CBS >> CBS Prediction Servers >> NetPhosK >> Output format
Prediction without filtering The output from NetPhosK contains four columns: Column 1: position of the residue being analyzed Column 2: the residue Column 3: the predicted kinase (above the threshold ,default 0.500) Column 4: output score (value in the range [0.000-1.000]) Prediction with ESS filtering Here the prediction is refined by a filtering process based on the evolutionary information obtained from sequence similarity and taxonomy. The Evolutionary Stable Sites (ESS) filter tests the same kinase prediction on homologues sites obtained from other homologues from higher eukaryotes. As most phosphorylation sites should be conserved in this taxonomic group, sites which are not positively predicted in all or a greater subset of the homologues can be filtered out. The output from NetPhosK with ESS filtering contains six columns: Column 1: position of the residue being analyzed Column 2: the residue Column 3: the predicted kinase (above the threshold ,default 0.500) Column 4: output score (value in the range [0.000-1.000]) Column 5: number of homologues with positive prediction Column 6: number of homologues with negative prediction Kinase Landscapes Consider the kinase specificity prediction along a amino acid sequence only at STY sites - if the prediction for different kinase are represented by different letters with heights equally to the prediction values and plotted along the sequence position, one can recognize kinase landscape - a potential region of the sliding kinase motif. Prediction of kinase specificity along an amino acid sequence is normally done at serine, threonine, or tyrosine residues. However, if kinase specificity is additionally predicted at non-STY sites, one can notice that the individual kinase predictions tend to cluster.
Method: NetPhosK without ESS filtering: Name: q_EFTU_HUMAN Pos AA Kinase Score: 5 T: PKC 0.777000 5 T: cdc2 0.520333 14 S: cdc2 0.547333 50 T: PKC 0.699500 72 T: PKC 0.655750 74 T: PKC 0.638000 107 T: PKA 0.579000 116 S: PKC 0.691750 141 T: PKC 0.536250 189 S: CKII 0.554000 273 T: PKA 0.624750 296 S: PKA 0.589000 296 S: cdc2 0.515000 304 T: CKII 0.532667 304 T: PKG 0.501000 345 S: PKC 0.874500 360 S: CKII 0.566333 423 T: PKC 0.724750 433 T: PKC 0.725750 443 T: CKII 0.678333 Highest Score: 0.874500 PKC at position 345
Method: NetPhosK with ESS filtering Name: SYN1_HUMAN Pos: AA: Kinase: Score: Positiv: Negative: ========================================== 9 S cdc2 0.530333333333 1 6 9 S PKA 0.88575 1 6 9 S PKG 0.554 1 6 55 S cdc2 0.563666666667 1 6 55 S PKA 0.62825 1 6 78 S cdc2 0.524666666667 6 1 79 S cdc2 0.526666666667 6 1 81 S PKC 0.68325 1 6 124 T CKII 0.523666666667 6 1 177 S PKC 0.5165 1 6 177 S PKG 0.565 1 6 191 S PKC 0.738 2 5 218 S PKC 0.53725 5 2 260 S PKA 0.52575 1 6 293 S PKC 0.5485 6 1 298 T PKC 0.76775 6 1 330 S PKC 0.62725 6 1 332 S PKC 0.79425 6 1 350 S PKC 0.77475 7 0 359 T CKII 0.511666666667 6 1 359 T PKG 0.531 6 1 432 S PKC 0.63475 6 1 432 S PKA 0.595 5 2 448 T PKA 0.5395 5 2 494 S cdc2 0.579666666667 6 1 502 S cdc2 0.523666666667 6 1 510 S PKG 0.547 6 1 513 S cdc2 0.508333333333 5 2 533 S PKC 0.52075 6 1 567 T PKA 0.5075 4 3 567 T PKG 0.506 4 3 568 S CaM-II 0.5325 6 1 570 S PKC 0.7195 7 0 605 S CaM-II 0.518 6 1 624 S PKA 0.52875 7 0 663 S cdc2 0.524666666667 6 1 667 T PKC 0.68 5 2 681 S PKA 0.7365 1 6 683 S CKII 0.524333333333 1 6 694 S PKC 0.827 2 5 698 S PKA 0.64075 1 6
