GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Band_7_1 - SPFH domain-Band 7 family
Pfam: PF13421 (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: 211
Sequences: 3569
Seq/Len: 16.91
HH_delta: 0.565 (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
33_I36_V0.870723.935
113_D116_L0.812253.671
162_H165_E0.58192.630
172_E176_P0.566362.560
29_N34_A0.559792.530
110_R184_E0.555182.509
19_V25_A0.550842.490
23_Q72_F0.547272.473
20_R23_Q0.525642.376
165_E169_A0.525142.373
168_E172_E0.509332.302
112_V184_E0.508672.299
201_K205_K0.497752.250
24_C75_T0.462222.089
151_E169_A0.446332.017
110_R186_V0.418791.893
17_L37_F0.414231.872
155_S158_D0.39471.784
158_D162_H0.378761.712
24_C114_P0.376771.703
164_D168_E0.368551.666
197_E201_K0.366981.659
18_I41_R0.349641.580
169_A172_E0.347071.569
140_E174_L0.345591.562
198_E201_K0.344651.558
137_L178_F0.335251.515
168_E171_K0.324441.466
158_D161_A0.318271.438
15_S43_T0.31711.433
171_K175_N0.310731.404
88_P93_D0.305231.380
22_G75_T0.30361.372
89_I93_D0.302591.368
16_Q41_R0.299011.351
116_L119_R0.298041.347
194_S200_Q0.292211.321
37_F42_Y0.286781.296
146_A150_A0.275881.247
175_N184_E0.275311.244
148_A169_A0.272451.231
105_G141_I0.272371.231
25_A72_F0.26391.193
19_V72_F0.260391.177
73_V118_I0.259991.175
24_C38_G0.2591.171
175_N179_E0.258221.167
91_Y159_I0.257471.164
88_P102_R0.255141.153
77_E186_V0.252431.141
169_A173_K0.250951.134
196_P199_V0.250121.130
27_F37_F0.248811.125
26_V118_I0.244111.103
148_A151_E0.24161.092
33_I115_V0.240751.088
149_L159_I0.239561.083
195_F199_V0.2381.076
173_K176_P0.237861.075
112_V179_E0.237471.073
154_I169_A0.236911.071
197_E200_Q0.234951.062
143_Q147_D0.233531.055
178_F185_L0.227991.030
165_E168_E0.227141.027
92_R155_S0.226931.026
176_P179_E0.225781.020
14_G17_L0.224071.013
21_E39_P0.222211.004
104_F191_E0.221951.003
31_G182_G0.219760.993
84_G102_R0.21810.986
136_Q181_Y0.2130.963
200_Q204_D0.211310.955
102_R194_S0.211290.955
136_Q140_E0.210410.951
17_L42_Y0.209860.948
30_D41_R0.209730.948
154_I166_I0.209520.947
116_L180_R0.208960.944
17_L25_A0.208180.941
74_N77_E0.20440.924
140_E177_E0.203960.922
28_V71_Y0.203570.920
165_E172_E0.202670.916
79_T109_F0.201080.909
117_F133_I0.200110.904
141_I174_L0.19820.896
109_F114_P0.192260.869
28_V32_K0.191040.863
35_D115_V0.190890.863
156_I160_P0.190540.861
26_V36_V0.190510.861
103_A149_L0.187520.848
132_E135_E0.187220.846
90_P98_P0.186510.843
24_C28_V0.183790.831
27_F35_D0.183140.828
144_A173_K0.180520.816
103_A141_I0.179180.810
144_A170_L0.178090.805
167_S189_G0.177540.802
83_W188_F0.17690.800
24_C36_V0.176160.796
36_V115_V0.176040.796
143_Q150_A0.175230.792
19_V42_Y0.174330.788
35_D42_Y0.173510.784
16_Q43_T0.173480.784
171_K184_E0.173020.782
111_I182_G0.172860.781
147_D173_K0.17150.775
171_K188_F0.170530.771
203_I206_R0.170.768
181_Y189_G0.16980.767
151_E173_K0.169750.767
140_E181_Y0.16890.763
177_E180_R0.168710.763
179_E184_E0.168710.763
93_D156_I0.16870.762
147_D151_E0.1680.759
193_I203_I0.167470.757
113_D182_G0.167030.755
14_G18_I0.166370.752
83_W141_I0.165620.749
90_P93_D0.16560.748
29_N89_I0.16480.745
145_I177_E0.16260.735
159_I195_F0.162060.732
112_V172_E0.161410.730
178_F181_Y0.161330.729
149_L166_I0.159170.719
38_G135_E0.159160.719
147_D177_E0.158910.718
109_F134_N0.15670.708
143_Q189_G0.156450.707
110_R113_D0.15620.706
38_G201_K0.155960.705
105_G188_F0.155730.704
22_G74_N0.154930.700
196_P204_D0.154070.696
163_L191_E0.153880.695
31_G113_D0.153390.693
185_L188_F0.153110.692
73_V149_L0.152870.691
156_I190_I0.152830.691
177_E187_D0.151930.687
31_G34_A0.151650.685
150_A163_L0.151620.685
73_V111_I0.151460.685
108_S186_V0.150840.682
119_R177_E0.150560.680
146_A163_L0.150330.679
24_C199_V0.149920.678
26_V73_V0.149680.676
139_S174_L0.148870.673
82_K179_E0.148220.670
103_A145_I0.148220.670
189_G206_R0.147940.669
82_K180_R0.147790.668
141_I144_A0.146990.664
26_V115_V0.146570.662
157_L160_P0.146260.661
88_P100_R0.145730.659
135_E179_E0.145730.659
150_A196_P0.145560.658
154_I162_H0.145130.656
34_A180_R0.145020.655
143_Q146_A0.144840.655
168_E184_E0.144830.655
91_Y149_L0.14380.650
87_N143_Q0.143520.649
156_I195_F0.14330.648
142_V192_S0.142980.646
189_G199_V0.142840.646
99_V170_L0.142810.645
118_I160_P0.142730.645
87_N142_V0.142420.644
32_K39_P0.142060.642
73_V83_W0.141930.641
22_G105_G0.141530.640
111_I117_F0.140730.636
16_Q30_D0.140690.636
28_V33_I0.14020.634
22_G133_I0.140170.634
24_C39_P0.140.633
175_N185_L0.139790.632
99_V159_I0.139610.631
77_E82_K0.139560.631
109_F162_H0.139370.630
140_E144_A0.139220.629
30_D183_I0.138640.627
91_Y98_P0.138480.626
71_Y191_E0.138370.625
83_W148_A0.137480.621
118_I203_I0.13740.621
172_E201_K0.137350.621
192_S204_D0.137340.621
170_L178_F0.13720.620
175_N178_F0.137160.620
114_P202_A0.136940.619
38_G42_Y0.136720.618
28_V31_G0.136690.618
33_I42_Y0.136650.618
140_E195_F0.136650.618
160_P195_F0.13650.617
111_I114_P0.13620.616
183_I198_E0.136170.615
76_K82_K0.135410.612
193_I199_V0.135240.611
146_A160_P0.134190.606
109_F200_Q0.133770.605
109_F186_V0.132750.600
170_L174_L0.132310.598
13_N116_L0.131860.596
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
4fvgA0.630399.70.565
3bk6A0.616199.70.586
1winA0.658899.70.599
2rpbA0.535599.50.644
2zuoA0.938495.10.878
1rq8A0.346230.938
1jo0A0.350711.20.946
4em8A0.28919.80.947
4fglA0.30818.70.948
2acmB0.24178.10.949
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0285 seconds.