GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MADF_DNA_bdg - Alcohol dehydrogenase transcription factor MybSANT-like
Pfam: PF10545 (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: CL0123
Length: 85
Sequences: 864
Seq/Len: 10.16
HH_delta: 0.581 (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
5_V49_W0.649943.515
9_P13_D0.433622.345
59_E79_Y0.429642.324
4_L35_E0.414512.242
8_H31_E0.411282.225
56_Y83_S0.38142.063
10_C28_A0.34231.851
50_K54_D0.313381.695
29_W45_C0.294331.592
4_L8_H0.275371.489
4_L32_I0.270491.463
26_E46_K0.269081.455
3_E6_K0.26561.437
56_Y60_L0.256571.388
4_L7_K0.255431.382
48_R51_N0.253711.372
33_A45_C0.244851.324
50_K57_R0.239141.293
32_I36_L0.234661.269
40_F45_C0.232261.256
52_L78_Y0.231411.252
2_I52_L0.229361.241
29_W49_W0.225531.220
12_W57_R0.222781.205
3_E81_E0.221661.199
33_A42_V0.219151.185
49_W54_D0.21741.176
55_R76_W0.216781.173
2_I78_Y0.210911.141
56_Y85_L0.208271.126
59_E62_K0.208271.126
59_E63_I0.205521.112
80_E83_S0.204381.105
8_H28_A0.204041.104
31_E35_E0.203311.100
59_E74_P0.198431.073
18_D24_L0.19791.070
52_L82_L0.196481.063
56_Y79_Y0.195661.058
12_W40_F0.19541.057
53_R61_K0.193991.049
48_R55_R0.187341.013
16_H19_Y0.187321.013
1_L36_L0.187131.012
11_L49_W0.182950.990
63_I74_P0.182520.987
79_Y83_S0.177630.961
42_V46_K0.176120.953
82_L85_L0.169870.919
75_T79_Y0.169150.915
29_W32_I0.168760.913
6_K34_R0.165360.894
41_S44_D0.164720.891
5_V54_D0.162750.880
19_Y25_R0.16270.880
17_P43_D0.1620.876
76_W81_E0.158520.857
49_W82_L0.157270.851
23_Q27_E0.157160.850
29_W48_R0.156850.848
55_R59_E0.156560.847
12_W53_R0.156140.845
62_K74_P0.154810.837
30_Q34_R0.152290.824
60_L79_Y0.150890.816
75_T80_E0.149160.807
64_K73_V0.148250.802
51_N82_L0.146510.792
8_H13_D0.14590.789
30_Q42_V0.145430.787
54_D58_R0.14520.785
5_V29_W0.145040.784
59_E72_Y0.143940.779
48_R78_Y0.143480.776
48_R76_W0.143150.774
26_E42_V0.142050.768
11_L28_A0.141880.767
5_V32_I0.140640.761
47_K54_D0.140430.760
32_I45_C0.139540.755
29_W76_W0.139520.755
23_Q26_E0.13810.747
26_E70_E0.137650.745
51_N55_R0.136880.740
13_D16_H0.135950.735
1_L54_D0.13570.734
54_D77_S0.13540.732
35_E61_K0.134820.729
13_D75_T0.132960.719
71_E82_L0.132480.717
53_R57_R0.131830.713
1_L55_R0.131380.711
27_E34_R0.130970.708
53_R59_E0.130520.706
11_L19_Y0.130210.704
26_E30_Q0.129820.702
37_G76_W0.129660.701
7_K41_S0.129420.700
58_R84_F0.129240.699
18_D21_N0.129020.698
62_K76_W0.128970.698
5_V76_W0.128640.696
8_H32_I0.128490.695
58_R63_I0.127950.692
8_H12_W0.127710.691
74_P79_Y0.126830.686
20_K23_Q0.125970.681
16_H20_K0.125370.678
64_K70_E0.12520.677
47_K56_Y0.123360.667
27_E30_Q0.12330.667
7_K35_E0.123250.667
78_Y81_E0.122570.663
23_Q64_K0.121720.658
8_H51_N0.12170.658
71_E74_P0.120810.653
36_L40_F0.120640.653
59_E76_W0.120460.652
44_D47_K0.120280.651
73_V80_E0.119760.648
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
2ebiA0.811898.20.581
2llkA0.470686.10.803
2k9nA0.517686.10.804
2m2eA0.705985.60.805
1gv2A0.458880.50.815
1h89C0.458879.40.817
1h8aC0.458879.40.817
3sjmA0.494179.10.818
2cqrA0.529476.80.822
3osgA0.635375.80.823
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