GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UvrD-helicase - UvrDREP helicase N-terminal domain
Pfam: PF00580 (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: CL0023
Length: 315
Sequences: 6003
Seq/Len: 19.06
HH_delta: 0.167 (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
47_R258_D1.157514.760
6_R10_R0.87633.604
244_R274_R0.747013.072
238_L241_E0.615862.533
34_I50_V0.596012.451
93_Y257_Y0.586792.413
101_C239_A0.574182.361
4_E7_R0.567732.335
60_E64_R0.566652.330
44_P47_R0.563282.317
224_L234_D0.55242.272
219_E222_E0.518252.131
11_S16_L0.517242.127
305_E309_E0.513892.113
95_S100_F0.510542.100
222_E226_E0.508782.092
223_Q227_R0.507512.087
241_E245_K0.498952.052
230_I238_L0.479971.974
36_Y40_E0.477531.964
236_L271_L0.475071.954
244_R278_K0.472981.945
240_L274_R0.47251.943
223_Q226_E0.471621.940
18_V287_F0.470851.936
32_E68_L0.468671.927
250_R254_R0.457931.883
16_L287_F0.454841.871
220_Y231_D0.450161.851
37_L259_H0.44611.835
28_T32_E0.44151.816
49_L260_I0.425271.749
247_P250_R0.420911.731
30_L261_L0.41211.695
98_H236_L0.407671.677
219_E223_Q0.40311.658
243_L250_R0.398291.638
121_L229_L0.396991.633
104_L239_A0.393641.619
10_R36_Y0.3931.616
240_L275_I0.391081.608
115_D228_G0.390941.608
108_Y252_K0.384541.581
270_P303_D0.384241.580
63_E67_E0.378791.558
33_R287_F0.377951.554
265_F273_L0.376281.548
38_L69_L0.374571.540
49_L257_Y0.374151.539
187_K233_D0.371491.528
221_E224_L0.367481.511
8_I18_V0.360961.485
104_L253_I0.360561.483
218_E222_E0.360391.482
19_N292_P0.358721.475
98_H235_L0.358231.473
34_I65_I0.355711.463
309_E312_E0.355361.461
35_A68_L0.353351.453
251_E255_Q0.348991.435
247_P251_E0.347911.431
109_G230_I0.346161.424
108_Y253_I0.341461.404
34_I48_I0.340741.401
31_L65_I0.339761.397
260_I280_F0.33441.375
274_R277_K0.329191.354
100_F104_L0.32461.335
17_L288_I0.321781.323
95_S99_S0.321641.323
262_I276_L0.321141.321
3_D6_R0.319011.312
65_I94_I0.318461.310
11_S14_G0.317631.306
50_V61_M0.316821.303
291_D294_Q0.31671.302
243_L278_K0.316621.302
246_D249_I0.315671.298
134_L223_Q0.315061.296
230_I235_L0.312791.286
59_Q62_R0.311431.281
114_I238_L0.309571.273
297_Y300_R0.306511.261
189_I199_Q0.305761.257
187_K191_E0.302981.246
111_E249_I0.302121.243
240_L244_R0.301541.240
21_G24_S0.301111.238
100_F253_I0.30081.237
259_H285_N0.299281.231
212_E215_E0.296181.218
198_E201_K0.29471.212
3_D7_R0.294441.211
14_G285_N0.293331.206
104_L243_L0.292021.201
33_R259_H0.290851.196
240_L278_K0.288451.186
251_E254_R0.287991.184
51_L100_F0.28781.184
111_E246_D0.287761.183
22_A293_N0.286931.180
195_E198_E0.284521.170
137_E223_Q0.282491.162
52_T57_A0.281771.159
109_G112_I0.281361.157
7_R10_R0.280461.153
108_Y111_E0.279961.151
270_P274_R0.279011.147
207_K210_R0.277831.143
295_S298_G0.275491.133
37_L43_V0.275281.132
191_E233_D0.273261.124
215_E218_E0.272521.121
225_R238_L0.271951.118
276_L286_L0.271781.118
114_I230_I0.27151.117
264_E294_Q0.271461.116
185_F189_I0.268861.106
89_I92_I0.266361.095
119_E125_E0.266111.094
105_L239_A0.264741.089
304_P308_E0.262361.079
257_Y260_I0.261331.075
138_I219_E0.260341.071
221_E225_R0.260211.070
290_G294_Q0.259621.068
102_Y106_R0.257621.060
186_I190_K0.256771.056
33_R37_L0.256421.055
59_Q63_E0.253791.044
268_T306_L0.252761.040
111_E248_E0.251551.035
264_E267_D0.244921.007
98_H233_D0.243251.000
240_L271_L0.241670.994
304_P307_F0.241560.993
239_A275_I0.239880.987
254_R282_N0.239770.986
253_I257_Y0.237110.975
261_L287_F0.235890.970
250_R278_K0.234660.965
20_A53_F0.234180.963
97_F268_T0.234150.963
197_K218_E0.233060.959
93_Y103_R0.23250.956
180_E183_K0.230060.946
236_L275_I0.228930.942
295_S299_F0.227250.935
112_I242_L0.227140.934
200_E218_E0.225950.929
265_F288_I0.223750.920
112_I246_D0.222230.914
265_F307_F0.222110.913
57_A60_E0.220830.908
66_R90_D0.220390.906
273_L277_K0.219530.903
138_I216_I0.21920.902
2_T5_Q0.218490.899
37_L48_I0.217740.895
57_A64_R0.217540.895
194_L199_Q0.217060.893
20_A289_V0.216250.889
104_L242_L0.216020.888
107_E252_K0.215120.885
269_S272_Q0.213740.879
101_C275_I0.21260.874
53_F267_D0.212480.874
265_F268_T0.21240.874
192_K303_D0.211990.872
288_I310_F0.211190.869
102_Y120_I0.209960.864
267_D294_Q0.209520.862
274_R278_K0.209330.861
269_S300_R0.20910.860
193_Q271_L0.206840.851
295_S302_A0.206380.849
56_A60_E0.205640.846
268_T272_Q0.205340.845
242_L249_I0.204670.842
19_N307_F0.203390.836
18_V29_T0.202970.835
180_E184_E0.202560.833
110_Y116_P0.201670.829
98_H269_S0.200070.823
20_A267_D0.199860.822
107_E256_R0.199110.819
264_E291_D0.198830.818
214_A218_E0.198590.817
188_R192_K0.198510.816
182_L213_I0.198270.815
181_E184_E0.198240.815
43_V47_R0.198150.815
103_R107_E0.196680.809
11_S287_F0.196610.809
5_Q29_T0.194480.800
33_R285_N0.193340.795
117_N228_G0.19270.793
36_Y41_G0.192320.791
52_T58_A0.191250.787
12_T259_H0.191030.786
224_L231_D0.190880.785
209_E213_I0.190880.785
39_Y72_E0.19040.783
21_G265_F0.189890.781
28_T64_R0.188740.776
53_F97_F0.18790.773
64_R289_V0.187850.773
98_H231_D0.187760.772
221_E237_L0.187740.772
215_E219_E0.18750.771
53_F264_E0.187490.771
33_R261_L0.187160.770
135_F216_I0.18680.768
101_C236_L0.186190.766
308_E311_K0.18610.765
260_I279_L0.185860.764
62_R66_R0.18560.763
248_E251_E0.185120.761
237_L271_L0.185080.761
20_A264_E0.184850.760
267_D296_I0.184450.759
239_A243_L0.183450.754
31_L68_L0.183420.754
9_I33_R0.18270.751
13_E259_H0.182220.749
251_E282_N0.182210.749
109_G114_I0.182210.749
51_L97_F0.182050.749
37_L261_L0.181870.748
35_A65_I0.181030.745
211_E215_E0.181010.744
9_I29_T0.180770.743
132_R180_E0.180690.743
30_L289_V0.18010.741
12_T37_L0.179720.739
123_E131_Q0.179010.736
53_F297_Y0.178510.734
135_F183_K0.178010.732
270_P309_E0.177820.731
254_R283_P0.177790.731
8_I29_T0.177420.730
277_K281_K0.17650.726
35_A39_Y0.17590.723
28_T31_L0.175530.722
132_R136_K0.175270.721
200_E214_A0.175250.721
16_L33_R0.174840.719
95_S103_R0.174760.719
51_L276_L0.17460.718
252_K256_R0.17410.716
22_A95_S0.173710.714
131_Q134_L0.173630.714
3_D10_R0.173610.714
221_E238_L0.173380.713
119_E229_L0.173020.712
268_T302_A0.172340.709
137_E227_R0.172270.708
133_E137_E0.172020.707
109_G113_G0.171660.706
255_Q282_N0.171580.706
23_G26_K0.171030.703
133_E136_K0.170530.701
12_T41_G0.169840.699
20_A57_A0.16960.698
23_G264_E0.169030.695
17_L307_F0.16860.693
32_E35_A0.168580.693
118_F230_I0.168330.692
267_D290_G0.167580.689
53_F272_Q0.167280.688
27_T64_R0.166840.686
239_A242_L0.166810.686
21_G60_E0.166170.683
189_I196_P0.166140.683
68_L71_E0.166120.683
147_L154_L0.165760.682
31_L35_A0.165480.681
134_L138_I0.164760.678
31_L61_M0.164450.676
54_T272_Q0.164340.676
36_Y39_Y0.164230.675
181_E185_F0.164140.675
302_A306_L0.16370.673
137_E140_E0.163030.670
255_Q258_D0.162940.670
120_I235_L0.162670.669
96_T99_S0.162540.668
189_I194_L0.162310.668
50_V65_I0.162270.667
49_L93_Y0.162080.667
189_I213_I0.161920.666
8_I287_F0.161490.664
2_T28_T0.161120.663
9_I28_T0.16080.661
65_I92_I0.160410.660
96_T267_D0.159810.657
188_R191_E0.159130.654
20_A297_Y0.158140.650
24_S28_T0.157750.649
23_G291_D0.157410.647
53_F98_H0.157360.647
149_L154_L0.157270.647
208_N211_E0.157170.646
2_T8_I0.157140.646
23_G290_G0.156850.645
23_G294_Q0.156720.645
269_S306_L0.156690.644
198_E202_K0.156440.643
66_R72_E0.156330.643
58_A61_M0.156220.642
55_N235_L0.155850.641
243_L253_I0.155020.638
267_D297_Y0.1550.637
150_D154_L0.154280.635
206_S210_R0.153990.633
17_L265_F0.15390.633
286_L310_F0.153130.630
34_I38_L0.152880.629
54_T57_A0.152680.628
20_A265_F0.152440.627
7_R11_S0.152110.626
295_S304_P0.151990.625
195_E241_E0.151880.625
21_G297_Y0.151640.624
307_F310_F0.151590.623
31_L57_A0.151120.622
39_Y42_G0.151110.621
255_Q283_P0.15090.621
12_T287_F0.150610.619
264_E290_G0.150490.619
49_L95_S0.150450.619
20_A98_H0.150340.618
194_L202_K0.149940.617
131_Q220_Y0.149730.616
22_A53_F0.149640.615
28_T60_E0.149480.615
236_L240_L0.149260.614
231_D234_D0.149230.614
139_L155_E0.149210.614
33_R36_Y0.149140.613
12_T36_Y0.149010.613
124_E132_R0.148720.612
37_L41_G0.14870.612
2_T24_S0.148670.611
123_E183_K0.148550.611
54_T60_E0.148550.611
11_S15_P0.148290.610
111_E252_K0.14810.609
93_Y256_R0.147890.608
51_L268_T0.147750.608
308_E312_E0.147740.608
233_D236_L0.14750.607
53_F300_R0.147410.606
28_T68_L0.147360.606
190_K234_D0.147260.606
98_H101_C0.147190.605
46_E91_R0.146960.604
35_A69_L0.146940.604
17_L310_F0.146880.604
131_Q183_K0.146840.604
44_P71_E0.146750.604
264_E297_Y0.146290.602
124_E133_E0.146170.601
217_Y221_E0.145760.599
223_Q229_L0.145760.599
61_M276_L0.144530.594
24_S51_L0.144230.593
38_L45_P0.143970.592
57_A289_V0.143810.591
51_L55_N0.143660.591
103_R136_K0.143660.591
236_L301_G0.143620.591
65_I68_L0.143390.590
237_L241_E0.143360.590
307_F311_K0.143220.589
10_R40_E0.142720.587
135_F139_L0.142470.586
276_L288_I0.14240.586
188_R193_Q0.14230.585
236_L269_S0.142110.584
148_N151_K0.142010.584
280_F285_N0.141780.583
183_K187_K0.141420.582
252_K255_Q0.141390.581
235_L239_A0.141160.581
30_L57_A0.14110.580
280_F286_L0.14090.579
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
1pjrA0.83811000.167
1uaaA0.83811000.193
3lfuA0.83491000.207
3u4qA0.99681000.209
1w36B0.98731000.275
3u4qB0.77461000.401
4b3fX0.72381000.513
3upuA0.492199.90.615
2xzlA0.67399.90.616
2gk6A0.676299.80.651

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