GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PMT - Dolichyl-phosphate-mannose-protein mannosyltransferase
Pfam: PF02366 (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: CL0111
Length: 245
Sequences: 2111
Seq/Len: 8.62
HH_delta: 0.65 (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
99_L146_L0.449053.409
104_L117_A0.39783.020
95_L142_F0.386982.938
93_G131_S0.374842.845
146_L174_A0.355112.696
104_L114_A0.345772.625
92_F142_F0.328272.492
101_Y118_A0.313442.379
137_D182_K0.299622.274
106_R153_R0.294232.233
97_V118_A0.28562.168
81_N84_A0.280392.128
150_C174_A0.279472.121
103_I152_L0.267352.029
143_F181_T0.264712.009
154_W168_L0.256991.951
121_L127_L0.247741.881
101_Y111_R0.231451.757
91_L95_L0.231081.754
176_G226_I0.228651.736
150_C170_L0.227351.726
105_R111_R0.223671.698
73_G84_A0.222791.691
150_C167_W0.220811.676
105_R114_A0.219321.665
99_L142_F0.213921.624
147_A175_L0.210941.601
114_A118_A0.208751.585
193_G200_L0.207381.574
83_W87_L0.20591.563
177_L181_T0.203371.544
104_L108_F0.198641.508
102_L149_Y0.19661.492
96_T145_L0.194711.478
217_H221_R0.194391.476
109_G113_A0.190261.444
74_F85_A0.188311.429
38_H59_L0.187671.425
143_F177_L0.186631.417
47_P52_L0.185331.407
103_I145_L0.181891.381
92_F139_I0.177971.351
25_E29_D0.177191.345
219_F222_L0.173111.314
84_A87_L0.172251.308
103_I149_Y0.170981.298
172_G219_F0.170481.294
147_A178_A0.171.290
107_L152_L0.169551.287
100_V121_L0.168281.277
97_V122_A0.163881.244
99_L145_L0.163511.241
96_T142_F0.161551.226
172_G176_G0.159091.208
37_E40_R0.158171.201
178_A185_G0.157691.197
73_G88_P0.156421.187
101_Y114_A0.155851.183
178_A186_L0.155651.182
192_A196_F0.153331.164
221_R225_L0.151051.147
43_D75_Y0.150991.146
72_I76_Y0.150221.140
203_K209_F0.150111.139
96_T127_L0.149891.138
136_L182_K0.149751.137
155_Y198_W0.149381.134
230_W234_V0.147581.120
218_L222_L0.147151.117
99_L149_Y0.146421.111
206_D209_F0.146311.111
174_A177_L0.141731.076
29_D134_A0.141651.075
27_H30_E0.141321.073
51_L67_Y0.140911.070
48_L51_L0.140831.069
104_L107_L0.14041.066
73_G87_L0.13981.061
100_V117_A0.138491.051
149_Y153_R0.137371.043
73_G77_F0.137211.042
96_T121_L0.136751.038
140_L182_K0.135371.028
23_F26_V0.13481.023
51_L54_A0.134221.019
166_L169_L0.134081.018
179_I223_L0.133861.016
43_D71_A0.133521.014
165_W169_L0.132961.009
203_K206_D0.132721.007
74_F80_V0.132291.004
230_W233_Y0.132011.002
86_R134_A0.131831.001
68_W137_D0.131811.001
96_T141_L0.131590.999
77_F87_L0.131440.998
144_I178_A0.130790.993
119_L122_A0.130320.989
183_G233_Y0.130180.988
220_A234_V0.130030.987
24_D27_H0.129390.982
25_E30_E0.128920.979
218_L221_R0.128680.977
204_R207_K0.128480.975
112_R116_L0.128410.975
45_H52_L0.128160.973
151_L171_A0.128110.972
122_A127_L0.12760.969
87_L91_L0.127510.968
83_W152_L0.126870.963
222_L226_I0.126750.962
101_Y105_R0.12570.954
89_S134_A0.12560.953
69_I92_F0.125540.953
140_L185_G0.12540.952
98_P102_L0.125230.951
140_L178_A0.124630.946
196_F200_L0.12440.944
228_I232_I0.123780.940
61_G135_L0.123620.938
90_A132_R0.123190.935
143_F146_L0.122810.932
94_A97_V0.122730.932
45_H48_L0.122390.929
173_I177_L0.122190.928
63_P68_W0.121730.924
169_L224_L0.120840.917
173_I218_L0.120650.916
105_R109_G0.120310.913
59_L136_L0.11950.907
65_L181_T0.1180.896
108_F113_A0.117850.895
137_D176_G0.11740.891
96_T116_L0.117050.889
42_M68_W0.116890.887
47_P50_K0.116880.887
62_Y183_G0.116250.882
151_L199_L0.11580.879
131_S138_S0.115630.878
86_R89_S0.115490.877
100_V127_L0.115280.875
30_E34_R0.114710.871
66_Y136_L0.112480.854
163_K166_L0.112210.852
36_A62_Y0.112190.852
106_R161_R0.112050.851
137_D140_L0.111830.849
18_P24_D0.111370.845
155_Y199_L0.111220.844
25_E31_F0.110830.841
114_A117_A0.110690.840
111_R115_L0.110670.840
206_D221_R0.110580.839
169_L222_L0.110530.839
169_L218_L0.110450.838
165_W220_A0.110070.836
62_Y68_W0.109740.833
93_G97_V0.109730.833
151_L168_L0.109110.828
38_H42_M0.109020.828
142_F146_L0.108670.825
54_A59_L0.108020.820
76_Y170_L0.107990.820
131_S139_I0.107630.817
70_S85_A0.107620.817
104_L113_A0.107540.816
105_R207_K0.106630.809
78_G191_P0.106620.809
42_M62_Y0.105620.802
30_E42_M0.105520.801
229_P232_I0.105260.799
100_V104_L0.105260.799
39_T85_A0.104930.797
24_D28_F0.104850.796
93_G132_R0.104570.794
122_A128_I0.104320.792
50_K68_W0.104170.791
227_V231_L0.103660.787
223_L230_W0.103570.786
76_Y94_A0.103190.783
86_R137_D0.103080.782
66_Y139_I0.102990.782
217_H220_A0.102930.781
99_L150_C0.102640.779
25_E86_R0.102550.778
162_R228_I0.102490.778
69_I139_I0.102080.775
41_F52_L0.101950.774
36_A74_F0.101920.774
169_L172_G0.101690.772
151_L155_Y0.101590.771
206_D210_S0.101440.770
28_F31_F0.101250.769
94_A98_P0.100870.766
196_F221_R0.100680.764
41_F59_L0.10060.764
219_F231_L0.100510.763
28_F35_Y0.100390.762
26_V29_D0.100020.759
93_G118_A0.099580.756
86_R182_K0.099330.754
172_G234_V0.099220.753
49_G171_A0.099170.753
26_V30_E0.098750.750
219_F223_L0.098530.748
163_K202_R0.098370.747
120_L123_L0.098360.747
28_F39_T0.098350.747
119_L123_L0.097880.743
87_L97_V0.097810.742
34_R197_L0.09760.741
220_A224_L0.097370.739
40_R44_E0.097180.738
175_L223_L0.097040.737
59_L63_P0.096860.735
119_L202_R0.096710.734
179_I227_V0.096680.734
100_V164_W0.096560.733
194_L231_L0.096290.731
169_L176_G0.095850.728
225_L229_P0.095740.727
99_L103_I0.095180.723
105_R225_L0.095070.722
197_L216_K0.094870.720
102_L106_R0.094390.717
200_L221_R0.094380.716
182_K186_L0.094290.716
93_G127_L0.094220.715
27_H135_L0.093990.713
35_Y136_L0.093920.713
176_G183_G0.093910.713
93_G121_L0.09380.712
62_Y182_K0.093790.712
89_S138_S0.093790.712
25_E28_F0.093630.711
103_I107_L0.093560.710
23_F28_F0.093550.710
170_L174_A0.09350.710
35_Y135_L0.093440.709
42_M45_H0.093270.708
176_G180_L0.093180.707
150_C171_A0.093030.706
135_L140_L0.092770.704
78_G81_N0.09270.704
86_R132_R0.09220.700
145_L152_L0.092140.699
180_L230_W0.092130.699
223_L227_V0.092070.699
192_A232_I0.091960.698
115_L118_A0.091920.698
224_L228_I0.091880.697
162_R170_L0.091720.696
23_F130_Q0.091650.696
48_L52_L0.091620.695
18_P21_G0.091520.695
50_K60_F0.09150.695
66_Y130_Q0.091490.694
99_L174_A0.091460.694
61_G136_L0.091450.694
208_R211_W0.091390.694
96_T192_A0.091370.694
77_F200_L0.091290.693
139_I143_F0.091210.692
96_T100_V0.091190.692
164_W167_W0.091190.692
186_L191_P0.091170.692
62_Y67_Y0.091070.691
99_L143_F0.091020.691
86_R90_A0.091010.691
67_Y183_G0.090940.690
49_G56_G0.09090.690
86_R131_S0.09080.689
102_L112_R0.090740.689
87_L176_G0.090730.689
35_Y38_H0.09070.688
100_V103_I0.090690.688
203_K217_H0.090680.688
34_R38_H0.090520.687
98_P101_Y0.090480.687
163_K228_I0.090390.686
102_L105_R0.090250.685
23_F27_H0.090230.685
219_F230_W0.090190.685
42_M47_P0.090030.683
66_Y70_S0.090.683
42_M183_G0.089790.682
43_D46_P0.089790.682
227_V232_I0.089720.681
90_A93_G0.089640.680
66_Y135_L0.08950.679
155_Y195_L0.089420.679
113_A117_A0.089030.676
96_T113_A0.088850.674
178_A182_K0.088820.674
66_Y138_S0.088770.674
194_L197_L0.088770.674
93_G155_Y0.088720.673
93_G122_A0.088720.673
188_L193_G0.088620.673
142_F174_A0.088610.673
26_V31_F0.088550.672
62_Y65_L0.088550.672
231_L235_L0.088380.671
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
3rceA0.926599.40.65
2kncB0.25716.10.95
2h3oA0.20412.50.958
2ks1B0.17962.30.959
2k1kA0.15512.20.959
4he8L0.64492.20.96
4hg6A0.48161.80.961
1xrdA0.13881.70.962
3rkoL0.26121.50.963
1wazA0.17141.50.963
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