Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU0418 lys1
saccharopine dehydrogenase
Functional Annotations (6)
Function | System |
---|---|
Saccharopine dehydrogenase and related proteins | cog/ cog |
saccharopine dehydrogenase (NAD+, L-lysine-forming) activity | go/ molecular_function |
lysine biosynthetic process | go/ biological_process |
Lysine biosynthesis | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
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Regulation information for DVU0418
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0813 DVU0230 |
119 | combiner |
DVU0813 DVU1517 |
119 | combiner |
DVU1572 DVU0269 |
119 | combiner |
DVU1572 DVU3255 |
119 | combiner |
DVU1788 | 119 | tf |
DVU2675 DVU3186 |
119 | combiner |
DVU2909 DVU1788 |
119 | combiner |
DVU3255 DVU1584 |
119 | combiner |
DVU0030 | 236 | tf |
DVU0110 DVU0813 |
236 | combiner |
DVU0110 DVU1083 |
236 | combiner |
DVU0110 DVU1419 |
236 | combiner |
DVU0619 | 236 | tf |
DVU0653 DVU0813 |
236 | combiner |
DVU1584 | 236 | tf |
DVU1645 DVU2644 |
236 | combiner |
DVU1744 | 236 | tf |
DVU2423 DVU0653 |
236 | combiner |
DVU2423 DVU0936 |
236 | combiner |
DVU2644 DVU3066 |
236 | combiner |
DVU2836 | 236 | tf |
DVU3167 | 236 | tf |
DVU3167 DVU0309 |
236 | combiner |
DVU3167 DVU0813 |
236 | combiner |
DVU3193 DVU0813 |
236 | 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 |
---|---|---|---|---|
229 | 1.60e+03 | CTgCTTGcaCggcA.gGctCGC |
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RegPredict |
230 | 1.30e+04 | ATCATACATAcAA |
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RegPredict |
451 | 2.90e+02 | AgTcaTc.CATTtTT |
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RegPredict |
452 | 7.90e+03 | CatcActggaGgAA |
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RegPredict |
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Functional Enrichment for DVU0418
Function | System |
---|---|
Saccharopine dehydrogenase and related proteins | cog/ cog |
saccharopine dehydrogenase (NAD+, L-lysine-forming) activity | go/ molecular_function |
lysine biosynthetic process | go/ biological_process |
Lysine biosynthesis | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
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Module neighborhood information for DVU0418
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0090 | wcaG | GDP-fucose synthetase | 137, 236 |
DVU0093 | glycosyl transferase domain-containing protein | 119, 289 | |
DVU0146 | hypothetical protein DVU0146 | 53, 119 | |
DVU0159 | thioesterase family protein | 57, 119 | |
DVU0160 | carbohydrate isomerase KpsF/GutQ family protein | 57, 119 | |
DVU0243 | lipoprotein | 57, 119 | |
DVU0274 | hypothetical protein DVU0274 | 188, 236 | |
DVU0290 | lipoprotein | 115, 236 | |
DVU0319 | NAD-dependent epimerase/dehydratase | 62, 119 | |
DVU0322 | eno | phosphopyruvate hydratase | 229, 236 |
DVU0359 | HesB-like domain-containing protein | 119, 226 | |
DVU0378 | thioredoxin | 137, 236 | |
DVU0380 | sulfatase | 119, 305 | |
DVU0398 | HMGL-like domain-containing protein | 236, 292 | |
DVU0417 | speA | arginine decarboxylase | 57, 119 |
DVU0418 | lys1 | saccharopine dehydrogenase | 119, 236 |
DVU0761 | lipoprotein | 35, 236 | |
DVU0831 | PTS system transporter subunit IID | 64, 119 | |
DVU0870 | frr | ribosome recycling factor | 27, 236 |
DVU1072 | hypothetical protein DVU1072 | 99, 236 | |
DVU1192 | acylphosphatase | 66, 119 | |
DVU1368 | rhodanese-like domain-containing protein | 35, 236 | |
DVU1412 | glycerate dehydrogenase | 236, 274 | |
DVU1467 | hslU | ATP-dependent protease ATP-binding subunit HslU | 119, 227 |
DVU1613 | glutamate synthase subunit beta | 192, 236 | |
DVU1722 | hypothetical protein DVU1722 | 119, 167 | |
DVU1868 | dapA | dihydrodipicolinate synthase | 62, 236 |
DVU1886 | hypothetical protein DVU1886 | 128, 236 | |
DVU1980 | hypothetical protein DVU1980 | 115, 236 | |
DVU2082 | flagellin | 62, 236 | |
DVU2108 | hypothetical protein DVU2108 | 66, 236 | |
DVU2109 | hypothetical protein DVU2109 | 236, 348 | |
DVU2112 | hypothetical protein DVU2112 | 27, 236 | |
DVU2143 | fba | fructose-1,6-bisphosphate aldolase, class II | 186, 236 |
DVU2203 | L-PSP family endoribonuclease | 62, 236 | |
DVU2258 | ruvC | Holliday junction resolvase | 65, 119 |
DVU2313 | pgl | 6-phosphogluconolactonase | 115, 236 |
DVU2420 | hypothetical protein DVU2420 | 119, 236 | |
DVU2460 | hypothetical protein DVU2460 | 229, 236 | |
DVU2486 | acetyltransferase | 119, 167 | |
DVU2490 | histidinol phosphatase | 35, 236 | |
DVU2554 | hypothetical protein DVU2554 | 119, 227 | |
DVU2555 | MATE efflux family protein | 119, 120 | |
DVU2641 | lipoprotein | 119, 254 | |
DVU2658 | hypothetical protein DVU2658 | 119, 215 | |
DVU2659 | exsB protein | 119, 215 | |
DVU2667 | phosphate ABC transporter periplasmic phosphate-binding protein | 119, 137 | |
DVU2735 | paaK-3 | phenylacetate-coenzyme A ligase | 62, 236 |
DVU2752 | rhodanese-like domain-containing protein | 97, 119 | |
DVU2769 | hypothetical protein DVU2769 | 27, 236 | |
DVU2876 | terminase large subunit | 7, 119 | |
DVU3212 | pyridine nucleotide-disulfide oxidoreductase | 5, 236 | |
DVU3351 | queA | S-adenosylmethionine:tRNA ribosyltransferase-isomerase | 50, 236 |
DVU3352 | lipoprotein | 27, 236 |
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 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;![](/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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