Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
hypothetical protein (NCBI)
Functional Annotations (1)
Regulation information for RSP_0384(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_0384
Module neighborhood information for RSP_0384
|Gene||Common Name||Description||Module membership|
|RSP_0203||RSP_0203||signal transduction kinase protein (NCBI)||1, 329|
|RSP_0282||ppsR||Transcriptional regulator, PpsR (NCBI)||358, 381|
|RSP_0384||RSP_0384||hypothetical protein (NCBI)||329, 381|
|RSP_0415||RSP_0415||sigma-24 (NCBI)||308, 381|
|RSP_0429||RSP_0429||Probable ABC drug/toxin efflux transporter; fused ATPase and inner membrane subunits (NCBI)||176, 329|
|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_0599||RSP_0599||Probable DNA/pantothenate metabolism flavoprotein (NCBI)||242, 381|
|RSP_0678||RSP_0678||hypothetical protein (NCBI)||23, 329|
|RSP_0708||RSP_0708||NUDIX hydrolase (NCBI)||242, 381|
|RSP_0709||cpdB||2',3'-cyclic-nucleotide 2'-phosphodiesterase (NCBI)||285, 329|
|RSP_0710||dnaX||DNA polymerase III tau and gamma subunits (NCBI)||173, 381|
|RSP_0881||RSP_0881||Putative soluble lytic transglycosylase (NCBI)||294, 329|
|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_1188||wcaG||Nucleotide sugar epimerase/dehydratase (NCBI)||59, 381|
|RSP_1214||RSP_1214||putative branched-chain amino acid aminotransferase (NCBI)||215, 381|
|RSP_1215||ilvE||putative IlvE, Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase (NCBI)||68, 381|
|RSP_1342||dnaA||chromosomal replication initiator protein, DnaA (NCBI)||25, 381|
|RSP_1404||RSP_1404||Orotidine 5'-phosphate decarboxylase (NCBI)||311, 381|
|RSP_1405||RSP_1405||ROK family protein (NCBI)||285, 381|
|RSP_1415||RSP_1415||putative polysaccharide deacetylase (NCBI)||23, 329|
|RSP_1416||RSP_1416||hypothetical protein (NCBI)||23, 329|
|RSP_1520||prrB||Sensor histidine kinase PrrB (RegB) (NCBI)||16, 381|
|RSP_1553||RSP_1553||Probable glyoxylate induced protein (NCBI)||102, 381|
|RSP_1554||RSP_1554||Possible polysaccharide deacetylase (NCBI)||102, 381|
|RSP_1555||RSP_1555||Transthyretin-like protein (NCBI)||329, 381|
|RSP_1566||RSP_1566||hypothetical protein (NCBI)||176, 381|
|RSP_1621||RSP_1621||Deoxyguanosinetriphosphate triphosphohydrolase-like protein (NCBI)||93, 381|
|RSP_1844||RSP_1844||hypothetical protein (NCBI)||35, 329|
|RSP_1894||RSP_1894||hypothetical protein (NCBI)||323, 381|
|RSP_1908||RSP_1908||outer membrane protein, OmpA/MotB family (NCBI)||72, 381|
|RSP_1909||RSP_1909||Outer membrane general secretion pathway protein, Secretin (NCBI)||221, 381|
|RSP_1946||RSP_1946||Cytochrome P450 hydroxylase (NCBI)||175, 381|
|RSP_2006||amsA||hypothetical protein (NCBI)||92, 329|
|RSP_2093||RSP_2093||Putative Mrp (Multidrug resistance-associated proteins) family protein (NCBI)||278, 329|
|RSP_2119||RSP_2119||hypothetical protein (NCBI)||10, 381|
|RSP_2694||RSP_2694||hypothetical protein (NCBI)||357, 381|
|RSP_2869||RSP_2869||Possible tellurite resistance protein (NCBI)||329, 381|
|RSP_2882||RSP_2882||two component transcriptional regulator, LuxR family (NCBI)||62, 381|
|RSP_2942||RSP_2942||hypothetical protein (NCBI)||349, 381|
|RSP_3071||RSP_3071||putative hydroxypyruvate reductase/glycerate kinase (NCBI)||107, 329|
|RSP_3226||RSP_3226||Silent information regulator protein, Sir2 (NCBI)||99, 381|
|RSP_3325||RSP_3325||Polysaccharide export transporter, PST Family (NCBI)||195, 329|
|RSP_3376||aroQ||3 dehydroquinase dehydratase, class II (NCBI)||240, 381|
|RSP_3419||RSP_3419||hypothetical protein (NCBI)||175, 381|
|RSP_3507||RSP_3507||hypothetical protein (NCBI)||381, 384|
|RSP_3553||dnaE||DNA polymerase III alpha chain (NCBI)||291, 381|
|RSP_3679||RSP_3679||hypothetical protein (NCBI)||308, 329|
|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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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
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