GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ail_Lom - Enterobacterial AilLom protein
Pfam: PF06316 (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: 199
Sequences: 2636
Seq/Len: 13.25
HH_delta: 0.385 (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
175_D194_G0.569883.663
173_V196_G0.562873.618
116_L161_G0.537063.452
111_V166_F0.424792.730
59_F65_V0.358892.307
121_Y154_K0.356012.288
169_N172_V0.350312.252
71_Y95_K0.32992.120
30_T54_K0.323552.080
52_N70_S0.29731.911
178_Y189_N0.293081.884
172_V197_Y0.29131.872
168_P174_I0.290421.867
119_V156_T0.280971.806
180_G189_N0.27281.753
111_V164_V0.270691.740
114_Y175_D0.264791.702
112_S165_Q0.258161.659
58_E64_G0.255071.639
22_A25_A0.254241.634
66_I102_G0.253951.632
107_V113_L0.253551.630
50_G194_G0.246191.582
172_V195_V0.24581.580
54_K66_I0.24261.559
109_E113_L0.242121.556
35_Y47_N0.240011.543
118_G159_A0.236051.517
110_Y166_F0.233611.502
121_Y156_T0.231751.490
64_G104_A0.230711.483
19_G23_S0.223791.438
120_A157_S0.222411.430
114_Y163_G0.220961.420
171_N197_Y0.217271.397
100_M103_P0.215071.382
63_L103_P0.207781.336
160_Y180_G0.206781.329
57_Y67_T0.196991.266
36_A72_A0.19651.263
32_S35_Y0.193121.241
154_K157_S0.190071.222
32_S196_G0.182411.172
32_S70_S0.178851.150
173_V198_R0.178521.147
167_N198_R0.178021.144
68_S177_G0.178011.144
166_F169_N0.177991.144
177_G192_N0.177741.142
30_T56_R0.174371.121
68_S179_E0.174011.118
74_G98_S0.170541.096
66_I161_G0.170191.094
60_D63_L0.169631.090
165_Q175_D0.168811.085
65_V101_A0.168041.080
62_P105_Y0.167021.074
67_T92_V0.165881.066
175_D196_G0.16451.057
64_G179_E0.16411.055
110_Y168_P0.163471.051
20_L23_S0.16281.046
111_V162_A0.161621.039
21_P24_A0.159581.026
69_F99_L0.157031.009
110_Y167_N0.156891.008
164_V167_N0.154970.996
106_R109_E0.154880.996
51_V69_F0.153830.989
100_M159_A0.151710.975
66_I177_G0.150840.970
157_S165_Q0.150770.969
29_S33_V0.150660.968
56_R104_A0.149470.961
102_G176_V0.149470.961
113_L120_A0.148340.953
45_F48_L0.147770.950
68_S100_M0.146790.944
166_F176_V0.146310.940
175_D179_E0.145770.937
109_E112_S0.145640.936
34_G197_Y0.145130.933
116_L120_A0.144320.928
165_Q173_V0.144180.927
56_R64_G0.142180.914
29_S57_Y0.141160.907
98_S120_A0.139220.895
176_V193_V0.138560.891
52_N55_Y0.136580.878
55_Y68_S0.135950.874
51_V71_Y0.135410.870
182_G186_W0.134660.866
33_V49_R0.13390.861
70_S179_E0.133760.860
171_N198_R0.133540.858
35_Y158_L0.132920.854
178_Y181_S0.132890.854
114_Y177_G0.13280.854
57_Y89_D0.130860.841
68_S72_A0.130810.841
188_T192_N0.129830.834
32_S54_K0.128960.829
48_L52_N0.128780.828
54_K68_S0.128150.824
19_G22_A0.127910.822
114_Y118_G0.127810.822
106_R112_S0.127650.820
78_S151_S0.12760.820
32_S165_Q0.126870.815
64_G180_G0.126680.814
56_R106_R0.126530.813
183_S190_G0.126430.813
61_D97_Y0.126170.811
61_D71_Y0.125980.810
123_K126_D0.125810.809
96_Y159_A0.125560.807
122_T157_S0.125270.805
166_F197_Y0.12420.798
79_S124_V0.124160.798
71_Y75_D0.124150.798
124_V186_W0.124120.798
158_L181_S0.123570.794
62_P106_R0.123460.794
38_S75_D0.123220.792
40_V101_A0.122930.790
119_V160_Y0.122870.790
31_L93_R0.122620.788
115_A162_A0.121330.780
104_A177_G0.120840.777
66_I116_L0.120790.776
30_T173_V0.120650.775
75_D188_T0.120630.775
152_S158_L0.120540.775
92_V191_F0.119860.770
102_G161_G0.119370.767
19_G109_E0.119340.767
66_I175_D0.119110.766
22_A37_Q0.1190.765
37_Q193_V0.11890.764
122_T155_K0.118670.763
23_S26_A0.118470.761
32_S68_S0.118360.761
56_R175_D0.117450.755
191_F196_G0.117260.754
180_G195_V0.117230.754
28_Q61_D0.117190.753
56_R66_I0.11690.751
102_G177_G0.116850.751
189_N192_N0.116430.748
34_G194_G0.116430.748
110_Y171_N0.116290.747
71_Y97_Y0.116190.747
50_G72_A0.115910.745
104_A165_Q0.114490.736
188_T191_F0.114360.735
52_N68_S0.114340.735
63_L110_Y0.114160.734
57_Y60_D0.114080.733
54_K179_E0.113980.733
117_A123_K0.11380.731
54_K161_G0.113740.731
98_S104_A0.112780.725
54_K102_G0.11260.724
31_L92_V0.112410.723
19_G153_S0.112380.722
97_Y123_K0.112340.722
20_L78_S0.112310.722
108_N167_N0.112130.721
161_G177_G0.112110.721
126_D151_S0.111720.718
28_Q56_R0.111620.717
109_E171_N0.110890.713
176_V179_E0.110770.712
105_Y168_P0.110750.712
74_G176_V0.110590.711
59_F64_G0.110090.708
162_A180_G0.110070.707
71_Y188_T0.109690.705
116_L177_G0.109520.704
50_G53_V0.109430.703
76_D111_V0.108990.701
42_V184_G0.108570.698
102_G114_Y0.108440.697
34_G163_G0.108330.696
164_V172_V0.108270.696
185_D198_R0.108170.695
98_S101_A0.108160.695
44_G151_S0.107890.693
64_G106_R0.107890.693
104_A112_S0.107780.693
40_V96_Y0.107690.692
34_G175_D0.107660.692
35_Y49_R0.107460.691
176_V191_F0.107360.690
34_G118_G0.107220.689
100_M104_A0.107130.689
19_G79_S0.1070.688
46_K50_G0.106680.686
193_V197_Y0.106520.685
99_L109_E0.106340.684
50_G55_Y0.106270.683
179_E192_N0.106190.683
66_I104_A0.10590.681
50_G113_L0.105890.681
152_S174_I0.105720.680
64_G157_S0.105610.679
118_G121_Y0.105260.677
32_S180_G0.104440.671
20_L25_A0.104380.671
44_G78_S0.103690.666
27_H61_D0.103670.666
46_K185_D0.103530.665
110_Y174_I0.103510.665
38_S96_Y0.10330.664
122_T181_S0.103270.664
49_R97_Y0.103020.662
116_L121_Y0.102520.659
35_Y43_Q0.102080.656
74_G96_Y0.101690.654
165_Q196_G0.101520.653
115_A123_K0.101390.652
46_K113_L0.101360.652
108_N111_V0.101150.650
36_A68_S0.101010.649
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
3nb3A0.869399.80.385
3qraA0.773999.70.452
2k0lA0.849299.60.489
1ormA0.738799.50.523
2x27X0.844299.50.526
1qjpA0.783999.50.538
2jmmA0.723699.40.562
1p4tA0.738799.30.576
2f1vA0.80999.30.577
2lhfA0.733799.20.6

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