Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_3498(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_3498
|Gene||Common Name||Description||Module membership|
|RSP_0134||RSP_0134||hypothetical protein (NCBI)||103, 183|
|RSP_0186||RSP_0186||Transcriptional regulator, TetR family (NCBI)||92, 370|
|RSP_0204||RSP_0204||metallo-beta-lactamase family protein (NCBI)||285, 370|
|RSP_0209||RSP_0209||possible prophage Lp3 protein 18 (NCBI)||103, 138|
|RSP_0297||RSP_0297||ABC branched chain amino acid transporter, ATPase subunit (NCBI)||103, 304|
|RSP_0298||RSP_0298||ABC branched chain amino acid transporter, ATPase subunit (NCBI)||103, 313|
|RSP_0299||RSP_0299||ABC branched chain amino acid transporter, inner membrane subunit (NCBI)||103, 313|
|RSP_0300||RSP_0300||ABC branched chain amino acid transporter, inner membrane subunit (NCBI)||103, 147|
|RSP_0477||RSP_0477||hypothetical protein (NCBI)||97, 103|
|RSP_0605||RSP_0605||hypothetical protein (NCBI)||249, 370|
|RSP_0607||RSP_0607||sigma 24 (NCBI)||77, 103|
|RSP_0617||RSP_0617||hypothetical protein (NCBI)||103, 325|
|RSP_0952||RSP_0952||Transglutaminase-like protein (NCBI)||249, 370|
|RSP_1294||RSP_1294||possible 2-oxoisovalerate dehydrogenase; E1 component, alpha and beta subunit (NCBI)||103, 217|
|RSP_1611||RSP_1611||sensor histidine kinase (NCBI)||35, 370|
|RSP_1612||RSP_1612||Sigma-54 dependent transcriptional regulator (NCBI)||370, 379|
|RSP_1933||RSP_1933||Outer membrane protein, OmpA/MotB family (NCBI)||103, 280|
|RSP_2019||RSP_2019||hypothetical protein (NCBI)||103, 120|
|RSP_2022||RSP_2022||Cytochrome b/diheme cytochrome c hybrid protein (NCBI)||103, 229|
|RSP_2026||RSP_2026||transcriptional regulator, AraC family (NCBI)||103, 176|
|RSP_2055||RSP_2055||hypothetical protein (NCBI)||103, 379|
|RSP_2105||RSP_2105||hypothetical protein (NCBI)||103, 325|
|RSP_2291||RSP_2291||hypothetical protein (NCBI)||14, 370|
|RSP_2385||RSP_2385||hypothetical protein (NCBI)||103, 124|
|RSP_2429||RSP_2429||Glutathione-regulated potassium-efflux system protein, kefB (NCBI)||36, 370|
|RSP_2432||RSP_2432||hypothetical protein (NCBI)||31, 370|
|RSP_2433||cheY2||Chemotaxis response regulator, CheY2 (NCBI)||285, 370|
|RSP_2434||cheR1||Putative MCP methyltransferase, CheR1 (NCBI)||31, 370|
|RSP_2435||cheW1||Putative chemotaxis scaffold protein, CheW1 (NCBI)||31, 370|
|RSP_2436||cheA1||Chemotaxis histidine protein kinase, CheA1 (NCBI)||31, 370|
|RSP_2437||cheY1||chemotaxis response regulator, CheY1 (NCBI)||31, 370|
|RSP_2438||cheX||Putative CheX protein (NCBI)||31, 370|
|RSP_2439||cheD||putative chemotaxis protein, CheD (NCBI)||31, 370|
|RSP_2440||mcpA||Methyl accepting chemotaxis protein (NCBI)||31, 370|
|RSP_2721||RSP_2721||hypothetical protein (NCBI)||38, 370|
|RSP_2792||RSP_2792||putative monooxygenase alpha subunit (NCBI)||77, 103|
|RSP_2793||RSP_2793||Putative reductase component of monooxygenase (NCBI)||103, 313|
|RSP_2794||RSP_2794||Putative monooxygenase beta subunit (NCBI)||103, 193|
|RSP_2795||RSP_2795||Putative regulatory protein of multicomponent monooxygenase (NCBI)||103, 193|
|RSP_2796||RSP_2796||hypothetical protein (NCBI)||77, 103|
|RSP_2798||groEL3||Putative chaperonin groEL (NCBI)||77, 103|
|RSP_3018||RSP_3018||putative acyl-CoA dehydrogenase (NCBI)||304, 370|
|RSP_3060||cysE||possible O-acetylserine synthase (NCBI)||141, 370|
|RSP_3062||fabG||3-oxoacyl-(acyl-carrier-protein) reductase (NCBI)||141, 370|
|RSP_3116||RSP_3116||Conserved hypothetical membrane/transport protein (NCBI)||246, 370|
|RSP_3230||RSP_3230||hypothetical protein (NCBI)||103, 279|
|RSP_3334||RSP_3334||HyuE hydantoin racemase (NCBI)||44, 103|
|RSP_3360||RSP_3360||Adenine specific DNA methyltransferase, D12 class (NCBI)||103, 342|
|RSP_3451||RSP_3451||TRAP-T family transporter, large (12TMs) inner membrane subunit (NCBI)||61, 370|
|RSP_3493||RSP_3493||hypothetical protein (NCBI)||220, 370|
|RSP_3495||RSP_3495||hypothetical protein (NCBI)||116, 370|
|RSP_3496||RSP_3496||Zinc carboxypeptidase A metalloprotease (M14) (NCBI)||220, 370|
|RSP_3497||RSP_3497||Caspase-1, p20 (NCBI)||103, 168|
|RSP_3498||RSP_3498||Antifreeze protein, type I (NCBI)||103, 370|
|RSP_3541||RSP_3541||hypothetical protein (NCBI)||103, 242|
|RSP_3576||RSP_3576||hypothetical protein (NCBI)||103, 249|
|RSP_3812||RSP_3812||recombinase (NCBI)||103, 189|
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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