GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_29 - P-loop containing region of AAA domain
Pfam: PF13555 (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: CL0023
Length: 62
Sequences: 7862
Seq/Len: 126.81
HH_delta: 0.06 (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
3_R16_T2.398274.321
5_Q16_T1.810073.262
3_R18_D1.434952.586
11_S38_T1.297352.338
5_Q14_G1.128912.034
7_V14_G1.05871.908
28_I39_L0.933741.682
6_L12_F0.866421.561
8_N13_D0.807361.455
10_G38_T0.787661.419
12_F15_E0.748821.349
10_G41_D0.720261.298
32_N38_T0.704431.269
19_F26_T0.680261.226
6_L42_A0.654281.179
44_Q49_G0.607371.094
9_W42_A0.599671.081
32_N35_G0.599361.080
2_T18_D0.592251.067
10_G27_L0.581141.047
10_G32_N0.571291.029
20_D26_T0.559171.008
18_D21_P0.54270.978
8_N14_G0.539760.973
2_T20_D0.522370.941
31_P34_S0.52110.939
15_E21_P0.505580.911
10_G37_S0.497410.896
2_T5_Q0.486720.877
44_Q48_Y0.483680.872
9_W45_T0.477580.861
41_D47_L0.461070.831
21_P26_T0.453110.816
12_F38_T0.446970.805
4_L19_F0.435840.785
9_W32_N0.426090.768
29_T40_L0.422190.761
42_A50_N0.421920.760
17_I39_L0.42150.759
40_L44_Q0.415240.748
6_L39_L0.414220.746
42_A49_G0.413910.746
11_S40_L0.411540.742
45_T49_G0.408180.735
33_G37_S0.403350.727
34_S37_S0.38920.701
9_W38_T0.3850.694
13_D21_P0.382150.689
44_Q50_N0.379850.684
25_V32_N0.366320.660
32_N41_D0.364830.657
25_V48_Y0.361390.651
21_P42_A0.354220.638
41_D44_Q0.351550.633
42_A47_L0.347010.625
45_T48_Y0.347010.625
27_L41_D0.341810.616
30_G36_K0.332540.599
25_V37_S0.328430.592
26_T48_Y0.324620.585
32_N36_K0.32070.578
12_F42_A0.313010.564
11_S41_D0.312910.564
10_G51_T0.30860.556
29_T33_G0.307810.555
15_E19_F0.304210.548
9_W29_T0.303390.547
29_T32_N0.302490.545
28_I34_S0.30050.541
30_G34_S0.30010.541
28_I45_T0.299750.540
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
3zgxA0.967799.20.06
4i99A0.967799.20.079
3qktA0.967799.20.086
4ad8A0.967799.10.094
3auyA0.967799.10.098
1e69A0.967799.10.12
3ktaA0.967799.10.13
3qksA0.9677990.136
4abyA0.9677990.138
3qf7A0.9677990.138

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