Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Glycoside hydrolase, family 25 (NCBI)
Functional Annotations (5)
|Lyzozyme M1 (1,4-beta-N-acetylmuramidase)||cog/ cog|
|lysozyme activity||go/ molecular_function|
|peptidoglycan catabolic process||go/ biological_process|
|cell wall macromolecule catabolic process||go/ biological_process|
|cation binding||go/ molecular_function|
Regulation information for RSP_3565(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|
Functional Enrichment for RSP_3565
Module neighborhood information for RSP_3565
|Gene||Common Name||Description||Module membership|
|RSP_0015||RSP_0015||ABC spermidine/putrescine transporter, ATPase subunit (NCBI)||221, 358|
|RSP_0202||RSP_0202||putative membrane protein (NCBI)||221, 340|
|RSP_0677||RSP_0677||Putative malonate transporter, mdcF, AEC family (NCBI)||130, 221|
|RSP_0923||map1||Methionine aminopeptidase, subfamily 1 (NCBI)||84, 286|
|RSP_0925||yobR||Putative acetyl transferase (NCBI)||84, 286|
|RSP_0926||RSP_0926||OmpA/MotB family protein (NCBI)||84, 286|
|RSP_0963||RSP_0963||Inner membrane protein (NCBI)||208, 221|
|RSP_0987||RSP_0987||Putative transporter, RarD family, DMT superfamily (NCBI)||84, 126|
|RSP_1263||RSP_1263||hypothetical protein (NCBI)||84, 307|
|RSP_1264||RSP_1264||hypothetical protein (NCBI)||84, 307|
|RSP_1265||kdpA||Potassium-transporting P-type ATPase, A chain, KdpA (NCBI)||84, 307|
|RSP_1266||kdpB||Potassium-transporting P-type ATPase, B chain, KdpB (NCBI)||84, 307|
|RSP_1267||kdpC||Potassium-transporting P-type ATPase C chain, kdpC (NCBI)||84, 307|
|RSP_1268||kdpD||Osmosensitive K+ channel histidine kinase (NCBI)||84, 307|
|RSP_1269||kdpE||two component transcriptional regulator, winged helix family (NCBI)||84, 307|
|RSP_1339||RSP_1339||Formamidopyrimidine-DNA glycolase (NCBI)||84, 331|
|RSP_1462||lpxK||Putative Tetraacyldisaccharide-1-P 4'-kinase (NCBI)||84, 234|
|RSP_1470||rnhB||ribonuclease HII (NCBI)||84, 164|
|RSP_1677||RSP_1677||hypothetical protein (NCBI)||221, 383|
|RSP_1810||mviN||putative virulence factor, MviN (NCBI)||221, 374|
|RSP_1811||glnD||uridylyltransferase (NCBI)||221, 374|
|RSP_1812||RSP_1812||hypothetical protein (NCBI)||81, 221|
|RSP_1813||RSP_1813||hypothetical protein (NCBI)||121, 221|
|RSP_1814||RSP_1814||hypothetical protein (NCBI)||197, 221|
|RSP_1815||gshB||glutathione synthetase (NCBI)||184, 221|
|RSP_1909||RSP_1909||Outer membrane general secretion pathway protein, Secretin (NCBI)||221, 381|
|RSP_1970||RSP_1970||Phosphoribosylglycinamide formyltransferase (NCBI)||84, 209|
|RSP_2107||murG||UDP-N-acetylglucosamine:N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI)||221, 349|
|RSP_2108||murC||UDP-N-acetylmuramate-alanine ligase (NCBI)||5, 221|
|RSP_2109||RSP_2109||hypothetical protein (NCBI)||5, 221|
|RSP_2110||murB||UDP-N-acetylenolpyruvoylglucosamine reductase/dehydrogenase (NCBI)||5, 221|
|RSP_2111||ddlA||D-alanine--D-alanine ligase (NCBI)||221, 349|
|RSP_2256||dtd||D-tyrosyl-tRNA(Tyr) deacylase (NCBI)||221, 374|
|RSP_2257||RSP_2257||putative Fructokinase (NCBI)||221, 374|
|RSP_2358||RSP_2358||possible phage phi-C31 gp36-like protein / Major capsid protein, HK97 family (NCBI)||221, 331|
|RSP_2534||RSP_2534||Predicted hydrolase of the metallo-beta-lactamase superfamily (NCBI)||84, 361|
|RSP_2583||RSP_2583||hypothetical protein (NCBI)||26, 221|
|RSP_2584||RSP_2584||hypothetical protein (NCBI)||221, 363|
|RSP_2599||phoB||Phosphate regulon transcriptional regulator, PhoR (NCBI)||84, 155|
|RSP_2790||RSP_2790||hypothetical protein (NCBI)||84, 356|
|RSP_2815||xerD||Probable integrase/recombinase XerD (NCBI)||84, 326|
|RSP_2818||aroB||Putative 3-dehydroquinate synthase (NCBI)||84, 234|
|RSP_2941||RSP_2941||Putative Glycoside hydrolase (NCBI)||221, 259|
|RSP_3091||RSP_3091||Coserved hypothetical protein (NCBI)||54, 84|
|RSP_3448||RSP_3448||transcriptional regulator, GntR-family (NCBI)||84, 220|
|RSP_3449||RSP_3449||Putative allophanate hydrolase subunit 2 (NCBI)||61, 84|
|RSP_3450||RSP_3450||hypothetical protein (NCBI)||61, 84|
|RSP_3565||RSP_3565||Glycoside hydrolase, family 25 (NCBI)||84, 221|
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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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.
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.
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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
- 3. Target genes (other module members)
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