GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_M48 - Peptidase family M48
Pfam: PF01435 (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: 226
Sequences: 3953
Seq/Len: 17.49
HH_delta: 0.169 (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
98_G168_Y0.832263.811
57_D78_S0.741113.394
94_A169_A0.676113.096
76_V93_L0.629922.885
39_E90_A0.615712.820
212_S222_E0.598442.741
32_E86_E0.563972.583
163_Y222_E0.563072.579
37_V53_V0.512042.345
167_R171_R0.483432.214
84_L195_K0.482052.208
222_E225_A0.469892.152
88_E195_K0.45392.079
38_E42_R0.427811.959
34_R38_E0.42741.957
40_L97_L0.418861.918
27_P38_E0.410321.879
104_H164_E0.404081.851
88_E191_S0.394241.805
34_R50_P0.3881.777
36_I90_A0.382661.752
85_S88_E0.372661.707
103_R106_L0.361441.655
64_F75_V0.355761.629
151_Q155_N0.355171.627
56_I75_V0.351951.612
95_H162_E0.341421.564
32_E36_I0.338751.551
32_E35_R0.337551.546
44_A172_L0.334911.534
76_V89_L0.333771.529
102_H168_Y0.331851.520
65_A100_I0.329111.507
99_H162_E0.32311.480
221_E225_A0.317851.456
33_L76_V0.315691.446
219_S222_E0.314651.441
104_H161_Q0.314581.441
36_I86_E0.310611.422
31_P34_R0.310451.422
184_Y224_I0.301931.383
168_Y172_L0.287421.316
31_P35_R0.28621.311
37_V41_A0.285231.306
76_V80_L0.281821.291
84_L88_E0.276181.265
95_H99_H0.271261.242
108_S161_Q0.269141.233
35_R38_E0.269121.232
65_A75_V0.263361.206
101_K168_Y0.262011.200
35_R39_E0.261151.196
96_E217_H0.259861.190
160_R163_Y0.258321.183
59_P82_E0.257891.181
122_L125_L0.256291.174
156_A159_R0.255041.168
218_P223_R0.253031.159
101_K172_L0.250491.147
114_L118_L0.248151.136
81_L89_L0.247881.135
91_A179_L0.247021.131
215_S219_S0.246621.129
39_E43_R0.243631.116
76_V81_L0.242471.110
107_K164_E0.241211.105
98_G101_K0.240731.102
80_L92_V0.238771.093
115_L150_F0.237561.088
203_R207_D0.237291.087
155_N215_S0.236251.082
40_L172_L0.236241.082
155_N216_T0.236221.082
88_E185_K0.234071.072
171_R181_R0.233361.069
52_R70_P0.232831.066
27_P35_R0.232641.065
184_Y188_A0.23221.063
95_H217_H0.231321.059
39_E86_E0.230531.056
108_S111_I0.230181.054
30_D34_R0.229681.052
91_A189_A0.228331.046
38_E50_P0.226321.036
160_R164_E0.224741.029
39_E42_R0.221741.015
65_A74_I0.221281.013
191_S195_K0.220171.008
30_D55_V0.219811.007
66_T105_I0.218861.002
164_E168_Y0.218311.000
96_E162_E0.215010.985
102_H164_E0.213390.977
67_G105_I0.212910.975
124_A128_G0.211740.970
41_A53_V0.21120.967
97_L100_I0.210650.965
220_T224_I0.210250.963
62_N77_T0.209450.959
60_S77_T0.208020.953
187_A191_S0.206260.945
131_S135_A0.204850.938
191_S194_E0.204770.938
162_E217_H0.204060.935
80_L84_L0.203090.930
107_K161_Q0.199590.914
66_T75_V0.199390.913
98_G102_H0.197380.904
74_I93_L0.196440.900
27_P31_P0.195690.896
62_N96_E0.195180.894
195_K198_E0.194220.889
84_L183_L0.193870.888
61_P83_S0.193860.888
190_I224_I0.19150.877
96_E99_H0.191150.875
108_S154_T0.188420.863
158_S216_T0.187510.859
83_S189_A0.18710.857
61_P77_T0.186670.855
53_V74_I0.186510.854
62_N217_H0.18630.853
153_L157_F0.186250.853
63_A217_H0.185350.849
84_L186_P0.185130.848
148_F151_Q0.18510.848
182_A186_P0.184770.846
98_G172_L0.18410.843
87_D188_A0.184040.843
41_A49_P0.183310.839
194_E198_E0.183120.839
187_A220_T0.18240.835
63_A80_L0.181540.831
124_A127_I0.181530.831
97_L101_K0.181190.830
33_L37_V0.180620.827
181_R184_Y0.180330.826
56_I77_T0.179910.824
156_A160_R0.179250.821
85_S188_A0.178850.819
211_S214_F0.177790.814
104_H107_K0.176650.809
28_L31_P0.175810.805
126_L129_S0.175370.803
127_I143_G0.174120.797
32_E37_V0.173630.795
203_R206_S0.173420.794
211_S215_S0.173340.794
59_P78_S0.172620.791
111_I160_R0.172020.788
193_L196_L0.170410.780
91_A172_L0.170190.779
148_F214_F0.170070.779
105_I109_L0.16980.778
162_E165_A0.169540.776
39_E171_R0.169530.776
189_A193_L0.16950.776
185_K188_A0.169470.776
158_S161_Q0.169440.776
36_I39_E0.168940.774
110_L114_L0.167320.766
58_S77_T0.166750.764
36_I44_A0.16650.763
35_R86_E0.166250.761
30_D36_I0.165690.759
48_I101_K0.165590.758
163_Y167_R0.16430.752
30_D44_A0.162550.744
50_P53_V0.162370.744
131_S203_R0.162270.743
169_A180_A0.161780.741
129_S132_L0.161590.740
61_P79_G0.16120.738
30_D37_V0.161150.738
166_D223_R0.16110.738
40_L93_L0.160460.735
82_E196_L0.159640.731
131_S134_S0.159540.731
87_D90_A0.159470.730
41_A44_A0.158360.725
150_F155_N0.157690.722
88_E188_A0.157330.721
97_L170_A0.157090.719
187_A221_E0.157040.719
83_S192_A0.156890.719
74_I169_A0.156760.718
130_M134_S0.155710.713
36_I40_L0.155260.711
36_I43_R0.155040.710
31_P49_P0.154630.708
37_V54_Y0.153690.704
62_N95_H0.153460.703
161_Q164_E0.153150.701
158_S165_A0.153110.701
188_A193_L0.152850.700
147_A150_F0.15230.697
212_S215_S0.152130.697
181_R185_K0.151220.693
217_H223_R0.151070.692
86_E90_A0.150650.690
40_L89_L0.150370.689
204_P207_D0.150260.688
111_I115_L0.150160.688
62_N92_V0.150050.687
164_E167_R0.149990.687
111_I154_T0.149970.687
58_S61_P0.149380.684
85_S185_K0.149230.683
62_N158_S0.149040.683
212_S219_S0.148950.682
65_A77_T0.147260.674
187_A190_I0.147220.674
192_A196_L0.146550.671
37_V44_A0.146380.670
119_F153_L0.146260.670
194_E207_D0.14580.668
83_S89_L0.145080.664
29_E32_E0.144910.664
106_L110_L0.144850.663
114_L119_F0.144420.661
30_D33_L0.144120.660
40_L44_A0.143690.658
197_A221_E0.143210.656
51_P100_I0.143210.656
128_G137_G0.142580.653
63_A92_V0.142540.653
116_S120_F0.142510.653
111_I150_F0.141830.650
163_Y219_S0.141650.649
29_E34_R0.141540.648
77_T193_L0.141440.648
92_V217_H0.140790.645
122_L144_I0.140410.643
211_S221_E0.139940.641
108_S158_S0.139290.638
155_N158_S0.139250.638
126_L131_S0.138780.636
194_E206_S0.138680.635
64_F100_I0.13830.633
53_V76_V0.138010.632
116_S119_F0.137860.631
115_L154_T0.137770.631
168_Y193_L0.136890.627
169_A179_L0.136840.627
70_P100_I0.136620.626
37_V93_L0.136410.625
48_I97_L0.135950.623
92_V192_A0.135770.622
82_E192_A0.135730.622
37_V40_L0.135670.621
55_V81_L0.135460.620
63_A95_H0.135180.619
28_L34_R0.134650.617
143_G147_A0.13440.616
169_A182_A0.134290.615
109_L113_L0.134120.614
91_A169_A0.134080.614
127_I135_A0.133970.614
180_A186_P0.133930.613
69_G164_E0.133740.612
36_I89_L0.133330.611
132_L135_A0.133270.610
89_L93_L0.131770.603
209_R212_S0.131770.603
133_F147_A0.131670.603
112_S147_A0.13140.602
169_A189_A0.131130.601
78_S82_E0.131090.600
92_V96_E0.130840.599
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
4aw6A0.94251000.169
4il3A0.94251000.207
3c37A0.89821000.297
3cqbA0.442599.70.592
3dteA0.783296.60.858
4jiuA0.4513950.877
4jixA0.477994.80.878
2xdtA0.876164.20.919
4fkeA0.893846.20.927
2gtqA0.911544.10.928

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