Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0353
iron-containing alcohol dehydrogenase
Functional Annotations (6)
Function | System |
---|---|
Alcohol dehydrogenase, class IV | cog/ cog |
alcohol dehydrogenase activity, metal ion-independent | go/ molecular_function |
alcohol dehydrogenase activity, zinc-dependent | go/ molecular_function |
alcohol dehydrogenase activity, iron-dependent | go/ molecular_function |
metabolic process | go/ biological_process |
metal ion binding | go/ molecular_function |
Regulation information for DVU0353
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0110 | 250 | tf |
DVU0110 DVU0569 |
250 | combiner |
DVU0277 | 250 | tf |
DVU0309 DVU0110 |
250 | combiner |
DVU0309 DVU0653 |
250 | combiner |
DVU0653 | 250 | tf |
DVU0653 DVU2251 |
250 | combiner |
DVU1518 DVU0030 |
250 | combiner |
DVU1518 DVU1561 |
250 | combiner |
DVU1561 DVU0230 |
250 | combiner |
DVU1759 | 250 | tf |
DVU3167 | 250 | tf |
DVU3167 DVU0569 |
250 | combiner |
DVU3313 | 250 | tf |
DVU0277 DVU0309 |
180 | combiner |
DVU0309 DVU0110 |
180 | combiner |
DVU0569 | 180 | tf |
DVU1518 DVU1561 |
180 | combiner |
DVU1561 | 180 | tf |
DVU1561 DVU0230 |
180 | combiner |
DVU1561 DVUA0024 |
180 | combiner |
DVU2036 DVU0110 |
180 | combiner |
DVU3023 | 180 | tf |
DVU3023 DVU0110 |
180 | combiner |
DVU3023 DVU0569 |
180 | combiner |
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.
Motif Id | e-value | Consensus | Motif Logo | RegPredict |
---|---|---|---|---|
343 | 8.10e+02 | c.cgacGCcG.Acgc | RegPredict | |
344 | 2.60e+04 | gccC.gcCatcaCga | RegPredict | |
477 | 1.20e+03 | gTgCgGcgt.g.a.caac.a.cg | RegPredict | |
478 | 1.50e+04 | ctTgcCacggaAgGG | RegPredict |
Functional Enrichment for DVU0353
Function | System |
---|---|
Alcohol dehydrogenase, class IV | cog/ cog |
alcohol dehydrogenase activity, metal ion-independent | go/ molecular_function |
alcohol dehydrogenase activity, zinc-dependent | go/ molecular_function |
alcohol dehydrogenase activity, iron-dependent | go/ molecular_function |
metabolic process | go/ biological_process |
metal ion binding | go/ molecular_function |
Module neighborhood information for DVU0353
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0142 | trpS | tryptophanyl-tRNA synthetase | 9, 180 |
DVU0169 | oligopeptide/dipeptide ABC transporter periplasmic oligopeptide/dipeptide-binding protein | 174, 250 | |
DVU0255 | hypothetical protein DVU0255 | 172, 250 | |
DVU0326 | hypE | hydrogenase expression/formation protein HypE | 117, 250 |
DVU0337 | hypothetical protein DVU0337 | 81, 250 | |
DVU0338 | HAD superfamily hydrolase | 180, 250 | |
DVU0342 | NAD-dependent epimerase/dehydratase family protein | 81, 250 | |
DVU0343 | HPCH/HPAI aldolase family protein | 81, 250 | |
DVU0348 | hypothetical protein DVU0348 | 23, 250 | |
DVU0349 | NeuB family protein | 62, 250 | |
DVU0350 | spsF | spore coat polysaccharide biosynthesis protein spsF | 180, 250 |
DVU0353 | iron-containing alcohol dehydrogenase | 180, 250 | |
DVU0492 | argC | N-acetyl-gamma-glutamyl-phosphate reductase | 172, 250 |
DVU0495 | hypothetical protein DVU0495 | 172, 180 | |
DVU0653 | sigma-54 dependent transcriptional regulator /response regulator | 126, 180 | |
DVU1039 | lipoprotein | 23, 180 | |
DVU1040 | hisB | imidazoleglycerol-phosphate dehydratase | 23, 180 |
DVU1185 | colicin V production family protein | 9, 180 | |
DVU1252 | hypothetical protein DVU1252 | 150, 250 | |
DVU1424 | gcvPB | glycine dehydrogenase subunit 2 | 180, 250 |
DVU1426 | gcvH | glycine cleavage system protein H | 176, 250 |
DVU1772 | pyridine nucleotide-disulfide oxidoreductase | 250, 327 | |
DVU1913 | aspartate kinase | 220, 250 | |
DVU1927 | ileS | isoleucyl-tRNA synthetase | 23, 180 |
DVU1945 | 2-oxoglutarate ferredoxin oxidoreductase subunit alpha | 250, 337 | |
DVU1946 | 2-oxoglutarate ferredoxin oxidoreductase subunit beta | 250, 337 | |
DVU2210 | hypothetical protein | 180, 223 | |
DVU2530 | tkt | transketolase | 81, 250 |
DVU2575 | M20/M25/M40 family peptidase | 180, 277 | |
DVU2757 | radical SAM domain-containing protein | 180, 327 | |
DVU2892 | GTP cyclohydrolase | 180, 223 | |
DVU2942 | purB | adenylosuccinate lyase | 180, 327 |
DVU2951 | glnS | glutaminyl-tRNA synthetase | 180, 250 |
DVU3006 | polysaccharide biosynthesis protein/methyltransferase | 22, 180 | |
DVU3154 | deoxyribonucleotide triphosphate pyrophosphatase | 23, 250 | |
DVU3157 | hypothetical protein DVU3157 | 145, 250 | |
DVU3167 | heme biosynthesis protein | 180, 327 | |
DVU3198 | DNA polymerase III subunits gamma/tau | 23, 180 | |
DVU3215 | response regulator | 87, 250 | |
DVU3348 | pyruvate ferredoxin/flavodoxin oxidoreductase subunit beta | 220, 250 | |
DVU3349 | 2-ketoisovalerate ferredoxin reductase | 220, 250 | |
DVU3350 | iron-sulfur cluster-binding protein | 220, 250 | |
DVU3373 | ilvD | dihydroxy-acid dehydratase | 81, 250 |
DVU3374 | permease | 81, 250 |
Gene Page Help
Network Tab
If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.
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Regulation Tab
Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".
For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
Motifs Tab
Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.
Functions Tab
Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
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Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.
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CircVis
Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;- 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
- 2. Source gene
- 3. Target genes (other module members)
- 4. Interactions between source and target genes for a particular module
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