Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0193(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_0193
|Gene||Common Name||Description||Module membership|
|RSP_0150||RSP_0150||chase sensor signal transducdtion histidine kinase (NCBI)||87, 214|
|RSP_0193||RSP_0193||hypothetical protein (NCBI)||87, 372|
|RSP_0194||RSP_0194||possible ABC transporter, substrate-binding protein (NCBI)||87, 349|
|RSP_0195||RSP_0195||NADH-ubiquinone oxidoreductase 17.2 kD subunit (NCBI)||87, 372|
|RSP_0247||RSP_0247||aminomethyltransferase related to GcvT (NCBI)||317, 372|
|RSP_0359||cbbI||Ribose-5-phosphate isomerase (NCBI)||127, 372|
|RSP_0553||ruvB||Holiday junction DNA helicase RuvB (NCBI)||299, 372|
|RSP_0843||RSP_0843||Conserved protein containing sulfotransfer domain (NCBI)||87, 361|
|RSP_0844||RSP_0844||hypothetical protein (NCBI)||87, 361|
|RSP_0882||DapA||Dihydrodipicolinate synthetase (NCBI)||182, 372|
|RSP_0896||RSP_0896||hypothetical protein (NCBI)||7, 87|
|RSP_1200||RSP_1200||putative membrane protein (NCBI)||152, 372|
|RSP_1225||spo0J||ParB-like partition protein (NCBI)||87, 182|
|RSP_1228||gidB||putative GidB, Glucose inhibited division protein (NCBI)||87, 182|
|RSP_1229||gidA||Glucose-inhibited division protein, A family (NCBI)||87, 182|
|RSP_1230||thdF||Predicted GTPase (NCBI)||87, 182|
|RSP_1233||maf||putative Maf/YceF/YhdE family protein (NCBI)||87, 234|
|RSP_1235||coaE||Dephospho-CoA kinase (NCBI)||87, 267|
|RSP_1236||dnaQ||putative DNA polymerase III, epsilon subunit and related 3'-5' exonucleases (NCBI)||87, 267|
|RSP_1343||RSP_1343||DNA polymerase III, beta chain (NCBI)||25, 372|
|RSP_1346||RSP_1346||DNA gyrase, subunit B (NCBI)||192, 372|
|RSP_1490||RSP_1490||Putative ATP-dependent protease La, LON (NCBI)||231, 372|
|RSP_1511||RSP_1511||hypothetical protein (NCBI)||215, 372|
|RSP_1562||RSP_1562||fumarylacetoacetate hydrolase family protein (NCBI)||294, 372|
|RSP_1686||RSP_1686||Putative Phosphocarrier HPr protein (NCBI)||87, 341|
|RSP_1776||greA||Transcription elongation factor greA (NCBI)||240, 372|
|RSP_1833||RSP_1833||putative ribosomal-protein-alanine acetyltransferase (NCBI)||326, 372|
|RSP_1875||RSP_1875||hypothetical protein (NCBI)||345, 372|
|RSP_1947||cbbJ||Triosephosphate isomerase (NCBI)||278, 372|
|RSP_1969||purM||Phosphoribosylformylglycinamidine cyclo-ligase (NCBI)||258, 372|
|RSP_2009||argF||Aspartate/ornithine carbamoyltransferase (NCBI)||192, 372|
|RSP_2038||RSP_2038||possible acetyltransferase (NCBI)||213, 372|
|RSP_2081||RSP_2081||putative acetyltransferase, GNAT family (NCBI)||87, 267|
|RSP_2082||RSP_2082||putative NADH-ubiquinone oxidoreductase-related protein (NCBI)||58, 372|
|RSP_2083||uvrB||Putative Excinuclease subunit B (NCBI)||152, 372|
|RSP_2325||rodA||RodA, Rod Cell shape determining protein (NCBI)||47, 87|
|RSP_2328||mreC||Rod shape-determining protein, MreC (NCBI)||87, 356|
|RSP_2458||RSP_2458||ABC transporter, ATPase subunit (NCBI)||87, 130|
|RSP_2459||RSP_2459||ABC transporter, inner membrane subunit (NCBI)||87, 374|
|RSP_2519||RSP_2519||hypothetical protein (NCBI)||269, 372|
|RSP_2533||RSP_2533||Putative transcriptional regulator (NCBI)||361, 372|
|RSP_2542||RSP_2542||ATPase (NCBI)||130, 372|
|RSP_2647||RSP_2647||Predicted SAM-dependent methyltransferases (NCBI)||192, 372|
|RSP_2777||RSP_2777||3-oxoacyl-(acyl-carrier-protein) synthase (NCBI)||87, 361|
|RSP_2811||RSP_2811||Putative ABC transporter, periplasmic substrate-binding protein (NCBI)||87, 294|
|RSP_2812||RSP_2812||hypothetical protein (NCBI)||87, 240|
|RSP_2902||RSP_2902||Putative organic solvent tolerance protein (NCBI)||87, 268|
|RSP_2904||pdxA1||Putative4-hydroxythreonine-4-phosphate dehydrogenase 1 (NCBI)||87, 130|
|RSP_2905||ksgA||Putative ribosomal RNA adenine dimethylase (NCBI)||87, 267|
|RSP_2943||argS||Arginyl-tRNA synthetase, class I (NCBI)||160, 372|
|RSP_2976||RSP_2976||hypothetical protein (NCBI)||58, 372|
|RSP_3261||bioA||Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (BioA) (NCBI)||354, 372|
|RSP_3262||RSP_3262||Putative thioesterase (NCBI)||259, 372|
|RSP_4315||RSP_4315||tRNA-Met (NCBI)||75, 372|
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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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
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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