GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RelB - RelB antitoxin
Pfam: PF04221 (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: CL0057
Length: 83
Sequences: 1321
Seq/Len: 15.92
HH_delta: 0.167 (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
20_L38_I0.734672.380
30_A34_F0.688782.232
26_T29_D0.669592.169
54_N57_T0.614151.990
64_A67_G0.59441.926
62_A66_K0.580591.881
19_I39_V0.568891.843
12_L39_V0.554921.798
37_Q41_E0.54021.750
16_A20_L0.517421.676
60_A63_E0.491331.592
57_T60_A0.454921.474
10_E14_E0.445061.442
16_A35_L0.430681.395
74_K79_M0.420161.361
8_I35_L0.417571.353
6_V31_I0.399621.295
20_L30_A0.390611.266
17_E27_L0.389271.261
25_L33_M0.378541.226
31_I35_L0.377011.222
59_K63_E0.372491.207
75_S78_E0.371381.203
67_G73_A0.357691.159
4_I31_I0.355661.152
28_S32_N0.349091.131
57_T61_I0.342011.108
60_A64_A0.331871.075
23_L46_F0.331541.074
58_I62_A0.326951.059
74_K77_E0.32641.058
13_K27_L0.321411.041
7_R13_K0.318541.032
19_I38_I0.318111.031
7_R28_S0.314751.020
30_A38_I0.312641.013
32_N36_K0.31061.006
56_E60_A0.30240.980
35_L38_I0.299440.970
12_L32_N0.298360.967
59_K62_A0.298120.966
18_A21_E0.29350.951
12_L36_K0.29150.944
9_D12_L0.29020.940
25_L29_D0.290190.940
15_E39_V0.277870.900
8_I31_I0.277540.899
76_A79_M0.277270.898
33_M40_R0.276690.896
73_A76_A0.275780.894
5_N32_N0.272930.884
62_A65_E0.272390.883
74_K78_E0.27230.882
16_A39_V0.271220.879
19_I23_L0.265250.859
61_I64_A0.26160.848
12_L15_E0.256250.830
13_K17_E0.251890.816
19_I35_L0.246990.800
63_E67_G0.24120.781
58_I61_I0.239090.775
57_T67_G0.236530.766
8_I13_K0.235190.762
63_E66_K0.233940.758
60_A65_E0.233850.758
73_A79_M0.230360.746
22_E42_G0.229940.745
60_A67_G0.226810.735
17_E26_T0.226530.734
22_E40_R0.222950.722
4_I13_K0.222170.720
72_K78_E0.2190.710
30_A33_M0.215180.697
14_E18_A0.214910.696
8_I32_N0.214030.693
66_K76_A0.213330.691
20_L25_L0.21310.690
36_K40_R0.211770.686
4_I28_S0.211530.685
58_I65_E0.210810.683
20_L34_F0.209490.679
55_E62_A0.20740.672
37_Q46_F0.204920.664
26_T55_E0.203160.658
37_Q40_R0.199860.648
10_E62_A0.199360.646
36_K39_V0.197060.638
14_E72_K0.196860.638
21_E33_M0.196120.635
34_F46_F0.195660.634
4_I17_E0.19540.633
27_L35_L0.193540.627
61_I65_E0.192610.624
34_F38_I0.191250.620
22_E26_T0.189460.614
3_T9_D0.18640.604
14_E77_E0.185670.602
29_D32_N0.185430.601
56_E64_A0.184110.597
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
4fxeA0.927799.40.167
2ay0A0.674797.50.581
2gpeA0.602497.50.586
2k5jA0.867597.40.596
1p94A0.518197.40.598
2k9iA0.566397.10.618
2cpgA0.530197.10.622
2kelA0.530196.90.634
1k87A0.903696.70.645
1u9pA0.963996.60.651

Page generated in 0.011 seconds.