GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_ligase_A_C - ATP dependent DNA ligase C terminal region
Pfam: PF04679 (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: 97
Sequences: 1752
Seq/Len: 18.06
HH_delta: 0.136 (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
14_D21_V0.744013.178
39_R43_E0.617882.639
42_L66_V0.590312.521
45_L69_E0.52772.254
34_E37_E0.472282.017
11_G52_F0.447621.912
76_F79_I0.441421.885
47_I67_E0.403121.722
31_S34_E0.385091.645
72_V90_F0.378381.616
71_V96_D0.377361.612
12_V23_V0.37211.589
75_K91_K0.369091.576
45_L70_L0.359951.537
41_R70_L0.35871.532
15_P18_G0.35811.529
36_R40_E0.357821.528
37_E41_R0.352251.504
28_T89_R0.331771.417
33_E36_R0.327151.397
10_L26_V0.326631.395
33_E37_E0.320631.369
6_G27_G0.320331.368
77_A87_F0.313431.339
72_V93_I0.308721.319
6_G35_L0.297881.272
90_F93_I0.29561.262
30_F35_L0.292781.250
71_V94_R0.284051.213
41_R69_E0.279121.192
12_V79_I0.277231.184
13_Y19_R0.274341.172
25_K89_R0.271461.159
9_L22_Y0.26231.120
25_K88_P0.261951.119
14_D19_R0.258141.103
43_E46_W0.253611.083
8_L42_L0.249511.066
94_R97_K0.249181.064
73_E92_R0.2391.021
7_S27_G0.238861.020
85_L88_P0.235751.007
9_L25_K0.233690.998
41_R95_E0.230940.986
77_A89_R0.230140.983
40_E44_P0.226440.967
25_K97_K0.220470.942
10_L23_V0.220.940
73_E94_R0.218550.933
82_S89_R0.218290.932
23_V79_I0.217730.930
13_Y20_L0.216710.926
48_K65_W0.215250.919
37_E40_E0.212060.906
25_K63_D0.210050.897
24_G74_V0.208610.891
61_R65_W0.208060.889
71_V97_K0.206620.882
41_R45_L0.206440.882
30_F90_F0.206420.882
24_G76_F0.203120.868
22_Y26_V0.201710.861
5_I39_R0.201620.861
4_G39_R0.200250.855
43_E48_K0.196510.839
35_L90_F0.194210.829
34_E41_R0.191180.817
4_G36_R0.191130.816
76_F85_L0.1910.816
3_G12_V0.190520.814
5_I35_L0.190180.812
12_V77_A0.189130.808
46_W64_V0.188290.804
84_S87_F0.187920.803
42_L70_L0.187120.799
6_G28_T0.186990.799
36_R68_P0.186880.798
12_V21_V0.186410.796
20_L64_V0.186140.795
2_G6_G0.185660.793
47_I50_P0.184710.789
37_E95_E0.184510.788
11_G96_D0.183240.783
32_D35_L0.180950.773
47_I65_W0.178990.764
70_L93_I0.177140.757
4_G15_P0.175940.751
30_F42_L0.175640.750
79_I85_L0.175580.750
7_S25_K0.174510.745
91_K95_E0.174070.743
38_L42_L0.172040.735
92_R95_E0.171960.734
25_K87_F0.170260.727
5_I30_F0.169270.723
33_E44_P0.168970.722
13_Y25_K0.168080.718
73_E97_K0.167650.716
78_E89_R0.167310.715
40_E43_E0.166870.713
7_S62_P0.1650.705
27_G30_F0.162130.692
9_L63_D0.16210.692
77_A88_P0.162050.692
22_Y65_W0.16190.691
11_G50_P0.161820.691
9_L80_T0.161270.689
60_E63_D0.160730.686
11_G65_W0.159630.682
48_K81_P0.159190.680
20_L49_K0.157380.672
34_E90_F0.157030.671
73_E96_D0.155220.663
71_V91_K0.155210.663
41_R44_P0.154280.659
45_L67_E0.15410.658
5_I78_E0.153910.657
26_V76_F0.153120.654
20_L68_P0.15010.641
51_P67_E0.148490.634
23_V88_P0.147810.631
8_L70_L0.147570.630
24_G85_L0.14720.629
46_W93_I0.1470.628
44_P68_P0.146640.626
4_G90_F0.145780.623
5_I44_P0.145710.622
3_G45_L0.145650.622
83_G87_F0.144460.617
9_L65_W0.143520.613
2_G14_D0.143510.613
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
2hivA0.979499.90.136
1x9nA199.90.136
1vs0A0.979499.90.141
3w1bA0.989799.90.141
3gdeA0.896999.90.147
2cfmA0.896999.90.188
3l2pA199.80.203
1a0iA0.876399.60.368
1fviA0.70199.40.468
1p16A0.70197.70.719

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