Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_1760(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_1760
|Gene||Common Name||Description||Module membership|
|RSP_0230||RSP_0230||Neutral zinc metallopeptidase (NCBI)||108, 377|
|RSP_0258||pufA||LHI alpha, Light-harvesting B875 protein (NCBI)||172, 377|
|RSP_0314||pucB||LHII beta, light-harvesting B800/850 protein (NCBI)||172, 377|
|RSP_0388||RSP_0388||hypothetical protein (NCBI)||107, 377|
|RSP_0549||RSP_0549||hypothetical protein (NCBI)||71, 171|
|RSP_0768||RSP_0768||transcriptional regulator, LuxR family (NCBI)||27, 377|
|RSP_0769||RSP_0769||Glutathione S-transferase (NCBI)||23, 71|
|RSP_0823||SHMT||serine hydroxymethyltransferase protein (NCBI)||71, 85|
|RSP_0885||SseA||Thiosulfate sulfurtransferase, Rhodanese-like (NCBI)||71, 171|
|RSP_0924||cinA||Predicted nucleotide-utilizing enzyme/competence-damage associated protein (NCBI)||71, 286|
|RSP_1008||RSP_1008||4-hydroxybenzoate octaprenyltransferase (NCBI)||71, 164|
|RSP_1009||RSP_1009||possible outer membrane protein, OmpA family (NCBI)||71, 164|
|RSP_1033||RSP_1033||OmpA family protein (NCBI)||16, 71|
|RSP_1460||RSP_1460||hypothetical protein (NCBI)||71, 93|
|RSP_1489||RSP_1489||Protein containing thioredoxin domain (NCBI)||30, 71|
|RSP_1592||acsA||Possible acyl-CoA sythetase (NCBI)||305, 377|
|RSP_1760||RSP_1760||hypothetical protein (NCBI)||71, 377|
|RSP_1808||trpS||tryptophanyl-tRNA synthetase (NCBI)||71, 360|
|RSP_1817||RSP_1817||hypothetical protein (NCBI)||172, 377|
|RSP_1818||feoB||Fe2+ transport system protein B (NCBI)||172, 377|
|RSP_1819||feoA1||ferrous iron transport protein A (NCBI)||172, 377|
|RSP_1843||ftsY||Signal recognition particle-docking protein FtsY (NCBI)||71, 309|
|RSP_1851||metZ||O-succinylhomoserine sulfhydrylase (NCBI)||71, 360|
|RSP_1860||RSP_1860||hypothetical protein (NCBI)||43, 377|
|RSP_1987||RSP_1987||hypothetical protein (NCBI)||36, 377|
|RSP_2007||RSP_2007||conservd hypothetical protein (NCBI)||64, 71|
|RSP_2147||cysK||O-acetylserine (Thiol)-lyase, cysteine synthase (NCBI)||71, 184|
|RSP_2193||gcvT||predicted aminomethyltransferase, tetrahydrofolate dependent (NCBI)||71, 309|
|RSP_2336||RSP_2336||hypothetical protein (NCBI)||71, 181|
|RSP_2338||RSP_2338||hypothetical protein (NCBI)||358, 377|
|RSP_2387||RSP_2387||hypothetical protein (NCBI)||71, 286|
|RSP_2408||RSP_2408||hypothetical protein (NCBI)||71, 322|
|RSP_2453||RSP_2453||putative oxidoreductase (NAD/NADP dependent) (NCBI)||71, 166|
|RSP_2507||ompW||outer membrane protein (NCBI)||270, 377|
|RSP_2573||RSP_2573||hypothetical protein (NCBI)||139, 377|
|RSP_2768||RSP_2768||5-methyltetrahydrofolate S-homocysteine methyltransferase (NCBI)||27, 71|
|RSP_2975||RSP_2975||hypothetical protein (NCBI)||71, 309|
|RSP_2983||RSP_2983||hypothetical protein (NCBI)||108, 377|
|RSP_2985||RSP_2985||hypothetical protein (NCBI)||71, 181|
|RSP_2986||RSP_2986||ArgE/DapE/Acy1 family protein (NCBI)||52, 71|
|RSP_2987||RSP_2987||probable acetyltransferase (NCBI)||71, 181|
|RSP_3044||dorS||DMSO/TMAO-sensor hybrid histidine kinase (NCBI)||36, 377|
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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