Organism : Halobacterium salinarum NRC-1
| Module List :
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VNG1542G sucD
hypothetical protein VNG1542G
Functional Annotations (12)
Function | System |
---|---|
Succinyl-CoA synthetase, alpha subunit | cog/ cog |
succinate-CoA ligase (ADP-forming) activity | go/ molecular_function |
metabolic process | go/ biological_process |
succinate-CoA ligase complex (ADP-forming) | go/ cellular_component |
Citrate cycle (TCA cycle) | kegg/ kegg pathway |
Propanoate metabolism | kegg/ kegg pathway |
C5-Branched dibasic acid metabolism | kegg/ kegg pathway |
Carbon fixation pathways in prokaryotes | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
Microbial metabolism in diverse environments | kegg/ kegg pathway |
sucCoAalpha | tigr/ tigrfam |
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Regulation information for VNG1542G
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
VNG0101G VNG2441G |
124 | combiner |
VNG6389G | 124 | tf |
VNG6389G | 114 | tf |
VNG2661G VNG0424C |
45 | combiner |
VNG2661G VNG1029C |
45 | combiner |
VNG6143H | 45 | tf |
VNG6389G | 45 | tf |
VNG0101G | 33 | tf |
VNG1496G | 33 | tf |
VNG6143H | 33 | tf |
VNG0194H | 67 | tf |
VNG1899G VNG2243G |
67 | combiner |
VNG2661G VNG1029C |
67 | combiner |
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Motif information (de novo identified motifs for modules)
There are 10 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
1043 | 1.70e+00 | GaggacGc.gTCGAa |
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1044 | 1.70e+03 | cgtcgaC.AgctcGAcg.CgaGaa |
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1067 | 6.20e+01 | AcaACGT |
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1068 | 6.80e+03 | AATCAAaaTTGTtT |
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1109 | 6.20e+00 | CagtaAcAaTgA |
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1110 | 2.00e+02 | Gtaagg.Ga.g..cTaTt.Gt |
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1201 | 8.30e+00 | AtaAttgtTTt |
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1202 | 1.30e+01 | CaacgccGAataCaA |
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1221 | 4.40e-03 | CaTCGAcGA |
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1222 | 2.00e+02 | AtcgCAcgTcCgCtAAtccattC |
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Functional Enrichment for VNG1542G
Function | System |
---|---|
Succinyl-CoA synthetase, alpha subunit | cog/ cog |
succinate-CoA ligase (ADP-forming) activity | go/ molecular_function |
metabolic process | go/ biological_process |
succinate-CoA ligase complex (ADP-forming) | go/ cellular_component |
Citrate cycle (TCA cycle) | kegg/ kegg pathway |
Propanoate metabolism | kegg/ kegg pathway |
C5-Branched dibasic acid metabolism | kegg/ kegg pathway |
Carbon fixation pathways in prokaryotes | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
Microbial metabolism in diverse environments | kegg/ kegg pathway |
sucCoAalpha | tigr/ tigrfam |
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Module neighborhood information for VNG1542G
Gene | Common Name | Description | Module membership |
---|---|---|---|
VNG0002G | yvrO | amino acid ABC transporter ATP-binding protein | 124, 263 |
VNG0040C | hypothetical protein VNG0040C | 67, 263 | |
VNG0043H | hypothetical protein VNG0043H | 45, 114 | |
VNG0207H | hypothetical protein VNG0207H | 2, 3, 7, 12, 16, 49, 67, 71, 78, 79, 113, 123 | |
VNG0208H | hypothetical protein VNG0208H | 2, 3, 7, 12, 16, 24, 29, 49, 67, 71, 78, 79, 113, 123 | |
VNG0209H | hypothetical protein VNG0209H | 2, 3, 7, 12, 16, 24, 29, 49, 67, 71, 78, 79, 113, 123 | |
VNG0451G | phoU | hypothetical protein VNG0451G | 6, 76, 124, 163, 174, 205, 226 |
VNG0452G | pstB2 | phosphate ABC transporter ATP-binding protein | 6, 76, 124, 163, 174, 205, 226 |
VNG0453G | pstA2 | phosphate ABC transporter permease | 6, 76, 124, 163, 174, 205, 226 |
VNG0455G | pstC2 | phosphate ABC transporter permease | 6, 76, 124, 163, 174, 205, 226 |
VNG0457G | phoX | phosphate ABC transporter periplasmic phosphate-binding protein | 6, 76, 124, 163, 174, 205, 226 |
VNG0458G | prp1 | phosphate regulatory protein-like protein | 6, 76, 124, 163, 174, 205, 226 |
VNG0540G | imp | hypothetical protein VNG0540G | 114, 119 |
VNG0548C | H/ACA RNA-protein complex component Nop10p | 1, 10, 33, 39, 66, 82, 99, 137, 161, 180 | |
VNG0549G | eif2a | translation initiation factor IF-2 subunit alpha | 10, 33, 66, 82, 99, 137, 180 |
VNG0550G | rps27e | 30S ribosomal protein S27e | 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180 |
VNG0551G | rpl44e | 50S ribosomal protein L44E | 1, 10, 33, 39, 66, 82, 99, 137, 161, 180 |
VNG0640G | nolD | NADH dehydrogenase/oxidoreductase-like protein | 2, 3, 16, 19, 24, 29, 45, 123 |
VNG0641C | NADH dehydrogenase subunit J | 19, 24, 29, 45, 199 | |
VNG0642C | hypothetical protein VNG0642C | 2, 24, 29, 45 | |
VNG0646G | nuoL | F420H2:quinone oxidoreductase subunit L | 29, 45 |
VNG0789C | hypothetical protein VNG0789C | 10, 33, 99 | |
VNG0790G | rps15p | 30S ribosomal protein S15P | 10, 33, 99, 161 |
VNG1048G | udg1 | UDP-glucose dehydrogenase | 45 |
VNG1132G | rps13p | 30S ribosomal protein S13P | 1, 10, 33, 39, 66, 82, 137, 161, 165, 180 |
VNG1133G | rps4p | 30S ribosomal protein S4P | 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180 |
VNG1134G | rps11p | 30S ribosomal protein S11P | 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180 |
VNG1137G | rpl18e | 50S ribosomal protein L18e | 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180 |
VNG1138G | rpl13p | 50S ribosomal protein L13P | 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180 |
VNG1140G | rpoN | DNA-directed RNA polymerase subunit N | 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180 |
VNG1141G | rpoK | DNA-directed RNA polymerase subunit K | 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180 |
VNG1149Cm | metallo-beta-lactamase superfamily hydrolase | 2, 16, 23, 33 | |
VNG1150G | idsA | IdsA | 33 |
VNG1292H | hypothetical protein VNG1292H | 24, 33 | |
VNG1294G | slyD | peptidyl-prolyl cis-trans isomerase | 23, 67, 184 |
VNG1542G | sucD | hypothetical protein VNG1542G | 33, 45, 67, 114, 124 |
VNG1543G | zim | CTAG modification methylase | 114, 124, 174, 184 |
VNG1550G | cbiT | cobalamin biosynthesis protein | 45, 67, 114, 227 |
VNG1551G | cbiL | cobalt-precorrin-2 C(20)-methyltransferase | 45, 67, 114, 124, 227 |
VNG1553G | cbiF | cobalamin biosynthesis protein | 45, 114, 227 |
VNG1554G | cbiG | cobalamin biosynthesis protein CbiG | 45, 61, 67, 114, 124, 227 |
VNG1557G | cbiH | cobalamin biosynthesis protein | 45, 61, 67, 114, 124, 174, 227 |
VNG1558H | hypothetical protein VNG1558H | 45, 61, 67, 114, 124, 174, 227 | |
VNG1559H | hypothetical protein VNG1559H | 45, 114, 124, 174, 227 | |
VNG1562H | hypothetical protein VNG1562H | 45, 114, 124, 174, 205, 227 | |
VNG1564H | hypothetical protein VNG1564H | 114, 124, 174, 205, 226, 227 | |
VNG1566G | cobN | hypothetical protein VNG1566G | 61, 124 |
VNG1567G | cbiC | precorrin isomerase | 61, 114, 124 |
VNG1568G | cbiJ | cobalt-precorrin-6Y C(5)-methyltransferase | 61, 114, 124 |
VNG1632G | cbiQ | hypothetical protein VNG1632G | 76, 114, 163, 174, 205, 226, 227 |
VNG1691G | rplW | 50S ribosomal protein L23P | 1, 10, 23, 33, 39, 66, 82, 99, 137, 161, 165, 180 |
VNG1695G | rpl22p | 50S ribosomal protein L22P | 1, 10, 23, 33, 39, 66, 82, 99, 137, 161, 165, 180 |
VNG1697G | rps3p | 30S ribosomal protein S3P | 1, 10, 23, 33, 39, 66, 82, 99, 137, 165, 180 |
VNG1713G | rpl19e | 50S ribosomal protein L19e | 1, 10, 23, 33, 39, 66, 99, 137, 180 |
VNG2053G | rpoE' | DNA-directed RNA polymerase subunit E' | 33, 59 |
VNG2098H | hypothetical protein VNG2098H | 33 | |
VNG2099C | hypothetical protein VNG2099C | 33, 45 | |
VNG2138G | atpB | V-type ATP synthase subunit B | 45, 67, 114, 124, 227 |
VNG2139G | atpA | V-type ATP synthase subunit A | 23, 24, 33, 39, 45, 67, 114, 124, 227 |
VNG2140G | atpF | V-type ATP synthase subunit F | 33, 39, 45, 67, 114, 124, 227 |
VNG2141G | atpC | V-type ATP synthase subunit C | 23, 39, 45, 67, 114, 124, 227 |
VNG2142G | atpE | V-type ATP synthase subunit E | 19, 24, 45, 67, 114, 227 |
VNG2143G | atpK | H+-transporting ATP synthase subunit K | 2, 19, 23, 24, 45, 67, 75, 114, 124, 227 |
VNG2144G | atpI | H+-transporting ATP synthase subunit I | 19, 23, 24, 45, 67, 75, 124, 227 |
VNG2146H | hypothetical protein VNG2146H | 2, 16, 19, 24, 45, 67, 124, 227 | |
VNG2150G | etfB | electron transfer flavoprotein subunit beta | 45, 124 |
VNG2151G | etfA | electron transfer flavoprotein subunit alpha | 33, 45, 61, 124 |
VNG2217G | pdhA2 | pyruvate dehydrogenase alpha subunit | 45, 61, 124 |
VNG2218G | pdhB | hypothetical protein VNG2218G | 45, 61, 124, 174 |
VNG2219G | dsa | branched-chain alpha-keto acid dehydrogenase subunit E2 | 45, 61, 124, 174 |
VNG2220G | lpdA | LpdA | 45, 61, 124, 174, 184 |
VNG2462G | dpa | signal recognition particle receptor | 90, 124, 184 |
VNG2465C | hypothetical protein VNG2465C | 33, 184 | |
VNG2467G | rpl31e | 50S ribosomal protein L31e | 1, 33, 66, 82, 99, 137, 161, 165, 180 |
VNG2469G | rpl39e | 50S ribosomal protein L39e | 1, 33, 66, 82, 99, 137, 161, 165, 180 |
VNG2658G | rps12P | 30S ribosomal protein S12P | 23, 39, 40, 45, 98, 110, 137 |
VNG2662G | rpoC | DNA-directed RNA polymerase subunit A'' | 45, 98 |
VNG2674H | hypothetical protein VNG2674H | 67, 225 | |
VNG2679G | csg | cell surface glycoprotein | 67 |
VNG6081G | crt_1 | isopentenyl pyrophosphate isomerase | 114 |
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.
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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.
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;![](/static/images/help_images/circvis-help.png)
- 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
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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.