GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mem_trans - Membrane transport protein
Pfam: PF03547 (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: CL0064
Length: 385
Sequences: 1927
Seq/Len: 5.01
HH_delta: 0.815 (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
239_L243_K0.394924.231
47_F256_I0.393594.217
47_F252_L0.289063.097
248_I252_L0.280843.009
331_G334_G0.253862.720
316_L380_T0.251242.692
11_L274_S0.223842.398
18_L22_F0.215542.309
327_V337_A0.214272.296
348_T373_S0.208382.232
93_W362_D0.200812.151
41_F281_A0.194842.087
110_G346_M0.188652.021
19_L40_V0.186782.001
36_L41_F0.183311.964
276_S280_A0.182361.954
36_L281_A0.17611.887
44_A278_L0.171791.840
19_L288_F0.17151.837
48_S279_G0.169641.817
312_V373_S0.1681.800
256_I261_P0.158351.696
36_L288_F0.157551.688
41_F282_A0.152971.639
20_G292_A0.148941.596
290_L350_I0.148931.596
324_I341_I0.145151.555
30_S292_A0.144091.544
379_P382_P0.143381.536
333_D337_A0.141141.512
48_S275_L0.139881.499
26_D32_G0.139871.498
20_G295_A0.139641.496
345_A381_L0.136821.466
101_A314_V0.136061.458
314_V318_I0.135271.449
308_S372_W0.133761.433
293_S353_F0.132351.418
46_I249_A0.132281.417
38_F353_F0.132171.416
12_I288_F0.130671.400
235_K239_L0.130611.399
44_A275_L0.12981.391
99_L103_F0.129471.387
316_L376_L0.129171.384
50_I253_G0.126551.356
78_L82_L0.126481.355
38_F108_F0.126371.354
100_A369_I0.126251.353
48_S276_S0.125891.349
316_L373_S0.125871.348
334_G337_A0.125461.344
312_V316_L0.125351.343
84_S94_R0.125051.340
256_I263_R0.124771.337
14_L18_L0.123081.319
26_D29_A0.12281.316
7_L270_F0.122241.310
331_G337_A0.121351.300
251_I255_I0.121091.297
48_S272_T0.121091.297
12_I278_L0.120991.296
322_I326_I0.118011.264
236_K239_L0.115891.242
69_A129_F0.115881.241
44_A249_A0.115241.235
114_L123_V0.114811.230
269_S273_D0.114361.225
21_R295_A0.113981.221
356_A361_L0.113971.221
341_I384_W0.113811.219
321_L325_G0.111921.199
272_T276_S0.111791.198
118_F339_V0.111751.197
51_A256_I0.111561.195
31_K35_K0.111531.195
75_L259_I0.111331.193
356_A366_A0.110581.185
40_V288_F0.109881.177
313_L317_I0.109531.173
51_A253_G0.109431.172
281_A285_L0.108931.167
113_I346_M0.108741.165
75_L322_I0.108671.164
37_V41_F0.107141.148
34_S286_A0.107041.147
323_G344_A0.106881.145
49_S315_R0.106481.141
379_P383_L0.10611.137
28_E32_G0.10571.132
255_I259_I0.104781.123
13_I246_P0.10461.121
37_V282_A0.104541.120
20_G23_G0.10421.116
109_L346_M0.103691.111
7_L11_L0.103651.110
377_S381_L0.103471.109
249_A253_G0.102811.101
74_I78_L0.102731.101
325_G328_F0.102541.099
250_I354_V0.102461.098
250_I349_A0.102251.095
48_S52_N0.101161.084
335_D339_V0.100571.077
259_I262_L0.100561.077
108_F355_I0.100531.077
317_I383_L0.099951.071
46_I250_I0.099931.071
20_G296_R0.09981.069
273_D276_S0.099751.069
37_V285_L0.099721.068
138_W142_Y0.099661.068
35_K358_L0.09951.066
101_A315_R0.099381.065
68_F326_I0.099351.064
360_G363_E0.098741.058
5_A8_P0.098611.056
241_L247_L0.098571.056
139_S142_Y0.098341.054
141_G317_I0.098121.051
317_I321_L0.098121.051
353_F370_V0.097891.049
129_F135_I0.097891.049
96_V366_A0.097751.047
252_L317_I0.097451.044
10_F380_T0.09681.037
85_R255_I0.096751.037
321_L384_W0.096631.035
352_S370_V0.096141.030
83_L87_F0.095921.028
20_G27_P0.095841.027
246_P287_L0.095741.026
11_L15_L0.095711.025
138_W141_G0.09571.025
375_L379_P0.095561.024
45_L282_A0.095461.023
252_L255_I0.095391.022
23_G325_G0.095381.022
126_A343_Q0.095071.019
29_A33_L0.094791.016
4_S270_F0.094341.011
324_I328_F0.09431.010
249_A285_L0.094181.009
45_L284_P0.094111.008
377_S382_P0.094031.007
256_I262_L0.094011.007
337_A341_I0.093931.006
15_L74_I0.093461.001
313_L322_I0.093110.998
5_A117_L0.092970.996
252_L256_I0.092770.994
114_L339_V0.092710.993
43_P342_L0.092220.988
118_F338_R0.092220.988
15_L40_V0.092030.986
108_F290_L0.09190.985
253_G257_G0.09190.985
312_V372_W0.091850.984
326_I329_L0.091840.984
82_L339_V0.091290.978
35_K39_N0.091220.977
350_I384_W0.091080.976
114_L122_G0.09090.974
24_I39_N0.090480.969
315_R319_L0.090180.966
12_I32_G0.090070.965
15_L236_K0.090.964
37_V286_A0.089860.963
142_Y359_Y0.088970.953
289_V353_F0.088840.952
282_A315_R0.088510.948
94_R98_V0.088150.944
26_D376_L0.087990.943
115_Q123_V0.087820.941
332_L340_L0.087770.940
275_L279_G0.087480.937
104_G315_R0.087410.936
75_L255_I0.087220.934
15_L274_S0.087130.933
38_F244_N0.087080.933
108_F354_V0.086930.931
50_I255_I0.086430.926
127_I130_D0.086420.926
327_V332_L0.0860.921
254_L309_I0.085850.920
281_A284_P0.085770.919
68_F72_I0.08570.918
309_I376_L0.085680.918
357_S360_G0.085640.917
103_F138_W0.085440.915
311_A369_I0.085330.914
99_L145_L0.084750.908
110_G374_T0.084220.902
38_F351_N0.084090.901
42_L286_A0.083510.895
264_P269_S0.083350.893
95_G98_V0.083320.893
103_F359_Y0.083310.893
263_R271_I0.083220.892
115_Q120_E0.083170.891
117_L290_L0.083160.891
38_F142_Y0.083020.889
78_L269_S0.082710.886
326_I376_L0.082620.885
5_A367_S0.082540.884
6_I315_R0.08250.884
114_L126_A0.082440.883
335_D338_R0.082390.883
348_T370_V0.082390.883
145_L361_L0.08190.877
131_V135_I0.081850.877
83_L328_F0.081780.876
39_N108_F0.081670.875
107_G135_I0.081560.874
57_E379_P0.081330.871
320_P345_A0.081260.871
348_T352_S0.081160.869
135_I139_S0.081060.868
346_M381_L0.080960.867
370_V374_T0.080950.867
251_I317_I0.08090.867
145_L356_A0.080820.866
276_S360_G0.08080.866
66_P69_A0.080760.865
71_I260_P0.080660.864
292_A359_Y0.080540.863
277_Y281_A0.080410.861
251_I379_P0.080410.861
102_S141_G0.080370.861
10_F142_Y0.080350.861
6_I382_P0.080050.858
61_S271_I0.079970.857
134_N138_W0.079960.857
241_L244_N0.079920.856
136_I139_S0.079880.856
36_L285_L0.079510.852
334_G338_R0.079340.850
6_I381_L0.079310.850
70_F318_I0.079120.848
50_I108_F0.078870.845
61_S377_S0.078640.843
4_S326_I0.078260.838
80_G314_V0.078220.838
104_G346_M0.078130.837
57_E147_S0.077930.835
74_I317_I0.077930.835
74_I333_D0.07790.835
255_I258_L0.077740.833
244_N253_G0.07770.832
107_G371_F0.077660.832
100_A366_A0.077590.831
252_L379_P0.077340.829
99_L141_G0.077290.828
45_L48_S0.077250.828
79_L306_K0.077190.827
99_L102_S0.077180.827
77_L98_V0.077160.827
98_V102_S0.077090.826
104_G349_A0.077040.825
135_I138_W0.076980.825
273_D279_G0.076890.824
273_D377_S0.076840.823
80_G290_L0.076760.822
316_L377_S0.076720.822
104_G110_G0.076680.822
325_G329_L0.076650.821
125_Y336_M0.076630.821
5_A9_I0.076540.820
103_F133_N0.076420.819
71_I326_I0.076140.816
283_V286_A0.07610.815
83_L383_L0.075880.813
80_G144_L0.075820.812
111_L123_V0.075810.812
316_L345_A0.075770.812
78_L306_K0.075640.810
349_A352_S0.075620.810
367_S371_F0.075480.809
34_S289_V0.075470.809
367_S377_S0.075470.809
242_F251_I0.07540.808
139_S284_P0.075360.807
364_E368_S0.074860.802
324_I337_A0.074840.802
41_F110_G0.074690.800
29_A32_G0.074690.800
289_V356_A0.074580.799
346_M352_S0.074350.797
46_I50_I0.07430.796
150_E255_I0.074230.795
357_S363_E0.074110.794
75_L79_L0.074070.794
363_E376_L0.074020.793
8_P47_F0.073940.792
249_A277_Y0.073890.792
51_A257_G0.073830.791
345_A380_T0.073760.790
110_G264_P0.073690.789
337_A340_L0.073620.789
62_L65_I0.073490.787
71_I330_L0.073230.785
97_F311_A0.073170.784
271_I274_S0.073070.783
345_A384_W0.07290.781
66_P118_F0.072830.780
292_A352_S0.072650.778
103_F118_F0.072610.778
141_G377_S0.07240.776
47_F51_A0.072360.775
74_I238_I0.072280.774
127_I131_V0.072280.774
45_L111_L0.072210.774
110_G245_P0.07220.774
279_G329_L0.072050.772
14_L61_S0.072010.771
112_P350_I0.071950.771
346_M371_F0.07180.769
122_G125_Y0.071790.769
137_L142_Y0.071730.768
372_W376_L0.071540.766
328_F337_A0.071490.766
41_F286_A0.071470.766
110_G370_V0.071460.766
362_D365_E0.071440.765
309_I313_L0.071360.765
312_V376_L0.071240.763
21_R317_I0.071170.762
109_L113_I0.071160.762
349_A374_T0.071080.762
71_I85_R0.071070.761
8_P290_L0.071040.761
129_F141_G0.071010.761
90_P93_W0.070920.760
29_A281_A0.070760.758
52_N78_L0.070720.758
290_L371_F0.070710.758
145_L248_I0.070630.757
116_A290_L0.070620.757
65_I76_G0.070490.755
39_N358_L0.070450.755
129_F146_E0.070390.754
66_P330_L0.070340.754
369_I372_W0.070290.753
89_L93_W0.070270.753
114_L118_F0.070240.753
86_L325_G0.070.750
138_W285_L0.069780.748
67_V74_I0.06970.747
99_L355_I0.06970.747
244_N353_F0.069610.746
7_L262_L0.069570.745
90_P360_G0.06950.745
287_L348_T0.069480.744
235_K261_P0.069390.743
108_F315_R0.069320.743
130_D246_P0.069310.743
88_R325_G0.069260.742
255_I270_F0.069140.741
249_A278_L0.069110.740
19_L36_L0.069080.740
348_T371_F0.068920.738
66_P76_G0.068920.738
18_L21_R0.068670.736
63_W79_L0.06860.735
100_A289_V0.068550.734
137_L342_L0.068510.734
257_G287_L0.06850.734
320_P356_A0.068480.734
36_L132_V0.068340.732
39_N44_A0.068260.731
61_S336_M0.068120.730
54_D257_G0.06810.730
134_N137_L0.068060.729
111_L130_D0.067880.727
75_L318_I0.067840.727
86_L239_L0.067770.726
11_L87_F0.067770.726
30_S289_V0.067710.725
78_L313_L0.067640.725
238_I241_L0.067540.724
10_F14_L0.067530.723
9_I37_V0.067520.723
99_L283_V0.067510.723
306_K383_L0.06750.723
139_S246_P0.067310.721
111_L116_A0.06730.721
79_L243_K0.067260.721
69_A349_A0.067190.720
295_A317_I0.067120.719
9_I50_I0.067070.719
106_T131_V0.067020.718
111_L357_S0.066980.718
18_L52_N0.066980.718
14_L271_I0.066970.717
17_Y275_L0.066910.717
91_K94_R0.06690.717
240_K243_K0.066850.716
344_A351_N0.066850.716
30_S286_A0.066780.715
76_G254_L0.066770.715
12_I277_Y0.066710.715
236_K322_I0.066710.715
82_L269_S0.06670.715
140_L376_L0.06670.715
49_S290_L0.066690.714
105_N339_V0.066590.713
27_P295_A0.066570.713
56_L61_S0.066560.713
262_L383_L0.066430.712
248_I325_G0.066310.710
122_G126_A0.06630.710
31_K360_G0.066190.709
10_F316_L0.066150.709
6_I348_T0.066110.708
99_L139_S0.066020.707
100_A117_L0.065980.707
256_I273_D0.065960.707
100_A348_T0.065860.706
75_L78_L0.065780.705
106_T344_A0.065740.704
99_L138_W0.065720.704
258_L375_L0.065620.703
14_L258_L0.065610.703
140_L380_T0.065560.702
348_T381_L0.065490.702
50_I342_L0.065440.701
50_I250_I0.065390.701
313_L318_I0.065380.700
285_L343_Q0.065290.699
248_I340_L0.065240.699
29_A112_P0.065240.699
57_E75_L0.064990.696
96_V107_G0.064980.696
51_A263_R0.064970.696
3_F113_I0.064960.696
146_E149_S0.064910.695
310_I383_L0.064760.694
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
3zuxA0.392299.30.815
3zuxA0.418297.80.896
4j05A0.420878.50.949
3o7qA0.755854.50.956
1pw4A0.815648.20.958
1zcdA0.389635.20.961
4apsA0.410422.60.964
4iu9B0.392219.50.965
4jr9A0.37418.80.965
3giaA0.402613.70.967
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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