GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4217 - Domain of unknown function (DUF4217)
Pfam: PF13959 (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: 65
Sequences: 719
Seq/Len: 11.06
HH_delta: 0.736 (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
47_D50_H0.63833.602
42_N45_K0.451162.546
10_V16_L0.32421.830
3_Q7_E0.316881.788
49_G53_K0.302751.709
22_K25_V0.300451.696
17_K21_Q0.278791.573
7_E58_L0.275271.554
18_E22_K0.25351.431
31_Y34_H0.24841.402
23_A55_F0.244961.383
25_V29_R0.228381.289
24_F28_V0.224171.265
38_K43_V0.216251.220
28_V48_L0.215371.216
48_L63_V0.209251.181
36_E39_D0.208651.178
2_I5_K0.208381.176
27_Y38_K0.197761.116
4_Q18_E0.195261.102
34_H37_L0.191341.080
39_D42_N0.187611.059
22_K45_K0.186661.053
13_D16_L0.18241.029
29_R45_K0.181151.022
8_K43_V0.178451.007
5_K9_L0.178351.007
34_H51_L0.178021.005
3_Q53_K0.177641.003
51_L55_F0.173550.979
7_E53_K0.17330.978
32_A43_V0.172090.971
29_R50_H0.169140.955
23_A29_R0.167830.947
27_Y37_L0.167780.947
9_L16_L0.167580.946
19_L26_S0.166680.941
4_Q8_K0.162520.917
18_E62_K0.160510.906
2_I6_L0.160060.903
25_V62_K0.159110.898
27_Y55_F0.159110.898
3_Q9_L0.157320.888
29_R33_S0.155750.879
14_R19_L0.155230.876
33_S47_D0.154460.872
20_A58_L0.153720.868
27_Y30_A0.153450.866
10_V20_A0.151420.855
51_L57_L0.151070.853
51_L54_S0.150830.851
23_A40_I0.149870.846
4_Q11_A0.149710.845
14_R60_A0.148930.841
16_L19_L0.148880.840
17_K56_G0.147040.830
11_A17_K0.146090.825
18_E21_Q0.145120.819
12_K44_K0.14510.819
31_Y37_L0.144490.815
38_K42_N0.142810.806
38_K63_V0.140250.792
29_R39_D0.139320.786
9_L36_E0.139240.786
10_V17_K0.139030.785
48_L52_A0.138190.780
21_Q43_V0.137670.777
42_N60_A0.137550.776
6_L10_V0.13740.775
19_L25_V0.137080.774
28_V53_K0.136850.772
31_Y41_F0.136390.770
36_E50_H0.135040.762
53_K58_L0.134750.761
6_L12_K0.133720.755
37_L56_G0.13320.752
44_K49_G0.132580.748
16_L40_I0.13250.748
11_A34_H0.132010.745
57_L61_P0.131580.743
5_K11_A0.130440.736
17_K59_E0.130250.735
38_K41_F0.129250.729
8_K11_A0.127920.722
21_Q56_G0.127870.722
9_L37_L0.127510.720
30_A55_F0.126210.712
11_A16_L0.125880.710
21_Q30_A0.125590.709
30_A34_H0.12530.707
28_V32_A0.125190.707
11_A18_E0.124920.705
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
2z83A0.953894.50.736
1yksA0.969293.50.748
2jlqA0.969289.30.774
2whxA0.969288.90.775
3i5xA0.907787.90.779
3sqwA0.907781.10.797
2wv9A0.953856.50.829
4b4tR0.815442.30.842
3txnA0.923116.90.87
4b4tQ0.923116.30.87
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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