GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YjbR - YjbR
Pfam: PF04237 (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: 92
Sequences: 1901
Seq/Len: 20.66
HH_delta: 0.016 (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
10_D21_R0.818063.589
7_V27_F0.752413.301
4_L86_D0.711613.122
38_N62_M0.549112.409
9_E18_P0.454521.994
12_P21_R0.424841.864
56_F84_L0.423631.858
45_E87_E0.377661.657
59_A69_S0.374041.641
41_C46_Q0.364511.599
45_E48_A0.351481.542
62_M69_S0.333321.462
78_D82_R0.325781.429
63_N66_H0.323641.420
8_E24_G0.319821.403
4_L89_Y0.317151.391
13_W19_V0.301751.324
57_F71_R0.293721.288
28_A85_I0.288811.267
52_Q83_E0.284311.247
80_E83_E0.282231.238
19_V29_L0.278311.221
77_D80_E0.266371.169
41_C68_V0.265331.164
28_A39_V0.262921.153
3_S82_R0.256861.127
43_P66_H0.253971.114
79_E83_E0.247631.086
20_F30_L0.245061.075
27_F89_Y0.241431.059
87_E90_R0.241411.059
26_M29_L0.241311.059
4_L22_V0.240861.057
55_G74_G0.240761.056
36_D71_R0.239291.050
68_V84_L0.2391.048
50_R68_V0.235981.035
9_E20_F0.234331.028
28_A72_L0.234041.027
40_K67_W0.232521.020
64_K88_S0.23181.017
28_A37_V0.231331.015
44_E52_Q0.228211.001
77_D83_E0.228061.000
48_A52_Q0.226750.995
38_N69_S0.222830.978
6_G23_G0.222220.975
11_Y18_P0.217040.952
64_K67_W0.214380.940
43_P65_K0.213350.936
59_A63_N0.213240.935
35_D71_R0.213110.935
80_E84_L0.211080.926
47_E50_R0.210620.924
45_E90_R0.20930.918
79_E82_R0.208740.916
15_W19_V0.208170.913
27_F72_L0.206810.907
29_L62_M0.204620.898
42_D46_Q0.203960.895
59_A62_M0.203420.892
52_Q80_E0.200380.879
45_E83_E0.199890.877
82_R86_D0.199690.876
42_D87_E0.197030.864
58_P62_M0.196140.860
83_E86_D0.195470.857
27_F88_S0.191790.841
56_F80_E0.191040.838
22_V89_Y0.190720.837
47_E51_E0.190410.835
5_P86_D0.189160.830
60_Y63_N0.188710.828
38_N59_A0.188180.826
50_R54_D0.187950.825
50_R56_F0.187580.823
62_M67_W0.18670.819
63_N68_V0.185050.812
13_W29_L0.184160.808
49_L80_E0.183910.807
58_P61_H0.181590.797
40_K88_S0.181560.796
46_Q68_V0.179880.789
61_H64_K0.178380.783
39_V81_L0.177620.779
70_V81_L0.175720.771
86_D90_R0.175570.770
29_L60_Y0.174990.768
22_V25_K0.17460.766
75_D79_E0.172750.758
79_E86_D0.169390.743
39_V70_V0.168210.738
42_D91_L0.167210.734
14_G31_G0.16620.729
6_G22_V0.16530.725
39_V69_S0.164780.723
48_A83_E0.163420.717
60_Y64_K0.163140.716
23_G75_D0.163020.715
72_L77_D0.162790.714
12_P26_M0.162590.713
67_W88_S0.161380.708
43_P77_D0.160020.702
38_N61_H0.159580.700
33_D74_G0.159240.699
4_L7_V0.159020.698
13_W64_K0.158820.697
46_Q63_N0.158710.696
13_W40_K0.156070.685
3_S7_V0.155260.681
37_V72_L0.155110.680
5_P22_V0.154590.678
88_S91_L0.15450.678
58_P69_S0.154490.678
32_E35_D0.153780.675
66_H91_L0.153230.672
10_D14_G0.153070.671
64_K69_S0.152590.669
50_R55_G0.151870.666
5_P79_E0.149470.656
33_D38_N0.148880.653
13_W18_P0.148420.651
14_G19_V0.148180.650
72_L76_V0.147930.649
3_S8_E0.146780.644
12_P18_P0.146630.643
55_G75_D0.146370.642
38_N60_Y0.145410.638
38_N65_K0.145350.638
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
2fkiA199.80.016
2a1vA199.80.042
2kfpA0.989199.70.07
2oc6A0.945798.80.475
2i8dA0.934898.70.477
2kl4A0.945798.70.48
2od0A0.934898.10.585
3w1oA0.347840.10.851
3ohwB0.391324.40.867
3pruC0.337200.871

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