GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HA - Helicase associated domain
Pfam: PF03457 (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: 68
Sequences: 762
Seq/Len: 11.21
HH_delta: 0.134 (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
18_Y24_H0.809173.320
12_Y61_R0.665322.730
56_P60_E0.633082.598
42_L67_F0.605722.485
41_W45_Q0.481371.975
11_R14_A0.478711.964
49_Y63_D0.470391.930
15_L25_L0.445691.829
9_E61_R0.44441.823
8_W45_Q0.443911.821
19_K25_L0.375121.539
15_L67_F0.344721.414
25_L67_F0.344441.413
11_R36_F0.336821.382
60_E64_A0.332691.365
27_V38_L0.330431.356
49_Y59_I0.309131.268
12_Y45_Q0.30851.266
14_A35_G0.305661.254
15_L42_L0.299591.229
41_W54_L0.284911.169
59_I63_D0.27541.130
48_K51_K0.27221.117
12_Y64_A0.27221.117
27_V42_L0.26831.101
12_Y16_K0.25841.060
46_R63_D0.250131.026
35_G39_G0.246491.011
44_N47_R0.239560.983
45_Q58_R0.232980.956
41_W58_R0.231670.951
16_K65_L0.231160.949
16_K61_R0.229820.943
28_P31_Y0.229180.940
60_E63_D0.221420.909
15_L19_K0.217250.891
7_S10_E0.214950.882
54_L59_I0.211960.870
25_L42_L0.211720.869
36_F39_G0.211040.866
6_R10_E0.209340.859
63_D66_G0.20570.844
47_R51_K0.204540.839
15_L27_V0.200320.822
40_Q47_R0.200290.822
51_K54_L0.200140.821
25_L65_L0.194870.800
40_Q44_N0.189550.778
55_T58_R0.189520.778
38_L42_L0.186350.765
31_Y35_G0.178620.733
14_A36_F0.175090.718
8_W41_W0.175090.718
8_W61_R0.173850.713
24_H27_V0.173620.712
18_Y28_P0.172330.707
29_R51_K0.17130.703
5_D9_E0.170090.698
18_Y22_H0.169490.695
39_G42_L0.169130.694
42_L46_R0.167550.688
45_Q48_K0.167410.687
47_R56_P0.166770.684
46_R67_F0.165380.679
12_Y65_L0.164220.674
25_L66_G0.163860.672
57_E60_E0.163610.671
8_W12_Y0.162960.669
35_G58_R0.161220.662
43_N46_R0.160040.657
18_Y31_Y0.159320.654
29_R43_N0.158940.652
29_R47_R0.158430.650
11_R37_P0.157080.645
21_E59_I0.156430.642
46_R58_R0.154820.635
27_V39_G0.15330.629
19_K66_G0.152170.624
30_D43_N0.151910.623
12_Y41_W0.149520.614
11_R35_G0.14880.611
30_D36_F0.148580.610
17_A21_E0.14730.604
43_N47_R0.14710.604
21_E31_Y0.1460.599
13_E16_K0.144180.592
6_R9_E0.144150.591
24_H38_L0.142950.587
10_E21_E0.142480.585
18_Y59_I0.142370.584
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
2ktaA0.911899.50.134
4i43B0.985338.30.838
2daiA0.6176230.854
2v7kA0.9118160.863
3gzaA0.720614.30.866
3gjaA0.3529140.867
1dv0A0.2513.60.867
3hy0A0.867612.60.87
4j27A0.7512.30.87
1ceoA0.588212.10.87

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