GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Haemolytic - Haemolytic domain
Pfam: PF01809 (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: 68
Sequences: 1577
Seq/Len: 23.19
HH_delta: 0.907 (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
34_A50_T2.080574.840
5_A43_L1.254782.919
6_I35_K1.165832.712
42_G46_G1.019882.373
20_K23_R0.919262.139
48_W52_D0.873452.032
26_F61_S0.819411.906
10_R13_Q0.782651.821
13_Q35_K0.759631.767
13_Q32_E0.754981.756
32_E36_Q0.734111.708
11_F15_Y0.715351.664
52_D58_N0.683291.590
35_K39_R0.675251.571
27_Y65_Y0.651581.516
52_D56_R0.646541.504
38_I50_T0.624751.453
56_R61_S0.612911.426
26_F62_K0.604021.405
36_Q68_V0.587651.367
38_I43_L0.577981.345
38_I47_L0.569391.325
5_A38_I0.559691.302
10_R35_K0.545641.269
9_I34_A0.520941.212
41_Y68_V0.5171.203
10_R14_R0.508971.184
7_G11_F0.505981.177
9_I38_I0.502371.169
25_R61_S0.48571.130
32_E35_K0.467971.089
36_Q40_K0.461461.074
26_F56_R0.449031.045
37_A49_L0.445971.038
9_I13_Q0.424140.987
2_K39_R0.419720.976
49_L52_D0.415240.966
51_A55_L0.393630.916
2_K38_I0.392840.914
15_Y20_K0.390710.909
2_K43_L0.387620.902
24_C30_C0.386940.900
15_Y19_L0.365720.851
55_L58_N0.363730.846
27_Y32_E0.358320.834
54_I58_N0.353310.822
6_I10_R0.350450.815
58_N61_S0.345010.803
16_I20_K0.343760.800
6_I39_R0.337380.785
11_F14_R0.337090.784
25_R59_P0.332870.774
30_C57_C0.330570.769
48_W55_L0.329170.766
15_Y18_P0.326720.760
4_L7_G0.324980.756
37_A68_V0.317190.738
2_K6_I0.31650.736
60_F65_Y0.310650.723
24_C57_C0.307430.715
47_L50_T0.306030.712
16_I21_G0.305120.710
38_I46_G0.29340.683
46_G50_T0.29310.682
19_L22_P0.29140.678
3_K7_G0.289290.673
49_L68_V0.286680.667
37_A41_Y0.28460.662
27_Y63_G0.282450.657
32_E39_R0.280730.653
9_I12_Y0.273280.636
41_Y45_K0.270660.630
5_A47_L0.267850.623
12_Y30_C0.264660.616
16_I23_R0.255840.595
14_R20_K0.254520.592
44_F51_A0.2530.589
52_D61_S0.249420.580
36_Q67_P0.247250.575
9_I35_K0.246860.574
34_A54_I0.241690.562
27_Y62_K0.24030.559
12_Y24_C0.240220.559
7_G10_R0.239260.557
50_T54_I0.231030.537
47_L51_A0.229620.534
34_A47_L0.22810.531
14_R19_L0.225520.525
12_Y57_C0.222780.518
41_Y49_L0.221140.514
45_K49_L0.220850.514
23_R62_K0.217870.507
17_S21_G0.210490.490
4_L8_L0.209530.487
3_K39_R0.203040.472
27_Y67_P0.201230.468
2_K5_A0.200690.467
40_K45_K0.200350.466
38_I68_V0.199240.464
38_I42_G0.194860.453
3_K14_R0.194390.452
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
4djdC0.779412.40.907
3qz6A0.58826.10.919
1di1A0.70595.50.92
3eiqC0.926550.922
4fwiB0.941250.922
2h9aA0.77944.20.924
1apyA0.42653.70.926
3aoeE0.82353.60.926
3qpiA0.44123.20.928
2yfqA0.82353.20.928
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 0.0734 seconds.