Organism : Clostridium acetobutylicum | Module List :
ABC transporter, permease component (NCBI ptt file)
Functional Annotations (1)
|ABC-type multidrug transport system, permease component||cog/ cog|
Regulation information for CAC0237(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 CAC0237
|ABC-type multidrug transport system, permease component||cog/ cog|
Module neighborhood information for CAC0237
|Gene||Common Name||Description||Module membership|
|CAC0111||CAC0111||Glutamine-binding periplasmic protein fused to glutamine permease (NCBI ptt file)||106, 278|
|CAC0112||glnQ||Glutamine ABC transporter (ATP-binding protein) (NCBI ptt file)||106, 302|
|CAC0237||CAC0237||ABC transporter, permease component (NCBI ptt file)||106, 287|
|CAC0291||CAC0291||FUSION: methionine sintase I (cobalamin dependent) and 5,10 methylenetetrahydrofolate reductase (NCBI ptt file)||259, 287|
|CAC0371||CAC0371||Response regulator (CheY-like domain and HTH domain) (NCBI ptt file)||71, 287|
|CAC0418||CAC0418||Predicted phosphatase, HAD family (NCBI ptt file)||261, 287|
|CAC0584||CAC0584||Precorrin-6B methylase 1 CobL1/CbiE (NCBI ptt file)||106, 117|
|CAC0605||CAC0605||Predicted phosphatase (NCBI ptt file)||287, 356|
|CAC0607||CAC0607||Aspartyl aminopeptidase (NCBI ptt file)||287, 309|
|CAC1018||CAC1018||Predicted membrane protein (NCBI ptt file)||287, 326|
|CAC1046||CAC1046||Transcriptional regulator, LysR family (NCBI ptt file)||71, 287|
|CAC1272||CAC1272||Predicted membrane protein (NCBI ptt file)||106, 215|
|CAC1279||hemN||Coproporphyrinogen III oxidase (NCBI ptt file)||3, 106|
|CAC1330||CAC1330||Metal-dependent hydrolases of the beta-lactamase superfamily, possible sulfatase (NCBI ptt file)||287, 356|
|CAC1424||CAC1424||Zn-dependent hydrolase, glyoxylase II family (NCBI ptt file)||287, 326|
|CAC1516||CAC1516||Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file)||140, 287|
|CAC1582||CAC1582||Membrane associated histidine kinase-like ATPase (NCBI ptt file)||259, 287|
|CAC1760||CAC1760||Signal peptidase I (NCBI ptt file)||106, 194|
|CAC1821||purB||Adenylosuccinate lyase (NCBI ptt file)||106, 297|
|CAC1852||CAC1852||Magnesium and cobalt transport protein (NCBI ptt file)||106, 346|
|CAC1858||CAC1858||MoxR-like ATPase (NCBI ptt file)||64, 106|
|CAC1969||CAC1969||Possible plasmid transfer factor, TraK (NCBI ptt file)||287, 291|
|CAC2253||CAC2253||Membrane-associated sensory histidine kinase-like ATPase (NCBI ptt file)||82, 106|
|CAC2265||CAC2265||Uncharacterized conserved membrane protein (NCBI ptt file)||106, 297|
|CAC2266||CAC2266||Uncharacterized conserved membrane protein (fragment) (NCBI ptt file)||106, 297|
|CAC2370||CAC2370||Uncharacterized protein, YrfI family (NCBI ptt file)||106, 194|
|CAC2371||CAC2371||S-adenosylmethionine-dependent methyltransferase (NCBI ptt file)||106, 194|
|CAC2397||CAC2397||Hypothetical protein (NCBI ptt file)||106, 296|
|CAC2432||CAC2432||Predicted permease (NCBI ptt file)||82, 106|
|CAC2472||CAC2472||Alpha/beta superfamily hydrolase (NCBI ptt file)||261, 287|
|CAC2658||glnA||Glutamine synthetase type III (NCBI ptt file)||99, 106|
|CAC2735||CAC2735||Response regulator (CheY-like receiver domain and HTH-type DNA-binding) (NCBI ptt file)||74, 287|
|CAC2996||CAC2996||Superfamily II DNA/RNA helicase, SNF2 family (NCBI ptt file)||259, 287|
|CAC3010||CAC3010||ATP-dependent RNA helicase (superfamily II), YDBR B.subtilis ortholog (NCBI ptt file)||84, 106|
|CAC3088||CAC3088||NtrC family transcriptional regulator, ATPase domain fused to two PAS domains (NCBI ptt file)||113, 287|
|CAC3099||truA||Pseudouridylate synthase, TRUA (NCBI ptt file)||106, 255|
|CAC3100||CAC3100||Predicted permease (Cobalt permease subfamily) (NCBI ptt file)||84, 106|
|CAC3457||CAC3457||Predicted membrane protein (NCBI ptt file)||287, 356|
|CAC3509||CAC3509||Transcriptional regulator, MerR family (duplicated domains) (NCBI ptt file)||287, 356|
|CAC3587||CAC3587||DNA replication protein DnaD (NCBI ptt file)||13, 287|
|CAC3675||CAC3675||Hypothetical secreted protein (NCBI ptt file)||106, 151|
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.
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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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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