GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_M17_N - Cytosol aminopeptidase family N-terminal domain
Pfam: PF02789 (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: CL0223
Length: 126
Sequences: 1287
Seq/Len: 10.21
HH_delta: 0.177 (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
18_D23_G0.500443.268
72_R110_E0.443562.896
3_G60_L0.403862.637
119_F122_Y0.387652.531
36_G59_G0.362552.367
79_A112_A0.341992.233
82_L90_V0.338532.211
111_G115_G0.333122.175
33_D54_R0.323142.110
76_A114_L0.318682.081
111_G114_L0.313942.050
6_E62_K0.308672.016
67_T70_S0.296521.936
83_K118_R0.290391.896
71_L108_A0.288521.884
43_L56_L0.287721.879
60_L74_A0.261611.708
75_G111_G0.251321.641
62_K65_K0.246991.613
6_E37_K0.240121.568
34_F42_L0.236231.543
18_D26_S0.229891.501
1_V78_A0.228681.493
39_G77_A0.228321.491
76_A111_G0.227811.488
107_A110_E0.211331.380
41_T56_L0.20971.369
69_E72_R0.207231.353
102_D106_E0.203841.331
18_D21_L0.195151.274
93_D108_A0.194241.268
69_E110_E0.188231.229
80_R115_G0.187371.224
69_E73_K0.186691.219
106_E110_E0.181891.188
75_G115_G0.181051.182
33_D45_P0.17821.164
42_L57_L0.175431.146
101_S104_A0.173571.133
34_F59_G0.170631.114
21_L46_G0.17061.114
119_F124_S0.170471.113
25_L71_L0.164411.074
58_V74_A0.159141.039
92_I95_P0.158491.035
5_F11_S0.156531.022
1_V82_L0.152280.994
5_F66_L0.152050.993
71_L95_P0.150420.982
77_A81_A0.15030.981
74_A78_A0.14850.970
79_A116_S0.147070.960
75_G79_A0.1460.953
103_E106_E0.145310.949
110_E115_G0.145020.947
32_G54_R0.144250.942
16_A20_A0.144180.941
36_G61_G0.143590.938
56_L78_A0.141940.927
60_L64_E0.141770.926
16_A23_G0.141420.923
65_K109_A0.14010.915
38_A70_S0.139310.910
77_A80_R0.139170.909
110_E114_L0.139110.908
41_T81_A0.138540.905
90_V93_D0.138420.904
27_R53_K0.136290.890
75_G114_L0.135950.888
81_A84_K0.135860.887
24_L27_R0.135260.883
75_G78_A0.134590.879
26_S30_K0.132950.868
66_L70_S0.132480.865
21_L24_L0.132070.862
120_D123_K0.131760.860
76_A95_P0.131430.858
102_D105_A0.131370.858
72_R107_A0.129620.846
26_S121_K0.128780.841
38_A74_A0.128670.840
120_D124_S0.128520.839
105_A111_G0.12720.831
76_A82_L0.126270.825
5_F60_L0.126260.824
20_A66_L0.125530.820
32_G41_T0.125070.817
58_V78_A0.123640.807
6_E40_E0.123410.806
82_L87_V0.123010.803
10_L16_A0.1230.803
30_K42_L0.122740.801
71_L91_A0.120690.788
66_L71_L0.119330.779
3_G94_L0.119140.778
110_E113_L0.117880.770
93_D109_A0.117650.768
1_V11_S0.11760.768
20_A65_K0.117420.767
34_F124_S0.116670.762
68_A107_A0.115740.756
83_K112_A0.11550.754
2_V67_T0.11520.752
62_K123_K0.11490.750
12_P15_K0.114720.749
35_K59_G0.114390.747
33_D57_L0.11420.746
23_G27_R0.113970.744
12_P105_A0.11360.742
20_A52_A0.112140.732
113_L116_S0.111890.731
40_E43_L0.111520.728
72_R76_A0.111420.728
36_G40_E0.111230.726
5_F12_P0.111070.725
38_A73_K0.110950.724
3_G17_L0.110420.721
102_D109_A0.110340.721
28_L56_L0.11020.720
4_V101_S0.109810.717
2_V44_L0.109790.717
49_G52_A0.109010.712
31_A112_A0.108830.711
54_R57_L0.108520.709
85_L109_A0.108040.705
15_K63_K0.108030.705
54_R61_G0.107980.705
58_V112_A0.107870.704
60_L69_E0.107860.704
101_S106_E0.107690.703
65_K70_S0.107630.703
12_P16_A0.107270.700
56_L93_D0.106610.696
68_A104_A0.106450.695
71_L104_A0.106320.694
66_L74_A0.106210.694
44_L94_L0.10620.693
29_I57_L0.105940.692
75_G92_I0.105920.692
57_L124_S0.105650.690
71_L107_A0.105440.689
33_D85_L0.105380.688
31_A53_K0.105360.688
27_R51_K0.105140.687
49_G68_A0.104520.683
84_K118_R0.104330.681
16_A22_D0.104140.680
48_G86_K0.103840.678
20_A23_G0.103530.676
3_G58_V0.103520.676
38_A92_I0.103170.674
67_T88_K0.103070.673
40_E123_K0.102980.672
34_F41_T0.102360.668
109_A112_A0.102110.667
44_L47_P0.102090.667
2_V58_V0.101930.666
75_G81_A0.101850.665
56_L82_L0.101820.665
56_L117_Y0.101820.665
107_A111_G0.101550.663
35_K121_K0.101190.661
40_E71_L0.101170.661
46_G49_G0.100940.659
52_A55_V0.100460.656
18_D22_D0.10010.654
39_G106_E0.100060.653
63_K73_K0.100020.653
83_K86_K0.09990.652
70_S78_A0.099420.649
31_A89_S0.099340.649
41_T77_A0.099320.649
31_A121_K0.099060.647
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
3jruB199.70.177
3h8gF199.70.18
3kr4A0.984199.70.193
3kzwA199.70.2
1gytA199.60.236
4ksiA0.960399.60.243
3peiA0.920699.60.258
1lamA0.936599.50.302
3ij3A0.857199.10.454
2hc9A0.841374.80.834

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