GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Nodulin_late - Late nodulin protein
Pfam: PF07127 (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: 54
Sequences: 412
Seq/Len: 7.63
HH_delta: 0.78 (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
3_K6_K0.270312.003
12_I20_V0.222621.649
4_I13_I0.219861.629
41_P47_K0.21231.573
5_L13_I0.199461.478
7_F37_P0.188271.395
7_F20_V0.18111.342
9_Y42_P0.174411.292
17_L24_V0.170171.261
44_F49_I0.16761.242
8_V12_I0.166111.231
46_P54_K0.164861.221
15_L46_P0.163331.210
15_L45_I0.15911.179
6_K11_M0.158821.177
30_C35_D0.157781.169
15_L52_I0.156111.157
34_S38_K0.154921.148
28_I31_K0.152441.129
19_L35_D0.151551.123
49_I54_K0.149481.108
32_T42_P0.14681.088
6_K24_V0.146691.087
32_T51_N0.144131.068
11_M29_P0.143891.066
21_V24_V0.142511.056
15_L42_P0.141681.050
14_F38_K0.140781.043
18_F44_F0.138241.024
50_N54_K0.138061.023
14_F18_F0.135311.003
8_V51_N0.13480.999
2_A38_K0.134740.998
37_P47_K0.134310.995
16_S19_L0.132610.983
12_I16_S0.132140.979
9_Y16_S0.131420.974
33_D47_K0.128380.951
4_I18_F0.127220.943
32_T38_K0.125850.932
33_D46_P0.12550.930
11_M21_V0.125310.928
34_S47_K0.123530.915
15_L39_D0.122340.906
6_K13_I0.121780.902
5_L49_I0.119040.882
31_K51_N0.118770.880
16_S21_V0.118740.880
4_I22_T0.117470.870
3_K24_V0.116980.867
48_C53_C0.116840.866
17_L33_D0.116590.864
5_L18_F0.11560.856
2_A50_N0.115260.854
10_A34_S0.113740.843
3_K22_T0.112360.832
25_D52_I0.111540.826
23_N34_S0.110840.821
41_P51_N0.109330.810
31_K47_K0.108920.807
15_L30_C0.108880.807
18_F23_N0.107670.798
6_K21_V0.107220.794
44_F54_K0.107120.794
18_F52_I0.105870.784
3_K12_I0.103620.768
45_I52_I0.103420.766
12_I27_I0.10340.766
10_A32_T0.102380.759
24_V29_P0.101430.751
43_P51_N0.101330.751
1_M16_S0.101010.748
32_T50_N0.100810.747
27_I42_P0.100260.743
12_I30_C0.099750.739
31_K39_D0.098410.729
25_D43_P0.097320.721
31_K34_S0.097170.720
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
1pvzA0.53781.20.78
1wz5A0.518569.60.8
2axkA0.5926690.8
1c49A0.518568.30.801
1quzA0.568.20.801
1n8mA0.555667.50.802
1c55A0.629667.40.802
1qkyA0.555667.20.802
1oigA0.407466.80.803
1wmtA0.574166.10.804
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