GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SSF - Sodiumsolute symporter family
Pfam: PF00474 (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: CL0062
Length: 406
Sequences: 15671
Seq/Len: 38.6
HH_delta: 0.205 (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
230_S233_T0.808333.490
163_I167_S0.729663.150
9_G229_K0.674532.912
345_I349_V0.638322.756
76_E86_R0.636492.748
125_L355_I0.604622.610
80_G83_A0.570722.464
335_S338_Q0.559132.414
119_P122_T0.551492.381
329_I342_V0.536192.315
8_L144_A0.530962.292
292_G296_L0.516882.231
330_K338_Q0.492292.125
10_W233_T0.491052.120
79_Y83_A0.48642.100
14_A240_I0.476472.057
49_A246_I0.467782.019
76_E81_S0.463182.000
13_V228_A0.462141.995
283_Y287_Q0.461751.993
328_F331_P0.459631.984
283_Y286_A0.455281.965
165_V258_I0.453541.958
10_W236_K0.448051.934
9_G12_V0.447141.930
121_N125_L0.445411.923
10_W240_I0.441071.904
321_S331_P0.437751.890
10_W14_A0.43661.885
233_T236_K0.424121.831
295_G299_A0.423911.830
341_R345_I0.420631.816
337_K341_R0.417391.802
229_K233_T0.414661.790
133_I348_V0.407161.758
332_N342_V0.404411.746
152_V156_I0.401921.735
134_Y138_G0.396921.714
18_V244_F0.393051.697
156_I160_V0.389461.681
334_A338_Q0.388111.676
159_I163_I0.386721.670
324_I328_F0.385251.663
236_K240_I0.384941.662
335_S341_R0.381341.646
239_L243_I0.378391.634
141_R145_W0.377221.628
125_L129_V0.374291.616
352_I356_L0.36911.593
327_P330_K0.366751.583
75_L89_A0.35881.549
228_A233_T0.355291.534
72_P323_D0.355221.534
227_A318_S0.345631.492
157_G300_G0.34011.468
19_A151_G0.339441.465
342_V346_A0.337561.457
50_I54_L0.336711.454
12_V148_F0.336241.452
122_T125_L0.331241.430
329_I332_N0.328351.418
219_P223_Q0.326211.408
162_L251_L0.325541.405
146_T150_Q0.325431.405
118_I122_T0.324721.402
128_G355_I0.323491.397
286_A294_A0.319171.378
113_S120_Y0.318881.377
8_L12_V0.318451.375
11_W15_F0.31751.371
325_Y334_A0.316721.367
232_K236_K0.316271.365
32_G36_S0.315081.360
341_R344_R0.314981.360
122_T126_I0.314571.358
94_I347_I0.309041.334
34_A41_G0.304971.317
188_D191_N0.303011.308
243_I247_I0.299091.291
342_V345_I0.295681.276
121_N124_I0.295321.275
286_A291_P0.294841.273
82_K88_L0.293911.269
118_I123_A0.290661.255
160_V164_F0.290621.255
155_I159_I0.289651.250
290_P293_L0.288041.243
73_E77_K0.287441.241
46_I250_F0.286891.239
171_G174_G0.286841.238
87_I91_I0.286571.237
328_F332_N0.286561.237
231_P235_R0.286081.235
332_N341_R0.282731.221
140_L227_A0.279881.208
367_I372_F0.276621.194
304_A307_S0.275611.190
69_V73_E0.275251.188
33_F37_Y0.274831.186
17_L241_A0.273811.182
91_I95_V0.273611.181
292_G295_G0.272331.176
335_S339_L0.271591.172
79_Y82_K0.269691.164
201_P204_F0.269581.164
132_I351_G0.269421.163
150_Q307_S0.269331.163
206_S209_I0.26871.160
356_L359_L0.267981.157
14_A244_F0.267871.156
11_W148_F0.267161.153
108_G127_V0.266861.152
145_W148_F0.264751.143
44_Y207_F0.264041.140
28_I107_G0.263851.139
78_R83_A0.263271.137
210_A214_G0.262881.135
18_V151_G0.260291.124
289_L293_L0.259841.122
220_H315_A0.258321.115
367_I371_L0.258041.114
16_S224_R0.257781.113
97_M312_L0.257771.113
160_V163_I0.257511.112
162_L165_V0.257091.110
167_S171_G0.256041.105
20_T311_S0.255851.105
321_S324_I0.254931.101
7_S229_K0.254761.100
123_A127_V0.254511.099
63_L74_Y0.253451.094
160_V293_L0.252241.089
11_W145_W0.250621.082
247_I251_L0.249931.079
77_K80_G0.24971.078
246_I250_F0.249191.076
161_V285_A0.249131.076
164_F168_A0.24771.069
131_V306_M0.246961.066
322_R326_K0.246281.063
119_P124_I0.246141.063
326_K330_K0.245641.060
368_D371_L0.244961.058
78_R81_S0.244431.055
7_S141_R0.2441.053
101_L354_A0.243891.053
232_K235_R0.243211.050
76_E80_G0.242071.045
317_S344_R0.241651.043
279_L283_Y0.240571.039
313_L317_S0.240271.037
8_L13_V0.240251.037
53_L239_L0.23961.034
13_V237_G0.2391.032
135_T146_T0.238951.032
94_I320_F0.238521.030
235_R238_M0.237461.025
105_L309_A0.236761.022
16_S20_T0.236731.022
138_G142_A0.236161.020
338_Q341_R0.235371.016
330_K334_A0.235061.015
45_A249_Y0.234921.014
202_L205_L0.234571.013
242_I246_I0.23431.011
134_Y137_F0.233391.008
101_L309_A0.233381.008
112_L123_A0.233061.006
356_L360_F0.232791.005
349_V353_I0.232661.004
53_L57_L0.232091.002
164_F290_P0.232031.002
120_Y124_I0.230670.996
78_R82_K0.229620.991
108_G305_I0.229430.990
27_F158_A0.229280.990
188_D192_P0.228870.988
316_I320_F0.22680.979
132_I309_A0.225650.974
316_I350_I0.225310.973
15_F148_F0.225270.973
301_I305_I0.225230.972
40_S204_F0.224950.971
313_L351_G0.224460.969
67_G73_E0.224360.969
353_I356_L0.224070.967
277_P283_Y0.223940.967
125_L128_G0.22390.967
70_T73_E0.22320.964
68_A77_K0.222210.959
346_A349_V0.221960.958
259_A280_A0.221920.958
355_I359_L0.221580.957
112_L116_F0.22140.956
330_K346_A0.221020.954
344_R348_V0.220770.953
259_A262_L0.220.950
88_L92_I0.219390.947
91_I326_K0.217340.938
260_I264_G0.21720.938
132_I313_L0.216320.934
69_V74_Y0.215750.931
131_V309_A0.215730.931
69_V72_P0.215620.931
204_F207_F0.215360.930
324_I327_P0.214810.927
204_F208_W0.213290.921
316_I347_I0.212450.917
125_L359_L0.21190.915
346_A350_I0.210750.910
57_L239_L0.210580.909
258_I262_L0.209950.906
129_V133_I0.209630.905
124_I128_G0.209120.903
206_S210_A0.208830.902
166_L169_V0.208630.901
147_D311_S0.208190.899
32_G278_D0.207820.897
225_F234_A0.207820.897
100_Y312_L0.207750.897
144_A147_D0.20760.896
366_I372_F0.20750.896
133_I344_R0.206830.893
153_I303_A0.206550.892
73_E323_D0.206140.890
147_D310_D0.206050.890
239_L242_I0.205850.889
75_L83_A0.205440.887
119_P123_A0.205110.885
361_F366_I0.204780.884
322_R331_P0.20460.883
68_A73_E0.204460.883
12_V145_W0.204160.881
191_N194_G0.204150.881
105_L128_G0.203350.878
65_R231_P0.202790.875
48_Y211_L0.202770.875
352_I355_I0.20240.874
369_L372_F0.202170.873
345_I348_V0.201980.872
109_G124_I0.201580.870
200_S203_F0.201290.869
146_T310_D0.200990.868
189_L192_P0.20080.867
70_T318_S0.199440.861
184_P188_D0.19930.860
130_I134_Y0.199130.860
30_F34_A0.199070.859
23_S30_F0.198870.859
54_L58_F0.198310.856
75_L78_R0.198270.856
325_Y330_K0.198020.855
161_V165_V0.197980.855
81_S87_I0.197910.854
203_F207_F0.197890.854
264_G287_Q0.197810.854
236_K239_L0.197630.853
21_W245_L0.197570.853
190_F194_G0.197130.851
306_M310_D0.197050.851
106_V110_A0.196720.849
16_S19_A0.195680.845
224_R314_L0.195340.843
33_F41_G0.195240.843
263_F287_Q0.194510.840
26_T29_G0.194370.839
34_A37_Y0.194010.838
77_K81_S0.19390.837
132_I136_F0.193890.837
340_L343_S0.193860.837
100_Y103_A0.193370.835
245_L249_Y0.193370.835
226_L322_R0.193230.834
12_V144_A0.193180.834
158_A252_T0.192650.832
183_H188_D0.192260.830
137_F345_I0.19210.829
277_P280_A0.191940.829
92_I96_F0.191470.827
66_S69_V0.191450.827
261_A264_G0.191250.826
154_M307_S0.191150.825
49_A215_T0.190780.824
170_G173_G0.190710.823
110_A113_S0.190590.823
98_I347_I0.189930.820
321_S326_K0.188660.814
136_F348_V0.188490.814
331_P334_A0.188420.813
300_G303_A0.188240.813
135_T310_D0.188010.812
63_L222_W0.18780.811
142_A146_T0.187150.808
282_P286_A0.186780.806
14_A17_L0.186740.806
315_A319_I0.186370.805
368_D372_F0.186170.804
14_A237_G0.185990.803
60_A234_A0.185910.803
124_I127_V0.185820.802
366_I371_L0.185510.801
155_I248_F0.185350.800
128_G132_I0.185320.800
113_S117_G0.184430.796
68_A226_L0.184420.796
23_S26_T0.184330.796
291_P295_G0.184160.795
325_Y338_Q0.183830.794
325_Y329_I0.183820.794
326_K339_L0.183820.794
291_P294_A0.183740.793
11_W14_A0.183490.792
9_G141_R0.183320.791
188_D193_G0.183090.790
285_A289_L0.183020.790
15_F151_G0.182850.789
284_L288_Y0.182630.788
329_I334_A0.182470.788
52_F241_A0.182460.788
46_I50_I0.181970.786
147_D224_R0.181820.785
334_A339_L0.181780.785
112_L302_L0.181310.783
7_S140_L0.181180.782
137_F341_R0.181060.782
93_I319_I0.180790.780
150_Q310_D0.180660.780
108_G302_L0.180340.779
93_I97_M0.180240.778
72_P90_A0.180080.777
340_L344_R0.180030.777
52_F218_A0.179750.776
299_A303_A0.179590.775
127_V131_V0.179560.775
25_W249_Y0.179480.775
205_L208_W0.179160.773
126_I130_I0.1790.773
70_T74_Y0.17860.771
53_L242_I0.178430.770
320_F324_I0.178420.770
108_G306_M0.178380.770
201_P205_L0.178190.769
26_T30_F0.177940.768
133_I137_F0.17770.767
164_F285_A0.177460.766
162_L166_L0.177030.764
229_K232_K0.176770.763
121_N359_L0.176380.761
24_A107_G0.176260.761
101_L105_L0.175850.759
358_A362_P0.175620.758
215_T218_A0.175340.757
61_P235_R0.17530.757
358_A361_F0.174970.755
95_V99_P0.174910.755
190_F193_G0.17430.752
51_G54_L0.173920.751
240_I243_I0.173140.747
42_L250_F0.172790.746
65_R77_K0.172770.746
147_D154_M0.172740.746
40_S194_G0.172170.743
45_A49_A0.172020.743
24_A305_I0.171630.741
336_E339_L0.171560.741
43_W46_I0.171520.740
133_I345_I0.171390.740
150_Q303_A0.171310.740
287_Q291_P0.170540.736
317_S343_S0.170490.736
124_I358_A0.170340.735
204_F211_L0.170240.735
363_D368_D0.169920.734
33_F36_S0.169860.733
105_L124_I0.169620.732
111_L301_I0.169410.731
38_G41_G0.169340.731
366_I369_L0.169120.730
320_F326_K0.168980.729
167_S170_G0.168910.729
76_E327_P0.167830.725
253_I257_L0.167790.724
74_Y78_R0.167740.724
166_L170_G0.167680.724
101_L316_I0.167630.724
123_A126_I0.167060.721
327_P331_P0.167050.721
99_P103_A0.166720.720
159_I162_L0.166590.719
7_S10_W0.166240.718
344_R347_I0.166130.717
8_L140_L0.16560.715
72_P76_E0.165340.714
209_I212_M0.164970.712
104_Q309_A0.164960.712
98_I102_A0.164820.712
103_A107_G0.164310.709
324_I330_K0.163840.707
325_Y342_V0.163660.707
28_I111_L0.163350.705
22_I25_W0.163240.705
101_L351_G0.162970.704
230_S236_K0.162780.703
76_E323_D0.162710.702
274_L277_P0.162590.702
209_I213_L0.162210.700
104_Q308_T0.161940.699
168_A172_F0.161390.697
93_I347_I0.161320.696
24_A27_F0.160730.694
105_L109_G0.160630.693
26_T31_P0.160450.693
27_F100_Y0.160450.693
100_Y104_Q0.160290.692
184_P189_L0.159790.690
307_S310_D0.159390.688
262_L284_L0.159240.687
130_I348_V0.159220.687
139_G142_A0.159160.687
282_P298_L0.15910.687
357_L360_F0.159030.687
53_L56_A0.158990.686
167_S172_F0.158950.686
153_I157_G0.158940.686
67_G77_K0.158840.686
241_A245_L0.158830.686
338_Q342_V0.158750.685
149_I152_V0.158740.685
140_L314_L0.158420.684
307_S313_L0.158350.684
13_V224_R0.157960.682
68_A74_Y0.157840.681
307_S311_S0.157830.681
320_F346_A0.157740.681
326_K329_I0.157720.681
164_F167_S0.157360.679
230_S235_R0.157110.678
151_G154_M0.156850.677
9_G145_W0.156850.677
348_V351_G0.156550.676
334_A337_K0.15650.676
120_Y123_A0.156490.676
30_F33_F0.156460.675
94_I98_I0.156370.675
26_T158_A0.156270.675
308_T312_L0.155850.673
248_F251_L0.155790.673
303_A307_S0.155430.671
19_A147_D0.155030.669
9_G233_T0.154730.668
14_A18_V0.154160.666
258_I261_A0.154120.665
140_L224_R0.153810.664
49_A245_L0.153740.664
114_V298_L0.153560.663
31_P284_L0.153510.663
49_A158_A0.153250.662
262_L265_L0.153240.662
26_T252_T0.153160.661
57_L101_L0.153130.661
57_L235_R0.153070.661
106_V314_L0.153070.661
144_A310_D0.15290.660
313_L348_V0.152770.660
39_I42_L0.152290.657
240_I244_F0.152270.657
166_L251_L0.152060.656
124_I355_I0.151960.656
101_L313_L0.151830.655
321_S330_K0.151690.655
241_A244_F0.151640.655
144_A148_F0.151610.655
9_G13_V0.151380.654
150_Q306_M0.151190.653
114_V279_L0.15110.652
6_R227_A0.150730.651
26_T214_G0.150710.651
120_Y362_P0.150560.650
332_N337_K0.15040.649
32_G35_Y0.150220.649
18_V22_I0.150160.648
104_Q312_L0.150130.648
140_L144_A0.149960.647
317_S347_I0.149920.647
285_A293_L0.149840.647
18_V21_W0.149760.647
165_V169_V0.149610.646
143_V154_M0.149510.645
91_I324_I0.149350.645
59_F71_I0.148910.643
28_I31_P0.148880.643
62_R65_R0.148670.642
349_V352_I0.148490.641
225_F238_M0.14840.641
183_H261_A0.148240.640
300_G304_A0.148130.639
57_L60_A0.148130.639
145_W149_I0.148020.639
65_R78_R0.147950.639
211_L215_T0.147930.639
96_F315_A0.14760.637
60_A238_M0.147260.636
343_S347_I0.146790.634
260_I265_L0.146770.634
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
3dh4A0.99011000.205
2xq2A0.99011000.214
3l1lA0.92861000.447
3giaA0.911399.90.496
4djkA0.933599.90.546
2jlnA0.869599.30.743
2a65A0.918798.70.807
2wswA0.913896.10.893
4ainA0.938495.80.896
4he8J0.43355.90.961

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