GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mpv17_PMP22 - Mpv17 PMP22 family
Pfam: PF04117 (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. )
Length: 68
Sequences: 1020
Seq/Len: 15
HH_delta: 0.877 (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_A50_F0.700062.944
15_K19_D0.530112.229
24_L28_W0.515692.169
49_L52_N0.47732.007
30_F54_V0.465891.959
8_S11_E0.425911.791
23_T65_I0.408561.718
13_K17_K0.401751.690
34_A54_V0.383231.612
25_K29_K0.382121.607
35_Q38_N0.375741.580
53_V57_F0.365971.539
20_Y24_L0.365211.536
10_E13_K0.346291.456
2_G12_I0.334441.407
30_F57_F0.330811.391
58_W61_Y0.326421.373
21_W25_K0.323961.362
48_V52_N0.319721.345
14_E18_R0.316421.331
26_A29_K0.313411.318
9_W13_K0.301231.267
21_W28_W0.291871.227
12_I16_L0.289321.217
44_P47_R0.28471.197
14_E17_K0.283591.193
35_Q51_V0.279011.173
15_K66_A0.278661.172
10_E14_E0.2671.123
23_T62_L0.262931.106
58_W62_L0.26171.101
19_D66_A0.245191.031
24_L27_S0.243331.023
56_F60_T0.241821.017
26_A30_F0.239681.008
51_V55_S0.238771.004
3_L14_E0.235980.992
30_F34_A0.235230.989
5_E66_A0.228490.961
38_N50_F0.228120.959
38_N47_R0.227010.955
35_Q59_N0.221090.930
37_V50_F0.213820.899
16_L20_Y0.207480.873
35_Q48_V0.206790.870
55_S58_W0.206630.869
27_S35_Q0.204350.859
38_N42_V0.201810.849
56_F63_S0.197990.833
7_K15_K0.197480.831
4_L47_R0.193240.813
9_W12_I0.193020.812
3_L9_W0.190360.801
11_E17_K0.189780.798
17_K21_W0.189770.798
26_A61_Y0.189470.797
3_L7_K0.18770.789
27_S55_S0.187320.788
42_V50_F0.186590.785
50_F54_V0.185810.781
48_V61_Y0.185740.781
36_I40_R0.178910.752
9_W33_P0.178110.749
14_E36_I0.175840.740
37_V41_Y0.175620.739
10_E18_R0.174310.733
22_P65_I0.173910.731
60_T66_A0.173550.730
7_K11_E0.170810.718
35_Q46_Y0.170780.718
39_F63_S0.168790.710
27_S47_R0.166770.701
34_A37_V0.164830.693
4_L16_L0.164070.690
2_G7_K0.16350.688
11_E18_R0.163450.687
13_K16_L0.162390.683
61_Y65_I0.161170.678
48_V56_F0.161160.678
17_K37_V0.156140.657
19_D23_T0.156120.657
11_E57_F0.155520.654
4_L25_K0.15480.651
29_K61_Y0.153490.646
31_W62_L0.153130.644
39_F65_I0.151080.635
51_V58_W0.15050.633
30_F33_P0.149440.628
38_N51_V0.149330.628
60_T64_Y0.14890.626
29_K45_H0.148180.623
52_N58_W0.147740.621
6_G45_H0.145970.614
47_R58_W0.145060.610
55_S61_Y0.144930.610
10_E21_W0.144760.609
58_W66_A0.143540.604
44_P48_V0.142450.599
5_E38_N0.142110.598
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
1szwA0.705913.90.877
1z2zA0.94129.60.885
2c5uA0.470680.889
1te7A0.57.10.891
3qufA0.38246.20.894
2heuA0.36765.40.896
2lbfB0.39715.20.898
2zyoA0.42654.70.899
3l0zA0.38244.20.902
3oo8A0.36763.40.906
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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