GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Crystall - BetaGamma crystallin
Pfam: PF00030 (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: CL0333
Length: 82
Sequences: 1246
Seq/Len: 15.2
HH_delta: 0.005 (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
45_L76_I0.406072.172
3_T16_E0.40492.165
38_V41_G0.39742.125
44_V57_V0.375652.009
17_I79_V0.342161.830
3_T39_P0.314941.684
47_E54_R0.301751.614
4_L33_V0.301691.613
44_V55_Q0.29691.588
46_Y55_Q0.280381.499
7_H74_D0.279611.495
34_S73_N0.27631.478
6_E32_R0.272811.459
7_H11_Q0.269551.442
56_Y69_W0.268471.436
34_S74_D0.264511.415
21_C51_F0.259941.390
4_L17_I0.255911.369
42_C57_V0.253541.356
7_H34_S0.252681.351
66_L69_W0.250721.341
40_S60_P0.248261.328
37_K62_E0.242821.299
31_D77_S0.239371.280
20_D80_R0.238491.275
49_P77_S0.233891.251
22_P51_F0.233131.247
8_E11_Q0.229961.230
11_Q76_I0.22791.219
24_L79_V0.227321.216
22_P50_N0.225731.207
45_L58_L0.221021.182
47_E75_K0.220471.179
36_I45_L0.21781.165
5_Y72_F0.212931.139
30_N48_H0.207131.108
24_L29_F0.205861.101
66_L71_G0.204521.094
42_C59_E0.203951.091
48_H54_R0.19991.069
49_P52_Q0.196911.053
48_H75_K0.196821.053
56_Y71_G0.195011.043
4_L79_V0.190881.021
44_V59_E0.184570.987
2_I79_V0.182690.977
65_D69_W0.179710.961
23_N29_F0.179140.958
3_T38_V0.178710.956
3_T14_S0.177610.950
28_G33_V0.177070.947
23_N26_S0.176630.945
9_N26_S0.174970.936
44_V56_Y0.174440.933
30_N77_S0.174360.932
58_L63_Y0.172190.921
25_S45_L0.170230.910
48_H52_Q0.167810.897
35_S38_V0.164740.881
38_V58_L0.164630.880
20_D81_P0.164470.880
45_L56_Y0.164440.879
48_H77_S0.163090.872
9_N31_D0.160190.857
4_L16_E0.157070.840
24_L76_I0.155060.829
47_E53_G0.154420.826
68_A81_P0.154130.824
11_Q75_K0.153320.820
72_F77_S0.152060.813
26_S62_E0.151640.811
20_D51_F0.147970.791
75_K81_P0.145860.780
7_H40_S0.144320.772
5_Y37_K0.143620.768
43_W63_Y0.143350.767
46_Y64_P0.142920.764
4_L15_I0.142430.762
15_I30_N0.142250.761
58_L70_G0.141590.757
11_Q15_I0.139560.746
41_G46_Y0.13930.745
7_H31_D0.138190.739
37_K61_G0.137140.733
45_L60_P0.136290.729
72_F76_I0.135990.727
14_S21_C0.135390.724
69_W73_N0.135380.724
43_W69_W0.134530.719
46_Y51_F0.134450.719
3_T40_S0.134430.719
36_I72_F0.134130.717
4_L32_R0.134070.717
9_N33_V0.134040.717
24_L67_N0.13360.714
17_I21_C0.132940.711
2_I58_L0.132640.709
65_D79_V0.130140.696
71_G80_R0.130120.696
43_W55_Q0.129610.693
3_T61_G0.129570.693
51_F81_P0.129470.692
36_I76_I0.129230.691
6_E71_G0.12920.691
11_Q74_D0.128790.689
38_V63_Y0.128790.689
31_D48_H0.127870.684
51_F78_S0.125750.672
12_G35_S0.125710.672
6_E12_G0.125240.670
51_F58_L0.124830.668
9_N22_P0.124670.667
6_E34_S0.123820.662
52_Q81_P0.123360.660
5_Y14_S0.123270.659
5_Y50_N0.122980.658
70_G79_V0.122830.657
39_P43_W0.122550.655
13_R47_E0.122470.655
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
1ytqA199.80.005
1ha4A199.80.008
1okiA199.80.009
1bd7A199.80.01
2bv2A199.80.013
3hz2A0.987899.80.015
3qk3A199.80.021
1zwmA0.987899.80.024
1h4aX0.975699.80.029
1zwmA0.975699.80.035

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