GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DER1 - Der1-like family
Pfam: PF04511 (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: CL0207
Length: 197
Sequences: 2694
Seq/Len: 13.68
HH_delta: 0.41 (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
49_F93_A0.767464.445
41_Q44_R0.723734.192
92_G120_A0.573513.322
95_L172_V0.554373.211
5_T85_Y0.491682.848
100_S162_S0.420652.436
48_S97_L0.393562.280
9_L63_L0.392212.272
13_V59_F0.356652.066
12_T89_L0.355322.058
55_F60_L0.34271.985
43_W47_T0.339881.969
58_N166_D0.334521.938
70_S85_Y0.334231.936
12_T63_L0.333371.931
52_F58_N0.332341.925
93_A117_L0.327411.896
58_N62_N0.32691.893
62_N166_D0.312441.810
61_F65_F0.309361.792
115_S119_F0.304921.766
45_L101_L0.296111.715
151_L155_S0.288071.669
9_L67_Y0.282421.636
123_Y170_I0.271931.575
88_F92_G0.270171.565
4_V80_G0.267371.549
52_F62_N0.265321.537
155_S163_P0.265191.536
114_G117_L0.263791.528
52_F166_D0.240281.392
167_L171_L0.238931.384
58_N115_S0.230421.335
87_W91_F0.22921.328
42_I46_F0.221591.283
115_S118_S0.22111.281
115_S166_D0.21981.273
169_G173_G0.216211.252
5_T74_E0.214251.241
32_D35_L0.212321.230
92_G172_V0.212241.229
69_Y121_L0.212051.228
10_I14_A0.210251.218
53_G112_F0.207981.205
66_L70_S0.205431.190
117_L120_A0.204731.186
14_A18_L0.203341.178
96_I168_L0.203221.177
88_F124_I0.202281.172
62_N115_S0.200871.163
6_R10_I0.199471.155
116_S166_D0.198691.151
12_T16_S0.198351.149
45_L97_L0.198211.148
88_F176_Y0.197471.144
9_L12_T0.195551.133
143_K146_Y0.193371.120
162_S165_P0.192831.117
52_F115_S0.1881.089
23_I26_P0.187381.085
31_F36_V0.183821.065
99_L168_L0.182861.059
44_R74_E0.182721.058
153_A157_L0.18151.051
85_Y89_L0.181381.051
4_V86_L0.180071.043
164_I168_L0.179941.042
49_F117_L0.179591.040
8_W89_L0.17931.039
8_W12_T0.17911.037
3_P80_G0.178111.032
155_S162_S0.178071.031
94_S98_I0.176941.025
114_G118_S0.176061.020
135_S141_T0.175271.015
35_L41_Q0.174951.013
11_S15_L0.174911.013
13_V63_L0.174851.013
116_S165_P0.174271.009
100_S104_G0.173141.003
83_A87_W0.171170.991
165_P173_G0.170910.990
97_L100_S0.170850.990
44_R47_T0.170580.988
130_P134_V0.169750.983
136_F142_I0.169590.982
62_N116_S0.169270.980
166_D169_G0.168430.976
89_L117_L0.167940.973
92_G96_I0.166870.967
62_N114_G0.166810.966
7_Y11_S0.166090.962
60_L64_Y0.165810.960
9_L13_V0.163790.949
66_L118_S0.163380.946
65_F147_L0.160320.929
8_W66_L0.159540.924
79_Q113_L0.158960.921
165_P168_L0.158160.916
72_S132_A0.158070.916
7_Y10_I0.157860.914
3_P7_Y0.157580.913
60_L67_Y0.156670.907
90_L94_S0.154490.895
172_V176_Y0.153550.889
71_S75_E0.152870.885
58_N165_P0.152470.883
148_P151_L0.152120.881
89_L92_G0.151050.875
116_S169_G0.15070.873
16_S19_V0.150090.869
3_P6_R0.149660.867
12_T50_F0.149050.863
52_F173_G0.148270.859
36_V45_L0.14760.855
29_L32_D0.146570.849
116_S120_A0.144840.839
123_Y127_R0.144620.838
152_L170_I0.144140.835
65_F68_Q0.1440.834
89_L96_I0.14380.833
89_L114_G0.142890.828
5_T71_S0.142480.825
135_S140_F0.141060.817
64_Y68_Q0.140840.816
49_F97_L0.140190.812
123_Y174_H0.13980.810
18_L22_G0.139240.806
17_L21_F0.138870.804
95_L176_Y0.138680.803
149_W153_A0.137750.798
63_L66_L0.137740.798
84_D87_W0.136840.793
99_L103_I0.136780.792
20_S55_F0.13650.791
134_V144_A0.136390.790
113_L120_A0.13570.786
131_N143_K0.13570.786
8_W86_L0.135080.782
19_V54_P0.13480.781
36_V40_F0.134730.780
79_Q84_D0.134360.778
4_V85_Y0.134020.776
15_L19_V0.133670.774
131_N147_L0.133060.771
117_L121_L0.132770.769
150_V153_A0.1320.765
64_Y155_S0.131890.764
19_V25_S0.131520.762
46_F94_S0.131060.759
88_F177_Y0.131060.759
133_Q143_K0.131030.759
16_S54_P0.129670.751
61_F101_L0.129560.750
59_F63_L0.128930.747
71_S80_G0.128920.747
51_Y96_I0.128420.744
62_N93_A0.127770.740
113_L116_S0.127120.736
49_F94_S0.126450.732
123_Y177_Y0.12630.732
41_Q45_L0.126070.730
58_N169_G0.125950.730
48_S112_F0.125670.728
166_D173_G0.125660.728
89_L93_A0.125330.726
129_N132_A0.125320.726
94_S97_L0.124370.720
31_F44_R0.123940.718
58_N116_S0.123910.718
10_I98_I0.12340.715
30_Y34_E0.123220.714
96_I100_S0.123210.714
57_L64_Y0.123180.713
52_F169_G0.123030.713
103_I164_I0.122980.712
111_P162_S0.122560.710
70_S74_E0.122190.708
79_Q168_L0.122010.707
88_F123_Y0.121670.705
11_S14_A0.121360.703
113_L118_S0.121130.702
148_P174_H0.120980.701
100_S111_P0.120940.700
35_L39_K0.120830.700
58_N173_G0.120590.698
76_G129_N0.120120.696
37_F101_L0.119750.694
8_W16_S0.11960.693
19_V51_Y0.119330.691
145_K149_W0.11850.686
42_I45_L0.118460.686
11_S86_L0.118210.685
134_V154_F0.118180.685
54_P159_G0.118030.684
114_G120_A0.1180.683
29_L43_W0.117780.682
6_R67_Y0.117570.681
114_G122_T0.117360.680
123_Y126_S0.117010.678
52_F113_L0.116870.677
37_F98_I0.116810.677
62_N169_G0.116610.675
24_I27_Y0.116470.675
115_S120_A0.116320.674
90_L98_I0.115930.671
79_Q115_S0.11570.670
168_L172_V0.115490.669
75_E80_G0.11470.664
111_P119_F0.114470.663
44_R126_S0.114330.662
99_L164_I0.11420.661
4_V9_L0.114140.661
91_F95_L0.114130.661
19_V29_L0.113850.659
122_T126_S0.113810.659
171_L175_L0.11360.658
19_V26_P0.112920.654
154_F158_F0.112680.653
72_S125_W0.112590.652
126_S148_P0.112550.652
122_T147_L0.112410.651
127_R177_Y0.112410.651
86_L90_L0.112030.649
115_S165_P0.111980.649
37_F132_A0.111490.646
131_N153_A0.111470.646
13_V17_L0.111430.645
153_A156_L0.111370.645
27_Y60_L0.11090.642
11_S76_G0.110780.642
29_L138_G0.110510.640
51_Y170_I0.11030.639
57_L127_R0.110270.639
72_S110_I0.110170.638
119_F155_S0.109670.635
61_F68_Q0.109580.635
131_N146_Y0.109550.635
69_Y148_P0.109370.633
18_L109_N0.109320.633
63_L166_D0.109180.632
15_L51_Y0.109170.632
66_L89_L0.109120.632
173_G177_Y0.108990.631
118_S163_P0.108830.630
49_F60_L0.108810.630
89_L121_L0.108750.630
50_F168_L0.108230.627
125_W170_I0.108020.626
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
2nr9A0.923999.90.41
2xovA0.86899.90.411
1tifA0.1321.60.959
4h44E0.15741.50.959
4g6vB0.18781.50.96
1jb0L0.375610.963
1utyA0.29440.80.965
2ab9A0.05580.70.967
2ww9C0.14720.70.967
1dbfA0.21830.60.968

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