GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SRP54_N - SRP54-type protein helical bundle domain
Pfam: PF02881 (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: 75
Sequences: 3078
Seq/Len: 41.04
HH_delta: 0.267 (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
24_E52_K1.150173.667
50_N74_E1.042833.325
46_K50_N0.72532.312
69_K73_E0.712662.272
44_A48_I0.54491.737
5_L8_T0.536321.710
49_E53_K0.528181.684
23_I56_I0.503531.605
45_E49_E0.50071.596
35_I44_A0.494951.578
49_E52_K0.494911.578
50_N53_K0.493831.574
47_I51_I0.481131.534
55_L59_K0.452741.443
27_L52_K0.443171.413
7_K10_K0.440551.405
33_A36_E0.418331.334
41_V45_E0.401321.279
3_K7_K0.399511.274
55_L70_A0.398911.272
63_P66_E0.388551.239
27_L56_I0.386121.231
55_L73_E0.384561.226
32_E35_I0.384111.225
19_T22_D0.382871.221
21_K24_E0.378181.206
10_K14_G0.376981.202
65_E68_K0.372941.189
39_V47_I0.37211.186
7_K11_K0.343811.096
32_E36_E0.342981.093
24_E28_E0.340451.085
4_G8_T0.333711.064
55_L74_E0.331221.056
29_E32_E0.328481.047
28_E45_E0.323061.030
42_E45_E0.317391.012
15_S33_A0.317061.011
10_K15_S0.315411.006
51_I74_E0.310870.991
15_S22_D0.305870.975
40_G44_A0.301240.960
3_K6_S0.293610.936
6_S10_K0.292870.934
4_G36_E0.289710.924
1_L4_G0.284490.907
22_D67_V0.282960.902
23_I26_F0.280720.895
27_L48_I0.279450.891
46_K49_E0.279030.890
4_G9_F0.276530.882
45_E48_I0.271780.866
12_L26_F0.268840.857
23_I27_L0.268730.857
26_F67_V0.266850.851
70_A74_E0.266120.848
40_G66_E0.265860.848
27_L51_I0.264690.844
9_F12_L0.264490.843
26_F64_R0.261970.835
53_K58_K0.26050.830
12_L16_I0.257920.822
70_A73_E0.256030.816
62_N65_E0.252050.804
66_E69_K0.251930.803
28_E32_E0.251110.801
1_L5_L0.250760.799
10_K62_N0.248620.793
31_E48_I0.248560.792
68_K72_K0.246940.787
47_I74_E0.245180.782
18_L23_I0.244330.779
11_K25_E0.243450.776
27_L30_L0.239420.763
56_I67_V0.237870.758
33_A38_D0.235020.749
27_L67_V0.229420.731
20_E56_I0.229390.731
71_L74_E0.22770.726
8_T32_E0.220960.704
66_E70_A0.220560.703
68_K75_L0.217520.693
61_I66_E0.215230.686
34_L39_V0.212630.678
9_F16_I0.21220.677
24_E58_K0.210990.673
18_L22_D0.210450.671
69_K72_K0.207980.663
29_E33_A0.207840.663
65_E69_K0.207650.662
12_L33_A0.207310.661
47_I61_I0.205040.654
33_A42_E0.203580.649
10_K69_K0.199460.636
4_G26_F0.199430.636
57_K75_L0.199240.635
7_K59_K0.198340.632
6_S24_E0.19680.627
7_K29_E0.195190.622
19_T67_V0.192510.614
59_K73_E0.190940.609
11_K15_S0.18980.605
6_S13_S0.188950.602
20_E30_L0.187990.599
28_E31_E0.187640.598
2_K8_T0.186760.595
56_I64_R0.186210.594
8_T40_G0.186060.593
31_E35_I0.185910.593
43_V47_I0.184730.589
31_E38_D0.184610.589
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
2xxaA198.60.267
2ffhA198.60.271
3e70C0.986798.60.274
2yhsA0.986798.60.277
1rj9A0.8898.60.288
1j8mF198.50.302
3dm5A0.986798.50.304
3b9qA0.973398.50.307
2og2A0.986798.50.313
2j37W198.40.323

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