GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Asp-Al_Ex - Predicted Permease Membrane Region
Pfam: PF06826 (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: 169
Sequences: 1148
Seq/Len: 6.79
HH_delta: 0.9 (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
8_L32_V0.239492.218
90_G94_T0.228612.117
12_L15_I0.214731.988
117_A133_A0.197761.831
115_I148_G0.181011.676
8_L12_L0.170021.574
105_G116_A0.169031.565
99_L103_V0.165271.530
72_G158_I0.163971.518
48_P52_P0.163681.516
7_A11_L0.162861.508
61_A82_G0.157981.463
16_K22_S0.15071.395
148_G152_T0.144061.334
104_I109_F0.14341.328
127_T149_Y0.14241.319
103_V108_L0.14231.318
64_L132_A0.141291.308
125_T156_G0.139351.290
123_A156_G0.138951.287
33_G147_V0.138231.280
74_G77_S0.137551.274
102_L118_G0.137381.272
33_G118_G0.137011.269
64_L128_P0.135451.254
95_L99_L0.135381.254
71_A74_G0.134871.249
8_L15_I0.134451.245
11_L162_L0.134351.244
83_G143_P0.13371.238
138_S143_P0.1331.232
127_T132_A0.131651.219
92_I100_I0.130771.211
17_I23_L0.130551.209
112_N115_I0.129421.198
125_T153_Y0.129121.196
72_G76_F0.128371.189
34_L83_G0.127521.181
28_G121_A0.125681.164
26_A164_V0.12561.163
78_S128_P0.124111.149
37_G156_G0.123231.141
49_I52_P0.123171.141
102_L106_R0.122951.138
95_L103_V0.122551.135
14_R22_S0.12251.134
127_T153_Y0.120411.115
99_L108_L0.119841.110
67_V148_G0.119031.102
48_P54_F0.118791.100
10_Y60_L0.118521.097
33_G60_L0.117851.091
59_G72_G0.117371.087
160_V164_V0.11711.084
92_I96_V0.117021.084
101_A119_I0.115251.067
98_L131_A0.115161.066
118_G133_A0.115111.066
31_F35_I0.114551.061
12_L23_L0.114221.058
63_F128_P0.114061.056
31_F157_V0.113961.055
85_K89_L0.113461.051
24_G159_G0.113111.047
75_F129_A0.112931.046
72_G118_G0.111791.035
88_L92_I0.111481.032
30_L149_Y0.111461.032
52_P144_A0.111191.030
116_A120_L0.110941.027
30_L63_F0.110471.023
95_L159_G0.109681.016
126_S129_A0.109481.014
106_R112_N0.108981.009
12_L32_V0.108881.008
3_F131_A0.10881.007
34_L49_I0.108171.002
124_L156_G0.108121.001
82_G92_I0.107981.000
67_V160_V0.107830.998
5_G160_V0.107680.997
129_A133_A0.107670.997
63_F125_T0.107570.996
29_V132_A0.107470.995
84_L103_V0.107370.994
31_F95_L0.107350.994
103_V106_R0.107280.993
77_S80_K0.107210.993
8_L138_S0.106830.989
159_G163_F0.10650.986
132_A154_P0.105880.980
33_G129_A0.105590.978
17_I55_L0.104820.971
25_A29_V0.10460.969
29_V127_T0.104130.964
100_I103_V0.104120.964
8_L11_L0.103990.963
116_A133_A0.103930.962
101_A127_T0.103880.962
56_R64_L0.103790.961
117_A135_E0.103720.960
11_L15_I0.10350.958
136_A144_A0.103220.956
3_F86_L0.103170.955
33_G150_A0.102630.950
30_L67_V0.102560.950
62_L90_G0.102530.949
61_A161_I0.10190.944
132_A160_V0.101230.937
112_N164_V0.100970.935
6_I55_L0.100950.935
37_G104_I0.100860.934
71_A131_A0.100670.932
14_R62_L0.10030.929
82_G87_L0.100280.929
35_I39_L0.10020.928
11_L138_S0.099840.924
99_L140_S0.099570.922
7_A71_A0.098850.915
10_Y112_N0.098820.915
28_G51_A0.098810.915
4_L92_I0.098710.914
60_L69_L0.098670.914
64_L130_L0.098590.913
15_I25_A0.098590.913
36_L114_G0.098560.913
59_G83_G0.098560.913
15_I84_L0.09810.908
95_L100_I0.097880.906
34_L126_S0.097680.904
53_S56_R0.097350.901
161_I165_Q0.097130.899
67_V77_S0.097090.899
110_K167_I0.096880.897
51_A55_L0.096830.897
3_F7_A0.096670.895
33_G143_P0.096530.894
95_L106_R0.09640.893
71_A78_S0.096150.890
29_V59_G0.095910.888
152_T157_V0.095850.888
4_L162_L0.095810.887
34_L37_G0.095780.887
63_F122_G0.095380.883
48_P53_S0.095360.883
112_N158_I0.095230.882
32_V84_L0.09520.882
140_S143_P0.094350.874
121_A124_L0.094250.873
83_G87_L0.093810.869
122_G153_Y0.093540.866
79_L84_L0.093520.866
126_S132_A0.093330.864
39_L93_I0.093320.864
127_T130_L0.093230.863
37_G102_L0.093160.863
15_I54_F0.093110.862
90_G164_V0.0930.861
34_L129_A0.09290.860
80_K83_G0.092870.860
97_P147_V0.092860.860
56_R130_L0.092170.853
62_L71_A0.092160.853
33_G69_L0.092130.853
37_G49_I0.092020.852
35_I136_A0.091970.852
62_L134_Q0.091830.850
74_G78_S0.091830.850
30_L125_T0.091810.850
79_L155_F0.091810.850
69_L138_S0.091560.848
88_L103_V0.091380.846
15_I20_G0.091290.845
61_A118_G0.091150.844
88_L99_L0.090860.841
57_Q72_G0.090650.839
129_A160_V0.09060.839
28_G149_Y0.090410.837
136_A152_T0.090310.836
77_S108_L0.090230.836
70_S84_L0.090190.835
98_L102_L0.089930.833
11_L100_I0.08990.832
56_R152_T0.089830.832
79_L117_A0.089720.831
5_G65_A0.089710.831
97_P160_V0.089610.830
20_G35_I0.089450.828
24_G55_L0.089360.827
58_L62_L0.089130.825
86_L101_A0.089050.825
96_V166_L0.089040.824
85_K92_I0.089040.824
106_R121_A0.089040.824
69_L83_G0.088880.823
12_L81_R0.088760.822
77_S103_V0.088720.822
129_A152_T0.088670.821
65_A75_F0.088530.820
38_A60_L0.088280.817
149_Y153_Y0.088080.816
70_S74_G0.087920.814
90_G97_P0.08790.814
60_L127_T0.08790.814
34_L154_P0.087830.813
91_V141_G0.087720.812
30_L57_Q0.08750.810
12_L85_K0.087450.810
62_L72_G0.087410.809
91_V99_L0.087190.807
150_A163_F0.087130.807
15_I141_G0.087110.807
58_L71_A0.087080.806
114_G123_A0.087070.806
90_G108_L0.087050.806
6_I66_A0.086910.805
64_L154_P0.08670.803
64_L160_V0.086650.802
106_R111_L0.086440.800
79_L82_G0.086290.799
88_L104_I0.086220.798
2_L53_S0.086060.797
28_G118_G0.086020.797
105_G141_G0.085970.796
99_L106_R0.08590.795
6_I22_S0.085850.795
55_L149_Y0.08580.794
98_L167_I0.085710.794
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
3zuxA0.934981.40.9
1zcdA0.89355.60.948
3llqA0.52074.10.951
4dveA0.86983.20.953
2o9gA0.526630.954
3cn5A0.63312.80.955
3v5uA0.54442.60.955
4i7zE0.11832.50.956
2kegA0.17752.50.956
1vf5E0.11832.40.956
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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