Organism : Bacillus subtilis | Module List :
Regulation information for BSU25920(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 BSU25920
|Gene||Common Name||Description||Module membership|
|BSU02380||ybgB||hypothetical protein (RefSeq)||206, 285|
|BSU02660||ycbU||putative cysteine desulfurase (RefSeq)||26, 371|
|BSU06990||yesQ||rhamnogalacturonan permease (RefSeq)||360, 371|
|BSU08280||yfiI||putative oxidoreductase (RefSeq)||360, 371|
|BSU08330||yfiN||putative ABC transporter (permease) (RefSeq)||175, 371|
|BSU10580||yhjO||hypothetical protein (RefSeq)||175, 371|
|BSU10590||yhjP||hypothetical protein (RefSeq)||130, 371|
|BSU10870||yisU||putative aminoacid related metabolite efflux transporter (RefSeq)||52, 206|
|BSU17740||ynzB||hypothetical protein (RefSeq)||39, 206|
|BSU23530||spoIIM||autolysin component for dissolution of the septal cell wall (stage II sporulation) (RefSeq)||206, 286|
|BSU25900||cwlA||N-acetylmuramoyl-L-alanine amidase; skin element (RefSeq)||44, 206|
|BSU25910||yqxH||putative holin; skin element (RefSeq)||44, 206|
|BSU25920||yqxG||putative phage-related lytic exoenzyme; skin element (RefSeq)||206, 371|
|BSU25930||yqcE||conserved hypothetical protein; skin element (RefSeq)||205, 206|
|BSU26140||yqbE||putative phage capsid protein; skin element (RefSeq)||206, 371|
|BSU26150||yqbD||putative DNA wielding protein; skin element (RefSeq)||129, 206|
|BSU26250||yqaN||putative Holliday junction resolvase; skin element (RefSeq)||52, 206|
|BSU26260||yqaM||hypothetical protein (RefSeq)||371, 372|
|BSU26270||yqaL||putative DNA-binding protein; skin element (RefSeq)||371, 372|
|BSU26280||yqaK||putative DNA recombination protein; skin element (RefSeq)||130, 371|
|BSU26290||yqaJ||putative nuclease; skin element (RefSeq)||130, 371|
|BSU26300||yqaI||hypothetical protein; skin element (RefSeq)||205, 371|
|BSU26310||yqaH||hypothetical protein; skin element (RefSeq)||88, 371|
|BSU26320||yqaG||putative transcriptional regulator; skin element (RefSeq)||88, 371|
|BSU26330||yqdA||hypothetical protein; skin element (RefSeq)||205, 206|
|BSU26340||yqaF||putative transcriptional regulator; skin element (RefSeq)||205, 206|
|BSU26840||sigZ||RNA polymerase sigma factor SigZ (RefSeq)||44, 206|
|BSU26850||yrpG||putative oxidoreductase (RefSeq)||206, 301|
|BSU29270||ytoI||hypothetical protein (RefSeq)||206, 404|
|BSU29320||ytnI||putative redoxin (RefSeq)||206, 333|
|BSU30090||yteU||putative membrane enzyme for rhamnogalaturonan degradation (RefSeq)||305, 371|
|BSU30100||yteT||putative dehydrogenase of rhamnogalaturonan degradation (RefSeq)||360, 371|
|BSU30110||yteS||putative lipoprotein required for rhamnogalaturonan degradation (RefSeq)||360, 371|
|BSU30120||yteR||unsaturated rhamnogalacturonyl hydrolase (RefSeq)||360, 371|
|BSU30150||ytdP||putative membrane bound transcriptional regulator (AraC/XylS family) (RefSeq)||26, 371|
|BSU31590||yufS||putative bacteriocin (RefSeq)||39, 206|
|BSU37280||narG||nitrate reductase (alpha subunit) (RefSeq)||371, 405|
|BSU37450||ywhK||factor interacting with DNA helicase PcrA (RefSeq)||108, 206|
|BSU38060||ywcJ||formate/nitrite transporter (RefSeq)||74, 206|
|BSU38820||yxkF||putative transcriptional regulator (RefSeq)||330, 371|
|BSU39040||yxiS||hypothetical protein (RefSeq)||47, 206|
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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