GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HEM4 - Uroporphyrinogen-III synthase HemD
Pfam: PF02602 (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. )
Length: 231
Sequences: 2457
Seq/Len: 10.64
HH_delta: 0.09 (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
7_L12_A0.753914.393
201_A207_A0.627833.658
43_Y144_T0.595113.467
177_P209_A0.531873.099
207_A220_V0.510342.974
126_E150_E0.447052.605
45_W77_F0.443292.583
171_A200_V0.429922.505
119_R142_E0.423642.468
124_R145_E0.385162.244
78_A84_A0.36482.126
181_R209_A0.361742.108
43_Y121_L0.359372.094
48_F54_V0.344112.005
136_L141_I0.343081.999
135_K138_E0.339321.977
199_I215_F0.337711.968
76_I92_F0.335781.956
207_A211_R0.334321.948
201_A220_V0.329031.917
174_F183_F0.326661.903
44_D118_K0.316651.845
23_E150_E0.314181.831
174_F180_V0.312331.820
6_L10_L0.308521.798
203_G206_T0.305761.782
208_K211_R0.299691.746
32_E60_A0.295871.724
4_A16_E0.294531.716
221_A228_A0.291351.698
201_A210_L0.287491.675
200_V229_L0.283651.653
77_F107_L0.282381.645
209_A212_E0.282311.645
86_A89_E0.276351.610
224_P228_A0.274321.598
124_R128_G0.27011.574
108_A135_K0.266911.555
180_V210_L0.265841.549
7_L14_V0.264231.540
126_E147_I0.263181.533
55_R86_A0.262651.530
104_S132_L0.259031.509
103_S106_G0.255961.491
48_F57_F0.254681.484
22_I52_N0.253151.475
202_I206_T0.253011.474
175_T179_A0.249781.455
45_W120_V0.247571.442
22_I151_T0.246381.436
20_I151_T0.239711.397
105_E129_R0.239111.393
4_A14_V0.236161.376
134_E137_R0.236111.376
56_A148_V0.232771.356
119_R144_T0.230231.341
6_L227_E0.228621.332
130_P134_E0.227461.325
24_P56_A0.227041.323
225_T228_A0.226121.317
78_A87_L0.225531.314
151_T178_S0.225461.314
48_F123_L0.222381.296
96_F110_L0.22191.293
58_F90_Y0.219971.282
177_P206_T0.21361.245
198_P219_I0.213161.242
98_P102_G0.211621.233
54_V83_T0.210741.228
223_R228_A0.209171.219
173_V200_V0.20791.211
128_G151_T0.20521.196
177_P205_R0.203571.186
15_I169_I0.202331.179
44_D119_R0.202251.178
37_Q42_N0.201471.174
209_A213_L0.201441.174
59_K90_Y0.200571.169
136_L143_V0.199561.163
133_P145_E0.199091.160
200_V219_I0.196681.146
162_E166_R0.195271.138
174_F199_I0.194591.134
101_E106_G0.194511.133
127_G147_I0.194381.133
6_L9_A0.192941.124
88_R93_Q0.190941.113
184_L213_L0.187851.095
75_K95_D0.186991.090
112_K139_A0.185321.080
210_L217_V0.184931.078
8_R14_V0.184291.074
45_W75_K0.18391.071
79_V83_T0.182791.065
199_I210_L0.18221.062
122_I133_P0.181341.057
33_A36_E0.180751.053
55_R59_K0.180211.050
181_R213_L0.179091.043
173_V229_L0.179071.043
127_G178_S0.176621.029
171_A198_P0.176061.026
104_S108_A0.175591.023
133_P137_R0.174141.015
210_L215_F0.173651.012
80_G149_Y0.172271.004
125_G148_V0.172071.003
99_S110_L0.171911.002
46_V123_L0.171581.000
3_L7_L0.170140.991
127_G151_T0.167990.979
4_A8_R0.166860.972
21_E153_P0.165490.964
153_P182_A0.1650.961
200_V218_D0.164920.961
88_R94_P0.164360.958
129_R205_R0.164150.956
178_S203_G0.16380.954
174_F179_A0.163730.954
184_L215_F0.163730.954
51_P82_K0.163150.951
210_L214_G0.162480.947
47_I111_L0.161640.942
167_G196_R0.161380.940
208_K212_E0.160560.936
104_S131_D0.16040.935
20_I182_A0.160190.933
80_G83_T0.15950.929
104_S128_G0.158250.922
221_A224_P0.156230.910
46_V121_L0.155510.906
172_V197_V0.154380.900
204_P224_P0.153770.896
84_A88_R0.153710.896
5_A8_R0.153650.895
106_G109_E0.151620.883
50_S79_V0.151310.882
128_G205_R0.150120.875
47_I136_L0.148290.864
104_S178_S0.145580.848
105_E131_D0.144560.842
20_I176_S0.143580.837
104_S151_T0.143060.834
23_E42_N0.143030.833
122_I175_T0.142030.828
122_I145_E0.141820.826
50_S83_T0.141560.825
52_N56_A0.141360.824
120_V141_I0.14040.818
51_P86_A0.140290.817
159_E162_E0.139820.815
135_K139_A0.13970.814
8_R13_E0.139350.812
85_E88_R0.138880.809
204_P208_K0.138140.805
21_E154_E0.137740.803
174_F206_T0.137190.799
5_A9_A0.136820.797
79_V107_L0.136720.797
199_I218_D0.136540.796
131_D135_K0.135970.792
3_L173_V0.135730.791
3_L82_K0.135250.788
81_P102_G0.135250.788
182_A186_L0.134140.782
86_A90_Y0.133910.780
198_P218_D0.133550.778
121_L146_V0.13340.777
45_W96_F0.133280.777
83_T104_S0.132910.774
134_E138_E0.132870.774
206_T221_A0.132670.773
102_G225_T0.131740.768
33_A37_Q0.131620.767
102_G224_P0.131590.767
124_R175_T0.131380.765
103_S204_P0.131110.764
52_N55_R0.130920.763
42_N119_R0.129310.753
151_T203_G0.129130.752
50_S149_Y0.12880.750
125_G151_T0.128260.747
69_R72_K0.127940.745
79_V205_R0.12790.745
54_V87_L0.127850.745
185_E188_K0.127790.745
128_G178_S0.127680.744
81_P225_T0.126420.737
46_V76_I0.126150.735
122_I143_V0.125370.730
85_E89_E0.125330.730
79_V202_I0.125080.729
80_G125_G0.124790.727
158_P162_E0.124530.726
161_K165_D0.124320.724
50_S53_A0.123980.722
137_R142_E0.12370.721
53_A122_I0.123060.717
104_S205_R0.123020.717
77_F95_D0.123010.717
108_A112_K0.122990.717
78_A97_V0.122850.716
108_A139_A0.122750.715
112_K135_K0.122680.715
54_V86_A0.122570.714
79_V104_S0.12230.713
53_A128_G0.121620.709
3_L175_T0.121540.708
19_L182_A0.120970.705
16_E226_I0.12020.700
49_T151_T0.120050.699
169_I172_V0.120030.699
15_I163_A0.119960.699
174_F203_G0.119720.698
58_F92_F0.11970.697
152_P185_E0.119650.697
128_G145_E0.119570.697
62_Q68_L0.119290.695
217_V220_V0.1190.693
37_Q144_T0.118220.689
175_T226_I0.117560.685
159_E163_A0.117090.682
49_T104_S0.117030.682
172_V199_I0.116940.681
20_I178_S0.116230.677
20_I179_A0.116180.677
180_V203_G0.115940.676
204_P220_V0.115840.675
118_K141_I0.115350.672
49_T221_A0.115290.672
122_I128_G0.114180.665
98_P110_L0.113880.664
168_E196_R0.11360.662
102_G173_V0.113490.661
47_I132_L0.113170.659
125_G149_Y0.112320.654
203_G221_A0.112250.654
115_L120_V0.111810.651
79_V125_G0.11170.651
109_E112_K0.111440.649
138_E188_K0.111190.648
96_F107_L0.111140.648
8_R16_E0.111020.647
125_G178_S0.111020.647
60_A146_V0.110790.646
171_A219_I0.110590.644
105_E108_A0.11050.644
32_E168_E0.10990.640
31_L229_L0.109720.639
45_W111_L0.109380.637
37_Q93_Q0.109350.637
50_S124_R0.10930.637
3_L226_I0.109220.636
15_I18_P0.108850.634
175_T224_P0.108260.631
47_I110_L0.108150.630
77_F96_F0.108040.629
122_I132_L0.107820.628
47_I107_L0.107680.627
129_R151_T0.107240.625
45_W95_D0.107220.625
47_I77_F0.106440.620
111_L120_V0.10620.619
57_F123_L0.10620.619
78_A94_P0.106050.618
55_R207_A0.105560.615
124_R130_P0.105320.614
103_S224_P0.104930.611
103_S173_V0.104910.611
106_G110_L0.104470.609
151_T206_T0.104370.608
103_S203_G0.104280.608
211_R220_V0.104220.607
200_V217_V0.103750.605
88_R167_G0.103710.604
19_L125_G0.103440.603
9_A138_E0.103410.603
137_R143_V0.103390.602
19_L183_F0.103250.602
117_G141_I0.103240.602
53_A149_Y0.103110.601
122_I127_G0.103090.601
163_A166_R0.102310.596
93_Q158_P0.102020.594
161_K186_L0.101880.594
205_R224_P0.101870.594
46_V226_I0.101810.593
84_A97_V0.101720.593
181_R185_E0.10160.592
111_L139_A0.101530.592
202_I221_A0.101430.591
179_A182_A0.101320.590
121_L167_G0.101190.590
211_R216_K0.100910.588
49_T206_T0.100810.587
8_R155_E0.100770.587
204_P207_A0.100760.587
103_S129_R0.100740.587
44_D169_I0.100660.586
174_F210_L0.100560.586
3_L16_E0.100490.586
115_L118_K0.100470.585
50_S80_G0.100440.585
77_F175_T0.10040.585
123_L146_V0.100380.585
32_E35_L0.099490.580
180_V202_I0.099480.580
203_G226_I0.09940.579
144_T147_I0.09930.579
162_E165_D0.09910.577
6_L230_V0.098940.576
187_L198_P0.098510.574
104_S129_R0.098350.573
125_G147_I0.098310.573
201_A204_P0.097880.570
31_L123_L0.097770.570
128_G131_D0.097750.570
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
3re1A0.9741000.09
4es6A0.9741000.095
1jr2A0.97841000.113
3d8tA0.96971000.123
3mw8A0.94811000.125
1wcwA0.96971000.129
3p9zA0.91341000.169
4es6A0.519599.60.62
3mw8A0.476299.50.637
1wcwA0.515299.50.645

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