GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Methyltransf_1N - 6-O-methylguanine DNA methyltransferase ribonuclease-like domain
Pfam: PF02870 (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: 77
Sequences: 2722
Seq/Len: 35.35
HH_delta: 0.116 (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
61_E67_R1.258663.423
19_S76_D0.985382.680
58_Q71_F0.857742.333
8_D13_P0.822422.237
19_S22_G0.731161.989
61_E66_E0.71241.938
16_L23_L0.680621.851
9_S12_G0.646931.760
5_T56_K0.629781.713
16_L55_A0.591881.610
58_Q73_L0.578531.574
10_P63_F0.577291.570
54_E58_Q0.575731.566
18_A52_L0.551791.501
6_T13_P0.544631.481
58_Q67_R0.54371.479
58_Q68_T0.541861.474
22_G76_D0.532321.448
19_S24_C0.529511.440
54_E57_Q0.498021.355
21_K76_D0.464391.263
59_L63_F0.461761.256
23_L55_A0.459221.249
17_A24_C0.458871.248
11_L14_L0.455951.240
7_I60_D0.442461.203
7_I56_K0.435481.184
14_L26_I0.429921.169
67_R71_F0.414821.128
6_T15_L0.413861.126
9_S14_L0.409061.113
39_L42_W0.407071.107
62_Y65_G0.402261.094
60_D64_A0.401141.091
23_L26_I0.399361.086
16_L52_L0.397281.081
17_A25_G0.393871.071
56_K60_D0.392091.066
57_Q61_E0.391531.065
18_A55_A0.378961.031
49_A52_L0.36530.994
59_L62_Y0.363210.988
57_Q60_D0.359550.978
24_C76_D0.354480.964
18_A21_K0.350620.954
15_L29_E0.350410.953
68_T71_F0.340740.927
58_Q72_D0.334960.911
4_Y17_A0.327440.891
51_L54_E0.326250.887
22_G74_P0.325780.886
15_L27_D0.321860.875
58_Q61_E0.32170.875
62_Y71_F0.311830.848
38_D42_W0.306930.835
60_D63_F0.306050.832
41_K44_P0.298430.812
27_D31_Q0.297440.809
40_P45_Q0.284790.775
67_R72_D0.281020.764
22_G75_L0.280290.762
48_E53_A0.276770.753
52_L55_A0.275910.750
67_R70_E0.26950.733
18_A51_L0.263860.718
13_P32_D0.262660.714
18_A49_A0.256740.698
37_A40_P0.255850.696
39_L43_F0.255410.695
25_G31_Q0.255320.694
31_Q34_E0.25160.684
4_Y44_P0.248380.676
53_A57_Q0.247780.674
37_A45_Q0.247030.672
26_I59_L0.24520.667
38_D41_K0.244830.666
16_L26_I0.241380.657
6_T29_E0.233370.635
11_L63_F0.228030.620
5_T52_L0.226940.617
57_Q64_A0.22540.613
61_E68_T0.225330.613
37_A42_W0.223850.609
7_I14_L0.223740.609
54_E73_L0.217210.591
55_A58_Q0.215870.587
43_F46_D0.215240.585
14_L28_F0.214880.584
14_L23_L0.213410.580
4_Y15_L0.213260.580
26_I55_A0.209720.570
14_L62_Y0.209070.569
15_L32_D0.206210.561
16_L58_Q0.205320.558
33_F37_A0.204720.557
40_P43_F0.204040.555
13_P29_E0.203170.553
58_Q62_Y0.202390.550
48_E52_L0.201490.548
11_L59_L0.200730.546
25_G33_F0.195770.532
5_T53_A0.195220.531
4_Y34_E0.195180.531
65_G70_E0.194930.530
31_Q45_Q0.192120.523
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
4bhbA0.922198.90.116
1sfeA0.98798.90.127
1wrjA0.857198.80.149
3l00A0.97498.80.159
1eh6A0.97498.70.187
2g7hA0.935197.70.421
1mgtA0.987970.501
4kwyA0.88317.20.832
3f9mA16.50.835
3k9tA0.93516.10.837

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