GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ectoine_synth - Ectoine synthase
Pfam: PF06339 (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. )
Clan: CL0029
Length: 126
Sequences: 1508
Seq/Len: 11.97
HH_delta: 0.371 (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
66_G101_M0.637883.366
63_E102_R0.637333.363
65_E80_K0.615253.247
65_E78_P0.485582.563
67_E96_R0.436042.301
5_S83_T0.397232.096
65_E98_K0.391292.065
67_E98_K0.378041.995
5_S8_D0.372061.964
65_E99_T0.358071.890
67_E76_V0.357571.887
39_E102_R0.341391.802
47_E96_R0.334361.765
43_Y100_D0.327651.729
69_E94_Y0.307331.622
67_E78_P0.299851.582
70_D73_T0.299431.580
61_C103_L0.282861.493
53_K93_H0.281951.488
63_E100_D0.277061.462
73_T91_D0.275451.454
66_G79_I0.274521.449
44_A99_T0.268931.419
76_V96_R0.266621.407
70_D75_E0.255011.346
51_H93_H0.250721.323
63_E81_P0.250471.322
69_E76_V0.238381.258
61_C79_I0.238011.256
41_T100_D0.236821.250
78_P98_K0.23251.227
15_D22_E0.230361.216
39_E104_V0.221181.167
42_I46_T0.221181.167
41_T102_R0.217551.148
80_K83_T0.215141.135
62_I104_V0.212921.124
33_M56_L0.212161.120
66_G78_P0.209241.104
4_R8_D0.205341.084
56_L89_K0.202661.070
44_A97_A0.199151.051
49_H94_Y0.198951.050
69_E74_G0.197711.043
88_D91_D0.191651.011
66_G98_K0.191441.010
38_H57_E0.187880.992
35_F108_N0.18780.991
38_H105_C0.186840.986
70_D91_D0.186210.983
49_H92_R0.1850.976
68_V85_Y0.184860.976
47_E94_Y0.184540.974
36_S105_C0.184520.974
20_N46_T0.183720.970
22_E48_T0.179050.945
51_H104_V0.178190.940
60_Y84_M0.176660.932
61_C101_M0.175740.927
44_A100_D0.17030.899
20_N48_T0.170.897
38_H107_F0.167920.886
27_L68_V0.167680.885
17_D43_Y0.166210.877
50_I94_Y0.162340.857
68_V95_L0.160210.846
68_V87_L0.154960.818
5_S80_K0.153980.813
84_M87_L0.153420.810
59_V93_H0.15220.803
45_G65_E0.151660.800
42_I103_L0.150470.794
40_T107_F0.149980.792
74_G91_D0.149970.791
7_D80_K0.148570.784
48_T107_F0.147790.780
31_D106_V0.14580.769
35_F58_A0.145610.768
40_T95_L0.14520.766
16_V19_E0.145110.766
10_R15_D0.144490.763
69_E96_R0.144090.760
29_K36_S0.143920.760
95_L101_M0.143680.758
50_I69_E0.143380.757
98_K101_M0.142980.755
33_M86_A0.142970.755
10_R24_R0.14260.753
36_S40_T0.141830.749
97_A101_M0.141750.748
25_R57_E0.141090.745
4_R9_I0.141060.744
24_R41_T0.140510.742
35_F106_V0.138990.734
59_V95_L0.138780.732
68_V101_M0.138480.731
17_D22_E0.138320.730
9_I27_L0.137720.727
28_L38_H0.136790.722
37_F55_H0.136570.721
37_F104_V0.136560.721
15_D24_R0.135660.716
4_R7_D0.135010.713
37_F58_A0.134070.708
5_S9_I0.134050.707
36_S55_H0.133230.703
51_H59_V0.131460.694
97_A100_D0.130910.691
20_N30_D0.12980.685
37_F105_C0.129660.684
68_V79_I0.129260.682
22_E25_R0.129230.682
3_V70_D0.129070.681
44_A98_K0.128960.681
5_S10_R0.12820.677
24_R94_Y0.12730.672
38_H93_H0.12710.671
25_R105_C0.126740.669
49_H53_K0.126480.667
3_V7_D0.126260.666
38_H59_V0.125920.665
40_T103_L0.125390.662
15_D30_D0.125340.661
29_K88_D0.124820.659
56_L86_A0.124750.658
20_N43_Y0.124150.655
4_R41_T0.123930.654
80_K98_K0.123920.654
74_G77_H0.122720.648
42_I101_M0.122620.647
62_I73_T0.12210.644
28_L37_F0.122060.644
103_L107_F0.122040.644
29_K56_L0.120880.638
27_L32_G0.120530.636
61_C66_G0.120350.635
43_Y102_R0.119930.633
16_V59_V0.119750.632
41_T63_E0.11940.630
22_E54_N0.119270.629
51_H85_Y0.119190.629
6_L66_G0.118040.623
46_T50_I0.117950.622
79_I101_M0.117840.622
68_V77_H0.116670.616
25_R39_E0.11660.615
26_L36_S0.116420.614
40_T87_L0.116230.613
50_I92_R0.116180.613
26_L60_Y0.116060.613
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
4e2qA0.88199.50.371
3ibmA0.928699.50.381
3ht1A0.976299.50.389
3kgzA0.928699.50.389
1lr5A0.960399.50.39
1sfnA0.896899.40.405
1sq4A0.936599.40.408
1vj2A0.88199.40.414
1rc6A0.88199.40.416
3jzvA0.928699.40.418

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