Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_2327(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 RSP_2327
|Gene||Common Name||Description||Module membership|
|RSP_0313||RSP_0313||hypothetical protein (NCBI)||115, 383|
|RSP_0818||carB||carbamoyl phosphate synthase large subunit (RefSeq)||209, 383|
|RSP_0821||RSP_0821||Esterase/lipase/thioesterase (NCBI)||72, 356|
|RSP_0939||RSP_0939||hypothetical protein (NCBI)||140, 356|
|RSP_1045||trmD||tRNA (guanine-N1-)-methyltransferase (NCBI)||279, 356|
|RSP_1101||RSP_1101||hypothetical protein (NCBI)||129, 356|
|RSP_1108||TruB||tRNA pseudouridine synthase B (NCBI)||209, 383|
|RSP_1149||gltD||Glutamate synthase (beta subunit) (NCBI)||98, 356|
|RSP_1152||rnd||Ribonuclease D (NCBI)||192, 356|
|RSP_1154||RSP_1154||hypothetical protein (NCBI)||129, 356|
|RSP_1155||RSP_1155||OstA-like protein (NCBI)||129, 356|
|RSP_1288||RSP_1288||ABC branched chain amino acid family transporter, ATPase subunit (NCBI)||263, 383|
|RSP_1290||RSP_1290||ABC branched chain amino acid family transporter, inner membrane subunit (NCBI)||263, 383|
|RSP_1670||spoT/relA||RelA/SpoT family protein (NCBI)||130, 383|
|RSP_1675||rnc||Ribonuclease III (NCBI)||263, 383|
|RSP_1677||RSP_1677||hypothetical protein (NCBI)||221, 383|
|RSP_1712||rpoC||RNA polymerase I subunit A, (NCBI)||104, 383|
|RSP_1830||surf-1||Surf1 protein (NCBI)||126, 356|
|RSP_1847||PurD||Phosphoribosylamine--glycine ligase (NCBI)||160, 356|
|RSP_1865||RSP_1865||ketol-acid reductoisomerase (NCBI)||261, 356|
|RSP_1866||RSP_1866||Transcriptional regulator, AsnC family (NCBI)||187, 356|
|RSP_1867||RSP_1867||transcriptional regulator, AsnC family (NCBI)||189, 356|
|RSP_1950||RSP_1950||hypothetical protein (NCBI)||213, 383|
|RSP_2097||RSP_2097||Putative FtsL (NCBI)||374, 383|
|RSP_2099||murE||UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase (NCBI)||374, 383|
|RSP_2100||murF||UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase (NCBI)||374, 383|
|RSP_2101||mraY||Phospho-N-acetylmuramoyl-pentapeptidetransferase (NCBI)||374, 383|
|RSP_2170||RSP_2170||Phosphate transporter, Pit family (NCBI)||263, 383|
|RSP_2191||pccA||Propionyl-CoA carboxylase alpha subunit (NCBI)||121, 356|
|RSP_2284||RSP_2284||Histidinol-phosphate aminotransferase (NCBI)||311, 356|
|RSP_2327||RSP_2327||hypothetical protein (NCBI)||356, 383|
|RSP_2328||mreC||Rod shape-determining protein, MreC (NCBI)||87, 356|
|RSP_2403||RSP_2403||ABC cobalamin/Fe3+-siderophore transporter, periplasmic substrate-binding subunit (NCBI)||167, 383|
|RSP_2404||RSP_2404||ABC cobalamin/Fe3+-siderophore transporter, inner membrane subunit (NCBI)||167, 383|
|RSP_2405||RSP_2405||ABC cobalamin/Fe3+-siderophore transporter, ATPase subunit (NCBI)||167, 383|
|RSP_2406||RSP_2406||hypothetical protein (NCBI)||167, 383|
|RSP_2612||fabH||3-oxoacyl-(acyl-carrier-protein) synthase III (NCBI)||263, 383|
|RSP_2619||trmU||tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI)||187, 356|
|RSP_2648||RSP_2648||hypothetical protein (NCBI)||209, 383|
|RSP_2748||RSP_2748||possible transcriptional regulator, CopG family (NCBI)||152, 356|
|RSP_2790||RSP_2790||hypothetical protein (NCBI)||84, 356|
|RSP_2912||RSP_2912||Predicted pyrophosphatase (NCBI)||279, 356|
|RSP_2917||RSP_2917||putative cystathionine gamma-synthase beta-lyase (NCBI)||7, 383|
|RSP_2970||RSP_2970||Transporter, Major facilitator superfamily (MFS) (NCBI)||231, 356|
|RSP_3170||RSP_3170||Demethylmenaquinone methyltransferase (NCBI)||337, 356|
|RSP_3171||RSP_3171||3-hydroxyisobutyrate dehydrogenase (NCBI)||337, 356|
|RSP_3172||RSP_3172||hypothetical protein (NCBI)||337, 356|
|RSP_3200||RSP_3200||Molecular chaperone, DnaK (NCBI)||146, 356|
|RSP_3227||RSP_3227||Lysine 2,3-aminomutase (NCBI)||289, 356|
|RSP_3344||RSP_3344||PAS sensor diguanylate cyclase (NCBI)||174, 356|
|RSP_3593||RSP_3593||hypothetical protein (NCBI)||214, 356|
|RSP_3607||RSP_3607||hypothetical protein (NCBI)||129, 356|
|RSP_3712||RSP_3712||Multisubunit Na+/H+ antiporter MnhE subunit (NCBI)||311, 383|
|RSP_3713||RSP_3713||pH adaptation potassium efflux system, phaD subunit (NCBI)||311, 383|
|RSP_3777||RSP_3777||hypothetical protein (NCBI)||29, 356|
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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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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CircVisOur 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
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