Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Putative peptidyl-dipeptidase (NCBI)
Functional Annotations (5)
|Zn-dependent oligopeptidases||cog/ cog|
|metalloendopeptidase activity||go/ molecular_function|
|zinc ion binding||go/ molecular_function|
|peptidyl-dipeptidase Dcp activity||go/ molecular_function|
Regulation information for RSP_0596(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_0596
Module neighborhood information for RSP_0596
|Gene||Common Name||Description||Module membership|
|RSP_0004||RSP_0004||hypothetical protein (NCBI)||97, 303|
|RSP_0123||cerI||Autoinducer synthesis protein (NCBI)||97, 309|
|RSP_0203||RSP_0203||signal transduction kinase protein (NCBI)||1, 329|
|RSP_0384||RSP_0384||hypothetical protein (NCBI)||329, 381|
|RSP_0429||RSP_0429||Probable ABC drug/toxin efflux transporter; fused ATPase and inner membrane subunits (NCBI)||176, 329|
|RSP_0430||cobD||cobalamin biosynthesis protein CobD (NCBI)||97, 171|
|RSP_0477||RSP_0477||hypothetical protein (NCBI)||97, 103|
|RSP_0491||hupT||Hydrogen uptake histidine-kinase (NCBI)||308, 329|
|RSP_0595||RSP_0595||hypothetical protein (NCBI)||285, 329|
|RSP_0596||RSP_0596||Putative peptidyl-dipeptidase (NCBI)||97, 329|
|RSP_0606||RSP_0606||Putative redox protein (NCBI)||97, 285|
|RSP_0678||RSP_0678||hypothetical protein (NCBI)||23, 329|
|RSP_0709||cpdB||2',3'-cyclic-nucleotide 2'-phosphodiesterase (NCBI)||285, 329|
|RSP_0751||RSP_0751||hypothetical protein (NCBI)||62, 97|
|RSP_0881||RSP_0881||Putative soluble lytic transglycosylase (NCBI)||294, 329|
|RSP_0955||RSP_0955||5'-nucleotidase (NCBI)||97, 195|
|RSP_0985||RSP_0985||adenine deaminase (NCBI)||285, 329|
|RSP_1055||RSP_1055||transcriptional regulator, LysR family (NCBI)||97, 329|
|RSP_1083||RSP_1083||two component transcriptional regulator, winged helix family (NCBI)||285, 329|
|RSP_1415||RSP_1415||putative polysaccharide deacetylase (NCBI)||23, 329|
|RSP_1416||RSP_1416||hypothetical protein (NCBI)||23, 329|
|RSP_1435||RSP_1435||regulatory protein TetR family (NCBI)||62, 97|
|RSP_1473||RSP_1473||hypothetical protein (NCBI)||97, 244|
|RSP_1521||RSP_1521||hypothetical protein (NCBI)||97, 116|
|RSP_1555||RSP_1555||Transthyretin-like protein (NCBI)||329, 381|
|RSP_1824||adh||Zinc-containing alcohol dehydrogenase (NCBI)||35, 97|
|RSP_1844||RSP_1844||hypothetical protein (NCBI)||35, 329|
|RSP_1962||RSP_1962||hypothetical protein (NCBI)||13, 97|
|RSP_1990||RSP_1990||Transcriptional regulator, AsnC family (NCBI)||97, 195|
|RSP_2006||amsA||hypothetical protein (NCBI)||92, 329|
|RSP_2053||RSP_2053||Possible transporter, RarD family, DMT superfamily (NCBI)||73, 97|
|RSP_2093||RSP_2093||Putative Mrp (Multidrug resistance-associated proteins) family protein (NCBI)||278, 329|
|RSP_2167||RSP_2167||hypothetical protein (NCBI)||97, 262|
|RSP_2376||kbl||2-amino-3-ketobutyrate CoA ligase (NCBI)||97, 239|
|RSP_2641||RSP_2641||hypothetical protein (NCBI)||97, 237|
|RSP_2869||RSP_2869||Possible tellurite resistance protein (NCBI)||329, 381|
|RSP_2932||hutC||Histidine utilization repressor, gntR family (NCBI)||95, 97|
|RSP_2933||hutF||Formiminoglutamate deiminase (NCBI)||95, 97|
|RSP_2934||hutI||Imidazolone-5-propionate hydrolase (NCBI)||95, 97|
|RSP_2935||hutH||Probable histidine ammonia-lyase (NCBI)||95, 97|
|RSP_2936||hutU||Urocanase (NCBI)||95, 97|
|RSP_3029||RSP_3029||transcriptional regulator, GntR family (NCBI)||97, 157|
|RSP_3031||RSP_3031||ABC peptide/opine transporter, inner membrane subunit (NCBI)||97, 157|
|RSP_3052||RSP_3052||transcriptional regulator, LysR family (NCBI)||97, 176|
|RSP_3053||RSP_3053||Possible dioxygenase/glyoxalase family protein (NCBI)||97, 176|
|RSP_3071||RSP_3071||putative hydroxypyruvate reductase/glycerate kinase (NCBI)||107, 329|
|RSP_3087||dgkA||diacylglycerol kinase (NCBI)||97, 176|
|RSP_3180||RSP_3180||Transglutaminase-like enzyme (NCBI)||38, 97|
|RSP_3325||RSP_3325||Polysaccharide export transporter, PST Family (NCBI)||195, 329|
|RSP_3400||RSP_3400||transcriptional regulator, LysR family (NCBI)||19, 97|
|RSP_3679||RSP_3679||hypothetical protein (NCBI)||308, 329|
|RSP_3748||ampR||transcriptional regulator, LysR family (NCBI)||97, 362|
|RSP_3836||RSP_3836||Putative metal-dependent hydrolase (NCBI)||10, 329|
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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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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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.
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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;
- 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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