GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Zn_ribbon_recom - Recombinase zinc beta ribbon domain
Pfam: PF13408 (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: 58
Sequences: 2173
Seq/Len: 37.47
HH_delta: 0.706 (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
7_R14_K1.020613.029
46_E50_E0.841112.496
27_Y46_E0.817712.427
13_S31_N0.802272.381
10_H40_P0.696182.066
45_R48_E0.602031.787
2_L50_E0.592461.758
2_L46_E0.585571.738
8_C11_C0.535611.590
17_R27_Y0.533121.582
17_R46_E0.495621.471
15_M41_N0.483621.435
8_C29_C0.481311.429
11_C29_C0.471371.399
18_R28_R0.457281.357
31_N35_K0.42751.269
6_L49_I0.424211.259
27_Y50_E0.414381.230
32_R43_S0.409521.215
1_L50_E0.406391.206
25_R46_E0.400781.190
8_C39_C0.395211.173
26_Y43_S0.395051.173
15_M27_Y0.389291.155
7_R10_H0.381181.131
32_R39_C0.372961.107
2_L53_V0.36871.094
28_R33_R0.354981.054
10_H42_K0.354021.051
31_N38_G0.349131.036
32_R42_K0.34161.014
49_I53_V0.333970.991
30_S34_R0.331920.985
2_L6_L0.33020.980
1_L27_Y0.329110.977
6_L27_Y0.325670.967
47_E51_E0.323020.959
6_L15_M0.320260.951
26_Y45_R0.31370.931
51_E55_E0.305160.906
5_L53_V0.304090.903
1_L54_L0.298560.886
52_A56_A0.289780.860
35_K38_G0.287290.853
30_S33_R0.272130.808
30_S36_G0.263410.782
19_K25_R0.26340.782
9_G12_G0.262980.781
50_E54_L0.260780.774
18_R33_R0.246260.731
4_G14_K0.243380.722
48_E51_E0.242830.721
18_R57_L0.241110.716
2_L49_I0.240360.713
10_H41_N0.238080.707
54_L57_L0.235970.700
16_T30_S0.227170.674
52_A55_E0.220320.654
34_R56_A0.217360.645
53_V57_L0.216540.643
17_R56_A0.21650.643
50_E53_V0.216280.642
17_R25_R0.212540.631
34_R43_S0.211220.627
48_E52_A0.210.623
9_G41_N0.209040.620
20_R43_S0.20790.617
32_R40_P0.201340.598
5_L16_T0.200390.595
5_L27_Y0.199850.593
24_Y45_R0.197930.587
13_S45_R0.196490.583
24_Y54_L0.195350.580
3_S13_S0.194150.576
14_K47_E0.191520.568
15_M28_R0.191130.567
20_R24_Y0.189380.562
44_I48_E0.188840.560
1_L53_V0.187530.557
34_R38_G0.184560.548
4_G53_V0.181960.540
11_C39_C0.17740.527
18_R26_Y0.177390.527
29_C39_C0.177230.526
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
1twfI0.965568.90.706
3qt1I0.982866.40.712
2riqA0.913866.30.712
3h0gI0.9655620.719
3ga8A0.827647.70.741
2lcqA0.379345.60.744
2gaiA0.913842.20.749
4esjA135.30.759
1ee8A0.620733.80.761
3q87A0.534529.90.767
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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