GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SbmA_BacA - SbmABacA-like family
Pfam: PF05992 (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: CL0241
Length: 315
Sequences: 23197
Seq/Len: 73.64
HH_delta: 0.273 (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
142_P146_E1.326113.162
38_D271_G1.133532.703
308_R312_A1.129652.694
215_Q218_T1.059562.526
261_P265_A1.014322.419
98_H102_L0.965512.302
145_W152_S0.960442.290
115_D306_R0.939292.240
38_D269_T0.936322.233
177_I181_F0.931962.222
148_S262_S0.912262.175
60_L64_W0.90032.147
257_I261_P0.851682.031
145_W149_S0.836641.995
223_F227_R0.834061.989
262_S267_A0.825611.969
185_K188_G0.797491.902
196_V229_N0.793331.892
34_G38_D0.783011.867
57_A61_N0.776681.852
56_Y60_L0.757971.807
34_G275_Q0.750441.789
218_T222_L0.74921.786
231_F235_F0.744241.775
196_V199_A0.743821.774
269_T272_V0.737241.758
207_G210_D0.73371.749
93_E97_S0.712981.700
215_Q219_L0.705641.683
191_F305_K0.691661.649
221_E225_N0.682071.626
304_Y308_R0.677541.616
197_E201_R0.671541.601
88_R92_N0.669791.597
18_V75_L0.665971.588
21_F72_L0.663551.582
138_I142_P0.662121.579
98_H311_E0.661631.578
18_V72_L0.658071.569
217_P221_E0.65041.551
151_V276_I0.647641.544
166_W170_I0.645271.539
53_D57_A0.632841.509
97_S101_K0.632761.509
149_S166_W0.632461.508
144_L276_I0.628891.500
170_I173_L0.62781.497
95_Y310_F0.62481.490
90_A94_Y0.624791.490
225_N229_N0.623431.487
220_R224_S0.617571.473
192_N196_V0.617191.472
31_E35_P0.614761.466
219_L222_L0.611521.458
51_T54_E0.609621.454
219_L223_F0.604461.441
211_A216_P0.60381.440
150_H267_A0.603021.438
258_I262_S0.598931.428
147_L272_V0.597291.424
30_N279_A0.593261.415
89_T93_E0.58661.399
301_R305_K0.571241.362
118_R303_I0.569781.359
34_G272_V0.561881.340
54_E57_A0.558071.331
82_H86_R0.555931.326
224_S228_R0.555361.324
195_K198_A0.551441.315
206_Y210_D0.548951.309
94_Y98_H0.548271.307
227_R231_F0.544821.299
27_V139_A0.536481.279
150_H262_S0.535561.277
95_Y307_L0.53461.275
213_R216_P0.533431.272
199_A229_N0.532571.270
148_S151_V0.528511.260
194_Q197_E0.527751.258
57_A60_L0.524421.250
229_N233_L0.52371.249
218_T221_E0.522941.247
18_V79_F0.517811.235
195_K199_A0.51121.219
188_G192_N0.510771.218
118_R299_E0.51031.217
213_R223_F0.506171.207
24_Q28_A0.505981.206
145_W169_I0.504521.203
229_N232_R0.504161.202
143_I146_E0.503961.202
235_F239_Y0.502631.198
212_N219_L0.501751.196
35_P39_L0.500961.195
259_L273_L0.500481.193
95_Y112_I0.498211.188
271_G275_Q0.498031.188
192_N233_L0.497931.187
232_R236_H0.496231.183
140_F282_Q0.49621.183
217_P220_R0.495351.181
185_K189_L0.495191.181
173_L177_I0.493191.176
144_L152_S0.492971.175
233_L236_H0.492161.174
242_I246_S0.490911.171
148_S268_I0.490421.169
198_A202_K0.490011.168
180_A184_I0.489391.167
226_V229_N0.483511.153
146_E149_S0.482691.151
260_I264_V0.482311.150
35_P38_D0.48111.147
167_A258_I0.480731.146
307_L311_E0.479581.144
190_E194_Q0.475121.133
222_L226_V0.473191.128
181_F185_K0.472951.128
212_N216_P0.471211.124
191_F195_K0.466711.113
203_E206_Y0.462611.103
35_P58_Q0.462081.102
228_R232_R0.462051.102
285_S289_Y0.461081.099
94_Y311_E0.460391.098
141_L152_S0.459421.095
228_R231_F0.458271.093
300_L303_I0.45621.088
196_V233_L0.455861.087
133_S289_Y0.455471.086
258_I261_P0.455211.085
64_W68_I0.454671.084
122_I300_L0.451291.076
222_L225_N0.451111.076
96_M100_P0.449171.071
176_T180_A0.4491.071
210_D219_L0.448771.070
71_V75_L0.44611.064
39_L54_E0.444441.060
171_W251_D0.44261.055
199_A226_V0.441121.052
61_N64_W0.440891.051
114_E117_M0.440181.050
143_I147_L0.439871.049
60_L63_L0.439871.049
189_L236_H0.438871.046
226_V230_Y0.437021.042
98_H101_K0.433161.033
192_N195_K0.432961.032
177_I180_A0.43071.027
75_L79_F0.430691.027
262_S265_A0.427951.020
221_E224_S0.426651.017
32_W58_Q0.426181.016
263_I268_I0.425731.015
246_S250_F0.425321.014
111_R309_A0.423931.011
236_H239_Y0.422341.007
17_F21_F0.416610.993
58_Q61_N0.41650.993
245_I249_Q0.41620.992
232_R235_F0.416160.992
19_T76_N0.415660.991
115_D303_I0.41020.978
148_S152_S0.409380.976
121_K125_D0.407770.972
25_V72_L0.40720.971
262_S266_G0.406560.969
31_E143_I0.406170.968
254_F258_I0.405470.967
184_I188_G0.405410.967
95_Y311_E0.404970.966
186_L190_E0.404850.965
105_I108_A0.399170.952
19_T132_R0.399030.951
94_Y97_S0.398620.950
37_Y274_Q0.39560.943
67_M71_V0.395470.943
38_D42_K0.393740.939
25_V68_I0.393710.939
239_Y242_I0.392250.935
246_S249_Q0.391370.933
108_A198_A0.388490.926
260_I263_I0.388070.925
31_E34_G0.387220.923
88_R120_A0.384530.917
189_L193_N0.382820.913
59_I63_L0.382030.911
31_E147_L0.381990.911
85_F88_R0.38190.911
88_R116_T0.381510.910
74_V78_F0.381010.908
22_Q73_A0.380240.907
86_R90_A0.378250.902
27_V30_N0.377740.901
238_M242_I0.375980.896
234_Y238_M0.375830.896
305_K309_A0.375730.896
150_H166_W0.374270.892
235_F238_M0.37220.887
216_P220_R0.372010.887
140_F279_A0.370670.884
147_L275_Q0.370560.884
62_F66_A0.37040.883
132_R136_T0.369950.882
187_P191_F0.369380.881
91_M116_T0.366560.874
206_Y209_D0.364840.870
189_L192_N0.363720.867
259_L263_I0.360990.861
23_V27_V0.359010.856
272_V275_Q0.355320.847
139_A142_P0.35440.845
70_V74_V0.353130.842
230_Y234_Y0.352890.841
151_V262_S0.351770.839
90_A93_E0.351740.839
115_D119_F0.351160.837
237_Y241_N0.349350.833
213_R219_L0.348090.830
32_W65_I0.347930.830
111_R115_D0.346930.827
198_A201_R0.34680.827
145_W166_W0.345610.824
236_H240_F0.345110.823
116_T307_L0.344510.821
303_I306_R0.343730.820
149_S152_S0.343650.819
25_V28_A0.34320.818
146_E150_H0.342990.818
245_I248_L0.342770.817
128_V131_I0.3420.815
233_L237_Y0.341610.815
31_E275_Q0.339570.810
80_V128_V0.337330.804
259_L262_S0.336710.803
187_P301_R0.336590.803
268_I272_V0.336530.802
253_I257_I0.336010.801
121_K296_T0.335880.801
268_I273_L0.335830.801
112_I116_T0.33470.798
39_L42_K0.334230.797
53_D56_Y0.333190.794
308_R311_E0.332410.793
185_K240_F0.331960.792
81_S85_F0.33190.791
117_M120_A0.33110.789
95_Y116_T0.330930.789
68_I72_L0.329740.786
227_R230_Y0.329120.785
118_R121_K0.328190.783
56_Y59_I0.328180.783
189_L233_L0.328080.782
85_F89_T0.328050.782
150_H258_I0.325980.777
32_W61_N0.325890.777
137_L141_L0.323690.772
117_M121_K0.323220.771
142_P145_W0.323040.770
34_G37_Y0.322840.770
79_F83_Y0.322120.768
119_F304_Y0.321640.767
196_V200_Y0.320580.764
84_I124_E0.317860.758
202_K205_V0.317840.758
129_S289_Y0.317720.758
168_A280_F0.317480.757
78_F82_H0.317320.757
29_I33_Y0.31650.755
43_A51_T0.315740.753
83_Y87_W0.315550.752
32_W35_P0.315240.752
86_R89_T0.315230.752
23_V26_S0.3150.751
152_S276_I0.314670.750
38_D41_Q0.313870.748
141_L145_W0.313820.748
168_A173_L0.313440.747
134_I138_I0.313380.747
193_N234_Y0.313080.747
225_N228_R0.313070.746
99_W102_L0.312790.746
21_F68_I0.312010.744
199_A202_K0.311470.743
28_A65_I0.311340.742
27_V279_A0.310620.741
100_P103_R0.30930.738
110_Q115_D0.309270.737
181_F184_I0.308710.736
18_V21_F0.308290.735
77_S81_S0.307710.734
239_Y243_A0.307020.732
198_A306_R0.306280.730
25_V69_Y0.305510.728
232_R239_Y0.30550.728
102_L310_F0.305050.727
115_D118_R0.304510.726
293_S297_I0.303420.723
28_A31_E0.301940.720
63_L67_M0.301830.720
25_V65_I0.301670.719
279_A282_Q0.301240.718
66_A69_Y0.300760.717
174_F178_L0.300680.717
123_M126_L0.300640.717
241_N244_R0.300310.716
244_R248_L0.297870.710
110_Q114_E0.297530.709
61_N65_I0.297190.709
297_I301_R0.297120.708
306_R309_A0.296760.708
115_D194_Q0.296760.708
140_F283_V0.296650.707
223_F230_Y0.295040.704
55_F59_I0.294760.703
252_V255_P0.2940.701
152_S169_I0.29390.701
140_F286_S0.293830.701
190_E193_N0.29330.699
252_V256_Y0.293120.699
151_V259_L0.293110.699
193_N197_E0.292590.698
186_L189_L0.291430.695
243_A247_Y0.291140.694
34_G147_L0.291090.694
54_E58_Q0.291030.694
69_Y73_A0.290970.694
192_N236_H0.290780.693
296_T299_E0.290410.692
190_E237_Y0.289840.691
22_Q26_S0.28930.690
209_D213_R0.288250.687
252_V281_G0.28810.687
130_F134_I0.28780.686
263_I273_L0.287790.686
122_I297_I0.287340.685
275_Q279_A0.287090.685
28_A35_P0.287080.685
119_F307_L0.28660.683
18_V22_Q0.284330.678
52_I56_Y0.283860.677
79_F82_H0.28310.675
143_I279_A0.282550.674
192_N229_N0.281770.672
298_V301_R0.281040.670
21_F25_V0.280920.670
276_I279_A0.280810.670
179_L183_G0.28080.670
66_A70_V0.280560.669
89_T227_R0.280460.669
91_M119_F0.280220.668
240_F244_R0.278790.665
67_M70_V0.277620.662
84_I120_A0.276980.660
273_L277_S0.27620.659
95_Y99_W0.27610.658
31_E279_A0.275160.656
23_V135_M0.274830.655
224_S227_R0.274440.654
29_I66_A0.273520.652
27_V143_I0.273390.652
111_R198_A0.272610.650
200_Y230_Y0.272510.650
301_R304_Y0.272440.650
92_N99_W0.27160.648
85_F120_A0.271410.647
246_S251_D0.270320.645
33_Y278_N0.269680.643
234_Y237_Y0.269450.642
139_A143_I0.269070.642
32_W36_F0.267960.639
72_L75_L0.267440.638
167_A171_W0.267070.637
19_T23_V0.266990.637
113_Q117_M0.266810.636
40_I43_A0.266410.635
169_I173_L0.266330.635
279_A286_S0.266190.635
194_Q302_S0.265210.632
99_W310_F0.264590.631
205_V210_D0.264560.631
78_F81_S0.264330.630
194_Q198_A0.263780.629
212_N227_R0.263550.628
166_W169_I0.263280.628
214_A219_L0.261710.624
292_N296_T0.261560.624
111_R306_R0.261290.623
175_G179_L0.260980.622
195_K306_R0.260790.622
109_S113_Q0.260040.620
275_Q278_N0.259870.620
184_I187_P0.259410.619
204_L219_L0.259340.618
129_S133_S0.258970.617
62_F65_I0.258790.617
194_Q202_K0.258730.617
107_G202_K0.258330.616
210_D215_Q0.257340.614
150_H167_A0.256560.612
52_I55_F0.25640.611
148_S276_I0.256210.611
56_Y257_I0.256110.611
208_E212_N0.25550.609
108_A203_E0.255340.609
22_Q72_L0.254650.607
278_N281_G0.254270.606
20_W24_Q0.25420.606
257_I260_I0.253450.604
212_N226_V0.253450.604
273_L276_I0.253210.604
108_A111_R0.25310.603
253_I256_Y0.252780.603
16_L19_T0.25270.603
187_P305_K0.252110.601
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
4f4cA0.958799.90.273
3qf4B0.939799.90.281
3b60A0.939799.90.294
3b5xA0.939799.90.296
4a82A0.949299.90.3
3qf4A0.939799.90.3
2yl4A0.94699.90.31
3g5uA0.958799.90.324
4f4cA0.94699.90.405
3g5uA0.952499.80.44

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