GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Holin_BlyA - holin BlyA family
Pfam: PF05102 (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: 61
Sequences: 838
Seq/Len: 13.74
HH_delta: 0.826 (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
19_I26_T0.555152.167
30_L33_I0.497241.941
45_S49_G0.463081.807
50_K54_N0.40051.563
7_T11_S0.380551.485
19_I25_I0.380131.484
46_I50_K0.362191.414
16_I19_I0.357741.396
18_L23_I0.354921.385
42_D46_I0.340471.329
33_I37_K0.339381.325
46_I53_K0.337411.317
49_G52_F0.334321.305
17_K25_I0.330851.291
10_L14_N0.328621.283
8_E11_S0.324421.266
17_K20_I0.319221.246
43_I52_F0.31671.236
46_I49_G0.311391.215
49_G53_K0.306231.195
7_T10_L0.305191.191
31_P35_I0.287261.121
17_K26_T0.286661.119
42_D45_S0.27081.057
38_P42_D0.261361.020
35_I38_P0.2571.003
20_I24_F0.255930.999
40_L55_G0.244020.952
9_F14_N0.242620.947
43_I55_G0.241110.941
26_T48_I0.236120.922
23_I29_I0.235450.919
26_T30_L0.232650.908
19_I27_V0.231050.902
40_L44_L0.229980.898
43_I46_I0.228870.893
35_I39_Q0.225570.880
28_L32_L0.222820.870
9_F13_L0.220890.862
19_I44_L0.216990.847
23_I36_I0.216690.846
27_V51_L0.216270.844
41_K45_S0.215760.842
17_K21_L0.214850.839
44_L48_I0.213040.831
6_I10_L0.210750.822
37_K41_K0.209470.818
7_T14_N0.208340.813
6_I14_N0.207060.808
30_L34_I0.205940.804
43_I50_K0.205560.802
45_S53_K0.204260.797
19_I24_F0.202620.791
23_I28_L0.200650.783
37_K48_I0.200190.781
47_L50_K0.199530.779
6_I9_F0.199290.778
8_E13_L0.197570.771
39_Q52_F0.197430.771
49_G54_N0.195910.765
6_I53_K0.194280.758
32_L35_I0.192970.753
31_P48_I0.188550.736
9_F12_N0.185990.726
14_N38_P0.184490.720
44_L47_L0.183160.715
38_P45_S0.181890.710
16_I21_L0.181430.708
34_I39_Q0.181080.707
6_I46_I0.180290.704
40_L45_S0.179160.699
25_I33_I0.17820.695
24_F30_L0.177790.694
16_I37_K0.177790.694
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
3sokA0.737720.70.826
1oqwA0.737716.80.833
2hi2A0.737716.10.834
1zcdA0.88529.80.849
4gl3A0.98367.40.856
3eu8A0.98366.40.86
2lzrA0.77055.30.865
1ciyA0.819740.872
2w3zA0.90163.90.873
2kdcA0.95083.50.875
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0486 seconds.