GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MHC_I - Class I Histocompatibility antigen domains alpha 1 and 2
Pfam: PF00129 (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: CL0343
Length: 179
Sequences: 2263
Seq/Len: 12.64
HH_delta: -0.056 (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
77_N80_D0.748454.075
143_T147_W0.579363.154
45_A67_L0.563563.068
24_A67_L0.539592.938
63_E66_K0.525592.862
63_E67_L0.488962.662
24_A45_A0.430982.347
97_R114_W0.417442.273
144_K148_E0.404492.202
67_L70_S0.401912.188
9_F24_A0.364461.984
156_W160_L0.350011.906
95_L116_Y0.349431.903
77_N81_L0.348741.899
76_M80_D0.339471.848
34_L45_A0.338531.843
70_S74_F0.332651.811
3_H29_D0.330761.801
114_W156_W0.328991.791
175_G179_L0.327821.785
45_A63_E0.32471.768
152_E155_K0.317441.728
66_K70_S0.317121.727
47_P60_W0.315861.720
7_Y26_G0.311181.694
151_R154_T0.302641.648
11_A74_F0.302431.647
73_F76_M0.301231.640
24_A66_K0.289651.577
97_R116_Y0.279421.521
15_P107_G0.278931.519
124_L143_T0.277141.509
93_H119_D0.275341.499
36_Y71_E0.27461.495
103_L165_P0.259341.412
9_F22_F0.258671.408
126_F154_T0.258621.408
9_F67_L0.257641.403
52_M55_E0.257161.400
24_A34_L0.249661.359
163_D167_W0.245261.335
45_A66_K0.240251.308
34_L67_L0.236221.286
124_L147_W0.235591.283
34_L63_E0.233291.270
79_K82_M0.232121.264
15_P18_G0.231221.259
151_R155_K0.230381.254
71_E74_F0.229551.250
77_N95_L0.228181.242
67_L71_E0.226051.231
55_E154_T0.225791.229
97_R156_W0.223431.217
116_Y156_W0.222341.211
62_E66_K0.222211.210
69_E74_F0.221831.208
110_V169_R0.214241.166
157_K161_E0.213951.165
9_F74_F0.212661.158
153_A156_W0.21081.148
63_E171_Y0.210791.148
156_W163_D0.210181.144
145_Q148_E0.209681.142
144_K177_E0.209031.138
45_A70_S0.202891.105
74_F97_R0.202161.101
26_G33_F0.200681.093
170_K174_Y0.199291.085
9_F70_S0.199131.084
109_S154_T0.198921.083
61_E65_Q0.195371.064
70_S73_F0.194931.061
79_K158_H0.194031.056
176_K179_L0.192171.046
27_Y30_D0.188271.025
77_N116_Y0.186851.017
138_P142_I0.183861.001
54_E90_G0.182520.994
141_Q145_Q0.181440.988
173_E176_K0.180350.982
12_V23_S0.180070.980
149_S152_E0.179050.975
149_S155_K0.178520.972
109_S151_R0.175380.955
17_P121_E0.174920.952
41_Q79_K0.174740.951
80_D95_L0.174430.950
134_T148_E0.173740.946
93_H96_Q0.1720.936
96_Q101_C0.171670.935
138_P151_R0.171230.932
144_K158_H0.171210.932
69_E73_F0.168660.918
141_Q149_S0.168350.917
135_A140_A0.168330.917
128_L131_G0.168150.916
121_E169_R0.166440.906
35_R45_A0.164660.897
102_E111_R0.163940.893
9_F45_A0.163350.889
83_K90_G0.163320.889
10_T14_Q0.162370.884
77_N99_Y0.161810.881
164_C168_L0.161590.880
150_D155_K0.161190.878
123_F140_A0.160620.875
124_L144_K0.160270.873
152_E156_W0.160250.873
57_P61_E0.160030.871
70_S97_R0.159890.871
101_C164_C0.15970.870
50_P53_K0.159550.869
161_E174_Y0.15880.865
4_S7_Y0.157990.860
167_W171_Y0.15750.858
26_G34_L0.157120.855
148_E154_T0.156020.849
40_S169_R0.154690.842
172_L176_K0.154690.842
9_F99_Y0.153960.838
87_Q118_Y0.153840.838
127_D130_T0.153370.835
138_P141_Q0.153050.833
7_Y34_L0.152820.832
110_V113_F0.151580.825
166_E174_Y0.151160.823
126_F130_T0.15060.820
9_F97_R0.150210.818
150_D154_T0.149490.814
158_H163_D0.148340.808
80_D84_R0.147820.805
32_Q35_R0.147580.804
12_V15_P0.146380.797
84_R123_F0.145320.791
40_S68_K0.145080.790
79_K169_R0.144730.788
133_W148_E0.14410.785
111_R178_T0.143950.784
66_K69_E0.143150.779
69_E76_M0.142980.778
62_E67_L0.142720.777
58_E65_Q0.142650.777
121_E174_Y0.142470.776
115_Q122_D0.142030.773
39_N44_R0.141840.772
44_R61_E0.141470.770
53_K56_L0.141420.770
116_Y147_W0.141390.770
56_L170_K0.141040.768
6_R30_D0.140980.768
49_Q52_M0.140890.767
18_G21_E0.140840.767
114_W144_K0.140640.766
103_L109_S0.140460.765
66_K163_D0.140190.763
77_N82_M0.140160.763
17_P90_G0.139650.760
175_G178_T0.139460.759
114_W138_P0.139020.757
59_Y63_E0.138590.755
74_F116_Y0.138180.752
101_C120_G0.137960.751
129_E157_K0.137840.751
27_Y40_S0.137590.749
33_F60_W0.137490.749
74_F114_W0.137060.746
162_G166_E0.136330.742
104_D110_V0.135710.739
14_Q18_G0.135570.738
24_A70_S0.135290.737
9_F159_Y0.134520.732
3_H7_Y0.134440.732
121_E137_D0.133440.727
131_G149_S0.133210.725
33_F45_A0.133110.725
8_F32_Q0.133020.724
74_F77_N0.132910.724
96_Q120_G0.132210.720
132_T139_E0.131740.717
41_Q71_E0.13130.715
67_L74_F0.130650.711
103_L166_E0.130470.710
22_F45_A0.130390.710
36_Y41_Q0.130230.709
34_L66_K0.130.708
95_L124_L0.129910.707
159_Y171_Y0.129780.707
65_Q69_E0.129690.706
9_F66_K0.129210.704
116_Y124_L0.129180.703
67_L73_F0.128810.701
7_Y33_F0.128760.701
52_M59_Y0.12850.700
121_E144_K0.128390.699
3_H6_R0.128350.699
80_D83_K0.128320.699
121_E151_R0.128130.698
23_S37_D0.127970.697
35_R48_K0.127720.695
113_F126_F0.127240.693
99_Y156_W0.12720.693
52_M73_F0.127140.692
41_Q44_R0.127020.692
104_D111_R0.126640.690
67_L156_W0.126630.689
46_E57_P0.126230.687
32_Q49_Q0.126050.686
17_P58_E0.125740.685
31_Q35_R0.125490.683
10_T25_V0.125190.682
47_P64_T0.124940.680
12_V18_G0.124670.679
34_L52_M0.124630.679
33_F49_Q0.124160.676
81_L95_L0.123750.674
14_Q30_D0.123410.672
125_S136_A0.123280.671
77_N114_W0.122820.669
121_E158_H0.122790.669
161_E177_E0.122760.668
172_L175_G0.12270.668
117_A158_H0.122490.667
171_Y174_Y0.122460.667
5_L26_G0.122360.666
23_S58_E0.122280.666
27_Y31_Q0.12170.663
5_L34_L0.121580.662
128_L161_E0.121550.662
39_N50_P0.121450.661
94_T117_A0.121370.661
59_Y171_Y0.121110.659
72_Q76_M0.120960.659
162_G173_E0.120410.656
103_L106_D0.120090.654
130_T139_E0.119440.650
35_R46_E0.119160.649
84_R146_K0.119160.649
70_S156_W0.119120.649
149_S158_H0.119070.648
136_A145_Q0.118940.648
5_L9_F0.118830.647
169_R173_E0.118590.646
15_P27_Y0.118490.645
105_E169_R0.118280.644
68_K72_Q0.117890.642
78_L84_R0.117840.642
109_S153_A0.117840.642
5_L67_L0.117750.641
120_G140_A0.117640.641
34_L59_Y0.117340.639
109_S155_K0.117250.638
103_L138_P0.11710.638
113_F173_E0.117070.637
131_G145_Q0.116890.636
121_E177_E0.116870.636
27_Y32_Q0.11660.635
131_G178_T0.116570.635
20_P23_S0.116390.634
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
4g59A0.9665100-0.056
4gupA0.9721100-0.017
1kcgC0.97211000.001
1jfmA0.96091000.005
3p73A0.97771000.022
1s7qA11000.035
4g43A0.97771000.036
3nwmA11000.037
3bevA0.97771000.04
1k5nA11000.042

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