GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Copine - Copine
Pfam: PF07002 (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: CL0128
Length: 146
Sequences: 6032
Seq/Len: 41.32
HH_delta: 0.275 (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
86_T117_D0.85522.653
95_A112_L0.822662.552
21_G78_P0.772772.398
87_N90_P0.706032.191
88_F114_I0.692.141
25_Q70_L0.683492.121
100_K136_L0.641051.989
11_N14_Q0.620811.926
94_H97_K0.620031.924
96_A133_A0.617511.916
37_G51_C0.606941.883
111_I141_I0.581211.803
96_A136_L0.559031.734
128_D131_V0.550281.707
34_P54_L0.550121.707
86_T118_G0.548511.702
42_I94_H0.547491.699
36_Y91_I0.5441.688
21_G74_R0.541351.680
38_F88_F0.534091.657
105_N108_Q0.525991.632
132_E135_K0.522261.620
93_N129_A0.520251.614
36_Y94_H0.516321.602
28_D31_K0.512481.590
18_R22_E0.502371.559
96_A129_A0.486321.509
131_V135_K0.481141.493
24_L33_I0.48021.490
93_N132_E0.470241.459
92_I133_A0.467211.450
112_L140_I0.463721.439
14_Q17_I0.458891.424
126_T130_I0.450571.398
92_I112_L0.444481.379
115_L145_V0.43651.354
128_D132_E0.42851.329
113_L143_V0.418941.300
16_A20_V0.418041.297
99_A110_F0.414891.287
71_E75_K0.41041.273
42_I91_I0.40771.265
93_N97_K0.406121.260
22_E25_Q0.401331.245
92_I96_A0.387611.203
71_E74_R0.374151.161
129_A132_E0.372711.156
125_E128_D0.370991.151
22_E26_D0.362791.126
44_P94_H0.362031.123
92_I140_I0.349081.083
13_Y17_I0.346931.076
130_I134_S0.346361.075
44_P98_I0.343951.067
21_G70_L0.343841.067
86_T116_T0.342371.062
77_L80_V0.341081.058
90_P93_N0.338881.051
10_P18_R0.338121.049
94_H98_I0.337711.048
40_A84_G0.337081.046
25_Q74_R0.336511.044
15_Q18_R0.334671.038
88_F120_I0.328991.021
89_A126_T0.328891.020
70_L73_Y0.322661.001
42_I90_P0.32110.996
13_Y82_L0.317070.984
36_Y42_I0.315480.979
124_E128_D0.313010.971
34_P99_A0.311160.965
89_A129_A0.307980.956
87_N120_I0.301610.936
13_Y19_A0.296510.920
19_A27_Y0.293410.910
44_P53_P0.293090.909
109_Y139_S0.292130.906
87_N121_T0.290340.901
114_I140_I0.289170.897
120_I123_M0.288820.896
69_V74_R0.286430.889
40_A85_P0.282140.875
88_F92_I0.280470.870
52_F55_N0.277510.861
14_Q18_R0.275960.856
69_V72_A0.274780.853
89_A130_I0.270590.840
96_A100_K0.268740.834
76_A79_K0.267890.831
91_I95_A0.267540.830
122_D126_T0.266020.825
17_I77_L0.255610.793
131_V134_S0.254850.791
35_A52_F0.254490.790
34_P98_I0.250330.777
36_Y95_A0.250030.776
16_A145_V0.249950.775
21_G25_Q0.249940.775
10_P14_Q0.249360.774
20_V35_A0.246630.765
97_K101_Q0.24660.765
36_Y44_P0.245960.763
13_Y16_A0.239550.743
134_S137_P0.239470.743
127_I131_V0.239440.743
37_G43_P0.23910.742
12_P15_Q0.237230.736
110_F136_L0.236470.734
41_K90_P0.235910.732
112_L138_L0.235540.731
53_P56_G0.234980.729
36_Y98_I0.234550.728
90_P94_H0.233710.725
96_A99_A0.233010.723
28_D58_P0.232590.722
123_M126_T0.232580.722
16_A115_L0.232510.721
114_I142_I0.230620.716
129_A133_A0.228980.710
19_A38_F0.228240.708
99_A138_L0.227280.705
59_Q69_V0.226530.703
12_P16_A0.22630.702
111_I139_S0.224350.696
23_I27_Y0.224010.695
75_K79_K0.22070.685
116_T142_I0.22040.684
39_G84_G0.219510.681
130_I133_A0.216350.671
89_A93_N0.215510.669
92_I114_I0.214810.666
86_T121_T0.213390.662
127_I130_I0.212940.661
75_K78_P0.211850.657
38_F86_T0.211510.656
98_I101_Q0.210310.653
39_G83_S0.210270.652
69_V76_A0.209830.651
17_I80_V0.208250.646
19_A23_I0.208120.646
27_Y141_I0.207730.645
27_Y31_K0.207460.644
10_P15_Q0.207210.643
58_P70_L0.206980.642
126_T131_V0.206860.642
13_Y27_Y0.206290.640
69_V73_Y0.203690.632
87_N125_E0.202540.628
39_G87_N0.201870.626
124_E127_I0.201070.624
39_G82_L0.201040.624
85_P116_T0.200780.623
18_R93_N0.198960.617
70_L74_R0.197240.612
133_A143_V0.197240.612
85_P121_T0.196120.608
24_L69_V0.195710.607
89_A120_I0.19440.603
20_V77_L0.194190.602
27_Y33_I0.19290.598
137_P141_I0.192810.598
133_A138_L0.192260.597
42_I57_N0.192170.596
133_A140_I0.192160.596
36_Y115_L0.190250.590
29_S58_P0.189740.589
87_N122_D0.18920.587
89_A124_E0.188130.584
52_F69_V0.187880.583
37_G82_L0.185340.575
30_D33_I0.184950.574
34_P116_T0.184560.573
19_A82_L0.184330.572
18_R21_G0.184210.572
132_E136_L0.182330.566
95_A99_A0.182070.565
100_K132_E0.1820.565
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
4hqoA0.904199.60.275
4hqfA0.931599.60.287
3k6sA0.897399.60.287
1ijbA0.890499.60.3
3hrzD0.904199.60.307
2odpA0.904199.60.315
1mf7A0.890499.60.323
1v7pC0.883699.50.33
2xggA0.904199.50.33
4jduA0.869999.50.335

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