GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_ligase_A_M - ATP dependent DNA ligase domain
Pfam: PF01068 (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: CL0078
Length: 202
Sequences: 4642
Seq/Len: 22.98
HH_delta: 0.089 (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
23_V182_L0.758662.618
131_L135_E0.750442.589
42_R50_D0.730862.522
43_L55_F0.707312.440
161_S164_E0.692612.390
171_E175_Q0.684862.363
157_Y171_E0.67772.338
20_P185_P0.665452.296
166_E170_E0.661842.283
34_I43_L0.613742.118
37_D72_D0.572661.976
132_P135_E0.562441.941
24_E183_K0.555311.916
139_L143_L0.552341.906
135_E138_E0.539041.860
134_E185_P0.527021.818
34_I62_L0.525091.812
77_G115_F0.522191.802
160_N164_E0.520451.796
120_I139_L0.506241.747
31_R76_D0.495471.709
22_Y133_Y0.491771.697
139_L142_E0.486381.678
126_K131_L0.480811.659
25_P172_A0.451161.557
119_D136_R0.449841.552
165_L182_L0.449691.552
27_Y80_V0.440121.518
37_D41_V0.439621.517
32_C43_L0.431961.490
138_E142_E0.431771.490
32_C115_F0.427331.474
134_E158_V0.424551.465
159_V164_E0.422461.458
164_E167_E0.419111.446
163_E167_E0.413561.427
91_P112_P0.407191.405
20_P158_V0.404911.397
80_V116_V0.392461.354
167_E171_E0.391541.351
138_E141_E0.380751.314
170_E173_I0.379951.311
158_V185_P0.379551.310
35_H74_V0.378631.306
32_C51_I0.37681.300
162_K166_E0.373671.289
126_K139_L0.373511.289
75_L117_V0.371641.282
91_P94_E0.367661.268
32_C79_L0.367221.267
22_Y134_E0.365671.262
23_V168_L0.363491.254
22_Y185_P0.361911.249
89_P176_G0.361671.248
99_L104_K0.361481.247
88_S91_P0.360841.245
81_V95_L0.356771.231
60_E114_Q0.354751.224
20_P160_N0.353571.220
123_L139_L0.35171.213
172_A177_F0.344641.189
33_Q74_V0.336471.161
27_Y116_V0.335761.158
35_H42_R0.335731.158
128_L139_L0.333421.150
34_I115_F0.333181.150
90_L94_E0.331551.144
114_Q146_P0.328331.133
97_G101_R0.325151.122
40_G55_F0.323251.115
24_E137_R0.322091.111
134_E138_E0.321931.111
168_L180_L0.321841.110
32_C55_F0.321481.109
31_R119_D0.31931.102
132_P185_P0.317431.095
97_G100_N0.313881.083
23_V165_L0.311591.075
94_E97_G0.308711.065
93_Q97_G0.308091.063
25_P177_F0.304571.051
98_R102_R0.303131.046
94_E98_R0.303061.046
46_R78_E0.301861.041
35_H44_F0.299871.035
35_H72_D0.299141.032
136_R187_S0.293091.011
23_V159_V0.288940.997
170_E174_D0.287310.991
157_Y168_L0.286650.989
186_D189_Y0.286480.988
134_E186_D0.285760.986
33_Q121_L0.282890.976
30_V51_I0.282020.973
163_E166_E0.281950.973
159_V165_L0.275910.952
22_Y137_R0.275350.950
133_Y136_R0.273130.942
56_P63_R0.272990.942
45_S51_I0.271750.938
36_K39_G0.27140.936
171_E174_D0.268220.925
98_R112_P0.263330.909
72_D125_G0.262790.907
120_I140_L0.26190.904
26_K29_G0.261780.903
73_F143_L0.260970.900
88_S114_Q0.257850.890
26_K78_E0.257630.889
98_R110_S0.255510.882
167_E170_E0.254920.880
30_V45_S0.254150.877
81_V91_P0.249370.860
33_Q44_F0.249160.860
52_T59_A0.248340.857
128_L131_L0.247620.854
20_P186_D0.245430.847
25_P168_L0.244410.843
53_S107_P0.244070.842
55_F79_L0.24360.840
133_Y137_R0.243140.839
73_F123_L0.243020.838
120_I136_R0.242780.838
172_A180_L0.242360.836
59_A63_R0.239960.828
81_V111_E0.236010.814
127_D130_D0.235620.813
26_K46_R0.235220.812
55_F58_L0.233550.806
96_S99_L0.233230.805
80_V114_Q0.227120.784
57_E111_E0.225210.777
58_L79_L0.224260.774
98_R101_R0.222930.769
43_L56_P0.222710.768
21_W165_L0.221790.765
26_K178_E0.221570.764
168_L171_E0.221090.763
92_F96_S0.214650.741
50_D53_S0.214490.740
38_G72_D0.214090.739
57_E112_P0.212610.734
30_V49_K0.211350.729
30_V99_L0.210890.728
36_K41_V0.210670.727
81_V178_E0.209340.722
31_R118_F0.209010.721
22_Y158_V0.208890.721
136_R140_L0.208740.720
44_F47_N0.208610.720
36_K73_F0.208270.719
144_L147_P0.20780.717
131_L139_L0.207750.717
92_F95_L0.207460.716
32_C45_S0.206740.713
165_L180_L0.20660.713
56_P98_R0.204310.705
34_I40_G0.203420.702
20_P184_D0.20280.700
28_D78_E0.202570.699
29_G78_E0.200820.693
118_F121_L0.200280.691
28_D46_R0.200230.691
93_Q100_N0.199890.690
114_Q149_P0.196650.678
24_E133_Y0.195490.674
43_L79_L0.194340.671
81_V97_G0.193920.669
99_L102_R0.193720.668
60_E63_R0.19360.668
58_L61_A0.192540.664
103_S107_P0.191940.662
138_E151_I0.190940.659
178_E183_K0.189980.655
162_K165_L0.189740.655
91_P114_Q0.189670.654
131_L186_D0.189490.654
137_R141_E0.188940.652
91_P95_L0.188670.651
57_E98_R0.18860.651
128_L136_R0.188210.649
123_L128_L0.187610.647
138_E167_E0.186680.644
81_V113_L0.186120.642
94_E112_P0.183020.631
33_Q182_L0.182810.631
150_R175_Q0.182750.631
47_N96_S0.182420.629
96_S100_N0.18210.628
28_D92_F0.181970.628
21_W182_L0.181350.626
168_L172_A0.181340.626
115_F119_D0.179550.619
122_Y125_G0.178980.618
103_S109_Q0.178750.617
41_V59_A0.178440.616
106_I109_Q0.178410.616
101_R104_K0.1780.614
133_Y187_S0.177570.613
55_F113_L0.177280.612
48_G51_I0.177110.611
130_D139_L0.176910.610
29_G46_R0.176840.610
136_R189_Y0.175170.604
34_I61_A0.17470.603
103_S106_I0.173820.600
101_R181_V0.173240.598
21_W184_D0.173050.597
123_L136_R0.172660.596
22_Y187_S0.172110.594
51_I54_Q0.171960.593
135_E139_L0.170720.589
79_L95_L0.170220.587
123_L126_K0.169070.583
148_P151_I0.168050.580
72_D124_D0.166290.574
141_E147_P0.165290.570
68_P142_E0.164590.568
27_Y133_Y0.164060.566
120_I123_L0.163160.563
137_R151_I0.162450.560
169_F182_L0.161790.558
134_E142_E0.161460.557
62_L65_L0.160750.555
122_Y127_D0.160620.554
132_P186_D0.160570.554
51_I79_L0.160460.554
24_E27_Y0.159120.549
130_D188_P0.159110.549
43_L51_I0.15840.547
37_D42_R0.157710.544
73_F140_L0.157450.543
26_K179_G0.157070.542
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
1x9nA0.9951000.089
2hivA0.98511000.09
2cfmA0.98021000.101
3gdeA0.95541000.11
3w1bA0.97521000.124
3l2pA0.94551000.127
1vs0A0.88121000.204
1a0iA0.94061000.212
1fviA0.85151000.246
1p16A0.856499.90.364

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