Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_2457(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_2457
|Gene||Common Name||Description||Module membership|
|RSP_0349||RSP_0349||ABC transporter, ATPase subunit (NCBI)||267, 293|
|RSP_0369||RSP_0369||hypothetical protein (NCBI)||47, 267|
|RSP_0452||recA||Recombinase A, DNA recombination protein (NCBI)||30, 93|
|RSP_0459||RSP_0459||hypothetical protein (NCBI)||47, 267|
|RSP_0657||RSP_0657||hypothetical protein (NCBI)||30, 72|
|RSP_0658||RSP_0658||Probable ATP-dependent helicase (NCBI)||30, 72|
|RSP_0659||RSP_0659||Putative metallo-phosphoesterase (NCBI)||30, 72|
|RSP_0772||parE||DNA topoisomerase II/DNA gyrase, subunit B (NCBI)||69, 267|
|RSP_0863||leuC||3-isopropylmalate dehydratase large subunit (NCBI)||30, 203|
|RSP_1013||RSP_1013||possible Hemolysin (NCBI)||68, 267|
|RSP_1069||RSP_1069||hypothetical protein (NCBI)||233, 267|
|RSP_1170||RSP_1170||OmpA family protein (NCBI)||267, 355|
|RSP_1235||coaE||Dephospho-CoA kinase (NCBI)||87, 267|
|RSP_1236||dnaQ||putative DNA polymerase III, epsilon subunit and related 3'-5' exonucleases (NCBI)||87, 267|
|RSP_1293||RSP_1293||putative acyl-carrier protein (NCBI)||267, 380|
|RSP_1360||RSP_1360||hypothetical protein (NCBI)||30, 93|
|RSP_1410||RSP_1410||hypothetical protein (NCBI)||2, 30|
|RSP_1489||RSP_1489||Protein containing thioredoxin domain (NCBI)||30, 71|
|RSP_1503||RSP_1503||hypothetical protein (NCBI)||265, 267|
|RSP_1673||RSP_1673||Probable holo-acyl carrier protein synthase (NCBI)||265, 267|
|RSP_1683||RSP_1683||putative kinase/phosphatase (NCBI)||267, 341|
|RSP_1997||lexA||LexA repressor (NCBI)||30, 93|
|RSP_1998||RSP_1998||Molybdenum cofactor biosynthesis protein A (NCBI)||30, 114|
|RSP_2000||RSP_2000||molybdenum cofactor biosynthesis protein C (NCBI)||30, 207|
|RSP_2081||RSP_2081||putative acetyltransferase, GNAT family (NCBI)||87, 267|
|RSP_2212||rimI||putative acetyltransferase (NCBI)||159, 267|
|RSP_2260||ydjG||hypothetical protein (NCBI)||267, 342|
|RSP_2326||pbpA||Cell division protein FtsI (NCBI)||47, 267|
|RSP_2457||RSP_2457||hypothetical protein (NCBI)||30, 267|
|RSP_2460||alr||alanine racemase (NCBI)||30, 369|
|RSP_2567||sqdC||putative sulfolipid biosynthesis protein (NCBI)||47, 267|
|RSP_2624||RSP_2624||hypothetical protein (NCBI)||30, 93|
|RSP_2628||gltX/glnS||glutamyl-/ glutaminyl-tRNA synthetase (NCBI)||65, 267|
|RSP_2722||cysS||Cysteinyl-tRNA synthetase, class Ia (NCBI)||30, 214|
|RSP_2851||RSP_2851||multidrug (bicyclomycin) efflux pump, Major facilitator superfamily (MFS) (NCBI)||12, 30|
|RSP_2905||ksgA||Putative ribosomal RNA adenine dimethylase (NCBI)||87, 267|
|RSP_3249||RSP_3249||ABC peptide transporter, duplicated ATPase domains (NCBI)||267, 362|
|RSP_3250||RSP_3250||ABC peptide transporter, inner membrane subunit (NCBI)||267, 340|
|RSP_3251||RSP_3251||ABC peptide transporter, inner membrane subunit (NCBI)||267, 362|
|RSP_3301||eda||2-dehydro-3-deoxyphosphogluconate aldolase (NCBI)||265, 267|
|RSP_3373||RSP_3373||ABC efflux transporter, inner membrane subunit (NCBI)||42, 267|
|RSP_3572||galM||putative aldose 1-epimerase protein (NCBI)||23, 30|
|RSP_3822||RSP_3822||GTP1/OBG family protein (NCBI)||30, 279|
|RSP_3823||proB1||glutamate 5-kinase (NCBI)||30, 240|
|RSP_3824||proA||Gamma-glutamyl phosphate reductase GPR (NCBI)||30, 101|
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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