GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Dynamin_N - Dynamin family
Pfam: PF00350 (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: CL0023
Length: 168
Sequences: 6111
Seq/Len: 36.38
HH_delta: 0.262 (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
63_E67_E0.475562.332
107_D110_G0.405641.989
3_V133_I0.3941.932
70_E74_E0.389031.907
14_L135_V0.358631.758
2_A129_A0.35731.752
64_E67_E0.351771.725
94_S98_P0.337211.653
27_G31_C0.332131.628
12_S16_N0.325021.594
3_V14_L0.319221.565
73_D78_S0.30961.518
133_I164_V0.304651.494
58_G110_G0.304071.491
113_S118_H0.302341.482
92_V95_I0.297811.460
69_R73_D0.296641.454
55_F58_G0.289991.422
77_D80_E0.283691.391
134_F146_D0.281361.379
24_L38_I0.280981.378
95_I98_P0.280521.375
54_E58_G0.279821.372
136_V142_L0.269181.320
67_E70_E0.264711.298
152_Q155_D0.262921.289
68_L72_I0.261551.282
137_D140_Q0.259321.271
105_L109_P0.256821.259
8_S31_C0.256021.255
6_Q9_S0.251191.232
69_R72_I0.249841.225
56_K59_S0.247971.216
131_V162_I0.244911.201
97_S100_L0.243881.196
120_E124_E0.243191.192
93_I103_L0.243141.192
114_T117_E0.241931.186
67_E71_Q0.239811.176
2_A126_L0.239051.172
115_N119_T0.238431.169
71_Q77_D0.238051.167
32_T38_I0.236641.160
127_P130_D0.236641.160
93_I97_S0.23391.147
96_S100_L0.233481.145
148_E151_K0.23091.132
14_L18_L0.230871.132
72_I77_D0.230181.129
30_P37_E0.229591.126
53_I57_D0.229491.125
59_S64_E0.229231.124
65_L69_R0.22771.116
106_V110_G0.22671.111
6_Q112_N0.225831.107
72_I75_E0.225441.105
60_E64_E0.225321.105
140_Q146_D0.224751.102
19_L38_I0.223861.098
55_F61_E0.220911.083
107_D111_L0.219841.078
116_S120_E0.218761.073
53_I56_K0.21771.067
141_D146_D0.217351.066
73_D77_D0.216371.061
149_F153_M0.21581.058
15_I105_L0.214571.052
63_E66_N0.21431.051
149_F154_L0.21431.051
148_E152_Q0.21371.048
72_I76_F0.212851.044
10_G13_T0.212051.040
24_L32_T0.212031.040
29_G32_T0.211941.039
24_L29_G0.211711.038
137_D142_L0.2111.034
13_T26_S0.208881.024
65_L71_Q0.208841.024
113_S119_T0.20851.022
76_F79_I0.208271.021
54_E57_D0.208121.020
8_S11_K0.208061.020
2_A106_V0.205711.009
152_Q156_P0.204141.001
108_T111_L0.203650.998
104_T107_D0.203540.998
3_V15_I0.203020.995
151_K155_D0.202470.993
118_H121_I0.202370.992
103_L107_D0.202360.992
95_I104_T0.202030.991
73_D76_F0.201240.987
92_V102_N0.200640.984
32_T35_P0.200370.982
115_N118_H0.200340.982
94_S97_S0.198210.972
58_G63_E0.197530.968
2_A130_D0.197370.968
92_V97_S0.196020.961
61_E66_N0.1960.961
123_E153_M0.195330.958
25_P31_C0.194650.954
59_S72_I0.194580.954
66_N70_E0.194330.953
136_V140_Q0.194290.953
71_Q78_S0.192810.945
136_V146_D0.192630.944
119_T122_T0.192220.942
42_D45_E0.191840.941
9_S12_S0.191620.939
106_V109_P0.190760.935
112_N145_S0.190370.933
157_D160_R0.189990.931
24_L30_P0.189140.927
6_Q12_S0.188660.925
71_Q74_E0.187470.919
112_N141_D0.186980.917
149_F152_Q0.186140.913
75_E78_S0.184690.905
64_E124_E0.184630.905
5_G11_K0.184070.902
66_N75_E0.183410.899
44_P58_G0.18330.899
111_L122_T0.183260.898
120_E123_E0.181470.890
116_S119_T0.179770.881
67_E79_I0.177740.871
70_E80_E0.177640.871
138_A143_T0.177450.870
143_T146_D0.175820.862
74_E79_I0.175540.861
8_S118_H0.175030.858
56_K61_E0.174860.857
91_I94_S0.174690.856
12_S22_P0.174340.855
59_S69_R0.174130.854
69_R78_S0.173730.852
119_T123_E0.173710.852
91_I96_S0.173170.849
65_L68_L0.172390.845
147_M151_K0.172390.845
62_F67_E0.172250.845
155_D158_K0.171850.843
8_S27_G0.171820.842
61_E64_E0.171080.839
30_P112_N0.170890.838
149_F159_S0.170550.836
138_A146_D0.169960.833
56_K68_L0.169670.832
113_S139_N0.168850.828
40_Y101_R0.168560.826
16_N19_L0.16840.826
97_S103_L0.167920.823
4_V122_T0.167440.821
113_S146_D0.16740.821
54_E59_S0.167130.819
98_P103_L0.166720.817
136_V163_F0.166510.816
60_E63_E0.166390.816
41_G44_P0.166210.815
29_G35_P0.165650.812
155_D161_T0.164050.804
70_E77_D0.16380.803
60_E65_L0.163590.802
157_D162_I0.163250.800
26_S29_G0.163020.799
140_Q144_E0.162890.799
91_I98_P0.162610.797
32_T36_T0.162210.795
60_E79_I0.161270.791
73_D80_E0.161010.789
79_I111_L0.15970.783
24_L35_P0.159460.782
147_M150_L0.159440.782
136_V141_D0.159340.781
62_F68_L0.159290.781
24_L36_T0.159040.780
62_F65_L0.158530.777
6_Q146_D0.158520.777
63_E71_Q0.158260.776
3_V16_N0.157960.774
21_R117_E0.15790.774
68_L71_Q0.157750.773
142_L145_S0.157370.772
97_S102_N0.157320.771
114_T119_T0.157310.771
137_D150_L0.156720.768
12_S53_I0.156660.768
113_S140_Q0.156180.766
5_G13_T0.156120.765
73_D79_I0.155870.764
8_S137_D0.155690.763
131_V150_L0.15510.760
9_S140_Q0.155040.760
113_S141_D0.154960.760
63_E69_R0.154690.758
153_M156_P0.154590.758
121_I125_Y0.154530.758
8_S17_A0.153540.753
1_V162_I0.153260.751
115_N123_E0.153250.751
58_G62_F0.153180.751
19_L40_Y0.153110.751
66_N80_E0.152580.748
74_E80_E0.151430.742
76_F80_E0.150770.739
2_A108_T0.150760.739
94_S99_L0.150670.739
144_E148_E0.150440.738
40_Y100_L0.150220.736
75_E80_E0.149620.734
18_L32_T0.149220.732
30_P33_A0.148880.730
12_S31_C0.148420.728
68_L75_E0.148180.726
91_I95_I0.148160.726
62_F71_Q0.147860.725
92_V104_T0.147840.725
37_E105_L0.14750.723
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
2j69A0.958399.80.262
3zvrA0.976299.80.266
4bejA0.99499.70.318
3t34A0.99499.70.322
1jwyB0.99499.70.33
2x2eA0.976299.70.363
2akaB0.976299.60.379
2qptA0.898899.60.384
3ievA0.672699.60.403
3szrA0.982199.50.423

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