GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cathelicidins - Cathelicidin
Pfam: PF00666 (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. )
Clan: CL0121
Length: 67
Sequences: 842
Seq/Len: 12.57
HH_delta: 0.018 (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
29_E49_T0.606553.163
26_R53_T0.430722.246
14_F17_Q0.409262.134
28_L51_K0.377931.971
36_W41_S0.354291.848
21_G52_E0.346631.808
38_E43_P0.316111.648
32_P47_N0.28391.480
30_L33_P0.255891.334
9_L13_D0.251731.313
31_D49_T0.241621.260
25_F50_I0.234491.223
13_D17_Q0.232171.211
22_E28_L0.218371.139
19_S57_K0.213321.112
34_P45_P0.213091.111
35_G54_V0.211221.101
56_P59_E0.210761.099
19_S22_E0.204331.066
14_F18_G0.199811.042
25_F54_V0.199381.040
20_S37_D0.199251.039
12_V15_Y0.19741.029
36_W39_D0.19611.023
8_V48_F0.193521.009
15_Y50_I0.192941.006
33_P38_E0.192851.006
12_V50_I0.190940.996
23_N56_P0.187490.978
6_E34_P0.183780.958
26_R39_D0.182340.951
15_Y34_P0.180480.941
38_E41_S0.179190.934
27_L50_I0.178310.930
31_D47_N0.1770.923
8_V27_L0.176270.919
12_V16_N0.172750.901
6_E35_G0.172480.899
29_E32_P0.165990.866
22_E56_P0.164940.860
32_P51_K0.164470.858
37_D42_T0.163610.853
7_A11_A0.163470.852
47_N50_I0.163190.851
6_E14_F0.162590.848
21_G55_C0.161490.842
31_D42_T0.160880.839
16_N52_E0.160060.835
37_D41_S0.159690.833
6_E37_D0.159290.831
12_V24_L0.156490.816
6_E29_E0.155560.811
25_F53_T0.153580.801
16_N24_L0.151830.792
38_E44_K0.150490.785
39_D42_T0.149940.782
27_L48_F0.149890.782
7_A10_R0.149750.781
10_R27_L0.149530.780
48_F55_C0.14690.766
5_E19_S0.146890.766
11_A18_G0.146310.763
32_P46_L0.146230.763
33_P46_L0.146040.762
36_W44_K0.144110.752
8_V46_L0.143830.750
35_G42_T0.143780.750
9_L25_F0.143670.749
15_Y19_S0.14240.743
8_V33_P0.141020.735
9_L42_T0.140190.731
29_E54_V0.135720.708
24_L53_T0.135660.707
21_G37_D0.132510.691
23_N43_P0.132450.691
8_V45_P0.13230.690
19_S55_C0.131220.684
54_V58_T0.130390.680
28_L56_P0.130090.678
29_E34_P0.129940.678
39_D43_P0.129550.676
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
4eycA199.50.018
2ch9A0.985199.40.081
3gaxA0.970199.40.099
1yvbI0.970199.30.121
3mwzA0.985199.30.126
1roaA0.970199.30.136
1kwiA199.20.16
3l0rA0.955299.20.191
1cyuA0.955298.50.375
3ul5A0.865798.40.415

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