GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Band_7 - SPFH domain Band 7 family
Pfam: PF01145 (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: CL0433
Length: 179
Sequences: 5003
Seq/Len: 27.95
HH_delta: 0.367 (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
13_R33_Q1.329644.825
74_D77_K0.956183.470
17_V20_V0.855993.106
71_R138_E0.76162.764
4_P7_E0.716822.601
71_R140_T0.685062.486
122_D126_E0.668812.427
126_E130_E0.627772.278
107_S123_E0.607812.206
119_E123_E0.605352.197
38_Y79_V0.598592.172
7_E37_V0.598482.172
13_R18_K0.592162.149
3_V9_G0.588362.135
8_V40_T0.560142.033
77_K81_N0.552232.004
73_E138_E0.551432.001
8_V75_P0.550581.998
68_V97_V0.546181.982
109_S112_E0.541081.963
151_Q155_E0.534231.939
155_E159_E0.517271.877
116_N119_E0.50931.848
9_G35_V0.505181.833
12_V80_Q0.47811.735
19_D33_Q0.465981.691
42_V140_T0.455451.653
112_E116_N0.449731.632
123_E126_E0.449641.632
125_R129_Q0.444861.614
56_T113_I0.442171.605
159_E162_R0.431071.564
64_V105_I0.429861.560
57_K109_S0.42941.558
96_I128_L0.42741.551
159_E166_E0.422281.532
11_V33_Q0.419251.521
9_G37_V0.41871.519
53_T63_D0.408671.483
129_Q133_E0.407741.480
29_I32_I0.40641.475
88_D91_N0.405151.470
118_E122_D0.393991.430
21_L26_H0.37311.354
122_D125_R0.369291.340
119_E122_D0.36571.327
104_V123_E0.363621.319
129_Q138_E0.358321.300
18_K33_Q0.355131.289
17_V76_P0.35321.282
93_L132_L0.349751.269
164_E167_A0.348031.263
148_D154_E0.347841.262
2_T25_L0.347461.261
78_F89_P0.346311.257
6_G40_T0.336071.220
162_R166_E0.334521.214
161_Q165_Q0.325581.181
29_I33_Q0.322551.170
14_F32_I0.32131.166
158_E161_Q0.320111.162
77_K136_G0.319481.159
45_I70_Y0.317041.150
8_V22_G0.316011.147
108_Y123_E0.310761.128
43_Q90_E0.308961.121
151_Q154_E0.306711.113
77_K80_Q0.306651.113
10_V79_V0.304941.107
96_I131_A0.304781.106
38_Y72_I0.303491.101
123_E127_Q0.29971.088
127_Q130_E0.290951.056
132_L139_I0.290261.053
65_D145_T0.284031.031
68_V139_I0.276971.005
46_E65_D0.276211.002
66_V101_L0.27581.001
152_E155_E0.273810.994
8_V12_V0.272990.991
92_L135_Y0.269920.979
105_I113_I0.268680.975
12_V36_Y0.266970.969
54_V105_I0.266360.967
73_E133_E0.266080.966
99_S103_E0.262230.952
6_G39_P0.259820.943
5_P23_P0.255220.926
11_V21_L0.254920.925
108_Y120_I0.254790.925
45_I94_R0.254780.925
11_V35_V0.252570.917
96_I100_A0.251970.914
160_K164_E0.250740.910
104_V107_S0.250660.910
12_V34_K0.250440.909
3_V37_V0.248770.903
150_P153_V0.245260.890
49_R63_D0.244370.887
42_V141_S0.243770.885
14_F25_L0.242910.881
17_V80_Q0.241290.876
97_V128_L0.240680.873
53_T61_P0.239920.871
10_V20_V0.239880.870
153_V161_Q0.239720.870
102_R106_S0.239150.868
149_P153_V0.236640.859
68_V142_V0.234310.850
157_I160_K0.234270.850
39_P43_Q0.233190.846
6_G41_R0.23230.843
125_R138_E0.231650.841
76_P80_Q0.229910.834
154_E158_E0.229840.834
7_E39_P0.229830.834
48_T52_I0.226880.823
103_E127_Q0.225340.818
20_V76_P0.223810.812
28_V32_I0.22310.810
131_A134_E0.222480.807
82_Y135_Y0.220340.800
82_Y92_L0.217780.790
38_Y75_P0.216520.786
160_K165_Q0.21570.783
8_V20_V0.213690.775
72_I75_P0.213310.774
96_I135_Y0.211750.768
22_G26_H0.210430.764
43_Q70_Y0.203680.739
101_L124_V0.202070.733
3_V26_H0.201770.732
59_G165_Q0.201090.730
77_K133_E0.200660.728
128_L132_L0.200420.727
58_D111_E0.200380.727
158_E162_R0.198450.720
161_Q164_E0.197280.716
92_L96_I0.197240.716
99_S143_Q0.196960.715
155_E162_R0.196040.711
81_N134_E0.195770.710
131_A141_S0.195650.710
21_L35_V0.19550.709
60_V150_P0.19530.709
156_A163_A0.194040.704
70_Y137_I0.193690.703
28_V33_Q0.190410.691
130_E133_E0.189350.687
14_F18_K0.189120.686
56_T62_V0.189070.686
103_E107_S0.188320.683
3_V35_V0.187890.682
133_E138_E0.186980.678
65_D146_D0.186140.675
42_V71_R0.186060.675
131_A135_Y0.183150.665
46_E145_T0.181950.660
69_T141_S0.180680.656
134_E155_E0.180230.654
149_P167_A0.180060.653
60_V158_E0.179940.653
64_V102_R0.179430.651
95_Q128_L0.179020.650
27_F30_P0.178380.647
67_T145_T0.17710.643
56_T110_L0.17690.642
97_V100_A0.176110.639
49_R65_D0.175870.638
96_I99_S0.174440.633
62_V113_I0.174430.633
67_T99_S0.173990.631
13_R29_I0.173930.631
60_V149_P0.1730.628
91_N133_E0.172540.626
66_V142_V0.170630.619
110_L147_I0.170530.619
114_Y157_I0.170460.619
63_D148_D0.169110.614
18_K76_P0.169090.614
106_S114_Y0.168790.612
107_S127_Q0.168660.612
152_E166_E0.167230.607
53_T149_P0.167130.606
124_V128_L0.166960.606
99_S102_R0.166540.604
100_A124_V0.166120.603
89_P137_I0.165450.600
100_A127_Q0.165280.600
60_V157_I0.164380.596
74_D78_F0.164150.596
155_E158_E0.1620.588
66_V97_V0.160970.584
44_T69_T0.160940.584
121_A143_Q0.160140.581
43_Q87_E0.160.581
43_Q79_V0.159990.581
13_R32_I0.159820.580
119_E126_E0.159570.579
15_G18_K0.158620.576
114_Y149_P0.157970.573
153_V162_R0.157760.572
73_E119_E0.15730.571
55_R106_S0.156140.567
100_A104_V0.155260.563
69_T96_I0.155240.563
73_E77_K0.154960.562
120_I144_I0.154740.562
14_F17_V0.153690.558
45_I90_E0.153590.557
103_E143_Q0.153570.557
4_P34_K0.153130.556
60_V153_V0.15270.554
55_R61_P0.151570.550
72_I89_P0.150940.548
87_E91_N0.150810.547
55_R102_R0.150660.547
102_R105_I0.150630.547
9_G22_G0.150320.545
158_E165_Q0.150050.544
143_Q147_I0.150010.544
143_Q154_E0.149880.544
110_L114_Y0.149410.542
43_Q164_E0.14920.541
104_V108_Y0.149070.541
153_V158_E0.149010.541
127_Q131_A0.148890.540
55_R121_A0.148640.539
118_E121_A0.148350.538
15_G24_G0.148220.538
107_S164_E0.148150.538
58_D110_L0.14750.535
56_T105_I0.147340.535
148_D151_Q0.147210.534
9_G26_H0.146670.532
79_V157_I0.146560.532
110_L165_Q0.146140.530
90_E94_R0.145930.530
100_A103_E0.145140.527
11_V19_D0.145070.526
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
3bk6A0.798999.90.367
4fvgA0.74399.80.398
1winA0.770999.70.466
2rpbA0.631399.60.518
2zuoA0.983297.60.787
3h4zA0.631335.80.915
4jkvA0.508430.80.918
3elnA0.396613.30.93
4ieuA0.396613.30.93
2ptmA0.46377.30.938

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