GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HhH-GPD - HhH-GPD superfamily base excision DNA repair protein
Pfam: PF00730 (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: CL0198
Length: 108
Sequences: 5533
Seq/Len: 51.23
HH_delta: 0.239 (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
29_T32_A1.768443.350
37_S40_E1.413642.678
43_E46_R1.226182.323
24_R44_L1.223452.318
31_E66_L1.188012.251
1_V58_I1.173342.223
24_R40_E1.159572.197
96_E100_K1.144722.169
53_R57_Y1.092382.070
31_E35_E1.084642.055
4_I61_L1.048411.986
59_I63_R1.038691.968
28_P32_A1.007491.909
80_R98_T0.993311.882
41_L59_I0.991821.879
53_R56_K0.96431.827
38_E59_I0.941221.783
13_A16_K0.937641.776
57_Y60_E0.927951.758
38_E42_R0.907261.719
89_I101_K0.887941.682
20_R23_E0.884851.676
9_T13_A0.876691.661
60_E64_A0.832511.577
25_Y36_A0.808661.532
60_E63_R0.795511.507
6_S11_I0.781221.480
42_R51_S0.758571.437
19_R23_E0.758441.437
16_K20_R0.722561.369
10_S13_A0.70661.339
56_K60_E0.700591.327
94_T97_E0.698041.322
38_E56_K0.63661.206
39_E42_R0.624431.183
30_P66_L0.607971.152
36_A41_L0.604551.145
38_E55_A0.593421.124
83_L102_L0.592251.122
37_S59_I0.590071.118
12_K16_K0.578141.095
18_Y22_F0.562561.066
20_R44_L0.555791.053
15_R19_R0.553691.049
9_T48_L0.542381.028
16_K19_R0.539491.022
40_E43_E0.536461.016
25_Y28_P0.530281.005
28_P33_L0.511250.969
34_A62_A0.491550.931
17_I20_R0.490570.929
97_E101_K0.487920.924
34_A66_L0.48720.923
91_E98_T0.484690.918
25_Y44_L0.483320.916
33_L62_A0.471590.893
34_A63_R0.47070.892
75_V79_V0.468960.888
33_L41_L0.462340.876
61_L64_A0.461030.873
44_L47_P0.452020.856
12_K15_R0.450580.854
63_R66_L0.447310.847
55_A59_I0.447110.847
2_R18_Y0.447080.847
77_T81_R0.445660.844
30_P62_A0.441230.836
36_A40_E0.434840.824
82_V85_R0.432230.819
13_A47_P0.428040.811
13_A17_I0.427230.809
40_E44_L0.423590.803
20_R47_P0.422380.800
91_E97_E0.420480.797
1_V4_I0.419130.794
61_L65_I0.417630.791
41_L55_A0.41350.783
2_R6_S0.411420.779
81_R84_Q0.410140.777
32_A35_E0.410040.777
96_E99_E0.40630.770
98_T102_L0.405810.769
5_L21_L0.401420.761
1_V22_F0.396250.751
34_A59_I0.393140.745
83_L86_L0.392180.743
91_E94_T0.391650.742
84_Q89_I0.391430.742
80_R84_Q0.389520.738
42_R45_I0.385090.730
82_V86_L0.373990.709
5_L18_Y0.372970.707
22_F28_P0.372760.706
30_P65_I0.370440.702
79_V83_L0.367640.697
20_R24_R0.365990.693
16_K47_P0.365030.692
3_A14_A0.35770.678
13_A48_L0.356350.675
38_E63_R0.354590.672
21_L25_Y0.353330.669
62_A65_I0.351160.665
5_L14_A0.343590.651
14_A48_L0.342850.650
2_R11_I0.341350.647
84_Q98_T0.340440.645
73_P102_L0.339780.644
8_Q53_R0.333270.631
81_R85_R0.330.625
45_I58_I0.329730.625
3_A74_P0.32680.619
76_D81_R0.325940.618
87_G90_P0.325920.617
68_R72_F0.323250.612
51_S54_K0.321370.609
62_A66_L0.319610.606
58_I62_A0.319180.605
1_V62_A0.314880.597
55_A58_I0.313930.595
39_E43_E0.312620.592
95_K100_K0.312150.591
48_L54_K0.310590.588
1_V61_L0.30970.587
6_S78_H0.309450.586
73_P83_L0.309240.586
42_R56_K0.30910.586
89_I98_T0.301790.572
95_K99_E0.299340.567
34_A37_S0.29760.564
30_P33_L0.296580.562
99_E102_L0.295130.559
4_I57_Y0.29470.558
97_E100_K0.293640.556
68_R71_P0.292650.554
6_S79_V0.292580.554
9_T17_I0.290030.549
92_K95_K0.285670.541
17_I48_L0.285460.541
21_L33_L0.284730.539
78_H81_R0.283950.538
83_L89_I0.28290.536
42_R46_R0.282470.535
3_A68_R0.281180.533
95_K98_T0.281090.533
11_I77_T0.275160.521
78_H82_V0.274840.521
6_S9_T0.274420.520
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
1ornA0.981599.70.239
4b21A0.953799.70.251
2abkA0.972299.70.256
3fspA0.972299.70.257
3n5nX0.972299.70.266
1pu6A0.972299.60.288
1keaA0.981599.60.293
1kg2A0.972299.60.293
3i0wA0.935299.60.298
3s6iA0.944499.60.302

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