GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SpoA - Surface presentation of antigens (SPOA)
Pfam: PF01052 (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: 77
Sequences: 1624
Seq/Len: 21.09
HH_delta: 0.037 (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
56_R72_E0.790753.153
60_G67_A0.708432.824
47_L57_G0.629892.511
21_L26_L0.585392.334
46_E53_P0.580982.316
15_E18_E0.577622.303
57_G68_V0.543172.166
47_L68_V0.520372.075
21_L29_L0.517152.062
22_T25_E0.473041.886
62_V67_A0.438751.749
14_V45_V0.43741.744
18_E48_R0.413971.650
46_E56_R0.409141.631
44_P71_T0.379191.512
17_G37_L0.364721.454
61_R64_G0.360561.438
39_K46_E0.356161.420
15_E46_E0.354761.414
29_L33_D0.33491.335
15_E48_R0.330991.320
16_L19_A0.327241.305
48_R53_P0.324861.295
58_E69_R0.293051.168
8_V55_F0.285121.137
66_L69_R0.282921.128
58_E71_T0.278051.109
55_F73_L0.263861.052
14_V68_V0.263771.052
14_V60_G0.261761.044
48_R51_G0.255561.019
45_V59_L0.251921.004
44_P72_E0.239430.955
6_S24_G0.23770.948
24_G28_N0.236040.941
34_V53_P0.235020.937
13_S48_R0.232610.927
40_P43_E0.230440.919
19_A38_D0.219980.877
29_L35_I0.215930.861
11_E50_N0.213750.852
42_D61_R0.212230.846
55_F60_G0.209060.834
13_S51_G0.2090.833
4_S35_I0.208660.832
21_L35_I0.208310.831
47_L70_I0.208070.830
28_N31_V0.206940.825
12_L55_F0.206270.822
53_P74_I0.203080.810
14_V47_L0.200410.799
51_G66_L0.198750.792
50_N66_L0.198290.791
19_A37_L0.196280.783
59_L66_L0.196190.782
6_S27_L0.195730.780
37_L44_P0.194260.775
36_P39_K0.193790.773
17_G39_K0.193180.770
8_V67_A0.189020.754
8_V48_R0.18880.753
47_L55_F0.187040.746
5_L8_V0.185480.739
60_G64_G0.184270.735
7_D24_G0.182520.728
33_D60_G0.179290.715
31_V64_G0.1790.714
56_R62_V0.178730.713
49_V54_I0.178140.710
16_L70_I0.177190.706
11_E30_K0.176690.704
47_L59_L0.176650.704
38_D66_L0.176350.703
30_K33_D0.174330.695
26_L29_L0.174070.694
10_V49_V0.171640.684
46_E74_I0.171080.682
13_S34_V0.170530.680
28_N72_E0.170510.680
52_Q56_R0.169040.674
12_L19_A0.167050.666
52_Q65_R0.1670.666
54_I67_A0.164570.656
54_I59_L0.164350.655
30_K73_L0.161270.643
21_L25_E0.161020.642
4_S54_I0.160870.641
15_E37_L0.160320.639
16_L22_T0.159910.638
62_V65_R0.159750.637
25_E28_N0.159320.635
12_L49_V0.15870.633
42_D64_G0.158060.630
36_P40_P0.156660.625
40_P69_R0.153270.611
22_T73_L0.153150.611
39_K52_Q0.152770.609
30_K36_P0.152430.608
12_L28_N0.151260.603
12_L51_G0.151070.602
36_P41_A0.149040.594
12_L31_V0.148580.592
48_R71_T0.147880.590
44_P56_R0.146620.585
18_E40_P0.14630.583
35_I39_K0.146110.583
46_E69_R0.145080.578
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
1o6aA199.60.037
1o9yA199.60.058
3uepA199.60.063
4f27A0.857118.10.853
2ekdA0.662316.10.856
3pgwB0.636414.20.86
1r17A0.857112.80.862
3gr4A1120.863
4drsA111.50.865
3hqnD111.20.866

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