GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Capsule_synth - Capsule polysaccharide biosynthesis protein
Pfam: PF05159 (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: CL0113
Length: 269
Sequences: 2488
Seq/Len: 9.25
HH_delta: 0.545 (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
2_A28_I0.429363.018
12_Y52_I0.361142.538
67_L71_L0.360912.537
64_P68_E0.349962.460
68_E72_N0.34122.398
3_V20_A0.327582.302
54_P66_D0.320352.252
157_K185_V0.306772.156
122_V146_L0.295252.075
150_A183_N0.292092.053
119_Y199_Q0.287362.020
119_Y200_S0.286732.015
120_V202_A0.281221.977
118_K155_D0.279481.964
5_V27_V0.271061.905
122_V158_L0.267971.883
167_R171_K0.266581.874
4_V28_I0.263321.851
28_I60_D0.252481.775
118_K201_D0.249851.756
78_D81_E0.249491.754
53_D59_A0.239831.686
193_L210_V0.237661.670
6_W12_Y0.23561.656
65_S68_E0.234611.649
197_L219_K0.232451.634
148_S152_E0.228311.605
204_V224_F0.22351.571
118_K156_A0.222861.566
81_E86_Y0.221941.560
13_H51_T0.218131.533
63_L66_D0.217441.528
197_L203_V0.209631.473
82_H86_Y0.208591.466
203_V214_A0.208321.464
68_E71_L0.204471.437
156_A201_D0.202881.426
148_S151_K0.202751.425
120_V158_L0.200121.407
159_V196_L0.198221.393
64_P67_L0.196961.384
119_Y201_D0.195561.374
61_S70_L0.195381.373
2_A58_N0.194211.365
2_A26_P0.193311.359
202_A222_I0.192451.353
200_S219_K0.188391.324
144_D147_E0.187941.321
197_L200_S0.186791.313
81_E85_A0.184811.299
169_G172_Y0.183811.292
120_V204_V0.183191.288
108_L111_L0.18251.283
124_L160_V0.180531.269
147_E151_K0.179571.262
203_V219_K0.177751.249
162_P167_R0.177551.248
168_G172_Y0.177191.245
118_K157_K0.174211.224
140_A144_D0.173541.220
208_S225_G0.173371.219
96_R198_E0.173271.218
50_L54_P0.17311.217
31_E164_P0.172921.215
20_A27_V0.168941.187
108_L112_L0.167891.180
36_R40_L0.167711.179
117_K157_K0.166281.169
55_Q66_D0.164861.159
198_E217_H0.164111.153
87_Y212_L0.162011.139
55_Q69_Q0.161951.138
197_L214_A0.161911.138
50_L205_T0.160451.128
146_L158_L0.160061.125
121_L146_L0.159621.122
162_P170_N0.159591.122
61_S66_D0.159451.121
107_K111_L0.158911.117
146_L150_A0.158131.111
31_E163_H0.158081.111
30_F60_D0.157491.107
115_K118_K0.154921.089
194_Y217_H0.154641.087
6_W212_L0.153661.080
83_D86_Y0.152861.074
197_L210_V0.152571.072
149_F204_V0.152161.069
82_H85_A0.151231.063
142_F145_M0.149851.053
3_V24_G0.147951.040
39_G43_D0.14791.040
187_I190_D0.146861.032
150_A181_L0.146541.030
46_P49_S0.146341.029
120_V156_A0.145551.023
139_Q142_F0.145071.020
84_R87_Y0.144391.015
97_I194_Y0.143481.008
125_Q208_S0.142621.002
41_G47_P0.142221.000
215_L221_V0.141220.993
139_Q145_M0.140890.990
40_L43_D0.140860.990
5_V12_Y0.140250.986
219_K223_V0.139840.983
54_P77_L0.139720.982
31_E87_Y0.139710.982
53_D70_L0.139120.978
6_W62_S0.137640.967
157_K186_I0.137220.964
155_D183_N0.136010.956
168_G171_K0.135990.956
143_L186_I0.135870.955
167_R188_D0.135810.955
123_P203_V0.135740.954
106_S110_S0.135610.953
116_N199_Q0.135580.953
88_L91_R0.135380.952
40_L47_P0.135330.951
144_D148_S0.134220.943
141_D144_D0.133670.940
143_L147_E0.133320.937
31_E212_L0.13320.936
175_L209_T0.133180.936
82_H87_Y0.132820.934
195_E199_Q0.132380.930
87_Y90_S0.131370.923
147_E180_N0.131240.922
8_D29_F0.131050.921
139_Q143_L0.130490.917
32_D61_S0.130420.917
167_R170_N0.130340.916
126_V208_S0.130060.914
69_Q72_N0.129990.914
195_E198_E0.129820.912
72_N78_D0.128790.905
143_L150_A0.128160.901
119_Y156_A0.12810.900
6_W31_E0.128050.900
27_V55_Q0.127270.895
120_V166_E0.127070.893
107_K110_S0.126630.890
122_V149_F0.126560.890
45_Y48_D0.126440.889
72_N151_K0.125880.885
64_P71_L0.125670.883
121_L197_L0.124830.877
147_E181_L0.124590.876
29_F55_Q0.1240.872
214_A221_V0.123240.866
117_K155_D0.122010.858
40_L57_V0.121960.857
205_T214_A0.121920.857
98_S101_N0.121470.854
111_L114_S0.121450.854
56_G59_A0.12140.853
208_S212_L0.121310.853
89_I92_I0.121190.852
26_P56_G0.120190.845
85_A88_L0.118920.836
106_S147_E0.117930.829
120_V221_V0.117910.829
71_L82_H0.117840.828
20_A25_I0.117480.826
61_S87_Y0.117410.825
26_P58_N0.117090.823
191_V195_E0.116860.821
124_L224_F0.11680.821
162_P186_I0.11650.819
31_E125_Q0.116290.817
78_D110_S0.116210.817
159_V200_S0.116110.816
67_L84_R0.115950.815
8_D33_G0.115580.812
5_V170_N0.115110.809
86_Y89_I0.115080.809
163_H167_R0.114630.806
193_L197_L0.114350.804
203_V210_V0.114320.804
62_S88_L0.113970.801
122_V139_Q0.113760.800
6_W9_K0.113650.799
85_A90_S0.113320.796
110_S116_N0.112780.793
145_M148_S0.112460.790
128_N169_G0.112370.790
198_E219_K0.111660.785
19_V23_L0.111580.784
105_F111_L0.111450.783
155_D172_Y0.110860.779
53_D56_G0.110840.779
124_L142_F0.11080.779
116_N152_E0.110760.778
70_L73_E0.110720.778
125_Q129_D0.110170.774
37_S105_F0.109830.772
26_P57_V0.109690.771
151_K178_L0.109420.769
8_D207_N0.109410.769
81_E87_Y0.109310.768
108_L185_V0.108970.766
153_N202_A0.108880.765
18_E22_E0.108460.762
37_S40_L0.108310.761
60_D83_D0.108310.761
123_P210_V0.108190.760
201_D219_K0.107980.759
7_G31_E0.107460.755
141_D145_M0.107310.754
30_F52_I0.106970.752
212_L215_L0.10690.751
49_S53_D0.106580.749
61_S67_L0.106490.748
174_Y209_T0.106460.748
150_A184_V0.106130.746
78_D82_H0.106070.746
126_V206_I0.10590.744
137_P141_D0.105750.743
31_E129_D0.105720.743
160_V166_E0.105580.742
101_N198_E0.105360.741
129_D225_G0.105180.739
161_K188_D0.105140.739
163_H171_K0.105140.739
125_Q207_N0.105090.739
106_S192_N0.104710.736
8_D13_H0.104710.736
189_D192_N0.104560.735
32_D59_A0.104490.734
119_Y219_K0.103950.731
69_Q86_Y0.103930.730
186_I226_R0.103830.730
72_N117_K0.103350.726
82_H110_S0.103290.726
204_V222_I0.103180.725
174_Y178_L0.103170.725
92_I159_V0.102950.724
119_Y187_I0.102760.722
129_D211_G0.102650.721
6_W193_L0.102560.721
110_S182_P0.102530.721
88_L97_I0.102390.720
120_V149_F0.102320.719
215_L223_V0.102260.719
109_I115_K0.102220.718
23_L152_E0.102170.718
80_A83_D0.101930.716
29_F70_L0.101920.716
147_E150_A0.101850.716
124_L139_Q0.101790.715
73_E146_L0.101380.713
119_Y159_V0.101190.711
151_K182_P0.101120.711
208_S211_G0.100820.709
47_P184_V0.100290.705
47_P215_L0.100040.703
29_F125_Q0.099890.702
44_G49_S0.099640.700
37_S145_M0.099630.700
67_L83_D0.099560.700
115_K144_D0.099550.700
67_L79_D0.099540.700
6_W215_L0.099490.699
140_A148_S0.099450.699
29_F49_S0.099340.698
141_D151_K0.099330.698
77_L82_H0.099310.698
99_K144_D0.099210.697
64_P84_R0.099160.697
141_D148_S0.099120.697
32_D49_S0.099050.696
64_P173_S0.099040.696
206_I225_G0.098690.694
18_E21_K0.098670.694
212_L225_G0.098560.693
33_G49_S0.098560.693
138_S141_D0.098210.690
137_P145_M0.097770.687
192_N200_S0.09770.687
76_F190_D0.09770.687
48_D51_T0.097680.687
31_E126_V0.097650.686
197_L217_H0.09730.684
9_K126_V0.097160.683
122_V224_F0.097130.683
106_S154_P0.097110.683
61_S98_S0.097060.682
188_D226_R0.097030.682
176_E186_I0.096770.680
147_E171_K0.096450.678
68_E144_D0.096090.675
129_D163_H0.095930.674
125_Q206_I0.095850.674
94_K98_S0.095720.673
121_L200_S0.095720.673
76_F86_Y0.095690.673
31_E36_R0.095620.672
129_D208_S0.09540.671
7_G121_L0.095310.670
175_L186_I0.095230.669
109_I112_L0.095180.669
77_L81_E0.095030.668
62_S209_T0.094970.667
105_F109_I0.094850.667
54_P195_E0.094770.666
45_Y70_L0.094630.665
10_R21_K0.094530.664
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
4hwgA0.918299.90.545
3ot5A0.907199.90.571
3dzcA0.925799.80.582
4fkzA0.903399.80.617
3beoA0.929499.40.707
1v4vA0.888599.40.71
1vgvA0.951799.40.716
3okpA0.9257990.766
3c48A0.9405990.772
2gekA0.895998.90.781
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