Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU0640(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 GSU0640
|Gene||Common Name||Description||Module membership|
|GSU0061||GSU0061||hypothetical protein (VIMSS)||9, 95|
|GSU0116||GSU0116||transglycosylase (VIMSS)||95, 200|
|GSU0214||GSU0214||conserved hypothetical protein (VIMSS)||6, 95|
|GSU0307||hypC||hydrogenase assembly chaperone hypC/hupF (NCBI)||42, 158|
|GSU0357||GSU0357||cytochrome c family protein (VIMSS)||6, 95|
|GSU0533||GSU0533||cytochrome c family protein, putative (NCBI)||54, 95|
|GSU0638||GSU0638||conserved hypothetical protein (VIMSS)||70, 158|
|GSU0639||GSU0639||hypothetical protein (NCBI)||70, 158|
|GSU0640||GSU0640||conserved hypothetical protein (VIMSS)||95, 158|
|GSU0707||sugE||sugE protein (NCBI)||95, 234|
|GSU0743||GSU0743||NAD-dependent dehydrogenase subunit (VIMSS)||158, 265|
|GSU0806||citG||ATP:dephospho-CoA triphosphoribosyl transferase (NCBI)||95, 133|
|GSU0816||GSU0816||ABC transporter, ATP-binding protein (VIMSS)||88, 158|
|GSU0843||GSU0843||NADH oxidase, putative (VIMSS)||9, 95|
|GSU0845||GSU0845||Rieske 2Fe-2S family protein (VIMSS)||9, 95|
|GSU0926||GSU0926||mce-related protein (NCBI)||20, 95|
|GSU1192||GSU1192||conserved hypothetical protein (VIMSS)||98, 158|
|GSU1231||GSU1231||response regulator (VIMSS)||87, 158|
|GSU1255||GSU1255||conserved hypothetical protein (NCBI)||95, 104|
|GSU1256||GSU1256||conserved domain protein (NCBI)||6, 95|
|GSU1291||GSU1291||response regulator (VIMSS)||147, 158|
|GSU1507||GSU1507||heptosyltransferase family protein, putative (VIMSS)||105, 158|
|GSU1595||dut||deoxyuridine 5'-triphosphate nucleotidohydrolase (NCBI)||124, 158|
|GSU1655||GSU1655||sensory box histidine kinase/response regulator (VIMSS)||17, 158|
|GSU1658||GSU1658||response regulator/GGDEF domain protein (NCBI)||158, 218|
|GSU1783||GSU1783||type IV pilus biogenesis protein PilB, putative (VIMSS)||17, 158|
|GSU1785||GSU1785||cytochrome c family protein, putative (NCBI)||158, 179|
|GSU1794||GSU1794||HAM1 protein (NCBI)||158, 248|
|GSU1795||rph||ribonuclease PH (NCBI)||35, 158|
|GSU1844||GSU1844||IPT/TIG domain protein, putative (VIMSS)||9, 95|
|GSU1940||GSU1940||sigma-54 dependent DNA-binding response regulator (VIMSS)||158, 335|
|GSU1953||asnB||asparagine synthase, glutamine-hydrolyzing (NCBI)||158, 333|
|GSU2199||GSU2199||conserved hypothetical protein (VIMSS)||95, 273|
|GSU2377||GSU2377||hypothetical protein (VIMSS)||51, 158|
|GSU2509||GSU2509||glycosyl transferase, group 2 family protein (VIMSS)||9, 95|
|GSU2515||GSU2515||cytochrome c family protein, putative (NCBI)||9, 95|
|GSU2561||GSU2561||conserved domain protein (NCBI)||95, 193|
|GSU2611||GSU2611||hypothetical protein (VIMSS)||158, 191|
|GSU2620||queA||S-adenosylmethionine:tRNA ribosyltransferase-isomerase (NCBI)||76, 158|
|GSU2640||GSU2640||hypothetical protein (VIMSS)||66, 95|
|GSU2641||GSU2641||hypothetical protein (VIMSS)||66, 95|
|GSU2775||GSU2775||hypothetical protein (VIMSS)||9, 95|
|GSU2787||GSU2787||transcriptional regulator, LysR family (VIMSS)||95, 224|
|GSU2896||GSU2896||ankyrin-related protein (VIMSS)||6, 95|
|GSU3048||flgH||flagellar L-ring protein FlgH (NCBI)||95, 186|
|GSU3071||murD||UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI)||95, 264|
|GSU3128||GSU3128||hypothetical protein (VIMSS)||95, 183|
|GSU3238||GSU3238||Rieske 2Fe-2S family protein (VIMSS)||95, 264|
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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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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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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- 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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