Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC2511(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 CAC2511
|Gene||Common Name||Description||Module membership|
|CAC0004||recF||RecF, ABC family ATPase (NCBI ptt file)||26, 272|
|CAC0181||CAC0181||Similar to beta-lactamase (NCBI ptt file)||314, 320|
|CAC0182||CAC0182||Beta-glucosidase homolog (NCBI ptt file)||236, 320|
|CAC0214||CAC0214||Endoglucanase, aminopeptidase M42 family (NCBI ptt file)||22, 320|
|CAC0253||nifH||Nitrogenase iron protein (nitrogenase component II) gene nifH (NCBI ptt file)||98, 320|
|CAC0328||CAC0328||Predicted metal-dependent hydrolase (NCBI ptt file)||72, 272|
|CAC0436||CAC0436||Predicted xylanase/chitin deacetilase, similar to yxkH B.subtilis (NCBI ptt file)||320, 353|
|CAC0514||CAC0514||CBS domain, similar to B.subtilis ytoI (NCBI ptt file)||64, 272|
|CAC0707||rpoN||RNA polymerase sigma-54 factor (NCBI ptt file)||170, 272|
|CAC0794||CAC0794||Nucleoside-diphosphate-sugar epimerase (UDP-glucose 4-epimerase) (NCBI ptt file)||98, 320|
|CAC0832||CAC0832||Fusion: transcriptional regulator and conserved domain (NCBI ptt file)||38, 320|
|CAC1087||CAC1087||Hypothetical protein (NCBI ptt file)||139, 272|
|CAC1094||CAC1094||Cation efflux system protein (NCBI ptt file)||208, 320|
|CAC1134||CAC1134||Phage related protein, YonF B.subtilis homolog (NCBI ptt file)||195, 272|
|CAC1137||CAC1137||Hypothetical protein (NCBI ptt file)||30, 272|
|CAC1321||glpK||Glycerol kinase, GLPK (NCBI ptt file)||272, 342|
|CAC1414||CAC1414||TerE family protein, ortholog of stress responce protein SCP2 (YCEC) B.subtilis (NCBI ptt file)||272, 298|
|CAC1418||CAC1418||Nitroreductase family protein (NCBI ptt file)||57, 272|
|CAC1462||CAC1462||Levanase/invertase (NCBI ptt file)||98, 320|
|CAC1477||CAC1477||Hypothetical protein (NCBI ptt file)||272, 301|
|CAC1512||nirC||Formate/nitrite family of transporter (NCBI ptt file)||240, 320|
|CAC1550||CAC1550||Methionine sulfoxide reductase C-terminal domain related protein, YPPQ ortholog (NCBI ptt file)||179, 320|
|CAC1647||CAC1647||Hypothetical protein (NCBI ptt file)||244, 320|
|CAC1849||CAC1849||Predicted flavoprotein, YhiN family (NCBI ptt file)||64, 272|
|CAC1947||CAC1947||Phage related transcriptional regulator (Xre family) (NCBI ptt file)||270, 272|
|CAC2079||CAC2079||Hypothetical protein (NCBI ptt file)||86, 272|
|CAC2099||CAC2099||Hypothetical protein (NCBI ptt file)||270, 320|
|CAC2103||CAC2103||General secretion pathway protein, pilin family (NCBI ptt file)||54, 320|
|CAC2105||CAC2105||General secretion pathway protein E, ATPase (NCBI ptt file)||256, 320|
|CAC2474||def||N-formylmethionyl-tRNA deformylase (NCBI ptt file)||57, 272|
|CAC2511||CAC2511||Predicted membrane protein (NCBI ptt file)||272, 320|
|CAC2516||CAC2516||Hypothetical protein (NCBI ptt file)||89, 320|
|CAC2569||CAC2569||NimC/NimA family protein (NCBI ptt file)||279, 320|
|CAC2609||CAC2609||Cytidine deaminase family enzyme (NCBI ptt file)||270, 320|
|CAC2805||CAC2805||Possible selenocysteine lyase (aminotransferase of NifS family) (NCBI ptt file)||148, 272|
|CAC3045||CAC3045||CPSB/CAPC ortholog, PHP family hydrolase (NCBI ptt file)||272, 333|
|CAC3275||CAC3275||Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file)||22, 320|
|CAC3337||CAC3337||Predicted amidohodrolase (dihydroorotase family) (NCBI ptt file)||320, 347|
|CAC3439||CAC3439||Uncharacterized conserved membrane protein, YGAE B.subtilis homolog (NCBI ptt file)||144, 320|
|CAC3475||CAC3475||Transcriptional regulator, merR family (NCBI ptt file)||14, 320|
|CAC3543||CAC3543||Predicted membrane protein (NCBI ptt file)||265, 320|
|CAC3654||CAC3654||Heavy-metal binding protein (similar to N-terminal domain of MerA) (NCBI ptt file)||73, 320|
|CAC3658||CAC3658||Uncharacterized conserved membrane protein, SapB/MtgC family (NCBI ptt file)||41, 272|
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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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;
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