GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_26 - AAA domain
Pfam: PF13500 (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: 199
Sequences: 18891
Seq/Len: 94.93
HH_delta: 0.225 (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
18_S104_L1.826774.002
25_L102_V1.765853.868
137_S167_R1.527163.345
33_G100_Y1.523933.338
30_I102_V1.49793.281
5_I21_L1.176992.578
31_K101_D1.166032.554
17_V164_I1.094082.397
4_F107_G1.03182.260
175_E179_E0.992882.175
18_S34_Y0.981152.149
30_I101_D0.956532.095
25_L104_L0.93592.050
23_R27_R0.920382.016
22_A104_L0.913122.000
24_A28_R0.905361.983
17_V166_N0.902221.976
22_A34_Y0.866991.899
31_K100_Y0.860351.885
2_T97_A0.797671.747
20_G23_R0.785361.720
13_G166_N0.730961.601
131_P161_L0.727111.593
7_G12_V0.726121.591
5_I133_I0.720811.579
165_L174_L0.717341.571
9_D12_V0.7061.547
174_L178_R0.704711.544
2_T105_V0.696561.526
133_I164_I0.6871.505
94_K97_A0.681871.494
176_A179_E0.67581.480
52_R59_E0.66911.466
138_G165_L0.655721.436
150_I154_K0.655721.436
24_A27_R0.628751.377
2_T130_A0.628421.377
68_T100_Y0.621021.360
38_I42_P0.615491.348
65_S68_T0.614161.345
176_A180_K0.602751.320
4_F129_G0.594811.303
25_L32_V0.589771.292
5_I18_S0.570321.249
46_E49_E0.567991.244
131_P162_G0.565531.239
31_K99_E0.553531.213
147_L180_K0.552431.210
66_P69_F0.552371.210
51_I54_L0.547931.200
119_D122_A0.545651.195
168_V171_P0.540681.184
33_G96_L0.535651.173
172_E175_E0.533891.169
32_V101_D0.529171.159
2_T93_Y0.526741.154
49_E53_E0.526261.153
67_Y70_D0.521811.143
15_T106_E0.520381.140
2_T129_G0.516041.130
14_K109_G0.515751.130
94_K98_E0.515691.130
35_F105_V0.509281.116
100_Y103_V0.506621.110
151_E154_K0.506071.109
35_F103_V0.504071.104
147_L151_E0.501861.099
135_V166_N0.501421.098
4_F126_K0.497591.090
123_D127_A0.495841.086
39_Q42_P0.494621.083
32_V102_V0.494541.083
33_G103_V0.492781.079
63_D95_E0.492441.079
37_P105_V0.489881.073
34_Y43_E0.489261.072
56_G59_E0.486421.066
134_L149_T0.482541.057
53_E56_G0.482271.056
69_F100_Y0.474041.038
97_A103_V0.472761.036
23_R26_R0.472091.034
136_A142_T0.471471.033
17_V21_L0.470531.031
50_L53_E0.468431.026
77_L81_L0.465591.020
148_L152_A0.465191.019
2_T103_V0.463551.015
75_P78_A0.460221.008
67_Y100_Y0.458361.004
17_V135_V0.455610.998
3_I102_V0.455090.997
26_R32_V0.447320.980
11_G106_E0.441010.966
7_G14_K0.439940.964
175_E178_R0.439730.963
93_Y97_A0.439620.963
66_P70_D0.438440.960
131_P134_L0.438270.960
123_D126_K0.436390.956
87_D90_R0.432860.948
40_T43_E0.431430.945
76_H80_E0.429220.940
119_D123_D0.425750.933
172_E176_A0.425230.931
86_I89_E0.422740.926
22_A32_V0.421110.922
50_L54_L0.418360.916
121_N125_A0.415820.911
148_L151_E0.413060.905
96_L99_E0.412150.903
125_A128_L0.411220.901
6_T132_V0.409830.898
149_T153_L0.408930.896
38_I43_E0.407920.894
173_N180_K0.406130.890
142_T145_H0.405810.889
151_E155_Q0.40550.888
177_L181_S0.404810.887
47_D50_L0.403630.884
74_S78_A0.402870.882
132_V153_L0.400220.877
178_R184_P0.398850.874
38_I41_G0.396430.868
77_L80_E0.393730.862
78_A81_L0.393690.862
65_S69_F0.392840.861
37_P40_T0.391820.858
95_E99_E0.391280.857
8_T12_V0.389380.853
162_G184_P0.386220.846
50_L60_P0.383910.841
73_A77_L0.383260.840
32_V104_L0.38250.838
21_L25_L0.380990.835
35_F38_I0.380050.833
19_L43_E0.377780.828
93_Y105_V0.377720.827
9_D145_H0.375950.824
122_A126_K0.373970.819
57_L60_P0.372810.817
165_L177_L0.37260.816
173_N176_A0.371290.813
129_G159_R0.366430.803
35_F93_Y0.365370.800
89_E127_A0.364950.799
4_F121_N0.362170.793
34_Y104_L0.361610.792
86_I90_R0.361290.791
62_D99_E0.358330.785
3_I104_L0.358320.785
136_A146_T0.35790.784
52_R55_F0.357850.784
6_T107_G0.357450.783
76_H79_A0.355210.778
154_K159_R0.354610.777
89_E94_K0.354490.777
124_I128_L0.353280.774
72_P78_A0.35080.768
120_L123_D0.350220.767
147_L181_S0.348250.763
142_T146_T0.344250.754
70_D73_A0.343090.752
5_I17_V0.342220.750
8_T149_T0.341490.748
53_E59_E0.341470.748
153_L158_I0.340720.746
53_E57_L0.339170.743
78_A82_E0.338610.742
3_I133_I0.337480.739
13_G135_V0.335810.736
68_T71_E0.335630.735
18_S22_A0.335620.735
182_G185_V0.335160.734
5_I104_L0.333930.731
144_N148_L0.332840.729
58_S61_P0.330340.724
174_L185_V0.330260.723
10_T36_K0.329420.722
48_A52_R0.328890.720
4_F105_V0.32860.720
135_V138_G0.328320.719
71_E74_S0.326860.716
73_A76_H0.324690.711
174_L177_L0.324670.711
88_L91_I0.323160.708
54_L57_L0.322740.707
136_A139_R0.322170.706
134_L137_S0.321210.704
20_G24_A0.318520.698
95_E98_E0.316830.694
137_S142_T0.316590.693
69_F72_P0.315170.690
60_P63_D0.313470.687
146_T150_I0.312540.685
96_L100_Y0.311610.683
178_R185_V0.311520.682
75_P79_A0.311170.682
165_L185_V0.3110.681
20_G166_N0.31050.680
13_G106_E0.309660.678
25_L30_I0.309640.678
179_E182_G0.308120.675
72_P76_H0.307930.675
141_G144_N0.304420.667
26_R57_L0.303930.666
126_K159_R0.303750.665
26_R31_K0.302980.664
178_R182_G0.302530.663
72_P77_L0.301280.660
120_L126_K0.300780.659
134_L139_R0.299880.657
66_P71_E0.298420.654
56_G60_P0.298280.653
67_Y71_E0.297140.651
47_D56_G0.296970.651
145_H149_T0.294570.645
3_I25_L0.294560.645
50_L57_L0.292930.642
29_G32_V0.292110.640
150_I183_I0.291710.639
5_I14_K0.291580.639
85_D89_E0.291350.638
49_E52_R0.29040.636
135_V139_R0.289770.635
9_D106_E0.289670.635
142_T150_I0.289670.635
55_F60_P0.288880.633
156_R159_R0.288720.632
172_E180_K0.287980.631
14_K107_G0.286320.627
112_M149_T0.285550.626
155_Q158_I0.285260.625
36_K40_T0.28370.621
143_I147_L0.282270.618
37_P42_P0.282140.618
91_I96_L0.28130.616
136_A163_V0.279780.613
22_A106_E0.279770.613
11_G15_T0.278230.609
120_L127_A0.277790.609
77_L82_E0.277570.608
14_K38_I0.27740.608
137_S141_G0.27340.599
133_I136_A0.272850.598
90_R94_K0.27120.594
19_L34_Y0.270880.593
147_L150_I0.270240.592
44_D47_D0.269950.591
139_R142_T0.269380.590
87_D91_I0.269230.590
37_P43_E0.268850.589
165_L168_V0.268760.589
181_S184_P0.268560.588
131_P159_R0.268350.588
149_T152_A0.268310.588
145_H148_L0.268240.588
2_T7_G0.268080.587
137_S140_L0.266270.583
163_V183_I0.26530.581
135_V164_I0.26470.580
4_F132_V0.264620.580
119_D124_I0.263110.576
19_L22_A0.260990.572
93_Y96_L0.260260.570
134_L160_V0.25930.568
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
3vx3A0.969899.90.225
1byiA0.984999.90.225
3endA0.959899.90.255
1hyqA0.954899.90.26
2ph1A0.959899.90.26
1g3qA0.949799.90.26
3ea0A0.949799.90.266
3q9lA0.949799.90.269
2ynmA0.959899.90.269
3k9gA0.944799.90.272

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