Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC3400(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 CAC3400
Module neighborhood information for CAC3400
|Gene||Common Name||Description||Module membership|
|CAC0002||dnaN||DNA polymerase III beta subunit (NCBI ptt file)||3, 283|
|CAC0010||CAC0010||Uncharacterized conserved protein, possible metal-binding (NCBI ptt file)||283, 312|
|CAC0174||CAC0174||Response regulator, CheY-like receiver domain and HTH DNA-binding domain (NCBI ptt file)||140, 283|
|CAC0222||exoA||Exodeoxyribonuclease (exoA) (NCBI ptt file)||72, 207|
|CAC0282||CAC0282||Cytosine/guanine deaminase related protein (NCBI ptt file)||283, 366|
|CAC0328||CAC0328||Predicted metal-dependent hydrolase (NCBI ptt file)||72, 272|
|CAC0421||CAC0421||Uncharacterized membrane protein (NCBI ptt file)||72, 259|
|CAC0458||CAC0458||Permease (NCBI ptt file)||283, 286|
|CAC0519||pyrC||Dihydroorotase (NCBI ptt file)||72, 286|
|CAC0627||CAC0627||Transcriptional regulator, MarR/EmrR family (NCBI ptt file)||278, 283|
|CAC0728||CAC0728||SAM-dependent methyltransferase (NCBI ptt file)||72, 283|
|CAC0855||CAC0855||Predicted phosphatase (NCBI ptt file)||72, 241|
|CAC0856||CAC0856||Transcriptional regulator, LacI family (probably maltose operon transcriptional repressor) (NCBI ptt file)||72, 206|
|CAC0900||CAC0900||Possible Zn-finger containing protein (NCBI ptt file)||72, 206|
|CAC0920||CAC0920||Protein related to MIFH/DOPD protein family, function in bacteria is unknown (NCBI ptt file)||72, 206|
|CAC1138||CAC1138||Hypothetical protein (NCBI ptt file)||72, 167|
|CAC1292||CAC1292||Membrane protein containing HD superfamily hydrolase domain, YQFF ortholog (NCBI ptt file)||51, 283|
|CAC1419||CAC1419||Uncharacterized proteins, homologs of microcin C7 resistance protein MccF (NCBI ptt file)||283, 346|
|CAC1542||CAC1542||Predicted membrane protein (NCBI ptt file)||278, 283|
|CAC1632||CAC1632||Endonuclease IV (NCBI ptt file)||34, 72|
|CAC1651||CAC1651||Predicted GTPase with uncharacterized domain, ortholog of T.maritima (4980952) (NCBI ptt file)||109, 283|
|CAC1749||CAC1749||BioB/LipA-like protein (NCBI ptt file)||5, 283|
|CAC1962||CAC1962||Predicted esterase of alpha/beta hydrolase superfamily, YBBA B.subtilis ortholog (NCBI ptt file)||71, 72|
|CAC2116||CAC2116||General stress protein, DnaK suppressor DskA, YTEA B.subtilis ortholog (NCBI ptt file)||239, 283|
|CAC2129||murE||UDP-N-acetylmuramyl tripeptide synthase, MurE (NCBI ptt file)||2, 283|
|CAC2169||CAC2169||UDP-galactopyranose mutase (NCBI ptt file)||283, 286|
|CAC2170||CAC2170||Predicted membrane protein (NCBI ptt file)||282, 283|
|CAC2231||murG||Undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNAc GlcNAc transferase, MurG (NCBI ptt file)||283, 286|
|CAC2410||recX||Uncharacterized protein recX (NCBI ptt file)||282, 283|
|CAC2413||CAC2413||Predicted membrane protein (NCBI ptt file)||105, 283|
|CAC2414||CAC2414||Uncharacterized conserved protein, related to alpha-amylase/alpha-mannosidase (NCBI ptt file)||283, 345|
|CAC2424||CAC2424||Predicted phosphoesterase (NCBI ptt file)||72, 148|
|CAC2585||CAC2585||6-pyruvoyl-tetrahydropterin synthase related domain; conserved membrane protein (NCBI ptt file)||72, 328|
|CAC2603||CAC2603||Predicted membrane protein (NCBI ptt file)||15, 72|
|CAC2661||ftsX||Cell division protein FtsX (NCBI ptt file)||72, 346|
|CAC2676||CAC2676||Predicted pseudouridylate synthase (NCBI ptt file)||72, 179|
|CAC3074||CAC3074||Uncharacterized conserved protein (NCBI ptt file)||72, 206|
|CAC3089||CAC3089||Hypothetical protein (NCBI ptt file)||3, 283|
|CAC3185||CAC3185||Membrane-associated protein containing a homolog of PilT-like ATPase N-terminal domain, YACL B.subtilis ortholog (NCBI ptt file)||283, 295|
|CAC3203||hprT||Hypoxanthine-guanine phosphoribosyltransferase (NCBI ptt file)||58, 283|
|CAC3207||CAC3207||Hypothetical protein (NCBI ptt file)||25, 283|
|CAC3216||mfd||Transcription-repair coupling factor, MFD (superfamily II helicase ) (NCBI ptt file)||58, 283|
|CAC3242||CAC3242||Uncharacterized Fe-S protein, PflX (pyruvate formate lyase activating protein) homolog (NCBI ptt file)||72, 301|
|CAC3383||CAC3383||Uncharacterized conserved protein, RtcB/UPF0027 family (NCBI ptt file)||72, 233|
|CAC3400||CAC3400||Predicted dehydrogenase (NCBI ptt file)||72, 283|
|CAC3410||CAC3410||HD-GYP domain (HD superfamily hydrolase) (NCBI ptt file)||70, 72|
|CAC3465||CAC3465||Amidase from nicotinamidase family (NCBI ptt file)||115, 283|
|CAC3466||CAC3466||Transcriptional regulator, LysR family (NCBI ptt file)||115, 283|
|CAC3467||CAC3467||Uncharacterized conserved protein, phnB family (NCBI ptt file)||115, 283|
|CAC3657||CAC3657||NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file)||239, 283|
|CAC3673||xylR||XylR transcriptional regulator (NCBI ptt file)||72, 283|
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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