GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HA2 - Helicase associated domain (HA2)
Pfam: PF04408 (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: 102
Sequences: 2218
Seq/Len: 21.75
HH_delta: 0.124 (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
25_M35_A1.035094.029
11_A25_M0.82083.195
40_Y43_Q0.694882.705
37_M50_A0.67622.632
34_L54_A0.670172.609
41_G47_L0.582382.267
69_K72_N0.581032.262
13_D17_N0.56462.198
56_I101_L0.517052.013
3_L12_L0.508111.978
36_K40_Y0.4891.904
4_E7_K0.477851.860
66_P73_A0.410481.598
40_Y44_F0.409741.595
9_L32_P0.376251.465
24_K42_I0.356041.386
21_L36_K0.344911.343
48_D52_I0.342011.331
3_L7_K0.326461.271
66_P69_K0.319781.245
3_L16_G0.318381.239
53_I99_L0.316751.233
70_E73_A0.314671.225
93_D96_S0.307711.198
20_P23_R0.300231.169
61_S96_S0.299811.167
53_I102_L0.299241.165
5_L33_R0.2991.164
28_L35_A0.297941.160
2_A63_F0.29411.145
97_D100_T0.293771.144
4_E8_S0.28451.108
46_C51_L0.273021.063
30_L35_A0.27281.062
42_I47_L0.272411.060
69_K73_A0.259291.009
5_L37_M0.253420.987
5_L30_L0.253230.986
7_K14_E0.250240.974
12_L16_G0.249320.971
46_C50_A0.247570.964
95_E100_T0.246950.961
54_A62_P0.246030.958
7_K16_G0.24310.946
50_A53_I0.238620.929
3_L43_Q0.234740.914
24_K39_L0.23170.902
36_K44_F0.231250.900
19_T22_G0.230690.898
38_L65_N0.226870.883
5_L32_P0.226410.881
4_E14_E0.223450.870
72_N92_S0.222460.866
2_A64_I0.219930.856
60_R68_D0.217740.848
6_L11_A0.214620.835
37_M54_A0.2130.829
2_A6_L0.21160.824
56_I98_H0.210850.821
62_P101_L0.210060.818
33_R61_S0.209370.815
67_D70_E0.203770.793
32_P101_L0.203420.792
54_A93_D0.202780.789
67_D72_N0.202520.788
17_N42_I0.201440.784
44_F48_D0.199390.776
36_K52_I0.19610.763
60_R65_N0.195690.762
32_P98_H0.195570.761
38_L51_L0.195170.760
25_M36_K0.192760.750
49_E102_L0.192470.749
24_K43_Q0.1920.747
43_Q49_E0.191910.747
8_S26_S0.190710.742
20_P27_Q0.188460.734
30_L94_D0.188130.732
35_A38_L0.188120.732
93_D99_L0.18740.730
96_S99_L0.185110.721
46_C98_H0.183140.713
33_R54_A0.181990.708
11_A39_L0.181960.708
64_I67_D0.179010.697
64_I68_D0.178950.697
39_L44_F0.178660.696
31_D42_I0.177980.693
41_G50_A0.177240.690
13_D19_T0.176760.688
71_E92_S0.176450.687
27_Q30_L0.171080.666
97_D101_L0.171060.666
6_L22_G0.170870.665
10_G45_G0.170390.663
98_H101_L0.17030.663
21_L57_L0.169290.659
16_G62_P0.169210.659
13_D16_G0.168950.658
38_L49_E0.165910.646
35_A94_D0.164340.640
56_I62_P0.163990.638
56_I59_V0.163890.638
48_D51_L0.163230.635
4_E12_L0.162420.632
64_I92_S0.162040.631
71_E95_E0.161210.628
35_A42_I0.159820.622
49_E101_L0.158420.617
9_L30_L0.157670.614
4_E26_S0.157350.613
49_E95_E0.15730.612
5_L8_S0.156880.611
61_S65_N0.156550.609
58_S61_S0.154720.602
2_A96_S0.154190.600
4_E48_D0.153890.599
41_G66_P0.15330.597
63_F68_D0.15310.596
62_P99_L0.15270.594
51_L58_S0.152340.593
12_L33_R0.152270.593
38_L54_A0.152270.593
57_L62_P0.152080.592
21_L39_L0.152030.592
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
3i4uA0.892299.90.124
2xauA0.892299.80.197
4bgdA0.960899.20.52
2va8A0.980498.70.601
2zj8A198.70.609
2p6rA0.960898.60.625
4bgdA0.9706970.757
4f92B0.970692.40.822
4f92B0.960890.60.83
2xgjA0.95178.10.856

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