Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3661

TRAP-T family transporter, periplasmic binding protein (NCBI)

CircVis
Functional Annotations (4)
Function System
TRAP-type C4-dicarboxylate transport system, periplasmic component cog/ cog
transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
dctP tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3661
(Mouseover regulator name to see its description)

RSP_3661 is regulated by 17 influences and regulates 0 modules.
Regulators for RSP_3661 (17)
Regulator Module Operator
RSP_0386 342 tf
RSP_1518 342 tf
RSP_1607 342 tf
RSP_2867 342 tf
RSP_3064 342 tf
RSP_3238 342 tf
RSP_3322 342 tf
RSP_3445 342 tf
RSP_3464 342 tf
RSP_0623 208 tf
RSP_0722 208 tf
RSP_0760 208 tf
RSP_1164 208 tf
RSP_1225 208 tf
RSP_1712 208 tf
RSP_1739 208 tf
RSP_1890 208 tf

Warning: RSP_3661 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
8136 2.70e-04 TTtatcctta.ctAaaaaAA
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8137 1.30e+00 CCC.tt.ctGtTG.tt.gaGg
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8386 2.60e-02 tctcCtTaggTCgcAtTtTtT
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8387 1.90e+00 TctggcgGaAagg.cttac.gAac
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for RSP_3661

RSP_3661 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
TRAP-type C4-dicarboxylate transport system, periplasmic component cog/ cog
transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
dctP tigr/ tigrfam
Module neighborhood information for RSP_3661

RSP_3661 has total of 54 gene neighbors in modules 208, 342
Gene neighbors (54)
Gene Common Name Description Module membership
RSP_0009 RSP_0009 hypothetical protein (NCBI) 98, 208
RSP_0181 RSP_0181 ABC nitrate/sulfonate/bicarbonate transporter, inner membrane subunit (NCBI) 193, 342
RSP_0189 RSP_0189 NADPH-dependent glutamate synthase beta chain and related oxidoreductase (NCBI) 43, 208
RSP_0190 accB Biotin carboxyl carrier protein, AccB (NCBI) 43, 208
RSP_0191 accC Biotin carboxylase (NCBI) 43, 208
RSP_0192 aat possible leucyl/phenylalanyl-tRNA--protein transferase (NCBI) 43, 208
RSP_0221 RSP_0221 plasma membrane H+-transporting two-sector ATPase, C subunit (NCBI) 14, 342
RSP_0620 RSP_0620 hypothetical protein (NCBI) 313, 342
RSP_0838 RSP_0838 putative DNA polymerase III, delta subunit / DNA binding (NCBI) 141, 342
RSP_0962 RSP_0962 Dihydrolipoamide dehydrogenase (NCBI) 190, 208
RSP_0963 RSP_0963 Inner membrane protein (NCBI) 208, 221
RSP_0964 sucB Dihydrolipoamide transsuccinylase (NCBI) 208, 297
RSP_0965 sucA 2-oxoglutarate dehydrogenase E1 component (RefSeq) 208, 297
RSP_0966 sucD Succinyl-CoA synthetase, alpha subunit (NCBI) 208, 297
RSP_0967 sucC Succinyl-CoA synthetase, beta subunit (NCBI) 208, 297
RSP_0970 RSP_0970 Putative citrate lyase beta chain (NCBI) 208, 263
RSP_1060 rnpA Ribonuclease P protein component (NCBI) 182, 208
RSP_1061 RSP_1061 hypothetical protein (NCBI) 65, 208
RSP_1071 moaE Molybdopterin converting factor subunit 2 (NCBI) 154, 208
RSP_1074 uvrC Excinuclease ABC, C subunit (NCBI) 208, 340
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_1622 RSP_1622 Putative DNA-binding protein (NCBI) 93, 208
RSP_1624 RSP_1624 hypothetical protein (NCBI) 48, 208
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_1975 RSP_1975 aminopeptidase P (NCBI) 208, 326
RSP_2260 ydjG hypothetical protein (NCBI) 267, 342
RSP_2297 atpA F0F1-type ATP synthase alpha subunit (NCBI) 208, 369
RSP_2423 RSP_2423 putative Heat shock protein 15 (HSP15) (NCBI) 65, 208
RSP_2924 RSP_2924 ABC branched-chain amino acid transporter family, ATPase subunit (NCBI) 65, 208
RSP_2925 RSP_2925 ABC branched-chain amino acid transporter family, ATPase subunit (NCBI) 65, 208
RSP_2926 RSP_2926 ABC branched-chain amino acid transporter family, inner membrane subunit (NCBI) 65, 208
RSP_2928 RSP_2928 hypothetical protein (NCBI) 65, 208
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_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_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_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_3781 RSP_3781 putative phage terminase large subunit (NCBI) 150, 342
Gene Page Help

Network Tab

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.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

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.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

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.

Functions Tab

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.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our 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
  • 6. Visualisation legend
Comments for RSP_3661
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our 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
  • 6. Visualisation legend