Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0365(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_0365
|Gene||Common Name||Description||Module membership|
|RSP_0148||RSP_0148||Signal transduction histidine kinase (NCBI)||107, 335|
|RSP_0149||RSP_0149||CheY-like receiver protein (NCBI)||107, 112|
|RSP_0153||RSP_0153||hypothetical protein (NCBI)||107, 278|
|RSP_0198||RSP_0198||Phosphatidylglycerophosphate synthase (NCBI)||107, 121|
|RSP_0365||RSP_0365||hypothetical protein (NCBI)||107, 185|
|RSP_0388||RSP_0388||hypothetical protein (NCBI)||107, 377|
|RSP_0392||RSP_0392||probable lactoylglutathione lyase (NCBI)||107, 239|
|RSP_0393||RSP_0393||probable riboflavin biosynthesis protein (NCBI)||107, 323|
|RSP_0460||RSP_0460||AcrB/AcrD/AcrF family cation/multidrug efflux pump (NCBI)||111, 185|
|RSP_0461||RSP_0461||multidrug/cation efflux pump, membrane fusion protein (MFP) family (NCBI)||111, 185|
|RSP_0548||RSP_0548||hypothetical protein (NCBI)||185, 250|
|RSP_0552||RSP_0552||putative multidrug transporter, SMR family, DMT Superfamily (NCBI)||107, 302|
|RSP_0589||RSP_0589||hypothetical protein (NCBI)||185, 250|
|RSP_0795||RSP_0795||hypothetical protein (NCBI)||107, 185|
|RSP_0865||RSP_0865||hypothetical protein (NCBI)||107, 345|
|RSP_0935||RSP_0935||MiaB-like Radical SAM protein (NCBI)||63, 107|
|RSP_1023||RSP_1023||hypothetical protein (NCBI)||185, 200|
|RSP_1032||RSP_1032||possible O6-methylguanine-DNA methyltransferase (NCBI)||76, 107|
|RSP_1234||aroE||putative shikimate 5-dehydrogenase (NCBI)||107, 308|
|RSP_1292||RSP_1292||putative Aldehyde dehydrogenase (NCBI)||91, 107|
|RSP_1558||RSP_1558||putative 2-dehydropantoate 2-reductase (NCBI)||107, 136|
|RSP_1834||RSP_1834||hypothetical protein (NCBI)||10, 185|
|RSP_1880||RSP_1880||hypothetical protein (NCBI)||64, 185|
|RSP_1939||RSP_1939||NADPH-ferredoxin reductase (NCBI)||86, 185|
|RSP_1945||RSP_1945||Transcriptional Regulator, AsnC family (NCBI)||86, 185|
|RSP_1965||RSP_1965||Putative Membrane Fusion Protein Family member (NCBI)||107, 247|
|RSP_1971||rnd||Ribonuclease D (NCBI)||51, 107|
|RSP_1984||RSP_1984||histidinol-phosphate-aminotransferase (NCBI)||107, 171|
|RSP_2122||mtbC||Putative dimethylamine corrinoid protein (NCBI)||185, 285|
|RSP_2127||purS||Component of phosphoribosylformylglycinamidine (FGAM) synthetase (NCBI)||107, 261|
|RSP_2165||putR||transcriptional regulator, AsnC family (NCBI)||107, 126|
|RSP_2241||hisI||Phosphoribosyl-ATP pyrophosphohydrolase (NCBI)||107, 294|
|RSP_2282||chrA||Chromate efflux pump, ChrA (NCBI)||10, 107|
|RSP_2287||RSP_2287||ChaC-like protein (NCBI)||107, 317|
|RSP_2330||leuA||2-Isopropylmalate synthase (NCBI)||185, 286|
|RSP_2411||RSP_2411||hypothetical protein (NCBI)||20, 107|
|RSP_2642||RSP_2642||hypothetical protein (NCBI)||107, 121|
|RSP_2671||RSP_2671||hypothetical protein (NCBI)||35, 185|
|RSP_2847||RSP_2847||hypothetical protein (NCBI)||185, 250|
|RSP_2889||RSP_2889||Transcriptional regulator (NCBI)||185, 229|
|RSP_2890||RSP_2890||Copper-translocating P-type ATPase (NCBI)||185, 229|
|RSP_2891||RSP_2891||Putative copper chaperone (NCBI)||185, 229|
|RSP_2892||RSP_2892||hypothetical protein (NCBI)||185, 308|
|RSP_2903||RSP_2903||Probable PpiC-type peptidyl-prolyl cis-trans isomerase (NCBI)||107, 223|
|RSP_2982||gcpE||Probable 4-hydroxy-3-methylbut-2-en-1-yl diphosphate (NCBI)||64, 185|
|RSP_3071||RSP_3071||putative hydroxypyruvate reductase/glycerate kinase (NCBI)||107, 329|
|RSP_3082||RSP_3082||hypothetical protein (NCBI)||185, 213|
|RSP_3228||RSP_3228||Predicted mannose-6-phosphate isomerase (NCBI)||35, 185|
|RSP_3263||RSP_3263||Putative copper binding protein (NCBI)||27, 185|
|RSP_3307||RSP_3307||hypothetical protein (NCBI)||35, 185|
|RSP_3309||RSP_3309||transcriptional regulator, AraC family (NCBI)||63, 107|
|RSP_3350||RSP_3350||Lipocalin-related protein (NCBI)||107, 293|
|RSP_3594||RSP_3594||Antifreeze protein, type I (NCBI)||35, 185|
|RSP_3695||argE||putative acetylornithine deacetylase (acetylornithinase) (NCBI)||1, 107|
|RSP_4312||RSP_4312||tRNA-Glu (NCBI)||185, 225|
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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