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ProOpDB specifications


Unique identifier OMICS_03207
Name ProOpDB
Alternative name Prokaryotic Operon DataBase
Restrictions to use None
Data access Browse
Maintained No

Publications for Prokaryotic Operon DataBase

ProOpDB citations


Outer membrane phospholipase A’s roles in Helicobacter pylori acid adaptation

PMCID: 5469174
PMID: 28616083
DOI: 10.1186/s13099-017-0184-y

[…] ProOpDB [] predicts operon structures of prokaryotic genomes, and presents results in figures in which all genes in a clusters of ortholog genes (COG) have the same colour. We used this software to de […]


Identification of Preferred DNA Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA

PLoS One
PMCID: 4948773
PMID: 27428627
DOI: 10.1371/journal.pone.0159408
call_split See protocol

[…] identify potential promoter elements [,]. Operons were identified using databases at the University of Georgia (DOOR2, and the Universidad Nacional Autónoma de México (ProOpDB, [,]. Information on identified/postulated protein functions for potential SbtR-regulated genes was obtained from both the KEGG Genome database (Th […]


Carboxydotrophic growth of Geobacter sulfurreducens

Appl Microbiol Biotechnol
PMCID: 4703632
PMID: 26481622
DOI: 10.1007/s00253-015-7033-z
call_split See protocol

[…] IMG (; Markowitz et al. ) and BlastP (; Altschul et al. ) searches against proteins of known CO-utilizing organisms. Operon prediction was provided by the Prokaryotic Operon Database (; Taboada et al. ). Gene clusters related to the CODH cluster in G. sulfurreducens were investigated using BlastP, by comparison […]


OperomeDB: A Database of Condition Specific Transcription Units in Prokaryotic Genomes

Biomed Res Int
PMCID: 4620388
PMID: 26543854
DOI: 10.1155/2015/318217

[…] database, which contains predicted operons for 675 sequenced prokaryotic genomes. It provides similarity scores between operons by which user can search for related operons in different organisms []. ProOpDB (prokaryotic operon database) predicts operons in more than 1200 prokaryotic genomes using a neural network based approach. It provides several options for retrieving operon information. In Pr […]


Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine

PLoS One
PMCID: 4411035
PMID: 25915650
DOI: 10.1371/journal.pone.0126694

[…] rized proteins was extracted from Pfam version 27.0 (available at and InterPro version 47.0 (available at Operon structures were retrieved from ProOpDB [] (available at […]


Plasmids are vectors for redundant chromosomal genes in the Bacillus cereus group

BMC Genomics
PMCID: 4326196
PMID: 25608745
DOI: 10.1186/s12864-014-1206-5

[…] osition was analyzed using G-language [], and a CAI (codon adaptation index) analysis was performed using codonW software (version 1.4.4, operons were predicted by ProOpDB []. To compare the promoters and terminators of shared genes between chromosomes and plasmids, we collected 200-bp upstream and 100-bp downstream sequences for each coding region of all these […]


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ProOpDB institution(s)
Centro de Ciencias Aplicadas y Desarrollo Tecnológico, Universidad Nacional Autónoma de México, México, DF, México; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
ProOpDB funding source(s)
This work was supported by grants PAPIIT IN201714 and CONACyT 154817.

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