GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CAP - Cysteine-rich secretory protein family
Pfam: PF00188 (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: 124
Sequences: 4204
Seq/Len: 33.9
HH_delta: 0.135 (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
20_D103_R1.859634.897
19_W24_A1.409593.712
31_A121_V1.307473.443
28_Q32_K1.24733.284
93_F97_L0.992842.614
26_A123_N0.809542.132
106_C122_C0.788432.076
21_P24_A0.739991.949
28_Q107_A0.739041.946
4_H124_Y0.721171.899
30_H33_Y0.687141.809
10_A13_G0.671941.769
108_V118_Y0.670981.767
65_V101_T0.65381.722
18_K103_R0.651261.715
3_L6_E0.638371.681
2_D6_E0.624261.644
14_L99_P0.619531.631
32_K109_A0.612881.614
66_E70_S0.604011.591
84_N88_N0.602391.586
31_A107_A0.595971.569
1_L104_I0.593861.564
69_Y72_S0.589531.552
44_S48_G0.582611.534
31_A109_A0.57041.502
4_H104_I0.57031.502
69_Y96_L0.554441.460
27_A105_G0.553721.458
98_W101_T0.549481.447
90_P94_T0.544071.433
1_L19_W0.534861.408
71_E92_H0.52871.392
17_L101_T0.508231.338
42_H92_H0.496331.307
24_A105_G0.495661.305
12_N93_F0.490741.292
5_N8_R0.482871.272
110_N118_Y0.481811.269
11_A14_L0.471271.241
83_F86_W0.47091.240
7_Y11_A0.455541.200
10_A16_P0.451041.188
25_K29_A0.446271.175
21_P25_K0.443731.168
1_L106_C0.442941.166
87_M96_L0.429381.131
87_M93_F0.413571.089
7_Y87_M0.412161.085
95_N101_T0.41091.082
65_V68_W0.391391.031
12_N97_L0.389341.025
33_Y37_S0.388471.023
94_T98_W0.387851.021
7_Y93_F0.382961.008
4_H122_C0.381921.006
72_S85_S0.371770.979
30_H53_R0.369170.972
84_N90_P0.367730.968
19_W106_C0.366620.965
24_A28_Q0.364030.959
35_A109_A0.358980.945
45_G48_G0.353090.930
104_I122_C0.349720.921
86_W89_S0.345150.909
7_Y69_Y0.345120.909
14_L93_F0.344010.906
4_H96_L0.335360.883
54_F57_Y0.333870.879
70_S73_K0.332480.876
33_Y39_S0.32720.862
69_Y97_L0.317660.836
50_Q53_R0.316840.834
95_N98_W0.316240.833
59_D103_R0.315760.831
65_V96_L0.314690.829
17_L102_T0.313880.827
108_V120_W0.31320.825
38_N42_H0.311020.819
1_L17_L0.308150.811
89_S92_H0.307620.810
34_C119_Y0.307140.809
30_H121_V0.304340.801
30_H34_C0.301350.794
18_K21_P0.30.790
50_Q54_F0.29840.786
34_C39_S0.298380.786
3_L7_Y0.296370.780
38_N41_S0.293540.773
6_E11_A0.293390.773
84_N87_M0.292930.771
34_C38_N0.288720.760
33_Y45_G0.288610.760
12_N99_P0.284250.749
69_Y93_F0.281630.742
90_P93_F0.279480.736
24_A106_C0.277720.731
46_E49_S0.275350.725
32_K36_N0.275110.724
34_C111_C0.272890.719
111_C114_G0.272810.718
23_L105_G0.269990.711
86_W90_P0.269560.710
19_W104_I0.268990.708
24_A107_A0.268770.708
17_L104_I0.268640.707
49_S67_N0.268470.707
7_Y12_N0.268120.706
13_G97_L0.265590.699
41_S44_S0.263640.694
26_A29_A0.262170.690
53_R56_S0.260030.685
95_N122_C0.259260.683
54_F61_Q0.258880.682
72_S93_F0.255710.673
47_N53_R0.255430.673
49_S52_S0.255340.672
40_L68_W0.255050.672
110_N114_G0.252130.664
68_W71_E0.251530.662
34_C121_V0.25040.659
28_Q109_A0.248950.656
23_L104_I0.247330.651
74_N87_M0.246760.650
22_E25_K0.246680.650
39_S45_G0.246680.650
22_E103_R0.245650.647
35_A111_C0.240280.633
101_T104_I0.238750.629
3_L66_E0.235970.621
76_N84_N0.235180.619
31_A34_C0.2350.619
1_L5_N0.234880.619
33_Y44_S0.234170.617
73_K77_F0.232020.611
26_A44_S0.231430.609
106_C111_C0.22950.604
29_A57_Y0.225250.593
66_E69_Y0.224620.591
7_Y97_L0.223010.587
35_A119_Y0.22220.585
83_F87_M0.220070.580
67_N70_S0.216490.570
20_D23_L0.214470.565
46_E123_N0.213210.561
15_P102_T0.212040.558
4_H83_F0.208360.549
45_G49_S0.208220.548
71_E74_N0.207980.548
85_S89_S0.207220.546
55_G61_Q0.206530.544
23_L26_A0.206320.543
53_R59_D0.204360.538
6_E10_A0.204090.537
85_S88_N0.20320.535
23_L44_S0.202890.534
51_S59_D0.2020.532
51_S54_F0.201530.531
13_G99_P0.201430.530
87_M90_P0.201170.530
3_L69_Y0.198160.522
67_N95_N0.196970.519
30_H123_N0.195130.514
26_A30_H0.19440.512
26_A53_R0.193530.510
94_T97_L0.19340.509
72_S113_N0.193130.509
71_E75_Y0.192060.506
75_Y106_C0.192030.506
12_N69_Y0.189770.500
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
4aiwA0.911399.80.135
1cfeA0.927499.70.152
4ifaA0.903299.70.168
4h0aA0.895299.70.198
1qnxA0.983999.70.209
2vznA0.991999.70.22
4g2uA0.983999.60.224
3u3lC0.991999.60.224
3nt8A0.951699.60.229
1xtaA0.943599.60.231

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