GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NifU - NifU-like domain
Pfam: PF01106 (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: CL0232
Length: 68
Sequences: 1303
Seq/Len: 19.16
HH_delta: -0.051 (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_E32_R0.808622.944
13_Q18_D0.66582.424
28_V64_R0.658042.395
1_V24_V0.609362.218
48_K52_E0.542571.975
52_E56_R0.535931.951
2_E21_L0.534431.946
9_R18_D0.507961.849
19_V51_I0.493881.798
29_V55_L0.477481.738
28_V66_V0.467521.702
23_D30_Y0.423731.543
21_L24_V0.410891.496
33_L46_T0.387351.410
21_L29_V0.385621.404
45_M49_Q0.375831.368
37_C40_C0.37111.351
15_D37_C0.360211.311
20_E34_T0.359191.308
22_V32_R0.355481.294
6_E9_R0.343881.252
4_V55_L0.34261.247
54_A58_A0.341321.243
7_E58_A0.331131.205
42_S45_M0.317571.156
54_A57_E0.304961.110
27_G63_K0.293791.069
12_L41_P0.288791.051
10_P46_T0.281491.025
3_E7_E0.278831.015
60_P63_K0.26680.971
25_D30_Y0.266090.969
11_Y50_G0.26490.964
29_V62_V0.262470.955
24_V29_V0.262390.955
15_D46_T0.261180.951
36_A43_S0.258390.941
30_Y66_V0.252510.919
4_V58_A0.249450.908
18_D58_A0.248750.906
52_E64_R0.248640.905
33_L47_L0.247790.902
38_S41_P0.243330.886
47_L51_I0.241110.878
15_D36_A0.24050.875
11_Y14_S0.240250.875
56_R63_K0.237580.865
4_V54_A0.237330.864
11_Y49_Q0.235180.856
4_V59_V0.232720.847
7_E31_V0.232660.847
39_G44_D0.231870.844
53_Q57_E0.230390.839
56_R64_R0.22560.821
41_P44_D0.223610.814
30_Y44_D0.22280.811
17_G46_T0.219580.799
19_V31_V0.218330.795
2_E6_E0.216970.790
31_V47_L0.216740.789
24_V62_V0.215380.784
14_S63_K0.214540.781
26_D63_K0.21280.775
15_D50_G0.211960.772
37_C46_T0.209690.763
33_L43_S0.209350.762
32_R61_E0.206490.752
17_G40_C0.203930.742
10_P51_I0.201860.735
33_L48_K0.200630.730
17_G37_C0.199570.727
22_V26_D0.193870.706
12_L53_Q0.192360.700
18_D34_T0.191970.699
49_Q53_Q0.191190.696
7_E57_E0.190710.694
2_E18_D0.188550.686
38_S44_D0.188520.686
38_S42_S0.185520.675
36_A47_L0.183810.669
15_D40_C0.183530.668
21_L47_L0.183520.668
55_L59_V0.18310.667
3_E6_E0.182390.664
32_R67_P0.181250.660
11_Y19_V0.179960.655
3_E54_A0.179690.654
2_E58_A0.178780.651
28_V63_K0.177570.646
2_E54_A0.177550.646
1_V5_L0.176310.642
12_L24_V0.175120.637
19_V47_L0.173450.631
5_L44_D0.172440.628
15_D51_I0.169910.619
25_D56_R0.168930.615
9_R15_D0.164620.599
48_K64_R0.16410.597
6_E31_V0.163730.596
41_P67_P0.163480.595
20_E26_D0.161340.587
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
1xhjA199.9-0.051
2m5oA199.8-0.035
1vehA199.8-0.023
2z51A199.8-0.018
1th5A0.941299.70.09
2z51A0.941299.70.109
3cq1A0.970696.50.709
1uwdA0.970695.50.736
3lnoA0.985394.90.747
3ksyA0.897169.10.827

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