PathPred statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PathPred

Tool usage distribution map

This map represents all the scientific publications referring to PathPred per scientific context
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PathPred specifications


Unique identifier OMICS_03569
Name PathPred
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Kae Morishima

Publication for PathPred

PathPred citations


Aerobic Growth of Rhodococcus aetherivorans BCP1 Using Selected Naphthenic Acids as the Sole Carbon and Energy Sources

Front Microbiol
PMCID: 5906575
PMID: 29706937
DOI: 10.3389/fmicb.2018.00672

[…] Rhodococcus aetherivorans BCP1 genome analysis was performed to detect the possible genes involved in NA degradation. Using Pathpred software and in silico comparative analyses, we identified genes encoding cyclohexanone monooxygenases and genes possibly encoding enzymes involved in oxidative degradation processes (Supplem […]


Identifying enriched drug fragments as possible candidates for metabolic engineering

BMC Med Genomics
PMCID: 4980782
PMID: 27510651
DOI: 10.1186/s12920-016-0205-6
call_split See protocol

[…] ding the names of the enzymes catalyzing the reactions.The next step in pathway annotation was to determine the synthesis pathway from fragments to drug compound. To accomplish this task, we used the Pathpred webserver (, which predicts the synthesis pathway given the substrates and the final product. The Pathpred webserver is linked to the KEGG database and the […]


Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3

PLoS One
PMCID: 4547698
PMID: 26301592
DOI: 10.1371/journal.pone.0132881

[…] e genes was also performed as above by GO function enrichment analysis. Possible enzyme-catalyzed metabolic pathways for multi-step reactions involved in naphthenic acid degradation were predicted by PathPred [], which was based on the local RDM pattern (KEGG atom type changes at the reaction center (R), the difference region (D), and the matched region (M) for each reactant pair.) match and the g […]


Integration of bioinformatics to biodegradation

PMCID: 4012781
PMID: 24808763
DOI: 10.1186/1480-9222-16-8

[…] romo-4-nitrophenol. For the prediction, users may enter a compound into the system by either drawing the structure and generating SMILES or entering SMILES directly.Another pathway prediction system, PathPred (, is a knowledge based prediction system that uses data derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) in the form of the KEGG REACTION […]

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PathPred institution(s)
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan

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