Organism : Halobacterium salinarum NRC-1 | Module List :
VNG2139G atpA

V-type ATP synthase subunit A

CircVis
Functional Annotations (12)
Function System
Archaeal/vacuolar-type H+-ATPase subunit A cog/ cog
hydrogen-transporting two-sector ATPase activity go/ molecular_function
ATP binding go/ molecular_function
ATP synthesis coupled proton transport go/ biological_process
integral to membrane go/ cellular_component
proton-transporting ATP synthase complex go/ cellular_component
hydrogen ion transporting ATP synthase activity, rotational mechanism go/ molecular_function
proton-transporting ATPase activity, rotational mechanism go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
ATP_syn_A_arch tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG2139G
(Mouseover regulator name to see its description)

VNG2139G is regulated by 27 influences and regulates 0 modules.
Regulators for VNG2139G atpA (27)
Regulator Module Operator
VNG0101G 23 tf
VNG1383G 23 tf
VNG2661G
VNG1029C
23 combiner
VNG6143H 23 tf
VNG6389G 114 tf
VNG0101G 39 tf
VNG0258H 39 tf
VNG2661G 39 tf
VNG6143H 39 tf
VNG1922G
VNG1405C
227 combiner
VNG6193H 227 tf
VNG6389G 227 tf
VNG0101G
VNG2441G
124 combiner
VNG6389G 124 tf
VNG0194H 67 tf
VNG1899G
VNG2243G
67 combiner
VNG2661G
VNG1029C
67 combiner
VNG0101G
VNG2163H
24 combiner
VNG0194H 24 tf
VNG2661G
VNG1029C
24 combiner
VNG2661G
VNG0424C
45 combiner
VNG2661G
VNG1029C
45 combiner
VNG6143H 45 tf
VNG6389G 45 tf
VNG0101G 33 tf
VNG1496G 33 tf
VNG6143H 33 tf

Warning: VNG2139G Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 18 motifs predicted.

Motif Table (18)
Motif Id e-value Consensus Motif Logo
1023 1.00e+03 GaTtcaaAAgcaTaGa
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1024 2.90e+03 gTAAaA
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1025 3.90e-02 tttaaaacgtTtgc
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1026 8.10e+02 cACgaAgA.cc
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1043 1.70e+00 GaggacGc.gTCGAa
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1044 1.70e+03 cgtcgaC.AgctcGAcg.CgaGaa
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1055 3.40e+03 TTTTAA
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1056 3.90e+03 GaGtCCgaGaa
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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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1395 5.80e+02 CAtAATtGtTT
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1396 4.10e+03 AAaTcaAGTaGTTcTaTcTAA
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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 VNG2139G

VNG2139G is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
Archaeal/vacuolar-type H+-ATPase subunit A cog/ cog
hydrogen-transporting two-sector ATPase activity go/ molecular_function
ATP binding go/ molecular_function
ATP synthesis coupled proton transport go/ biological_process
integral to membrane go/ cellular_component
proton-transporting ATP synthase complex go/ cellular_component
hydrogen ion transporting ATP synthase activity, rotational mechanism go/ molecular_function
proton-transporting ATPase activity, rotational mechanism go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
ATP_syn_A_arch tigr/ tigrfam
Module neighborhood information for VNG2139G

VNG2139G has total of 133 gene neighbors in modules 23, 24, 33, 39, 45, 67, 114, 124, 227
Gene neighbors (133)
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
VNG0584H hypothetical protein VNG0584H 2, 16, 24
VNG0585H hypothetical protein VNG0585H 2, 16, 24
VNG0635G nolB NADH dehydrogenase/oxidoreductase-like protein 2, 16, 19, 24, 29, 199
VNG0636G ndhG1 NADH dehydrogenase/oxidoreductase 19, 24, 29
VNG0637G ndhG5 NADH dehydrogenase/oxidoreductase 2, 16, 19, 24, 29
VNG0639G ndhG4 NADH dehydrogenase/oxidoreductase 19, 24, 29, 199
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
VNG0940Gm ACS3 Acetyl-CoA synthetase 7, 19, 24, 25, 29, 49
VNG0964C hypothetical protein VNG0964C 12, 24, 49, 100, 109
VNG1048G udg1 UDP-glucose dehydrogenase 45
VNG1103G rpl12p 50S ribosomal protein L12P 1, 10, 39, 66, 82, 99, 137, 150, 161, 165, 180
VNG1104G rplP0 acidic ribosomal protein P0 1, 10, 39, 66, 82, 99, 137, 150, 161, 165, 180
VNG1105G rpl1P 50S ribosomal protein L1P 1, 10, 39, 66, 82, 99, 137, 150, 161, 165, 180
VNG1125G korB KorB 7, 12, 24, 29
VNG1128G korA KorA 3, 7, 12, 24, 29, 49, 71, 78, 113
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
VNG1136G rpb3 DNA-directed RNA polymerase II 1, 10, 39, 66, 82, 137, 161, 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
VNG1139Gm rps9p 30S ribosomal protein S9P 1, 10, 39, 161
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
VNG1142G eno phosphopyruvate hydratase 1, 10, 39, 161
VNG1149Cm metallo-beta-lactamase superfamily hydrolase 2, 16, 23, 33
VNG1150G idsA IdsA 33
VNG1158G rps28e 30S ribosomal protein S28e 23, 283
VNG1160G ndk nucleoside diphosphate kinase 23, 283
VNG1169C hypothetical protein VNG1169C 23, 66, 82, 137, 161, 165, 180
VNG1170G rpl21e 50S ribosomal protein L21e 23, 66, 82, 137, 161, 165
VNG1292H hypothetical protein VNG1292H 24, 33
VNG1294G slyD peptidyl-prolyl cis-trans isomerase 23, 67, 184
VNG1310G sdhC hypothetical protein VNG1310G 2, 24, 236
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
VNG1555G cobH hypothetical protein VNG1555G 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
VNG1561Cm ferredoxin 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
VNG1635G cbiM cobalt transport protein CbiM 76, 163, 205, 226, 227
VNG1689G rpl3p 50S ribosomal protein L3P 1, 10, 23, 39, 66, 82, 99, 137, 180
VNG1690G rpl4lp 50S ribosomal protein L4P 1, 10, 39, 66, 82, 99, 137, 161, 165, 180
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
VNG1699C ribonuclease P protein component 1 1, 10, 23, 39, 99, 180, 227
VNG1701G rpl14p 50S ribosomal protein L14P 1, 10, 23, 137, 221
VNG1702G rpl24p 50S ribosomal protein L24P 1, 10, 23, 39, 66, 82, 99, 137, 165
VNG1705G rpl5p 50S ribosomal protein L5P 1, 10, 23, 39, 99, 180
VNG1706G rps14P 30S ribosomal protein S14P 10, 23, 221
VNG1709G rpl6p 50S ribosomal protein L6P 1, 10, 23, 39, 66, 99, 137, 165, 180
VNG1713G rpl19e 50S ribosomal protein L19e 1, 10, 23, 33, 39, 66, 99, 137, 180
VNG1714G rpl18p 50S ribosomal protein L18P 10, 39, 99
VNG1718G rpl15p 50S ribosomal protein L15P 1, 10, 23, 39, 99, 180
VNG1719G secY preprotein translocase subunit SecY 1, 10, 23, 39, 99
VNG1768G eif5a translation initiation factor IF-5A 23, 24, 40, 59
VNG1933G ftsZ3 cell division protein 7, 25, 61, 227
VNG1934H hypothetical protein VNG1934H 227
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
VNG2243G tbpE transcription factor 19, 24, 29, 128
VNG2244H hypothetical protein VNG2244H 24, 29
VNG2251G achY S-adenosyl-L-homocysteine hydrolase 24, 29, 49, 71, 79, 113
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
VNG2499G gcdH glutaryl-CoA dehydrogenase 7, 24, 25, 50, 61, 78
VNG2574G can aconitate hydratase 23, 29
VNG2575G rimI Pab N-terminal acetyltransferase 23
VNG2648G rps10p 30S ribosomal protein S10P 2, 3, 16, 23, 24, 29, 40, 110
VNG2649G eef1a elongation factor 1-alpha 2, 3, 16, 24, 29, 40, 79, 110
VNG2654Gm EEF2 elongation factor EF-2 2, 23, 110
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
VNG6294G perA peroxidase / catalase 23, 24, 29, 52
VNG6312G argS arginine-tRNA synthetase 24, 29
VNG7015 gvpM gas vesicle protein GvpM 227
VNG7017 gvpK gas vesicle protein GvpK 227
VNG7018 gvpJ gas vesicle protein GvpJ 227
VNG7021 gvpG gas vesicle protein GvpG 227
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.

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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.

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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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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)
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  • 5. Module(s) that source gene and target genes belong to
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Comments for VNG2139G
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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