GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Exo_endo_phos - EndonucleaseExonucleasephosphatase family
Pfam: PF03372 (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: CL0530
Length: 249
Sequences: 6394
Seq/Len: 25.68
HH_delta: 0.286 (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
34_A162_M1.259835.361
36_Q126_N0.837943.566
34_A126_N0.812153.456
31_D81_R0.683032.907
78_I126_N0.666582.837
35_L38_V0.632932.693
34_A124_V0.60332.567
158_P229_D0.570732.429
162_M224_I0.549062.337
80_S83_P0.525372.236
2_T36_Q0.508972.166
227_S230_L0.504242.146
151_Y229_D0.502192.137
192_G226_V0.501112.132
127_V161_V0.456831.944
34_A78_I0.44451.892
127_V165_F0.439691.871
30_P33_I0.427021.817
24_W28_L0.419281.784
37_E164_D0.411781.752
80_S84_I0.411081.749
129_L140_W0.399981.702
136_R139_Q0.398931.698
32_I124_V0.393931.676
38_V77_A0.392171.669
23_Q26_A0.390871.663
160_I226_V0.380991.621
23_Q27_E0.376641.603
125_V159_V0.375341.597
161_V225_F0.371761.582
159_V189_F0.364791.552
141_R145_A0.361351.538
140_W144_L0.349361.487
20_E23_Q0.348641.484
138_E142_E0.338271.440
5_V35_L0.336951.434
190_K195_D0.336521.432
144_L182_D0.335011.426
228_S231_R0.326631.390
142_E145_A0.326221.388
192_G234_F0.325321.384
43_L46_L0.321231.367
124_V224_I0.311981.328
191_D220_R0.304631.296
1_M30_P0.303031.290
190_K231_R0.299471.274
197_H200_C0.298951.272
124_V160_I0.294361.253
19_R23_Q0.293311.248
84_I87_S0.29081.238
182_D186_E0.290391.236
144_L148_Q0.290381.236
195_D231_R0.290171.235
169_P181_R0.289481.232
146_R150_I0.288711.229
2_T224_I0.285771.216
25_I30_P0.283911.208
149_K152_A0.282721.203
226_V231_R0.280371.193
214_K217_E0.279531.190
3_W21_I0.279391.189
190_K228_S0.276791.178
191_D194_R0.275781.174
180_I225_F0.275621.173
206_P241_W0.274761.169
1_M28_L0.273821.165
160_I224_I0.272891.161
1_M33_I0.271351.155
181_R186_E0.266651.135
25_I33_I0.266321.133
200_C205_S0.263321.121
37_E166_N0.262651.118
29_D81_R0.26261.117
38_V128_H0.261911.115
161_V165_F0.261471.113
158_P233_R0.256221.090
140_W143_L0.255731.088
166_N248_D0.25191.072
28_L240_L0.251051.068
165_F225_F0.247421.053
22_A26_A0.247261.052
61_F64_G0.24671.050
51_L54_Y0.244951.042
159_V227_S0.244091.039
126_N162_M0.243111.035
39_R128_H0.242161.031
39_R74_Y0.24131.027
49_E52_R0.24081.025
142_E146_R0.239231.018
52_R56_G0.238121.013
78_I124_V0.237671.011
188_G191_D0.23671.007
168_R219_S0.23460.998
53_G56_G0.234210.997
123_T159_V0.233150.992
164_D248_D0.232870.991
50_Q53_G0.231570.985
96_S100_I0.231220.984
220_R223_Y0.230920.983
125_V147_I0.23080.982
170_D181_R0.230580.981
122_I230_L0.229610.977
64_G97_K0.228290.971
193_F200_C0.227870.970
33_I79_L0.227570.968
140_W167_S0.224970.957
234_F239_T0.224160.954
193_F206_P0.223330.950
129_L139_Q0.223230.950
163_G166_N0.221920.944
61_F89_S0.221550.943
123_T153_D0.221240.941
191_D198_P0.220270.937
197_H206_P0.219120.932
189_F193_F0.218360.929
99_G102_I0.218260.929
87_S90_Y0.217990.928
43_L47_L0.217880.927
165_F223_Y0.217760.927
39_R75_G0.216790.923
147_I189_F0.215970.919
200_C206_P0.215950.919
74_Y221_I0.21410.911
4_N164_D0.212870.906
49_E53_G0.212210.903
1_M25_I0.211630.901
7_G39_R0.211520.900
135_E139_Q0.21150.900
226_V230_L0.210160.894
138_E141_R0.209910.893
139_Q146_R0.209250.890
4_N37_E0.205390.874
35_L79_L0.205150.873
50_Q54_Y0.203980.868
232_A235_V0.203830.867
196_L234_F0.202150.860
80_S85_F0.201530.858
44_S47_L0.201110.856
169_P223_Y0.200790.854
21_I25_I0.199240.848
207_G211_T0.19810.843
26_A29_D0.198080.843
233_R236_E0.19790.842
94_L142_E0.196870.838
148_Q151_Y0.196740.837
98_P102_I0.19540.832
128_H131_S0.194990.830
55_L58_Y0.194120.826
44_S48_E0.193990.826
51_L136_R0.193740.824
38_V44_S0.192410.819
231_R234_F0.191770.816
148_Q152_A0.191460.815
136_R140_W0.191150.813
131_S221_I0.191130.813
213_S218_P0.189410.806
35_L77_A0.189350.806
58_Y61_F0.189020.804
39_R131_S0.188220.801
194_R197_H0.188110.801
180_I223_Y0.187560.798
8_W128_H0.187160.796
84_I119_G0.185950.791
197_H238_S0.185740.790
45_E49_E0.185370.789
60_S65_N0.184380.785
94_L97_K0.184350.785
125_V150_I0.183910.783
129_L165_F0.18380.782
37_E221_I0.182210.775
180_I183_F0.181510.772
168_R221_I0.181470.772
141_R144_L0.181370.772
39_R130_P0.180960.770
91_V101_R0.180410.768
98_P101_R0.177660.756
6_R9_N0.177410.755
3_W35_L0.177390.755
3_W6_R0.17710.754
220_R225_F0.17680.752
7_G74_Y0.176250.750
9_N46_L0.176180.750
58_Y62_W0.175710.748
56_G59_G0.175230.746
143_L146_R0.175050.745
47_L55_L0.175050.745
38_V129_L0.174780.744
180_I185_P0.174750.744
151_Y154_N0.173930.740
18_R22_A0.173890.740
27_E243_P0.173040.736
26_A54_Y0.172850.736
123_T154_N0.172590.734
5_V77_A0.171740.731
62_W65_N0.171360.729
182_D187_Y0.171020.728
193_F196_L0.170740.727
55_L83_P0.17060.726
229_D233_R0.170510.726
160_I230_L0.169170.720
223_Y226_V0.168960.719
76_V130_P0.168680.718
237_S241_W0.168580.717
37_E248_D0.168460.717
132_S136_R0.168350.716
192_G196_L0.168330.716
27_E242_D0.167610.713
128_H164_D0.167150.711
59_G63_P0.167130.711
55_L61_F0.167020.711
226_V234_F0.167010.711
7_G73_G0.166770.710
94_L138_E0.166120.707
136_R143_L0.166090.707
238_S242_D0.1660.706
78_I162_M0.165230.703
205_S209_T0.164690.701
60_S63_P0.164340.699
209_T220_R0.164080.698
49_E54_Y0.163210.695
168_R220_R0.162540.692
150_I154_N0.162120.690
213_S217_E0.1620.689
52_R55_L0.161970.689
59_G80_S0.161960.689
96_S99_G0.161740.688
81_R84_I0.161370.687
74_Y128_H0.16120.686
196_L200_C0.161120.686
181_R185_P0.160990.685
236_E240_L0.16040.683
235_V238_S0.160350.682
164_D222_D0.159960.681
48_E52_R0.159850.680
76_V128_H0.15870.675
96_S101_R0.158590.675
208_T212_Y0.15810.673
207_G210_P0.157880.672
39_R220_R0.157540.670
188_G192_G0.157470.670
52_R61_F0.156280.665
52_R79_L0.156220.665
193_F197_H0.155950.664
85_F122_I0.155620.662
1_M24_W0.15490.659
47_L51_L0.154870.659
128_H167_S0.154840.659
36_Q128_H0.154550.658
63_P66_S0.154190.656
169_P210_P0.154160.656
32_I119_G0.154050.656
230_L234_F0.153670.654
144_L186_E0.153570.654
124_V162_M0.152880.651
194_R198_P0.152760.650
158_P227_S0.15250.649
216_G219_S0.152420.649
148_Q182_D0.152370.648
54_Y58_Y0.151290.644
193_F239_T0.151250.644
151_Y227_S0.15120.643
3_W247_S0.150680.641
240_L243_P0.150490.640
3_W243_P0.150130.639
27_E149_K0.150110.639
96_S102_I0.149590.637
236_E239_T0.149550.636
145_A149_K0.149320.635
49_E56_G0.149110.635
195_D198_P0.149010.634
193_F208_T0.148690.633
129_L217_E0.148580.632
167_S218_P0.148480.632
210_P218_P0.148460.632
123_T161_V0.148360.631
209_T212_Y0.148290.631
195_D234_F0.148230.631
189_F192_G0.148170.631
1_M34_A0.147820.629
74_Y131_S0.147490.628
130_P223_Y0.147430.627
238_S243_P0.147170.626
237_S240_L0.146940.625
121_P158_P0.146780.625
185_P188_G0.146770.625
132_S167_S0.14670.624
18_R50_Q0.146330.623
150_I159_V0.145840.621
43_L51_L0.145590.620
208_T237_S0.145340.618
38_V75_G0.145090.617
80_S86_S0.145060.617
95_F142_E0.1450.617
196_L236_E0.144720.616
8_W42_D0.14450.615
149_K153_D0.144460.615
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
4gewA0.875599.90.286
3tebA0.923799.90.3
4f1rA0.879599.90.308
4jg3A0.875599.90.316
2j63A0.955899.90.316
1akoA0.891699.90.32
4gz1A0.899699.90.321
3g91A0.871599.90.328
4fvaA0.875599.90.332
3i41A0.951899.90.332

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