GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YiiD_Cterm - Putative thioesterase (yiiD_Cterm)
Pfam: PF09500 (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: CL0050
Length: 144
Sequences: 4055
Seq/Len: 28.16
HH_delta: 0.078 (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
23_T33_S1.244993.001
31_E96_R1.14232.754
96_R127_Y1.115172.688
79_A119_R1.094532.639
24_S31_E1.085642.617
24_S29_R1.053222.539
29_R98_S0.963852.324
31_E94_T0.927782.237
21_K33_S0.905092.182
32_L58_A0.903412.178
29_R96_R0.890232.146
125_E132_L0.883732.130
26_T29_R0.858882.071
55_A136_F0.852382.055
52_Y81_S0.848872.046
87_K131_E0.820881.979
34_A50_S0.798411.925
128_S131_E0.795091.917
33_S94_T0.746361.799
98_S125_E0.723041.743
80_D84_R0.716791.728
123_E135_E0.699691.687
52_Y83_I0.692481.669
23_T31_E0.692281.669
58_A95_A0.672611.621
14_L50_S0.648981.565
56_T78_I0.645541.556
125_E135_E0.641681.547
100_P123_E0.627171.512
98_S123_E0.624761.506
51_L134_A0.619241.493
63_V120_I0.608161.466
89_V133_A0.5861.413
49_G53_S0.571491.378
99_L115_G0.559271.348
59_G138_G0.558551.347
59_G124_V0.550151.326
114_R119_R0.549771.325
123_E137_T0.549481.325
55_A124_V0.54711.319
52_Y85_Y0.529951.278
55_A126_I0.528781.275
54_L95_A0.512381.235
34_A54_L0.511621.233
36_L46_M0.497741.200
83_I134_A0.481671.161
95_A124_V0.475911.147
86_L135_E0.458861.106
89_V93_F0.448831.082
127_Y130_G0.430951.039
33_S92_D0.427971.032
127_Y132_L0.422071.018
14_L53_S0.409570.987
100_P135_E0.405150.977
84_R135_E0.403830.974
46_M93_F0.403760.973
95_A126_I0.403250.972
82_N137_T0.402160.970
45_T77_V0.402120.969
21_K35_P0.402090.969
121_T139_R0.393010.947
118_A141_V0.389040.938
51_L126_I0.387990.935
35_P92_D0.387860.935
96_R125_E0.384670.927
41_N45_T0.383910.926
22_V32_L0.37430.902
51_L133_A0.372820.899
13_P16_K0.368860.889
114_R121_T0.354990.856
81_S136_F0.354510.855
15_S57_L0.353510.852
51_L85_Y0.350030.844
39_N50_S0.346960.836
59_G140_Y0.345030.832
20_I32_L0.339480.818
20_I34_A0.339330.818
63_V122_L0.337490.814
18_M53_S0.336870.812
94_T127_Y0.324090.781
36_L40_I0.320430.772
115_G120_I0.319880.771
94_T128_S0.318720.768
86_L132_L0.318170.767
79_A141_V0.317610.766
59_G122_L0.315720.761
93_F126_I0.313170.755
78_I81_S0.310460.748
80_D139_R0.309880.747
15_S20_I0.308770.744
99_L122_L0.303050.731
17_A37_A0.302190.729
87_K114_R0.296220.714
19_G37_A0.294770.711
41_N47_F0.293110.707
14_L18_M0.291320.702
64_W75_D0.286430.691
116_G121_T0.285610.689
47_F57_L0.284880.687
80_D137_T0.28310.682
28_Q65_L0.283030.682
97_C124_V0.282180.680
51_L89_V0.280480.676
93_F133_A0.279960.675
63_V140_Y0.278980.673
62_L99_L0.277460.669
132_L135_E0.276190.666
55_A83_I0.275090.663
86_L121_T0.274680.662
84_R139_R0.273980.660
92_D128_S0.273670.660
56_T60_W0.272510.657
43_H75_D0.271620.655
64_W76_I0.271410.654
83_I136_F0.269650.650
38_P91_G0.268440.647
45_T88_P0.26760.645
40_I91_G0.267350.645
46_M89_V0.264690.638
121_T137_T0.264480.638
120_I140_Y0.264370.637
81_S85_Y0.259670.626
84_R137_T0.258250.623
58_A61_G0.255610.616
60_W63_V0.255330.616
79_A139_R0.251870.607
25_Y30_L0.251330.606
87_K128_S0.249370.601
22_V61_G0.244940.590
97_C122_L0.241230.582
32_L54_L0.238290.574
35_P39_N0.237740.573
36_L39_N0.236110.569
84_R121_T0.235070.567
48_G52_Y0.234750.566
42_H60_W0.231450.558
28_Q99_L0.231370.558
96_R130_G0.230770.556
22_V30_L0.229920.554
41_N60_W0.229440.553
30_L97_C0.229120.552
46_M51_L0.228460.551
99_L120_I0.226690.546
20_I54_L0.22580.544
58_A97_C0.224830.542
41_N49_G0.224120.540
119_R141_V0.222480.536
86_L114_R0.222370.536
48_G78_I0.222160.536
48_G88_P0.220760.532
23_T32_L0.219950.530
50_S93_F0.219950.530
45_T90_T0.219880.530
77_V141_V0.219560.529
81_S138_G0.219020.528
118_A121_T0.218010.526
124_V138_G0.215940.521
13_P38_P0.214360.517
82_N139_R0.213870.516
48_G85_Y0.213680.515
54_L126_I0.212030.511
25_Y28_Q0.208890.504
36_L91_G0.208160.502
61_G64_W0.206320.497
69_E74_G0.205870.496
57_L61_G0.205390.495
122_L140_Y0.205010.494
78_I138_G0.203060.490
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
3lmbA199.90.078
1t82A0.965399.90.17
1sh8A0.979299.90.227
1yocA0.888999.90.247
3hduA0.902899.90.256
1sc0A0.87599.90.259
3e8pA0.902899.80.275
3gekA0.812599.80.278
3f1tA0.881999.80.279
3dkzA0.881999.80.293

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