GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
META - META domain
Pfam: PF03724 (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. )
Clan: CL0116
Length: 101
Sequences: 1098
Seq/Len: 10.87
HH_delta: 0.092 (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
43_C69_C1.041195.397
47_S63_A0.948594.917
48_G62_L0.632863.280
39_G46_F0.573092.971
41_A81_L0.511912.654
41_A77_E0.491572.548
44_N65_T0.418142.167
37_V59_F0.390982.027
46_F80_F0.350441.817
6_T29_T0.348811.808
9_L80_F0.328021.700
45_R67_M0.321881.668
37_V62_L0.30131.562
87_V99_L0.292971.519
44_N77_E0.288651.496
65_T68_A0.287011.488
6_T27_T0.28341.469
78_Q82_S0.273371.417
37_V48_G0.266671.382
64_S81_L0.266451.381
39_G81_L0.254461.319
77_E81_L0.252831.311
41_A64_S0.246431.277
38_S47_S0.235511.221
26_P42_G0.232941.207
89_S100_S0.225941.171
9_L12_I0.221791.150
16_G19_G0.219831.139
39_G42_G0.21791.129
93_D96_Q0.213341.106
41_A46_F0.208781.082
49_T60_G0.204691.061
74_M77_E0.203041.052
59_F87_V0.201371.044
57_L87_V0.19941.034
92_I97_L0.19941.034
75_A79_A0.193991.006
70_P74_M0.193831.005
39_G84_L0.193711.004
45_R66_R0.19311.001
7_W90_Y0.192841.000
4_G29_T0.191490.993
5_G32_F0.191450.992
90_Y97_L0.188640.978
39_G80_F0.184060.954
10_T96_Q0.183450.951
93_D98_T0.182530.946
4_G33_E0.179510.930
48_G63_A0.177590.921
45_R63_A0.17540.909
11_S19_G0.174220.903
40_S45_R0.170550.884
73_L76_Q0.169160.877
91_R100_S0.167970.871
63_A68_A0.167610.869
49_T78_Q0.167370.868
56_T89_S0.166960.865
36_R68_A0.166370.862
35_G50_Y0.164430.852
47_S64_S0.163310.847
27_T46_F0.162350.842
67_M74_M0.162010.840
39_G77_E0.160240.831
38_S45_R0.158640.822
46_F59_F0.157360.816
83_A88_S0.152850.792
30_F50_Y0.152280.789
78_Q85_Q0.14830.769
9_L28_L0.147220.763
32_F50_Y0.146240.758
44_N67_M0.145640.755
61_P66_R0.145440.754
35_G90_Y0.145130.752
44_N68_A0.144450.749
46_F62_L0.144270.748
52_I57_L0.143780.745
60_G95_D0.142390.738
46_F81_L0.141530.734
6_T25_K0.140830.730
91_R98_T0.138590.718
36_R49_T0.138190.716
59_F91_R0.137820.714
63_A66_R0.137810.714
32_F91_R0.137590.713
34_D50_Y0.137230.711
8_Q25_K0.135910.704
9_L38_S0.135630.703
37_V46_F0.135590.703
11_S21_P0.135360.702
9_L97_L0.134610.698
82_S85_Q0.134170.695
11_S22_P0.134150.695
59_F78_Q0.133950.694
96_Q100_S0.133650.693
57_L88_S0.132730.688
4_G53_E0.132490.687
45_R68_A0.129570.672
44_N66_R0.129530.671
11_S16_G0.129090.669
59_F84_L0.126680.657
12_I34_D0.126060.653
5_G50_Y0.12560.651
92_I96_Q0.123990.643
29_T38_S0.123810.642
55_N89_S0.122990.638
35_G52_I0.122610.636
34_D54_G0.122570.635
12_I80_F0.122560.635
59_F99_L0.122380.634
28_L59_F0.122080.633
10_T72_E0.121610.630
35_G54_G0.121310.629
10_T76_Q0.121220.628
47_S67_M0.121110.628
26_P46_F0.120970.627
28_L37_V0.120670.625
17_K27_T0.120560.625
72_E75_A0.120140.623
53_E85_Q0.120.622
45_R96_Q0.118980.617
36_R47_S0.118730.615
78_Q81_L0.117920.611
33_E72_E0.116460.604
28_L46_F0.116280.603
23_P91_R0.116250.603
27_T30_F0.116040.601
7_W42_G0.115120.597
35_G81_L0.114950.596
55_N90_Y0.114940.596
45_R61_P0.114940.596
55_N87_V0.114760.595
23_P78_Q0.113860.590
21_P24_A0.113340.588
80_F97_L0.113340.588
19_G53_E0.11270.584
41_A83_A0.112180.581
68_A74_M0.112010.581
26_P75_A0.111920.580
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
2ktsA0.960499.80.092
2la7A199.80.11
1sluA0.90142.90.866
2y6tE0.910941.70.866
2x8sA0.8713150.891
3s9zA0.98029.50.9
1z0pA0.27727.50.904
1stzA0.79216.80.906
3l6iA0.51496.70.906
2zouA0.70360.908

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