GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OmpA_membrane - OmpA-like transmembrane domain
Pfam: PF01389 (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: 183
Sequences: 3821
Seq/Len: 20.88
HH_delta: 0.249 (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
148_Y169_H1.138265.024
145_R174_G0.852923.765
150_Y169_H0.761093.359
93_L136_Y0.733443.237
138_L144_L0.695673.070
101_A126_V0.644022.843
93_L134_L0.636112.808
143_S176_S0.623032.750
142_W177_Y0.582192.570
98_K131_G0.561312.477
139_T142_W0.515722.276
47_F53_L0.452131.996
145_R176_S0.422861.866
96_Y147_E0.412421.820
92_D136_Y0.404971.787
135_E145_R0.389751.720
96_Y145_R0.385021.699
42_F176_S0.376761.663
82_S98_K0.360331.590
143_S178_R0.354151.563
142_W175_L0.346011.527
141_N177_Y0.333091.470
48_N51_F0.332091.466
46_Q52_A0.331931.465
147_E172_S0.329771.456
52_A86_S0.328331.449
89_L95_L0.324981.434
40_G58_D0.323551.428
79_I103_Y0.316441.397
94_D135_E0.31151.375
96_Y133_G0.310031.368
137_A178_R0.303981.342
99_A128_P0.296071.307
103_Y124_D0.295111.303
82_S129_L0.286111.263
96_Y100_G0.277061.223
135_E176_S0.275691.217
95_L134_L0.275241.215
42_F54_E0.275091.214
132_L148_Y0.274011.209
92_D137_A0.264661.168
51_F85_F0.262571.159
138_L175_L0.26211.157
96_Y131_G0.258951.143
137_A143_S0.256391.132
88_P91_D0.256191.131
40_G149_Q0.255871.129
135_E143_S0.251671.111
98_K149_Q0.250721.107
149_Q172_S0.250491.106
86_S94_D0.249021.099
51_F87_Y0.236921.046
89_L94_D0.236831.045
50_Y87_Y0.236621.044
94_D137_A0.235591.040
50_Y88_P0.234371.034
52_A84_K0.232381.026
99_A130_A0.230071.015
64_K67_Y0.228631.009
105_Q122_S0.224690.992
150_Y167_D0.223960.988
78_G82_S0.221850.979
130_A150_Y0.221630.978
54_E84_K0.22140.977
52_A100_G0.221190.976
104_W127_S0.220540.973
129_L151_I0.21910.967
102_A129_L0.218970.966
149_Q170_F0.218840.966
54_E98_K0.218020.962
82_S86_S0.217850.962
128_P132_L0.214070.945
81_L103_Y0.210320.928
146_L173_L0.208110.919
63_F67_Y0.207960.918
47_F51_F0.20750.916
94_D127_S0.207480.916
42_F56_G0.207160.914
51_F83_L0.20640.911
56_G80_T0.206170.910
82_S149_Q0.204650.903
38_G174_G0.201930.891
146_L171_F0.200210.884
159_T165_N0.199120.879
55_L81_L0.198590.877
103_Y126_V0.198230.875
57_Y77_Q0.196740.868
90_T93_L0.196590.868
144_L173_L0.195390.862
103_Y106_S0.194930.860
84_K147_E0.190370.840
145_R172_S0.190210.840
78_G102_A0.189020.834
132_L150_Y0.188320.831
157_D173_L0.186840.825
88_P137_A0.185840.820
128_P152_N0.185380.818
68_S111_S0.185310.818
96_Y99_A0.185080.817
92_D139_T0.184910.816
100_G129_L0.184910.816
104_W154_V0.184590.815
171_F175_L0.184520.814
66_S111_S0.18370.811
94_D143_S0.183550.810
102_A127_S0.181820.803
123_D165_N0.18110.799
165_N170_F0.180420.796
54_E100_G0.179410.792
87_Y94_D0.179130.791
59_D78_G0.179080.790
97_A132_L0.178810.789
67_Y70_G0.177270.782
86_S135_E0.176950.781
39_Y59_D0.176210.778
52_A88_P0.175970.777
67_Y72_Y0.175130.773
56_G98_K0.17480.772
54_E147_E0.173130.764
84_K98_K0.171370.756
151_I154_V0.171150.755
56_G129_L0.16830.743
42_F145_R0.165820.732
71_N119_I0.165360.730
46_Q94_D0.165310.730
32_C64_K0.16520.729
129_L149_Q0.1650.728
38_G172_S0.16450.726
79_I106_S0.164280.725
74_Y79_I0.16350.722
37_T41_L0.163430.721
40_G145_R0.163240.720
80_T100_G0.162960.719
57_Y61_G0.162170.716
106_S125_G0.162030.715
153_D167_D0.161810.714
136_Y144_L0.161260.712
72_Y78_G0.160220.707
101_A128_P0.159710.705
119_I160_G0.159070.702
92_D138_L0.158270.699
44_G86_S0.155950.688
102_A152_N0.155750.687
46_Q178_R0.155310.685
80_T102_A0.154710.683
48_N55_L0.154380.681
32_C67_Y0.153690.678
40_G172_S0.153390.677
99_A132_L0.15170.670
148_Y171_F0.151530.669
44_G56_G0.150.662
66_S70_G0.149630.660
72_Y75_S0.149550.660
52_A56_G0.1480.653
155_G158_S0.147340.650
136_Y177_Y0.146960.649
158_S166_P0.146350.646
71_N120_T0.146250.646
54_E131_G0.145880.644
104_W107_D0.145830.644
82_S145_R0.144710.639
52_A98_K0.144570.638
131_G149_Q0.144550.638
82_S88_P0.14450.638
69_G111_S0.143190.632
91_D95_L0.143160.632
34_D74_Y0.143140.632
68_S73_S0.142610.629
104_W125_G0.141640.625
81_L101_A0.141470.624
64_K119_I0.140550.620
46_Q50_Y0.140050.618
64_K69_G0.139380.615
50_Y85_F0.139360.615
35_D123_D0.138970.613
40_G56_G0.137680.608
107_D122_S0.136960.605
84_K131_G0.136640.603
34_D155_G0.136490.602
76_A106_S0.136320.602
44_G52_A0.136070.601
78_G81_L0.136030.600
39_Y62_E0.135980.600
141_N179_F0.135940.600
86_S147_E0.135490.598
94_D97_A0.134840.595
99_A103_Y0.134570.594
52_A131_G0.134520.594
169_H173_L0.133860.591
89_L92_D0.133490.589
98_K132_L0.133370.589
68_S157_D0.133290.588
41_L45_Y0.132770.586
145_R148_Y0.132710.586
105_Q151_I0.132480.585
110_S120_T0.13240.584
108_Y119_I0.132020.583
38_G56_G0.132010.583
130_A152_N0.131640.581
154_V157_D0.131640.581
110_S160_G0.131320.580
37_T129_L0.131250.579
66_S158_S0.130850.578
131_G147_E0.130790.577
70_G111_S0.130760.577
105_Q126_V0.130760.577
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
2k0lA0.989199.80.249
3nb3A0.945499.80.265
1qjpA0.92999.80.282
2jmmA0.803399.80.316
2x27X0.983699.80.329
2f1vA0.994599.70.37
1p4tA0.836199.70.375
3qraA0.84799.60.406
2lhfA0.907199.60.415
1ormA0.803399.40.491

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