GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
POTRA_2 - POTRA domain ShlB-type
Pfam: PF08479 (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: CL0191
Length: 76
Sequences: 3048
Seq/Len: 40.11
HH_delta: 0.088 (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
47_Y75_E0.872542.478
7_R70_T0.762122.164
46_Y50_K0.759162.156
9_E70_T0.753432.140
16_E20_Q0.674361.915
11_N75_E0.63081.792
8_F19_L0.62041.762
15_P18_E0.600511.706
11_N16_E0.59661.694
41_D45_N0.587031.667
32_T35_D0.582711.655
57_V71_I0.56871.615
31_L36_L0.544471.546
4_K68_V0.541271.537
14_L50_K0.522651.484
40_A59_L0.519331.475
35_D38_Q0.488741.388
34_A38_Q0.487191.384
40_A44_T0.480941.366
37_Q40_A0.480531.365
63_D66_D0.474121.347
13_L52_Y0.472711.343
9_E72_R0.469341.333
38_Q41_D0.464091.318
25_P39_L0.461031.309
36_L69_L0.444851.263
42_A45_N0.430051.221
45_N49_E0.426521.211
48_R54_T0.422911.201
18_E46_Y0.42081.195
56_R74_V0.413621.175
26_Y29_R0.409011.162
33_L37_Q0.407151.156
5_G27_I0.403831.147
14_L75_E0.396661.127
43_L57_V0.391881.113
29_R35_D0.390611.109
11_N47_Y0.390081.108
6_I69_L0.380771.081
44_T55_S0.379381.077
5_G68_V0.378171.074
22_I46_Y0.368331.046
36_L71_I0.366751.042
8_F16_E0.348830.991
37_Q41_D0.346210.983
64_I67_G0.345510.981
58_Y72_R0.343770.976
26_Y39_L0.332540.944
38_Q42_A0.329120.935
14_L19_L0.327560.930
3_I6_I0.322270.915
4_K66_D0.320910.911
45_N48_R0.319050.906
2_P30_C0.317070.901
10_G75_E0.310120.881
6_I27_I0.30970.880
48_R55_S0.308090.875
17_E20_Q0.305670.868
59_L62_Q0.305660.868
11_N19_L0.298970.849
14_L46_Y0.293150.833
8_F73_V0.291450.828
48_R53_I0.289860.823
48_R56_R0.289660.823
14_L47_Y0.288670.820
18_E50_K0.283890.806
20_Q24_A0.280230.796
10_G47_Y0.27820.790
46_Y49_E0.271560.771
6_I26_Y0.269970.767
41_D44_T0.268550.763
44_T56_R0.263720.749
18_E21_A0.263320.748
39_L59_L0.262630.746
33_L59_L0.261530.743
8_F11_N0.260640.740
39_L71_I0.254430.723
24_A42_A0.253570.720
44_T48_R0.247490.703
23_L39_L0.246650.701
58_Y74_V0.244730.695
17_E21_A0.243110.690
23_L43_L0.240140.682
44_T57_V0.237970.676
8_F20_Q0.235950.670
4_K28_G0.234520.666
63_D67_G0.234290.665
60_P72_R0.233780.664
22_I42_A0.232160.659
15_P19_L0.232110.659
4_K70_T0.229510.652
18_E22_I0.227880.647
47_Y55_S0.226880.644
12_T75_E0.226350.643
13_L50_K0.224120.637
23_L27_I0.222420.632
2_P66_D0.221110.628
54_T76_G0.218910.622
43_L52_Y0.218640.621
8_F43_L0.21640.615
8_F23_L0.210820.599
25_P42_A0.210780.599
65_S68_V0.207890.590
6_I25_P0.205610.584
2_P27_I0.205280.583
3_I23_L0.203010.577
36_L76_G0.201920.573
69_L73_V0.201640.573
31_L59_L0.199750.567
11_N23_L0.199010.565
6_I52_Y0.198280.563
63_D69_L0.198020.562
36_L40_A0.197970.562
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
2qdzA199.20.088
3mc9A1990.168
3q6bA1990.175
2x8xX198.90.224
3efcA198.80.232
3efcA198.80.246
2qdfA198.70.268
2qdfA198.70.28
3mc9A0.934298.10.408
2x8xX0.934297.80.459

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