GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MDMPI_N - Mycothiol maleylpyruvate isomerase N-terminal domain
Pfam: PF11716 (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: CL0310
Length: 140
Sequences: 4380
Seq/Len: 31.29
HH_delta: 0.197 (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
16_D19_D1.360244.626
9_A90_R0.930943.166
104_D107_A0.899753.060
21_D32_R0.778542.648
19_D22_R0.743292.528
81_P84_E0.73142.487
30_T33_D0.656052.231
29_W33_D0.579721.972
94_A98_A0.559551.903
20_W82_P0.539041.833
107_A110_R0.524841.785
87_A91_A0.508181.728
12_V35_V0.499091.697
42_A96_L0.457151.555
42_A93_A0.454741.547
37_H135_H0.446081.517
39_A88_R0.439321.494
13_A90_R0.431981.469
43_R88_R0.431351.467
15_L31_V0.422541.437
83_A87_A0.418541.423
50_R95_A0.414851.411
6_D10_A0.399691.359
8_L38_L0.39591.346
17_D21_D0.395731.346
131_E134_V0.381271.297
111_P118_P0.380531.294
43_R92_A0.380341.293
130_V133_V0.3741.272
10_A13_A0.37281.268
13_A86_L0.370831.261
8_L89_L0.358181.218
20_W32_R0.349131.187
32_R36_A0.347661.182
131_E136_G0.339921.156
97_A101_A0.335081.140
42_A132_L0.333721.135
86_L90_R0.333511.134
45_F127_A0.333061.133
90_R94_A0.33291.132
32_R82_P0.329441.120
120_P123_D0.328681.118
99_A102_A0.326861.112
127_A130_V0.326771.111
15_L19_D0.326621.111
98_A102_A0.319731.087
131_E135_H0.313181.065
87_A90_R0.312611.063
80_L84_E0.307251.045
100_L125_A0.301571.026
44_A48_A0.301461.025
106_D109_V0.300851.023
119_M123_D0.298991.017
89_L93_A0.296941.010
103_L107_A0.295051.003
7_A10_A0.293971.000
17_D81_P0.286280.974
93_A97_A0.285810.972
9_A89_L0.284290.967
126_R130_V0.283690.965
18_E22_R0.283110.963
46_A96_L0.281020.956
88_R91_A0.280580.954
45_F124_A0.280490.954
17_D83_A0.279610.951
124_A127_A0.278530.947
91_A95_A0.277330.943
113_G116_G0.275310.936
96_L128_R0.275120.936
17_D82_P0.272210.926
84_E87_A0.271110.922
8_L136_G0.270150.919
38_L89_L0.268880.914
39_A92_A0.268540.913
32_R85_L0.267850.911
82_P86_L0.267350.909
123_D127_A0.266240.905
7_A11_L0.263890.897
24_T28_G0.263210.895
81_P85_L0.263110.895
23_P28_G0.262940.894
49_L121_L0.262710.893
93_A96_L0.260510.886
24_T30_T0.257880.877
132_L136_G0.257550.876
20_W35_V0.25720.875
23_P33_D0.255770.870
36_A85_L0.253790.863
18_E21_D0.251970.857
89_L132_L0.249710.849
95_A99_A0.248830.846
92_A96_L0.245540.835
46_A92_A0.240590.818
95_A98_A0.240390.818
9_A86_L0.238690.812
109_V122_A0.237550.808
46_A128_R0.237240.807
51_G54_A0.23530.800
94_A97_A0.234720.798
112_V124_A0.231710.788
21_D30_T0.22870.778
29_W134_V0.22260.757
108_W125_A0.221660.754
41_W45_F0.22140.753
111_P120_P0.221280.753
38_L132_L0.21970.747
128_R132_L0.219220.746
123_D130_V0.218230.742
110_R121_L0.216690.737
113_G118_P0.216550.736
28_G131_E0.216110.735
45_F128_R0.215640.733
11_L14_A0.214650.730
33_D36_A0.214620.730
130_V134_V0.214580.730
24_T27_P0.212260.722
96_L99_A0.211680.720
129_L133_V0.211120.718
10_A101_A0.210980.718
39_A89_L0.210250.715
42_A128_R0.208230.708
19_D24_T0.208190.708
108_W111_P0.207290.705
40_S43_R0.206580.703
9_A13_A0.203260.691
127_A131_E0.203120.691
133_V136_G0.202950.690
105_P109_V0.201710.686
87_A98_A0.20170.686
15_L22_R0.200460.682
29_W131_E0.200150.681
53_P56_P0.199810.680
36_A40_S0.198620.675
29_W37_H0.198550.675
36_A81_P0.19850.675
112_V120_P0.198430.675
43_R47_A0.197760.673
42_A45_F0.197190.671
35_V85_L0.196030.667
46_A99_A0.195880.666
14_A17_D0.195410.665
13_A83_A0.194230.661
7_A136_G0.193850.659
36_A80_L0.192710.655
23_P27_P0.191810.652
123_D128_R0.190510.648
89_L97_A0.189570.645
129_L132_L0.186840.635
25_P34_L0.186650.635
128_R131_E0.185510.631
37_H131_E0.18510.630
39_A85_L0.184960.629
87_A102_A0.184810.629
74_V77_R0.184210.626
42_A92_A0.183910.625
54_A114_G0.18040.614
74_V78_R0.178550.607
113_G117_G0.178220.606
110_R120_P0.177650.604
128_R133_V0.176930.602
85_L88_R0.176370.600
111_P115_P0.175790.598
46_A95_A0.175630.597
39_A42_A0.175580.597
50_R99_A0.175490.597
10_A14_A0.175410.597
42_A133_V0.174790.594
104_D108_W0.173890.591
83_A86_L0.173540.590
13_A16_D0.172580.587
125_A128_R0.172170.586
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
1rxqA0.978699.60.197
2rd9A0.964399.60.209
3di5A0.885799.60.244
3e4xA0.878699.50.258
3dkaA0.878699.50.261
3gorA0.878699.50.263
2yqyA0.985799.50.275
2ou6A0.978699.50.281
2p1aA0.907199.50.298
3cexA0.992999.40.33

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