Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU2115(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Module neighborhood information for GSU2115
|Gene||Common Name||Description||Module membership|
|GSU0012||hemG||protoporphyrinogen oxidase (VIMSS)||16, 134|
|GSU0014||dnaJ||phage prohead protease, HK97 family/dnaJ domain protein (NCBI)||16, 134|
|GSU0133||GSU0133||hypothetical protein (VIMSS)||16, 86|
|GSU0177||GSU0177||acetyltransferase, GNAT family (NCBI)||16, 60|
|GSU0191||GSU0191||cold-shock domain family protein (VIMSS)||16, 248|
|GSU0209||GSU0209||hypothetical protein (VIMSS)||16, 109|
|GSU0467||GSU0467||hypothetical protein (VIMSS)||16, 86|
|GSU0491||rhlE-1||ATP-dependent RNA helicase RhlE (NCBI)||16, 25|
|GSU0550||GSU0550||conserved hypothetical protein (VIMSS)||16, 55|
|GSU0558||GSU0558||hypothetical protein (VIMSS)||16, 174|
|GSU0674||hcP-1||hydroxylamine reductase (RefSeq)||16, 214|
|GSU0731||lpxC||UDP-3-0-acyl N-acetylglucosamine deacetylase (NCBI)||16, 140|
|GSU0733||GSU0733||cell shape-determining protein MreB/Mrl family (VIMSS)||15, 16|
|GSU0771||GSU0771||alcohol dehydrogenase, zinc-containing (VIMSS)||16, 257|
|GSU0773||GSU0773||multidrug resistance protein, putative (VIMSS)||16, 257|
|GSU0852||GSU0852||lipoprotein, putative (VIMSS)||16, 65|
|GSU0919||GSU0919||hypothetical protein (VIMSS)||16, 110|
|GSU1024||cyd-4||cytochrome c3 (NCBI)||16, 20|
|GSU1032||GSU1032||methyl-accepting chemotaxis protein (VIMSS)||1, 337|
|GSU1037||GSU1037||sensory box/response regulator (VIMSS)||1, 224|
|GSU1082||GSU1082||conserved hypothetical protein (VIMSS)||16, 77|
|GSU1095||phoU||phosphate transport system regulatory protein PhoU (NCBI)||1, 96|
|GSU1096||pstB||phosphate ABC transporter, ATP-binding protein (NCBI)||16, 236|
|GSU1407||GSU1407||hypothetical protein (VIMSS)||1, 268|
|GSU2094||GSU2094||response regulator (VIMSS)||1, 287|
|GSU2095||GSU2095||NADH oxidase, putative (VIMSS)||1, 79|
|GSU2098||cooS||carbon monoxide dehydrogenase subunit (NCBI)||1, 178|
|GSU2115||GSU2115||hypothetical protein (VIMSS)||1, 16|
|GSU2152||GSU2152||hypothetical protein (VIMSS)||1, 213|
|GSU2154||GSU2154||hypothetical protein (VIMSS)||1, 337|
|GSU2156||GSU2156||hypothetical protein (VIMSS)||1, 70|
|GSU2158||norQ||cobS protein, putative (NCBI)||1, 322|
|GSU2162||GSU2162||hypothetical protein (VIMSS)||1, 224|
|GSU2165||GSU2165||hypothetical protein (VIMSS)||1, 78|
|GSU2166||GSU2166||hypothetical protein (VIMSS)||1, 300|
|GSU2167||GSU2167||CHC2 zinc finger domain protein (VIMSS)||1, 78|
|GSU2168||radC||DNA repair protein RadC (NCBI)||1, 163|
|GSU2389||GSU2389||ABC transporter, periplasmic substrate-binding protein, putative (NCBI)||16, 55|
|GSU2421||GSU2421||hypothetical protein (VIMSS)||1, 190|
|GSU2661||GSU2661||conserved hypothetical protein (VIMSS)||1, 287|
|GSU2695||GSU2695||outer membrane efflux protein (VIMSS)||16, 86|
|GSU2696||GSU2696||AcrB/AcrD/AcrF family protein (VIMSS)||16, 26|
|GSU2697||GSU2697||multidrug resistance protein (NCBI)||16, 86|
|GSU2776||GSU2776||conserved hypothetical protein (NCBI)||1, 9|
|GSU3091||cvpA||CvpA family protein (NCBI)||16, 236|
|GSU3121||GSU3121||EF hand domain protein (VIMSS)||1, 224|
|GSU3154||GSU3154||cytochrome c nitrite reductase, catalytic subunit NrfA, putative (VIMSS)||16, 82|
|GSU3156||GSU3156||methyl-accepting chemotaxis protein, putative (VIMSS)||16, 153|
|GSU3180||GSU3180||conserved hypothetical protein (VIMSS)||1, 180|
|GSU3225||GSU3225||NHL repeat domain protein (VIMSS)||16, 155|
|GSU3400||GSU3400||heavy metal efflux pump, CzcA family (VIMSS)||1, 337|
Gene Page Help
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 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.
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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.
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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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- 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.
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