GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Semialdhyde_dh - Semialdehyde dehydrogenase NAD binding domain
Pfam: PF01118 (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: CL0063
Length: 121
Sequences: 32774
Seq/Len: 270.86
HH_delta: 0.183 (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
3_A67_V3.080183.655
1_R26_E1.879282.230
2_V69_V1.583321.879
1_R27_L1.574121.868
73_A96_L1.566791.859
1_R68_D1.558351.849
35_R39_K1.526081.811
8_T32_S1.525881.810
80_K84_P1.472081.747
39_K43_E1.345961.597
2_V25_F1.334241.583
79_S97_S1.330841.579
61_P88_K1.281171.520
28_V67_V1.266161.502
1_R28_V1.255811.490
18_L22_H1.24621.479
61_P85_K1.191371.414
81_E85_K1.190681.413
5_V72_L1.184171.405
14_E17_R1.177791.397
4_I16_L1.173961.393
15_L71_F1.169391.387
61_P89_A1.160141.376
59_A62_E1.141381.354
39_K42_S1.103761.310
15_L73_A1.100561.306
1_R29_A1.092911.297
81_E84_P1.083181.285
36_S40_P1.075461.276
69_V92_K1.063661.262
60_D63_E1.047041.242
54_L59_A1.034441.227
2_V19_L1.001931.189
72_L95_D0.998361.185
3_A63_E0.979351.162
18_L21_E0.975071.157
64_L67_V0.97021.151
36_S39_K0.939661.115
13_R44_V0.91711.088
40_P43_E0.913291.084
88_K91_I0.912381.082
4_I71_F0.906211.075
53_D56_V0.905261.074
40_P44_V0.900411.068
72_L93_V0.8971.064
34_S37_A0.884531.049
85_K89_A0.880991.045
29_A67_V0.863191.024
13_R17_R0.849681.008
17_R44_V0.83640.992
83_A86_L0.832760.988
14_E18_L0.828770.983
84_P87_L0.824040.978
17_R21_E0.822630.976
92_K95_D0.816730.969
37_A40_P0.80340.953
42_S45_F0.796530.945
32_S38_G0.789640.937
62_E65_S0.776420.921
10_Y14_E0.769070.912
30_L54_L0.767970.911
27_L31_V0.767630.911
3_A31_V0.759130.901
70_V91_I0.757620.899
38_G42_S0.755980.897
5_V74_L0.755170.896
8_T30_L0.748990.889
66_D91_I0.743880.883
11_V73_A0.738690.876
41_L45_F0.73760.875
22_H25_F0.733720.871
85_K88_K0.725530.861
32_S35_R0.725380.861
78_A81_E0.722880.858
2_V71_F0.721620.856
29_A66_D0.711110.844
4_I12_G0.703290.834
67_V91_I0.69840.829
8_T16_L0.690320.819
1_R67_V0.679220.806
3_A70_V0.679220.806
72_L79_S0.677950.804
1_R66_D0.677270.804
60_D85_K0.675580.802
53_D57_E0.671650.797
9_G12_G0.66790.792
84_P88_K0.664390.788
5_V82_L0.658260.781
55_S58_D0.653060.775
64_L70_V0.649850.771
71_F94_I0.647850.769
15_L19_L0.637750.757
16_L30_L0.62970.747
70_V93_V0.626750.744
96_L99_D0.626020.743
52_E56_V0.62120.737
52_E55_S0.617670.733
16_L20_A0.616850.732
75_P78_A0.606660.720
16_L29_A0.601970.714
10_Y98_G0.601480.714
59_A63_E0.600770.713
28_V66_D0.59970.712
83_A87_L0.597950.709
79_S95_D0.596840.708
61_P65_S0.595760.707
69_V94_I0.595740.707
17_R20_A0.595180.706
11_V96_L0.590360.700
19_L71_F0.589030.699
63_E67_V0.587180.697
86_L91_I0.581620.690
86_L93_V0.576760.684
33_S37_A0.574420.682
10_Y13_R0.574170.681
62_E66_D0.56980.676
5_V70_V0.568180.674
13_R40_P0.566980.673
6_G9_G0.563090.668
82_L85_K0.560970.666
10_Y77_G0.560560.665
70_V86_L0.556090.660
4_I19_L0.555040.659
28_V52_E0.547860.650
82_L86_L0.547730.650
76_H98_G0.546070.648
77_G99_D0.544470.646
33_S36_S0.544060.646
72_L97_S0.542780.644
42_S46_P0.542670.644
72_L75_P0.538830.639
95_D98_G0.534940.635
11_V95_D0.528110.627
74_L82_L0.524370.622
41_L44_V0.518760.615
74_L78_A0.517150.614
11_V15_L0.510120.605
63_E66_D0.508080.603
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
4dplA0.991799.40.183
4dpkA0.991799.40.183
3dr3A199.40.208
1vknA0.958799.40.212
3pwkA0.942199.40.213
3tz6A0.942199.40.217
2nqtA0.983599.40.219
2ozpA0.975299.40.223
1xygA0.966999.40.224
3hskA199.30.235

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