GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_pol_A_exo1 - 3-5 exonuclease
Pfam: PF01612 (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: CL0219
Length: 176
Sequences: 5337
Seq/Len: 30.32
HH_delta: 0.078 (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
82_G85_A1.291414.476
83_H106_T1.116983.871
80_K102_N0.670022.322
120_S123_D0.630792.186
110_A119_Y0.630592.186
26_D160_D0.616682.137
75_D78_I0.616562.137
170_K174_Q0.556371.928
70_K74_E0.547041.896
28_E160_D0.545021.889
104_F109_A0.533891.850
76_P101_K0.53061.839
84_N87_F0.530051.837
88_D160_D0.519611.801
118_S123_D0.508731.763
25_F92_L0.505071.751
125_A163_V0.497131.723
28_E88_D0.487391.689
75_D80_K0.483451.676
26_D88_D0.483211.675
23_L72_L0.461211.599
156_Y160_D0.458611.590
29_T87_F0.457771.587
22_V81_V0.447381.551
25_F82_G0.442871.535
70_K98_I0.441521.530
162_V166_R0.429511.489
110_A124_L0.425071.473
104_F172_K0.424611.472
159_Q162_V0.424571.472
125_A167_L0.42111.459
30_T38_N0.404921.403
24_A165_F0.400311.387
125_A134_L0.393171.363
168_Y172_K0.392991.362
22_V168_Y0.389481.350
170_K173_P0.3861.338
68_A71_E0.385831.337
123_D126_E0.384921.334
150_S153_Q0.38321.328
126_E133_D0.382311.325
151_E155_E0.378731.313
67_D71_E0.376431.305
141_S153_Q0.373871.296
49_G169_E0.357291.238
69_L73_L0.354981.230
157_A161_A0.354551.229
81_V168_Y0.354031.227
113_L174_Q0.353841.226
149_L152_E0.353531.225
67_D70_K0.351541.218
152_E155_E0.349581.212
25_F73_L0.346161.200
72_L78_I0.344541.194
129_L167_L0.333321.155
165_F169_E0.326991.133
128_Y167_L0.319071.106
128_Y174_Q0.318731.105
47_A50_E0.310891.078
104_F168_Y0.310151.075
22_V79_I0.309961.074
34_P90_K0.309621.073
107_M111_Y0.30751.066
31_G87_F0.307081.064
43_L54_I0.306571.063
93_Y99_D0.305141.058
126_E132_I0.303281.051
169_E173_P0.302321.048
63_N67_D0.302191.047
110_A171_L0.297141.030
40_K156_Y0.296921.029
114_D174_Q0.295881.025
29_T91_W0.294691.021
47_A52_C0.293371.017
52_C158_A0.290951.008
45_Q157_A0.289991.005
56_D147_R0.289491.003
26_D156_Y0.289311.003
74_E99_D0.28830.999
113_L171_L0.285790.991
27_T91_W0.285410.989
46_L169_E0.284780.987
89_L100_L0.284360.986
110_A115_P0.283220.982
121_L167_L0.282520.979
81_V165_F0.281790.977
75_D102_N0.28070.973
88_D156_Y0.280360.972
166_R169_E0.276090.957
161_A165_F0.275610.955
136_K140_M0.275010.953
107_M110_A0.274570.952
122_K133_D0.273220.947
27_T92_L0.272650.945
26_D157_A0.271530.941
24_A81_V0.271450.941
166_R170_K0.270020.936
157_A160_D0.269790.935
79_I168_Y0.268420.930
24_A164_T0.267650.928
28_E156_Y0.266640.924
114_D117_R0.265580.920
110_A114_D0.26090.904
33_D37_Y0.259390.899
73_L80_K0.259280.899
32_L38_N0.25630.888
47_A162_V0.250920.870
74_E98_I0.247830.859
121_L164_T0.247780.859
81_V164_T0.246690.855
136_K139_Q0.243470.844
82_G88_D0.242270.840
79_I104_F0.241930.839
31_G37_Y0.241820.838
162_V165_F0.239450.830
138_E152_E0.239050.829
108_L112_L0.236320.819
109_A112_L0.235380.816
121_L160_D0.234850.814
62_D67_D0.231810.803
158_A161_A0.231260.802
114_D128_Y0.231080.801
30_T144_R0.22960.796
66_L70_K0.227080.787
159_Q163_V0.226820.786
124_L167_L0.226670.786
125_A129_L0.226430.785
109_A168_Y0.225470.781
139_Q148_P0.224290.777
74_E102_N0.224040.777
127_E174_Q0.223310.774
143_W153_Q0.222260.770
88_D157_A0.221130.766
81_V106_T0.221050.766
132_I163_V0.218060.756
83_H124_L0.217680.754
48_T169_E0.217060.752
21_K47_A0.216560.751
117_R127_E0.216160.749
47_A161_A0.215450.747
137_K140_M0.214740.744
34_P37_Y0.213610.740
21_K78_I0.213020.738
169_E172_K0.212930.738
84_N107_M0.212770.737
27_T41_I0.210680.730
90_K93_Y0.209430.726
127_E167_L0.209360.726
128_Y170_K0.208570.723
167_L171_L0.207910.721
27_T39_P0.207680.720
23_L45_Q0.207560.719
150_S154_I0.206940.717
84_N91_W0.20630.715
55_I58_I0.206250.715
100_L103_V0.205220.711
89_L93_Y0.205150.711
106_T164_T0.204570.709
29_T84_N0.204330.708
21_K77_N0.202830.703
101_K172_K0.202240.701
125_A128_Y0.201670.699
73_L100_L0.200870.696
21_K45_Q0.200350.694
27_T88_D0.200110.694
158_A162_V0.19990.693
123_D127_E0.199560.692
65_I68_A0.197490.684
85_A89_L0.197120.683
48_T165_F0.196350.681
38_N94_R0.195910.679
44_I54_I0.195460.677
43_L157_A0.195360.677
151_E154_I0.195030.676
133_D163_V0.194160.673
138_E141_S0.193680.671
149_L153_Q0.191930.665
129_L166_R0.190970.662
89_L103_V0.190.659
69_L72_L0.187410.650
23_L43_L0.187030.648
22_V169_E0.18670.647
114_D171_L0.185980.645
106_T110_A0.185240.642
25_F80_K0.184680.640
29_T32_L0.183760.637
143_W157_A0.183430.636
107_M119_Y0.182410.632
163_V166_R0.181620.629
161_A164_T0.181470.629
47_A165_F0.180620.626
129_L132_I0.180410.625
84_N160_D0.180290.625
115_P127_E0.180240.625
27_T157_A0.180040.624
24_A161_A0.179970.624
139_Q152_E0.179450.622
93_Y100_L0.179330.622
143_W149_L0.178930.620
31_G91_W0.178730.619
85_A103_V0.177550.615
120_S160_D0.176450.612
135_D138_E0.176250.611
21_K79_I0.176190.611
77_N130_G0.175780.609
137_K142_D0.175780.609
31_G39_P0.174170.604
124_L128_Y0.174060.603
42_A144_R0.173980.603
100_L105_D0.173810.602
125_A132_I0.17330.601
84_N105_D0.172640.598
21_K75_D0.17240.598
54_I158_A0.171810.595
66_L96_F0.171590.595
109_A172_K0.170630.591
144_R147_R0.170560.591
116_T127_E0.170440.591
167_L170_K0.170140.590
30_T91_W0.170040.589
54_I154_I0.169620.588
154_I158_A0.169430.587
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
3safA0.960299.90.078
2hbjA0.960299.90.145
1yt3A0.960299.90.152
2e6mA0.977399.90.192
1vk0A0.948999.90.213
3cymA0.954599.80.248
2kfnA0.971699.80.265
3pv8A0.920599.80.33
1x9mA0.835299.70.338
4dfkA0.721699.50.458

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