GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HlyD_2 - HlyD family secretion protein
Pfam: PF12700 (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: CL0105
Length: 328
Sequences: 10957
Seq/Len: 33.41
HH_delta: 0.222 (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
33_S50_E1.481193.089
305_K318_S1.448343.020
43_K142_D1.375162.867
290_Y301_K1.337912.790
47_V136_Q1.262592.633
302_R324_D1.261282.630
231_G248_V1.20412.511
18_E199_E1.126052.348
279_K314_V1.105462.305
64_Q129_Q1.102152.298
4_R322_E1.08712.267
98_K102_S1.054492.199
234_S249_S1.047052.183
43_K46_Q1.04412.177
35_N50_E1.040052.169
115_K119_E1.039052.167
293_V302_R1.036452.161
276_V313_Y1.021832.131
97_A106_I1.019762.126
118_Y122_Q1.019312.125
98_K115_K1.012142.110
53_S57_Q0.966282.015
288_K303_P0.964282.011
17_V198_V0.961272.004
5_G313_Y0.94821.977
97_A114_A0.942221.965
47_V138_K0.941661.964
108_K112_D0.941511.963
321_K324_D0.937341.955
101_Y111_L0.934461.949
35_N47_V0.933741.947
50_E136_Q0.932661.945
4_R273_N0.924631.928
146_S191_A0.919691.918
215_K230_T0.903461.884
200_A265_V0.896831.870
5_G276_V0.887631.851
41_K144_V0.878951.833
68_E71_E0.862071.798
307_G315_E0.861341.796
307_G317_I0.848431.769
27_P134_L0.844831.762
61_E64_Q0.842811.757
217_E230_T0.840111.752
119_E122_Q0.829691.730
305_K317_I0.821621.713
197_Y247_R0.81681.703
227_K256_N0.813591.696
101_Y108_K0.811591.692
299_A327_V0.80491.678
215_K232_K0.80291.674
57_Q61_E0.800011.668
44_K142_D0.798681.665
32_V175_V0.781711.630
200_A248_V0.758061.581
139_A190_I0.755161.575
60_L64_Q0.754521.573
94_Y111_L0.754521.573
306_V314_V0.750351.565
6_T272_E0.748721.561
10_T266_S0.746261.556
293_V324_D0.743951.551
308_E315_E0.741111.545
2_V323_G0.726461.515
199_E245_K0.72551.513
217_E228_S0.725491.513
94_Y98_K0.725251.512
71_E75_E0.721031.503
291_V304_V0.720861.503
32_V49_A0.71641.494
304_V316_V0.714621.490
110_E113_Q0.711661.484
216_V248_V0.696891.453
126_N129_Q0.692091.443
20_N192_D0.684251.427
198_V263_V0.683321.425
12_E266_S0.671191.400
94_Y118_Y0.669241.395
37_K40_D0.668691.394
30_G51_L0.665731.388
17_V196_L0.659181.375
75_E78_Q0.659011.374
145_V188_F0.654691.365
12_E264_E0.654091.364
78_Q95_E0.648921.353
203_P206_D0.647951.351
240_A244_F0.637711.330
113_Q117_N0.636141.326
23_S186_P0.630781.315
21_E189_T0.628431.310
277_V326_V0.625691.305
279_K312_D0.625011.303
64_Q68_E0.624341.302
198_V265_V0.618561.290
219_T266_S0.616791.286
232_K249_S0.615861.284
33_S177_P0.615371.283
48_L188_F0.613921.280
285_E301_K0.613441.279
192_D195_N0.613071.278
201_Y245_K0.607261.266
275_L322_E0.605231.262
2_V275_L0.604931.261
74_L78_Q0.603741.259
6_T273_N0.599761.251
274_G315_E0.595091.241
36_V46_Q0.593081.237
111_L115_K0.589841.230
182_A185_Q0.584221.218
96_R112_D0.577221.204
284_E289_Y0.576841.203
100_L104_I0.576371.202
67_L71_E0.575081.199
235_S247_R0.57361.196
47_V50_E0.570761.190
23_S189_T0.557791.163
29_S183_A0.557721.163
112_D115_K0.556221.160
233_V246_V0.554151.156
294_V299_A0.546641.140
220_I263_V0.544511.135
59_Q62_Q0.542541.131
34_V177_P0.54191.130
127_K131_Q0.541061.128
173_I176_N0.53911.124
56_L135_A0.535261.116
139_A142_D0.534971.116
109_E113_Q0.529011.103
95_E98_K0.527561.100
57_Q132_S0.523051.091
199_E247_R0.520691.086
99_K103_Q0.520461.085
310_D313_Y0.519451.083
207_A244_F0.517281.079
172_K189_T0.514331.072
195_N249_S0.514281.072
40_D46_Q0.509891.063
38_E172_K0.508291.060
279_K309_E0.506961.057
49_A188_F0.506691.057
117_N121_A0.505111.053
41_K255_G0.503171.049
49_A137_I0.502891.049
316_V320_L0.498521.040
309_E314_V0.493761.030
295_E300_E0.493581.029
217_E268_I0.493141.028
252_N255_G0.490211.022
73_Q76_Q0.488831.019
219_T228_S0.488771.019
29_S182_A0.487421.016
282_I314_V0.486481.014
129_Q133_Q0.486351.014
294_V325_K0.485851.013
197_Y249_S0.485651.013
277_V291_V0.48521.012
104_I107_S0.484211.010
289_Y306_V0.483511.008
26_A137_I0.482941.007
62_Q66_E0.473470.987
95_E99_K0.472550.985
99_K102_S0.470130.980
59_Q127_K0.469390.979
22_V141_F0.467420.975
173_I188_F0.460250.960
98_K111_L0.459970.959
36_V145_V0.455760.950
66_E69_Q0.455520.950
17_V257_L0.455070.949
232_K251_D0.454560.948
9_Q209_K0.453880.946
8_S268_I0.451630.942
36_V173_I0.451620.942
141_F190_I0.447270.933
37_K173_I0.447230.933
268_I271_S0.446760.932
93_S109_E0.444770.927
32_V181_V0.444460.927
49_A187_L0.442740.923
117_N120_Q0.440720.919
94_Y115_K0.44060.919
206_D209_K0.436540.910
17_V263_V0.432430.902
78_Q122_Q0.431440.900
233_V248_V0.431050.899
195_N251_D0.430810.898
285_E288_K0.430660.898
121_A125_L0.430480.898
128_A131_Q0.430430.898
69_Q73_Q0.429130.895
130_L134_L0.427840.892
307_G314_V0.427630.892
93_S97_A0.427040.890
26_A49_A0.425530.887
130_L133_Q0.424520.885
217_E266_S0.422810.882
36_V188_F0.422680.881
49_A173_I0.422520.881
59_Q63_A0.420980.878
27_P31_R0.420760.877
221_D264_E0.420470.877
220_I250_L0.419790.875
59_Q131_Q0.418970.874
174_N189_T0.416780.869
237_S245_K0.413050.861
60_L129_Q0.412180.859
181_V187_L0.410810.857
16_T242_R0.409030.853
50_E53_S0.405150.845
26_A181_V0.405030.845
15_G263_V0.402590.839
8_S271_S0.402530.839
34_V49_A0.401680.838
115_K118_Y0.401450.837
93_S113_Q0.39910.832
196_L259_P0.399030.832
7_I310_D0.398740.831
41_K142_D0.398480.831
293_V300_E0.395410.825
218_V250_L0.395220.824
282_I289_Y0.394970.824
278_P281_A0.39380.821
74_L118_Y0.393210.820
63_A128_A0.392790.819
306_V316_V0.390990.815
121_A124_Q0.389610.812
223_P229_F0.389070.811
292_Y301_K0.387560.808
76_Q93_S0.387520.808
114_A117_N0.387390.808
100_L107_S0.386980.807
2_V320_L0.386830.807
61_E126_N0.386470.806
236_I246_V0.386380.806
20_N177_P0.383470.800
106_I114_A0.383170.799
28_V56_L0.3790.790
6_T271_S0.378770.790
104_I108_K0.377980.788
292_Y299_A0.377250.787
3_K322_E0.3760.784
67_L125_L0.375580.783
302_R319_G0.374840.782
223_P226_G0.373290.778
212_V236_I0.37270.777
97_A110_E0.37250.777
110_E114_A0.371850.775
24_V140_P0.371620.775
202_V210_I0.370340.772
57_Q60_L0.369830.771
9_Q270_G0.368840.769
60_L132_S0.367310.766
294_V327_V0.366450.764
19_P259_P0.365020.761
132_S135_A0.363060.757
283_I290_Y0.362760.756
10_T268_I0.362440.756
202_V246_V0.361360.754
285_E290_Y0.360150.751
297_G325_K0.36010.751
13_A200_A0.359680.750
66_E70_A0.359250.749
70_A73_Q0.358920.748
101_Y104_I0.358660.748
24_V188_F0.354510.739
11_I269_L0.35380.738
18_E197_Y0.353190.736
295_E298_K0.352980.736
277_V281_A0.352330.735
96_R100_L0.351240.732
41_K193_L0.350310.730
224_D227_K0.349090.728
78_Q118_Y0.346220.722
106_I110_E0.345880.721
114_A118_Y0.342030.713
21_E191_A0.340870.711
174_N186_P0.339530.708
63_A67_L0.338870.707
290_Y303_P0.338460.706
116_A120_Q0.337520.704
292_Y327_V0.335950.701
31_R180_Y0.334080.697
69_Q124_Q0.332910.694
55_D59_Q0.332450.693
307_G316_V0.331530.691
198_V218_V0.331010.690
219_T230_T0.329880.688
295_E302_R0.328750.686
24_V141_F0.328640.685
291_V320_L0.328490.685
143_G190_I0.327690.683
197_Y234_S0.326930.682
219_T226_G0.325840.679
128_A132_S0.325160.678
20_N176_N0.32440.676
294_V297_G0.324250.676
200_A267_I0.324160.676
15_G198_V0.323920.675
27_P55_D0.323870.675
4_R275_L0.320460.668
204_E262_F0.319720.667
258_R261_M0.318430.664
229_F254_N0.315760.658
63_A66_E0.315130.657
291_V326_V0.314780.656
210_I233_V0.313870.654
282_I304_V0.312590.652
25_S185_Q0.312070.651
59_Q128_A0.310630.648
7_I315_E0.309170.645
231_G250_L0.308610.644
307_G319_G0.307770.642
13_A202_V0.307240.641
277_V282_I0.306060.638
146_S172_K0.304840.636
107_S110_E0.304440.635
211_K214_Q0.303470.633
13_A267_I0.303360.633
64_Q67_L0.302770.631
281_A326_V0.302250.630
7_I308_E0.302020.630
293_V326_V0.300480.627
26_A187_L0.298850.623
282_I306_V0.298340.622
302_R321_K0.297880.621
53_S136_Q0.297270.620
44_K140_P0.292760.610
220_I223_P0.29270.610
218_V248_V0.292510.610
201_Y243_T0.292410.610
277_V314_V0.292050.609
60_L63_A0.291170.607
131_Q134_L0.291050.607
218_V231_G0.290880.607
53_S135_A0.289670.604
101_Y106_I0.288980.603
24_V137_I0.288910.602
73_Q77_A0.288540.602
11_I206_D0.287040.599
200_A216_V0.286990.598
106_I111_L0.286680.598
38_E146_S0.285370.595
108_K111_L0.285020.594
283_I292_Y0.283990.592
23_S179_Q0.283910.592
207_A261_M0.28360.591
194_S255_G0.283040.590
96_R109_E0.281760.588
144_V193_L0.281740.587
36_V49_A0.281110.586
65_A123_A0.279280.582
108_K115_K0.279240.582
62_Q127_K0.279010.582
58_A130_L0.278540.581
325_K328_T0.277070.578
5_G310_D0.275830.575
320_L324_D0.275060.574
36_V40_D0.274910.573
42_V48_L0.274890.573
118_Y121_A0.274760.573
74_L122_Q0.27460.573
56_L128_A0.274130.572
13_A206_D0.274010.571
93_S96_R0.2740.571
191_A238_P0.273960.571
111_L118_Y0.273690.571
233_V236_I0.273220.570
219_T264_E0.273120.570
62_Q124_Q0.2730.569
191_A259_P0.271370.566
234_S247_R0.271040.565
109_E112_D0.27070.564
276_V315_E0.270630.564
42_V46_Q0.269220.561
20_N141_F0.268540.560
29_S180_Y0.268040.559
38_E173_I0.268020.559
71_E74_L0.26670.556
198_V250_L0.265570.554
97_A109_E0.265230.553
35_N46_Q0.264750.552
96_R104_I0.264750.552
291_V319_G0.264490.552
7_I276_V0.263980.550
2_V324_D0.26380.550
18_E21_E0.2630.548
32_V187_L0.262880.548
25_S186_P0.261920.546
275_L319_G0.261770.546
45_G142_D0.261420.545
248_V265_V0.260530.543
44_K139_A0.259610.541
22_V140_P0.258430.539
295_E324_D0.256970.536
31_R52_D0.256760.535
74_L125_L0.256310.534
100_L105_A0.255770.533
58_A62_Q0.255630.533
112_D116_A0.255590.533
218_V265_V0.255350.532
222_A261_M0.255120.532
240_A262_F0.254680.531
137_I187_L0.253820.529
275_L320_L0.253380.528
116_A123_A0.253160.528
220_I257_L0.252770.527
45_G138_K0.25270.527
119_E123_A0.252450.526
118_Y125_L0.252350.526
221_D266_S0.251330.524
25_S180_Y0.250820.523
100_L106_I0.249610.520
216_V267_I0.249520.520
30_G181_V0.248320.518
17_V220_I0.248060.517
196_L252_N0.246660.514
120_Q124_Q0.245490.512
227_K254_N0.245220.511
19_P191_A0.245120.511
53_S56_L0.245050.511
282_I290_Y0.243940.509
13_A265_V0.243020.507
26_A51_L0.24210.505
9_Q269_L0.241760.504
46_Q142_D0.241540.504
306_V317_I0.240640.502
175_V179_Q0.240510.502
67_L74_L0.240060.501
176_N179_Q0.239310.499
200_A246_V0.239070.499
252_N256_N0.238720.498
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
4dk0A0.90241000.222
3fppA0.90241000.232
3lnnA0.86591000.253
1vf7A0.86281000.258
4l8jA0.85671000.26
3ne5B0.83231000.304
2f1mA0.76521000.414
2k32A0.347699.60.71
2d5dA0.222698.90.805
1z6hA0.216598.80.807

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