GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sulfate_tra_GLY - Sulfate transporter N-terminal domain with GLY motif
Pfam: PF13792 (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: CL0062
Length: 84
Sequences: 2592
Seq/Len: 30.86
HH_delta: 0.828 (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
11_S15_N0.874123.127
11_S14_S0.752262.691
59_Y70_V0.614262.197
10_Y16_L0.552041.975
34_G73_T0.515331.843
43_V47_Y0.509411.822
10_Y19_D0.501771.795
16_L20_L0.494651.769
23_G27_A0.489771.752
22_A26_V0.486081.739
37_Y74_A0.470721.684
34_G52_A0.393251.407
69_I75_A0.389051.392
51_A72_P0.381951.366
34_G37_Y0.380711.362
79_L83_V0.358881.284
59_Y62_F0.358591.283
58_I62_F0.355761.273
9_R17_R0.341691.222
14_S17_R0.337571.207
42_G81_A0.333341.192
17_R21_L0.332671.190
9_R15_N0.332211.188
27_A73_T0.322071.152
9_R14_S0.320141.145
47_Y50_Y0.316471.132
69_I79_L0.309531.107
55_P59_Y0.306971.098
59_Y63_G0.304161.088
15_N18_G0.301611.079
56_P69_I0.295681.058
33_Q40_L0.291711.043
54_I58_I0.287911.030
15_N19_D0.281891.008
30_A72_P0.279691.000
29_V33_Q0.275990.987
33_Q69_I0.274790.983
39_L45_P0.274320.981
59_Y64_S0.273460.978
10_Y15_N0.273380.978
37_Y77_S0.272160.974
55_P76_M0.261920.937
31_I72_P0.260940.933
30_A56_P0.260760.933
29_V37_Y0.257770.922
10_Y14_S0.255270.913
46_I73_T0.252980.905
36_A78_L0.250430.896
36_A73_T0.25030.895
33_Q72_P0.247470.885
47_Y51_A0.246870.883
69_I73_T0.246060.880
76_M80_I0.244690.875
17_R20_L0.244140.873
27_A47_Y0.243920.872
35_M44_P0.240360.860
57_L62_F0.231520.828
18_G21_L0.231260.827
33_Q77_S0.229740.822
30_A69_I0.228890.819
10_Y59_Y0.228790.818
79_L82_S0.227610.814
41_A77_S0.226280.809
25_T70_V0.226250.809
26_V74_A0.223890.801
28_L78_L0.22330.799
35_M47_Y0.222440.796
16_L54_I0.21880.783
51_A54_I0.217610.778
9_R16_L0.217110.777
49_L78_L0.215570.771
40_L73_T0.214340.767
14_S18_G0.213720.764
60_A69_I0.213140.762
52_A71_G0.211580.757
37_Y41_A0.211130.755
17_R81_A0.209140.748
35_M52_A0.209110.748
60_A66_R0.2070.740
16_L19_D0.206570.739
45_P63_G0.205610.735
25_T31_I0.203810.729
24_L32_P0.203520.728
38_A44_P0.203490.728
10_Y71_G0.202390.724
14_S57_L0.202080.723
60_A68_M0.201510.721
17_R66_R0.200560.717
15_N46_I0.20.715
11_S16_L0.199580.714
52_A63_G0.199460.713
53_I72_P0.198890.711
22_A60_A0.198820.711
40_L77_S0.198620.710
11_S58_I0.198520.710
38_A45_P0.197660.707
14_S54_I0.197350.706
26_V55_P0.196110.701
40_L69_I0.19610.701
55_P74_A0.195780.700
25_T28_L0.194790.697
63_G68_M0.193690.693
37_Y55_P0.193490.692
60_A64_S0.190.680
46_I50_Y0.18990.679
37_Y70_V0.189370.677
78_L82_S0.189120.676
50_Y53_I0.188890.676
17_R25_T0.188390.674
14_S61_L0.188330.674
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
3qe7A0.976286.80.828
2xq2A119.80.893
1btsA0.30958.30.909
2d10E0.19053.90.921
2d11E0.19053.80.922
3me0B0.35713.60.922
3dh4A13.50.923
1sghB0.19053.50.923
2wb0X0.3693.20.924
3o0qA0.57141.60.935
If you are interested in a protein containing this domain,
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