GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF772 - Transposase domain (DUF772)
Pfam: PF05598 (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: 77
Sequences: 1462
Seq/Len: 18.99
HH_delta: 0.831 (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
26_R53_H0.742513.183
31_R35_N0.68412.933
17_K28_L0.56762.433
13_A32_L0.526752.258
8_R12_K0.516752.215
34_D37_S0.489412.098
32_L42_C0.453361.944
25_D60_R0.446751.915
27_E31_R0.417051.788
54_S58_R0.376761.615
70_E74_D0.370561.589
13_A56_L0.345511.481
72_L76_V0.32571.396
10_M59_F0.318051.364
13_A51_P0.30631.313
16_L38_F0.299431.284
71_K75_Q0.28151.207
16_L20_F0.278161.192
67_G71_K0.26831.150
5_Y9_M0.267211.146
26_R54_S0.266061.141
39_R50_V0.264341.133
69_I73_F0.261311.120
10_M55_T0.252181.081
25_D41_F0.250221.073
20_F38_F0.240221.030
52_D60_R0.240071.029
7_P18_Y0.23951.027
57_S61_K0.239171.025
31_R38_F0.233621.002
8_R42_C0.23220.995
54_S57_S0.230750.989
55_T59_F0.230340.987
33_R39_R0.230170.987
70_E73_F0.230170.987
25_D59_F0.229270.983
29_E53_H0.22630.970
12_K41_F0.2250.965
29_E50_V0.22360.959
29_E33_R0.221430.949
12_K39_R0.221130.948
7_P10_M0.220290.944
16_L28_L0.218890.938
57_S60_R0.217330.932
71_K74_D0.21720.931
13_A42_C0.214060.918
55_T58_R0.21090.904
30_E65_Q0.204570.877
5_Y59_F0.204250.876
22_L38_F0.204250.876
16_L41_F0.204170.875
7_P59_F0.203590.873
30_E33_R0.20110.862
20_F30_E0.20040.859
19_L73_F0.19680.844
56_L60_R0.196140.841
17_K31_R0.196040.840
61_K65_Q0.195780.839
36_L39_R0.193060.828
17_K25_D0.192710.826
68_L71_K0.192530.825
44_L50_V0.192090.824
44_L48_E0.191780.822
27_E74_D0.189980.814
66_H76_V0.189850.814
67_G70_E0.186770.801
14_L34_D0.184210.790
73_F76_V0.183870.788
20_F31_R0.183770.788
22_L31_R0.182470.782
52_D58_R0.181810.779
14_L68_L0.181630.779
61_K64_I0.180850.775
58_R72_L0.180560.774
2_R20_F0.178950.767
50_V75_Q0.178440.765
11_L69_I0.175870.754
30_E34_D0.174410.748
8_R11_L0.173950.746
12_K16_L0.169560.727
53_H57_S0.168080.721
66_H70_E0.166750.715
6_P9_M0.16620.713
72_L75_Q0.165470.709
67_G74_D0.164860.707
14_L28_L0.162810.698
30_E40_Y0.16240.696
19_L40_Y0.162190.695
12_K42_C0.160840.690
21_G65_Q0.160680.689
9_M44_L0.160610.689
22_L27_E0.157680.676
21_G67_G0.155460.666
52_D62_R0.155440.666
5_Y51_P0.155430.666
12_K51_P0.15360.658
1_G43_G0.153540.658
18_Y36_L0.151870.651
25_D56_L0.151330.649
10_M14_L0.150420.645
9_M49_P0.150230.644
35_N41_F0.150030.643
5_Y15_L0.150010.643
32_L51_P0.149190.640
68_L73_F0.149060.639
5_Y55_T0.148870.638
15_L19_L0.148280.636
44_L51_P0.146980.630
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
4dyqA0.779243.10.831
3osjA0.6364350.839
3ohwB0.636433.90.84
3nphB0.792225.80.849
2ky4A0.766219.10.857
2xigA0.831217.50.86
2o03A0.831216.60.861
1tc3C0.649416.40.862
2w57A0.831216.30.862
3ploX0.688315.30.863
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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