GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DiS_P_DiS - Bacterial Peptidase A24 N-terminal domain
Pfam: PF06750 (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: 1177
Seq/Len: 12.79
HH_delta: 0.882 (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_D62_R1.340494.810
33_R42_P0.991133.556
6_L10_L0.731782.626
79_T83_F0.612782.199
47_D63_Y0.601612.159
29_I32_P0.585252.100
54_Y70_P0.578712.076
43_L63_Y0.564522.025
41_H63_Y0.529811.901
13_L17_L0.523021.877
41_H47_D0.513171.841
3_G80_G0.471541.692
70_P74_L0.455511.634
4_A51_I0.455351.634
52_L56_L0.446781.603
38_H66_A0.425761.528
4_A80_G0.425671.527
43_L48_L0.424471.523
84_L88_W0.412281.479
47_D57_L0.40441.451
37_P68_I0.379941.363
28_S32_P0.379741.362
58_R65_G0.371971.335
39_C64_C0.370921.331
51_I77_L0.370111.328
11_N75_I0.35471.273
20_G29_I0.341011.224
44_S47_D0.330771.187
21_E35_H0.317281.138
48_L57_L0.316551.136
41_H44_S0.312951.123
3_G7_G0.309961.112
83_F86_L0.304731.093
20_G28_S0.300391.078
47_D53_S0.294761.058
71_R75_I0.292991.051
49_I53_S0.292461.049
88_W91_G0.292191.048
11_N14_A0.289721.040
36_C39_C0.28861.035
28_S31_F0.283731.018
14_A75_I0.282081.012
44_S63_Y0.279241.002
36_C64_C0.275610.989
8_S34_S0.275540.989
54_Y59_G0.262360.941
61_C64_C0.260660.935
10_L14_A0.254880.914
45_W48_L0.25160.903
15_Y71_R0.25150.902
69_P73_P0.245580.881
39_C61_C0.245250.880
51_I73_P0.244650.878
20_G32_P0.242270.869
75_I79_T0.241880.868
44_S62_R0.23860.856
12_V18_P0.238170.855
49_I52_L0.237160.851
74_L78_L0.23630.848
46_W62_R0.23560.845
3_G83_F0.233530.838
7_G16_R0.231650.831
36_C61_C0.228610.820
35_H40_G0.219720.788
85_L89_R0.218920.785
69_P72_Y0.218610.784
15_Y35_H0.218260.783
83_F87_Y0.214750.771
35_H43_L0.211530.759
2_L6_L0.211350.758
19_R28_S0.211210.758
43_L47_D0.205250.736
67_P81_I0.20460.734
74_L77_L0.20370.731
82_L86_L0.203560.730
13_L30_I0.202770.728
3_G16_R0.202480.726
7_G75_I0.201460.723
7_G79_T0.200710.720
4_A53_S0.199940.717
37_P72_Y0.199330.715
41_H62_R0.195890.703
8_S16_R0.19530.701
42_P74_L0.194710.699
61_C68_I0.194570.698
33_R44_S0.190610.684
49_I56_L0.19050.684
43_L52_L0.189350.679
10_L13_L0.188280.676
46_W78_L0.187890.674
10_L79_T0.18740.672
15_Y21_E0.186250.668
42_P86_L0.185840.667
70_P73_P0.184860.663
80_G84_L0.184250.661
5_C89_R0.183540.659
73_P77_L0.181030.650
9_F48_L0.179560.644
46_W56_L0.178750.641
75_I78_L0.178010.639
70_P89_R0.177990.639
2_L5_C0.177750.638
86_L89_R0.177730.638
5_C30_I0.174550.626
12_V68_I0.174550.626
11_N72_Y0.173930.624
9_F34_S0.172290.618
83_F89_R0.172150.618
43_L46_W0.170320.611
15_Y19_R0.169430.608
6_L14_A0.16790.602
14_A18_P0.167270.600
31_F51_I0.166060.596
3_G84_L0.163110.585
9_F16_R0.161610.580
1_I5_C0.16030.575
4_A73_P0.159570.573
5_C53_S0.158850.570
33_R70_P0.156820.563
59_G70_P0.156470.561
8_S12_V0.156170.560
87_Y91_G0.155960.560
53_S57_L0.155540.558
84_L90_F0.154140.553
18_P28_S0.152840.548
84_L87_Y0.152670.548
81_I88_W0.151210.543
61_C91_G0.150710.541
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
2jneA0.815253.60.882
2fiyA0.869641.80.89
3k1lB0.673936.70.893
2k5cA0.695731.60.896
1iymA0.456529.90.898
3py7A0.793521.50.904
2m3lA0.739118.50.907
1qypA0.58718.50.907
2eclA0.619617.60.908
4aybP0.514.70.91
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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