GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AFT - Transcription factor AFT
Pfam: PF08731 (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: CL0274
Length: 111
Sequences: 590
Seq/Len: 5.32
HH_delta: 0.838 (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
1_F10_W0.328612.794
11_L85_F0.274652.336
2_D6_E0.267212.272
7_I89_A0.235922.006
11_L15_F0.209341.780
15_F20_I0.203991.735
6_E16_Y0.192361.636
37_K79_R0.190881.623
2_D97_K0.187591.595
40_K80_K0.177341.508
42_Y78_S0.1761.497
14_I85_F0.170611.451
14_I18_Q0.164931.402
21_G37_K0.164451.398
11_L20_I0.162461.381
8_K24_I0.159451.356
41_R82_T0.153031.301
14_I105_N0.151771.291
24_I27_S0.151631.289
29_K105_N0.14931.270
70_K74_K0.145871.240
15_F19_G0.144831.232
12_Q73_K0.143431.220
14_I20_I0.143241.218
23_V80_K0.142561.212
11_L14_I0.142441.211
38_N94_K0.140671.196
81_N108_N0.138531.178
28_D88_R0.134961.148
19_G98_W0.134261.142
25_E35_K0.133951.139
32_I43_R0.131931.122
30_K33_V0.1311.114
38_N81_N0.129811.104
38_N105_N0.126961.080
16_Y98_W0.125991.071
8_K34_F0.124321.057
23_V35_K0.124021.055
39_G80_K0.122381.041
13_K97_K0.119071.013
24_I42_Y0.119011.012
4_K32_I0.117561.000
22_I26_R0.117490.999
3_D6_E0.117270.997
38_N72_K0.116280.989
41_R80_K0.115780.985
71_K74_K0.11570.984
72_K75_R0.115550.983
72_K77_K0.115470.982
42_Y79_R0.11470.975
93_K102_V0.114620.975
91_Y110_P0.114590.974
25_E34_F0.114440.973
73_K76_T0.11270.958
84_P104_N0.111920.952
11_L89_A0.111540.948
13_K41_R0.108470.922
40_K76_T0.106020.902
74_K110_P0.10590.901
12_Q22_I0.104610.890
28_D33_V0.10450.889
78_S98_W0.104430.888
10_W40_K0.1040.884
73_K77_K0.103250.878
4_K89_A0.103110.877
93_K106_E0.103040.876
32_I89_A0.101930.867
87_I100_L0.100120.851
10_W37_K0.099950.850
8_K81_N0.099640.847
14_I40_K0.098970.842
12_Q27_S0.098890.841
5_D108_N0.09840.837
35_K40_K0.097910.833
43_R100_L0.097450.829
43_R90_N0.096880.824
7_I19_G0.09660.821
36_C40_K0.096070.817
1_F11_L0.095030.808
4_K90_N0.094910.807
13_K104_N0.094910.807
87_I90_N0.09440.803
5_D41_R0.094140.801
11_L39_G0.094130.800
27_S32_I0.094030.800
73_K89_A0.093840.798
23_V85_F0.093510.795
5_D24_I0.093260.793
39_G108_N0.093220.793
40_K108_N0.092630.788
35_K42_Y0.092620.788
25_E80_K0.092440.786
3_D95_N0.092390.786
6_E91_Y0.09220.784
93_K104_N0.091920.782
35_K39_G0.091850.781
40_K81_N0.091740.780
29_K34_F0.09170.780
17_P45_K0.091690.780
19_G23_V0.091460.778
29_K39_G0.091270.776
22_I46_K0.091060.774
2_D82_T0.091040.774
7_I11_L0.090620.771
2_D24_I0.090510.770
25_E31_K0.090410.769
30_K72_K0.089760.763
18_Q99_T0.089580.762
5_D9_P0.089570.762
5_D47_K0.089220.759
23_V39_G0.089140.758
9_P74_K0.089110.758
32_I99_T0.0890.757
6_E17_P0.088730.755
78_S81_N0.088260.751
44_H110_P0.08810.749
89_A102_V0.087550.744
34_F98_W0.087470.744
73_K110_P0.087290.742
15_F90_N0.087260.742
15_F21_G0.087250.742
12_Q15_F0.087030.740
25_E28_D0.086660.737
12_Q90_N0.086580.736
44_H71_K0.086390.735
73_K78_S0.085850.730
3_D106_E0.085750.729
8_K87_I0.085740.729
11_L23_V0.085440.727
2_D94_K0.084860.722
4_K24_I0.08430.717
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
2rprA0.585687.60.838
1wj2A0.567684.20.845
2aydA0.612680.70.851
2ljuA0.387428.10.894
4ggoA0.333318.30.902
2cr4A0.333315.50.905
2jyaA0.441415.50.905
3ugjA0.819813.50.907
2dm0A0.333313.30.908
3lo3A0.315313.30.908
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