GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HSF_DNA-bind - HSF-type DNA-binding
Pfam: PF00447 (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: 103
Sequences: 1036
Seq/Len: 10.06
HH_delta: -0.027 (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
20_R31_H0.532132.996
35_E39_E0.456622.571
25_G88_R0.414072.331
32_D35_E0.412242.321
90_Q93_L0.399922.252
27_S80_E0.357262.012
55_R58_N0.344881.942
52_S58_N0.344291.938
87_R90_Q0.340671.918
52_S55_R0.33751.900
22_S27_S0.315031.774
26_D87_R0.314641.772
85_N96_K0.295871.666
46_K49_N0.263081.481
47_H58_N0.248531.399
56_Q60_Y0.246051.385
15_N40_V0.241971.362
10_L15_N0.238711.344
83_H101_K0.234631.321
54_V60_Y0.22391.261
56_Q99_R0.222351.252
44_Y47_H0.220791.243
54_V64_K0.207881.170
58_N64_K0.20251.140
52_S56_Q0.201241.133
56_Q59_M0.200831.131
7_Y94_L0.198691.119
47_H52_S0.197631.113
22_S29_I0.194961.098
11_E21_W0.193951.092
50_F79_W0.193681.090
26_D29_I0.192081.081
54_V79_W0.191691.079
49_N53_F0.190861.075
49_N52_S0.189851.069
9_M79_W0.182491.027
45_F52_S0.178991.008
47_H55_R0.178091.003
30_I50_F0.177851.001
64_K99_R0.176660.995
47_H60_Y0.175980.991
66_S82_Y0.175070.986
13_P16_S0.173090.975
18_I35_E0.173020.974
37_E49_N0.170430.960
45_F49_N0.17030.959
18_I31_H0.168750.950
58_N99_R0.168280.947
55_R99_R0.167920.945
2_F56_Q0.167560.943
8_E91_P0.167340.942
60_Y64_K0.164720.927
49_N54_V0.161640.910
98_K101_K0.161490.909
47_H64_K0.161430.909
28_F57_L0.161190.908
35_E38_K0.160420.903
6_L30_I0.15990.900
12_D19_I0.157860.889
2_F5_K0.157790.888
84_P87_R0.157780.888
34_E98_K0.15760.887
4_S22_S0.157580.887
55_R60_Y0.156020.878
64_K81_F0.15580.877
42_P48_S0.155620.876
47_H56_Q0.15540.875
4_S8_E0.155360.875
11_E89_G0.15340.864
3_L59_M0.15240.858
25_G101_K0.150050.845
45_F56_Q0.149590.842
4_S32_D0.148980.839
94_L97_I0.14870.837
12_D15_N0.148490.836
46_K56_Q0.148270.835
22_S80_E0.14810.834
41_L100_R0.147190.829
69_S101_K0.145910.822
55_R64_K0.145370.818
6_L31_H0.14530.818
68_D91_P0.144790.815
39_E43_K0.143930.810
86_F97_I0.143680.809
11_E98_K0.142470.802
14_E17_D0.142340.801
14_E18_I0.142240.801
46_K60_Y0.140680.792
57_L60_Y0.14010.789
13_P17_D0.139950.788
8_E39_E0.139810.787
33_P37_E0.139530.786
59_M63_K0.139130.783
29_I36_F0.138820.782
5_K89_G0.138010.777
7_Y11_E0.137920.777
25_G30_I0.137280.773
83_H95_S0.137220.773
20_R29_I0.136820.770
48_S58_N0.136010.766
10_L19_I0.13480.759
84_P101_K0.134120.755
16_S19_I0.133910.754
69_S85_N0.133560.752
36_F50_F0.133540.752
46_K58_N0.133510.752
65_V82_Y0.132770.748
46_K64_K0.132540.746
7_Y50_F0.132540.746
27_S82_Y0.1320.743
6_L67_S0.13180.742
64_K80_E0.131290.739
86_F89_G0.130780.736
2_F53_F0.130760.736
53_F60_Y0.130450.734
33_P50_F0.130450.734
18_I39_E0.130190.733
17_D24_D0.129360.728
51_S56_Q0.128840.725
67_S70_N0.127870.720
34_E38_K0.127740.719
49_N81_F0.127160.716
32_D42_P0.127020.715
6_L19_I0.126920.715
3_L6_L0.126570.713
4_S83_H0.126370.712
25_G34_E0.126130.710
15_N100_R0.125170.705
29_I80_E0.125150.705
27_S87_R0.125080.704
33_P81_F0.124880.703
20_R30_I0.124560.701
7_Y33_P0.124360.700
14_E30_I0.124270.700
37_E51_S0.123290.694
44_Y61_G0.122630.690
23_P32_D0.122340.689
10_L16_S0.122290.689
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
2lduA1100-0.027
1hksA0.9709100-0.009
3htsB0.844799.90.185
3zp5A0.854493.90.833
2nnyA0.951590.40.85
1gvjA0.951589.30.853
1hbxG0.951588.40.855
1awcA0.951587.60.857
1fliA0.873887.40.858
1bc8C0.844786.90.859

Page generated in 0.0199 seconds.