fimbrial genes resulted in phenotypes that included biofilm formation, adhesion to eukaryotic epithelial cells and microscopically observable pili.

  • A new function was assigned to the ChiP protein - reported to be an outer membrane porin for chitooligosaccharides. ChiP expression is controlled by a novel mechanism of gene regulation in E. coli K-12, whereby the induction of an mRNA 'trap' leads to selective degradation of a small regulatory RNA molecule. In this particular case the chitobiose operon (chb) mRNA 'traps' and degrades the constitutively expressed regulatory RNA MicM, resulting in the induction of chiP mRNA translation and ultimately transport of chitooligosaccharides.

  • The motif obtained from aligning OxyR binding sites is highly variable due to the length of sequences, even though, through manipulation of the alignment it is possible to detect four conserved regions. For this reason we have relocated, reassigned, and corrected binding sites of the OxyR regulon, corresponding to 19 transcription units. Toledano et al. (1994) showed that OxyR binds in tandem to four ATAG elements and defines a consensus motif, ATAGntnnnanCTATnnnnnnnATAGntnnnanCTAT covering around 40 bp. We now propose a new consensus sequence, GATAGGTTnAACCTATCnnnnnGATAGGTTnAACCTATC, which contains two inverted repeat motifs, GATAGGTTnAACCTATC, of 17 bp separated by 5 bp. This sequence consensus is based on agreement of alignments realized by the curator of these upstream regions and on the corresponding evidence, obtained in the bibliography for every operon, including the similarity to the consensus sequence, data from footprinting assays, computational analysis of these sequences, and profiling of OxyR-dependent gene expression. In the database the OxyR-binding sites are represented by an inverted repeat motif of 17 bp.

  • During this last period, we have updated curation on transcription initiation including publications until end of April, 2010.

Release Notes for EcoCyc Version 14.0

Released on March 18, 2010.

EcoCyc KB Statistics
Pathways 248
Reactions 1815
Enzymes 1430
Transporters 249
Genes 4497
Transcription Units 3386
Citations 19,563

  • We have added one new metabolic pathway and one new signal transduction pathway to EcoCyc:

  • Crystal structures of a number of proteins that are thought to form a carboxysome-like proteinaceous microcompartment that functions in ethanolamine utilization were recently reported by Tanaka et al. (PMID 20044574). The structures of EutS, EutL, EutK and EutM are suggestive of their functions, and we are looking forward to their functional characterization in E. coli.

  • Curation of transport proteins has included the newly charcterised YtfQ galactofuranose binding protein - the periplasmic component of a predicted ABC type transporter (YtfQRT/YjfF).

  • Summaries relating to the cytochrome c biogenesis proteins (CcmA-H) have been updated based on a recent study which sought to purify and characterise the various complexes in order to elucidate the mechanism of haem binding and trafficking.

  • We have corrected and relocated the binding sites of the CytR transcription factor. This regulator negatively controls the expression of genes that encode the proteins required for transport and utilization of ribonunucleosides and deoxyribonucleosides. The CytR binding sites were previously represented as long regions which were determined by footprinting of several promoter sequences.

    Computational analysis of these sequences showed that the optimal CytR binding site consists of two octamer repeats, GTTGCATT, in direct o invert orientation and preferably separated by 2 bp. Experimental support of this consensus sequence was obtained from footprinting, site-directed mutagenesis experiments and gene expression. (Pedersen et al. (1997), Jorgensen et al. (1998))

  • We have updated curation on transcription initiation including publications until end of December, 2009.


Release Notes for EcoCyc Version 13.6

Released on November 21, 2009.

EcoCyc KB Statistics
Pathways 246
Reactions 1800
Enzymes 1425
Transporters 247
Genes 4495
Transcription Units 3370
Citations 19,156

  • We have made many smaller updates to protein summaries to reflect information from recent publications. Updated proteins include HscA, a chaperone required for the assembly of iron-sulfur clusters, and SufA, a protein that transports iron-sulfur clusters during cluster assembly.

  • Curation of membrane proteins has included the recent experimental confirmation of YjdL as a dipeptide transporter, while the function of the ChaA protein as a calcium ion transporter was disputed.

  • The cytoplasmic protein UspC was reported to act as a scaffolding protein of the KdpD/KdpE two component signal cascade. Under conditions of salt stress the KdpD/KdpE system acts to increase intracellular K+ levels. The stabilizing effect of UspC on the KdpD/KdpE/DNA complex is thought to attenuate the inhibiting effect of increasing intracellular K+ on the kinase activity of KdpD.

  • OmpA was reported to influence cellulose production and biofilm formation though the CpxR/CpxA two-component signaling pathway.


Release Notes for EcoCyc Version 13.5

Released on October 7, 2009.

EcoCyc KB Statistics
Pathways 246
Reactions 1805
Enzymes 1422
Transporters 246
Genes 4495
Transcription Units 3369
Citations 18,969

Data Content Improvements

  • We have added two new metabolic pathways and one new signal transduction pathway to EcoCyc:

  • The DpiAB Two-Component Signal Transduction System was added to the database. This pathway describes the regulatory system that activates the set of genes involved in citrate fermentation in E. coli.

  • Curation of transport proteins has included two recently described members of the ATP binding cassette (ABC) family of transporters - the MlaBCDEF transporter, an inner membrane phospholipid transporter involved in the trafficking system that maintains outer membrane organisation in E. coli, and LptABCFG, a lipopolysaccharide transporter.

  • New functions were assigned for the membrane protein complexes YnfEFGH - reported to be a selenate reductase - and YagTSR - an aldehyde ferredoxin oxidoreductase with a role in the detoxification of aromatic aldehydes in E. coli.

  • Our curation update project for transcriptional regulation is progressing; we have substantially curated published information on regulation of transcription initiation up to the end of June 2009.

  • FASTA files in the exported flatfiles: protseq.fasta was renamed to protseq.fsa, and contains the amino acid sequences for all protein-coding genes in EcoCyc. The new file dnaseq.fsa was added, containing the nucleotide sequences for every gene in EcoCyc.

Improvements to EcoCyc Web Site and Desktop EcoCyc

  • Genome browser tracks improvements:When displaying external data tracks, a new bar graph mode was added, which fills the rectangular area between the horizontal line and the baseline (corresponding to the score zero) with a solid color. This mode is useful for features that are very narrow, which might otherwise be hard to see. In the graph modes, a single color is assigned to each track. The color can be chosen by adding a special header comment into the GFF file, to allow users to follow their own color conventions. Many common colors can be specified, using this syntax (without quotes): "##color green" . The original graph mode was changed to show scores as horizontal lines spanning the length of the features, instead of showing a dot in the center. On the desktop version, the ordering of the tracks can be changed. In the graph modes, score values that fall outside the selected range are visually indicated. Error reporting of syntactic problems in the GFF files has been improved.

EcoCyc Web Site Improvements

  • Web Regulatory Overview: The Regulatory Overview diagram that depicts the transcriptional regulatory network of an organism is now available through the Web. Try toolbar command Tools → Regulatory Overview.

  • Quick search enhancements: Make your quick searches more precise as follows. By default a quick search for a term such as "argA" returns a list of all genes, proteins, pathways, compounds, etc that contain that string as a substring. By including additional qualifiers in the search, you can further constrain the search to go directly to the information page you want. For example, by searching for "argA type:gene" you will go directly to the gene page. If you prefer an exact search to a substring search, add the qualifier search:exact. Example: "argA search:exact". The search and type qualifiers can be combined in one search.

  • Find Current Object in Other Database: From a protein page, new toolbar commands are available that allow you to display the equivalent protein(s) from one or more other databases in this Web site (such as other E. coli strains). Similar functionality is available for genes, pathways, reactions, and compounds. See these toolbar commands:

    • Protein → Show This Protein in Another Database (equivalent object found based on orthology and name search)
    • Protein → Show This Protein in All Databases (orthology and name search)
    • Gene → Show This Gene in Another Database (orthology and name search)
    • Gene → Show This Gene in All Databases (orthology and name search)
    • Pathway → Show This Pathway in Another Database (frame-id search)
    • Pathway → Show This Pathway in All Databases (frame-id search)
    • Peaction → Show This Reaction in Another Database (frame-id search)
    • Reaction → Show This Reaction in All Databases (frame-id search)
    • Compound → Show This Compound in Another Database (frame-id search)
    • Compound → Show This Compound in All Databases (frame-id search)

EcoCyc Desktop Software Improvements

  • Manipulation of Object Groups for Omics Data Analysis: A new facility is available for manipulating groups of objects, such as a group of genes that are up-regulated in a gene expression experiment, or a group of metabolites that are up-regulated in a metabolomics experiment. The facility allows users to:
    • Define and store a group of objects
    • Transform the group into another group (such as to transform a gene list into a list of pathways containing those genes, or into an expanded list of genes that includes all genes in the same operon as the original genes)
    • Perform over-representation analysis on a group, such as asking if the group is statistically enriched for genes in one or more metabolic pathways, for genes in a Gene Ontology biological process, or for genes controlled by a given regulator.
    See the Groups menu and Section 3.8.13 of the Pathway Tools User's Guide.

  • Omics data graphing capabilities: The Omics Viewers now have the capability to show a graph of the set of data values (such as for a time series experiment) for a given object or set of objects (such as all the genes in a pathway) in a small popup overlay that the user can drag to reposition as desired. The graph can be customized to display either as a heat map, a bar graph or a plot. In addition, the software remembers the most recently loaded omics dataset so that these graphs can be added to any object display (such as for genes in an individual pathway display). To show the omics graph popup, right click on any object (such as a gene or reaction in any of the Omics Viewers, or a reaction in a pathway display). If there is omics data associated with that object, the menu will include the command "Show Omics Data in Popup". In the Cellular Overview, this command will also appear in the Pathway submenu, which shows the graph for all the objects in the pathway. Right-clicking on any omics graph popup allows you to change the display preferences.

  • 13 Additional E. coli and Shigella genomes available: You can download a configuration of the EcoCyc software that contains 13 E. coli and Shigella genomes in addition to EcoCyc.

Release Notes for EcoCyc Version 13.1

Released on June 19, 2009.

EcoCyc KB Statistics
Pathways 242
Reactions 1784
Enzymes 1415
Transporters 244
Genes 4496
Transcription Units 3356
Citations 18,469

  • We have added four new metabolic pathways to EcoCyc:

  • A number of membrane and transporter proteins have been updated, including the PuuP protein recently confirmed as a putrescine importer and DtpB, a peptide transporter.

  • 18 newly identified small proteins (16-50 amino acids) reported by Hemm et al. (PMID 19121005) were added to the database, reflecting an increased recognition of the significance of such proteins in cellular processes.

  • We have now completed summaries for all 170 Transcription Factors (TFs) that have at least one experimentally characterized binding site or interaction. These regulators represent 33 families of TFs, and the summaries describe relevant characteristics of each regulatory protein. A list of TFs within EcoCyc, organized by the Gene Ontology, is available here. A summary of the functions of these 170 TFs is the following:

    • Seven TFs are considered to be global regulators and are involved in regulating multiple operons and genes of different functional classes or gene ontologies, including DNA architecture, such as: anaerobiosis (ArcA and FNR), carbon source (CRP), factor for inversion stimulation (FIS), organization, maintenance of nucleoid, as well as other cellular processes (HNS, Lrp, and IHF).
    • Additionally, 21 response regulators belong to two-component systems, 42 TFs are included in the carbon sources system, 17 TFs are related to processes such as transport, biosynthesis and catabolism of the amino acids, 13 TFs are involved in the transport and metabolism of different nitrogen sources, and 8 TFs are classified as metallo-regulators. Note that the TFs can be involved in more than one function.
    • The rest of the TFs are considered to be local regulators that control the genetic transcription of different cellular processes and functional classes, for instance, flagellar and chemotaxis systems, metabolism of nucleosides, transport and synthesis of fatty acids, DNA replication, quorum sensing, toxin-antitoxin systems, adaptation and resistance to different conditions of stress, among others.

  • We have completed adding references and evidence codes to 210 promoters. Now every manually curated promoter has a reference and an evidence code associated with it.


Release Notes for EcoCyc Version 13.0

Released on March 9, 2009.

EcoCyc KB Statistics
Pathways 237
Reactions 1751
Enzymes 1409
Transporters 243
Genes 4477
Transcription Units 3375
Citations 17,842

  • The EcoCyc Web site has been redesigned to provide a new toolbar and new search commands. For quick instructions on how to use it, click here, or watch the webinar on how to use the new site.

  • EcoCyc now provides full-text searches of an E. coli literature corpus of 24,000 articles and 6,000 abstracts. It is available from the new search toolbar at Search → Textpresso. We are grateful to the EcoliHub project for providing the E. coli literature corpus.

  • Curation of peptidoglycan metabolizing enzymes has incorporated recent discoveries such as the identification of RodZ filaments that form within the E. coli cell to direct the peptidoglycan synthesis machinery to maintain the cell's rod shape. Also, the MurJ flippase has been identified as being responsible for moving lipid II molecules synthesized on the inner face of the inner membrane to the outer face where they can act as substrates for peptidoglycan biosynthesis enzymes. The identification of this transporter at last makes the connection between peptidoglycan precursor molecule synthesis and polymerization.

  • Our curation update project is progressing; we have substantially curated information on regulation of transcription initiation up to the end of Nov 2008.

  • We have imported many protein features from UniProt. EcoCyc now contains more than 18,500 protein features such as phosphorylation sites, enzyme active sites, and transmembrane regions. More than half of these features are supported by experimental evidence. Features are highlighted as regions on the protein sequence, at the bottom of protein pages, directly above the References section.

  • We updated our GO term assignments by re-importing term assignments from UniProt, as of December 2008. More than 10,000 new annotations were added. The total number of GO term assignments in EcoCyc increased from 33,259 (in version 12.5) to 41,541.
    • Note that the GOAFF file deposited with the Gene Ontology Consortium now carries the more specific taxon ID 511145 (for strain E. coli K-12 MG1655) rather than the more generic taxon ID 83333 (for the group of E. coli K-12 strains).

  • To aid the development of flux-balance models of E. coli metabolism, we have calculated and stored the predicted protonation state at pH 7.3 of all chemical compounds in EcoCyc, and we subsequently computationally proton-balanced all EcoCyc reactions.

  • A large number of chemicals referred to in enzymatic reactions have been converted to database objects. Chemical structures were added if possible.


Release Notes for EcoCyc Version 12.5

Released on October 15, 2008.

EcoCyc KB Statistics
Pathways 237
Reactions 1714
Enzymes 1397
Transporters 241
Genes 4472
Transcription Units 3359
Citations 17,258

  • EcoCyc can now display electron transfer pathways with the correct localization of the component reactions, as well as proton transport across the membrane. Eleven new pathways were created:

  • We have added two new metabolic pathways to EcoCyc: In addition, the pathway of initiation of fatty acid biosynthesis was reorganized into three component pathways.

  • ErfK, YcfS, YbiS, YcbB, and YnhG, the recently identified L,D-transpeptidases involved in peptidoglycan structure and anchoring to the outer membrane, along with a number of other enzymes important for maintaining the rod-shaped structure of E. coli through growth and cell division, have been curated.

  • We are now beginning to curate new types of E. coli regulatory processes in EcoCyc in addition to regulation of transcription initiation. Look for information about regulation by attenuation, and regulation by small RNAs, which appears in the transcription unit diagrams present on gene pages, RNA pages, and transcription unit pages.
    Examples:
    • Trp operon page depicts attenuation
    • GlmZ small RNA page lists all transcription units regulated by GlmZ, and depicts its binding sites
    Click below to generate lists of all:

  • Our general curation update project is progressing; this version contains curated information on regulation of transcription initiation up to end of May 2008.

  • Regulatory Overview (desktop EcoCyc): This tool for viewing and exploring the complete E. coli transcriptional regulatory network has been modified so that the inner ring of genes now contains master regulators (defined as the top 15% of regulatory genes based on the number of genes regulated, plus all sigma factors). Mousing over a regulatory arrow pops up a tooltip displaying the name of the regulatory gene and the list of the genes that it regulates, organized by operon. There is a new command in the right-click highlighting menu on a gene: This command shows regulatory arrows for the direct regulatees of the gene, and for all direct regulators of those regulatees.

  • Graph tracks for ChIP-chip data: The genome browser graph-track capability was designed for analysis of ChIP-chip datasets. It plots protein binding strength from ChIP-chip datasets as a function of genome position. First released in version 12.0 of Pathway Tools for Web mode only, this capability is now available in desktop mode in addition to Web mode.

    For more information, go to the genome browser and click on the green "?" to the right of the navigation control, and read Section "View Positional Data with External Tracks."

  • Many improvements have been made to the Structured Advanced Query Form, which allows you to execute complex queries against EcoCyc through the Web.

  • A new reference list at the bottom of each pathway page includes all references cited in the pathway, and in all enzymes belonging to the pathway.


Release Notes for EcoCyc Version 12.1

Released on June 27, 2008.

EcoCyc KB Statistics
Pathways 230
Reactions 1676
Enzymes 1374
Transporters 229
Genes 4472
Transcription Units 3356
Citations 16,909

  • A number of DNA repair enzymes, transporters, and other membrane proteins have been updated including the recent identification of LpxT as the protein responsible for attaching phosphate groups to lipopolysaccharide, the identification of MltF as a new lytic transglycosylase involved in peptidoglycan metabolism, and the identification of YgaZ/YgaH as a valine exporter.

  • This release includes a collection of 259 new transcription start sites that have been experimentally determined in a high throughput experimental modified RACE approach (with the corresponding new evidence code: EV-EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP). The experiments were performed in the laboratory of Dr. Enrique Morett, Institute of Biotechnology, in collaboration with the laboratory of Dr. Julio Collado-Vides, both at UNAM. This mapping has been supported by NIGMS grant RO1-GM71962.

  • This version contains curated information on regulation of transcription initiation up to end of March, 2008.


Release Notes for EcoCyc Version 12.0

Released on April 1, 2008.

EcoCyc KB Statistics
Pathways 224
Reactions 1658
Enzymes 1361
Transporters 227
Genes 4472
Transcription Units 3277
Citations 16,297

  • We have greatly expanded EcoCyc assignments to Gene Ontology terms by importing term assignments from UniProt. Previously, EcoCyc contained nearly 4000 GO term assignments covering approximately half of the gene products of E. coli; about one third of those GO terms had an experimental evidence code associated with them. We added more than 1000 GO term assignments with experimental evidence codes and approximately 30,000 GO term assignments with computational evidence codes from UniProt, now covering more than 80% of the gene products of E. coli. Note that GO term assignments in EcoCyc are made to gene products (monomers and multimeric complexes, depending on their function) to optimize the accuracy of annotation. GO term assignments will be updated on an ongoing basis by the EcoCyc curators.

  • Updates were made to approximately 40 membrane, transporter, and membrane structure-related proteins. Included are the recent assignments of MdtJI as a sperimidine exporter and YddG as an aromatic amino acid exporter.

  • We are currently updating our curation related to transcriptional regulation in E. coli, including the recent literature. In this release we have initiated the annotation of some promoters and DNA binding sites from computational predictions and from high-throughput experiments such as microarrays and ChIP-chip experiments. Only promoters or DNA binding sites that have evidence from at least two of these three types of experiments have been added to EcoCyc. Some examples are: Fur DNA binding sites identified by computational prediction and binding of purified protein in Chen et al. (2007), Sigma32 promoters identified by ChIP-chip, microarray analysis and in vitro transcription assays in Wade et al. (2006), and Sigma32 promoters identified by microarray analysis, transcription initiation mapping and in vitro transcription assays in Nonaka et al. (2006). Promoters identified by libraries of fluorescent transcriptional fusions (Zaslaver et al. (2006)) are also included in this release.


Release Notes for EcoCyc Version 11.6

Released on December 5, 2007.

EcoCyc KB Statistics
Pathways 225
Reactions 1661
Enzymes 1357
Transporters 226
Genes 4470
Transcription Units 3199
Citations 15,883

  • We have added two new pathways to EcoCyc: In addition, a number of pathways were re-organized into superpathways with shorter component pathways.

  • Data on the regulation of transcription initiation is now up-to-date. EcoCyc contains all promoters, transcription units, regulatory interactions, transcription factors and terminators that were published up to approximately four months before the release date. To achieve this goal, we have used four main strategies: curation by publication year, by regulon, by sigmulon and by biological systems. Note that our current curation does not include plausible interactions derived from high-throughput experiments, such as ChIP-chip and microarrays.

  • Updates were made to 28 transporters and 13 membrane and transport-related proteins.

  • Using the EC-to-GO mappings of enzymes to the Gene Ontology, we have added GO molecular function terms to every protein that catalyzes a reaction with a full EC number. All terms that were added were assigned computational evidence codes, although experimental evidence exists for the majority of the assignments. As part of our ongoing curation efforts, we will update the evidence codes to the proper experimental evidence codes when appropriate.


Release Notes for EcoCyc Version 11.5

Released on August 15, 2007.

EcoCyc KB Statistics
Pathways 224
Reactions 1615
Enzymes 1342
Transporters 224
Genes 4471
Transcription Units 3187
Citations 16,154

  • We have added one pathway to EcoCyc:

  • In addition to adding new pathways, we have begun to systematically update pathways that were entered into EcoCyc in the early years of the project. All enzymes participating in a pathway are re-curated, and the pathway summary is updated and expanded. Recently updated pathways include the methylerythritol phosphate pathway for the biosynthesis of isoprene units, serine biosynthesis, and glycine biosynthesis.

  • We have corrected and relocated the binding sites of the ArcA response regulator. ArcA is considered to be a global regulator and is involved in respiratory metabolism and controlling the expression of about 60 transcription units. The ArcA binding sites were previously represented as long regions of 60 bp, which were determined by foot printing of several promoter sequences. Computational analysis of these sequences showed a shorter 15 bp site, GTTAnnnnnnnGTTA, consisting of two direct repeats of 4 bp separated by 7 bp. Experimental support of this consensus sequence was obtained from foot printing, site-directed mutagenesis experiments and profiling ArcA-P dependent gene expression.

  • A number of newly predicted genes were recently added to the E. coli K-12 MG1655 GenBank and RefSeq sequence annotation files. These genes have been added to EcoCyc.


Release Notes for EcoCyc Version 11.1

Released on May 25, 2007.

EcoCyc KB Statistics
Pathways 223
Reactions 5220
Enzymes 1338
Transporters 223
Genes 4436
Transcription Units 3156
Citations 15,953

  • We have added six pathways to EcoCyc:

  • In an ongoing effort, we are updating the curation of metabolic pathways and enzymes that were initially added to EcoCyc more than ten years ago.

  • Acid resistance mechanisms have been curated, including updates to twelve acid resistance proteins, the addition of arginine and glutamate dependent acid resistance pathways (see above), and an update of the lysine degradation I pathway.

  • Updates were made to 43 membrane and transport related proteins.

  • The annotation of transcriptional promoters regulated by the sigma factors sigma19 (FecI), sigma28 (FliA), and sigma54 (RpoN) has been reviewed and updated. These factors are required for the transcription of specific sets of genes involved in the iron stress response, the flagellar system, and in nitrogen metabolism, respectively. Where experimental data was available, appropriate literature citations and notes were added.

  • The TyrR, TrpR and Lrp regulons have been updated. These regulons are related to processes such as transport, biosynthesis and catabolism of the amino acids tyrosine, phenylalanine, and tryptophan (aromatic), and also serine, glycine, glutamate, leucine, isoleucine, valine and threonine. The Lrp regulon is also important for the assimilation of ammonia in poor nitrogen conditions.

  • All transcription factors have now been assigned Gene Ontology and MultiFun terms.


Release Notes for EcoCyc Version 11.0

Released on March 16, 2007.

EcoCyc KB Statistics
Pathways 215
Reactions 5003
Enzymes 1323
Transporters 214
Genes 4461
Transcription Units 3063
Citations 15,335

  • We have significantly revised a number of pathways in EcoCyc:

  • We updated a number of protein function annotations with predictions from an updated annotation of the E. coli genome performed by the Paulsen group at TIGR.

  • We finished curation of information about transcriptional regulation of genes involved in the transport and metabolism of different nitrogen sources (including the preferred source, ammonia). This curation included the annotation of sigma54 promoters and nine trancription factors and their regulons, involved in nitrogen metabolism: NtrC, FlhA, NorR, PspF, PspR, HyfR, NacC, ZraR and RtcR.


Release Notes for EcoCyc Version 10.6

Released on January 10, 2007.

EcoCyc KB Statistics
Pathways 205
Reactions 4956
Enzymes 1307
Transporters 211
Genes 4465
Transcription Units 3133
Citations 14,951

  • We have updated evidence codes for a large number of proteins that were lacking this information.

  • Curation of flagellar proteins has been updated to include information regarding structure and function of several sub-complexes of the flagellum.

  • Approximately thirty transporters and other membrane proteins have been curated.

  • Notes for 30 regulatory proteins have been expanded and now include short summaries about the evolutionary family to which they belong, their domain composition, and the cellular processes in which the regulated genes are involved. When available, an indication of the active conformation of a complex (dimer, tetramer...) is given. Relevant physiological data about the effectors of transcription factors is also covered, with the aim of helping the understanding of regulation physiology. These summaries also have descriptive information about binding site features (size, consensus sequence, relative position to the transcription start, spatial arrangement of the site sequences).

  • We have computationally predicted transcription units for all E. coli genes that were not part of an existing transcription unit. Please be aware of the evidence codes on the right side of many pages that indicate what information was derived from experiments versus from computational predictions. Click on the evidence-code icons (such as the flask) for more information, and citations. Also be aware of the graphical conventions for distinguishing computationally predicted promoters and transcription factor binding sites in operon displays.


Release Notes for EcoCyc Version 10.5

Released on September 8, 2006.

EcoCyc KB Statistics
Pathways 197
Reactions 4854
Enzymes 1276
Transporters 211
Genes 4516
Transcription Units 1662
Citations 14,269

  • EcoCyc has reached a major curation milestone: the EcoCyc team has manually curated all E. coli gene products. For many years our curation staff has been performing literature searches for E. coli genes, and writing mini-review summaries describing the gene products for which we found published experimental information. We have completed our first pass of literature searches, resulting in summaries covering 3257 E. coli gene products in EcoCyc. The summaries are present in EcoCyc protein and RNA pages. For the remaining genes, no information was found in the literature.

  • We have added two new pathways to EcoCyc: In addition, a small number of pathways have been reorganized and split into two or more separate pathways.

  • We finished curating information on the transcriptional regulation of genes involved in both flagellar and chemotaxis systems; eight new promoters and five new transcription units as well as 21 new DNA-binding sites for the transcriptional regulator FlhDC were added.

  • We have completed the curation of 364 transcription units based on single-gene directons. A directon is one or a set of genes transcribed in the same direction, organized into one or several transcription units and operons (Salgado et al. (2000)). In other words, these 364 genes are surrounded by genes that are transcribed in a different direction, and therefore they must be transcribed in isolation.

  • Several transporters, DNA metabolism enzymes, proteins involved in peptidoglycan metabolism, lipopolysaccharide and colanic acid biosynthesis enzymes, and other membrane proteins have been curated.

  • We have curated the individual ribosomal subunit polypeptides.

  • The key players in transcription have been curated, including the core RNA polymerase, Sigma70, Sigma54 and the transcriptional regulators NusA, NusB, NusG and Rho.

  • We have updated links to the Swiss-Model and Modbase databases and removed links that were not connected to a model in these databases.


Release Notes for EcoCyc Version 10.1

Released on May 19, 2006.

EcoCyc KB Statistics
Pathways 190
Reactions 4469
Enzymes 1257
Transporters 209
Genes 4517
Transcription Units 1304
Citations 13,274

  • We have added one new pathway to EcoCyc: In addition, a small number of pathways have been reorganized and split into two separate pathways.

  • We have added or updated links to several databases:
    • Links from EcoCyc proteins to UniProt were updated.
    • Links were added from EcoCyc proteins to MODBASE and Swiss-Model. Please note that for many E. coli proteins, protein structure models are not yet available.

  • Our general curation update project is progressing. Of the 4517 gene products within EcoCyc, 4349 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 13274 literature citations. Specific areas that were updated include:
    • All 82 tRNAs are now curated
    • Leader peptides of various operons that are regulated by attenuation
    • Proteins involved in transcriptional regulation, including histidine kinases of two-component systems and several transcription factors
    • More than 30 membrane proteins, transporters, and DNA repair enzymes
    • Curation of Escherichia coli strain EDL933, serotype O157:H7 continues, with updates from the literature for approximately 20 proteins.

Release Notes for EcoCyc Version 10.0

Released on March 13, 2006.

EcoCyc KB Statistics
Pathways 187
Reactions 4308
Enzymes 1232
Transporters 208
Genes 4521
Transcription Units 1261
Citations 12,489
  • EcoCyc has been updated to reflect many aspects of the revised E. coli genome annotation published in Riley et al. (2006). Specific updates include:
    • 31 genes were deleted from the genome annotation. They have moved to the class "Phantom-Genes" in EcoCyc -- the class of entities previously thought to be genes, but no longer believed to be genes.
    • Approximately 60 new genes were created in EcoCyc to reflect newly discovered genes in the genome.
    • Start and end positions of EcoCyc genes were adjusted where necessary to make them the same as in the revised genome annotation.
    No sequence changes were made as part of the revised genome annotation.

  • We have added or updated links to several databases:
    • Links from EcoCyc proteins to PDB were updated.
    • Links were added from EcoCyc proteins to Pfam.
    • Links were added from EcoCyc genes to EchoBASE.
    • Links from EcoCyc to EcoGene now use the new EcoGene web site.
  • EcoCyc and RegulonDB have recently been updated with additional regulatory information and represent the largest comprehensive and constantly curated regulatory network of E. coli K-12. A report on our progress has been published in Salgado et al. (2006).

  • Our general curation update project is progressing. Of the 4480 polypeptides within EcoCyc, 3848 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 12489 citations. Specific areas that were updated include:
    • More than 60 membrane proteins, transporters, flagellar proteins, and DNA repair enzymes
    • Expansion of coverage of DNA replication to include additional helicases, DNA polymerase I, DNA gyrase and DNA ligase
    • Curation of Escherichia coli strain EDL933, serotype O157:H7 is underway, with updates from the literature for 82 proteins.

  • Regulation of degradation pathways: We expanded a project to curate within EcoCyc information about transcriptional regulation of gene expression for genes involved in the degradation of carbon sources, including the catabolism of sugars, polysaccharides and sugar derivatives. Pathways whose gene regulation has been curated are:
      CATABOLISM OF SUGAR DERIVATIVES: SUGAR CARBOXYLATES
    • Methylcitrate cycle
    • Methylmalonyl pathway
    • Conversion of succinate to propionate
    • Acetate utilization
    • Glycolate degradation I
    • Glyoxylate degradation
    • L-ascorbate degradation
      CATABOLISM OF SUGAR DERIVATIVES: SUGAR ALCOHOLS
    • Glycerol degradation I
    • Glycerol degradation II
    • Superpathway of glycol metabolism and degradation
      CATABOLISM OF AROMATIC COMPOUNDS
    • 3-phenylpropionate and 3-(3-hydroxyphenyl)propionate degradation
      Regulation of expression of enzymes involved in the degradation or utilization of melibiose, maltose, fructose, chitobiose, N-acetylgalactosamine, and beta-glucosides was curated.
      Regulation of the following additional pathways was curated:
      • Gluconeogenesis
      • Superpathway of gluconate degradation
      • Glycogen biosynthesis

Release Notes for EcoCyc Version 9.6

Released on December 15, 2005.

EcoCyc KB Statistics
Pathways 187
Reactions 4260
Enzymes 1222
Transporters 206
Genes 4480
Transcription Units 1232
Citations 12,026
  • We have added two new pathways to EcoCyc:

  • We have added Gene Ontology (GO) classifications to our gene pages. GO terms were added automatically based on the existing MultiFun terms and the mapping provided at the GO site. Both GO and MultiFun provide a classification scheme for attributes such as molecular function and biological process. We are planning to curate genes and proteins according to both classification schemes for a period of time.

  • Annotations of more than 70 membrane proteins, transporters, and flagellar proteins have been updated and expanded. Annotation of membrane proteins of E. coli strain CFT073 is underway.

  • We have curated RNA degradation and processing, including fourteen RNases and related proteins and the degradosome.

  • Twenty-four DNA replication genes have been curated, including most of the DNA polymerases, the DNA polymerase III holoenzyme complex and the primosome.

  • We have curated within EcoCyc gene regulatory interactions identified in datasets from Ma et al. (2004) and Shen-Orr et al. (2002) that were not present in EcoCyc.

  • Regulation of respiration pathways: We completed a project to curate within EcoCyc information about transcriptional regulation of gene expression for genes involved in respiration pathways in E. coli, which include aerobic and anaerobic phases, as well as those for electron transfer, electron donors and electron acceptors. Specific attention involved modifying all NarL binding sites with new central positions resulting from a consensus sequence of the site now defined by 7 nucleotides. Pathways whose gene regulation has been curated are:
    • Aerobic electron transfer
    • Aerobic respiration (electron donors reaction list)
    • Electron transfer (anaerobic)
    • Respiration (anaerobic)
    • Respiration (anaerobic)-electron acceptors reaction list
    • Respiration (anaerobic)-electron donors reaction list

  • Regulation of degradation pathways: We completed a project to curate within EcoCyc information about transcriptional regulation of gene expression for genes involved in the degradation of carbon sources, including the catabolism of sugars, polysaccharides and sugar derivatives. Regulation of operons encoding enzymes of glycolysis, the pentose phosphate pathway, the TCA cycle, and the Entner-Doudoroff pathway were also curated in this phase. Pathways whose gene regulation has been curated are:
      CATABOLISM OF SUGAR AND POLYSACCHARIDES
    • Lactose degradation III
    • D-allose degradation
    • D-arabinose degradation
    • Fucose degradation
    • Galactose degradation I
    • Glucose and glucose-1-phosphate degradation
    • Glycogen degradation
    • L-arabinose degradation
    • L-xylose degradation
    • Mannose degradation
    • Rhamnose degradation
    • Ribose degradation
    • Trehalose biosynthesis and degradation-low osmolarity
    • Xylose degradation
      CATABOLISM OF SUGAR DERIVATIVES: SUGAR ACIDS
    • beta-D-glucuronide degradation
    • D-galactarate degradation
    • D-galacturonate degradation
    • D-glucarate degradation
    • Galactonate degradation
    • Ketogluconate metabolism
    • L-idonate degradation
      CATABOLISM OF SUGAR DERIVATIVES: SUGAR ALCOHOLS
    • Galactitol degradation
    • Mannitol degradation
    • Sorbitol degradation
    • Superpathway of hexitol degradation
    • Fructoselysine degradation
    • Glucosamine degradation
      CATABOLISM OF SUGAR DERIVATIVES: AMINO SUGARS
    • Glucosamine degradation
    • N-acetylglucosamine
    • N-acetylmannosamine
    • N-acetylneuraminic acid dissimilation

      Regulation of the following additional pathways was curated:
    • Glycolysis I
    • Methylglyoxal pathway
    • Non-oxidative branch of the pentose phosphate pathway
    • Oxidative branch of the pentose phosphate pathway
    • TCA cycle
    • Glyoxylate cycle
    • Pyruvate dehydrogenase
    • Pyruvate oxidation pathway
    • Entner-Doudoroff pathway I

  • Our general curation update project is progressing. Of the 4471 polypeptides within EcoCyc, 3758 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 12026 citations.


Release Notes for EcoCyc Version 9.5

Released on September 30th, 2005.

EcoCyc KB Statistics
Pathways 184
Reactions 3939
Enzymes 1198
Transporters 198
Genes 4481
Transcription Units 1127
Citations 11,079
  • There have been many enhancements to the Pathway Tools software used to query EcoCyc. Please see the Pathway Tools Release Notes for more details. Highlights include:

    • Many improvements to the Cellular Overview and Omics Viewer, including abilities to magnify the display of a pathway within the Overview and Omics Viewer, and the ability to generate a table of omics-colored pathway drawings for all pathways whose omics values exceed some threshold.

    • A new suite of comparative genomics tools allows you to perform global comparisons among the 170 BioCyc DBs including EcoCyc. See the new Comparative Analysis section in the BioCyc Query Page.

    • A new comparative genome browser allows you to visualize chromosomal regions containing orthologous genes from EcoCyc and the other 170 BioCyc databases.

  • We have added one new pathway to EcoCyc:

  • Annotations of 57 transcriptional regulators have been updated and checked. Where experimental data was available, appropriate literature citations were added. In addition, annotations of membrane proteins have been updated and expanded, and we have added significant curation of proteins involved in RNA degradation and processing.

  • In an ongoing effort to eliminate duplicate information, we have combined the display of polypeptides and their homomultimers. Due to this update, the reported number of proteins that have comments in EcoCyc has declined since version 9.1.


Release Notes for EcoCyc Version 9.1

Released on May 23, 2005.

EcoCyc KB Statistics
Pathways 183
Reactions 3873
Enzymes 1186
Transporters 197
Genes 4477
Transcription Units 1113
Citations 10,747
  • EcoCyc has passed the 10,000 citation milestone!

    The information in EcoCyc has been derived from 10,747 peer-reviewed publications which are cited in the database. EcoCyc curators integrate information from many biomedical publications. They produce mini reviews of protein and RNA gene products that are stored as comments within those database objects. Of the 4465 polypeptides within EcoCyc, 3722 now have comments or citations or are components of a complex that has a comment or citations.

  • We have curated protein degradation and processing, including twenty-eight proteases and peptidases and a number of functionally related proteins.

  • We have added one new pathway to EcoCyc:

  • We have analyzed the E. coli regulatory network in RegulonDB and EcoCyc in detail. Differences between the two databases were mentioned in Ma HW, et al., 2004, Nucleic Acids Res. 2004 32(22):6643-9. We have identified all differences and have generated a unified description of the regulatory network in terms of regulatory and regulated genes and proteins.

  • Annotations of transcriptional regulators have been updated and expanded.


Release Notes for EcoCyc Version 9.0

Released on February 25, 2005.

EcoCyc KB Statistics
Pathways 183
Reactions 3634
Enzymes 1148
Transporters 196
Genes 4476
Transcription Units 983
Citations 9873
  • EcoCyc's coverage of complex cellular systems has grown. We have recently entered or updated comments on essential and non-essential cell division proteins in E. coli. This curation was performed under the guidance of Dr. William Margolin at the University of Texas, Houston. In addition, we have curated a number of flagellar proteins and membrane lipoproteins.

  • Our general curation update project is progressing. Of the 4463 polypeptides within EcoCyc, 3609 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 9873 citations.

  • We have added one new pathway to EcoCyc:

  • Due to our ongoing effort to eliminate duplicate binding sites of transcriptional regulatory proteins in the promoter regions of divergently transcribed genes and operons, the number of reactions reported in EcoCyc has declined.

  • We have substantially reorganized and expanded our display of genes and transcription units on the gene pages. In addition to the gene and operon, we now display information on the surrounding genes and their regulatory sites. This allows visualization of potentially overlapping regulatory regions, and thus the formulation of new hypotheses concerning transcriptional regulation. For example, see ybjC.

  • A new genome browser with expanded features implemented in the more common horizontal display format is available. For example, see the browser centered around dnaA. Some of the key features are:

    • At the top of the page, the full chromosome is shown at low resolution. A selected region of the chromosome is displayed at higher magnification in the lower part of the screen.
    • The full chromosome view at the very top indicates the magnified region by means of a red, rectangular cursor.
    • Magnified regions are wrapped over several lines, thus showing more context.
    • Several levels of semantic zooming show increasing detail upon increased magnification.
    • Protein ORFs are visually distinguished from RNA genes, and genes belonging to the same operon are assigned the same color.
    • An improved navigation interface offers a panel of control arrows that allow movement and zooming. Additionally, base-pair positions or a gene name can be manually entered into text entry boxes to position the browser.
    • Mouse-over of genes shows gene names and intergenic distances to the neighbors in base pairs. Mouse-over of promoters shows the activating and inhibiting transcription factors.

Release Notes for EcoCyc Version 8.6

Released on November 8, 2004.

EcoCyc KB Statistics
Pathways 182
Reactions 3676
Enzymes 1144
Transporters 197
Genes 4476
Transcription Units 977
Citations 9305
  • This EcoCyc release includes updates derived from the revised 2004 E. coli K-12 GenBank entry U00096.2, which supersedes the GenBank entry U00096.1 deposited by the Blattner laboratory in 1997. A summary of the updates to EcoCyc is listed below. Please note that due to changes in U00096.1, the genes encoded by successive b-numbers above b4409 are not necessarily adjacent on the chromosome.

  • Our curation update project is progressing. Of the 4458 polypeptides within EcoCyc, 3503 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 9305 citations.

  • We have reorganized and added comments to three pathways in EcoCyc:

  • Summary of the EcoCyc updates performed as a result of incorporating GenBank entry U00096.2:

    • The nucleotide sequence has been revised in 254 locations. The revisions include insertions, deletions, and substitutions. The Blattner laboratory provides a full list of sequence updates at URL http://www.genome.wisc.edu/sequencing/MG1655_update.xls.

    • Those sequence revisions necessitated updating all sequence features in EcoCyc including the locations of genes, transcription start sites, terminators, and transcription factor binding sites. We are grateful to Tatiana Tatusov and James Ostell of NCBI for assistance in computing the new coordinates of these sequence features. All EcoCyc version 8.6 gene sequence coordinates were obtained directly from U00096.2, with the exception that in approximately 25 cases, the EcoCyc project has modified the extents of the genes based on information from the experimental literature. However, coordinates of transcription start sites, terminators, and transcription factor binding sites in EcoCyc version 8.6 were derived from the EcoCyc version 8.5 coordinates, transformed to reflect the nucleotide sequence insertions and deletions.

    • U00096.2 modifies the E. coli gene list with deletions, additions, merges, and splits, and those modifications have been imported into EcoCyc as follows. Please note that gene names and product names were not imported from U00096.2 into EcoCyc on a large scale because of the careful curation of these fields that has occurred in EcoCyc for many years. However, for the genes below we did review all gene names and product names from U00096.2 and import them into EcoCyc when appropriate (e.g., for the created genes listed below).

      • The following genes were deleted: b0302 b0322 b0332 b0395 b0663 b0667 b0669 b0671 b1017 b1030 b1031 b2391 b3122 b3837

      • The following genes were created: b4409 b4411 b4412 b4415 b4419 b4420 b4421 b4422 b4423 b4424 b4425 b4428 b4429 b4447 b4455

      • The following genes were merged:
        • b2612 and b2613 were merged and became b4461
        • b1898 and b1899 were merged and became b4460
        • b2655 and b2656 were merged and became b4462
        • b2772 and b2773 were merged and became b4463
        • b2884 and b2885 were merged and became b4464
        • b2931 and b2932 were merged and became b4465
        • b2973 and b2974 were merged and became b4466
        • b3015 and b3016 were merged and became b4469
        • b3108 and b3109 were merged and became b4470
        • b3111 and b3112 were merged and became b4471
        • b3245 and b3246 were merged and became b4472
        • b3285 and b3286 were merged and became b4473
        • b3372 and b3373 were merged and became b4474
        • b3419 and b3420 were merged and became b4475
        • b3435 and b3436 were merged and became b4476
        • b3694 and b3695 were merged and became b4479
        • b3762 and b3763 were merged and became b4480
        • b3814 and b3815 were merged and became b4482
        • b3840 and b3841 were merged and became b4483
        • b3913 and b3914 were merged and became b4484
        • b4228 and b4229 were merged and became b4485
        • b4343 and b4344 were merged and became b4486
        • b4404 and b4405 were merged and became b4481
        • b3948 was merged into b3947

      • The following genes were split:
        • b2978 was split into b4467 and b4468
        • b3692 was split into b4477 and b4478

      • The following genes changed b-numbers. Many of these genes are interrupted genes that contain distinct IDs within EcoCyc, but are assigned a single b-number in U00096.2.
        • b3767 and b3768 became b4488
        • b1016 became b4490
        • b1169 and b1170 became b4491
        • b1401 and b1405 became b4492
        • b1416 and b1417 became b4493
        • b1720 and b1721 became b4494
        • b1933 and b1934 became b4495
        • b1964, b1965 and b1966 became b4496
        • b1979 and b1980 became b4497
        • b2087 and b2090 became b4498
        • b2115, b2116 and b2117 became b4499
        • b2227 and b2228 became b4500
        • b4091 became b4487

Release Notes for EcoCyc Version 8.5

Released on Sept. 17, 2004.

EcoCyc KB Statistics
Pathways 182
Reactions 3629
Enzymes 1133
Transporters 197
Genes 4497
Transcription Units 956
Citations 8862
  • Our curation update project is progressing. Of the 4478 polypeptides within EcoCyc, 3461 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 8862 citations.

  • Coverage of regulation of transcription initiation has grown. EcoCyc now describes 2393 specific interactions of transcription initiation (promoters and binding sites for regulators), including more than 1000 mapped transcription initiation sites with nearly 1400 binding sites for specific transcriptional regulatory factors (TFs). Furthermore, the names of TFs have been standardized, describing whether a TF acts as a repressor, activator, or has a dual effect. Comments on regulatory proteins have been expanded and updated. Annotations include the active conformation of TFs with the associated signal metabolites, the evolutionary family to which they belong, and whether they are auto regulated.

  • The EcoCyc Cellular Overview diagram has been re-organized. Metabolic pathways within the Overview are now grouped by classes, for example, all amino-acid biosynthetic pathways are grouped together on the diagram. Mousing-over a shaded background region of the Overview will identify the class of pathways in that region.

  • Please note that EcoCyc has not yet been modified to include the recent update to the E. coli genome sequence deposited in Genbank. We plan to include the updated E. coli sequence in our November 2004 release.

  • EcoCyc is now an open database, meaning it is free to all users, and that it can be redistributed, with or without modifications. See the license agreement that you click through on the way to the data files for more details. EcoCyc continues to be available in the following forms:


Release Notes for EcoCyc Version 8.1

Released on June 23, 2004.

EcoCyc KB Statistics
Pathways 182
Reactions 3547
Enzymes 1132
Transporters 197
Genes 4491
Transcription Units 931
Citations 8696
  • Our curation update project is progressing. Of the 4479 polypeptides within EcoCyc, 3395 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 8696 citations.

  • We have added five new pathways to EcoCyc:

  • We have completed curation of DNA repair enzymes in E. coli. In E. coli, there are a wide range of DNA repair systems. These systems include those for the direct reversal of DNA damage (photo reactivation, alkyl transfer) as well as indirect repair through the excision of damaged bases/sections of DNA and subsequent re-synthesis using the intact strand as template (base excision repair, nucleotide excision repair, mismatch repair) and homologous recombination. This curation work was performed at TIGR under the guidance of Dr. Jonathan Eisen.

  • EcoCyc is now an open database, meaning it is free to all users, and that it can be redistributed, with or without modifications. See the license agreement that you click through on the way to the data files for more details. EcoCyc continues to be available in the following forms:
    • Bundled with the Pathway Tools software in a form that you can run on a PC/Windows, PC/Linux, or SUN computer as a desktop application, or that you can run as a local EcoCyc Web server on your intranet
    • As a set of flat files you can load into your proprietary database

  • A Web page generated at each EcoCyc release contains a list of unsequenced enzymes of E. coli. These are enzymes that have been characterized biochemically and reported in the experimental literature, but whose gene has not been identified in the E. coli genome. Identification of these genes represents a challenge to the experimental community. A link to this page can be found under Information on the right menu on the EcoCyc.org page. A commentary on the larger topic of enzyme activities for which no sequence is known has been published by P. Karp in Genome Biology.

  • Conferences of interest to the E. coli community are now tabulated on our Web site. See the Conferences link under Services on the right menu on the EcoCyc.org page, or click here.

  • EcoCyc gene pages now contain links to corresponding pages in the EcoGene database.

Release Notes for EcoCyc Version 8.0

Released on March 12, 2004.

EcoCyc KB Statistics
Pathways 178
Reactions 3331
Enzymes 1043
Transporters 183
Genes 4479
Transcription Units 858
Citations 8014
  • Our curation update project is progressing. Of the 4474 polypeptides within EcoCyc, 2595 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 8014 citations.

  • The reactions contained within the superpathway of arginine degradation have been organized into separate subpathways:

  • We have made extensive updates to the database links within EcoCyc. The links from EcoCyc to Swiss-Prot were previously incomplete; we have added links to virtually all EcoCyc polypeptides, so that 99% of EcoCyc entries now contain links to Swiss-Prot. We have also added links from most EcoCyc polypeptides to RefSeq. The preceding links are all displayed under the heading "Unification Links," meaning links to information about the same biological object in a different database.

Release Notes for EcoCyc Version 7.6

Released on November 4, 2003.

EcoCyc KB Statistics
Pathways 176
Reactions 3177
Enzymes 992
Transporters 169
Genes 4477
Transcription Units 828
Citations 6223

Release Notes for EcoCyc Version 7.5

Released on August 29, 2003.

EcoCyc KB Statistics
Pathways 173
Reactions 3090
Enzymes 975
Transporters 168
Genes 4399
Transcription Units 810
Citations 4710
  • We are currently updating and expanding our curation of all E. coli gene products. As part of this expansion, we are authoring extended comments and curating updated reference lists. This information is typically found in the display windows for gene products in EcoCyc (rather than in the gene windows). Of the 4468 polypeptides within EcoCyc, 1600 now have comments or citations or are components of a complex that has a comment or citation. Our goal is to complete this expansion within the next few years.

  • EcoCyc database windows now feature full lists of references in addition to the links to abstracts that have been supplied previously. The list of references associated with each database object (e.g., polypeptide, pathway, transcription unit, etc.) is located at the bottom of the display window.

  • The pathway class hierarchy within EcoCyc has been updated and improved to facilitate browsing of metabolic pathways within the BioCyc databases. The pathway hierarchy may be viewed here.

  • The Pathway Tools software now supports association of evidence codes with information in the database. Currently, EcoCyc uses these codes most frequently for transcription units and promoters to indicate the type of evidence for the existence of these entities (for example, was a promoter predicted computationally or elucidated experimentally?). In subsequent releases, more evidence information will be available. The presence of a computer icon or a flask icon, respectively, indicate computational versus experimental evidence for an entity. Click on those icons to obtain more details about the evidence for an entity.

  • Many other miscellaneous corrections and updates have been applied.


Release Notes for EcoCyc Version 7.1

Released on May 20, 2003.

EcoCyc KB Statistics
Pathways 173
Reactions 3001
Enzymes 944
Transporters 168
Genes 4396
Transcription Units 777
Citations 4406
  • We are pleased to announce that new releases of EcoCyc at the BioCyc web site now occur quarterly, rather than twice a year. Newly updated EcoCyc flat files are also released quarterly. (The downloadable executable Pathway Tools containing EcoCyc is still released twice per year.)

  • The following pathways have been added to EcoCyc:
    • cyclopropane fatty acid (CFA) biosynthesis
    • fructoselysine degradation
    • lipoate biosynthesis and modification
    • lipoate salvage and modification

  • The y-gene names created by Dr. K. Rudd have been added to all ORFs within EcoCyc to enable searching for E. coli genes by those names. For example, the gene b1806 is now named yeaY.

  • Many other miscellaneous corrections and updates have been applied.


Release Notes for EcoCyc Version 7.0

Released on February 28, 2003.

EcoCyc KB Statistics
Pathways 169
Reactions 2909
Enzymes 930
Transporters 169
Genes 4392
Transcription Units 747
Citations 3780
  • In 2001, Serres et al. (Genome Biol 2(9)RESEARCH0035) published an update to the annotation of the E. coli genome in which new functions for unidentified E. coli ORFs were listed, based on experimental reports in the literature, and based on sequence analysis. We have loaded an even newer version of the annotation updates by Riley's group (from Riley's GenProtEC database) into EcoCyc. These updates involved changes to the function of ORFs only, and not to other genes with functions already assigned. In many cases, the new functional information was partial, such as indicating only that a protein is a putative membrane protein.

  • The pathways describing synthesis of nucleotides have been updated and divided into de novo and salvage synthesis pathways. The salvage synthesis pathways have been moved within the pathway hierarchy from the Network of nucleotide interconversions class (a subclass of Central intermediary metabolism) to the Nucleotides class (a subclass of Biosynthesis). The pathway objects replaced by these new updated pathways have been removed from EcoCyc.
    • The pathway de novo biosynthesis of pyrimidine ribonucleotides replaces and extends the former pyrimidine biosynthesis pathway. The pyrimidine biosynthesis pathway ended with the synthesis of UMP; the new de novo biosynthesis of pyrimidine ribonucleotides pathway extends to UDP, UTP, CDP, and CTP.
    • The new salvage pathways of pyrimidine ribonucleotides replace the former pyrimidine ribonucleotide/ribonucleoside metabolism pathway.
    • The pathways de novo biosynthesis of pyrimidine deoxyribonucleotides and salvage pathways of pyrimidine deoxyribonucleotides replace the former deoxypyrimidine nucleotide/side metabolism. The pathway de novo biosynthesis of pyrimidine deoxyribonucleotides includes the reduction of the nucleoside di- and tri-phosphates to the corresponding deoxyribonucleotides, which was not depicted within deoxypyrimidine nucleotide/side metabolism.
    • The pathway de novo biosynthesis of purine nucleotides replaces and extends the former purine biosynthesis pathway to include the reductions of the nucleoside di- and triphosphates to the corresponding deoxyribonucleotides.
    • Two salvage pathways of purine nucleoside biosynthesis have been added, salvage pathways of adenine, hypoxanthine, and their nucleosides and salvage pathways of guanine, xanthine, and their nucleosides, which replace the former purine ribonucleotide/ribonucleoside metabolism pathway.
    • Because the reduction of each ribonucleotide to the corresponding deoxyribonucleotide has been added to the pathways describing the de novo biosyntheses, the pathway that formerly comprised this group of reactions (entitled deoxyribonucleotide metabolism) has been removed.

  • The following other pathways have been added:
    • phenylacetate degradation, aerobic
    • L-ascorbate degradation

  • We have added 17 new promoters, 25 new DNA-binding sites for specific transcriptional regulators and 23 new transcription units. As a result of identifying the promoter, we verified and modified the precise position of the initiation of 21 genes (aldB, aspA, focA, gntK, livJ, slp, tdcR, caiF, upp, fixA, aroK, tauA, gcvR,nmpC, zraP, phoA, rbsD, ilvI, csiD, sugE, fxsA), whose initiation was overlapping transcription initiation.

  • Many other miscellaneous corrections and updates have been applied.


Release Notes for EcoCyc Version 6.5

Released on August 30, 2002.

EcoCyc KB Statistics
Pathways 164
Reactions 2862
Enzymes 918
Transporters 168
Genes 4393
Transcription Units 724
Citations 3701
  • Note that the reaction count includes metabolic reactions, transport reactions, and reactions related to transcriptional control of gene expression

  • Approximately 40 new transcription units have been added to EcoCyc since the last release. We have currently gathered information for 110 transcriptional regulators, 956 associated operator sites and interactions, and 812 mapped promoters. We estimate that these numbers correspond to approximately 25% of the interactions and knowledge necessary to describe the regulatory network of E. coli. Some general properties of this fraction of the network are the following. Around 80% of all transcription units are composed of one to three genes. These genes are mostly transcribed by a single promoter (80% of the cases) with few genes having two to six different promoters. We estimate that more than 85% of these are of the type recognized by sigma 70 RNA polymerase. More than 90% of genes are regulated by at most 3 different regulatory proteins. This significant fraction of the regulatory network in E. coli is a powerful resource for analysis of global experimental studies of transription and proteome, as well as in studies of properties of regulatory networks.


Release Notes for EcoCyc Version 6.0

Released on February 15, 2002.

EcoCyc KB Statistics
Pathways 164
Reactions 2760
Enzymes 914
Transporters 164
Genes 4393
Transcription Units 684
Citations 3636
  • Note that the reaction count includes metabolic reactions, transport reactions, and reactions related to transcriptional control of gene expression

  • EcoCyc contains many updates to the descriptions of E. coli genes, enzymes, pathways, and transporters

  • Approximately 50 new transcription units have been added to EcoCyc since the last release


Release Notes for EcoCyc Version 5.6

Released on June 15, 2001.

EcoCyc KB Statistics
Pathways 165
Reactions 2604
Enzymes 905
Transporters 162
Genes 4393
Transcription Units 629
Citations 3508
  • EcoCyc contains many updates to the descriptions of E. coli genes, enzymes, and transporters
  • Over 100 new E. coli transcription units have been added since the last version
  • EcoCyc proteins now contain WWW links to the PIR database
  • The following pathways were added to EcoCyc since the last release:
    • threonine biosynthesis from homoserine
    • alkanesulfonate monooxygenase two-component system
    • conversion of succinate to propionate
    • propionate metabolism, methylcitrate cycle
    • allantoin assimilation
    • D-allose catabolism
    • ketogluconate metabolism
    • tRNA charging reactions
    • biosynthesis of 2'-(5"-triphosphoribosyl)-3'-dephospho-CoA
    • BarA-UvrY Two-Component Signal Transduction System

Release Notes for EcoCyc Version 5.4

Released on Sept 1, 2000.

EcoCyc KB Statistics
Pathways 165
Reactions 2115
Enzymes 884
Transporters 158
Genes 4393
Chemical Compounds 773
Citations 3208
  • Dr. Julio Collado's RegulonDB database has been integrated with EcoCyc. EcoCyc therefore contains descriptions of many transcription units, where a transcription unit is defined as a promoter, its associated regulatory elements, and its downstream genes. EcoCyc also contains descriptions of many transcription factors, and their interactions with the transcription units they control.

    This information may be accessed within EcoCyc in several ways. Gene-display windows now show schematic diagrams of known transcription units for the gene. Within that transcription unit:

    • Clicking on the transcription unit as a whole will produce a new type of window that displays information about the transcription unit and all of its internal regulatory sites.
    • Clicking on a transcription-factor binding site within the transcription unit will produce a display window for the transcription factor that lists all transcription units that it controls.
    • Clicking on the promoter ...
    • Clicking on a gene within the transcription unit will display a window for that gene.
  • Because MetaCyc is now meant as our general-purpose metabolic-pathway database, we have removed non-E. coli specific metabolic information from EcoCyc, such as metabolic reactions and compounds that do not occur in E. coli. That data had previously been present in EcoCyc for general reference purposes.
  • A new version of Dr. Monica Riley's classification system for E. coli genes has been added to EcoCyc.
  • An assignment of E. coli genes to paralogous groups by Dr. Riley and Dr. Bernard Labedan has been added to EcoCyc. When a gene is a member of a paralogous group, the name of the group will be displayed in the EcoCyc gene window. Clicking on the group name will display a list of all genes within the group. See: Labedan, B and M. Riley. (1999) Genetic inventory: Escherichia coli as a window on ancestral proteins .In Organization of the Prokaryotic Genome (Robert Charlebois, editor) Chapter 17, pages 311-329, ASM Press, Washington, D.C.
  • Many revisions to E. coli gene names and to the functions of E. coli gene products have been incorporated in EcoCyc.

Release Notes for EcoCyc Version 5.0

Released on June 16, 1999.

EcoCyc KB Statistics
Pathways 159
Reactions 946
Enzymes 629
Transporters 13
Genes 4390
Chemical Compounds 1868
Citations 1944
Notes: "Pathways" includes both pathways of small-molecule metabolism and signalling pathways. "Reactions" includes enzymatic and transport reactions.

Changes to the EcoCyc Data

  • Drs. Ian Paulsen and Milton Saier of UC San Diego have recently joined the EcoCyc collaboration. Their group will be annotating the transport proteins of E. coli using the same detailed, literature-based approach as used for E. coli enzymes and pathways. Version 5.0 of EcoCyc contains all of the E. coli phosphotransferase system (PTS) transporters. Subsequent versions of Ecocyc will include detailed descriptions of the primary and secondary transporters and channel proteins present in E. coli.
    The PTS functions by transporting and concomitantly phosphorylating their sugar substrates using phosphoenolpyruvate as a phosphate donor. Each PTS transporter characteristically consists of a sugar-specific multidomain Enzyme II complex with between one and four protein subunits and two general energy coupling proteins, Enzyme I and Hpr. The Version 5.0 release describes each of the 20 Enzyme II complexes and the two general energy coupling proteins of the PTS.
  • New pathways in this version are:
    • isopentenyl diphosphate biosynthesis, mevalonate-independent
    • acetate utilization
    • dissimilation of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminic acid
    • ammonia assimilation cycle
    • L-idonate catabolism
    • arginine catabolism
  • A variety of miscellaneous updates have been applied to EcoCyc genes and enzymes.

Modifications to the Pathway/Genome Navigator Interface

  • You must now use Netscape 4.0 or Internet Explorer 4.0 (or higher) to access EcoCyc because older versions of these programs do not have proper support for Javascript.
  • The EcoCyc web site has been upgraded and reorganized. Although the location of the EcoCyc home page has not changed, the URL of the main EcoCyc query page has changed to [old URL removed]. Please update any bookmarks you may have to the old server page.
  • Users may now issue structured queries to the EcoCyc database using an HTML query form that is available at [old URL removed].
  • X-Windows version: In Overview mode, the menu that appears when the user right clicks on a compound or reaction in the Overview has been reorganized and has additional functionality. A new function is the ability to show all connections from one occurrence of a compound in the Overview to all other occurrences of that compound.
  • X-windows version: A new user preference allows the Overview diagram to be scaled as desired.
  • X-windows version: The user can now print the contents of the Answer List and the History List using commands under the Special menu.
  • X-Windows version: Users can now control the font size using a newly defined user preference

Release Notes for EcoCyc Version 4.5

Released September 4, 1998.

The most significant changes are marked with a "*".

Changes to the EcoCyc Data

  • The gene descriptions within EcoCyc have undergone extensive curation to update gene name and synonym information, as well as product descriptions for all E. coli genes.
  • EcoCyc is very careful to distinguish genes whose functions have been determined experimentally, from those whose functions have been determined through sequence analysis. The names of gene products whose functions have been determined through sequence analysis always contain the word "putative" and, very occasionally for a high certainty hit, "probable." The level of assurance for each functional assignment is given in the following way. If an orf sequence shows similarity to a number of hydrolases, all of which act on on sugars, the orf is identified as, for instance, a "putative sugar hydrolase" . In other cases an assignment may be "putative amidotransferase" or "putative aminotransferase" or "putative formyl acetyltransferase". More often a degree of uncertainty is signified by by confining the assignment to a general class such as "putative transferase" or sometimes only as an "enzyme" if the orf can be identified as an enzyme, but not what kind of enzyme. the same gradations are used throughout for all types of gene products such as regulators, transport components, rnas.

Modifications to the EcoCyc Graphical User Interface (GUI)

  • *EcoCyc pathway diagrams now include arrows showing regulatory interactions between small molecules and enzymes of a pathway. Each arrow portraying feedback inhibition or activation leads from a small molecule in the pathway to a "+" or "-" sign adjacent to the enzyme whose activity it moderates. The presence of the "+" or "-" indicates whether activators, inhibitors, or both, are known for a given enzyme.
  • The Overview diagram now uses different icons for different classes of compounds:
    square = carbohydrate
    triangle = amino acid
    diamond = lipid
    horiz elipse = purine
    vert elipse = pyrimidine
    hexagon = protein
    circle = all other compound types
    Solid icons mean the compound is phosphorylated
  • *EcoCyc now generates automatic layouts of signal-transduction pathways, and the Overview diagram now includes signal-transduction pathways. For example, query the proteins PhoB or NarQ, and you will see links to their pathways, which can be displayed.

X-Windows EcoCyc GUI Modifications

  • *The Highlighting menu for Overview mode has been redesigned and has a number of additional features and query operations, including the ability to paint expression data on the Overview diagram.
  • A new user preference controls whether the "Next Answer" command retrieves only one answer per click, or N answers, when there are N display panes active.
  • The main menu now includes commands called Fix and Unfix, which allow the user to fix a display pane, thus preventing additional object displays from replacing the object shown in that pane. Fix a pane if you wish to see the same object across a number of queries. If all panes are fixed and the user displays an additional object, it will be displayed in a pop-up window (an existing window will be reused; otherwise a new window will be created).

Current knowledge base size:

   :::: Ecocyc KB statistics on Fri Sep 4, 1998 ::::

Reactions: 4607 total
  180 have no EC#
  904 occur in E. coli

Polypeptides: 1265
Protein complexes: 576
Enzymes: 802
Two-component sig trans: 45

Pathways:
  Small-molecule metabolism: 131
  Signaling: 20
  Superpathways: 34

Compounds: 1308   (975 have structures)

Genes:  4391 
  1400 ORFs

tRNAs: 79


Release Notes for EcoCyc Version 4.0

Released April 15, 1998.

The most significant changes are marked with a "*".

Changes to the EcoCyc Data

  • EcoCyc describes all published pathways of E. coli metabolism. The following pathways were added since version 3.7:
    • carnitine metabolism, CoA-linked
    • enterobactin synthesis
    • phenylethylamine degradation
  • *EcoCyc now describes E. coli two-component signal transduction proteins.
  • EcoCyc now describes E. coli tRNAs.
  • *Data from the full E. coli nucleotide sequence determined by the Blattner laboratory (Science 277:1453 1997) are now included within EcoCyc. The included data were obtained from the Genbank entry submitted by the Blattner laboratory.
  •  All genes defined in this Genbank entry (which we term the "Blattner genes") were loaded into EcoCyc by merging the Blattner genes with gene objects that existed previously in EcoCyc. The initial merging was performed programmatically by matching the gene names assigned to the Blattner genes against the gene names and synonyms maintained in EcoCyc. These matches were confirmed by checking the Swiss-Prot links provided for many genes by the Blattner group with the Swiss-Prot links that exist for many EcoCyc genes. 2497 matches were found of which 2265 were confirmed using the Swiss-Prot links. A number of additional gene correspondences were determined through manual inspection.

    Therefore, EcoCyc now contains three classes of E. coli genes: (a) Genes that existed previously in EcoCyc that no Blattner gene matched, (b) Genes that existed previously in EcoCyc that were merged with a matching Blattner gene, and (c) Genes defined in the Blattner Genbank record that were not found to match any EcoCyc gene. The class of each gene is indicated in EcoCyc using a history entry that is displayed within the gene window. Over time, we expect more gene correspondences to be discovered.

  • Many more citations are now linked to PubMed.

Modifications to the EcoCyc Graphical User Interface (GUI)

  • The display of chemical structures within compound windows now uses a concept called superatoms, which is a hierarchical structuring of chemical structures. For example, when displaying the structure for succinyl-CoA, the structure is initially displayed with the word "CoA" in place of the structure of the CoA moiety. If the user clicks on the word CoA, however, the full structure of that moiety will be displayed (clicking on the name to expand works only in the X-windows version).
  • Pathway displays now include a small circular genome map, marked with the positions of all genes that encode the enzymes within the current pathway. Moving the mouse over the mark for a given gene flashes the gene name at the bottom of the screen, and also (X-Windows version only) highlights the arrows within the pathway for the reaction(s) catalyzed by the gene product. Clicking on a gene navigates to the gene display.
  • Circular pathways are now drawn with curved reaction arrows.
  • *EcoCyc uses a new scheme for displaying iterative pathways of synthesis or degradation of polymeric compounds. For each iteration the polymer increases or decreases a fixed number of monomers. The repeating iterations are indicated with a dashed line.
  • Displays for gene classes now show gene name and gene product (where known) rather than just gene name.
  • In the display of compounds and proteins, the presentation of the reactions in which a compound or protein is a substrate has been reorganized. Each reaction is listed under the pathway(s) (if any) in which it occurs.

Modifications Specific to the X-windows GUI

  • *Overview Mode is now available for the first time in the X-windows Ecocyc. This mode displays the full metabolic map of E. coli. A number of queries are supported including highlighting reactions within the map according to EC number, enzyme name, gene name, and according to activation or inhibition of an enzyme by a specified compound.
  • Enzyme command mode has been renamed Protein Mode because it can be used to query and display other types of proteins in addition to enzymes.
  • A new command called Get Rxn by Substrates allows you to query all reactions that contain a specified set of reactants and/or products.
  • EcoCyc uses a dedicated Netscape window for looking up citations.
  • Cloned windows now have forward and back buttons.
  • Hard copy printing of Greek letters now works, and some lines that previously were drawn with an extremely thin width are now drawn wider.
  • Short comments are now displayed in the pointer documentation window when the mouse is passed over them. (Longer comments still need to be displayed in a pop-up window)
  • The EcoCyc history list now stores the window scrolling position within the history, so that when the user moves forward and backward in the history, the scrolled position is remembered.

Modifications Specific to the World-Wide Web GUI

  • We are now using client-side image maps, rather than server-side image maps, with imbedded javascript to show object names/descriptions instead of URLs.

Current knowledge base size:

   :::: Ecocyc KB statistics on Fri Dec 12, 1997 ::::

Reactions: 4412 total;  988 occur in ECOLI;  166 have no EC#

Polypeptides: 1196;  Protein complexes: 563; Enzymes: 804

Genes: 4909   (4357 have assigned map positions)

Base pathways: 123;  Superpathways: 34

Compounds: 1303   (977 have structures)


EcoCyc Version 3.7, released March 7, 1997

Changes introduced in this version include:
  • An Overview diagram of the entire E. coli metabolic map is now available
  • We believe that EcoCyc now describes all published pathways of E. coli metabolism. The following pathways were added since version 3.1:
    • trehalose biosynthesis
    • NAD phosphorylation and dephosphorylation
    • betaine biosynthetic pathway
    • mannose and GDP-mannose metabolism
    • formylTHF biosynthesis
    • methylglyoxal metabolism
    • nucleotide metabolism
    • arginine utilization
    • L-serine degradation
    • glutamine utilization
    • glutamate utilization
    • L-cysteine catabolism
    • tryptophan utilization
    • ornithine degradation
    • putrescine degradation
    • D-galactarate catabolism
    • galactitol catabolism pathway
    • mannitol degradation
    • sorbitol degradation
    • trehalose degradation, low osmolarity
    • D-glucarate catabolism
    • cobalamin biosynthesis
    • glutathione-glutaredoxin redox reactions
    • anaerobic respiration, electron acceptors reaction list
    • aerobic electron transfer
    • aerobic respiration, electron donors reaction list
    • anaerobic respiration, electron donors reaction list
    • anaerobic respiration
    • anaerobic electron transfer
  • Compound displays now sort the set of reactions that contain the compound according to the pathways that contain the reactions.
  • The X-window version of EcoCyc now displays links to other databases; if you click on a link then EcoCyc will invoke Netscape to query the linked object via the WWW.
  • In the X-window version, most modes that allow you to query objects by their exact name allow you to enter in several names within one pop-up window, separated by commas, e.g., "Find Gene by Name" allows you to enter "hisA, hisB, hisC." The exception is compound mode, because many compounds have commas within their names.
  • Links have been added from EcoCyc to the Swiss-Model database (thanks to Manuel Peitsch for assistance).
  • A second gene-classification system has been added to EcoCyc. This second system, also developed by Riley, is much simpler than the first system, and classifies genes according to the type of their product, e.g., enzyme, regulator, transport protein.
  • EcoCyc executables are now available for Solaris but are no longer available for SunOS.
  • EcoCyc does not yet contain the full annotation of the E. coli genome; that task is next on our list. Thus, the data in slots centisome-position, left-end-position, and right-end-position, are all derived from EcoGene7.
Current knowledge base size:

    :::: Ecocyc KB statistics on Thu Feb 20, 1997 ::::

Reactions: 3241 total;  736 occur in ECOLI;  165 have no EC#

Polypeptides: 1029;  Protein complexes: 419; Enzymes: 731

Genes: 3025   (2571 are mapped)

Base pathways: 131;  Superpathways: 26

Compounds: 1294   (964 have structures)

EcoCyc Version 3.1, released July 17, 1996

Improvements introduced in this version include:
  • EcoCyc executables are now available for Solaris in addition to SunOS.
  • This version contains detailed descriptions of pathways that were only superficially encoded in the previous version, including detailed information on 125 new enzymes. It also contains a number of new reactions that connect to many pathways, and hence are not recorded as being part of specific pathway.
  • Many data corrections and additions have been made.
  • The following pathways were added since version 2.7:
    • lactose degradation
    • (deoxy)ribose phosphate metabolism
    • riboflavin, FMN and FAD biosynthesis
    • pyridoxal 5'-phosphate biosynthesis
    • menaquinone biosynthesis
    • biosynthesis of proto- and siroheme
  • EcoCyc now displays superscripts, subscripts, and Greek characters in appropriate places.
  • Database links -- EcoCyc is now linked to the CGSC in addition to SwissProt and PDB.
  • The Clone Window command in the X-window EcoCyc allows a display of any object to be cloned in a separate window. Replaces the Fix-Item and Unfix-Item commands.
  • The EcoCyc class hierarchy can now be queried through the WWW interface, and users can navigate the hierarchy within individual object displays by following the Superclass, Subclass, and Instance links.
  • EcoCyc genes are now classified according to two hierarchies developed by Riley: one hierarchy considers the physiological role of the gene product, the other hierarchy considers the type of the product (enzyme, regulator, etc)
  • The WWW map browser now allows the user to expand the map to show a gene that is specified by the user
  • The representation of cofactors and coenzymes in EcoCyc has been revised.
  • The X-window version of EcoCyc now queries Medline and Entrez using Netscape, which must be installed on your system for these queries to work
  • For the bracketed numbers that refer to citations and comments in EcoCyc displays, such as [1], if the number is italicized it is a comment, otherwise it is a citation.
Current knowledge base size:

Reactions: 2965 total;  690 occur in ECOLI;  87 have no EC#

Polypeptides: 598;  Protein complexes: 312; Enzymes: 523

Genes: 2957   (2571 are mapped)

Base pathways: 101;  Superpathways: 26

Compounds: 1274

Publications: 765

EcoCyc Version 2.7, released Feb 19, 1996

Improvements introduced in this version include:
  • A number of minor programming enhancements
  • The following pathways were added since version 2.4:
    • methyl-donor molecule biosynthesis
    • propionate metabolism, methylmalonyl pathway
    • UDP-N-acetylglucosamine biosynthesis
    • peptidoglycan precursor and lipid a precursor biosynthesis
    • ppGpp metabolism
    • glycolate metabolism
    • glucosamine catabolism
    • pyrimidine ribonucleotide/ribonucleoside metabolism
    • glycine biosynthesis
    • asparagine biosynthesis
    • glycogen biosynthesis
    • peptidoglycan precursor biosynthesis
    • peptidoglycan biosynthesis
    • dTDP-rhamnose biosynthesis
    • KDO biosynthesis
    • lipid-A-precursor biosynthesis
    • degradation of short-chain fatty acids
    • galactose, galactoside and glucose catabolism
    • glyoxylate degradation
    • rhamnose catabolism
Current knowledge base size:

    Reactions: 2929 total;  627 occur in E. coli;  87 have no EC#
    
    Polypeptides: 523;  Protein complexes: 264
    
    Enzymes: 397
    
    Genes: 2956   (2571 are mapped)
    
    Total Pathways: 94;  Superpathways: 11
    
    Compounds: 1253
    
    Publications: 565

EcoCyc Version 2.6, released Dec 11, 1995

(This version was released on our WWW server only.)

Improvements introduced in this version include:

  • New gene data -- EcoCyc now contains Rudd's EcoGene.7, which describes 1000 more mapped E. coli genes than EcoGene.6
  • Database links -- EcoCyc is now linked to SwissProt and PDB
  • Gene-Reaction schematics summarize gene/enzyme/reaction relationships
  • Several new pathways have been added
  • Pathway windows now contain commands called More Detail / Less Detail, which apply different levels of information filtering to pathway displays
Knowledge base size:

    Reactions: 2910 total;  598 in E. coli;  87 w/ no EC#
    
    Polypeptides: 491;  Protein complexes: 250
    
    Enzymes: 348
    
    Genes: 2962   (2577 are mapped)
    
    Total Pathways: 97;  Superpathways: 11
    
    Compounds: 1241
    
    Publications: 470

EcoCyc Version 2.4, released Oct 4, 1995

Improvements introduced in this version include:
  • More data -- EcoCyc now contains 100 metabolic pathways
  • The circular genomic-map viewer is introduced (see Gene Map Mode command)
  • Any EcoCyc window can be saved to a postscript file for printing (see Print To File command)
  • All reactions known to occur in E. coli are now marked as such, even if EcoCyc does not yet describe the corresponding enzyme
  • Many citations were added to the KB
  • A new user preference controls whether reactions are drawn in the systematic direction defined by Enzyme Nomenclature, or in the direction they proceed in the context of a pathway
  • Different enzyme names can now be explicitly associated with the different activities of an enzyme
  • Citations and Genbank sequences can be saved to a file
  • Relationships among components of an enzyme complex are displayed more accurately, and reactions catalyzed by the components are shown
  • The curved arcs adjacent to side compounds are now drawn in pathway displays