GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fapy_DNA_glyco - Formamidopyrimidine-DNA glycosylase N-terminal domain
Pfam: PF01149 (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. )
Length: 116
Sequences: 1993
Seq/Len: 17.18
HH_delta: 0.061 (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
54_E63_H0.976223.716
20_K100_D0.686912.615
14_R18_V0.673892.565
61_F69_V0.64672.462
48_R66_G0.589742.245
29_R111_R0.576612.195
24_S97_R0.56482.150
26_E97_R0.557132.121
35_N114_R0.552332.102
94_L115_V0.5091.938
10_R60_L0.502891.914
72_V80_L0.499591.902
7_E55_R0.478491.821
24_S46_Q0.437731.666
92_T107_V0.413651.575
72_V115_V0.405541.544
51_T65_D0.403221.535
7_E11_R0.391461.490
63_H69_V0.388041.477
10_R14_R0.385911.469
48_R65_D0.382861.457
64_L70_L0.374741.426
20_K99_E0.374591.426
21_R99_E0.369871.408
20_K102_S0.369561.407
22_I64_L0.3641.386
79_R109_P0.36221.379
14_R52_D0.358091.363
21_R49_K0.357451.361
95_R103_R0.350181.333
52_D63_H0.347341.322
72_V106_F0.342951.305
7_E10_R0.341911.302
27_V94_L0.339271.291
34_R75_G0.33921.291
34_R114_R0.334591.274
23_E99_E0.330141.257
40_E43_K0.327451.246
80_L106_F0.323681.232
28_R95_R0.322111.226
49_K65_D0.319091.215
17_L98_F0.318721.213
93_R111_R0.313581.194
17_L50_I0.312021.188
53_V62_F0.311911.187
41_F115_V0.308331.174
50_I64_L0.296561.129
40_E44_A0.296191.127
44_A68_L0.294711.122
22_I96_L0.2911.108
26_E95_R0.28881.099
106_F115_V0.285481.087
42_R46_Q0.281881.073
25_V45_L0.281491.072
88_P105_R0.279531.064
59_Y71_V0.273341.040
58_K78_G0.26651.014
18_V52_D0.266411.014
83_D86_D0.263771.004
62_F72_V0.26230.998
6_V76_M0.259980.990
3_L7_E0.256440.976
50_I62_F0.252820.962
80_L96_L0.251520.957
98_F102_S0.250560.954
80_L115_V0.249550.950
5_E113_G0.248550.946
31_K111_R0.247110.941
3_L8_T0.244940.932
92_T105_R0.243680.928
4_P7_E0.242090.922
79_R107_V0.240810.917
14_R53_V0.240630.916
3_L55_R0.238850.909
76_M91_H0.235150.895
62_F70_L0.234290.892
13_L60_L0.232560.885
39_E42_R0.229710.874
22_I50_I0.229370.873
37_E40_E0.228120.868
92_T95_R0.227480.866
9_V81_R0.225390.858
58_K73_H0.224880.856
50_I98_F0.223430.851
20_K98_F0.221330.843
73_H78_G0.220310.839
54_E69_V0.220050.838
1_P78_G0.217810.829
9_V74_L0.215260.819
3_L6_V0.212520.809
29_R75_G0.212360.808
106_F113_G0.210170.800
9_V12_G0.210120.800
25_V94_L0.208160.792
44_A100_D0.20740.789
84_P103_R0.206820.787
96_L115_V0.205090.781
33_L36_P0.202660.771
28_R93_R0.20190.769
33_L114_R0.201080.765
97_R103_R0.20050.763
18_V21_R0.199790.761
16_A80_L0.199640.760
76_M110_R0.198580.756
11_R14_R0.196670.749
22_I98_F0.194890.742
59_Y74_L0.194470.740
41_F72_V0.192950.734
77_T91_H0.192910.734
58_K76_M0.192450.733
36_P40_E0.191340.728
92_T103_R0.190770.726
88_P95_R0.189460.721
9_V59_Y0.187590.714
87_W105_R0.187510.714
56_R59_Y0.18650.710
82_L102_S0.185550.706
44_A66_G0.18430.702
5_E55_R0.184040.701
1_P58_K0.182960.696
76_M112_F0.182960.696
74_L112_F0.182230.694
41_F64_L0.181990.693
50_I53_V0.180340.686
1_P110_R0.179540.683
89_P101_G0.17860.680
10_R53_V0.178350.679
10_R57_G0.176720.673
75_G114_R0.176580.672
18_V53_V0.175220.667
17_L62_F0.173860.662
30_P42_R0.173740.661
14_R60_L0.173530.661
56_R61_F0.173190.659
89_P107_V0.173180.659
8_T79_R0.172510.657
17_L82_L0.170650.650
11_R43_K0.170480.649
16_A82_L0.169360.645
73_H76_M0.168330.641
108_D113_G0.167180.636
19_G48_R0.166780.635
81_R107_V0.166150.632
12_G82_L0.166090.632
60_L74_L0.165050.628
2_E5_E0.164880.628
4_P55_R0.164830.627
58_K110_R0.164640.627
27_V57_G0.164340.626
66_G85_P0.163960.624
60_L73_H0.163720.623
23_E44_A0.163120.621
48_R51_T0.162950.620
7_E91_H0.161260.614
90_K93_R0.159840.608
18_V43_K0.159790.608
25_V64_L0.159580.607
6_V112_F0.159250.606
77_T93_R0.158610.604
58_K74_L0.158350.603
77_T80_L0.158060.602
1_P6_V0.158010.601
24_S51_T0.157920.601
86_D105_R0.157140.598
23_E46_Q0.157120.598
8_T12_G0.156540.596
75_G111_R0.156430.595
5_E112_F0.156270.595
77_T109_P0.155390.592
12_G81_R0.155260.591
59_Y73_H0.155090.590
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
3u6pA0.99141000.061
3twlA11000.062
2xzfA0.97411000.074
1k82A0.97411000.083
3vk8A0.95691000.099
1ee8A0.90521000.13
1k3xA0.939799.90.193
1tdhA0.956999.90.195
3w0fA0.965599.60.469
2v0cA0.56920.20.917

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