GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Virul_fac_BrkB - Virulence factor BrkB
Pfam: PF03631 (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. )
Length: 260
Sequences: 2424
Seq/Len: 9.32
HH_delta: 0.927 (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
3_N251_E0.554144.812
4_D97_R0.36483.168
200_F252_L0.32222.798
10_A15_Y0.319822.777
6_F244_L0.311732.707
95_L250_A0.276022.397
197_G253_N0.271482.357
205_W242_S0.269482.340
7_Y11_A0.259382.252
208_L241_F0.247312.148
178_F198_A0.244942.127
181_Y201_A0.242532.106
54_D57_E0.237272.060
96_N185_P0.228241.982
196_P253_N0.210091.824
178_F191_W0.20741.801
89_A113_R0.206741.795
3_N100_G0.21.737
96_N186_N0.195691.699
174_F199_L0.195511.698
182_R191_W0.194991.693
12_L243_A0.194061.685
117_L121_I0.192821.674
57_E60_E0.191571.664
216_L234_I0.188971.641
4_D93_R0.18771.630
73_G80_L0.182041.581
114_L118_L0.181481.576
200_F204_L0.18111.573
174_F202_A0.180161.564
99_Y253_N0.179581.559
92_Q116_A0.176981.537
12_L94_A0.175891.527
92_Q184_L0.175711.526
13_A243_A0.174111.512
201_A249_G0.173341.505
181_Y249_G0.172911.501
96_N101_V0.172651.499
9_A247_L0.172361.497
212_F216_L0.172361.497
194_A198_A0.170921.484
214_L218_Y0.170861.484
85_S113_R0.170761.483
95_L184_L0.16741.454
76_G79_I0.167161.452
98_I247_L0.165721.439
47_L51_L0.165451.437
206_F209_S0.159821.388
10_A13_A0.159761.387
113_R116_A0.159411.384
136_F139_S0.157361.366
215_Y219_V0.156541.359
110_W114_L0.156211.356
171_L195_L0.151081.312
15_Y19_S0.149971.302
174_F195_L0.147411.280
16_A239_L0.147211.278
238_W242_S0.145271.261
179_L183_F0.14461.256
44_L56_A0.144481.255
12_L91_L0.143861.249
99_Y209_S0.143451.246
74_L78_L0.142751.240
60_E64_E0.141831.232
91_L121_I0.141661.230
44_L48_R0.141191.226
94_A247_L0.140451.220
106_R186_N0.139941.215
19_S87_F0.13941.210
212_F222_Y0.138241.200
5_G251_E0.135241.174
9_A244_L0.135181.174
98_I251_E0.134611.169
108_S111_K0.133751.161
207_L211_G0.13341.158
174_F178_F0.132651.152
22_P227_G0.130911.137
196_P200_F0.128831.119
189_V194_A0.128071.112
91_L243_A0.127931.111
178_F195_L0.127541.108
205_W228_S0.127511.107
92_Q113_R0.127511.107
170_F202_A0.126071.095
41_D45_N0.125891.093
13_A240_Y0.125361.089
46_F50_L0.125071.086
203_V207_L0.124771.083
111_K115_I0.124581.082
61_S64_E0.124311.079
5_G244_L0.124291.079
195_L199_L0.123371.071
205_W209_S0.122631.065
228_S231_S0.12211.060
21_F52_P0.122051.060
92_Q237_L0.120991.051
85_S120_L0.120131.043
26_L88_F0.120031.042
11_A90_S0.119721.040
12_L247_L0.119611.039
177_F205_W0.11911.034
89_A92_Q0.118921.033
13_A239_L0.118871.032
38_E41_D0.117941.024
177_F246_L0.117261.018
190_R193_A0.117141.017
225_V230_G0.116931.015
91_L94_A0.11641.011
107_R115_I0.116041.008
198_A202_A0.115731.005
222_Y226_Y0.115641.004
141_L161_W0.115070.999
53_P57_E0.114620.995
164_I167_L0.114060.990
58_Q61_S0.113270.984
125_V128_I0.113270.984
21_F66_I0.113140.982
6_F9_A0.112880.980
207_L210_Y0.112740.979
88_F92_Q0.11170.970
14_Y246_L0.111660.970
43_L62_F0.110670.961
7_Y93_R0.11050.960
10_A14_Y0.10980.953
177_F202_A0.109630.952
8_L14_Y0.109220.948
87_F243_A0.109120.948
42_Q45_N0.108790.945
52_P212_F0.108720.944
8_L97_R0.108690.944
11_A89_A0.108680.944
162_N165_R0.108680.944
17_L47_L0.10860.943
210_Y214_L0.108250.940
205_W239_L0.10820.940
26_L80_L0.107470.933
189_V193_A0.106570.925
23_L120_L0.105670.918
14_Y18_L0.10550.916
83_S90_S0.105430.916
225_V243_A0.105340.915
34_L38_E0.105250.914
240_Y245_I0.104640.909
8_L11_A0.104290.906
15_Y83_S0.104260.905
130_S236_L0.104080.904
248_L252_L0.103980.903
90_S93_R0.103680.900
71_S75_I0.103530.899
37_P41_D0.103420.898
211_G214_L0.103250.897
255_V258_K0.103030.895
14_Y237_L0.103020.895
51_L131_L0.102980.894
110_W152_L0.102390.889
75_I79_I0.101930.885
94_A123_L0.101910.885
101_V186_N0.101660.883
208_L242_S0.101430.881
134_S239_L0.100760.875
173_L206_F0.100680.874
84_A238_W0.100520.873
17_L239_L0.100010.868
195_L198_A0.099930.868
16_A243_A0.099890.867
178_F194_A0.099860.867
212_F234_I0.099210.862
96_N107_R0.099130.861
171_L175_L0.098840.858
76_G80_L0.098760.858
93_R162_N0.098750.858
201_A241_F0.098690.857
85_S116_A0.098230.853
37_P40_I0.09810.852
14_Y236_L0.098050.851
202_A206_F0.09780.849
2_R210_Y0.097710.848
190_R195_L0.097570.847
149_L163_L0.097520.847
177_F201_A0.097460.846
29_S76_G0.097440.846
105_E232_L0.096880.841
120_L181_Y0.096310.836
21_F233_I0.096120.835
18_L233_I0.095910.833
15_Y90_S0.095440.829
75_I78_L0.095240.827
101_V107_R0.095160.826
227_G231_S0.095150.826
19_S183_F0.095110.826
94_A251_E0.094890.824
205_W253_N0.09460.821
55_I58_Q0.09450.821
197_G249_G0.094480.820
40_I43_L0.094230.818
209_S253_N0.094090.817
222_Y234_I0.094030.817
52_P66_I0.093740.814
29_S33_L0.093730.814
215_Y238_W0.093730.814
6_F86_S0.093570.813
87_F92_Q0.093450.811
88_F177_F0.093420.811
168_V171_L0.093270.810
75_I132_A0.093230.810
81_L175_L0.09310.808
169_S201_A0.092990.807
125_V129_L0.09260.804
34_L65_Q0.092570.804
130_S133_L0.092570.804
7_Y82_W0.092560.804
212_F249_G0.09250.803
53_P58_Q0.092470.803
187_R257_E0.092460.803
13_A17_L0.092430.803
15_Y82_W0.092420.803
95_L246_L0.092350.802
193_A256_L0.092240.801
116_A194_A0.09220.801
42_Q46_F0.092180.800
149_L152_L0.092120.800
57_E160_L0.091790.797
85_S89_A0.091790.797
220_S237_L0.091740.797
95_L247_L0.091620.796
7_Y90_S0.09160.795
136_F172_L0.091550.795
134_S209_S0.09150.795
151_L164_I0.09150.795
230_G234_I0.091460.794
174_F198_A0.091390.794
212_F235_L0.091370.793
91_L95_L0.091190.792
164_I168_V0.091150.792
59_L127_L0.090790.788
17_L76_G0.090690.788
2_R207_L0.090450.785
222_Y227_G0.090330.784
19_S40_I0.090230.784
134_S206_F0.090210.783
130_S176_L0.090190.783
49_R175_L0.089920.781
13_A235_L0.089870.780
201_A245_I0.08970.779
224_S242_S0.089570.778
209_S238_W0.089540.778
139_S246_L0.089390.776
150_G161_W0.089360.776
29_S93_R0.089150.774
84_A120_L0.089030.773
226_Y238_W0.088850.772
98_I250_A0.088680.770
189_V257_E0.088370.767
4_D7_Y0.088330.767
27_L123_L0.08820.766
18_L181_Y0.088180.766
72_L87_F0.088170.766
19_S189_V0.088110.765
235_L238_W0.088060.765
228_S232_L0.0880.764
183_F191_W0.08790.763
5_G238_W0.087890.763
54_D175_L0.087650.761
196_P199_L0.087630.761
162_N200_F0.087540.760
105_E187_R0.087460.759
66_I70_S0.087410.759
82_W181_Y0.087130.757
25_I29_S0.087130.757
92_Q201_A0.087090.756
4_D236_L0.086950.755
107_R167_L0.086840.754
177_F250_A0.086790.754
190_R207_L0.086780.754
64_E171_L0.086620.752
197_G201_A0.086460.751
71_S74_L0.086290.749
137_L140_V0.086260.749
35_P65_Q0.086250.749
39_L247_L0.086130.748
82_W196_P0.086010.747
25_I226_Y0.0860.747
6_F212_F0.085980.747
88_F120_L0.08590.746
39_L80_L0.085830.745
86_S224_S0.085820.745
163_L167_L0.08570.744
16_A137_L0.085560.743
23_L33_L0.08550.742
98_I176_L0.085390.741
19_S201_A0.085320.741
42_Q47_L0.085310.741
65_Q68_S0.08530.741
100_G129_L0.085280.741
18_L22_P0.08520.740
212_F239_L0.085120.739
33_L237_L0.085070.739
225_V228_S0.084990.738
142_Q190_R0.084860.737
73_G81_L0.084850.737
4_D8_L0.084810.736
69_S169_S0.084710.736
223_S228_S0.084670.735
142_Q163_L0.084640.735
25_I132_A0.084630.735
10_A240_Y0.08460.735
209_S228_S0.084570.734
129_L168_V0.084370.733
19_S127_L0.084350.732
137_L172_L0.084320.732
124_G243_A0.084260.732
34_L40_I0.084190.731
193_A257_E0.084120.730
115_I187_R0.083970.729
161_W164_I0.083760.727
63_L67_S0.083740.727
171_L199_L0.083720.727
126_L130_S0.083610.726
100_G208_L0.083580.726
77_I80_L0.083530.725
19_S246_L0.083410.724
229_L232_L0.083380.724
135_V220_S0.083350.724
121_I199_L0.083290.723
76_G245_I0.083230.723
81_L133_L0.083170.722
94_A224_S0.083060.721
212_F215_Y0.082910.720
57_E213_S0.082810.719
78_L167_L0.082660.718
8_L94_A0.082460.716
52_P55_I0.082320.715
54_D133_L0.082310.715
99_Y185_P0.082190.714
133_L150_G0.081970.712
32_G95_L0.081840.711
181_Y250_A0.081780.710
81_L86_S0.081730.710
10_A73_G0.081590.708
9_A107_R0.081550.708
94_A194_A0.081520.708
87_F116_A0.081390.707
20_L204_L0.081380.707
180_L184_L0.081360.707
14_Y180_L0.081330.706
26_L136_F0.08120.705
85_S243_A0.081080.704
43_L184_L0.081010.703
14_Y223_S0.080990.703
71_S80_L0.080910.703
225_V250_A0.080860.702
3_N255_V0.080820.702
26_L124_G0.080660.700
95_L101_V0.080610.700
27_L258_K0.08060.700
18_L88_F0.08060.700
181_Y247_L0.080590.700
136_F140_V0.080550.699
177_F194_A0.080270.697
52_P229_L0.080230.697
233_I246_L0.080140.696
254_A258_K0.080120.696
94_A248_L0.080090.695
64_E68_S0.080070.695
209_S239_L0.079960.694
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
4humA0.826965.60.927
3rlfF0.484649.10.933
1hgvA0.17698.20.954
4a82A0.307750.958
3mktA0.82693.40.961
4hygA0.53462.60.963
2iubA0.55772.50.963
1a87A0.24232.40.964
3kp9A0.58081.90.965
3effK0.38461.80.966
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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