Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC2855(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 CAC2855
|Gene||Common Name||Description||Module membership|
|CAC0013||CAC0013||Uncharacterized small conserved protein, ortholog of T.maritima (4981999) and P.abyssi (5457704) (NCBI ptt file)||59, 253|
|CAC0680||CAC0680||Predicted membrane protein (NCBI ptt file)||52, 59|
|CAC1015||CAC1015||Pseudouridylate synthase (NCBI ptt file)||76, 306|
|CAC1065||CAC1065||Uncharacterized protein, related stage III sporulation protein AH of Bacillus sp. (NCBI ptt file)||59, 304|
|CAC1234||pheB||Chorismate mutase PheB of B.subtilis ortholog (NCBI ptt file)||76, 215|
|CAC1251||rodA||Cell division protein, rodA/ftsW/spoVE family (NCBI ptt file)||76, 281|
|CAC1501||CAC1501||DNA-methyltransferase (cytosine-specific), ortholog of BSP6I Bsubtilis (NCBI ptt file)||76, 79|
|CAC1538||CAC1538||Predicted permease, YCXC B.subtilis ortholog (NCBI ptt file)||59, 151|
|CAC1612||CAC1612||Probable cation efflux pump, multidrug resistance protein (FS) (NCBI ptt file)||76, 149|
|CAC1613||CAC1613||ABC-type multidrug/protein/lipid transport system, membrane ATPase component (NCBI ptt file)||76, 249|
|CAC1740||CAC1740||Uncharcaterized membrane protein, YLBJ B.subtilis homolog (NCBI ptt file)||59, 304|
|CAC1744||CAC1744||Predicted Zn-finger-like protein, possible nucleic acid binding (NCBI ptt file)||59, 61|
|CAC1757||CAC1757||RimM protein, required for 16S rRNA processing (NCBI ptt file)||76, 297|
|CAC1758||trmD||TRNA-(guanine-N1)-methyltransferase, TrmD (NCBI ptt file)||76, 297|
|CAC1787||rpsB||Ribosomal protein S2 (NCBI ptt file)||59, 61|
|CAC2062||CAC2062||TRNA nucleotidyltransferase family enzyme (NCBI ptt file)||76, 211|
|CAC2228||CAC2228||Hypothetical protein (NCBI ptt file)||76, 281|
|CAC2229||CAC2229||Pyruvate:ferredoxin oxidoreductase (NCBI ptt file)||59, 63|
|CAC2339||CAC2339||Uncharacterized protein, YBBK B.subtilis ortholog (NCBI ptt file)||76, 123|
|CAC2373||CAC2373||Predicted membrane protein (NCBI ptt file)||76, 84|
|CAC2409||CAC2409||Transglutaminase-like enzyme, putative cysteine protease (NCBI ptt file)||59, 105|
|CAC2656||CAC2656||Protein containing uncharacterized domain from NimC family (NCBI ptt file)||59, 296|
|CAC2657||CAC2657||Polyferredoxin (NCBI ptt file)||59, 296|
|CAC2709||etfA||Electron transfer flavoprotein alpha-subunit (NCBI ptt file)||10, 59|
|CAC2713||CAC2713||AT-rich DNA-binding protein (NCBI ptt file)||76, 281|
|CAC2748||deaD||ATP dependent RNA helicase DeaD, superfamily II (NCBI ptt file)||59, 333|
|CAC2852||comFC||Predicted amidophosphoribosyltransferase, ComFC B.suntilis ortholog (NCBI ptt file)||76, 149|
|CAC2855||CAC2855||Predicted membrane protein (NCBI ptt file)||59, 76|
|CAC2865||atpD||FoF1-type ATP synthase beta subunit (NCBI ptt file)||59, 304|
|CAC2866||atpG||FoF1-type ATP synthase gamma subunit (NCBI ptt file)||59, 335|
|CAC2867||atpA||FoF1-type ATP synthase alpha subunit (NCBI ptt file)||59, 335|
|CAC2868||atpH||FoF1-type ATP synthase delta subunit (NCBI ptt file)||59, 335|
|CAC2870||atpE||FoF1-type ATP synthase C subunit (NCBI ptt file)||59, 304|
|CAC2871||atpB||FoF1-type ATP synthase A subunit (NCBI ptt file)||59, 79|
|CAC2872||CAC2872||Predicted membrane protein in FoF1-type ATP synthase operon (NCBI ptt file)||76, 162|
|CAC2881||CAC2881||Protein-tyrosine-phosphatase, YWLE B.subtilis ortholog (NCBI ptt file)||35, 76|
|CAC2887||tdk||Thymidine kinase (NCBI ptt file)||59, 337|
|CAC2896||CAC2896||Uncharacterized protein, YPEB B.subtilis ortholog (NCBI ptt file)||59, 179|
|CAC2990||csp||Cold shock protein (NCBI ptt file)||32, 76|
|CAC3103||rplQ||Ribosomal protein L17 (NCBI ptt file)||20, 59|
|CAC3106||rpsK||Ribosomal protein S11 (NCBI ptt file)||59, 362|
|CAC3114||rplO||Ribosomal protein L15 (NCBI ptt file)||59, 335|
|CAC3121||rplE||Ribosomal protein L5 (NCBI ptt file)||59, 241|
|CAC3200||CAC3200||Predicted transcriptional regulator, homolog of Bvg accessory factor (NCBI ptt file)||76, 116|
|CAC3215||prsA||Parvulin-like peptidyl-prolyl isomerase, PRSA B.subtilis ortholog (NCBI ptt file)||53, 59|
|CAC3437||CAC3437||Predicted membrane-associated Zn-dependent protease, HtpX family (BlaR subfamily) (NCBI ptt file)||59, 253|
|CAC3537||CAC3537||Fragment of SECA (fragment) (NCBI ptt file)||76, 229|
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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