GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HsdM_N - HsdM N-terminal domain
Pfam: PF12161 (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: 137
Sequences: 1901
Seq/Len: 13.88
HH_delta: 0.14 (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_K36_D0.520112.851
74_E79_N0.470352.578
7_N10_D0.454962.494
20_E23_D0.452832.482
39_E78_S0.436472.393
17_D22_K0.431762.367
3_S7_N0.408732.241
41_R44_E0.396412.173
11_I132_K0.364151.996
89_E93_N0.356061.952
10_D13_R0.305931.677
9_A21_Y0.302071.656
81_K134_I0.300291.646
128_K132_K0.296871.627
11_I136_E0.276971.518
75_Y97_G0.276951.518
38_F70_Y0.272031.491
79_N82_K0.26451.450
10_D14_G0.25681.408
59_E63_K0.250851.375
88_G92_N0.246281.350
7_N136_E0.243011.332
83_N90_N0.239561.313
124_K133_L0.234961.288
80_L134_I0.232211.273
33_R37_K0.231211.267
15_D129_K0.230991.266
124_K129_K0.228611.253
74_E93_N0.227851.249
132_K135_D0.221651.215
59_E101_S0.218951.200
41_R45_L0.218931.200
35_S77_W0.214191.174
7_N11_I0.213721.172
41_R64_S0.212891.167
61_K66_G0.212331.164
72_P97_G0.211631.160
8_I136_E0.207621.138
6_W9_A0.207581.138
58_L62_Y0.204571.121
41_R66_G0.203091.113
84_P87_L0.202941.112
97_G100_E0.197561.083
11_I32_K0.196791.079
24_Y95_F0.193561.061
83_N86_N0.192541.055
81_K135_D0.192371.055
87_L131_K0.192071.053
44_E66_G0.191711.051
60_E64_S0.190911.047
24_Y126_R0.187591.028
131_K135_D0.186971.025
72_P75_Y0.186961.025
8_I75_Y0.185781.018
31_L80_L0.18541.016
80_L90_N0.185171.015
19_S23_D0.1841.009
93_N97_G0.183931.008
17_D36_D0.183691.007
18_A21_Y0.181850.997
96_P100_E0.181230.993
78_S82_K0.180170.988
95_F109_F0.180170.988
80_L91_L0.176440.967
87_L134_I0.175780.964
18_A22_K0.175680.963
39_E76_R0.173970.954
38_F76_R0.173220.950
93_N96_P0.172670.947
15_D27_G0.169460.929
28_L133_L0.167170.916
92_N113_D0.167020.916
132_K136_E0.166060.910
105_L114_F0.165590.908
77_W81_K0.164750.903
39_E42_K0.164120.900
40_D43_E0.16390.898
40_D44_E0.16320.895
12_L16_I0.161640.886
35_S39_E0.159110.872
95_F99_E0.159060.872
60_E66_G0.158770.870
129_K137_F0.158550.869
14_G19_S0.15820.867
41_R68_G0.157240.862
9_A12_L0.157170.862
7_N107_G0.157090.861
88_G102_N0.157080.861
128_K137_F0.155920.855
126_R129_K0.155570.853
99_E109_F0.155530.853
43_E78_S0.155140.850
9_A26_L0.155130.850
6_W21_Y0.154360.846
19_S22_K0.153670.842
86_N89_E0.153560.842
86_N103_P0.153540.842
4_K136_E0.152520.836
62_Y66_G0.151270.829
9_A27_G0.150570.825
13_R17_D0.150260.824
61_K110_S0.149570.820
75_Y94_A0.149490.819
44_E64_S0.147860.811
73_P79_N0.147590.809
13_R21_Y0.147190.807
5_L114_F0.146390.802
14_G18_A0.146060.801
35_S78_S0.145290.796
75_Y125_E0.145240.796
31_L109_F0.145020.795
24_Y127_N0.144330.791
25_I137_F0.143980.789
31_L75_Y0.143770.788
86_N90_N0.143770.788
8_I133_L0.14350.787
88_G127_N0.143030.784
28_L124_K0.141730.777
8_I25_I0.141510.776
29_L130_L0.141240.774
77_W95_F0.140870.772
92_N96_P0.140390.770
61_K64_S0.14010.768
20_E114_F0.138550.759
4_K33_R0.137750.755
115_F126_R0.136970.751
22_K133_L0.136470.748
74_E82_K0.136030.746
75_Y93_N0.135220.741
22_K35_S0.133820.734
58_L61_K0.132950.729
37_K40_D0.132370.726
21_Y108_I0.131930.723
92_N100_E0.131450.721
37_K67_N0.131340.720
6_W26_L0.131220.719
35_S42_K0.130650.716
3_S44_E0.130570.716
58_L64_S0.130110.713
42_K82_K0.130090.713
31_L98_I0.129260.709
43_E106_K0.129120.708
37_K41_R0.129010.707
42_K45_L0.128960.707
9_A20_E0.128680.705
28_L134_I0.128520.705
13_R18_A0.128320.703
31_L68_G0.128040.702
108_I113_D0.127020.696
129_K135_D0.125830.690
20_E126_R0.125780.689
29_L32_K0.125210.686
94_A105_L0.125210.686
106_K109_F0.124860.684
36_D77_W0.124840.684
41_R67_N0.124030.680
79_N102_N0.122950.674
60_E63_K0.122780.673
86_N128_K0.122690.673
88_G105_L0.122560.672
7_N133_L0.122520.672
13_R26_L0.122280.670
80_L98_I0.122150.670
45_L104_D0.121760.667
103_P107_G0.121690.667
39_E103_P0.12160.667
113_D124_K0.120910.663
116_S127_N0.120050.658
113_D116_S0.119930.657
33_R36_D0.119410.655
32_K77_W0.119340.654
64_S67_N0.119310.654
89_E133_L0.119290.654
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
3lkdA0.992799.90.14
3khkA0.934399.90.144
3ufbA0.861399.50.452
2ar0A0.744599.40.462
2okcA0.766499.40.47
2f8lA0.532864.30.875
3q6mA0.817523.20.903
3hjcA0.832122.50.904
2cgeA0.802916.30.909
3pryA0.817512.30.914

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