Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0313(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_0313
|Gene||Common Name||Description||Module membership|
|RSP_0163||RSP_0163||putative iron(III) ABC transporter, fused inner membrane subunits (NCBI)||115, 234|
|RSP_0313||RSP_0313||hypothetical protein (NCBI)||115, 383|
|RSP_0818||carB||carbamoyl phosphate synthase large subunit (RefSeq)||209, 383|
|RSP_1108||TruB||tRNA pseudouridine synthase B (NCBI)||209, 383|
|RSP_1113||RSP_1113||Hemolysin-type calcium-binding region; RTX toxin (NCBI)||74, 115|
|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_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_1950||RSP_1950||hypothetical protein (NCBI)||213, 383|
|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_2170||RSP_2170||Phosphate transporter, Pit family (NCBI)||263, 383|
|RSP_2226||glgX||Glycosidase (NCBI)||115, 296|
|RSP_2227||glgC||ADP-glucose pyrophosphorylase (NCBI)||115, 296|
|RSP_2254||RSP_2254||ABC efflux transporter, fused ATPase and inner membrane subunits (NCBI)||115, 316|
|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_2612||fabH||3-oxoacyl-(acyl-carrier-protein) synthase III (NCBI)||263, 383|
|RSP_2648||RSP_2648||hypothetical protein (NCBI)||209, 383|
|RSP_2661||RSP_2661||Iron-containing alcohol dehydrogenase (NCBI)||115, 122|
|RSP_2662||glpK||Glycerol kinase (NCBI)||115, 122|
|RSP_2663||RSP_2663||ABC sugar (glycerol) transporter, periplasmic binding protein (NCBI)||115, 122|
|RSP_2664||RSP_2664||hypothetical protein (NCBI)||115, 122|
|RSP_2665||RSP_2665||ABC sugar (glycerol) transporter, inner membrane subunit (NCBI)||115, 122|
|RSP_2666||RSP_2666||ABC sugar (glycerol) transporter, inner membrane subunit (NCBI)||115, 122|
|RSP_2667||RSP_2667||ABC sugar (glycerol) transporter, ATPase subunit (NCBI)||115, 122|
|RSP_2669||RSP_2669||ABC sugar (glycerol) transporter, ATPase subunit (NCBI)||115, 122|
|RSP_2670||glpD||putative FAD-dependent glycerol-3-phosphate dehydrogenase (NCBI)||115, 122|
|RSP_2917||RSP_2917||putative cystathionine gamma-synthase beta-lyase (NCBI)||7, 383|
|RSP_3287||upgC||ABC glycerol-3-phosphate transporter, ATPase subunit UpgC (NCBI)||115, 233|
|RSP_3288||ugpE||ABC glycerol-3-phosphate transporter, inner membrane subunit UgpE (NCBI)||115, 233|
|RSP_3289||ugpA||ABC glycerol-3-phosphate transporter, inner membrane subunit UgpA (NCBI)||115, 233|
|RSP_3290||ugpB||ABC glycerol-3-phosphate transporter, periplasmic binding protein, UgpB (NCBI)||115, 233|
|RSP_3666||RSP_3666||putative membrane protein (NCBI)||115, 155|
|RSP_3667||RSP_3667||transcriptional regulator, AraC family with Parallel beta-helix repeat (NCBI)||115, 155|
|RSP_3669||RSP_3669||hypothetical protein (NCBI)||115, 155|
|RSP_3671||RSP_3671||putative D-tagatose 3-epimerase (NCBI)||88, 115|
|RSP_3672||RSP_3672||ABC sugar transporter, inner membrane subunit (NCBI)||88, 115|
|RSP_3673||RSP_3673||ABC sugar transporter, inner membrane subunit (NCBI)||88, 115|
|RSP_3674||RSP_3674||ABC sugar transporter, periplasmic binding protein (NCBI)||26, 115|
|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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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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