GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MFS_3 - Transmembrane secretion effector
Pfam: PF05977 (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: CL0015
Length: 524
Sequences: 3155
Seq/Len: 6.02
HH_delta: 0.538 (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
336_V344_V0.20172.802
212_R216_S0.194872.707
293_L320_A0.178042.473
381_A385_L0.176942.458
93_A173_L0.171712.385
66_G342_G0.16712.321
104_W108_I0.164732.288
66_G70_D0.163512.271
84_L116_G0.156612.175
70_D342_G0.152642.120
74_R130_E0.150092.085
337_P340_V0.148952.069
266_G315_F0.140151.947
384_L388_L0.136871.901
138_P279_R0.135591.883
88_V109_L0.135011.875
275_P279_R0.13361.856
269_L273_L0.130411.811
132_V140_A0.12941.797
73_D76_R0.125961.750
74_R126_A0.125761.747
65_A119_F0.125331.741
57_P111_F0.125281.740
300_L313_A0.124751.733
160_G257_G0.123121.710
129_P137_L0.120891.679
184_L188_R0.119711.663
103_P107_L0.118081.640
262_A311_L0.117311.629
377_L381_A0.114911.596
365_F369_H0.114911.596
102_S105_L0.113211.572
292_L296_L0.113031.570
228_F355_G0.111881.554
43_S46_M0.110941.541
90_L94_V0.110561.536
20_L151_A0.109311.518
283_S334_L0.108251.504
295_A384_L0.108231.503
61_L118_A0.106811.484
276_R280_R0.106581.480
54_S110_T0.105221.461
268_I272_L0.105111.460
297_A313_A0.103621.439
296_L303_L0.10291.429
88_V112_L0.102651.426
133_P136_D0.102241.420
87_L91_L0.101511.410
252_G255_G0.101321.407
79_I183_I0.101241.406
101_L105_L0.09931.379
57_P61_L0.09861.370
110_T113_L0.098171.364
32_A172_F0.097151.349
266_G318_G0.096761.344
91_L109_L0.096531.341
73_D77_I0.096191.336
282_S286_L0.096141.335
330_T334_L0.096021.334
45_L368_D0.095761.330
81_S119_F0.095261.323
70_D74_R0.095091.321
91_L94_V0.094841.317
302_A380_G0.094721.316
83_L87_L0.094391.311
73_D110_T0.093891.304
53_A107_L0.093761.302
181_I187_L0.093541.299
158_L161_I0.092961.291
262_A315_F0.092671.287
138_P275_P0.092571.286
297_A320_A0.092421.284
308_W312_I0.092381.283
323_I327_S0.091141.266
25_G28_M0.091031.264
58_I62_S0.090911.263
79_I186_L0.089771.247
69_A74_R0.089691.246
279_R283_S0.089451.242
230_F234_A0.08871.232
73_D114_G0.087941.221
17_I181_I0.087881.221
78_L127_I0.087731.219
306_S309_L0.087641.217
295_A387_A0.087571.216
137_L334_L0.087341.213
73_D137_L0.087231.212
295_A380_G0.087061.209
170_A173_L0.086561.202
307_F311_L0.086411.200
282_S285_R0.086131.196
184_L187_L0.086021.195
361_L365_F0.08581.192
70_D343_R0.085331.185
355_G359_G0.085291.185
58_I353_F0.085271.184
281_L285_R0.084961.180
53_A111_F0.08371.163
79_I187_L0.083491.160
366_L370_F0.083131.155
48_A364_G0.083061.154
397_Q400_E0.082671.148
273_L276_R0.082611.147
202_R205_S0.082541.146
274_L323_I0.082511.146
292_L295_A0.082441.145
177_L181_I0.082061.140
176_A180_L0.081981.139
362_L366_L0.081751.135
17_I24_L0.081671.134
95_L105_L0.081541.133
56_L354_G0.08141.131
160_G318_G0.081341.130
281_L286_L0.081281.129
251_G255_G0.0811.125
93_A176_A0.080841.123
186_L190_K0.080731.121
277_L289_L0.080331.116
95_L109_L0.080311.115
90_L176_A0.080261.115
62_S341_R0.079511.104
108_I205_S0.079471.104
59_L354_G0.079261.101
142_A275_P0.07921.100
258_L311_L0.079121.099
47_V287_V0.078651.092
292_L387_A0.078621.092
88_V116_G0.078461.090
295_A300_L0.078071.084
49_L52_A0.077941.083
211_L220_L0.077891.082
292_L399_E0.077791.080
125_Q132_V0.077571.077
218_P221_R0.077541.077
130_E341_R0.077311.074
162_L174_I0.077211.072
221_R332_V0.0771.070
72_F77_I0.076751.066
162_L170_A0.076741.066
145_S148_F0.076661.065
172_F275_P0.076561.063
68_L72_F0.076361.061
114_G341_R0.076231.059
270_G319_A0.076161.058
139_A354_G0.07611.057
183_I187_L0.076021.056
51_Q239_A0.075551.049
124_W144_N0.075541.049
383_L387_A0.075531.049
68_L287_V0.075351.047
262_A266_G0.075011.042
286_L290_A0.074961.041
285_R289_L0.074931.041
160_G258_L0.074921.041
37_V103_P0.074911.040
282_S397_Q0.07471.038
128_I287_V0.07461.036
267_A322_I0.074511.035
85_R116_G0.07441.033
61_L138_P0.07431.032
370_F374_T0.074181.030
25_G168_A0.074141.030
160_G253_A0.07391.026
151_A238_W0.073821.025
74_R131_L0.073611.022
27_W52_A0.073541.021
57_P114_G0.073511.021
83_L180_L0.073431.020
87_L197_S0.07341.020
73_D119_F0.072911.013
46_M107_L0.07261.008
86_A180_L0.072551.008
228_F313_A0.072381.005
187_L381_A0.072251.004
111_F237_V0.072231.003
20_L153_I0.072081.001
173_L177_L0.071971.000
296_L378_I0.071880.998
147_S151_A0.071730.996
126_A342_G0.071720.996
102_S106_L0.071720.996
165_F296_L0.071670.995
50_V53_A0.071620.995
153_I265_V0.07150.993
55_T172_F0.071440.992
306_S311_L0.071180.989
402_D405_P0.071170.989
35_W253_A0.071170.989
66_G346_S0.071140.988
20_L148_F0.071050.987
299_L303_L0.071050.987
327_S330_T0.071010.986
170_A177_L0.070980.986
174_I406_S0.070890.985
75_R79_I0.070780.983
79_I185_A0.070730.982
275_P376_L0.07070.982
89_A113_L0.070380.978
310_A354_G0.07010.974
227_S328_L0.070010.972
39_Q43_S0.069730.969
309_L316_L0.069410.964
308_W311_L0.069290.962
258_L261_A0.069180.961
241_L362_L0.069130.960
84_L112_L0.069040.959
87_L90_L0.068820.956
367_A375_A0.068770.955
43_S368_D0.068630.953
66_G69_A0.068520.952
61_L115_I0.06850.951
61_L367_A0.068360.950
296_L300_L0.068350.949
66_G119_F0.068350.949
110_T114_G0.068280.948
75_R190_K0.068140.946
22_S82_Q0.068070.945
83_L319_A0.068070.945
187_L192_P0.067780.941
222_S389_I0.067770.941
16_W147_S0.067730.941
138_P283_S0.067650.940
395_L402_D0.067650.940
121_N125_Q0.067630.939
171_A263_F0.067610.939
371_G374_T0.067580.939
22_S175_N0.067580.939
378_I381_A0.067570.939
48_A257_G0.067530.938
269_L315_F0.067510.938
286_L289_L0.067450.937
73_D336_V0.067430.937
168_A179_F0.067370.936
61_L334_L0.067320.935
274_L277_L0.067220.934
70_D336_V0.067110.932
304_S310_A0.066970.930
145_S325_N0.066920.930
33_L51_Q0.066820.928
174_I177_L0.066790.928
85_R120_F0.066780.928
362_L379_A0.066720.927
146_I150_I0.066380.922
402_D406_S0.066350.922
244_F249_L0.066220.920
118_A122_P0.066220.920
228_F387_A0.066190.919
75_R271_A0.066150.919
16_W78_L0.066120.918
128_I144_N0.06610.918
396_R402_D0.066090.918
38_T41_T0.066050.917
23_N26_D0.065910.915
285_R296_L0.065890.915
17_I204_F0.065890.915
226_R231_N0.065860.915
22_S58_I0.065810.914
62_S120_F0.065660.912
78_L231_N0.065650.912
157_A261_A0.065640.912
128_I235_S0.06560.911
102_S195_P0.065520.910
277_L281_L0.065510.910
233_F236_A0.065510.910
299_L380_G0.065490.910
397_Q403_L0.065450.909
291_S295_A0.065410.909
172_F314_L0.065380.908
60_L64_F0.065370.908
78_L81_S0.065330.907
155_G253_A0.065270.907
57_P73_D0.065270.907
117_S346_S0.065250.906
209_E366_L0.065240.906
183_I246_R0.065170.905
41_T44_P0.065130.905
237_V314_L0.065120.905
28_M171_A0.065060.904
312_I381_A0.065050.904
211_L381_A0.065040.903
108_I195_P0.065030.903
401_L405_P0.064940.902
95_L102_S0.064910.902
110_T168_A0.064830.900
235_S238_W0.064810.900
42_G103_P0.06480.900
138_P334_L0.064730.899
142_A271_A0.064710.899
196_S380_G0.064680.898
137_L278_R0.064620.898
137_L343_R0.064530.896
36_L172_F0.064490.896
340_V343_R0.064370.894
312_I316_L0.064180.891
85_R89_A0.06410.890
201_E205_S0.063940.888
52_A131_L0.063820.886
39_Q150_I0.063720.885
129_P341_R0.063710.885
110_T123_A0.063650.884
56_L107_L0.063630.884
138_P278_R0.063610.884
374_T378_I0.063580.883
208_R211_L0.06350.882
385_L389_I0.063470.882
338_D341_R0.063420.881
39_Q174_I0.06340.881
244_F275_P0.063380.880
192_P312_I0.063320.880
200_R204_F0.06330.879
128_I267_A0.063220.878
227_S294_F0.06320.878
158_L162_L0.06320.878
108_I369_H0.063190.878
331_L334_L0.063180.878
161_I254_S0.063160.877
312_I400_E0.063160.877
297_A316_L0.063110.877
188_R194_P0.063060.876
101_L104_W0.063050.876
86_A176_A0.063030.875
228_F296_L0.062980.875
299_L381_A0.062960.875
61_L353_F0.062880.873
108_I112_L0.06280.872
200_R203_F0.062780.872
210_G340_V0.062770.872
284_R393_F0.062720.871
86_A90_L0.062690.871
137_L244_F0.062670.870
222_S391_L0.062630.870
27_W151_A0.062620.870
104_W311_L0.062550.869
247_D368_D0.062520.868
289_L296_L0.062520.868
255_G307_F0.062520.868
154_I405_P0.06250.868
332_V336_V0.062450.867
255_G258_L0.062360.866
247_D390_A0.062350.866
259_L318_G0.06230.865
124_W151_A0.06230.865
309_L312_I0.062250.865
289_L292_L0.062250.865
81_S116_G0.062220.864
326_S330_T0.062180.864
83_L208_R0.062180.864
290_A294_F0.062180.864
227_S231_N0.062090.862
197_S220_L0.062070.862
270_G347_I0.062020.861
114_G118_A0.062020.861
290_A320_A0.061980.861
377_L380_G0.061960.861
66_G122_P0.06190.860
87_L150_I0.06180.858
23_N152_R0.061790.858
105_L108_I0.061710.857
17_I21_I0.061650.856
135_E204_F0.061640.856
61_L122_P0.061630.856
109_L124_W0.061620.856
167_G171_A0.061570.855
43_S51_Q0.061570.855
311_L335_S0.061560.855
50_V103_P0.061550.855
244_F264_G0.061510.854
170_A335_S0.061510.854
380_G387_A0.06150.854
188_R385_L0.061490.854
137_L283_S0.061410.853
231_N325_N0.061330.852
45_L396_R0.061220.850
365_F368_D0.061090.849
25_G179_F0.060980.847
236_A287_V0.060940.846
163_V171_A0.060870.845
156_P241_L0.060850.845
319_A395_L0.060830.845
318_G332_V0.06070.843
44_P269_L0.060650.842
65_A342_G0.060610.842
35_W242_P0.060590.842
292_L384_L0.060590.842
106_L271_A0.060550.841
371_G375_A0.06050.840
397_Q401_L0.060460.840
56_L88_V0.060460.840
270_G274_L0.060450.840
83_L183_I0.06040.839
238_W383_L0.060390.839
261_A265_V0.060280.837
88_V91_L0.060260.837
270_G273_L0.060210.836
287_V328_L0.060210.836
62_S353_F0.06020.836
52_A357_P0.060150.835
158_L165_F0.060130.835
87_L277_L0.060040.834
403_L406_S0.060030.834
241_L375_A0.059890.832
21_I181_I0.059890.832
49_L107_L0.059870.832
20_L147_S0.059870.832
200_R269_L0.059870.832
208_R369_H0.059860.831
224_L347_I0.059860.831
60_L289_L0.059780.830
287_V291_S0.059780.830
68_L80_L0.059760.830
145_S329_N0.059740.830
80_L83_L0.059730.830
270_G325_N0.059670.829
326_S332_V0.059630.828
266_G357_P0.059620.828
157_A364_G0.059620.828
273_L277_L0.05960.828
49_L361_L0.059590.828
173_L229_L0.059560.827
34_A179_F0.059550.827
149_N230_F0.059540.827
272_L384_L0.059540.827
307_F315_F0.059530.827
161_I170_A0.059460.826
373_R377_L0.059440.826
93_A168_A0.059440.826
50_V112_L0.059420.825
256_Y259_L0.059410.825
82_Q85_R0.05940.825
110_T124_W0.059370.825
201_E269_L0.059370.825
60_L313_A0.059360.825
94_V198_L0.059320.824
153_I227_S0.059260.823
32_A36_L0.059230.823
284_R396_R0.059190.822
311_L370_F0.059080.821
289_L302_A0.059080.821
295_A321_W0.059040.820
304_S309_L0.058990.819
278_R327_S0.058980.819
240_L346_S0.058980.819
34_A38_T0.058920.818
211_L385_L0.058870.818
370_F378_I0.058840.817
261_A354_G0.058820.817
290_A323_I0.058780.816
139_A279_R0.05870.815
292_L388_L0.058650.815
231_N240_L0.058650.815
64_F199_P0.058620.814
155_G270_G0.058610.814
69_A342_G0.058590.814
292_L378_I0.058550.813
383_L386_S0.058540.813
82_Q120_F0.058530.813
122_P349_Q0.058520.813
399_E402_D0.058420.811
292_L362_L0.05840.811
362_L365_F0.05840.811
248_V252_G0.058380.811
25_G178_S0.058320.810
359_G364_G0.05830.810
297_A317_A0.058240.809
364_G368_D0.058240.809
32_A159_G0.058170.808
356_M379_A0.058130.807
48_A372_V0.058080.807
69_A123_A0.058080.807
90_L400_E0.058060.806
82_Q182_S0.057980.805
69_A346_S0.057970.805
180_L187_L0.057960.805
265_V402_D0.057960.805
48_A341_R0.057890.804
230_F321_W0.057890.804
291_S386_S0.057880.804
213_Y217_S0.057870.804
101_L193_P0.057850.804
19_Q179_F0.057790.803
88_V174_I0.057790.803
224_L235_S0.057710.802
49_L56_L0.057630.800
89_A116_G0.05760.800
266_G270_G0.057570.800
26_D58_I0.057490.799
138_P330_T0.057470.798
50_V110_T0.05740.797
59_L103_P0.057280.796
229_L233_F0.057240.795
31_V47_V0.057240.795
305_P309_L0.057210.795
339_W345_F0.057190.794
86_A183_I0.057160.794
161_I164_A0.057150.794
87_L308_W0.057140.794
164_A361_L0.057140.794
380_G388_L0.057080.793
18_A124_W0.057010.792
221_R282_S0.056960.791
37_V47_V0.056960.791
214_V347_I0.056940.791
242_P267_A0.056940.791
315_F319_A0.056920.791
229_L385_L0.056890.790
331_L336_V0.056890.790
131_L352_F0.056850.790
17_I72_F0.056820.789
64_F358_L0.056790.789
357_P363_W0.056790.789
128_I331_L0.056790.789
120_F346_S0.056750.788
84_L182_S0.056660.787
173_L216_S0.056640.787
128_I133_P0.056630.787
58_I350_M0.056620.786
290_A324_A0.056610.786
87_L365_F0.05660.786
23_N27_W0.056570.786
112_L197_S0.056570.786
195_P400_E0.056570.786
17_I161_I0.056560.786
24_L364_G0.056540.785
156_P333_Q0.056510.785
141_N326_S0.056510.785
63_L152_R0.05650.785
36_L127_I0.056440.784
165_F250_G0.056420.784
263_F266_G0.056390.783
324_A334_L0.056360.783
295_A386_S0.05630.782
389_I400_E0.056260.781
149_N347_I0.056240.781
373_R381_A0.056230.781
182_S405_P0.056220.781
178_S186_L0.056190.780
277_L280_R0.056140.780
110_T137_L0.056090.779
289_L391_L0.056010.778
295_A398_G0.055880.776
45_L365_F0.055870.776
19_Q148_F0.055860.776
119_F342_G0.055860.776
89_A179_F0.055830.775
107_L402_D0.055830.775
52_A107_L0.05580.775
68_L306_S0.055780.775
73_D129_P0.055740.774
156_P266_G0.055730.774
141_N357_P0.055680.773
244_F301_L0.055680.773
265_V404_D0.055680.773
253_A313_A0.055680.773
108_I373_R0.055660.773
113_L168_A0.055650.773
193_P196_S0.055620.773
296_L302_A0.055560.772
354_G389_I0.055540.771
290_A297_A0.055530.771
328_L332_V0.055520.771
147_S168_A0.055470.770
18_A263_F0.055450.770
211_L358_L0.055410.770
269_L319_A0.055360.769
351_V355_G0.055360.769
302_A377_L0.055340.769
180_L218_P0.055340.769
336_V341_R0.055270.768
173_L176_A0.055250.767
60_L201_E0.055240.767
34_A355_G0.055230.767
185_A189_W0.055210.767
81_S120_F0.055190.767
166_F170_A0.055180.766
162_L255_G0.055170.766
180_L296_L0.055170.766
165_F168_A0.05510.765
108_I277_L0.055080.765
88_V113_L0.055070.765
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
1pw4A0.78051000.538
4j05A0.79391000.538
3o7qA0.74621000.558
2gfpA0.7081000.582
4apsA0.77671000.592
4iu9B0.75571000.604
4jr9A0.74051000.607
4gc0A0.7921000.616
2cfqA0.77481000.617
2xutA0.78051000.633
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