Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU2200(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 GSU2200
|Gene||Common Name||Description||Module membership|
|GSU0083||GSU0083||conserved hypothetical protein TIGR00726 (VIMSS)||3, 40|
|GSU0154||GSU0154||mutT/nudix family protein (NCBI)||112, 289|
|GSU0155||GSU0155||hypothetical protein (VIMSS)||160, 289|
|GSU0156||argH||argininosuccinate lyase (NCBI)||222, 289|
|GSU0205||GSU0205||transcriptional regulator, TetR family (VIMSS)||112, 289|
|GSU0224||GSU0224||conserved hypothetical protein (VIMSS)||40, 258|
|GSU0272||GSU0272||hypothetical protein (VIMSS)||285, 289|
|GSU0460||fabF-1||3-oxoacyl-(acyl-carrier-protein) synthase II (NCBI)||40, 114|
|GSU0474||GSU0474||sensory box/GGDEF family protein (VIMSS)||40, 253|
|GSU0483||GSU0483||exsB protein (VIMSS)||112, 289|
|GSU0520||GSU0520||conserved hypothetical protein (VIMSS)||40, 212|
|GSU0793||GSU0793||hypothetical protein (VIMSS)||202, 289|
|GSU0847||GSU0847||rubredoxin (VIMSS)||208, 289|
|GSU0850||GSU0850||hypothetical protein (NCBI)||258, 289|
|GSU0997||mutM||formamidopyrimidine-DNA glycosylase (NCBI)||40, 164|
|GSU1197||GSU1197||RNA methyltransferase, TrmH family, group 2, putative (NCBI)||40, 47|
|GSU1249||GSU1249||sensory box histidine kinase (VIMSS)||40, 113|
|GSU1269||GSU1269||hypothetical protein (VIMSS)||40, 159|
|GSU1548||GSU1548||hypothetical protein (VIMSS)||40, 253|
|GSU1832||GSU1832||conserved hypothetical protein (NCBI)||112, 289|
|GSU2192||cbbZ||phosphoglycolate phosphatase (NCBI)||4, 40|
|GSU2200||GSU2200||hypothetical protein (VIMSS)||40, 289|
|GSU2283||GSU2283||diacylglycerol kinase, putative (NCBI)||207, 289|
|GSU2339||GSU2339||monovalent cation/proton antiporter, MrpF/PhaF family (NCBI)||94, 289|
|GSU2341||GSU2341||NADH-ubiquinone/plastoquinone family protein (VIMSS)||40, 289|
|GSU2431||GSU2431||membrane protein, putative (NCBI)||40, 49|
|GSU2434||lipB||lipoate-protein ligase B (NCBI)||40, 128|
|GSU2451||GSU2451||PilB-related protein (VIMSS)||40, 258|
|GSU2452||GSU2452||copper-translocating P-type ATPase (VIMSS)||40, 59|
|GSU2475||GSU2475||sigma-54 dependent transcriptional regulator (NCBI)||40, 49|
|GSU2552||GSU2552||lipoprotein, putative (VIMSS)||231, 289|
|GSU2575||GSU2575||sensor histidine kinase/response regulator (VIMSS)||40, 141|
|GSU2718||hoxH||NAD-reducing hydrogenase, beta subunit (NCBI)||40, 289|
|GSU2721||hoxF||NAD-reducing hydrogenase, alpha subunit (NCBI)||40, 128|
|GSU2990||cobD||cobalamin biosynthesis protein CobD (NCBI)||112, 289|
|GSU3137||GSU3137||cytochrome c family protein (NCBI)||40, 128|
|GSU3353||rluD||RNA pseudouridine synthase family protein (NCBI)||147, 289|
|GSU3383||gatC||glutamyl-tRNA(Gln) amidotransferase, C subunit (NCBI)||112, 289|
|GSU3446||GSU3446||thioredoxin family protein, selenocysteine-containing (NCBI)||40, 49|
|GSU3457||GSU3457||glycine cleavage system transcriptional repressor, putative (VIMSS)||112, 289|
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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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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