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Archive: 2012 - 2013
Claudin_3 - Tight junction protein Claudin-like
Pfam: PF06653 (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: CL0375
Length: 163
Sequences: 1477
Seq/Len: 9.06
HH_delta: 0.912 (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
37_S42_I0.446123.244
43_V47_S0.345952.515
25_T136_S0.329672.397
20_A24_F0.261481.901
81_V120_S0.259221.885
42_I47_S0.258881.882
39_S42_I0.257951.875
35_K42_I0.257941.875
22_G140_C0.257791.874
58_W62_I0.250431.821
61_Y65_A0.24551.785
106_I110_I0.243081.767
30_T134_G0.228971.665
44_P47_S0.222491.618
37_S40_I0.221871.613
23_V60_M0.216551.574
108_T143_S0.212781.547
74_Y97_I0.211861.540
35_K43_V0.211151.535
51_G55_A0.210821.533
43_V46_S0.208831.518
36_I39_S0.206421.501
133_L141_V0.205711.496
111_A115_F0.202851.475
22_G143_S0.1951.418
16_F67_F0.189441.377
63_S108_T0.189321.376
121_S124_N0.186721.358
113_I117_V0.185671.350
60_M108_T0.182221.325
98_S151_F0.180851.315
18_L143_S0.173281.260
73_F78_V0.172991.258
14_I139_L0.171111.244
106_I113_I0.169371.231
113_I116_A0.167591.218
42_I46_S0.167221.216
18_L139_L0.166521.211
35_K40_I0.16651.211
12_I101_S0.165561.204
79_Y91_R0.164891.199
36_I42_I0.161051.171
12_I70_M0.160421.166
138_W141_V0.158441.152
137_A141_V0.157421.145
96_I104_I0.155741.132
25_T135_Y0.153731.118
38_I41_G0.151811.104
69_I72_I0.151531.102
82_R120_S0.151491.101
22_G76_I0.151421.101
36_I40_I0.15121.099
100_F103_L0.150131.092
19_N67_F0.147211.070
142_A149_I0.147051.069
124_N132_S0.146711.067
47_S127_D0.145311.056
73_F108_T0.143291.042
38_I42_I0.14321.041
144_A153_L0.142251.034
19_N144_A0.142091.033
107_L143_S0.141921.032
105_V151_F0.140021.018
17_I21_V0.139721.016
98_S109_I0.138871.010
21_V25_T0.138531.007
126_Y129_F0.137611.000
95_H100_F0.136770.994
22_G136_S0.136590.993
138_W142_A0.136240.991
98_S105_V0.133210.969
39_S43_V0.132910.966
24_F27_C0.130190.947
62_I65_A0.129420.941
49_E112_V0.129150.939
137_A150_N0.129150.939
108_T112_V0.128540.935
58_W141_V0.128310.933
27_C135_Y0.127910.930
52_W56_A0.126990.923
19_N133_L0.12640.919
40_I43_V0.126290.918
102_L151_F0.126260.918
35_K47_S0.125870.915
110_I114_L0.125380.912
23_V57_S0.125180.910
37_S43_V0.124880.908
73_F97_I0.124280.904
65_A71_I0.123940.901
10_F72_I0.12310.895
95_H139_L0.122740.892
65_A72_I0.122160.888
66_C100_F0.12210.888
105_V153_L0.121650.884
42_I45_Y0.121390.883
10_F136_S0.120720.878
11_L14_I0.120580.877
35_K39_S0.120560.877
116_A119_I0.120470.876
56_A133_L0.120130.873
105_V148_L0.119490.869
64_F149_I0.118730.863
109_I113_I0.118690.863
16_F68_I0.118490.861
116_A141_V0.118190.859
58_W61_Y0.117570.855
53_F77_I0.116860.850
99_I102_L0.116830.849
37_S41_G0.116410.846
41_G47_S0.116250.845
118_N128_P0.116210.845
18_L72_I0.116190.845
60_M78_V0.1160.843
15_G150_N0.115970.843
23_V61_Y0.115660.841
145_I149_I0.115430.839
81_V128_P0.115360.839
92_K103_L0.115320.838
75_I103_L0.115290.838
111_A114_L0.115230.838
65_A69_I0.115190.837
57_S61_Y0.115040.836
79_Y101_S0.114680.834
111_A147_S0.114270.831
96_I100_F0.113640.826
90_I93_W0.113630.826
59_L107_L0.113610.826
10_F94_F0.11340.824
14_I30_T0.112390.817
57_S109_I0.111930.814
66_C76_I0.111650.812
54_A58_W0.111620.812
149_I153_L0.111370.810
23_V26_P0.110980.807
57_S116_A0.110620.804
116_A138_W0.11060.804
119_I131_L0.110580.804
31_D115_F0.110030.800
57_S141_V0.108360.788
114_L137_A0.107980.785
67_F70_M0.107640.783
15_G151_F0.107260.780
54_A57_S0.107220.780
21_V143_S0.107190.779
62_I92_K0.106630.775
135_Y139_L0.10650.774
75_I146_L0.106470.774
52_W115_F0.10630.773
104_I128_P0.106260.773
108_T144_A0.105870.770
74_Y79_Y0.105810.769
14_I71_I0.105180.765
39_S47_S0.104940.763
92_K95_H0.104760.762
24_F71_I0.104740.762
39_S45_Y0.104360.759
68_I72_I0.104190.758
21_V24_F0.104170.757
13_L75_I0.10410.757
50_P96_I0.103880.755
19_N22_G0.10360.753
146_L151_F0.103080.749
63_S67_F0.103070.749
141_V151_F0.103050.749
110_I117_V0.102970.749
18_L145_I0.102950.748
36_I127_D0.102610.746
98_S104_I0.10260.746
65_A100_F0.102580.746
65_A70_M0.10240.744
98_S114_L0.102380.744
15_G108_T0.10230.744
27_C39_S0.101950.741
29_I119_I0.101780.740
34_Y143_S0.101450.738
22_G60_M0.100580.731
117_V138_W0.100510.731
10_F78_V0.099770.725
20_A64_F0.099620.724
58_W110_I0.099430.723
13_L18_L0.099430.723
59_L62_I0.09940.723
20_A118_N0.09930.722
26_P153_L0.099030.720
70_M97_I0.098650.717
40_I46_S0.098610.717
66_C96_I0.098490.716
32_S133_L0.098350.715
44_P90_I0.098210.714
33_N123_N0.098160.714
63_S69_I0.097830.711
72_I89_S0.097740.711
36_I43_V0.097510.709
31_D43_V0.09750.709
55_A66_C0.097440.708
14_I20_A0.097360.708
20_A76_I0.097070.706
118_N131_L0.096980.705
15_G136_S0.096650.703
35_K44_P0.096640.703
50_P112_V0.096520.702
103_L109_I0.096090.699
15_G147_S0.095890.697
15_G21_V0.095760.696
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
2jp3A0.269926.90.912
4hytG0.325218.50.919
2zxeG0.257716.60.92
2jo1A0.263813.90.923
4ev6A0.39887.10.932
2wswA0.48476.10.934
2jwaA0.25775.40.935
2hi7B0.80374.50.938
4i0uA0.39884.40.938
1lghA0.239340.939
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