GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NLE - NLE (NUC135) domain
Pfam: PF08154 (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: 65
Sequences: 409
Seq/Len: 6.29
HH_delta: 0.803 (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
4_V22_V0.380082.866
52_I57_L0.24261.830
8_T14_E0.226531.708
5_Q17_G0.196031.478
32_S49_D0.190931.440
36_N47_P0.187411.413
7_V52_I0.183191.382
29_K47_P0.177251.337
15_V48_F0.175471.323
30_E34_L0.174681.317
42_E46_V0.173051.305
59_T63_E0.172821.303
57_L64_H0.172411.300
17_G56_E0.168881.274
49_D58_R0.167421.263
45_P61_L0.160571.211
32_S54_G0.156381.179
32_S35_V0.155881.176
25_N37_Q0.155771.175
30_E37_Q0.155681.174
51_L54_G0.154381.164
51_L58_R0.152541.150
43_E46_V0.152521.150
43_E47_P0.14951.127
26_I30_E0.143611.083
25_N46_V0.141931.070
3_Q11_G0.140411.059
2_V35_V0.138581.045
7_V11_G0.137431.036
28_R45_P0.136351.028
21_S61_L0.135891.025
11_G14_E0.132270.998
24_S62_E0.130280.983
4_V9_E0.129330.975
22_V34_L0.128610.970
7_V33_E0.12690.957
32_S58_R0.126030.950
46_V57_L0.125280.945
16_P22_V0.1250.943
19_P38_L0.12450.939
55_E65_L0.124270.937
35_V47_P0.124180.937
6_F62_E0.121910.919
30_E49_D0.120820.911
35_V38_L0.120520.909
19_P65_L0.119190.899
41_D63_E0.119170.899
37_Q65_L0.117620.887
27_T30_E0.116160.876
18_T55_E0.116140.876
19_P64_H0.116110.876
6_F53_N0.115640.872
28_R32_S0.115580.872
24_S44_E0.115530.871
8_T26_I0.114960.867
39_L65_L0.112150.846
41_D53_N0.111730.843
3_Q9_E0.111680.842
21_S24_S0.111520.841
6_F28_R0.11130.839
61_L64_H0.110260.832
23_P47_P0.109720.827
14_E33_E0.109550.826
14_E53_N0.10930.824
9_E34_L0.109120.823
34_L59_T0.108620.819
60_S63_E0.108540.819
44_E62_E0.108250.816
27_T50_F0.107810.813
19_P39_L0.107320.809
45_P65_L0.107210.809
44_E55_E0.105860.798
5_Q56_E0.105620.797
2_V64_H0.105490.796
29_K45_P0.105160.793
55_E62_E0.105010.792
11_G21_S0.104520.788
20_I26_I0.104020.784
41_D57_L0.103240.779
19_P33_E0.103180.778
35_V64_H0.102910.776
29_K35_V0.102680.774
10_D21_S0.102540.773
2_V10_D0.102260.771
20_I45_P0.102050.770
10_D61_L0.101870.768
32_S39_L0.101440.765
2_V65_L0.101410.765
5_Q18_T0.101160.763
11_G56_E0.101140.763
9_E19_P0.100660.759
9_E24_S0.100540.758
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
2i1sA0.938562.50.803
2c2xA0.830845.10.822
4gdkA0.9846440.822
1b0aA0.830843.20.823
4a26A0.830842.70.824
4a5oA0.830842.30.824
3ngxA0.815442.30.824
3l07A0.830840.70.826
1a4iA0.830839.40.827
3p2oA0.830839.20.828
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0645 seconds.