GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PS_Dcarbxylase - Phosphatidylserine decarboxylase
Pfam: PF02666 (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. )
Length: 202
Sequences: 1749
Seq/Len: 8.66
HH_delta: 0.78 (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
93_E128_E0.559563.376
89_D160_K0.5483.307
27_A84_N0.485532.930
29_G74_I0.474282.862
25_S194_V0.461112.782
160_K163_E0.448272.705
68_G180_K0.420692.539
154_K157_D0.379692.291
148_V169_R0.361942.184
91_R158_E0.359392.169
90_G127_I0.349072.106
189_K192_Q0.329591.989
91_R128_E0.328981.985
88_V134_V0.321331.939
23_I88_V0.314571.898
80_D193_K0.314091.895
97_Y121_E0.304721.839
136_V165_L0.292281.764
133_K179_P0.269991.629
19_D22_A0.268621.621
128_E133_K0.266721.609
36_E70_T0.2651.599
25_S74_I0.260211.570
14_R28_D0.257961.557
11_D164_E0.257381.553
24_V161_K0.25031.510
86_A159_V0.248371.499
17_P22_A0.246511.487
83_R164_E0.244191.473
9_F13_A0.241191.455
16_I161_K0.239831.447
195_R198_E0.239351.444
17_P24_V0.237671.434
139_V173_T0.226521.367
104_P107_P0.224071.352
92_V127_I0.218491.318
39_E67_Q0.21641.306
9_F12_P0.216211.305
151_V159_V0.215241.299
93_E133_K0.213441.288
102_L145_G0.212231.281
98_I124_V0.211941.279
16_I162_G0.211581.277
36_E68_G0.208531.258
27_A196_A0.207161.250
179_P182_K0.206581.247
129_T134_V0.204311.233
150_T167_Y0.204241.232
86_A165_L0.202661.223
9_F170_F0.202211.220
16_I24_V0.198961.201
95_V123_V0.194741.175
34_I190_P0.194261.172
81_Y85_H0.19421.172
73_V173_T0.193691.169
123_V149_L0.192821.164
94_E126_V0.191951.158
94_E155_E0.191581.156
88_V127_I0.189511.144
86_A151_V0.189091.141
148_V167_Y0.188951.140
101_K119_E0.188161.135
76_L82_H0.187621.132
126_V135_A0.187381.131
124_V137_V0.185411.119
176_L201_G0.184811.115
25_S200_I0.182931.104
84_N138_Q0.182641.102
27_A74_I0.181361.094
82_H172_S0.181171.093
143_L170_F0.179051.080
18_D24_V0.178611.078
58_D157_D0.178491.077
89_D130_K0.178341.076
99_P121_E0.177831.073
136_V176_L0.17661.066
20_P130_K0.175711.060
151_V157_D0.171711.036
31_V194_V0.171421.034
4_F7_R0.170421.028
6_T167_Y0.169941.025
75_Y141_A0.169161.021
66_F69_G0.168641.018
84_N166_G0.168171.015
76_L196_A0.167521.011
188_V192_Q0.165150.997
95_V154_K0.16490.995
105_V144_V0.16480.994
84_N174_V0.162690.982
105_V141_A0.162180.979
147_I171_G0.160240.967
19_D187_S0.158780.958
75_Y78_P0.157760.952
127_I134_V0.157250.949
120_N141_A0.156140.942
21_D130_K0.155860.940
151_V163_E0.15520.936
122_R137_V0.154790.934
37_I177_L0.154660.933
149_L165_L0.154570.933
17_P199_T0.153260.925
86_A127_I0.1530.923
70_T186_W0.151810.916
92_V125_L0.151580.915
70_T180_K0.15130.913
75_Y105_V0.151260.913
35_G71_F0.148610.897
55_L137_V0.147920.893
30_K80_D0.147880.892
129_T132_G0.147790.892
17_P20_P0.147230.888
154_K158_E0.146520.884
2_N6_T0.144680.873
74_I194_V0.144220.870
84_N165_L0.144080.869
168_F172_S0.144060.869
38_E68_G0.14380.868
8_F167_Y0.143470.866
17_P161_K0.143420.865
87_P136_V0.143190.864
23_I134_V0.142750.861
38_E189_K0.14250.860
127_I136_V0.142120.858
95_V149_L0.14160.854
34_I192_Q0.141150.852
27_A174_V0.140370.847
137_V177_L0.140310.847
76_L168_F0.139920.844
70_T181_D0.139870.844
31_V72_I0.138960.839
120_N147_I0.138240.834
92_V159_V0.138160.834
144_V168_F0.138020.833
55_L71_F0.137620.830
100_G145_G0.136980.827
26_P74_I0.136360.823
141_A145_G0.136160.822
86_A89_D0.136120.821
23_I188_V0.136020.821
196_A201_G0.135680.819
102_L140_G0.135650.819
76_L174_V0.13540.817
77_S80_D0.135380.817
78_P85_H0.134790.813
104_P109_A0.134740.813
19_D89_D0.133990.809
134_V178_F0.133820.807
71_F177_L0.133820.807
76_L81_Y0.133220.804
58_D154_K0.132870.802
30_K110_L0.132310.798
85_H196_A0.131480.793
76_L172_S0.131290.792
2_N169_R0.130550.788
73_V175_V0.130430.787
24_V188_V0.130190.786
4_F79_F0.129190.780
7_R81_Y0.129180.779
181_D186_W0.127850.771
141_A144_V0.127620.770
56_L69_G0.127340.768
18_D155_E0.126330.762
19_D199_T0.126130.761
90_G134_V0.125890.760
138_Q165_L0.125670.758
83_R167_Y0.125610.758
39_E56_L0.125490.757
156_G159_V0.125140.755
92_V151_V0.12510.755
32_L104_P0.124740.753
26_P176_L0.124680.752
76_L150_T0.124430.751
138_Q149_L0.123850.747
125_L149_L0.122360.738
26_P177_L0.122020.736
186_W190_P0.121990.736
110_L170_F0.12190.736
69_G180_K0.121450.733
108_P111_S0.119990.724
147_I175_V0.119830.723
52_L193_K0.119750.723
53_R91_R0.119160.719
76_L80_D0.118460.715
26_P31_V0.118130.713
76_L140_G0.117970.712
98_I122_R0.117360.708
122_R171_G0.117210.707
9_F85_H0.116960.706
92_V128_E0.116780.705
139_V196_A0.116530.703
176_L200_I0.116260.702
66_F135_A0.116250.701
82_H168_F0.116210.701
75_Y82_H0.115820.699
123_V146_S0.115780.699
186_W189_K0.115620.698
100_G166_G0.115570.697
141_A173_T0.115320.696
4_F143_L0.115250.695
151_V165_L0.114750.692
82_H139_V0.114460.691
140_G168_F0.113830.687
67_Q180_K0.113770.687
156_G178_F0.113470.685
107_P142_L0.113430.684
82_H144_V0.11310.682
187_S200_I0.112940.681
13_A164_E0.11290.681
36_E180_K0.112660.680
187_S193_K0.11250.679
30_K109_A0.112470.679
125_L136_V0.112420.678
85_H197_G0.112330.678
37_I71_F0.111440.672
105_V120_N0.111390.672
84_N149_L0.111340.672
1_F4_F0.11110.670
75_Y138_Q0.11090.669
52_L55_L0.11070.668
81_Y174_V0.110630.668
186_W192_Q0.110480.667
96_R139_V0.110390.666
3_D6_T0.110120.664
72_I193_K0.110030.664
102_L121_E0.109860.663
25_S142_L0.109630.662
8_F11_D0.109510.661
125_L138_Q0.10950.661
7_R83_R0.109430.660
195_R199_T0.109160.659
18_D180_K0.109110.658
105_V173_T0.108950.657
34_I187_S0.108880.657
155_E199_T0.108860.657
96_R99_P0.108730.656
83_R168_F0.108660.656
55_L175_V0.108640.656
8_F12_P0.108470.655
131_F187_S0.108450.654
106_N142_L0.108330.654
91_R160_K0.108240.653
1_F5_F0.10820.653
33_V37_I0.107350.648
88_V131_F0.10720.647
88_V201_G0.107150.647
185_E199_T0.107120.646
140_G146_S0.1070.646
7_R161_K0.106970.645
157_D181_D0.106840.645
125_L151_V0.106650.644
91_R156_G0.106620.643
96_R126_V0.106330.642
4_F164_E0.106210.641
72_I175_V0.106180.641
95_V151_V0.105940.639
58_D155_E0.105840.639
84_N136_V0.105750.638
123_V138_Q0.105350.636
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
2gprA0.693199.10.78
1ax3A0.717899.10.785
1f3zA0.69898.90.805
3ourB0.747597.70.868
2gprA0.534795.60.903
1ax3A0.564495.30.906
1z6hA0.316892.40.917
1bdoA0.336690.80.92
2dn8A0.405989.60.922
2xhaA0.638685.90.927
If you are interested in a protein containing this domain,
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