Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0002(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_0002
Module neighborhood information for RSP_0002
|Gene||Common Name||Description||Module membership|
|RSP_0002||spbB||Histone-like nucleoid-structuring protein H-NS (NCBI)||48, 93|
|RSP_0019||RSP_0019||hypothetical protein (NCBI)||48, 285|
|RSP_0146||glnB||Nitrogen regulatory protein P-II (NCBI)||93, 108|
|RSP_0147||glnA||Glutamine synthetase class-I (NCBI)||25, 93|
|RSP_0196||clpX||ATP-dependent protease Clp, ATPase subunit (NCBI)||48, 52|
|RSP_0197||clpP||Protease subunit of ATP-dependent Clp proteases (NCBI)||48, 345|
|RSP_0223||RSP_0223||hypothetical protein (NCBI)||93, 358|
|RSP_0224||RSP_0224||ATP-dependent helicase (NCBI)||93, 358|
|RSP_0452||recA||Recombinase A, DNA recombination protein (NCBI)||30, 93|
|RSP_0555||ruvA||Holliday junction DNA helicase ruvA (NCBI)||4, 48|
|RSP_0556||ruvC||Holliday junction nuclease RuvC (NCBI)||4, 48|
|RSP_0557||RSP_0557||hypothetical protein (NCBI)||3, 48|
|RSP_0717||RSP_0717||hypothetical protein (NCBI)||48, 81|
|RSP_0718||rpsU||30S ribosomal protein S21 (RpsU) (NCBI)||48, 56|
|RSP_0797||gltX-1||Glutamyl-tRNA synthetase, class Ic (NCBI)||51, 93|
|RSP_0831||trpA||Tryptophan synthase, alpha chain (NCBI)||51, 93|
|RSP_0981||RSP_0981||Transcriptional regulator, GntR family (NCBI)||93, 277|
|RSP_0982||RSP_0982||zinc metallopeptidases-like protein (NCBI)||93, 277|
|RSP_0983||RSP_0983||hypothetical protein (NCBI)||93, 277|
|RSP_1085||RSP_1085||hypothetical protein (NCBI)||75, 93|
|RSP_1360||RSP_1360||hypothetical protein (NCBI)||30, 93|
|RSP_1383||RSP_1383||hypothetical protein (NCBI)||48, 277|
|RSP_1459||RSP_1459||hypothetical protein (NCBI)||93, 279|
|RSP_1460||RSP_1460||hypothetical protein (NCBI)||71, 93|
|RSP_1517||spbA||Histone-like protein of HNS family (NCBI)||48, 327|
|RSP_1621||RSP_1621||Deoxyguanosinetriphosphate triphosphohydrolase-like protein (NCBI)||93, 381|
|RSP_1622||RSP_1622||Putative DNA-binding protein (NCBI)||93, 208|
|RSP_1623||RSP_1623||hypothetical protein (NCBI)||93, 130|
|RSP_1624||RSP_1624||hypothetical protein (NCBI)||48, 208|
|RSP_1741||RSP_1741||Possible LuxR family protein (NCBI)||48, 181|
|RSP_1772||accA||Acetyl-CoA carboxylase, alpha subunit (NCBI)||48, 182|
|RSP_1793||RSP_1793||Single-strand DNA binding protein (NCBI)||48, 261|
|RSP_1864||RSP_1864||hypothetical protein (NCBI)||48, 309|
|RSP_1977||cobS||cobalt chelatase, CobS small subunit (NCBI)||93, 261|
|RSP_1978||RSP_1978||molecular chaperone, DnaJ family (NCBI)||93, 261|
|RSP_1979||RSP_1979||stress induced morphogen, BolA (NCBI)||93, 261|
|RSP_1985||RSP_1985||hypothetical protein (NCBI)||48, 368|
|RSP_1997||lexA||LexA repressor (NCBI)||30, 93|
|RSP_2175||RSP_2175||ABC transporter, ATPase subunit (NCBI)||48, 341|
|RSP_2246||hisB||Imidazoleglycerol-phosphate dehydratase (NCBI)||93, 182|
|RSP_2329||mreB||Cell shape determining protein MreB/Mrl (NCBI)||93, 309|
|RSP_2356||RSP_2356||hypothetical protein (NCBI)||93, 114|
|RSP_2361||RSP_2361||putative integrase/resolvase recombinase protein phage-related integrase (NCBI)||93, 161|
|RSP_2540||tatA||twin-arginine translocation system protein, TatA (NCBI)||48, 237|
|RSP_2624||RSP_2624||hypothetical protein (NCBI)||30, 93|
|RSP_2625||nifU||NifU-related protein involved in Fe-S cluster formation (NCBI)||46, 48|
|RSP_2674||RSP_2674||hypothetical protein (NCBI)||48, 285|
|RSP_2763||RSP_2763||hypothetical protein (NCBI)||48, 64|
|RSP_2764||RSP_2764||hypothetical protein (NCBI)||48, 112|
|RSP_2773||RSP_2773||hypothetical protein (NCBI)||26, 48|
|RSP_2776||acpP||Acyl carrier protein, AcpP (NCBI)||46, 48|
|RSP_3003||RSP_3003||hypothetical protein (NCBI)||93, 108|
|RSP_3007||RSP_3007||hypothetical protein (NCBI)||48, 250|
|RSP_3589||ihfB||Integration host factor beta-subunit (NCBI)||48, 81|
|RSP_3634||RSP_3634||hypothetical protein (NCBI)||48, 379|
|RSP_3644||RSP_3644||Metal dependent phosphohydrolase (NCBI)||93, 130|
|RSP_4301||RSP_4301||tRNA-Leu (NCBI)||48, 327|
|RSP_4314||RSP_4314||tRNA-Ser (NCBI)||35, 48|
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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