GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Semialdhyde_dhC - Semialdehyde dehydrogenase dimerisation domain
Pfam: PF02774 (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: CL0139
Length: 184
Sequences: 3518
Seq/Len: 19.12
HH_delta: 0.194 (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
2_A6_K1.137293.946
25_A51_F0.775082.689
138_R159_D0.770182.672
13_R114_E0.748862.598
59_L101_V0.744252.582
22_V55_I0.714772.480
146_P161_G0.696152.415
136_F157_F0.613192.127
7_A128_A0.595262.065
123_E127_E0.574321.992
124_E127_E0.56981.977
12_E114_E0.567561.969
4_L115_L0.560781.946
18_T109_A0.555321.927
127_E131_K0.548051.901
17_D110_T0.545511.893
136_F156_N0.538361.868
138_R157_F0.530771.841
69_R78_L0.511771.775
7_A124_E0.501011.738
16_V111_I0.498641.730
125_I173_L0.497251.725
1_L14_V0.496631.723
122_V173_L0.48681.689
15_I112_Y0.484191.680
119_P165_V0.483831.679
124_E128_A0.457591.588
57_F152_V0.456841.585
103_V148_P0.452781.571
108_L148_P0.440711.529
9_F120_V0.436051.513
106_G181_N0.43211.499
122_V165_V0.42791.485
156_N183_R0.419591.456
1_L113_V0.41771.449
6_K129_F0.411941.429
118_T121_D0.405651.407
126_Y163_V0.396551.376
111_I177_S0.383251.330
111_I175_V0.379561.317
63_I69_R0.377121.308
56_A104_F0.373751.297
64_G75_E0.368441.278
108_L176_W0.364851.266
113_V175_V0.363011.259
137_V163_V0.358941.245
105_R182_L0.358541.244
62_Y143_G0.355361.233
4_L173_L0.353451.226
122_V163_V0.34871.210
19_Y101_V0.348421.209
113_V173_L0.348151.208
158_V179_I0.342891.190
105_R181_N0.342761.189
147_T150_D0.338221.173
65_G75_E0.337731.172
158_V177_S0.336261.167
59_L148_P0.335151.163
93_R170_P0.326951.134
132_G135_P0.319941.110
140_D144_D0.317051.100
25_A60_I0.314251.090
108_L178_V0.312931.086
4_L126_Y0.306721.064
14_V113_V0.305791.061
28_K47_S0.305121.059
16_V109_A0.303321.052
122_V126_Y0.300221.042
99_V110_T0.299661.040
4_L125_I0.297931.034
127_E130_Y0.295231.024
95_S112_Y0.29251.015
136_F155_T0.289781.005
17_D112_Y0.288291.000
123_E126_Y0.286530.994
121_D165_V0.285810.992
155_T159_D0.285370.990
60_I147_T0.281880.978
121_D124_E0.279630.970
58_N147_T0.273090.947
106_G151_V0.272340.945
2_A81_I0.271080.940
151_V159_D0.269580.935
101_V148_P0.266690.925
53_S147_T0.265860.922
118_T124_E0.265160.920
130_Y137_V0.265110.920
134_E184_K0.264810.919
129_F132_G0.264280.917
48_P51_F0.264260.917
48_P54_Q0.263460.914
20_Q24_G0.262650.911
145_Y161_G0.260060.902
19_Y99_V0.258770.898
61_P176_W0.25760.894
3_P130_Y0.256570.890
112_Y174_V0.254570.883
77_E80_M0.254170.882
126_Y137_V0.253010.878
115_L173_L0.249960.867
5_H10_G0.249030.864
145_Y176_W0.247980.860
95_S174_V0.247190.858
2_A5_H0.246980.857
22_V52_P0.245350.851
123_E142_E0.244710.849
163_V173_L0.244240.847
126_Y130_Y0.243730.846
110_T174_V0.243260.844
1_L111_I0.241460.838
150_D159_D0.239040.829
149_K152_V0.238040.826
17_D99_V0.237890.825
129_F137_V0.237550.824
5_H11_L0.236950.822
145_Y164_R0.236860.822
78_L82_A0.234530.814
7_A118_T0.234460.813
61_P99_V0.229960.798
75_E168_R0.229960.798
79_K82_A0.227270.788
59_L99_V0.22560.783
120_V124_E0.225580.783
160_V175_V0.225330.782
19_Y112_Y0.225110.781
153_G180_D0.224990.781
67_E78_L0.223090.774
73_E78_L0.222050.770
105_R152_V0.221570.769
109_A177_S0.221230.768
24_G100_R0.219960.763
53_S143_G0.219050.760
115_L165_V0.216510.751
93_R168_R0.215520.748
4_L113_V0.215270.747
164_R176_W0.215150.746
126_Y139_V0.214610.745
136_F159_D0.214310.744
63_I80_M0.213830.742
16_V96_F0.213610.741
10_G114_E0.212850.738
156_N184_K0.212250.736
120_V142_E0.211050.732
69_R73_E0.210880.732
61_P147_T0.209740.728
93_R169_D0.207080.718
127_E141_P0.206090.715
27_R48_P0.205530.713
18_T24_G0.205030.711
151_V179_I0.204570.710
55_I100_R0.203630.706
7_A10_G0.201350.699
11_L113_V0.199440.692
115_L120_V0.196030.680
129_F175_V0.196030.680
148_P152_V0.193930.673
59_L103_V0.193260.670
104_F152_V0.19260.668
49_G60_I0.192510.668
14_V111_I0.192190.667
128_A131_K0.191680.665
58_N149_K0.190330.660
21_G105_R0.190250.660
129_F135_P0.190090.659
2_A129_F0.189370.657
157_F179_I0.187790.651
24_G107_H0.187640.651
23_S104_F0.18760.651
27_R106_G0.187370.650
79_K85_R0.187050.649
20_Q100_R0.187010.649
5_H14_V0.186870.648
78_L167_P0.186830.648
15_I19_Y0.186280.646
140_D143_G0.186210.646
57_F104_F0.186180.646
73_E167_P0.185930.645
1_L16_V0.1850.642
110_T176_W0.184050.639
161_G164_R0.183160.635
61_P145_Y0.182940.635
9_F128_A0.18260.633
173_L176_W0.18230.632
52_P56_A0.18220.632
97_T174_V0.181930.631
61_P108_L0.181130.628
47_S50_L0.180880.628
119_P171_R0.180740.627
98_C105_R0.180390.626
152_V181_N0.179810.624
21_G98_C0.179180.622
165_V173_L0.178870.621
27_R54_Q0.178530.619
4_L9_F0.178310.619
19_Y103_V0.178020.618
13_R113_V0.17720.615
130_Y141_P0.177090.614
120_V125_I0.176880.614
15_I110_T0.176690.613
22_V53_S0.176580.613
16_V74_I0.176480.612
96_F112_Y0.175990.611
139_V163_V0.175420.609
165_V171_R0.174930.607
47_S51_F0.174580.606
80_M98_C0.174510.605
28_K50_L0.174340.605
82_A85_R0.174330.605
123_E143_G0.173870.603
101_V107_H0.17350.602
98_C177_S0.173410.602
52_P55_I0.172820.600
75_E79_K0.172650.599
146_P176_W0.172460.598
9_F124_E0.172160.597
20_Q107_H0.172160.597
114_E171_R0.172130.597
96_F110_T0.171640.595
100_R107_H0.171330.594
138_R150_D0.171080.594
5_H9_F0.170640.592
119_P123_E0.170560.592
140_D159_D0.16960.588
55_I58_N0.168730.585
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
3uw3A0.9621000.194
3pzrA0.9621000.203
3tz6A0.94021000.225
3pwkA0.9621000.239
1t4bA0.9621000.26
1vknA0.84241000.264
2hjsA0.94571000.284
2nqtA0.84781000.296
2r00A0.95651000.299
2yv3A0.94021000.305

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