Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_2648(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|
Module neighborhood information for RSP_2648
|Gene||Common Name||Description||Module membership|
|RSP_0313||RSP_0313||hypothetical protein (NCBI)||115, 383|
|RSP_0448||RSP_0448||EF-Tu; elongation factor Tu (NCBI)||209, 271|
|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_0818||carB||carbamoyl phosphate synthase large subunit (RefSeq)||209, 383|
|RSP_0819||rhlE2||DEAD/DEAH box helicase (NCBI)||209, 316|
|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_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_1288||RSP_1288||ABC branched chain amino acid family transporter, ATPase subunit (NCBI)||263, 383|
|RSP_1290||RSP_1290||ABC branched chain amino acid family transporter, inner membrane subunit (NCBI)||263, 383|
|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_1670||spoT/relA||RelA/SpoT family protein (NCBI)||130, 383|
|RSP_1675||rnc||Ribonuclease III (NCBI)||263, 383|
|RSP_1677||RSP_1677||hypothetical protein (NCBI)||221, 383|
|RSP_1712||rpoC||RNA polymerase I subunit A, (NCBI)||104, 383|
|RSP_1799||secF||protein-export membrane protein SecF (NCBI)||209, 224|
|RSP_1950||RSP_1950||hypothetical protein (NCBI)||213, 383|
|RSP_1970||RSP_1970||Phosphoribosylglycinamide formyltransferase (NCBI)||84, 209|
|RSP_2097||RSP_2097||Putative FtsL (NCBI)||374, 383|
|RSP_2099||murE||UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase (NCBI)||374, 383|
|RSP_2100||murF||UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase (NCBI)||374, 383|
|RSP_2101||mraY||Phospho-N-acetylmuramoyl-pentapeptidetransferase (NCBI)||374, 383|
|RSP_2118||recN||DNA repair protein RecN (NCBI)||209, 339|
|RSP_2170||RSP_2170||Phosphate transporter, Pit family (NCBI)||263, 383|
|RSP_2327||RSP_2327||hypothetical protein (NCBI)||356, 383|
|RSP_2403||RSP_2403||ABC cobalamin/Fe3+-siderophore transporter, periplasmic substrate-binding subunit (NCBI)||167, 383|
|RSP_2404||RSP_2404||ABC cobalamin/Fe3+-siderophore transporter, inner membrane subunit (NCBI)||167, 383|
|RSP_2405||RSP_2405||ABC cobalamin/Fe3+-siderophore transporter, ATPase subunit (NCBI)||167, 383|
|RSP_2406||RSP_2406||hypothetical protein (NCBI)||167, 383|
|RSP_2552||exoU||Glycosyl transferase, family 2 (NCBI)||209, 316|
|RSP_2612||fabH||3-oxoacyl-(acyl-carrier-protein) synthase III (NCBI)||263, 383|
|RSP_2648||RSP_2648||hypothetical protein (NCBI)||209, 383|
|RSP_2917||RSP_2917||putative cystathionine gamma-synthase beta-lyase (NCBI)||7, 383|
|RSP_3004||RSP_3004||Possible Protein kinase (NCBI)||209, 214|
|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_3712||RSP_3712||Multisubunit Na+/H+ antiporter MnhE subunit (NCBI)||311, 383|
|RSP_3713||RSP_3713||pH adaptation potassium efflux system, phaD subunit (NCBI)||311, 383|
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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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;
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