GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NOP5NT - NOP5NT (NUC127) domain
Pfam: PF08156 (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: 67
Sequences: 385
Seq/Len: 5.75
HH_delta: 0.65 (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
62_N66_E0.244751.792
21_D24_G0.238991.750
13_L47_A0.233761.712
20_K26_D0.230811.690
3_V21_D0.217011.589
22_E25_S0.205511.505
1_M27_E0.19511.429
51_F57_A0.189061.384
39_F50_P0.187141.370
13_L46_K0.186211.364
21_D25_S0.184531.351
33_F39_F0.179391.314
36_P40_S0.174611.279
12_A17_K0.169921.244
20_K25_S0.169541.241
58_L66_E0.16761.227
6_E10_G0.166391.218
17_K41_K0.161731.184
20_K23_I0.160241.173
3_V6_E0.159591.169
55_E59_E0.157831.156
56_E63_A0.157291.152
24_G43_V0.154661.132
46_K49_S0.152481.117
58_L65_S0.15241.116
44_K56_E0.150521.102
1_M54_A0.147931.083
39_F43_V0.147711.082
8_A54_A0.147241.078
16_V53_S0.144051.055
54_A58_L0.143731.052
14_F45_L0.142111.041
48_F61_A0.141961.039
31_K34_S0.139781.024
29_V65_S0.138281.013
2_L5_F0.136871.002
14_F61_A0.136751.001
11_Y58_L0.135940.995
8_A42_I0.132180.968
7_T28_E0.131540.963
57_A67_G0.131330.962
12_A45_L0.13070.957
3_V59_E0.128770.943
32_S35_D0.128630.942
7_T27_E0.127210.931
14_F40_S0.127080.931
11_Y60_N0.126230.924
2_L15_K0.125980.922
16_V52_K0.124830.914
2_L44_K0.12470.913
2_L46_K0.124660.913
2_L33_F0.124570.912
27_E56_E0.124540.912
62_N65_S0.122730.899
40_S67_G0.12260.898
29_V35_D0.122540.897
59_E64_I0.12220.895
27_E46_K0.122010.893
5_F20_K0.121980.893
12_A49_S0.121410.889
9_A52_K0.121320.888
43_V47_A0.118840.870
21_D60_N0.118570.868
12_A48_F0.118130.865
54_A59_E0.117380.860
58_L62_N0.116880.856
53_S59_E0.116210.851
39_F60_N0.116140.850
30_Q40_S0.115740.847
2_L53_S0.115610.847
30_Q39_F0.115340.845
30_Q34_S0.11350.831
24_G39_F0.112630.825
23_I42_I0.111480.816
43_V58_L0.110960.812
3_V36_P0.110930.812
22_E26_D0.110170.807
31_K55_E0.110080.806
6_E12_A0.108960.798
9_A48_F0.108520.795
41_K49_S0.10830.793
1_M14_F0.107910.790
38_K46_K0.107660.788
40_S49_S0.107120.784
34_S55_E0.106620.781
14_F39_F0.106510.780
25_S38_K0.105430.772
31_K38_K0.105110.770
31_K64_I0.103840.760
42_I63_A0.103710.759
56_E59_E0.103360.757
31_K49_S0.102780.753
28_E38_K0.102320.749
34_S42_I0.102110.748
33_F55_E0.102070.747
29_V32_S0.101360.742
32_S44_K0.101130.741
35_D38_K0.100980.739
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
3id6A0.626997.60.65
3plaA0.626997.40.669
2nnwA0.59795.80.734
1owxA0.970122.90.872
3g5bA0.746316.50.88
2fy1A0.925413.30.885
1x5tA0.8955130.885
3md1A0.835810.30.89
3sdeA0.97019.10.892
3zzyA0.82098.90.893
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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