Organism : Bacillus subtilis | Module List :
Regulation information for BSU33560(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 BSU33560
|Gene||Common Name||Description||Module membership|
|BSU00180||tadA||tRNA specific adenosine deaminase (RefSeq)||111, 123|
|BSU02440||glnJ||two-component sensor histidine kinase [GlnL] for glutamine degradation (RefSeq)||318, 361|
|BSU03560||ycxD||putative PLP-dependent transcriptional regulator (RefSeq)||71, 318|
|BSU05580||ydgC||putative transcriptional regulator (RefSeq)||111, 262|
|BSU05590||ydgD||hypothetical protein (RefSeq)||111, 262|
|BSU05600||ydgE||putative N-acetyltransferase (RefSeq)||111, 216|
|BSU05610||vmlR||ATP-binding cassette efflux transporter (RefSeq)||111, 354|
|BSU08380||yfiS||putative efflux transporter (RefSeq)||152, 318|
|BSU09320||yhcY||two-component sensor histidine kinase [YhcZ] (RefSeq)||114, 318|
|BSU09330||yhcZ||two-component response regulator [YhcY] (RefSeq)||114, 318|
|BSU09490||yhdJ||putative acetyltransferase (RefSeq)||145, 318|
|BSU10880||yisV||putative PLP-dependent transcriptional regulator (RefSeq)||64, 318|
|BSU10890||yisX||hypothetical protein (RefSeq)||111, 262|
|BSU12380||uxaB||altronate oxidoreductase (RefSeq)||71, 318|
|BSU12390||uxaA||altronate hydrolase (RefSeq)||180, 318|
|BSU13150||ohrR||transcriptional regulator sensing organic peroxides (RefSeq)||111, 123|
|BSU13850||zosA||Zn transporter (RefSeq)||111, 249|
|BSU15060||ylbM||hypothetical protein (RefSeq)||111, 123|
|BSU19560||yodD||putative hydrolase (RefSeq)||50, 111|
|BSU19570||yodE||putative lyase/dioxygenase (RefSeq)||50, 111|
|BSU21870||ilvD||dihydroxy-acid dehydratase (RefSeq)||28, 111|
|BSU23640||yqkD||putative hydrolase (RefSeq)||111, 373|
|BSU26180||yqbA||putative phage capsid protein; skin element (RefSeq)||318, 387|
|BSU32440||pucK||uric acid permease (RefSeq)||84, 318|
|BSU32520||pucG||putative ureidoglycolate lyase (ureidoglycolase) (RefSeq)||219, 318|
|BSU32530||yurH||allantoate amidohydrolase (RefSeq)||89, 318|
|BSU32770||yusE||putative thiol-disulfide oxidoreductase with thioredoxin domain (RefSeq)||111, 354|
|BSU33230||sigO||alternative sigma factor (RefSeq)||111, 341|
|BSU33560||yvaD||putative integral inner membrane protein (RefSeq)||111, 318|
|BSU33570||yvaE||putative metabolite-efflux transporter (RefSeq)||111, 318|
|BSU33580||yvaF||putative transcriptional regulator (RefSeq)||111, 318|
|BSU34060||yvfU||two-component response regulator [YvfT] (RefSeq)||318, 361|
|BSU34070||yvfT||two-component sensor histidine kinase [YvfU] (RefSeq)||318, 361|
|BSU34080||yvfS||putative ABC transporter (permease) (RefSeq)||318, 326|
|BSU34090||yvfR||putative ABC efflux transporter (ATP-binding protein) (RefSeq)||318, 326|
|BSU34630||mdxR||putative transcriptional regulator (LacI family) (RefSeq)||90, 318|
|BSU35880||pgsA||capsular polyglutamate synthetase (RefSeq)||64, 318|
|BSU36320||ywpG||hypothetical protein (RefSeq)||64, 318|
|BSU36340||ywpE||putative sortase (RefSeq)||291, 318|
|BSU37540||ywhB||4-oxalocrotonate tautomerase (RefSeq)||111, 115|
|BSU37550||ywhA||putative transcriptional regulator (MarR family) (RefSeq)||111, 123|
|BSU37960||ywdH||putative aldehyde dehydrogenase (RefSeq)||111, 243|
|BSU37990||ywdE||putative integral inner membrane protein (RefSeq)||38, 111|
|BSU38000||ywdD||putative integral inner membrane protein (RefSeq)||38, 111|
|BSU38640||yxlH||putative efflux transporter (RefSeq)||180, 318|
|BSU39860||aldX||putative aldehyde dehydrogenase (RefSeq)||156, 318|
|BSU40110||bglA||aryl-6-phospho-beta-glucosidase (RefSeq)||61, 318|
|BSU40120||yyzE||putative phosphotransferase system enzyme IIA component (RefSeq)||248, 318|
|BSU40130||yydK||putative transcriptional regulator (GntR family) (RefSeq)||171, 318|
|BSU40260||yycQ||putative conserved membrane protein (RefSeq)||248, 318|
|BSU40700||yybB||putative hydrolase (RefSeq)||318, 378|
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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