GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_photolyase - DNA photolyase
Pfam: PF00875 (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: CL0039
Length: 165
Sequences: 2170
Seq/Len: 13.15
HH_delta: 0.034 (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
94_F120_V0.548452.686
59_Q63_R0.532752.609
93_Y123_F0.531772.604
94_F122_T0.455612.231
59_Q68_P0.451782.213
5_F62_L0.450682.207
5_F29_P0.444752.178
3_V16_A0.428692.099
3_V14_N0.422632.070
74_G79_V0.421392.064
92_V113_L0.419762.056
14_N95_N0.405281.985
5_F58_L0.362621.776
15_P125_D0.355221.740
91_A119_K0.352131.725
2_L89_A0.350831.718
72_L79_V0.3491.709
91_A121_H0.347531.702
7_R97_E0.347311.701
29_P67_I0.340731.669
30_V83_L0.338531.658
57_D61_S0.334741.639
6_R106_D0.321381.574
30_V80_L0.318961.562
49_R53_E0.318321.559
129_V152_W0.317521.555
149_R153_E0.317291.554
84_A89_A0.312711.531
28_L70_L0.306281.500
83_L87_Y0.303941.489
92_V120_V0.302381.481
72_L86_E0.297411.457
50_F54_S0.29491.444
110_R122_T0.294671.443
79_V82_E0.287391.407
99_T102_E0.283171.387
35_P73_R0.280941.376
82_E86_E0.275191.348
28_L87_Y0.273211.338
63_R68_P0.271651.330
3_V93_Y0.269511.320
30_V72_L0.269261.319
18_H22_Q0.267511.310
128_L152_W0.265991.303
31_F51_L0.265911.302
98_Y127_T0.264641.296
97_E105_R0.262141.284
75_D78_E0.262021.283
2_L30_V0.261311.280
81_P116_H0.256681.257
84_A113_L0.250781.228
77_E81_P0.249341.221
33_F71_V0.245461.202
77_E108_R0.245251.201
85_K116_H0.244071.195
76_P81_P0.242631.188
62_L67_I0.241811.184
4_W94_F0.239441.173
19_A22_Q0.237481.163
61_S65_L0.2371.161
32_V79_V0.235821.155
32_V76_P0.234731.150
32_V80_L0.231981.136
52_L56_A0.231441.133
62_L69_L0.231031.131
70_L83_L0.230951.131
78_E82_E0.230751.130
103_R107_E0.230571.129
47_R50_F0.230191.127
50_F53_E0.228631.120
95_N125_D0.228421.119
56_A60_E0.22791.116
36_E75_D0.224141.098
53_E57_D0.222111.088
110_R114_K0.221721.086
11_L65_L0.220931.082
147_P150_K0.2181.068
147_P151_K0.216971.063
97_E102_E0.216551.061
136_K140_E0.216251.059
84_A87_Y0.212721.042
49_R54_S0.208641.022
34_D37_E0.206411.011
94_F110_R0.205111.005
4_W76_P0.204331.001
31_F55_L0.203810.998
8_D13_D0.203220.995
60_E64_K0.200870.984
145_F149_R0.200360.981
35_P45_P0.199590.977
96_E122_T0.198640.973
33_F55_L0.197790.969
137_K151_K0.193180.946
4_W109_V0.193010.945
2_L84_A0.192980.945
124_D130_P0.192290.942
146_T150_K0.189630.929
96_E124_D0.188240.922
34_D47_R0.188060.921
140_E143_K0.187740.919
23_N26_P0.185530.909
102_E105_R0.184290.903
4_W80_L0.18110.887
144_V147_P0.178640.875
33_F38_F0.178590.875
59_Q71_V0.177530.869
96_E130_P0.176820.866
20_A93_Y0.175660.860
19_A123_F0.174630.855
16_A95_N0.174610.855
111_K115_K0.174390.854
4_W113_L0.173710.851
61_S64_K0.173660.850
50_F97_E0.173170.848
23_N91_A0.171550.840
151_K154_K0.17090.837
124_D127_T0.170510.835
34_D74_G0.169740.831
43_I47_R0.16890.827
128_L156_L0.168860.827
136_K142_Y0.168440.825
84_A92_V0.168410.825
81_P85_K0.167070.818
32_V74_G0.166990.818
28_L89_A0.163960.803
10_R13_D0.163810.802
84_A118_I0.163650.801
33_F52_L0.163150.799
136_K139_G0.161810.792
21_A27_V0.161180.789
124_D129_V0.161140.789
151_K155_Q0.16010.784
127_T131_P0.160060.784
94_F106_D0.158190.775
2_L87_Y0.157410.771
36_E101_Y0.157250.770
82_E85_K0.156330.766
138_D142_Y0.156270.765
81_P112_A0.155780.763
19_A93_Y0.155470.761
142_Y145_F0.155080.759
110_R120_V0.154790.758
14_N50_F0.154540.757
142_Y147_P0.154310.756
9_L58_L0.154110.755
3_V29_P0.153240.750
95_N124_D0.152490.747
74_G78_E0.152020.745
3_V27_V0.151310.741
57_D60_E0.15130.741
33_F51_L0.151290.741
129_V149_R0.150740.738
135_P139_G0.150290.736
107_E110_R0.148940.729
114_K117_G0.148640.728
72_L83_L0.148080.725
92_V109_V0.147190.721
134_I151_K0.147030.720
33_F48_R0.146910.719
104_R115_K0.146180.716
15_P95_N0.146110.716
81_P84_A0.146080.715
5_F9_L0.145330.712
98_Y130_P0.145080.711
136_K141_P0.144370.707
7_R102_E0.144150.706
55_L69_L0.143830.704
37_E43_I0.14380.704
95_N123_F0.142920.700
86_E104_R0.142550.698
112_A115_K0.142020.696
47_R102_E0.141590.693
134_I143_K0.140490.688
7_R99_T0.140070.686
55_L68_P0.139950.685
101_Y105_R0.139720.684
38_F102_E0.139670.684
53_E152_W0.139450.683
6_R9_L0.139230.682
150_K154_K0.138960.681
8_D95_N0.138880.680
7_R92_V0.138150.677
36_E108_R0.138130.676
43_I48_R0.138110.676
63_R116_H0.136990.671
148_F152_W0.136980.671
31_F48_R0.136070.666
109_V112_A0.135350.663
9_L31_F0.1350.661
107_E122_T0.134170.657
142_Y152_W0.134150.657
102_E106_D0.1340.656
55_L61_S0.133970.656
9_L69_L0.133860.656
3_V62_L0.133810.655
65_L115_K0.132890.651
46_R127_T0.132490.649
116_H119_K0.131590.644
96_E132_D0.131440.644
59_Q62_L0.131350.643
95_N98_Y0.131070.642
59_Q69_L0.130840.641
144_V150_K0.130620.640
100_P105_R0.130590.640
78_E108_R0.129730.635
104_R108_R0.129660.635
146_T153_E0.12920.633
76_P97_E0.129040.632
145_F148_F0.128990.632
143_K146_T0.128770.631
98_Y124_D0.128570.630
50_F152_W0.128170.628
18_H121_H0.127860.626
76_P83_L0.12720.623
146_T149_R0.127080.622
132_D135_P0.126780.621
20_A27_V0.126460.619
133_D155_Q0.126420.619
74_G81_P0.125740.616
3_V20_A0.125570.615
28_L83_L0.125550.615
18_H156_L0.124770.611
85_K108_R0.124690.611
25_D111_K0.124320.609
31_F102_E0.124140.608
11_L17_L0.124090.608
38_F43_I0.1240.607
130_P133_D0.123620.605
137_K142_Y0.123590.605
129_V133_D0.123260.604
104_R107_E0.123210.603
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
3fy4A11000.034
3tvsA11000.061
4k0rA0.99391000.067
1owlA11000.087
1dnpA0.98791000.094
1np7A11000.105
2wq7A11000.114
2j4dA11000.118
2e0iA0.95151000.128
1u3dA0.99391000.132

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