Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_3682(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_3682
|Gene||Common Name||Description||Module membership|
|RSP_0151||RSP_0151||hypothetical protein (NCBI)||38, 74|
|RSP_0152||RSP_0152||P-loop ATPase (NCBI)||74, 280|
|RSP_0211||RSP_0211||hypothetical protein (NCBI)||74, 191|
|RSP_0212||RSP_0212||HNH nuclease (NCBI)||74, 193|
|RSP_0297||RSP_0297||ABC branched chain amino acid transporter, ATPase subunit (NCBI)||103, 304|
|RSP_0330||RSP_0330||hypothetical protein (NCBI)||74, 116|
|RSP_0512||RSP_0512||multisensor hybrid histidine kinase (NCBI)||94, 304|
|RSP_0524||RSP_0524||hypothetical protein (NCBI)||74, 168|
|RSP_0609||RSP_0609||hypothetical protein (NCBI)||146, 304|
|RSP_0856||btaA||S-adenosylmethionine-diacylglycerol 3-amino-3-carboxypropyl transferase (NCBI)||6, 304|
|RSP_0938||RSP_0938||hypothetical protein (NCBI)||304, 313|
|RSP_0946||RSP_0946||putative DNA topoisomerase I protein (NCBI)||74, 150|
|RSP_1113||RSP_1113||Hemolysin-type calcium-binding region; RTX toxin (NCBI)||74, 115|
|RSP_1195||comF||Competence protein F (NCBI)||74, 150|
|RSP_1323||RSP_1323||hypothetical protein (NCBI)||116, 304|
|RSP_1357||RSP_1357||cytoplasmic sensor hybrid histidine kinase (NCBI)||74, 137|
|RSP_1500||RSP_1500||possible anti-sigma regulatory kinase (NCBI)||29, 304|
|RSP_1501||RSP_1501||Antisigma-factor antagonist (STAS) domain protein (NCBI)||74, 292|
|RSP_1618||RSP_1618||hypothetical protein (NCBI)||62, 304|
|RSP_1651||RSP_1651||hypothetical protein (NCBI)||304, 313|
|RSP_1694||RSP_1694||Probable short-chain dehydrogenase/reductase (NCBI)||233, 304|
|RSP_1753||RSP_1753||hypothetical protein (NCBI)||304, 355|
|RSP_1954||RSP_1954||hypothetical protein (NCBI)||155, 304|
|RSP_2023||RSP_2023||hypothetical protein (NCBI)||229, 304|
|RSP_2068||RSP_2068||putative ClpP-like protease (NCBI)||235, 304|
|RSP_2070||RSP_2070||Putative Phage-related terminase (NCBI)||77, 304|
|RSP_2071||RSP_2071||hypothetical protein (NCBI)||77, 304|
|RSP_2259||RSP_2259||Transmembrane protein (NCBI)||288, 304|
|RSP_2351||RSP_2351||hypothetical protein (NCBI)||74, 362|
|RSP_2352||RSP_2352||putative terminase large subunit / phage terminase (NCBI)||74, 83|
|RSP_2353||RSP_2353||hypothetical protein (NCBI)||74, 83|
|RSP_2441||tlpS||Putative transducer like protein (NCBI)||304, 320|
|RSP_2497||RSP_2497||ATPase (NCBI)||74, 238|
|RSP_2679||RSP_2679||ATP-dependent DNA ligase (NCBI)||74, 191|
|RSP_2755||RSP_2755||hypothetical protein (NCBI)||74, 77|
|RSP_2769||RSP_2769||probable 5,10-methylenetetrahydrofolate reductase (NCBI)||238, 304|
|RSP_2813||mttB||putative trimethylamine methyltransferase protein (NCBI)||73, 304|
|RSP_3014||RSP_3014||putative aldolase protein (NCBI)||137, 304|
|RSP_3018||RSP_3018||putative acyl-CoA dehydrogenase (NCBI)||304, 370|
|RSP_3063||RSP_3063||AMP-dependent synthetase and ligase (NCBI)||74, 137|
|RSP_3096||RSP_3096||hypothetical protein (NCBI)||168, 304|
|RSP_3098||qoxB||QoxB, Quinol oxidase subunit II (NCBI)||168, 304|
|RSP_3103||RSP_3103||hypothetical protein (NCBI)||19, 304|
|RSP_3104||fdh||Putative Glutathione-dependent formaldehyde dehydrogenase (NCBI)||288, 304|
|RSP_3204||RSP_3204||putative Oxidoreductase (NCBI)||124, 304|
|RSP_3206||RSP_3206||Putative xanthine dehydrogenase (NCBI)||74, 236|
|RSP_3283||RSP_3283||myo-inositol 2-dehydrogenase (NCBI)||116, 304|
|RSP_3353||RSP_3353||Phage related tail protein (NCBI)||74, 150|
|RSP_3357||gpU||putative phage tail protein U (NCBI)||40, 304|
|RSP_3358||gpX||Phage tail component protein X (NCBI)||282, 304|
|RSP_3414||RSP_3414||ABC Fe+3-siderophore transporter, inner membrane subunit (NCBI)||74, 196|
|RSP_3415||RSP_3415||ABC Fe+3-siderophore transporter, inner membrane subunit (NCBI)||74, 138|
|RSP_3416||RSP_3416||ABC Fe+3-siderophore transporter, periplasmic binding protein (NCBI)||74, 331|
|RSP_3577||gvpG||putative gas vesicle synthesis protein (NCBI)||253, 304|
|RSP_3659||RSP_3659||Predicted amidohydrolase (NCBI)||288, 304|
|RSP_3682||RSP_3682||hypothetical protein (NCBI)||74, 304|
|RSP_3774||RSP_3774||hypothetical protein (NCBI)||304, 380|
|RSP_3775||RSP_3775||hypothetical protein (NCBI)||304, 380|
|RSP_3814||RSP_3814||hypothetical protein (NCBI)||189, 304|
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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