GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Permease - Permease
Pfam: PF02405 (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. )
Length: 215
Sequences: 1633
Seq/Len: 7.6
HH_delta: 0.945 (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
170_I207_I0.731115.889
174_I203_A0.51794.171
7_I113_A0.414743.340
182_A192_A0.396813.196
3_F108_L0.388153.126
3_F112_V0.285422.299
19_L120_I0.278312.242
110_M172_A0.273932.206
57_E163_K0.258272.080
22_S121_F0.252762.036
57_E208_D0.24671.987
8_Y13_Q0.245051.974
19_L124_I0.244121.966
107_L169_L0.241461.945
99_I103_V0.237021.909
79_L102_L0.235191.894
166_V207_I0.223731.802
65_L201_I0.222241.790
178_Y195_R0.2211.780
54_L125_A0.220451.776
163_K208_D0.214111.725
9_F13_Q0.213531.720
10_I75_I0.203091.636
75_I176_C0.19561.575
178_Y199_R0.195241.573
7_I112_V0.19421.564
23_F128_G0.190661.536
98_P180_L0.186941.506
111_V168_G0.186681.504
55_V126_L0.186491.502
130_Y145_L0.185861.497
83_R181_R0.185761.496
129_G144_F0.184461.486
6_Q106_R0.18411.483
72_G175_A0.184021.482
14_S71_S0.18211.467
38_S43_Q0.18071.455
76_A196_A0.178361.437
166_V211_L0.178221.435
83_R180_L0.176391.421
111_V169_L0.1761.418
187_E191_R0.17431.404
118_T122_D0.170841.376
130_Y141_F0.169851.368
87_E201_I0.166841.344
20_L202_V0.16471.327
122_D160_G0.164521.325
37_L49_I0.161711.302
33_G49_I0.160691.294
162_L215_F0.159361.284
29_L53_A0.157371.268
20_L203_A0.156881.264
118_T160_G0.154331.243
57_E167_F0.152951.232
130_Y134_V0.152811.231
169_L173_L0.152061.225
167_F208_D0.151221.218
114_M118_T0.151181.218
170_I203_A0.150841.215
111_V165_L0.150761.214
158_L162_L0.149131.201
161_L165_L0.148321.195
15_L120_I0.148241.194
170_I174_I0.147511.188
70_R193_T0.147471.188
46_V133_A0.146421.179
178_Y181_R0.145091.169
122_D157_L0.142761.150
104_V107_L0.142341.146
67_L114_M0.141911.143
175_A200_S0.141561.140
63_T121_F0.140991.136
3_F7_I0.14041.131
59_G122_D0.140241.130
97_D100_R0.139621.125
163_K167_F0.138941.119
84_V185_G0.137421.107
92_E98_P0.136871.102
63_T69_G0.134141.080
185_G189_V0.133891.078
90_A189_V0.133611.076
68_A212_S0.133531.076
134_V141_F0.131881.062
88_I102_L0.130951.055
6_Q9_F0.130811.054
81_T84_V0.130321.050
126_L148_F0.130121.048
27_L176_C0.129671.044
78_E82_M0.129541.043
83_R88_I0.129211.041
83_R92_E0.128661.036
80_G182_A0.127981.031
19_L47_G0.127341.026
197_V208_D0.12681.021
56_R152_L0.126351.018
155_W162_L0.126061.015
123_V210_L0.125831.013
91_L101_Y0.125821.013
50_L129_G0.125511.011
155_W158_L0.125161.008
24_F61_L0.125011.007
59_G125_A0.123870.998
71_S74_A0.122150.984
64_A208_D0.120460.970
186_A189_V0.120190.968
18_V121_F0.119650.964
21_V87_E0.1180.950
84_V189_V0.116760.940
33_G37_L0.116710.940
177_Y181_R0.11670.940
95_G182_A0.116260.936
211_L215_F0.116180.936
88_I180_L0.115540.931
177_Y180_L0.115470.930
67_L171_I0.115290.929
73_S197_V0.115190.928
162_L166_V0.115040.927
87_E96_I0.114430.922
144_F149_R0.114390.921
64_A204_I0.114170.920
81_T190_G0.114170.920
60_P98_P0.114040.919
30_A50_L0.113860.917
67_L71_S0.113040.910
81_T189_V0.112880.909
91_L168_G0.112720.908
153_T162_L0.112530.906
182_A188_G0.112180.904
2_E6_Q0.112120.903
69_G198_V0.112030.902
75_I175_A0.111160.895
64_A73_S0.110830.893
48_S147_S0.110610.891
102_L170_I0.110450.890
165_L169_L0.110360.889
77_A190_G0.109920.885
56_R156_D0.109030.878
144_F148_F0.108860.877
81_T186_A0.108750.876
210_L214_L0.108260.872
51_G152_L0.108250.872
119_V161_L0.108230.872
14_S87_E0.107990.870
92_E180_L0.107850.869
103_V176_C0.107370.865
166_V170_I0.107190.863
108_L113_A0.106740.860
18_V191_R0.106720.860
91_L94_M0.10640.857
43_Q46_V0.106380.857
29_L206_V0.105920.853
130_Y135_F0.105370.849
104_V108_L0.104780.844
111_V207_I0.104740.844
86_E190_G0.104460.841
64_A68_A0.104390.841
32_Q212_S0.104290.840
40_F128_G0.104130.839
154_P158_L0.103750.836
2_E5_R0.103650.835
52_I56_R0.103470.833
112_V134_V0.102950.829
64_A167_F0.102490.825
52_I152_L0.102440.825
195_R199_R0.102310.824
23_F131_L0.101640.819
196_A202_V0.101540.818
65_L68_A0.101210.815
42_A214_L0.10090.813
120_I149_R0.100810.812
1_R4_L0.10070.811
92_E95_G0.100690.811
146_D150_S0.100630.811
159_V215_F0.100590.810
74_A186_A0.100530.810
91_L186_A0.100510.810
68_A190_G0.100190.807
134_V142_G0.100180.807
129_G133_A0.100140.807
36_Q144_F0.100040.806
63_T118_T0.099830.804
17_I66_L0.09970.803
156_D188_G0.099380.800
191_R195_R0.099230.799
5_R146_D0.09920.799
9_F16_P0.098940.797
147_S211_L0.098380.792
26_G32_Q0.098240.791
24_F28_V0.098180.791
9_F64_A0.097920.789
69_G194_T0.097390.784
30_A144_F0.097190.783
127_L158_L0.097050.782
80_G175_A0.097020.781
78_E106_R0.096950.781
108_L138_G0.096430.777
115_P194_T0.096380.776
30_A133_A0.096330.776
79_L123_V0.096020.773
159_V162_L0.095930.773
99_I180_L0.095930.773
107_L172_A0.095590.770
27_L144_F0.095490.769
67_L102_L0.095450.769
45_F48_S0.095430.769
112_V168_G0.095310.768
184_G190_G0.095110.766
76_A194_T0.095090.766
127_L130_Y0.095010.765
5_R8_Y0.094930.765
161_L172_A0.094510.761
171_I200_S0.093840.756
63_T124_I0.093150.750
102_L190_G0.093080.750
70_R82_M0.092910.748
9_F119_V0.092860.748
142_G171_I0.092620.746
45_F206_V0.092560.746
21_V28_V0.09250.745
107_L195_R0.092460.745
185_G188_G0.092360.744
194_T197_V0.092330.744
162_L211_L0.092250.743
53_A125_A0.09210.742
47_G192_A0.09150.737
72_G91_L0.091470.737
105_P194_T0.091160.734
111_V140_S0.0910.733
42_A45_F0.0910.733
156_D189_V0.090780.731
125_A162_L0.090760.731
86_E94_M0.090710.731
17_I34_G0.090680.730
132_V136_F0.090630.730
209_F213_V0.090630.730
39_Q120_I0.090620.730
89_D184_G0.090370.728
25_I68_A0.090350.728
177_Y195_R0.090190.726
125_A128_G0.090180.726
38_S45_F0.089930.724
69_G115_P0.089760.723
18_V206_V0.08970.722
171_I204_I0.089630.722
113_A196_A0.089540.721
79_L106_R0.089430.720
60_P196_A0.089410.720
147_S178_Y0.089280.719
8_Y154_P0.089090.718
97_D181_R0.089050.717
114_M168_G0.088870.716
158_L206_V0.088790.715
57_E83_R0.088740.715
34_G137_L0.08870.714
194_T198_V0.08870.714
157_L161_L0.088680.714
133_A144_F0.088680.714
99_I107_L0.088680.714
84_V202_V0.088630.714
51_G148_F0.088060.709
4_L7_I0.088050.709
102_L175_A0.088040.709
127_L210_L0.087910.708
204_I207_I0.087890.708
90_A173_L0.087830.707
75_I90_A0.087580.705
42_A52_I0.087530.705
133_A145_L0.087520.705
111_V172_A0.087370.704
113_A121_F0.087170.702
34_G157_L0.087170.702
182_A189_V0.087130.702
108_L180_L0.087110.702
6_Q75_I0.08710.702
49_I168_G0.086970.700
82_M193_T0.086960.700
30_A160_G0.086930.700
25_I50_L0.08690.700
55_V161_L0.086870.700
28_V209_F0.086770.699
87_E205_L0.086630.698
76_A178_Y0.086560.697
89_D102_L0.086450.696
10_I113_A0.086440.696
67_L182_A0.086350.695
61_L205_L0.086330.695
123_V146_D0.086260.695
28_V62_L0.086250.695
73_S121_F0.086230.695
68_A181_R0.086120.694
185_G190_G0.085910.692
148_F152_L0.085830.691
188_G192_A0.085810.691
14_S70_R0.085750.691
55_V122_D0.085730.691
121_F184_G0.085640.690
99_I125_A0.085640.690
68_A200_S0.085610.690
90_A179_G0.085170.686
14_S66_L0.085050.685
74_A81_T0.084950.684
8_Y210_L0.08490.684
97_D213_V0.084860.683
168_G204_I0.084680.682
10_I109_A0.084670.682
74_A87_E0.084560.681
5_R210_L0.08450.681
134_V140_S0.084470.680
82_M85_S0.084320.679
42_A56_R0.084260.679
77_A89_D0.084060.677
27_L177_Y0.083920.676
1_R5_R0.083910.676
17_I70_R0.083790.675
148_F189_V0.083770.675
4_L187_E0.083730.674
88_I125_A0.083640.674
17_I25_I0.08360.673
22_S124_I0.083560.673
185_G192_A0.083460.672
52_I140_S0.08340.672
16_P172_A0.08340.672
5_R187_E0.08320.670
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
2zy9A0.488456.40.945
3tuiA0.83724.90.966
3d31C0.85123.60.968
1otsA0.95813.20.969
3rlfF0.81862.60.97
2ls2A0.11632.10.972
4humA0.88841.90.972
3kpbA0.19071.90.972
2yvyA0.27911.80.973
2pfiA0.25581.70.973
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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