GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF951 - Bacterial protein of unknown function (DUF951)
Pfam: PF06107 (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: 57
Sequences: 339
Seq/Len: 5.95
HH_delta: 0.9 (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
18_S36_G0.668953.040
31_K40_Q0.577772.625
9_E54_K0.540532.456
5_G22_E0.398021.809
47_K51_R0.377091.713
22_E33_K0.370231.682
24_I40_Q0.363661.652
9_E19_N0.355321.615
22_E35_L0.346241.573
4_V26_I0.337311.533
15_P36_G0.325861.481
20_E57_K0.325581.479
36_G39_R0.319831.453
48_F52_L0.317961.445
4_V24_I0.315131.432
31_K42_M0.29411.336
2_Y23_I0.27771.262
2_Y48_F0.267731.217
7_I57_K0.258681.175
10_M48_F0.257331.169
10_M55_V0.2571.168
9_E53_K0.25671.166
8_V48_F0.255331.160
17_G39_R0.253151.150
7_I17_G0.251521.143
24_I31_K0.232761.058
20_E35_L0.229591.043
31_K46_S0.225451.024
10_M32_I0.221381.006
23_I26_I0.221181.005
15_P47_K0.217790.990
26_I52_L0.216690.985
3_E23_I0.214180.973
24_I32_I0.210560.957
13_P19_N0.20860.948
4_V43_L0.197320.897
47_K50_K0.196550.893
9_E56_I0.194660.885
2_Y8_V0.192940.877
22_E40_Q0.192230.873
2_Y15_P0.183330.833
38_G42_M0.183170.832
44_P47_K0.180090.818
2_Y49_E0.179890.817
10_M42_M0.174630.794
5_G17_G0.174250.792
5_G24_I0.17340.788
26_I30_I0.171760.780
33_K57_K0.170520.775
6_D53_K0.169620.771
39_R51_R0.169570.771
25_R28_A0.16690.758
7_I35_L0.165060.750
35_L57_K0.162130.737
16_C37_C0.159190.723
26_I46_S0.157430.715
8_V23_I0.156950.713
20_E56_I0.156130.709
40_Q52_L0.15460.702
6_D36_G0.151210.687
2_Y52_L0.150330.683
3_E57_K0.150210.683
32_I41_I0.149060.677
32_I48_F0.148730.676
28_A46_S0.148630.675
29_D37_C0.147470.670
33_K40_Q0.147420.670
3_E7_I0.146870.667
47_K55_V0.146560.666
22_E57_K0.144260.656
8_V43_L0.14360.653
30_I51_R0.143130.650
5_G32_I0.142930.649
10_M51_R0.141560.643
2_Y43_L0.138890.631
8_V41_I0.137890.627
16_C29_D0.135770.617
22_E31_K0.134210.610
15_P49_E0.132310.601
53_K56_I0.132180.601
28_A42_M0.132140.600
41_I48_F0.131560.598
11_K24_I0.130070.591
28_A41_I0.129850.590
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
4aybP0.789529.50.9
3ec1A0.526328.80.9
1d1nA0.333325.30.903
3na7A0.947418.70.909
4aybN0.526318.30.909
1zo1I0.333317.20.91
2vv5A0.894716.20.911
1twfJ0.5263160.911
1vq8Z0.947415.50.912
3sgiA0.947415.40.912
If you are interested in a protein containing this domain,
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