Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3387

TRAP-T family transporter, fused small and large inner membrane subunits (NCBI)

CircVis
Functional Annotations (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3387
(Mouseover regulator name to see its description)

RSP_3387 is regulated by 21 influences and regulates 0 modules.
Regulators for RSP_3387 (21)
Regulator Module Operator
RSP_0068 220 tf
RSP_0186 220 tf
RSP_0402 220 tf
RSP_1231 220 tf
RSP_2011 220 tf
RSP_2410 220 tf
RSP_3029 220 tf
RSP_3064 220 tf
RSP_3124 220 tf
RSP_3385 220 tf
RSP_3445 220 tf
RSP_3528 220 tf
RSP_3616 220 tf
RSP_3676 220 tf
RSP_0616 133 tf
RSP_1191 133 tf
RSP_1867 133 tf
RSP_2182 133 tf
RSP_2932 133 tf
RSP_3055 133 tf
RSP_3514 133 tf

Warning: RSP_3387 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
7986 4.70e+02 aAg.GgcGGtGcc..cGaT
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7987 6.40e+03 accCTtcCCGAa
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8160 3.40e+02 aTtTcaagAT
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8161 7.30e+03 TCCTTGCGGGAAAAAGA
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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_3387

RSP_3387 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
Module neighborhood information for RSP_3387

RSP_3387 has total of 51 gene neighbors in modules 133, 220
Gene neighbors (51)
Gene Common Name Description Module membership
RSP_0003 RSP_0003 putative site-specific recombinase (NCBI) 220, 303
RSP_0010 RSP_0010 homoserine O-succinyltransferase (NCBI) 91, 133
RSP_0135 RSP_0135 hypothetical protein (NCBI) 29, 133
RSP_0201 RSP_0201 ABC transporter, fused inner membrane subunits (NCBI) 121, 133
RSP_0219 RSP_0219 hypothetical protein (NCBI) 168, 220
RSP_0307 RSP_0307 Antifreeze protein, type I (NCBI) 133, 265
RSP_0492 hupU hydrogenase small subunit (NCBI) 83, 133
RSP_0563 RSP_0563 putative site-specific recombinase (NCBI) 220, 323
RSP_0786 RSP_0786 possible Endonuclease/Exonuclease/phosphatase fa (NCBI) 13, 220
RSP_0950 RSP_0950 Arginine utilization protein RocB (NCBI) 23, 133
RSP_0954 RSP_0954 Transglutaminase-like domain (NCBI) 82, 220
RSP_1121 RSP_1121 acetyl transferase, Isoleucine patch superfamily (NCBI) 133, 242
RSP_1226 RSP_1226 hypothetical protein (NCBI) 133, 187
RSP_1320 flhA Flagellar biosynthesis pathway, component FlhA (NCBI) 220, 342
RSP_1366 RSP_1366 Class I peptide chain release factor (NCBI) 53, 133
RSP_1400 RSP_1400 DNA polymerase IV (RefSeq) 11, 133
RSP_1417 RSP_1417 hypothetical protein (NCBI) 23, 133
RSP_1846 RSP_1846 hypothetical protein (NCBI) 133, 164
RSP_1899 RSP_1899 Predicted ATPase (NCBI) 91, 220
RSP_1931 RSP_1931 Probable ATPase, AAA family (NCBI) 1, 220
RSP_1932 RSP_1932 hypothetical protein (NCBI) 220, 325
RSP_1938 RSP_1938 Conserved hypotetical protein (NCBI) 181, 220
RSP_1967 RSP_1967 hypothetical protein (NCBI) 11, 133
RSP_2185 RSP_2185 nuclease (SNase-like) (NCBI) 220, 355
RSP_2234 RSP_2234 Predicted DNA-binding protein (NCBI) 220, 346
RSP_2251 RSP_2251 putative beta-ketoadipate enol-lactone hydrolase (NCBI) 23, 220
RSP_2420 RSP_2420 hypothetical protein (NCBI) 82, 133
RSP_2490 RSP_2490 hypothetical protein (NCBI) 220, 355
RSP_2747 RSP_2747 possible glycosyltransferase (NCBI) 133, 335
RSP_3008 RSP_3008 None 133, 313
RSP_3084 RSP_3084 hypothetical protein (NCBI) 133, 183
RSP_3140 RSP_3140 hypothetical protein (NCBI) 133, 158
RSP_3308 RSP_3308 possible transporter, DME family, DMT superfamily (NCBI) 133, 375
RSP_3329 RSP_3329 hypothetical protein (NCBI) 133, 331
RSP_3340 rarD possible transporter, RarD, DMT superfamily (NCBI) 133, 308
RSP_3349 RSP_3349 hypothetical protein (NCBI) 133, 166
RSP_3375 RSP_3375 Membrane fusion protein, HlyD family (NCBI) 22, 133
RSP_3379 RSP_3379 hypothetical protein (NCBI) 133, 146
RSP_3385 RSP_3385 transcriptional regulator, LysR family (NCBI) 11, 220
RSP_3386 RSP_3386 TRAP-T family transporter, periplasmic binding protein (NCBI) 220, 331
RSP_3387 RSP_3387 TRAP-T family transporter, fused small and large inner membrane subunits (NCBI) 133, 220
RSP_3388 RSP_3388 putative Isocitrate/isopropylmalate dehydrogenase / tartrate dehydrogenase ttuC (NCBI) 83, 220
RSP_3389 RSP_3389 Isocitrate/isopropylmalate dehydrogenase / tartrate dehydrogenase (NCBI) 220, 355
RSP_3448 RSP_3448 transcriptional regulator, GntR-family (NCBI) 84, 220
RSP_3493 RSP_3493 hypothetical protein (NCBI) 220, 370
RSP_3496 RSP_3496 Zinc carboxypeptidase A metalloprotease (M14) (NCBI) 220, 370
RSP_3615 groEL Chaperonin Cpn60 (NCBI) 188, 220
RSP_3619 RSP_3619 hypothetical protein (NCBI) 133, 188
RSP_3762 RSP_3762 patch repair protein (NCBI) 150, 220
RSP_3830 RSP_3830 hypothetical protein (NCBI) 116, 220
RSP_4319 RSP_4319 tRNA-Gly (NCBI) 181, 220
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_3387
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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