GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PNP_UDP_1 - Phosphorylase superfamily
Pfam: PF01048 (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: CL0408
Length: 234
Sequences: 5329
Seq/Len: 22.77
HH_delta: 0.098 (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
125_D190_P1.147544.004
133_K145_E0.946213.302
149_A170_A0.818512.856
87_K90_D0.769082.684
38_K43_N0.755472.636
92_V172_A0.752332.625
132_L192_I0.707372.468
72_L190_P0.689312.405
90_D144_H0.637862.226
164_L168_F0.632592.207
83_D171_D0.629512.197
79_C197_I0.611042.132
95_Q145_E0.609082.125
184_A191_F0.581872.030
65_L189_I0.570451.991
172_A197_I0.557961.947
36_T45_V0.550261.920
2_I72_L0.543661.897
127_D190_P0.538571.879
86_I144_H0.531221.854
163_E167_K0.527361.840
130_E134_E0.526471.837
177_S193_A0.511731.786
96_D123_P0.51091.783
130_E133_K0.508741.775
53_P152_D0.502181.752
20_L23_T0.493341.722
129_R145_E0.480011.675
38_K41_G0.472311.648
149_A165_L0.469521.638
128_L192_I0.461091.609
93_I143_V0.456211.592
93_I129_R0.454361.586
62_Q187_R0.434231.515
96_D147_P0.432841.510
133_K137_K0.427751.493
63_R66_E0.42061.468
151_G165_L0.417611.457
160_A163_E0.412451.439
79_C172_A0.407521.422
22_E38_K0.40531.414
136_A143_V0.402181.403
34_Y45_V0.395131.379
59_I183_A0.389941.361
73_V184_A0.387171.351
135_A139_L0.383221.337
94_P148_I0.381871.333
127_D130_E0.3811.330
92_V197_I0.364661.272
148_I172_A0.360621.258
33_T48_S0.359081.253
13_E17_D0.358791.252
3_G70_P0.355751.241
100_Y151_G0.352811.231
2_I42_K0.352271.229
63_R67_E0.351771.228
101_D150_S0.350521.223
174_D177_S0.348261.215
72_L128_L0.347781.214
81_G200_Y0.347381.212
93_I133_K0.345681.206
83_D86_I0.344691.203
4_I15_L0.342871.196
146_G171_D0.341581.192
61_T73_V0.341331.191
73_V189_I0.339731.185
9_P48_S0.339551.185
126_P130_E0.338261.180
200_Y203_G0.337861.179
129_R133_K0.335431.170
66_E187_R0.33151.157
122_A181_A0.329571.150
77_G195_R0.32911.148
82_L173_V0.328811.147
81_G197_I0.328651.147
134_E137_K0.327551.143
3_G64_L0.325821.137
25_Y28_E0.322811.126
53_P179_A0.322271.125
79_C195_R0.322141.124
84_P166_Q0.321881.123
6_C12_A0.321711.123
148_I174_D0.319441.115
85_D144_H0.317491.108
114_P117_P0.313721.095
97_A177_S0.31361.094
62_Q66_E0.304991.064
162_I202_D0.300371.048
5_I73_V0.29971.046
54_V152_D0.297091.037
98_I170_A0.296711.035
5_I49_T0.294741.029
133_K143_V0.29391.026
126_P129_R0.293521.024
87_K200_Y0.293071.023
91_V196_G0.292931.022
92_V171_D0.292891.022
81_G86_I0.290341.013
96_D121_P0.285850.997
135_A138_A0.285770.997
97_A193_A0.284290.992
12_A46_I0.281060.981
121_P126_P0.280650.979
131_A135_A0.277470.968
12_A35_Y0.277340.968
134_E138_A0.27720.967
7_A75_M0.275140.960
26_F47_V0.274990.960
3_G45_V0.274050.956
60_A64_L0.273410.954
95_Q147_P0.272630.951
71_D189_I0.272230.950
69_G189_I0.270860.945
157_E160_A0.270590.944
131_A134_E0.269580.941
14_A17_D0.26920.939
124_A128_L0.268640.937
97_A181_A0.267830.935
181_A191_F0.267130.932
21_E24_P0.266820.931
116_A119_S0.265840.928
102_G152_D0.264710.924
86_I92_V0.264050.921
36_T43_N0.262760.917
165_L170_A0.262630.916
129_R192_I0.262530.916
37_G44_V0.26150.913
90_D142_P0.26040.909
24_P36_T0.259360.905
65_L73_V0.251670.878
175_M199_D0.251130.876
162_I199_D0.250450.874
53_P150_S0.249850.872
54_V57_A0.249730.871
52_G55_N0.248550.867
110_D186_E0.24840.867
59_I63_R0.248380.867
107_F152_D0.247780.865
148_I195_R0.247430.863
99_R178_A0.247310.863
14_A38_K0.246560.860
94_P172_A0.245810.858
130_E137_K0.245380.856
162_I203_G0.24470.854
80_G173_V0.244430.853
95_Q129_R0.244410.853
87_K142_P0.243640.850
103_D107_F0.242510.846
150_S177_S0.240580.840
20_L24_P0.240270.838
82_L165_L0.239760.837
164_L167_K0.238610.833
115_Y118_V0.237830.830
26_F36_T0.23740.828
21_E38_K0.236060.824
88_L200_Y0.234370.818
56_A179_A0.234260.817
199_D202_D0.234040.817
45_V68_F0.232850.813
163_E166_Q0.232340.811
53_P101_D0.232070.810
157_E199_D0.231470.808
127_D134_E0.231420.808
154_F175_M0.231150.807
103_D152_D0.230040.803
162_I165_L0.229920.802
53_P57_A0.229290.800
93_I145_E0.2290.799
128_L132_L0.228990.799
5_I75_M0.228060.796
3_G65_L0.22750.794
7_A11_E0.227010.792
34_Y64_L0.226250.790
86_I171_D0.225580.787
99_R182_Q0.224880.785
162_I201_A0.224550.784
61_T183_A0.223050.778
137_K142_P0.222840.778
98_I168_F0.221690.774
128_L131_A0.221170.772
64_L68_F0.22040.769
177_S195_R0.219890.767
173_V199_D0.219490.766
114_P118_V0.219130.765
98_I149_A0.219050.764
75_M180_V0.218440.762
150_S178_A0.217840.760
179_A183_A0.216740.756
22_E27_R0.216280.755
173_V201_A0.215110.751
159_E163_E0.214830.750
27_R33_T0.214120.747
86_I197_I0.214030.747
100_Y149_A0.212540.742
121_P124_A0.212190.740
47_V60_A0.211670.739
127_D131_A0.211270.737
126_P133_K0.209730.732
23_T26_F0.209510.731
104_S155_Y0.209340.730
151_G155_Y0.207450.724
65_L70_P0.205970.719
101_D152_D0.204790.715
144_H171_D0.204740.714
158_T162_I0.204580.714
5_I62_Q0.203480.710
9_P13_E0.203480.710
150_S193_A0.202810.708
124_A129_R0.202090.705
117_P120_R0.201230.702
78_I199_D0.200130.698
81_G90_D0.199990.698
75_M193_A0.197370.689
94_P193_A0.197090.688
82_L151_G0.19670.686
162_I166_Q0.195950.684
98_I123_P0.195390.682
104_S107_F0.193290.674
77_G177_S0.193230.674
75_M181_A0.192170.671
99_R102_G0.191630.669
90_D93_I0.19130.668
158_T161_E0.190650.665
32_F48_S0.189540.661
64_L67_E0.18910.660
34_Y68_F0.188510.658
93_I194_I0.188120.656
32_F47_V0.187090.653
11_E194_I0.186710.652
124_A130_E0.186510.651
149_A164_L0.186210.650
57_A183_A0.185180.646
37_G146_G0.185030.646
7_A49_T0.184960.645
123_P185_R0.18490.645
150_S179_A0.184630.644
70_P189_I0.18390.642
26_F68_F0.182290.636
37_G45_V0.182040.635
61_T180_V0.181740.634
82_L202_D0.181540.633
43_N71_D0.181520.633
93_I192_I0.180960.631
32_F60_A0.180950.631
9_P16_A0.180680.630
96_D120_R0.180350.629
157_E162_I0.180310.629
31_G48_S0.180170.629
178_A181_A0.179950.628
100_Y173_V0.17880.624
92_V193_A0.178720.624
65_L71_D0.17870.624
151_G173_V0.178330.622
12_A16_A0.178260.622
20_L27_R0.177850.621
159_E202_D0.177680.620
47_V64_L0.176860.617
125_D128_L0.175440.612
114_P119_S0.17520.611
52_G176_E0.175140.611
148_I177_S0.174410.609
11_E39_Y0.174330.608
59_I62_Q0.174180.608
39_Y44_V0.173810.607
55_N59_I0.173150.604
56_A180_V0.17290.603
105_P110_D0.172730.603
88_L199_D0.172510.602
100_Y165_L0.171620.599
98_I121_P0.171520.599
15_L46_I0.171220.597
105_P153_S0.171140.597
75_M191_F0.169310.591
120_R185_R0.169230.591
82_L201_A0.168920.589
130_E145_E0.16880.589
106_S110_D0.168790.589
156_R161_E0.168340.587
105_P108_F0.168310.587
34_Y47_V0.168090.587
129_R132_L0.168060.586
125_D131_A0.16730.584
80_G201_A0.166560.581
126_P145_E0.166180.580
15_L18_L0.165520.578
98_I164_L0.165430.577
161_E165_L0.165120.576
149_A173_V0.165060.576
105_P160_A0.164580.574
116_A120_R0.164570.574
14_A18_L0.164340.573
66_E71_D0.163980.572
124_A181_A0.163310.570
102_G106_S0.162950.569
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
4g41A0.96151000.098
4josA0.95731000.141
4kn5A0.96151000.141
3dp9A0.96151000.144
4f1wA0.96151000.145
3eeiA0.96151000.147
3nm6B0.96151000.148
3o4vA0.96151000.148
4jwtA0.96151000.155
3bl6A0.96151000.174

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