GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_16 - AAA ATPase domain
Pfam: PF13191 (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: 185
Sequences: 15453
Seq/Len: 83.53
HH_delta: 0.466 (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
22_G25_R1.970634.169
41_L155_V1.677943.550
91_R95_R1.365172.888
57_S67_P1.15342.440
94_L98_L1.090252.306
46_D49_A0.983452.080
23_S152_L0.950092.010
163_D166_S0.901561.907
92_S96_E0.824071.743
78_L152_L0.822691.740
67_P70_P0.813891.722
80_D151_P0.780971.652
39_S43_A0.779661.649
168_D172_A0.773371.636
33_S166_S0.744671.575
72_R76_R0.733641.552
127_P131_E0.728411.541
31_G35_S0.717081.517
49_A69_S0.714651.512
139_R143_R0.708911.500
126_D129_S0.690711.461
56_I60_C0.684761.449
127_P130_L0.683451.446
125_L131_E0.659011.394
93_P96_E0.649881.375
176_R179_N0.649131.373
172_A176_R0.635121.344
33_S158_D0.632621.338
29_L40_L0.630341.333
26_N178_Q0.629741.332
126_D131_E0.623311.319
167_L171_R0.596291.261
90_T93_P0.595711.260
26_N185_V0.591141.251
158_D161_W0.589021.246
178_Q183_L0.587541.243
172_A175_R0.58591.239
74_A77_Q0.581071.229
123_S131_E0.578961.225
126_D130_L0.577051.221
45_L155_V0.574881.216
51_R55_V0.573881.214
55_V58_I0.573781.214
140_E143_R0.571141.208
93_P97_K0.56721.200
166_S169_L0.566411.198
120_E128_D0.551581.167
95_R99_A0.550681.165
43_A46_D0.536841.136
120_E130_L0.536481.135
94_L97_K0.533591.129
98_L103_D0.529171.119
100_A104_D0.527761.116
162_A170_L0.523311.107
101_S104_D0.521031.102
121_A125_L0.519761.100
120_E124_A0.519271.098
32_E35_S0.515461.090
121_A124_A0.514091.088
101_S105_D0.509771.078
77_Q81_Q0.501361.061
167_L173_L0.50021.058
97_K100_A0.498581.055
58_I62_D0.494131.045
59_N62_D0.488571.034
140_E146_A0.487091.030
41_L45_L0.481991.020
42_R45_L0.47631.008
156_I159_L0.474781.004
77_Q80_D0.47080.996
98_L102_L0.469420.993
139_R142_L0.462650.979
170_L174_A0.461660.977
63_S71_F0.460560.974
128_D131_E0.456530.966
124_A131_E0.454170.961
33_S162_A0.451320.955
74_A78_L0.449930.952
63_S70_P0.447490.947
120_E123_S0.446530.945
78_L81_Q0.446430.944
143_R148_R0.443580.938
177_L182_L0.440910.933
169_L172_A0.439980.931
95_R98_L0.438510.928
152_L182_L0.437820.926
170_L173_L0.436440.923
169_L174_A0.423480.896
125_L129_S0.418230.885
80_D84_D0.417460.883
139_R144_E0.417170.882
87_Q90_T0.415910.880
162_A167_L0.415170.878
92_S95_R0.415080.878
147_A151_P0.41190.871
122_A130_L0.410670.869
91_R94_L0.409720.867
148_R151_P0.409630.867
124_A130_L0.408790.865
173_L181_P0.408670.865
102_L105_D0.408570.864
39_S42_R0.408060.863
81_Q84_D0.404940.857
142_L145_L0.401260.849
90_T97_K0.395720.837
98_L104_D0.392960.831
83_L86_S0.392940.831
97_K101_S0.392830.831
120_E127_P0.391890.829
57_S60_C0.390250.826
55_V59_N0.388120.821
120_E125_L0.386980.819
38_T41_L0.386720.818
176_R180_D0.38590.816
55_V62_D0.385190.815
96_E99_A0.385120.815
178_Q181_P0.383430.811
71_F74_A0.383110.810
148_R181_P0.382580.809
38_T157_D0.380930.806
169_L173_L0.379830.804
145_L148_R0.378980.802
56_I59_N0.378470.801
168_D171_R0.375670.795
140_E144_E0.373210.789
43_A51_R0.371660.786
75_L79_I0.36950.782
43_A50_E0.368610.780
157_D160_D0.367140.777
26_N175_R0.366890.776
22_G27_L0.36340.769
165_A169_L0.363240.768
174_A181_P0.36220.766
122_A129_S0.36110.764
167_L174_A0.359060.760
156_I174_A0.357990.757
96_E100_A0.356030.753
124_A128_D0.3560.753
45_L81_Q0.35430.749
42_R48_L0.35380.748
173_L178_Q0.350040.740
123_S127_P0.347710.736
175_R178_Q0.34760.735
82_L159_L0.34530.730
83_L87_Q0.344990.730
125_L130_L0.344410.729
26_N183_L0.343180.726
143_R147_A0.339930.719
99_A104_D0.338280.716
99_A102_L0.33790.715
99_A103_D0.336580.712
33_S161_W0.336420.712
43_A47_R0.33560.710
123_S126_D0.334140.707
73_S77_Q0.333540.706
38_T158_D0.333280.705
90_T94_L0.333270.705
94_L99_A0.33140.701
88_A96_E0.330710.700
75_L78_L0.329850.698
33_S160_D0.329750.698
177_L180_D0.327210.692
159_L162_A0.326690.691
44_L155_V0.326560.691
39_S158_D0.326540.691
143_R146_A0.326360.690
38_T42_R0.324110.686
43_A48_L0.323670.685
92_S97_K0.318540.674
28_L33_S0.317740.672
33_S156_I0.317650.672
140_E145_L0.316720.670
142_L146_A0.315320.667
171_R175_R0.315210.667
67_P71_F0.313440.663
125_L128_D0.312280.661
34_G39_S0.312260.661
72_R77_Q0.312260.661
178_Q185_V0.311930.660
58_I68_Y0.311650.659
93_P98_L0.310390.657
94_L102_L0.309330.654
41_L184_V0.309230.654
86_S91_R0.305660.647
82_L85_Q0.303640.642
63_S67_P0.3030.641
98_L101_S0.302410.640
58_I61_D0.300880.636
76_R80_D0.300720.636
174_A178_Q0.300510.636
86_S98_L0.300340.635
181_P185_V0.299960.635
63_S74_A0.299640.634
86_S90_T0.298990.632
140_E147_A0.298180.631
171_R174_A0.298010.630
57_S69_S0.295960.626
92_S99_A0.295140.624
30_T158_D0.294890.624
71_F78_L0.292180.618
104_D176_R0.291890.617
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
1w5sA0.751499.30.466
1fnnA0.751499.30.467
2v1uA0.751499.30.469
2qbyA0.751499.30.476
2qbyB0.740599.20.496
2qenA0.810899.20.499
2fnaA0.843299.20.501
3te6A0.740599.20.504
1qvrA0.691999.10.529
3uk6A0.918999.10.532

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