Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0182(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_0182
|Gene||Common Name||Description||Module membership|
|RSP_0302||ureG||Urease accessory protein G (NCBI)||175, 307|
|RSP_0303||ureF||Urease accessory protein UreF (NCBI)||175, 307|
|RSP_0304||ureE||urease accessory protein UreE (NCBI)||175, 307|
|RSP_0305||RSP_0305||hypothetical protein (NCBI)||175, 307|
|RSP_0306||RSP_0306||Class I diheme cytochrome c (NCBI)||175, 307|
|RSP_0329||RSP_0329||GAF sensor diguanylate cyclase (GGDEF) (NCBI)||174, 175|
|RSP_0406||RSP_0406||periplasmic sensor diguanylate cyclase (GGDEF) (NCBI)||126, 175|
|RSP_0407||RSP_0407||putative lactate dehydrogenase (NCBI)||175, 384|
|RSP_0610||RSP_0610||Putative 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI)||95, 273|
|RSP_0796||cobQ||cobyric acid synthase (NCBI)||95, 158|
|RSP_0803||DppF||ABC dipeptide transporter, ATPase subunit DppF (NCBI)||174, 175|
|RSP_0894||RSP_0894||hypothetical protein (NCBI)||175, 384|
|RSP_0895||RSP_0895||phosphodiesterase-like (NCBI)||7, 175|
|RSP_0943||yhxA||probable adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI)||25, 175|
|RSP_1086||sdh||saccharopine dehydrogenase (NAD+, L-lysine forming) (NCBI)||72, 175|
|RSP_1377||RSP_1377||Carbonic anhydrase (NCBI)||112, 175|
|RSP_1378||RSP_1378||hypothetical protein (NCBI)||175, 189|
|RSP_1379||RSP_1379||Cytosol aminopeptidase (NCBI)||175, 384|
|RSP_1380||RSP_1380||hypothetical protein (NCBI)||7, 175|
|RSP_1434||RSP_1434||Putative Zn-dependent oxidoreductase (NCBI)||95, 113|
|RSP_1590||RSP_1590||two component, sigma54 specific, transcriptional regulator, fis family (NCBI)||175, 358|
|RSP_1758||RSP_1758||Probable succinyl-diaminopimelate desuccinylase (NCBI)||95, 102|
|RSP_1946||RSP_1946||Cytochrome P450 hydroxylase (NCBI)||175, 381|
|RSP_2012||RSP_2012||NUDIX hydrolase, MutT (NCBI)||175, 242|
|RSP_2168||RSP_2168||hypothetical protein (NCBI)||126, 175|
|RSP_2188||RSP_2188||hypothetical protein (NCBI)||175, 214|
|RSP_2252||RSP_2252||Threonine dehydratase (NCBI)||145, 175|
|RSP_2253||RSP_2253||predicted hydrolases or acyltransferases (NCBI)||16, 175|
|RSP_2632||argI||Arginase (NCBI)||95, 168|
|RSP_2730||RSP_2730||Transcriptional regulator, ArsR family (NCBI)||67, 95|
|RSP_2853||RSP_2853||Transcriptional regulator, TetR family (NCBI)||12, 95|
|RSP_2854||RSP_2854||Cation/multidrug efflux pump, Membrane fusion protein (MFP) family (NCBI)||12, 95|
|RSP_2855||RSP_2855||Cation/multidrug efflux pump, RND superfamily (NCBI)||12, 95|
|RSP_2883||pgm||Probable phosphoglucomutase/phosphomannomutase (NCBI)||175, 384|
|RSP_2898||RSP_2898||putative DNA polymerase III chi subunit (NCBI)||4, 175|
|RSP_2899||RSP_2899||Probable cytosol aminopeptidase (NCBI)||4, 175|
|RSP_2932||hutC||Histidine utilization repressor, gntR family (NCBI)||95, 97|
|RSP_2933||hutF||Formiminoglutamate deiminase (NCBI)||95, 97|
|RSP_2934||hutI||Imidazolone-5-propionate hydrolase (NCBI)||95, 97|
|RSP_2935||hutH||Probable histidine ammonia-lyase (NCBI)||95, 97|
|RSP_2936||hutU||Urocanase (NCBI)||95, 97|
|RSP_3246||RSP_3246||putative D-alanyl-D-alanine carboxypeptidase (NCBI)||175, 384|
|RSP_3298||RSP_3298||transcriptional regulator, LysR family (NCBI)||95, 273|
|RSP_3381||RSP_3381||NAD(P)H -dependent quinone oxidoreductase (NCBI)||57, 175|
|RSP_3403||RSP_3403||hypothetical protein (NCBI)||95, 102|
|RSP_3404||RSP_3404||hypothetical protein (NCBI)||95, 244|
|RSP_3405||gntR||transcriptional regulator, GntR family (NCBI)||95, 244|
|RSP_3419||RSP_3419||hypothetical protein (NCBI)||175, 381|
|RSP_3520||RSP_3520||ABC peptide transporter, fused ATPase domains (NCBI)||95, 170|
|RSP_3522||RSP_3522||ABC peptide transporter, inner membrane subunit (NCBI)||95, 170|
|RSP_3523||RSP_3523||ABC peptide transporter, inner membrane subunit (NCBI)||95, 170|
|RSP_3524||RSP_3524||ABC peptide transporter, periplasmic binding protein (NCBI)||95, 170|
|RSP_3525||RSP_3525||ABC peptide transporter, periplasmic binding protein (NCBI)||95, 170|
|RSP_3526||RSP_3526||Amidase (NCBI)||95, 170|
|RSP_3527||RSP_3527||Probable acetylpolyamine aminohydrolase (NCBI)||95, 170|
|RSP_3584||RSP_3584||hypothetical protein (NCBI)||95, 242|
|RSP_3759||RSP_3759||Putative endonuclease (NCBI)||130, 175|
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;
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