GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_24 - AAA domain
Pfam: PF13479 (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: 213
Sequences: 1653
Seq/Len: 7.76
HH_delta: 0.577 (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
45_D69_Y0.500033.473
36_D39_K0.49953.470
25_K70_D0.476173.308
51_S90_R0.446943.105
86_E90_R0.44483.090
89_C118_F0.435373.024
113_Q117_R0.408412.837
42_D46_V0.371962.584
81_E107_G0.355222.467
8_I20_A0.336612.338
20_A73_V0.318462.212
116_M128_K0.304562.116
59_L72_I0.294672.047
54_D57_E0.293892.041
21_A147_Y0.287781.999
51_S54_D0.286161.988
133_T158_V0.28531.982
114_E118_F0.274171.904
61_E67_A0.258251.794
24_P71_T0.258141.793
2_K127_G0.246661.713
136_A149_R0.24561.706
47_I57_E0.243651.692
60_D66_E0.242971.688
28_F42_D0.241621.678
25_K69_Y0.23111.605
27_L69_Y0.225491.566
49_I57_E0.221811.541
169_V172_L0.214741.492
8_I19_L0.212071.473
13_G18_T0.211661.470
55_F80_L0.209341.454
27_L61_E0.20361.414
53_E90_R0.200881.395
168_V172_L0.198071.376
39_K48_P0.193181.342
57_E61_E0.189161.314
27_L62_L0.187951.306
21_A41_L0.18611.293
29_I58_A0.18541.288
24_P70_D0.184671.283
33_N52_W0.179131.244
57_E60_D0.176431.226
86_E89_C0.176231.224
72_I128_K0.172691.200
20_A28_F0.172091.195
7_L166_F0.166181.154
60_D65_D0.1641.139
81_E111_L0.163151.133
151_K154_L0.158541.101
13_G17_T0.157811.096
47_I50_T0.157491.094
3_P34_G0.157431.094
16_K75_D0.156191.085
107_G110_E0.155651.081
4_I37_S0.15561.081
46_V49_I0.151481.052
28_F73_V0.151021.049
53_E91_Q0.150651.046
157_K164_G0.148241.030
122_L175_E0.147661.026
77_I115_F0.147541.025
69_Y74_I0.145631.012
61_E69_Y0.144581.004
44_G51_S0.144461.003
61_E66_E0.144361.003
2_K68_D0.14290.993
13_G121_K0.142370.989
111_L114_E0.142170.988
109_G125_A0.141930.986
25_K68_D0.140980.979
13_G153_K0.140820.978
35_S80_L0.135510.941
133_T170_G0.135210.939
7_L169_V0.134630.935
26_P71_T0.133340.926
83_M86_E0.132640.921
26_P30_D0.132340.919
111_L118_F0.13180.916
6_I73_V0.131710.915
26_P45_D0.131020.910
160_N174_V0.129620.900
4_I30_D0.126650.880
120_D128_K0.126140.876
136_A174_V0.125240.870
56_L60_D0.123030.855
89_C135_H0.122970.854
114_E117_R0.122790.853
3_P127_G0.122320.850
154_L170_G0.121450.844
2_K24_P0.120950.840
10_G172_L0.120410.836
124_N135_H0.12020.835
27_L53_E0.120170.835
70_D148_T0.119350.829
145_G153_K0.119350.829
80_L100_G0.118890.826
65_D113_Q0.11880.825
3_P14_S0.117940.819
78_S134_A0.117720.818
15_G75_D0.117490.816
14_S20_A0.116660.810
129_N169_V0.116350.808
57_E124_N0.116160.807
53_E57_E0.115980.806
67_A149_R0.115680.804
2_K70_D0.11530.801
110_E114_E0.115280.801
29_I74_I0.114130.793
8_I175_E0.113920.791
43_D46_V0.112830.784
60_D67_A0.112530.782
2_K39_K0.111670.776
61_E65_D0.111110.772
132_F152_P0.111040.771
10_G16_K0.110430.767
113_Q116_M0.109650.762
18_T21_A0.109550.761
3_P168_V0.109420.760
71_T129_N0.108850.756
50_T69_Y0.108840.756
30_D133_T0.108770.756
101_D105_G0.108240.752
115_F167_D0.10820.752
2_K29_I0.108030.750
6_I168_V0.107770.749
43_D53_E0.107470.747
35_S49_I0.106780.742
116_M132_F0.106710.741
81_E114_E0.106260.738
4_I48_P0.105960.736
54_D66_E0.105920.736
12_P163_P0.105590.733
40_F114_E0.105480.733
106_K115_F0.10440.725
35_S55_F0.104190.724
123_L128_K0.104160.724
51_S58_A0.103480.719
27_L72_I0.103330.718
8_I131_I0.103270.717
5_K59_L0.103180.717
165_W169_V0.102850.714
69_Y118_F0.102810.714
77_I112_Q0.102510.712
72_I131_I0.102060.709
83_M90_R0.101770.707
31_T68_D0.101440.705
61_E74_I0.101380.704
32_E76_S0.101320.704
121_K145_G0.101170.703
74_I118_F0.100950.701
31_T74_I0.100880.701
100_G122_L0.100580.699
30_D56_L0.100380.697
36_D61_E0.10.695
146_K151_K0.09970.693
35_S46_V0.099280.690
41_L119_I0.099260.689
25_K45_D0.099040.688
116_M120_D0.098860.687
40_F49_I0.098840.687
32_E170_G0.098720.686
22_S38_L0.098140.682
50_T90_R0.098140.682
29_I72_I0.097990.681
67_A71_T0.097790.679
77_I150_Y0.097710.679
160_N169_V0.097460.677
31_T49_I0.097220.675
17_T37_S0.096840.673
76_S163_P0.096110.668
36_D40_F0.096010.667
27_L67_A0.095920.666
5_K119_I0.095890.666
86_E160_N0.095780.665
161_E164_G0.095720.665
14_S39_K0.095650.664
65_D90_R0.095650.664
157_K167_D0.095520.664
4_I49_I0.095210.661
14_S156_K0.095060.660
34_G87_Y0.095050.660
32_E78_S0.094770.658
67_A117_R0.094750.658
86_E91_Q0.094360.655
18_T80_L0.093990.653
49_I54_D0.093980.653
61_E83_M0.093880.652
34_G52_W0.09370.651
65_D68_D0.093350.648
120_D152_P0.093130.647
59_L91_Q0.093110.647
3_P6_I0.092790.645
80_L111_L0.092720.644
46_V121_K0.092660.644
24_P44_G0.092540.643
4_I50_T0.092450.642
18_T41_L0.092410.642
27_L44_G0.092340.641
101_D153_K0.091980.639
5_K72_I0.09190.638
29_I49_I0.091670.637
79_W171_R0.091340.634
2_K118_F0.09120.634
105_G108_Y0.09110.633
133_T156_K0.091050.632
25_K56_L0.09090.631
111_L119_I0.090790.631
31_T56_L0.09070.630
11_P136_A0.090670.630
91_Q100_G0.090660.630
136_A165_W0.090440.628
67_A86_E0.090330.627
39_K130_V0.090070.626
40_F109_G0.089980.625
162_L174_V0.089970.625
24_P53_E0.089930.625
38_L78_S0.08990.624
27_L70_D0.089860.624
101_D155_G0.08980.624
130_V133_T0.089790.624
46_V50_T0.089580.622
52_W108_Y0.089520.622
19_L135_H0.089430.621
3_P7_L0.089370.621
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
3cmuA0.906199.70.577
3cmwA0.887399.70.583
3cmuA0.901499.70.591
4a1fA0.887399.60.597
3cmwA0.840499.60.6
2i1qA0.849899.60.601
3bh0A0.835799.60.602
3bgwA0.835799.60.603
1v5wA0.854599.60.605
3ldaA0.863899.60.606
If you are interested in a protein containing this domain,
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