Organism : Geobacter sulfurreducens | Module List :
modification methylase, HemK family (NCBI)
Functional Annotations (5)
|Methylase of polypeptide chain release factors||cog/ cog|
|nucleic acid binding||go/ molecular_function|
|protein methylation||go/ biological_process|
|protein methyltransferase activity||go/ molecular_function|
Regulation information for GSU3103(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 GSU3103
Module neighborhood information for GSU3103
|Gene||Common Name||Description||Module membership|
|GSU0030||GSU0030||oxygen-independent coproporphyrinogen III oxidase, putative (VIMSS)||118, 266|
|GSU0035||GSU0035||2',5' RNA ligase, putative (NCBI)||229, 294|
|GSU0143||GSU0143||competence/damage-inducible protein CinA (VIMSS)||109, 118|
|GSU0168||GSU0168||Fic family protein (NCBI)||118, 319|
|GSU0188||GSU0188||conserved domain protein (VIMSS)||294, 339|
|GSU0204||GSU0204||radical SAM domain protein (NCBI)||118, 206|
|GSU0245||GSU0245||glycosyl transferase, group 2 family protein (VIMSS)||119, 294|
|GSU0266||GSU0266||transcriptional regulator, LysR family (VIMSS)||118, 294|
|GSU0267||GSU0267||transcriptional regulator, GntR family (VIMSS)||118, 206|
|GSU0355||GSU0355||hypothetical protein (VIMSS)||118, 319|
|GSU0518||GSU0518||sodium/solute symporter family protein (VIMSS)||118, 220|
|GSU0676||GSU0676||lipoprotein, putative (VIMSS)||118, 312|
|GSU0770||GSU0770||transcriptional regulator, TetR family (VIMSS)||104, 118|
|GSU0840||GSU0840||hypothetical protein (VIMSS)||282, 294|
|GSU0884||GSU0884||radical SAM domain protein (NCBI)||217, 294|
|GSU0908||GSU0908||moaD family protein (NCBI)||13, 294|
|GSU0917||GSU0917||conserved hypothetical protein (VIMSS)||45, 294|
|GSU1044||GSU1044||MutT/nudix family protein (VIMSS)||118, 266|
|GSU1090||GSU1090||signal transduction protein-related protein (VIMSS)||200, 294|
|GSU1147||GSU1147||conserved hypothetical protein (NCBI)||109, 294|
|GSU1148||GSU1148||sensor histidine kinase (VIMSS)||110, 118|
|GSU1306||GSU1306||PHP domain protein (NCBI)||118, 188|
|GSU1309||GSU1309||hypothetical protein (VIMSS)||118, 166|
|GSU1431||GSU1431||conserved hypothetical protein (VIMSS)||118, 229|
|GSU1661||GSU1661||hypothetical protein (VIMSS)||27, 118|
|GSU1663||GSU1663||phosphorylase family protein (VIMSS)||84, 118|
|GSU1664||GSU1664||conserved hypothetical protein (VIMSS)||110, 118|
|GSU1723||GSU1723||mechanosensitive ion channel family protein (NCBI)||104, 294|
|GSU2144||GSU2144||sensor histidine kinase (VIMSS)||121, 294|
|GSU2145||vicR||DNA-binding response regulator (NCBI)||294, 319|
|GSU2317||GSU2317||trkA domain protein (NCBI)||110, 118|
|GSU2318||mma4||cyclopropane-fatty-acyl-phospholipid synthase, putative (NCBI)||118, 220|
|GSU2320||GSU2320||hypothetical protein (VIMSS)||92, 294|
|GSU2326||GSU2326||outer membrane lipoprotein (VIMSS)||118, 226|
|GSU2331||GSU2331||conserved hypothetical protein (VIMSS)||118, 148|
|GSU2460||GSU2460||ribonuclease BN, putative (VIMSS)||118, 266|
|GSU2734||GSU2734||hypothetical protein (VIMSS)||118, 206|
|GSU3015||GSU3015||flagellin FlaG, putative (VIMSS)||217, 294|
|GSU3056||flhA||flagellar biosynthetic protein FlhA (NCBI)||294, 312|
|GSU3103||hemK||modification methylase, HemK family (NCBI)||118, 294|
|GSU3395||putA||proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI)||178, 294|
|GSU3460||GSU3460||glycosyl transferase, group 2 family protein (VIMSS)||118, 294|
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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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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