GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SAF - SAF domain
Pfam: PF08666 (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: CL0489
Length: 63
Sequences: 3502
Seq/Len: 55.59
HH_delta: 0.131 (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_P14_T1.320192.776
47_A51_I1.294382.722
10_I47_A1.233852.594
6_A51_I1.108292.330
8_R20_D1.103452.320
4_V23_L1.013242.131
6_A10_I0.981682.064
55_E61_M0.91821.931
6_A57_I0.911261.916
17_T20_D0.861581.812
3_V26_V0.856051.800
52_P55_E0.739671.555
58_T61_M0.738531.553
9_D53_A0.710011.493
49_R61_M0.702511.477
7_A22_T0.692391.456
12_A50_D0.67891.428
2_R23_L0.658241.384
11_P50_D0.652391.372
2_R25_R0.645921.358
15_V46_V0.645311.357
9_D52_P0.645261.357
37_D40_E0.640351.346
14_T20_D0.634671.335
24_V54_G0.584221.228
5_V56_P0.560091.178
16_I47_A0.545741.148
8_R19_E0.513661.080
31_P34_I0.496521.044
35_F42_V0.474540.998
5_V24_V0.453660.954
9_D50_D0.430880.906
16_I20_D0.430610.905
5_V22_T0.401880.845
9_D12_A0.396290.833
26_V56_P0.389110.818
12_A26_V0.384970.809
21_L42_V0.378080.795
15_V44_G0.374860.788
16_I62_L0.372960.784
10_I20_D0.372870.784
37_D41_E0.37070.779
18_A43_V0.363830.765
59_P62_L0.355340.747
2_R35_F0.345660.727
8_R14_T0.328790.691
3_V56_P0.324010.681
23_L32_P0.32230.678
3_V33_G0.320160.673
16_I43_V0.315810.664
34_I45_K0.314060.660
39_I43_V0.308280.648
17_T43_V0.308110.648
21_L43_V0.302290.636
10_I16_I0.300540.632
14_T47_A0.296440.623
15_V19_E0.294770.620
3_V27_P0.294410.619
43_V46_V0.292550.615
4_V35_F0.291960.614
31_P48_R0.291180.612
51_I61_M0.291160.612
49_R55_E0.291070.612
32_P35_F0.290320.610
4_V34_I0.288820.607
27_P34_I0.287050.604
18_A39_I0.285910.601
4_V39_I0.281650.592
15_V43_V0.278070.585
49_R60_S0.275610.580
34_I56_P0.272220.572
48_R62_L0.271990.572
50_D60_S0.267740.563
51_I57_I0.267130.562
4_V42_V0.264790.557
10_I14_T0.260830.548
25_R55_E0.260040.547
23_L39_I0.246340.518
36_P53_A0.245810.517
2_R36_P0.245110.515
6_A54_G0.244630.514
2_R39_I0.244050.513
2_R37_D0.242270.509
9_D13_G0.24190.509
3_V36_P0.236840.498
16_I44_G0.230020.484
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
1wvoA0.952498.70.131
3teeA0.984198.70.138
2wqpA0.936598.70.156
3g8rA0.968398.60.163
3frnA0.984198.60.179
1vliA0.984198.50.194
1opsA0.952497.40.419
1msiA0.952497.30.433
1ucsA0.952497.30.437
3uplA0.968397.10.46

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