GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Molybdop_Fe4S4 - Molybdopterin oxidoreductase Fe4S4 domain
Pfam: PF04879 (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. )
Length: 55
Sequences: 3765
Seq/Len: 68.45
HH_delta: -0.053 (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
20_Y30_E1.073012.045
3_T18_D1.07232.044
5_P18_D1.065792.031
4_V21_V1.046111.994
3_T20_Y1.042141.986
18_D33_P1.001081.908
15_C43_C0.987191.882
16_G35_H0.977891.864
11_C15_C0.957491.825
8_C43_C0.911241.737
19_V26_I0.891651.699
19_V29_V0.881211.680
8_C46_G0.822731.568
18_D32_D0.821781.566
8_C15_C0.807161.538
11_C43_C0.787871.502
8_C11_C0.766481.461
6_T19_V0.753151.435
22_K27_V0.704331.342
5_P32_D0.693361.321
15_C46_G0.690621.316
25_K54_Y0.668041.273
7_V14_G0.65331.245
43_C46_G0.650211.239
16_G32_D0.638891.218
44_P48_F0.594581.133
3_T30_E0.585111.115
5_P16_G0.53661.023
18_D30_E0.514440.980
20_Y28_K0.513280.978
49_G52_F0.498550.950
11_C46_G0.478470.912
31_G40_G0.471780.899
21_V26_I0.470480.897
17_I42_L0.469880.896
44_P47_R0.46430.885
24_G27_V0.4590.875
21_V24_G0.448730.855
29_V50_Y0.444560.847
13_S47_R0.41810.797
26_I53_V0.410810.783
16_G38_N0.410.781
50_Y54_Y0.39980.762
9_P13_S0.392230.748
41_R47_R0.384590.733
22_K25_K0.379620.724
41_R44_P0.372340.710
30_E33_P0.368020.701
37_I44_P0.363250.692
21_V27_V0.361520.689
34_D39_Q0.358550.683
7_V17_I0.338210.645
10_Y52_F0.333870.636
10_Y49_G0.328730.627
8_C45_K0.32580.621
17_I29_V0.320030.610
10_Y13_S0.316980.604
32_D35_H0.313570.598
10_Y48_F0.312970.596
14_G35_H0.308640.588
12_S37_I0.301570.575
46_G49_G0.299780.571
5_P34_D0.29670.565
16_G31_G0.290240.553
6_T17_I0.290120.553
14_G37_I0.28890.551
14_G41_R0.285750.545
9_P52_F0.284360.542
28_K31_G0.284340.542
29_V49_G0.283510.540
37_I41_R0.281810.537
14_G51_Q0.277580.529
33_P41_R0.276720.527
6_T44_P0.276520.527
35_H38_N0.27480.524
7_V38_N0.267490.510
31_G38_N0.266630.508
9_P14_G0.265610.506
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
3ml1A199.4-0.053
1h0hA199.4-0.021
2vpzA199.3-0.017
2iv2X0.981899.3-0.012
3i9v3199.3-0.011
2napA0.981899.3-0.009
2e7zA0.963699.3-0.005
1g8kA199.30.002
1kqfA199.30.013
2ivfA199.10.103

Page generated in 0.0168 seconds.