Organism : Bacillus subtilis | Module List :
Regulation information for BSU12260(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 BSU12260
|Gene||Common Name||Description||Module membership|
|BSU03080||ycgE||putative transcriptional regulator (RefSeq)||132, 339|
|BSU03580||yczE||integral inner membrane protein regulating antibiotic production (RefSeq)||132, 319|
|BSU05470||ydfM||putative divalent cation efflux transporter (RefSeq)||132, 197|
|BSU05480||ydfN||putative oxidoreductase (RefSeq)||107, 178|
|BSU08290||yfiJ||two-component sensor histidine kinase [YfiK] (RefSeq)||132, 307|
|BSU08700||ygaE||hypothetical protein (RefSeq)||132, 397|
|BSU10150||yhgD||putative transcriptional regulator (RefSeq)||1, 132|
|BSU12240||yjkA||putative ABC transporter (permease) (RefSeq)||132, 339|
|BSU12250||yjkB||putative phosphate ABC transporter (ATP-binding protein) (RefSeq)||132, 339|
|BSU12260||yjlA||putative permease (RefSeq)||107, 132|
|BSU16960||ymdA||phosphodiesterase (RefSeq)||107, 266|
|BSU17790||yndH||hypothetical protein (RefSeq)||107, 339|
|BSU22610||tyrA||prephenate dehydrogenase (RefSeq)||107, 187|
|BSU22620||hisC||histidinol-phosphate aminotransferase (RefSeq)||4, 107|
|BSU22630||trpA||tryptophan synthase subunit alpha (RefSeq)||4, 107|
|BSU22640||trpB||tryptophan synthase subunit beta (RefSeq)||4, 107|
|BSU22650||trpF||N-(5'-phosphoribosyl)anthranilate isomerase (RefSeq)||4, 107|
|BSU22660||trpC||indole-3-glycerol-phosphate synthase (RefSeq)||4, 107|
|BSU22670||trpD||anthranilate phosphoribosyltransferase (RefSeq)||4, 107|
|BSU22680||trpE||anthranilate synthase component I (RefSeq)||4, 107|
|BSU22690||aroH||chorismate mutase (RefSeq)||107, 343|
|BSU22700||aroB||3-dehydroquinate synthase (RefSeq)||107, 343|
|BSU22710||aroF||chorismate synthase (RefSeq)||107, 343|
|BSU28650||ysgA||putative RNA methylase (RefSeq)||132, 339|
|BSU29900||trmB||tRNA (guanine-N(7)-)-methyltransferase (RefSeq)||132, 397|
|BSU30740||mntD||manganese ABC transporter (permease) (RefSeq)||4, 107|
|BSU30750||mntC||manganese ABC transporter (permease) (RefSeq)||4, 107|
|BSU30760||mntB||manganese ABC transporter (ATP-binding protein) (RefSeq)||4, 107|
|BSU30770||mntA||manganese ABC transporter (manganese binding lipoprotein) (RefSeq)||4, 107|
|BSU30810||ytxM||putative esterase (RefSeq)||132, 339|
|BSU30820||menD||2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase (RefSeq)||132, 319|
|BSU31400||alaT||hypothetical protein (RefSeq)||67, 132|
|BSU31510||yufK||putative integral inner membrane protein (RefSeq)||132, 240|
|BSU33460||yvgT||putative integral inner membrane protein (RefSeq)||132, 339|
|BSU33470||bdbC||thiol-disulfide oxidoreductase (RefSeq)||4, 132|
|BSU33480||bdbD||thiol-disulfide oxidoreductase (RefSeq)||4, 107|
|BSU33740||yvaV||putative transcriptional regulator (RefSeq)||132, 339|
|BSU34100||rsbQ||regulator of RsbP phosphatase (RefSeq)||132, 319|
|BSU34110||rsbP||serine phosphatase (RefSeq)||75, 132|
|BSU35200||yvkB||putative transcriptional regulator (TetR/AcrR family) (RefSeq)||38, 132|
|BSU36610||ywnC||putative integral inner membrane protein (RefSeq)||132, 319|
|BSU38140||qoxD||cytochrome aa3-600 quinol oxidase (subunit IV) (RefSeq)||107, 343|
|BSU38150||qoxC||cytochrome aa3-600 quinol oxidase (subunit III) (RefSeq)||107, 343|
|BSU38160||qoxB||cytochrome aa3-600 quinol oxidase (subunit I) (RefSeq)||107, 343|
|BSU38170||qoxA||cytochrome aa3-600 quinol oxidase (subunit II) (RefSeq)||107, 343|
|BSU38320||ywbH||holin-like protein (RefSeq)||132, 409|
|BSU40490||yycA||putative integral inner membrane protein; putative glycosyl transferase (RefSeq)||132, 339|
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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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
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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