Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_3544(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_3544
|Gene||Common Name||Description||Module membership|
|RSP_0116||RSP_0116||hypothetical protein (NCBI)||14, 229|
|RSP_0181||RSP_0181||ABC nitrate/sulfonate/bicarbonate transporter, inner membrane subunit (NCBI)||193, 342|
|RSP_0221||RSP_0221||plasma membrane H+-transporting two-sector ATPase, C subunit (NCBI)||14, 342|
|RSP_0381||RSP_0381||hypothetical protein (NCBI)||14, 43|
|RSP_0620||RSP_0620||hypothetical protein (NCBI)||313, 342|
|RSP_0621||RSP_0621||Possible DNA helicase (NCBI)||14, 36|
|RSP_0838||RSP_0838||putative DNA polymerase III, delta subunit / DNA binding (NCBI)||141, 342|
|RSP_0961||MeaA||similiar to methylmalonyl-CoA mutases (NCBI)||14, 253|
|RSP_1320||flhA||Flagellar biosynthesis pathway, component FlhA (NCBI)||220, 342|
|RSP_1333||RSP_1333||hypothetical protein (NCBI)||320, 342|
|RSP_1334||RSP_1334||possible chemotactic signal-response protein CheL (NCBI)||320, 342|
|RSP_1335||RSP_1335||hypothetical protein (NCBI)||320, 342|
|RSP_1336||RSP_1336||Possible FlgD protein (NCBI)||320, 342|
|RSP_1616||RSP_1616||hypothetical protein (NCBI)||141, 342|
|RSP_1620||RSP_1620||hypothetical protein (NCBI)||235, 342|
|RSP_1656||RSP_1656||hypothetical protein (NCBI)||325, 342|
|RSP_1658||RSP_1658||hypothetical protein (NCBI)||325, 342|
|RSP_1659||RSP_1659||hypothetical protein (NCBI)||325, 342|
|RSP_2011||RSP_2011||putative transcription elongation factor (NCBI)||14, 128|
|RSP_2260||ydjG||hypothetical protein (NCBI)||267, 342|
|RSP_2291||RSP_2291||hypothetical protein (NCBI)||14, 370|
|RSP_2807||RSP_2807||putative cytochrome b (NCBI)||14, 229|
|RSP_2808||RSP_2808||hypothetical protein (NCBI)||14, 229|
|RSP_2991||RSP_2991||hypothetical protein (NCBI)||14, 189|
|RSP_2996||RSP_2996||putative prohead protease (NCBI)||14, 235|
|RSP_2997||RSP_2997||putative head portal protein (NCBI)||14, 235|
|RSP_2998||RSP_2998||Hypothetical Terminase large subunit (NCBI)||14, 189|
|RSP_2999||RSP_2999||hypothetical protein (NCBI)||14, 189|
|RSP_3000||RSP_3000||hypothetical protein (NCBI)||14, 325|
|RSP_3001||RSP_3001||Possible Endonuclease (NCBI)||14, 189|
|RSP_3057||RSP_3057||ABC proline/glycine betaine transporter, ATPase subunit (NCBI)||105, 342|
|RSP_3058||RSP_3058||ABC proline/glycine betaine transporter, inner membrane subunit (NCBI)||105, 342|
|RSP_3059||RSP_3059||ABC proline/glycine betaine transporter, periplasmic substrate-binding protein (NCBI)||105, 342|
|RSP_3110||RSP_3110||Putative Glutathione S-transferase (NCBI)||62, 342|
|RSP_3119||RSP_3119||conserved hypothetical protein / putative esterase (NCBI)||14, 38|
|RSP_3175||RSP_3175||hypothetical protein (NCBI)||14, 19|
|RSP_3203||RSP_3203||transcriptional regulator, AraC family (NCBI)||14, 19|
|RSP_3240||RSP_3240||periplasmic sensor signal transduction histidine kinase (NCBI)||14, 19|
|RSP_3252||RSP_3252||ABC peptide transporter, fused ATPase domains (NCBI)||14, 325|
|RSP_3264||RSP_3264||probable c-type cytochrome (NCBI)||14, 27|
|RSP_3312||RSP_3312||hypothetical protein (NCBI)||14, 188|
|RSP_3343||RSP_3343||putative glycosyl transferase (NCBI)||14, 168|
|RSP_3360||RSP_3360||Adenine specific DNA methyltransferase, D12 class (NCBI)||103, 342|
|RSP_3406||pdxA||4-hydroxythreonine-4-phosphate dehydrogenase 2 (NCBI)||61, 342|
|RSP_3428||RSP_3428||hypothetical protein (NCBI)||14, 116|
|RSP_3434||RSP_3434||hypothetical protein (NCBI)||14, 144|
|RSP_3445||RSP_3445||transcriptional regulator, GntR family (NCBI)||61, 342|
|RSP_3518||RSP_3518||ABC polyamine/opine transporter, inner membrane subunit (NCBI)||31, 342|
|RSP_3544||RSP_3544||hypothetical protein (NCBI)||14, 342|
|RSP_3545||RSP_3545||hypothetical protein (NCBI)||325, 342|
|RSP_3573||gvpA||Gas vesicle protein GVPa (NCBI)||14, 27|
|RSP_3661||RSP_3661||TRAP-T family transporter, periplasmic binding protein (NCBI)||208, 342|
|RSP_3662||RSP_3662||TRAP-T family transporter, large (12TMs) inner membrane subunit (NCBI)||208, 342|
|RSP_3663||RSP_3663||TRAP-T family transporter, small (4TMs) inner membrane subunit (NCBI)||141, 342|
|RSP_3753||RSP_3753||hypothetical protein (NCBI)||14, 183|
|RSP_3781||RSP_3781||putative phage terminase large subunit (NCBI)||150, 342|
|RSP_4294||RSP_4294||16S ribosomal RNA (NCBI)||14, 43|
|RSP_4295||RSP_4295||23S ribosomal RNA (NCBI)||14, 310|
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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