GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
JmjC - JmjC domain hydroxylase
Pfam: PF02373 (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: CL0029
Length: 114
Sequences: 2657
Seq/Len: 23.31
HH_delta: 0.114 (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
31_S86_K1.131364.500
33_V82_R0.772573.073
33_V104_L0.592082.355
14_H99_H0.588552.341
31_S105_G0.57652.293
26_H90_F0.575672.290
31_S84_V0.564272.244
41_D79_P0.531752.115
39_P97_A0.513872.044
25_Y34_W0.477141.898
41_D44_K0.470041.870
33_V84_V0.453081.802
34_W93_I0.446521.776
11_T101_V0.437221.739
35_Y82_R0.424511.688
37_V80_V0.377941.503
67_F71_E0.346341.378
11_T14_H0.341611.359
3_Y11_T0.328241.306
5_G103_N0.314591.251
86_K89_E0.313731.248
7_K105_G0.301911.201
103_N109_S0.298631.188
85_Q91_V0.292441.163
3_Y21_S0.285491.136
73_L78_I0.28481.133
34_W101_V0.284771.133
14_H32_K0.282231.123
84_V104_L0.28091.117
108_I111_A0.280161.114
92_F95_P0.279061.110
36_I93_I0.278631.108
11_T17_D0.278191.106
83_F91_V0.273911.089
72_Q76_A0.27371.089
25_Y109_S0.270951.078
31_S87_P0.26991.074
48_F52_K0.268221.067
5_G9_S0.266171.059
35_Y100_Q0.264951.054
3_Y14_H0.261321.039
33_V102_F0.260671.037
68_V72_Q0.260031.034
19_G92_F0.258461.028
62_D65_N0.257421.024
103_N107_N0.256811.021
64_K69_S0.25661.021
42_A98_Y0.25581.017
38_P80_V0.255781.017
28_F108_I0.255251.015
74_K77_G0.253761.009
3_Y111_A0.251270.999
20_L111_A0.251110.999
4_I108_I0.249760.993
38_P97_A0.245320.976
63_H66_I0.244080.971
65_N71_E0.243820.970
66_I69_S0.240370.956
73_L76_A0.239720.953
11_T16_E0.238940.950
3_Y103_N0.238660.949
72_Q75_K0.238010.947
69_S72_Q0.236970.943
34_W85_Q0.234340.932
15_I98_Y0.230480.917
25_Y85_Q0.224260.892
88_G94_P0.223280.888
47_K50_R0.221760.882
36_I97_A0.221510.881
47_K51_S0.21830.868
44_K77_G0.21710.863
41_D78_I0.214780.854
45_F49_L0.214540.853
7_K106_D0.214270.852
20_L103_N0.209950.835
13_W98_Y0.209750.834
49_L52_K0.208960.831
61_L65_N0.208140.828
61_L64_K0.206480.821
9_S15_I0.206190.820
16_E20_L0.202490.805
29_G105_G0.202310.805
36_I83_F0.202250.804
32_K109_S0.200370.797
5_G98_Y0.200220.796
61_L66_I0.198660.790
9_S12_P0.198250.789
16_E111_A0.19750.786
21_S90_F0.197260.785
107_N110_E0.195210.776
28_F32_K0.194850.775
99_H111_A0.193540.770
17_D96_G0.192940.767
48_F78_I0.192570.766
38_P79_P0.190740.759
63_H67_F0.19060.758
64_K68_V0.190240.757
26_H30_G0.189760.755
48_F51_S0.188910.751
31_S104_L0.187570.746
26_H109_S0.185510.738
83_F89_E0.184880.735
3_Y99_H0.183580.730
62_D67_F0.183410.729
81_Y89_E0.182650.726
107_N111_A0.182150.724
61_L70_P0.18210.724
17_D103_N0.181890.723
29_G87_P0.179930.716
27_H85_Q0.179040.712
16_E99_H0.178230.709
40_E48_F0.177640.707
44_K47_K0.177060.704
93_I101_V0.17670.703
26_H89_E0.175440.698
10_Y100_Q0.172190.685
2_L50_R0.1720.684
3_Y85_Q0.171050.680
11_T32_K0.17090.680
15_I39_P0.170430.678
9_S103_N0.169550.674
89_E94_P0.169490.674
11_T99_H0.167510.666
20_L25_Y0.167310.665
37_V45_F0.166720.663
32_K99_H0.166090.661
27_H103_N0.166020.660
19_G95_P0.165980.660
44_K48_F0.165780.659
47_K98_Y0.165370.658
41_D52_K0.165140.657
25_Y32_K0.165030.656
14_H101_V0.164820.656
3_Y34_W0.164740.655
41_D46_E0.164510.654
44_K50_R0.164440.654
16_E88_G0.164430.654
68_V71_E0.164190.653
93_I97_A0.162730.647
9_S20_L0.162360.646
81_Y97_A0.161920.644
12_P35_Y0.161680.643
65_N69_S0.161190.641
16_E94_P0.160790.640
34_W103_N0.160.636
37_V41_D0.159880.636
17_D111_A0.159620.635
3_Y17_D0.159030.633
36_I39_P0.158570.631
40_E44_K0.158540.631
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
4gjzA0.947499.80.114
2ox0A199.80.121
3dxtA199.80.125
3optA199.80.13
4igqA199.80.13
3avrA0.956199.80.14
2xxzA0.956199.80.144
3kv5D0.88699.80.148
4askA0.956199.80.153
3k2oA0.982599.80.163

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