GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DMRL_synthase - 67-dimethyl-8-ribityllumazine synthase
Pfam: PF00885 (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: 144
Sequences: 1661
Seq/Len: 11.53
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
7_A57_L0.864973.225
65_A134_A0.822533.066
22_L41_V0.787612.936
93_D97_E0.742682.769
40_E63_Y0.678882.531
28_E128_R0.664612.478
4_L138_A0.600662.239
26_L30_K0.577382.153
54_A68_A0.548842.046
42_I57_L0.544392.030
10_V22_L0.518051.931
74_R110_D0.516221.925
55_K97_E0.514091.917
76_E117_E0.506691.889
15_E19_D0.491981.834
16_E116_L0.48821.820
126_K129_E0.485461.810
68_A91_L0.467451.743
72_V83_V0.45551.698
50_L106_V0.451981.685
59_E99_G0.443291.653
86_A89_R0.442021.648
3_G38_N0.441341.645
29_L34_V0.438991.637
55_K59_E0.438961.636
78_D81_E0.431371.608
28_E132_E0.421831.573
103_I133_A0.417771.557
89_R93_D0.405891.513
44_V53_A0.396341.478
81_E84_A0.394371.470
87_V106_V0.388341.448
12_R136_E0.387071.443
52_L141_L0.377841.409
6_I138_A0.370071.380
29_L131_A0.368511.374
19_D43_R0.364031.357
10_V41_V0.361561.348
17_I71_C0.360821.345
53_A141_L0.357641.333
27_E31_R0.355841.327
10_V18_T0.353381.317
29_L67_I0.349031.301
15_E43_R0.346541.292
113_E117_E0.345221.287
48_F104_F0.343111.279
51_P90_G0.335361.250
9_V50_L0.331621.236
80_F84_A0.331411.236
78_D110_D0.3261.215
58_A66_V0.32411.208
55_K99_G0.322511.202
16_E112_E0.321171.197
23_E27_E0.319311.190
52_L95_S0.313981.171
54_A66_V0.311271.160
78_D82_Y0.308541.150
20_R23_E0.30631.142
55_K96_L0.302741.129
35_A38_N0.28961.080
103_I130_A0.285731.065
56_R99_G0.284641.061
105_G130_A0.283311.056
58_A100_I0.282771.054
4_L142_R0.281311.049
17_I116_L0.27721.033
48_F88_S0.276791.032
9_V54_A0.268531.001
112_E121_G0.267550.997
69_L105_G0.266510.994
32_H135_L0.264860.987
10_V43_R0.264670.987
5_R38_N0.263760.983
103_I134_A0.263070.981
19_D23_E0.262690.979
26_L39_I0.261750.976
128_R132_E0.257830.961
11_S18_T0.257380.960
6_I34_V0.257240.959
11_S50_L0.25670.957
88_S104_F0.254330.948
58_A94_L0.253850.946
110_D114_Q0.24940.930
7_A63_Y0.248560.927
87_V104_F0.246060.917
134_A138_A0.243590.908
122_K125_N0.243310.907
50_L87_V0.240080.895
82_Y85_N0.239350.892
28_E31_R0.238350.889
72_V84_A0.237230.884
18_T71_C0.236570.882
30_K39_I0.236440.881
74_R78_D0.236290.881
55_K98_Y0.235880.879
20_R119_A0.23230.866
92_M95_S0.231420.863
45_P137_M0.231420.863
93_D96_L0.231080.861
79_H118_R0.228840.853
26_L41_V0.226790.845
90_G94_L0.225770.842
58_A98_Y0.224040.835
85_N89_R0.223110.832
117_E121_G0.222650.830
7_A42_I0.221960.827
56_R141_L0.220050.820
121_G124_G0.219720.819
54_A58_A0.218870.816
23_E26_L0.218340.814
94_L98_Y0.21610.806
51_P92_M0.214920.801
67_I131_A0.214890.801
56_R59_E0.213920.798
119_A125_N0.211770.789
17_I119_A0.210020.783
66_V102_V0.209280.780
22_L43_R0.20910.780
6_I29_L0.206150.769
112_E116_L0.205750.767
130_A133_A0.204660.763
94_L102_V0.202880.756
85_N88_S0.201840.752
21_L127_G0.201010.749
126_K130_A0.200870.749
65_A138_A0.200120.746
4_L139_K0.199730.745
14_N71_C0.197080.735
3_G62_R0.1970.734
48_F82_Y0.196790.734
77_T118_R0.196310.732
80_F130_A0.196050.731
62_R142_R0.195390.728
34_V135_L0.195270.728
8_I25_A0.190750.711
59_E97_E0.189140.705
67_I134_A0.18880.704
52_L94_L0.188650.703
52_L56_R0.188640.703
39_I131_A0.187210.698
65_A101_P0.186910.697
8_I67_I0.186880.697
50_L68_A0.186770.696
6_I68_A0.185810.693
116_L121_G0.185610.692
108_T126_K0.185190.690
6_I38_N0.185110.690
8_I22_L0.183890.686
78_D85_N0.183750.685
60_S63_Y0.183720.685
65_A103_I0.183560.684
3_G142_R0.182480.680
52_L99_G0.182470.680
132_E136_E0.182370.680
109_P115_A0.181140.675
91_L102_V0.180360.672
135_L139_K0.179160.668
54_A94_L0.177980.664
28_E32_H0.177240.661
50_L91_L0.177080.660
52_L96_L0.177060.660
63_Y100_I0.176490.658
78_D84_A0.176380.658
21_L24_G0.176160.657
66_V98_Y0.175720.655
6_I131_A0.174930.652
54_A91_L0.174810.652
95_S98_Y0.174110.649
46_G49_E0.17250.643
59_E98_Y0.172210.642
22_L25_A0.170810.637
30_K35_A0.169920.633
112_E117_E0.167310.624
105_G115_A0.166930.622
42_I53_A0.166860.622
27_E89_R0.166030.619
80_F110_D0.16480.614
5_R61_G0.164560.613
6_I67_I0.164510.613
53_A137_M0.163080.608
11_S109_P0.162650.606
24_G127_G0.16140.602
74_R83_V0.161270.601
17_I107_L0.15870.592
86_A90_G0.15850.591
5_R62_R0.157360.587
82_Y104_F0.155970.581
68_A84_A0.155570.580
52_L101_P0.155290.579
103_I137_M0.154830.577
34_V131_A0.154280.575
137_M140_L0.154030.574
60_S98_Y0.153490.572
80_F107_L0.152690.569
6_I134_A0.152380.568
78_D88_S0.15220.567
111_T114_Q0.149940.559
64_D142_R0.149770.558
72_V85_N0.149740.558
14_N18_T0.149290.557
17_I112_E0.149170.556
61_G100_I0.147450.550
28_E131_A0.146960.548
120_G124_G0.14640.546
24_G119_A0.146140.545
8_I39_I0.145050.541
66_V101_P0.143670.536
40_E62_R0.143610.535
95_S103_I0.142710.532
32_H40_E0.142550.531
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
3nq4A11000.001
1c41A11000.01
1rvvA11000.01
1hqkA11000.01
1c2yA0.99311000.011
1di0A11000.016
1kz1A0.99311000.018
2obxA11000.021
2i0fA0.97921000.025
1ejbA11000.032

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