GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YjgF_endoribonc - YjgFchorismate_mutase-like putative endoribonuclease
Pfam: PF14588 (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: CL0534
Length: 148
Sequences: 4229
Seq/Len: 28.57
HH_delta: 0.024 (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
64_R116_E1.782873.517
89_K143_E1.484012.927
71_L81_L1.304292.573
37_L138_A1.279362.524
74_L146_A1.245392.457
70_A144_L1.23682.440
79_G83_R1.154682.278
27_V147_E1.113132.196
93_F129_V1.089572.149
130_G133_S1.068492.108
64_R68_L1.063982.099
71_L75_K1.050282.072
62_A139_P1.026832.026
60_Y112_D0.936581.848
90_L144_L0.898281.772
68_L117_V0.888891.753
26_R29_N0.884071.744
32_Y145_I0.879611.735
31_L79_G0.870921.718
68_L71_L0.840731.658
38_P138_A0.84031.658
65_L69_N0.808931.596
27_V88_V0.803861.586
26_R31_L0.803041.584
127_S143_E0.790811.560
29_N147_E0.761041.501
133_S137_N0.744231.468
64_R117_V0.741071.462
99_D139_P0.740331.460
30_L147_E0.729331.439
94_V128_A0.724651.429
60_Y102_E0.715041.411
80_D83_R0.669941.322
95_N99_D0.646821.276
75_K80_D0.644771.272
31_L77_A0.631831.246
20_N112_D0.617941.219
91_T127_S0.60631.196
38_P66_C0.605261.194
97_T130_G0.600761.185
84_V118_F0.595051.174
33_V73_A0.590691.165
119_G123_R0.586621.157
36_Q73_A0.584381.153
99_D102_E0.571131.127
14_P23_P0.548071.081
67_A114_L0.545961.077
13_E75_K0.545281.076
91_T143_E0.542731.071
114_L126_R0.538261.062
93_F127_S0.53721.060
96_S99_D0.52761.041
65_L68_L0.525821.037
120_E123_R0.522881.031
95_N137_N0.52171.029
113_L116_E0.521311.028
35_G141_E0.510871.008
81_L84_V0.506891.000
95_N133_S0.504050.994
26_R79_G0.501050.988
24_A77_A0.500980.988
33_V144_L0.49950.985
40_D43_K0.496080.979
28_G147_E0.49170.970
72_A75_K0.490130.967
18_V136_L0.477830.943
61_E64_R0.474220.935
102_E112_D0.472280.932
71_L117_V0.467790.923
95_N131_V0.459720.907
93_F131_V0.459490.906
97_T133_S0.457470.902
64_R113_L0.457080.902
74_L79_G0.4440.876
24_A73_A0.4420.872
24_A31_L0.44040.869
27_V32_Y0.438560.865
30_L145_I0.433430.855
36_Q69_N0.432660.853
37_L136_L0.430990.850
98_P133_S0.419740.828
90_L114_L0.417580.824
112_D115_V0.416520.822
60_Y113_L0.409450.808
30_L88_V0.408260.805
84_V144_L0.406660.802
67_A117_V0.403570.796
89_K145_I0.40110.791
63_A140_V0.394810.779
115_V123_R0.390830.771
66_C142_I0.382780.755
34_S125_A0.38040.750
74_L84_V0.37960.749
112_D116_E0.378920.747
25_V125_A0.369710.729
75_K78_L0.363410.717
40_D65_L0.361770.714
88_V147_E0.360480.711
95_N139_P0.358480.707
51_G61_E0.35790.706
113_L117_V0.355810.702
18_V21_Y0.355020.700
84_V146_A0.348020.687
100_F128_A0.345450.681
95_N132_A0.345060.681
13_E42_G0.342030.675
68_L72_A0.340030.671
66_C70_A0.339640.670
36_Q66_C0.33910.669
21_Y37_L0.334380.660
94_V97_T0.330140.651
24_A33_V0.329680.650
134_L141_E0.329620.650
81_L117_V0.329220.649
89_K127_S0.324870.641
100_F135_P0.32380.639
96_S133_S0.322830.637
70_A142_I0.320010.631
26_R77_A0.319470.630
96_S139_P0.315950.623
60_Y116_E0.314640.621
25_V88_V0.307860.607
27_V30_L0.306850.605
60_Y64_R0.304170.600
22_V123_R0.303750.599
82_D119_G0.30370.599
74_L78_L0.302840.597
36_Q70_A0.301550.595
71_L118_F0.29780.587
12_P16_A0.292210.576
38_P62_A0.291410.575
92_G126_R0.289660.571
22_V25_V0.288180.568
30_L33_V0.286740.566
90_L118_F0.284580.561
79_G147_E0.284190.561
63_A142_I0.279070.551
78_L83_R0.279060.550
38_P139_P0.277610.548
92_G140_V0.277060.547
39_R138_A0.272910.538
71_L80_D0.27280.538
31_L73_A0.272720.538
98_P132_A0.272380.537
18_V23_P0.270940.534
69_N72_A0.270840.534
74_L144_L0.27060.534
67_A140_V0.270530.534
22_V124_H0.270290.533
24_A70_A0.268910.530
37_L66_C0.26850.530
67_A142_I0.26760.528
82_D120_E0.267320.527
92_G142_I0.26650.526
69_N73_A0.264890.523
33_V70_A0.264710.522
126_R135_P0.264110.521
89_K125_A0.263710.520
29_N79_G0.262030.517
83_R147_E0.26040.514
41_D72_A0.260170.513
91_T145_I0.257020.507
70_A73_A0.256340.506
131_V134_L0.256070.505
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
2otmA11000.024
3d01A11000.058
3k0tA0.86491000.153
1qahA0.86491000.173
3quwA0.86491000.173
3r0pA0.85811000.175
3vczA0.86491000.177
3m1xA0.87161000.179
3lybA0.87841000.179
3l7qA0.83781000.179

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