GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Marek_A - Mareks disease glycoprotein A
Pfam: PF02124 (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: CL0011
Length: 211
Sequences: 2158
Seq/Len: 10.23
HH_delta: 0.387 (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
96_C155_C0.495013.981
159_G162_D0.354962.854
139_R142_R0.326452.625
111_S156_R0.30772.474
61_W64_D0.265542.135
148_D153_Y0.247121.987
112_V150_P0.243841.961
150_P153_Y0.239371.925
100_C104_G0.233271.876
112_V153_Y0.219981.769
12_F58_Q0.218641.758
13_E50_S0.186531.500
9_F61_W0.185681.493
189_I193_C0.184131.481
186_I190_G0.18191.463
140_S144_L0.181191.457
170_T173_Y0.180271.450
138_I141_R0.175731.413
191_V194_G0.174341.402
191_V195_A0.173791.398
187_S191_V0.173631.396
98_A108_L0.171651.380
188_I192_I0.167041.343
162_D168_E0.166981.343
190_G194_G0.163721.317
112_V148_D0.163181.312
13_E53_P0.161.287
113_G117_S0.158161.272
10_R58_Q0.157881.270
168_E172_T0.157781.269
124_E127_G0.156311.257
185_V189_I0.155761.253
183_P198_L0.15541.250
187_S198_L0.154761.245
13_E55_I0.154721.244
188_I193_C0.153591.235
192_I196_G0.153221.232
136_V139_R0.152851.229
138_I142_R0.150441.210
199_G204_I0.149541.203
144_L149_G0.149351.201
187_S194_G0.148471.194
43_L46_N0.147251.184
51_P55_I0.147031.182
100_C103_R0.146951.182
46_N50_S0.146581.179
189_I198_L0.146441.178
98_A102_P0.144361.161
12_F17_P0.143051.150
194_G199_G0.142021.142
193_C197_A0.141531.138
186_I194_G0.141421.137
183_P197_A0.140611.131
185_V194_G0.139621.123
183_P186_I0.13871.115
194_G197_A0.138061.110
79_V82_K0.137781.108
57_C71_F0.137141.103
141_R144_L0.13681.100
194_G198_L0.136271.096
190_G204_I0.1361.094
43_L62_Y0.134621.083
10_R17_P0.134531.082
177_P181_G0.132891.069
183_P187_S0.131021.054
50_S53_P0.130941.053
171_A175_A0.130131.046
78_S81_P0.129421.041
187_S193_C0.129321.040
103_R107_T0.128021.029
189_I196_G0.127571.026
186_I193_C0.127231.023
185_V190_G0.126721.019
187_S204_I0.126321.016
58_Q68_E0.126221.015
196_G199_G0.125951.013
160_Y164_L0.124531.001
189_I197_A0.123660.994
190_G197_A0.122780.987
166_V169_D0.122740.987
195_A198_L0.122190.983
49_D55_I0.122120.982
50_S55_I0.122020.981
13_E18_V0.121940.981
162_D166_V0.121630.978
198_L203_L0.121230.975
125_I129_C0.120760.971
12_F16_N0.120710.971
183_P188_I0.120440.969
197_A203_L0.119370.960
133_P136_V0.119160.958
192_I199_G0.118390.952
181_G185_V0.118090.950
11_W41_L0.117890.948
184_M191_V0.117440.944
135_L138_I0.116840.940
10_R60_T0.116580.937
11_W110_W0.116040.933
178_S182_F0.115910.932
108_L157_L0.115880.932
65_S69_T0.115430.928
47_S56_R0.114730.923
41_L110_W0.114450.920
8_R18_V0.114410.920
98_A104_G0.113910.916
183_P190_G0.113880.916
193_C196_G0.113290.911
98_A157_L0.113270.911
53_P68_E0.113160.910
40_T51_P0.11280.907
186_I196_G0.112790.907
12_F56_R0.112630.906
183_P189_I0.112540.905
134_G139_R0.112480.905
55_I94_A0.112190.902
196_G203_L0.111870.900
173_Y176_S0.111290.895
191_V199_G0.111160.894
192_I197_A0.111030.893
191_V203_L0.110910.892
185_V192_I0.110690.890
14_D18_V0.110220.886
183_P191_V0.110140.886
43_L50_S0.109940.884
111_S154_T0.109830.883
59_V63_R0.109740.882
84_R157_L0.109460.880
15_G56_R0.109160.878
184_M187_S0.108920.876
77_P80_Y0.10850.873
133_P137_N0.108410.872
161_P164_L0.10840.872
182_F197_A0.108190.870
179_A182_F0.107850.867
184_M188_I0.10770.866
10_R56_R0.106790.859
178_S181_G0.105910.852
12_F15_G0.10590.852
182_F185_V0.10580.851
179_A184_M0.105670.850
46_N53_P0.105260.846
185_V197_A0.105190.846
58_Q100_C0.105170.846
59_V72_N0.104880.843
43_L56_R0.104870.843
58_Q61_W0.104760.842
65_S72_N0.104140.837
180_Q183_P0.103820.835
44_P47_S0.10340.832
89_F146_D0.103370.831
183_P196_G0.103280.831
104_G159_G0.10290.827
41_L46_N0.102790.827
146_D149_G0.102510.824
129_C133_P0.102310.823
9_F108_L0.102240.822
139_R143_P0.102080.821
112_V117_S0.102060.821
54_S70_R0.101720.818
98_A101_V0.101610.817
9_F13_E0.101510.816
12_F18_V0.101470.816
63_R72_N0.101440.816
42_T174_D0.101430.816
150_P155_C0.101360.815
177_P183_P0.101040.813
40_T50_S0.100030.804
112_V199_G0.099850.803
94_A153_Y0.09980.803
111_S116_P0.099460.800
45_G61_W0.099350.799
15_G65_S0.099270.798
189_I194_G0.099030.796
59_V193_C0.099020.796
80_Y84_R0.0990.796
182_F186_I0.098950.796
181_G184_M0.09880.795
46_N55_I0.09880.795
57_C153_Y0.098720.794
139_R150_P0.098670.793
166_V173_Y0.098440.792
94_A108_L0.098110.789
184_M189_I0.098080.789
60_T195_A0.097860.787
139_R144_L0.097470.784
190_G203_L0.097290.782
103_R134_G0.097270.782
114_D117_S0.097230.782
66_V69_T0.096970.780
184_M195_A0.096950.780
186_I189_I0.096510.776
56_R69_T0.096230.774
110_W159_G0.096150.773
192_I204_I0.095660.769
172_T175_A0.095440.767
169_D172_T0.095370.767
188_I191_V0.094840.763
138_I144_L0.094320.758
124_E128_V0.09410.757
185_V191_V0.093750.754
183_P194_G0.093520.752
171_A174_D0.093510.752
113_G116_P0.093170.749
182_F193_C0.092840.747
188_I194_G0.092810.746
127_G136_V0.092740.746
168_E173_Y0.09270.745
174_D177_P0.092630.745
127_G130_A0.092450.743
88_R146_D0.092330.742
41_L81_P0.09210.741
187_S190_G0.092080.740
82_K85_V0.091970.740
187_S197_A0.091950.739
47_S50_S0.091910.739
165_P169_D0.091850.739
12_F65_S0.091530.736
59_V77_P0.091490.736
144_L155_C0.091410.735
56_R158_I0.091170.733
56_R68_E0.090940.731
194_G203_L0.090850.731
42_T45_G0.090670.729
71_F77_P0.090430.727
58_Q69_T0.090340.726
42_T49_D0.090170.725
185_V203_L0.090080.724
180_Q199_G0.089910.723
14_D53_P0.089750.722
193_C199_G0.089730.722
51_P95_V0.088970.715
184_M199_G0.088720.713
62_Y71_F0.088680.713
43_L91_D0.088520.712
189_I192_I0.088520.712
8_R60_T0.088470.711
186_I198_L0.088080.708
159_G194_G0.088030.708
98_A103_R0.08780.706
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
3b43A0.905299.80.387
4fa8A0.78299.80.394
3b43A0.734699.80.408
2rcjC0.786799.80.409
4fqpA0.772599.80.409
3zo0A0.786799.80.413
1zvoC0.843699.70.421
1igtB0.786799.70.422
3qs7E0.767899.70.424
1igyB0.786799.70.424

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