GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MIF - Macrophage migration inhibitory factor (MIF)
Pfam: PF01187 (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: CL0082
Length: 114
Sequences: 1534
Seq/Len: 13.46
HH_delta: -0.04 (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
6_K42_E0.393262.282
68_D71_Q0.386962.246
28_E78_A0.357022.072
80_T94_I0.353992.054
5_I22_L0.35162.041
21_E86_E0.340081.974
81_E85_E0.319661.855
76_S98_F0.31751.843
24_K28_E0.316171.835
76_S107_G0.309261.795
77_A81_E0.303821.763
69_P104_W0.275161.597
41_V46_R0.269181.562
6_K40_T0.265831.543
24_K34_E0.257631.495
69_P73_K0.254831.479
9_V43_D0.250051.451
3_L22_L0.249531.448
84_E91_P0.2391.387
72_N105_N0.238661.385
72_N100_D0.235411.366
101_L106_V0.232221.348
21_E82_F0.230371.337
62_K99_H0.229751.333
74_K78_A0.229331.331
23_S27_A0.228211.324
4_E60_E0.224151.301
47_M56_A0.221491.285
101_L105_N0.220481.280
20_K24_K0.220231.278
3_L61_L0.219581.274
15_P46_R0.217621.263
30_L63_S0.217261.261
33_P36_Y0.217121.260
78_A81_E0.2161.254
19_L36_Y0.214861.247
23_S39_V0.213971.242
24_K82_F0.213491.239
107_G110_G0.209771.217
66_G100_D0.2091.213
84_E88_G0.196081.138
19_L48_S0.192831.119
23_S37_I0.192311.116
21_E85_E0.188661.095
60_E99_H0.188171.092
38_M95_Y0.186111.080
100_D105_N0.184811.073
74_K77_A0.182511.059
63_S72_N0.179921.044
70_E73_K0.177511.030
25_L82_F0.177321.029
92_D110_G0.175921.021
13_K88_G0.174941.015
70_E74_K0.174911.015
97_N101_L0.174571.013
19_L29_L0.171170.993
3_L59_V0.166570.967
4_E40_T0.166350.965
25_L78_A0.163760.950
68_D72_N0.16370.950
75_Y79_I0.163410.948
16_D53_D0.161660.938
23_S34_E0.159780.927
67_L75_Y0.159520.926
52_S93_R0.158870.922
62_K97_N0.158760.921
33_P93_R0.157430.914
58_F97_N0.15620.907
64_I103_A0.155760.904
3_L26_V0.155610.903
78_A82_F0.152340.884
20_K81_E0.152180.883
40_T45_Q0.152040.882
53_D93_R0.151610.880
73_K77_A0.151380.879
65_G103_A0.151290.878
15_P41_V0.151180.877
21_E84_E0.150980.876
37_I63_S0.150560.874
90_P110_G0.149580.868
10_S13_K0.14940.867
7_T41_V0.149240.866
23_S51_G0.148220.860
60_E97_N0.147730.857
19_L23_S0.147550.856
54_D93_R0.145940.847
17_D86_E0.145640.845
63_S66_G0.145560.845
32_K95_Y0.145320.843
26_V37_I0.145020.842
18_F82_F0.1450.842
82_F86_E0.144460.838
43_D46_R0.144240.837
81_E91_P0.142860.829
10_S44_G0.142520.827
30_L80_T0.142220.825
23_S26_V0.142030.824
27_A34_E0.140870.818
84_E87_L0.14070.817
36_Y95_Y0.140570.816
24_K74_K0.14050.815
77_A91_P0.138930.806
16_D20_K0.138320.803
45_Q49_F0.13780.800
95_Y108_W0.137770.800
29_L78_A0.137740.799
72_N76_S0.137390.797
64_I76_S0.137280.797
53_D61_L0.136520.792
69_P100_D0.135650.787
28_E82_F0.133470.775
36_Y64_I0.132330.768
67_L72_N0.131740.765
20_K34_E0.131730.765
5_I83_L0.131140.761
7_T15_P0.130470.757
64_I101_L0.130070.755
24_K27_A0.129780.753
19_L39_V0.129620.752
17_D21_E0.129310.750
16_D85_E0.129210.750
99_H105_N0.129130.749
27_A103_A0.129020.749
9_V12_S0.128990.749
66_G75_Y0.127120.738
24_K86_E0.126740.736
19_L22_L0.126190.732
72_N98_F0.1260.731
97_N100_D0.125680.729
31_G51_G0.125320.727
83_L86_E0.124950.725
30_L37_I0.124880.725
12_S43_D0.124680.724
16_D46_R0.12460.723
30_L64_I0.124550.723
21_E87_L0.124170.721
70_E92_D0.123840.719
37_I101_L0.123420.716
31_G78_A0.123140.715
80_T96_I0.123110.714
35_S50_G0.1220.708
49_F89_I0.121940.708
98_F110_G0.121770.707
88_G94_I0.121430.705
34_E51_G0.121410.705
89_I92_D0.121190.703
14_V55_P0.121070.703
55_P93_R0.119840.696
19_L37_I0.119230.692
14_V17_D0.119160.692
83_L91_P0.118230.686
9_V81_E0.11790.684
7_T14_V0.117830.684
18_F88_G0.117610.683
20_K48_S0.117530.682
64_I99_H0.117290.681
63_S98_F0.116670.677
7_T43_D0.11660.677
17_D54_D0.116420.676
10_S14_V0.116270.675
56_A95_Y0.114950.667
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
3djhA199.9-0.04
4dh4A0.991299.9-0.037
3kanA199.9-0.02
3t5sA0.982599.9-0.012
2wkbA199.90.011
3fwuA0.973799.90.012
1uizA199.90.013
1hfoA0.991299.90.013
2xczA199.90.013
3fwtA0.973799.90.015

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