Horizontally transferred genes in Methanosarcina spp.

This archive contains detailed information about horizontally transferred genes in Methanosarcina, such as list of genes of bacterial origin in 3 Methanosarcina species, corresponding alignments (produced by MUSCLE), neighbor-joining (NJ) trees with 100 bootstrap replicas generated by ClustalW software with default parameters (BLOSUM distance matrix), and a maximum-likelihood (ML) cladograms produced with PhyML v3.0 with default parameters

Results for the external statistical test of the scoring function for the MMPs protein substrates collected in CutDB database.

<p>Results for the external statistical test of the scoring function for the MMPs protein substrates collected in CutDB database.</p

Workflow of the CleavPredict Web server.

<p>Top: the types of input queries; middle: the first tier of the output data; bottom: the second tier of the results obtained using a Uniprot id as for the input protein substrate. Blast program and mapping is used for determining the Uniprot id.</p

Distribution of PWM scores for peptide substrates of MMP-2 and MMP-9 from Prudova <i>et al</i>. [65].

<p>Red and black lines are distributions of PWM score values for experimentally identified cleaved peptide bonds and for all other peptide bonds, respectively. For both MMP-2 and MMP-9 the Kolmogorov-Smirnov test yields <i>D</i> = 0.60.</p

Snapshots of the result pages.

<p>As an example the prediction of the cleavage positions in Q15848 protein for MMP2 enzyme is demonstrated. This section contains information about signal peptide prediction, subcellular location, co-expression and co-localization information, known cleavages in CutDB, data on experimentally identified SNPs and PTMs, congregated into tables.</p

ROC curves for prediction cleavage sites in proteins collected in CutDB for MMP-2, MMP-3, MMP-8, MMP-9 and MMP-14.

<p>ROC curves for prediction cleavage sites in proteins collected in CutDB for MMP-2, MMP-3, MMP-8, MMP-9 and MMP-14.</p

CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

<div><p>CleavPredict (<a href="http://cleavpredict.sanfordburnham.org" target="_blank">http://cleavpredict.sanfordburnham.org</a>) is a Web server for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events. CleavPredict offers <i>in silico</i> prediction of cleavage sites specific for 11 human MMPs. The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results. To augment the substrate cleavage prediction process, CleavPredict provides information about the structural features of potential cleavage sites that influence proteolysis. These include: secondary structure, disordered regions, transmembrane domains, and solvent accessibility. The server also provides information about subcellular location, co-localization, and co-expression of proteinase and potential substrates, along with experimentally determined positions of single nucleotide polymorphism (SNP), and posttranslational modification (PTM) sites in substrates. All this information will provide the user with perspectives in reasoning about proteolytic events. CleavPredict is freely accessible, and there is no login required.</p></div

Distribution of PWM scores for peptide substrates of MMP-2 from Schilling <i>et al</i>. [66].

<p>Red line—distribution of PWM score values for experimentally identified cleaved peptide bonds, black line—distribution of scores for all other peptide bonds. Red—dashed line represents distribution of scores for set of cleaved peptide bonds corrected by replacing poorly scored peptide bonds by those that have their scores above the threshold and were located in the vicinity of experimentally predicted positions. The separation between the cleavage site scores and the scores for other peptide bonds was subject to Kolmogorov-Smirnov test yielding <i>D</i> = 0.60 and <i>D</i> = 0.66 for red and red-dashed distributions, respectively, when tested against the black one.</p

Results for the external statistical test of the scoring function for the MMP-2 and MMP-9 cleavages in peptide substrates identified by Overall <i>et al</i>.

<p>Results for the external statistical test of the scoring function for the MMP-2 and MMP-9 cleavages in peptide substrates identified by Overall <i>et al</i>.</p

Genomic arrangement of the synthetase and glutaminase components in NAD synthetase and other families of ATP-dependent amidotransferases.

1<p>Gene names are as in <i>E. coli</i> except <i>gatABC</i> and <i>yaaDE</i> that are as in <i>B. subtilis</i> (not present in <i>E. coli</i>). ² A current classification of glutaminase domains (subunits) of amidotransferases includes four classes of nonhomologous enzymes: Class I (contains a catalytic triad in the active site); Class II (contains a catalytic Cys at the N-terminus); Class III (a relatively poorly explored glutaminase subunit of GatABC complex); and Class IV (nitrilase-like glutaminase component of NADS). ³ Percentage (%) of total number of arrangements within analyzed genomes.</p