Organism : Geobacter sulfurreducens | Module List :
cytochrome d ubiquinol oxidase, subunit I (NCBI)
Functional Annotations (6)
|Cytochrome bd-type quinol oxidase, subunit 1||cog/ cog|
|electron transport||go/ biological_process|
|oxidoreductase activity||go/ molecular_function|
|Oxidative phosphorylation||kegg/ kegg pathway|
|Metabolic pathways||kegg/ kegg pathway|
Regulation information for GSU1640(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 GSU1640
Module neighborhood information for GSU1640
|Gene||Common Name||Description||Module membership|
|GSU0098||GSU0098||MglB protein (VIMSS)||114, 264|
|GSU0164||GSU0164||conserved hypothetical protein (VIMSS)||113, 315|
|GSU0352||psaD||thiol peroxidase (NCBI)||130, 315|
|GSU0353||GSU0353||membrane protein, putative (NCBI)||314, 315|
|GSU0388||GSU0388||conserved hypothetical protein (NCBI)||89, 264|
|GSU0476||GSU0476||conserved hypothetical protein (VIMSS)||77, 264|
|GSU0654||moeB||thiF family protein (NCBI)||11, 315|
|GSU0657||GSU0657||hypothetical protein (VIMSS)||53, 315|
|GSU0780||GSU0780||formate dehydrogenase accessory protein FdhD (VIMSS)||184, 264|
|GSU1117||GSU1117||response regulator (VIMSS)||94, 264|
|GSU1118||GSU1118||universal stress protein family (VIMSS)||264, 276|
|GSU1119||GSU1119||sensor histidine kinase/response regulator (VIMSS)||94, 264|
|GSU1386||GSU1386||conserved hypothetical protein (VIMSS)||18, 315|
|GSU1503||GSU1503||glycosyl transferase, group 2 family protein (VIMSS)||103, 315|
|GSU1584||bioB||biotin synthetase (Dmitry Rodionov)||120, 315|
|GSU1631||GSU1631||metallo-beta-lactamase family protein (VIMSS)||81, 315|
|GSU1639||GSU1639||Rrf2 family protein (NCBI)||264, 315|
|GSU1640||cydA||cytochrome d ubiquinol oxidase, subunit I (NCBI)||264, 315|
|GSU1641||cydB||cytochrome d ubiquinol oxidase, subunit II (NCBI)||264, 315|
|GSU1817||GSU1817||outer membrane lipoprotein, Slp family, putative (VIMSS)||53, 264|
|GSU1867||GSU1867||hypothetical protein (VIMSS)||258, 264|
|GSU1906||leuA||2-isopropylmalate synthase (NCBI)||137, 315|
|GSU1949||GSU1949||hypothetical protein (VIMSS)||65, 264|
|GSU1992||GSU1992||transcriptional regulator, Crp/Fnr family (VIMSS)||264, 279|
|GSU1999||hfq||hfq protein (NCBI)||42, 315|
|GSU2014||GSU2014||hypothetical protein (VIMSS)||108, 315|
|GSU2044||GSU2044||sensory box/GGDEF family protein (VIMSS)||100, 264|
|GSU2553||GSU2553||glycosyl transferase, group 2 family protein (VIMSS)||231, 315|
|GSU2730||GSU2730||hypothetical protein (NCBI)||113, 264|
|GSU2844||rpsN||ribosomal protein S14 (NCBI)||315, 340|
|GSU3063||ftsZ||cell division protein FtsZ (NCBI)||230, 264|
|GSU3065||ftsQ||cell division protein FtsQ (NCBI)||200, 264|
|GSU3066||ddl||D-alanine--D-alanine ligase (NCBI)||35, 264|
|GSU3067||murB||UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI)||94, 264|
|GSU3068||murC||UDP-N-acetylmuramate--alanine ligase (NCBI)||94, 264|
|GSU3069||murG||UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI)||140, 264|
|GSU3070||GSU3070||cell division protein, rodA/ftsW/spoVE family (VIMSS)||60, 264|
|GSU3071||murD||UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI)||95, 264|
|GSU3072||mraY||phospho-N-acetylmuramoyl-pentapeptide-transferase (NCBI)||140, 264|
|GSU3098||hisB||imidazoleglycerol-phosphate dehydratase (NCBI)||203, 315|
|GSU3238||GSU3238||Rieske 2Fe-2S family protein (VIMSS)||95, 264|
|GSU3240||GSU3240||radical SAM domain protein (NCBI)||100, 264|
|GSU3246||GSU3246||thioredoxin peroxidase (VIMSS)||264, 315|
|GSU3293||GSU3293||conserved hypothetical protein (VIMSS)||35, 315|
|GSU3466||GSU3466||membrane protein, putative (VIMSS)||230, 315|
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;
- 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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