GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ion_trans - Ion transport protein
Pfam: PF00520 (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: CL0030
Length: 200
Sequences: 6103
Seq/Len: 30.52
HH_delta: 0.192 (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
111_F183_S0.799583.593
11_I45_I0.739463.323
115_G180_F0.614182.760
115_G119_F0.519842.336
153_L184_F0.491532.209
4_I8_V0.447452.011
14_I38_F0.438771.972
109_L113_C0.433431.948
14_I28_Y0.426641.917
66_R69_R0.418621.881
145_S148_E0.416441.871
116_Y119_F0.39061.755
194_N198_A0.381171.713
14_I18_F0.359381.615
40_S43_P0.35711.605
163_G167_P0.349531.571
116_Y120_G0.349431.570
28_Y37_D0.340321.529
8_V11_I0.334351.502
28_Y34_N0.333041.497
160_E163_G0.326761.468
159_G163_G0.326661.468
146_F150_L0.325261.462
174_S177_A0.32521.461
8_V12_L0.323041.452
109_L146_F0.319881.437
13_E17_R0.318471.431
63_R66_R0.316071.420
5_I8_V0.311981.402
89_A93_S0.309241.390
156_T161_G0.304871.370
49_I53_Y0.299281.345
26_R30_R0.29471.324
156_T164_D0.294321.323
116_Y145_S0.29131.309
161_G164_D0.281481.265
185_I190_I0.272421.224
14_I17_R0.271041.218
32_W35_W0.268291.206
162_W165_V0.267511.202
36_F40_S0.26691.199
96_D100_F0.265971.195
27_R30_R0.265451.193
18_F29_F0.265241.192
17_R20_A0.264771.190
116_Y149_S0.264721.190
174_S178_V0.264021.186
37_D41_V0.263721.185
155_Q186_I0.263441.184
14_I41_V0.26221.178
35_W39_I0.261481.175
31_S34_N0.260461.170
14_I29_F0.259171.165
86_L89_A0.259031.164
156_T159_G0.258021.159
49_I52_S0.257581.157
156_T162_W0.255011.146
65_F69_R0.253211.138
158_T161_G0.248131.115
72_R75_R0.247621.113
159_G162_W0.2471.110
12_L16_L0.24671.109
177_A180_F0.245951.105
152_W156_T0.245131.101
155_Q158_T0.243771.095
7_D11_I0.243751.095
162_W167_P0.242771.091
148_E178_V0.240851.082
159_G164_D0.239881.078
85_R88_R0.239671.077
156_T160_E0.239171.075
34_N37_D0.238161.070
119_F177_A0.237181.066
155_Q160_E0.236211.061
141_E168_S0.235061.056
112_A115_G0.233841.051
75_R79_R0.232551.045
155_Q163_G0.23231.044
3_E69_R0.231111.038
164_D167_P0.229661.032
121_G144_D0.229171.030
155_Q161_G0.226791.019
13_E20_A0.22361.005
41_V44_S0.223291.003
46_V49_I0.220930.993
29_F35_W0.220010.989
84_R87_L0.21960.987
176_L180_F0.218630.982
37_D75_R0.218020.980
69_R72_R0.217440.977
111_F115_G0.217320.977
63_R74_L0.216990.975
175_W187_I0.216480.973
32_W36_F0.214330.963
64_I68_L0.213420.959
110_F113_C0.21340.959
181_F186_I0.213270.958
144_D148_E0.213070.957
160_E167_P0.212430.955
84_R88_R0.21220.954
17_R21_L0.211790.952
141_E144_D0.211510.950
115_G118_L0.209520.941
184_F188_V0.208890.939
48_V51_R0.207310.932
116_Y146_F0.206720.929
152_W160_E0.206360.927
5_I9_I0.206360.927
7_D41_V0.205980.926
10_F41_V0.205730.924
112_A119_F0.205180.922
39_I43_P0.203810.916
15_V19_F0.203060.912
77_L84_R0.202120.908
61_L64_I0.202110.908
194_N197_I0.201470.905
11_I41_V0.19990.898
151_Y162_W0.19980.898
166_M181_F0.198960.894
114_I120_G0.198470.892
7_D44_S0.1980.890
28_Y31_S0.19760.888
62_L66_R0.197140.886
17_R28_Y0.19680.884
77_L81_R0.196640.884
85_R89_A0.195260.877
155_Q159_G0.194910.876
185_I188_V0.194580.874
156_T163_G0.19280.866
96_D99_K0.192090.863
162_W166_M0.192050.863
112_A150_L0.191190.859
96_D103_L0.190960.858
21_L28_Y0.189710.852
99_K113_C0.189240.850
188_V191_L0.189180.850
119_F122_S0.189130.850
37_D40_S0.189130.850
112_A116_Y0.188970.849
3_E10_F0.188960.849
113_C117_Q0.188040.845
23_F26_R0.187680.843
114_I180_F0.187090.841
151_Y163_G0.185210.832
108_L153_L0.184820.830
18_F38_F0.184040.827
160_E165_V0.183480.824
88_R91_I0.183410.824
151_Y164_D0.182420.820
106_I113_C0.18220.819
163_G166_M0.181760.817
65_F68_L0.181490.816
189_S198_A0.181460.815
180_F185_I0.181110.814
109_L115_G0.18080.812
99_K199_V0.180680.812
99_K106_I0.179830.808
151_Y166_M0.179580.807
107_V117_Q0.179240.805
96_D104_L0.179130.805
157_M188_V0.179030.804
140_Y144_D0.178970.804
70_L74_L0.178660.803
165_V180_F0.178490.802
175_W178_V0.178160.801
29_F34_N0.177490.798
90_L97_L0.17610.791
153_L195_L0.175740.790
51_R54_G0.175710.790
95_P99_K0.175290.788
185_I189_S0.175280.788
87_L91_I0.175230.787
26_R53_Y0.175090.787
113_C146_F0.175070.787
6_F9_I0.175060.787
70_L80_F0.174990.786
99_K114_I0.174290.783
152_W161_G0.174070.782
13_E16_L0.173650.780
193_L196_L0.173190.778
191_L197_I0.173060.778
176_L179_I0.172680.776
98_F102_L0.171930.773
14_I34_N0.171330.770
155_Q162_W0.171270.770
3_E6_F0.171160.769
164_D168_S0.171150.769
177_A181_F0.170430.766
152_W163_G0.170320.765
51_R55_S0.170290.765
152_W162_W0.170170.765
17_R34_N0.169850.763
74_L79_R0.169590.762
155_Q167_P0.169440.761
112_A146_F0.169260.761
13_E37_D0.168140.756
74_L77_L0.167710.754
47_S66_R0.167140.751
112_A149_S0.166730.749
76_L82_S0.166140.747
30_R35_W0.165640.744
142_N148_E0.165330.743
161_G190_I0.164720.740
192_L198_A0.16440.739
30_R34_N0.164360.739
157_M189_S0.163940.737
10_F13_E0.163790.736
175_W181_F0.162910.732
97_L122_S0.162670.731
19_F23_F0.161940.728
73_L82_S0.161670.726
77_L83_L0.161410.725
79_R82_S0.160860.723
22_G27_R0.160780.722
90_L95_P0.160470.721
149_S153_L0.160190.720
44_S47_S0.160030.719
143_F149_S0.160020.719
70_L76_L0.159810.718
71_L76_L0.159630.717
180_F184_F0.159540.717
71_L77_L0.159420.716
97_L196_L0.159390.716
108_L112_A0.159010.715
69_R110_F0.158750.713
104_L108_L0.158660.713
151_Y160_E0.157850.709
193_L197_I0.157620.708
145_S177_A0.15750.708
195_L199_V0.157210.706
68_L74_L0.157170.706
120_G123_D0.157140.706
83_L87_L0.156550.703
191_L195_L0.156330.702
28_Y38_F0.156270.702
142_N146_F0.155940.701
145_S149_S0.155860.700
151_Y156_T0.15520.697
188_V197_I0.155120.697
146_F149_S0.155120.697
93_S196_L0.15450.694
158_T165_V0.154220.693
111_F185_I0.154030.692
61_L73_L0.153570.690
160_E164_D0.153490.690
80_F85_R0.15310.688
156_T177_A0.153070.688
61_L114_I0.151840.682
181_F194_N0.151830.682
7_D45_I0.151770.682
4_I7_D0.151720.682
161_G167_P0.151650.681
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
2r9rB0.88599.90.192
3rvyA0.8599.90.205
4dxwA0.8799.90.206
3behA0.83599.80.314
1orqC0.8599.70.341
4f4lA0.465990.593
2a9hA0.6698.90.602
1orsC0.4698.80.626
2ih3C0.54598.70.629
2kyhA0.44598.20.693

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