GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OrfB_Zn_ribbon - Putative transposase DNA-binding domain
Pfam: PF07282 (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: CL0167
Length: 69
Sequences: 2971
Seq/Len: 43.06
HH_delta: 0.725 (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
32_P61_N1.596923.309
12_A19_V1.48843.084
5_R21_E1.449833.004
3_Q7_R1.442232.988
7_R10_Y1.078382.234
22_V66_I1.041152.157
41_R44_G0.95041.969
31_C34_C0.912461.890
9_E21_E0.903071.871
30_T37_R0.854281.770
48_T55_E0.82611.712
4_F8_L0.805631.669
33_R54_F0.779531.615
27_T66_I0.772541.601
49_C52_C0.759341.573
3_Q6_Q0.74991.554
56_M60_V0.721971.496
32_P64_R0.701461.453
31_C52_C0.695191.440
12_A17_I0.691931.434
26_Y29_Q0.684891.419
36_H50_P0.677851.404
9_E13_E0.676631.402
64_R68_R0.658981.365
7_R11_K0.634681.315
34_C52_C0.623541.292
45_R58_R0.620271.285
42_R45_R0.618871.282
31_C49_C0.616631.278
34_C49_C0.585361.213
29_Q39_K0.569411.180
24_E27_T0.552811.145
11_K14_E0.53591.110
47_F54_F0.534021.106
2_G5_R0.530481.099
38_N47_F0.516481.070
2_G6_Q0.49721.030
10_Y14_E0.490941.017
46_V55_E0.489281.014
62_A65_N0.471340.977
38_N41_R0.467760.969
36_H51_N0.458080.949
9_E19_V0.453560.940
47_F56_M0.453440.939
38_N50_P0.440170.912
8_L19_V0.439450.910
61_N65_N0.430320.892
42_R58_R0.408880.847
56_M64_R0.397280.823
60_V64_R0.389210.806
32_P56_M0.37520.777
11_K15_Y0.368140.763
46_V56_M0.354370.734
29_Q38_N0.352060.729
15_Y18_Q0.35010.725
63_A66_I0.335910.696
29_Q41_R0.333830.692
26_Y37_R0.329460.683
28_S41_R0.3280.680
60_V63_A0.325560.675
1_F17_I0.322970.669
24_E62_A0.313310.649
23_D26_Y0.308930.640
5_R9_E0.305260.632
44_G47_F0.303950.630
54_F60_V0.297520.616
30_T39_K0.295920.613
56_M61_N0.295040.611
29_Q37_R0.292150.605
32_P68_R0.283070.586
13_E18_Q0.282830.586
5_R19_V0.279550.579
41_R45_R0.272480.565
44_G58_R0.267670.555
40_K47_F0.264570.548
64_R67_L0.260880.541
48_T54_F0.258820.536
46_V57_D0.258640.536
32_P54_F0.249060.516
59_D63_A0.243090.504
4_F13_E0.240520.498
30_T36_H0.238740.495
13_E20_V0.237980.493
45_R57_D0.235820.489
36_H47_F0.234050.485
7_R14_E0.232670.482
4_F12_A0.231110.479
14_E17_I0.229950.476
12_A15_Y0.229810.476
52_C59_D0.228380.473
33_R51_N0.22630.469
48_T51_N0.225080.466
6_Q10_Y0.222530.461
5_R14_E0.222480.461
33_R60_V0.221920.460
27_T30_T0.221880.460
26_Y30_T0.220550.457
14_E27_T0.218540.453
43_S47_F0.217340.450
3_Q12_A0.21460.445
22_V25_A0.214490.444
38_N51_N0.214130.444
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
1h7bA0.94295.10.725
3u6pA0.782691.40.761
1vk6A191.20.763
1ee8A0.826189.40.771
1k82A0.782688.20.776
1k3xA0.768188.10.777
2xzfA0.797187.70.778
1vq8Z0.869678.40.801
2fiyA0.97177.50.802
3cngA0.637776.60.803
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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