GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAS_11 - PAS domain
Pfam: PF14598 (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: CL0183
Length: 111
Sequences: 37565
Seq/Len: 338.42
HH_delta: -0.295 (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
73_T77_G2.648062.649
70_R80_W2.347862.349
73_T79_V2.306742.308
20_R24_S2.251822.253
66_S82_Q2.239082.240
72_R78_Y2.072342.073
82_Q104_T1.997871.999
70_R78_Y1.940591.941
23_S30_P1.926311.927
9_S13_K1.867121.868
17_V22_V1.85631.857
82_Q109_E1.852551.853
6_T101_C1.849331.850
28_Y74_K1.84271.843
83_T103_N1.704051.705
13_K37_S1.649661.650
36_R40_D1.628051.629
17_V23_S1.564081.565
69_Y83_T1.562971.564
7_R98_F1.553821.554
7_R16_Y1.547421.548
19_S24_S1.546391.547
43_H46_D1.502651.503
90_N93_T1.49131.492
29_L32_E1.468631.469
57_E61_K1.450671.451
30_P34_V1.448981.450
89_Y96_P1.421991.423
6_T14_I1.410951.412
68_Y82_Q1.407931.409
66_S84_K1.389771.390
17_V33_L1.364661.365
87_L96_P1.359111.360
52_K56_R1.340091.341
19_S23_S1.3381.339
23_S29_L1.276311.277
90_N95_K1.262971.264
16_Y30_P1.198721.199
71_F81_V1.175711.176
7_R100_V1.164241.165
28_Y32_E1.150121.151
15_T98_F1.137081.138
10_L96_P1.136341.137
22_V26_L1.127561.128
81_V103_N1.113511.114
56_R60_Q1.109961.110
32_E74_K1.105491.106
79_V105_V1.104881.105
53_Q57_E1.088681.089
84_K104_T1.059121.060
43_H78_Y1.033051.033
27_G75_N1.029911.030
6_T22_V1.02761.028
19_S30_P1.026131.027
37_S40_D1.014771.015
9_S15_T1.013161.014
46_D70_R1.009181.010
26_L71_F0.998570.999
7_R15_T0.996270.997
88_F100_V0.984570.985
8_H101_C0.971720.972
86_T100_V0.958360.959
85_A101_C0.94350.944
20_R25_L0.927660.928
90_N97_E0.9190.919
54_H57_E0.916370.917
6_T103_N0.901670.902
26_L103_N0.88550.886
106_L109_E0.866550.867
23_S33_L0.865750.866
39_Y52_K0.862420.863
80_W107_S0.861210.862
39_Y47_L0.856810.857
49_R54_H0.848040.848
42_V46_D0.8250.825
88_F98_F0.822510.823
48_Q53_Q0.81990.820
8_H55_H0.815450.816
28_Y33_L0.811130.811
7_R88_F0.809880.810
56_R59_L0.803660.804
71_F79_V0.802090.802
36_R41_F0.801570.802
5_T102_T0.799310.800
42_V47_L0.798120.798
14_I17_V0.796650.797
90_N96_P0.786040.786
44_P47_L0.78320.784
8_H38_I0.778580.779
46_D51_L0.768780.769
8_H14_I0.767320.768
10_L97_E0.762110.762
25_L81_V0.761540.762
10_L13_K0.755520.756
46_D49_R0.738310.739
42_V45_D0.724480.725
85_A99_I0.724350.725
47_L52_K0.721350.722
58_V61_K0.715280.716
51_L54_H0.712960.713
43_H47_L0.696630.697
8_H99_I0.695840.696
57_E60_Q0.689180.689
55_H85_A0.684640.685
17_V26_L0.672310.673
8_H12_G0.669740.670
27_G77_G0.669370.670
54_H67_P0.66170.662
23_S26_L0.654090.654
10_L95_K0.652930.653
68_Y109_E0.644250.645
64_S84_K0.6410.641
104_T109_E0.639490.640
64_S86_T0.63590.636
90_N94_S0.63140.632
58_V63_Q0.629920.630
58_V62_G0.627290.628
54_H58_V0.627040.627
5_T18_D0.626060.626
57_E63_Q0.625610.626
51_L69_Y0.624860.625
25_L103_N0.624510.625
32_E36_R0.624230.624
25_L79_V0.620470.621
89_Y94_S0.617980.618
18_D22_V0.615260.616
97_E101_C0.609150.609
49_R53_Q0.608310.609
27_G73_T0.606880.607
42_V69_Y0.605490.606
47_L51_L0.604150.604
43_H72_R0.602470.603
52_K55_H0.598280.599
28_Y41_F0.594570.595
48_Q52_K0.592920.593
54_H65_V0.592920.593
80_W106_L0.592440.593
17_V30_P0.58980.590
99_I103_N0.589120.589
68_Y106_L0.58830.589
8_H85_A0.583850.584
20_R104_T0.582440.583
93_T96_P0.580970.581
62_G89_Y0.579260.580
69_Y72_R0.577660.578
55_H59_L0.575760.576
89_Y97_E0.573270.574
8_H13_K0.57320.573
26_L79_V0.572780.573
82_Q106_L0.572470.573
34_V37_S0.570970.571
12_G56_R0.566670.567
65_V69_Y0.565640.566
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
3f1pA0.98299.3-0.295
3f1pB0.98299.3-0.29
4f3lB0.98299.3-0.287
4f3lA0.98299.2-0.281
4ehoA0.96499.2-0.264
2wkqA0.97399.2-0.259
3p7nA0.97399.2-0.248
4hiaA0.97399.2-0.247
2gj3A0.96499.1-0.243
3ewkA0.945999.1-0.223

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