Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC2600(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 CAC2600
|Gene||Common Name||Description||Module membership|
|CAC0093||CAC0093||Transcriptional regulators, LysR family (NCBI ptt file)||216, 301|
|CAC0133||CAC0133||Hypothetical protein, CF-4 family (NCBI ptt file)||150, 300|
|CAC0154||MtlA||PTS system, mannitol-specific IIBC component (gene MtlA) (NCBI ptt file)||301, 342|
|CAC0332||manB||Beta-mannanase (NCBI ptt file)||191, 301|
|CAC0388||CAC0388||Hypothetical protein (NCBI ptt file)||301, 361|
|CAC0501||bacA||Bacitracin resistance protein (bacA) (NCBI ptt file)||69, 300|
|CAC0534||pps||Phosphoenolpyruvate synthase (gene pps) (NCBI ptt file)||65, 301|
|CAC0613||CAC0613||Spore coat protein F (NCBI ptt file)||203, 300|
|CAC0614||CAC0614||Spore coat protein F (NCBI ptt file)||203, 300|
|CAC0695||CAC0695||Altronate oxidoreductase (NCBI ptt file)||170, 301|
|CAC0810||hypF||Hydrogenase maturation factor (hypF) (NCBI ptt file)||95, 300|
|CAC0863||CAC0863||Sensory transduction histidine kinase (NCBI ptt file)||39, 300|
|CAC1140||CAC1140||Hypothetical protein (NCBI ptt file)||16, 301|
|CAC1423||CAC1423||Predicted dehydrogenase of short-chain alcohol dehydrogenase family, ortholog of YHDF B.subtilis (NCBI ptt file)||118, 300|
|CAC1477||CAC1477||Hypothetical protein (NCBI ptt file)||272, 301|
|CAC1508||CAC1508||Hypothetical protein (NCBI ptt file)||39, 300|
|CAC1526||CAC1526||Amidase, related to GSP of E.coli (NCBI ptt file)||26, 301|
|CAC1676||CAC1676||Uncharacterized conserved protein (NCBI ptt file)||301, 332|
|CAC1839||CAC1839||Hypothetical protein (NCBI ptt file)||39, 300|
|CAC1867||CAC1867||Transcriptional regulator (phage-related) (Xre family) (NCBI ptt file)||301, 342|
|CAC1985||CAC1985||Hypothetical protein (NCBI ptt file)||279, 300|
|CAC2247||CAC2247||Site-specific recombinase, DNA invertase Pin homolog (NCBI ptt file)||270, 301|
|CAC2249||CAC2249||C-terminal domain of asparagine synthase (NCBI ptt file)||114, 300|
|CAC2300||CAC2300||Uncharacterized secreted protein, YunB B.subtilis homolog (NCBI ptt file)||39, 300|
|CAC2438||CAC2438||Predicted phosphatase (NCBI ptt file)||174, 300|
|CAC2509||CAC2509||Predicted acetyltransferase (NCBI ptt file)||165, 301|
|CAC2540||CAC2540||Co/Zn/Cd efflux system component (NCBI ptt file)||207, 301|
|CAC2582||CAC2582||Uncharacterized conserved membrane protein, YHGE B.subtilis homolog (NCBI ptt file)||39, 300|
|CAC2583||CAC2583||Uncharacterized conserved membrane protein, YHGE B.subtilis homolog (NCBI ptt file)||150, 300|
|CAC2600||CAC2600||Predicted membrane protein (NCBI ptt file)||300, 301|
|CAC2666||CAC2666||Hypothetical protein (NCBI ptt file)||300, 330|
|CAC2682||CAC2682||Hypothetical protein (NCBI ptt file)||62, 300|
|CAC2683||cotF||Related to spore coat protein F (NCBI ptt file)||62, 300|
|CAC2790||CAC2790||Hypothetical protein (NCBI ptt file)||39, 300|
|CAC2794||CAC2794||Transcriptional regulator, Lrp family (possible nitrite reductase regulator NirD) (NCBI ptt file)||300, 330|
|CAC2796||CAC2796||MoaA/NirJ family Fe-S oxidoreductase (NCBI ptt file)||188, 300|
|CAC2822||CAC2822||TPR-repeat-containing protein (NCBI ptt file)||165, 301|
|CAC3015||CAC3015||Glycosyltransferase (NCBI ptt file)||39, 300|
|CAC3164||CAC3164||Lysine-specific permease (NCBI ptt file)||265, 301|
|CAC3237||msmX||Multiple sugar-binding ABC-transporter, MSMX ATP-binding protein (NCBI ptt file)||301, 312|
|CAC3241||CAC3241||Uncharacterized conserved membrane protein, YYAD B.subtilis ortholog (NCBI ptt file)||150, 301|
|CAC3242||CAC3242||Uncharacterized Fe-S protein, PflX (pyruvate formate lyase activating protein) homolog (NCBI ptt file)||72, 301|
|CAC3330||CAC3330||Cytochrome P450 family protein, YBDT B.subtilis ortholog (NCBI ptt file)||154, 300|
|CAC3451||CAC3451||Sugar/Na+(H+) simporter (NCBI ptt file)||170, 301|
|CAC3468||uvrC||Excinuclease ABC, subunit C (uvrC) (NCBI ptt file)||207, 301|
|CAC3471||CAC3471||GMP reductase (NCBI ptt file)||223, 301|
|CAC3490||CAC3490||DNA gyrase inhibitory protein, GyrI (NCBI ptt file)||205, 301|
|CAC3546||CAC3546||Highly conserved protein containing a domain related to cellulase catalitic domain and a thioredoxin domain (NCBI ptt file)||259, 300|
|CAC3590||CAC3590||Predicted flavoprotein, YhiN family (NCBI ptt file)||174, 301|
|CAC3644||CAC3644||Oligopeptide ABC transporter, permease component (NCBI ptt file)||217, 301|
|CAC3674||CAC3674||Two CBS domain containing protein (NCBI ptt file)||114, 300|
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.
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