GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_MA_2 - Peptidase MA superfamily
Pfam: PF13485 (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: 128
Sequences: 4001
Seq/Len: 31.26
HH_delta: 0.198 (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
113_E118_R0.867963.105
31_H35_H0.75652.706
32_E35_H0.74162.653
58_E61_E0.65262.335
116_Y120_K0.643632.303
59_Y113_E0.618942.214
120_K123_A0.614882.200
31_H102_Y0.614842.200
122_K126_R0.590562.113
118_R122_K0.585522.095
123_A126_R0.564362.019
63_R113_E0.563312.015
58_E106_Y0.552381.976
123_A127_E0.541691.938
31_H54_E0.538141.925
32_E102_Y0.537261.922
35_H102_Y0.520561.862
35_H54_E0.478631.712
54_E102_Y0.45761.637
27_R61_E0.457181.636
56_L125_L0.456631.634
34_A57_A0.439811.573
32_E54_E0.424231.518
55_G109_V0.395811.416
55_G105_G0.385131.378
34_A60_V0.38411.374
110_R113_E0.369911.323
38_F56_L0.356781.276
108_F111_F0.354691.269
53_N97_D0.35441.268
85_E98_D0.346441.239
23_D66_D0.338291.210
58_E103_Y0.335771.201
63_R118_R0.330211.181
44_G53_N0.32951.179
51_W55_G0.32921.178
117_G120_K0.31661.133
56_L109_V0.314811.126
99_S103_Y0.310021.109
39_G53_N0.308811.105
63_R122_K0.300931.077
27_R58_E0.299351.071
33_L36_Q0.298311.067
97_D101_A0.296011.059
50_R53_N0.292171.045
69_D73_K0.2911.041
37_W104_Q0.285541.022
39_G47_N0.282621.011
76_I79_G0.280651.004
110_R114_E0.28021.002
66_D69_D0.276670.990
111_F115_K0.275790.987
120_K127_E0.274170.981
40_N53_N0.27370.979
38_F125_L0.272430.975
113_E121_F0.271870.973
47_N53_N0.268330.960
46_D49_P0.25990.930
119_E123_A0.257190.920
38_F42_F0.256070.916
78_S96_E0.249490.893
42_F47_N0.244470.875
116_Y124_F0.244130.873
24_W27_R0.24330.870
83_P86_P0.240650.861
30_A61_E0.238970.855
112_L116_Y0.238940.855
107_L111_F0.237740.851
94_S97_D0.237220.849
51_W87_L0.237170.848
121_F124_F0.233910.837
119_E122_K0.227280.813
75_A81_L0.224710.804
124_F127_E0.224250.802
66_D70_E0.223720.800
120_K124_F0.223570.800
74_Q103_Y0.222430.796
112_L115_K0.221770.793
74_Q78_S0.219090.784
59_Y63_R0.218230.781
76_I85_E0.216420.774
44_G52_F0.215150.770
40_N47_N0.215070.769
36_Q40_N0.214760.768
39_G44_G0.214330.767
70_E74_Q0.212970.762
67_E73_K0.212490.760
24_W28_V0.212230.759
70_E77_E0.211230.756
59_Y110_R0.210710.754
40_N50_R0.210620.754
81_L89_S0.209840.751
39_G43_G0.208440.746
39_G42_F0.208120.745
51_W112_L0.206070.737
65_E127_E0.205710.736
78_S81_L0.205670.736
66_D92_D0.204710.732
39_G104_Q0.203890.729
76_I89_S0.203060.726
86_P89_S0.201070.719
30_A33_L0.200750.718
102_Y105_G0.200420.717
62_G68_F0.198960.712
43_G53_N0.198030.708
50_R97_D0.197830.708
25_L57_A0.197230.706
64_I67_E0.195470.699
66_D74_Q0.195330.699
27_R103_Y0.195310.699
34_A38_F0.195160.698
74_Q95_W0.193820.693
28_V102_Y0.193120.691
45_D49_P0.192860.690
111_F114_E0.192210.688
87_L90_S0.191210.684
33_L37_W0.191080.684
69_D72_L0.190540.682
91_F96_E0.190140.680
72_L76_I0.190080.680
107_L110_R0.189360.677
60_V63_R0.188350.674
49_P88_N0.188280.674
81_L85_E0.184750.661
78_S84_L0.184690.661
71_D103_Y0.184530.660
104_Q116_Y0.184380.660
75_A82_P0.184050.658
69_D123_A0.184030.658
59_Y127_E0.183910.658
114_E118_R0.183050.655
77_E81_L0.183020.655
74_Q99_S0.182850.654
65_E69_D0.182250.652
77_E80_S0.180730.647
78_S83_P0.180420.645
37_W42_F0.17920.641
49_P52_F0.179070.641
100_L104_Q0.177410.635
36_Q57_A0.176160.630
57_A98_D0.173940.622
43_G56_L0.173650.621
35_H55_G0.173640.621
27_R60_V0.173380.620
69_D114_E0.172330.617
40_N43_G0.172060.616
39_G50_R0.171560.614
73_K77_E0.171490.614
30_A110_R0.170480.610
62_G72_L0.170430.610
43_G46_D0.170270.609
59_Y105_G0.170040.608
116_Y121_F0.169710.607
71_D74_Q0.169520.606
68_F73_K0.169490.606
84_L87_L0.168960.604
101_A105_G0.168930.604
68_F71_D0.168570.603
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
3u9wA0.992299.70.198
4fkeA199.70.199
4gaaA0.992299.70.206
2xdtA199.70.208
3se6A199.70.209
3ebhA199.70.215
1z5hA199.70.22
2xq0A0.992299.70.232
3ciaA0.992299.70.232
3b34A199.70.233

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