GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YkuD - LD-transpeptidase catalytic domain
Pfam: PF03734 (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: CL0508
Length: 144
Sequences: 4225
Seq/Len: 29.34
HH_delta: 0.153 (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
15_Y22_L0.869412.705
24_Y131_W0.865722.693
17_Y22_L0.841032.616
44_T141_P0.806322.508
26_Y131_W0.786582.447
7_D10_E0.745312.319
41_P98_I0.709522.207
131_W135_N0.708332.204
8_K42_R0.702812.186
50_K133_Y0.675222.101
44_T143_I0.65862.049
38_T119_H0.618161.923
102_G126_N0.617271.920
137_P140_T0.604081.879
35_E38_T0.578011.798
4_I136_V0.572791.782
26_Y124_L0.569811.773
28_V124_L0.563981.755
47_I142_V0.562551.750
10_E15_Y0.559331.740
3_W143_I0.556051.730
124_L129_A0.55171.716
6_V122_I0.546371.700
8_K30_T0.542771.689
29_S117_A0.531971.655
130_K134_D0.505061.571
125_S128_D0.501221.559
13_L28_V0.490151.525
16_L135_N0.487921.518
6_V28_V0.474861.477
4_I132_L0.46431.444
56_W59_P0.463941.443
100_I124_L0.436781.359
12_R25_T0.434541.352
40_T122_I0.42861.333
87_V90_W0.424841.322
101_H121_C0.420541.308
60_P64_G0.417671.299
106_P109_F0.415411.292
18_E23_V0.405761.262
28_V122_I0.404871.260
6_V100_I0.402341.252
103_T109_F0.396431.233
87_V93_F0.392211.220
36_G39_P0.389531.212
15_Y25_T0.384681.197
102_G106_P0.366561.140
128_D131_W0.362191.127
30_T116_P0.355721.107
90_W93_F0.35041.090
18_E135_N0.342771.066
49_E92_G0.342751.066
118_S123_R0.33961.057
51_V54_P0.334931.042
91_V94_F0.329221.024
26_Y128_D0.327721.020
117_A123_R0.325391.012
46_R141_P0.323751.007
89_P92_G0.321541.000
5_V17_Y0.321260.999
13_L25_T0.320620.997
51_V99_G0.317540.988
66_E119_H0.316770.985
124_L128_D0.316380.984
5_V143_I0.315390.981
88_I94_F0.314370.978
41_P45_Y0.305620.951
48_S95_G0.29620.921
93_F99_G0.295580.920
60_P63_G0.2950.918
29_S123_R0.29090.905
89_P93_F0.290470.904
7_D15_Y0.285580.888
106_P117_A0.277470.863
103_T106_P0.276040.859
118_S121_C0.271390.844
22_L25_T0.266470.829
61_S64_G0.265940.827
88_I93_F0.265420.826
63_G66_E0.264780.824
63_G67_P0.259490.807
16_L24_Y0.255360.794
101_H118_S0.254970.793
4_I16_L0.25350.789
90_W94_F0.253070.787
12_R27_P0.250340.779
87_V91_V0.248630.773
16_L132_L0.248060.772
38_T66_E0.247060.769
4_I100_I0.246070.766
50_K137_P0.244080.759
52_R133_Y0.243770.758
12_R15_Y0.242750.755
58_Y62_I0.242170.753
136_V140_T0.24060.749
40_T45_Y0.240480.748
3_W17_Y0.23850.742
59_P62_I0.235370.732
29_S108_S0.234080.728
89_P94_F0.233040.725
105_A109_F0.230910.718
100_I142_V0.230760.718
49_E138_V0.230690.718
45_Y98_I0.229680.715
37_D40_T0.228820.712
104_P109_F0.228130.710
45_Y95_G0.226260.704
58_Y63_G0.225960.703
98_I122_I0.223220.694
26_Y125_S0.222590.692
87_V92_G0.221480.689
99_G102_G0.21990.684
100_I132_L0.219720.684
88_I91_V0.218810.681
108_S117_A0.218330.679
39_P42_R0.216330.673
90_W99_G0.215980.672
64_G67_P0.214040.666
30_T122_I0.213150.663
131_W134_D0.2130.663
3_W19_N0.212580.661
26_Y100_I0.21180.659
54_P59_P0.21130.657
27_P128_D0.210830.656
108_S115_G0.21040.655
43_G91_V0.209640.652
60_P67_P0.208360.648
126_N129_A0.203180.632
61_S65_G0.202610.630
35_E39_P0.201690.627
52_R134_D0.201330.626
51_V55_T0.201230.626
21_K143_I0.201040.625
97_G119_H0.200450.624
64_G68_N0.200250.623
118_S129_A0.200180.623
53_N88_I0.199620.621
26_Y132_L0.19870.618
4_I140_T0.197250.614
88_I92_G0.196170.610
29_S114_G0.1950.607
87_V94_F0.194380.605
114_G117_A0.194220.604
3_W15_Y0.194170.604
17_Y20_G0.193070.601
15_Y18_E0.192720.600
50_K91_V0.192270.598
16_L23_V0.191550.596
52_R89_P0.191530.596
62_I65_G0.190280.592
40_T144_I0.189920.591
38_T61_S0.188710.587
10_E13_L0.187730.584
7_D143_I0.185850.578
52_R130_K0.185750.578
31_G40_T0.185470.577
17_Y23_V0.185080.576
41_P144_I0.184990.576
5_V15_Y0.183790.572
29_S118_S0.182490.568
104_P126_N0.181130.564
58_Y64_G0.180210.561
108_S114_G0.180190.561
132_L136_V0.179720.559
18_E137_P0.178940.557
12_R116_P0.178450.555
3_W7_D0.177040.551
48_S93_F0.176330.549
24_Y135_N0.176280.548
41_P61_S0.175220.545
48_S94_F0.17450.543
43_G96_S0.173760.541
132_L135_N0.1730.538
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
1zatA0.854299.90.153
3turA0.861199.90.171
3vynA0.861199.90.174
3vypA0.861199.90.175
4k73A0.861199.90.198
4a1kA0.7599.90.22
1qksA0.34036.80.925
1nirA0.3754.70.93
3c8lA0.38894.20.932
1nkzB0.15973.90.933

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