Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC1502(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 CAC1502
|Gene||Common Name||Description||Module membership|
|CAC0055||CAC0055||Uncharacterized predicted metal-binding protein, ortholog of Streptomyces (2808777) (NCBI ptt file)||71, 185|
|CAC0113||CAC0113||Transcriptional regulator of sugar metabolism (NCBI ptt file)||20, 346|
|CAC0235||CAC0235||Chloramphenicol acetyltransferase (NCBI ptt file)||140, 346|
|CAC0236||CAC0236||ABC-type multidrug transport system, ATP-ase component (NCBI ptt file)||140, 346|
|CAC0238||CAC0238||ABC transporter, permease component (NCBI ptt file)||259, 346|
|CAC0239||CAC0239||Histidine kinase-like ATPase (NCBI ptt file)||185, 346|
|CAC0371||CAC0371||Response regulator (CheY-like domain and HTH domain) (NCBI ptt file)||71, 287|
|CAC0400||CAC0400||Hypothetical protein, CF-19 family (NCBI ptt file)||91, 346|
|CAC0417||CAC0417||Similar to arsenate reductase (NCBI ptt file)||71, 185|
|CAC0536||dltE||Short-chain dehydrodenase (gene dltE) (NCBI ptt file)||71, 108|
|CAC0547||CAC0547||Lactoylglutation lyase (NCBI ptt file)||346, 366|
|CAC0600||CAC0600||Predicted membrane protein (NCBI ptt file)||10, 71|
|CAC0648||CAC0648||Molecular chaperone, DnaJ family (contain C-term. Zn finger domain) (NCBI ptt file)||149, 346|
|CAC0745||CAC0745||Transcriptional regulator, LysR family (NCBI ptt file)||71, 83|
|CAC0858||CAC0858||Phosphinothricin acetyltransferase (NCBI ptt file)||71, 216|
|CAC0968||CAC0968||Hypothetical protein (NCBI ptt file)||140, 346|
|CAC1040||CAC1040||Predicted amidohydrolases (NCBI ptt file)||185, 346|
|CAC1046||CAC1046||Transcriptional regulator, LysR family (NCBI ptt file)||71, 287|
|CAC1076||CAC1076||Hypothetical protein, CF-32 family (NCBI ptt file)||140, 346|
|CAC1419||CAC1419||Uncharacterized proteins, homologs of microcin C7 resistance protein MccF (NCBI ptt file)||283, 346|
|CAC1482||CAC1482||Uncharacterized membrane protein,ortholog of YDFK B.subtilis (NCBI ptt file)||158, 346|
|CAC1493||CAC1493||Zn-finger DNA-binding domain (NCBI ptt file)||71, 74|
|CAC1496||CAC1496||Uncharacterized protein, homolog of YCGL B.subtilis (NCBI ptt file)||71, 137|
|CAC1502||CAC1502||Hypothetical protein (NCBI ptt file)||71, 346|
|CAC1507||phoR||Sensory transduction histidine kinase (with HAMP domain) (NCBI ptt file)||205, 346|
|CAC1540||CAC1540||Uncharacterized ATP-grasp enzyme (NCBI ptt file)||71, 91|
|CAC1558||CAC1558||ABC-type transport system,membrane ATPase component (NCBI ptt file)||1, 346|
|CAC1577||CAC1577||Ncharacterized conserved protein (NCBI ptt file)||71, 239|
|CAC1618||CAC1618||Hypothetical protein (NCBI ptt file)||71, 132|
|CAC1619||CAC1619||Hypothetical protein (NCBI ptt file)||71, 259|
|CAC1621||CAC1621||Predicted Fe-S oxidoreductase (NCBI ptt file)||71, 261|
|CAC1852||CAC1852||Magnesium and cobalt transport protein (NCBI ptt file)||106, 346|
|CAC1962||CAC1962||Predicted esterase of alpha/beta hydrolase superfamily, YBBA B.subtilis ortholog (NCBI ptt file)||71, 72|
|CAC2174||CAC2174||Glycosyltransferase (NCBI ptt file)||82, 346|
|CAC2453||CAC2453||CBS domain containing protein (NCBI ptt file)||13, 346|
|CAC2520||CAC2520||Multimeric flavodoxin (WrbA) domain containing protein (NCBI ptt file)||49, 71|
|CAC2554||CAC2554||Hypothetical protein (NCBI ptt file)||13, 346|
|CAC2568||CAC2568||Predicted transcriptional regulator (NCBI ptt file)||71, 223|
|CAC2661||ftsX||Cell division protein FtsX (NCBI ptt file)||72, 346|
|CAC2696||CAC2696||Predicted membrane protein (NCBI ptt file)||117, 346|
|CAC2734||CAC2734||ABC-type multidrug transport system, ATPase component (NCBI ptt file)||71, 98|
|CAC2759||CAC2759||Response regulator (CheY receiver domain and HTH-type DNA-binding domain) (NCBI ptt file)||71, 185|
|CAC2930||CAC2930||Uncharacterized conserved membrane protein (NCBI ptt file)||71, 223|
|CAC2931||CAC2931||Uncharacterized conserved membrane protein (NCBI ptt file)||71, 223|
|CAC2962||CAC2962||Transcriptional regulators of the LacI family (NCBI ptt file)||261, 346|
|CAC3303||CAC3303||Superfamily II DNA/RNA helicases, SNF2 family (NCBI ptt file)||71, 294|
|CAC3364||CAC3364||Barstar-like protein, ribonuclease (barnase) inhibitor (NCBI ptt file)||92, 346|
|CAC3529||CAC3529||Hypothetical protein (NCBI ptt file)||71, 259|
|CAC3530||CAC3530||Hypothetical protein (NCBI ptt file)||71, 259|
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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