GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Flavodoxin_4 - Flavodoxin
Pfam: PF12682 (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: CL0042
Length: 156
Sequences: 4180
Seq/Len: 26.79
HH_delta: 0.171 (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
80_G109_F0.843332.704
14_K18_E0.820572.631
13_T80_G0.773072.478
32_E70_D0.739142.370
4_V21_A0.705492.262
76_T105_T0.702042.251
110_C121_L0.679922.180
87_T123_D0.661492.121
2_T76_T0.640722.054
21_A25_G0.579891.859
3_L74_Y0.579631.858
88_P93_R0.527961.693
70_D73_D0.508811.631
81_T89_P0.508571.630
108_P121_L0.497611.595
20_I78_F0.491151.575
119_N123_D0.478141.533
93_R97_E0.464251.488
78_F107_I0.460081.475
19_K22_E0.44171.416
90_P93_R0.439151.408
5_V95_F0.412031.321
83_V110_C0.411181.318
71_L77_I0.405691.301
34_V63_E0.404251.296
7_Y89_P0.388921.247
20_I80_G0.386351.239
6_Y14_K0.38221.225
82_P89_P0.380251.219
112_S117_F0.378611.214
122_E125_K0.376681.208
4_V17_A0.37621.206
106_V125_K0.37451.201
90_P97_E0.369051.183
21_A33_P0.358881.151
23_K26_A0.35591.141
32_E73_D0.355711.140
112_S116_G0.354551.137
71_L101_F0.347381.114
20_I109_F0.342731.099
2_T24_T0.338791.086
81_T124_L0.33861.085
39_S63_E0.331141.062
18_E21_A0.330671.060
123_D126_K0.330071.058
13_T111_T0.328741.054
9_R90_P0.328731.054
21_A31_I0.319481.024
22_E25_G0.319261.023
2_T78_F0.31431.008
25_G28_I0.3131.003
8_S91_P0.312391.001
88_P92_V0.310130.994
74_Y77_I0.309280.992
105_T108_P0.304130.975
68_I99_Y0.299950.962
64_I68_I0.298510.957
15_K18_E0.298380.957
17_A80_G0.29750.954
125_K129_P0.296890.952
28_I31_I0.296020.949
96_L127_L0.295590.948
77_I106_V0.294710.945
76_T107_I0.294560.944
27_D74_Y0.293960.942
106_V128_C0.292230.937
79_L128_C0.292180.937
86_G119_N0.291520.935
75_D104_K0.287850.923
69_P73_D0.284540.912
12_N15_K0.279770.897
106_V129_P0.278590.893
88_P120_S0.278040.891
119_N122_E0.277740.890
90_P94_T0.276780.887
23_K27_D0.276160.885
117_F121_L0.275550.883
114_G118_G0.275340.883
70_D74_Y0.27480.881
14_K30_E0.274620.880
13_T109_F0.265870.852
77_I104_K0.263370.844
79_L106_V0.262530.842
71_L99_Y0.261050.837
83_V86_G0.260870.836
94_T97_E0.259110.831
96_L124_L0.254650.816
25_G31_I0.250430.803
94_T98_Q0.249820.801
33_P91_P0.247910.795
86_G110_C0.245960.789
122_E126_K0.245380.787
83_V117_F0.245230.786
6_Y17_A0.244310.783
78_F109_F0.243370.780
112_S115_S0.242720.778
81_T120_S0.240130.770
34_V70_D0.239410.768
95_F99_Y0.239160.767
36_P95_F0.2360.757
69_P72_S0.235940.756
110_C117_F0.233950.750
101_F104_K0.233760.749
88_P127_L0.232660.746
35_K38_P0.232490.745
39_S68_I0.231860.743
10_T84_W0.231730.743
86_G112_S0.231070.741
88_P124_L0.230770.740
7_Y81_T0.230250.738
4_V24_T0.228330.732
7_Y91_P0.2260.725
18_E25_G0.224930.721
5_V77_I0.224840.721
8_S13_T0.224140.719
19_K23_K0.220430.707
15_K19_K0.220120.706
84_W113_G0.219490.704
25_G30_E0.219450.704
27_D31_I0.218010.699
108_P124_L0.217550.697
10_T14_K0.217260.697
37_Y91_P0.2170.696
2_T29_F0.215110.690
8_S11_G0.214820.689
20_I23_K0.214710.688
6_Y33_P0.214690.688
7_Y92_V0.211490.678
32_E74_Y0.210910.676
73_D129_P0.210730.676
6_Y109_F0.209160.671
2_T69_P0.207530.665
3_L34_V0.207020.664
13_T112_S0.206430.662
121_L125_K0.206040.661
64_I94_T0.20480.657
126_K129_P0.203940.654
17_A109_F0.202440.649
83_V119_N0.202250.648
3_L70_D0.198490.636
31_I75_D0.197670.634
7_Y84_W0.196230.629
81_T92_V0.196160.629
81_T91_P0.195450.627
16_V111_T0.194270.623
112_S118_G0.193320.620
89_P95_F0.193050.619
4_V20_I0.192920.618
10_T15_K0.192790.618
86_G122_E0.192360.617
100_D108_P0.191340.613
79_L118_G0.190680.611
5_V71_L0.190040.609
116_G121_L0.18970.608
119_N126_K0.189070.606
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
4j8pA0.961599.90.171
3klbA0.993699.90.189
4iciA0.987299.90.198
3edoA0.929599.80.303
1sqsA0.980899.80.312
1t5bA199.80.325
3lcmA0.974499.80.335
1d4aA0.980899.80.343
2hpvA199.80.346
3temA0.980899.80.358

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