Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Potassium-transporting P-type ATPase C chain, kdpC (NCBI)
Functional Annotations (6)
|K+-transporting ATPase, c chain||cog/ cog|
|potassium ion transport||go/ biological_process|
|potassium-transporting ATPase activity||go/ molecular_function|
|Two-component system||kegg/ kegg pathway|
Regulation information for RSP_1267(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_1267
Module neighborhood information for RSP_1267
|Gene||Common Name||Description||Module membership|
|RSP_0302||ureG||Urease accessory protein G (NCBI)||175, 307|
|RSP_0303||ureF||Urease accessory protein UreF (NCBI)||175, 307|
|RSP_0304||ureE||urease accessory protein UreE (NCBI)||175, 307|
|RSP_0305||RSP_0305||hypothetical protein (NCBI)||175, 307|
|RSP_0306||RSP_0306||Class I diheme cytochrome c (NCBI)||175, 307|
|RSP_0923||map1||Methionine aminopeptidase, subfamily 1 (NCBI)||84, 286|
|RSP_0925||yobR||Putative acetyl transferase (NCBI)||84, 286|
|RSP_0926||RSP_0926||OmpA/MotB family protein (NCBI)||84, 286|
|RSP_0987||RSP_0987||Putative transporter, RarD family, DMT superfamily (NCBI)||84, 126|
|RSP_1263||RSP_1263||hypothetical protein (NCBI)||84, 307|
|RSP_1264||RSP_1264||hypothetical protein (NCBI)||84, 307|
|RSP_1265||kdpA||Potassium-transporting P-type ATPase, A chain, KdpA (NCBI)||84, 307|
|RSP_1266||kdpB||Potassium-transporting P-type ATPase, B chain, KdpB (NCBI)||84, 307|
|RSP_1267||kdpC||Potassium-transporting P-type ATPase C chain, kdpC (NCBI)||84, 307|
|RSP_1268||kdpD||Osmosensitive K+ channel histidine kinase (NCBI)||84, 307|
|RSP_1269||kdpE||two component transcriptional regulator, winged helix family (NCBI)||84, 307|
|RSP_1339||RSP_1339||Formamidopyrimidine-DNA glycolase (NCBI)||84, 331|
|RSP_1449||RSP_1449||Putative transcriptional regulator of sugar metabolism (NCBI)||155, 307|
|RSP_1462||lpxK||Putative Tetraacyldisaccharide-1-P 4'-kinase (NCBI)||84, 234|
|RSP_1470||rnhB||ribonuclease HII (NCBI)||84, 164|
|RSP_1970||RSP_1970||Phosphoribosylglycinamide formyltransferase (NCBI)||84, 209|
|RSP_2186||RSP_2186||Transcriptional Regulator, MerR family (NCBI)||238, 307|
|RSP_2187||RSP_2187||multidrug efflux pump, Major Facilitator Superfamily ( MFS) (NCBI)||19, 307|
|RSP_2534||RSP_2534||Predicted hydrolase of the metallo-beta-lactamase superfamily (NCBI)||84, 361|
|RSP_2599||phoB||Phosphate regulon transcriptional regulator, PhoR (NCBI)||84, 155|
|RSP_2790||RSP_2790||hypothetical protein (NCBI)||84, 356|
|RSP_2815||xerD||Probable integrase/recombinase XerD (NCBI)||84, 326|
|RSP_2818||aroB||Putative 3-dehydroquinate synthase (NCBI)||84, 234|
|RSP_2872||aglF||ABC alpha-glucoside transporter, inner membrane subunit AglF (NCBI)||281, 307|
|RSP_2873||aglE||ABC alpha-glucoside transporter, perplasmic substrate-binding protein (NCBI)||73, 307|
|RSP_3068||RSP_3068||hypothetical protein (NCBI)||38, 307|
|RSP_3091||RSP_3091||Coserved hypothetical protein (NCBI)||54, 84|
|RSP_3448||RSP_3448||transcriptional regulator, GntR-family (NCBI)||84, 220|
|RSP_3449||RSP_3449||Putative allophanate hydrolase subunit 2 (NCBI)||61, 84|
|RSP_3450||RSP_3450||hypothetical protein (NCBI)||61, 84|
|RSP_3565||RSP_3565||Glycoside hydrolase, family 25 (NCBI)||84, 221|
|RSP_3624||RSP_3624||hypothetical protein (NCBI)||235, 307|
|RSP_3792||RSP_3792||hypothetical protein (NCBI)||307, 346|
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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