GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LacAB_rpiB - RiboseGalactose Isomerase
Pfam: PF02502 (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. )
Length: 140
Sequences: 1662
Seq/Len: 11.87
HH_delta: -0.033 (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
133_Q137_D1.183163.547
43_D138_K1.087833.262
20_Y120_D0.935582.805
15_E18_K0.805412.415
24_K120_D0.755312.265
82_A104_C0.687832.062
3_A31_F0.68512.054
96_E128_E0.683152.048
5_G48_V0.654311.962
31_F51_A0.652841.957
18_K22_E0.647731.942
13_L115_A0.638361.914
83_A94_A0.634431.902
3_A57_A0.62831.884
1_K27_E0.583011.748
16_A112_E0.578281.734
51_A56_E0.57691.730
88_P117_E0.572951.718
10_G63_I0.564481.692
3_A51_A0.555991.667
86_S90_S0.543561.630
111_G114_L0.51271.537
14_K30_D0.509881.529
19_E23_E0.503171.509
19_E22_E0.497971.493
92_K96_E0.4951.484
12_E107_A0.492081.475
46_E77_V0.490611.471
62_L74_A0.488411.464
29_I57_A0.487571.462
50_E54_S0.484641.453
89_Y93_M0.47881.436
100_A122_F0.474151.422
12_E36_E0.469031.406
46_E50_E0.462891.388
45_A70_M0.460341.380
120_D124_N0.459931.379
113_E116_K0.458151.374
53_A77_V0.454681.363
87_D90_S0.453541.360
49_A80_I0.441771.325
65_G108_R0.441111.323
62_L70_M0.44061.321
62_L104_C0.4371.310
61_I119_V0.436491.309
11_F15_E0.435611.306
48_V60_G0.433921.301
96_E125_T0.425731.276
89_Y109_V0.425431.276
20_Y116_K0.420541.261
16_A116_K0.415771.247
94_A122_F0.413321.239
92_K117_E0.410411.231
82_A102_V0.406161.218
20_Y24_K0.399391.197
40_D134_R0.389921.169
121_A125_T0.389281.167
70_M104_C0.383871.151
3_A55_G0.381831.145
38_S134_R0.381281.143
71_S84_L0.378591.135
94_A100_A0.377151.131
64_C70_M0.37491.124
22_E28_V0.372631.117
9_A108_R0.372381.116
88_P121_A0.371861.115
71_S104_C0.369411.108
105_L119_V0.366911.100
93_M96_E0.366651.099
53_A80_I0.365171.095
17_I119_V0.364641.093
106_G109_V0.364131.092
24_K124_N0.361181.083
59_R122_F0.36021.080
45_A62_L0.357561.072
132_H135_R0.354431.063
13_L112_E0.352741.058
55_G58_D0.3511.052
4_I18_K0.349561.048
105_L110_I0.349011.046
61_I103_L0.348281.044
68_I83_A0.345251.035
85_C103_L0.343871.031
49_A53_A0.342691.027
89_Y111_G0.339531.018
59_R95_R0.337721.013
48_V62_L0.336111.008
5_G31_F0.329670.988
17_I63_I0.325430.976
3_A58_D0.325320.975
97_H135_R0.313510.940
6_S30_D0.3090.926
49_A77_V0.304090.912
4_I28_V0.304080.912
92_K121_A0.299010.897
47_K51_A0.297130.891
80_I102_V0.294230.882
74_A82_A0.293350.880
31_F57_A0.292820.878
49_A102_V0.286450.859
30_D34_Y0.283340.850
15_E19_E0.27920.837
91_A118_I0.277050.831
117_E121_A0.276780.830
86_S110_I0.27430.822
1_K29_I0.273320.819
73_A77_V0.269430.808
71_S82_A0.264150.792
11_F14_K0.261170.783
97_H132_H0.258170.774
4_I63_I0.257640.772
6_S10_G0.256040.768
13_L107_A0.255010.765
29_I51_A0.253840.761
93_M97_H0.252660.758
60_G102_V0.251390.754
11_F35_S0.25110.753
133_Q136_V0.250690.752
90_S109_V0.248960.746
2_I26_Y0.246610.739
103_L118_I0.245670.737
130_G133_Q0.243690.731
118_I121_A0.243320.730
95_R125_T0.242930.728
85_C118_I0.242280.726
29_I34_Y0.240730.722
76_K140_N0.239130.717
129_G133_Q0.237050.711
6_S33_T0.236060.708
90_S106_G0.235060.705
48_V102_V0.234020.702
134_R137_D0.233630.700
6_S11_F0.233140.699
6_S34_Y0.232280.696
131_R135_R0.232260.696
8_H40_D0.232180.696
1_K58_D0.232120.696
40_D138_K0.231850.695
16_A19_E0.230440.691
110_I115_A0.229940.689
22_E27_E0.229890.689
112_E116_K0.229110.687
87_D111_G0.228010.684
95_R122_F0.227710.683
40_D43_D0.226580.679
38_S44_F0.225880.677
5_G62_L0.225670.677
5_G14_K0.225180.675
106_G111_G0.224010.672
55_G59_R0.222180.666
6_S15_E0.220310.661
52_V79_G0.219230.657
117_E120_D0.219180.657
91_A103_L0.218860.656
45_A64_C0.217910.653
68_I94_A0.217190.651
73_A139_I0.21690.650
88_P114_L0.216560.649
17_I116_K0.214910.644
52_V77_V0.21470.644
98_N132_H0.214680.644
67_G84_L0.214550.643
16_A20_Y0.214280.642
95_R99_D0.213780.641
64_C71_S0.213130.639
99_D127_F0.211820.635
97_H131_R0.211410.634
39_V43_D0.210690.632
63_I84_L0.209890.629
87_D114_L0.20940.628
2_I123_L0.209220.627
4_I17_I0.209120.627
68_I98_N0.20770.623
10_G40_D0.207220.621
33_T39_V0.206970.621
5_G44_F0.205040.615
23_E116_K0.203960.612
68_I71_S0.203290.610
25_G28_V0.202210.606
11_F34_Y0.202020.606
76_K139_I0.201250.603
90_S111_G0.201150.603
34_Y37_D0.20060.601
17_I61_I0.200240.600
29_I56_E0.199960.600
20_Y23_E0.197650.593
137_D140_N0.197220.591
3_A48_V0.195340.586
89_Y106_G0.193720.581
82_A100_A0.193030.579
20_Y119_V0.191820.575
59_R99_D0.190910.572
1_K26_Y0.190450.571
86_S106_G0.19010.570
76_K79_G0.188850.566
18_K34_Y0.188360.565
68_I90_S0.188260.564
39_V44_F0.187870.563
81_R99_D0.187270.561
86_S109_V0.18710.561
68_I86_S0.186630.560
51_A57_A0.185020.555
4_I61_I0.184720.554
86_S105_L0.184410.553
8_H32_G0.183920.551
110_I118_I0.183040.549
86_S89_Y0.182990.549
90_S114_L0.182130.546
28_V57_A0.181410.544
33_T44_F0.181370.544
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
3s5pA1100-0.033
3he8A1100-0.031
3ph3A1100-0.03
1o1xA1100-0.026
3k7pA1100-0.023
2vvrA1100-0.021
3sgwA1100-0.017
4em8A0.9857100-0.014
2vvpA1100-0.014
2ppwA0.99291000.057

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