GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SpoU_sub_bind - RNA 2-O ribose methyltransferase substrate binding
Pfam: PF08032 (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: CL0101
Length: 76
Sequences: 3694
Seq/Len: 48.61
HH_delta: 0.099 (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
19_K71_K1.153153.050
20_K47_Y1.08812.878
8_V68_A1.021882.703
54_L67_V1.020972.700
21_L68_A0.810512.144
20_K69_V0.690171.825
53_V56_K0.666541.763
18_I68_A0.623091.648
51_K55_D0.61361.623
49_V53_V0.585791.549
2_I11_A0.584611.546
58_S67_V0.581871.539
21_L39_A0.580081.534
24_T51_K0.571261.511
26_E51_K0.556591.472
49_V54_L0.55581.470
25_E50_S0.540391.429
52_K55_D0.519911.375
2_I70_V0.514481.361
11_A15_G0.492341.302
2_I7_A0.483991.280
17_R71_K0.466721.234
10_E64_Q0.465451.231
6_H10_E0.463541.226
23_V46_V0.451361.194
38_L41_K0.44731.183
9_E13_K0.444051.174
70_V73_P0.443691.173
25_E48_E0.443411.173
19_K69_V0.438481.160
1_L67_V0.42591.126
49_V67_V0.422011.116
8_V66_V0.412161.090
57_L67_V0.409181.082
5_R64_Q0.399351.056
4_G49_V0.388941.029
1_L69_V0.388231.027
34_E38_L0.380471.006
54_L64_Q0.380211.006
18_I70_V0.376230.995
10_E13_K0.376150.995
3_E59_D0.373610.988
17_R73_P0.356940.944
55_D63_H0.355140.939
13_K38_L0.350830.928
5_R9_E0.349680.925
54_L63_H0.347750.920
52_K56_K0.337040.891
22_F57_L0.334450.885
38_L42_K0.334310.884
7_A60_T0.324650.859
5_R66_V0.323770.856
11_A16_P0.316830.838
23_V66_V0.315590.835
31_R34_E0.310110.820
60_T64_Q0.309720.819
35_I39_A0.309190.818
39_A46_V0.307750.814
23_V48_E0.304880.806
8_V64_Q0.302330.800
36_L48_E0.295860.782
8_V21_L0.292830.774
22_F69_V0.292240.773
20_K45_P0.289470.766
11_A70_V0.281120.744
27_K31_R0.280090.741
2_I10_E0.279310.739
59_D62_N0.279090.738
16_P73_P0.277770.735
3_E67_V0.27770.734
3_E60_T0.277050.733
37_K40_K0.276370.731
2_I6_H0.273220.723
30_K33_K0.272460.721
36_L40_K0.268630.710
21_L46_V0.266280.704
5_R31_R0.266070.704
36_L39_A0.264030.698
48_E51_K0.263760.698
5_R35_I0.260870.690
23_V28_A0.260190.688
22_F47_Y0.25850.684
6_H9_E0.255860.677
50_S53_V0.255730.676
10_E70_V0.252490.668
37_K41_K0.250440.662
9_E38_L0.2480.656
30_K37_K0.247320.654
24_T27_K0.244150.646
1_L58_S0.24340.644
12_L44_I0.241580.639
59_D64_Q0.240690.637
29_D36_L0.240550.636
9_E34_E0.239490.633
62_N69_V0.238550.631
7_A11_A0.237950.629
3_E62_N0.237390.628
22_F49_V0.235490.623
12_L21_L0.234680.621
56_K59_D0.230740.610
63_H72_P0.229970.608
6_H60_T0.226370.599
2_I18_I0.224780.594
23_V65_G0.22410.593
34_E37_K0.22320.590
18_I21_L0.221830.587
7_A64_Q0.219380.580
21_L66_V0.218670.578
11_A68_A0.217820.576
28_A50_S0.215170.569
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
1gz0A199.10.099
3nk6A0.973799.10.1
1ipaA1990.114
1x7oA0.960598.80.187
2i6dA0.894798.70.218
3zf7g0.986892.80.647
2qi2A0.947492.40.651
3agkA0.947492.20.653
3j15A0.934290.10.67
3obwA0.934289.90.672

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