GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BPD_transp_1 - Binding-protein-dependent transport system inner membrane component
Pfam: PF00528 (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: CL0404
Length: 185
Sequences: 48283
Seq/Len: 260.99
HH_delta: 0.14 (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
96_Q100_K2.632143.364
93_S96_Q2.443213.122
88_R97_I2.359333.015
95_W99_R2.162922.764
73_Y77_R2.010362.569
87_A97_I1.95012.492
84_I97_I1.800172.301
94_R97_I1.766622.258
84_I102_I1.687612.157
92_A96_Q1.670362.135
88_R94_R1.662642.125
83_Y105_N1.587192.028
87_A92_A1.551751.983
84_I88_R1.53091.956
75_A109_G1.481021.893
139_T143_N1.467061.875
174_I178_L1.462051.868
11_R84_I1.431281.829
14_R17_K1.372641.754
87_A101_V1.372431.754
142_I146_S1.340691.713
141_L144_A1.319661.687
82_E85_E1.316281.682
56_I128_V1.303861.666
96_Q99_R1.303781.666
178_L181_R1.300181.662
72_I110_I1.29841.659
15_K19_I1.287461.645
76_L106_I1.252411.601
5_G9_A1.236461.580
3_P7_L1.196291.529
15_K18_R1.175661.502
30_I35_I1.151821.472
149_D152_F1.136441.452
93_S97_I1.129181.443
12_K94_R1.120411.432
3_P6_I1.117081.428
13_N17_K1.116051.426
86_A90_L1.08951.392
115_I176_Q1.049391.341
138_G141_L1.029591.316
16_F19_I1.025751.311
140_L143_N1.008421.289
153_I156_A1.003031.282
127_V131_L0.996651.274
68_A113_A0.984641.258
65_F69_I0.982241.255
81_K84_I0.979871.252
141_L145_I0.96391.232
68_A117_S0.959591.226
175_L178_L0.950581.215
17_K72_I0.94641.209
92_A97_I0.942181.204
81_K85_E0.942061.204
18_R22_P0.939811.201
170_L174_I0.939491.201
142_I145_I0.938561.199
75_A102_I0.933911.194
14_R18_R0.933551.193
176_Q180_E0.928681.187
52_G55_P0.915961.171
53_F57_I0.911451.165
94_R98_F0.896741.146
19_I22_P0.889671.137
76_L102_I0.887141.134
56_I60_Y0.880541.125
19_I23_L0.878031.122
11_R81_K0.872211.115
17_K77_R0.857951.096
21_R73_Y0.857761.096
178_L182_R0.854031.091
78_S83_Y0.847861.084
4_L8_L0.844981.080
54_L58_L0.843741.078
143_N146_S0.835121.067
113_A117_S0.829561.060
97_I102_I0.816671.044
13_N18_R0.810881.036
169_N173_N0.808381.033
60_Y121_A0.805311.029
144_A147_Q0.803251.027
18_R21_R0.803021.026
139_T142_I0.798621.021
125_F129_E0.793351.014
9_A76_L0.792511.013
8_L69_I0.785511.004
74_N77_R0.785131.003
140_L147_Q0.784691.003
98_F103_L0.782851.000
165_I169_N0.769670.984
99_R102_I0.763670.976
72_I76_L0.761420.973
112_S116_L0.760530.972
143_N147_Q0.754880.965
22_P25_N0.753480.963
140_L144_A0.751350.960
17_K21_R0.74580.953
84_I94_R0.739450.945
79_I105_N0.732980.937
157_A161_L0.72840.931
166_I170_L0.728110.931
24_I69_I0.726170.928
85_E88_R0.725930.928
99_R103_L0.723090.924
162_A165_I0.719260.919
171_I175_L0.717910.917
12_K15_K0.717190.917
145_I148_Y0.712540.911
78_S81_K0.712370.910
140_L152_F0.711250.909
67_F117_S0.706890.903
4_L7_L0.706090.902
4_L20_L0.702980.898
174_I177_R0.700990.896
74_N78_S0.69970.894
79_I102_I0.699180.894
106_I109_G0.69750.891
117_S121_A0.68890.880
68_A72_I0.684450.875
57_I60_Y0.676310.864
35_I39_L0.674750.862
135_P139_T0.672150.859
75_A106_I0.67210.859
51_F54_L0.668950.855
16_F20_L0.664090.849
13_N16_F0.660570.844
49_F54_L0.65850.842
169_N176_Q0.653990.836
166_I169_N0.652370.834
173_N176_Q0.646630.826
71_I75_A0.645630.825
11_R14_R0.642540.821
72_I106_I0.640060.818
167_L171_I0.639350.817
54_L57_I0.63820.816
148_Y154_S0.636430.813
69_I73_Y0.635320.812
5_G72_I0.63290.809
72_I113_A0.629780.805
57_I61_V0.629050.804
8_L65_F0.625340.799
124_D127_V0.624980.799
117_S120_S0.624070.798
97_I100_K0.623820.797
137_L140_L0.620010.792
144_A153_I0.615840.787
148_Y151_P0.610320.780
75_A79_I0.610170.780
115_I172_L0.609680.779
61_V65_F0.60870.778
138_G144_A0.608550.778
60_Y64_W0.607950.777
9_A72_I0.607080.776
51_F134_G0.603850.772
32_S63_F0.603360.771
23_L27_P0.602850.770
172_L176_Q0.602380.770
6_I98_F0.600850.768
140_L145_I0.600330.767
105_N108_P0.598650.765
120_S124_D0.59650.762
6_I72_I0.595590.761
6_I75_A0.595130.761
98_F102_I0.594760.760
124_D128_V0.593860.759
48_S51_F0.593460.758
156_A160_A0.591030.755
138_G142_I0.590870.755
161_L165_I0.588310.752
144_A152_F0.586810.750
147_Q150_Y0.586310.749
109_G113_A0.585060.748
39_L58_L0.581710.743
92_A100_K0.580690.742
150_Y153_I0.580480.742
148_Y152_F0.574590.734
7_L16_F0.573210.733
102_I105_N0.571980.731
25_N29_S0.571410.730
110_I114_F0.565540.723
144_A148_Y0.565150.722
137_L141_L0.561690.718
168_L172_L0.560310.716
90_L101_V0.559680.715
175_L179_L0.559160.715
83_Y86_A0.554810.709
81_K88_R0.553530.707
22_P26_I0.551420.705
21_R25_N0.54990.703
78_S106_I0.54860.701
71_I113_A0.545090.697
146_S149_D0.542250.693
162_A166_I0.540440.691
144_A149_D0.538390.688
39_L131_L0.536920.686
95_W100_K0.536850.686
177_R180_E0.536740.686
85_E89_I0.534160.683
32_S35_I0.533280.682
51_F55_P0.532120.680
140_L148_Y0.531920.680
173_N177_R0.530770.678
107_K110_I0.530520.678
154_S158_A0.530370.678
169_N172_L0.529540.677
9_A79_I0.526950.673
36_G128_V0.52630.673
163_L167_L0.525310.671
64_W117_S0.524860.671
146_S150_Y0.524220.670
156_A159_A0.52290.668
8_L20_L0.522740.668
126_A129_E0.518060.662
107_K111_L0.5180.662
67_F113_A0.517910.662
80_P83_Y0.516350.660
170_L173_N0.51550.659
63_F66_P0.514960.658
39_L59_A0.513510.656
95_W98_F0.513160.656
158_A161_L0.512690.655
77_R81_K0.51090.653
167_L170_L0.508410.650
35_I63_F0.50730.648
59_A63_F0.505050.645
72_I109_G0.504530.645
97_I101_V0.504290.644
141_L146_S0.50130.641
58_L61_V0.500660.640
25_N70_I0.500060.639
151_P154_S0.497060.635
6_I9_A0.497050.635
30_I34_V0.495160.633
162_A169_N0.492960.630
32_S36_G0.492910.630
137_L164_I0.488770.625
86_A89_I0.488570.624
147_Q152_F0.488520.624
103_L110_I0.488080.624
93_S100_K0.487560.623
61_V64_W0.484780.620
83_Y101_V0.483910.618
141_L147_Q0.483820.618
9_A75_A0.482980.617
177_R181_R0.482160.616
166_I173_N0.479130.612
103_L107_K0.47820.611
12_K17_K0.478180.611
140_L146_S0.477130.610
86_A91_G0.476710.609
158_A162_A0.476130.608
5_G68_A0.474450.606
78_S102_I0.473670.605
25_N28_L0.473630.605
60_Y128_V0.472350.604
141_L161_L0.469920.601
55_P59_A0.469280.600
141_L157_A0.467660.598
27_P31_P0.46760.598
49_F52_G0.464210.593
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
3d31C0.967699.90.14
2onkC0.967699.80.155
3rlfF0.989299.80.155
3tuiA0.97399.80.189
3rlfG0.989299.80.215
3tuiA0.967690.50.824
3qf4A0.49733.40.926
3qnqA0.43783.20.927
3w4tA0.57842.80.929
2ifoA0.10812.70.929

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