GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TP_methylase - Tetrapyrrole (CorrinPorphyrin) Methylases
Pfam: PF00590 (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: 210
Sequences: 7984
Seq/Len: 38.02
HH_delta: 0.109 (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
13_D21_E1.839694.066
20_L24_K1.393673.080
124_R199_E1.381713.054
26_A80_V1.296952.867
192_E200_R1.196312.644
184_P207_E1.160212.564
3_Y22_A1.130592.499
191_G194_L1.129142.496
204_G208_E1.083832.396
21_E25_N1.060062.343
5_V80_V1.028062.272
117_S164_L0.995192.200
27_D77_K0.986732.181
27_D78_D0.982142.171
1_K110_E0.98172.170
36_L82_L0.971272.147
1_K108_E0.963912.131
17_L20_L0.957452.116
193_R198_D0.954752.110
72_A77_K0.952642.106
121_A194_L0.913062.018
74_K105_R0.900271.990
188_V209_L0.894481.977
205_T208_E0.872761.929
5_V19_A0.869551.922
3_Y78_D0.83261.840
204_G209_L0.828011.830
72_A75_E0.799351.767
6_G112_I0.788341.742
11_D18_R0.784361.734
3_Y110_E0.762411.685
13_D18_R0.739771.635
191_G201_I0.733781.622
99_A105_R0.731.614
99_A102_A0.706471.561
28_V72_A0.7061.560
25_N78_D0.700311.548
18_R110_E0.690281.526
22_A112_I0.688331.521
70_I105_R0.684721.513
21_E24_K0.678681.500
150_L153_N0.673241.488
1_K78_D0.672691.487
125_L189_A0.6641.468
2_L100_L0.661921.463
176_L179_E0.661371.462
121_A191_G0.659671.458
175_E179_E0.647311.431
174_A178_L0.644891.425
70_I74_K0.64461.425
71_E75_E0.630941.395
65_E71_E0.627141.386
189_A203_R0.617941.366
29_V43_L0.600831.328
185_D207_E0.595941.317
62_E65_E0.594841.315
22_A80_V0.593051.311
116_S164_L0.583011.289
6_G87_P0.582791.288
124_R201_I0.579811.282
178_L184_P0.575561.272
174_A206_L0.57361.268
73_A107_I0.572461.265
116_S119_Q0.568661.257
193_R196_Y0.564451.248
88_L93_G0.559931.238
15_L20_L0.55751.232
4_I93_G0.554181.225
2_L73_A0.553961.224
118_F164_L0.544651.204
172_E175_E0.543761.202
3_Y112_I0.542941.200
178_L206_L0.534681.182
15_L19_A0.533081.178
65_E99_A0.520911.151
19_A112_I0.515961.140
66_I71_E0.50631.119
3_Y26_A0.500761.107
37_E41_D0.49751.100
74_K107_I0.497331.099
169_R172_E0.494851.094
102_A105_R0.494331.093
122_A129_L0.491791.087
30_I79_V0.491761.087
20_L42_L0.488491.080
30_I67_I0.483631.069
111_I123_A0.48241.066
6_G86_D0.482231.066
176_L180_R0.481741.065
189_A201_I0.481271.064
86_D123_A0.471051.041
14_L18_R0.462921.023
70_I99_A0.460041.017
16_T115_I0.458721.014
147_R176_L0.45831.013
33_E52_D0.457361.011
81_V96_L0.45721.011
147_R172_E0.457131.010
171_A175_E0.454661.005
28_V77_K0.453931.003
9_P14_L0.452591.000
88_L111_I0.449640.994
71_E74_K0.445310.984
172_E176_L0.443910.981
183_P186_T0.443220.980
28_V79_V0.44270.978
188_V206_L0.437010.966
152_E179_E0.436720.965
36_L40_R0.435410.962
111_I201_I0.434650.961
177_L206_L0.434040.959
17_L21_E0.431160.953
66_I72_A0.430340.951
97_V109_V0.420870.930
87_P91_S0.420310.929
100_L107_I0.419310.927
120_A195_G0.417920.924
22_A25_N0.417760.923
64_A99_A0.417220.922
26_A78_D0.412470.912
60_Y95_Y0.411570.910
13_D17_L0.408330.903
131_D135_I0.407840.901
3_Y80_V0.407770.901
174_A209_L0.406130.898
152_E180_R0.406080.898
97_V101_R0.40490.895
63_I66_I0.404580.894
30_I72_A0.403930.893
178_L207_E0.402040.889
83_V91_S0.40190.888
18_R112_I0.401060.886
94_S98_R0.400150.884
187_P203_R0.399240.882
23_L29_V0.39860.881
15_L39_V0.396250.876
170_L209_L0.395040.873
18_R21_E0.392730.868
153_N157_N0.389730.861
40_R43_L0.389440.861
170_L174_A0.386230.854
30_I66_I0.385520.852
18_R22_A0.384410.850
11_D14_L0.380410.841
101_R203_R0.378210.836
153_N156_A0.374730.828
139_G159_D0.373310.825
83_V92_T0.372860.824
152_E155_L0.368350.814
70_I100_L0.363770.804
135_I159_D0.362250.801
120_A194_L0.361410.799
187_P205_T0.360390.797
94_S130_T0.360390.797
73_A79_V0.357740.791
163_I166_D0.355830.786
27_D44_P0.34950.772
185_D205_T0.349330.772
127_I189_A0.348150.770
93_G97_V0.347860.769
124_R195_G0.347580.768
89_F129_L0.347550.768
6_G120_A0.346370.766
152_E176_L0.345290.763
89_F138_H0.342440.757
138_H162_V0.34180.755
155_L180_R0.341010.754
5_V22_A0.340520.753
22_A110_E0.340150.752
16_T19_A0.337040.745
190_V204_G0.336230.743
64_A67_I0.336050.743
133_G159_D0.331720.733
11_D195_G0.331290.732
61_D99_A0.330710.731
5_V112_I0.330620.731
202_F209_L0.330090.730
148_E176_L0.328170.725
139_G150_L0.328070.725
59_S62_E0.326840.722
174_A188_V0.326830.722
101_R109_V0.326810.722
56_L59_S0.325740.720
152_E156_A0.323310.715
12_P38_I0.322390.713
101_R126_G0.321520.711
94_S131_D0.319990.707
61_D64_A0.319420.706
35_A38_I0.317550.702
19_A80_V0.316930.701
22_A26_A0.315660.698
19_A39_V0.314680.696
137_L159_D0.314080.694
87_P111_I0.311720.689
15_L43_L0.311540.689
148_E152_E0.310230.686
150_L156_A0.309410.684
74_K77_K0.309390.684
165_T169_R0.308330.681
31_G36_L0.308050.681
64_A70_I0.306850.678
138_H150_L0.306710.678
17_L24_K0.306160.677
60_Y64_A0.305850.676
118_F162_V0.29840.660
39_V42_L0.2980.659
26_A29_V0.296460.655
37_E40_R0.294940.652
36_L43_L0.293750.649
154_L161_L0.290690.643
4_I97_V0.289680.640
38_I41_D0.288660.638
135_I150_L0.28770.636
93_G111_I0.287350.635
124_R194_L0.286540.633
94_S128_P0.285670.631
24_K44_P0.28560.631
139_G158_G0.285010.630
22_A78_D0.281650.623
190_V209_L0.28090.621
125_L201_I0.280430.620
88_L97_V0.280430.620
62_E66_I0.280120.619
61_D65_E0.279150.617
17_L42_L0.278380.615
192_E202_F0.27580.610
2_L81_V0.275480.609
141_R147_R0.275190.608
33_E53_R0.274220.606
6_G115_I0.274150.606
23_L80_V0.273520.605
53_R168_R0.272110.601
52_D55_S0.271890.601
98_R102_A0.270320.597
133_G157_N0.269740.596
39_V43_L0.267880.592
29_V80_V0.266550.589
70_I107_I0.265060.586
53_R56_L0.263350.582
32_P92_T0.263070.581
146_E149_K0.262190.580
10_G196_Y0.261470.578
62_E71_E0.261230.577
170_L190_V0.260640.576
194_L201_I0.260420.576
106_G109_V0.259320.573
88_L94_S0.258970.572
141_R146_E0.257670.570
24_K42_L0.256240.566
92_T165_T0.255190.564
138_H164_L0.254340.562
167_P192_E0.25430.562
154_L157_N0.25280.559
20_L43_L0.251880.557
147_R150_L0.248520.549
7_L82_L0.248180.549
10_G14_L0.247840.548
36_L44_P0.247660.547
12_P41_D0.246790.545
58_E66_I0.246370.545
122_A194_L0.245520.543
32_P83_V0.244470.540
151_L179_E0.244220.540
53_R63_I0.242490.536
6_G116_S0.241550.534
111_I124_R0.240110.531
58_E62_E0.238160.526
88_L123_A0.238020.526
6_G124_R0.236980.524
137_L154_L0.235960.522
54_E183_P0.23570.521
9_P195_G0.235180.520
120_A124_R0.235150.520
86_D111_I0.233020.515
30_I63_I0.232020.513
100_L109_V0.231410.511
16_T114_G0.230640.510
23_L43_L0.229630.508
1_K73_A0.229190.507
163_I173_I0.228740.506
119_Q122_A0.228460.505
112_I120_A0.228340.505
14_L195_G0.22810.504
131_D134_F0.227780.503
119_Q129_L0.227670.503
155_L161_L0.227290.502
117_S122_A0.2260.500
136_S139_G0.225470.498
151_L176_L0.224970.497
111_I126_G0.224440.496
90_F134_F0.224320.496
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
1pjqA0.96191000.109
1s4dA0.97621000.111
2yboA0.97141000.116
3ndcA0.95241000.117
4e16A0.95241000.121
1cbfA0.95241000.137
3kwpA0.94761000.139
1ve2A0.92381000.156
2e0nA0.93331000.157
1va0A0.93331000.157

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