GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thioredoxin_5 - Thioredoxin
Pfam: PF13743 (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: 176
Sequences: 4355
Seq/Len: 24.74
HH_delta: 0.197 (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
107_L121_K0.81952.624
88_A112_E0.769712.464
91_E96_E0.713832.285
73_A123_D0.705332.258
6_P71_Y0.705032.257
111_E117_V0.621551.990
138_Q142_E0.611681.958
98_K108_E0.61031.954
116_D119_M0.608281.947
131_Q135_E0.585691.875
103_E125_H0.582141.864
66_P103_E0.555811.779
65_Y134_Q0.546381.749
77_Q119_M0.533771.709
121_K125_H0.513631.644
117_V121_K0.513141.643
108_E112_E0.50881.629
8_C11_C0.490331.570
92_A109_I0.476761.526
107_L111_E0.476581.526
105_L108_E0.473581.516
6_P86_L0.452791.450
139_L143_M0.450191.441
70_A120_F0.447631.433
20_K24_E0.444621.423
139_L142_E0.439581.407
85_F89_L0.436611.398
74_A115_L0.436051.396
72_K136_D0.435831.395
118_E122_E0.426311.365
11_C148_F0.422811.354
135_E139_L0.419321.342
77_Q123_D0.418521.340
98_K105_L0.411231.317
14_F151_L0.406881.303
138_Q141_R0.403531.292
10_W13_G0.399541.279
135_E138_Q0.397521.273
69_L130_K0.394511.263
74_A78_G0.394151.262
72_K75_Q0.390681.251
127_D131_Q0.389991.249
91_E95_L0.384991.233
8_C148_F0.383411.227
102_D105_L0.379681.216
109_I113_L0.377181.207
15_E87_R0.376881.207
107_L117_V0.376651.206
85_F113_L0.375651.203
34_I136_D0.372371.192
86_L90_Q0.370461.186
20_K23_E0.362081.159
16_P87_R0.359261.150
119_M123_D0.358311.147
88_A109_I0.357381.144
76_L128_E0.354651.135
34_I139_L0.352711.129
19_R23_E0.350131.121
103_E107_L0.344061.101
36_G148_F0.343481.100
6_P67_A0.342841.098
15_E19_R0.339551.087
87_R91_E0.333111.066
140_A145_I0.331741.062
71_Y85_F0.331321.061
21_L25_Y0.331151.060
7_L64_S0.329641.055
67_A100_Y0.328331.051
99_N102_D0.327031.047
3_F139_L0.325211.041
33_F83_R0.325211.041
92_A105_L0.32391.037
37_G137_Q0.323041.034
147_G150_T0.320871.027
132_A136_D0.318771.021
134_Q137_Q0.317351.016
72_K133_F0.311550.997
137_Q141_R0.311190.996
119_M122_E0.310790.995
5_D8_C0.310460.994
22_K29_I0.305860.979
88_A91_E0.305120.977
143_M152_V0.301650.966
72_K76_L0.300080.961
110_A120_F0.298910.957
92_A112_E0.297070.951
32_R75_Q0.296640.950
65_Y130_K0.294660.943
3_F140_A0.293730.940
35_P136_D0.293560.940
88_A96_E0.292920.938
61_R64_S0.291220.932
131_Q134_Q0.29050.930
108_E111_E0.288890.925
76_L132_A0.287950.922
36_G140_A0.287440.920
35_P72_K0.2860.916
70_A106_L0.285960.915
7_L93_L0.28560.914
126_S129_A0.282480.904
123_D129_A0.281310.901
5_D64_S0.279770.896
37_G64_S0.278380.891
100_Y105_L0.276050.884
77_Q116_D0.272190.871
6_P68_C0.27120.868
71_Y86_L0.270980.868
134_Q138_Q0.2690.861
73_A77_Q0.268760.860
17_E20_K0.266810.854
36_G39_M0.265910.851
145_I150_T0.262940.842
73_A76_L0.262680.841
76_L129_A0.258710.828
9_S148_F0.258090.826
104_E121_K0.25710.823
13_G17_E0.254070.813
11_C146_T0.253150.810
88_A113_L0.252920.810
64_S68_C0.251630.806
19_R87_R0.250740.803
130_K134_Q0.25060.802
4_V86_L0.249750.800
83_R87_R0.248180.795
3_F35_P0.247920.794
66_P69_L0.247710.793
145_I152_V0.244290.782
89_L109_I0.242130.775
74_A85_F0.241510.773
108_E117_V0.241250.772
62_S101_S0.239740.768
12_W16_P0.239430.767
14_F18_L0.238250.763
34_I38_L0.237670.761
122_E128_E0.237120.759
132_A135_E0.237120.759
80_K84_R0.236460.757
11_C15_E0.236220.756
21_L24_E0.232740.745
72_K129_A0.231230.740
111_E125_H0.228240.731
70_A85_F0.227450.728
3_F34_I0.225620.722
104_E108_E0.225420.722
88_A92_A0.2250.720
90_Q93_L0.224480.719
89_L106_L0.222970.714
120_F123_D0.21980.704
70_A124_L0.218730.700
129_A132_A0.217680.697
99_N105_L0.217620.697
98_K112_E0.21740.696
38_L41_D0.217360.696
73_A120_F0.216580.693
106_L109_I0.212210.679
36_G145_I0.212020.679
72_K132_A0.211740.678
3_F136_D0.211550.677
16_P19_R0.211550.677
4_V11_C0.211380.677
87_R90_Q0.210150.673
119_M128_E0.207910.666
79_K84_R0.207150.663
15_E83_R0.206970.663
18_L31_F0.206130.660
4_V33_F0.206060.660
85_F110_A0.2050.656
107_L110_A0.204870.656
123_D126_S0.203070.650
76_L123_D0.202920.650
111_E121_K0.202680.649
128_E131_Q0.202620.649
77_Q115_L0.202580.649
3_F143_M0.201110.644
66_P70_A0.200370.641
10_W147_G0.200280.641
127_D130_K0.199760.640
93_L97_G0.196950.631
84_R113_L0.1950.624
7_L100_Y0.193690.620
104_E107_L0.193430.619
73_A110_A0.192020.615
9_S68_C0.191180.612
69_L133_F0.190840.611
16_P20_K0.18950.607
92_A108_E0.189270.606
14_F17_E0.18730.600
19_R83_R0.186610.597
10_W150_T0.185980.595
37_G148_F0.184990.592
133_F137_Q0.184850.592
8_C13_G0.184760.591
66_P124_L0.184330.590
118_E121_K0.183660.588
32_R139_L0.183430.587
60_P63_S0.183240.587
77_Q117_V0.182440.584
6_P90_Q0.182330.584
12_W148_F0.181650.582
122_E126_S0.180580.578
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
3kzqA0.977399.90.197
3fz5A0.943299.90.209
3gl5A0.948999.90.231
2imfA0.920599.90.232
1r4wA0.971699.90.237
2in3A0.977399.90.243
3rppA0.965999.90.256
3ghaA0.840999.90.271
3bciA0.840999.90.278
4jrrA0.829599.90.291

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