Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2885
iron-containing alcohol dehydrogenase
Functional Annotations (14)
Function | System |
---|---|
Alcohol dehydrogenase, class IV | cog/ cog |
alcohol dehydrogenase activity, metal ion-independent | go/ molecular_function |
alcohol dehydrogenase activity, zinc-dependent | go/ molecular_function |
alcohol dehydrogenase activity, iron-dependent | go/ molecular_function |
metabolic process | go/ biological_process |
metal ion binding | go/ molecular_function |
Glycolysis / Gluconeogenesis | kegg/ kegg pathway |
Fatty acid metabolism | kegg/ kegg pathway |
Tyrosine metabolism | kegg/ kegg pathway |
Chloroalkane and chloroalkene degradation | kegg/ kegg pathway |
Naphthalene degradation | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
Microbial metabolism in diverse environments | kegg/ kegg pathway |
Regulation information for DVU2885
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0277 | 87 | tf |
DVU0436 | 87 | tf |
DVU0436 DVU0529 |
87 | combiner |
DVU0529 DVU1083 |
87 | combiner |
DVU0653 | 87 | tf |
DVU1517 | 87 | tf |
DVU2195 DVU0529 |
87 | combiner |
DVU2785 DVU0230 |
87 | combiner |
DVUA0024 | 87 | tf |
DVUA0057 | 87 | tf |
DVU0653 | 334 | tf |
DVU1063 | 334 | tf |
DVU1517 | 334 | tf |
DVU1518 | 334 | tf |
DVU1744 | 334 | tf |
DVU2114 DVU1744 |
334 | combiner |
DVU2633 DVU1744 |
334 | combiner |
DVU2785 DVU0230 |
334 | combiner |
DVU2832 DVU1745 |
334 | combiner |
DVU2953 | 334 | tf |
DVU3142 DVU0529 |
334 | combiner |
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.
Motif Id | e-value | Consensus | Motif Logo | RegPredict |
---|---|---|---|---|
171 | 1.70e-04 | GggcttC.GCaaCg | RegPredict | |
172 | 7.10e+02 | ttTcgctGTGcTgCGgtGcgCt | RegPredict | |
633 | 9.50e-04 | tTcTtAaaGaCTTcaCATCgcTG | RegPredict | |
634 | 2.80e+00 | acCCcGcCTtG.CGc.CGtcAGC | RegPredict |
Functional Enrichment for DVU2885
Function | System |
---|---|
Alcohol dehydrogenase, class IV | cog/ cog |
alcohol dehydrogenase activity, metal ion-independent | go/ molecular_function |
alcohol dehydrogenase activity, zinc-dependent | go/ molecular_function |
alcohol dehydrogenase activity, iron-dependent | go/ molecular_function |
metabolic process | go/ biological_process |
metal ion binding | go/ molecular_function |
Glycolysis / Gluconeogenesis | kegg/ kegg pathway |
Fatty acid metabolism | kegg/ kegg pathway |
Tyrosine metabolism | kegg/ kegg pathway |
Chloroalkane and chloroalkene degradation | kegg/ kegg pathway |
Naphthalene degradation | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
Microbial metabolism in diverse environments | kegg/ kegg pathway |
Module neighborhood information for DVU2885
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0077 | hypothetical protein DVU0077 | 87, 162 | |
DVU0103 | cation ABC transporter ATP-binding protein | 247, 334 | |
DVU0124 | hypothetical protein DVU0124 | 206, 334 | |
DVU0154 | hypothetical protein DVU0154 | 162, 334 | |
DVU0194 | terminase large subunit | 162, 334 | |
DVU0258 | sensory box histidine kinase/response regulator | 83, 87 | |
DVU0295 | amine oxidase, flavin-containing | 87, 162 | |
DVU0297 | hypothetical protein DVU0297 | 214, 334 | |
DVU0362 | hypothetical protein DVU0362 | 174, 334 | |
DVU0363 | pabB | para-aminobenzoate synthase, component I | 181, 334 |
DVU0446 | sodium/solute symporter family protein | 247, 334 | |
DVU0651 | hypothetical protein DVU0651 | 9, 334 | |
DVU0661 | dihydrouridine synthase family protein | 87, 185 | |
DVU0731 | hypothetical protein DVU0731 | 87, 126 | |
DVU0740 | hypothetical protein DVU0740 | 87, 162 | |
DVU0742 | hypothetical protein DVU0742 | 83, 87 | |
DVU0743 | sensory box histidine kinase | 14, 87 | |
DVU1036 | hypothetical protein DVU1036 | 69, 334 | |
DVU1081 | iron-sulfur cluster-binding protein | 126, 334 | |
DVU1150 | hypothetical protein DVU1150 | 33, 334 | |
DVU1187 | hypothetical protein DVU1187 | 87, 176 | |
DVU1357 | hypothetical protein DVU1357 | 75, 87 | |
DVU1371 | HAD family hydrolase | 87, 126 | |
DVU1391 | hypothetical protein DVU1391 | 69, 87 | |
DVU1435 | hypothetical protein DVU1435 | 69, 87 | |
DVU1439 | hypothetical protein DVU1439 | 87, 155 | |
DVU1459 | hypothetical protein DVU1459 | 9, 334 | |
DVU1460 | hypothetical protein DVU1460 | 145, 334 | |
DVU1461 | hemA | glutamyl-tRNA reductase | 117, 334 |
DVU1463 | siroheme synthase | 117, 334 | |
DVU1465 | CgeB family protein | 87, 334 | |
DVU1869 | methyl-accepting chemotaxis protein | 87, 122 | |
DVU1903 | mfd | transcription-repair coupling factor | 176, 334 |
DVU2276 | hypothetical protein DVU2276 | 69, 334 | |
DVU2279 | hypothetical protein DVU2279 | 94, 334 | |
DVU2280 | amino acid permease family protein | 94, 334 | |
DVU2843 | DNA mismatch endonuclease Vsr | 214, 334 | |
DVU2844 | hypothetical protein DVU2844 | 214, 334 | |
DVU2885 | iron-containing alcohol dehydrogenase | 87, 334 | |
DVU2888 | cobalt ABC transporter ATP-binding protein | 316, 334 | |
DVU2908 | hypothetical protein DVU2908 | 69, 334 | |
DVU2949 | hypothetical protein DVU2949 | 33, 334 | |
DVU2954 | GGDEF domain-containing protein | 69, 334 | |
DVU2955 | hypothetical protein DVU2955 | 69, 334 | |
DVU2993 | glycosyl transferase group 1/2 family protein | 83, 87 | |
DVU2996 | NAD-dependent epimerase/dehydratase family protein | 87, 150 | |
DVU2997 | hypothetical protein DVU2997 | 87, 150 | |
DVU2998 | hypothetical protein DVU2998 | 87, 150 | |
DVU3008 | NeuB family protein | 87, 176 | |
DVU3015 | hypothetical protein DVU3015 | 83, 87 | |
DVU3017 | hypothetical protein DVU3017 | 69, 87 | |
DVU3043 | hypothetical protein DVU3043 | 181, 334 | |
DVU3072 | ABC transporter permease | 126, 334 | |
DVU3096 | hypothetical protein DVU3096 | 17, 334 | |
DVU3115 | hypothetical protein DVU3115 | 33, 334 | |
DVU3126 | None | 87, 150 | |
DVU3180 | GGDEF domain-containing protein | 33, 87 | |
DVU3196 | twin-arginine translocation pathway signal sequence domain-containing protein | 87, 214 | |
DVU3215 | response regulator | 87, 250 | |
DVU3224 | sfsA | sugar fermentation stimulation protein | 83, 87 |
DVU3233 | flhB | flagellar biosynthesis protein FlhB | 81, 334 |
DVU3297 | tryptophan-specific transport protein | 9, 334 | |
DVU3320 | hypothetical protein DVU3320 | 83, 334 | |
DVU3343 | hypothetical protein DVU3343 | 330, 334 | |
DVUA0103 | invX | HrpO family type III secretion protein | 131, 334 |
Gene Page Help
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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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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.
- 2. Source gene
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