GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peripla_BP_3 - Periplasmic binding protein-like domain
Pfam: PF13377 (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: CL0144
Length: 160
Sequences: 17458
Seq/Len: 109.11
HH_delta: -0.009 (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
9_H70_D2.615923.346
93_R96_Q2.52113.225
9_H99_S2.208852.825
28_L32_R2.208132.824
105_D120_D1.920672.457
129_E132_E1.687272.158
5_I38_H1.60442.052
87_L98_I1.593092.038
61_L90_L1.532451.960
74_C83_V1.463221.872
30_G34_A1.420941.817
13_A69_P1.395961.786
14_F75_S1.389071.777
120_D153_E1.377891.762
122_D125_E1.370071.752
3_Y7_R1.367711.749
61_L86_A1.363541.744
125_E128_R1.361241.741
57_R89_E1.342541.717
136_D141_P1.324531.694
93_R97_D1.310771.677
135_L139_E1.303871.668
115_P158_E1.280111.637
5_I34_A1.255621.606
101_V117_T1.252961.603
92_I97_D1.240281.586
65_R90_L1.226631.569
125_E129_E1.218471.558
86_A90_L1.198331.533
86_A89_E1.168661.495
4_L71_A1.120751.434
88_R113_S1.099391.406
29_E33_E1.09831.405
60_Q83_V1.094171.400
57_R86_A1.065271.363
3_Y156_P1.054971.349
11_R68_R1.046191.338
84_L100_V1.045451.337
15_I83_V1.042241.333
82_G86_A1.033691.322
11_R70_D1.03081.318
34_A37_E1.028041.315
13_A63_W1.017941.302
9_H71_A1.016421.300
105_D157_R1.013651.297
87_L92_I1.011171.293
60_Q72_I1.008191.290
32_R36_K1.00231.282
11_R43_E1.001231.281
56_A82_G0.997321.276
77_D118_T0.997141.275
124_R128_R0.995341.273
57_R61_L0.989711.266
124_R127_G0.989661.266
127_G131_V0.988211.264
31_F35_L0.985091.260
14_F28_L0.971481.243
3_Y6_E0.970531.241
26_E29_E0.969751.240
132_E136_D0.951841.217
129_E133_L0.945021.209
43_E46_I0.941781.205
12_I35_L0.933551.194
134_L138_I0.903931.156
34_A38_H0.902571.154
129_E148_I0.886921.134
7_R156_P0.884461.131
122_D150_V0.877791.123
25_R29_E0.869341.112
60_Q87_L0.867021.109
74_C80_A0.866961.109
74_C79_L0.852611.091
12_I71_A0.850191.087
104_D121_Q0.848391.085
61_L89_E0.844321.080
29_E32_R0.836961.071
10_R70_D0.82961.061
31_F73_I0.828051.059
153_E156_P0.827421.058
72_I83_V0.825121.055
33_E37_E0.822351.052
54_E58_E0.815041.042
60_Q64_L0.812011.039
128_R132_E0.811441.038
77_D105_D0.808711.034
57_R85_R0.806441.031
22_S26_E0.802121.026
7_R99_S0.801471.025
5_I40_I0.800561.024
6_E38_H0.799481.023
59_A62_L0.79341.015
102_S118_T0.786961.007
54_E57_R0.784671.004
5_I10_R0.784031.003
26_E30_G0.781921.000
14_F73_I0.781380.999
77_D102_S0.777710.995
45_L48_F0.764320.978
55_D58_E0.76330.976
122_D153_E0.762390.975
131_V135_L0.761990.975
11_R41_E0.76080.973
35_L40_I0.760360.973
58_E62_L0.750960.961
42_F45_L0.747350.956
56_A60_Q0.744620.952
129_E150_V0.736330.942
73_I101_V0.734070.939
120_D155_I0.71650.916
72_I98_I0.708450.906
33_E36_K0.707820.905
111_F114_P0.694120.888
56_A59_A0.693060.886
32_R42_F0.683170.874
77_D80_A0.681320.871
16_G28_L0.680090.870
121_Q126_M0.678880.868
92_I98_I0.677730.867
3_Y117_T0.67380.862
133_L136_D0.669780.857
62_L66_R0.669590.856
105_D155_I0.658240.842
84_L112_F0.657560.841
80_A102_S0.642480.822
15_I74_C0.639370.818
55_D59_A0.635620.813
52_D55_D0.633010.810
68_R92_I0.632390.809
61_L65_R0.624050.798
10_R40_I0.623860.798
85_R88_R0.621650.795
21_S24_S0.620620.794
14_F31_F0.618850.792
136_D140_G0.610090.780
87_L100_V0.608010.778
44_E47_F0.606670.776
5_I35_L0.605510.774
85_R89_E0.603550.772
13_A72_I0.602560.771
103_F121_Q0.599130.766
64_L86_A0.596330.763
76_N79_L0.593990.760
58_E61_L0.589680.754
109_L118_T0.587190.751
50_D55_D0.586790.751
137_R140_G0.58230.745
12_I31_F0.580140.742
60_Q86_A0.578510.740
20_N25_R0.577760.739
81_L112_F0.572440.732
122_D126_M0.570290.729
24_S75_S0.561580.718
64_L90_L0.559520.716
76_N104_D0.558630.715
4_L101_V0.556630.712
70_D99_S0.556460.712
105_D109_L0.553560.708
117_T157_R0.551780.706
62_L65_R0.550570.704
117_T154_L0.54840.701
81_L108_L0.548040.701
57_R60_Q0.544230.696
71_A101_V0.540210.691
133_L148_I0.539530.690
74_C102_S0.536060.686
85_R113_S0.536050.686
12_I70_D0.534930.684
85_R115_P0.534930.684
40_I44_E0.532770.681
78_R106_S0.532740.681
60_Q63_W0.531180.679
80_A100_V0.529460.677
4_L73_I0.525940.673
81_L85_R0.525740.672
81_L106_S0.520840.666
123_P127_G0.520460.666
126_M130_A0.515660.660
73_I103_F0.512140.655
130_A134_L0.510910.653
115_P157_R0.505740.647
42_F46_I0.504870.646
17_G24_S0.504590.645
126_M150_V0.499390.639
119_I152_P0.49830.637
75_S79_L0.498030.637
28_L75_S0.494560.633
53_S57_R0.49310.631
69_P92_I0.492760.630
87_L90_L0.492030.629
92_I95_P0.490570.627
154_L157_R0.484370.620
77_D106_S0.475290.608
35_L42_F0.47420.607
110_E114_P0.471820.603
53_S56_A0.469440.600
32_R44_E0.467490.598
112_F115_P0.467360.598
22_S25_R0.461870.591
43_E47_F0.456860.584
63_W67_L0.454020.581
133_L137_R0.453620.580
103_F119_I0.45250.579
88_R93_R0.450460.576
110_E115_P0.448020.573
71_A99_S0.447120.572
66_R69_P0.446830.572
79_L82_G0.446590.571
52_D56_A0.445380.570
134_L137_R0.443630.567
27_R30_G0.441640.565
27_R104_D0.439470.562
95_P99_S0.438760.561
77_D104_D0.437860.560
149_L152_P0.436510.558
24_S76_N0.435420.557
53_S85_R0.435190.557
16_G24_S0.434670.556
17_G51_D0.434410.556
137_R143_A0.432940.554
105_D118_T0.430950.551
74_C100_V0.429640.550
3_Y154_L0.428190.548
69_P72_I0.42660.546
27_R103_F0.425830.545
107_P111_F0.425410.544
51_D55_D0.4250.544
46_I49_S0.423230.541
9_H12_I0.419690.537
101_V119_I0.419550.537
11_R69_P0.416490.533
77_D109_L0.414230.530
104_D123_P0.411490.526
23_V76_N0.410630.525
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
3jvdA0.981299.9-0.009
3hcwA0.987599.90.004
3kjxA199.90.006
3e3mA199.90.007
3qk7A199.90.007
3mizA0.993899.90.014
2o20A0.993899.90.014
3huuA0.981299.90.014
2hsgA199.90.014
1qpzA199.90.014

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