Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_1459(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_1459
|Gene||Common Name||Description||Module membership|
|RSP_0002||spbB||Histone-like nucleoid-structuring protein H-NS (NCBI)||48, 93|
|RSP_0146||glnB||Nitrogen regulatory protein P-II (NCBI)||93, 108|
|RSP_0147||glnA||Glutamine synthetase class-I (NCBI)||25, 93|
|RSP_0223||RSP_0223||hypothetical protein (NCBI)||93, 358|
|RSP_0224||RSP_0224||ATP-dependent helicase (NCBI)||93, 358|
|RSP_0446||RSP_0446||Isocitrate dehydrogenase (NCBI)||279, 297|
|RSP_0452||recA||Recombinase A, DNA recombination protein (NCBI)||30, 93|
|RSP_0561||RSP_0561||Transaldolase (NCBI)||279, 349|
|RSP_0562||RSP_0562||hypothetical protein (NCBI)||54, 279|
|RSP_0584||RSP_0584||Lysyl-tRNA synthetase (NCBI)||109, 279|
|RSP_0756||ribH1||6,7-dimethyl-8-ribityllumazine synthase beta chain (NCBI)||203, 279|
|RSP_0757||ribBA||Bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2butanone-4-phosphate synthase (NCBI)||203, 279|
|RSP_0797||gltX-1||Glutamyl-tRNA synthetase, class Ic (NCBI)||51, 93|
|RSP_0831||trpA||Tryptophan synthase, alpha chain (NCBI)||51, 93|
|RSP_0873||RSP_0873||N-formylmethionyl tRNA deformylase (NCBI)||279, 306|
|RSP_0883||RSP_0883||SmpB protein (NCBI)||277, 279|
|RSP_0981||RSP_0981||Transcriptional regulator, GntR family (NCBI)||93, 277|
|RSP_0982||RSP_0982||zinc metallopeptidases-like protein (NCBI)||93, 277|
|RSP_0983||RSP_0983||hypothetical protein (NCBI)||93, 277|
|RSP_1045||trmD||tRNA (guanine-N1-)-methyltransferase (NCBI)||279, 356|
|RSP_1085||RSP_1085||hypothetical protein (NCBI)||75, 93|
|RSP_1350||serB||phosphoserine phosphatase (NCBI)||258, 279|
|RSP_1360||RSP_1360||hypothetical protein (NCBI)||30, 93|
|RSP_1459||RSP_1459||hypothetical protein (NCBI)||93, 279|
|RSP_1460||RSP_1460||hypothetical protein (NCBI)||71, 93|
|RSP_1461||kdtA||Putative 3-deoxy-D-manno-octulosonic-acid transferase (NCBI)||184, 279|
|RSP_1621||RSP_1621||Deoxyguanosinetriphosphate triphosphohydrolase-like protein (NCBI)||93, 381|
|RSP_1622||RSP_1622||Putative DNA-binding protein (NCBI)||93, 208|
|RSP_1623||RSP_1623||hypothetical protein (NCBI)||93, 130|
|RSP_1806||RSP_1806||aconitate hydratase (RefSeq)||279, 297|
|RSP_1977||cobS||cobalt chelatase, CobS small subunit (NCBI)||93, 261|
|RSP_1978||RSP_1978||molecular chaperone, DnaJ family (NCBI)||93, 261|
|RSP_1979||RSP_1979||stress induced morphogen, BolA (NCBI)||93, 261|
|RSP_1994||gltA||Citrate synthase (NCBI)||279, 309|
|RSP_1997||lexA||LexA repressor (NCBI)||30, 93|
|RSP_2246||hisB||Imidazoleglycerol-phosphate dehydratase (NCBI)||93, 182|
|RSP_2306||RSP_2306||putative HAD superfamily protein (NCBI)||234, 279|
|RSP_2329||mreB||Cell shape determining protein MreB/Mrl (NCBI)||93, 309|
|RSP_2356||RSP_2356||hypothetical protein (NCBI)||93, 114|
|RSP_2361||RSP_2361||putative integrase/resolvase recombinase protein phage-related integrase (NCBI)||93, 161|
|RSP_2624||RSP_2624||hypothetical protein (NCBI)||30, 93|
|RSP_2845||RSP_2845||putative penicillin acylase (penicillin amidase) (NCBI)||195, 279|
|RSP_2910||RSP_2910||Predicted Metal-dependent amidase/aminoacylase/carboxypeptidase (NCBI)||98, 279|
|RSP_2912||RSP_2912||Predicted pyrophosphatase (NCBI)||279, 356|
|RSP_3003||RSP_3003||hypothetical protein (NCBI)||93, 108|
|RSP_3230||RSP_3230||hypothetical protein (NCBI)||103, 279|
|RSP_3231||RSP_3231||ABC peptide transporter, periplasmic binding protein (NCBI)||195, 279|
|RSP_3232||RSP_3232||ABC peptide transporter, inner membrane subunit (NCBI)||279, 297|
|RSP_3233||RSP_3233||ABC peptide transporter, inner membrane subunit (NCBI)||279, 297|
|RSP_3235||RSP_3235||ABC peptide transporter, ATPase subunit (NCBI)||279, 297|
|RSP_3236||RSP_3236||ABC peptide transporter, ATPase subunit (NCBI)||279, 297|
|RSP_3328||RSP_3328||hypothetical protein (NCBI)||279, 306|
|RSP_3644||RSP_3644||Metal dependent phosphohydrolase (NCBI)||93, 130|
|RSP_3716||selD||selenide, water dikinase (selenophosphate synthetase) (NCBI)||279, 311|
|RSP_3749||ampC||putative beta-lactamase precursor (NCBI)||279, 362|
|RSP_3822||RSP_3822||GTP1/OBG family protein (NCBI)||30, 279|
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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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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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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