Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Ppx/GppA phosphatase (NCBI)
Functional Annotations (1)
Regulation information for RSP_0782(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_0782
Module neighborhood information for RSP_0782
|Gene||Common Name||Description||Module membership|
|RSP_0014||RSP_0014||transcriptional regulator, TetR family (NCBI)||91, 215|
|RSP_0332||RSP_0332||possible cellulose synthase (NCBI)||240, 259|
|RSP_0337||RSP_0337||possible phospodiesterase (NCBI)||120, 215|
|RSP_0338||RSP_0338||hypothetical protein (NCBI)||120, 215|
|RSP_0363||RSP_0363||hypothetical protein (NCBI)||215, 218|
|RSP_0586||RSP_0586||probable nicotinate-nucleotide adenylyltransferase (NCBI)||7, 215|
|RSP_0726||RSP_0726||arginosuccinate lyase 1 (NCBI)||51, 240|
|RSP_0755||nusB||putative N utilization substance protein B (NCBI)||234, 240|
|RSP_0763||aatA||aspartate aminotransferase A (NCBI)||162, 240|
|RSP_0782||RSP_0782||Ppx/GppA phosphatase (NCBI)||215, 240|
|RSP_0783||RSP_0783||hypothetical protein (NCBI)||116, 240|
|RSP_0784||RSP_0784||putative acetyltransferase, GNAT family (NCBI)||215, 240|
|RSP_0814||RSP_0814||Acetyltransferase (NCBI)||215, 248|
|RSP_0841||RSP_0841||hypothetical protein (NCBI)||218, 240|
|RSP_0931||ialA||NUDIX hydrolase (NCBI)||23, 240|
|RSP_1072||moaD||putative molybdopterin MPT converting factor, subunit 1 protein (NCBI)||154, 240|
|RSP_1098||RSP_1098||hypothetical protein (NCBI)||240, 262|
|RSP_1189||wcaJ||sugar transferase (NCBI)||47, 215|
|RSP_1190||RSP_1190||hypothetical protein (NCBI)||215, 368|
|RSP_1191||RSP_1191||transcriptional regulator, MarR family (NCBI)||215, 368|
|RSP_1214||RSP_1214||putative branched-chain amino acid aminotransferase (NCBI)||215, 381|
|RSP_1275||RSP_1275||Crp-Fnr family transciptional regulator (NCBI)||215, 340|
|RSP_1276||RSP_1276||hypothetical protein (NCBI)||215, 368|
|RSP_1287||RSP_1287||ABC branched chain amino acid family transporter, ATPase subunit (NCBI)||215, 263|
|RSP_1369||RSP_1369||Short-chain dehydrogenase/reductase SDR (NCBI)||126, 215|
|RSP_1483||RSP_1483||hypothetical protein (NCBI)||240, 293|
|RSP_1511||RSP_1511||hypothetical protein (NCBI)||215, 372|
|RSP_1775||RSP_1775||hypothetical protein (NCBI)||7, 240|
|RSP_1776||greA||Transcription elongation factor greA (NCBI)||240, 372|
|RSP_1839||RSP_1839||putative acetyltransferase, GNAT family (NCBI)||240, 337|
|RSP_1850||ptsI||phosphoenolpyruvate-protein phosphotransferase, PtsI(Ntr) (NCBI)||213, 240|
|RSP_1861||RSP_1861||probable dihydroneopterin aldolase (NCBI)||215, 326|
|RSP_1893||RSP_1893||Inositol monophosphatase family protein (NCBI)||214, 240|
|RSP_2312||RSP_2312||hypothetical protein (NCBI)||215, 231|
|RSP_2375||RSP_2375||hypothetical protein (NCBI)||215, 366|
|RSP_2382||RSP_2382||hypothetical protein (NCBI)||215, 294|
|RSP_2391||RSP_2391||2'-5' RNA ligase (NCBI)||126, 215|
|RSP_2616||RSP_2616||hypothetical protein (NCBI)||223, 240|
|RSP_2629||gid||Glucose-inhibited division protein A (NCBI)||65, 240|
|RSP_2634||ccmH||Cytochrome c maturation protein, CcmH (NCBI)||215, 368|
|RSP_2678||RSP_2678||hypothetical protein (NCBI)||215, 340|
|RSP_2698||RSP_2698||putative quinoprotein (NCBI)||166, 240|
|RSP_2716||lpxB||putative lipid-A-disaccharide synthase (NCBI)||7, 240|
|RSP_2784||cycG||Diheme class I cytochrome c (NCBI)||240, 274|
|RSP_2785||CycF||Cytochrome c-554 (NCBI)||240, 274|
|RSP_2788||RSP_2788||hypothetical protein (NCBI)||36, 215|
|RSP_2812||RSP_2812||hypothetical protein (NCBI)||87, 240|
|RSP_2836||nifR3||tRNA-dihydrouridine synthase, nifR3 (NCBI)||240, 318|
|RSP_2960||RSP_2960||pantetheine-phosphate adenylyltransferase (NCBI)||223, 240|
|RSP_3023||RSP_3023||hypothetical protein (NCBI)||215, 303|
|RSP_3376||aroQ||3 dehydroquinase dehydratase, class II (NCBI)||240, 381|
|RSP_3402||RSP_3402||multisensor diguanylate cyclase/phosphodiesterase (NCBI)||17, 215|
|RSP_3564||RSP_3564||Generic methyltransferase (NCBI)||7, 215|
|RSP_3680||RSP_3680||transcriptional regulator, TetR family (NCBI)||143, 215|
|RSP_3823||proB1||glutamate 5-kinase (NCBI)||30, 240|
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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Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.
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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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