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A comparative account of pathways, feature-validations and application-based categorizations : Pathways in bacteria
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
BiGG - Biochemical Genetic and Genomic knowledgebase
http://bigg.ucsd.edu
Knowledgebase of biochemically, genetically and genomically structured genome scale reconstructions, uses one standarad nomenclature allowing comparison across different species.
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol. 2011 Jan 18;5:8. PubMed PMID: 21244678; PubMed Central PMCID: PMC3032673.
2011
100
BioCyc
http://biocyc.org
Gene interactions in dynamic graphical models, depicts molecular relationships.
Krummenacker M, Paley S, Mueller L, Yan T, Karp PD. Querying and computing with BioCyc databases. Bioinformatics. 2005 Aug 15;21(16):3454-5. Epub 2005 Jun16. PubMed PMID: 15961440; PubMed Central PMCID: PMC1450015.
2005
100
Bionemo
http://bionemo.bioinfo.cnio.es
Biodegradation network database.
Carbajosa G, Trigo A, Valencia A, Cases I. Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res. 2009 Jan;37(Database issue):D598-602. Epub 2008 Nov 5.PubMed PMID: 18986994; PubMed Central PMCID:PMC2686592.
2008
100
Biopath - Database on Biochemical Pathways
http://www.molecular-networks.com/databases/biopath
Contains biological transformation and regulations derived from the Roche Applied Science "biochemical pathways" wall chart.
Schreiber F. High quality visualization of biochemical pathways in BioPath. In Silico Biol. 2002;2(2):59-73. PubMed PMID: 12066841.
2002
100
BSD - Biodegradability Strain Database
http://bsd.cme.msu.edu
Information on the biodegradation pathways based on the strain or the substance involved.
Urbance JW, Cole J, Saxman P, Tiedje JM. BSD: the Biodegradative Strain Database. Nucleic Acids Res. 2003 Jan 1;31(1):152-5. PubMed PMID: 12519970; PubMed Central PMCID: PMC165479.
2003
100
CPA - Comparative Pathway Analyzer
http://cpa.cebitec.uni-bielefeld.de
Investigates reaction content of a set of organisms.
Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A. Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W433-7. Epub 2008 Jun 6. PubMed PMID: 18539612; PubMed Central PMCID: PMC2447754.
2008
100
EMP - Enzymes and Metabolic Pathways Database
http://www.empproject.com
Electronic source of biochemical data that stores details like chemical reactions and Km.
Selkov E, Basmanova S, Gaasterland T, Goryanin I, Gretchkin Y, Maltsev N, Nenashev V, Overbeek R, Panyushkina E, Pronevitch L, Selkov E Jr, Yunus I. The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucleic Acids Res. 1996 Jan 1;24(1):26-8. PubMed PMID: 8594593; PubMed Central PMCID: PMC145618.
1996
100
URL could not be retrieved (10/01/2012).
ERGO - ERGO Genome Analysis and Discovery System
http://www.ergo-light.com
Curated database of genomic DNA with functional annotation and pathway information.
Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P,KapatralV,Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N. The ERGO genome analysis and discovery system. Nucleic Acids Res. 2003 Jan 1;31(1):164-71. PubMed PMID: 12519973; PubMed Central PMCID: PMC165577.
2003
100
FMM - From Metabolite to Metabolite
http://FMM.mbc.nctu.edu.tw
Reconstruct the pathway from one metabolite to another, comparison of the pathway among species.
Chou CH, Chang WC, Chiu CM, Huang CC, Huang HD. FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W129-34. Epub 2009 Apr 28. PubMed PMID: 19401437; PubMed Central PMCID: PMC2703958.
2009
100
IMG - Integrated Microbial Genomes
http://img.jgi.doe.gov
Data management, analysis and annotation platform for all publicly available genomes.
Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 2008 Jan;36(Database issue):D528-33. Epub 2007 Oct 12. PubMed PMID: 17933782; PubMed Central PMCID: PMC2238897.
2007
100
Indigo
http://chlora.lgi.infobiogen.fr:1234/Indigo
Contains information on codon usage, operons, gene neighbours in case of E. coli and Bacillus subtilis.
Nitschké P, Guerdoux-Jamet P, Chiapello H, Faroux G, Hénaut C, Hénaut A, Danchin A. Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol Rev. 1998 Oct;22(4):207-27. Review. PubMed PMID: 9862121.
1998
100
KEGG - Kyoto Encyclopedia of Genes and Genomes
http://www.genome.jp/kegg
Database of metabolic pathways from different organisms, also provides reference pathways that describe a general pathway which is then projected onto a genome based on the presence of pathway enzymes in that genome.
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999 Jan 1;27(1):29-34.PubMed PMID: 9847135; PubMed Central PMCID: PMC148090.
1999
100
MassTRIX
http://metabolomics.helmholtz-muenchen.de/masstrix2
Annotates metabolites in high precision mass spectrometry data.
Suhre K, Schmitt-Kopplin P. MassTRIX: mass translator into pathways. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W481-4. Epub 2008 Apr 28. PubMed PMID:18442993; PubMed Central PMCID: PMC2447776.
2007
100
MetaCyc - Metabolic Pathway Database
http://metacyc.org
Contains pathways from different organisms.
Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D438-42. PubMed PMID: 14681452; PubMed Central PMCID: PMC308834.
2004
100
Metagrowth
http://igs-server.cnrs-mrs.fr/axenic
Study of culture condition of obligate parasitic bacteria.
Ogata H, Claverie JM. Metagrowth: a new resource for the building of metabolic hypotheses in microbiology. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D321-4. PubMed PMID: 15608207; PubMed Central PMCID: PMC539996.
2005
100
METAPATH
http://scopes.biologie.hu-berlin.de/index.php?m=path
Calculation of minimal synthesis pathway.
Handorf T, Ebenhöh O. MetaPath Online: a web server implementation of the network expansion algorithm. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W613-8. Epub 2007 May 5. PubMed PMID: 17483511; PubMed Central PMCID:PMC1933239.
2007
100
MetExplore
http://metexplore.toulouse.inra.fr/metexploreJoomla/index.php
A web resource that offers the possibility to link the metabolites identified in untargetted metabolomics experiments within the context of genome scale reconstructed metabolic network.
Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W132-7. Epub 2010 May 5. PubMed PMID: 20444866; PubMed Central PMCID: PMC2896158.
2010
100
MiMI - Michigan Molecular Interactions
http://mimi.ncibi.org/MimiWeb/main-page.jsp
Contains pathway diagrams from KEGG and Reactome.
Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27. PubMed PMID: 17130145; PubMed Central PMCID: PMC1716720.
2006
100
MiST - Microbial Signal Transduction database
http://genomics.ornl.gov/mist
Signal transduction proteins in bacterial and archeal organisms.
Ulrich LE, Zhulin IB. MiST: a microbial signal transduction database. Nucleic Acids Res. 2007 Jan;35(Database issue):D386-90. Epub 2006 Nov 28. PubMed PMID:17135192; PubMed Central PMCID: PMC1747179.
2007
100
NCBI BioSystems
http://www.ncbi.nlm.nih.gov/biosystems
Connects biosystem records with the associated literature, molecular and chemical data.
Evsikov AV, Dolan ME, Genrich MP, Patek E, Bult CJ. MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol. 2009;10(8):R84. Epub 2009 Aug 14. PubMed PMID: 19682380; PubMed Central PMCID:PMC2745765.
2009
100
NMPDR - National Microbial Pathogen Data Resource
http://www.nmpdr.org
Microbial pathogen data resource with emphasis on food-borne pathogens.
McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53.Epub 2006 Dec 1. PubMed PMID: 17145713; PubMed Central PMCID: PMC1751540.
2007
100
P2CS - Prokaryotic 2-Component Systems
http://www.p2cs.org
Database of prokaryotic two-component system signal transduction proteins.
Barakat M, Ortet P, Jourlin-Castelli C, Ansaldi M, Méjean V, Whitworth DE. P2CS: a two-component system resource for prokaryotic signal transduction research. BMC Genomics. 2009 Jul 15;10:315. PubMed PMID: 19604365 ; PubMed Central PMCID: PMC2716373.
2009
100
PANTHER - Protein ANalysis Through Evolutionary Relationships
http://www.pantherdb.org
Gene expression data analysis, comparison of gene lists.
Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD. The PANTHERdatabase of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8. PubMed PMID: 15608197; PubMed Central PMCID: PMC540032.
2005
100
PathPred - Pathway Prediction server
http://www.genome.jp/tools/pathpred
Enzyme catalyzed metabolic pathway prediction server.
Moriya Y, Shigemizu D, Hattori M, Tokimatsu T, Kotera M, Goto S, Kanehisa M.PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W138-43. Epub 2010 Apr 30. PubMed PMID:20435670; PubMed Central PMCID: PMC2896155.
2010
100
Pathway Commons
http://www.pathwaycommons.org/pc/
Provides researchers with convenient access to the collection of publicly available pathways from many different organisms.
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90. Epub 2010 Nov 10. PubMed PMID: 21071392; PubMed Central PMCID: PMC3013659.
2010
100
PATRIC - PathoSystems Resource Integration Center
http://patric.vbi.vt.edu
Pathway resources for bacteria and viruses.
Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BW. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. 2007 Jan;35(Database issue):D401-6. Epub 2006 Nov 16. PubMed PMID: 17142235; PubMed Central PMCID: PMC1669763.
2006
100
PHT - Pathway Hunter Tool
http://pht.tu-bs.de
Finds all the shortest valid pathways that connect two molecules, statistical information about different pathways in different organisms.
Rahman SA, Advani P, Schunk R, Schrader R, Schomburg D. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics. 2005 Apr1;21(7):1189-93. Epub 2004 Nov 30. PubMed PMID: 15572476.
2005
100
Prodonet
http://www.prodonet.tu-bs.de
Visualization network for regulatory tools.
Klein J, Leupold S, Münch R, Pommerenke C, Johl T, Kärst U, Jänsch L, Jahn D, Retter I. ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W460-4. Epub 2008 Apr 25. PubMed PMID: 18440972; PubMed Central PMCID:PMC2447764.
2008
100
Protein Lounge
http://www.proteinlounge.com
Contains curated pathways for many different organisms.
Not available
Not available
100
RegAnalyst
http://www.nii.ac.in/~deepak/RegAnalyst
Tool for analysis of regulatory network that integrates motif prediction program and pattern detection tool.
Sharma D, Mohanty D, Surolia A. RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W193-201. Epub 2009 May 21. PubMed PMID: 19465400; PubMed Central PMCID: PMC2703886.
2009
100
SENTRA
http://compbio.mcs.anl.gov/sentra
Database of microbial signal transduction.
D'Souza M, Romine MF, Maltsev N. SENTRA, a database of signal transduction proteins. Nucleic Acids Res. 2000 Jan 1;28(1):335-6. PubMed PMID: 10592266; PubMed Central PMCID: PMC102390.
2000
100
URL could not be retrieved (10/01/2012).
SYSTOMONAS - SYSTems biology of pseudOMONAS
http://systomonas.tu-bs.de
Provides broad range of information on the genes, proteins, metabolome experiment results as well as regulatory network.
Choi C, Münch R, Leupold S, Klein J, Siegel I, Thielen B, Benkert B, Kucklick M, Schobert M, Barthelmes J, Ebeling C, Haddad I, Scheer M, Grote A, Hiller K,Bunk B, Schreiber K, Retter I, Schomburg D, Jahn D. SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas. Nucleic Acids Res. 2007 Jan;35(Database issue):D533-7. PubMed PMID: 17202169; PubMed Central PMCID:PMC1899106.
2007
100
The SEED
http://theseed.uchicago.edu/FIG/index.cgi
Annotation and analysis tool for microbial genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A,Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I,Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005. PubMed PMID: 16214803; PubMed Central PMCID: PMC1251668.
2005
100
TRRD - Transcription Regulatory Regions Database
http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd
Information on the structural and functional organization of transcription regulatory regions in the eukaryotic genes.
Kel' AE, Kolchanov NA, Kel' OV, Romashchenko AG, Anan'ko EA, Ignat'eva EV, Merkulova TI, Podkolodnaia OA, Stepanenko IL, Kochetov AV, Kolpakov FA,Podkolodnyi NL, Naumochkin AA. [TRRD: a database of transcription regulatory regions in eukaryotic genes]. Mol Biol (Mosk). 1997 Jul-Aug;31(4):626-36.Russian. PubMed PMID: 9340490.
1997
100
UM-BBD - University of Minnesota Biocatalysis/Biodegradation Database
http://umbbd.msi.umn.edu
Exclusively showcases the biocatalysis and biodegradation pathways, pathway prediction system.
Ellis LB, Speedie SM, McLeish R. Representing metabolic pathway information: an object-oriented approach. Bioinformatics. 1998;14(9):803-6. PubMed PMID:9918950.
1998
100
VisANT
http://visant.bu.edu
Visual analysis tool for biological networks, predict the function of a network module.
Hu Z, Mellor J, Wu J, DeLisi C. VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics. 2004 Feb 19;5:17. PubMed PMID: 15028117; PubMed Central PMCID: PMC368431.
2004
100
WikiPathways
http://wikipathways.org
Open, public space for pathway editing.
Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C.WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184.PubMed PMID: 18651794; PubMed Central PMCID: PMC2475545.
2008
100
 
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