Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0123(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|
Functional Enrichment for RSP_0123
Module neighborhood information for RSP_0123
|Gene||Common Name||Description||Module membership|
|RSP_0004||RSP_0004||hypothetical protein (NCBI)||97, 303|
|RSP_0123||cerI||Autoinducer synthesis protein (NCBI)||97, 309|
|RSP_0124||RSP_0124||hypothetical protein (NCBI)||161, 309|
|RSP_0217||int||possible phage-related integrase (NCBI)||171, 309|
|RSP_0430||cobD||cobalamin biosynthesis protein CobD (NCBI)||97, 171|
|RSP_0477||RSP_0477||hypothetical protein (NCBI)||97, 103|
|RSP_0596||RSP_0596||Putative peptidyl-dipeptidase (NCBI)||97, 329|
|RSP_0606||RSP_0606||Putative redox protein (NCBI)||97, 285|
|RSP_0751||RSP_0751||hypothetical protein (NCBI)||62, 97|
|RSP_0890||RSP_0890||possible protein yrbC precursor (NCBI)||182, 309|
|RSP_0891||vacJ||putative lipoprotein (NCBI)||182, 309|
|RSP_0892||RSP_0892||ABC protein toxin exporter, fused ATPase and inner membrane domain (NCBI)||182, 309|
|RSP_0893||RSP_0893||RTX secretion protein D, HlyD family (NCBI)||182, 309|
|RSP_0929||accD||Acetyl-CoA carboxylase carboxyl transferase, beta subunit (NCBI)||309, 360|
|RSP_0955||RSP_0955||5'-nucleotidase (NCBI)||97, 195|
|RSP_1055||RSP_1055||transcriptional regulator, LysR family (NCBI)||97, 329|
|RSP_1435||RSP_1435||regulatory protein TetR family (NCBI)||62, 97|
|RSP_1473||RSP_1473||hypothetical protein (NCBI)||97, 244|
|RSP_1521||RSP_1521||hypothetical protein (NCBI)||97, 116|
|RSP_1824||adh||Zinc-containing alcohol dehydrogenase (NCBI)||35, 97|
|RSP_1843||ftsY||Signal recognition particle-docking protein FtsY (NCBI)||71, 309|
|RSP_1864||RSP_1864||hypothetical protein (NCBI)||48, 309|
|RSP_1948||RSP_1948||Protein of unknown function, HesB/YadR/YfhF (NCBI)||161, 309|
|RSP_1949||RSP_1949||hypothetical protein (NCBI)||161, 309|
|RSP_1962||RSP_1962||hypothetical protein (NCBI)||13, 97|
|RSP_1986||gatB||Glutamyl-tRNA amidotransferase subunit B (NCBI)||25, 309|
|RSP_1990||RSP_1990||Transcriptional regulator, AsnC family (NCBI)||97, 195|
|RSP_1991||RSP_1991||Putative Ornithine decarboxylase (NCBI)||309, 365|
|RSP_1994||gltA||Citrate synthase (NCBI)||279, 309|
|RSP_2053||RSP_2053||Possible transporter, RarD family, DMT superfamily (NCBI)||73, 97|
|RSP_2167||RSP_2167||hypothetical protein (NCBI)||97, 262|
|RSP_2193||gcvT||predicted aminomethyltransferase, tetrahydrofolate dependent (NCBI)||71, 309|
|RSP_2329||mreB||Cell shape determining protein MreB/Mrl (NCBI)||93, 309|
|RSP_2376||kbl||2-amino-3-ketobutyrate CoA ligase (NCBI)||97, 239|
|RSP_2641||RSP_2641||hypothetical protein (NCBI)||97, 237|
|RSP_2718||RSP_2718||possible outer membrane protein (NCBI)||3, 309|
|RSP_2783||lipA||lipoic acid synthetase (NCBI)||161, 309|
|RSP_2914||RSP_2914||Nucleoside hydrolase (NCBI)||126, 309|
|RSP_2921||RSP_2921||phospho-2-dehydro-3-deoxyheptonate (NCBI)||182, 309|
|RSP_2922||RSP_2922||Transcriptional regulator, AraC family (NCBI)||182, 309|
|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_2975||RSP_2975||hypothetical protein (NCBI)||71, 309|
|RSP_3029||RSP_3029||transcriptional regulator, GntR family (NCBI)||97, 157|
|RSP_3031||RSP_3031||ABC peptide/opine transporter, inner membrane subunit (NCBI)||97, 157|
|RSP_3052||RSP_3052||transcriptional regulator, LysR family (NCBI)||97, 176|
|RSP_3053||RSP_3053||Possible dioxygenase/glyoxalase family protein (NCBI)||97, 176|
|RSP_3074||ilvD||Dihydroxy-acid and 6-phosphogluconate dehydratase (NCBI)||15, 309|
|RSP_3087||dgkA||diacylglycerol kinase (NCBI)||97, 176|
|RSP_3180||RSP_3180||Transglutaminase-like enzyme (NCBI)||38, 97|
|RSP_3400||RSP_3400||transcriptional regulator, LysR family (NCBI)||19, 97|
|RSP_3748||ampR||transcriptional regulator, LysR family (NCBI)||97, 362|
|RSP_3820||rpmA||Ribosomal protein L27 (NCBI)||169, 309|
|RSP_3821||RSP_3821||Putative acetyltransferase (NCBI)||297, 309|
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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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.
- 2. Source gene
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