Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_3004(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_3004
Module neighborhood information for RSP_3004
|Gene||Common Name||Description||Module membership|
|RSP_0150||RSP_0150||chase sensor signal transducdtion histidine kinase (NCBI)||87, 214|
|RSP_0448||RSP_0448||EF-Tu; elongation factor Tu (NCBI)||209, 271|
|RSP_0613||RSP_0613||hypothetical protein (NCBI)||214, 325|
|RSP_0684||RSP_0684||Possible oxidoreductase; Short-chain dehydrogenase/reductase SDR (NCBI)||196, 209|
|RSP_0685||RSP_0685||Possible ribosomal RNA small subunit methyltransferase C RsmC (NCBI)||209, 340|
|RSP_0686||RSP_0686||ATP-dependent Clp protease adaptor protein clpS (NCBI)||209, 227|
|RSP_0687||RSP_0687||Predicted hydrolase (haloacid dehalogenase (HAD) superfamily) (NCBI)||192, 209|
|RSP_0760||mucS||transcriptional regulator, MarR family (NCBI)||17, 214|
|RSP_0818||carB||carbamoyl phosphate synthase large subunit (RefSeq)||209, 383|
|RSP_0819||rhlE2||DEAD/DEAH box helicase (NCBI)||209, 316|
|RSP_1041||RSP_1041||Malonyl CoA synthetase (NCBI)||214, 363|
|RSP_1062||RSP_1062||ATPases of the PP superfamily (NCBI)||110, 209|
|RSP_1065||RSP_1065||hypothetical protein (NCBI)||130, 209|
|RSP_1075||RSP_1075||Short-chain dehydrogenase/reductase SDR (NCBI)||209, 218|
|RSP_1108||TruB||tRNA pseudouridine synthase B (NCBI)||209, 383|
|RSP_1110||RSP_1110||hypothetical protein (NCBI)||209, 271|
|RSP_1127||ElaA||acetyltransferase, GNAT family (NCBI)||214, 231|
|RSP_1197||HemH||Ferrochelatase (NCBI)||209, 311|
|RSP_1202||TrmA||putative RNA SAM-dependent methyltransferase, TrmA family (NCBI)||47, 209|
|RSP_1203||RSP_1203||ABC multidrug efflux pump, fused ATPase and inner membrane subunits (NCBI)||196, 209|
|RSP_1218||mutS||DNA mismatch repair protein MutS (NCBI)||209, 299|
|RSP_1426||RSP_1426||RNA-binding region RNP-1 (NCBI)||209, 316|
|RSP_1427||RSP_1427||hypothetical protein (NCBI)||209, 316|
|RSP_1484||RSP_1484||hypothetical protein (NCBI)||209, 268|
|RSP_1485||RSP_1485||ATP-dependent RNA helicase (NCBI)||209, 268|
|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_1799||secF||protein-export membrane protein SecF (NCBI)||209, 224|
|RSP_1893||RSP_1893||Inositol monophosphatase family protein (NCBI)||214, 240|
|RSP_1926||RSP_1926||tRNA-Dihydrouridine synthase (NCBI)||214, 311|
|RSP_1970||RSP_1970||Phosphoribosylglycinamide formyltransferase (NCBI)||84, 209|
|RSP_2118||recN||DNA repair protein RecN (NCBI)||209, 339|
|RSP_2188||RSP_2188||hypothetical protein (NCBI)||175, 214|
|RSP_2189||pccB||propionyl-CoA carboxylase beta chain (NCBI)||121, 214|
|RSP_2230||RSP_2230||response regulator receiver domain protein (NCBI)||214, 353|
|RSP_2552||exoU||Glycosyl transferase, family 2 (NCBI)||209, 316|
|RSP_2648||RSP_2648||hypothetical protein (NCBI)||209, 383|
|RSP_2696||RSP_2696||ABC transporter, fused ATPase and inner membrane subunits (NCBI)||214, 311|
|RSP_2717||RSP_2717||putative UUP ATPase (NCBI)||214, 311|
|RSP_2722||cysS||Cysteinyl-tRNA synthetase, class Ia (NCBI)||30, 214|
|RSP_2744||RSP_2744||hypothetical protein (NCBI)||214, 299|
|RSP_2915||phoR||Probable two-component sensor histidine kinase (NCBI)||213, 214|
|RSP_3004||RSP_3004||Possible Protein kinase (NCBI)||209, 214|
|RSP_3102||RSP_3102||putative sec-independent protein translocase protein, TatE (NCBI)||214, 306|
|RSP_3273||RSP_3273||ABC multidrug/carbohydrate efflux transporter, inner membrane subunit (NCBI)||116, 209|
|RSP_3274||RSP_3274||ABC multidrug/carbohydrate efflux transporter, ATPase subunit (NCBI)||116, 209|
|RSP_3591||RSP_3591||cytidylate kinase (NCBI)||209, 271|
|RSP_3593||RSP_3593||hypothetical protein (NCBI)||214, 356|
|RSP_3665||RSP_3665||transcriptional regulator, LuxR family (NCBI)||214, 384|
|RSP_4298||RSP_4298||tRNA-Trp (NCBI)||75, 214|
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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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.
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