Organism : Bacillus cereus ATCC14579 | Module List :
D-alanyl-D-alanine carboxypeptidase (NCBI ptt file)
Functional Annotations (4)
|D-alanyl-D-alanine carboxypeptidase||cog/ cog|
|calcium ion binding||go/ molecular_function|
|serine-type D-Ala-D-Ala carboxypeptidase activity||go/ molecular_function|
Regulation information for BC5389(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 BC5389
Module neighborhood information for BC5389
|Gene||Common Name||Description||Module membership|
|BC0203||BC0203||hypothetical protein (NCBI ptt file)||204, 340|
|BC0436||BC0436||Permease (NCBI ptt file)||58, 204|
|BC0481||BC0481||Glutaminase (NCBI ptt file)||27, 133|
|BC1309||BC1309||TerC-like protein (NCBI ptt file)||204, 410|
|BC1363||BC1363||Leucine-responsive regulatory protein (NCBI ptt file)||204, 428|
|BC1432||BC1432||Proton/sodium-glutamate symport protein (NCBI ptt file)||133, 337|
|BC1571||BC1571||hypothetical Membrane Spanning Protein (NCBI ptt file)||204, 214|
|BC1709||BC1709||malate-2H+/lactate-NA+ antiporter (NCBI ptt file)||67, 204|
|BC1793||BC1793||Chlorohydrolase/deaminase family protein (NCBI ptt file)||92, 133|
|BC2021||BC2021||High-affinity zinc uptake system protein znuA precursor (NCBI ptt file)||92, 133|
|BC2399||BC2399||Serine--pyruvate aminotransferase (NCBI ptt file)||204, 341|
|BC2400||BC2400||Threonine dehydratase (NCBI ptt file)||204, 341|
|BC2627||BC2627||hypothetical protein (NCBI ptt file)||150, 204|
|BC2628||BC2628||hypothetical protein (NCBI ptt file)||150, 204|
|BC2900||BC2900||CcdC protein (NCBI ptt file)||204, 341|
|BC2901||BC2901||ABC transporter permease protein (NCBI ptt file)||30, 204|
|BC3251||BC3251||hypothetical protein (NCBI ptt file)||204, 410|
|BC3706||BC3706||Transcriptional regulator, MerR family (NCBI ptt file)||133, 142|
|BC3765||BC3765||Phosphoglycerol transferase (NCBI ptt file)||133, 382|
|BC3892||BC3892||Ribosomal large subunit pseudouridine synthase D (NCBI ptt file)||133, 192|
|BC4507||BC4507||Aquaporin (NCBI ptt file)||92, 133|
|BC4795||BC4795||hypothetical Membrane Spanning Protein (NCBI ptt file)||133, 221|
|BC4911||BC4911||Arsenical pump membrane protein (NCBI ptt file)||133, 236|
|BC5012||BC5012||Chloramphenicol resistance protein (NCBI ptt file)||92, 133|
|BC5117||BC5117||ABC transporter permease protein (NCBI ptt file)||204, 410|
|BC5118||BC5118||ABC transporter ATP-binding protein (NCBI ptt file)||204, 410|
|BC5119||BC5119||hypothetical protein (NCBI ptt file)||204, 410|
|BC5120||BC5120||hypothetical Cytosolic Protein (NCBI ptt file)||204, 410|
|BC5121||BC5121||hypothetical protein (NCBI ptt file)||204, 410|
|BC5122||BC5122||hypothetical Cytosolic Protein (NCBI ptt file)||204, 410|
|BC5123||BC5123||hypothetical protein (NCBI ptt file)||204, 410|
|BC5124||BC5124||hypothetical protein (NCBI ptt file)||204, 410|
|BC5125||BC5125||hypothetical protein (NCBI ptt file)||204, 410|
|BC5235||BC5235||Nucleoside permease nupC (NCBI ptt file)||92, 133|
|BC5237||BC5237||N-acetylglucosaminyltransferase (NCBI ptt file)||204, 431|
|BC5241||BC5241||IG hypothetical 16680 (NCBI ptt file)||204, 410|
|BC5242||BC5242||Membrane protein with C2C2 zinc finger (NCBI ptt file)||62, 204|
|BC5243||BC5243||hypothetical protein (NCBI ptt file)||204, 410|
|BC5263||BC5263||UDP-glucose 4-epimerase (NCBI ptt file)||204, 214|
|BC5265||BC5265||Transcriptional regulator, LytR family (NCBI ptt file)||133, 396|
|BC5314||BC5314||hypothetical protein (NCBI ptt file)||133, 182|
|BC5330||BC5330||Thymidine kinase (NCBI ptt file)||133, 142|
|BC5389||BC5389||D-alanyl-D-alanine carboxypeptidase (NCBI ptt file)||133, 204|
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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