Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2298
glycine/betaine/L-proline ABC transporter permease
Functional Annotations (6)
Function | System |
---|---|
ABC-type proline/glycine betaine transport system, permease component | cog/ cog |
transport | go/ biological_process |
quaternary-ammonium-compound-transporting ATPase activity | go/ molecular_function |
glycine betaine/proline porter activity | go/ molecular_function |
membrane | go/ cellular_component |
ABC transporters | kegg/ kegg pathway |
Regulation information for DVU2298
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0063 | 235 | tf |
DVU0063 DVU1949 |
235 | combiner |
DVU0118 | 235 | tf |
DVU0118 DVU2690 |
235 | combiner |
DVU0682 | 235 | tf |
DVU0682 DVU1584 |
235 | combiner |
DVU1419 | 235 | tf |
DVU1572 | 235 | tf |
DVU1572 DVU2111 |
235 | combiner |
DVU2394 | 235 | tf |
DVU2547 | 235 | tf |
DVU0118 | 94 | tf |
DVU1572 DVU1730 |
94 | combiner |
DVU1572 DVU2319 |
94 | combiner |
DVU1572 DVU2423 |
94 | combiner |
DVU1572 DVU2956 |
94 | combiner |
DVU1572 DVU3313 |
94 | combiner |
DVU1745 | 94 | tf |
DVU1759 | 94 | tf |
DVU1759 DVU2275 |
94 | combiner |
DVU2111 DVU3186 |
94 | combiner |
DVU2275 | 94 | tf |
DVU2989 | 94 | tf |
DVU3167 | 94 | tf |
DVU3305 | 94 | tf |
DVU3313 | 94 | tf |
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 |
---|---|---|---|---|
181 | 2.20e-02 | ATCGCTtgTatGcaaGTtaaT | RegPredict | |
182 | 1.70e+02 | CaTcaACCgga.a.aaggAAca.c | RegPredict | |
449 | 4.00e+02 | ctcTTcCc.t | RegPredict | |
450 | 1.40e+04 | AAAAAG | RegPredict |
Functional Enrichment for DVU2298
Function | System |
---|---|
ABC-type proline/glycine betaine transport system, permease component | cog/ cog |
transport | go/ biological_process |
quaternary-ammonium-compound-transporting ATPase activity | go/ molecular_function |
glycine betaine/proline porter activity | go/ molecular_function |
membrane | go/ cellular_component |
ABC transporters | kegg/ kegg pathway |
Module neighborhood information for DVU2298
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0060 | RND family efflux transporter MFP subunit | 5, 94 | |
DVU0061 | multidrug resistance protein | 5, 94 | |
DVU0062 | RND efflux system outer membrane lipoprotein | 5, 94 | |
DVU0063 | MarR family transcriptional regulator | 5, 94 | |
DVU0224 | hypothetical protein DVU0224 | 94, 156 | |
DVU0399 | hypothetical protein DVU0399 | 10, 235 | |
DVU0503 | pnp | polynucleotide phosphorylase/polyadenylase | 10, 235 |
DVU0507 | hypothetical protein DVU0507 | 10, 235 | |
DVU0508 | infB | translation initiation factor IF-2 | 10, 235 |
DVU0510 | nusA | transcription elongation factor NusA | 10, 235 |
DVU0603 | hypothetical protein DVU0603 | 5, 94 | |
DVU0753 | amino acid ABC transporter ATP-binding protein | 235, 292 | |
DVU0809 | gatC | glutamyl-tRNA(Gln) amidotransferase subunit C | 29, 235 |
DVU0810 | hypothetical protein DVU0810 | 29, 235 | |
DVU1201 | ribD | riboflavin biosynthesis protein RibD | 94, 169 |
DVU1247 | hypothetical protein DVU1247 | 28, 235 | |
DVU1248 | argS | arginyl-tRNA synthetase | 29, 235 |
DVU1298 | rpsL | 30S ribosomal protein S12 | 10, 235 |
DVU1299 | rpsG | 30S ribosomal protein S7 | 10, 235 |
DVU1300 | fusA-1 | elongation factor G | 10, 235 |
DVU1332 | selD | selenide, water dikinase, selenocysteine-containing | 30, 94 |
DVU1571 | rho | transcription termination factor Rho | 5, 235 |
DVU1622 | purQ | phosphoribosylformylglycinamidine synthase I | 10, 235 |
DVU1775 | ribB | 3,4-dihydroxy-2-butanone 4-phosphate synthase | 12, 94 |
DVU1791 | GatB/Yqey family protein | 28, 94 | |
DVU1862 | GGDEF domain-containing protein | 94, 229 | |
DVU1892 | glycosyl transferase group 2 family protein | 94, 277 | |
DVU2130 | hypothetical protein DVU2130 | 5, 94 | |
DVU2216 | infA | translation initiation factor IF-1 | 235, 308 |
DVU2256 | ruvA | Holliday junction DNA helicase RuvA | 94, 275 |
DVU2279 | hypothetical protein DVU2279 | 94, 334 | |
DVU2280 | amino acid permease family protein | 94, 334 | |
DVU2298 | glycine/betaine/L-proline ABC transporter permease | 94, 235 | |
DVU2299 | glycine/betaine/L-proline ABC transporter ATP binding protein | 5, 235 | |
DVU2738 | methyl-accepting chemotaxis protein | 94, 179 | |
DVU2771 | hypothetical protein DVU2771 | 27, 94 | |
DVU2913 | lipoprotein | 10, 235 | |
DVU2914 | prfA | peptide chain release factor 1 | 10, 235 |
DVU3116 | prfC | peptide chain release factor 3 | 235, 278 |
DVU3151 | tRNA modifying protein | 5, 94 | |
DVU3194 | engA | GTP-binding protein EngA | 5, 94 |
DVU3204 | purA | adenylosuccinate synthetase | 5, 94 |
DVU3205 | transglycosylase | 5, 94 | |
DVU3206 | phosphoribosylaminoimidazolecarboxamide formyltransferase | 5, 235 | |
DVU3307 | ubiX | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase | 29, 235 |
DVU3308 | metallo-beta-lactamase family protein | 10, 235 | |
DVU3310 | DEAD-box ATP dependent DNA helicase | 10, 235 | |
DVU3327 | SMR family multidrug efflux pump | 94, 279 |
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.
Module Members Tab
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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