GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA - ATPase family associated with various cellular activities (AAA)
Pfam: PF00004 (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: 132
Sequences: 43093
Seq/Len: 326.46
HH_delta: -0.073 (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
46_I56_S2.004143.161
63_F108_T1.632872.575
118_A123_R1.608772.537
15_A63_F1.240231.956
15_A108_T1.173821.851
17_A21_Y1.164011.836
48_D51_K1.014341.600
13_T17_A0.991961.564
67_I107_A0.967741.526
45_K57_A0.966081.524
68_D109_T0.9631.519
15_A106_I0.953141.503
112_P117_P0.918861.449
12_T65_D0.911241.437
17_A20_Q0.904771.427
107_A124_F0.872881.377
6_P9_T0.865041.364
91_S95_N0.863941.362
66_E110_N0.847371.336
26_F63_F0.825151.301
50_F53_A0.820761.294
104_I107_A0.810731.279
62_L105_V0.809441.277
16_R28_E0.793881.252
61_V104_I0.79331.251
68_D110_N0.789471.245
54_K57_A0.783821.236
12_T91_S0.770991.216
5_G9_T0.760971.200
52_K55_K0.758471.196
88_Q91_S0.754861.190
43_E47_R0.753061.188
69_K111_S0.747971.180
111_S114_K0.747141.178
32_S87_N0.744751.174
41_D44_Q0.723341.141
25_P60_C0.721351.138
88_Q92_L0.708871.118
40_G44_Q0.702311.108
27_I31_G0.699961.104
71_F74_S0.699431.103
112_P120_L0.696881.099
51_K55_K0.696521.098
11_K65_D0.687011.083
103_V107_A0.68581.082
67_I70_L0.682541.076
44_Q48_D0.681481.075
49_F52_K0.677961.069
13_T16_R0.672451.060
30_D33_E0.670971.058
5_G8_G0.669781.056
92_L98_S0.667831.053
48_D52_K0.665231.049
86_L90_L0.661311.043
106_I110_N0.657151.036
112_P115_I0.656511.035
45_K49_F0.650451.026
87_N91_S0.648731.023
117_P120_L0.644971.017
24_F59_P0.635951.003
49_F53_A0.634011.000
92_L95_N0.629380.993
91_S94_D0.628010.990
27_I60_C0.624490.985
19_A26_F0.617480.974
3_L15_A0.614690.969
4_H112_P0.614570.969
5_G10_G0.614230.969
39_A42_S0.61220.965
52_K56_S0.611230.964
41_D45_K0.611010.964
37_S41_D0.60930.961
118_A122_S0.605540.955
112_P116_D0.601770.949
18_L106_I0.59120.932
119_L123_R0.588250.928
31_G64_I0.584550.922
43_E46_I0.572760.903
5_G11_K0.568610.897
90_L94_D0.561730.886
38_Y41_D0.561020.885
70_L74_S0.559850.883
115_I118_A0.558070.880
116_D119_L0.557560.879
34_L37_S0.556620.878
51_K54_K0.555730.876
42_S46_I0.544620.859
26_F31_G0.542410.855
43_E48_D0.539860.851
39_A88_Q0.537720.848
48_D54_K0.532030.839
19_A63_F0.52970.835
120_L123_R0.52970.835
16_R20_Q0.528650.834
86_L114_K0.528560.834
2_L109_T0.527040.831
40_G43_E0.525670.829
66_E123_R0.522160.823
115_I120_L0.521580.823
115_I119_L0.520310.821
3_L14_L0.519710.820
38_Y45_K0.518530.818
53_A57_A0.514640.812
87_N90_L0.511320.806
46_I54_K0.510340.805
53_A56_S0.50980.804
89_L94_D0.506470.799
46_I50_F0.503520.794
38_Y44_Q0.500460.789
71_F119_L0.497070.784
94_D97_S0.496870.784
40_G48_D0.495040.781
59_P103_V0.494550.780
22_L61_V0.493820.779
61_V106_I0.492930.777
49_F57_A0.492270.776
31_G37_S0.490730.774
31_G34_L0.490540.774
119_L122_S0.489620.772
2_L115_I0.487830.769
16_R95_N0.486630.767
116_D120_L0.486220.767
32_S69_K0.485520.766
115_I122_S0.481020.759
95_N98_S0.480890.758
94_D123_R0.478780.755
26_F30_D0.478470.755
39_A43_E0.475870.750
68_D111_S0.474930.749
2_L107_A0.471310.743
104_I108_T0.470040.741
15_A26_F0.46920.740
94_D98_S0.468490.739
39_A45_K0.468250.738
68_D107_A0.467060.737
86_L116_D0.465840.735
115_I124_F0.464060.732
38_Y74_S0.463850.732
40_G45_K0.463580.731
53_A62_L0.461490.728
111_S118_A0.460410.726
26_F34_L0.457990.722
44_Q47_R0.457340.721
108_T111_S0.457140.721
43_E50_F0.456180.719
92_L96_P0.455130.718
36_S41_D0.453990.716
43_E57_A0.453960.716
51_K56_S0.452790.714
86_L111_S0.449790.709
1_I106_I0.447690.706
90_L93_L0.447450.706
45_K54_K0.446330.704
19_A61_V0.445910.703
43_E54_K0.445630.703
3_L106_I0.44550.703
12_T28_E0.444440.701
86_L92_L0.44370.700
89_L93_L0.44180.697
7_P110_N0.441680.697
15_A19_A0.441190.696
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
3cf2A0.984899.8-0.073
3cf2A0.977399.8-0.056
3eieA0.984899.70.029
2zanA0.984899.70.037
2qp9X0.984899.70.04
1xwiA0.984899.70.04
3hu3A0.984899.70.059
1ypwA0.977399.70.063
4b4tH0.984899.70.065
4b4tM0.984899.70.071

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