GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Whib - Transcription factor WhiB
Pfam: PF02467 (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. )
Length: 66
Sequences: 748
Seq/Len: 11.33
HH_delta: 0.864 (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
38_R42_L0.694473.640
29_R62_E0.688443.608
42_L56_G0.350071.835
50_E55_W0.322921.692
16_F56_G0.312661.639
45_A55_W0.293461.538
59_T63_R0.281441.475
19_R23_R0.277521.454
42_L46_L0.273541.434
24_S27_E0.262761.377
46_L60_E0.244331.281
11_D28_A0.241021.263
33_A38_R0.237011.242
44_Y52_H0.230241.207
44_Y50_E0.225011.179
43_E47_D0.223631.172
14_L64_R0.222781.168
9_G12_P0.217971.142
49_R54_V0.21071.104
52_H60_E0.203911.069
23_R54_V0.20081.052
18_E23_R0.199941.048
57_G60_E0.199911.048
3_E10_T0.199761.047
20_G63_R0.197381.034
15_F28_A0.1971.032
18_E26_R0.193181.012
4_R33_A0.190380.998
31_I37_V0.189490.993
6_A31_I0.188690.989
10_T14_L0.188690.989
59_T62_E0.181570.952
4_R36_P0.180130.944
10_T30_A0.179710.942
15_F60_E0.177880.932
6_A9_G0.17680.927
48_T51_E0.175520.920
4_R34_R0.174560.915
28_A31_I0.174140.913
15_F26_R0.173290.908
11_D30_A0.171010.896
23_R44_Y0.170680.895
16_F20_G0.170640.894
11_D57_G0.170.891
39_A43_E0.168690.884
30_A33_A0.167920.880
13_D16_F0.167740.879
45_A56_G0.167460.878
27_E30_A0.167430.877
42_L62_E0.165140.865
60_E63_R0.162510.852
11_D16_F0.162380.851
4_R27_E0.162150.850
56_G59_T0.160430.841
16_F28_A0.1580.828
10_T49_R0.1570.823
40_E48_T0.156260.819
4_R39_A0.155680.816
17_P63_R0.155620.816
42_L58_L0.154990.812
18_E44_Y0.154440.809
5_A30_A0.153040.802
6_A39_A0.152660.800
34_R43_E0.1510.791
49_R58_L0.150740.790
19_R40_E0.148390.778
33_A39_A0.147020.771
50_E56_G0.143830.754
10_T13_D0.143280.751
3_E36_P0.142960.749
3_E49_R0.141110.740
26_R34_R0.140880.738
19_R44_Y0.138940.728
30_A47_D0.138690.727
14_L58_L0.137810.722
51_E61_R0.13620.714
26_R52_H0.134310.704
29_R53_G0.133780.701
38_R58_L0.133060.697
34_R49_R0.132310.693
28_A55_W0.131810.691
23_R37_V0.131750.690
40_E43_E0.131570.690
19_R27_E0.129640.679
4_R40_E0.129150.677
14_L34_R0.128750.675
25_A61_R0.128370.673
6_A26_R0.12820.672
29_R45_A0.127470.668
38_R57_G0.126770.664
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
1pxqA0.424230.30.864
3fspA112.40.885
1z9tA0.515250.903
1kg2A0.87884.40.905
1keaA0.72734.30.906
2abkA0.74243.20.911
1rv9A0.56062.60.915
3hi7A0.36362.50.915
1xfjA0.53031.80.921
2xfrA0.71211.70.923
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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