GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SRCR - Scavenger receptor cysteine-rich domain
Pfam: PF00530 (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: CL0550
Length: 99
Sequences: 2720
Seq/Len: 27.47
HH_delta: -0.101 (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
29_S32_E1.191893.823
24_C88_C1.096593.518
7_C42_Y1.081573.470
90_H93_D1.047573.361
11_V36_V0.898112.881
26_D92_E0.66922.147
30_M45_A0.627652.013
28_W94_A0.606411.945
63_L80_H0.585461.878
11_V94_A0.5711.832
22_T93_D0.534291.714
68_C78_C0.527921.694
4_S8_E0.517281.659
65_N81_S0.509251.634
61_I90_H0.508311.631
49_S97_I0.502261.611
28_W32_E0.498111.598
25_D92_E0.476431.528
34_N44_G0.462161.483
30_M34_N0.445581.429
62_W84_T0.438441.406
22_T90_H0.432181.386
63_L66_V0.423811.360
27_G65_N0.420751.350
35_V72_E0.414531.330
82_P85_S0.409491.314
65_N87_S0.405581.301
11_V96_V0.400551.285
7_C43_G0.394121.264
27_G67_N0.391191.255
26_D87_S0.387911.244
10_R22_T0.385711.237
39_Q76_S0.385231.236
8_E97_I0.382311.226
49_S53_S0.379111.216
19_S60_P0.37791.212
3_G8_E0.357411.147
39_Q74_S0.35621.143
64_S87_S0.353461.134
34_N45_A0.351241.127
54_F95_G0.348761.119
11_V23_V0.348581.118
35_V70_G0.344611.105
28_W36_V0.338921.087
5_S8_E0.322171.033
52_S55_G0.318091.020
67_N79_T0.31251.002
81_S85_S0.312491.002
48_T94_A0.31130.999
76_S83_W0.306310.983
76_S79_T0.305730.981
32_E66_V0.297830.955
33_A48_T0.297460.954
10_R93_D0.293740.942
73_T77_E0.292540.938
64_S86_S0.289920.930
32_E35_V0.285360.915
28_W66_V0.284920.914
33_A94_A0.28240.906
62_W83_W0.274090.879
22_T61_I0.272020.873
10_R95_G0.271240.870
14_C39_Q0.269740.865
45_A48_T0.26880.862
69_S79_T0.260220.835
12_E20_W0.258750.830
38_R70_G0.258410.829
74_S77_E0.255070.818
61_I93_D0.253390.813
8_E42_Y0.24760.794
6_P42_Y0.245460.787
36_V75_L0.244410.784
36_V96_V0.2440.783
13_V63_L0.243460.781
28_W33_A0.24050.772
37_C98_C0.240140.770
94_A98_C0.239150.767
49_S95_G0.233610.749
30_M46_S0.232160.745
50_S53_S0.230680.740
13_V23_V0.230450.739
59_G93_D0.229150.735
80_H83_W0.227710.730
54_F97_I0.226740.727
21_G61_I0.226610.727
28_W48_T0.2260.725
64_S84_T0.225750.724
52_S56_S0.225580.724
89_S92_E0.225560.724
87_S92_E0.220410.707
47_S97_I0.217130.697
48_T52_S0.216710.695
31_N34_N0.214770.689
9_G12_E0.213790.686
31_N67_N0.211790.679
71_N76_S0.211770.679
64_S92_E0.210770.676
21_G63_L0.210210.674
35_V75_L0.208330.668
68_C75_L0.208160.668
72_E78_C0.208110.668
37_C41_G0.208090.668
47_S53_S0.206180.661
21_G62_W0.205880.660
76_S80_H0.204940.657
15_F62_W0.204780.657
39_Q43_G0.203030.651
60_P67_N0.20250.650
12_E22_T0.201590.647
59_G90_H0.198930.638
85_S89_S0.197230.633
34_N71_N0.196370.630
75_L78_C0.195930.629
2_G7_C0.195570.627
68_C72_E0.193860.622
39_Q75_L0.193340.620
5_S42_Y0.192380.617
10_R57_G0.192380.617
33_A96_V0.18990.609
21_G66_V0.189430.608
10_R21_G0.188550.605
22_T59_G0.186990.600
11_V33_A0.186130.597
18_G21_G0.181720.583
66_V80_H0.181220.581
18_G59_G0.180070.578
31_N91_S0.178660.573
28_W96_V0.177050.568
7_C76_S0.176660.567
14_C30_M0.174480.560
30_M47_S0.171990.552
27_G79_T0.169840.545
30_M77_E0.168070.539
53_S60_P0.167910.539
4_S97_I0.167130.536
50_S81_S0.166450.534
79_T89_S0.165830.532
7_C44_G0.165750.532
33_A47_S0.165480.531
46_S49_S0.164840.529
85_S91_S0.164810.529
14_C17_N0.164590.528
67_N85_S0.163720.525
56_S59_G0.162420.521
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
1by2A0.989999.9-0.101
2oyaA0.939499.9-0.035
2xrcA0.969799.80.034
2jopA0.888999.80.045
2ja4A0.888999.80.058
1z8gA0.89999.50.265
2qsfA0.82834.90.905
3zwuA0.7984.20.908
1uhuA0.67682.50.917
3b8bA0.68691.90.922

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