Organism : Campylobacter jejuni | Module List :
lepA GTP-binding protein homolog (NCBI ptt file)
Functional Annotations (6)
|Membrane GTPase LepA||cog/ cog|
|GTPase activity||go/ molecular_function|
|GTP binding||go/ molecular_function|
|protein-synthesizing GTPase activity||go/ molecular_function|
Regulation information for Cj1030c(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 Cj1030c
Module neighborhood information for Cj1030c
|Gene||Common Name||Description||Module membership|
|Cj0028||recJ||putative single-stranded-DNA-specific exonuclease (NCBI ptt file)||24, 160|
|Cj0164c||ubiA||putative 4-hydroxybenzoate octaprenyltransferase (NCBI ptt file)||63, 149|
|Cj0194||folE||GTP cyclohydrolase I (NCBI ptt file)||95, 160|
|Cj0202c||Cj0202c||hypothetical protein Cj0202c (NCBI ptt file)||63, 155|
|Cj0265c||Cj0265c||putative cytochrome C-type haem-binding periplasmic protein (NCBI ptt file)||82, 160|
|Cj0270||Cj0270||possible isomserase (NCBI ptt file)||130, 160|
|Cj0271||Cj0271||bacterioferritin comigratory protein homolog (NCBI ptt file)||52, 63|
|Cj0287c||greA||transcription elongation factor (NCBI ptt file)||95, 160|
|Cj0387||aroK||shikimate kinase (NCBI ptt file)||6, 63|
|Cj0388||trpS||tryptophanyl-tRNA synthetase (NCBI ptt file)||63, 166|
|Cj0398||gatC||putative Glu-tRNAGln amidotransferase subunit C (NCBI ptt file)||132, 160|
|Cj0434||pgm||phosphoglycerate mutase (NCBI ptt file)||24, 160|
|Cj0549||fliS||flagellar protein (NCBI ptt file)||130, 160|
|Cj0646||Cj0646||putative lipoprotein (NCBI ptt file)||19, 63|
|Cj0663c||hslV||putative heat shock protein (NCBI ptt file)||137, 160|
|Cj0668||Cj0668||putative ATP /GTP-binding protein (NCBI ptt file)||158, 160|
|Cj0713||trmD||tRNA (guanine-N1)-methyltransferase (NCBI ptt file)||132, 160|
|Cj0730||Cj0730||putative ABC transport system permease (NCBI ptt file)||63, 164|
|Cj0820c||fliP||flagellar biosynthesis protein (NCBI ptt file)||104, 160|
|Cj0854c||Cj0854c||putative periplasmic protein (NCBI ptt file)||63, 120|
|Cj0891c||serA||D-3-phosphoglycerate dehydrogenase (NCBI ptt file)||63, 148|
|Cj0965c||Cj0965c||hypothetical protein Cj0965c (NCBI ptt file)||139, 160|
|Cj1000||Cj1000||putative transcriptional regulator (lysR family) (NCBI ptt file)||44, 63|
|Cj1024c||Cj1024c||signal-transduction regulatory protein (NCBI ptt file)||132, 160|
|Cj1030c||lepA||lepA GTP-binding protein homolog (NCBI ptt file)||63, 160|
|Cj1060c||Cj1060c||small hydrophobic protein (NCBI ptt file)||110, 160|
|Cj1086c||Cj1086c||hypothetical protein Cj1086c (NCBI ptt file)||63, 81|
|Cj1117c||prmA||possible ribosomal protein methyltransferase (NCBI ptt file)||60, 160|
|Cj1146c||waaV||putative glucosyltransferase (NCBI ptt file)||63, 149|
|Cj1181c||tsf||elongation factor TS (NCBI ptt file)||30, 160|
|Cj1204c||atpB||ATP synthase F0 sector A subunit (NCBI ptt file)||160, 166|
|Cj1218c||ribA||putative riboflavin synthase alpha chain (NCBI ptt file)||110, 160|
|Cj1234||glyS||glycyl-tRNA synthetase beta chain (NCBI ptt file)||132, 160|
|Cj1242||Cj1242||hypothetical protein Cj1242 (NCBI ptt file)||130, 160|
|Cj1288c||gltX2||glutamyl-tRNA synthetase (NCBI ptt file)||34, 160|
|Cj1316c||Cj1316c||hypothetical protein Cj1316c (NCBI ptt file)||63, 144|
|Cj1327||neuB2||N-acetylneuraminic acid synthetase (NCBI ptt file)||63, 117|
|Cj1331||ptmB||acylneuraminate cytidylyltransferase (flagellin modification) (NCBI ptt file)||63, 146|
|Cj1332||ptmA||putative oxidoreductase (flagellin modification) (NCBI ptt file)||63, 77|
|Cj1333||Cj1333||hypothetical protein Cj1333 (1318 family) (NCBI ptt file)||63, 109|
|Cj1458c||thiL||putative thiamin-monophosphate kinase (NCBI ptt file)||44, 63|
|Cj1562||Cj1562||hypothetical protein Cj1562 (NCBI ptt file)||19, 63|
|Cj1634c||aroC||chorismate synthase (NCBI ptt file)||63, 110|
|Cj1642||Cj1642||hypothetical protein Cj1642 (NCBI ptt file)||57, 160|
|Cj1672c||eno||enolase (NCBI ptt file)||137, 160|
|Cj1714||Cj1714||small hydrophobic protein (NCBI ptt file)||11, 160|
|Cj1727c||metY||putative O-acetylhomoserine (thiol)-lyase (NCBI ptt file)||63, 83|
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.
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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.
- 2. Source gene
- 3. Target genes (other module members)
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