Organism : Clostridium acetobutylicum | Module List :
Predicted transcriptional regulator (HTH winged helix type) (NCBI ptt file)
Functional Annotations (2)
|Predicted transcriptional regulator||cog/ cog|
Regulation information for CAC1675(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 CAC1675
|Predicted transcriptional regulator||cog/ cog|
Module neighborhood information for CAC1675
|Gene||Common Name||Description||Module membership|
|CAC0076||CAC0076||Predicted permease (NCBI ptt file)||31, 262|
|CAC0162||CAC0162||Transcriptional regulator MarR/EmrR family (NCBI ptt file)||83, 276|
|CAC0310||abrB||Regulators of stationary/sporulation gene expression, abrB B.subtilis ortholog (NCBI ptt file)||31, 303|
|CAC0394||kdgA||Deoxyphosphogluconate aldolase (gene kdgA) (NCBI ptt file)||83, 326|
|CAC0548||CAC0548||Predicted metal-dependent hydrolase (NCBI ptt file)||27, 31|
|CAC0560||CAC0560||Integral membrane protein similar to antibiotic resistance protein B.subtilis (NCBI ptt file)||83, 165|
|CAC0594||CAC0594||Predicted phosphate-utilizing enzyme involved in pyridoxine/purine/histidine biosynthesis (NCBI ptt file)||83, 266|
|CAC0595||CAC0595||Glutamine amidotranspherase (possibly involved in histidine and purine biosinthesis) (NCBI ptt file)||83, 291|
|CAC0669||CAC0669||Hypothetical protein (NCBI ptt file)||83, 266|
|CAC0718||CAC0718||Ortholog ycnD B.subtilis, nitroreductase (NCBI ptt file)||83, 326|
|CAC0745||CAC0745||Transcriptional regulator, LysR family (NCBI ptt file)||71, 83|
|CAC0869||CAC0869||Thioredoxine reductase (NCBI ptt file)||31, 209|
|CAC1029||CAC1029||FeoA-like protein, involved in iron transport (NCBI ptt file)||83, 214|
|CAC1030||CAC1030||FeoA-like protein, involved in iron transport (NCBI ptt file)||83, 266|
|CAC1031||feoB||FeoB-like GTPase, responsible for iron uptake (NCBI ptt file)||80, 83|
|CAC1032||CAC1032||Predicted transcriptional regulator (NCBI ptt file)||83, 214|
|CAC1050||nadE||NH(3)-dependent NAD(+) synthetase (NCBI ptt file)||31, 276|
|CAC1063||CAC1063||TPR-repeat-containing protein (NCBI ptt file)||31, 182|
|CAC1262||CAC1262||Predicted nucleotidyltransferases of NarD/TagD family (N-term. domain) , yqeJ ortholog (NCBI ptt file)||31, 238|
|CAC1325||CAC1325||Uncharacterized conserved protein, YitT (B.subtilis) family (NCBI ptt file)||27, 31|
|CAC1478||rpsD||Ribosomal protein S4 (NCBI ptt file)||83, 214|
|CAC1549||bsaA||Glutathione peroxidase (NCBI ptt file)||83, 266|
|CAC1603||CAC1603||Diverged enzyme related to 2'-5' RNA ligase, ortholog YJCG B.subtilis (NCBI ptt file)||70, 83|
|CAC1675||CAC1675||Predicted transcriptional regulator (HTH winged helix type) (NCBI ptt file)||31, 83|
|CAC1764||CAC1764||Predicted glutamine amidotransferase (NCBI ptt file)||31, 209|
|CAC2070||CAC2070||Hypothetical protein (NCBI ptt file)||31, 162|
|CAC2637||lonA||ATP-dependent Lon protease (NCBI ptt file)||31, 182|
|CAC2659||CAC2659||Putative stress-responsive transcriptional regulator PspC (NCBI ptt file)||31, 162|
|CAC2684||CAC2684||Sugar kinase, ribokinase family (NCBI ptt file)||83, 326|
|CAC2738||CAC2738||Uncharacterized conserved protein (NCBI ptt file)||31, 262|
|CAC2778||CAC2778||Rubredoxin (NCBI ptt file)||31, 259|
|CAC3028||CAC3028||Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file)||31, 206|
|CAC3073||CAC3073||Sugar transferase involved in lipopolysaccharide synthesis (NCBI ptt file)||25, 31|
|CAC3233||CAC3233||Uncharacterized conserved protein, YITC B.subtilis ortholog (NCBI ptt file)||31, 182|
|CAC3289||CAC3289||Iron-regulated ABC-type transporter membrane component (SufB) (NCBI ptt file)||31, 182|
|CAC3338||CAC3338||Predicted transcriptional regulator (NCBI ptt file)||31, 182|
|CAC3387||CAC3387||Pectate lyase (NCBI ptt file)||83, 261|
|CAC3503||CAC3503||Nucleoside-diphosphate-sugar epimerase (NCBI ptt file)||83, 240|
|CAC3556||CAC3556||Probable S-layer protein (NCBI ptt file)||31, 93|
|CAC3580||CAC3580||Dioxygenase related to 2-nitropropane dioxygenase (NCBI ptt file)||31, 276|
|CAC3607||CAC3607||Possible ketopantoate reductase PanE/ApbA (NCBI ptt file)||83, 216|
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.
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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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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- 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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