GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AlaDh_PNT_N - Alanine dehydrogenasePNT N-terminal domain
Pfam: PF05222 (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: CL0325
Length: 136
Sequences: 2325
Seq/Len: 17.1
HH_delta: 0.047 (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
84_P108_G1.005653.532
98_K102_E0.920123.231
29_E53_E0.901553.166
45_E48_E0.857173.010
102_E106_K0.825052.897
57_R60_E0.824812.897
45_E49_E0.779612.738
4_K33_E0.760792.672
20_V52_A0.717442.520
70_K78_E0.709572.492
34_S54_I0.696932.447
119_R122_R0.660932.321
31_L55_V0.63632.235
91_F128_V0.593452.084
34_S44_D0.573872.015
35_G44_D0.561341.971
92_L111_A0.538541.891
79_L103_A0.526421.849
119_R125_S0.524021.840
83_K86_Q0.52311.837
48_E53_E0.522971.837
66_D83_K0.516761.815
21_K25_K0.515681.811
1_G65_A0.477771.678
87_T110_T0.458421.610
34_S56_S0.453591.593
15_L19_D0.446571.568
122_R125_S0.444131.560
14_A69_L0.44211.553
92_L104_L0.427951.503
56_S60_E0.422881.485
6_S75_S0.418741.471
118_P123_A0.413461.452
35_G38_E0.413071.451
76_E103_A0.412061.447
97_N100_L0.406751.428
60_E64_D0.398641.400
31_L65_A0.39551.389
13_V36_A0.383831.348
67_I87_T0.382511.343
43_S46_E0.374791.316
62_Y81_L0.369391.297
99_E102_E0.363441.276
2_I15_L0.361811.271
80_A107_K0.352851.239
1_G61_V0.347911.222
7_K72_K0.346361.216
93_H115_E0.337561.185
72_K93_H0.33111.163
103_A106_K0.330731.161
88_L104_L0.330571.161
22_K26_L0.328491.154
11_R39_G0.317751.116
55_V61_V0.314941.106
93_H96_Q0.313661.102
85_G109_I0.312841.099
84_P107_K0.310261.090
16_T19_D0.302861.064
104_L111_A0.298771.049
61_V68_I0.289681.017
15_L20_V0.289241.016
13_V47_Y0.287921.011
46_E49_E0.287131.008
38_E43_S0.285661.003
94_P104_L0.281880.990
90_G114_L0.28060.985
68_I86_Q0.279450.981
77_E81_L0.278720.979
119_R123_A0.276450.971
31_L53_E0.274240.963
76_E99_E0.27170.954
103_A107_K0.269120.945
3_P70_K0.266660.936
130_S134_N0.261860.920
82_L109_I0.260630.915
102_E105_A0.258690.908
58_A61_V0.250790.881
3_P62_Y0.249720.877
87_T112_F0.24870.873
86_Q109_I0.248390.872
88_L109_I0.243290.854
82_L88_L0.241520.848
2_I32_V0.24050.845
118_P121_S0.240140.843
34_S48_E0.236760.831
129_L133_A0.236470.830
63_S83_K0.232030.815
80_A103_A0.231710.814
20_V50_A0.231590.813
30_V52_A0.230170.808
74_P88_L0.227830.800
96_Q115_E0.226230.794
15_L69_L0.22560.792
6_S33_E0.221010.776
81_L86_Q0.220840.776
19_D23_L0.219610.771
31_L64_D0.217490.764
76_E79_L0.216770.761
42_F46_E0.216580.761
6_S77_E0.213010.748
24_V30_V0.211490.743
127_D131_S0.211060.741
96_Q100_L0.20940.735
33_E58_A0.20910.734
114_L117_I0.209060.734
44_D48_E0.208520.732
75_S79_L0.207840.730
73_P90_G0.207660.729
95_A115_E0.205860.723
39_G42_F0.20530.721
61_V65_A0.204220.717
96_Q101_L0.203520.715
130_S135_I0.203470.715
48_E54_I0.201520.708
62_Y86_Q0.201350.707
17_P42_F0.199510.701
95_A116_L0.198490.697
18_E42_F0.19810.696
117_I126_M0.197610.694
118_P122_R0.195210.686
58_A62_Y0.19470.684
125_S130_S0.194420.683
31_L61_V0.192170.675
132_Q135_I0.192070.675
2_I23_L0.189990.667
98_K101_L0.188140.661
24_V29_E0.188130.661
18_E134_N0.187560.659
91_F114_L0.187360.658
105_A108_G0.187080.657
94_P130_S0.186010.653
5_E10_E0.183450.644
34_S63_S0.183190.643
82_L86_Q0.183040.643
53_E64_D0.181110.636
95_A132_Q0.179760.631
129_L132_Q0.178870.628
72_K113_A0.177550.624
95_A113_A0.177130.622
3_P68_I0.176010.618
70_K74_P0.175470.616
76_E80_A0.174990.615
121_S127_D0.174020.611
94_P127_D0.173920.611
2_I20_V0.172790.607
71_V128_V0.171710.603
117_I123_A0.171130.601
112_F125_S0.169960.597
26_L125_S0.169780.596
22_K25_K0.169130.594
18_E21_K0.169020.594
67_I89_I0.167980.590
24_V53_E0.167880.590
51_G54_I0.167580.589
90_G117_I0.167010.587
118_P127_D0.166850.586
77_E80_A0.166040.583
16_T42_F0.165780.582
60_E63_S0.165750.582
48_E67_I0.165280.580
57_R63_S0.164930.579
123_A127_D0.164450.578
36_A40_A0.16370.575
49_E106_K0.16370.575
91_F116_L0.163540.574
19_D40_A0.16350.574
62_Y100_L0.162330.570
118_P125_S0.161890.569
116_L126_M0.161350.567
34_S38_E0.160560.564
12_R69_L0.160130.562
38_E63_S0.159890.562
119_R130_S0.159550.560
85_G107_K0.159080.559
62_Y135_I0.158820.558
77_E102_E0.157270.552
20_V30_V0.156820.551
19_D22_K0.156480.550
26_L31_L0.155360.546
56_S80_A0.155280.545
28_H115_E0.154920.544
88_L92_L0.154530.543
15_L30_V0.154490.543
38_E46_E0.154310.542
28_H95_A0.154260.542
96_Q135_I0.154230.542
73_P93_H0.153670.540
119_R127_D0.152960.537
12_R133_A0.152820.537
53_E60_E0.152450.535
129_L136_A0.152370.535
55_V60_E0.152070.534
16_T135_I0.151960.534
75_S78_E0.151730.533
79_L100_L0.151570.532
32_V52_A0.150940.530
9_G40_A0.150830.530
19_D134_N0.150590.529
114_L128_V0.150560.529
4_K35_G0.150380.528
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
4dioA0.98531000.047
3p2yA0.96321000.062
2qrjA0.91911000.248
2eezA0.97061000.257
1l7dA11000.264
2vhwA0.98531000.27
1x13A0.98531000.273
1pjcA0.97791000.275
2rirA0.889798.40.791
3d4oA0.860397.80.823

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