GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NusB - NusB family
Pfam: PF01029 (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: 134
Sequences: 2789
Seq/Len: 20.81
HH_delta: 0.024 (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
64_D88_R1.264973.913
55_G92_Y1.148683.553
90_A109_A0.873952.704
91_I132_I0.855492.646
114_K122_A0.774222.395
86_I113_A0.765652.369
59_N62_E0.75242.328
7_A52_L0.678172.098
131_R134_R0.640521.981
100_I105_A0.625031.934
5_E115_K0.588351.820
63_L92_Y0.54811.696
113_A125_V0.537021.661
101_P104_V0.529641.638
8_L89_L0.528591.635
63_L91_I0.51611.597
48_F100_I0.511351.582
95_L132_I0.500421.548
62_E96_F0.490151.516
74_W78_R0.487991.510
71_L124_F0.480141.485
107_N111_E0.477141.476
9_Q116_Y0.475871.472
8_L85_A0.467231.445
81_P84_R0.464881.438
71_L79_L0.459211.421
66_L132_I0.459041.420
10_A49_A0.458761.419
59_N96_F0.455231.408
86_I109_A0.439691.360
52_L89_L0.436721.351
110_V126_N0.435781.348
51_E97_L0.422621.307
7_A53_V0.422591.307
50_R54_Y0.417181.291
67_I91_I0.414181.281
14_V57_L0.411911.274
110_V122_A0.411341.272
3_A49_A0.410051.268
94_L105_A0.409671.267
111_E114_K0.392751.215
93_E109_A0.385941.194
94_L133_A0.38341.186
106_I133_A0.382251.182
70_L132_I0.373281.155
51_E58_R0.372231.151
80_P83_D0.369771.144
68_S76_L0.368061.139
51_E92_Y0.367631.137
86_I125_V0.362321.121
92_Y96_F0.357571.106
5_E116_Y0.355851.101
66_L91_I0.353721.094
63_L96_F0.352821.091
119_E122_A0.347671.076
102_P133_A0.347451.075
83_D121_S0.346681.072
90_A105_A0.342011.058
108_E111_E0.340031.052
127_A131_R0.338151.046
71_L128_V0.337741.045
8_L112_L0.337731.045
89_L112_L0.327321.013
79_L124_F0.326061.009
84_R88_R0.32541.007
94_L102_P0.325131.006
3_A7_A0.323621.001
52_L92_Y0.3210.993
64_D84_R0.315640.976
92_Y97_L0.314540.973
47_A51_E0.313160.969
85_A88_R0.312490.967
56_V92_Y0.310110.959
12_Y85_A0.305590.945
66_L95_L0.305150.944
65_A69_K0.303290.938
49_A53_V0.300710.930
13_Q24_E0.299370.926
118_D121_S0.295370.914
5_E9_Q0.294810.912
56_V88_R0.289320.895
110_V114_K0.284540.880
68_S77_E0.283050.876
86_I112_L0.282780.875
27_F30_E0.28070.868
70_L131_R0.278820.863
8_L116_Y0.278080.860
48_F97_L0.277620.859
11_L89_L0.271510.840
10_A53_V0.271220.839
106_I110_V0.270750.838
28_L50_R0.267780.828
60_K64_D0.267030.826
119_E123_G0.266090.823
111_E115_K0.26310.814
8_L86_I0.262580.812
87_L125_V0.260830.807
104_V108_E0.254480.787
25_G31_A0.253090.783
33_E37_E0.251830.779
80_P121_S0.250720.776
48_F52_L0.250240.774
83_D117_G0.249180.771
12_Y82_V0.248880.770
54_Y58_R0.247680.766
60_K85_A0.244260.756
81_P85_A0.243220.752
117_G121_S0.239330.740
67_I87_L0.238390.737
48_F51_E0.238030.736
43_E47_A0.237520.735
8_L82_V0.23730.734
60_K88_R0.237220.734
62_E66_L0.236840.733
25_G28_L0.235760.729
11_L85_A0.233860.723
63_L88_R0.231690.717
103_H130_R0.231390.716
14_V53_V0.22970.711
62_E95_L0.228810.708
90_A129_L0.226210.700
7_A55_G0.223910.693
6_L10_A0.223290.691
106_I130_R0.223130.690
70_L134_R0.223010.690
83_D125_V0.22230.688
80_P124_F0.220110.681
64_D67_I0.218920.677
56_V89_L0.218820.677
107_N114_K0.2180.674
8_L12_Y0.216970.671
39_S43_E0.216580.670
7_A56_V0.214010.662
10_A31_A0.213760.661
110_V130_R0.213520.661
90_A94_L0.212550.658
5_E112_L0.21250.657
93_E97_L0.211860.655
61_E65_A0.209040.647
11_L60_K0.208890.646
93_E105_A0.207060.641
100_I104_V0.205950.637
110_V125_V0.204680.633
79_L83_D0.202450.626
4_R93_E0.199940.619
90_A93_E0.198890.615
73_N124_F0.19880.615
80_P118_D0.198560.614
6_L9_Q0.197910.612
13_Q26_Q0.196970.609
125_V128_V0.196920.609
67_I71_L0.196730.609
4_R11_L0.196170.607
48_F93_E0.195870.606
12_Y116_Y0.195430.605
65_A68_S0.194940.603
4_R7_A0.194940.603
26_Q30_E0.194310.601
82_V117_G0.193060.597
120_K123_G0.192960.597
12_Y24_E0.192510.596
56_V63_L0.19220.595
126_N130_R0.191180.591
39_S42_S0.189850.587
127_A130_R0.188680.584
11_L56_V0.18850.583
12_Y81_P0.188080.582
42_S46_R0.186330.576
3_A44_E0.185490.574
9_Q24_E0.185270.573
76_L84_R0.183710.568
64_D85_A0.18220.564
71_L76_L0.182170.564
91_I130_R0.181770.562
40_E43_E0.181030.560
106_I126_N0.179550.555
13_Q78_R0.179230.554
24_E68_S0.178230.551
58_R65_A0.178020.551
6_L49_A0.177730.550
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
1tzvA0.94031000.024
3r2dA0.94781000.024
3d3bA0.94031000.036
1eyvA0.94781000.066
2yxlA0.925499.90.191
1sqgA0.917999.90.192
1q8cA0.955276.20.876
1u6gC0.947862.30.887
1k87A0.888159.80.888
3e2qA0.895542.30.899

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