Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_2930(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_2930
|Gene||Common Name||Description||Module membership|
|RSP_0117||RSP_0117||Cytochrome c oxidase, subunit I (NCBI)||38, 238|
|RSP_0206||RSP_0206||hypothetical protein (NCBI)||235, 303|
|RSP_0234||tlpL||TlpL, putative cytoplasmic chemoreceptor (NCBI)||138, 235|
|RSP_0864||RSP_0864||Puative heme-binding hypothetical protein (NCBI)||168, 238|
|RSP_0918||RSP_0918||hypothetical protein (NCBI)||150, 238|
|RSP_0951||RSP_0951||hypothetical protein (NCBI)||168, 238|
|RSP_1319||RSP_1319||possible invasion protein (NCBI)||73, 238|
|RSP_1332||RSP_1332||H+-transporting two-sector ATPase, alpha/beta subunit (NCBI)||235, 359|
|RSP_1619||RSP_1619||hypothetical protein (NCBI)||189, 235|
|RSP_1620||RSP_1620||hypothetical protein (NCBI)||235, 342|
|RSP_1782||RSP_1782||hypothetical membrane protein (NCBI)||233, 235|
|RSP_1783||RSP_1783||Predicted membrane protein (NCBI)||233, 235|
|RSP_1816||RSP_1816||Mg chelatase-related protein (NCBI)||238, 282|
|RSP_1822||RSP_1822||hypothetical protein (NCBI)||229, 238|
|RSP_1872||RSP_1872||Glycosyl transferase, family 2 (NCBI)||236, 238|
|RSP_1957||RSP_1957||hypothetical protein (NCBI)||138, 235|
|RSP_1961||RSP_1961||hypothetical protein (NCBI)||235, 355|
|RSP_1968||RSP_1968||Possible integrase/recombinase (NCBI)||236, 238|
|RSP_1992||RSP_1992||hypothetical protein (NCBI)||128, 238|
|RSP_2033||RSP_2033||hypothetical protein (NCBI)||19, 238|
|RSP_2034||RSP_2034||possible CAAX amino terminal protease family (NCBI)||235, 380|
|RSP_2040||RSP_2040||possible Transposase fragment (NCBI)||138, 235|
|RSP_2043||RSP_2043||hypothetical protein (NCBI)||235, 380|
|RSP_2059||RSP_2059||Potential phage tail tape measure protein (NCBI)||31, 238|
|RSP_2068||RSP_2068||putative ClpP-like protease (NCBI)||235, 304|
|RSP_2153||RSP_2153||hypothetical protein (NCBI)||238, 249|
|RSP_2186||RSP_2186||Transcriptional Regulator, MerR family (NCBI)||238, 307|
|RSP_2378||cypC||putative fatty acid beta hydroxylase (cytochrome P450) (NCBI)||236, 238|
|RSP_2413||lig2||putative ATP-dependent DNA Ligase (NCBI)||82, 238|
|RSP_2466||RSP_2466||hypothetical protein (NCBI)||193, 235|
|RSP_2471||RSP_2471||Predicted phage phi-C31 gp36 major capsid-like protein (NCBI)||193, 235|
|RSP_2472||RSP_2472||hypothetical protein (NCBI)||193, 235|
|RSP_2478||RSP_2478||hypothetical protein (NCBI)||193, 235|
|RSP_2479||RSP_2479||putative phage host specificity protein (NCBI)||235, 320|
|RSP_2480||RSP_2480||hypothetical protein (NCBI)||193, 235|
|RSP_2497||RSP_2497||ATPase (NCBI)||74, 238|
|RSP_2501||RSP_2501||hypothetical protein (NCBI)||238, 292|
|RSP_2769||RSP_2769||probable 5,10-methylenetetrahydrofolate reductase (NCBI)||238, 304|
|RSP_2770||RSP_2770||hypothetical protein (NCBI)||73, 238|
|RSP_2871||aglG||ABC alpha-glucoside transporter, inner membrane subunit AglG (NCBI)||229, 235|
|RSP_2930||RSP_2930||hypothetical protein (NCBI)||235, 238|
|RSP_2988||RSP_2988||Pirin-related protein (NCBI)||155, 238|
|RSP_2990||RSP_2990||hypothetical protein (NCBI)||235, 380|
|RSP_2996||RSP_2996||putative prohead protease (NCBI)||14, 235|
|RSP_2997||RSP_2997||putative head portal protein (NCBI)||14, 235|
|RSP_3043||RSP_3043||hypothetical protein (NCBI)||238, 249|
|RSP_3064||RSP_3064||transcriptional regulator, DeoR family (NCBI)||235, 292|
|RSP_3201||RSP_3201||putative oxidoreductase (NCBI)||138, 235|
|RSP_3322||acoR||acetoin transcriptional regulator, sigma54 specific, AcoR (NCBI)||238, 338|
|RSP_3390||RSP_3390||ABC Fe3+-siderophores transporter, ATPase subunit (NCBI)||146, 235|
|RSP_3417||RSP_3417||TonB dependent outer membrane ferrichrome-iron receptor (NCBI)||235, 380|
|RSP_3427||RSP_3427||hypothetical protein (NCBI)||137, 238|
|RSP_3433||RSP_3433||transcriptionalregulator, CopG family (NCBI)||1, 238|
|RSP_3608||RSP_3608||hypothetical protein (NCBI)||147, 238|
|RSP_3613||RSP_3613||Glycosyltransferase (NCBI)||238, 292|
|RSP_3614||RSP_3614||hypothetical protein (NCBI)||150, 238|
|RSP_3624||RSP_3624||hypothetical protein (NCBI)||235, 307|
|RSP_3657||RSP_3657||putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase (NCBI)||196, 238|
|RSP_3684||solR||transcriptional regulator, LuxR family (NCBI)||116, 235|
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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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.
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