GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_S41 - Peptidase family S41
Pfam: PF03572 (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: CL0127
Length: 169
Sequences: 3672
Seq/Len: 21.73
HH_delta: 0.114 (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
41_G98_D1.558245.632
112_L118_A1.386985.013
97_T125_T1.380274.989
99_E123_E1.013853.664
109_A120_I0.770852.786
7_I16_F0.747572.702
101_T105_A0.710152.567
2_I34_G0.694822.511
113_K156_Q0.650492.351
124_P164_E0.633682.290
37_I108_F0.630162.278
34_G92_P0.620622.243
3_G27_L0.615862.226
1_N33_D0.602132.176
97_T120_I0.600842.172
7_I53_L0.5732.071
32_T35_L0.572832.070
17_D52_E0.536911.941
26_K30_K0.515271.862
94_Y121_V0.508761.839
54_L108_F0.501871.814
113_K166_D0.473581.712
23_F26_K0.469651.697
53_L108_F0.454591.643
164_E168_E0.441331.595
19_E22_E0.430591.556
68_D71_G0.421951.525
121_V167_I0.421171.522
21_D56_Y0.399521.444
17_D49_Y0.384291.389
102_A126_A0.381711.380
20_L57_L0.379621.372
42_N45_G0.375711.358
55_S63_I0.374451.353
119_T167_I0.374061.352
37_I93_V0.373521.350
128_A132_Q0.372741.347
34_G94_Y0.370641.340
44_G103_S0.356231.288
114_D152_N0.355461.285
3_G32_T0.353861.279
3_G35_L0.349331.263
21_D25_D0.347941.258
24_L88_R0.345141.247
110_S163_I0.337271.219
130_G159_E0.330361.194
68_D72_S0.330321.194
134_G142_I0.32941.191
15_S18_E0.328961.189
18_E22_E0.32511.175
42_N103_S0.324611.173
149_R157_K0.322291.165
110_S114_D0.321481.162
45_G103_S0.320211.157
110_S152_N0.317421.147
58_I115_N0.306821.109
106_E127_G0.304871.102
35_L91_G0.303531.097
28_K91_G0.302571.094
22_E26_K0.302321.093
43_G101_T0.300331.085
131_G148_S0.299881.084
133_T147_T0.296551.072
67_R73_N0.295251.067
62_I65_Y0.293721.062
27_L32_T0.293061.059
24_L35_L0.281621.018
15_S49_Y0.281551.018
119_T166_D0.281211.016
123_E168_E0.279191.009
64_F107_I0.278151.005
161_I164_E0.277811.004
132_Q146_P0.276951.001
128_A146_P0.275370.995
151_Y157_K0.27370.989
17_D21_D0.272990.987
95_V112_L0.272270.984
102_A106_E0.26840.970
109_A163_I0.268310.970
5_L20_L0.263720.953
108_F112_L0.263710.953
86_K90_N0.262450.949
114_D154_D0.259270.937
50_A54_L0.257130.929
72_S75_K0.257090.929
135_F145_I0.255060.922
152_N156_Q0.252970.914
27_L35_L0.252530.913
94_Y119_T0.252170.911
102_A128_A0.251480.909
50_A108_F0.250070.904
37_I95_V0.245880.889
120_I125_T0.244570.884
5_L23_F0.243860.881
39_L97_T0.242490.876
9_S43_G0.241760.874
48_E52_E0.240110.868
10_F108_F0.236780.856
1_N30_K0.236530.855
10_F42_N0.236290.854
70_I73_N0.235840.852
137_L140_G0.234460.847
47_D107_I0.228730.827
54_L58_I0.228250.825
46_S49_Y0.226150.817
151_Y155_G0.225540.815
95_V109_A0.225270.814
93_V118_A0.224770.812
12_E46_S0.222880.806
95_V118_A0.22270.805
25_D29_S0.222090.803
4_Y36_I0.221070.799
130_G157_K0.220650.798
25_D28_K0.219770.794
93_V117_R0.219680.794
22_E29_S0.218750.791
68_D73_N0.218030.788
16_F53_L0.217680.787
132_Q144_S0.21680.784
136_S142_I0.214340.775
58_I117_R0.212880.769
129_G146_P0.21260.768
67_R151_Y0.212020.766
93_V112_L0.21180.766
43_G100_N0.211430.764
126_A132_Q0.21120.763
152_N163_I0.208980.755
150_Y158_I0.208020.752
49_Y52_E0.207990.752
97_T109_A0.207530.750
39_L105_A0.206560.747
41_G100_N0.205480.743
113_K164_E0.203620.736
10_F104_A0.203270.735
28_K31_D0.202280.731
51_I63_I0.202080.730
59_P90_N0.200040.723
50_A57_L0.199760.722
54_L63_I0.197860.715
105_A128_A0.197620.714
125_T162_G0.197470.714
44_G104_A0.197010.712
120_I163_I0.19650.710
129_G132_Q0.196360.710
23_F27_L0.196270.709
11_S46_S0.195650.707
33_D91_G0.195620.707
99_E124_P0.195060.705
10_F102_A0.194810.704
101_T106_E0.193490.699
134_G144_S0.193220.698
20_L56_Y0.19290.697
40_R96_L0.192650.696
54_L111_A0.192610.696
28_K89_F0.192180.695
135_F147_T0.191440.692
32_T89_F0.191060.691
55_S79_T0.191060.691
113_K116_K0.190690.689
42_N104_A0.189960.687
16_F20_L0.189870.686
75_K78_S0.188870.683
29_S59_P0.187070.676
20_L53_L0.186880.675
50_A104_A0.186570.674
88_R91_G0.185480.670
111_A152_N0.184950.668
17_D53_L0.18390.665
106_E128_A0.183850.664
127_G162_G0.183390.663
130_G152_N0.183280.662
26_K29_S0.183080.662
124_P168_E0.182340.659
151_Y159_E0.182320.659
20_L37_I0.181670.657
47_D131_G0.180870.654
22_E25_D0.180770.653
7_I37_I0.18070.653
106_E162_G0.179910.650
104_A128_A0.178930.647
40_R98_D0.178850.646
36_I94_Y0.17880.646
107_I148_S0.177450.641
107_I132_Q0.177080.640
106_E125_T0.176460.638
22_E70_I0.174830.632
73_N80_I0.174390.630
21_D88_R0.174250.630
39_L101_T0.173560.627
110_S156_Q0.17340.627
42_N102_A0.172940.625
29_S33_D0.172510.624
112_L117_R0.172310.623
77_V80_I0.171950.621
76_W79_T0.171480.620
128_A162_G0.171310.619
47_D51_I0.171270.619
113_K118_A0.171010.618
17_D56_Y0.170220.615
130_G146_P0.169310.612
58_I62_I0.169040.611
28_K90_N0.168970.611
115_N118_A0.16860.609
106_E126_A0.168110.608
138_P141_S0.168110.608
106_E111_A0.167950.607
39_L108_F0.167890.607
47_D54_L0.16740.605
74_K77_V0.167290.605
130_G150_Y0.167110.604
36_I42_N0.167060.604
55_S87_N0.166410.601
142_I147_T0.164450.594
156_Q161_I0.163250.590
97_T165_P0.162930.589
67_R150_Y0.162560.588
97_T101_T0.162260.586
107_I131_G0.162210.586
28_K35_L0.162050.586
18_E21_D0.161730.585
99_E160_G0.161650.584
63_I66_Y0.161470.584
24_L57_L0.161350.583
11_S19_E0.161170.583
21_D24_L0.161120.582
1_N21_D0.16080.581
47_D104_A0.160070.579
76_W135_F0.160.578
47_D148_S0.159750.577
158_I163_I0.158640.573
106_E146_P0.158280.572
124_P149_R0.157820.570
124_P161_I0.157470.569
113_K152_N0.156890.567
65_Y73_N0.156860.567
149_R159_E0.15680.567
150_Y159_E0.155710.563
25_D60_K0.155080.561
128_A131_G0.155080.561
35_L89_F0.154360.558
87_N90_N0.153580.555
114_D153_P0.153330.554
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
1fc6A0.96451000.114
1j7xA0.98221000.142
3k50A11000.154
4ghnA0.91721000.158
3dorA0.99411000.175
1k32A0.91121000.191
3bf0A0.78787.70.884
1y7oA0.751584.10.889
3rstA0.727874.50.898
4jcsA0.899458.50.908

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