GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OMP_b-brl_2 - Outer membrane protein beta-barrel domain
Pfam: PF13568 (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: CL0193
Length: 173
Sequences: 2039
Seq/Len: 11.79
HH_delta: 0.613 (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
12_G43_F0.531143.038
105_Y151_G0.529293.027
41_G59_S0.514572.943
60_Y86_H0.50262.874
58_L90_I0.414652.371
51_R96_Y0.410362.347
54_V92_L0.381312.181
9_F44_F0.380972.179
88_L116_L0.377722.160
107_F149_G0.371112.122
89_E113_S0.367222.100
111_Y145_G0.367092.099
57_G163_R0.365562.091
90_I114_F0.359062.053
17_F36_I0.343081.962
93_L147_Q0.328041.876
143_D169_N0.296871.698
53_S95_R0.295691.691
18_N61_S0.282031.613
45_N95_R0.281121.608
48_L54_V0.277581.588
87_Y115_L0.275931.578
114_F141_K0.273231.563
10_S45_N0.271961.555
52_F94_L0.271421.552
62_Q84_K0.269941.544
144_F169_N0.267251.528
19_F34_P0.26041.489
93_L163_R0.256011.464
62_Q86_H0.250881.435
143_D167_G0.245011.401
46_Y56_T0.243971.395
63_R89_E0.241341.380
19_F36_I0.240891.378
115_L118_G0.239921.372
108_A146_L0.238891.366
35_G64_G0.238371.363
14_K41_G0.235751.348
57_G91_P0.234421.341
9_F46_Y0.234141.339
95_R151_G0.229261.311
60_Y88_L0.227951.304
107_F161_E0.225231.288
14_K57_G0.222251.271
112_F142_F0.221921.269
55_Q93_L0.221521.267
16_G39_S0.217851.246
14_K59_S0.210361.203
97_N152_Y0.206761.182
87_Y143_D0.198791.137
148_L166_Y0.198261.134
91_P145_G0.196981.127
146_L168_L0.196751.125
86_H116_L0.192391.100
95_R105_Y0.191491.095
153_E159_F0.190391.089
113_S143_D0.187981.075
105_Y161_E0.185011.058
87_Y113_S0.183371.049
14_K43_F0.179881.029
85_L115_L0.178821.023
43_F55_Q0.178081.018
52_F96_Y0.177691.016
49_N94_L0.177151.013
145_G151_G0.176521.010
53_S97_N0.174971.001
95_R107_F0.174470.998
65_Y81_Y0.173790.994
48_L52_F0.172340.986
55_Q107_F0.168210.962
56_T110_P0.166240.951
151_G161_E0.16610.950
105_Y147_Q0.166080.950
146_L166_Y0.165660.947
11_I42_L0.164260.939
10_S153_E0.163720.936
89_E111_Y0.163190.933
63_R113_S0.15950.912
152_Y157_K0.159240.911
111_Y147_Q0.159110.910
107_F147_Q0.159090.910
68_N80_K0.158020.904
112_F144_F0.157990.904
166_Y170_N0.15710.898
43_F57_G0.156180.893
49_N52_F0.155540.890
45_N97_N0.154880.886
53_S56_T0.153670.879
89_E165_S0.152780.874
86_H117_S0.151290.865
53_S105_Y0.150090.858
61_S89_E0.149270.854
154_I160_V0.148870.851
55_Q95_R0.148760.851
50_N88_L0.148270.848
145_G165_S0.148160.847
22_F65_Y0.145880.834
94_L108_A0.145350.831
118_G141_K0.143640.821
151_G164_Y0.143180.819
104_F157_K0.142190.813
100_K103_R0.142170.813
92_L135_D0.141630.810
63_R143_D0.141180.807
155_G158_I0.139970.801
43_F56_T0.139030.795
18_N37_G0.13790.789
159_F162_L0.137420.786
21_N34_P0.137260.785
25_D34_P0.137210.785
104_F111_Y0.135280.774
88_L91_P0.134840.771
146_L167_G0.134840.771
51_R99_G0.134650.770
95_R104_F0.134180.767
98_F104_F0.134150.767
94_L98_F0.133840.765
98_F106_V0.133650.764
111_Y143_D0.133040.761
110_P147_Q0.132530.758
93_L107_F0.131920.754
48_L108_A0.131410.752
61_S87_Y0.131290.751
19_F24_N0.130070.744
12_G57_G0.129820.742
55_Q161_E0.129390.740
55_Q59_S0.129360.740
32_Y36_I0.128170.733
57_G110_P0.12630.722
114_F142_F0.12610.721
59_S90_I0.126010.721
149_G161_E0.125870.720
93_L110_P0.125150.716
111_Y165_S0.124750.713
92_L112_F0.124370.711
63_R87_Y0.124040.709
47_P95_R0.123940.709
33_K136_N0.123610.707
91_P111_Y0.123510.706
112_F148_L0.123380.706
85_L139_F0.123270.705
39_S59_S0.122390.700
10_S47_P0.122220.699
40_I60_Y0.122150.699
24_N152_Y0.121670.696
20_S35_G0.121480.695
92_L119_K0.120710.690
66_N82_K0.120540.689
39_S163_R0.120530.689
66_N80_K0.12050.689
93_L109_G0.119680.684
95_R161_E0.119510.683
149_G163_R0.119250.682
25_D31_S0.119010.681
43_F159_F0.118920.680
39_S161_E0.11860.678
167_G170_N0.11840.677
146_L150_V0.118150.676
9_F13_L0.118010.675
41_G91_P0.117910.674
94_L112_F0.117150.670
55_Q110_P0.117120.670
45_N53_S0.116810.668
78_D82_K0.116460.666
147_Q151_G0.116170.664
151_G159_F0.116030.664
33_K68_N0.115990.663
96_Y99_G0.115830.662
161_E165_S0.115830.662
81_Y89_E0.114040.652
108_A148_L0.113690.650
36_I79_Y0.112720.645
18_N38_F0.112650.644
25_D79_Y0.11260.644
25_D98_F0.112440.643
47_P53_S0.111690.639
105_Y153_E0.111430.637
70_D78_D0.111270.636
48_L96_Y0.111170.636
152_Y155_G0.110950.635
43_F155_G0.110880.634
45_N153_E0.110850.634
20_S25_D0.110320.631
54_V94_L0.109960.629
103_R152_Y0.109720.627
22_F170_N0.109420.626
54_V112_F0.109140.624
106_V116_L0.108870.623
50_N100_K0.108680.622
68_N82_K0.108530.621
105_Y111_Y0.107510.615
45_N105_Y0.107490.615
37_G62_Q0.107270.613
57_G90_I0.107180.613
104_F165_S0.107030.612
45_N107_F0.106920.611
155_G159_F0.106840.611
45_N159_F0.106830.611
95_R98_F0.106510.609
66_N140_N0.105820.605
105_Y159_F0.105790.605
66_N70_D0.104830.600
48_L107_F0.104820.599
53_S120_Y0.104720.599
93_L145_G0.104630.598
39_S61_S0.104510.598
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
3nb3A0.878698.80.613
2x27X0.953898.60.639
2k0lA0.913398.30.671
2lhfA0.803598.30.674
2f1vA0.913398.30.677
1qjpA0.867198.20.689
3qraA0.838298.10.696
1p4tA0.780398.10.698
2jmmA0.76397.80.723
1ormA0.780397.30.755
If you are interested in a protein containing this domain,
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