Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
hypothetical protein (NCBI)
Functional Annotations (1)
|Uncharacterized conserved protein||cog/ cog|
Regulation information for RSP_3403(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|
Functional Enrichment for RSP_3403
|Uncharacterized conserved protein||cog/ cog|
Module neighborhood information for RSP_3403
|Gene||Common Name||Description||Module membership|
|RSP_0161||RSP_0161||Spermidine/putrescine-binding periplasmic protein (NCBI)||70, 102|
|RSP_0184||RSP_0184||putative N-carbamyl-L-amino acid amidohydrolase (NCBI)||92, 102|
|RSP_0185||RSP_0185||Transcriptional regulator, TetR family (NCBI)||92, 102|
|RSP_0610||RSP_0610||Putative 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI)||95, 273|
|RSP_0796||cobQ||cobyric acid synthase (NCBI)||95, 158|
|RSP_0851||RSP_0851||Putative transporter, AEC family (NCBI)||16, 102|
|RSP_0852||fghA||S-formylglutathione hydrolase (NCBI)||16, 102|
|RSP_0853||RSP_0853||hypothetical protein (NCBI)||16, 102|
|RSP_1308||RSP_1308||hypothetical protein (NCBI)||92, 102|
|RSP_1355||RSP_1355||Glycosyl transferase, family 51 (NCBI)||92, 102|
|RSP_1413||RSP_1413||TRAP-T family transporter, periplasmic binding component (NCBI)||70, 102|
|RSP_1434||RSP_1434||Putative Zn-dependent oxidoreductase (NCBI)||95, 113|
|RSP_1553||RSP_1553||Probable glyoxylate induced protein (NCBI)||102, 381|
|RSP_1554||RSP_1554||Possible polysaccharide deacetylase (NCBI)||102, 381|
|RSP_1747||bztA||ABC glutamate/glutamine/aspartate/asparagine transporter, periplasmic substrate-binding protein (NCBI)||70, 102|
|RSP_1758||RSP_1758||Probable succinyl-diaminopimelate desuccinylase (NCBI)||95, 102|
|RSP_2141||RSP_2141||ABC polyamine transporter, periplasmic substrate-binding protein (NCBI)||102, 204|
|RSP_2317||RSP_2317||Iron-containing alcohol dehydrogenase (NCBI)||16, 102|
|RSP_2318||RSP_2318||putative Aldehyde dehydrogenase (NCBI)||16, 102|
|RSP_2319||glnA||Glutamine synthetase class-I (NCBI)||16, 102|
|RSP_2321||RSP_2321||Putative TRAP-T family transporter, DctM (12TMs) subunit (NCBI)||16, 102|
|RSP_2322||RSP_2322||TRAP-T family transporter, DctQ (4TMs) subunit (NCBI)||16, 102|
|RSP_2323||RSP_2323||hypothetical protein (NCBI)||16, 102|
|RSP_2324||RSP_2324||transcriptional regulator, RpiR family (NCBI)||16, 102|
|RSP_2632||argI||Arginase (NCBI)||95, 168|
|RSP_2730||RSP_2730||Transcriptional regulator, ArsR family (NCBI)||67, 95|
|RSP_2853||RSP_2853||Transcriptional regulator, TetR family (NCBI)||12, 95|
|RSP_2854||RSP_2854||Cation/multidrug efflux pump, Membrane fusion protein (MFP) family (NCBI)||12, 95|
|RSP_2855||RSP_2855||Cation/multidrug efflux pump, RND superfamily (NCBI)||12, 95|
|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_3225||RSP_3225||periplasmic sensor signal transduction histidine kinase (NCBI)||102, 118|
|RSP_3241||RSP_3241||Two-component transcriptional regulator, winged helix family (NCBI)||102, 195|
|RSP_3298||RSP_3298||transcriptional regulator, LysR family (NCBI)||95, 273|
|RSP_3364||proC||Pyrroline-5-carboxylate reductase (NCBI)||102, 171|
|RSP_3365||csaA||Protein secretion chaperonine (NCBI)||102, 171|
|RSP_3366||RSP_3366||D-isomer specific 2-hydroxyacid dehydrogenase (NCBI)||102, 171|
|RSP_3382||RSP_3382||hypothetical protein (NCBI)||57, 102|
|RSP_3383||RSP_3383||hypothetical protein (NCBI)||57, 102|
|RSP_3403||RSP_3403||hypothetical protein (NCBI)||95, 102|
|RSP_3404||RSP_3404||hypothetical protein (NCBI)||95, 244|
|RSP_3405||gntR||transcriptional regulator, GntR family (NCBI)||95, 244|
|RSP_3520||RSP_3520||ABC peptide transporter, fused ATPase domains (NCBI)||95, 170|
|RSP_3522||RSP_3522||ABC peptide transporter, inner membrane subunit (NCBI)||95, 170|
|RSP_3523||RSP_3523||ABC peptide transporter, inner membrane subunit (NCBI)||95, 170|
|RSP_3524||RSP_3524||ABC peptide transporter, periplasmic binding protein (NCBI)||95, 170|
|RSP_3525||RSP_3525||ABC peptide transporter, periplasmic binding protein (NCBI)||95, 170|
|RSP_3526||RSP_3526||Amidase (NCBI)||95, 170|
|RSP_3527||RSP_3527||Probable acetylpolyamine aminohydrolase (NCBI)||95, 170|
|RSP_3584||RSP_3584||hypothetical protein (NCBI)||95, 242|
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.
Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
Module Members Tab
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
- 3. Target genes (other module members)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
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