Organism : Clostridium acetobutylicum | Module List :
ABC-type MDR transport system, permease component (NCBI ptt file)
Functional Annotations (1)
|ABC-type multidrug transport system, permease component||cog/ cog|
Regulation information for CAC3610(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 CAC3610
|ABC-type multidrug transport system, permease component||cog/ cog|
Module neighborhood information for CAC3610
|Gene||Common Name||Description||Module membership|
|CAC0071||CAC0071||Uncharacterized conserved protein, YTFE E.coli ortholog (NCBI ptt file)||24, 108|
|CAC0075||CAC0075||Ferredoxin (NCBI ptt file)||69, 150|
|CAC0124||CAC0124||Hypothetical protein (NCBI ptt file)||108, 150|
|CAC0133||CAC0133||Hypothetical protein, CF-4 family (NCBI ptt file)||150, 300|
|CAC0202||CAC0202||Hydrolase of the alpha/beta superfamily (NCBI ptt file)||24, 288|
|CAC0203||CAC0203||Flavodoxin (NCBI ptt file)||24, 288|
|CAC0206||CAC0206||Uncharacterized conserved membrane protein (NCBI ptt file)||98, 150|
|CAC0326||CAC0326||ATPase related to the helicase subunit of Holliday junction resolvase (NCBI ptt file)||24, 89|
|CAC0577||CAC0577||Endo-arabinase related enzyme (family 43 glycosyl hydrolase domain and ricin B-like domain) (NCBI ptt file)||150, 216|
|CAC0598||gerKC||Spore germination protein, gerKC (NCBI ptt file)||24, 145|
|CAC0625||CAC0625||Possible periplasmic aspartyl protease (NCBI ptt file)||24, 266|
|CAC0719||CAC0719||Epoxide hydrolase, similar to eukaryotic (NCBI ptt file)||150, 356|
|CAC0741||CAC0741||Methyl-accepting chemotaxis protein (NCBI ptt file)||24, 285|
|CAC0805||CAC0805||Methyl-accepting chemotaxis protein (NCBI ptt file)||24, 207|
|CAC0813||CAC0813||Hypothetical protein (NCBI ptt file)||123, 150|
|CAC0921||CAC0921||Metal-dependent amidohydrolase (NCBI ptt file)||24, 108|
|CAC0955||CAC0955||ATP-dependent Zn protease (NCBI ptt file)||150, 190|
|CAC1332||uxuA||D-mannonate hydrolase (NCBI ptt file)||150, 169|
|CAC1351||CAC1351||Periplasmic sugar-binding protein (NCBI ptt file)||24, 267|
|CAC1359||CAC1359||Predicted xylanase/chitin deacetylase (NCBI ptt file)||150, 190|
|CAC1458||CAC1458||PTS system, fructose(mannose)-specific IIB (NCBI ptt file)||136, 150|
|CAC1521||CAC1521||Uncharacterized membrane protein, yetF/ydfS/ykjA/yrbG/ydfR B.subtilis ortholog (NCBI ptt file)||150, 208|
|CAC1536||CAC1536||Transcriptional regulator, AcrR family (NCBI ptt file)||150, 165|
|CAC2528||CAC2528||Multimeric flavodoxin WrbA fused to cytochrome c-like domain (NCBI ptt file)||7, 24|
|CAC2583||CAC2583||Uncharacterized conserved membrane protein, YHGE B.subtilis homolog (NCBI ptt file)||150, 300|
|CAC2587||CAC2587||GGDEF domain containing protein (NCBI ptt file)||150, 169|
|CAC2588||CAC2588||Glycosyltransferase (NCBI ptt file)||150, 169|
|CAC2592||CAC2592||6-pyruvoyl-tetrahydropterin synthase related domain; conserved membrane protein (NCBI ptt file)||24, 240|
|CAC2596||CAC2596||Rieske FeS-domain containing oxidoreductase (NCBI ptt file)||65, 150|
|CAC2691||CAC2691||D-lactate dehydrogenase (NCBI ptt file)||150, 338|
|CAC2761||CAC2761||Thiamine biosynthesis lipoprotein ApbE (NCBI ptt file)||150, 183|
|CAC2762||CAC2762||Polyferredoxin (NCBI ptt file)||26, 150|
|CAC2812||CAC2812||Hypothetical protein (NCBI ptt file)||24, 115|
|CAC2898||spoIIR||Stage II sporulation protein R (NCBI ptt file)||24, 179|
|CAC2919||CAC2919||Hypothetical protein (NCBI ptt file)||24, 73|
|CAC3240||CAC3240||Predicted membrane protein (NCBI ptt file)||13, 150|
|CAC3241||CAC3241||Uncharacterized conserved membrane protein, YYAD B.subtilis ortholog (NCBI ptt file)||150, 301|
|CAC3301||gerKB||Spore germination protein GerKB, membrane protein (NCBI ptt file)||24, 240|
|CAC3324||CAC3324||Predicted transcriptional regulator (NCBI ptt file)||24, 227|
|CAC3329||CAC3329||Putative Mn transporter, NRAMP family (NCBI ptt file)||24, 40|
|CAC3331||CAC3331||Alanine racemase (NCBI ptt file)||24, 353|
|CAC3332||CAC3332||Predicted amidohydrolase (dihydroorothase family) (NCBI ptt file)||150, 360|
|CAC3346||CAC3346||MDR-type permease (NCBI ptt file)||4, 150|
|CAC3361||CAC3361||Transcriptional regulator, LysR family (NCBI ptt file)||150, 240|
|CAC3370||CAC3370||Predicted transcriptional regulator (NCBI ptt file)||150, 240|
|CAC3433||CAC3433||Transcriptional regulators, AcrR family (NCBI ptt file)||150, 344|
|CAC3549||CAC3549||Subtilisin-like serine protease (NCBI ptt file)||150, 190|
|CAC3609||CAC3609||ABC-type MDR transport system, permease component (NCBI ptt file)||26, 150|
|CAC3610||CAC3610||ABC-type MDR transport system, permease component (NCBI ptt file)||24, 150|
|CAC3697||CAC3697||Uncharacterized, Zn-finger domain containing protein, YXKC B.subtilis homolog (NCBI ptt file)||123, 150|
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.
- 2. Source gene
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