Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Serine/threonine protein kinase (NCBI)
Functional Annotations (5)
|Serine/threonine protein kinase||cog/ cog|
|protein serine/threonine kinase activity||go/ molecular_function|
|protein tyrosine kinase activity||go/ molecular_function|
|ATP binding||go/ molecular_function|
|protein phosphorylation||go/ biological_process|
Regulation information for RSP_3134(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_3134
Module neighborhood information for RSP_3134
|Gene||Common Name||Description||Module membership|
|RSP_0187||RSP_0187||Dihydroorotate dehydrogenase (NCBI)||83, 244|
|RSP_0328||nnrS||hypothetical protein (NCBI)||168, 249|
|RSP_0360||RSP_0360||hypothetical protein (NCBI)||150, 249|
|RSP_0361||sda||probable L-serine dehydratase protein (NCBI)||150, 244|
|RSP_0410||RSP_0410||sensor diguanylate cyclase (GGDEF) (NCBI)||249, 282|
|RSP_0470||RSP_0470||hypothetical protein (NCBI)||168, 249|
|RSP_0498||hupC||Ni, Fe hydrogenase I cytochrome b subunit (NCBI)||244, 300|
|RSP_0542||RSP_0542||hypothetical protein (NCBI)||244, 300|
|RSP_0543||fixU||hypothetical protein (NCBI)||141, 244|
|RSP_0604||RSP_0604||hypothetical protein (NCBI)||29, 249|
|RSP_0605||RSP_0605||hypothetical protein (NCBI)||249, 370|
|RSP_0614||RSP_0614||hypothetical protein (NCBI)||249, 325|
|RSP_0952||RSP_0952||Transglutaminase-like protein (NCBI)||249, 370|
|RSP_1077||RSP_1077||transcriptional regulator, LysR family (NCBI)||216, 249|
|RSP_1458||RSP_1458||Putative DNA repair enzyme (NCBI)||244, 282|
|RSP_1473||RSP_1473||hypothetical protein (NCBI)||97, 244|
|RSP_1751||RSP_1751||putative 2Fe-2S ferredoxin protein (NCBI)||244, 300|
|RSP_2056||RSP_2056||hypothetical protein (NCBI)||244, 347|
|RSP_2123||RSP_2123||Radical SAM domain protein (NCBI)||73, 244|
|RSP_2150||RSP_2150||predicted Glycosyl transferase, family 2 (NCBI)||138, 249|
|RSP_2151||yohD||putative DedA family, membrane protein (NCBI)||138, 249|
|RSP_2152||RSP_2152||putative ceramide glucosyltransferase (NCBI)||138, 249|
|RSP_2153||RSP_2153||hypothetical protein (NCBI)||238, 249|
|RSP_2392||RSP_2392||putative membrane protein, similar to periplasmic nitrate reductase NnuR (NCBI)||249, 303|
|RSP_2700||RSP_2700||ABC oligo/dipeptide transporter, fused ATPase subunits (NCBI)||19, 249|
|RSP_2701||RSP_2701||ABC oligo/dipeptide transporter, inner membrane subunit (NCBI)||19, 249|
|RSP_2964||RSP_2964||hypothetical protein (NCBI)||229, 244|
|RSP_3043||RSP_3043||hypothetical protein (NCBI)||238, 249|
|RSP_3122||RSP_3122||putative Glutathione S-transferase (NCBI)||233, 249|
|RSP_3129||RSP_3129||serine/threonine protein kinase (NCBI)||244, 249|
|RSP_3130||RSP_3130||Putative serine protease (NCBI)||83, 244|
|RSP_3131||RSP_3131||ABC (antimicrobial peptide) transporter, ATPase subunit (NCBI)||244, 249|
|RSP_3132||RSP_3132||hypothetical protein (NCBI)||244, 249|
|RSP_3133||RSP_3133||hypothetical protein (NCBI)||244, 249|
|RSP_3134||RSP_3134||Serine/threonine protein kinase (NCBI)||244, 249|
|RSP_3135||RSP_3135||ppkA-related protein (NCBI)||244, 292|
|RSP_3188||RSP_3188||ApbE family protein (NCBI)||244, 300|
|RSP_3190||RSP_3190||2Fe-2S ferredoxin (NCBI)||68, 244|
|RSP_3191||fprA||Flavodoxin (NCBI)||244, 300|
|RSP_3199||RSP_3199||hypothetical protein (NCBI)||244, 300|
|RSP_3211||cbiO||ABC cobalt transporter, ATPase subunit, CbiO (NCBI)||23, 244|
|RSP_3404||RSP_3404||hypothetical protein (NCBI)||95, 244|
|RSP_3405||gntR||transcriptional regulator, GntR family (NCBI)||95, 244|
|RSP_3576||RSP_3576||hypothetical protein (NCBI)||103, 249|
|RSP_3628||RSP_3628||hypothetical protein (NCBI)||150, 244|
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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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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