Organism : Geobacter sulfurreducens | Module List :
GSU3095 hisF
imidazoleglycerol phosphate synthase, cyclase subunit (NCBI)
Functional Annotations (9)
Function | System |
---|---|
Imidazoleglycerol-phosphate synthase | cog/ cog |
histidine biosynthetic process | go/ biological_process |
imidazoleglycerol-phosphate synthase activity | go/ molecular_function |
cytoplasm | go/ cellular_component |
imidazoleglycerol-phosphate synthase complex | go/ cellular_component |
Histidine metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
hisF | tigr/ tigrfam |
Regulation information for GSU3095
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
GSU1320 | 99 | tf |
GSU1495 | 99 | tf |
GSU1569 | 99 | tf |
GSU2033 | 99 | tf |
GSU2113 | 99 | tf |
GSU2520 | 99 | tf |
GSU3109 | 99 | tf |
GSU0732 | 53 | tf |
GSU1218 | 53 | tf |
GSU1320 | 53 | tf |
GSU1525 | 53 | tf |
GSU1692 | 53 | tf |
GSU1989 | 53 | tf |
GSU1992 | 53 | tf |
GSU2945 | 53 | tf |
GSU3089 | 53 | tf |
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
2266 | 6.10e+02 | taaaGTTctTacagg | |
2267 | 2.40e+03 | aAAATCAaaCaAcTgC.AA | |
2358 | 6.50e+01 | GtTcCt.CGGGctTTtTtgtTTT | |
2359 | 8.60e+02 | tc.ccctGgCggcgGcaAgcg |
Functional Enrichment for GSU3095
Function | System |
---|---|
Imidazoleglycerol-phosphate synthase | cog/ cog |
histidine biosynthetic process | go/ biological_process |
imidazoleglycerol-phosphate synthase activity | go/ molecular_function |
cytoplasm | go/ cellular_component |
imidazoleglycerol-phosphate synthase complex | go/ cellular_component |
Histidine metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
hisF | tigr/ tigrfam |
Module neighborhood information for GSU3095
Gene | Common Name | Description | Module membership |
---|---|---|---|
GSU0144 | GSU0144 | sensory box histidine kinase (VIMSS) | 53, 85 |
GSU0222 | GSU0222 | cytochrome c oxidase, subunit II (VIMSS) | 99, 257 |
GSU0283 | GSU0283 | sensor histidine kinase (VIMSS) | 99, 203 |
GSU0304 | pepN | aminopeptidase N (NCBI) | 53, 290 |
GSU0318 | GSU0318 | peptidase, M48 family (NCBI) | 99, 336 |
GSU0437 | ubiD | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (NCBI) | 99, 235 |
GSU0454 | GSU0454 | conserved hypothetical protein (VIMSS) | 99, 160 |
GSU0500 | typA | GTP-binding protein TypA (NCBI) | 53, 320 |
GSU0519 | GSU0519 | conserved hypothetical protein (VIMSS) | 99, 225 |
GSU0575 | cstA | carbon starvation protein A (NCBI) | 99, 127 |
GSU0585 | GSU0585 | fumarylacetoacetate hydrolase family protein (VIMSS) | 44, 99 |
GSU0586 | GSU0586 | radical SAM protein, TIGR01212 family (NCBI) | 99, 133 |
GSU0588 | thiG | thiamine biosynthesis protein ThiG (NCBI) | 44, 99 |
GSU0589 | GSU0589 | conserved hypothetical protein (VIMSS) | 60, 99 |
GSU0605 | thiD | thiamine-phosphate pyrophosphorylase/phosphomethylpyrimidine kinase (NCBI) | 99, 287 |
GSU0657 | GSU0657 | hypothetical protein (VIMSS) | 53, 315 |
GSU0681 | GSU0681 | sensory box histidine kinase (VIMSS) | 53, 85 |
GSU0768 | GSU0768 | AzlC family protein (VIMSS) | 99, 122 |
GSU0827 | GSU0827 | hypothetical protein (VIMSS) | 27, 53 |
GSU0829 | GSU0829 | heavy metal efflux pump, CzcB family (VIMSS) | 27, 53 |
GSU0921 | rne | ribonuclease, Rne/Rng family protein (NCBI) | 20, 99 |
GSU1036 | GSU1036 | sensor histidine kinase (VIMSS) | 53, 157 |
GSU1325 | GSU1325 | hypothetical protein (NCBI) | 99, 142 |
GSU1414 | GSU1414 | sensory box histidine kinase/response regulator (VIMSS) | 53, 275 |
GSU1427 | GSU1427 | anti-anti-sigma factor (VIMSS) | 53, 268 |
GSU1430 | GSU1430 | hypothetical protein (VIMSS) | 53, 229 |
GSU1553 | GSU1553 | conserved hypothetical protein (VIMSS) | 99, 220 |
GSU1642 | GSU1642 | conserved hypothetical protein (VIMSS) | 27, 53 |
GSU1673 | GSU1673 | hypothetical protein (VIMSS) | 53, 200 |
GSU1817 | GSU1817 | outer membrane lipoprotein, Slp family, putative (VIMSS) | 53, 264 |
GSU1857 | GSU1857 | hypothetical protein (VIMSS) | 53, 203 |
GSU1989 | GSU1989 | sigma-54 dependent DNA-binding response regulator (VIMSS) | 53, 268 |
GSU1990 | GSU1990 | sensor histidine kinase (VIMSS) | 53, 200 |
GSU1998 | GSU1998 | transporter, putative (VIMSS) | 8, 99 |
GSU2002 | GSU2002 | conserved domain protein (NCBI) | 99, 127 |
GSU2300 | GSU2300 | hypothetical protein (VIMSS) | 99, 287 |
GSU2492 | GSU2492 | sensory box histidine kinase (VIMSS) | 99, 160 |
GSU2665 | GSU2665 | efflux transporter, RND family, MFP subunit (NCBI) | 53, 244 |
GSU2666 | GSU2666 | transcriptional regulator, TetR family (VIMSS) | 53, 244 |
GSU2668 | GSU2668 | hypothetical protein (VIMSS) | 53, 244 |
GSU2669 | GSU2669 | sensor histidine kinase (VIMSS) | 53, 244 |
GSU2678 | hsp | heat shock protein, Hsp20 family (NCBI) | 53, 200 |
GSU2685 | GSU2685 | membrane protein, putative (VIMSS) | 99, 107 |
GSU2692 | GSU2692 | immunogenic protein family protein (VIMSS) | 53, 194 |
GSU2701 | GSU2701 | ABC transporter, permease protein (VIMSS) | 99, 133 |
GSU2813 | ccpA-2 | cytochrome c551 peroxidase (NCBI) | 65, 99 |
GSU3058 | GSU3058 | dihydroorotate dehydrogenase, electron transfer subunit, putative (NCBI) | 99, 145 |
GSU3086 | GSU3086 | conserved hypothetical protein (VIMSS) | 53, 258 |
GSU3088 | GSU3088 | ybaK/ebsC protein (VIMSS) | 53, 324 |
GSU3089 | rpoD | RNA polymerase sigma factor RpoD (NCBI) | 53, 267 |
GSU3095 | hisF | imidazoleglycerol phosphate synthase, cyclase subunit (NCBI) | 53, 99 |
GSU3109 | GSU3109 | transcriptional regulator, IclR family (NCBI) | 99, 133 |
GSU3139 | GSU3139 | conserved hypothetical protein (VIMSS) | 53, 216 |
GSU3161 | msrA | peptide methionine sulfoxide reductase (NCBI) | 60, 99 |
GSU3347 | GSU3347 | peptidase, U32 family (NCBI) | 99, 127 |
GSU3360 | GSU3360 | peptidase, M16 family (NCBI) | 99, 127 |
Gene Page Help
Network Tab
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.
Functions Tab
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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CircVis
Our 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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