GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Wyosine_form - Wyosine base formation
Pfam: PF08608 (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: 62
Sequences: 384
Seq/Len: 6.19
HH_delta: 0.625 (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
13_M18_S0.352421.896
47_E57_V0.343261.847
24_M52_H0.313751.688
7_V13_M0.284761.532
10_K55_S0.283041.523
18_S22_L0.270321.454
12_Y22_L0.269091.448
25_G31_E0.264031.421
49_T57_V0.259881.398
12_Y33_V0.245051.318
11_A28_P0.241951.302
53_E56_R0.236441.272
12_Y27_M0.235241.266
2_A10_K0.227271.223
52_H57_V0.222011.194
34_L58_V0.21631.164
10_K18_S0.216231.163
6_F27_M0.213451.148
19_R57_V0.212781.145
49_T61_A0.211271.137
28_P55_S0.208871.124
47_E54_H0.198781.070
18_S27_M0.19661.058
28_P61_A0.195271.051
48_I59_L0.192171.034
54_H61_A0.189251.018
1_R29_W0.186341.003
32_E61_A0.180870.973
23_T26_N0.180490.971
33_V36_F0.177930.957
5_D31_E0.177550.955
25_G37_A0.174220.937
37_A47_E0.174090.937
31_E35_D0.17250.928
10_K28_P0.172270.927
11_A37_A0.171720.924
35_D48_I0.17120.921
3_E35_D0.169880.914
34_L51_E0.167890.903
1_R26_N0.165420.890
1_R25_G0.163680.881
8_E60_L0.162870.876
29_W32_E0.159360.857
4_P60_L0.158490.853
46_Y54_H0.157770.849
3_E34_L0.157580.848
22_L60_L0.157580.848
32_E59_L0.156840.844
27_M33_V0.153450.826
18_S30_H0.151870.817
54_H58_V0.145750.784
6_F60_L0.144960.780
48_I51_E0.144680.778
52_H59_L0.144370.777
9_V59_L0.143910.774
35_D58_V0.141310.760
1_R51_E0.14080.758
2_A59_L0.140090.754
25_G47_E0.139930.753
11_A18_S0.139480.750
46_Y53_E0.136680.735
3_E31_E0.135890.731
46_Y55_S0.13480.725
26_N51_E0.133610.719
7_V50_D0.13230.712
19_R35_D0.13190.710
9_V37_A0.131740.709
7_V34_L0.130760.704
33_V49_T0.128370.691
30_H33_V0.127610.687
11_A36_F0.125820.677
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
2z2uA198.20.625
2yx0A197.90.658
4fh3A0.677447.50.864
2r6zA0.62914.30.893
1n8pA0.709712.20.897
4ihqA0.9032120.897
2eapA0.774211.60.897
1j5uA0.532310.60.899
3a9lA0.6299.50.901
2fq6A0.66138.80.902
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