Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Alpha amylase, catalytic subdomain (NCBI)
Functional Annotations (6)
|catalytic activity||go/ molecular_function|
|transporter activity||go/ molecular_function|
|carbohydrate metabolic process||go/ biological_process|
|cation binding||go/ molecular_function|
Regulation information for RSP_0937(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_0937
Module neighborhood information for RSP_0937
|Gene||Common Name||Description||Module membership|
|RSP_0008||RSP_0008||possible transporter, DME family, DMT superfamily (NCBI)||323, 340|
|RSP_0202||RSP_0202||putative membrane protein (NCBI)||221, 340|
|RSP_0473||RSP_0473||phospholipase-D family protein (NCBI)||40, 134|
|RSP_0551||RSP_0551||putative thymidylate kinase (NCBI)||234, 340|
|RSP_0560||priA||Probable pimosomal protein N' (NCBI)||54, 340|
|RSP_0685||RSP_0685||Possible ribosomal RNA small subunit methyltransferase C RsmC (NCBI)||209, 340|
|RSP_0937||RSP_0937||Alpha amylase, catalytic subdomain (NCBI)||40, 340|
|RSP_1057||merA1||Putative mercuric reductase protein (NCBI)||134, 340|
|RSP_1074||uvrC||Excinuclease ABC, C subunit (NCBI)||208, 340|
|RSP_1275||RSP_1275||Crp-Fnr family transciptional regulator (NCBI)||215, 340|
|RSP_1286||cbbR||RuBisCO operon transcriptional regulator, CbbR (NCBI)||54, 340|
|RSP_1321||fliR||Flagellar biosynthesis pathway, component FliR (NCBI)||146, 340|
|RSP_1364||RSP_1364||hypothetical protein (NCBI)||146, 340|
|RSP_1820||RSP_1820||hypothetical protein (NCBI)||40, 325|
|RSP_2080||RSP_2080||Putative Tyrosine recombinase (NCBI)||251, 340|
|RSP_2223||RSP_2223||AcrB/AcrD/AcrF multidrug efflux pump (NCBI)||171, 340|
|RSP_2240||RSP_2240||hypothetical protein (NCBI)||213, 340|
|RSP_2250||RSP_2250||hypothetical protein (NCBI)||44, 340|
|RSP_2390||acuC1||putative Acetoin utilization protein (NCBI)||126, 340|
|RSP_2443||cheY5||putative Chemotaxis response regulator, CheY5 (NCBI)||40, 320|
|RSP_2444||RSP_2444||hypothetical protein (NCBI)||40, 320|
|RSP_2445||RSP_2445||putative Alpha amylase (NCBI)||40, 320|
|RSP_2446||RSP_2446||Putative trehalose synthase (NCBI)||40, 320|
|RSP_2448||glgB1||1,4-alpha-glucan branching enzyme (Glycogen branching enzyme) (NCBI)||40, 320|
|RSP_2449||RSP_2449||Putative glycosyl hydrolase (NCBI)||40, 320|
|RSP_2450||RSP_2450||putative Alpha-amylase (NCBI)||40, 320|
|RSP_2451||RSP_2451||putative 4-alpha-glucanotransferase (NCBI)||40, 320|
|RSP_2452||RSP_2452||Alpha amylase, catalytic domain/subdomain (NCBI)||40, 320|
|RSP_2650||RSP_2650||hypothetical protein (NCBI)||121, 340|
|RSP_2678||RSP_2678||hypothetical protein (NCBI)||215, 340|
|RSP_2850||mfd||transcription-repair coupling factor (helicase) (NCBI)||54, 340|
|RSP_2884||glgX||glycogen debranching enzyme (NCBI)||233, 340|
|RSP_3005||RSP_3005||hypothetical protein (NCBI)||40, 316|
|RSP_3006||RSP_3006||conserved hypothetical protein containing Von Willebrand factor, type A domain (NCBI)||40, 316|
|RSP_3105||RSP_3105||PAS sensor protein (NCBI)||83, 340|
|RSP_3250||RSP_3250||ABC peptide transporter, inner membrane subunit (NCBI)||267, 340|
|RSP_3291||RSP_3291||Putative Na+/phosphate symporter (NCBI)||40, 338|
|RSP_3357||gpU||putative phage tail protein U (NCBI)||40, 304|
|RSP_3418||RSP_3418||transcriptional regulator, AraC family (NCBI)||146, 340|
|RSP_3610||RSP_3610||hypothetical protein (NCBI)||177, 340|
|RSP_6183||RSP_6183||hypothetical protein (NCBI)||40, 142|
|RSP_6254||RSP_6254||hypothetical protein (NCBI)||40, 364|
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.
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