Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU0608
methyl-accepting chemotaxis protein
Functional Annotations (7)
Function | System |
---|---|
Signal transduction histidine kinase regulating C4-dicarboxylate transport system | cog/ cog |
signal transducer activity | go/ molecular_function |
chemotaxis | go/ biological_process |
signal transduction | go/ biological_process |
membrane | go/ cellular_component |
Two-component system | kegg/ kegg pathway |
Bacterial chemotaxis | kegg/ kegg pathway |
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Regulation information for DVU0608
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0063 | 105 | tf |
DVU1561 DVU2588 |
105 | combiner |
DVU1584 DVU2275 |
105 | combiner |
DVU2036 DVU2275 |
105 | combiner |
DVU2195 | 105 | tf |
DVU2423 DVU1547 |
105 | combiner |
DVU2423 DVU2588 |
105 | combiner |
DVU2547 DVU0539 |
105 | combiner |
DVU3220 | 105 | tf |
DVU0063 DVU0529 |
198 | combiner |
DVU0309 DVU2275 |
198 | combiner |
DVU0529 DVU2989 |
198 | combiner |
DVU0916 | 198 | tf |
DVU2036 DVU2547 |
198 | combiner |
DVU2275 | 198 | tf |
DVU2547 | 198 | tf |
DVU2547 DVU0619 |
198 | combiner |
DVU2547 DVU0946 |
198 | combiner |
DVU2547 DVU1628 |
198 | combiner |
DVU2557 | 198 | tf |
DVU2934 | 198 | tf |
DVUA0143 DVU2989 |
198 | combiner |
DVUA0151 | 198 | tf |
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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 |
---|---|---|---|---|
203 | 4.80e+02 | tcGtCGacatcCCCCTcCGgttCt |
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RegPredict |
204 | 1.30e+01 | GCcgcaa.cgcCttc.tca |
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RegPredict |
379 | 3.50e+01 | CAAgGAgCaca |
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RegPredict |
380 | 2.20e+04 | TcTTCaGg |
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RegPredict |
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Functional Enrichment for DVU0608
Function | System |
---|---|
Signal transduction histidine kinase regulating C4-dicarboxylate transport system | cog/ cog |
signal transducer activity | go/ molecular_function |
chemotaxis | go/ biological_process |
signal transduction | go/ biological_process |
membrane | go/ cellular_component |
Two-component system | kegg/ kegg pathway |
Bacterial chemotaxis | kegg/ kegg pathway |
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Module neighborhood information for DVU0608
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0112 | deoxyribodipyrimidine photolyase | 198, 318 | |
DVU0118 | sigma-54 dependent transcriptional regulator/response regulator | 105, 112 | |
DVU0221 | tail fiber assembly protein | 198, 314 | |
DVU0254 | hypothetical protein DVU0254 | 105, 167 | |
DVU0289 | moaC | molybdenum cofactor biosynthesis protein C | 105, 112 |
DVU0294 | glycosyl transferase group 2 family protein | 31, 105 | |
DVU0482 | sensory box histidine kinase/response regulator | 105, 112 | |
DVU0540 | sensor histidine kinase | 162, 198 | |
DVU0581 | response regulator/anti-anti-sigma factor | 105, 112 | |
DVU0582 | sensory box histidine kinase | 105, 112 | |
DVU0584 | transposase | 105, 304 | |
DVU0608 | methyl-accepting chemotaxis protein | 105, 198 | |
DVU0615 | hypothetical protein DVU0615 | 150, 198 | |
DVU0619 | sigma-54 dependent transcriptional regulator | 63, 198 | |
DVU0634 | hypothetical protein DVU0634 | 105, 112 | |
DVU0640 | pomA | chemotaxis protein PomA | 105, 296 |
DVU0676 | His/Glu/Gln/Arg/opine ABC transporter permease | 153, 198 | |
DVU0683 | hflC protein | 194, 198 | |
DVU0721 | sensory box histidine kinase | 198, 318 | |
DVU0741 | hypothetical protein DVU0741 | 115, 198 | |
DVU0744 | sigma-54 dependent transcriptional regulator/response regulator | 115, 198 | |
DVU0755 | sensor histidine kinase | 105, 198 | |
DVU0803 | sensor histidine kinase | 198, 201 | |
DVU0855 | radical SAM domain-containing protein | 57, 198 | |
DVU0903 | HD domain-containing protein | 17, 198 | |
DVU0910 | fliM | flagellar motor switch protein FliM | 194, 198 |
DVU0992 | cheV-3 | chemotaxis protein CheV | 105, 198 |
DVU1030 | universal stress protein | 105, 201 | |
DVU1279 | folP | dihydropteroate synthase | 198, 330 |
DVU1338 | hypothetical protein DVU1338 | 112, 198 | |
DVU1359 | hypothetical protein DVU1359 | 105, 115 | |
DVU1404 | radical SAM domain-containing protein | 86, 105 | |
DVU1447 | CgeB family protein | 198, 318 | |
DVU1448 | hypothetical protein DVU1448 | 198, 318 | |
DVU1535 | hypothetical protein DVU1535 | 31, 105 | |
DVU1549 | hypothetical protein DVU1549 | 112, 198 | |
DVU1771 | hydC | [Fe] hydrogenase gamma [Desulfovibrio vulgaris str. Hildenborough] | 175, 198 |
DVU1803 | glycosyl transferase group 1 family protein | 12, 198 | |
DVU1830 | hypothetical protein DVU1830 | 194, 198 | |
DVU1853 | hypothetical protein DVU1853 | 105, 175 | |
DVU1939 | anaerobic glycerol-3-phosphate dehydrogenase subunit B | 198, 267 | |
DVU1986 | hypothetical protein DVU1986 | 192, 198 | |
DVU2019 | hypothetical protein DVU2019 | 175, 198 | |
DVU2091 | thiE-1 | thiamine-phosphate pyrophosphorylase | 198, 225 |
DVU2138 | hypothetical protein DVU2138 | 105, 178 | |
DVU2141 | nucleic acid-binding protein | 105, 115 | |
DVU2142 | surE | acid phosphatase SurE | 176, 198 |
DVU2195 | hypothetical protein DVU2195 | 105, 311 | |
DVU2312 | hypothetical protein DVU2312 | 105, 123 | |
DVU2361 | hypothetical protein DVU2361 | 161, 198 | |
DVU2391 | hypothetical protein DVU2391 | 198, 214 | |
DVU2410 | sodB | superoxide dismutase, Fe | 105, 321 |
DVU2429 | hypothetical protein DVU2429 | 105, 109 | |
DVU2472 | hypothetical protein DVU2472 | 105, 112 | |
DVU2556 | hypothetical protein DVU2556 | 105, 115 | |
DVU2668 | glmU | bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase | 105, 106 |
DVU2707 | virion morphogenesis protein | 105, 239 | |
DVU2708 | virion morphogenesis protein | 105, 239 | |
DVU2763 | TPR/GGDEF domain-containing protein | 175, 198 | |
DVU2813 | hypothetical protein DVU2813 | 175, 198 | |
DVU2934 | sigma-54 dependent transcriptional regulator/response regulator | 198, 291 | |
DVU3062 | sensor histidine kinase/response regulator | 105, 321 | |
DVU3220 | sigma-54 dependent transcriptional regulator/response regulator | 115, 198 | |
DVU3222 | pgi | glucose-6-phosphate isomerase | 83, 198 |
DVU3225 | hypothetical protein DVU3225 | 37, 198 | |
DVU3266 | hypothetical protein DVU3266 | 123, 198 | |
DVU3268 | hypothetical protein DVU3268 | 105, 175 | |
DVU3388 | lipoprotein | 105, 112 |
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.
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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.
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.
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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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