Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0381(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_0381
|Gene||Common Name||Description||Module membership|
|RSP_0116||RSP_0116||hypothetical protein (NCBI)||14, 229|
|RSP_0189||RSP_0189||NADPH-dependent glutamate synthase beta chain and related oxidoreductase (NCBI)||43, 208|
|RSP_0190||accB||Biotin carboxyl carrier protein, AccB (NCBI)||43, 208|
|RSP_0191||accC||Biotin carboxylase (NCBI)||43, 208|
|RSP_0192||aat||possible leucyl/phenylalanyl-tRNA--protein transferase (NCBI)||43, 208|
|RSP_0221||RSP_0221||plasma membrane H+-transporting two-sector ATPase, C subunit (NCBI)||14, 342|
|RSP_0381||RSP_0381||hypothetical protein (NCBI)||14, 43|
|RSP_0444||RSP_0444||hypothetical protein (NCBI)||43, 360|
|RSP_0621||RSP_0621||Possible DNA helicase (NCBI)||14, 36|
|RSP_0842||RSP_0842||putative porin (NCBI)||43, 310|
|RSP_0887||MrcB||Glycosyl transferase, family 51 (NCBI)||43, 112|
|RSP_0961||MeaA||similiar to methylmalonyl-CoA mutases (NCBI)||14, 253|
|RSP_0971||RSP_0971||Putative membrane protein (NCBI)||43, 118|
|RSP_0972||RSP_0972||hypothetical protein (NCBI)||43, 118|
|RSP_1039||atpI||FoF1 ATP synthase, subunit I (NCBI)||43, 369|
|RSP_1064||RSP_1064||Putative preprotein translocase, YidC (NCBI)||43, 369|
|RSP_1157||PSrp1||Ribosomal subunit interface protein Y (NCBI)||43, 310|
|RSP_1169||secA||preprotein translocase, SecA subunit, ATPase (NCBI)||43, 277|
|RSP_1201||RSP_1201||hypothetical protein (NCBI)||43, 327|
|RSP_1231||rho||Transcription termination factor rho (NCBI)||43, 182|
|RSP_1519||prrC||PrrC (NCBI)||43, 360|
|RSP_1667||RSP_1667||hypothetical protein (NCBI)||43, 112|
|RSP_1668||FolK||2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase (NCBI)||43, 112|
|RSP_1860||RSP_1860||hypothetical protein (NCBI)||43, 377|
|RSP_2011||RSP_2011||putative transcription elongation factor (NCBI)||14, 128|
|RSP_2258||purC||SAICAR synthetase (NCBI)||43, 109|
|RSP_2291||RSP_2291||hypothetical protein (NCBI)||14, 370|
|RSP_2425||RSP_2425||putative CarD-like transcriptional regulator (NCBI)||43, 112|
|RSP_2536||rhlE||ATP-dependent helicase, DEAD-box (NCBI)||43, 195|
|RSP_2630||gyrA||DNA gyrase/topoisomerase IV, subunit A (NCBI)||43, 182|
|RSP_2711||RSP_2711||putative outer membrane protein (NCBI)||43, 360|
|RSP_2807||RSP_2807||putative cytochrome b (NCBI)||14, 229|
|RSP_2808||RSP_2808||hypothetical protein (NCBI)||14, 229|
|RSP_2974||RSP_2974||Putative metalopeptidase (NCBI)||43, 118|
|RSP_2991||RSP_2991||hypothetical protein (NCBI)||14, 189|
|RSP_2996||RSP_2996||putative prohead protease (NCBI)||14, 235|
|RSP_2997||RSP_2997||putative head portal protein (NCBI)||14, 235|
|RSP_2998||RSP_2998||Hypothetical Terminase large subunit (NCBI)||14, 189|
|RSP_2999||RSP_2999||hypothetical protein (NCBI)||14, 189|
|RSP_3000||RSP_3000||hypothetical protein (NCBI)||14, 325|
|RSP_3001||RSP_3001||Possible Endonuclease (NCBI)||14, 189|
|RSP_3119||RSP_3119||conserved hypothetical protein / putative esterase (NCBI)||14, 38|
|RSP_3175||RSP_3175||hypothetical protein (NCBI)||14, 19|
|RSP_3203||RSP_3203||transcriptional regulator, AraC family (NCBI)||14, 19|
|RSP_3240||RSP_3240||periplasmic sensor signal transduction histidine kinase (NCBI)||14, 19|
|RSP_3252||RSP_3252||ABC peptide transporter, fused ATPase domains (NCBI)||14, 325|
|RSP_3264||RSP_3264||probable c-type cytochrome (NCBI)||14, 27|
|RSP_3312||RSP_3312||hypothetical protein (NCBI)||14, 188|
|RSP_3343||RSP_3343||putative glycosyl transferase (NCBI)||14, 168|
|RSP_3428||RSP_3428||hypothetical protein (NCBI)||14, 116|
|RSP_3434||RSP_3434||hypothetical protein (NCBI)||14, 144|
|RSP_3544||RSP_3544||hypothetical protein (NCBI)||14, 342|
|RSP_3573||gvpA||Gas vesicle protein GVPa (NCBI)||14, 27|
|RSP_3595||metK||S-adenosylmethionine synthetase (NCBI)||43, 85|
|RSP_3753||RSP_3753||hypothetical protein (NCBI)||14, 183|
|RSP_4294||RSP_4294||16S ribosomal RNA (NCBI)||14, 43|
|RSP_4295||RSP_4295||23S ribosomal RNA (NCBI)||14, 310|
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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