Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1758

Probable succinyl-diaminopimelate desuccinylase (NCBI)

CircVis
Functional Annotations (11)
Function System
Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases cog/ cog
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
succinyl-diaminopimelate desuccinylase activity go/ molecular_function
lysine biosynthetic process go/ biological_process
metal ion binding go/ molecular_function
protein dimerization activity go/ molecular_function
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
DapE-ArgE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1758
(Mouseover regulator name to see its description)

RSP_1758 is regulated by 18 influences and regulates 0 modules.
Regulators for RSP_1758 (18)
Regulator Module Operator
RSP_0014 102 tf
RSP_0032 102 tf
RSP_0087 102 tf
RSP_0527 102 tf
RSP_0728 102 tf
RSP_1191 102 tf
RSP_1866 102 tf
RSP_2130 102 tf
RSP_2171 102 tf
RSP_2182 102 tf
RSP_2610 102 tf
RSP_2681 102 tf
RSP_2730 102 tf
RSP_2939 102 tf
RSP_3238 102 tf
RSP_3676 102 tf
RSP_1790 95 tf
RSP_2730 95 tf

Warning: RSP_1758 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
7910 1.40e-15 tgcgCAca.Aa.GgAtccTGtcaA
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7911 2.40e-05 AAAaTtaacGaCcAAtCAATC
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7924 2.30e-07 aagAAaaatccttgaaagagt
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7925 2.00e-09 aaGCggttaagAaaTTTac.Gcga
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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_1758

RSP_1758 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases cog/ cog
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
succinyl-diaminopimelate desuccinylase activity go/ molecular_function
lysine biosynthetic process go/ biological_process
metal ion binding go/ molecular_function
protein dimerization activity go/ molecular_function
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
DapE-ArgE tigr/ tigrfam
Module neighborhood information for RSP_1758

RSP_1758 has total of 54 gene neighbors in modules 95, 102
Gene neighbors (54)
Gene Common Name Description Module membership
RSP_0161 RSP_0161 Spermidine/putrescine-binding periplasmic protein (NCBI) 70, 102
RSP_0182 RSP_0182 None 95, 175
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

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_1758
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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