Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_1473(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 RSP_1473
|Gene||Common Name||Description||Module membership|
|RSP_0004||RSP_0004||hypothetical protein (NCBI)||97, 303|
|RSP_0123||cerI||Autoinducer synthesis protein (NCBI)||97, 309|
|RSP_0187||RSP_0187||Dihydroorotate dehydrogenase (NCBI)||83, 244|
|RSP_0361||sda||probable L-serine dehydratase protein (NCBI)||150, 244|
|RSP_0430||cobD||cobalamin biosynthesis protein CobD (NCBI)||97, 171|
|RSP_0477||RSP_0477||hypothetical protein (NCBI)||97, 103|
|RSP_0498||hupC||Ni, Fe hydrogenase I cytochrome b subunit (NCBI)||244, 300|
|RSP_0542||RSP_0542||hypothetical protein (NCBI)||244, 300|
|RSP_0543||fixU||hypothetical protein (NCBI)||141, 244|
|RSP_0596||RSP_0596||Putative peptidyl-dipeptidase (NCBI)||97, 329|
|RSP_0606||RSP_0606||Putative redox protein (NCBI)||97, 285|
|RSP_0751||RSP_0751||hypothetical protein (NCBI)||62, 97|
|RSP_0955||RSP_0955||5'-nucleotidase (NCBI)||97, 195|
|RSP_1055||RSP_1055||transcriptional regulator, LysR family (NCBI)||97, 329|
|RSP_1435||RSP_1435||regulatory protein TetR family (NCBI)||62, 97|
|RSP_1458||RSP_1458||Putative DNA repair enzyme (NCBI)||244, 282|
|RSP_1473||RSP_1473||hypothetical protein (NCBI)||97, 244|
|RSP_1521||RSP_1521||hypothetical protein (NCBI)||97, 116|
|RSP_1751||RSP_1751||putative 2Fe-2S ferredoxin protein (NCBI)||244, 300|
|RSP_1824||adh||Zinc-containing alcohol dehydrogenase (NCBI)||35, 97|
|RSP_1962||RSP_1962||hypothetical protein (NCBI)||13, 97|
|RSP_1990||RSP_1990||Transcriptional regulator, AsnC family (NCBI)||97, 195|
|RSP_2053||RSP_2053||Possible transporter, RarD family, DMT superfamily (NCBI)||73, 97|
|RSP_2056||RSP_2056||hypothetical protein (NCBI)||244, 347|
|RSP_2123||RSP_2123||Radical SAM domain protein (NCBI)||73, 244|
|RSP_2167||RSP_2167||hypothetical protein (NCBI)||97, 262|
|RSP_2376||kbl||2-amino-3-ketobutyrate CoA ligase (NCBI)||97, 239|
|RSP_2641||RSP_2641||hypothetical protein (NCBI)||97, 237|
|RSP_2932||hutC||Histidine utilization repressor, gntR family (NCBI)||95, 97|
|RSP_2933||hutF||Formiminoglutamate deiminase (NCBI)||95, 97|
|RSP_2934||hutI||Imidazolone-5-propionate hydrolase (NCBI)||95, 97|
|RSP_2935||hutH||Probable histidine ammonia-lyase (NCBI)||95, 97|
|RSP_2936||hutU||Urocanase (NCBI)||95, 97|
|RSP_2964||RSP_2964||hypothetical protein (NCBI)||229, 244|
|RSP_3029||RSP_3029||transcriptional regulator, GntR family (NCBI)||97, 157|
|RSP_3031||RSP_3031||ABC peptide/opine transporter, inner membrane subunit (NCBI)||97, 157|
|RSP_3052||RSP_3052||transcriptional regulator, LysR family (NCBI)||97, 176|
|RSP_3053||RSP_3053||Possible dioxygenase/glyoxalase family protein (NCBI)||97, 176|
|RSP_3087||dgkA||diacylglycerol kinase (NCBI)||97, 176|
|RSP_3129||RSP_3129||serine/threonine protein kinase (NCBI)||244, 249|
|RSP_3130||RSP_3130||Putative serine protease (NCBI)||83, 244|
|RSP_3131||RSP_3131||ABC (antimicrobial peptide) transporter, ATPase subunit (NCBI)||244, 249|
|RSP_3132||RSP_3132||hypothetical protein (NCBI)||244, 249|
|RSP_3133||RSP_3133||hypothetical protein (NCBI)||244, 249|
|RSP_3134||RSP_3134||Serine/threonine protein kinase (NCBI)||244, 249|
|RSP_3135||RSP_3135||ppkA-related protein (NCBI)||244, 292|
|RSP_3180||RSP_3180||Transglutaminase-like enzyme (NCBI)||38, 97|
|RSP_3188||RSP_3188||ApbE family protein (NCBI)||244, 300|
|RSP_3190||RSP_3190||2Fe-2S ferredoxin (NCBI)||68, 244|
|RSP_3191||fprA||Flavodoxin (NCBI)||244, 300|
|RSP_3199||RSP_3199||hypothetical protein (NCBI)||244, 300|
|RSP_3211||cbiO||ABC cobalt transporter, ATPase subunit, CbiO (NCBI)||23, 244|
|RSP_3400||RSP_3400||transcriptional regulator, LysR family (NCBI)||19, 97|
|RSP_3404||RSP_3404||hypothetical protein (NCBI)||95, 244|
|RSP_3405||gntR||transcriptional regulator, GntR family (NCBI)||95, 244|
|RSP_3628||RSP_3628||hypothetical protein (NCBI)||150, 244|
|RSP_3748||ampR||transcriptional regulator, LysR family (NCBI)||97, 362|
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.
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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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.
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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.
- 2. Source gene
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