GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA-ATPase_like - Predicted AAA-ATPase
Pfam: PF09820 (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: 284
Sequences: 2177
Seq/Len: 7.67
HH_delta: 0.553 (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
40_R151_E0.274622.626
227_E231_E0.228312.183
40_R153_D0.203161.943
226_T229_E0.199731.910
52_E56_D0.194491.860
253_E256_E0.193271.848
231_E251_L0.190171.818
151_E194_G0.186951.788
227_E255_K0.179961.721
227_E252_E0.17791.701
132_D136_Y0.17251.649
187_L190_A0.172391.648
25_K29_D0.166551.593
174_R202_S0.164721.575
134_I137_L0.164481.573
151_E154_K0.163251.561
144_K188_R0.159121.522
248_E252_E0.156851.500
47_N222_Y0.15471.479
41_R151_E0.154641.479
22_M26_E0.152821.461
24_I51_L0.152391.457
228_E232_T0.15121.446
38_R42_F0.148731.422
48_L148_L0.147791.413
46_L50_M0.144211.379
230_V251_L0.143821.375
80_K86_L0.14351.372
234_L251_L0.143081.368
232_T235_K0.142661.364
147_L187_L0.141281.351
110_I113_E0.140581.344
46_L263_F0.139391.333
17_Y46_L0.136951.310
225_F233_L0.136761.308
96_F100_E0.135351.294
21_T229_E0.133871.280
80_K143_K0.133591.277
231_E235_K0.133021.272
138_Y186_Y0.131921.261
109_D135_E0.131631.259
151_E156_I0.131121.254
116_Y124_I0.130891.252
40_R263_F0.13051.248
105_E132_D0.129841.242
227_E251_L0.129731.240
40_R194_G0.129611.239
80_K83_V0.129591.239
193_T196_L0.129281.236
108_S112_K0.127381.218
222_Y262_H0.126271.207
95_S98_E0.126021.205
50_M53_A0.12591.204
224_G258_Y0.125631.201
40_R195_I0.125351.199
123_E132_D0.125241.198
48_L193_T0.124751.193
230_V255_K0.121991.166
175_N178_S0.121911.166
193_T198_I0.121371.161
82_P86_L0.121221.159
41_R153_D0.121091.158
233_L237_Y0.120811.155
128_D132_D0.120751.155
252_E256_E0.120211.149
37_S45_S0.119571.143
229_E232_T0.119331.141
37_S212_D0.118781.136
80_K84_I0.118251.131
28_L54_Y0.118181.130
203_I206_G0.118181.130
235_K247_R0.118121.129
81_Y84_I0.117281.121
153_D156_I0.116211.111
105_E124_I0.115851.108
27_L51_L0.115441.104
115_R120_S0.115061.100
104_K123_E0.114961.099
20_K46_L0.114921.099
128_D131_K0.114531.095
94_S98_E0.114391.094
42_F261_Y0.113911.089
156_I159_A0.113831.088
225_F262_H0.11361.086
49_S52_E0.113271.083
41_R152_Y0.112611.077
232_T236_Y0.112511.076
104_K125_D0.11151.066
24_I229_E0.111331.065
45_S150_D0.111251.064
19_D38_R0.111071.062
230_V260_G0.110911.061
240_N247_R0.110831.060
112_K117_L0.110481.056
131_K135_E0.108931.042
45_S140_K0.108791.040
22_M25_K0.108261.035
96_F99_L0.108051.033
50_M54_Y0.107471.028
98_E106_I0.107411.027
100_E124_I0.107361.027
45_S85_F0.107281.026
24_I47_N0.107211.025
148_L191_F0.106541.019
105_E128_D0.106421.018
188_R194_G0.105811.012
41_R261_Y0.105551.009
27_L190_A0.104731.001
151_E195_I0.104390.998
23_F222_Y0.104310.997
47_N51_L0.103930.994
109_D115_R0.103920.994
150_D153_D0.10330.988
102_S125_D0.102970.985
116_Y125_D0.102970.985
51_L153_D0.10280.983
38_R41_R0.102740.982
147_L212_D0.102650.982
234_L254_L0.102370.979
52_E85_F0.102220.977
109_D112_K0.10140.970
35_F48_L0.101080.967
41_R87_D0.100980.966
235_K251_L0.10080.964
178_S206_G0.100090.957
183_D187_L0.099970.956
98_E105_E0.099690.953
131_K138_Y0.099650.953
151_E261_Y0.09960.952
192_I196_L0.099070.947
257_W264_G0.098930.946
111_F129_S0.098840.945
40_R205_S0.098680.944
201_E206_G0.098520.942
102_S106_I0.09850.942
30_S101_E0.098490.942
18_V236_Y0.098110.938
17_Y21_T0.097920.936
189_F197_P0.097910.936
82_P133_L0.097880.936
33_Y254_L0.097720.934
109_D113_E0.097390.931
199_S213_I0.097120.929
20_K38_R0.096750.925
153_D195_I0.096680.924
20_K42_F0.096660.924
247_R251_L0.096430.922
97_E101_E0.096410.922
19_D153_D0.096380.922
142_G231_E0.096240.920
204_F212_D0.096190.920
104_K117_L0.096020.918
231_E248_E0.095970.918
27_L47_N0.095620.914
81_Y88_F0.095580.914
101_E105_E0.095380.912
171_E174_R0.094830.907
151_E263_F0.094720.906
201_E205_S0.094580.904
51_L234_L0.094170.900
39_P42_F0.093860.897
200_K207_L0.093830.897
174_R178_S0.09370.896
20_K23_F0.093460.894
23_F27_L0.093150.891
23_F56_D0.092970.889
188_R197_P0.09280.887
45_S255_K0.092610.886
114_H129_S0.092580.885
104_K118_Y0.092540.885
56_D157_N0.092470.884
21_T259_D0.092460.884
101_E116_Y0.092370.883
230_V240_N0.091740.877
105_E131_K0.091620.876
171_E256_E0.091430.874
105_E109_D0.091420.874
101_E128_D0.091170.872
196_L261_Y0.091090.871
252_E255_K0.090730.868
98_E102_S0.09070.867
79_N143_K0.090640.867
200_K229_E0.090290.863
40_R152_Y0.090040.861
94_S126_L0.089750.858
107_L134_I0.089680.858
112_K118_Y0.089590.857
80_K85_F0.089250.853
102_S105_E0.088980.851
173_L205_S0.088940.850
191_F198_I0.088410.845
48_L85_F0.088370.845
28_L55_F0.088130.843
253_E257_W0.088070.842
201_E204_F0.088050.842
189_F194_G0.088040.842
97_E221_E0.087830.840
15_Y46_L0.087820.840
205_S208_N0.087660.838
40_R261_Y0.087450.836
190_A200_K0.087250.834
125_D129_S0.0870.832
48_L52_E0.086930.831
107_L176_F0.086890.831
19_D50_M0.086880.831
38_R261_Y0.086880.831
246_D249_E0.086870.831
173_L179_V0.086850.830
104_K189_F0.086760.830
230_V253_E0.086740.829
49_S53_A0.086580.828
35_F99_L0.08640.826
124_I128_D0.086180.824
127_A132_D0.086180.824
112_K123_E0.086090.823
19_D42_F0.086060.823
104_K132_D0.086020.823
26_E228_E0.085920.822
22_M29_D0.085890.821
104_K126_L0.085890.821
150_D194_G0.085390.817
153_D261_Y0.085360.816
96_F105_E0.085310.816
31_G234_L0.085270.815
94_S104_K0.085130.814
41_R195_I0.084990.813
42_F195_I0.084770.811
80_K91_V0.084280.806
115_R142_G0.084280.806
258_Y264_G0.084260.806
152_Y263_F0.084060.804
108_S211_E0.084030.804
118_Y127_A0.083930.803
22_M97_E0.083750.801
188_R196_L0.083720.801
13_E18_V0.08370.800
51_L123_E0.083640.800
33_Y209_N0.083630.800
178_S210_L0.083590.799
194_G197_P0.083560.799
143_K252_E0.083370.797
41_R263_F0.083290.796
16_Y236_Y0.083260.796
258_Y261_Y0.083250.796
40_R174_R0.08320.796
102_S107_L0.082890.793
38_R263_F0.082790.792
147_L157_N0.082780.792
98_E101_E0.082750.791
89_S173_L0.08250.789
194_G258_Y0.082350.787
86_L92_K0.082340.787
34_V223_F0.082280.787
117_L140_K0.082190.786
28_L34_V0.082010.784
94_S108_S0.082010.784
109_D119_E0.081990.784
151_E258_Y0.081910.783
246_D254_L0.081850.783
93_G178_S0.081720.781
143_K235_K0.081640.781
52_E148_L0.081610.780
109_D117_L0.081520.780
173_L229_E0.081480.779
98_E143_K0.081340.778
55_F146_V0.081290.777
108_S116_Y0.081170.776
38_R46_L0.081090.775
199_S206_G0.081090.775
84_I132_D0.081060.775
18_V225_F0.0810.775
147_L248_E0.080960.774
14_N252_E0.080850.773
235_K249_E0.080780.772
29_D109_D0.080680.771
98_E136_Y0.080470.769
95_S120_S0.080340.768
85_F148_L0.080330.768
81_Y86_L0.080230.767
104_K127_A0.080080.766
157_N202_S0.080020.765
106_I136_Y0.079850.764
39_P258_Y0.079780.763
117_L123_E0.079760.763
158_D225_F0.079740.762
82_P186_Y0.07970.762
135_E171_E0.079630.761
170_R177_F0.079410.759
100_E104_K0.079390.759
99_L197_P0.079290.758
83_V86_L0.079280.758
112_K140_K0.079140.757
42_F209_N0.078970.755
42_F207_L0.078950.755
228_E231_E0.078690.752
84_I111_F0.078670.752
32_K36_L0.078650.752
20_K261_Y0.078560.751
90_G105_E0.078440.750
52_E113_E0.078210.748
36_L222_Y0.078140.747
46_L152_Y0.078020.746
255_K258_Y0.078010.746
240_N249_E0.077970.746
174_R206_G0.077960.745
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
2qenA0.834599.80.553
2fnaA0.83199.80.557
1w5sA0.862799.70.603
2v1uA0.845199.70.607
1z6tA0.785299.70.619
3sfzA0.795899.70.622
2qbyA0.83899.70.625
1fnnA0.823999.60.633
2a5yB0.792399.60.642
2qbyB0.83199.60.647
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