GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Formyl_trans_C - Formyl transferase C-terminal domain
Pfam: PF02911 (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: 100
Sequences: 2694
Seq/Len: 26.94
HH_delta: 0.017 (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
91_S94_D1.3033.073
9_I18_I1.242272.930
13_Q17_E1.21892.875
19_Y45_A1.013862.391
13_Q21_L0.988132.330
22_V45_A0.940312.218
46_E78_R0.934452.204
81_E89_P0.933562.202
44_K81_E0.918132.165
46_E80_R0.897662.117
93_K97_N0.861092.031
14_S17_E0.860842.030
94_D97_N0.851692.009
44_K80_R0.844531.992
43_L89_P0.833231.965
9_I42_I0.823051.941
38_K85_E0.813291.918
69_L78_R0.777761.834
11_W33_T0.762351.798
18_I77_L0.730691.723
69_L76_A0.69371.636
45_A77_L0.676251.595
10_D13_Q0.652191.538
16_E20_N0.637941.505
33_T42_I0.614191.449
8_R34_T0.601491.419
19_Y47_P0.600181.416
8_R32_F0.584321.378
81_E91_S0.579381.366
79_I82_L0.573981.354
82_L95_F0.573391.352
67_G78_R0.543851.283
22_V31_A0.513631.211
84_P90_M0.50611.194
19_Y23_R0.480641.134
20_N23_R0.475271.121
68_L79_I0.473311.116
15_A72_C0.472771.115
68_L92_A0.468471.105
61_V76_A0.465971.099
15_A47_P0.465471.098
15_A74_D0.4651.097
7_G28_Y0.464391.095
42_I79_I0.45651.077
26_N43_L0.448341.057
70_V79_I0.442391.043
1_K6_D0.441631.042
84_P95_F0.441531.041
14_S74_D0.432841.021
7_G25_L0.4291.012
33_T40_I0.428411.010
1_K7_G0.425991.005
87_K90_M0.424351.001
17_E20_N0.423410.999
39_R85_E0.422580.997
83_Q89_P0.419170.989
21_L25_L0.406210.958
55_N59_T0.400540.945
59_T71_A0.39960.942
40_I82_L0.398940.941
3_T6_D0.398920.941
34_T37_G0.394450.930
17_E21_L0.392390.925
18_I72_C0.391830.924
54_S59_T0.386920.913
5_E8_R0.385230.909
48_L78_R0.379650.895
84_P87_K0.379490.895
7_G32_F0.377570.890
95_F99_Y0.364540.860
66_N78_R0.362680.855
19_Y77_L0.359660.848
38_K84_P0.357040.842
64_D67_G0.347010.818
71_A76_A0.344910.813
40_I84_P0.344860.813
92_A96_L0.33670.794
43_L83_Q0.335930.792
41_K83_Q0.335750.792
7_G30_G0.335340.791
16_E19_Y0.329960.778
32_F39_R0.329570.777
48_L69_L0.323850.764
63_I66_N0.319460.753
68_L78_R0.316670.747
72_C76_A0.310730.733
62_Y69_L0.309940.731
64_D69_L0.305050.719
60_I70_V0.303730.716
88_K94_D0.299140.706
61_V71_A0.298080.703
20_N24_A0.297510.702
7_G26_N0.291660.688
2_I28_Y0.287110.677
2_I6_D0.286230.675
12_N73_G0.285230.673
42_I45_A0.28060.662
51_D74_D0.272130.642
30_G43_L0.269870.636
34_T39_R0.267910.632
90_M94_D0.264340.623
15_A73_G0.260770.615
4_K7_G0.26060.615
6_D21_L0.258230.609
19_Y22_V0.257780.608
11_W70_V0.254790.601
68_L82_L0.253470.598
84_P99_Y0.25280.596
26_N30_G0.252230.595
30_G41_K0.251690.594
26_N44_K0.25120.592
41_K98_G0.249220.588
95_F98_G0.247380.583
47_P75_G0.24710.583
57_P72_C0.246590.582
6_D30_G0.243720.575
34_T74_D0.239850.566
57_P71_A0.238410.562
43_L80_R0.237090.559
15_A75_G0.235780.556
87_K98_G0.233470.551
21_L31_A0.230050.543
4_K28_Y0.229840.542
49_E53_S0.228220.538
26_N89_P0.225670.532
82_L92_A0.223610.527
57_P73_G0.22020.519
63_I68_L0.21920.517
34_T85_E0.219090.517
64_D78_R0.214340.506
5_E34_T0.212950.502
49_E75_G0.209810.495
25_L31_A0.205590.485
16_E74_D0.205180.484
65_K93_K0.204980.483
7_G29_P0.204940.483
18_I21_L0.204450.482
50_D54_S0.204260.482
94_D98_G0.203630.480
90_M98_G0.203560.480
7_G20_N0.197610.466
9_I21_L0.195020.460
67_G92_A0.193440.456
48_L76_A0.192890.455
14_S73_G0.192490.454
81_E88_K0.192270.453
7_G21_L0.191350.451
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
3q0iA0.9999.90.017
3tqqA0.9999.90.019
3rfoA0.9999.90.025
1fmtA0.9999.90.034
4iqfA0.9999.90.053
2blnA0.9799.80.092
1z7eA0.9799.80.122
2bw0A0.9499.80.132
1zghA0.6598.90.518
3n75A0.8320.90.89

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