Organism : Geobacter sulfurreducens | Module List :
GSU3009 cobT
nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NCBI)
Functional Annotations (8)
Function | System |
---|---|
NaMN:DMB phosphoribosyltransferase | cog/ cog |
nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity | go/ molecular_function |
starch synthase activity | go/ molecular_function |
cobalamin biosynthetic process | go/ biological_process |
Riboflavin metabolism | kegg/ kegg pathway |
Porphyrin and chlorophyll metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
cobT_DBIPRT | tigr/ tigrfam |
Regulation information for GSU3009
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
GSU0372 | 101 | tf |
GSU1270 | 101 | tf |
GSU1483 | 101 | tf |
GSU2237 | 101 | tf |
GSU2524 | 101 | tf |
GSU3087 | 101 | tf |
GSU0372 | 169 | tf |
GSU0655 | 169 | tf |
GSU1129 | 169 | tf |
GSU1692 | 169 | tf |
GSU1989 | 169 | tf |
GSU2041 | 169 | tf |
GSU2237 | 169 | tf |
GSU2354 | 169 | tf |
GSU2524 | 169 | tf |
GSU2666 | 169 | tf |
GSU3087 | 169 | tf |
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
2362 | 4.20e-02 | TaaAcAAA | |
2363 | 3.40e+00 | aAAgTGTaTaCagtAtgC | |
2498 | 2.00e+02 | acaaGcaAcTGa.aa | |
2499 | 2.40e+03 | TtAtTtc.TAaAccc |
Functional Enrichment for GSU3009
Function | System |
---|---|
NaMN:DMB phosphoribosyltransferase | cog/ cog |
nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity | go/ molecular_function |
starch synthase activity | go/ molecular_function |
cobalamin biosynthetic process | go/ biological_process |
Riboflavin metabolism | kegg/ kegg pathway |
Porphyrin and chlorophyll metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
cobT_DBIPRT | tigr/ tigrfam |
Module neighborhood information for GSU3009
Gene | Common Name | Description | Module membership |
---|---|---|---|
GSU0088 | GSU0088 | heterodisulfide reductase subunit (VIMSS) | 169, 214 |
GSU0111 | atpA | ATP synthase F1, alpha subunit (NCBI) | 10, 169 |
GSU0159 | dapA | dihydrodipicolinate synthase (NCBI) | 101, 214 |
GSU0197 | GSU0197 | oxidoreductase, short chain dehydrogenase/reductase family (VIMSS) | 80, 169 |
GSU0298 | GSU0298 | sigma-54 dependent DNA-binding response regulator, interruption-C (VIMSS) | 116, 169 |
GSU0509 | sfrA | Fe(III) reductase, alpha subunit (NCBI) | 101, 243 |
GSU0510 | sfrB | Fe(III) reductase, beta subunit (NCBI) | 101, 243 |
GSU0864 | GSU0864 | conserved hypothetical protein TIGR00251 (VIMSS) | 101, 214 |
GSU0871 | GSU0871 | radical SAM domain protein/B12 binding domain protein (NCBI) | 50, 169 |
GSU0994 | fumB | fumarate hydratase, class I (NCBI) | 101, 243 |
GSU1106 | GSU1106 | citrate synthase (NCBI) | 101, 243 |
GSU1126 | GSU1126 | phage SPO1 DNA polymerase-related protein (VIMSS) | 101, 225 |
GSU1176 | GSU1176 | fumarate reductase, cytochrome b subunit, putative (VIMSS) | 101, 228 |
GSU1177 | frdA | fumarate reductase, flavoprotein subunit (NCBI) | 101, 214 |
GSU1375 | GSU1375 | hypothetical protein (VIMSS) | 169, 225 |
GSU1465 | icd | isocitrate dehydrogenase, NADP-dependent (NCBI) | 101, 297 |
GSU1466 | mdh | malate dehydrogenase (NCBI) | 101, 297 |
GSU1496 | GSU1496 | pilin domain protein (VIMSS) | 117, 169 |
GSU1497 | GSU1497 | hypothetical protein (VIMSS) | 117, 169 |
GSU1515 | thrS | threonyl-tRNA synthetase (NCBI) | 101, 116 |
GSU1599 | rpmF | ribosomal protein L32 (NCBI) | 62, 169 |
GSU1660 | acnB | aconitate hydratase 2 (NCBI) | 101, 169 |
GSU1886 | yfiA | ribosomal subunit interface protein (NCBI) | 169, 238 |
GSU1902 | leuD | 3-isopropylmalate dehydratase, small subunit, putative (NCBI) | 101, 169 |
GSU2223 | cheY-6 | chemotaxis protein CheY (NCBI) | 101, 238 |
GSU2237 | rpoZ | DNA-directed RNA polymerase, omega subunit (NCBI) | 169, 228 |
GSU2427 | GSU2427 | hypothetical protein (VIMSS) | 101, 225 |
GSU2642 | GSU2642 | cytochrome c family protein (NCBI) | 136, 169 |
GSU2645 | GSU2645 | cytochrome c family protein (NCBI) | 169, 215 |
GSU2707 | ackA-1 | acetate kinase (NCBI) | 101, 168 |
GSU2708 | GSU2708 | ferredoxin family protein (VIMSS) | 101, 228 |
GSU2998 | GSU2998 | nitroimidazole resistance protein, putative (VIMSS) | 89, 169 |
GSU3005 | thiC-2 | thiamine biosynthesis protein ThiC (NCBI) | 101, 169 |
GSU3007 | GSU3007 | phosphoglycerate mutase family, putative (VIMSS) | 101, 169 |
GSU3009 | cobT | nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NCBI) | 101, 169 |
GSU3011 | GSU3011 | hypothetical protein (VIMSS) | 97, 101 |
GSU3278 | GSU3278 | hypothetical protein (VIMSS) | 169, 276 |
GSU3401 | GSU3401 | branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative (NCBI) | 117, 169 |
GSU3402 | GSU3402 | hypothetical protein (VIMSS) | 117, 169 |
GSU3403 | GSU3403 | hypothetical protein (VIMSS) | 117, 169 |
GSU3406 | GSU3406 | amino acid ABC transporter, periplasmic amino acid-binding protein (NCBI) | 117, 169 |
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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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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Motifs Tab
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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