Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC0050(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 CAC0050
|Gene||Common Name||Description||Module membership|
|CAC0036||CAC0036||Predicted membrane protein, containing FHA domain (NCBI ptt file)||102, 183|
|CAC0050||CAC0050||Hypothetical protein, CF-3 family K28 (NCBI ptt file)||183, 246|
|CAC0051||CAC0051||Hypothetical protein, CF-3 family (NCBI ptt file)||224, 246|
|CAC0067||CAC0067||(FS) similar to ABC transporter (permease), YXDM B.subtilis ortholog (NCBI ptt file)||176, 246|
|CAC0068||CAC0068||(FS) similar to ABC transporter (permease), YXDM B.subtilis ortholog (NCBI ptt file)||40, 246|
|CAC0186||CAC0186||Xre family DNA-binding domain and TPR-repeat-containing protein (NCBI ptt file)||68, 183|
|CAC0349||CAC0349||Predicted membrane protein (NCBI ptt file)||246, 351|
|CAC0484||CAC0484||Phosphomannomutase (NCBI ptt file)||40, 246|
|CAC0576||CAC0576||Hypothetical protein (NCBI ptt file)||115, 183|
|CAC0652||CAC0652||Uncharacterized conserved membrane protein, similar to MDR (VANZ) ORF of Enterococcus (NCBI ptt file)||246, 353|
|CAC0780||tyrZ||Tyrosyl-tRNA synthetase (NCBI ptt file)||246, 306|
|CAC0799||psd||Phosphatidylserine decarboxylase (NCBI ptt file)||183, 236|
|CAC0800||ubiA||4-hydroxybenzoate octaprenyltranferase related protein (NCBI ptt file)||183, 267|
|CAC0818||CAC0818||Diguanylate cyclase/phosphodiesterase domain (GGDEF) containing protein (NCBI ptt file)||183, 202|
|CAC1061||CAC1061||Uncharcterized protein, shares conserved domain among different RHS family proteins and WAPA of B.subtilis (NCBI ptt file)||183, 253|
|CAC1070||CAC1070||Transcriptional regulator, AcrR family (NCBI ptt file)||183, 282|
|CAC1167||CAC1167||Hypothetical protein (NCBI ptt file)||246, 351|
|CAC1188||CAC1188||Hypothetical protein (NCBI ptt file)||187, 246|
|CAC1213||CAC1213||Predicted membrane protein (NCBI ptt file)||246, 351|
|CAC1397||CAC1397||Predicted hydrolase of PHP superfamily (NCBI ptt file)||246, 306|
|CAC1400||CAC1400||ABC transporter, periplasmic binding component (NCBI ptt file)||246, 306|
|CAC1401||CAC1401||ABC transporter, ATPase component (NCBI ptt file)||246, 306|
|CAC1527||CAC1527||Spore germination protein GerKB (NCBI ptt file)||26, 183|
|CAC1589||malS||Malic enzyme (NCBI ptt file)||92, 183|
|CAC1704||CAC1704||Hypothetical protein (NCBI ptt file)||183, 336|
|CAC1779||CAC1779||Hypothetical protein (NCBI ptt file)||183, 282|
|CAC1780||CAC1780||Nicotinic acid phosphoribosyltransferase (NCBI ptt file)||246, 306|
|CAC1782||nadE||NH(3)-dependent NAD(+) synthase (nadE) fused to amidohydrolase domain (NCBI ptt file)||246, 306|
|CAC1920||CAC1920||Zn-finger containing protein (NCBI ptt file)||54, 246|
|CAC1922||CAC1922||Hypothetical protein (NCBI ptt file)||117, 246|
|CAC1984||CAC1984||Predicted permease (NCBI ptt file)||176, 183|
|CAC1986||CAC1986||Hypothetical protein (NCBI ptt file)||68, 183|
|CAC2051||CAC2051||Predicted membrane protein (NCBI ptt file)||246, 336|
|CAC2443||CAC2443||Iron (III) ABC transporter, ATPase component (NCBI ptt file)||183, 282|
|CAC2559||CAC2559||Hypothetical protein (NCBI ptt file)||183, 351|
|CAC2753||CAC2753||Possible MDR-type permease, YQJV B.subtilis ortholog (NCBI ptt file)||183, 336|
|CAC2761||CAC2761||Thiamine biosynthesis lipoprotein ApbE (NCBI ptt file)||150, 183|
|CAC3404||CAC3404||Uncharactecterized conserved membrane protein, possible ABC-type MDR permease (NCBI ptt file)||246, 351|
|CAC3526||CAC3526||FMN-binding protein (NCBI ptt file)||66, 183|
|CAC3573||fabF||3-oxoacyl-(acyl-carrier-protein) synthase I (NCBI ptt file)||68, 183|
|CAC3666||CAC3666||Membrane transporters of cations and cationic drugs (NCBI ptt file)||132, 246|
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;
- 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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