GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bro-N - BRO family N-terminal domain
Pfam: PF02498 (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: 87
Sequences: 2240
Seq/Len: 25.75
HH_delta: 0.826 (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
32_I61_G1.084773.114
30_K34_K0.857422.462
15_V56_F0.837112.403
48_D52_Q0.723742.078
59_E63_Y0.692761.989
67_M82_T0.668361.919
73_K76_E0.663981.906
13_W58_N0.661421.899
17_K21_K0.652821.874
64_R78_R0.622191.786
27_N30_K0.603051.731
25_Y30_K0.582141.671
60_S83_D0.579761.664
47_N50_G0.563941.619
60_S82_T0.559021.605
25_Y28_P0.51951.491
77_F80_W0.515921.481
26_K30_K0.499481.434
15_V18_D0.469471.348
49_G52_Q0.462751.329
79_D83_D0.461241.324
24_G73_K0.459241.318
47_N52_Q0.448641.288
72_P76_E0.442771.271
43_T55_V0.440121.264
67_M78_R0.43681.254
19_V62_L0.43481.248
69_S74_A0.421381.210
63_Y81_V0.393831.131
58_N61_G0.391551.124
48_D54_T0.386251.109
68_R78_R0.383651.101
20_A25_Y0.366911.053
50_G54_T0.356321.023
57_I62_L0.355511.021
16_A65_L0.35371.015
31_A65_L0.346940.996
75_K79_D0.346750.996
36_V40_N0.346270.994
31_A35_Y0.338510.972
31_A34_K0.337330.968
60_S64_R0.333410.957
15_V54_T0.333260.957
64_R82_T0.331740.952
36_V61_G0.330680.949
22_A77_F0.327210.939
8_K13_W0.324230.931
16_A32_I0.319760.918
70_N73_K0.319090.916
14_F62_L0.305080.876
78_R82_T0.304370.874
68_R71_K0.304220.873
23_L66_I0.304080.873
19_V57_I0.301280.865
59_E81_V0.299260.859
8_K12_P0.293240.842
29_D33_K0.280040.804
28_P33_K0.279760.803
64_R67_M0.279580.803
27_N34_K0.275760.792
36_V46_E0.274630.788
21_K24_G0.273610.786
43_T53_K0.272820.783
46_E52_Q0.263750.757
70_N74_A0.263390.756
61_G65_L0.26310.755
13_W22_A0.262820.755
72_P75_K0.262230.753
8_K11_E0.261090.750
42_K52_Q0.260760.749
79_D82_T0.260690.748
71_K74_A0.259460.745
27_N31_A0.258530.742
64_R68_R0.257740.740
42_K50_G0.256760.737
29_D55_V0.255660.734
33_K37_D0.252570.725
64_R79_D0.252270.724
76_E79_D0.251650.722
60_S79_D0.249760.717
24_G72_P0.249240.716
46_E51_N0.248660.714
48_D51_N0.246460.708
17_K20_A0.246130.707
19_V77_F0.245980.706
69_S72_P0.243920.700
33_K43_T0.243820.700
36_V39_E0.243490.699
16_A55_V0.242350.696
20_A69_S0.240330.690
25_Y74_A0.239370.687
46_E54_T0.236590.679
34_K44_L0.2340.672
32_I35_Y0.233950.672
71_K78_R0.233750.671
79_D84_E0.231920.666
18_D21_K0.231910.666
31_A45_S0.231160.664
57_I65_L0.229790.660
27_N55_V0.229210.658
25_Y71_K0.228790.657
64_R75_K0.223840.643
17_K28_P0.223620.642
18_D56_F0.222640.639
43_T47_N0.222370.638
63_Y77_F0.222040.637
20_A62_L0.220030.632
47_N51_N0.219620.631
73_K84_E0.219240.629
37_D79_D0.218920.629
8_K56_F0.218130.626
62_L66_I0.212770.611
38_K75_K0.212720.611
72_P79_D0.211220.606
57_I61_G0.210250.604
34_K47_N0.209010.600
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
2kfsA0.965570.60.826
1qgpA0.666732.80.861
1tnsA0.839130.10.863
1xmkA0.747129.60.864
1g4dA0.758628.80.865
1j9iA0.7701280.866
1hsjA0.885118.30.876
2vn2A0.9655180.876
1oyiA0.7011150.881
3eqxA0.839114.20.881
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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