GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Spectrin - Spectrin repeat
Pfam: PF00435 (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: 105
Sequences: 1797
Seq/Len: 17.11
HH_delta: 0.068 (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
61_N86_N0.77164.391
21_E88_R0.55933.183
64_A82_L0.423932.413
54_Q58_E0.358062.038
50_I96_V0.347671.979
47_Q100_R0.344861.963
6_F64_A0.323991.844
30_G39_Q0.26471.506
32_D35_E0.262081.491
54_Q93_C0.256541.460
64_A78_I0.254511.448
49_E53_R0.249491.420
14_L81_K0.247771.410
6_F10_A0.242941.383
13_L53_R0.241221.373
30_G35_E0.238081.355
68_I75_S0.234841.336
43_H96_V0.233891.331
62_E66_Q0.228951.303
17_L92_L0.228921.303
36_L39_Q0.227931.297
87_Q91_A0.227211.293
49_E52_S0.222381.266
65_Q69_D0.220891.257
98_E102_K0.212331.208
13_L57_L0.207581.181
83_E87_Q0.206861.177
65_Q82_L0.20661.176
85_L99_R0.205361.169
20_T49_E0.202611.153
72_P78_I0.200881.143
50_I53_R0.200411.141
94_E98_E0.199011.133
39_Q99_R0.198011.127
97_E100_R0.197381.123
21_E91_A0.195731.114
55_E58_E0.195581.113
16_W53_R0.195471.112
66_Q70_S0.195251.111
61_N82_L0.19141.089
46_L50_I0.19031.083
43_H99_R0.188571.073
30_G99_R0.186491.061
35_E40_L0.184611.051
9_E63_Q0.183851.046
3_L72_P0.183831.046
8_Q12_E0.183041.042
68_I72_P0.182071.036
84_E87_Q0.181621.034
5_Q9_E0.179231.020
29_P102_K0.179221.020
16_W20_T0.177231.009
17_L20_T0.177051.008
72_P75_S0.176851.006
61_N64_A0.175030.996
79_Q83_E0.174670.994
58_E62_E0.173480.987
74_D83_E0.173050.985
45_E49_E0.173040.985
73_E78_I0.172420.981
90_E94_E0.171030.973
70_S85_L0.170510.970
5_Q38_E0.170130.968
33_L39_Q0.167480.953
10_A82_L0.166820.949
3_L7_Q0.162890.927
16_W43_H0.162210.923
47_Q78_I0.161830.921
47_Q51_E0.157540.897
13_L20_T0.157430.896
38_E48_E0.157430.896
79_Q90_E0.157390.896
98_E101_Q0.156610.891
18_Q88_R0.156470.890
13_L64_A0.154910.882
16_W49_E0.153850.876
39_Q43_H0.151870.864
86_N90_E0.151670.863
14_L88_R0.149240.849
31_S35_E0.149070.848
10_A72_P0.148670.846
6_F23_K0.147030.837
64_A67_L0.146390.833
81_K84_E0.145950.831
99_R103_L0.143160.815
51_E59_S0.142810.813
67_L72_P0.142790.813
40_L58_E0.142380.810
4_Q39_Q0.141470.805
48_E58_E0.141020.803
68_I77_E0.140650.800
43_H48_E0.140620.800
30_G36_L0.140460.799
15_D84_E0.140280.798
60_L89_W0.139990.797
34_E47_Q0.139490.794
50_I100_R0.139050.791
19_E32_D0.139010.791
13_L24_L0.138710.789
29_P39_Q0.138610.789
35_E39_Q0.138470.788
18_Q94_E0.138280.787
25_S95_L0.137720.784
45_E48_E0.137660.783
24_L92_L0.135440.771
37_E53_R0.135160.769
17_L66_Q0.13480.767
12_E32_D0.134710.767
97_E101_Q0.134080.763
19_E22_A0.133530.760
46_L53_R0.133420.759
89_W95_L0.133230.758
16_W19_E0.132720.755
36_L103_L0.132170.752
37_E41_K0.131730.750
58_E90_E0.131720.750
3_L74_D0.131470.748
61_N65_Q0.131440.748
93_C98_E0.131140.746
57_L61_N0.130920.745
5_Q37_E0.130590.743
50_I55_E0.130370.742
24_L53_R0.130090.740
91_A98_E0.12970.738
67_L77_E0.128950.734
32_D38_E0.128350.730
84_E94_E0.12780.727
20_T24_L0.127270.724
5_Q63_Q0.127250.724
69_D101_Q0.126690.721
6_F82_L0.126270.719
76_D79_Q0.125910.717
15_D79_Q0.125140.712
68_I71_G0.1250.711
90_E100_R0.124920.711
57_L69_D0.12490.711
18_Q102_K0.124710.710
7_Q10_A0.124660.709
20_T50_I0.123910.705
87_Q98_E0.12350.703
27_S39_Q0.122570.698
17_L26_S0.122290.696
20_T46_L0.122030.694
41_K56_R0.121610.692
47_Q63_Q0.121130.689
29_P42_K0.12070.687
65_Q72_P0.120490.686
19_E80_E0.120320.685
14_L85_L0.120220.684
51_E93_C0.11990.682
43_H103_L0.119710.681
9_E34_E0.119660.681
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
1u5pA199.30.068
3lbxA0.990599.30.073
2spcA199.30.076
1cunA0.990599.30.077
2iakA199.30.08
3eduA199.30.084
3r6nA199.30.089
1s35A199.30.091
3edvA199.30.092
3f31A0.990599.30.094

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