Organism : Desulfovibrio vulgaris Hildenborough | Module List :
ABC transporter permease
Functional Annotations (2)
|ABC-type antimicrobial peptide transport system, permease component||cog/ cog|
Regulation information for DVUA0023(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.
|Motif Id||e-value||Consensus||Motif Logo||RegPredict|
Functional Enrichment for DVUA0023
|ABC-type antimicrobial peptide transport system, permease component||cog/ cog|
Module neighborhood information for DVUA0023
|Gene||Common Name||Description||Module membership|
|DVU0111||response regulator||143, 274|
|DVU0175||tungsten formylmethanofuran dehydrogenase family protein/molybdopterin binding protein||192, 348|
|DVU0239||hypothetical protein DVU0239||153, 274|
|DVU0453||ATP-dependent DNA helicase UvrD||71, 274|
|DVU0456||DHH family protein||153, 192|
|DVU0577||formate dehydrogenase formation protein FdhE||274, 281|
|DVU0579||molybdopterin-guanine dinucleotide biosynthesis protein A||274, 281|
|DVU0580||moaA||molybdenum cofactor biosynthesis protein A||192, 281|
|DVU0587||fdnG-1||formate dehydrogenase subunit alpha, selenocysteine-containing||167, 274|
|DVU0600||ldh||L-lactate dehydrogenase||192, 281|
|DVU0626||ilvN-1||acetolactate synthase small subunit||192, 298|
|DVU0701||glcB||malate synthase G||192, 348|
|DVU0819||FMN reductase, NADPH-dependent||153, 274|
|DVU1037||mercuric reductase||181, 192|
|DVU1396||hypothetical protein DVU1396||192, 274|
|DVU1412||glycerate dehydrogenase||236, 274|
|DVU1413||hypothetical protein DVU1413||192, 296|
|DVU1420||Hpt domain-containing protein||109, 192|
|DVU1471||HSP20 family protein||71, 192|
|DVU1472||ATP-dependent protease||115, 192|
|DVU1564||hypothetical protein DVU1564||263, 274|
|DVU1592||arginine N-succinyltransferase subunit beta||192, 274|
|DVU1593||cheY-1||chemotaxis protein CheY||123, 274|
|DVU1594||cheA-1||chemotaxis protein CheA||192, 274|
|DVU1595||cheR-1||chemotaxis protein methyltransferase||274, 277|
|DVU1596||cheB-1||protein-glutamate methylesterase CheB||192, 274|
|DVU1597||sulfite reductase, assimilatory-type||123, 274|
|DVU1613||glutamate synthase subunit beta||192, 236|
|DVU1614||iron-sulfur cluster-binding protein||6, 192|
|DVU1958||sensory box histidine kinase||69, 192|
|DVU1973||rhodanese-like domain-containing protein||269, 274|
|DVU1974||pyridine nucleotide-disulfide oxidoreductase||274, 283|
|DVU1986||hypothetical protein DVU1986||192, 198|
|DVU2349||carbohydrate phosphorylase family protein||60, 192|
|DVU2360||FAD/NAD-binding family oxidoreductase||115, 192|
|DVU2421||4-oxalocrotonate tautomerase family protein||192, 274|
|DVU2422||nitroreductase family protein||192, 274|
|DVU2482||fdnG-2||formate dehydrogenase subunit alpha, selenocysteine-containing||192, 348|
|DVU2895||hypothetical protein DVU2895||115, 192|
|DVU2968||sensor histidine kinase/response regulator||148, 192|
|DVU2972||chemotaxis protein CheD||37, 274|
|DVU2976||hypothetical protein DVU2976||83, 192|
|DVU3037||rhodanese-like domain-containing protein||192, 348|
|DVU3041||cytochrome c553||178, 274|
|DVU3076||hypothetical protein DVU3076||269, 274|
|DVU3077||AhpC/TSA family protein||192, 269|
|DVU3079||glyoxalase family protein||110, 274|
|DVU3135||flavodoxin-like fold domain-containing protein||110, 274|
|DVU3136||nitroreductase family protein||110, 274|
|DVU3217||hypothetical protein DVU3217||109, 192|
|DVU3282||ADP-ribosylglycohydrolase family protein||109, 192|
|DVUA0021||hypothetical protein DVUA0021||61, 192|
|DVUA0023||ABC transporter permease||192, 274|
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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If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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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)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
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