EcoCyc Update History

This document summarizes the history of updates to EcoCyc.

EcoCyc Knowledgebase Cumulative Statistics by Year
  2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 Description
Pathways 376 365 363 359 354 352 347 342 338 328 320 300 281 276 Metabolic plus signaling pathways. Excludes super-pathways.
Reactions 3226 3057 3017 2968 2911 2831 2728 2659 2478 2361 2284 2120 1991 1907 Includes metabolic reactions and transport reactions.
Enzymes 1734 1714 1703 1682 1641 1617 1593 1568 1555 1533 1505 1485 1470 1451 Number of enzymes that catalyze biochemical reactions.
Transporters 298 291 290 288 286 286 284 282 284 277 269 264 257 254 Number of transporters.
Gene product summaries 4170 4148 4129 4087 4070 4012 3940 3884 3852 3804 3751 3706 3710 3676 Number of gene products containing written summaries.
Genes 4557 4546 4545 4518 4534 4499 4496 4497 4500 4501 4501 4499 4503 4490 Number of genes, including some that have not been pinned to the DNA sequence.
Transcription Units 3718 3695 3697 3705 3597 3552 3555 3556 3549 3538 4510 4490 4463 3412 Number of transcription units -- includes operons and single-gene transcription-units.
Citations 44,142 42,700 41,490 39,865 37,929 36,151 34,421 32,534 30,224 27,887 25,406 23,909 22,039 20,890 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 27.5

Released on December 08, 2023.

EcoCyc KB Statistics
Pathways 376
Reactions 3226
Enzymes 1734
Transporters 298
Genes 4557
Transcription Units 3718
Citations 44,142

Improvements to the EcoCyc Database

For this release of the EcoCyc database, we have curated new pathways and reactions, new functions for existing proteins and small RNAs, and new regulatory interactions:

Release Notes for EcoCyc Version 27.1

Released on August 28, 2023.

EcoCyc KB Statistics
Pathways 372
Reactions 3212
Enzymes 1732
Transporters 297
Genes 4557
Transcription Units 3705
Citations 43,542

Improvements to the EcoCyc Database

Several new pathways and reactions were added:

Significant upgrades to major nucleotide binding and cell division proteins:

Additional upgrades of note include:

Release Notes for EcoCyc Version 27.0

Released on April 12, 2023.

EcoCyc KB Statistics
Pathways 367
Reactions 3073
Enzymes 1717
Transporters 292
Genes 4556
Transcription Units 3305
Citations 42,963

Highlights of EcoCyc Database Improvements

Multiple new genes, including two new proteins and several small RNAs, and new functions for existing proteins have been added and curated with summaries for each new gene product and regulatory interactions for the small RNAs with functions identified.

New genes:

New small RNAs added to Ecocyc:

New gene functions curated:

Other updates include:

Release Notes for EcoCyc Version 26.5

Released on December 13, 2022.

EcoCyc KB Statistics
Pathways 365
Reactions 3057
Enzymes 1714
Transporters 291
Genes 4546
Transcription Units 3695
Citations 42,700

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 26.1

Released on August 24, 2022.

EcoCyc KB Statistics
Pathways 365
Reactions 3055
Enzymes 1714
Transporters 291
Genes 4546
Transcription Units 3694
Citations 42,357

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 26.0

Released on April 13, 2022.

EcoCyc KB Statistics
Pathways 364
Reactions 3052
Enzymes 1713
Transporters 291
Genes 4545
Transcription Units 3696
Citations 41,925

EcoCyc Modeling Tab Contains Predictions from E. coli Whole Cell Model

This version of EcoCyc contains predictions from computer simulations of an E. coli cell from the E. coli whole-cell modeling project. The aim of the project is to build a computational representation of an E. coli cell that fully captures the dynamics of every known molecule within an E. coli cell, using a heterogeneous set of parameters that are curated from decades of research conducted on this model microbe. The model ties together multiple submodels that each represent a particular domain of an E. coli cell, using the mathematical framework that is most appropriate for the given domain. Macklin et al., 2020 provides more details on how the model was constructed and how its outputs were validated.

The predictions are present on the new Modeling tab on EcoCyc gene pages (example). The Modeling tab contains predictions of the cellular copy numbers for the mRNA and protein product of that gene under three conditions of E. coli growth: aerobic and anaerobic growth under M9 medium with 0.4% glucose, and aerobic growth under M9-derived rich medium. The presented data were calculated by running a batch of computer simulations of an E. coli cell.

Through a collaborative effort between the EcoCyc team and the whole-cell modeling project team, we have built a pipeline that allows the whole-cell model to import a subset of the required input parameters, which includes genome annotations, RNA/protein sequences, metabolic reaction networks, transcription factor networks, and reaction stoichiometries, directly from the latest release of the EcoCyc database. With each updated release of EcoCyc, a new batch of simulations is initialized with the newly imported parameters from EcoCyc, and the outputs from the updated simulations are reported on the modeling tabs for EcoCyc gene pages.

The whole-cell model simulates the dynamics of individual cells, which allows it to capture how stochastic processes can lead to heterogeneity between cells that are grown under the same conditions. Thus, in addition to the mean values that are taken from the average of all simulated cells, we are also able to report the standard deviations of each value between the simulated cells, which are presented as error terms in the provided data.

The latest released version of the model code can be accessed for a closer look into the inner workings of the whole-cell model. Please note that the Modeling tab data were generated from the latest working version of the model that contains further updates that may lead to output values that are different from the released version.

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 25.5

Released on December 15, 2021.

EcoCyc KB Statistics
Pathways 363
Reactions 3017
Enzymes 1703
Transporters 290
Genes 4545
Transcription Units 3697
Citations 41,490

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 25.1

Released on August 5, 2021.

EcoCyc KB Statistics
Pathways 362
Reactions 3010
Enzymes 1701
Transporters 290
Genes 4523
Transcription Units 3697
Citations 41,037

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 25.0

Released on May 20, 2021.

EcoCyc KB Statistics
Pathways 360
Reactions 2995
Enzymes 1692
Transporters 288
Genes 4523
Transcription Units 3697
Citations 40,472

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 24.5

Released on January 7, 2021.

EcoCyc KB Statistics
Pathways 359
Reactions 2968
Enzymes 1682
Transporters 288
Genes 4518
Transcription Units 3705
Citations 39,865

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 24.1

Released on September 8, 2020.

EcoCyc KB Statistics
Pathways 359
Reactions 2965
Enzymes 1681
Transporters 287
Genes 4539
Transcription Units 3716
Citations 39,572

Highlights of EcoCyc Database Improvements

To improve the other E. coli PGDBs in BioCyc (meaning those PGDBs describing strains other than K-12 MG1655), we propagated gene and protein annotations from EcoCyc to the 480 other E. coli PGDBs in BioCyc. On average, each of those PGDBs received updates to 2535 gene or proteins. The information we propagated included gene and protein names, protein complex assignments, and the reactions assigned to each protein. Propagation was performed from a gene or protein in EcoCyc only if it had experimental support, and only if the existing annotations for the target gene or protein did not have experimental evidence. The target gene/protein is a computed ortholog of the source gene/protein. The propagation event was recorded in a "history entry" for the target gene/protein that is displayed on the gene/protein page and explains what information was propagated.

The following improvements were made to EcoCyc itself.


Release Notes for EcoCyc Version 24.0

Released on May 14, 2020.

EcoCyc KB Statistics
Pathways 355
Reactions 2934
Enzymes 1655
Transporters 286
Genes 4534
Transcription Units 3599
Citations 38,924

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements


Release Notes for EcoCyc Version 23.5

Released on December 18, 2019.

EcoCyc KB Statistics
Pathways 354
Reactions 2911
Enzymes 1641
Transporters 286
Genes 4534
Transcription Units 3597
Citations 37,929

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements


Release Notes for EcoCyc Version 23.1

Released on September 19, 2019.

EcoCyc KB Statistics
Pathways 354
Reactions 2896
Enzymes 1641
Transporters 286
Genes 4540
Transcription Units 3595
Citations 37,630

We propagated extensive information from EcoCyc to the BioCyc database for E. coli CFT073. For more details see the BioCyc release notes.

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 23.0

Released on April 29, 2019.

EcoCyc KB Statistics
Pathways 352
Reactions 2852
Enzymes 1619
Transporters 286
Genes 4501
Transcription Units 3553
Citations 36,585

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements

Highlights of Desktop Software Improvements


Release Notes for EcoCyc Version 22.6

Released on December 12, 2018.

EcoCyc KB Statistics
Pathways 352
Reactions 2831
Enzymes 1617
Transporters 286
Genes 4499
Transcription Units 3552
Citations 36,151

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 22.5

Released on September 25, 2018.

EcoCyc KB Statistics
Pathways 350
Reactions 2817
Enzymes 1611
Transporters 285
Genes 4500
Transcription Units 3550
Citations 35,788

New GenBank File for Escherichia coli K-12 MG1655 Released!

A new GenBank file of the E. coli K-12 MG1655 genome and annotation (U00096.3) was released on September 24, 2018. The updated genome annotation in this file was directly generated from EcoCyc Version 22.5 in a collaboration with Guy Plunkett III (University of Wisconsin), Andrea Auchincloss (UniProt/Swiss-Prot), and NCBI.

The most recent prior update to U00096.3 was released on August 1, 2014. The version suffix is changed only when the nucleotide sequence has changed -- thus the version number remains the same for this new release because no changes have been made to the nucleotide sequence. This new update does contain a large number of other changes based on publications in the past four years. The most significant updates include:

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements


Release Notes for EcoCyc Version 22.0

Released on April 24, 2018.

EcoCyc KB Statistics
Pathways 349
Reactions 2777
Enzymes 1599
Transporters 284
Genes 4501
Transcription Units 3560
Citations 35,024

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements


Release Notes for EcoCyc Version 21.5

Released on Nov 28, 2017.

EcoCyc KB Statistics
Pathways 347
Reactions 2728
Enzymes 1593
Transporters 284
Genes 4496
Transcription Units 3555
Citations 34,421

Highlights of EcoCyc Database Improvements

EcoCyc contains the equivalent of 3,000 textbook-pages of mini-review summaries.

Highlights of Website Improvements


Release Notes for EcoCyc Version 21.1

Released on Aug 15, 2017.

EcoCyc KB Statistics
Pathways 345
Reactions 2715
Enzymes 1585
Transporters 284
Genes 4489
Transcription Units 3555
Citations 33,843

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 21.0

Released on April 27, 2017.

EcoCyc KB Statistics
Pathways 343
Reactions 2686
Enzymes 1572
Transporters 283
Genes 4497
Transcription Units 3556
Citations 33,232

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements


Release Notes for EcoCyc Version 20.5

Released on December 17, 2016.

EcoCyc KB Statistics
Pathways 342
Reactions 2659
Enzymes 1568
Transporters 282
Genes 4497
Transcription Units 3556
Citations 32,534

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements


Release Notes for EcoCyc Version 20.1

Released on September 29, 2016.

EcoCyc KB Statistics
Pathways 341
Reactions 2653
Enzymes 1567
Transporters 282
Genes 4505
Transcription Units 3553
Citations 31,999

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 20.0

Released on May 6, 2016.

EcoCyc KB Statistics
Pathways 339
Reactions 2614
Enzymes 1564
Transporters 281
Genes 4506
Transcription Units 3547
Citations 31,054

EcoCyc now uses the updated U00096.3 sequence

Through release 19.5, EcoCyc used the U00096.2 version of the E. coli K-12 MG1655 genome sequence. We have now upgraded the sequence to version U00096.3. The nucleotide coordinates of genes and other features differ between U00096.2 and U00096.3. We are offering a coordinate mapping service as part of this new release, which is available here. This service will translate data files containing the old coordinates to contain new mapped coordinates.

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements


Release Notes for EcoCyc Version 19.5

Released on November 13, 2015.

EcoCyc KB Statistics
Pathways 338
Reactions 2478
Enzymes 1555
Transporters 284
Genes 4500
Transcription Units 3549
Citations 30,224

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements


Release Notes for EcoCyc Version 19.1

Released on June 25, 2015.

EcoCyc KB Statistics
Pathways 337
Reactions 2418
Enzymes 1545
Transporters 282
Genes 4500
Transcription Units 3543
Citations 29,227

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 19.0

Released on March 20, 2015.

EcoCyc KB Statistics
Pathways 329
Reactions 2384
Enzymes 1538
Transporters 279
Genes 4501
Transcription Units 3541
Citations 28,535

Highlights of Website Improvements

Highlights of EcoCyc Database Improvements


Release Notes for EcoCyc Version 18.5

Released on November 7, 2014.

EcoCyc KB Statistics
Pathways 328
Reactions 2361
Enzymes 1533
Transporters 277
Genes 4501
Transcription Units 3538
Citations 27,887