GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NAD_binding_8 - NAD(P)-binding Rossmann-like domain
Pfam: PF13450 (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: 68
Sequences: 12915
Seq/Len: 189.93
HH_delta: -0.084 (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
13_Y17_K1.924873.199
1_I8_G1.768292.939
16_A22_V1.535422.552
12_A24_V1.473342.449
14_Y17_K1.292662.148
10_A14_Y1.227112.039
14_Y18_A1.193751.984
20_Y23_T1.046571.739
4_A24_V1.021661.698
28_N36_R0.936981.557
39_R44_R0.916931.524
30_R36_R0.916521.523
11_A15_L0.914161.519
4_A31_L0.864281.436
1_I11_A0.78241.300
49_A53_F0.763151.268
34_R51_Y0.756211.257
50_H53_F0.753711.253
38_F47_L0.738611.227
6_I35_A0.697881.160
50_H54_P0.688961.145
19_G22_V0.67461.121
54_P59_P0.666551.108
47_L50_H0.663911.103
38_F41_P0.646991.075
15_L20_Y0.627721.043
1_I12_A0.624581.038
15_L19_G0.623071.035
34_R50_H0.620871.032
28_N37_S0.604981.005
6_I49_A0.593960.987
34_R48_G0.586420.975
35_A48_G0.57120.949
39_R43_Y0.570610.948
1_I24_V0.560940.932
39_R42_G0.555810.924
1_I22_V0.552160.918
15_L22_V0.544040.904
37_S46_D0.540480.898
47_L51_Y0.529870.881
10_A13_Y0.517480.860
54_P60_N0.516450.858
12_A22_V0.513040.853
49_A54_P0.503630.837
45_F50_H0.482830.802
45_F51_Y0.480170.798
53_F60_N0.479860.797
16_A21_R0.467120.776
44_R47_L0.46390.771
53_F61_L0.463860.771
6_I10_A0.455120.756
40_I43_Y0.454280.755
13_Y16_A0.453050.753
49_A52_F0.427410.710
40_I45_F0.42640.709
38_F43_Y0.412160.685
9_L24_V0.408880.680
51_Y54_P0.406110.675
48_G51_Y0.398420.662
37_S44_R0.394760.656
1_I5_G0.384270.639
38_F46_D0.383070.637
34_R49_A0.382980.636
47_L53_F0.382260.635
9_L46_D0.37160.618
36_R40_I0.366850.610
43_Y46_D0.366640.609
36_R47_L0.366360.609
30_R37_S0.363210.604
35_A49_A0.360590.599
48_G52_F0.358270.595
6_I34_R0.352690.586
36_R53_F0.347240.577
27_K30_R0.346760.576
4_A26_E0.346250.575
34_R53_F0.344410.572
12_A16_A0.333180.554
34_R45_F0.326780.543
33_G48_G0.325510.541
4_A12_A0.324960.540
46_D49_A0.324650.540
35_A46_D0.323110.537
4_A9_L0.31940.531
36_R39_R0.3180.528
7_S34_R0.317550.528
4_A8_G0.315020.524
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
4gdeA0.970699.3-0.084
4hsuA0.985399.2-0.04
2vvmA0.970699.10.005
4i59A0.970699.10.007
2ivdA0.970699.10.009
3i6dA0.970699.10.011
2b9wA0.970699.10.013
1sezA0.970699.10.02
1s3eA0.970699.10.021
3ka7A199.10.024

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