GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GPI-anchored - Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family
Pfam: PF10342 (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: CL0538
Length: 93
Sequences: 677
Seq/Len: 7.28
HH_delta: 0.731 (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
9_W15_I0.422893.377
48_A51_V0.327222.613
14_P59_T0.302172.413
47_I60_W0.277582.216
36_G87_Y0.275092.197
2_S18_T0.271792.170
73_F90_R0.243711.946
35_N71_D0.216791.731
31_I47_I0.210091.678
34_C73_F0.204921.636
16_T57_S0.194541.553
31_I76_I0.192841.540
63_P93_I0.18711.494
17_I31_I0.184951.477
31_I58_Y0.177911.421
30_T79_S0.165011.318
53_N56_G0.161921.293
34_C75_Q0.159781.276
21_S53_N0.157931.261
32_Y44_V0.153211.223
34_C43_F0.151051.206
17_I74_I0.144721.156
22_D87_Y0.142831.140
34_C87_Y0.142551.138
21_S56_G0.140761.124
51_V58_Y0.140641.123
75_Q87_Y0.138991.110
32_Y46_T0.137041.094
4_T7_T0.136711.092
38_N90_R0.136331.089
71_D76_I0.134581.075
73_F87_Y0.13281.060
68_S72_Y0.131721.052
17_I81_N0.131691.052
21_S25_D0.130171.039
18_T57_S0.130031.038
16_T59_T0.129531.034
36_G72_Y0.12851.026
7_T48_A0.127721.020
29_V53_N0.126421.009
2_S16_T0.126351.009
76_I86_A0.125130.999
36_G90_R0.1250.998
19_W29_V0.124470.994
22_D25_D0.124420.993
79_S82_N0.122710.980
32_Y75_Q0.12010.959
5_A89_P0.119410.953
15_I32_Y0.116910.934
16_T28_N0.113410.906
4_T89_P0.112920.902
45_Q88_S0.111740.892
32_Y77_V0.111620.891
13_Q93_I0.111270.888
61_T69_G0.111210.888
16_T61_T0.111170.888
11_A16_T0.111140.887
17_I76_I0.110880.885
29_V87_Y0.110440.882
23_G79_S0.109910.878
59_T67_P0.109680.876
73_F86_A0.109050.871
13_Q52_S0.108670.868
15_I49_S0.107940.862
20_T25_D0.107770.861
20_T65_D0.106320.849
25_D62_I0.106240.848
41_L87_Y0.10410.831
14_P29_V0.103950.830
37_N40_N0.103860.829
25_D34_C0.103810.829
38_N44_V0.103790.829
31_I74_I0.103720.828
69_G72_Y0.103250.824
12_G93_I0.103130.823
12_G27_G0.102990.822
22_D75_Q0.102650.820
18_T61_T0.101750.812
18_T80_S0.101240.808
50_N65_D0.1010.806
51_V81_N0.100870.805
20_T88_S0.100340.801
6_G80_S0.100130.800
14_P27_G0.099790.797
33_L44_V0.099220.792
37_N70_G0.098780.789
18_T59_T0.09820.784
62_I66_L0.098180.784
44_V76_I0.097990.782
78_N81_N0.097920.782
54_S58_Y0.09780.781
25_D81_N0.097740.780
2_S74_I0.097170.776
14_P61_T0.096830.773
75_Q85_Y0.096140.768
36_G73_F0.095920.766
11_A63_P0.095910.766
12_G63_P0.095750.765
8_V92_T0.095740.764
18_T28_N0.095150.760
35_N69_G0.094990.758
22_D53_N0.094770.757
9_W74_I0.094360.753
7_T81_N0.093940.750
49_S60_W0.093770.749
2_S5_A0.093520.747
31_I86_A0.093460.746
88_S93_I0.09290.742
17_I47_I0.092570.739
27_G61_T0.092390.738
34_C56_G0.092390.738
25_D53_N0.092380.738
3_P8_V0.092230.736
35_N72_Y0.091880.734
87_Y90_R0.091840.733
51_V80_S0.091630.732
3_P6_G0.091620.732
53_N81_N0.090450.722
54_S59_T0.090320.721
47_I67_P0.090110.720
11_A65_D0.08960.715
85_Y89_P0.089370.714
75_Q88_S0.089320.713
52_S70_G0.089220.712
10_T15_I0.088890.710
78_N85_Y0.088220.704
10_T93_I0.087590.699
41_L73_F0.087410.698
30_T77_V0.087390.698
53_N76_I0.087380.698
41_L44_V0.087360.698
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
3pddA0.860294.50.731
3pddA0.8602940.737
2vtcA0.989290.20.766
4b5qA0.989289.10.771
3pe9A0.8602860.782
3ejaA0.989284.60.786
3mpcA0.903284.10.787
3zudA0.989280.60.795
4eisA0.989279.70.796
2ic2A0.9677750.804
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