Organism : Clostridium acetobutylicum | Module List :
Predicted phosphatase (NCBI ptt file)
Functional Annotations (2)
|hydrolase activity||go/ molecular_function|
Regulation information for CAC2438(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 CAC2438
|hydrolase activity||go/ molecular_function|
Module neighborhood information for CAC2438
|Gene||Common Name||Description||Module membership|
|CAC0133||CAC0133||Hypothetical protein, CF-4 family (NCBI ptt file)||150, 300|
|CAC0193||CAC0193||Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file)||7, 174|
|CAC0194||CAC0194||Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file)||7, 174|
|CAC0444||napA||Na/H antiporter (napA) (NCBI ptt file)||62, 174|
|CAC0467||CAC0467||Uncharacterized membrane protein, homolog of YDAH B.subtilis (NCBI ptt file)||78, 174|
|CAC0492||CAC0492||Alanine racemase (NCBI ptt file)||174, 318|
|CAC0501||bacA||Bacitracin resistance protein (bacA) (NCBI ptt file)||69, 300|
|CAC0613||CAC0613||Spore coat protein F (NCBI ptt file)||203, 300|
|CAC0614||CAC0614||Spore coat protein F (NCBI ptt file)||203, 300|
|CAC0668||CAC0668||Predicted membrane protein (NCBI ptt file)||174, 305|
|CAC0678||CAC0678||CBS domains (NCBI ptt file)||160, 174|
|CAC0704||CAC0704||Sugar ABC transporter, permease protein (NCBI ptt file)||95, 174|
|CAC0810||hypF||Hydrogenase maturation factor (hypF) (NCBI ptt file)||95, 300|
|CAC0840||potA||Spermidine/putrescine ABC transporter, ATP-binding component (NCBI ptt file)||153, 174|
|CAC0863||CAC0863||Sensory transduction histidine kinase (NCBI ptt file)||39, 300|
|CAC1423||CAC1423||Predicted dehydrogenase of short-chain alcohol dehydrogenase family, ortholog of YHDF B.subtilis (NCBI ptt file)||118, 300|
|CAC1468||CAC1468||Predicted acetyltransferase (NCBI ptt file)||174, 315|
|CAC1508||CAC1508||Hypothetical protein (NCBI ptt file)||39, 300|
|CAC1588||CAC1588||Malolactic regulator, LysR family (NCBI ptt file)||174, 366|
|CAC1696||sigG||Specialized DNA-dependent RNA polymerase sigma subunit (NCBI ptt file)||174, 235|
|CAC1839||CAC1839||Hypothetical protein (NCBI ptt file)||39, 300|
|CAC1968||CAC1968||Pectate lyase related enzyme (NCBI ptt file)||174, 314|
|CAC1985||CAC1985||Hypothetical protein (NCBI ptt file)||279, 300|
|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|
|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|
|CAC2875||tagO||Undecaprenyl-phosphate (NCBI ptt file)||174, 235|
|CAC3015||CAC3015||Glycosyltransferase (NCBI ptt file)||39, 300|
|CAC3032||CAC3032||Galactose mutarotase related enzyme (NCBI ptt file)||174, 315|
|CAC3220||CAC3220||Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file)||44, 174|
|CAC3230||CAC3230||Hydrogenase subunit (ferredoxin) (NCBI ptt file)||174, 330|
|CAC3330||CAC3330||Cytochrome P450 family protein, YBDT B.subtilis ortholog (NCBI ptt file)||154, 300|
|CAC3357||CAC3357||Hypothetical protein (NCBI ptt file)||118, 174|
|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|
|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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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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- 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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