Organism : Geobacter sulfurreducens | Module List :
sensory box histidine kinase (VIMSS)
Functional Annotations (6)
|two-component sensor activity||go/ molecular_function|
|ATP binding||go/ molecular_function|
|signal transduction||go/ biological_process|
|peptidyl-histidine phosphorylation||go/ biological_process|
Regulation information for GSU0009(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 GSU0009
Module neighborhood information for GSU0009
|Gene||Common Name||Description||Module membership|
|GSU0009||GSU0009||sensory box histidine kinase (VIMSS)||217, 249|
|GSU0060||GSU0060||hypothetical protein (VIMSS)||163, 217|
|GSU0273||GSU0273||radical SAM domain protein (NCBI)||249, 278|
|GSU0276||GSU0276||secretion protein, HlyD family (VIMSS)||217, 293|
|GSU0310||GSU0310||conserved hypothetical protein (VIMSS)||217, 249|
|GSU0424||fliQ||flagellar biosynthetic protein FliQ (NCBI)||92, 217|
|GSU0440||ubiX||3-octaprenyl-4-hydroxybenzoate carboxy-lyase, putative (NCBI)||163, 217|
|GSU0442||GSU0442||radical SAM domain protein (NCBI)||217, 318|
|GSU0634||GSU0634||glycosyl transferase, group 1 family protein (VIMSS)||204, 249|
|GSU0748||GSU0748||hypothetical protein (VIMSS)||217, 293|
|GSU0884||GSU0884||radical SAM domain protein (NCBI)||217, 294|
|GSU0950||GSU0950||outer membrane efflux protein (VIMSS)||132, 217|
|GSU1010||GSU1010||transglycosylase, Slt family (VIMSS)||217, 282|
|GSU1136||GSU1136||5-formyltetrahydrofolate cyclo-ligase family protein (VIMSS)||249, 265|
|GSU1219||gltX||glutamyl-tRNA synthetase (NCBI)||217, 282|
|GSU1276||carB||carbamoyl-phosphate synthase, large subunit (NCBI)||132, 249|
|GSU1360||GSU1360||hypothetical protein (VIMSS)||179, 217|
|GSU1390||GSU1390||DNA-binding protein (NCBI)||88, 249|
|GSU1391||GSU1391||Fic family protein (NCBI)||249, 278|
|GSU1392||GSU1392||CRISPR-associated protein Cas1 (NCBI)||249, 336|
|GSU1393||GSU1393||CRISPR-associated protein, CT1978 family (NCBI)||163, 249|
|GSU1679||GSU1679||hypothetical protein (VIMSS)||51, 249|
|GSU1688||ribD||riboflavin biosynthesis protein RibD (NCBI)||217, 282|
|GSU1753||GSU1753||lysyl-tRNA synthetase-related protein (NCBI)||163, 249|
|GSU1758||purM||phosphoribosylformylglycinamidine cyclo-ligase (VIMSS)||30, 249|
|GSU1831||GSU1831||conserved hypothetical protein TIGR00281 (VIMSS)||217, 282|
|GSU1864||ksgA||dimethyladenosine transferase (NCBI)||199, 249|
|GSU1865||gcp||metalloendopeptidase, putative, glycoprotease family (NCBI)||199, 249|
|GSU1866||GSU1866||phoH family protein (VIMSS)||249, 333|
|GSU1868||GSU1868||aminotransferase, class V (VIMSS)||249, 308|
|GSU1869||GSU1869||lipoprotein, putative (VIMSS)||199, 249|
|GSU2093||GSU2093||ABC transporter, ATP-binding protein (VIMSS)||217, 249|
|GSU2110||GSU2110||hypothetical protein (VIMSS)||102, 249|
|GSU2111||GSU2111||hypothetical protein (VIMSS)||102, 249|
|GSU2264||lpxA||acyl-(acyl-carrier-protein)--UDP-N- acetylglucosamine O-acyltransferase (NCBI)||249, 277|
|GSU2542||GSU2542||hypothetical protein (VIMSS)||213, 217|
|GSU2778||GSU2778||hypothetical protein (VIMSS)||132, 217|
|GSU2889||GSU2889||hypothetical protein (VIMSS)||68, 249|
|GSU3015||GSU3015||flagellin FlaG, putative (VIMSS)||217, 294|
|GSU3064||ftsA||cell division protein FtsA (NCBI)||249, 265|
|GSU3346||GSU3346||potassium uptake protein, Kup system (VIMSS)||249, 295|
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.
Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
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Module Members Tab
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;
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