Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC2643(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 CAC2643
|Gene||Common Name||Description||Module membership|
|CAC0285||CAC0285||DNA-damage repair protein, dinP/uvrX ortholog (NCBI ptt file)||271, 314|
|CAC0301||CAC0301||Signal peptidase II (PSP1) homolog, YAAT B.subtilis ortholog (NCBI ptt file)||36, 271|
|CAC0367||rocB||Arginine degradation protein (gene rocB) (NCBI ptt file)||256, 271|
|CAC0368||CAC0368||4 animobutyrate aminotransferase (NCBI ptt file)||172, 271|
|CAC0472||dnaK||DnaK protein (heat shock protein), HSP70/DnaK family (NCBI ptt file)||14, 271|
|CAC0821||CAC0821||Transcriptional regulator (TetR/AcrR family) (NCBI ptt file)||14, 271|
|CAC0822||CAC0822||ABC transporter, ATP-binding protein (NCBI ptt file)||234, 271|
|CAC0823||CAC0823||Predicted membrane protein (NCBI ptt file)||14, 271|
|CAC1089||CAC1089||Serine kinase/phosphatase HPr (NCBI ptt file)||26, 159|
|CAC1090||CAC1090||5-formyltetrahydrofolate cyclo-ligase (NCBI ptt file)||159, 229|
|CAC1091||CAC1091||Aspartyl aminopeptidase (NCBI ptt file)||159, 234|
|CAC1300||sigA||RNA polymerase sigma factor RPOD (NCBI ptt file)||159, 256|
|CAC1303||CAC1303||Uncharacterized protein of YbgI/Acr family (NCBI ptt file)||10, 159|
|CAC1429||galE||UDP-glucose 4-epimerase (NCBI ptt file)||271, 329|
|CAC1715||CAC1715||PLP-dependent aminotransferase (NCBI ptt file)||159, 234|
|CAC1722||def||N-formylmethionyl-tRNA deformylase (NCBI ptt file)||6, 159|
|CAC1723||fmt||Methionyl-tRNA formyltransferase (NCBI ptt file)||159, 329|
|CAC1724||CAC1724||Predicted metal-dependent peptidase (NCBI ptt file)||159, 329|
|CAC1725||CAC1725||Predicted rRNA methylase, SUN family (NCBI ptt file)||159, 315|
|CAC1727||CAC1727||Protein serine/threonine phosphatases, PP2C family (YLOO B.subtilis ortholog) (NCBI ptt file)||6, 271|
|CAC1748||rncS||DsRNA-specific ribonuclease III (NCBI ptt file)||271, 335|
|CAC1828||CAC1828||TldD protein fragment (NCBI ptt file)||159, 172|
|CAC1835||miaA||TRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file)||159, 273|
|CAC1836||mutL||DNA mismatch repair enzyme, MutL (NCBI ptt file)||36, 159|
|CAC1837||mutS||Mismatch repair protein MutS, ATPase (NCBI ptt file)||159, 172|
|CAC1838||CAC1838||Predicted Fe-S oxidoreductase, YMCB B.subtilis ortholog (NCBI ptt file)||36, 159|
|CAC1953||CAC1953||Predicted membrane protein (NCBI ptt file)||271, 331|
|CAC2077||CAC2077||Deoxyxylulose-5-phosphate synthase (NCBI ptt file)||159, 229|
|CAC2081||xseB||Exonuclease VII small subunit (NCBI ptt file)||159, 310|
|CAC2262||addA||ATP-dependent exonuclease (exonuclease V) synthesis protein AddA (helicase and exonuclease domains) (NCBI ptt file)||14, 159|
|CAC2263||addB||ATP-dependent exonuclease synthesis protein AddB (superfamily I helicase) (NCBI ptt file)||159, 314|
|CAC2344||CAC2344||LPS biosynthesis protein , RfbU family (NCBI ptt file)||137, 159|
|CAC2435||CAC2435||Response regulator (CheY-like domain and HTH-type DNA-binding domain) (NCBI ptt file)||243, 271|
|CAC2436||CAC2436||Uncharacterized conserved membrane protein (NCBI ptt file)||44, 271|
|CAC2579||CAC2579||Uncharacterized conserved membrane protein (NCBI ptt file)||159, 163|
|CAC2631||CAC2631||Uncharacterized protein, ErfK family (NCBI ptt file)||159, 273|
|CAC2642||CAC2642||Predicted endonuclease (NCBI ptt file)||159, 352|
|CAC2643||CAC2643||Hypothetical protein (NCBI ptt file)||159, 271|
|CAC2703||groEL||Chaperonin GroEL, HSP60 family (NCBI ptt file)||204, 271|
|CAC2704||groES||Co-chaperonin GroES, HSP10 family (NCBI ptt file)||204, 271|
|CAC2726||CAC2726||Uncharacterized protein, possible ynzC B.subtilis homolog (NCBI ptt file)||159, 298|
|CAC3188||sms||Predicted ATP-dependent serine protease, RADA homolog (NCBI ptt file)||36, 271|
|CAC3218||CAC3218||Periplasmic trypsin-like serine protease (with PDZ domain), HtrA subfamily (NCBI ptt file)||81, 271|
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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If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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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.
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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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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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