GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
XhlA - Haemolysin XhlA
Pfam: PF10779 (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: 71
Sequences: 346
Seq/Len: 4.87
HH_delta: 0.724 (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
21_R26_E0.345142.548
41_K44_E0.291692.154
5_K9_N0.28642.115
42_Q47_K0.267461.975
17_N20_E0.261651.932
18_H22_I0.253941.875
10_R13_T0.243541.798
28_R33_E0.229651.696
27_K30_A0.229521.695
36_I39_L0.210651.555
52_W55_R0.193991.432
56_T59_G0.189541.399
52_W59_G0.180981.336
6_E10_R0.175771.298
19_E22_I0.16561.223
15_L63_T0.163011.204
21_R24_K0.161691.194
49_N55_R0.159561.178
50_T53_I0.156631.156
48_S55_R0.152771.128
6_E13_T0.14941.103
44_E58_I0.145131.072
10_R15_L0.144431.066
46_I69_I0.142621.053
18_H21_R0.142351.051
17_N38_N0.141751.047
15_L38_N0.141741.047
6_E9_N0.140781.039
53_I58_I0.134710.995
40_N43_L0.13470.995
58_I61_I0.133450.985
53_I56_T0.133390.985
20_E24_K0.131510.971
6_E37_K0.130850.966
55_R68_L0.129730.958
33_E36_I0.12920.954
64_A67_Y0.128660.950
53_I57_I0.128240.947
59_G63_T0.127820.944
25_L29_D0.126410.933
7_K12_E0.126310.933
48_S51_K0.125120.924
12_E16_D0.124050.916
56_T68_L0.123730.914
31_A34_K0.122450.904
37_K41_K0.121070.894
8_L61_I0.120380.889
15_L43_L0.119150.880
39_L43_L0.117510.868
40_N44_E0.117410.867
5_K13_T0.116780.862
14_K19_E0.116720.862
28_R31_A0.116680.862
54_W58_I0.115390.852
10_R14_K0.114710.847
26_E64_A0.113240.836
57_I60_A0.11320.836
18_H24_K0.112570.831
50_T57_I0.112380.830
14_K17_N0.11210.828
25_L43_L0.111930.826
51_K54_W0.11160.824
32_N66_I0.110870.819
8_L11_I0.110340.815
20_E25_L0.110260.814
9_N17_N0.108850.804
61_I66_I0.10770.795
22_I32_N0.107670.795
46_I67_Y0.107540.794
52_W60_A0.106950.790
40_N47_K0.106030.783
54_W68_L0.105720.781
29_D39_L0.105580.780
55_R61_I0.105260.777
10_R16_D0.104860.774
59_G65_I0.104540.772
60_A66_I0.10420.769
25_L36_I0.104090.769
62_I66_I0.102840.759
22_I26_E0.102250.755
35_D40_N0.100950.745
13_T16_D0.100610.743
7_K11_I0.099150.732
8_L13_T0.098310.726
49_N54_W0.097570.720
56_T61_I0.097280.718
35_D38_N0.097150.717
12_E15_L0.09680.715
8_L19_E0.096780.715
10_R24_K0.095940.708
45_K68_L0.095840.708
61_I64_A0.095820.707
55_R64_A0.095540.705
32_N36_I0.095140.702
49_N52_W0.094290.696
63_T69_I0.093780.692
14_K20_E0.0930.687
15_L64_A0.092680.684
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
3nmdA0.732482.20.724
3hnwA0.676174.20.743
2kogA168.80.752
3hd7B168.60.753
3vkgA0.971864.90.758
2oqqA0.535259.90.765
2ykoA1590.766
3hd7A153.90.774
1jcdA0.66253.80.774
3c9iA149.30.779
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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