GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
IspD - 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Pfam: PF01128 (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: CL0110
Length: 221
Sequences: 9461
Seq/Len: 42.81
HH_delta: 0.126 (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
28_K36_E1.936995.226
29_P32_E1.155743.118
32_E36_E1.013562.734
3_A44_I0.852392.300
46_E69_K0.844242.278
43_E111_D0.834782.252
2_A46_E0.820382.213
30_V206_I0.789192.129
14_M23_L0.75842.046
136_R145_E0.751592.028
23_L212_L0.74342.006
3_A38_F0.735771.985
115_E119_E0.71661.933
127_A196_I0.708251.911
38_F98_H0.707951.910
138_D142_F0.701181.892
50_V84_G0.690171.862
28_K33_Y0.672341.814
24_E216_E0.659751.780
206_I215_A0.654781.767
106_S109_L0.653771.764
163_F167_L0.641141.730
165_L192_K0.637381.720
54_E58_Y0.636331.717
46_E67_K0.632581.707
33_Y37_A0.63171.704
76_T79_E0.611631.650
39_L47_I0.608311.641
108_E112_R0.605781.634
28_K32_E0.605411.633
168_E172_K0.604051.630
19_P55_D0.602891.627
117_A124_A0.600211.619
112_R115_E0.598721.615
58_Y61_E0.597721.613
129_P198_E0.586961.584
94_I118_R0.586621.583
165_L187_V0.584251.576
142_F193_K0.582481.571
37_A40_A0.58221.571
209_P213_E0.581041.568
40_A107_P0.57781.559
104_F215_A0.572911.546
111_D115_E0.56441.523
24_E29_P0.547241.476
29_P33_Y0.544561.469
5_I38_F0.537521.450
116_A197_V0.531431.434
31_L59_V0.517591.396
5_I35_L0.513631.386
213_E216_E0.513581.386
9_G19_P0.513261.385
37_A107_P0.511181.379
48_V71_V0.505491.364
113_V160_A0.501411.353
122_G192_K0.499981.349
122_G162_R0.499241.347
35_L47_I0.499181.347
187_V192_K0.498981.346
109_L112_R0.494471.334
116_A195_A0.493521.331
24_E27_G0.492371.328
212_L216_E0.4841.306
32_E62_L0.480661.297
39_L67_K0.475341.282
107_P111_D0.464481.253
75_A79_E0.463361.250
23_L209_P0.461741.246
162_R165_L0.460721.243
172_K190_A0.457641.235
96_L160_A0.456361.231
13_R20_K0.45631.231
164_E168_E0.45561.229
94_I117_A0.454971.227
208_T211_D0.453291.223
36_E40_A0.452751.221
121_H195_A0.445711.202
98_H110_I0.442871.195
2_A48_V0.441741.192
136_R147_L0.441321.191
185_S189_A0.43971.186
82_Y86_K0.431441.164
137_V196_I0.427471.153
79_E83_N0.423551.143
116_A119_E0.415191.120
138_D144_T0.411621.111
213_E217_A0.410471.107
14_M209_P0.409911.106
4_I84_G0.408291.102
26_G33_Y0.407921.101
51_V55_D0.405711.095
113_V126_P0.404461.091
96_L114_I0.403261.088
35_L66_K0.402831.087
25_L215_A0.39911.077
6_L50_V0.395331.067
99_D102_R0.393151.061
57_D61_E0.389681.051
109_L202_R0.387511.045
14_M212_L0.386511.043
31_L49_V0.382381.032
112_R116_A0.38191.030
89_A167_L0.377111.017
210_E214_L0.374311.010
115_E118_R0.373581.008
2_A88_L0.373081.007
26_G216_E0.372811.006
125_I184_A0.368070.993
51_V70_I0.363920.982
35_L39_L0.36360.981
73_G76_T0.363580.981
122_G193_K0.362230.977
50_V80_S0.36120.974
7_A31_L0.358150.966
85_L171_E0.357720.965
109_L126_P0.357510.965
48_V87_A0.357240.964
7_A49_V0.357050.963
105_V110_I0.356530.962
51_V57_D0.356480.962
136_R144_T0.355180.958
4_I95_V0.354860.957
44_I114_I0.354530.956
4_I48_V0.352950.952
148_D151_K0.348990.942
43_E115_E0.348290.940
153_W156_Q0.346290.934
211_D214_L0.34510.931
168_E171_E0.344430.929
22_F58_Y0.343290.926
51_V59_V0.339110.915
5_I34_T0.336720.908
134_I154_A0.335150.904
94_I160_A0.333980.901
32_E35_L0.333610.900
2_A92_C0.333050.899
98_H105_V0.332320.897
204_I214_L0.328680.887
117_A162_R0.328050.885
125_I143_V0.326230.880
113_V124_A0.324960.877
60_E64_S0.323950.874
142_F195_A0.322960.871
106_S202_R0.321680.868
135_K188_E0.321230.867
53_P72_E0.317110.856
204_I215_A0.316280.853
206_I211_D0.316160.853
36_E39_L0.315150.850
4_I50_V0.315080.850
165_L168_E0.314530.849
35_L63_L0.313040.845
11_G19_P0.312060.842
69_K87_A0.3090.834
169_A190_A0.308670.833
94_I162_R0.307690.830
144_T147_L0.305910.825
97_I166_L0.305910.825
32_E63_L0.30560.824
79_E82_Y0.305150.823
62_L65_K0.30490.823
4_I81_V0.304610.822
92_C164_E0.304450.821
95_V163_F0.303170.818
85_L167_L0.302450.816
135_K146_T0.301870.814
25_L30_V0.30150.813
82_Y85_L0.300350.810
34_T37_A0.299980.809
71_V80_S0.299370.808
21_Q30_V0.298260.805
108_E111_D0.297840.804
38_F110_I0.297740.803
29_P62_L0.297350.802
167_L171_E0.296510.800
185_S188_E0.29590.798
156_Q159_Q0.295620.798
10_S52_P0.295420.797
22_F59_V0.29470.795
30_V34_T0.294040.793
48_V84_G0.293180.791
22_F62_L0.29310.791
81_V97_I0.291680.787
57_D60_E0.29140.786
172_K176_E0.290680.784
143_V196_I0.290560.784
168_E192_K0.289210.780
58_Y62_L0.289130.780
207_T211_D0.289110.780
87_A90_E0.288280.778
82_Y171_E0.28510.769
83_N86_K0.284930.769
168_E190_A0.284880.769
184_A188_E0.283870.766
25_L212_L0.283330.764
55_D58_Y0.2830.764
8_A21_Q0.282020.761
14_M21_Q0.281970.761
60_E72_E0.281880.760
44_I111_D0.28120.759
6_L81_V0.28070.757
5_I31_L0.279690.755
67_K83_N0.279330.754
132_D149_R0.27860.752
27_G33_Y0.277030.747
9_G13_R0.27690.747
35_L49_V0.276880.747
117_A160_A0.275390.743
111_D114_I0.274870.742
146_T188_E0.271740.733
51_V72_E0.270950.731
187_V190_A0.270810.731
31_L35_L0.269480.727
186_L190_A0.269250.726
129_P151_K0.269040.726
104_F204_I0.268650.725
22_F55_D0.268120.723
61_E64_S0.265310.716
8_A50_V0.265030.715
52_P55_D0.264690.714
60_E65_K0.259470.700
9_G55_D0.257550.695
6_L100_A0.254980.688
155_V159_Q0.254570.687
141_G144_T0.254050.685
74_G77_R0.253880.685
93_D162_R0.252960.682
131_T201_P0.252820.682
214_L217_A0.252090.680
8_A11_G0.251970.680
48_V88_L0.251340.678
93_D164_E0.251010.677
72_E75_A0.248350.670
39_L66_K0.247590.668
67_K70_I0.24750.668
54_E57_D0.247030.666
34_T38_F0.246780.666
86_K171_E0.244760.660
114_I160_A0.244660.660
2_A90_E0.244610.660
63_L68_V0.24410.659
24_E212_L0.241560.652
26_G104_F0.240860.650
188_E194_V0.240820.650
210_E213_E0.240520.649
113_V197_V0.240420.649
117_A126_P0.240310.648
86_K89_A0.239940.647
51_V60_E0.239830.647
130_V152_L0.239590.646
69_K72_E0.238110.642
55_D60_E0.237310.640
206_I212_L0.237230.640
66_K69_K0.234990.634
102_R205_K0.234910.634
3_A98_H0.23340.630
49_V70_I0.232540.627
59_V62_L0.231470.624
183_D186_L0.231380.624
48_V69_K0.230890.623
112_R197_V0.230840.623
73_G79_E0.230440.622
25_L216_E0.230380.622
80_S84_G0.22930.619
46_E89_A0.226160.610
31_L63_L0.225970.610
146_T149_R0.224840.607
80_S100_A0.224350.605
94_I114_I0.223970.604
44_I47_I0.223760.604
6_L99_D0.223570.603
109_L200_S0.222820.601
136_R151_K0.22210.599
34_T98_H0.221770.598
181_T185_S0.221720.598
123_A127_A0.220180.594
40_A111_D0.219280.592
60_E66_K0.219220.591
77_R81_V0.219060.591
77_R99_D0.217960.588
169_A187_V0.217810.588
180_F185_S0.217520.587
129_P153_W0.217320.586
46_E88_L0.217290.586
44_I96_L0.215910.583
39_L68_V0.215830.582
85_L89_A0.215440.581
11_G20_K0.215110.580
118_R121_H0.215070.580
14_M208_T0.214930.580
52_P72_E0.214910.580
33_Y36_E0.21460.579
116_A124_A0.214430.579
43_E114_I0.21360.576
105_V109_L0.213350.576
151_K154_A0.213350.576
64_S70_I0.212310.573
119_E122_G0.211590.571
101_A207_T0.210.567
10_S75_A0.209750.566
63_L66_K0.209330.565
196_I199_G0.208850.563
161_F183_D0.20880.563
163_F166_L0.208630.563
85_L88_L0.208590.563
34_T100_A0.208450.562
23_L216_E0.208210.562
37_A105_V0.20820.562
109_L203_N0.207260.559
9_G20_K0.206880.558
113_V117_A0.206830.558
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
3q80A0.99551000.126
4kt7A0.99551000.132
3f1cA0.99551000.148
2yc3A0.9911000.197
2vshA0.9911000.229
2xwlA0.98191000.235
1vpaA0.96831000.238
1vgwA0.97741000.244
1i52A0.98641000.248
2px7A0.94121000.253

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