GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HMG_CoA_synt_N - Hydroxymethylglutaryl-coenzyme A synthase N terminal
Pfam: PF01154 (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: CL0046
Length: 174
Sequences: 4849
Seq/Len: 27.87
HH_delta: 0.078 (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
58_A99_L1.522083.963
36_T42_E0.981782.556
128_V132_A0.956312.490
77_R141_A0.92512.409
61_A142_L0.919982.395
58_A62_K0.84442.198
127_A141_A0.835122.174
76_G140_K0.831422.165
20_D23_E0.828972.158
59_N62_K0.826222.151
58_A96_V0.804982.096
96_V144_V0.801172.086
55_T99_L0.790842.059
57_A96_V0.782992.039
18_Y43_K0.764491.990
64_L168_L0.760521.980
123_A143_V0.75411.963
74_D140_K0.734321.912
76_G139_R0.714081.859
124_L169_I0.702461.829
13_Y56_M0.697241.815
71_D74_D0.676111.760
65_L72_P0.656291.709
22_E25_A0.643851.676
70_I140_K0.64291.674
9_A67_R0.629791.640
53_I146_S0.627971.635
81_G123_A0.61831.610
11_E64_L0.603211.571
18_Y45_A0.596251.552
64_L68_Y0.587341.529
61_A100_L0.587171.529
62_K66_D0.582861.518
63_P67_R0.580671.512
77_R130_W0.568851.481
23_E26_E0.567881.479
79_I111_V0.559451.457
11_E63_P0.55511.445
111_V126_N0.553621.441
59_N63_P0.550321.433
48_P51_E0.539871.406
74_D139_R0.537071.398
28_R157_E0.532761.387
79_I127_A0.529131.378
131_V169_I0.529021.377
52_D55_T0.527151.372
20_D43_K0.523051.362
60_A166_A0.510051.328
33_G37_I0.508161.323
129_N133_S0.505191.315
63_P66_D0.500661.304
159_T162_A0.491641.280
70_I74_D0.490231.276
129_N135_P0.490091.276
131_V134_S0.485851.265
32_P36_T0.482791.257
57_A146_S0.477081.242
61_A144_V0.459261.196
80_V92_I0.458431.194
16_R51_E0.457361.191
47_P148_I0.452011.177
9_A68_Y0.451521.176
62_K72_P0.449711.171
118_Y121_T0.443691.155
83_E116_A0.441711.150
65_L75_I0.441161.149
127_A143_V0.438921.143
75_I102_L0.437911.140
41_Q44_M0.429471.118
56_M148_I0.429221.118
102_L108_C0.427371.113
131_V141_A0.423651.103
120_G167_M0.423481.103
58_A100_L0.421581.098
95_Y98_Q0.406851.059
19_V46_V0.404571.053
125_Q129_N0.40191.046
13_Y59_N0.398051.036
9_A64_L0.39721.034
78_L97_H0.396881.033
77_R109_R0.395811.031
79_I141_A0.39311.023
126_N130_W0.39141.019
8_D140_K0.390651.017
146_S164_A0.390451.017
22_E26_E0.39021.016
38_G41_Q0.388621.012
72_P102_L0.387111.008
70_I168_L0.38030.990
65_L70_I0.380270.990
17_Y48_P0.374270.974
113_M126_N0.3740.974
92_I95_Y0.36960.962
83_E114_K0.368490.959
87_D95_Y0.368360.959
51_E55_T0.367570.957
78_L102_L0.364560.949
12_F63_P0.36260.944
127_A169_I0.361610.941
95_Y99_L0.361050.940
54_V92_I0.360120.938
80_V146_S0.359820.937
81_G145_A0.358680.934
75_I140_K0.35640.928
143_V169_I0.355170.925
162_A166_A0.352560.918
157_E160_Q0.352420.918
19_V27_A0.352160.917
54_V86_V0.348330.907
83_E89_S0.343010.893
75_I142_L0.34210.891
75_I168_L0.337210.878
87_D90_K0.336610.876
93_S110_G0.334190.870
162_A165_V0.331980.864
17_Y23_E0.330930.862
55_T59_N0.328740.856
54_V99_L0.326290.850
62_K99_L0.325010.846
11_E60_A0.322080.839
51_E59_N0.321540.837
56_M164_A0.319810.833
60_A164_A0.318870.830
125_Q135_P0.318280.829
160_Q166_A0.318220.829
80_V96_V0.316070.823
62_K100_L0.315940.823
61_A65_L0.313870.817
126_N129_N0.31340.816
79_I113_M0.310190.808
109_R141_A0.296590.772
61_A64_L0.293120.763
83_E149_A0.292250.761
24_L28_R0.290040.755
160_Q165_V0.288120.750
79_I126_N0.286770.747
44_M47_P0.285880.744
89_S114_K0.28570.744
83_E147_D0.283640.738
19_V24_L0.276380.720
151_Y154_G0.275670.718
53_I92_I0.2750.716
16_R59_N0.274950.716
25_A33_G0.274330.714
150_R153_L0.273430.712
85_G88_K0.273330.712
157_E166_A0.27280.710
80_V144_V0.272650.710
16_R48_P0.272390.709
13_Y51_E0.271860.708
120_G165_V0.271730.707
153_L156_A0.270160.703
157_E162_A0.26870.700
82_T85_G0.267840.697
65_L71_D0.267770.697
142_L168_L0.266580.694
57_A144_V0.265960.692
6_G121_T0.264140.688
9_A168_L0.263710.687
90_K147_D0.26310.685
115_Q122_A0.262640.684
94_T110_G0.26260.684
97_H110_G0.261960.682
57_A80_V0.26150.681
157_E165_V0.26120.680
78_L108_C0.260660.679
21_Q44_M0.258030.672
54_V95_Y0.257730.671
40_G44_M0.257460.670
56_M146_S0.253130.659
6_G128_V0.252780.658
51_E56_M0.252580.658
17_Y46_V0.252550.658
7_I10_I0.25250.657
118_Y122_A0.252150.656
57_A60_A0.251290.654
122_A126_N0.249220.649
93_S112_E0.24830.646
34_K38_G0.246550.642
64_L142_L0.245340.639
129_N132_A0.243380.634
54_V96_V0.243290.633
91_S94_T0.243140.633
159_T165_V0.239830.624
86_V89_S0.23920.623
35_Y38_G0.239080.622
151_Y157_E0.238850.622
100_L142_L0.238120.620
159_T166_A0.237380.618
65_L68_Y0.23680.617
130_W135_P0.236780.616
86_V90_K0.231190.602
38_G44_M0.22990.599
115_Q119_G0.229820.598
35_Y153_L0.229370.597
61_A78_L0.228940.596
109_R122_A0.228490.595
158_P165_V0.227890.593
32_P42_E0.227090.591
132_A135_P0.226750.590
68_Y71_D0.222220.579
10_I167_M0.221890.578
70_I75_I0.220680.575
116_A159_T0.215790.562
39_L44_M0.215550.561
18_Y23_E0.214620.559
24_L46_V0.212750.554
68_Y72_P0.211710.551
83_E118_Y0.210690.549
150_R154_G0.208840.544
85_G92_I0.207220.540
57_A61_A0.206720.538
66_D69_N0.204110.531
23_E27_A0.201730.525
54_V58_A0.20150.525
94_T98_Q0.201480.525
82_T92_I0.199360.519
134_S139_R0.199150.519
16_R50_D0.198910.518
58_A69_N0.198470.517
96_V100_L0.198210.516
65_L102_L0.197520.514
91_S114_K0.197120.513
27_A152_D0.195740.510
22_E42_E0.195230.508
84_S116_A0.195110.508
17_Y49_P0.194870.507
47_P162_A0.194380.506
109_R125_Q0.191960.500
80_V93_S0.19190.500
61_A96_V0.191090.498
39_L45_A0.1910.497
149_A153_L0.189760.494
8_D70_I0.189610.494
76_G141_A0.189270.493
121_T148_I0.189120.492
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
2v4wA11000.078
2wyaA11000.083
2p8uA11000.108
2f82A0.99431000.124
3sqzA0.96551000.13
3gwaA0.9771000.136
4efiA0.9771000.141
3il3A0.97131000.141
3v4nA0.96551000.145
3il6A0.96551000.149

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