GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bac_surface_Ag - Surface antigen
Pfam: PF01103 (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: CL0193
Length: 323
Sequences: 3741
Seq/Len: 11.58
HH_delta: 0.333 (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
171_F235_Y0.521473.841
175_L233_A0.489913.609
254_A281_S0.466813.439
43_Y61_G0.41033.023
7_Q26_Y0.377322.780
36_L68_Y0.37612.771
44_Y60_F0.345542.545
180_G197_F0.344322.536
82_Y110_N0.321392.368
79_G115_G0.318922.349
80_Y112_S0.312882.305
120_Y133_W0.312862.305
7_Q28_N0.311442.294
205_V213_I0.309882.283
253_F284_G0.304142.240
156_E197_F0.281912.077
291_T294_G0.280322.065
10_S25_S0.279832.061
39_G65_S0.278772.054
283_V304_L0.276082.034
133_W161_Y0.273482.015
237_F250_L0.27081.995
158_S178_Q0.267941.974
256_A281_S0.267091.968
174_A236_R0.261991.930
251_V286_G0.261241.924
251_V288_R0.260981.923
11_V24_L0.258871.907
252_A285_V0.258581.905
181_Y227_Y0.253341.866
74_W118_L0.249061.835
182_I191_L0.247431.823
232_S255_D0.237931.753
288_R299_D0.234851.730
1_N4_G0.229331.689
298_F315_F0.228811.686
152_F195_E0.228491.683
171_F237_F0.22771.677
204_S230_T0.226671.670
205_V282_S0.226011.665
207_G282_S0.225231.659
135_L159_A0.224281.652
286_G299_D0.222091.636
12_S23_S0.218731.611
180_G228_Y0.213811.575
122_T133_W0.21361.574
281_S305_N0.212791.568
201_G204_S0.212381.565
173_L233_A0.211121.555
124_D130_T0.210211.549
84_R110_N0.204041.503
206_R255_D0.202871.494
236_R249_Y0.201151.482
3_F7_Q0.20021.475
27_T37_S0.199171.467
161_Y175_L0.198411.462
199_L230_T0.19521.438
208_Y280_R0.194681.434
8_S27_T0.194111.430
199_L257_G0.193011.422
129_P132_G0.189761.398
41_S63_S0.188341.387
251_V297_R0.18681.376
299_D316_Y0.186771.376
206_R234_E0.182951.348
81_S113_S0.182781.346
77_S117_S0.180371.329
206_R253_F0.179991.326
74_W120_Y0.178421.314
38_L66_L0.178021.311
9_L24_L0.177331.306
70_I76_L0.176051.297
208_Y305_N0.174511.286
258_N279_I0.174441.285
139_L153_Y0.173511.278
120_Y135_L0.172521.271
208_Y303_P0.172041.267
137_F157_L0.17191.266
41_S65_S0.170821.258
251_V299_D0.170661.257
200_G204_S0.166271.225
40_F64_L0.165271.217
76_L116_L0.164751.214
176_R232_S0.164561.212
300_Y313_N0.164011.208
303_P316_Y0.163391.204
254_A283_V0.159581.176
166_G171_F0.159241.173
37_S67_G0.159061.172
154_K182_I0.158281.166
22_L44_Y0.157891.163
76_L118_L0.157481.160
163_Y175_L0.157461.160
156_E178_Q0.157281.159
174_A234_E0.157261.158
113_S140_E0.151621.117
80_Y84_R0.151621.117
159_A177_L0.151571.117
197_F228_Y0.15151.116
206_R284_G0.15061.109
237_F252_A0.14961.102
117_S138_S0.149221.099
256_A279_I0.148021.090
123_R134_Y0.147661.088
154_K195_E0.147131.084
124_D131_K0.146021.076
140_E154_K0.145721.073
158_S176_R0.145721.073
199_L228_Y0.145371.071
233_A254_A0.144921.068
291_T295_P0.144871.067
71_S74_W0.144481.064
124_D132_G0.144161.062
141_F153_Y0.144131.062
139_L155_F0.142811.052
282_S316_Y0.142251.048
285_V302_Y0.141951.046
113_S152_F0.140441.035
300_Y315_F0.139431.027
179_G231_A0.139341.026
234_E253_F0.138881.023
2_L9_L0.138191.018
179_G228_Y0.137471.013
36_L66_L0.13731.011
239_L245_S0.13711.010
28_N31_F0.135961.002
162_Y172_V0.135530.998
160_R176_R0.134140.988
59_T85_N0.133610.984
248_L289_Y0.132920.979
135_L157_L0.132090.973
298_F317_F0.131890.972
258_N280_R0.131650.970
31_F38_L0.13110.966
205_V255_D0.131090.966
132_G137_F0.130310.960
191_L226_D0.130150.959
162_Y174_A0.129950.957
154_K180_G0.129470.954
15_Y20_Q0.129440.954
133_W159_A0.12930.953
80_Y114_L0.129150.951
285_V300_Y0.129080.951
175_L231_A0.128730.948
13_A22_L0.12870.948
200_G257_G0.12860.947
34_D37_S0.128190.944
199_L204_S0.127580.940
43_Y83_S0.127350.938
35_R69_R0.127210.937
175_L319_I0.126640.933
165_L235_Y0.126330.931
234_E255_D0.126310.930
239_L250_L0.126210.930
121_D134_Y0.126180.930
177_L229_F0.12610.929
80_Y143_G0.12610.929
255_D282_S0.125580.925
300_Y314_R0.125350.923
83_S195_E0.125290.923
283_V302_Y0.125270.923
198_Y214_G0.125240.923
206_R286_G0.124890.920
281_S304_L0.124780.919
227_Y262_D0.124590.918
69_R75_S0.124410.916
178_Q228_Y0.124190.915
173_L235_Y0.124140.914
178_Q230_T0.123950.913
234_E288_R0.123810.912
234_E286_G0.123480.910
123_R132_G0.12290.905
44_Y58_Q0.122860.905
177_L231_A0.122420.902
1_N323_F0.121580.896
196_R226_D0.120940.891
183_F226_D0.120790.890
199_L259_V0.120470.887
179_G229_F0.119780.882
70_I118_L0.119740.882
231_A256_A0.119430.880
133_W137_F0.119240.878
129_P162_Y0.11890.876
134_Y160_R0.118720.875
14_T21_S0.118360.872
67_G77_S0.11830.871
196_R215_P0.118180.871
165_L171_F0.117550.866
86_D108_K0.116890.861
213_I280_R0.116670.859
170_K238_P0.116530.858
288_R297_R0.115660.852
198_Y211_R0.115390.850
16_G289_Y0.115340.850
239_L287_L0.11490.846
78_L116_L0.114560.844
138_S156_E0.114440.843
160_R174_A0.114420.843
320_G323_F0.114210.841
157_L179_G0.114150.841
209_R212_S0.114140.841
182_I226_D0.114030.840
176_R319_I0.113920.839
113_S195_E0.113750.838
135_L161_Y0.11350.836
238_P249_Y0.113190.834
134_Y137_F0.112440.828
205_V257_G0.112420.828
132_G142_S0.11210.826
280_R307_P0.112010.825
140_E143_G0.111330.820
9_L26_Y0.111320.820
175_L235_Y0.111250.820
60_F84_R0.110740.816
213_I258_N0.11070.815
62_F66_L0.110480.814
250_L287_L0.110250.812
137_F141_F0.110020.810
247_N289_Y0.109630.808
132_G138_S0.109630.808
38_L64_L0.109590.807
248_L287_L0.109370.806
2_L26_Y0.109090.804
23_S41_S0.108770.801
58_Q88_S0.10870.801
42_L61_G0.10860.800
302_Y313_N0.108590.800
249_Y303_P0.108380.798
208_Y212_S0.108270.798
172_V236_R0.107150.789
117_S136_S0.107010.788
89_T93_S0.106850.787
209_R314_R0.106790.787
208_Y306_K0.106550.785
174_A321_Q0.106220.782
59_T62_F0.105890.780
143_G147_G0.105380.776
177_L233_A0.105290.776
178_Q197_F0.1050.773
143_G146_L0.104990.773
82_Y112_S0.104550.770
174_A299_D0.104520.770
119_S134_Y0.10440.769
112_S143_G0.104070.767
65_S77_S0.103930.766
112_S147_G0.103770.764
67_G70_I0.103440.762
171_F175_L0.103360.761
68_Y74_W0.103240.761
30_Y35_R0.10320.760
202_P316_Y0.102810.757
155_F183_F0.102570.756
23_S43_Y0.102520.755
25_S39_G0.102450.755
199_L215_P0.102360.754
159_A175_L0.102070.752
58_Q64_L0.101780.750
198_Y215_P0.101240.746
52_F93_S0.100820.743
124_D129_P0.100770.742
57_E194_S0.100660.742
121_D162_Y0.100450.740
5_T28_N0.099710.735
234_E251_V0.09960.734
234_E297_R0.099560.733
296_L317_F0.09930.732
295_P320_G0.099260.731
181_Y260_W0.098940.729
143_G148_S0.09870.727
174_A232_S0.098520.726
123_R129_P0.098460.725
121_D132_G0.09830.724
204_S207_G0.098280.724
215_P259_V0.098240.724
87_F194_S0.098090.723
8_S25_S0.097610.719
156_E228_Y0.097520.718
199_L205_V0.09750.718
202_P210_Y0.097210.716
58_Q86_D0.097150.716
68_Y226_D0.09690.714
180_G293_I0.096680.712
174_A251_V0.096510.711
132_G162_Y0.096460.711
63_S77_S0.096340.710
280_R310_D0.096320.710
136_S158_S0.096270.709
236_R299_D0.096250.709
13_A20_Q0.096150.708
139_L142_S0.095810.706
153_Y183_F0.095660.705
61_G317_F0.095430.703
124_D164_P0.095140.701
28_N38_L0.095120.701
76_L120_Y0.095060.700
234_E301_A0.095040.700
236_R297_R0.094990.700
116_L119_S0.09490.699
176_R320_G0.094880.699
289_Y292_P0.094770.698
113_S197_F0.094710.698
67_G75_S0.094670.697
165_L177_L0.094320.695
196_R304_L0.094080.693
52_F107_G0.094070.693
4_G238_P0.093570.689
57_E61_G0.093390.688
208_Y281_S0.093230.687
118_L135_L0.093140.686
250_L285_V0.092960.685
197_F317_F0.092910.684
207_G247_N0.092620.682
236_R251_V0.092570.682
302_Y314_R0.092480.681
132_G151_N0.092390.681
3_F15_Y0.092250.680
165_L173_L0.092220.679
175_L247_N0.092020.678
159_A228_Y0.092010.678
229_F256_A0.091840.677
251_V255_D0.091810.676
12_S178_Q0.091680.675
2_L183_F0.091090.671
231_A281_S0.091020.671
113_S142_S0.091020.671
180_G280_R0.090980.670
4_G284_G0.090740.668
130_T164_P0.09070.668
49_S56_D0.090560.667
40_F66_L0.090530.667
200_G208_Y0.090510.667
89_T94_P0.090290.665
66_L151_N0.090260.665
42_L62_F0.090240.665
226_D262_D0.090240.665
84_R108_K0.090220.665
254_A304_L0.089830.662
3_F11_V0.089790.661
111_I195_E0.089720.661
52_F55_Y0.089590.660
55_Y70_I0.089430.659
159_A233_A0.089410.659
196_R323_F0.089380.658
213_I303_P0.089360.658
297_R321_Q0.08910.656
116_L137_F0.088950.655
231_A254_A0.08890.655
230_T257_G0.088850.655
42_L60_F0.08880.654
81_S140_E0.088690.653
198_Y257_G0.088660.653
151_N191_L0.088410.651
202_P299_D0.088130.649
2_L31_F0.088040.649
297_R319_I0.087920.648
229_F258_N0.08790.648
141_F279_I0.087450.644
83_S230_T0.087260.643
164_P172_V0.087180.642
191_L196_R0.087020.641
129_P294_G0.086870.640
131_K137_F0.086870.640
191_L285_V0.08680.639
155_F254_A0.086540.638
13_A298_F0.086320.636
63_S81_S0.086210.635
4_G114_L0.085990.633
90_S114_L0.085980.633
43_Y148_S0.085830.632
79_G117_S0.085790.632
4_G206_R0.085780.632
45_S111_I0.085740.632
204_S228_Y0.085720.631
136_S139_L0.085660.631
70_I82_Y0.085540.630
42_L153_Y0.08540.629
201_G320_G0.085090.627
157_L161_Y0.084830.625
303_P306_K0.08480.625
132_G139_L0.084790.625
175_L306_K0.084680.624
81_S115_G0.084470.622
176_R234_E0.084380.622
157_L170_K0.084330.621
1_N284_G0.084140.620
234_E284_G0.084110.620
1_N5_T0.083930.618
136_S178_Q0.083810.617
64_L69_R0.083660.616
196_R214_G0.083630.616
81_S117_S0.083520.615
174_A297_R0.083460.615
53_S208_Y0.083460.615
192_P195_E0.083440.615
201_G301_A0.08340.614
59_T83_S0.083360.614
238_P253_F0.083180.613
301_A306_K0.083110.612
112_S148_S0.082920.611
14_T84_R0.082760.610
133_W139_L0.082710.609
32_F35_R0.08260.608
72_P76_L0.08260.608
232_S250_L0.082570.608
45_S105_Q0.082560.608
116_L139_L0.082450.607
255_D314_R0.082330.606
182_I228_Y0.082320.606
73_N256_A0.082120.605
202_P207_G0.082010.604
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
2qdzA0.88851000.333
2lhfA0.495476.50.927
3dwoX0.38741.40.941
3qraA0.436534.10.943
1ormA0.430326.20.946
3pguA0.35625.90.946
3kvnX0.77421.70.948
3bryA0.368421.70.948
3qlbA0.489220.70.949
3bs0A0.3653200.949

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