GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fil_haemagg_2 - Haemagluttinin repeat
Pfam: PF13332 (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: CL0268
Length: 170
Sequences: 1040
Seq/Len: 6.12
HH_delta: 0.877 (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
58_I126_I0.735384.495
130_G150_G0.579993.545
38_T59_N0.553843.385
124_V139_V0.545423.334
39_L42_S0.511083.124
37_I52_L0.5013.062
28_V44_I0.443582.711
133_N153_T0.427522.613
50_L118_I0.423792.590
60_I116_S0.402172.458
128_A132_L0.398832.438
141_A144_I0.375972.298
46_A50_L0.358162.189
59_N133_N0.356572.180
51_N125_T0.354642.168
62_A157_A0.351392.148
53_N127_N0.342732.095
57_N130_G0.341752.089
131_D151_N0.315551.929
34_N56_G0.307451.879
54_A129_G0.305981.870
20_S42_S0.303311.854
115_N137_A0.299811.833
132_L146_L0.298361.824
134_I137_A0.286711.753
113_H157_A0.28241.726
56_G130_G0.281.712
63_A114_Q0.273521.672
17_A63_A0.271061.657
64_E111_T0.259211.584
36_D56_G0.257871.576
17_A65_N0.251111.535
24_A28_V0.249571.526
62_A113_H0.242271.481
126_I139_V0.22571.380
132_L148_A0.225451.378
65_N114_Q0.224991.375
40_Q61_S0.223431.366
37_I58_I0.222381.359
22_I28_V0.209131.278
64_E113_H0.20831.273
113_H159_D0.206751.264
148_A152_L0.206351.261
108_S163_S0.19891.216
39_L60_I0.198491.213
14_S67_N0.196941.204
124_V141_A0.192911.179
116_S137_A0.19081.166
75_S102_G0.189081.156
19_G42_S0.186611.141
27_N121_G0.185351.133
43_N117_T0.185011.131
29_N51_N0.1851.131
132_L152_L0.182511.116
124_V128_A0.17981.099
131_D150_G0.175311.072
39_L44_I0.173911.063
22_I30_I0.172121.052
133_N155_E0.171971.051
115_N156_S0.171511.048
83_S96_S0.17071.043
144_I148_A0.170421.042
135_Q155_E0.169571.037
68_S109_N0.169011.033
115_N138_N0.167881.026
33_G55_G0.166031.015
73_N104_S0.164541.006
126_I146_L0.164481.005
31_T53_N0.16210.991
45_Q119_N0.15990.977
36_D55_G0.15910.973
115_N157_A0.157780.964
38_T61_S0.157440.962
20_S39_L0.157430.962
131_D153_T0.156620.957
48_G122_G0.148830.910
61_S135_Q0.148760.909
15_T66_T0.14830.907
32_A37_I0.14560.890
60_I137_A0.14550.889
41_G63_A0.145460.889
110_S161_Y0.144450.883
137_A159_D0.143950.880
33_G37_I0.143170.875
46_A49_D0.142260.870
49_D122_G0.141980.868
143_K148_A0.140860.861
50_L124_V0.1390.850
84_V97_V0.137420.840
114_Q118_I0.135450.828
24_A81_G0.135010.825
134_I139_V0.134560.823
123_N143_K0.134030.819
21_T43_N0.133810.818
32_A39_L0.130990.801
127_N147_N0.130110.795
134_I154_I0.12960.792
139_V154_I0.128930.788
79_S83_S0.127410.779
116_S119_N0.12680.775
107_N164_S0.126410.773
37_I54_A0.125480.767
116_S134_I0.125340.766
36_D57_N0.12440.760
148_A154_I0.124090.759
34_N55_G0.123370.754
48_G120_A0.123330.754
53_N56_G0.121810.745
52_L118_I0.121320.742
17_A41_G0.121190.741
109_N162_S0.120640.737
54_A57_N0.119660.731
46_A159_D0.119340.729
13_T30_I0.119310.729
94_G98_S0.118730.726
62_A155_E0.118020.721
28_V50_L0.116710.713
135_Q157_A0.116570.713
62_A111_T0.116340.711
22_I161_Y0.115820.708
139_V144_I0.114680.701
79_S96_S0.11460.701
50_L120_A0.114370.699
84_V94_G0.114020.697
56_G81_G0.113770.695
100_S115_N0.113040.691
46_A121_G0.112980.691
132_L137_A0.112370.687
27_N48_G0.111050.679
111_T160_T0.110410.675
85_S88_S0.109620.670
60_I115_N0.109520.669
49_D82_V0.109420.669
40_Q63_A0.108990.666
27_N120_A0.10830.662
143_K147_N0.107470.657
101_G105_K0.107440.657
11_N32_A0.106850.653
122_G150_G0.106450.651
79_S82_V0.106120.649
61_S64_E0.105980.648
81_G154_I0.105610.646
56_G150_G0.105250.643
72_E94_G0.105210.643
74_K79_S0.104680.640
71_S106_S0.104140.637
26_G48_G0.103660.634
41_G136_G0.103570.633
16_T32_A0.103370.632
36_D54_A0.102890.629
44_I118_I0.101360.620
27_N147_N0.100580.615
120_A140_S0.100080.612
32_A129_G0.099780.610
70_T107_N0.099250.607
75_S80_V0.099110.606
46_A160_T0.098950.605
76_S85_S0.098470.602
140_S144_I0.098430.602
138_N161_Y0.098190.600
42_S52_L0.098110.600
17_A114_Q0.097560.596
26_G31_T0.09730.595
34_N37_I0.09710.594
151_N155_E0.096290.589
26_G47_G0.096230.588
13_T68_S0.095930.586
71_S107_N0.095110.581
70_T109_N0.094890.580
64_E68_S0.094740.579
18_V40_Q0.094510.578
60_I134_I0.094280.576
80_V83_S0.094230.576
55_G151_N0.094160.576
31_T127_N0.093790.573
51_N68_S0.093730.573
104_S163_S0.093650.572
27_N49_D0.093590.572
32_A58_I0.093520.572
23_S26_G0.093430.571
27_N39_L0.093270.570
61_S155_E0.093210.570
12_S16_T0.093120.569
129_G132_L0.093030.569
41_G159_D0.092940.568
44_I139_V0.092530.566
67_N110_S0.092340.564
12_S110_S0.092310.564
115_N152_L0.09210.563
88_S99_A0.091780.561
13_T23_S0.091760.561
54_A128_A0.091760.561
69_S103_K0.091510.559
60_I118_I0.09150.559
23_S45_Q0.091430.559
57_N129_G0.091390.559
17_A120_A0.09130.558
80_V84_V0.091270.558
99_A104_S0.091130.557
25_G28_V0.090970.556
13_T18_V0.090660.554
142_G147_N0.090540.553
143_K162_S0.090480.553
137_A153_T0.090460.553
125_T145_N0.089990.550
12_S43_N0.089970.550
14_S162_S0.089740.549
39_L124_V0.089480.547
11_N30_I0.089430.547
142_G145_N0.089410.547
30_I40_Q0.089230.545
83_S87_G0.089110.545
19_G43_N0.088980.544
46_A69_S0.088810.543
107_N153_T0.088740.542
95_V99_A0.088630.542
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
1rwrA0.929472.20.877
1wthA0.428.70.905
3szeA0.75886.80.927
2odlA0.911840.934
3h09A0.83.30.937
3syjA0.82.10.943
2akkA0.34712.10.943
1s7mA0.36471.80.945
1wxrA0.81.70.945
3vtoA0.48241.30.948
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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