GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NRPS - Nonribosomal peptide synthase
Pfam: PF08415 (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: 58
Sequences: 486
Seq/Len: 8.38
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_F12_E0.569044.000
7_V11_R0.300262.111
12_E15_R0.278631.959
20_R26_V0.237221.668
11_R55_Q0.211571.487
31_M34_V0.202491.424
29_T58_Q0.192771.355
10_L44_S0.183551.290
10_L22_A0.170971.202
1_H15_R0.169511.192
10_L24_M0.168631.185
28_F32_L0.168151.182
29_T54_S0.167671.179
2_R44_S0.165611.164
36_D52_G0.164211.154
29_T52_G0.161281.134
8_E15_R0.157621.108
31_M36_D0.15741.107
13_L24_M0.156441.100
16_R32_L0.153411.078
45_S48_E0.152511.072
4_F8_E0.151561.065
35_D43_R0.149971.054
30_S54_S0.146461.030
32_L48_E0.144071.013
5_S56_T0.14311.006
35_D45_S0.142170.999
19_G46_F0.141830.997
41_S45_S0.141320.993
16_R51_Y0.14060.988
41_S44_S0.136950.963
38_D42_S0.135390.952
6_G13_L0.13320.936
40_D43_R0.132750.933
5_S34_V0.132650.933
32_L58_Q0.132640.932
19_G22_A0.130480.917
37_D41_S0.129460.910
14_A45_S0.128210.901
3_S43_R0.128150.901
3_S7_V0.126250.888
33_G58_Q0.125430.882
37_D49_L0.125410.882
9_V30_S0.124550.876
52_G56_T0.124290.874
27_V57_P0.124090.872
23_V41_S0.122910.864
5_S57_P0.122160.859
6_G55_Q0.121630.855
33_G52_G0.120420.847
41_S48_E0.119750.842
5_S8_E0.119590.841
43_R48_E0.118680.834
14_A20_R0.118560.833
16_R20_R0.118340.832
4_F19_G0.117680.827
11_R54_S0.1170.823
26_V43_R0.116190.817
18_G55_Q0.115990.815
30_S33_G0.115660.813
35_D38_D0.115570.812
4_F9_V0.114680.806
18_G22_A0.11340.797
12_E16_R0.113320.797
13_L22_A0.113220.796
16_R40_D0.112930.794
19_G23_V0.112450.791
42_S46_F0.111640.785
30_S58_Q0.111480.784
7_V27_V0.111070.781
54_S58_Q0.110250.775
5_S55_Q0.109710.771
14_A33_G0.108960.766
18_G21_A0.108850.765
8_E23_V0.108250.761
3_S40_D0.108220.761
29_T53_I0.108210.761
2_R52_G0.107980.759
2_R40_D0.106390.748
38_D50_V0.104630.736
12_E28_F0.10420.733
31_M42_S0.103320.726
42_S52_G0.103290.726
23_V45_S0.102330.719
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
3ot9A0.9655500.803
2i09A0.9655500.803
1l5aA0.896630.90.824
2jgpA0.982823.60.833
4jn3A0.844812.40.852
2vycA0.93111.30.854
4j15A0.94839.90.858
3lufA0.86216.60.868
4hvmA0.98286.20.87
3au8A0.9315.60.872
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