GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mrr_cat - Restriction endonuclease
Pfam: PF04471 (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: CL0236
Length: 115
Sequences: 2570
Seq/Len: 22.35
HH_delta: 0.221 (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
73_A81_G0.86763.133
13_V54_C0.793232.865
89_F105_L0.7242.615
35_G53_Q0.59292.141
69_L83_I0.576052.080
63_V67_R0.56132.027
69_L81_G0.539761.949
13_V84_V0.510251.843
107_D110_D0.49511.788
51_L78_A0.491581.775
65_A83_I0.475351.717
88_G107_D0.471591.703
64_K68_Q0.464431.677
10_E55_K0.462541.670
37_D55_K0.448231.619
67_R96_F0.447031.614
9_F54_C0.435241.572
70_I74_K0.433071.564
6_G56_R0.431041.557
17_L40_A0.414111.496
80_K104_E0.40371.458
60_K88_G0.400691.447
5_S8_E0.395111.427
14_A38_I0.394511.425
70_I96_F0.381821.379
91_P95_E0.378311.366
10_E53_Q0.374271.352
90_T93_A0.369831.336
33_D53_Q0.364631.317
6_G10_E0.362231.308
89_F93_A0.357571.291
38_I52_V0.350991.268
14_A27_V0.345151.246
36_I53_Q0.344611.245
48_E80_K0.343131.239
62_D65_A0.338311.222
65_A68_Q0.337721.220
41_E49_R0.337361.218
13_V17_L0.335111.210
25_V38_I0.328611.187
60_K90_T0.320161.156
84_V106_I0.318371.150
14_A18_R0.316991.145
70_I101_K0.314511.136
50_I80_K0.314131.134
85_T108_G0.30491.101
63_V96_F0.293421.060
57_Y61_V0.289531.046
6_G38_I0.285511.031
5_S56_R0.281431.016
17_L52_V0.280641.014
35_G72_K0.276891.000
75_K96_F0.276330.998
50_I82_I0.276020.997
36_I72_K0.272470.984
17_L22_Y0.271830.982
9_F56_R0.270840.978
40_A52_V0.26720.965
10_E37_D0.266810.964
49_R79_D0.261340.944
85_T88_G0.256180.925
57_Y65_A0.252880.913
37_D53_Q0.251550.908
13_V38_I0.249940.903
52_V84_V0.24860.898
95_E98_E0.247870.895
56_R86_S0.246820.891
85_T89_F0.244740.884
7_R30_G0.242670.876
106_I110_D0.241870.873
57_Y86_S0.240330.868
11_E27_V0.237780.859
57_Y69_L0.235390.850
81_G103_I0.235220.849
65_A69_L0.234320.846
81_G84_V0.229190.828
85_T105_L0.225790.815
69_L72_K0.225640.815
69_L73_A0.225350.814
61_V89_F0.224910.812
82_I104_E0.223920.809
8_E11_E0.223470.807
41_E44_D0.223290.806
17_L82_I0.219920.794
83_I89_F0.219350.792
9_F85_T0.217480.785
71_G96_F0.215260.777
97_A105_L0.214560.775
38_I54_C0.213810.772
6_G54_C0.213480.771
25_V28_T0.213310.770
13_V52_V0.212950.769
16_L20_L0.212250.767
14_A25_V0.210350.760
62_D90_T0.209960.758
34_G76_Y0.209610.757
67_R71_G0.209490.757
69_L86_S0.208150.752
67_R72_K0.207880.751
104_E109_E0.207360.749
104_E110_D0.204780.740
70_I79_D0.204060.737
68_Q71_G0.202040.730
67_R97_A0.201130.726
63_V92_E0.200660.725
7_R11_E0.199930.722
8_E56_R0.199640.721
35_G55_K0.198950.718
15_E19_K0.196480.710
26_E41_E0.194040.701
17_L21_G0.192940.697
32_G92_E0.192050.694
48_E79_D0.191550.692
10_E35_G0.190970.690
23_T44_D0.189750.685
64_K67_R0.189480.684
34_G63_V0.187910.679
94_K98_E0.186580.674
71_G74_K0.186510.674
39_I76_Y0.184420.666
14_A82_I0.183850.664
70_I103_I0.181970.657
20_L43_D0.181360.655
11_E15_E0.180440.652
44_D48_E0.179170.647
26_E49_R0.179020.647
88_G94_K0.177580.641
20_L51_L0.177320.640
30_G111_L0.177080.640
57_Y63_V0.176140.636
101_K109_E0.176110.636
74_K101_K0.175140.633
67_R75_K0.17430.629
6_G55_K0.174190.629
60_K110_D0.174110.629
108_G111_L0.174090.629
6_G53_Q0.173920.628
26_E32_G0.173860.628
103_I107_D0.17360.627
71_G75_K0.173170.625
93_A97_A0.172780.624
89_F97_A0.172770.624
66_V103_I0.171860.621
106_I111_L0.171680.620
51_L76_Y0.171460.619
28_T39_I0.171310.619
11_E14_A0.171060.618
39_I49_R0.170870.617
94_K107_D0.169610.613
22_Y52_V0.168590.609
62_D67_R0.168580.609
69_L78_A0.168550.609
63_V90_T0.166110.600
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
4f0qA0.982699.60.221
1y88A0.956599.60.222
1xmxA0.965297.80.62
1ob8A0.895797.60.638
2eo0A0.956597.60.64
1hh1A0.939197.60.643
1gefA0.878397.60.643
2wcwA0.956597.30.668
3fovA0.9043970.688
2vldA0.947895.30.739

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