GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribul_P_3_epim - Ribulose-phosphate 3 epimerase family
Pfam: PF00834 (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: CL0036
Length: 201
Sequences: 19612
Seq/Len: 97.57
HH_delta: 0.049 (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
53_R82_D1.769393.076
19_K55_I1.507482.620
180_I191_F1.425322.478
181_K185_E1.411132.453
22_E57_D1.375662.391
74_E78_E1.360082.364
20_R24_A1.339892.329
47_D50_K1.278662.223
19_K23_E1.192052.072
98_I102_K1.169932.034
170_E190_I1.152152.003
157_R189_D1.13521.973
102_K129_D1.109011.928
74_E100_Y1.09321.900
95_K99_K1.088041.891
154_R186_A1.087871.891
182_Q185_E1.07661.871
51_A54_K1.071281.862
154_R158_K1.039581.807
160_I167_F1.029181.789
176_N179_N1.020781.774
151_E154_R1.013341.761
22_E56_T0.983971.710
122_E159_L0.977931.700
46_P75_E0.959021.667
155_E159_L0.956881.663
15_E51_A0.946011.644
18_I52_I0.94291.639
74_E104_A0.939441.633
22_E58_L0.930971.618
100_Y103_E0.92731.612
15_E19_K0.922151.603
19_K22_E0.907671.578
157_R169_I0.904141.572
151_E155_E0.902711.569
75_E78_E0.884941.538
50_K54_K0.882391.534
184_V191_F0.867631.508
168_E189_D0.864421.503
47_D51_A0.861881.498
71_R75_E0.859761.494
16_E19_K0.832611.447
68_N71_R0.824181.433
46_P79_A0.823771.432
50_K79_A0.81981.425
123_P126_D0.81251.412
99_K103_E0.810171.408
141_G194_G0.79691.385
15_E55_I0.792241.377
177_E181_K0.787211.368
46_P50_K0.782921.361
44_F47_D0.777711.352
175_I183_L0.759061.319
119_E122_E0.746371.297
155_E158_K0.745821.296
62_V81_A0.737811.282
20_R23_E0.734921.277
193_A196_A0.718911.250
22_E55_I0.714451.242
122_E126_D0.707531.230
16_E20_R0.702491.221
18_I29_L0.683071.187
17_E20_R0.682271.186
96_E99_K0.670761.166
182_Q186_A0.66811.161
75_E79_A0.665631.157
95_K127_Q0.665481.157
150_L182_Q0.665071.156
152_K155_E0.665071.156
179_N182_Q0.658661.145
100_Y104_A0.649911.130
96_E100_Y0.646311.123
178_E182_Q0.644511.120
77_A106_I0.637091.107
22_E25_G0.633671.101
71_R74_E0.619741.077
53_R60_L0.616121.071
68_N72_Y0.614321.068
43_T75_E0.606851.055
50_K78_E0.606371.054
109_G130_M0.605651.053
178_E181_K0.599931.043
99_K127_Q0.596951.038
80_G106_I0.588181.022
122_E125_L0.586651.020
28_W83_Y0.586521.020
76_F81_A0.586311.019
45_G48_I0.585861.018
29_L58_L0.585431.018
101_I108_A0.582121.012
77_A104_A0.581931.012
183_L188_A0.581821.011
153_I188_A0.581251.010
72_Y75_E0.576861.003
83_Y109_G0.574690.999
135_S149_V0.573890.998
171_V188_A0.573680.997
130_M168_E0.570790.992
153_I157_R0.569810.990
27_D59_P0.564250.981
125_L167_F0.560120.974
171_V183_L0.553720.962
46_P78_E0.549570.955
118_V121_L0.549250.955
121_L124_Y0.548910.954
51_A55_I0.547740.952
61_D83_Y0.542160.942
84_I106_I0.540450.939
48_I51_A0.536890.933
85_T130_M0.528970.919
97_T100_Y0.528080.918
59_P82_D0.525250.913
153_I169_I0.524920.912
130_M190_I0.522130.908
49_I60_L0.518640.902
73_I100_Y0.517230.899
118_V122_E0.517090.899
98_I108_A0.513240.892
120_E123_P0.512710.891
49_I79_A0.51220.890
67_E92_E0.512010.890
92_E95_K0.510920.888
39_V43_T0.50930.885
117_P120_E0.508220.883
18_I56_T0.504070.876
117_P155_E0.486760.846
193_A197_I0.486440.846
85_T111_A0.484190.842
73_I101_I0.481680.837
153_I171_V0.480410.835
44_F48_I0.473980.824
74_E77_A0.473320.823
37_H67_E0.472750.822
31_I49_I0.471260.819
33_I36_G0.471190.819
56_T59_P0.470180.817
28_W59_P0.466950.812
156_L160_I0.465740.810
176_N196_A0.463330.805
177_E180_I0.46220.803
194_G198_F0.461840.803
157_R186_A0.460940.801
102_K108_A0.459850.799
86_F110_I0.459730.799
78_E104_A0.459220.798
157_R160_I0.458650.797
154_R182_Q0.456260.793
133_V156_L0.456110.793
118_V155_E0.456080.793
147_P182_Q0.449780.782
119_E123_P0.446950.777
110_I124_Y0.445690.775
177_E196_A0.445550.774
95_K98_I0.443130.770
53_R79_A0.437020.760
172_D192_V0.434440.755
180_I196_A0.429780.747
15_E18_I0.425910.740
73_I84_I0.424880.739
28_W190_I0.423460.736
170_E192_V0.421920.733
99_K102_K0.421840.733
150_L183_L0.420020.730
154_R185_E0.414830.721
150_L186_A0.41350.719
183_L191_F0.412420.717
69_P72_Y0.411170.715
86_F97_T0.410760.714
128_V167_F0.410130.713
133_V152_K0.407130.708
121_L159_L0.406410.706
63_H81_A0.406140.706
148_E151_E0.405210.704
168_E190_I0.402460.700
188_A191_F0.400780.697
150_L154_R0.400480.696
14_L18_I0.396380.689
21_L26_A0.394460.686
136_V171_V0.393130.683
61_D85_T0.39310.683
157_R161_P0.392890.683
98_I128_V0.389250.677
112_L120_E0.388840.676
110_I128_V0.388250.675
169_I188_A0.386310.671
108_A129_D0.385370.670
76_F80_G0.383860.667
33_I45_G0.383670.667
179_N183_L0.382320.665
156_L159_L0.382260.664
129_D168_E0.380710.662
59_P83_Y0.378970.659
56_T60_L0.378130.657
157_R188_A0.377470.656
87_H90_A0.377440.656
140_F143_Q0.376390.654
149_V152_K0.37420.650
127_Q167_F0.372670.648
98_I127_Q0.369990.643
18_I22_E0.369990.643
97_T101_I0.369980.643
53_R56_T0.367230.638
69_P96_E0.366620.637
49_I62_V0.365070.635
133_V149_V0.364880.634
147_P150_L0.363410.632
17_E198_F0.363080.631
66_V76_F0.362810.631
73_I77_A0.362310.630
43_T47_D0.361810.629
21_L197_I0.361320.628
85_T109_G0.359940.626
14_L17_E0.359380.625
107_K129_D0.35890.624
117_P121_L0.358840.624
88_A91_T0.352790.613
140_F195_S0.351580.611
134_M172_D0.350430.609
38_F72_Y0.350250.609
85_T172_D0.350090.609
77_A100_Y0.348840.606
76_F84_I0.348780.606
35_D38_F0.347810.605
152_K156_L0.347290.604
116_T119_E0.346480.602
31_I52_I0.34630.602
150_L153_I0.345950.601
183_L186_A0.345880.601
111_A132_L0.345780.601
118_V123_P0.345770.601
125_L160_I0.345070.600
43_T46_P0.344220.598
139_G142_G0.34330.597
160_I169_I0.342880.596
134_M138_P0.341220.593
74_E103_E0.340830.592
14_L52_I0.340410.592
31_I81_A0.336850.586
21_L24_A0.336760.585
49_I81_A0.331970.577
22_E60_L0.330060.574
180_I193_A0.329560.573
73_I104_A0.329260.572
146_I149_V0.328290.571
101_I106_I0.328160.570
104_A107_K0.3280.570
17_E21_L0.326140.567
31_I60_L0.324020.563
83_Y107_K0.321860.559
121_L125_L0.320620.557
109_G170_E0.319860.556
69_P73_I0.319090.555
133_V153_I0.318620.554
84_I108_A0.317730.552
48_I52_I0.317440.552
146_I183_L0.316640.550
60_L82_D0.315680.549
46_P76_F0.314950.547
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
3inpA11000.049
1tqjA11000.072
3ctlA0.9951000.072
3ovpA0.98011000.081
1h1yA0.98011000.1
3cu2A0.9999.90.125
1tqxA0.970199.90.127
1rpxA199.90.156
2fliA199.90.172
1geqA0.955299.80.303

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