GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NusA_N - NusA N-terminal domain
Pfam: PF08529 (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: 122
Sequences: 1250
Seq/Len: 10.25
HH_delta: -0.032 (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_R91_E0.596033.265
7_E17_K0.461272.527
60_E89_E0.435822.387
78_K85_E0.410712.250
54_K93_E0.396872.174
73_S76_E0.382032.093
60_E71_E0.374452.051
58_K91_E0.347851.906
65_V73_S0.331631.817
65_V71_E0.328781.801
25_E48_E0.326641.789
44_V55_V0.314671.724
66_E71_E0.298781.637
74_L78_K0.276541.515
59_K92_E0.270811.484
5_A32_Y0.266891.462
45_E54_K0.264281.448
61_V84_A0.26121.431
26_E30_K0.260991.430
103_A106_T0.258421.416
6_I10_A0.252761.385
74_L86_V0.251.370
67_D70_T0.248371.361
41_N58_K0.247831.358
95_D98_D0.246461.350
18_E48_E0.24351.334
43_R58_K0.238971.309
100_G103_A0.236671.297
21_I48_E0.231551.268
13_K119_E0.229061.255
58_K89_E0.226671.242
113_Q119_E0.22071.209
81_D88_D0.219721.204
23_A118_A0.218691.198
60_E87_G0.215861.183
74_L77_A0.215791.182
5_A9_I0.213691.171
30_K34_K0.213021.167
118_A121_E0.212671.165
21_I46_I0.212151.162
10_A16_D0.209191.146
63_E86_V0.206681.132
7_E11_R0.206481.131
29_I42_I0.204491.120
62_V65_V0.204241.119
27_A110_V0.203121.113
82_P85_E0.202961.112
27_A106_T0.19911.091
61_V77_A0.199011.090
78_K82_P0.196381.076
18_E22_E0.195851.073
72_I76_E0.194911.068
57_R92_E0.193821.062
84_A90_I0.193051.058
102_I105_Q0.192841.056
84_A88_D0.192711.056
75_S78_K0.191811.051
76_E80_I0.191351.048
8_Q115_I0.189191.036
16_D83_N0.189191.036
23_A114_K0.189151.036
102_I107_A0.188681.034
30_K33_K0.187151.025
103_A110_V0.185731.017
26_E106_T0.183961.008
107_A111_I0.183611.006
107_A113_Q0.18070.990
112_I117_E0.179730.985
100_G104_A0.179390.983
55_V95_D0.17930.982
32_Y96_P0.179240.982
51_G109_Q0.178930.980
20_V23_A0.178840.980
63_E66_E0.178710.979
81_D84_A0.172990.948
15_I115_I0.169450.928
44_V94_I0.16840.923
75_S79_K0.165590.907
26_E114_K0.164430.901
5_A10_A0.164170.899
112_I121_E0.164160.899
32_Y55_V0.164120.899
15_I26_E0.163460.895
28_L32_Y0.163090.893
74_L80_I0.16220.889
32_Y42_I0.162010.888
34_K116_R0.158230.867
28_L44_V0.158190.867
85_E88_D0.157860.865
3_L50_T0.156670.858
96_P111_I0.156660.858
3_L53_I0.156010.855
27_A113_Q0.155970.854
72_I77_A0.15540.851
77_A81_D0.155060.849
78_K84_A0.155020.849
64_D75_S0.155010.849
36_Y41_N0.154360.846
102_I110_V0.153890.843
105_Q120_R0.153780.842
65_V75_S0.153730.842
66_E69_D0.15370.842
76_E79_K0.153350.840
17_K21_I0.152380.835
116_R119_E0.150670.825
45_E56_Y0.150010.822
72_I90_I0.149160.817
29_I33_K0.14910.817
78_K83_N0.148010.811
18_E61_V0.147990.811
39_E70_T0.147760.809
4_E7_E0.147470.808
3_L6_I0.146790.804
34_K54_K0.146720.804
38_P49_D0.1460.800
67_D71_E0.145170.795
51_G104_A0.144970.794
58_K90_I0.144810.793
117_E121_E0.141830.777
64_D73_S0.141750.777
29_I99_F0.141680.776
68_P75_S0.141210.774
61_V88_D0.140990.772
34_K106_T0.139980.767
5_A121_E0.139910.766
47_D50_T0.139610.765
20_V106_T0.139460.764
17_K105_Q0.139450.764
107_A110_V0.136890.750
5_A115_I0.136630.748
46_I115_I0.136450.747
8_Q12_E0.135510.742
73_S79_K0.135140.740
5_A117_E0.134530.737
20_V55_V0.134260.735
114_K117_E0.133310.730
10_A24_L0.132910.728
9_I42_I0.131490.720
15_I21_I0.13140.720
81_D85_E0.131220.719
5_A112_I0.131090.718
40_A114_K0.130730.716
106_T110_V0.130480.715
34_K109_Q0.130440.715
26_E70_T0.12930.708
6_I48_E0.129220.708
24_L98_D0.128980.707
25_E45_E0.128360.703
6_I21_I0.128270.703
57_R95_D0.128110.702
55_V108_K0.128020.701
61_V67_D0.127780.700
6_I28_L0.127480.698
96_P120_R0.127040.696
10_A53_I0.126920.695
27_A31_A0.126750.694
12_E105_Q0.12670.694
108_K119_E0.126320.692
3_L21_I0.126210.691
77_A90_I0.126190.691
2_L27_A0.125850.689
108_K120_R0.125760.689
19_V118_A0.125620.688
9_I24_L0.125410.687
89_E111_I0.125380.687
25_E44_V0.125230.686
80_I84_A0.124720.683
40_A94_I0.124490.682
100_G114_K0.124080.680
2_L35_K0.123720.678
113_Q117_E0.123580.677
38_P97_E0.123120.674
99_F106_T0.122130.669
34_K118_A0.121980.668
31_A117_E0.121880.668
5_A14_G0.121840.667
30_K106_T0.120990.663
45_E85_E0.120620.661
103_A107_A0.119960.657
25_E51_G0.11950.655
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
2kwpA1100-0.032
1hh2P11000.091
1k0rA0.819799.90.288
2k5eA0.295130.60.912
3ku7A0.508230.60.912
2cpgA0.278724.80.916
1wlmA0.409821.70.918
3e2vA0.336120.50.919
2k53A0.327920.50.919
2y1hA0.336112.90.925

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