GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
2Fe-2S_thioredx - Thioredoxin-like 2Fe-2S ferredoxin
Pfam: PF01257 (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: 145
Sequences: 1676
Seq/Len: 11.56
HH_delta: 0.067 (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
66_H125_D1.02054.304
89_E95_K0.776253.274
91_E138_D0.712273.004
99_T106_T0.671952.834
16_L58_F0.641222.704
65_K104_K0.625412.637
89_E107_L0.588532.482
87_A138_D0.568162.396
38_A48_V0.503572.124
2_E40_A0.499592.107
85_L96_P0.495952.091
22_V37_I0.475652.006
91_E142_E0.460931.944
15_L43_I0.443951.872
92_L100_T0.413481.744
59_R63_K0.410571.731
86_E90_E0.401521.693
52_A60_L0.399341.684
104_K145_K0.394171.662
34_L52_A0.378261.595
84_L137_V0.37421.578
87_A91_E0.362651.529
94_I100_T0.359661.517
67_H106_T0.347211.464
68_I124_V0.345821.458
36_E39_E0.341241.439
12_R47_E0.34021.435
64_G106_T0.336921.421
15_L48_V0.331921.400
83_E86_E0.330321.393
94_I98_E0.327381.381
70_V85_L0.325351.372
66_H104_K0.32511.371
122_V132_V0.324421.368
11_K42_G0.318141.342
86_E89_E0.310411.309
34_L48_V0.30491.286
37_I48_V0.304611.285
94_I107_L0.304361.284
89_E96_P0.304211.283
22_V33_A0.301191.270
29_I52_A0.298441.259
79_R119_A0.295681.247
64_G99_T0.293711.239
46_A50_G0.29091.227
132_V140_I0.289391.220
133_T136_K0.287571.213
30_P33_A0.286051.206
113_L123_M0.284741.201
31_E35_E0.279431.178
2_E36_E0.278951.176
113_L121_V0.274731.159
68_I140_I0.2741.155
36_E40_A0.273911.155
95_K98_E0.273271.152
4_I21_E0.272761.150
20_H58_F0.271311.144
122_V140_I0.268761.133
44_P47_E0.264481.115
129_Y140_I0.263061.109
67_H108_E0.260961.100
94_I99_T0.260421.098
3_E6_A0.260331.098
71_C76_C0.25711.084
87_A137_V0.256251.081
139_E143_E0.25471.074
136_K139_E0.253771.070
88_L137_V0.2521.063
87_A90_E0.249191.051
35_E45_P0.247991.046
15_L51_V0.246331.039
115_A118_Q0.244611.032
118_Q130_G0.24131.018
87_A134_P0.240581.015
1_I5_I0.241.012
69_R110_T0.235860.995
22_V29_I0.229920.970
9_P13_S0.225240.950
72_T109_E0.224750.948
26_Y30_P0.224640.947
80_G83_E0.223960.944
20_H57_M0.222730.939
24_E126_G0.221280.933
77_H111_G0.219870.927
34_L49_Y0.219450.925
88_L141_L0.218470.921
27_G59_R0.218050.920
22_V25_E0.217910.919
127_E144_L0.217280.916
31_E60_L0.217210.916
17_P20_H0.217140.916
12_R43_I0.216840.914
124_V144_L0.214720.905
141_L144_L0.213530.900
74_T118_Q0.2130.898
76_C116_C0.212570.896
39_E42_G0.211710.893
73_G111_G0.211070.890
2_E6_A0.210590.888
68_I105_F0.210060.886
88_L122_V0.210030.886
29_I37_I0.209650.884
18_I41_L0.208330.879
63_K106_T0.208270.878
138_D142_E0.20640.870
127_E143_E0.205050.865
123_M126_G0.204970.864
70_V122_V0.202810.855
71_C116_C0.201440.849
110_T113_L0.201170.848
14_A18_I0.200350.845
35_E39_E0.199240.840
20_H24_E0.198770.838
91_E145_K0.198470.837
85_L89_E0.198040.835
1_I36_E0.196480.829
29_I34_L0.195010.822
69_R126_G0.192390.811
94_I97_G0.1920.810
69_R108_E0.190640.804
16_L51_V0.190210.802
142_E145_K0.190170.802
23_Q27_G0.189990.801
123_M128_W0.189450.799
82_E86_E0.188720.796
26_Y33_A0.188420.795
74_T78_L0.18790.792
14_A17_P0.187850.792
75_S78_L0.187120.789
124_V129_Y0.185050.780
8_Y21_E0.184870.780
100_T141_L0.184030.776
63_K67_H0.182090.768
72_T111_G0.181290.765
115_A121_V0.179990.759
61_E135_E0.176770.745
77_H117_D0.176360.744
57_M111_G0.17590.742
1_I18_I0.175440.740
39_E45_P0.174950.738
19_L51_V0.174210.735
59_R67_H0.173670.732
105_F129_Y0.172030.725
49_Y60_L0.17150.723
70_V88_L0.169750.716
14_A41_L0.168860.712
16_L33_A0.168410.710
100_T105_F0.166270.701
90_E138_D0.163970.691
59_R108_E0.163090.688
96_P109_E0.162630.686
122_V137_V0.161930.683
75_S119_A0.159730.674
89_E97_G0.159210.671
7_R21_E0.159060.671
115_A119_A0.158650.669
75_S79_R0.157970.666
100_T104_K0.157880.666
84_L134_P0.157840.666
104_K141_L0.157590.665
5_I36_E0.156530.660
66_H144_L0.155970.658
49_Y53_T0.155920.658
38_A43_I0.155370.655
61_E98_E0.154240.650
92_L102_D0.15360.648
13_S17_P0.153330.647
29_I58_F0.153130.646
129_Y144_L0.153130.646
4_I7_R0.153010.645
19_L48_V0.15280.644
139_E142_E0.151070.637
74_T84_L0.150910.636
29_I33_A0.150120.633
1_I21_E0.149970.632
63_K108_E0.149570.631
53_T60_L0.149440.630
74_T115_A0.148930.628
1_I40_A0.148350.626
84_L132_V0.147710.623
61_E106_T0.147540.622
93_G101_E0.146590.618
49_Y52_A0.146390.617
41_L48_V0.146220.617
74_T77_H0.145420.613
54_F58_F0.14490.611
10_S13_S0.144090.608
21_E24_E0.144060.608
5_I10_S0.143940.607
73_G118_Q0.143070.603
28_Y62_P0.143050.603
39_E101_E0.142160.599
8_Y18_I0.141990.599
93_G96_P0.141810.598
28_Y52_A0.141630.597
68_I93_G0.141580.597
38_A41_L0.140970.594
48_V51_V0.140310.592
75_S113_L0.140130.591
105_F144_L0.140040.591
122_V129_Y0.140040.591
39_E143_E0.139590.589
17_P69_R0.139260.587
74_T121_V0.138530.584
76_C113_L0.138520.584
83_E134_P0.13820.583
102_D139_E0.136970.578
10_S35_E0.136550.576
115_A130_G0.135510.571
71_C113_L0.134940.569
98_E101_E0.134920.569
4_I8_Y0.13490.569
63_K103_G0.134720.568
53_T64_G0.134070.565
75_S118_Q0.133610.563
11_K14_A0.133480.563
29_I48_V0.132910.560
19_L37_I0.132560.559
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
3i9v211000.067
2auvA0.586299.90.528
1m2dA0.551799.70.631
4gfjA0.827676.90.922
1r7jA0.586269.90.926
3ghaA0.703467.30.927
4fiwA0.524158.20.931
3f4sA0.703448.30.935
2wl8A0.324146.70.935
3s4wB0.903445.50.936

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