Organism : Clostridium acetobutylicum | Module List :
Intracellular protease/amidase related enzyme (ThiJ family) (NCBI ptt file)
Functional Annotations (1)
|Putative intracellular protease/amidase||cog/ cog|
Regulation information for CAC2826(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|
Functional Enrichment for CAC2826
|Putative intracellular protease/amidase||cog/ cog|
Module neighborhood information for CAC2826
|Gene||Common Name||Description||Module membership|
|CAC0012||CAC0012||Predicted dehydrogenase with iron-sulfur domain (NCBI ptt file)||86, 328|
|CAC0053||CAC0053||Hypothetical protein (NCBI ptt file)||70, 86|
|CAC0081||agrA||Accessory gene regulator protein A (NCBI ptt file)||53, 86|
|CAC0199||CAC0199||Hypothetical protein (NCBI ptt file)||86, 244|
|CAC0207||CAC0207||Hypothetical protein, CF-6 family (NCBI ptt file)||63, 273|
|CAC0309||CAC0309||Cell wall-associated hydrolase (NCBI ptt file)||4, 86|
|CAC0422||licT||Transcriptional antiterminator licT (NCBI ptt file)||86, 328|
|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|
|CAC0761||CAC0761||Predicted membrane protein (NCBI ptt file)||66, 86|
|CAC0947||CAC0947||Predicted membrane protein, hemolysin III homolog (NCBI ptt file)||38, 273|
|CAC1199||CAC1199||Hypothetical protein (NCBI ptt file)||86, 123|
|CAC1237||CAC1237||Hypothetical protein (NCBI ptt file)||86, 313|
|CAC1320||glpP||Glycerol-3-phosphate responsive antiterminator (mRNA-binding), GLPP (NCBI ptt file)||4, 86|
|CAC1406||CAC1406||Transcriptional antiterminator (BglG family) (NCBI ptt file)||86, 133|
|CAC1460||CAC1460||PTS system, fructose(mannose)-specific IID (NCBI ptt file)||86, 136|
|CAC1488||CAC1488||Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file)||63, 273|
|CAC1656||CAC1656||Hypothetical protein, CF-39 family (NCBI ptt file)||114, 273|
|CAC1835||miaA||TRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file)||159, 273|
|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|
|CAC2079||CAC2079||Hypothetical protein (NCBI ptt file)||86, 272|
|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|
|CAC2291||CAC2291||Hypothetical protein (NCBI ptt file)||86, 102|
|CAC2331||CAC2331||DTDP-4-dehydrorhamnose 3,5-epimerase (NCBI ptt file)||86, 211|
|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|
|CAC2469||CAC2469||Lactoylglutathione lyase (fragment) (NCBI ptt file)||78, 86|
|CAC2494||CAC2494||Predicted membrane protein (NCBI ptt file)||53, 86|
|CAC2631||CAC2631||Uncharacterized protein, ErfK family (NCBI ptt file)||159, 273|
|CAC2690||CAC2690||Transcriptional regulator, LysR family (NCBI ptt file)||86, 137|
|CAC2706||CAC2706||Uncharacterized conserved membrane protein, DedA family (NCBI ptt file)||53, 273|
|CAC2826||CAC2826||Intracellular protease/amidase related enzyme (ThiJ family) (NCBI ptt file)||86, 273|
|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|
|CAC3033||CAC3033||Uncharacterized protein containing conserved domain, related to YABE B.subtilis C-terminal domain (NCBI ptt file)||86, 233|
|CAC3186||CAC3186||Hypothetical protein (NCBI ptt file)||95, 273|
|CAC3202||ftsH||ATP-dependent Zn protease, FTSH (NCBI ptt file)||273, 292|
|CAC3213||CAC3213||Possible stage V sporulation protein B, predicted transporter (NCBI ptt file)||86, 118|
|CAC3226||CAC3226||Predicted membrane protein (NCBI ptt file)||86, 341|
|CAC3280||CAC3280||Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file)||4, 86|
|CAC3286||CAC3286||Chey-like receiver domain containing protein, YCBB B.subtilis ortholog (NCBI ptt file)||86, 328|
|CAC3313||CAC3313||Acyl carrier protein, ACP (NCBI ptt file)||86, 341|
|CAC3359||CAC3359||Nitroreductase family protein fused to ferredoxin domain (NCBI ptt file)||86, 266|
|CAC3395||CAC3395||Predicted membrane protein (NCBI ptt file)||57, 86|
|CAC3602||CAC3602||HD superfamily hydrolase (NCBI ptt file)||86, 109|
|CAC3661||CAC3661||Glycosyltransferase (NCBI ptt file)||210, 273|
|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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Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
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Module Members Tab
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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