GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PemK - PemK-like protein
Pfam: PF02452 (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: 110
Sequences: 2016
Seq/Len: 18.33
HH_delta: 0.084 (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
6_V87_L0.758312.826
2_R103_K0.728962.717
24_V102_I0.727162.710
40_V74_V0.644762.403
95_S98_D0.632462.357
55_H77_D0.599092.233
10_F23_A0.589712.198
7_W91_I0.587212.188
8_V23_A0.56052.089
4_D93_R0.521961.945
3_G99_L0.503151.875
26_L40_V0.495731.847
4_D90_Y0.469471.750
98_D101_E0.463131.726
16_E86_R0.462831.725
40_V76_C0.439761.639
39_V82_I0.438361.634
23_A39_V0.42841.597
74_V102_I0.427281.592
40_V79_I0.406571.515
42_I74_V0.406421.515
101_E105_A0.403981.506
8_V82_I0.40271.501
42_I72_S0.39771.482
17_M75_R0.374441.395
38_V109_V0.373121.391
57_E73_Y0.372581.388
5_I42_I0.368021.371
31_F109_V0.359091.338
12_D18_G0.326971.219
75_R78_Q0.326821.218
55_H73_Y0.324221.208
6_V90_Y0.322591.202
55_H75_R0.319511.191
60_P71_D0.316221.178
10_F80_R0.314811.173
26_L106_L0.31471.173
46_K73_Y0.295441.101
24_V94_L0.2951.099
46_K57_E0.294921.099
36_T81_T0.292681.091
83_D86_R0.289541.079
6_V23_A0.28881.076
38_V81_T0.285181.063
19_K22_P0.283591.057
79_I106_L0.282151.051
59_E98_D0.279341.041
17_M21_R0.277971.036
7_W89_K0.277691.035
44_S68_G0.274871.024
78_Q83_D0.269091.003
99_L102_I0.268020.999
100_E104_N0.26690.995
94_L98_D0.263320.981
56_V98_D0.263030.980
105_A108_R0.260960.973
9_D20_R0.259250.966
20_R89_K0.255230.951
27_S32_N0.252170.940
100_E107_R0.252120.940
41_P80_R0.247990.924
7_W20_R0.247620.923
80_R86_R0.245520.915
72_S92_G0.244580.911
56_V105_A0.242420.903
99_L103_K0.242170.902
23_A82_I0.239840.894
37_V84_K0.23880.890
48_N55_H0.238440.889
47_P73_Y0.238220.888
6_V25_V0.237720.886
16_E83_D0.234820.875
66_L92_G0.230870.860
56_V102_I0.229920.857
37_V87_L0.225560.841
28_N31_F0.225050.839
25_V39_V0.217690.811
42_I58_I0.217620.811
12_D80_R0.215550.803
103_K107_R0.215280.802
94_L99_L0.214720.800
36_T78_Q0.21040.784
105_A109_V0.209880.782
16_E36_T0.20980.782
82_I87_L0.206430.769
68_G92_G0.205650.766
57_E71_D0.204850.763
61_D98_D0.203410.758
74_V98_D0.202870.756
49_K55_H0.20270.755
22_P72_S0.201420.751
96_E100_E0.200950.749
27_S36_T0.198440.740
90_Y93_R0.197140.735
92_G95_S0.196220.731
22_P43_T0.194730.726
104_N107_R0.194630.725
44_S71_D0.193960.723
31_F38_V0.19370.722
65_G92_G0.19370.722
2_R99_L0.191770.715
44_S72_S0.191620.714
30_A108_R0.1880.701
2_R27_S0.184290.687
65_G68_G0.183760.685
19_K23_A0.182090.679
25_V37_V0.181960.678
76_C109_V0.181540.677
20_R88_R0.18140.676
10_F82_I0.180930.674
103_K106_L0.17750.661
97_E101_E0.176240.657
5_I94_L0.175950.656
14_G17_M0.175840.655
14_G83_D0.175040.652
49_K73_Y0.172650.643
84_K106_L0.171760.640
24_V40_V0.170380.635
59_E71_D0.169690.632
27_S31_F0.167910.626
8_V87_L0.167690.625
24_V42_I0.167670.625
17_M78_Q0.166780.622
28_N109_V0.166740.621
53_P56_V0.165350.616
11_P83_D0.165310.616
8_V39_V0.165120.615
30_A85_E0.164870.614
72_S87_L0.164760.614
7_W22_P0.164430.613
2_R29_N0.164170.612
31_F36_T0.163990.611
54_F77_D0.160870.600
5_I66_L0.160.596
9_D16_E0.159170.593
100_E103_K0.156080.582
60_P66_L0.155680.580
101_E104_N0.155020.578
30_A35_G0.15430.575
45_K73_Y0.153570.572
30_A47_P0.153180.571
18_G72_S0.150730.562
28_N77_D0.150710.562
43_T75_R0.148290.553
37_V81_T0.147610.550
96_E101_E0.146930.548
24_V74_V0.146740.547
104_N108_R0.14650.546
46_K71_D0.145350.542
33_E107_R0.144990.540
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
1m1fA0.954599.80.084
1ne8A0.963699.80.088
1ub4A0.909199.80.092
2kmtA0.890998.60.57
3vubA0.872795.10.771
2l89A0.830.70.877
3mxuA0.836429.40.878
3klrA0.854528.10.879
1h3zA0.818228.10.879
3hgbA0.890922.30.885

Page generated in 0.0375 seconds.