GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Formyl_trans_N - Formyl transferase
Pfam: PF00551 (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: 181
Sequences: 5316
Seq/Len: 29.37
HH_delta: 0.036 (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
131_E153_K1.751863.794
142_G145_A1.390423.011
94_K98_S1.339692.902
94_K141_E1.329542.880
160_D168_R1.328792.878
140_D145_A1.318842.856
4_V80_P1.205522.611
135_T148_I1.181432.559
152_K179_E1.09782.378
32_L78_L1.097032.376
114_K129_E1.076382.331
138_F149_I1.070652.319
115_Y129_E1.066512.310
160_D164_S1.00392.174
115_Y127_N0.998242.162
136_V180_A0.991792.148
122_Q162_A0.942242.041
76_E99_I0.92041.993
70_E73_E0.919151.991
73_E77_S0.876121.898
150_A176_L0.875811.897
119_S122_Q0.870211.885
4_V32_L0.850441.842
82_L181_I0.845311.831
152_K175_E0.839811.819
2_R31_V0.838311.816
105_I149_I0.792891.717
122_Q126_L0.780541.691
15_K19_E0.768851.665
91_I143_L0.768061.663
74_L77_S0.75631.638
150_A180_A0.745031.614
152_K172_A0.73151.584
22_K59_K0.729681.580
154_F172_A0.710571.539
157_E168_R0.706211.530
111_L133_G0.703851.524
41_R44_S0.691081.497
123_W126_L0.677171.467
44_S47_I0.675681.463
161_T164_S0.669311.450
125_I165_L0.668731.448
148_I151_Q0.664251.439
157_E160_D0.651991.412
57_D60_N0.640821.388
19_E23_A0.623921.351
131_E155_P0.617441.337
97_L104_I0.61431.330
135_T151_Q0.605161.311
80_P83_I0.592751.284
69_E95_E0.57891.254
83_I104_I0.569881.234
152_K176_L0.568981.232
55_V59_K0.556491.205
15_K45_R0.547121.185
69_E73_E0.545561.182
17_L181_I0.542561.175
14_L33_V0.541831.174
17_L107_I0.537861.165
4_V75_L0.536331.162
98_S141_E0.536021.161
19_E55_V0.528911.146
3_I82_L0.527961.143
72_L99_I0.52671.141
140_D147_P0.524231.135
120_P123_W0.523571.134
20_A178_V0.522761.132
18_L49_N0.519911.126
56_A67_N0.519471.125
121_I169_L0.517331.120
175_E179_E0.511671.108
123_W127_N0.509231.103
6_F83_I0.508431.101
22_K49_N0.508151.101
150_A179_E0.505191.094
2_R79_N0.501241.086
5_F14_L0.49831.079
162_A166_Y0.496331.075
121_I124_A0.491671.065
72_L76_E0.490931.063
84_V181_I0.487461.056
41_R47_I0.485841.052
164_S168_R0.483081.046
72_L100_P0.480471.041
54_Q57_D0.473981.027
2_R81_D0.473421.025
31_V80_P0.467381.012
154_F168_R0.466671.011
18_L51_I0.464311.006
41_R45_R0.464271.006
63_P66_E0.4641.005
100_P103_G0.462131.001
33_V46_A0.461631.000
150_A155_P0.460570.998
43_R53_A0.456760.989
38_D53_A0.455740.987
38_D41_R0.455560.987
107_I177_L0.45260.980
119_S123_W0.45070.976
44_S48_K0.449560.974
105_I177_L0.442520.958
10_S170_A0.441470.956
34_I71_L0.439940.953
18_L30_I0.438460.950
114_K131_E0.434890.942
166_Y170_A0.429630.931
136_V176_L0.425330.921
75_L80_P0.420180.910
17_L177_L0.419760.909
35_T43_R0.413250.895
52_P78_L0.410860.890
17_L86_A0.409950.888
156_I160_D0.405450.878
74_L78_L0.401240.869
132_T165_L0.40020.867
6_F34_I0.399360.865
170_A174_A0.395770.857
100_P104_I0.393990.853
134_V172_A0.393380.852
124_A156_I0.393310.852
72_L95_E0.391950.849
80_P99_I0.391550.848
73_E76_E0.389980.845
19_E49_N0.387850.840
31_V78_L0.383190.830
32_L80_P0.380330.824
85_V139_M0.380070.823
105_I136_V0.378630.820
16_A174_A0.375850.814
20_A175_E0.3750.812
54_Q74_L0.374880.812
130_K158_P0.373730.809
132_T156_I0.370750.803
95_E98_S0.370650.803
93_P96_F0.366950.795
157_E164_S0.366630.794
65_S95_E0.365510.792
24_R178_V0.360290.780
121_I166_Y0.358790.777
136_V150_A0.357560.774
92_L104_I0.356920.773
111_L151_Q0.356910.773
104_I139_M0.356190.771
54_Q58_E0.354450.768
22_K55_V0.35350.766
58_E90_R0.351460.761
84_V177_L0.351450.761
55_V58_E0.350570.759
172_A175_E0.349320.757
16_A19_E0.349240.756
62_Q66_E0.345560.748
11_G87_G0.345110.747
34_I88_Y0.342650.742
16_A20_A0.341870.740
130_K153_K0.337790.732
14_L18_L0.337290.731
67_N88_Y0.336720.729
53_A57_D0.336570.729
76_E79_N0.335110.726
41_R48_K0.335010.726
75_L83_I0.33460.725
106_N137_H0.334020.723
21_L30_I0.330510.716
167_E170_A0.327840.710
68_D93_P0.325150.704
112_L116_R0.324430.703
97_L139_M0.324390.703
36_N90_R0.320950.695
3_I81_D0.320760.695
33_V42_G0.320690.695
124_A129_E0.317640.688
20_A23_A0.316870.686
109_P121_I0.314360.681
2_R27_N0.312990.678
64_R68_D0.311970.676
176_L180_A0.310390.672
167_E171_E0.308720.669
69_E72_L0.307310.666
134_V176_L0.304590.660
36_N58_E0.304120.659
45_R49_N0.303750.658
35_T42_G0.303410.657
5_F17_L0.302990.656
66_E71_L0.301530.653
16_A170_A0.301510.653
16_A171_E0.299430.649
32_L74_L0.299220.648
125_I156_I0.299220.648
163_E167_E0.298980.648
171_E175_E0.298940.647
118_A121_I0.298760.647
125_I132_T0.297810.645
70_E74_L0.297380.644
35_T53_A0.295890.641
132_T169_L0.29510.639
15_K55_V0.293250.635
58_E64_R0.292520.634
18_L45_R0.291740.632
116_R145_A0.291710.632
172_A176_L0.291610.632
116_R142_G0.291180.631
4_V78_L0.289820.628
110_S120_P0.289650.627
124_A132_T0.289520.627
32_L61_F0.289160.626
95_E99_I0.288580.625
15_K49_N0.288560.625
39_K64_R0.288240.624
36_N39_K0.288080.624
67_N93_P0.288030.624
43_R55_V0.287310.622
92_L96_F0.287280.622
154_F160_D0.286660.621
53_A62_Q0.285970.619
82_L105_I0.283930.615
10_S45_R0.283090.613
105_I138_F0.281040.609
67_N71_L0.279810.606
76_E100_P0.277860.602
40_P43_R0.275030.596
75_L96_F0.273510.592
132_T154_F0.273260.592
135_T149_I0.273250.592
49_N57_D0.27240.590
140_D143_L0.271370.588
65_S69_E0.270080.585
159_D164_S0.268430.581
118_A123_W0.268280.581
120_P124_A0.268270.581
34_I83_I0.266710.578
98_S101_P0.265440.575
11_G40_P0.265140.574
66_E69_E0.265010.574
138_F147_P0.264950.574
109_P169_L0.264390.573
91_I137_H0.26390.572
15_K48_K0.263810.571
116_R120_P0.26330.570
156_I165_L0.262310.568
61_F70_E0.260990.565
149_I180_A0.259760.563
10_S41_R0.259690.562
114_K127_N0.259490.562
152_K155_P0.25850.560
61_F78_L0.257390.557
160_D165_L0.257120.557
4_V83_I0.256780.556
47_I53_A0.255580.554
38_D57_D0.255220.553
3_I21_L0.254940.552
93_P97_L0.253750.550
40_P44_S0.252470.547
110_S143_L0.250590.543
10_S50_G0.250270.542
72_L96_F0.249960.541
125_I162_A0.249240.540
83_I100_P0.247650.536
111_L153_K0.247390.536
64_R93_P0.246940.535
120_P132_T0.246380.534
86_A173_E0.245220.531
20_A24_R0.245140.531
88_Y106_N0.245070.531
6_F71_L0.243240.527
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
2ywrA11000.036
3aufA11000.038
1jkxA11000.041
3tqrA0.99451000.043
3p9xA11000.045
4ds3A11000.046
1meoA11000.049
3av3A11000.051
3da8A0.9891000.052
3tqqA0.97791000.066

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