Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_2732(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_2732
|Gene||Common Name||Description||Module membership|
|RSP_0013||RSP_0013||hypothetical protein (NCBI)||68, 91|
|RSP_0220||RSP_0220||hypothetical protein (NCBI)||68, 327|
|RSP_0301||RSP_0301||ABC branched chain amino acid transporter, substrate binding protein (NCBI)||68, 300|
|RSP_0326||RSP_0326||hypothetical protein (NCBI)||68, 188|
|RSP_0494||hypF||hydrogenase maturation factor F (NCBI)||292, 337|
|RSP_0571||RSP_0571||tRNA pseudouridine synthase (NCBI)||68, 108|
|RSP_0748||RSP_0748||N-6 Adenine-specific DNA methylase (NCBI)||68, 288|
|RSP_1013||RSP_1013||possible Hemolysin (NCBI)||68, 267|
|RSP_1115||RSP_1115||hypothetical protein (NCBI)||246, 292|
|RSP_1118||RSP_1118||group 1 glycosyltransferase (NCBI)||246, 292|
|RSP_1137||RSP_1137||Histone deacetylase family protein (NCBI)||68, 108|
|RSP_1215||ilvE||putative IlvE, Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase (NCBI)||68, 381|
|RSP_1224||hemN||putative Coproporphyrinogen III oxidase and related Fe-S oxidoreductases (NCBI)||68, 187|
|RSP_1423||RSP_1423||ParA family ATPase (NCBI)||68, 293|
|RSP_1425||RSP_1425||Plasmid replication initiation protein (NCBI)||42, 68|
|RSP_1443||RSP_1443||ABC sugar transporter, inner membrane subunit (NCBI)||68, 89|
|RSP_1445||RSP_1445||ABC sugar transporter, ATPase subunit (NCBI)||68, 89|
|RSP_1450||RSP_1450||Inositol monophosphatase family protein (NCBI)||105, 292|
|RSP_1501||RSP_1501||Antisigma-factor antagonist (STAS) domain protein (NCBI)||74, 292|
|RSP_1509||RSP_1509||Glycoprotease (M22) metalloprotease (NCBI)||292, 300|
|RSP_1577||putR||Proline dehydrogenase transcriptional activator (NCBI)||68, 112|
|RSP_1661||RSP_1661||hypothetical protein (NCBI)||292, 300|
|RSP_1752||RSP_1752||Putative creatinase (NCBI)||68, 346|
|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_1923||bioB||Biotin synthase (NCBI)||62, 292|
|RSP_2061||RSP_2061||hypothetical protein (NCBI)||292, 379|
|RSP_2315||RSP_2315||hypothetical protein (NCBI)||105, 292|
|RSP_2316||dadA||D-amino acid dehydrogenase (NCBI)||68, 375|
|RSP_2339||RSP_2339||hypothetical protein (NCBI)||28, 68|
|RSP_2348||RSP_2348||hypothetical protein (NCBI)||68, 293|
|RSP_2501||RSP_2501||hypothetical protein (NCBI)||238, 292|
|RSP_2732||RSP_2732||Major facilitator superfamily (MFS) transporter (NCBI)||68, 292|
|RSP_2867||rpoN4||Sigma-54 factor family protein (NCBI)||282, 292|
|RSP_3024||RSP_3024||transcriptional regulator, IclR family/MhpR (NCBI)||68, 73|
|RSP_3064||RSP_3064||transcriptional regulator, DeoR family (NCBI)||235, 292|
|RSP_3108||RSP_3108||Putative methyl accepting chemotaxis protein (NCBI)||246, 292|
|RSP_3128||RSP_3128||hypothetical protein (NCBI)||292, 337|
|RSP_3135||RSP_3135||ppkA-related protein (NCBI)||244, 292|
|RSP_3190||RSP_3190||2Fe-2S ferredoxin (NCBI)||68, 244|
|RSP_3471||RSP_3471||hypothetical protein (NCBI)||147, 292|
|RSP_3613||RSP_3613||Glycosyltransferase (NCBI)||238, 292|
|RSP_3650||RSP_3650||Periplasmic serine proteases (ClpP class) (NCBI)||68, 196|
|RSP_3743||speB1||putative agmatinase (NCBI)||61, 292|
|RSP_3746||RSP_3746||hypothetical protein (NCBI)||61, 292|
|RSP_3764||RSP_3764||hypothetical protein (NCBI)||292, 347|
|RSP_3780||RSP_3780||hypothetical protein (NCBI)||147, 292|
|RSP_3789||RSP_3789||hypothetical protein (NCBI)||88, 292|
|RSP_3790||RSP_3790||hypothetical protein (NCBI)||42, 68|
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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