GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PKD - PKD domain
Pfam: PF00801 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0159
Length: 69
Sequences: 2535
Seq/Len: 36.74
HH_delta: 0.096 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
34_D46_H1.285963.316
8_V11_G0.995792.568
18_A28_Y0.904812.333
8_V12_Q0.872352.249
28_Y42_S0.807482.082
32_F44_V0.688271.775
18_A58_L0.628551.621
9_P66_S0.610151.573
22_D62_N0.60311.555
28_Y58_L0.595431.535
13_P47_T0.594871.534
62_N66_S0.570681.472
33_G48_Y0.568411.466
41_G44_V0.568111.465
32_F48_Y0.553521.427
16_F56_V0.531061.369
31_D57_T0.514051.326
15_T45_T0.511371.319
13_P45_T0.507251.308
9_P14_V0.498191.285
29_S59_T0.479021.235
17_T43_S0.467531.206
29_S61_T0.455951.176
48_Y56_V0.448441.156
16_F32_F0.442091.140
39_S44_V0.440391.136
18_A42_S0.435021.122
33_G46_H0.433161.117
25_P28_Y0.416371.074
10_T51_P0.410711.059
32_F39_S0.399111.029
8_V14_V0.397521.025
18_A44_V0.393421.014
27_T61_T0.384180.991
37_T46_H0.375620.969
16_F44_V0.366830.946
16_F48_Y0.356350.919
26_V63_G0.341990.882
33_G36_G0.341040.879
22_D25_P0.318860.822
34_D37_T0.313190.808
32_F46_H0.311390.803
30_W58_L0.310320.800
16_F30_W0.303320.782
48_Y54_Y0.30090.776
22_D63_G0.298390.769
28_Y60_V0.291720.752
36_G46_H0.291610.752
31_D59_T0.288710.744
11_G14_V0.288340.744
15_T43_S0.287020.740
22_D66_S0.286440.739
24_S63_G0.28640.739
61_T65_G0.284640.734
26_V62_N0.28390.732
11_G49_S0.281080.725
59_T66_S0.279360.720
40_T50_S0.277480.716
23_G26_V0.274790.709
27_T40_T0.274260.707
31_D46_H0.267820.691
50_S54_Y0.259820.670
19_S50_S0.259010.668
9_P12_Q0.258440.666
36_G39_S0.24990.644
31_D34_D0.244770.631
17_T20_S0.244620.631
34_D38_V0.243830.629
39_S42_S0.24360.628
25_P62_N0.242560.625
53_T64_V0.236150.609
33_G55_T0.23590.608
16_F46_H0.235250.607
25_P61_T0.23160.597
20_S58_L0.225140.581
13_P50_S0.224160.578
27_T57_T0.223950.577
29_S38_V0.220710.569
34_D48_Y0.215260.555
15_T55_T0.214150.552
27_T59_T0.212330.548
15_T44_V0.211530.545
53_T57_T0.208910.539
47_T50_S0.20810.537
22_D26_V0.204180.526
19_S61_T0.203510.525
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
2y3uA0.97198.90.096
2kzwA0.956598.90.099
2c4xA0.985598.90.102
1b4rA0.97198.80.13
4aqoA0.97198.80.133
2y72A0.97198.80.139
1wgoA0.985598.30.275
2yrlA197.70.387
1l0qA0.956597.70.398
2c4xA0.884197.50.419

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