GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lactamase_B_4 - tRNase Z endonuclease
Pfam: PF13691 (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: CL0381
Length: 63
Sequences: 11844
Seq/Len: 188
HH_delta: 0.102 (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
22_R48_N2.601253.445
24_Y49_D2.295193.039
18_F23_R2.097652.778
22_R49_D1.447431.917
26_F53_T1.407321.864
23_R48_N1.280461.696
16_L23_R1.263171.673
28_N54_G1.178321.560
24_Y51_F1.131531.498
29_C50_I1.118951.482
23_R46_K1.104011.462
56_S59_E1.044711.383
55_L58_W0.98321.302
52_L61_I0.934831.238
29_C52_L0.90221.195
43_K46_K0.895181.185
41_K44_L0.893061.183
58_W62_G0.879811.165
31_E58_W0.831941.102
19_F22_R0.797361.056
15_L26_F0.78141.035
55_L61_I0.770191.020
53_T56_S0.769631.019
56_S60_N0.759171.005
23_R47_L0.728260.964
14_S31_E0.718250.951
22_R46_K0.71170.942
26_F51_F0.711170.942
35_R38_N0.700420.927
39_E42_I0.68970.913
38_N41_K0.674630.893
55_L62_G0.671360.889
54_G59_E0.660790.875
25_L47_L0.659430.873
36_A39_E0.650490.861
30_G52_L0.647590.858
52_L62_G0.639370.847
31_E36_A0.639010.846
54_G60_N0.635020.841
19_F24_Y0.634290.840
31_E62_G0.631190.836
13_P31_E0.590370.782
31_E55_L0.589620.781
28_N59_E0.589560.781
37_C41_K0.568070.752
49_D52_L0.55520.735
31_E34_Q0.550710.729
52_L58_W0.542930.719
14_S29_C0.537280.711
41_K46_K0.534190.707
25_L29_C0.532180.705
35_R39_E0.524220.694
13_P62_G0.516230.684
23_R42_I0.513950.681
52_L55_L0.512350.678
17_L26_F0.504660.668
16_L25_L0.503850.667
33_T37_C0.49680.658
13_P55_L0.496550.658
41_K45_S0.495230.656
32_G63_G0.49090.650
34_Q38_N0.485670.643
36_A40_H0.480290.636
28_N61_I0.452730.600
26_F29_C0.452350.599
18_F21_S0.434620.576
17_L24_Y0.429660.569
18_F42_I0.429370.569
33_T36_A0.429330.569
16_L47_L0.417980.553
29_C33_T0.416180.551
18_F45_S0.413690.548
28_N56_S0.413330.547
15_L53_T0.411960.546
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
3zwfA0.968399.10.102
2cbnA0.9683990.158
1y44A0.9683990.168
3tp9A0.968398.90.188
1zkpA0.952498.90.197
1p9eA0.968398.90.2
2i7xA0.968398.90.2
3r2uA0.968398.80.212
1ztcA0.968398.80.215
3zq4A0.968398.80.215

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