Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC1656(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 CAC1656
|Gene||Common Name||Description||Module membership|
|CAC0138||CAC0138||ABC transporter, ATP-binding component (NCBI ptt file)||36, 114|
|CAC0139||CAC0139||Predicted permease (NCBI ptt file)||36, 114|
|CAC0140||CAC0140||Predicted permease (NCBI ptt file)||67, 114|
|CAC0141||CAC0141||Membrane permease, predicted cation efflux pumps (NCBI ptt file)||36, 114|
|CAC0207||CAC0207||Hypothetical protein, CF-6 family (NCBI ptt file)||63, 273|
|CAC0672||CAC0672||Fision threonyl-tRNA synthetase (N-terminal part) and uridine kinase (NCBI ptt file)||64, 273|
|CAC0673||CAC0673||L-serine dehydratase, beta chain (NCBI ptt file)||64, 273|
|CAC0947||CAC0947||Predicted membrane protein, hemolysin III homolog (NCBI ptt file)||38, 273|
|CAC0970||CAC0970||Isopropylmalate synthase (NCBI ptt file)||114, 127|
|CAC0971||citB||Aconitase A (NCBI ptt file)||114, 127|
|CAC0972||citC||Isocitrate dehydrogenase (NCBI ptt file)||114, 127|
|CAC1336||CAC1336||Hypothetical protein (NCBI ptt file)||114, 127|
|CAC1337||CAC1337||Spore coat protein COTJB (NCBI ptt file)||114, 127|
|CAC1338||CAC1338||Spore coat protein COTJC (NCBI ptt file)||114, 127|
|CAC1469||CAC1469||Iron-dependent transcription repressor (NCBI ptt file)||114, 127|
|CAC1488||CAC1488||Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file)||63, 273|
|CAC1572||CAC1572||Fructose-1,6-bisphosphatase (YYDE B.subtils ortholog) (NCBI ptt file)||100, 114|
|CAC1633||CAC1633||Protein from bacterioferritin family (NCBI ptt file)||114, 127|
|CAC1656||CAC1656||Hypothetical protein, CF-39 family (NCBI ptt file)||114, 273|
|CAC1835||miaA||TRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file)||159, 273|
|CAC1866||CAC1866||Putative 4-Cys ferredoxin (NCBI ptt file)||114, 127|
|CAC2038||CAC2038||Hypothetical protein, CF-23 family (NCBI ptt file)||273, 312|
|CAC2072||CAC2072||Stage IV sporulation protein B, SpoIVB (NCBI ptt file)||63, 273|
|CAC2085||CAC2085||Uncharacterized protein from alkaline shock protein family, YQHY B.subtilis ortholog (NCBI ptt file)||64, 273|
|CAC2141||CAC2141||Hypothetical protein (NCBI ptt file)||57, 273|
|CAC2230||CAC2230||Uncharacterized protein of PR1 family, YkwD B.subtilis ortholog (NCBI ptt file)||63, 273|
|CAC2243||asnB||N-terminal domain of asparagine synthase (NCBI ptt file)||100, 114|
|CAC2249||CAC2249||C-terminal domain of asparagine synthase (NCBI ptt file)||114, 300|
|CAC2422||CAC2422||Oxygen-independent coproporphyrinogen III oxidase, Fe-S oxidoreductase (NCBI ptt file)||273, 298|
|CAC2461||CAC2461||Hypothetical protein, CF-13 family (NCBI ptt file)||264, 273|
|CAC2462||CAC2462||Hypothetical protein, CF-13 family (NCBI ptt file)||264, 273|
|CAC2631||CAC2631||Uncharacterized protein, ErfK family (NCBI ptt file)||159, 273|
|CAC2706||CAC2706||Uncharacterized conserved membrane protein, DedA family (NCBI ptt file)||53, 273|
|CAC2747||CAC2747||Protein containing LysM repeats (N-terminal domain) and domain related to chitinase (NCBI ptt file)||114, 127|
|CAC2797||CAC2797||Hypothetical protein (NCBI ptt file)||114, 127|
|CAC2826||CAC2826||Intracellular protease/amidase related enzyme (ThiJ family) (NCBI ptt file)||86, 273|
|CAC2909||CAC2909||Spore coat protein cotS related (diverged) (NCBI ptt file)||114, 190|
|CAC2968||CAC2968||Mannose-1-phosphate guanylyltransferase (NCBI ptt file)||114, 127|
|CAC2974||CAC2974||Predicted protease from collagenase family (NCBI ptt file)||210, 273|
|CAC2987||CAC2987||Primase-like protein, containing TOPRIM domain, YABF B.subtilis ortholog (NCBI ptt file)||57, 273|
|CAC3018||CAC3018||Rubrerythrin (NCBI ptt file)||114, 127|
|CAC3078||CAC3078||Uncharacterized secreted protein, YBBR Bacillus subtilis homolog (NCBI ptt file)||114, 142|
|CAC3186||CAC3186||Hypothetical protein (NCBI ptt file)||95, 273|
|CAC3202||ftsH||ATP-dependent Zn protease, FTSH (NCBI ptt file)||273, 292|
|CAC3661||CAC3661||Glycosyltransferase (NCBI ptt file)||210, 273|
|CAC3674||CAC3674||Two CBS domain containing protein (NCBI ptt file)||114, 300|
|CAC3716||lonB||Lon-like ATP-dependent protease (NCBI ptt file)||36, 114|
|CAC3717||rplI||Ribosomal protein L9 (NCBI ptt file)||114, 243|
|CAC3720||CAC3720||Hypothetical protein (NCBI ptt file)||273, 298|
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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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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