GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_M10 - Matrixin
Pfam: PF00413 (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: CL0126
Length: 154
Sequences: 1984
Seq/Len: 12.88
HH_delta: 0.045 (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
110_I128_V0.619783.701
24_R44_E0.492512.941
28_R44_E0.490592.930
143_E147_D0.485442.899
32_Q36_D0.484892.896
111_H115_H0.463282.767
91_N94_E0.438662.620
34_W149_I0.400182.390
6_T43_T0.384792.298
31_F113_I0.359992.150
88_I116_A0.354352.116
90_F109_A0.33842.021
117_L149_I0.337942.018
112_E115_H0.317371.895
111_H121_H0.306461.830
34_W141_L0.303441.812
144_D148_G0.30111.798
31_F42_F0.291791.743
33_A106_Q0.287341.716
6_T41_N0.284791.701
88_I113_I0.284461.699
34_W114_G0.278331.662
115_H121_H0.27381.635
27_I109_A0.270181.613
33_A110_I0.269531.610
76_H89_H0.262111.565
30_A34_W0.260191.554
77_A80_P0.260181.554
42_F117_L0.252391.507
127_S148_G0.239861.432
111_H114_G0.226861.355
127_S144_D0.225311.346
31_F35_N0.222241.327
112_E121_H0.217351.298
58_S93_D0.212531.269
25_D29_Q0.211191.261
45_V50_A0.200481.197
75_A89_H0.198631.186
35_N41_N0.192241.148
28_R32_Q0.19151.144
35_N40_L0.189081.129
29_Q106_Q0.189071.129
118_G121_H0.187791.121
12_S53_R0.185441.107
26_A106_Q0.182711.091
114_G129_M0.181481.084
20_Q23_Q0.181221.082
122_S127_S0.180631.079
27_I105_L0.175811.050
54_I113_I0.174621.043
35_N42_F0.173781.038
106_Q110_I0.172221.028
6_T46_S0.171871.026
23_Q27_I0.167861.002
106_Q139_K0.165390.988
89_H94_E0.165330.987
35_N113_I0.16510.986
74_L77_A0.164670.983
149_I153_Y0.16420.981
11_I24_R0.161530.965
146_I150_Q0.161350.964
30_A106_Q0.160320.957
37_V141_L0.160010.956
10_S53_R0.15990.955
8_T43_T0.158460.946
127_S145_D0.157830.943
25_D28_R0.157790.942
81_N85_S0.155940.931
89_H96_W0.155740.930
108_V133_Y0.155670.930
147_D151_Y0.15550.929
127_S130_Y0.155440.928
85_S92_D0.153980.920
105_L109_A0.153010.914
81_N87_D0.152430.910
75_A80_P0.151520.905
58_S92_D0.150860.901
11_I20_Q0.148810.889
104_D139_K0.148150.885
86_G89_H0.148030.884
30_A110_I0.147180.879
37_V150_Q0.1470.878
63_D66_S0.146920.877
21_S25_D0.146880.877
120_D148_G0.14590.871
50_A53_R0.145410.868
76_H80_P0.145340.868
65_Y79_F0.145280.868
61_H69_G0.14510.867
107_S132_Y0.145090.866
32_Q35_N0.144220.861
79_F120_D0.144170.861
6_T13_N0.144140.861
37_V146_I0.144030.860
76_H86_G0.143170.855
124_D142_S0.143140.855
46_S147_D0.141610.846
104_D107_S0.141010.842
104_D109_A0.140440.839
69_G91_N0.140330.838
27_I54_I0.140040.836
111_H129_M0.139830.835
34_W105_L0.139440.833
68_D71_G0.139280.832
49_N147_D0.138790.829
38_A41_N0.138770.829
27_I31_F0.138230.825
7_I38_A0.137060.819
127_S153_Y0.136610.816
7_I11_I0.136340.814
123_N131_P0.135930.812
23_Q56_F0.135580.810
60_N64_G0.13530.808
43_T134_R0.133610.798
52_I56_F0.133610.798
45_V53_R0.132990.794
61_H89_H0.13270.792
68_D74_L0.132510.791
10_S48_G0.13220.789
142_S146_I0.131670.786
75_A78_Y0.130460.779
8_T45_V0.130360.778
72_G76_H0.129550.774
88_I91_N0.12920.772
7_I12_S0.127050.759
11_I54_I0.127020.759
22_E25_D0.126760.757
141_L149_I0.126120.753
34_W144_D0.125730.751
98_I107_S0.125660.750
42_F56_F0.125270.748
129_M145_D0.124760.745
115_H129_M0.124750.745
36_D47_D0.123550.738
41_N44_E0.123420.737
61_H77_A0.122430.731
41_N46_S0.121780.727
111_H118_G0.121760.727
139_K142_S0.121650.726
40_L107_S0.121420.725
75_A79_F0.121290.724
13_N55_S0.121080.723
76_H93_D0.121060.723
127_S131_P0.120130.717
69_G72_G0.119950.716
107_S136_P0.119890.716
107_S139_K0.119660.715
49_N123_N0.119540.714
75_A90_F0.11940.713
52_I116_A0.118660.709
61_H76_H0.118650.709
122_S144_D0.118280.706
6_T12_S0.11810.705
128_V133_Y0.118060.705
75_A86_G0.11780.703
41_N54_I0.117530.702
110_I141_L0.117460.701
74_L78_Y0.11730.700
40_L51_D0.117110.699
120_D123_N0.1170.699
69_G94_E0.116990.699
103_N125_P0.116930.698
26_A105_L0.116790.697
134_R137_D0.115350.689
79_F132_Y0.11470.685
104_D136_P0.114510.684
70_S95_S0.114140.682
78_Y81_N0.113770.679
38_A42_F0.113630.679
49_N53_R0.113290.677
23_Q100_D0.113030.675
10_S50_A0.112620.673
108_V112_E0.11260.672
80_P86_G0.112550.672
15_T57_G0.112170.670
122_S130_Y0.112060.669
7_I40_L0.111840.668
65_Y126_N0.111710.667
142_S145_D0.111690.667
7_I37_V0.111390.665
21_S32_Q0.111010.663
38_A149_I0.11090.662
136_P139_K0.110810.662
59_N63_D0.110380.659
147_D150_Q0.110310.659
88_I92_D0.11020.658
113_I139_K0.109420.653
122_S131_P0.109330.653
70_S73_T0.108910.650
14_T20_Q0.108890.650
123_N134_R0.108890.650
143_E146_I0.108810.650
38_A128_V0.108740.649
88_I97_T0.108350.647
8_T15_T0.108090.645
71_G94_E0.1080.645
81_N88_I0.107810.644
133_Y141_L0.107230.640
145_D153_Y0.107170.640
74_L79_F0.107080.639
69_G86_G0.107070.639
11_I15_T0.107050.639
133_Y136_P0.106990.639
42_F152_L0.10690.638
124_D130_Y0.106550.636
75_A81_N0.106440.636
26_A98_I0.10620.634
126_N142_S0.105940.633
131_P145_D0.105870.632
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
1slmA11000.045
4h1qA11000.045
830cA11000.048
4in9A0.99351000.056
2ovxA0.99351000.057
1hv5A11000.06
3ma2D11000.061
2jsdA11000.064
2xs4A0.99351000.065
1hy7A11000.067

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