Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_3630(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_3630
|Gene||Common Name||Description||Module membership|
|RSP_0028||RSP_0028||Putative short-chain dehydrogenase/reductase (NCBI)||246, 251|
|RSP_0481||RSP_0481||possible 2-deoxy-D-gluconate 3-dehydrogenase (NCBI)||253, 301|
|RSP_0495||hupS||hydrogenase protein small subunit (NCBI)||253, 300|
|RSP_0496||hupL||hydrogenase protein large subunit (NCBI)||253, 300|
|RSP_0497||RSP_0497||HupE/UreJ accessory protein (NCBI)||253, 300|
|RSP_0522||RSP_0522||putative oxidoreductase (NCBI)||217, 246|
|RSP_0644||RSP_0644||ABC transporter, inner membrane subunit (NCBI)||253, 347|
|RSP_0645||RSP_0645||ABC transporter, ATPase subunit (NCBI)||253, 347|
|RSP_0646||RSP_0646||ABC transporter, substrate-binding protein (NCBI)||253, 347|
|RSP_0647||thiD||phosphomethylpyrimidine kinase (NCBI)||253, 347|
|RSP_0648||thiE||Thiamine-phosphate pyrophosphorylase (NCBI)||253, 347|
|RSP_0649||thiM||Putative hydoxyethylthiazole kinase (NCBI)||253, 347|
|RSP_0835||manB||phosphomannomutase (NCBI)||153, 246|
|RSP_0961||MeaA||similiar to methylmalonyl-CoA mutases (NCBI)||14, 253|
|RSP_1115||RSP_1115||hypothetical protein (NCBI)||246, 292|
|RSP_1116||RSP_1116||glycosyltransferase (NCBI)||196, 246|
|RSP_1117||RSP_1117||hypothetical protein (NCBI)||137, 246|
|RSP_1118||RSP_1118||group 1 glycosyltransferase (NCBI)||246, 292|
|RSP_1119||RSP_1119||ABC protein exporter, fused ATPase and inner membrane subunits (NCBI)||196, 246|
|RSP_1120||RSP_1120||protein secretion protein, HlyD family, membrane fusion protein (NCBI)||137, 246|
|RSP_1299||RSP_1299||putative binding domain (NCBI)||253, 303|
|RSP_1302||motB||putative chemotaxis MotB protein (NCBI)||31, 246|
|RSP_1303||flgE||putative flagellar hook protein (NCBI)||29, 246|
|RSP_1304||RSP_1304||putative flagellar hook protein (NCBI)||124, 246|
|RSP_1305||RSP_1305||putative flagellar hook-associated protein (NCBI)||138, 246|
|RSP_1307||flgI||putative flagellar P-ring protein (NCBI)||31, 246|
|RSP_1630||RSP_1630||hypothetical protein (NCBI)||31, 246|
|RSP_1639||RSP_1639||hypothetical protein (NCBI)||233, 253|
|RSP_1920||RSP_1920||Pyridoxal/pyridoxine/pyridoxamine kinase (NCBI)||99, 253|
|RSP_1921||RSP_1921||MOSC domain protein (NCBI)||99, 253|
|RSP_2063||RSP_2063||hypothetical protein (NCBI)||253, 303|
|RSP_2757||RSP_2757||hypothetical protein (NCBI)||236, 246|
|RSP_2758||RSP_2758||hypothetical protein (NCBI)||246, 251|
|RSP_2759||RSP_2759||hypothetical protein (NCBI)||246, 282|
|RSP_2760||RSP_2760||hypothetical protein (NCBI)||246, 251|
|RSP_2761||RSP_2761||putative P2-like prophage tail protein X (NCBI)||246, 282|
|RSP_3108||RSP_3108||Putative methyl accepting chemotaxis protein (NCBI)||246, 292|
|RSP_3116||RSP_3116||Conserved hypothetical membrane/transport protein (NCBI)||246, 370|
|RSP_3242||RSP_3242||Putative trypsin-like serine protease (NCBI)||253, 331|
|RSP_3284||iolD||Acetolactate synthase (NCBI)||176, 246|
|RSP_3285||iolE||possible sugar phosphate isomerases/epimerases, IolE (NCBI)||150, 246|
|RSP_3286||iolB||Uncharacterized enzyme involved in inositol metabolism, IolB (NCBI)||246, 380|
|RSP_3339||RSP_3339||transcriptional regulator, GntR family (NCBI)||38, 253|
|RSP_3391||RSP_3391||ABC Fe3+-siderophores transporter, inner membrane subunit (NCBI)||188, 253|
|RSP_3413||RSP_3413||ABC Fe+3-siderophore transporter, ATPase subunit (NCBI)||138, 253|
|RSP_3577||gvpG||putative gas vesicle synthesis protein (NCBI)||253, 304|
|RSP_3578||gvpF2||putative gas vesicle synthesis protein (NCBI)||153, 253|
|RSP_3579||RSP_3579||Heat shock protein Hsp20 (NCBI)||196, 253|
|RSP_3580||gvpJ||Gas vesicle protein GVPa (NCBI)||253, 282|
|RSP_3581||RSP_3581||hypothetical protein (NCBI)||196, 253|
|RSP_3582||gvpN||ATPase (NCBI)||153, 253|
|RSP_3630||RSP_3630||hypothetical protein (NCBI)||246, 253|
|RSP_3631||RSP_3631||hypothetical protein (NCBI)||73, 253|
|RSP_3690||RSP_3690||resiniferatoxin-binding, phosphotriesterase-related protein (NCBI)||31, 253|
|RSP_3796||RSP_3796||hypothetical protein (NCBI)||253, 282|
|RSP_3811||RSP_3811||hypothetical protein (NCBI)||138, 246|
|RSP_4345||RSP_4345||tRNA-Glu (NCBI)||34, 246|
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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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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