Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_1000(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_1000
|Gene||Common Name||Description||Module membership|
|RSP_0018||RSP_0018||Putative transcriptional regulator, gntR family (NCBI)||285, 326|
|RSP_0019||RSP_0019||hypothetical protein (NCBI)||48, 285|
|RSP_0119||RSP_0119||PA-phosphatase related phosphoesterase (NCBI)||2, 4|
|RSP_0204||RSP_0204||metallo-beta-lactamase family protein (NCBI)||285, 370|
|RSP_0354||RSP_0354||hypothetical protein (NCBI)||242, 285|
|RSP_0424||RSP_0424||hypothetical protein (NCBI)||216, 285|
|RSP_0440||sufB||putative SufB (NCBI)||2, 289|
|RSP_0558||RSP_0558||Possible ribosomal protein L11 methyltransferase (NCBI)||2, 218|
|RSP_0595||RSP_0595||hypothetical protein (NCBI)||285, 329|
|RSP_0606||RSP_0606||Putative redox protein (NCBI)||97, 285|
|RSP_0709||cpdB||2',3'-cyclic-nucleotide 2'-phosphodiesterase (NCBI)||285, 329|
|RSP_0730||RSP_0730||hypothetical protein (NCBI)||2, 54|
|RSP_0761||RSP_0761||hypothetical protein (NCBI)||2, 162|
|RSP_0969||RSP_0969||putative integral membrane protein (NCBI)||2, 280|
|RSP_0985||RSP_0985||adenine deaminase (NCBI)||285, 329|
|RSP_1000||RSP_1000||hypothetical protein (NCBI)||2, 285|
|RSP_1067||fixR||Short-chain alcohol dehydrogenase (NCBI)||39, 285|
|RSP_1083||RSP_1083||two component transcriptional regulator, winged helix family (NCBI)||285, 329|
|RSP_1096||RSP_1096||putative zinc protease (NCBI)||2, 184|
|RSP_1297||RSP_1297||transcriptional regulator, LysR family (NCBI)||171, 285|
|RSP_1405||RSP_1405||ROK family protein (NCBI)||285, 381|
|RSP_1409||RSP_1409||Beta-Ig-H3/Fasciclin (NCBI)||2, 161|
|RSP_1410||RSP_1410||hypothetical protein (NCBI)||2, 30|
|RSP_1411||RSP_1411||putative membrane protein (NCBI)||2, 4|
|RSP_1433||RSP_1433||hypothetical protein (NCBI)||141, 285|
|RSP_1778||RSP_1778||TPR domain protein (NCBI)||68, 285|
|RSP_1779||ispE||Putative 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (NCBI)||68, 285|
|RSP_1780||RSP_1780||hypothetical protein (NCBI)||285, 323|
|RSP_1807||RSP_1807||hypothetical protein (NCBI)||2, 287|
|RSP_1966||RSP_1966||possible ISSod13, transposase (NCBI)||19, 285|
|RSP_2003||yibQ||YibQ protein (NCBI)||176, 285|
|RSP_2122||mtbC||Putative dimethylamine corrinoid protein (NCBI)||185, 285|
|RSP_2132||RSP_2132||Protein of unknown function UPF0033 (NCBI)||2, 53|
|RSP_2134||ccdA||putative cytochrome c-type biogenesis protein CcdA (NCBI)||2, 242|
|RSP_2271||RSP_2271||hypothetical protein (NCBI)||2, 294|
|RSP_2396||RSP_2396||hypothetical protein (NCBI)||196, 285|
|RSP_2433||cheY2||Chemotaxis response regulator, CheY2 (NCBI)||285, 370|
|RSP_2609||dcd||putative deoxycytidine triphosphate deaminase (NCBI)||2, 98|
|RSP_2649||RSP_2649||Putative Zn-dependent protease (NCBI)||62, 285|
|RSP_2674||RSP_2674||hypothetical protein (NCBI)||48, 285|
|RSP_2731||ArsH||arsenical resistance protein, ArsH (NCBI)||285, 313|
|RSP_2765||RSP_2765||hypothetical protein (NCBI)||88, 285|
|RSP_2849||RSP_2849||hypothetical membrane protein (NCBI)||2, 4|
|RSP_2929||RSP_2929||putative disulfide bond formation protein DsbB (NCBI)||2, 331|
|RSP_3067||RSP_3067||hypothetical protein (NCBI)||2, 19|
|RSP_3109||RSP_3109||transcriptional regulator, MarR family (NCBI)||62, 285|
|RSP_3111||RSP_3111||Putative Glutathione S-transferase (NCBI)||62, 285|
|RSP_3112||RSP_3112||hypothetical protein (NCBI)||62, 285|
|RSP_3120||RSP_3120||hypothetical protein (NCBI)||2, 42|
|RSP_3218||RSP_3218||Putative oxidoreductase NAD protein (NCBI)||112, 285|
|RSP_3260||amiC||Putative negative amidase regulator, AmiC (NCBI)||285, 325|
|RSP_3327||RSP_3327||possible Rhomboid family membrane protein (NCBI)||2, 280|
|RSP_3423||xthA1||Probable exodeoxyribonuclease III (NCBI)||2, 280|
|RSP_3424||RSP_3424||hypothetical protein (NCBI)||38, 285|
|RSP_3787||RSP_3787||hypothetical protein (NCBI)||236, 285|
|RSP_3805||RSP_3805||possible integrase (NCBI)||157, 285|
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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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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- 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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