GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
A2M - Alpha-2-macroglobulin family
Pfam: PF00207 (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: CL0011
Length: 92
Sequences: 1216
Seq/Len: 13.22
HH_delta: -0.028 (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
28_S49_E0.509053.285
24_D27_T0.376542.430
29_W52_V0.361432.333
66_L72_I0.353222.280
53_F81_Y0.311042.007
8_V16_A0.309952.000
83_D87_E0.251551.623
60_L76_V0.244061.575
10_T13_N0.234291.512
2_W23_P0.232991.504
36_V42_F0.222471.436
87_E91_T0.218221.408
22_L52_V0.216851.400
31_V50_I0.213211.376
23_P29_W0.206861.335
43_G69_G0.198981.284
22_L29_W0.189511.223
58_I78_V0.187931.213
37_S41_G0.187471.210
18_F33_A0.183831.186
29_W67_R0.182191.176
26_I53_F0.180961.168
57_F81_Y0.180871.167
35_A43_G0.177251.144
56_F81_Y0.17631.138
30_R52_V0.174911.129
3_F20_F0.171941.110
17_T28_S0.171931.110
26_I81_Y0.171611.108
12_A17_T0.171231.105
12_A19_S0.166361.074
63_P66_L0.165611.069
26_I57_F0.162881.051
3_F18_F0.160211.034
50_I61_N0.160061.033
65_S70_D0.158011.020
2_W70_D0.156931.013
61_N77_T0.156911.013
72_I75_P0.156681.011
34_F66_L0.156561.010
84_K89_T0.155921.006
32_T45_A0.154630.998
2_W29_W0.154410.997
43_G55_P0.151880.980
55_P69_G0.150040.968
15_K46_E0.1490.962
34_F68_R0.148870.961
49_E52_V0.148430.958
15_K39_T0.148080.956
28_S34_F0.147960.955
57_F64_R0.147310.951
4_W34_F0.146850.948
60_L81_Y0.145530.939
41_G68_R0.143660.927
44_I71_Q0.143530.926
29_W57_F0.142680.921
59_Q86_Q0.142480.920
56_F82_T0.141410.913
5_S18_F0.140380.906
22_L50_I0.139320.899
3_F79_F0.137670.889
14_G39_T0.13740.887
58_I76_V0.137360.887
29_W54_K0.13730.886
18_F62_L0.1370.884
31_V46_E0.136770.883
8_V18_F0.135910.877
4_W80_N0.135770.876
20_F60_L0.134570.869
42_F87_E0.13440.867
4_W36_V0.133650.863
83_D86_Q0.133370.861
78_V90_V0.132370.854
31_V35_A0.131650.850
57_F79_F0.131430.848
35_A38_P0.131180.847
53_F78_V0.130840.844
51_T91_T0.130630.843
23_P50_I0.130480.842
46_E52_V0.130410.842
6_P10_T0.130080.840
33_A60_L0.129910.838
30_R46_E0.129660.837
6_P35_A0.127690.824
14_G33_A0.126690.818
76_V90_V0.126650.817
8_V12_A0.126480.816
62_L74_I0.126460.816
25_S29_W0.125570.810
56_F74_I0.124960.806
30_R49_E0.124850.806
36_V54_K0.124150.801
60_L73_Q0.122960.794
21_T78_V0.122740.792
8_V78_V0.122390.790
21_T84_K0.121820.786
9_V13_N0.12180.786
12_A66_L0.12170.785
71_Q74_I0.121620.785
35_A73_Q0.121560.785
7_I83_D0.121240.782
53_F57_F0.121110.782
16_A20_F0.121060.781
56_F78_V0.120860.780
18_F89_T0.120330.777
9_V38_P0.119640.772
12_A18_F0.11930.770
27_T64_R0.118960.768
16_A84_K0.118930.768
14_G37_S0.118050.762
58_I88_V0.117510.758
64_R70_D0.11690.754
4_W73_Q0.116690.753
39_T74_I0.116680.753
44_I73_Q0.116680.753
22_L28_S0.116370.751
32_T47_P0.116160.750
9_V89_T0.115860.748
15_K69_G0.115840.748
39_T90_V0.115070.743
71_Q87_E0.115040.742
33_A45_A0.114390.738
49_E84_K0.114210.737
43_G76_V0.114150.737
12_A51_T0.11310.730
59_Q79_F0.112680.727
37_S81_Y0.112330.725
54_K67_R0.112070.723
15_K91_T0.111980.723
25_S67_R0.111890.722
7_I17_T0.111590.720
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
4acqA0.989199.9-0.028
2b39A199.9-0.026
2hr0B199.9-0.023
3prxB199.9-0.023
4fxkB0.967499.9-0.016
3hrzB199.9-0.01
2pn5A0.989199.90.005
3cu7A0.956599.90.029
3es6B0.478398.40.581
2icnB0.478398.30.593

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