Organism : Bacillus subtilis | Module List :
Regulation information for BSU33140(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 BSU33140
|Gene||Common Name||Description||Module membership|
|BSU00640||spoIIE||serine phosphatase (RefSeq)||131, 141|
|BSU00650||yabS||hypothetical protein (RefSeq)||131, 141|
|BSU00660||yabT||putative serine/threonine-protein kinase (RefSeq)||137, 141|
|BSU01910||skfA||sporulation killing factor A (RefSeq)||33, 141|
|BSU01920||skfB||synthesis of sporulation killing factor A (RefSeq)||33, 141|
|BSU01960||skfF||sporulation killing factor biosynthesis and export; ABC transporter (permease) (RefSeq)||33, 141|
|BSU01980||skfH||sibling killing effect ; sporulation killing factor biosynthesis and export (RefSeq)||141, 304|
|BSU02040||ybdN||hypothetical protein (RefSeq)||25, 141|
|BSU02220||ybfI||putative transcriptional regulator (AraC/XylS family, cupin family) (RefSeq)||86, 141|
|BSU03470||hxlR||positive regulator of hxlAB expression (RefSeq)||91, 296|
|BSU05130||ydeB||putative transcriptional regulator (RefSeq)||91, 404|
|BSU10560||yhjM||transcriptional regulator of the ntd operon; (LacI family) (RefSeq)||49, 91|
|BSU11990||yjdB||hypothetical protein (RefSeq)||25, 91|
|BSU13640||spo0E||negative regulatory phosphatase acting on Spo0A-P (sporulation) (RefSeq)||70, 91|
|BSU14220||ykuU||putative 2-cys peroxiredoxin (RefSeq)||91, 359|
|BSU14230||ykuV||thiol-disulfide isomerase (RefSeq)||91, 359|
|BSU14560||def||peptide deformylase (RefSeq)||91, 373|
|BSU15090||ylbO||putative spore coat protein regulator protein YlbO (RefSeq)||91, 126|
|BSU15330||sigG||sporulation sigma factor SigG (RefSeq)||131, 141|
|BSU17100||pksC||malonyl-CoA-acyltransferase involved in polyketide synthesis (RefSeq)||25, 91|
|BSU17500||ynaB||hypothetical protein (RefSeq)||70, 91|
|BSU17690||yncM||hypothetical protein (RefSeq)||39, 91|
|BSU18530||yoaA||putative N-acetyltransferase (RefSeq)||91, 323|
|BSU19690||kamA||lysine 2,3-aminomutase (RefSeq)||141, 399|
|BSU19720||yodR||putative acyloate-acetoacetate CoA-transferase (RefSeq)||141, 399|
|BSU19730||yodS||putative aminoacyloate CoA-transferase (RefSeq)||141, 399|
|BSU22540||qcrC||menaquinol:cytochrome c oxidoreductase (cytochrome cc subunit) (RefSeq)||141, 210|
|BSU23300||ypuD||hypothetical protein (RefSeq)||59, 91|
|BSU25860||yqcG||putative phage DNA manipulating enzyme; skin element (RefSeq)||31, 91|
|BSU25870||yqcF||hypothetical protein; skin element (RefSeq)||31, 91|
|BSU26910||yraK||putative hydrolase (RefSeq)||91, 379|
|BSU29260||ytpI||hypothetical protein (RefSeq)||91, 304|
|BSU29630||yttP||putative transcriptional regulator (RefSeq)||12, 141|
|BSU30000||ythQ||putative ABC transporter (permease) (RefSeq)||91, 166|
|BSU30010||ythP||putative ABC transporter (ATP-binding protein) (RefSeq)||91, 166|
|BSU30020||ytzE||putative transcriptional regulator (DeoR family) (RefSeq)||91, 249|
|BSU30960||glgD||glucose-1-phosphate adenylyltransferase (ADP-glucose pyrophosphorylase) beta subunit (RefSeq)||126, 141|
|BSU30980||glgB||glycogen branching enzyme (RefSeq)||141, 304|
|BSU33140||yvqJ||putative efflux protein (RefSeq)||91, 141|
|BSU33960||araE||arabinose-related compounds permease (RefSeq)||91, 329|
|BSU34430||racX||amino acid racemase (RefSeq)||91, 329|
|BSU34440||pbpE||penicillin-binding protein 4* (RefSeq)||91, 329|
|BSU35050||yvnA||putative transcriptional regulator (RefSeq)||25, 91|
|BSU36380||rapD||response regulator aspartate phosphatase (RefSeq)||91, 237|
|BSU37800||yweA||member of the processed secretome (RefSeq)||25, 91|
|BSU39060||citH||secondary transporter of divalent metal ions/citrate complexes (RefSeq)||141, 278|
|BSU39080||licT||transcriptional antiterminator (BglG family) (RefSeq)||68, 91|
|BSU39090||yxiP||putative lipoprotein (RefSeq)||90, 91|
|BSU39260||bglH||aryl-phospho-beta-d-glucosidase (RefSeq)||141, 330|
|BSU39270||bglP||phosphotransferase system (PTS) beta-glucoside-specific enzyme IIBCA component (RefSeq)||141, 330|
|BSU39890||yxbB||putative S-adenosylmethionine-dependent methyltransferase (RefSeq)||19, 141|
|BSU39910||yxnB||hypothetical protein (RefSeq)||19, 141|
|BSU39920||asnH||asparagine synthetase (glutamine-hydrolyzing) (RefSeq)||141, 407|
|BSU39930||yxaM||putative efflux transporter (RefSeq)||85, 141|
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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CircVisOur circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
- 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.
- 2. Source gene
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