Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_1899(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|
Module neighborhood information for RSP_1899
|Gene||Common Name||Description||Module membership|
|RSP_0003||RSP_0003||putative site-specific recombinase (NCBI)||220, 303|
|RSP_0010||RSP_0010||homoserine O-succinyltransferase (NCBI)||91, 133|
|RSP_0011||RSP_0011||Predicted hydrolases or acyltransferases (alpha/beta hydrolase) (NCBI)||91, 366|
|RSP_0013||RSP_0013||hypothetical protein (NCBI)||68, 91|
|RSP_0014||RSP_0014||transcriptional regulator, TetR family (NCBI)||91, 215|
|RSP_0219||RSP_0219||hypothetical protein (NCBI)||168, 220|
|RSP_0563||RSP_0563||putative site-specific recombinase (NCBI)||220, 323|
|RSP_0774||RSP_0774||RNA binding protein (NCBI)||91, 184|
|RSP_0786||RSP_0786||possible Endonuclease/Exonuclease/phosphatase fa (NCBI)||13, 220|
|RSP_0954||RSP_0954||Transglutaminase-like domain (NCBI)||82, 220|
|RSP_1018||RSP_1018||Glycolate oxidase iron-sulfur subunit (NCBI)||91, 148|
|RSP_1019||RSP_1019||putative glycolate oxidase subunit protein (NCBI)||91, 148|
|RSP_1034||pdhR||Pyruvate dehydrogenase complex repressor (NCBI)||91, 148|
|RSP_1130||RSP_1130||hypothetical membrane protein (NCBI)||54, 91|
|RSP_1172||dnaJ||Chaperone, DnaJ (NCBI)||91, 297|
|RSP_1292||RSP_1292||putative Aldehyde dehydrogenase (NCBI)||91, 107|
|RSP_1320||flhA||Flagellar biosynthesis pathway, component FlhA (NCBI)||220, 342|
|RSP_1487||RSP_1487||hypothetical protein (NCBI)||91, 289|
|RSP_1488||RSP_1488||Possible glyoxalase (NCBI)||91, 289|
|RSP_1516||RSP_1516||putative S-adenosyl L-homocystein hydrolase (NCBI)||91, 197|
|RSP_1895||RSP_1895||Small-conductance mechanosensitive ion channel (NCBI)||91, 231|
|RSP_1899||RSP_1899||Predicted ATPase (NCBI)||91, 220|
|RSP_1900||RSP_1900||hypothetical protein (NCBI)||91, 233|
|RSP_1901||RSP_1901||Hypothetical protein with TPR repeat (NCBI)||91, 245|
|RSP_1931||RSP_1931||Probable ATPase, AAA family (NCBI)||1, 220|
|RSP_1932||RSP_1932||hypothetical protein (NCBI)||220, 325|
|RSP_1938||RSP_1938||Conserved hypotetical protein (NCBI)||181, 220|
|RSP_2185||RSP_2185||nuclease (SNase-like) (NCBI)||220, 355|
|RSP_2234||RSP_2234||Predicted DNA-binding protein (NCBI)||220, 346|
|RSP_2251||RSP_2251||putative beta-ketoadipate enol-lactone hydrolase (NCBI)||23, 220|
|RSP_2263||RSP_2263||hypothetical protein (NCBI)||91, 125|
|RSP_2456||radA||DNA Repair Protein (NCBI)||39, 91|
|RSP_2490||RSP_2490||hypothetical protein (NCBI)||220, 355|
|RSP_2605||RSP_2605||hypothetical protein (NCBI)||91, 197|
|RSP_2606||RSP_2606||ArsR family Arsenical Resistance Operon Repressor (NCBI)||91, 197|
|RSP_2607||RSP_2607||nitrilotriacetate monooxygenase component B (NCBI)||91, 197|
|RSP_2608||corA||magnesium/cobalt transport protein, MIT family (NCBI)||91, 197|
|RSP_2810||RSP_2810||ABC transporter, ATPase subunit (NCBI)||91, 294|
|RSP_3107||RSP_3107||hypothetical protein (NCBI)||91, 350|
|RSP_3384||RSP_3384||mandelate racemase/muconate lactonizing enzyme family protein (NCBI)||91, 346|
|RSP_3385||RSP_3385||transcriptional regulator, LysR family (NCBI)||11, 220|
|RSP_3386||RSP_3386||TRAP-T family transporter, periplasmic binding protein (NCBI)||220, 331|
|RSP_3387||RSP_3387||TRAP-T family transporter, fused small and large inner membrane subunits (NCBI)||133, 220|
|RSP_3388||RSP_3388||putative Isocitrate/isopropylmalate dehydrogenase / tartrate dehydrogenase ttuC (NCBI)||83, 220|
|RSP_3389||RSP_3389||Isocitrate/isopropylmalate dehydrogenase / tartrate dehydrogenase (NCBI)||220, 355|
|RSP_3435||RSP_3435||possible DNA-binding protein (NCBI)||91, 316|
|RSP_3448||RSP_3448||transcriptional regulator, GntR-family (NCBI)||84, 220|
|RSP_3456||RSP_3456||Putative dihydrodipicolinate synthase (NCBI)||61, 91|
|RSP_3493||RSP_3493||hypothetical protein (NCBI)||220, 370|
|RSP_3496||RSP_3496||Zinc carboxypeptidase A metalloprotease (M14) (NCBI)||220, 370|
|RSP_3615||groEL||Chaperonin Cpn60 (NCBI)||188, 220|
|RSP_3762||RSP_3762||patch repair protein (NCBI)||150, 220|
|RSP_3785||RSP_3785||putative bacteriophage-related protein (NCBI)||91, 105|
|RSP_3830||RSP_3830||hypothetical protein (NCBI)||116, 220|
|RSP_4319||RSP_4319||tRNA-Gly (NCBI)||181, 220|
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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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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