GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pectate_lyase_3 - Pectate lyase superfamily protein
Pfam: PF12708 (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: CL0268
Length: 225
Sequences: 3573
Seq/Len: 15.88
HH_delta: 0.299 (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
98_N127_N0.586013.181
170_N191_N0.552212.997
169_N190_S0.52142.830
171_C192_N0.403922.193
155_S158_F0.387142.101
25_I49_L0.377992.052
121_Q144_T0.377452.049
179_G194_F0.374232.031
101_I130_I0.367931.997
172_I193_T0.359081.949
100_T131_E0.352421.913
120_S123_V0.328051.781
128_V151_S0.325821.769
19_A23_A0.318831.731
168_V171_C0.31881.730
117_F125_I0.310621.686
174_N195_E0.310381.685
83_G87_S0.309741.681
127_N150_G0.307421.669
35_V58_R0.30291.644
117_F120_S0.30141.636
122_N145_D0.299341.625
91_N122_N0.299241.624
22_Q25_I0.297611.615
42_T68_F0.295821.606
21_I38_F0.291511.582
143_G146_Y0.29081.578
102_D131_E0.288531.566
117_F123_V0.281331.527
40_P60_A0.27921.516
200_N203_N0.277031.504
82_I87_S0.276571.501
125_I128_V0.27621.499
114_G130_I0.274141.488
97_R126_S0.273551.485
51_I57_L0.273361.484
25_I57_L0.270731.470
189_I192_N0.269311.462
126_S149_I0.265621.442
20_A24_A0.261061.417
165_N186_N0.260251.413
149_I169_N0.25911.406
96_I101_I0.25721.396
35_V56_T0.256491.392
173_F194_F0.254811.383
115_I138_I0.254231.380
164_N185_N0.253111.374
36_V55_V0.250581.360
21_I36_V0.249711.355
37_Y58_R0.246331.337
96_I99_L0.245861.335
150_G170_N0.240321.304
38_F45_I0.239791.302
82_I85_F0.239391.299
83_G86_D0.238481.294
22_Q28_A0.238141.293
20_A23_A0.237571.290
168_V189_I0.236081.281
167_I190_S0.231551.257
144_T164_N0.230771.253
72_S75_S0.227541.235
194_F202_I0.22611.227
123_V146_Y0.22261.208
37_Y60_A0.221991.205
18_T45_I0.220721.198
39_P60_A0.218571.186
36_V57_L0.218181.184
25_I55_V0.217991.183
44_R68_F0.212331.153
20_A39_P0.210691.144
140_F148_I0.210081.140
57_L99_L0.209821.139
68_F104_N0.209381.137
125_I130_I0.208831.134
130_I138_I0.20611.119
40_P64_S0.204951.112
39_P43_Y0.202261.098
95_Q124_S0.201861.096
160_D173_F0.20021.087
136_D139_Y0.199211.081
118_N142_T0.198891.080
40_P43_Y0.198641.078
172_I195_E0.195751.063
158_F181_I0.195491.061
130_I153_H0.195121.059
96_I125_I0.192871.047
20_A45_I0.192291.044
100_T129_R0.191881.042
57_L96_I0.191641.040
18_T22_Q0.191071.037
91_N94_I0.190851.036
147_R169_N0.190761.035
38_F57_L0.190121.032
151_S192_N0.18921.027
148_I151_S0.18781.019
63_N129_R0.187541.018
149_I170_N0.187031.015
130_I137_G0.185541.007
108_P111_N0.184831.003
145_D165_N0.184781.003
21_I45_I0.184421.001
204_I208_S0.180930.982
128_V192_N0.180570.980
24_A36_V0.180460.980
101_I128_V0.180460.980
23_A29_A0.179650.975
61_G104_N0.178440.969
168_V173_F0.17810.967
30_A34_G0.177980.966
182_L189_I0.177080.961
61_G64_S0.176830.960
203_N206_G0.176290.957
140_F166_V0.175050.950
125_I148_I0.174880.949
154_V174_N0.172880.938
46_S71_G0.172360.936
114_G133_S0.169960.923
144_T165_N0.16940.920
153_H158_F0.168750.916
199_G206_G0.168640.915
129_R152_T0.167760.911
135_G139_Y0.166820.906
70_S75_S0.166590.904
115_I130_I0.166010.901
54_N91_N0.165180.897
169_N191_N0.164670.894
42_T66_I0.164020.890
128_V171_C0.162690.883
166_V187_I0.162350.881
97_R121_Q0.16220.880
118_N141_N0.161690.878
151_S171_C0.160530.871
31_A53_S0.16040.871
81_G84_V0.15980.867
158_F161_N0.159050.863
40_P61_G0.158960.863
105_G108_P0.158110.858
116_R141_N0.157240.854
17_D20_A0.157230.853
24_A38_F0.156640.850
28_A32_G0.15650.849
203_N207_G0.15610.847
124_S147_R0.155820.846
85_F88_G0.154090.836
169_N188_T0.153610.834
34_G55_V0.152940.830
46_S70_S0.152580.828
152_T172_I0.152580.828
113_N116_R0.151350.822
28_A36_V0.151190.821
99_L128_V0.150610.818
133_S137_G0.150430.817
199_G205_E0.150160.815
82_I86_D0.150140.815
22_Q49_L0.149360.811
133_S176_G0.14860.807
140_F187_I0.148050.804
17_D24_A0.146710.796
100_T124_S0.146010.793
164_N186_N0.144580.785
89_N184_N0.144250.783
20_A38_F0.14420.783
126_S150_G0.143390.778
163_S185_N0.143090.777
103_G114_G0.142280.772
136_D158_F0.141490.768
56_T95_Q0.140420.762
181_I203_N0.139950.760
114_G137_G0.139840.759
175_G194_F0.138320.751
40_P44_R0.137950.749
106_I111_N0.13720.745
199_G203_N0.136910.743
181_I184_N0.136790.743
66_I100_T0.136680.742
17_D21_I0.136080.739
67_L99_L0.135840.737
73_G76_F0.135750.737
140_F146_Y0.135240.734
16_D45_I0.13510.733
99_L102_D0.134860.732
167_I188_T0.134820.732
59_G98_N0.134320.729
16_D19_A0.134230.729
31_A34_G0.134180.728
19_A22_Q0.134090.728
81_G85_F0.133810.726
168_V190_S0.132720.720
40_P121_Q0.132330.718
30_A33_G0.132060.717
183_G206_G0.131410.713
152_T174_N0.130890.710
138_I148_I0.13070.709
21_I67_L0.130220.707
33_G98_N0.129730.704
23_A31_A0.129350.702
106_I131_E0.128510.698
199_G202_I0.128430.697
46_S69_L0.128380.697
158_F205_E0.128230.696
62_G129_R0.128190.696
105_G109_N0.12720.690
51_I85_F0.126820.688
42_T67_L0.126140.685
195_E199_G0.124520.676
126_S169_N0.124090.674
74_D77_S0.123120.668
173_F192_N0.121950.662
113_N135_G0.12160.660
21_I25_I0.121530.660
89_N94_I0.121390.659
97_R127_N0.120990.657
205_E208_S0.12090.656
33_G56_T0.120750.655
178_N201_G0.120650.655
21_I24_A0.120430.654
49_L67_L0.120410.654
181_I205_E0.120340.653
155_S160_D0.120290.653
194_F207_G0.120190.652
177_D199_G0.119960.651
28_A53_S0.119890.651
29_A34_G0.119870.651
140_F143_G0.119040.646
135_G141_N0.11880.645
106_I110_N0.118720.644
45_I125_I0.118550.643
89_N181_I0.118510.643
23_A122_N0.118290.642
81_G88_G0.117310.637
153_H159_I0.117260.636
117_F143_G0.117170.636
94_I99_L0.117140.636
137_G179_G0.117090.636
204_I207_G0.116940.635
106_I116_R0.116730.634
59_G128_V0.116440.632
36_V100_T0.115810.629
153_H156_G0.11570.628
120_S143_G0.115380.626
106_I109_N0.115330.626
143_G163_S0.114950.624
185_N192_N0.114950.624
28_A43_Y0.114690.623
201_G204_I0.114670.622
22_Q52_P0.114590.622
46_S114_G0.114470.621
118_N143_G0.114210.620
112_N205_E0.114130.620
17_D41_G0.113980.619
40_P54_N0.113740.617
103_G205_E0.113660.617
96_I128_V0.113370.615
85_F193_T0.113360.615
54_N122_N0.113270.615
32_G53_S0.11310.614
178_N181_I0.112940.613
200_N206_G0.112880.613
32_G58_R0.112770.612
59_G67_L0.112630.611
30_A36_V0.112260.609
66_I102_D0.112120.609
166_V171_C0.11210.608
29_A35_V0.111990.608
19_A72_S0.111810.607
77_S144_T0.111210.604
180_I189_I0.111030.603
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
3gqnA0.955699.90.299
3gq8A0.955699.90.3
3eqnA0.893399.90.323
3jurA0.9699.90.328
2pygA0.991199.90.339
1rmgA0.928999.90.358
2uvfA0.955699.90.366
3zppA0.977899.90.37
1bheA0.928999.90.437
1h80A0.906799.80.453

Page generated in 0.0187 seconds.