Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_6219(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_6219
|Gene||Common Name||Description||Module membership|
|RSP_0157||RSP_0157||Beta-mannanase (NCBI)||147, 290|
|RSP_0158||RSP_0158||cellulose synthase-like protein (NCBI)||147, 290|
|RSP_0159||galE-2||UDP-glucose 4-epimerase (NCBI)||147, 290|
|RSP_0160||RSP_0160||NAD-dependent epimerase/dehydratase family protein (NCBI)||147, 290|
|RSP_1309||fliP||Type III secretion system inner membrane P protein (NCBI)||147, 290|
|RSP_1310||RSP_1310||hypothetical protein (NCBI)||147, 290|
|RSP_1311||fliH||putative flagellar biosynthesis/type III secretory pathway protein (NCBI)||147, 290|
|RSP_1312||fliF||flagellar MS-ring protein (RefSeq)||147, 290|
|RSP_1313||RSP_1313||possible flagellar synthesis protein (NCBI)||147, 290|
|RSP_1314||RSP_1314||hypothetical protein (NCBI)||147, 290|
|RSP_1315||RSP_1315||hypothetical protein (NCBI)||147, 290|
|RSP_1316||motA||Flagellar motor protein MotA (NCBI)||147, 290|
|RSP_3457||RSP_3457||ABC polar amino acid transporter, periplasmic binding protein (NCBI)||111, 143|
|RSP_3458||RSP_3458||ABC polar amino acid transporter, ATPase subunit (NCBI)||111, 143|
|RSP_3459||RSP_3459||ABC polar amino acid transporter, inner membrane subunit (NCBI)||111, 143|
|RSP_3460||RSP_3460||ABC polar amino acid transporter, inner membrane subunit (NCBI)||111, 143|
|RSP_3461||RSP_3461||N-carbamyl-D-amino acid amidohydrolase (NCBI)||111, 143|
|RSP_3462||RSP_3462||putative D-hydantoinase dihydropyrimidinase (NCBI)||111, 143|
|RSP_3463||RSP_3463||putative hydantoin racemase (NCBI)||111, 143|
|RSP_3464||RSP_3464||transcriptional regulator, LysR-family (NCBI)||111, 143|
|RSP_3465||RSP_3465||hypothetical protein (NCBI)||111, 143|
|RSP_3529||RSP_3529||hypothetical protein (NCBI)||79, 143|
|RSP_3530||RSP_3530||Oxidoreductase (NCBI)||79, 143|
|RSP_3532||RSP_3532||AMP-binding enzyme (NCBI)||79, 143|
|RSP_3533||RSP_3533||Aldehyde dehydrogenase family protein (NCBI)||79, 143|
|RSP_3534||RSP_3534||Aminotransferase class-III (NCBI)||79, 143|
|RSP_3535||RSP_3535||enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme (NCBI)||79, 143|
|RSP_3536||RSP_3536||Thiolase (NCBI)||79, 143|
|RSP_3680||RSP_3680||transcriptional regulator, TetR family (NCBI)||143, 215|
|RSP_3681||stcD2||putative NADH-dependent oxidase (NCBI)||61, 143|
|RSP_4346||RSP_4346||tRNA-Gln (NCBI)||8, 290|
|RSP_6091||RSP_6091||hypothetical protein (NCBI)||199, 290|
|RSP_6093||flgJ||FlgJ (NCBI)||123, 290|
|RSP_6139||RSP_6139||hypothetical protein (NCBI)||255, 290|
|RSP_6180||RSP_6180||conserved hypothetical membrane protein (NCBI)||290, 330|
|RSP_6219||RSP_6219||hypothetical protein (NCBI)||143, 290|
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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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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- 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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