GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF411 - Protein of unknown function DUF
Pfam: PF04214 (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: 70
Sequences: 491
Seq/Len: 7.01
HH_delta: 0.891 (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
36_I48_L0.573443.088
17_L30_V0.436432.350
14_K37_E0.417432.248
34_Y53_P0.369671.990
42_A68_P0.369671.990
47_R51_E0.33941.827
19_V35_V0.328261.768
28_T37_E0.32251.736
10_L14_K0.321321.730
14_K28_T0.308791.663
40_V48_L0.288291.552
63_M70_M0.281421.515
60_V65_A0.275031.481
34_Y48_L0.2621.411
62_G67_S0.252991.362
36_I40_V0.24511.320
36_I58_L0.237071.276
48_L55_A0.226211.218
34_Y52_K0.22461.209
15_Q24_A0.222941.200
32_G50_A0.210871.135
48_L52_K0.210131.131
11_S15_Q0.206561.112
29_A60_V0.204781.103
37_E59_A0.190621.026
14_K25_S0.187771.011
11_S21_P0.187421.009
36_I60_V0.185080.997
15_Q54_D0.184810.995
26_C63_M0.183460.988
42_A58_L0.182460.982
26_C70_M0.18060.972
19_V62_G0.179110.964
34_Y49_L0.176780.952
20_P59_A0.175750.946
39_H67_S0.175240.944
60_V66_G0.174820.941
49_L53_P0.173660.935
31_V48_L0.173190.933
20_P23_L0.170460.918
11_S54_D0.169760.914
67_S70_M0.168090.905
27_H63_M0.167040.899
21_P46_K0.166940.899
45_I58_L0.166310.895
13_I17_L0.1660.894
59_A62_G0.165590.892
1_E4_V0.165410.891
47_R52_K0.164590.886
32_G52_K0.163740.882
31_V40_V0.163010.878
22_E43_D0.162210.873
7_T10_L0.161690.871
25_S29_A0.15780.850
27_H70_M0.157670.849
5_V67_S0.157620.849
2_V32_G0.157090.846
22_E59_A0.156980.845
9_D30_V0.155730.839
8_D65_A0.153840.828
5_V61_P0.153490.826
12_A17_L0.153150.825
2_V15_Q0.152830.823
10_L35_V0.152440.821
44_D47_R0.151270.815
50_A54_D0.151260.814
24_A44_D0.150830.812
63_M67_S0.149560.805
60_V67_S0.148190.798
19_V24_A0.147760.796
33_G49_L0.147310.793
15_Q65_A0.146190.787
23_L60_V0.146060.786
25_S68_P0.143270.771
22_E30_V0.142670.768
53_P67_S0.142640.768
44_D58_L0.142150.765
2_V17_L0.142120.765
6_D13_I0.14210.765
9_D21_P0.140530.757
30_V35_V0.139330.750
16_R65_A0.13780.742
18_G28_T0.137650.741
53_P58_L0.137370.740
29_A37_E0.137070.738
5_V24_A0.136850.737
13_I45_I0.135460.729
36_I51_E0.135210.728
31_V44_D0.134710.725
25_S37_E0.132390.713
1_E12_A0.132010.711
8_D13_I0.131750.709
11_S16_R0.131440.708
7_T46_K0.130530.703
4_V35_V0.129930.700
34_Y58_L0.129620.698
1_E32_G0.129440.697
27_H39_H0.129170.696
31_V36_I0.12910.695
63_M68_P0.12770.688
8_D29_A0.127010.684
44_D60_V0.1260.678
35_V57_G0.125440.675
2_V55_A0.124620.671
55_A58_L0.123930.667
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
2fgxA0.642958.70.891
1z6mA0.728648.70.897
1t3bA0.736.80.904
1vs1A0.8286360.904
3gykA0.742928.50.909
3fz5A0.771426.70.91
3ic4A0.657125.80.91
4esqA0.471420.60.914
1nhoA0.714319.60.915
3kp9A0.871417.90.916
If you are interested in a protein containing this domain,
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