Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Siderophore-interacting protein (NCBI)
Functional Annotations (1)
|Siderophore-interacting protein||cog/ cog|
Regulation information for RSP_3678(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_3678
|Siderophore-interacting protein||cog/ cog|
Module neighborhood information for RSP_3678
|Gene||Common Name||Description||Module membership|
|RSP_0392||RSP_0392||probable lactoylglutathione lyase (NCBI)||107, 239|
|RSP_0398||RSP_0398||dehydrogenase (NCBI)||239, 278|
|RSP_0482||kduI||4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (NCBI)||24, 301|
|RSP_0525||RSP_0525||hypothetical protein (NCBI)||24, 161|
|RSP_0663||RSP_0663||Formate-tetrahydrofolate ligase (NCBI)||121, 239|
|RSP_0704||RSP_0704||ABC peptide transporter, substrate binding protein (NCBI)||63, 239|
|RSP_0773||RSP_0773||mannonate dehydratase (NCBI)||24, 301|
|RSP_0920||exbB||Biopolymer transport protein, ExbB (NCBI)||24, 232|
|RSP_0921||exbD||biopolymer transport protein, ExbD (NCBI)||24, 232|
|RSP_0922||RSP_0922||Putative TonB protein (NCBI)||24, 232|
|RSP_0960||RSP_0960||alcohol dehydrogenase (NCBI)||239, 325|
|RSP_1078||fdsG||NAD-dependent formate dehydrogenase, gamma subunit (24 kDa) (NCBI)||216, 239|
|RSP_1079||fdsB||NAD dependent formate dehydrogenase, beta subunit (51 kDa) (NCBI)||216, 239|
|RSP_1080||fdsA||NAD-dependent formate dehydrogenase, alpha subunit (NCBI)||216, 239|
|RSP_1081||fdsC||formate dehydrogenase chain C (NCBI)||216, 239|
|RSP_1082||fdsD||NAD-dependent formate dehydrogenase, delta subunit (NCBI)||216, 239|
|RSP_1437||RSP_1437||ABC Fe+3 hydroxamate (ferrichrome) transporter, ATPase subunit (NCBI)||24, 55|
|RSP_1438||RSP_1438||ABC Fe+3 hydroxamate (ferrichrome) transporter, fused inner membrane subunits (NCBI)||24, 55|
|RSP_1439||RSP_1439||ABC Fe+3 hydroxamate (ferrichrome) transporter, periplasmic siderophore binding protein (NCBI)||24, 55|
|RSP_1440||RSP_1440||TonB dependent, hydroxamate-type ferrisiderophore, outer membrane receptor (NCBI)||24, 55|
|RSP_1486||RSP_1486||regulatory protein, TetR family (NCBI)||239, 289|
|RSP_1548||RSP_1548||putative iron-regulated protein (NCBI)||24, 232|
|RSP_1980||glcB||malate synthase G protein (NCBI)||148, 239|
|RSP_2294||gloB||putative hydroxyacylglutathione hydrolase (glyoxalase II) (GLX II) protein (NCBI)||239, 280|
|RSP_2376||kbl||2-amino-3-ketobutyrate CoA ligase (NCBI)||97, 239|
|RSP_2734||zwf||Glucose-6-phosphate dehydrogenase (NCBI)||24, 301|
|RSP_2735||pgl||6-phosphogluconolactonase (NCBI)||24, 301|
|RSP_2736||pgi||Phosphoglucose isomerase (PGI) glucose-6-phosphate isomerase (NCBI)||24, 301|
|RSP_3056||RSP_3056||TonB dependent-iron siderophore receptor (NCBI)||24, 55|
|RSP_3081||RSP_3081||ABC multidrug efflux transporter, fused ATPase and inner membrane subunits (NCBI)||24, 55|
|RSP_3220||RSP_3220||ABC ferric siderophore transporter, inner membrane subunit (NCBI)||24, 55|
|RSP_3221||RSP_3221||ABC ferric siderophore transporter, inner membrane subunit (NCBI)||24, 55|
|RSP_3222||RSP_3222||ABC ferric siderophore transporter, ATPase subunit (NCBI)||24, 55|
|RSP_3272||ggt||Gamma-glutamyltranspeptidase (NCBI)||210, 239|
|RSP_3509||expE1||Hemolysin-type calcium-binding region, RTX (NCBI)||33, 239|
|RSP_3510||RSP_3510||hypothetical protein (NCBI)||33, 239|
|RSP_3511||RSP_3511||two component transcriptional regulator, winged helix family family (NCBI)||23, 239|
|RSP_3512||RSP_3512||periplasmic sensor signal transduction histidine kinase (NCBI)||33, 239|
|RSP_3678||RSP_3678||Siderophore-interacting protein (NCBI)||24, 239|
|RSP_4355||RSP_4355||hypothetical protein (NCBI)||24, 173|
|RSP_6176||RSP_6176||putative tail fiber assembly protein (NCBI)||24, 80|
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;
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