Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_2758(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_2758
|Gene||Common Name||Description||Module membership|
|RSP_0027||RSP_0027||hypothetical protein (NCBI)||62, 251|
|RSP_0028||RSP_0028||Putative short-chain dehydrogenase/reductase (NCBI)||246, 251|
|RSP_0522||RSP_0522||putative oxidoreductase (NCBI)||217, 246|
|RSP_0835||manB||phosphomannomutase (NCBI)||153, 246|
|RSP_1115||RSP_1115||hypothetical protein (NCBI)||246, 292|
|RSP_1116||RSP_1116||glycosyltransferase (NCBI)||196, 246|
|RSP_1117||RSP_1117||hypothetical protein (NCBI)||137, 246|
|RSP_1118||RSP_1118||group 1 glycosyltransferase (NCBI)||246, 292|
|RSP_1119||RSP_1119||ABC protein exporter, fused ATPase and inner membrane subunits (NCBI)||196, 246|
|RSP_1120||RSP_1120||protein secretion protein, HlyD family, membrane fusion protein (NCBI)||137, 246|
|RSP_1302||motB||putative chemotaxis MotB protein (NCBI)||31, 246|
|RSP_1303||flgE||putative flagellar hook protein (NCBI)||29, 246|
|RSP_1304||RSP_1304||putative flagellar hook protein (NCBI)||124, 246|
|RSP_1305||RSP_1305||putative flagellar hook-associated protein (NCBI)||138, 246|
|RSP_1307||flgI||putative flagellar P-ring protein (NCBI)||31, 246|
|RSP_1630||RSP_1630||hypothetical protein (NCBI)||31, 246|
|RSP_2080||RSP_2080||Putative Tyrosine recombinase (NCBI)||251, 340|
|RSP_2166||putA||Bifunctional putA protein; Proline dehydrogenase / Delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI)||38, 251|
|RSP_2757||RSP_2757||hypothetical protein (NCBI)||236, 246|
|RSP_2758||RSP_2758||hypothetical protein (NCBI)||246, 251|
|RSP_2759||RSP_2759||hypothetical protein (NCBI)||246, 282|
|RSP_2760||RSP_2760||hypothetical protein (NCBI)||246, 251|
|RSP_2761||RSP_2761||putative P2-like prophage tail protein X (NCBI)||246, 282|
|RSP_3108||RSP_3108||Putative methyl accepting chemotaxis protein (NCBI)||246, 292|
|RSP_3116||RSP_3116||Conserved hypothetical membrane/transport protein (NCBI)||246, 370|
|RSP_3143||RSP_3143||hypothetical protein (NCBI)||44, 251|
|RSP_3144||RSP_3144||hypothetical protein (NCBI)||44, 251|
|RSP_3145||ttdB||Putative Tartrate dehydratase beta subunit (NCBI)||44, 251|
|RSP_3146||ttdA||Putative Tartrate dehydratase alpha subunit (NCBI)||44, 251|
|RSP_3147||sdhA||putative succinate dehydrogenase/fumarate reductase, flavoprotein subunit (NCBI)||44, 251|
|RSP_3148||RSP_3148||putative succinate dehydrogenase cytochrome b-556 subunit (NCBI)||44, 251|
|RSP_3149||RSP_3149||putative succinate dehydrogenase membrane anchor (NCBI)||44, 251|
|RSP_3150||frdB||Succinate dehydrogenase/fumarate reductase Fe-S protein subunit (NCBI)||44, 251|
|RSP_3153||RSP_3153||ABC nitrate/sulfonate/bicarbonate transporter family, inner membrane subunit (NCBI)||110, 251|
|RSP_3154||RSP_3154||ABC nitrate/sulfonate/bicarbonate transporter family, ATPase subunit (NCBI)||105, 251|
|RSP_3155||RSP_3155||Thiamine pyrophosphate-requiring enzyme (NCBI)||251, 273|
|RSP_3284||iolD||Acetolactate synthase (NCBI)||176, 246|
|RSP_3285||iolE||possible sugar phosphate isomerases/epimerases, IolE (NCBI)||150, 246|
|RSP_3286||iolB||Uncharacterized enzyme involved in inositol metabolism, IolB (NCBI)||246, 380|
|RSP_3338||RSP_3338||ABC spermidine/putrescine transporter, ATPase subunit (NCBI)||236, 251|
|RSP_3420||RSP_3420||Methyl-accepting chemotaxis protein (NCBI)||77, 251|
|RSP_3422||RSP_3422||hypothetical protein (NCBI)||251, 323|
|RSP_3630||RSP_3630||hypothetical protein (NCBI)||246, 253|
|RSP_3700||RSP_3700||transcriptional regulator, LacI family (NCBI)||157, 251|
|RSP_3701||RSP_3701||ABC sugar transporter, periplasmic binding protein (NCBI)||157, 251|
|RSP_3702||RSP_3702||ABC sugar transporter, ATPase subunit (NCBI)||157, 251|
|RSP_3703||RSP_3703||ABC sugar transporter, inner membrane subunit (NCBI)||157, 251|
|RSP_3704||RSP_3704||ribitol 2-dehydrogenase (NCBI)||157, 251|
|RSP_3705||RSP_3705||D-ribulokinase (NCBI)||157, 251|
|RSP_3811||RSP_3811||hypothetical protein (NCBI)||138, 246|
|RSP_4345||RSP_4345||tRNA-Glu (NCBI)||34, 246|
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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If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.
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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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