GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HlyD_3 - HlyD family secretion protein
Pfam: PF13437 (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: CL0105
Length: 105
Sequences: 16353
Seq/Len: 155.74
HH_delta: -0.011 (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
74_S92_S2.698493.680
37_W90_E2.208693.012
56_K70_E2.137342.915
58_T68_T2.02942.768
11_V31_V1.959212.672
39_E88_R1.828372.494
58_T70_E1.827842.493
71_G91_I1.805252.462
22_S25_Q1.658882.262
57_V91_I1.639642.236
80_P87_Y1.602262.185
40_A91_I1.546142.109
75_S90_E1.41841.934
10_V28_A1.416351.932
35_D92_S1.396671.905
41_Y88_R1.38541.889
72_K94_D1.314511.793
32_D35_D1.296021.768
39_E90_E1.275141.739
56_K72_K1.273951.737
72_K92_S1.272231.735
13_I16_Q1.272121.735
67_K101_P1.267681.729
60_R68_T1.210411.651
43_P46_D1.094591.493
37_W92_S1.075341.467
77_S88_R1.063641.451
47_I87_Y1.058941.444
51_K55_Q1.050941.433
4_A30_I1.05011.432
12_S29_E1.024491.397
59_V71_G1.016531.386
4_A7_D1.009071.376
14_N29_E0.962321.312
37_W74_S0.950521.296
73_V89_V0.948371.293
59_V93_I0.933711.273
13_I28_A0.885381.207
41_Y86_T0.876821.196
21_V27_L0.876651.196
8_G30_I0.869351.186
16_Q19_E0.852891.163
73_V91_I0.845551.153
42_V89_V0.838821.144
6_F30_I0.83791.143
96_P99_D0.815891.113
95_N100_S0.81311.109
81_D84_G0.809141.104
42_V50_I0.785291.071
14_N26_P0.775351.057
46_D49_R0.772031.053
60_R66_E0.765871.045
38_V59_V0.75191.025
61_L64_G0.747941.020
31_V104_P0.745281.016
64_G67_K0.736811.005
70_E94_D0.698260.952
9_V33_T0.696150.949
64_G69_I0.676130.922
63_P67_K0.662950.904
26_P29_E0.645580.880
57_V71_G0.631550.861
76_I89_V0.630340.860
53_P74_S0.625790.853
36_L104_P0.625430.853
15_V27_L0.620350.846
54_G72_K0.609820.832
2_I27_L0.607610.829
59_V91_I0.604270.824
11_V77_S0.598310.816
9_V103_R0.594980.811
78_P103_R0.593110.809
95_N99_D0.589570.804
6_F32_D0.573840.783
74_S90_E0.572660.781
15_V19_E0.565120.771
38_V93_I0.560940.765
51_K54_G0.554850.757
11_V29_E0.554180.756
50_I73_V0.545050.743
35_D94_D0.542210.739
12_S75_S0.533550.728
41_Y81_D0.531850.725
11_V78_P0.528640.721
21_V25_Q0.526560.718
10_V13_I0.525270.716
15_V25_Q0.523940.715
69_I99_D0.517890.706
82_P85_G0.516630.705
12_S26_P0.516140.704
20_V24_G0.515330.703
19_E25_Q0.509990.696
61_L102_L0.505110.689
40_A89_V0.501570.684
69_I102_L0.500990.683
81_D85_G0.494610.675
4_A8_G0.489230.667
80_P85_G0.482830.658
58_T61_L0.482740.658
9_V78_P0.48040.655
31_V78_P0.477810.652
7_D34_D0.463410.632
44_E63_P0.459810.627
61_L69_I0.45870.626
15_V21_V0.451530.616
43_P86_T0.447370.610
69_I101_P0.446030.608
93_I102_L0.438720.598
40_A57_V0.432260.590
67_K99_D0.418870.571
54_G73_V0.413710.564
63_P66_E0.409810.559
53_P76_I0.409040.558
31_V79_S0.40750.556
57_V73_V0.406730.555
48_A53_P0.399570.545
61_L65_P0.393020.536
73_V76_I0.391560.534
41_Y84_G0.389860.532
70_E95_N0.384150.524
42_V46_D0.380880.519
47_I103_R0.378340.516
44_E86_T0.376390.513
77_S90_E0.376240.513
3_R7_D0.370380.505
33_T36_L0.369960.505
48_A64_G0.369760.504
48_A63_P0.368180.502
47_I76_I0.364150.497
14_N17_P0.363380.496
49_R53_P0.360640.492
41_Y44_E0.360320.491
36_L95_N0.359720.491
51_K101_P0.357710.488
76_I87_Y0.35720.487
66_E69_I0.353750.482
53_P56_K0.34890.476
64_G101_P0.343020.468
31_V86_T0.341420.466
38_V71_G0.337180.460
37_W40_A0.334390.456
11_V79_S0.330220.450
71_G93_I0.327930.447
14_N28_A0.326530.445
75_S79_S0.326430.445
35_D95_N0.325040.443
44_E85_G0.324990.443
86_T89_V0.322210.439
41_Y83_Q0.320560.437
13_I17_P0.319630.436
4_A10_V0.318290.434
6_F10_V0.315410.430
3_R6_F0.313080.427
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
3ne5B0.971499.7-0.011
3lnnA0.961999.60.069
3fppA0.971499.60.092
4dk0A0.971499.60.093
2f1mA0.971499.60.095
1vf7A0.971499.60.108
4l8jA0.98199.60.11
2k32A0.447698.20.522
2dn8A0.428697.50.613
1iyuA0.352497.20.633

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