GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PA - PA domain
Pfam: PF02225 (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: 101
Sequences: 2745
Seq/Len: 27.18
HH_delta: 0.138 (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
53_A58_A1.11223.591
91_Y95_E0.951763.073
39_V61_V0.788572.546
36_I60_G0.693612.239
40_E64_Y0.647262.090
40_E98_L0.631842.040
42_G49_K0.63162.039
38_L64_Y0.621122.005
52_N55_K0.611981.976
41_R46_F0.595951.924
34_G59_K0.583221.883
62_I87_V0.536981.734
90_S93_D0.501841.620
89_I93_D0.481771.555
64_Y98_L0.436561.409
50_V86_V0.433621.400
37_V53_A0.426911.378
51_R55_K0.423291.367
22_C25_S0.41951.354
54_Q83_D0.413771.336
70_N73_M0.409911.323
89_I97_L0.407591.316
32_V56_A0.387561.251
46_F63_I0.368691.190
38_L98_L0.366451.183
50_V61_V0.366291.183
46_F88_F0.366061.182
61_V86_V0.361431.167
39_V100_Y0.348821.126
95_E99_A0.347441.122
93_D96_A0.343031.107
28_N31_D0.342761.107
96_A99_A0.335511.083
54_Q82_I0.334311.079
65_N88_F0.32651.054
62_I89_I0.319471.031
64_Y94_G0.317491.025
37_V58_A0.313931.014
24_P55_K0.312281.008
54_Q84_I0.309210.998
23_C44_C0.304730.984
22_C26_D0.290950.939
32_V35_K0.286560.925
40_E91_Y0.286170.924
50_V54_Q0.284720.919
91_Y94_G0.28420.918
49_K65_N0.283770.916
31_D35_K0.28330.915
89_I94_G0.283150.914
71_G74_I0.282790.913
46_F49_K0.282550.912
45_S48_D0.274270.885
60_G85_P0.272060.878
50_V82_I0.269140.869
64_Y89_I0.269040.869
39_V53_A0.267640.864
32_V37_V0.265590.857
23_C26_D0.265110.856
21_D44_C0.264040.852
29_G56_A0.264030.852
41_R65_N0.254790.823
19_E22_C0.253780.819
52_N56_A0.251740.813
42_G46_F0.248770.803
92_E96_A0.246910.797
41_R63_I0.244660.790
40_E95_E0.243970.788
48_D51_R0.241440.779
46_F65_N0.237710.767
72_S78_D0.236960.765
97_L100_Y0.235230.759
82_I86_V0.23290.752
19_E23_C0.232540.751
22_C39_V0.23170.748
50_V56_A0.227290.734
59_K85_P0.223090.720
44_C49_K0.221350.715
26_D30_S0.220140.711
72_S89_I0.219730.709
27_Y52_N0.217680.703
38_L94_G0.214190.692
73_M76_S0.212480.686
51_R80_D0.211190.682
73_M81_P0.204780.661
49_K63_I0.204040.659
28_N32_V0.202180.653
34_G58_A0.201860.652
62_I78_D0.199350.644
22_C37_V0.196530.634
27_Y32_V0.195950.633
21_D24_P0.192290.621
50_V84_I0.191260.617
61_V64_Y0.190420.615
38_L90_S0.190140.614
48_D52_N0.189120.611
33_K59_K0.188580.609
53_A61_V0.188510.609
51_R54_Q0.18790.607
44_C77_E0.187740.606
20_G23_C0.187620.606
50_V83_D0.187240.604
87_V94_G0.186590.602
47_D72_S0.186560.602
47_D50_V0.186390.602
47_D51_R0.185610.599
72_S75_D0.185040.597
93_D97_L0.184270.595
63_I86_V0.182640.590
29_G99_A0.182290.589
96_A100_Y0.180750.584
28_N33_K0.18030.582
60_G96_A0.178720.577
57_G62_I0.178070.575
79_P84_I0.176710.571
92_E95_E0.176550.570
74_I77_E0.176450.570
44_C48_D0.175650.567
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
3icuA0.990199.50.138
3fedA0.990199.30.233
2ek8A0.930799.20.274
3kasA0.940699.20.276
3i6sA0.901990.331
3iibA0.9505990.342
1xf1A0.90198.70.422
1y9zA198.50.459
3vtaA0.891197.50.605
4kngE0.940696.60.664

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