Organism : Clostridium acetobutylicum | Module List :
Heavy-metal-associated domain (N-terminus) and membrane-bounded cytochrome biogenesis cycZ-like domain, possible membrane copper tolerance protein (NCBI ptt file)
Functional Annotations (3)
|Uncharacterized protein conserved in bacteria||cog/ cog|
|metal ion transport||go/ biological_process|
|metal ion binding||go/ molecular_function|
Regulation information for CAC1554(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 CAC1554
Module neighborhood information for CAC1554
|Gene||Common Name||Description||Module membership|
|CAC0022||asd||Aspartate-semialdehyde dehydrogenase (NCBI ptt file)||176, 231|
|CAC0067||CAC0067||(FS) similar to ABC transporter (permease), YXDM B.subtilis ortholog (NCBI ptt file)||176, 246|
|CAC0087||CAC0087||Predicted Co/Zn/Cd cation transporter (NCBI ptt file)||182, 206|
|CAC0130||CAC0130||Uncharacterized membrane protein, YTAF B.subtilis ortholog (NCBI ptt file)||176, 341|
|CAC0274||ansB||Aspartate ammonia-lyase (aspartase) gene ansB(aspA) (NCBI ptt file)||206, 238|
|CAC0315||CAC0315||Predicted acetyltransferase (NCBI ptt file)||11, 206|
|CAC0321||CAC0321||Response regulator (CheY-like domain, HTH domain) (NCBI ptt file)||182, 206|
|CAC0550||CAC0550||Possible sigma factor (NCBI ptt file)||176, 253|
|CAC0558||CAC0558||Hypothetical protein (NCBI ptt file)||201, 206|
|CAC0691||CAC0691||Uncharacterized conserved protein, VanW of Enterococcus faecalis related (NCBI ptt file)||176, 253|
|CAC0693||CAC0693||Transcriptional regulator of the LacI family (NCBI ptt file)||176, 238|
|CAC0777||CAC0777||Acetyltransferase (the isoleucine patch superfamily) (NCBI ptt file)||176, 306|
|CAC0816||CAC0816||Lipase-esterase related protein (NCBI ptt file)||176, 209|
|CAC0856||CAC0856||Transcriptional regulator, LacI family (probably maltose operon transcriptional repressor) (NCBI ptt file)||72, 206|
|CAC0860||CAC0860||Two-component response regulator (NCBI ptt file)||185, 206|
|CAC0875||CAC0875||Predicted permease (NCBI ptt file)||206, 253|
|CAC0900||CAC0900||Possible Zn-finger containing protein (NCBI ptt file)||72, 206|
|CAC0920||CAC0920||Protein related to MIFH/DOPD protein family, function in bacteria is unknown (NCBI ptt file)||72, 206|
|CAC1037||CAC1037||Predicted xylanase/chitin deacetylase (NCBI ptt file)||206, 261|
|CAC1045||CAC1045||Predicted permease (NCBI ptt file)||80, 176|
|CAC1068||CAC1068||Hypothetical protein, CF-25 family (NCBI ptt file)||176, 267|
|CAC1215||CAC1215||Hypothetical protein (NCBI ptt file)||4, 176|
|CAC1249||minD||Septum site-determining protein MinD, ATPase (NCBI ptt file)||206, 244|
|CAC1312||CAC1312||Hypothetical protein (NCBI ptt file)||109, 176|
|CAC1434||CAC1434||Alkaline phosphatase superfamily protein (NCBI ptt file)||176, 276|
|CAC1554||CAC1554||Heavy-metal-associated domain (N-terminus) and membrane-bounded cytochrome biogenesis cycZ-like domain, possible membrane copper tolerance protein (NCBI ptt file)||176, 206|
|CAC1648||CAC1648||Hypothetical protein, CF-7 family (NCBI ptt file)||206, 240|
|CAC1984||CAC1984||Predicted permease (NCBI ptt file)||176, 183|
|CAC2069||CAC2069||Hypothetical protein (NCBI ptt file)||152, 176|
|CAC2505||CAC2505||Uncharacterized membrane protein, YXJN B.subtilis homolog (NCBI ptt file)||134, 176|
|CAC2742||CAC2742||Predicted membrane protein (NCBI ptt file)||206, 240|
|CAC2751||CAC2751||Predicted acetyltransferase (NCBI ptt file)||176, 253|
|CAC2755||CAC2755||MDR-type ABC transporter (membrane associated ATPase) (NCBI ptt file)||140, 176|
|CAC2756||CAC2756||MDR-type ABC transporter (membrane associated ATPase) (NCBI ptt file)||102, 176|
|CAC2765||CAC2765||Similar to uncharacterized domain of sensory transducer protein (NCBI ptt file)||176, 309|
|CAC2967||CAC2967||Alpha-acetolactate decarboxylase (NCBI ptt file)||152, 206|
|CAC2993||CAC2993||Uncharacterized protein, YceG B.subtilis homolog (NCBI ptt file)||146, 206|
|CAC3022||CAC3022||Alpha/beta superfamily hydrolase (NCBI ptt file)||146, 206|
|CAC3028||CAC3028||Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file)||31, 206|
|CAC3074||CAC3074||Uncharacterized conserved protein (NCBI ptt file)||72, 206|
|CAC3354||CAC3354||Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file)||206, 266|
|CAC3360||CAC3360||Transcriptional regulator, LysR family (NCBI ptt file)||176, 277|
|CAC3373||CAC3373||Pectin methylesterase (NCBI ptt file)||206, 314|
|CAC3386||CAC3386||Hypothetical protein (NCBI ptt file)||132, 176|
|CAC3414||CAC3414||ABC-type multidrug/protein/lipid transport system, ATPase component (NCBI ptt file)||176, 253|
|CAC3464||CAC3464||Uncharacterized conserved protein (fragment) (NCBI ptt file)||182, 206|
|CAC3484||CAC3484||Short-chain alcohol dehydrogenase family protein (NCBI ptt file)||206, 216|
|CAC3485||CAC3485||Transcriptional regulator, MarR/EmrR family (NCBI ptt file)||206, 313|
|CAC3502||CAC3502||Transcriptional regulator, fadR family (NCBI ptt file)||57, 206|
|CAC3568||accA||Acetyl-CoA carboxylase alpha subunit (NCBI ptt file)||32, 206|
|CAC3599||CAC3599||Hypothetical protein (NCBI ptt file)||4, 206|
|CAC3600||dapA||Dihydrodipicolinate synthase (NCBI ptt file)||176, 277|
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.
Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
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.
- 2. Source gene
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