GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Eco57I - Eco57I restriction-modification methylase
Pfam: PF07669 (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: CL0063
Length: 106
Sequences: 4856
Seq/Len: 45.81
HH_delta: 0.134 (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
43_L47_L1.196633.482
67_K71_N1.069923.113
68_F72_N0.984072.863
76_K101_K0.853882.485
39_S47_L0.850412.474
46_Y101_K0.81332.367
36_I51_T0.796262.317
48_S99_I0.761242.215
40_L73_T0.750842.185
39_S49_F0.711792.071
38_K41_N0.697392.029
64_K67_K0.686381.997
8_G49_F0.655731.908
8_G39_S0.643191.872
46_Y76_K0.639871.862
53_N80_D0.634141.845
63_K67_K0.587121.708
51_T98_I0.572511.666
9_N12_Y0.532651.550
9_N88_F0.495561.442
5_V46_Y0.482821.405
47_L100_F0.479471.395
53_N94_Y0.467811.361
38_K42_L0.467341.360
6_V39_S0.463041.347
56_L78_I0.447431.302
33_I62_G0.447291.302
13_I31_L0.446851.300
32_Y55_F0.434381.264
36_I49_F0.411991.199
36_I98_I0.40021.164
44_N103_S0.394291.147
44_N101_K0.392451.142
84_R94_Y0.391641.140
37_E68_F0.387341.127
19_S22_K0.385591.122
74_N103_S0.382461.113
37_E41_N0.363791.059
32_Y52_P0.356771.038
79_I97_I0.354751.032
20_K24_K0.351041.021
73_T100_F0.350371.019
20_K23_K0.349231.016
34_L38_K0.349031.016
2_K42_L0.348011.013
81_F87_V0.34471.003
50_I88_F0.342530.997
40_L69_L0.338390.985
73_T76_K0.335250.975
69_L100_F0.333360.970
22_K25_K0.331880.966
84_R92_S0.33070.962
21_K24_K0.323360.941
83_E94_Y0.321240.935
74_N101_K0.320670.933
14_K18_L0.318580.927
50_I97_I0.318360.926
6_V43_L0.316920.922
40_L68_F0.316810.922
40_L74_N0.309640.901
75_I100_F0.308540.898
83_E92_S0.308540.898
5_V48_S0.30850.898
54_S62_G0.30670.892
13_I18_L0.301010.876
33_I54_S0.300010.873
77_K99_I0.292760.852
70_L75_I0.291250.847
64_K68_F0.291040.847
18_L21_K0.287930.838
55_F96_C0.287930.838
18_L22_K0.287920.838
14_K31_L0.287020.835
12_Y95_T0.286650.834
73_T102_K0.286010.832
46_Y99_I0.280660.817
21_K25_K0.280150.815
76_K99_I0.27990.814
12_Y32_Y0.27880.811
19_S24_K0.272430.793
51_T55_F0.271470.790
4_D44_N0.271360.790
80_D84_R0.269670.785
9_N48_S0.26450.770
62_G66_R0.2630.765
61_Y64_K0.257570.749
60_K63_K0.25710.748
12_Y55_F0.25370.738
78_I96_C0.251040.730
53_N96_C0.247750.721
40_L72_N0.246590.718
32_Y51_T0.242370.705
75_I78_I0.240460.700
22_K26_K0.239440.697
73_T103_S0.239050.696
81_F97_I0.239040.696
56_L96_C0.2370.690
30_D54_S0.235830.686
16_K26_K0.235580.685
66_R81_F0.234150.681
43_L102_K0.233250.679
12_Y93_V0.232360.676
70_L73_T0.230970.672
22_K41_N0.230720.671
40_L100_F0.229890.669
15_I28_K0.22970.668
16_K29_S0.226230.658
23_K26_K0.225940.657
59_G92_S0.225440.656
59_G62_G0.22450.653
13_I30_D0.223450.650
34_L37_E0.223320.650
75_I82_G0.222240.647
22_K27_K0.222130.646
15_I20_K0.222080.646
82_G95_T0.221670.645
94_Y97_I0.221420.644
89_E92_S0.221050.643
15_I29_S0.220950.643
50_I63_K0.215480.627
18_L26_K0.214420.624
4_D75_I0.21420.623
52_P88_F0.214090.623
12_Y35_F0.213530.621
13_I82_G0.213320.621
41_N72_N0.212540.618
15_I23_K0.210260.612
16_K21_K0.210120.611
68_F71_N0.209990.611
81_F84_R0.209240.609
65_L69_L0.208090.605
14_K30_D0.20610.600
73_T101_K0.205660.598
20_K27_K0.205130.597
17_S20_K0.204830.596
75_I98_I0.204720.596
34_L58_S0.202780.590
12_Y51_T0.20260.590
50_I70_L0.201040.585
23_K27_K0.201010.585
79_I82_G0.200220.583
13_I32_Y0.199640.581
50_I95_T0.199180.580
58_S61_Y0.198980.579
56_L80_D0.197850.576
88_F95_T0.196940.573
54_S59_G0.196920.573
58_S80_D0.195290.568
76_K89_E0.194420.566
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
3ufbA0.981199.80.134
3lkdA0.981199.70.181
3khkA0.981199.70.191
2ar0A0.981199.70.205
3s1sA0.990699.70.217
2okcA0.981199.60.284
2f8lA0.971799.40.331
2ih2A0.952899.40.361
3tmaA0.7736970.712
3lduA0.764296.90.717

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