Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC1277(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 CAC1277
|Gene||Common Name||Description||Module membership|
|CAC0009||CAC0009||Uncharacterized conserved protein, ortholog of YRXA B.subtilis (NCBI ptt file)||62, 312|
|CAC0010||CAC0010||Uncharacterized conserved protein, possible metal-binding (NCBI ptt file)||283, 312|
|CAC0012||CAC0012||Predicted dehydrogenase with iron-sulfur domain (NCBI ptt file)||86, 328|
|CAC0043||CAC0043||Hypothetical protein, CF-3 family (NCBI ptt file)||99, 312|
|CAC0044||CAC0044||Predicted membrane protein (NCBI ptt file)||264, 312|
|CAC0090||CAC0090||Xylanase/chitin deacetylase, NodB family (NCBI ptt file)||109, 312|
|CAC0172||CAC0172||Predicted membrane protein (NCBI ptt file)||123, 328|
|CAC0354||CAC0354||Uncharacterized membrane protein (NCBI ptt file)||279, 312|
|CAC0422||licT||Transcriptional antiterminator licT (NCBI ptt file)||86, 328|
|CAC0618||CAC0618||Uncharacterised permease, similar to ABC transporter (permease) (NCBI ptt file)||40, 312|
|CAC0726||CAC0726||Ribose 5-phosphate isomerase RpiB (NCBI ptt file)||288, 312|
|CAC0803||CAC0803||Hypothetical protein (NCBI ptt file)||328, 367|
|CAC0915||CAC0915||Endoglucanase A precursor (endo-1,4-beta-glucanase) (cellulase A), secreted; dockerin domain (NCBI ptt file)||26, 312|
|CAC1162||CAC1162||Hypothetical protein, CF-11 family (NCBI ptt file)||26, 328|
|CAC1166||CAC1166||Hypothetical protein (NCBI ptt file)||26, 328|
|CAC1271||CAC1271||ComC competence related protein (NCBI ptt file)||190, 312|
|CAC1277||CAC1277||Predicted membrane protein (NCBI ptt file)||312, 328|
|CAC1476||CAC1476||Proline/glycine betaine ABC-type transport system, permease component (NCBI ptt file)||313, 328|
|CAC1484||CAC1484||Nitroreductase family protein (NCBI ptt file)||142, 328|
|CAC1530||CAC1530||Sugar-proton symporter (NCBI ptt file)||169, 328|
|CAC1635||CAC1635||Predicted nucleic acid binding protein, containing 2 S1 domains, YITL B.subtilis ortholog (NCBI ptt file)||109, 312|
|CAC1829||CAC1829||Predicted inactivated Zn-dependent peptidase, PMBA ortholog (NCBI ptt file)||312, 315|
|CAC1860||CAC1860||Predicted flavodoxin oxidoreductase (NCBI ptt file)||62, 312|
|CAC1956||CAC1956||Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file)||102, 312|
|CAC2027||CAC2027||Hypothetical protein (NCBI ptt file)||270, 328|
|CAC2033||CAC2033||Hypothetical protein (NCBI ptt file)||99, 312|
|CAC2037||CAC2037||Hypothetical protein, CF-39 family (NCBI ptt file)||109, 312|
|CAC2038||CAC2038||Hypothetical protein, CF-23 family (NCBI ptt file)||273, 312|
|CAC2096||CAC2096||Hypothetical protein (NCBI ptt file)||69, 312|
|CAC2098||CAC2098||Hypothetical protein (NCBI ptt file)||267, 312|
|CAC2102||CAC2102||Prepilin peptidase (NCBI ptt file)||54, 312|
|CAC2226||CAC2226||Enzyme of ILVE/PABC family (branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase) (NCBI ptt file)||282, 328|
|CAC2251||CAC2251||Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file)||123, 312|
|CAC2348||CAC2348||Glycosyltransferase (NCBI ptt file)||13, 312|
|CAC2431||CAC2431||Alkaline phosphatase superfamily enzyme (NCBI ptt file)||62, 312|
|CAC2434||CAC2434||Membrane associatehistidine kinase with HAMP domain (NCBI ptt file)||44, 312|
|CAC2491||CAC2491||Predicted acetyltransferase (NCBI ptt file)||179, 312|
|CAC2585||CAC2585||6-pyruvoyl-tetrahydropterin synthase related domain; conserved membrane protein (NCBI ptt file)||72, 328|
|CAC2701||guaB||IMP dehydrogenase (NCBI ptt file)||222, 328|
|CAC2719||CAC2719||Ethanolamin permease (NCBI ptt file)||111, 312|
|CAC2831||CAC2831||Conserved membrane protein, YccA family (NCBI ptt file)||312, 366|
|CAC2908||CAC2908||Spore coat protein cotS related (NCBI ptt file)||190, 312|
|CAC2910||CAC2910||Spore coat protein cotS related (NCBI ptt file)||190, 312|
|CAC3222||gcaD||UDP-N-acetylglucosamine pyrophosphorylase (NCBI ptt file)||255, 312|
|CAC3236||CAC3236||Possible transcriptional regulator from YAEG/LRPR family (NCBI ptt file)||247, 312|
|CAC3237||msmX||Multiple sugar-binding ABC-transporter, MSMX ATP-binding protein (NCBI ptt file)||301, 312|
|CAC3286||CAC3286||Chey-like receiver domain containing protein, YCBB B.subtilis ortholog (NCBI ptt file)||86, 328|
|CAC3491||CAC3491||Protein, related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) (NCBI ptt file)||312, 341|
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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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
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.
- 2. Source gene
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