GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
gag_pre-integrs - GAG-pre-integrase domain
Pfam: PF13976 (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: 67
Sequences: 619
Seq/Len: 9.24
HH_delta: 0.673 (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
61_S65_G0.401732.910
62_C66_K0.363962.636
59_C62_C0.349612.532
34_P38_V0.249291.806
34_P48_L0.231761.679
25_D36_F0.211811.534
2_L5_L0.204291.480
59_C66_K0.182621.323
27_W30_R0.18081.309
30_R33_H0.17831.291
34_P39_L0.177611.286
60_E63_I0.177431.285
61_S64_L0.174311.262
40_K44_K0.173791.259
26_L44_K0.173421.256
38_V42_L0.167441.213
64_L67_Q0.166111.203
23_S50_G0.165711.200
6_D29_R0.164481.191
8_S12_S0.164221.189
46_G49_P0.162061.174
29_R51_L0.162021.173
27_W42_L0.160341.161
34_P61_S0.160311.161
48_L51_L0.15881.150
15_V35_S0.1581.144
40_K60_E0.157351.140
59_C65_G0.156161.131
41_K51_L0.154771.121
40_K57_S0.153511.112
9_S12_S0.151381.096
38_V67_Q0.147511.068
35_S38_V0.14561.055
27_W67_Q0.144711.048
35_S42_L0.142731.034
17_F20_K0.14071.019
8_S13_S0.139831.013
26_L43_S0.139331.009
62_C65_G0.135770.983
2_L64_L0.135640.982
47_L50_G0.133780.969
46_G50_G0.133070.964
31_L57_S0.131560.953
42_L48_L0.13020.943
14_S21_K0.130140.943
23_S37_Q0.128830.933
36_F40_K0.128830.933
41_K63_I0.127110.921
34_P67_Q0.122990.891
34_P47_L0.122730.889
35_S56_S0.12090.876
25_D29_R0.120720.874
57_S63_I0.120690.874
52_K56_S0.120180.870
28_H62_C0.120110.870
15_V32_G0.119360.864
3_Y12_S0.119230.864
44_K55_K0.119170.863
53_I60_E0.118770.860
52_K55_K0.117550.851
5_L29_R0.117470.851
9_S13_S0.116740.846
37_Q52_K0.114280.828
7_S12_S0.110770.802
58_V63_I0.110390.800
54_S58_V0.109870.796
3_Y11_P0.108520.786
10_I14_S0.108070.783
36_F56_S0.108010.782
2_L6_D0.106190.769
60_E67_Q0.105630.765
31_L55_K0.105190.762
40_K55_K0.103730.751
39_L52_K0.102370.741
31_L61_S0.102210.740
11_P37_Q0.10130.734
38_V43_S0.100770.730
10_I13_S0.098910.716
28_H33_H0.098750.715
24_T48_L0.097970.710
31_L44_K0.097460.706
43_S52_K0.097210.704
47_L52_K0.096880.702
41_K56_S0.096680.700
30_R65_G0.096510.699
22_S50_G0.094880.687
20_K23_S0.094740.686
36_F57_S0.094530.685
21_K45_K0.094470.684
8_S14_S0.094080.681
26_L29_R0.09380.679
31_L40_K0.093680.679
40_K53_I0.093140.675
57_S67_Q0.092560.670
28_H32_G0.092370.669
19_S25_D0.092360.669
44_K57_S0.092220.668
10_I21_K0.091620.664
9_S14_S0.091310.661
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
1k6yA0.701595.30.673
3oymA0.9851920.717
3f9kA0.716484.10.753
4fw2A0.671683.70.754
3hphA0.701582.50.757
3nnqA0.925416.10.847
3ephA0.7919.10.862
3oa5A0.83588.10.865
3cu0A0.73137.40.867
3gx8A0.55226.40.871
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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