GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YtxH - YtxH-like protein
Pfam: PF12732 (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: 74
Sequences: 533
Seq/Len: 7.2
HH_delta: 0.711 (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
21_P28_R0.304051.978
20_A28_R0.296751.930
20_A24_G0.295621.923
22_K30_K0.291331.895
17_L20_A0.27121.764
20_A27_T0.263191.712
11_A14_A0.255941.665
22_K26_E0.247041.607
29_E33_D0.23941.557
16_G20_A0.234651.526
12_G16_G0.231311.505
23_S26_E0.22571.468
18_L31_L0.223931.457
18_L21_P0.221961.444
65_K69_K0.218351.420
16_G27_T0.210151.367
61_A65_K0.202831.319
3_L6_L0.198961.294
18_L27_T0.191751.247
27_T31_L0.187671.221
15_A19_F0.185181.205
24_G28_R0.184471.200
44_D51_E0.181781.183
53_V57_A0.180031.171
53_V68_A0.179291.166
47_E55_E0.176161.146
21_P24_G0.174121.133
5_F11_A0.165591.077
15_A50_K0.158241.029
57_A64_A0.156941.021
3_L7_A0.156781.020
17_L24_G0.155691.013
7_A16_G0.152840.994
60_T63_E0.149690.974
53_V60_T0.149620.973
45_L48_E0.148110.963
17_L26_E0.147760.961
22_K41_K0.147160.957
63_E67_K0.146960.956
21_P27_T0.146620.954
29_E54_K0.146260.951
19_F24_G0.146220.951
16_G23_S0.144180.938
54_K58_E0.144110.937
5_F47_E0.142360.926
49_A57_A0.139790.909
57_A63_E0.139360.907
17_L28_R0.13930.906
17_L21_P0.137920.897
37_D59_E0.137850.897
39_K43_K0.137060.892
17_L27_T0.136120.885
31_L34_K0.133380.868
26_E40_D0.132710.863
50_K63_E0.132290.861
3_L14_A0.131390.855
61_A64_A0.130560.849
15_A32_K0.130310.848
3_L42_A0.129150.840
2_L10_A0.128050.833
11_A40_D0.128040.833
28_R31_L0.127270.828
18_L28_R0.126090.820
2_L46_Y0.126050.820
7_A23_S0.124990.813
45_L64_A0.123750.805
18_L24_G0.123340.802
36_E44_D0.121880.793
17_L23_S0.121380.790
35_A38_L0.121060.788
53_V64_A0.121060.788
62_D66_E0.11930.776
40_D43_K0.118810.773
50_K60_T0.118170.769
38_L48_E0.117860.767
12_G20_A0.117780.766
64_A68_A0.116960.761
22_K35_A0.116880.760
34_K54_K0.115950.754
4_G8_G0.115630.752
2_L30_K0.114530.745
33_D69_K0.114030.742
53_V62_D0.113910.741
47_E50_K0.11370.740
33_D64_A0.113480.738
61_A67_K0.112860.734
4_G14_A0.112710.733
30_K36_E0.11210.729
7_A19_F0.110590.719
59_E62_D0.10980.714
45_L53_V0.109720.714
26_E41_K0.108970.709
49_A56_K0.108710.707
4_G13_A0.108480.706
60_T67_K0.108470.706
29_E47_E0.108260.704
7_A51_E0.107560.700
9_A13_A0.107040.696
29_E62_D0.105570.687
4_G42_A0.105280.685
18_L23_S0.104830.682
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
2x43S0.702793.40.711
2j69A0.986585.70.755
3iyzA0.959566.10.792
3ldtA0.97360.30.799
1i5pA0.959554.80.805
1ciiA0.527480.813
2wscL0.405447.80.813
2qkgA0.9459440.817
1ji6A0.945939.10.822
2l16A0.959530.20.832
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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