GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BATS - Biotin and Thiamin Synthesis associated domain
Pfam: PF06968 (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: 93
Sequences: 2473
Seq/Len: 26.59
HH_delta: 0.327 (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
39_G63_N0.951583.858
51_R88_K0.588182.385
84_E88_K0.5692.307
21_D53_L0.529022.145
83_I87_E0.479651.945
80_D84_E0.455521.847
42_L57_T0.453781.840
7_P18_P0.447151.813
84_E87_E0.434291.761
7_P15_D0.431671.750
78_S81_E0.400061.622
51_R81_E0.377111.529
6_R74_S0.37221.509
20_S23_E0.371911.508
26_R30_A0.355931.443
55_P89_L0.338791.374
47_E75_G0.336751.365
13_L16_P0.336291.364
59_M89_L0.329131.335
10_G14_E0.328211.331
23_E27_I0.325591.320
35_L38_A0.323361.311
87_E93_P0.31891.293
72_T76_N0.317791.289
25_L57_T0.302671.227
65_I82_D0.301511.223
79_V83_I0.288221.169
7_P14_E0.287311.165
87_E92_E0.28051.137
40_I62_A0.278581.130
9_P14_E0.277861.127
65_I86_I0.273481.109
40_I56_L0.268761.090
28_I62_A0.265491.077
29_A61_G0.264561.073
81_E84_E0.264471.072
42_L62_A0.263761.069
30_A34_L0.261871.062
32_R63_N0.261221.059
41_R66_M0.260011.054
39_G93_P0.258151.047
86_I91_L0.253931.030
43_A66_M0.250771.017
41_R64_S0.246280.999
5_L8_I0.243410.987
19_L23_E0.24180.980
86_I93_P0.240270.974
47_E50_L0.236660.960
11_T15_D0.233640.947
28_I57_T0.232550.943
54_Q66_M0.231590.939
50_L53_L0.23090.936
31_F35_L0.230130.933
41_R71_L0.229590.931
58_F91_L0.226110.917
34_L38_A0.225890.916
55_P88_K0.224980.912
57_T62_A0.224970.912
22_E52_D0.223410.906
29_A33_L0.220020.892
52_D55_P0.219810.891
31_F40_I0.219020.888
48_A66_M0.215040.872
47_E53_L0.214430.869
45_G68_G0.214050.868
22_E53_L0.213970.868
8_I74_S0.213960.868
71_L76_N0.213760.867
11_T72_T0.213630.866
83_I92_E0.210180.852
20_S24_F0.209940.851
25_L60_S0.208030.844
80_D83_I0.207260.840
19_L27_I0.20630.837
5_L29_A0.204870.831
73_T76_N0.204310.828
58_F62_A0.20370.826
24_F49_L0.203420.825
45_G71_L0.201570.817
62_A79_V0.201310.816
43_A64_S0.200580.813
75_G81_E0.198410.805
5_L13_L0.197980.803
11_T14_E0.196680.797
62_A66_M0.195650.793
29_A32_R0.195450.793
16_P88_K0.19510.791
58_F61_G0.19480.790
19_L24_F0.194770.790
22_E88_K0.191460.776
16_P87_E0.188240.763
29_A42_L0.187930.762
28_I77_R0.187490.760
47_E74_S0.186850.758
46_R82_D0.184810.749
69_G77_R0.184450.748
47_E55_P0.183480.744
47_E78_S0.183420.744
46_R75_G0.183050.742
44_G65_I0.181740.737
49_L76_N0.181240.735
49_L66_M0.18040.731
24_F27_I0.177740.721
27_I51_R0.176770.717
22_E56_L0.17660.716
43_A69_G0.176320.715
37_E93_P0.175210.710
46_R57_T0.174290.707
63_N70_Y0.173830.705
25_L53_L0.173580.704
34_L37_E0.172560.700
68_G71_L0.172290.699
21_D52_D0.17190.697
43_A73_T0.171760.696
42_L54_Q0.171530.696
21_D50_L0.170630.692
11_T66_M0.16820.682
57_T60_S0.167860.681
44_G82_D0.167390.679
35_L74_S0.166660.676
40_I91_L0.165920.673
21_D24_F0.165750.672
52_D85_M0.165390.671
47_E81_E0.164670.668
51_R79_V0.164550.667
54_Q85_M0.164480.667
10_G13_L0.164370.666
22_E59_M0.163590.663
59_M91_L0.163540.663
54_Q82_D0.163330.662
30_A75_G0.162660.660
66_M72_T0.162470.659
15_D83_I0.161010.653
43_A70_Y0.160820.652
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
3t7vA0.978599.60.327
1r30A199.40.39
3iixA199.40.396
1h5yA0.91477.20.841
2w6rA0.903264.80.854
1thfD0.903263.30.856
3inpA0.881756.50.861
3tjxA0.978556.10.862
1ka9F0.903248.40.867
1tqxA0.903245.10.87

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