GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
dTDP_sugar_isom - dTDP-4-dehydrorhamnose 35-epimerase
Pfam: PF00908 (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: CL0029
Length: 176
Sequences: 2097
Seq/Len: 11.91
HH_delta: 0.001 (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
142_G171_A1.152493.943
77_E99_E1.073293.672
122_E125_A0.980473.354
78_I127_V0.967093.308
30_E41_E0.963483.296
79_F97_S0.789182.700
13_E106_R0.742352.540
58_L115_A0.741862.538
3_E10_Y0.732842.507
5_K94_K0.728842.493
149_D175_A0.720842.466
136_D139_D0.705712.414
5_K96_V0.697632.387
68_A109_Y0.691512.366
68_A132_T0.681132.330
75_R102_A0.667072.282
2_R13_E0.653352.235
55_L119_Q0.648872.220
62_S141_R0.637112.180
48_S118_F0.635752.175
45_D130_K0.630592.157
75_R124_D0.616732.110
34_A39_P0.615672.106
31_D134_Y0.607652.079
11_I106_R0.594732.035
112_P132_T0.584872.001
30_E34_A0.584552.000
166_E170_N0.565191.933
144_R173_S0.55341.893
52_K123_D0.54151.852
101_S104_N0.538341.842
68_A112_P0.524731.795
173_S176_E0.517651.771
74_L128_L0.507381.736
77_E122_E0.496921.700
3_E7_E0.492991.686
75_R126_E0.479991.642
166_E169_A0.479531.640
11_I98_V0.476751.631
47_I126_E0.463551.586
60_Y141_R0.445991.526
120_T125_A0.444571.521
143_I150_L0.44241.513
6_I114_V0.437131.495
79_F155_P0.435081.488
85_L115_A0.431941.478
47_I72_R0.421961.444
23_Y47_I0.414131.417
150_L174_L0.403081.379
65_Y133_N0.402791.378
4_T11_I0.401941.375
58_L117_G0.394971.351
77_E101_S0.392121.341
29_R32_E0.390971.337
149_D173_S0.381141.304
9_V82_A0.378341.294
49_V126_E0.376211.287
16_V105_P0.375581.285
31_D35_E0.373161.277
65_Y136_D0.355571.216
9_V96_V0.347171.188
145_W162_P0.346131.184
6_I9_V0.342711.172
40_P109_Y0.340941.166
49_V124_D0.337761.155
111_P114_V0.337661.155
29_R134_Y0.336391.151
24_F48_S0.333941.142
1_V10_Y0.329481.127
26_E67_Q0.325221.113
40_P112_P0.325021.112
81_V152_I0.320881.098
65_Y139_D0.31791.088
119_Q156_I0.314691.077
172_P176_E0.313411.072
82_A96_V0.312561.069
140_E171_A0.312491.069
26_E29_R0.309481.059
20_E166_E0.307441.052
119_Q155_P0.30691.050
112_P133_N0.305591.045
81_V154_W0.301931.033
78_I125_A0.301381.031
79_F95_W0.300991.030
82_A114_V0.29671.015
80_D116_H0.294441.007
42_F132_T0.293021.002
32_E36_A0.292391.000
66_A139_D0.287060.982
109_Y112_P0.285440.976
46_N131_V0.283020.968
115_A143_I0.282650.967
23_Y126_E0.281390.963
6_I96_V0.280440.959
15_K32_E0.279840.957
23_Y49_V0.27950.956
63_P66_A0.279420.956
6_I91_T0.279030.955
1_V33_F0.278980.954
11_I108_L0.277320.949
12_I32_E0.275010.941
1_V36_A0.27420.938
60_Y115_A0.271530.929
148_P173_S0.269890.923
26_E44_Q0.267990.917
144_R171_A0.267790.916
18_P51_K0.266360.911
95_W150_L0.265190.907
27_T45_D0.264610.905
47_I128_L0.264520.905
85_L143_I0.263680.902
98_V108_L0.25480.872
99_E121_L0.253610.868
2_R106_R0.250480.857
102_A126_E0.242760.830
2_R11_I0.240820.824
82_A110_I0.240520.823
100_L108_L0.235440.805
27_T47_I0.234790.803
40_P132_T0.234290.801
42_F45_D0.228750.783
1_V12_I0.228730.782
32_E35_E0.227850.779
120_T124_D0.225440.771
62_S139_D0.222180.760
109_Y132_T0.221410.757
97_S155_P0.220540.754
24_F129_Y0.217980.746
165_S168_D0.217090.743
26_E46_N0.215680.738
142_G172_P0.215140.736
71_V127_V0.214980.735
70_L109_Y0.21380.731
63_P136_D0.213520.730
163_I166_E0.211910.725
119_Q162_P0.211210.723
74_L126_E0.210870.721
60_Y143_I0.210860.721
60_Y85_L0.210290.719
1_V32_E0.208910.715
24_F46_N0.208740.714
58_L152_I0.208430.713
4_T9_V0.206490.706
93_G149_D0.204070.698
120_T123_D0.203920.698
10_Y109_Y0.20350.696
149_D174_L0.200770.687
29_R33_F0.199950.684
38_L112_P0.198110.678
9_V108_L0.198090.678
7_E91_T0.196870.673
55_L162_P0.196870.673
20_E163_I0.195230.668
47_I74_L0.194180.664
131_V141_R0.193830.663
11_I104_N0.19360.662
82_A98_V0.19270.659
16_V25_M0.1920.657
7_E90_P0.190410.651
20_E51_K0.189240.647
69_K80_D0.188440.645
8_G91_T0.187560.642
67_Q167_K0.18650.638
51_K124_D0.185190.634
27_T128_L0.182550.624
6_I82_A0.181670.621
10_Y111_P0.180420.617
135_Y165_S0.17970.615
28_F38_L0.179280.613
33_F72_R0.178070.609
96_V99_E0.17790.609
3_E8_G0.177520.607
63_P139_D0.177080.606
63_P133_N0.17650.604
145_W164_L0.176420.604
157_E162_P0.176070.602
128_L131_V0.175210.599
82_A108_L0.174260.596
158_N162_P0.173720.594
85_L93_G0.173570.594
166_E175_A0.172290.589
27_T72_R0.170750.584
11_I96_V0.170330.583
58_L150_L0.168930.578
43_V133_N0.167420.573
64_P136_D0.167270.572
88_G92_F0.165250.565
58_L83_V0.164790.564
137_P170_N0.164560.563
52_K157_E0.164250.562
43_V134_Y0.164060.561
98_V106_R0.163980.561
21_R56_R0.162940.557
71_V80_D0.162920.557
51_K163_I0.162750.557
64_P73_C0.161760.553
71_V78_I0.161540.553
141_R171_A0.161390.552
67_Q131_V0.160010.547
23_Y128_L0.159880.547
46_N129_Y0.159740.546
167_K171_A0.158460.542
150_L153_D0.158320.542
58_L85_L0.157760.540
42_F107_Q0.157050.537
55_L145_W0.156850.537
18_P105_P0.156780.536
145_W169_A0.156770.536
31_D34_A0.155790.533
27_T131_V0.155750.533
121_L155_P0.15540.532
77_E125_A0.1550.530
79_F121_L0.154470.528
50_S56_R0.152650.522
64_P139_D0.152530.522
78_I120_T0.152260.521
79_F153_D0.15210.520
158_N163_I0.151970.520
58_L143_I0.151350.518
117_G154_W0.150480.515
86_R114_V0.149830.513
7_E108_L0.149790.512
23_Y105_P0.148820.509
85_L111_P0.14880.509
26_E131_V0.148720.509
53_G66_A0.147670.505
72_R107_Q0.147660.505
87_K90_P0.147050.503
79_F99_E0.146960.503
141_R172_P0.146510.501
42_F130_K0.146240.500
48_S80_D0.145890.499
83_V150_L0.145330.497
1_V4_T0.145080.496
4_T106_R0.144370.494
146_N158_N0.143950.492
98_V170_N0.143770.492
1_V29_R0.143690.492
146_N169_A0.143140.490
163_I169_A0.142880.489
72_R126_E0.142870.489
6_I108_L0.142510.488
133_N137_P0.142440.487
81_V97_S0.142110.486
116_H140_E0.141670.485
34_A38_L0.141520.484
54_V121_L0.140340.480
25_M105_P0.139640.478
105_P126_E0.139610.478
66_A133_N0.139080.476
50_S54_V0.138230.473
27_T130_K0.13810.472
34_A175_A0.137960.472
28_F134_Y0.13690.468
73_C125_A0.136840.468
147_D150_L0.136710.468
19_D22_G0.136390.467
162_P166_E0.134940.462
1_V11_I0.134160.459
21_R69_K0.134020.458
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
4hn1A0.98861000.001
3rykA0.9831000.035
1oi6A0.98861000.052
1dzrA0.98861000.056
1upiA11000.058
2c0zA0.9831000.061
1ep0A0.99431000.061
2ixkA0.9831000.064
1wltA0.94891000.115
1nxmA0.94891000.12

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