GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UPAR_LY6 - u-PARLy-6 domain
Pfam: PF00021 (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: CL0117
Length: 77
Sequences: 820
Seq/Len: 10.65
HH_delta: 0.172 (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
52_C70_C0.685874.913
71_C76_C0.326192.337
19_P22_E0.280642.010
1_C4_C0.274231.964
46_C52_C0.256161.835
26_Y45_G0.224661.609
12_C18_C0.216851.553
4_C18_C0.215351.543
46_C71_C0.212271.521
4_C12_C0.192891.382
21_S50_S0.185311.327
2_Y77_N0.184931.325
1_C18_C0.180281.291
2_Y33_T0.174561.250
71_C77_N0.170671.223
12_C46_C0.167221.198
57_D61_G0.162721.166
1_C12_C0.161491.157
27_T42_V0.160541.150
46_C76_C0.159131.140
19_P55_L0.158781.137
66_V74_D0.158231.133
26_Y30_V0.157511.128
60_N64_I0.156571.122
60_N65_K0.153141.097
44_K77_N0.15251.092
44_K58_F0.152051.089
16_V20_G0.151691.087
2_Y75_L0.150911.081
10_S14_G0.14981.073
56_S59_S0.147141.054
28_A45_G0.146661.051
33_T62_G0.146411.049
16_V28_A0.144041.032
12_C52_C0.142861.023
3_S10_S0.142341.020
46_C77_N0.141971.017
31_T66_V0.140531.007
24_V44_K0.140091.004
43_S54_F0.138480.992
42_V50_S0.135260.969
40_T69_S0.130960.938
28_A66_V0.129320.926
27_T69_S0.127530.914
10_S22_E0.127050.910
16_V69_S0.125170.897
3_S45_G0.124470.892
2_Y14_G0.124130.889
24_V28_A0.118440.848
63_I69_S0.11830.847
11_S42_V0.117360.841
19_P30_V0.116590.835
51_S55_L0.115550.828
52_C63_I0.11420.818
55_L58_F0.113890.816
33_T74_D0.113110.810
9_S33_T0.113080.810
30_V73_T0.112960.809
17_T74_D0.112820.808
21_S41_L0.111950.802
41_L55_L0.111320.797
15_E19_P0.109870.787
42_V67_S0.109610.785
64_I69_S0.109560.785
39_V75_L0.10850.777
65_K69_S0.108470.777
19_P27_T0.108290.776
2_Y15_E0.108070.774
6_S9_S0.107590.771
3_S16_V0.107460.770
17_T40_T0.10620.761
14_G19_P0.106190.761
55_L65_K0.105790.758
17_T20_G0.105470.756
39_V73_T0.105170.753
3_S11_S0.105060.753
30_V59_S0.105030.752
30_V64_I0.104550.749
47_A59_S0.104540.749
50_S53_R0.10430.747
9_S31_T0.104090.746
29_T40_T0.104030.745
56_S60_N0.103260.740
23_D38_S0.102690.736
52_C71_C0.102640.735
26_Y47_A0.102630.735
21_S31_T0.102620.735
6_S32_V0.101950.730
40_T74_D0.101950.730
69_S72_N0.10130.726
62_G74_D0.100670.721
53_R56_S0.10030.718
29_T39_V0.100270.718
5_Y29_T0.09970.714
18_C25_C0.099280.711
54_F71_C0.099050.710
5_Y11_S0.0990.709
10_S74_D0.098760.707
41_L67_S0.098360.705
12_C25_C0.098120.703
17_T32_V0.097780.700
29_T73_T0.097770.700
47_A64_I0.097660.700
28_A40_T0.097650.700
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
1ywhA0.97498.90.172
3laqU0.97498.80.188
3laqU0.97498.80.205
2fd6U0.98798.70.238
1ywhA0.98798.70.241
2fd6U0.96198.60.255
2j8bA0.883198.50.287
2l03A0.909198.50.289
2h5fA0.857198.40.323
2h7zB0.844298.30.326

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