Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0915(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_0915
|Gene||Common Name||Description||Module membership|
|RSP_0147||glnA||Glutamine synthetase class-I (NCBI)||25, 93|
|RSP_0153||RSP_0153||hypothetical protein (NCBI)||107, 278|
|RSP_0250||RSP_0250||hypothetical protein (NCBI)||25, 278|
|RSP_0251||RSP_0251||Outer membrane efflux protein (NCBI)||223, 278|
|RSP_0252||RSP_0252||Protein-L-isoaspartatecarboxylmethyltransferase (NCBI)||262, 278|
|RSP_0253||RSP_0253||Glycine/D-amino acid oxidase (deaminating) (NCBI)||136, 278|
|RSP_0398||RSP_0398||dehydrogenase (NCBI)||239, 278|
|RSP_0423||RSP_0423||Aldo/keto reductase (NCBI)||121, 278|
|RSP_0550||RSP_0550||putative D-alanyl-D-alanine carboxypeptidase (NCBI)||25, 52|
|RSP_0745||RSP_0745||acetyl-CoA acetyltransferase (NCBI)||25, 195|
|RSP_0747||RSP_0747||Short-chain dehydrogenase/reductase (NCBI)||25, 195|
|RSP_0913||crt||Enoyl-CoA hydratase/isomerase (NCBI)||82, 278|
|RSP_0914||RSP_0914||Short-chain dehydrogenase/reductase SDR (NCBI)||82, 278|
|RSP_0915||RSP_0915||hypothetical protein (NCBI)||25, 278|
|RSP_0943||yhxA||probable adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI)||25, 175|
|RSP_0968||mdh||malate dehydrogenase (RefSeq)||25, 166|
|RSP_1002||pyrB||Aspartate/ornithine carbamoyltransferase (NCBI)||25, 224|
|RSP_1131||dapD||2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI)||25, 192|
|RSP_1242||RSP_1242||hypothetical protein (NCBI)||76, 278|
|RSP_1243||RSP_1243||transcriptional regulator, LacI family (NCBI)||76, 278|
|RSP_1244||RSP_1244||putative IolE, Sugar phosphate isomerases/epimerases (NCBI)||76, 278|
|RSP_1245||RSP_1245||predicted oxidoreductase, Gfo/Idh/MocA family (NCBI)||76, 278|
|RSP_1247||RSP_1247||ABC sugar transporter, ATPase subunit (NCBI)||76, 278|
|RSP_1249||RSP_1249||ABC ribose transporter, periplasmic solute-binding protein (NCBI)||76, 278|
|RSP_1342||dnaA||chromosomal replication initiator protein, DnaA (NCBI)||25, 381|
|RSP_1343||RSP_1343||DNA polymerase III, beta chain (NCBI)||25, 372|
|RSP_1345||RSP_1345||hypothetical protein (NCBI)||25, 262|
|RSP_1374||lpsB||putative lipopolysaccharide core biosynthesis mannosyltransferase protein (NCBI)||278, 308|
|RSP_1375||RSP_1375||hypothetical protein (NCBI)||72, 278|
|RSP_1492||RSP_1492||UbiH/COQ6 monooxygenase family (NCBI)||51, 278|
|RSP_1493||RSP_1493||Amidase (NCBI)||81, 278|
|RSP_1499||RSP_1499||Probable gamma-glutamyltranspeptidase (NCBI)||174, 278|
|RSP_1593||RSP_1593||NAD dependent malic enzyme (NCBI)||15, 25|
|RSP_1595||RSP_1595||Thymidine phosphorylase (NCBI)||15, 25|
|RSP_1598||RSP_1598||putative uracil phosphoribosyltransferase (NCBI)||15, 25|
|RSP_1613||RSP_1613||TRAP-T family transporter, DctP subunit (NCBI)||25, 291|
|RSP_1614||RSP_1614||TRAP-T family transporter with fused DctQ/DctM subunits (NCBI)||25, 112|
|RSP_1615||RSP_1615||hypothetical protein (NCBI)||25, 112|
|RSP_1757||panC||Probable pantoate--beta-alanine ligase (NCBI)||207, 278|
|RSP_1913||RSP_1913||3-oxoadipate CoA-transferase, beta subunit (NCBI)||25, 363|
|RSP_1914||RSP_1914||3-ketoacid CoA transferase alpha subunit (NCBI)||25, 363|
|RSP_1947||cbbJ||Triosephosphate isomerase (NCBI)||278, 372|
|RSP_1986||gatB||Glutamyl-tRNA amidotransferase subunit B (NCBI)||25, 309|
|RSP_2093||RSP_2093||Putative Mrp (Multidrug resistance-associated proteins) family protein (NCBI)||278, 329|
|RSP_2131||rne||Ribonuclease E (NCBI)||25, 223|
|RSP_2465||RSP_2465||hypothetical protein (NCBI)||25, 203|
|RSP_2576||adhI||Alcohol dehydrogenase class III (NCBI)||52, 278|
|RSP_2622||ligA||DNA ligase (NCBI)||25, 98|
|RSP_2781||RSP_2781||peroxiredoxin/glutaredoxin family protein (NCBI)||25, 184|
|RSP_2857||RSP_2857||D-beta-hydroxybutyrate dehydrogenase (NCBI)||242, 278|
|RSP_3583||RSP_3583||Class I monoheme cytochrome c (NCBI)||184, 278|
|RSP_3833||fadB||enoyl CoA hydratase (NCBI)||59, 278|
|RSP_4047||pdhAa||Pyruvate dehydrogenase E1 component, alpha subunit (NCBI)||25, 195|
|RSP_4049||pdhAb||Pyruvate dehydrogenase E1 component, beta subunit (NCBI)||25, 291|
|RSP_4050||pdhB||Dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase complex (NCBI)||25, 291|
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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