GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_gyraseB_C - DNA gyrase B subunit carboxyl terminus
Pfam: PF00986 (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: 65
Sequences: 1826
Seq/Len: 28.09
HH_delta: -0.139 (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
28_D31_T0.872292.981
11_F18_N0.690952.362
61_R65_E0.620742.122
47_E51_M0.610312.086
58_E62_E0.604762.067
44_E47_E0.529821.811
56_N59_P0.472111.614
27_M65_E0.439171.501
17_M22_L0.433441.481
42_A45_A0.423061.446
52_L63_F0.420251.436
46_D50_E0.409351.399
9_Q21_Q0.404191.381
43_E47_E0.377831.291
27_M56_N0.364351.245
50_E56_N0.35981.230
20_D28_D0.352211.204
11_F21_Q0.351711.202
42_A46_D0.346431.184
54_G64_I0.342381.170
20_D24_E0.341131.166
33_R48_L0.337461.153
40_E43_E0.336531.150
59_P62_E0.33391.141
44_E48_L0.328851.124
27_M64_I0.323631.106
23_W29_P0.318011.087
35_I58_E0.305681.045
41_D44_E0.304621.041
6_V39_I0.296521.013
46_D49_F0.294051.005
50_E55_K0.291970.998
11_F55_K0.290340.992
38_T43_E0.285790.977
13_G16_E0.280840.960
25_T32_R0.274050.937
62_E65_E0.274010.937
17_M21_Q0.271150.927
6_V18_N0.270570.925
44_E51_M0.269130.920
30_E36_R0.266230.910
48_L51_M0.262280.896
23_W28_D0.25980.888
6_V33_R0.259740.888
8_I38_T0.258780.884
15_G54_G0.258780.884
5_K50_E0.255620.874
11_F22_L0.253420.866
49_F64_I0.252660.864
58_E65_E0.241640.826
9_Q23_W0.240830.823
43_E62_E0.239020.817
11_F53_M0.23660.809
38_T46_D0.235720.806
11_F17_M0.231410.791
5_K39_I0.230920.789
12_K15_G0.230070.786
24_E28_D0.229360.784
37_V54_G0.228830.782
43_E56_N0.228070.780
18_N49_F0.225480.771
38_T42_A0.225480.771
12_K16_E0.223410.764
8_I41_D0.223320.763
39_I55_K0.220180.753
41_D47_E0.220.752
47_E50_E0.21890.748
5_K34_L0.217520.743
7_E19_P0.215610.737
7_E34_L0.212320.726
31_T38_T0.212080.725
31_T43_E0.211080.721
17_M25_T0.20950.716
35_I41_D0.208260.712
27_M63_F0.207870.710
17_M52_L0.207810.710
60_R64_I0.202780.693
11_F56_N0.202470.692
7_E31_T0.201520.689
22_L26_T0.201030.687
7_E56_N0.198150.677
57_V63_F0.197070.674
35_I56_N0.196540.672
22_L53_M0.1930.660
24_E47_E0.192940.659
7_E39_I0.190230.650
37_V63_F0.189490.648
22_L25_T0.188920.646
23_W38_T0.188610.645
51_M58_E0.188040.643
10_R13_G0.187750.642
10_R14_L0.186550.638
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
3nuhB1100-0.139
3k9fC199.90.073
3m4iA199.90.085
2xkjE199.90.116
2xcsB199.80.216
4gfhA0.953899.80.254
3qx3A0.953899.70.299
3l4jA0.953899.70.305
3encA0.692338.70.888
4h83A0.461512.10.911

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