GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1289 - Protein of unknown function (DUF1289)
Pfam: PF06945 (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: 51
Sequences: 679
Seq/Len: 13.31
HH_delta: 0.86 (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
33_M41_I0.809953.565
21_G49_R0.608292.677
35_D38_R0.433421.908
42_L45_L0.417121.836
6_G9_K0.413031.818
10_L27_I0.390191.717
40_A43_A0.377681.662
29_D37_E0.364921.606
9_K18_R0.347741.531
6_G10_L0.284781.253
22_R30_W0.27691.219
28_R31_K0.276731.218
34_S37_E0.260511.147
2_S24_L0.250281.102
33_M37_E0.248111.092
37_E40_A0.240211.057
38_R47_A0.240181.057
3_P8_C0.23721.044
29_D33_M0.233731.029
29_D32_S0.229751.011
37_E44_R0.227881.003
6_G24_L0.224650.989
39_R43_A0.221960.977
33_M45_L0.21810.960
31_K49_R0.214440.944
18_R29_D0.210290.926
44_R47_A0.209320.921
25_D32_S0.208420.917
24_L31_K0.208040.916
39_R49_R0.208030.916
32_S43_A0.201450.887
21_G45_L0.200610.883
10_L18_R0.19930.877
1_P35_D0.195450.860
2_S28_R0.191720.844
2_S25_D0.191680.844
31_K35_D0.190550.839
12_P21_G0.190540.839
38_R46_R0.186510.821
22_R27_I0.184710.813
32_S37_E0.184570.812
5_I18_R0.183540.808
10_L24_L0.179440.790
24_L27_I0.179210.789
6_G18_R0.179130.788
43_A47_A0.177980.783
1_P6_G0.177860.783
4_C8_C0.177780.782
12_P36_D0.176690.778
10_L14_D0.174060.766
32_S40_A0.173230.762
16_V37_E0.172070.757
5_I49_R0.169750.747
10_L31_K0.169190.745
22_R26_E0.169080.744
12_P46_R0.168730.743
36_D40_A0.167840.739
29_D40_A0.163870.721
17_C30_W0.163830.721
1_P39_R0.163470.719
11_D48_R0.162130.714
8_C17_C0.159750.703
30_W41_I0.158260.697
26_E30_W0.157440.693
27_I31_K0.156840.690
7_V24_L0.155530.685
5_I43_A0.154310.679
24_L28_R0.154310.679
2_S42_L0.153310.675
38_R42_L0.151760.668
2_S37_E0.151210.666
44_R48_R0.148270.653
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
2hw2A0.843118.40.86
4i8pA0.980416.70.863
2doaA0.843116.60.863
2e5nA0.823516.50.863
3l6wA0.54914.60.866
3k9dA0.745113.30.868
3awuA0.54910.80.873
3odnA0.803910.80.873
2o2pA110.30.874
4acrA0.803910.20.875
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