GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YolD - YolD-like protein
Pfam: PF08863 (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: 92
Sequences: 527
Seq/Len: 5.73
HH_delta: 0.851 (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
46_T59_T0.258132.357
38_A62_I0.251852.299
20_K88_D0.240482.196
38_A45_V0.219182.001
10_E14_E0.218541.995
1_L4_H0.197391.802
70_R87_D0.197371.802
2_P5_K0.19011.736
66_D69_N0.17211.571
7_A11_L0.170511.557
51_E56_Q0.169311.546
2_P26_Q0.15361.402
45_V72_L0.146821.341
21_P90_I0.14541.328
82_E86_F0.144811.322
85_P88_D0.144431.319
50_Y53_G0.142591.302
2_P6_E0.141951.296
83_K92_I0.14141.291
4_H21_P0.136391.245
44_P61_T0.134151.225
47_I50_Y0.132791.212
35_L72_L0.12961.183
5_K9_R0.129511.182
34_K65_I0.128851.176
42_N72_L0.127381.163
54_Y70_R0.126911.159
39_Y42_N0.125141.143
21_P55_Y0.120361.099
72_L89_I0.119361.090
11_L14_E0.118891.086
3_E14_E0.118351.081
12_I52_D0.118031.078
73_K81_T0.117751.075
22_E25_E0.117221.070
61_T75_K0.117221.070
4_H12_I0.115911.058
35_L86_F0.115441.054
19_E25_E0.114421.045
1_L12_I0.114131.042
35_L74_L0.113511.036
61_T84_I0.112861.030
2_P11_L0.112451.027
71_T83_K0.109150.997
24_D64_K0.108730.993
5_K12_I0.108110.987
36_S62_I0.107780.984
51_E88_D0.1060.968
21_P26_Q0.105750.966
23_L32_N0.104820.957
26_Q49_Y0.104770.957
75_K90_I0.104070.950
52_D55_Y0.103930.949
1_L33_E0.102440.935
25_E60_G0.102350.934
13_K16_N0.100960.922
69_N87_D0.100570.918
20_K87_D0.099750.911
17_K21_P0.09960.909
56_Q75_K0.099250.906
51_E76_D0.099030.904
24_D32_N0.098990.904
71_T92_I0.098960.904
18_V55_Y0.098860.903
15_Q23_L0.09880.902
2_P50_Y0.097760.893
43_Q88_D0.097750.892
62_I70_R0.0970.886
2_P8_L0.096380.880
11_L15_Q0.095420.871
54_Y59_T0.095070.868
9_R52_D0.094710.865
25_E89_I0.094270.861
1_L6_E0.094260.861
5_K11_L0.094080.859
14_E17_K0.093540.854
57_S66_D0.092760.847
7_A13_K0.092190.842
1_L5_K0.091240.833
32_N49_Y0.0910.831
45_V60_G0.090970.831
60_G74_L0.090920.830
48_T64_K0.09060.827
50_Y90_I0.090530.827
39_Y44_P0.090050.822
3_E11_L0.089890.821
23_L31_I0.089720.819
6_E73_K0.089660.819
39_Y49_Y0.088970.812
76_D82_E0.088610.809
31_I40_Q0.088510.808
10_E15_Q0.088210.805
69_N83_K0.087970.803
22_E28_L0.087950.803
13_K47_I0.087930.803
26_Q92_I0.087390.798
82_E87_D0.087270.797
39_Y63_H0.087080.795
48_T56_Q0.086980.794
84_I87_D0.086980.794
40_Q64_K0.086790.792
17_K55_Y0.086550.790
4_H8_L0.086120.786
40_Q63_H0.085780.783
39_Y92_I0.085610.782
26_Q31_I0.085140.777
48_T55_Y0.0850.776
38_A43_Q0.084280.770
5_K15_Q0.084130.768
46_T63_H0.084120.768
64_K67_E0.084050.767
16_N25_E0.084030.767
6_E10_E0.08370.764
19_E75_K0.082840.756
10_E29_E0.082590.754
29_E33_E0.082560.754
30_E65_I0.082450.753
8_L61_T0.082140.750
57_S83_K0.082040.749
49_Y66_D0.081820.747
58_V84_I0.081490.744
48_T91_D0.080810.738
39_Y47_I0.080710.737
22_E69_N0.080380.734
39_Y76_D0.079560.726
17_K88_D0.079460.725
82_E92_I0.079380.725
42_N57_S0.079260.724
30_E37_E0.079110.722
50_Y65_I0.078950.721
50_Y64_K0.078850.720
15_Q30_E0.078670.718
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
1mhnA0.58734.50.851
3ruxA0.91331.30.855
3h8zA0.565230.70.855
1ib8A0.956530.40.855
4a53A0.641330.40.855
3s6wA0.565229.80.856
2j0pA0.9891280.858
3ahuA0.728326.30.859
2qtxA0.7525.30.861
2hq2A0.945723.20.863
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