GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_10 - AAA-like domain
Pfam: PF12846 (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: 304
Sequences: 4302
Seq/Len: 14.15
HH_delta: 0.206 (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
11_G250_R1.026656.898
38_K251_K0.806245.417
247_R265_D0.615734.137
294_E297_E0.584473.927
18_L259_A0.545263.663
4_T257_I0.482143.239
3_H10_T0.477693.209
262_S277_A0.450383.026
227_D259_A0.4062.728
229_A242_L0.394792.652
246_L256_L0.376452.529
45_A183_V0.375412.522
10_T278_N0.372822.505
17_L283_I0.345582.322
8_G12_S0.343712.309
249_G254_V0.33692.263
34_I41_Y0.318412.139
22_L225_V0.313232.104
6_I18_L0.310372.085
4_T281_T0.296251.990
38_K248_E0.292481.965
226_I242_L0.284011.908
33_V222_K0.283621.906
223_I257_I0.283331.904
230_H260_T0.277131.862
15_T40_D0.269931.814
6_I17_L0.268461.804
130_D133_E0.264741.779
258_L279_C0.263621.771
231_N248_E0.262161.761
230_H247_R0.259761.745
5_L260_T0.257241.728
243_D247_R0.255371.716
230_H265_D0.254311.709
260_T266_L0.251221.688
19_K40_D0.24441.642
290_S294_E0.237491.596
30_P223_I0.237331.595
17_L285_F0.235411.582
54_D57_P0.23341.568
5_L279_C0.232221.560
39_G185_D0.230191.547
113_L131_L0.22551.515
225_V257_I0.224521.508
224_I254_V0.224041.505
293_A297_E0.218861.470
260_T265_D0.214751.443
264_S273_D0.214511.441
147_R151_L0.213651.435
148_A151_L0.212031.425
42_S46_R0.211871.423
40_D251_K0.211191.419
108_N157_R0.210951.417
129_S133_E0.210821.416
289_D292_D0.209921.410
113_L134_F0.204941.377
31_R220_R0.204781.376
6_I257_I0.204561.374
22_L32_V0.203981.370
31_R222_K0.203581.368
208_I224_I0.199651.341
224_I256_L0.19921.338
112_A134_F0.199171.338
88_K103_E0.198851.336
4_T283_I0.197951.330
45_A50_G0.19521.311
246_L258_L0.194851.309
10_T280_N0.19391.303
248_E251_K0.190461.280
245_L249_G0.190291.278
23_E27_R0.190221.278
8_G259_A0.18911.270
25_L223_I0.187381.259
129_S169_D0.1871.256
212_I254_V0.186221.251
24_Q27_R0.184671.241
67_D172_S0.184551.240
18_L225_V0.184081.237
229_A258_L0.184061.237
109_A112_A0.176881.188
267_P273_D0.175691.180
247_R278_N0.175321.178
32_V181_I0.172891.162
21_L257_I0.171311.151
248_E252_Y0.169731.140
230_H248_E0.168991.135
110_L131_L0.168311.131
243_D274_A0.168311.131
9_K280_N0.164681.106
15_T251_K0.1641.102
54_D185_D0.162081.089
15_T19_K0.161781.087
56_D59_D0.161431.085
229_A233_L0.16051.078
127_T169_D0.159971.075
127_T130_D0.159721.073
12_S286_R0.159551.072
51_Q179_G0.158751.067
3_H246_L0.157781.060
147_R150_D0.157581.059
244_E248_E0.157281.057
133_E136_S0.157091.055
51_Q180_R0.156031.048
11_G14_K0.15531.043
20_N24_Q0.154191.036
8_G285_F0.153491.031
4_T21_L0.152181.022
25_L30_P0.15211.022
234_S240_E0.151741.019
37_P40_D0.15061.012
223_I255_G0.150161.009
261_Q278_N0.150141.009
33_V184_F0.148660.999
107_E158_S0.148020.994
19_K41_Y0.147820.993
109_A131_L0.147440.991
108_N112_A0.146720.986
162_G165_G0.146650.985
41_Y227_D0.146240.983
282_K288_E0.145970.981
275_I279_C0.145940.981
227_D292_D0.14550.978
263_P287_L0.144650.972
128_L132_I0.144580.971
248_E254_V0.144480.971
95_D98_I0.144130.968
36_D39_G0.143610.965
277_A289_D0.14250.957
265_D274_A0.142080.955
3_H256_L0.141090.948
161_S165_G0.14050.944
279_C282_K0.140070.941
128_L131_L0.140020.941
84_V88_K0.139810.939
38_K252_Y0.139680.938
54_D188_G0.138560.931
209_Y212_I0.138160.928
48_L51_Q0.138060.928
246_L279_C0.138050.928
247_R274_A0.137670.925
30_P221_P0.137550.924
7_L284_I0.137490.924
18_L227_D0.137360.923
164_F168_F0.137160.922
80_I111_R0.136450.917
132_I153_A0.136240.915
3_H278_N0.136070.914
26_I32_V0.135860.913
229_A260_T0.135830.913
33_V224_I0.135790.912
11_G15_T0.135710.912
196_V199_A0.135690.912
6_I283_I0.13450.904
64_N67_D0.134080.901
15_T41_Y0.133860.899
50_G54_D0.133680.898
106_L110_L0.133160.895
196_V200_V0.132330.889
9_K12_S0.132260.889
35_F224_I0.131660.885
150_D153_A0.131610.884
26_I181_I0.131390.883
155_R158_S0.131210.882
35_F226_I0.13120.881
3_H249_G0.131060.881
12_S285_F0.130530.877
42_S183_V0.130030.874
211_R214_A0.129490.870
262_S274_A0.129390.869
228_E261_Q0.129230.868
133_E137_D0.128610.864
62_S173_T0.128550.864
76_N79_R0.127970.860
10_T261_Q0.127040.854
276_L279_C0.126930.853
284_I287_L0.126930.853
106_L135_L0.126690.851
84_V87_L0.126580.850
245_L256_L0.126280.848
175_D178_D0.125710.845
8_G13_G0.125660.844
31_R211_R0.125310.842
243_D265_D0.12340.829
104_T157_R0.122430.823
212_I252_Y0.122410.822
165_G169_D0.122370.822
15_T250_R0.12170.818
3_H254_V0.121420.816
145_R149_R0.121130.814
247_R260_T0.120980.813
209_Y245_L0.120950.813
273_D291_D0.120890.812
226_I229_A0.12060.810
87_L127_T0.120440.809
50_G57_P0.120160.807
229_A266_L0.119740.804
146_E149_R0.119280.801
263_P292_D0.119010.800
199_A202_L0.118560.797
207_W210_R0.118550.796
263_P276_L0.118550.796
102_E108_N0.118110.794
284_I295_L0.117970.793
17_L21_L0.117880.792
66_F110_L0.117750.791
221_P253_G0.117640.790
84_V107_E0.11740.789
277_A292_D0.117320.788
18_L41_Y0.116980.786
242_L258_L0.116680.784
134_F137_D0.116360.782
112_A138_P0.116230.781
176_L207_W0.116140.780
33_V208_I0.116030.780
108_N161_S0.115940.779
94_L97_S0.115830.778
51_Q178_D0.115680.777
79_R206_S0.115630.777
230_H287_L0.115550.776
118_E121_P0.115210.774
102_E106_L0.115170.774
38_K261_Q0.114870.772
262_S265_D0.114870.772
205_L226_I0.114460.769
146_E150_D0.114190.767
11_G251_K0.114060.766
132_I157_R0.113920.765
105_L109_A0.113670.764
291_D297_E0.113020.759
22_L34_I0.112640.757
62_S170_G0.11250.756
134_F138_P0.112440.755
102_E150_D0.111880.752
149_R153_A0.111650.750
111_R161_S0.111340.748
49_G180_R0.111290.748
136_S157_R0.111090.746
110_L113_L0.110850.745
179_G220_R0.110680.744
285_F289_D0.110220.741
67_D89_S0.110130.740
287_L295_L0.109280.734
197_F221_P0.109080.733
15_T186_L0.108820.731
49_G53_I0.108810.731
266_L273_D0.10880.731
34_I183_V0.107850.725
230_H263_P0.107650.723
119_G130_D0.107360.721
132_I136_S0.10730.721
83_L86_L0.107190.720
36_D251_K0.107010.719
5_L258_L0.106750.717
207_W211_R0.106710.717
38_K187_S0.106420.715
206_S209_Y0.106390.715
250_R255_G0.10620.714
226_I232_F0.106170.713
273_D289_D0.105520.709
153_A157_R0.105340.708
112_A118_E0.105190.707
42_S52_Y0.105080.706
165_G170_G0.105010.706
262_S278_N0.1050.705
50_G56_D0.104850.704
260_T287_L0.104470.702
77_P91_L0.104170.700
167_L200_V0.104110.699
140_E153_A0.103940.698
89_S92_G0.103930.698
86_L90_M0.103770.697
10_T19_K0.103460.695
201_L226_I0.102940.692
34_I181_I0.102840.691
157_R164_F0.102370.688
189_L204_L0.102250.687
104_T111_R0.102010.685
250_R261_Q0.101740.684
10_T15_T0.101710.683
99_E102_E0.101660.683
54_D59_D0.100780.677
6_I11_G0.100080.672
231_N247_R0.100030.672
157_R160_L0.099760.670
282_K289_D0.099630.669
137_D140_E0.09950.669
197_F212_I0.099420.668
20_N23_E0.099370.668
11_G255_G0.099160.666
264_S274_A0.099160.666
39_G42_S0.0990.665
263_P267_P0.098950.665
51_Q55_I0.09880.664
77_P81_S0.0980.658
67_D226_I0.09790.658
8_G11_G0.097720.657
199_A203_L0.097420.655
150_D154_R0.097130.653
247_R277_A0.097120.653
53_I56_D0.097060.652
100_D245_L0.096620.649
111_R114_Y0.096570.649
196_V202_L0.096480.648
118_E134_F0.096460.648
34_I227_D0.096410.648
83_L87_L0.096360.647
14_K228_E0.096320.647
18_L257_I0.096310.647
9_K287_L0.096260.647
6_I259_A0.096180.646
201_L207_W0.096170.646
130_D134_F0.096140.646
87_L106_L0.095960.645
156_L168_F0.09590.644
182_I186_L0.095840.644
245_L248_E0.095840.644
91_L95_D0.095680.643
206_S210_R0.095670.643
241_F249_G0.095670.643
289_D293_A0.095410.641
222_K254_V0.095340.641
159_L166_R0.095280.640
204_L208_I0.095280.640
104_T108_N0.095120.639
183_V189_L0.095080.639
106_L255_G0.094870.637
111_R133_E0.094750.637
195_K199_A0.094690.636
10_T252_Y0.094670.636
182_I191_D0.094670.636
133_E138_P0.094530.635
196_V210_R0.094350.634
258_L284_I0.094260.633
8_G14_K0.094230.633
37_P259_A0.094220.633
247_R261_Q0.094220.633
258_L266_L0.09410.632
64_N83_L0.094090.632
109_A135_L0.093770.630
66_F83_L0.093740.630
49_G55_I0.093670.629
30_P255_G0.093660.629
17_L20_N0.093630.629
25_L32_V0.093610.629
205_L209_Y0.093610.629
190_S244_E0.093430.628
230_H285_F0.093410.628
291_D294_E0.093410.628
249_G278_N0.093320.627
26_I180_R0.093270.627
52_Y183_V0.093150.626
5_L276_L0.093090.625
47_A153_A0.092940.624
241_F244_E0.09290.624
45_A52_Y0.092820.624
79_R83_L0.092820.624
55_I86_L0.092790.623
132_I137_D0.092770.623
49_G52_Y0.092680.623
64_N114_Y0.092150.619
15_T227_D0.092140.619
280_N288_E0.092030.618
2_P247_R0.091870.617
251_K276_L0.091740.616
114_Y130_D0.091570.615
292_D296_A0.091520.615
156_L160_L0.091510.615
203_L206_S0.091390.614
2_P255_G0.091250.613
196_V207_W0.091230.613
19_K44_L0.091140.612
90_M199_A0.091070.612
31_R253_G0.0910.611
19_K38_K0.090920.611
182_I232_F0.090860.610
287_L293_A0.090820.610
226_I233_L0.090740.610
290_S297_E0.090720.610
24_Q28_R0.090680.609
50_G53_I0.090680.609
55_I61_G0.090550.608
186_L232_F0.090480.608
199_A207_W0.09010.605
205_L224_I0.089930.604
9_K283_I0.089910.604
261_Q295_L0.089810.603
44_L84_V0.089670.602
191_D199_A0.089550.602
264_S277_A0.089550.602
231_N265_D0.089130.599
70_D85_S0.089110.599
132_I160_L0.088980.598
50_G55_I0.088770.596
44_L47_A0.088760.596
64_N130_D0.088670.596
235_N275_I0.088510.595
227_D261_Q0.08850.595
40_D227_D0.088220.593
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
4ag6A0.9771000.206
1e9rA0.90791000.359
2iutA0.661299.60.671
2iusA0.667899.30.724
4kfuA0.565898.80.781
2c9oA0.891498.30.819
2ehvA0.618498.10.826
2kjqA0.368498.10.831
4b4tJ0.4572980.833
4b4tL0.4572980.834

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