GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_S11 - D-alanyl-D-alanine carboxypeptidase
Pfam: PF00768 (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: CL0013
Length: 240
Sequences: 8772
Seq/Len: 36.55
HH_delta: 0.147 (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
62_K88_K1.365823.389
61_D113_H1.104972.742
90_T93_D1.052892.613
51_A124_M1.039732.580
50_E128_K1.035942.571
208_L220_L0.974562.418
27_S30_A0.967212.400
31_D155_Y0.959382.381
18_D21_T0.948662.354
48_V110_L0.932692.315
161_A221_V0.927152.301
58_S61_D0.899732.233
128_K131_E0.899432.232
98_L107_A0.890822.211
127_E131_E0.870712.161
43_M160_I0.826312.051
23_K172_I0.819832.034
89_Y103_A0.817812.029
161_A208_L0.809842.010
207_G226_R0.802911.992
17_M158_A0.799421.984
18_D23_K0.793041.968
36_P152_T0.792071.966
115_G124_M0.787661.955
64_T88_K0.780381.937
33_K151_Y0.74861.858
42_L164_A0.739361.835
14_A26_Y0.73891.834
124_M127_E0.722211.792
98_L106_A0.714761.774
65_I103_A0.691741.717
47_V128_K0.682341.693
157_L221_V0.66591.652
126_N130_K0.663271.646
134_M160_I0.655941.628
23_K175_T0.654371.624
15_I158_A0.64881.610
63_V113_H0.648671.610
39_L157_L0.642311.594
29_N32_E0.634811.575
93_D101_P0.630051.564
13_S34_R0.625681.553
39_L221_V0.622541.545
206_D223_T0.614521.525
15_I155_Y0.594671.476
60_D92_R0.589081.462
155_Y159_K0.58331.447
42_L161_A0.577581.433
18_D25_L0.576931.432
159_K168_Y0.57071.416
204_G226_R0.566551.406
89_Y93_D0.556311.381
62_K90_T0.553271.373
45_A99_L0.547571.359
40_T129_A0.54661.356
44_T107_A0.543731.349
38_S41_K0.535881.330
91_V110_L0.523031.298
127_E130_K0.513891.275
93_D100_L0.505521.254
195_N198_L0.504791.253
78_G81_I0.504231.251
46_Y132_L0.493721.225
19_A162_R0.490961.218
42_L221_V0.490041.216
162_R166_K0.487551.210
128_K132_L0.47771.185
42_L99_L0.474811.178
51_A114_I0.474011.176
17_M162_R0.46441.152
111_A125_M0.462841.149
15_I24_I0.458631.138
103_A106_A0.458051.137
15_I27_S0.455641.131
187_R191_L0.454991.129
67_K85_E0.454011.127
43_M129_A0.452921.124
45_A107_A0.451751.121
46_Y163_Y0.450121.117
159_K162_R0.448711.114
31_D136_N0.447871.111
13_S154_A0.447491.110
63_V109_A0.443471.100
102_S209_K0.441971.097
57_L91_V0.441231.095
157_L219_C0.435941.082
163_Y166_K0.43441.078
66_S109_A0.429391.066
154_A158_A0.42851.063
193_N197_L0.427661.061
47_V51_A0.426791.059
152_T157_L0.425811.057
57_L61_D0.424311.053
201_Y205_V0.423981.052
59_L92_R0.423291.050
66_S112_E0.421961.047
46_Y128_K0.419531.041
38_S209_K0.415391.031
132_L163_Y0.414591.029
57_L113_H0.412321.023
50_E131_E0.411781.022
207_G223_T0.410421.018
33_K136_N0.409511.016
138_H151_Y0.408251.013
38_S102_S0.404091.003
124_M128_K0.403331.001
168_Y171_E0.402080.998
102_S210_T0.398720.989
48_V91_V0.392090.973
137_T152_T0.387540.962
47_V114_I0.387160.961
165_L223_T0.386770.960
109_A113_H0.386160.958
17_M24_I0.385350.956
84_K87_E0.384790.955
47_V125_M0.381910.948
98_L110_L0.379040.941
51_A57_L0.378240.939
69_A112_E0.37710.936
165_L207_G0.37670.935
66_S69_A0.374540.929
135_T156_D0.374340.929
40_T150_H0.37050.919
65_I109_A0.370120.918
186_G190_N0.36840.914
17_M22_G0.367840.913
125_M129_A0.367780.913
47_V50_E0.364110.904
22_G162_R0.36190.898
45_A98_L0.360750.895
67_K71_S0.360220.894
51_A128_K0.358130.889
114_I124_M0.357390.887
14_A28_K0.355480.882
153_T156_D0.351090.871
65_I87_E0.350370.869
146_D215_E0.349630.868
182_F186_G0.348580.865
159_K163_Y0.346930.861
186_G189_Y0.34540.857
157_L160_I0.344480.855
15_I30_A0.343240.852
78_G82_G0.342750.851
108_Y112_E0.339690.843
201_Y204_G0.33920.842
68_E112_E0.338750.841
19_A165_L0.337980.839
163_Y167_N0.33510.832
41_K104_N0.334650.830
65_I89_Y0.332310.825
191_L194_T0.326890.811
81_I103_A0.326830.811
35_P215_E0.324520.805
213_T216_A0.323680.803
30_A155_Y0.32290.801
172_I175_T0.321150.797
134_M152_T0.32070.796
169_P173_V0.320190.795
46_Y167_N0.31940.793
91_V106_A0.315210.782
15_I154_A0.313520.778
171_E174_I0.310430.770
152_T156_D0.308780.766
48_V57_L0.307340.763
140_V150_H0.304850.757
134_M159_K0.304290.755
44_T125_M0.301250.748
39_L219_C0.300060.745
104_N108_Y0.299880.744
35_P146_D0.299780.744
65_I68_E0.296870.737
212_Y218_Y0.295410.733
16_V19_A0.294670.731
57_L63_V0.294450.731
27_S155_Y0.294050.730
163_Y168_Y0.287520.713
80_T83_L0.284950.707
117_S127_E0.28440.706
40_T44_T0.284140.705
129_A134_M0.2840.705
60_D90_T0.283870.704
64_T109_A0.282680.701
129_A132_L0.282460.701
80_T84_K0.281840.699
44_T111_A0.280990.697
43_M157_L0.279720.694
174_I177_S0.278920.692
109_A112_E0.278410.691
158_A221_V0.277290.688
24_I155_Y0.274450.681
63_V106_A0.274420.681
194_T197_L0.271910.675
41_K102_S0.271450.674
24_I27_S0.270910.672
114_I125_M0.270690.672
89_Y101_P0.269910.670
36_P157_L0.269870.670
83_L86_G0.269430.669
188_T192_K0.267760.664
105_D109_A0.266590.662
43_M137_T0.266590.662
205_V222_G0.266260.661
117_S124_M0.265710.659
42_L208_L0.264750.657
138_H141_N0.264720.657
37_A213_T0.263180.653
180_F186_G0.26140.649
191_L195_N0.259940.645
143_H146_D0.259290.643
193_N196_K0.257420.639
107_A110_L0.256720.637
48_V98_L0.256280.636
90_T106_A0.254740.632
65_I86_G0.254070.630
82_G85_E0.252420.626
43_M125_M0.250730.622
19_A166_K0.250260.621
43_M132_L0.249770.620
35_P147_D0.249440.619
190_N193_N0.249370.619
72_I108_Y0.248130.616
140_V147_D0.247960.615
38_S210_T0.246460.612
187_R190_N0.246180.611
27_S173_V0.244730.607
39_L42_L0.244530.607
140_V149_N0.24450.607
161_A164_A0.244080.606
126_N139_F0.243930.605
130_K135_T0.243680.605
47_V124_M0.242950.603
79_S83_L0.242280.601
188_T191_L0.241860.600
70_A112_E0.240580.597
57_L110_L0.239930.595
189_Y193_N0.238560.592
182_F190_N0.238340.591
171_E175_T0.238220.591
206_D224_A0.237330.589
42_L160_I0.237240.589
179_T190_N0.236850.588
137_T153_T0.23680.588
130_K136_N0.236080.586
38_S211_G0.23580.585
208_L223_T0.235250.584
189_Y192_K0.235070.583
175_T178_Y0.234820.583
137_T156_D0.234330.582
136_N156_D0.234320.581
35_P213_T0.234060.581
129_A139_F0.233460.579
12_K34_R0.232480.577
158_A162_R0.23210.576
73_S78_G0.232060.576
165_L225_K0.231310.574
128_K163_Y0.231060.573
35_P217_G0.229680.570
194_T198_L0.229620.570
181_T188_T0.228730.568
86_G103_A0.228720.568
144_G149_N0.22810.566
65_I83_L0.225910.561
134_M157_L0.225670.560
13_S32_E0.225430.559
34_R219_C0.225120.559
178_Y181_T0.22460.557
157_L161_A0.222640.552
173_V208_L0.222610.552
102_S211_G0.222370.552
135_T155_Y0.221960.551
173_V176_K0.220040.546
17_M155_Y0.219340.544
29_N217_G0.219190.544
45_A91_V0.218840.543
166_K169_P0.21810.541
36_P40_T0.217250.539
170_R174_I0.216740.538
132_L160_I0.216630.538
20_D166_K0.215890.536
170_R173_V0.215730.535
66_S87_E0.215560.535
33_K156_D0.215430.535
35_P219_C0.214160.531
209_K212_Y0.214120.531
159_K171_E0.213130.529
46_Y164_A0.212620.528
193_N198_L0.212130.526
141_N146_D0.211350.524
142_P145_L0.211060.524
198_L218_Y0.210550.522
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
3itaA0.98331000.147
3mzfA0.98331000.148
3hunA0.9751000.175
3a3jA0.96251000.176
1xp4A0.96671000.181
3mfdA0.93331000.192
1tvfA0.9751000.197
1es5A0.97081000.208
2bcfA0.94581000.223
4dxbA0.94171000.312

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