Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
TRAP-T family transporter, DctQ (4TMs) subunit (NCBI)
Functional Annotations (1)
|TRAP-type C4-dicarboxylate transport system, small permease component||cog/ cog|
Regulation information for RSP_1604(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Functional Enrichment for RSP_1604
|TRAP-type C4-dicarboxylate transport system, small permease component||cog/ cog|
Module neighborhood information for RSP_1604
|Gene||Common Name||Description||Module membership|
|RSP_0118||RSP_0118||Cytochrome c oxidase, subunit IIc (NCBI)||77, 229|
|RSP_0607||RSP_0607||sigma 24 (NCBI)||77, 103|
|RSP_0992||phaA/B||pH adaption potassium efflux system, PhaA/B subunit (NCBI)||32, 361|
|RSP_0993||phaC||pH adaption potassium efflux system, PhaC subunit (NCBI)||32, 361|
|RSP_0994||phaD||pH adaption potassium efflux system, PhaD subunit (NCBI)||32, 361|
|RSP_0995||phaE||pH adaption potassium efflux system, PhaE subunit (NCBI)||32, 361|
|RSP_0996||phaF||pH adaption potassium efflux system, PhaF subunit (NCBI)||32, 361|
|RSP_0997||phaG||pH adaption potassium efflux system, PhaG subunit (NCBI)||32, 361|
|RSP_1602||RSP_1602||TRAP-T family transporter, DctM (12TMs) subunit (NCBI)||32, 77|
|RSP_1604||RSP_1604||TRAP-T family transporter, DctQ (4TMs) subunit (NCBI)||32, 77|
|RSP_1605||RSP_1605||TRAP-T family transporter, periplasmic binding protein, DctP (NCBI)||32, 77|
|RSP_1606||RSP_1606||Putative regulatory protein, GntR family (NCBI)||32, 214|
|RSP_1607||RSP_1607||Putative regulatory protein, GntR family (NCBI)||77, 214|
|RSP_1608||RSP_1608||Putative Zn-dependent dehydrogenase (NCBI)||32, 214|
|RSP_1609||RSP_1609||Putative altronate dehydrogenase (NCBI)||32, 214|
|RSP_1610||RSP_1610||altronate hydrolase (NCBI)||32, 214|
|RSP_1636||RSP_1636||phage-related protein, probable phage tail tape meausure protein, lambda family (NCBI)||31, 77|
|RSP_2070||RSP_2070||Putative Phage-related terminase (NCBI)||77, 304|
|RSP_2071||RSP_2071||hypothetical protein (NCBI)||77, 304|
|RSP_2182||betI||transcriptional regulator, BetI (NCBI)||77, 303|
|RSP_2183||betB||Betaine aldehyde dehydrogenase (NCBI)||77, 303|
|RSP_2184||betA||Choline dehydrogenase (NCBI)||77, 303|
|RSP_2555||RSP_2555||hypothetical protein (NCBI)||77, 157|
|RSP_2556||RSP_2556||hypothetical protein (NCBI)||77, 157|
|RSP_2750||RSP_2750||hypothetical protein (NCBI)||77, 105|
|RSP_2753||RSP_2753||hypothetical protein (NCBI)||77, 105|
|RSP_2755||RSP_2755||hypothetical protein (NCBI)||74, 77|
|RSP_2792||RSP_2792||putative monooxygenase alpha subunit (NCBI)||77, 103|
|RSP_2796||RSP_2796||hypothetical protein (NCBI)||77, 103|
|RSP_2798||groEL3||Putative chaperonin groEL (NCBI)||77, 103|
|RSP_2944||RSP_2944||hypothetical protein (NCBI)||77, 153|
|RSP_2995||RSP_2995||possible phage major capsid protein, gp36 (NCBI)||77, 153|
|RSP_3012||RSP_3012||Probable transposase (NCBI)||77, 126|
|RSP_3065||RSP_3065||Putative transporter, Major facilitator superfamily (MFS) (NCBI)||77, 320|
|RSP_3114||RSP_3114||hypothetical protein (NCBI)||77, 282|
|RSP_3259||RSP_3259||Transcription antitermination protein (NCBI)||77, 236|
|RSP_3346||RSP_3346||5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI)||32, 135|
|RSP_3347||RSP_3347||methionine synthase, 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI)||32, 135|
|RSP_3380||RSP_3380||hypothetical protein (NCBI)||77, 236|
|RSP_3393||RSP_3393||ABC opine/polyamine transporter, inner membrane subunit (NCBI)||77, 88|
|RSP_3420||RSP_3420||Methyl-accepting chemotaxis protein (NCBI)||77, 251|
|RSP_3421||RSP_3421||hypothetical protein (NCBI)||77, 105|
|RSP_3605||RSP_3605||FAD-dependent pyridine nucleotide-disulphide oxidoreductase (NCBI)||77, 273|
|RSP_3696||cysA||ABC sulfate/thiosulfate transporter, ATPase subunit CysA (NCBI)||32, 86|
|RSP_3697||cysP||ABC sulfate/thiosulfate transporter, periplasmic binding protein CysP (NCBI)||32, 86|
|RSP_3698||cysT||ABC sulfate/thiosulfate transporter, inner membrane subunit CysT (NCBI)||32, 86|
|RSP_3699||cysW||ABC sulfate/thiosulfate transporter, inner membrane subunit CysW (NCBI)||32, 86|
|RSP_3788||RSP_3788||hypothetical protein (NCBI)||77, 233|
Gene Page Help
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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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.
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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.
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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CircVisOur 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)
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