Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU2674
succinate dehydrogenase and fumarate reductase iron-sulfur protein
Functional Annotations (13)
Function | System |
---|---|
Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit | cog/ cog |
succinate dehydrogenase activity | go/ molecular_function |
tricarboxylic acid cycle | go/ biological_process |
electron transport | go/ biological_process |
electron carrier activity | go/ molecular_function |
iron-sulfur cluster binding | go/ molecular_function |
Citrate cycle (TCA cycle) | kegg/ kegg pathway |
Oxidative phosphorylation | kegg/ kegg pathway |
Butanoate metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
Microbial metabolism in diverse environments | kegg/ kegg pathway |
dhsB | tigr/ tigrfam |
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Regulation information for DVU2674
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0309 DVU0525 |
318 | combiner |
DVU0525 | 318 | tf |
DVU0813 DVU0230 |
318 | combiner |
DVU0916 | 318 | tf |
DVU0946 | 318 | tf |
DVU1518 DVU1730 |
318 | combiner |
DVU1584 DVU0653 |
318 | combiner |
DVU1645 DVUA0151 |
318 | combiner |
DVU3255 DVU0653 |
318 | combiner |
DVUA0151 | 318 | tf |
DVU0110 | 172 | tf |
DVU0230 | 172 | tf |
DVU0653 | 172 | tf |
DVU0813 | 172 | tf |
DVU1518 DVU1730 |
172 | combiner |
DVU1674 | 172 | tf |
DVU1674 DVU0525 |
172 | combiner |
DVU1788 | 172 | tf |
DVU2086 | 172 | tf |
DVU2359 DVU2690 |
172 | combiner |
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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 |
---|---|---|---|---|
329 | 1.30e-02 | aGCaTaCaCccCcagAaCAggAca |
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RegPredict |
330 | 7.80e-01 | TAcTtaaCaTCATttCtGtGATAA |
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RegPredict |
605 | 3.40e+02 | CTtTTccg |
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RegPredict |
606 | 1.00e+04 | GCaTTCCGaCgTcG |
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RegPredict |
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Functional Enrichment for DVU2674
Function | System |
---|---|
Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit | cog/ cog |
succinate dehydrogenase activity | go/ molecular_function |
tricarboxylic acid cycle | go/ biological_process |
electron transport | go/ biological_process |
electron carrier activity | go/ molecular_function |
iron-sulfur cluster binding | go/ molecular_function |
Citrate cycle (TCA cycle) | kegg/ kegg pathway |
Oxidative phosphorylation | kegg/ kegg pathway |
Butanoate metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
Microbial metabolism in diverse environments | kegg/ kegg pathway |
dhsB | tigr/ tigrfam |
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Module neighborhood information for DVU2674
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0112 | deoxyribodipyrimidine photolyase | 198, 318 | |
DVU0255 | hypothetical protein DVU0255 | 172, 250 | |
DVU0492 | argC | N-acetyl-gamma-glutamyl-phosphate reductase | 172, 250 |
DVU0495 | hypothetical protein DVU0495 | 172, 180 | |
DVU0654 | U32 family peptidase | 172, 174 | |
DVU0697 | mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase | 172, 296 | |
DVU0721 | sensory box histidine kinase | 198, 318 | |
DVU0875 | fumarylacetoacetate hydrolase family protein | 318, 331 | |
DVU0876 | metallo-beta-lactamase family protein | 145, 172 | |
DVU0897 | RNA modification protein | 172, 304 | |
DVU0898 | hypothetical protein DVU0898 | 172, 304 | |
DVU0899 | hypothetical protein DVU0899 | 146, 172 | |
DVU0900 | gmk | guanylate kinase | 172, 304 |
DVU0941 | M16 family peptidase | 16, 318 | |
DVU0954 | organic solvent tolerance protein | 98, 318 | |
DVU1000 | M24 family peptidase | 172, 296 | |
DVU1001 | coenzyme A binding protein | 52, 172 | |
DVU1002 | hypothetical protein DVU1002 | 169, 172 | |
DVU1003 | dnaJ domain-containing protein | 169, 172 | |
DVU1182 | hypothetical protein DVU1182 | 26, 172 | |
DVU1266 | hypothetical protein DVU1266 | 172, 337 | |
DVU1268 | hypothetical protein DVU1268 | 82, 172 | |
DVU1269 | hypothetical protein DVU1269 | 69, 172 | |
DVU1353 | dnaE | DNA polymerase III subunit alpha | 65, 172 |
DVU1428 | pgm | phosphoglucomutase | 268, 318 |
DVU1446 | heptosyltransferase family protein | 318, 341 | |
DVU1447 | CgeB family protein | 198, 318 | |
DVU1448 | hypothetical protein DVU1448 | 198, 318 | |
DVU1449 | anti-anti-sigma factor | 71, 318 | |
DVU1450 | anti-sigma factor | 71, 318 | |
DVU1451 | response regulator | 318, 341 | |
DVU1452 | dtd | D-tyrosyl-tRNA(Tyr) deacylase | 14, 318 |
DVU1453 | fadD | long-chain-fatty-acid--CoA ligase | 230, 318 |
DVU1681 | mreB-2 | rod shape-determining protein MreB | 318, 348 |
DVU1683 | hypothetical protein DVU1683 | 181, 318 | |
DVU1684 | gcvT | glycine cleavage system T protein | 318, 348 |
DVU1685 | 16S ribosomal RNA methyltransferase RsmE | 318, 348 | |
DVU1686 | recombination factor protein RarA | 318, 348 | |
DVU1687 | glycosyl transferase group 2 family protein | 12, 318 | |
DVU1844 | septum formation initiator family protein | 318, 337 | |
DVU1914 | alpha-isopropylmalate/homocitrate synthase family transferase | 172, 196 | |
DVU2083 | relA | GTP pyrophosphokinase | 145, 318 |
DVU2238 | RNA methyltransferase | 55, 318 | |
DVU2332 | proC | pyrroline-5-carboxylate reductase | 64, 318 |
DVU2576 | oligopeptide ABC transporter ATP-binding protein | 174, 318 | |
DVU2674 | succinate dehydrogenase and fumarate reductase iron-sulfur protein | 172, 318 | |
DVU2677 | sensor histidine kinase/response regulator | 166, 172 | |
DVU3048 | asd | aspartate-semialdehyde dehydrogenase | 35, 172 |
DVU3156 | glmS | glucosamine--fructose-6-phosphate aminotransferase (isomerizing) | 172, 321 |
DVU3178 | hypothetical protein DVU3178 | 172, 292 | |
DVU3179 | ispB | octaprenyl-diphosphate synthase | 172, 174 |
DVU3192 | glycosyl transferase group 1 family protein | 172, 176 | |
DVU3379 | ribonucleotide-diphosphate reductase subunit alpha | 172, 195 |
Gene Page Help
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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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For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
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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.
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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.
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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;![](/static/images/help_images/circvis-help.png)
- 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
- 5. Module(s) that source gene and target genes belong to
- 6. Visualisation legend
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