Organism : Clostridium acetobutylicum | Module List :
Transcription elongation factor GreA (NCBI ptt file)
Functional Annotations (5)
|Transcription elongation factor||cog/ cog|
|DNA binding||go/ molecular_function|
|transcription elongation regulator activity||go/ molecular_function|
|regulation of transcription, DNA-dependent||go/ biological_process|
Regulation information for CAC1965(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 CAC1965
Module neighborhood information for CAC1965
|Gene||Common Name||Description||Module membership|
|CAC0034||CAC0034||Hypothetical protein (NCBI ptt file)||63, 298|
|CAC0089||serA||D-3 phosphoglycerate dehydrogenase (NCBI ptt file)||109, 343|
|CAC0090||CAC0090||Xylanase/chitin deacetylase, NodB family (NCBI ptt file)||109, 312|
|CAC0115||CAC0115||Uncharacterized protein, Yje/RRF2 family (NCBI ptt file)||63, 232|
|CAC0207||CAC0207||Hypothetical protein, CF-6 family (NCBI ptt file)||63, 273|
|CAC0225||CAC0225||Sensory transduction histidine kinase (NCBI ptt file)||57, 109|
|CAC0277||CAC0277||HD-GYP hydrolase domain containing protein (NCBI ptt file)||109, 298|
|CAC0452||CAC0452||Permease (NCBI ptt file)||99, 109|
|CAC0641||CAC0641||Uncharacterized conserved protein (NCBI ptt file)||109, 348|
|CAC0910||CAC0910||Probably cellulosomal scaffolding protein precursor, secreted; cellulose-binding and cohesin domain (NCBI ptt file)||53, 63|
|CAC0945||ssb||Single-stranded DNA-binding protein (NCBI ptt file)||63, 99|
|CAC1098||polA||DNA polymerase I, polA (NCBI ptt file)||99, 109|
|CAC1297||CAC1297||N-terminal fragment of elongation factor Ts (NCBI ptt file)||49, 109|
|CAC1312||CAC1312||Hypothetical protein (NCBI ptt file)||109, 176|
|CAC1313||CAC1313||Hypothetical protein (NCBI ptt file)||63, 295|
|CAC1404||CAC1404||Transcriptional regulator of sugar metabolism (deoR family) (NCBI ptt file)||64, 109|
|CAC1488||CAC1488||Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file)||63, 273|
|CAC1539||CAC1539||Gamma-glutamylcysteine synthetase (NCBI ptt file)||109, 222|
|CAC1559||CAC1559||Predicted transcriptional regulator (NCBI ptt file)||109, 151|
|CAC1635||CAC1635||Predicted nucleic acid binding protein, containing 2 S1 domains, YITL B.subtilis ortholog (NCBI ptt file)||109, 312|
|CAC1651||CAC1651||Predicted GTPase with uncharacterized domain, ortholog of T.maritima (4980952) (NCBI ptt file)||109, 283|
|CAC1652||aspA||Aspartate ammonia-lyase (NCBI ptt file)||109, 329|
|CAC1661||CAC1661||Predicted secreted nucleic acid binding protein (NCBI ptt file)||25, 109|
|CAC1855||CAC1855||Hypothetical protein (NCBI ptt file)||63, 210|
|CAC1955||CAC1955||Hypothetical protein (NCBI ptt file)||57, 109|
|CAC1965||greA||Transcription elongation factor GreA (NCBI ptt file)||63, 109|
|CAC2037||CAC2037||Hypothetical protein, CF-39 family (NCBI ptt file)||109, 312|
|CAC2072||CAC2072||Stage IV sporulation protein B, SpoIVB (NCBI ptt file)||63, 273|
|CAC2229||CAC2229||Pyruvate:ferredoxin oxidoreductase (NCBI ptt file)||59, 63|
|CAC2230||CAC2230||Uncharacterized protein of PR1 family, YkwD B.subtilis ortholog (NCBI ptt file)||63, 273|
|CAC2321||CAC2321||Predicted glycosyltransferase (NCBI ptt file)||63, 278|
|CAC2386||CAC2386||Predicted protein of beta-propeller fold (NCBI ptt file)||63, 321|
|CAC2437||CAC2437||Uncharacterized conserved protein (NCBI ptt file)||100, 109|
|CAC2787||CAC2787||Serine/threonine protein phosphatase (NCBI ptt file)||109, 128|
|CAC2858||mreV||Shape-determining protein envB (HSP70 family charepones) (NCBI ptt file)||36, 63|
|CAC2873||CAC2873||Acetyl-CoA acetyltransferase (NCBI ptt file)||10, 109|
|CAC2893||CAC2893||Hypothetical protein (NCBI ptt file)||63, 137|
|CAC2942||CAC2942||Uncharacterized conserved protein fron YGAG family, predicted metal-dependent enzyme (NCBI ptt file)||47, 63|
|CAC3152||CAC3152||DNA-dependent RNA polymerase sigma subunit (NCBI ptt file)||5, 109|
|CAC3155||CAC3155||Uncharacterized conserved protein, THY1 family (NCBI ptt file)||19, 109|
|CAC3217||spoVC||Stage V sporulation protein C, peptidyl-tRNA hydrolase (NCBI ptt file)||63, 105|
|CAC3219||CAC3219||Membrane associated histidine kinase with HAMP domain (NCBI ptt file)||19, 63|
|CAC3221||prs||Phosphoribosylpyrophosphate synthetase (NCBI ptt file)||109, 251|
|CAC3251||CAC3251||Sensory transduction protein containing HD_GYP domain (NCBI ptt file)||63, 225|
|CAC3307||CAC3307||TPR-repeats containing protein (NCBI ptt file)||109, 190|
|CAC3602||CAC3602||HD superfamily hydrolase (NCBI ptt file)||86, 109|
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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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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