Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_1956(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_1956
|Gene||Common Name||Description||Module membership|
|RSP_0152||RSP_0152||P-loop ATPase (NCBI)||74, 280|
|RSP_0339||RSP_0339||hypothetical protein (NCBI)||280, 286|
|RSP_0671||RSP_0671||ExbD/TolR family protein (NCBI)||286, 294|
|RSP_0672||TolQ||Biopolymer transport protein, TolQ (NCBI)||277, 286|
|RSP_0723||ald||alanine dehydrogenase (NCBI)||273, 280|
|RSP_0753||SspA||Salt-stress induced outer membrane protein (NCBI)||280, 368|
|RSP_0799||RSP_0799||hypothetical protein (NCBI)||286, 287|
|RSP_0923||map1||Methionine aminopeptidase, subfamily 1 (NCBI)||84, 286|
|RSP_0924||cinA||Predicted nucleotide-utilizing enzyme/competence-damage associated protein (NCBI)||71, 286|
|RSP_0925||yobR||Putative acetyl transferase (NCBI)||84, 286|
|RSP_0926||RSP_0926||OmpA/MotB family protein (NCBI)||84, 286|
|RSP_0958||RSP_0958||RAM domain protein (NCBI)||82, 286|
|RSP_0969||RSP_0969||putative integral membrane protein (NCBI)||2, 280|
|RSP_1258||RSP_1258||putative hydrolase (NCBI)||231, 280|
|RSP_1259||RSP_1259||hypothetical protein (NCBI)||280, 289|
|RSP_1260||RSP_1260||hypothetical protein (NCBI)||207, 286|
|RSP_1348||RSP_1348||hypothetical protein (NCBI)||280, 362|
|RSP_1421||RSP_1421||hypothetical protein (NCBI)||286, 366|
|RSP_1542||RSP_1542||ABC transporter, ATPase subunit (NCBI)||210, 286|
|RSP_1672||pdxJ||PNP synthase, pyridoxal phosphate biosynthetic protein PdxJ (NCBI)||181, 286|
|RSP_1863||RSP_1863||Phosphoglucomutase/phosphomannomutase (NCBI)||280, 308|
|RSP_1933||RSP_1933||Outer membrane protein, OmpA/MotB family (NCBI)||103, 280|
|RSP_1956||RSP_1956||hypothetical protein (NCBI)||280, 286|
|RSP_2201||RSP_2201||transcriptional regulator, MerR family (NCBI)||162, 286|
|RSP_2225||RSP_2225||hypothetical protein (NCBI)||117, 280|
|RSP_2294||gloB||putative hydroxyacylglutathione hydrolase (glyoxalase II) (GLX II) protein (NCBI)||239, 280|
|RSP_2330||leuA||2-Isopropylmalate synthase (NCBI)||185, 286|
|RSP_2374||RSP_2374||hypothetical protein (NCBI)||218, 286|
|RSP_2387||RSP_2387||hypothetical protein (NCBI)||71, 286|
|RSP_2414||RSP_2414||hypothetical protein (NCBI)||82, 280|
|RSP_2865||RSP_2865||putative transposase (NCBI)||132, 280|
|RSP_2965||RSP_2965||Transcriptional regulator, LysR family (NCBI)||19, 280|
|RSP_2973||RSP_2973||Peroxiredoxin (NCBI)||158, 286|
|RSP_3113||dadA||D-amino acid dehydrogenase small subunit (NCBI)||178, 280|
|RSP_3115||RSP_3115||Conserved hypothetical membrane protein (NCBI)||280, 368|
|RSP_3138||RSP_3138||Smp-30/Cgr1 family protein (NCBI)||210, 280|
|RSP_3141||RSP_3141||hypothetical protein (NCBI)||161, 280|
|RSP_3142||RSP_3142||Na+/solute symporter (NCBI)||161, 280|
|RSP_3305||abc1||putative ubiquinol-cytochrome-c reductase assembly protein (NCBI)||117, 280|
|RSP_3324||RSP_3324||transcriptional regulator, LuxR family (NCBI)||46, 286|
|RSP_3327||RSP_3327||possible Rhomboid family membrane protein (NCBI)||2, 280|
|RSP_3423||xthA1||Probable exodeoxyribonuclease III (NCBI)||2, 280|
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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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.
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