GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_ligase_OB - NAD-dependent DNA ligase OB-fold domain
Pfam: PF03120 (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: CL0021
Length: 82
Sequences: 1658
Seq/Len: 20.22
HH_delta: -0.068 (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
6_R25_E1.665964.093
44_Y47_E1.473953.622
32_T60_R1.23883.044
4_K55_T1.103532.711
59_T67_K1.059552.603
4_K25_E1.054032.590
23_V36_R1.049522.579
7_D52_I0.998142.453
9_E23_V0.981662.412
10_W18_I0.937772.304
77_T80_E0.907512.230
42_Y46_K0.878622.159
51_R82_P0.796731.958
60_R64_V0.794811.953
11_Q21_V0.791051.944
55_T75_K0.737911.813
32_T64_V0.736481.810
24_L56_V0.736031.808
7_D23_V0.692721.702
57_L70_G0.673491.655
28_E33_T0.655641.611
26_P33_T0.651881.602
2_E75_K0.651141.600
30_D60_R0.599551.473
46_K82_P0.590391.451
2_E55_T0.575421.414
21_V36_R0.550211.352
3_T24_L0.545411.340
59_T69_V0.524121.288
2_E72_V0.523271.286
51_R80_E0.515521.267
48_L67_K0.515311.266
30_D63_D0.514731.265
2_E57_L0.489771.203
22_A37_A0.488751.201
61_A67_K0.473121.162
12_V18_I0.465031.143
44_Y48_L0.455441.119
1_Q29_L0.446611.097
57_L72_V0.441251.084
58_V68_I0.418141.027
57_L69_V0.411171.010
49_D82_P0.400690.985
7_D81_Q0.398640.979
24_L58_V0.396010.973
10_W42_Y0.394750.970
5_V71_V0.363590.893
54_D76_R0.362530.891
9_E36_R0.355320.873
9_E21_V0.348470.856
13_G19_T0.345750.850
11_Q19_T0.32520.799
38_T67_K0.322560.793
5_V56_V0.304830.749
78_G81_Q0.290690.714
61_A69_V0.287060.705
13_G16_G0.285080.700
18_I42_Y0.275010.676
5_V70_G0.2730.671
53_G81_Q0.266030.654
17_K21_V0.26230.644
52_I81_Q0.259620.638
48_L71_V0.258750.636
39_L68_I0.257260.632
11_Q36_R0.254330.625
38_T44_Y0.253880.624
19_T67_K0.252690.621
14_R40_H0.250510.616
15_T61_A0.250250.615
6_R23_V0.244620.601
73_K78_G0.244110.600
79_D82_P0.243780.599
47_E50_I0.242210.595
55_T72_V0.23920.588
5_V22_A0.235670.579
24_L37_A0.234650.577
21_V24_L0.23420.575
37_A68_I0.233910.575
22_A39_L0.231590.569
28_E32_T0.228290.561
39_L43_D0.221120.543
70_G73_K0.219040.538
14_R67_K0.217420.534
10_W59_T0.215340.529
10_W61_A0.214690.528
7_D24_L0.214580.527
49_D76_R0.213290.524
5_V51_R0.212860.523
18_I24_L0.208120.511
22_A58_V0.205720.505
49_D54_D0.205660.505
71_V75_K0.205430.505
70_G82_P0.204960.504
3_T27_V0.202360.497
28_E62_G0.201110.494
38_T59_T0.200350.492
5_V45_I0.199390.490
16_G54_D0.198760.488
60_R63_D0.197980.486
14_R19_T0.194890.479
41_N60_R0.194670.478
34_V58_V0.194660.478
38_T64_V0.1930.474
4_K53_G0.189210.465
44_Y50_I0.188290.463
29_L35_S0.187770.461
17_K42_Y0.187260.460
30_D64_V0.186920.459
73_K81_Q0.185370.455
32_T63_D0.183030.450
1_Q30_D0.182030.447
20_P64_V0.18010.443
8_I51_R0.179450.441
78_G82_P0.179040.440
56_V68_I0.178070.438
55_T74_E0.177010.435
72_V75_K0.176240.433
40_H44_Y0.175680.432
1_Q27_V0.17550.431
21_V44_Y0.174760.429
6_R79_D0.174560.429
61_A68_I0.173960.427
46_K81_Q0.172440.424
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
2owoA1100-0.068
3sgiA1100-0.066
1dgsA1100-0.062
4glxA1100-0.061
3m7aA0.695144.30.888
1zq1A0.536632.40.895
3ixzA0.914631.50.896
2d6fA0.548827.60.898
3pjyA0.817117.70.907
3ar4A0.93913.30.912

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