GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Citrate_ly_lig - Citrate lyase ligase C-terminal domain
Pfam: PF08218 (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: CL0039
Length: 182
Sequences: 5499
Seq/Len: 30.21
HH_delta: 0.296 (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
28_W61_T1.203033.630
42_P45_D1.07283.237
11_F50_V1.034683.122
23_A59_N1.001953.023
166_D169_E0.900972.719
160_K164_E0.843052.544
30_H61_T0.827562.497
170_I174_V0.796162.402
48_E51_K0.739532.231
63_H72_S0.726892.193
9_N41_F0.712482.150
47_Y51_K0.675242.037
157_R161_L0.632361.908
45_D48_E0.593071.789
110_K139_E0.592711.788
48_E52_E0.591311.784
21_Q24_K0.563441.700
20_E57_L0.535291.615
11_F53_G0.524971.584
21_Q141_V0.519751.568
16_R54_T0.518471.564
108_I111_R0.513251.549
157_R160_K0.509011.536
13_L16_R0.500311.510
110_K141_V0.493651.489
45_D49_L0.487141.470
111_R116_E0.486891.469
11_F19_I0.47891.445
161_L166_D0.47341.428
41_F49_L0.46681.408
23_A27_D0.459171.385
26_C112_F0.458551.384
161_L169_E0.457771.381
54_T62_V0.457591.381
20_E56_D0.444691.342
21_Q25_E0.435541.314
145_R152_P0.424121.280
26_C29_L0.416031.255
30_H63_H0.409981.237
43_F47_Y0.409051.234
25_E28_W0.407731.230
133_L138_I0.405891.225
169_E172_K0.405661.224
17_Y21_Q0.402491.214
12_T158_V0.401791.212
16_R20_E0.40121.211
157_R173_L0.398551.203
47_Y62_V0.398481.202
33_V60_V0.391691.182
57_L60_V0.390771.179
41_F45_D0.384731.161
16_R53_G0.383421.157
162_L170_I0.381561.151
17_Y20_E0.379461.145
133_L140_V0.377331.139
57_L172_K0.374661.130
151_E157_R0.372481.124
96_T100_K0.370651.118
67_D71_S0.364191.099
96_T135_P0.354321.069
32_F63_H0.350691.058
112_F116_E0.347811.049
43_F62_V0.343131.035
115_E142_E0.336791.016
54_T57_L0.332421.003
20_E24_K0.329610.995
13_L172_K0.318810.962
118_F126_N0.317650.958
95_A98_F0.317540.958
20_E23_A0.317260.957
49_L52_E0.313920.947
160_K163_K0.313730.947
156_S159_R0.310190.936
153_I158_V0.305410.922
154_S159_R0.301390.909
158_V174_V0.301030.908
96_T99_K0.300190.906
51_K54_T0.299810.905
161_L173_L0.295410.891
9_N40_L0.295370.891
153_I173_L0.294420.888
128_A132_I0.294150.888
18_L143_I0.290910.878
120_P123_R0.290240.876
25_E141_V0.290040.875
19_I50_V0.286980.866
50_V62_V0.286070.863
99_K132_I0.285140.860
22_A112_F0.284240.858
134_P138_I0.28370.856
19_I33_V0.282680.853
158_V173_L0.277760.838
114_G117_P0.271860.820
19_I53_G0.271160.818
10_P34_V0.27010.815
16_R56_D0.270080.815
13_L174_V0.268330.810
11_F16_R0.266150.803
155_A159_R0.265740.802
105_A111_R0.265370.801
126_N129_M0.263530.795
47_Y60_V0.262360.792
124_I128_A0.262340.792
125_Y128_A0.261530.789
13_L153_I0.261030.788
12_T15_H0.259380.783
9_N39_S0.258420.780
12_T37_D0.257650.777
13_L17_Y0.257330.776
36_E39_S0.255550.771
123_R126_N0.255470.771
10_P15_H0.254380.768
17_Y151_E0.252830.763
115_E145_R0.251080.758
113_V116_E0.25070.756
108_I114_G0.248910.751
162_L174_V0.247640.747
50_V60_V0.246890.745
38_R163_K0.24240.731
116_E155_A0.239580.723
169_E173_L0.239290.722
96_T124_I0.238750.720
53_G57_L0.237650.717
119_S125_Y0.23750.717
158_V170_I0.233610.705
120_P124_I0.231750.699
99_K137_G0.230120.694
19_I60_V0.229320.692
99_K128_A0.226760.684
113_V117_P0.224670.678
21_Q139_E0.224460.677
16_R172_K0.223980.676
50_V54_T0.222810.672
119_S122_T0.221160.667
19_I31_V0.220460.665
31_V60_V0.217920.658
120_P125_Y0.217290.656
116_E145_R0.216160.652
140_V143_I0.214560.647
44_A48_E0.213770.645
95_A99_K0.211470.638
119_S123_R0.20870.630
10_P54_T0.205060.619
133_L145_R0.204140.616
105_A116_E0.202750.612
154_S157_R0.200420.605
9_N34_V0.200360.605
9_N14_G0.199850.603
56_D59_N0.199470.602
151_E172_K0.199470.602
127_E142_E0.199120.601
107_G116_E0.198370.599
159_R162_L0.198270.598
96_T132_I0.197860.597
113_V126_N0.19720.595
67_D72_S0.19680.594
133_L137_G0.19620.592
11_F49_L0.193160.583
23_A57_L0.192660.581
33_V50_V0.19160.578
51_K61_T0.190850.576
132_I135_P0.19070.575
24_K134_P0.190330.574
107_G114_G0.188920.570
19_I54_T0.187890.567
105_A110_K0.186660.563
95_A124_I0.185880.561
69_I72_S0.185330.559
107_G111_R0.185330.559
119_S132_I0.184640.557
123_R127_E0.184410.556
72_S109_T0.182410.550
19_I29_L0.181710.548
63_H138_I0.180850.546
32_F61_T0.179170.541
22_A26_C0.179050.540
105_A135_P0.178910.540
47_Y50_V0.178840.540
98_F116_E0.178710.539
118_F128_A0.178690.539
23_A58_P0.178340.538
111_R114_G0.177730.536
70_I98_F0.177170.535
21_Q144_P0.176860.534
122_T126_N0.176770.533
111_R119_S0.176330.532
52_E56_D0.176070.531
139_E142_E0.175860.531
47_Y64_P0.175270.529
18_L21_Q0.175090.528
105_A109_T0.174860.528
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
1yumA0.917699.90.296
1kqnA0.917699.90.312
3h05A0.763799.90.316
1nupA0.923199.90.318
1k4mA0.923199.90.319
2h29A0.862699.90.337
2qtrA0.862699.90.363
1kamA0.862699.90.364
3f3mA0.807799.90.383
3nd5A0.807799.90.389

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