Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
ATP-dependent RNA helicase (NCBI)
Functional Annotations (5)
|Superfamily II DNA and RNA helicases||cog/ cog|
|nucleic acid binding||go/ molecular_function|
|ATP binding||go/ molecular_function|
|ATP-dependent helicase activity||go/ molecular_function|
|RNA degradation||kegg/ kegg pathway|
Regulation information for RSP_1485(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 RSP_1485
Module neighborhood information for RSP_1485
|Gene||Common Name||Description||Module membership|
|RSP_0448||RSP_0448||EF-Tu; elongation factor Tu (NCBI)||209, 271|
|RSP_0684||RSP_0684||Possible oxidoreductase; Short-chain dehydrogenase/reductase SDR (NCBI)||196, 209|
|RSP_0685||RSP_0685||Possible ribosomal RNA small subunit methyltransferase C RsmC (NCBI)||209, 340|
|RSP_0686||RSP_0686||ATP-dependent Clp protease adaptor protein clpS (NCBI)||209, 227|
|RSP_0687||RSP_0687||Predicted hydrolase (haloacid dehalogenase (HAD) superfamily) (NCBI)||192, 209|
|RSP_0780||RSP_0780||hypothetical protein with ATP/GTP-binding site (NCBI)||13, 268|
|RSP_0818||carB||carbamoyl phosphate synthase large subunit (RefSeq)||209, 383|
|RSP_0819||rhlE2||DEAD/DEAH box helicase (NCBI)||209, 316|
|RSP_0848||xthA1||Exodeoxyribonuclease III (NCBI)||184, 268|
|RSP_0944||purU||PurU, Formyltetrahydrofolate deformylase (NCBI)||124, 268|
|RSP_0998||nhaD||Na+/H+ antiporter, NhaD (NCBI)||160, 268|
|RSP_1052||RSP_1052||possible Acetyltransferase (NCBI)||268, 271|
|RSP_1062||RSP_1062||ATPases of the PP superfamily (NCBI)||110, 209|
|RSP_1065||RSP_1065||hypothetical protein (NCBI)||130, 209|
|RSP_1075||RSP_1075||Short-chain dehydrogenase/reductase SDR (NCBI)||209, 218|
|RSP_1105||DapB||Dihydrodipicolinate reductase (DHPR) (NCBI)||268, 299|
|RSP_1108||TruB||tRNA pseudouridine synthase B (NCBI)||209, 383|
|RSP_1110||RSP_1110||hypothetical protein (NCBI)||209, 271|
|RSP_1197||HemH||Ferrochelatase (NCBI)||209, 311|
|RSP_1202||TrmA||putative RNA SAM-dependent methyltransferase, TrmA family (NCBI)||47, 209|
|RSP_1203||RSP_1203||ABC multidrug efflux pump, fused ATPase and inner membrane subunits (NCBI)||196, 209|
|RSP_1218||mutS||DNA mismatch repair protein MutS (NCBI)||209, 299|
|RSP_1381||RSP_1381||hypothetical protein (NCBI)||47, 268|
|RSP_1382||RSP_1382||radical SAM superfamily protein (NCBI)||266, 268|
|RSP_1426||RSP_1426||RNA-binding region RNP-1 (NCBI)||209, 316|
|RSP_1427||RSP_1427||hypothetical protein (NCBI)||209, 316|
|RSP_1484||RSP_1484||hypothetical protein (NCBI)||209, 268|
|RSP_1485||RSP_1485||ATP-dependent RNA helicase (NCBI)||209, 268|
|RSP_1706||RSP_1706||Putative acetyltransferase (NCBI)||13, 268|
|RSP_1799||secF||protein-export membrane protein SecF (NCBI)||209, 224|
|RSP_1832||RSP_1832||peptidase, M16 family (NCBI)||69, 268|
|RSP_1970||RSP_1970||Phosphoribosylglycinamide formyltransferase (NCBI)||84, 209|
|RSP_2004||trpE||Anthranilate synthase component I and chorismate binding protein (NCBI)||203, 268|
|RSP_2118||recN||DNA repair protein RecN (NCBI)||209, 339|
|RSP_2304||ribF||Riboflavin kinase / FAD synthetase = FMN adenylyltransferase, RibF (NCBI)||268, 343|
|RSP_2454||purF||Amidophosphoribosyltransferase (NCBI)||218, 268|
|RSP_2552||exoU||Glycosyl transferase, family 2 (NCBI)||209, 316|
|RSP_2648||RSP_2648||hypothetical protein (NCBI)||209, 383|
|RSP_2714||lpxA||Acyl-(acyl carrier protein))-UDP-N-acetylglucosamine O-acyltransferase (NCBI)||268, 281|
|RSP_2778||RSP_2778||hypothetical protein (NCBI)||224, 268|
|RSP_2841||trkA||potassium uptake tranporter, NAD-binding subunit, TrkA (NCBI)||63, 268|
|RSP_2902||RSP_2902||Putative organic solvent tolerance protein (NCBI)||87, 268|
|RSP_3004||RSP_3004||Possible Protein kinase (NCBI)||209, 214|
|RSP_3273||RSP_3273||ABC multidrug/carbohydrate efflux transporter, inner membrane subunit (NCBI)||116, 209|
|RSP_3274||RSP_3274||ABC multidrug/carbohydrate efflux transporter, ATPase subunit (NCBI)||116, 209|
|RSP_3549||hisG||ATP phosphoribosyltransferase (NCBI)||160, 268|
|RSP_3550||RSP_3550||Aminoacyl-transfer RNA synthetase, class II (NCBI)||212, 268|
|RSP_3591||RSP_3591||cytidylate kinase (NCBI)||209, 271|
|RSP_3664||RSP_3664||transcriptional regulator, GntR family (NCBI)||268, 331|
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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Module Members Tab
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.
- 2. Source gene
- 3. Target genes (other module members)
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