GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SRCR_2 - Scavenger receptor cysteine-rich domain
Pfam: PF15494 (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: 98
Sequences: 1376
Seq/Len: 14.04
HH_delta: 0.222 (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
25_N28_L0.812283.532
83_S86_V0.78483.412
58_Q61_V0.573952.495
68_N74_S0.563922.452
22_D85_S0.549492.389
24_W87_V0.479812.086
20_C81_C0.470622.046
6_L87_V0.46962.042
60_F63_L0.409721.781
70_T73_Q0.406861.769
21_S85_S0.383681.668
26_E41_S0.378771.647
6_L32_A0.375861.634
3_N38_Y0.366751.595
58_Q63_L0.366661.594
6_L89_L0.362981.578
65_S68_N0.36291.578
24_W32_A0.339611.477
6_L19_V0.329851.434
18_P83_S0.322941.404
18_P86_V0.319971.391
30_K40_S0.31121.353
57_S63_L0.307271.336
26_E30_K0.297791.295
57_S60_F0.293671.277
59_S62_K0.290721.264
66_N69_S0.286071.244
59_S63_L0.280071.218
35_Q72_Q0.2781.209
59_S77_P0.273621.190
24_W28_L0.270941.178
58_Q62_K0.270461.176
24_W29_S0.258911.126
72_Q75_L0.257641.120
15_S42_S0.252281.097
68_N71_L0.248211.079
30_K41_S0.246811.073
47_V51_D0.242831.056
71_L74_S0.239391.041
87_V91_C0.238341.036
70_T74_S0.237421.032
47_V50_S0.235161.022
81_C91_C0.233681.016
21_S88_S0.232621.011
6_L30_K0.229590.998
57_S62_K0.228640.994
35_Q42_S0.223650.972
28_L31_A0.222960.969
5_L86_V0.219090.953
68_N73_Q0.218740.951
49_L52_I0.218270.949
41_S44_S0.21770.947
20_C37_G0.216020.939
39_S92_S0.213510.928
80_S85_S0.20630.897
31_A68_N0.202630.881
32_A36_L0.201110.874
7_Q16_W0.199020.865
80_S84_G0.198860.865
57_S61_V0.197550.859
3_N90_Q0.194230.844
44_S87_V0.193980.843
75_L78_S0.191150.831
9_Y26_E0.186420.811
43_S78_S0.185140.805
5_L18_P0.181440.789
7_Q36_L0.179010.778
9_Y35_Q0.178990.778
69_S72_Q0.178350.775
48_N70_T0.178260.775
10_S75_L0.178090.774
35_Q39_S0.176590.768
45_S48_N0.176380.767
24_W44_S0.176330.767
4_S7_Q0.175690.764
4_S74_S0.174820.760
16_W81_C0.17220.749
9_Y70_T0.168980.735
17_L21_S0.16450.715
5_L16_W0.164470.715
50_S53_S0.161870.704
34_Q79_S0.160470.698
27_A40_S0.158940.691
9_Y15_S0.158880.691
19_V71_L0.157480.685
23_N46_S0.157070.683
29_S87_V0.155470.676
77_P84_G0.15490.673
29_S44_S0.15480.673
10_S14_G0.154050.670
48_N51_D0.153510.667
33_C91_C0.152470.663
5_L17_L0.152410.663
62_K76_S0.151790.660
22_D80_S0.151640.659
46_S53_S0.150870.656
29_S35_Q0.148110.644
10_S42_S0.147330.641
38_Y72_Q0.146490.637
23_N82_S0.145140.631
37_G81_C0.144930.630
40_S69_S0.144860.630
54_P58_Q0.144250.627
33_C37_G0.143320.623
43_S73_Q0.143110.622
28_L87_V0.142810.621
38_Y92_S0.142710.620
35_Q84_G0.142580.620
37_G64_S0.142360.619
22_D81_C0.141640.616
78_S82_S0.140480.611
38_Y42_S0.139690.607
11_A15_S0.13960.607
15_S43_S0.13840.602
38_Y90_Q0.135480.589
30_K92_S0.135430.589
27_A92_S0.135210.588
47_V52_I0.134480.585
47_V53_S0.134180.583
37_G40_S0.133880.582
46_S88_S0.133530.581
30_K51_D0.13330.580
5_L50_S0.133270.579
6_L28_L0.133120.579
23_N27_A0.132860.578
31_A74_S0.132830.578
27_A43_S0.132690.577
53_S57_S0.131790.573
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
2oyaA0.887899.70.222
1by2A0.969499.70.224
1z8gA0.969499.60.249
2jopA0.836799.60.282
2xrcA0.969499.50.303
2ja4A0.816399.50.311
2wjyA0.673521.80.882
2xzlA0.724518.60.886
3h0gL0.48989.60.899
3r8s10.17358.90.9

Page generated in 0.0114 seconds.