Organism : Bacillus subtilis | Module List :
putative efflux transporter (RefSeq)
Functional Annotations (3)
|transporter activity||go/ molecular_function|
|integral to membrane||go/ cellular_component|
Regulation information for BSU39930(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|
Functional Enrichment for BSU39930
|transporter activity||go/ molecular_function|
|integral to membrane||go/ cellular_component|
Module neighborhood information for BSU39930
|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|
|BSU10780||yisN||hypothetical protein (RefSeq)||85, 127|
|BSU10790||asnO||asparagine synthetase (RefSeq)||85, 127|
|BSU15330||sigG||sporulation sigma factor SigG (RefSeq)||131, 141|
|BSU17110||pksD||enzyme involved in polyketide synthesis (RefSeq)||85, 302|
|BSU17120||pksE||enzyme involved in polyketide synthesis (RefSeq)||85, 306|
|BSU17130||acpK||acyl carrier protein (RefSeq)||85, 306|
|BSU17140||pksF||polyketide beta-ketoacyl:acyl carrier protein synthase (RefSeq)||85, 306|
|BSU17150||pksG||acetyl-S-AcpK beta-ketothioester polyketide intermediate transferase (RefSeq)||85, 306|
|BSU17160||pksH||polyketide biosynthesis enoyl-CoA hydratase (RefSeq)||85, 306|
|BSU17170||pksI||polyketide biosynthesis enoyl-CoA hydratase (RefSeq)||85, 306|
|BSU17180||pksJ||polyketide synthase of type I (RefSeq)||85, 306|
|BSU17190||pksL||polyketide synthase of type I (RefSeq)||85, 306|
|BSU17200||pksM||polyketide synthase (RefSeq)||85, 306|
|BSU17210||pksN||polyketide synthase of type I (RefSeq)||85, 306|
|BSU17220||pksR||polyketide synthase (RefSeq)||85, 306|
|BSU18330||ppsB||plipastatin synthetase (RefSeq)||85, 306|
|BSU18340||ppsA||plipastatin synthetase (RefSeq)||85, 306|
|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|
|BSU27030||sacC||levanase (RefSeq)||85, 329|
|BSU27040||levG||phosphotransferase system (PTS) fructose-specific enzyme IID component (RefSeq)||85, 117|
|BSU27050||levF||phosphotransferase system (PTS) fructose-specific enzyme IIC component (RefSeq)||85, 117|
|BSU27060||levE||phosphotransferase system (PTS) fructose-specific enzyme IIB component (RefSeq)||85, 117|
|BSU27070||levD||phosphotransferase system (PTS) fructose-specific enzyme IIA component (RefSeq)||85, 329|
|BSU29630||yttP||putative transcriptional regulator (RefSeq)||12, 141|
|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|
|BSU39060||citH||secondary transporter of divalent metal ions/citrate complexes (RefSeq)||141, 278|
|BSU39260||bglH||aryl-phospho-beta-d-glucosidase (RefSeq)||141, 330|
|BSU39270||bglP||phosphotransferase system (PTS) beta-glucoside-specific enzyme IIBCA component (RefSeq)||141, 330|
|BSU39350||hutH||histidine ammonia-lyase (RefSeq)||85, 326|
|BSU39360||hutU||urocanate hydratase (RefSeq)||85, 326|
|BSU39370||hutI||imidazolonepropionase (RefSeq)||85, 326|
|BSU39380||hutG||formimidoylglutamase (RefSeq)||85, 326|
|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.
Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
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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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