Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU0019(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 GSU0019
|Gene||Common Name||Description||Module membership|
|GSU0015||GSU0015||PPIC-type PPIASE domain protein (NCBI)||4, 89|
|GSU0016||ppiD||PPIC-type PPIASE domain protein (NCBI)||4, 89|
|GSU0017||mfd||transcription-repair coupling factor (NCBI)||4, 262|
|GSU0018||GSU0018||transcriptional regulator, GntR family/aminotransferase class-I (VIMSS)||4, 89|
|GSU0019||GSU0019||pentapeptide repeat domain protein (VIMSS)||4, 89|
|GSU0253||GSU0253||sensory box histidine kinase (VIMSS)||4, 107|
|GSU0386||radC||DNA repair protein RadC (NCBI)||89, 283|
|GSU0387||GSU0387||undecaprenol kinase, putative (VIMSS)||89, 295|
|GSU0388||GSU0388||conserved hypothetical protein (NCBI)||89, 264|
|GSU0389||GSU0389||phosphate transporter, putative (VIMSS)||26, 89|
|GSU0443||GSU0443||ribonuclease D, putative (VIMSS)||89, 295|
|GSU0452||GSU0452||sensor histidine kinase (VIMSS)||4, 160|
|GSU0529||nfo||endonuclease IV (NCBI)||89, 225|
|GSU0876||GSU0876||diacylglycerol kinase catalytic domain protein (NCBI)||89, 322|
|GSU1002||GSU1002||isochorismatase family protein (NCBI)||89, 265|
|GSU1003||ntrC||nitrogen regulation protein NR(I) (NCBI)||89, 265|
|GSU1004||GSU1004||sensory box histidine kinase (VIMSS)||89, 265|
|GSU1066||GSU1066||hypothetical protein (NCBI)||4, 157|
|GSU1167||GSU1167||conserved hypothetical protein (VIMSS)||4, 86|
|GSU1237||GSU1237||pyridine nucleotide-disulphide oxidoreductase family protein (NCBI)||4, 72|
|GSU1654||GSU1654||response regulator, putative (NCBI)||4, 140|
|GSU1683||GSU1683||conserved hypothetical protein (VIMSS)||4, 235|
|GSU1835||glnA||glutamine synthetase, type I (NCBI)||4, 72|
|GSU1836||GSU1836||nitrogen regulatory protein P-II (VIMSS)||4, 72|
|GSU2060||GSU2060||pmbA protein, putative (VIMSS)||4, 88|
|GSU2061||argA||acetyltransferase, GNAT family (NCBI)||4, 88|
|GSU2062||GSU2062||GGDEF domain protein (VIMSS)||4, 88|
|GSU2063||GSU2063||HD domain protein (NCBI)||4, 88|
|GSU2192||cbbZ||phosphoglycolate phosphatase (NCBI)||4, 40|
|GSU2193||GSU2193||conserved hypothetical protein (VIMSS)||4, 193|
|GSU2551||GSU2551||LysM domain protein (VIMSS)||89, 231|
|GSU2619||tgt-2||queuine tRNA-ribosyltransferase (NCBI)||89, 231|
|GSU2712||GSU2712||hypothetical protein (VIMSS)||4, 12|
|GSU2713||GSU2713||conserved hypothetical protein (VIMSS)||4, 133|
|GSU2762||glpK||glycerol kinase (NCBI)||4, 252|
|GSU2763||GSU2763||conserved hypothetical protein (VIMSS)||4, 66|
|GSU2989||GSU2989||L-threonine-O-3-phosphate decarboxylase, putative (VIMSS)||89, 281|
|GSU2991||GSU2991||sensor histidine kinase (VIMSS)||89, 285|
|GSU2992||cobQ||cobyric acid synthase (NCBI)||89, 153|
|GSU2997||cbiD||cobalamin biosynthesis protein CbiD (NCBI)||89, 281|
|GSU2998||GSU2998||nitroimidazole resistance protein, putative (VIMSS)||89, 169|
|GSU3002||GSU3002||cobalt ABC transporter, permease protein (VIMSS)||89, 285|
|GSU3004||GSU3004||cobalt transport protein CbiM (RefSeq)||75, 89|
|GSU3010||cobU||bifunctional cobalamin biosynthesis protein CobU (NCBI)||30, 89|
|GSU3114||GSU3114||hypothetical protein (VIMSS)||4, 100|
|GSU3140||GSU3140||peptidase, M1 family protein (NCBI)||4, 100|
|GSU3141||GSU3141||hypothetical protein (VIMSS)||4, 216|
|GSU3142||GSU3142||phospho-2-dehydro-3-deoxyheptonate aldolase (NCBI)||4, 216|
|GSU3283||GSU3283||cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS)||44, 89|
|GSU3286||hemD||uroporphyrinogen III synthase/methyltransferase (NCBI)||89, 300|
|GSU3287||GSU3287||hydrolase, TatD family (NCBI)||30, 89|
|GSU3288||moeB||thiF family protein (NCBI)||30, 89|
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.
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