GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AntA - AntAAntB antirepressor
Pfam: PF08346 (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. )
Length: 71
Sequences: 327
Seq/Len: 4.61
HH_delta: 0.898 (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
15_R18_T0.616323.309
16_F55_Y0.466632.505
29_F61_M0.438742.355
14_K18_T0.40472.173
27_Y64_E0.398532.139
26_E70_R0.374822.012
9_F66_A0.322951.734
23_R69_E0.322171.730
64_E68_V0.295811.588
3_A16_F0.29171.566
61_M65_L0.283221.520
15_R21_K0.281011.509
30_V33_V0.266871.433
3_A55_Y0.260111.396
20_I24_I0.25421.365
64_E67_M0.240921.293
2_S56_H0.237291.274
57_L61_M0.237031.272
61_M70_R0.228121.225
24_I69_E0.225371.210
27_Y68_V0.219441.178
56_H59_L0.215721.158
45_N49_G0.211861.137
18_T21_K0.207791.116
1_V66_A0.206691.110
39_E43_K0.196341.054
32_N40_Q0.19571.051
60_D63_K0.191811.030
24_I68_V0.191181.026
47_G50_R0.190071.020
46_G49_G0.186311.000
48_G51_P0.186241.000
4_R11_E0.184680.991
45_N48_G0.183230.984
14_K21_K0.181550.975
61_M66_A0.178560.959
14_K17_S0.17510.940
17_S53_K0.174990.939
17_S39_E0.173610.932
8_E35_F0.172950.928
20_I69_E0.170690.916
18_T43_K0.170040.913
27_Y67_M0.168070.902
20_I55_Y0.16430.882
53_K59_L0.164290.882
65_L69_E0.163820.879
1_V56_H0.163050.875
49_G52_S0.161560.867
35_F71_N0.159330.855
32_N44_S0.156520.840
44_S49_G0.156360.839
46_G52_S0.155040.832
1_V8_E0.15490.832
5_D60_D0.153310.823
5_D9_F0.153140.822
24_I55_Y0.151520.813
40_Q54_D0.151520.813
2_S54_D0.151110.811
5_D54_D0.150580.808
6_L67_M0.149830.804
3_A57_L0.149710.804
27_Y70_R0.149360.802
37_V53_K0.148390.797
17_S21_K0.148230.796
55_Y58_T0.146860.788
23_R27_Y0.146360.786
33_V62_A0.145910.783
48_G52_S0.145250.780
15_R39_E0.143390.770
7_H23_R0.140110.752
37_V51_P0.139940.751
3_A56_H0.138130.742
44_S50_R0.137940.741
37_V50_R0.137550.738
9_F59_L0.136970.735
29_F70_R0.136590.733
26_E29_F0.136290.732
16_F25_E0.136210.731
27_Y61_M0.135920.730
57_L71_N0.135210.726
44_S51_P0.133570.717
7_H13_K0.133360.716
33_V36_I0.130960.703
37_V52_S0.130360.700
47_G51_P0.129360.694
2_S5_D0.127960.687
46_G50_R0.127260.683
43_K49_G0.126260.678
56_H66_A0.125240.672
21_K55_Y0.124710.670
4_R13_K0.124570.669
23_R70_R0.121180.651
34_D64_E0.121150.650
37_V45_N0.120950.649
62_A66_A0.120850.649
45_N52_S0.120650.648
37_V40_Q0.119970.644
1_V6_L0.119950.644
12_V71_N0.119250.640
53_K65_L0.116610.626
43_K48_G0.11630.624
55_Y59_L0.115750.621
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
3hpcX0.33835.50.898
3bbnI0.915529.90.902
2qlzA0.873227.10.904
3hrzD0.436623.40.907
3v33A0.915522.60.907
2vqeI0.9014210.908
3v32B0.788720.80.909
3r8nI0.901419.30.91
2flhA0.971815.20.914
2p4wA0.873214.80.914
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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