GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mur_ligase - Mur ligase family catalytic domain
Pfam: PF01225 (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: 83
Sequences: 5768
Seq/Len: 69.49
HH_delta: 0.031 (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
4_G16_A1.956853.486
20_A40_A1.600492.851
34_D38_K1.563752.786
26_V30_D1.200312.139
36_I63_V1.149112.047
34_D37_A1.098691.957
45_V65_V1.065791.899
6_S12_V1.058181.885
60_A63_V1.041041.855
19_F44_V1.036471.847
6_S11_K1.028661.833
6_S16_A1.024581.825
46_D71_T0.993611.770
73_Q77_E0.951551.695
13_S16_A0.943361.681
60_A64_P0.867281.545
22_K46_D0.864341.540
19_F75_L0.844761.505
72_R76_G0.809321.442
33_E36_I0.807031.438
17_L42_A0.798451.423
70_D73_Q0.744751.327
33_E37_A0.736481.312
77_E80_A0.716611.277
35_A40_A0.709461.264
48_D67_P0.69291.234
12_V40_A0.67541.203
9_S12_V0.664981.185
36_I43_V0.661431.178
29_H71_T0.632851.128
19_F71_T0.631991.126
23_G26_V0.618051.101
3_H15_G0.612151.091
9_S35_A0.606651.081
17_L38_K0.600171.069
20_A43_V0.597661.065
32_I43_V0.595341.061
7_I26_V0.562751.003
29_H46_D0.556970.992
3_H27_D0.52270.931
35_A39_G0.511810.912
68_V74_A0.510410.909
7_I75_L0.508360.906
46_D70_D0.507550.904
12_V16_A0.507440.904
2_I17_L0.489980.873
76_G80_A0.482890.860
4_G13_S0.478160.852
21_I72_R0.468490.835
2_I42_A0.46720.832
3_H16_A0.463770.826
20_A32_I0.461060.821
36_I41_A0.455950.812
22_K47_K0.452820.807
5_I17_L0.452220.806
45_V67_P0.44670.796
17_L20_A0.444040.791
21_I38_K0.440030.784
17_L44_V0.439290.783
26_V31_F0.434240.774
71_T74_A0.426450.760
6_S13_S0.421690.751
21_I75_L0.413980.738
76_G79_A0.400840.714
79_A82_F0.400430.713
43_V65_V0.399680.712
20_A44_V0.395620.705
74_A78_L0.393010.700
18_F31_F0.392780.700
10_R13_S0.385950.688
43_V63_V0.381690.680
44_V74_A0.37050.660
7_I76_G0.369960.659
21_I24_E0.365840.652
68_V71_T0.364250.649
29_H32_I0.363770.648
62_D65_V0.362010.645
42_A64_P0.358450.639
27_D47_K0.352040.627
77_E81_A0.350890.625
69_E74_A0.350540.625
18_F78_L0.343940.613
8_D34_D0.33770.602
23_G28_G0.336230.599
69_E73_Q0.333940.595
20_A45_V0.332730.593
18_F21_I0.331010.590
7_I72_R0.329180.586
29_H45_V0.326720.582
19_F74_A0.323050.576
42_A66_I0.317930.566
19_F78_L0.316530.564
10_R27_D0.312610.557
76_G82_F0.312320.556
5_I19_F0.311160.554
31_F44_V0.306440.546
4_G11_K0.301670.537
69_E77_E0.301110.536
7_I11_K0.298770.532
27_D43_V0.29670.529
2_I66_I0.290620.518
7_I82_F0.287980.513
32_I49_A0.28390.506
14_P17_L0.282670.504
12_V35_A0.282510.503
5_I29_H0.279840.499
47_K67_P0.278170.496
35_A38_K0.277760.495
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
1e8cA0.975999.50.031
2wtzA0.939899.50.045
1gg4A0.879599.30.151
2am1A0.855499.20.173
4hv4A194.20.68
3hn7A1940.682
1j6uA0.98892.60.698
3eagA190.60.713
2x5oA0.867585.40.737
2f00A0.975983.50.743

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