GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SMP_2 - Bacterial virulence factor haemolysin
Pfam: PF10144 (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: 210
Sequences: 7830
Seq/Len: 37.29
HH_delta: 0.567 (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
94_D98_V0.912993.759
9_R13_T0.874113.599
91_S143_R0.825963.401
42_S126_Q0.655092.697
129_V143_R0.65392.693
177_V181_R0.594732.449
180_A183_L0.584862.408
27_M31_S0.567032.335
176_G180_A0.558412.299
89_D145_T0.535672.206
93_Y99_L0.486792.004
186_K189_S0.481831.984
92_I142_L0.454871.873
9_R12_R0.429181.767
129_V141_F0.428761.766
89_D102_Q0.427211.759
131_P141_F0.424981.750
178_L182_S0.417921.721
93_Y143_R0.408751.683
127_Q143_R0.383171.578
34_S38_Q0.382261.574
180_A184_L0.367921.515
44_Q146_L0.359781.481
127_Q145_T0.356431.468
41_R151_L0.353331.455
42_S46_E0.352311.451
94_D97_G0.349811.440
36_S40_A0.345381.422
165_L169_L0.343491.414
11_H15_I0.343331.414
99_L102_Q0.341241.405
46_E50_R0.336361.385
93_Y141_F0.332931.371
166_R170_L0.32811.351
162_M166_R0.325591.341
28_Q32_W0.323881.334
134_S137_G0.322981.330
173_L177_V0.314081.293
163_N167_L0.311581.283
79_N82_A0.310911.280
94_D100_L0.310891.280
44_Q48_L0.309381.274
181_R186_K0.306591.262
160_Q163_N0.305581.258
179_L183_L0.30331.249
49_A53_V0.302861.247
162_M165_L0.295081.215
159_D163_N0.29331.208
148_T152_Q0.29041.196
31_S35_L0.288171.187
11_H14_V0.2871.182
14_V18_I0.283621.168
132_I140_G0.283191.166
43_N46_E0.282311.162
170_L174_L0.281491.159
72_E75_Q0.280791.156
91_S99_L0.27761.143
19_C23_L0.276461.138
10_L184_L0.276151.137
91_S145_T0.274021.128
39_Q42_S0.272521.122
31_S34_S0.272471.122
146_L151_L0.270251.113
22_L26_I0.267471.101
14_V180_A0.264321.088
27_M30_V0.259881.070
35_L39_Q0.25861.065
38_Q42_S0.258331.064
10_L14_V0.257891.062
74_L77_L0.255461.052
16_I19_C0.254971.050
73_Q76_Q0.254311.047
78_L90_A0.253411.043
185_R188_R0.252811.041
159_D162_M0.252431.039
30_V34_S0.251631.036
182_S185_R0.24991.029
70_D73_Q0.249761.028
94_D99_L0.248631.024
26_I165_L0.247081.017
178_L181_R0.245771.012
45_V49_A0.245431.011
25_I168_M0.245251.010
163_N166_R0.244781.008
15_I18_I0.244671.007
128_I131_P0.244251.006
104_G108_S0.242831.000
39_Q43_N0.241630.995
99_L103_S0.237030.976
37_S40_A0.236090.972
172_A180_A0.234680.966
8_K12_R0.233760.963
41_R44_Q0.231760.954
33_F36_S0.23110.952
52_L142_L0.230650.950
16_I20_L0.230640.950
30_V33_F0.23020.948
95_A137_G0.228980.943
112_R115_L0.227460.937
43_N47_N0.22660.933
181_R184_L0.225440.928
131_P140_G0.224580.925
151_L154_E0.224350.924
33_F154_E0.219110.902
54_R58_N0.21770.896
12_R15_I0.217110.894
58_N76_Q0.216210.890
29_G33_F0.216020.890
42_S45_V0.215780.889
169_L173_L0.214650.884
71_Q75_Q0.213820.880
34_S37_S0.213340.878
50_R54_R0.210890.868
37_S154_E0.210020.865
87_V90_A0.209880.864
11_H181_R0.209180.861
70_D74_L0.207090.853
12_R16_I0.206760.851
164_Q167_L0.206090.849
36_S39_Q0.203720.839
48_L51_S0.203630.838
46_E128_I0.203430.838
37_S41_R0.203010.836
28_Q31_S0.202610.834
104_G107_V0.202140.832
166_R181_R0.200980.828
40_A44_Q0.200960.827
128_I143_R0.200070.824
148_T151_L0.200060.824
91_S102_Q0.199830.823
152_Q159_D0.199310.821
185_R189_S0.198810.819
137_G140_G0.197780.814
44_Q47_N0.196970.811
174_L178_L0.195230.804
35_L38_Q0.19490.803
91_S129_V0.193690.798
78_L92_I0.193450.797
41_R146_L0.193430.796
183_L187_R0.192360.792
49_A128_I0.191920.790
41_R155_S0.191190.787
58_N83_K0.191140.787
43_N119_E0.191040.787
52_L55_Q0.190290.784
92_I100_L0.190080.783
45_V146_L0.189820.782
40_A43_N0.189660.781
21_A29_G0.189580.781
30_V162_M0.188940.778
34_S152_Q0.188850.778
54_R130_E0.188640.777
90_A144_I0.188170.775
50_R130_E0.187950.774
173_L181_R0.187410.772
151_L155_S0.187290.771
81_L89_D0.187190.771
24_V28_Q0.187050.770
48_L52_L0.18530.763
75_Q78_L0.184020.758
13_T30_V0.183710.756
37_S155_S0.18320.754
18_I21_A0.182720.752
95_A153_T0.181850.749
165_L172_A0.180520.743
183_L186_K0.180520.743
81_L90_A0.180450.743
92_I140_G0.17930.738
52_L144_I0.179150.738
172_A176_G0.178210.734
25_I29_G0.177910.733
74_L101_A0.177020.729
181_R185_R0.175920.724
49_A146_L0.175830.724
17_L179_L0.175180.721
30_V155_S0.172330.710
10_L180_A0.172160.709
26_I37_S0.172150.709
154_E161_S0.171940.708
54_R76_Q0.171580.707
40_A151_L0.171330.705
76_Q79_N0.171210.705
47_N54_R0.170350.701
56_A142_L0.170030.700
41_R45_V0.169840.699
111_E117_G0.169610.698
33_F37_S0.169580.698
166_R169_L0.168610.694
26_I169_L0.168260.693
177_V182_S0.168250.693
169_L172_A0.168210.693
14_V172_A0.168020.692
29_G165_L0.167860.691
11_H21_A0.167840.691
77_L80_Q0.166610.686
50_R55_Q0.166520.686
18_I180_A0.166470.685
57_A132_I0.165840.683
26_I54_R0.165730.682
182_S186_K0.165430.681
111_E116_D0.164070.676
20_L23_L0.162840.671
70_D79_N0.162150.668
97_G100_L0.161890.667
111_E115_L0.161790.666
117_G120_A0.161510.665
93_Y96_D0.161260.664
75_Q79_N0.161050.663
149_Q153_T0.160670.662
108_S120_A0.159850.658
32_W160_Q0.159640.657
175_I179_L0.159620.657
19_C26_I0.15930.656
184_L187_R0.159270.656
130_E176_G0.159150.655
150_Y153_T0.158870.654
174_L189_S0.158830.654
14_V17_L0.158030.651
53_V56_A0.157710.649
28_Q161_S0.157230.647
38_Q155_S0.157090.647
12_R23_L0.157020.647
49_A56_A0.156980.646
27_M34_S0.156330.644
177_V183_L0.156150.643
112_R118_P0.156110.643
20_L24_V0.156070.643
25_I176_G0.15590.642
180_A187_R0.15580.642
174_L177_V0.15570.641
154_E160_Q0.155040.638
17_L21_A0.153340.631
137_G185_R0.152870.629
49_A144_I0.152740.629
164_Q168_M0.15190.625
39_Q163_N0.151710.625
43_N167_L0.151630.624
29_G161_S0.151590.624
58_N159_D0.151550.624
74_L92_I0.150570.620
182_S189_S0.150470.620
12_R17_L0.150420.619
19_C22_L0.150340.619
53_V130_E0.15030.619
49_A142_L0.150290.619
43_N85_P0.150280.619
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
2kseA0.828698.80.567
4i5sA0.304897.60.7
2f95B0.51997.50.708
4gycB0.533397.10.736
2f93B0.528696.90.742
3b47A0.552496.50.758
3b42A0.552496.50.758
1p0zA0.542996.20.766
3cwfA0.528696.10.769
3by8A0.595295.90.773
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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