Organism : Clostridium acetobutylicum | Module List :
Membrane associated methyl-chemotaxis protein, HAMP domain containing (NCBI ptt file)
Functional Annotations (5)
|Methyl-accepting chemotaxis protein||cog/ cog|
|signal transducer activity||go/ molecular_function|
|signal transduction||go/ biological_process|
Regulation information for CAC2617(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 CAC2617
Module neighborhood information for CAC2617
|Gene||Common Name||Description||Module membership|
|CAC0246||CAC0246||Conserved membrane protein, predicted permease (NCBI ptt file)||66, 113|
|CAC0247||CAC0247||Predicted permease (NCBI ptt file)||66, 356|
|CAC0423||CAC0423||Fusion: PTS system, beta-glucosides specific IIABC component (NCBI ptt file)||284, 360|
|CAC0425||sacA||Sucrase-6-phosphate hydrolase (gene sacA) (NCBI ptt file)||92, 360|
|CAC0450||CAC0450||Response regulator (CheY-like and HTH domains) (NCBI ptt file)||13, 66|
|CAC0522||CAC0522||Predicted hydrolase of the HAD superfamily (NCBI ptt file)||66, 282|
|CAC0559||CAC0559||Transcriptional regulator, MarR/EmrR family (NCBI ptt file)||66, 214|
|CAC0570||CAC0570||PTS enzyme II, ABC component (NCBI ptt file)||237, 360|
|CAC0585||CAC0585||N-terminal CheY reciever domain fused to C-terminal uncharacterized CheX-like domain (NCBI ptt file)||66, 151|
|CAC0644||gerKA||Spore germination protein gerKA (NCBI ptt file)||324, 360|
|CAC0761||CAC0761||Predicted membrane protein (NCBI ptt file)||66, 86|
|CAC0766||CAC0766||Predicted transcriptional regulator (MerR family) (NCBI ptt file)||116, 360|
|CAC0778||CAC0778||ATP-dependent RNA helicase, superfamily II (NCBI ptt file)||13, 66|
|CAC0820||CAC0820||Conserved protein, ortholog YwqG B.subtilis (NCBI ptt file)||13, 66|
|CAC1396||purD||Phosphoribosylamine-glycine ligase (NCBI ptt file)||249, 360|
|CAC1470||CAC1470||2-Hydroxy-6-Oxo-6-Phenylhexa-2,4-Dienoate hydrolase (NCBI ptt file)||66, 227|
|CAC1471||arbA||Ketopantoate reductase (NCBI ptt file)||66, 227|
|CAC1590||CAC1590||2-oxoglutarate/malate translocator (NCBI ptt file)||66, 249|
|CAC1595||CAC1595||Integrase/recombinase, XerC/XerD family (NCBI ptt file)||249, 360|
|CAC1630||CAC1630||Zn-dependent peptidase from MPP family (NCBI ptt file)||22, 360|
|CAC1761||CAC1761||Predicted GTPase, YLQF B.subtilis ortholog (NCBI ptt file)||116, 360|
|CAC1789||smbA/pyrH||Uridylate kinase (NCBI ptt file)||310, 360|
|CAC2203||hag||Possible hook-associated protein, flagellin family (NCBI ptt file)||66, 93|
|CAC2617||CAC2617||Membrane associated methyl-chemotaxis protein, HAMP domain containing (NCBI ptt file)||66, 360|
|CAC2626||fabG||Possible 3-ketoacyl-acyl carrier protein reductase (NCBI ptt file)||310, 360|
|CAC2627||CAC2627||Predicted S-adenosylmethionine-dependent methyltransferase, YtmQ B.subtilis ortholog (NCBI ptt file)||310, 360|
|CAC2628||CAC2628||Predicted metal-dependent peptidase (NCBI ptt file)||310, 360|
|CAC2650||pyrD||Dihydroorotate dehydrogenase (NCBI ptt file)||116, 360|
|CAC2652||pyrF||Orotidine-5'-phosphate decarboxylase (NCBI ptt file)||116, 360|
|CAC2653||pyrI||Aspartate carbamoyltransferase regulatory subunit (NCBI ptt file)||116, 360|
|CAC2654||CAC2654||Aspartate carbamoyltransferase catalytic subunit (NCBI ptt file)||116, 360|
|CAC2902||CAC2902||Isopentenyl monophosphate kinase, IPK (NCBI ptt file)||66, 247|
|CAC2918||pmi||Mannose-6 phospate isomelase (NCBI ptt file)||270, 360|
|CAC2936||CAC2936||Alpha/beta superfamily hydrolase (NCBI ptt file)||236, 360|
|CAC3095||thiK||Hydroxyethylthiazole kinase ThiM/ThiK (FS!) (NCBI ptt file)||353, 360|
|CAC3332||CAC3332||Predicted amidohydrolase (dihydroorothase family) (NCBI ptt file)||150, 360|
|CAC3334||CAC3334||Multimeric flavodoxin WrbA family protein (NCBI ptt file)||66, 142|
|CAC3349||CAC3349||Transcriptional regulator, LysR family (NCBI ptt file)||66, 140|
|CAC3356||CAC3356||Lactoylglutathione lyase (LGUL) family protein, diverged (NCBI ptt file)||236, 360|
|CAC3440||CAC3440||Hypothetical protein (NCBI ptt file)||353, 360|
|CAC3526||CAC3526||FMN-binding protein (NCBI ptt file)||66, 183|
|CAC3527||CAC3527||Ferredoxin (NCBI ptt file)||66, 249|
|CAC3567||topB||Topoisomerase B (NCBI ptt file)||66, 270|
|CAC3686||CAC3686||Metallo-beta-lactamase superfamily hydrolase (NCBI ptt file)||33, 66|
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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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.
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