GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thioredoxin_6 - Thioredoxin-like domain
Pfam: PF13848 (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: CL0172
Length: 184
Sequences: 2897
Seq/Len: 15.74
HH_delta: 0.174 (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
60_D66_E0.472193.002
123_K179_E0.470062.989
45_V56_V0.453062.880
135_A142_L0.433332.755
63_T66_E0.411942.619
174_T177_S0.395542.515
11_I14_E0.360432.292
11_I64_P0.356112.264
28_T33_L0.351192.233
37_Y47_Y0.339542.159
11_I15_A0.328852.091
17_E20_K0.32862.089
18_K68_K0.320872.040
155_L178_I0.30971.969
116_E120_I0.273611.740
88_E144_Y0.272551.733
172_E177_S0.270881.722
44_I67_L0.270521.720
46_V70_F0.269081.711
100_I103_D0.268251.705
120_I175_P0.260641.657
82_L87_F0.253121.609
46_V74_N0.251071.596
133_V141_L0.25041.592
39_I42_P0.247041.571
34_A37_Y0.245571.561
128_I182_L0.243791.550
30_N33_L0.234211.489
39_I43_T0.228721.454
57_Y70_F0.226411.439
140_R143_K0.225731.435
15_A64_P0.220071.399
116_E119_D0.219891.398
100_I158_F0.219821.398
117_L130_F0.219451.395
70_F74_N0.218391.388
79_V132_Y0.217871.385
15_A67_L0.217121.380
119_D175_P0.215031.367
15_A19_L0.212691.352
74_N125_K0.212631.352
120_I130_F0.21211.348
15_A68_K0.211471.344
120_I124_F0.210241.337
166_Y169_P0.208741.327
18_K64_P0.207841.321
88_E92_S0.207171.317
83_T86_N0.206031.310
41_E62_F0.205981.310
22_D72_K0.205761.308
60_D63_T0.20461.301
14_E64_P0.203831.296
98_V102_F0.201561.281
66_E69_K0.197321.255
19_L25_F0.196681.250
12_F25_F0.193961.233
171_G177_S0.193921.233
179_E183_N0.189611.205
116_E175_P0.187381.191
164_K168_L0.185971.182
90_L131_V0.185851.182
175_P179_E0.185021.176
99_L130_F0.182291.159
102_F145_F0.179521.141
45_V54_P0.177551.129
145_F158_F0.176711.123
10_E15_A0.172561.097
111_E115_K0.171981.093
32_E35_K0.169191.076
9_F12_F0.168451.071
119_D123_K0.166621.059
99_L103_D0.164811.048
112_A116_E0.163761.041
33_L36_K0.161941.030
104_N110_T0.161251.025
19_L23_Y0.16041.020
89_K92_S0.160041.017
80_P90_L0.157851.004
86_N89_K0.155070.986
110_T115_K0.151420.963
120_I182_L0.150820.959
31_E35_K0.150760.958
176_E180_K0.149520.951
138_F141_L0.14550.925
109_S173_I0.145360.924
114_K118_Q0.14460.919
59_G66_E0.144430.918
147_I154_A0.144380.918
113_F116_E0.144170.917
101_L104_N0.144020.916
99_L155_L0.143450.912
87_F91_F0.143210.910
81_E132_Y0.141710.901
12_F71_I0.140870.896
78_L125_K0.140630.894
27_V34_A0.140.890
19_L68_K0.139130.885
163_G166_Y0.138760.882
10_E42_P0.138420.880
45_V62_F0.138290.879
10_E62_F0.138250.879
39_I45_V0.138150.878
164_K167_Y0.137960.877
80_P131_V0.137920.877
140_R144_Y0.137870.877
10_E13_E0.137690.875
117_L120_I0.137490.874
79_V130_F0.137150.872
40_K56_V0.136290.866
11_I123_K0.135350.861
68_K72_K0.135260.860
103_D132_Y0.134880.858
38_G45_V0.134530.855
80_P88_E0.133520.849
160_S163_G0.133450.848
141_L144_Y0.133140.846
133_V142_L0.1330.846
43_T62_F0.132330.841
114_K132_Y0.130530.830
165_Y168_L0.130070.827
12_F142_L0.12990.826
36_K47_Y0.129860.826
72_K75_S0.12960.824
79_V117_L0.128730.818
106_D115_K0.127880.813
142_L152_L0.127660.812
128_I157_I0.127560.811
98_V131_V0.12680.806
55_V59_G0.126450.804
57_Y60_D0.126150.802
101_L109_S0.125770.800
113_F117_L0.125570.798
122_K125_K0.125510.798
78_L122_K0.125370.797
37_Y45_V0.124870.794
121_A130_F0.124680.793
35_K38_G0.124420.791
84_P141_L0.124260.790
177_S180_K0.12420.790
12_F15_A0.123370.784
113_F135_A0.122790.781
115_K173_I0.122760.780
9_F27_V0.122490.779
22_D25_F0.122390.778
72_K118_Q0.122340.778
84_P147_I0.121410.772
106_D110_T0.120980.769
12_F16_A0.120870.768
9_F13_E0.120430.766
15_A25_F0.120320.765
117_L156_V0.12020.764
173_I177_S0.120070.763
130_F157_I0.119820.762
159_D162_K0.119820.762
47_Y54_P0.119770.761
169_P177_S0.119590.760
16_A25_F0.11950.760
124_F179_E0.119310.759
118_Q132_Y0.119150.758
34_A142_L0.1190.757
46_V71_I0.118670.754
110_T154_A0.118440.753
124_F183_N0.117820.749
9_F26_G0.117670.748
93_S140_R0.117450.747
120_I178_I0.117230.745
37_Y54_P0.117220.745
112_A115_K0.116850.743
139_P143_K0.116760.742
40_K60_D0.116750.742
65_E69_K0.116240.739
169_P172_E0.11580.736
114_K119_D0.115530.735
60_D70_F0.115030.731
9_F29_F0.114980.731
116_E174_T0.114610.729
10_E14_E0.114430.728
46_V66_E0.11410.725
26_G72_K0.114030.725
65_E68_K0.113830.724
10_E41_E0.113640.722
90_L129_N0.113640.722
11_I63_T0.113610.722
141_L155_L0.113380.721
174_T183_N0.113280.720
115_K119_D0.113090.719
13_E27_V0.112980.718
170_E180_K0.112780.717
37_Y43_T0.112640.716
64_P67_L0.112610.716
104_N136_D0.112580.716
109_S115_K0.112560.716
29_F39_I0.112390.715
10_E43_T0.112280.714
26_G29_F0.111820.711
101_L117_L0.111770.711
55_V58_D0.111250.707
58_D180_K0.111160.707
77_P121_A0.111070.706
134_D138_F0.110930.705
91_F144_Y0.110490.702
35_K41_E0.110360.702
34_A42_P0.110060.700
41_E151_D0.110020.699
120_I179_E0.109890.699
54_P181_F0.109870.699
101_L155_L0.109690.697
76_F80_P0.109610.697
43_T56_V0.109270.695
98_V129_N0.108960.693
62_F70_F0.108570.690
133_V138_F0.108430.689
162_K166_Y0.108380.689
12_F117_L0.108080.687
78_L86_N0.1080.687
50_F53_K0.107940.686
41_E121_A0.10770.685
87_F181_F0.107610.684
32_E92_S0.107520.684
147_I153_P0.10730.682
77_P98_V0.107270.682
69_K73_K0.107110.681
40_K62_F0.107080.681
99_L102_F0.107080.681
81_E101_L0.106810.679
56_V62_F0.106710.678
22_D122_K0.10650.677
10_E39_I0.10640.676
71_I93_S0.10640.676
99_L128_I0.106160.675
172_E176_E0.106110.675
81_E86_N0.106040.674
85_E102_F0.106030.674
92_S160_S0.105950.674
53_K119_D0.105850.673
37_Y41_E0.105760.672
82_L86_N0.105680.672
105_K108_E0.10540.670
96_P129_N0.104920.667
33_L55_V0.104830.666
48_K70_F0.104710.666
93_S106_D0.104620.665
71_I75_S0.104510.664
98_V101_L0.104510.664
13_E19_L0.104440.664
19_L41_E0.10430.663
67_L166_Y0.104180.662
12_F45_V0.104050.662
86_N131_V0.10380.660
144_Y158_F0.103720.659
28_T34_A0.103180.656
93_S104_N0.103080.655
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
4f9zD0.989199.90.174
3uemA0.989199.90.193
3us3A0.994699.90.228
1sjiA0.994699.90.237
4ekzA0.989199.90.245
2h8lA0.967499.90.265
3ec3A0.972899.90.265
3f8uA0.967499.80.324
2r2jA0.978399.80.335
3apoA0.967499.80.348

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