GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Myb_DNA-bind_3 - MybSANT-like DNA-binding domain
Pfam: PF12776 (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: CL0123
Length: 96
Sequences: 726
Seq/Len: 7.56
HH_delta: 0.542 (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_T57_K0.416883.203
34_W54_L0.256971.975
17_Q36_N0.254371.955
57_K60_T0.24881.912
65_Y69_K0.235451.809
55_K59_K0.21891.682
10_L54_L0.205121.576
49_Y54_L0.185631.426
38_A51_K0.184251.416
71_L77_F0.177341.363
16_E40_E0.176841.359
75_S78_G0.173191.331
40_E43_E0.172131.323
12_D15_I0.170161.307
50_T53_Q0.170061.307
38_A54_L0.167211.285
14_L53_Q0.162931.252
17_Q22_N0.161051.237
13_L40_E0.160531.233
5_E40_E0.159021.222
72_R77_F0.157621.211
14_L34_W0.154141.184
13_L41_F0.153941.183
49_Y53_Q0.153241.177
23_R29_F0.147721.135
43_E83_T0.146971.129
31_K73_N0.144741.112
26_N73_N0.14421.108
72_R79_W0.142941.098
56_N59_K0.139571.072
8_R12_D0.138561.065
39_E43_E0.135051.038
41_F49_Y0.134861.036
17_Q20_K0.13381.028
22_N36_N0.133541.026
38_A42_N0.133291.024
56_N71_L0.132731.020
27_G58_W0.131051.007
6_M49_Y0.129720.997
23_R62_K0.128350.986
11_L15_I0.128180.985
39_E46_G0.128050.984
15_I19_N0.12710.977
51_K54_L0.126940.975
59_K68_W0.126390.971
9_F45_T0.125940.968
78_G83_T0.125250.962
6_M11_L0.124740.958
18_I29_F0.124660.958
35_N43_E0.124430.956
80_D83_T0.123850.952
30_K63_K0.123540.949
48_N69_K0.12320.947
15_I54_L0.122550.942
9_F17_Q0.120620.927
17_Q55_K0.120140.923
29_F37_I0.119920.921
3_T14_L0.119490.918
7_T77_F0.118670.912
27_G41_F0.11830.909
21_G26_N0.117480.903
18_I71_L0.117350.902
37_I70_E0.116770.897
15_I18_I0.116610.896
12_D19_N0.11650.895
42_N47_L0.115110.884
8_R19_N0.114850.882
73_N84_G0.113690.874
57_K84_G0.113340.871
17_Q47_L0.113250.870
36_N43_E0.11310.869
39_E84_G0.111260.855
13_L37_I0.111050.853
10_L37_I0.110590.850
26_N58_W0.110220.847
32_E50_T0.109380.840
61_L66_R0.109380.840
9_F31_K0.10910.838
8_R84_G0.108550.834
26_N29_F0.108380.833
30_K33_G0.107750.828
42_N45_T0.107370.825
26_N74_H0.106750.820
42_N48_N0.106740.820
49_Y58_W0.10580.813
67_I83_T0.105770.813
35_N38_A0.105180.808
79_W83_T0.104690.804
57_K66_R0.104510.803
66_R82_E0.103890.798
3_T6_M0.103880.798
47_L82_E0.103270.794
30_K37_I0.103170.793
33_G56_N0.103020.792
43_E60_T0.102270.786
56_N60_T0.102110.785
4_P8_R0.101960.783
68_W71_L0.101690.781
22_N33_G0.101650.781
31_K34_W0.10050.772
28_G58_W0.09940.764
62_K65_Y0.099040.761
9_F13_L0.098870.760
30_K36_N0.098560.757
53_Q56_N0.098170.754
14_L29_F0.097620.750
39_E67_I0.097570.750
32_E38_A0.097540.749
34_W61_L0.097130.746
4_P7_T0.097030.746
3_T60_T0.09670.743
13_L29_F0.096440.741
52_K56_N0.095850.737
41_F54_L0.095220.732
10_L44_K0.095170.731
75_S79_W0.095130.731
56_N68_W0.094990.730
11_L68_W0.094690.728
36_N76_G0.094690.728
31_K38_A0.094530.726
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
2ebiA0.833398.70.542
2llkA0.510495.40.759
2cqqA0.656294.90.766
3osgA0.656294.80.768
2cqrA0.562594.20.775
1ug2A0.6354940.777
1ignA0.87593.80.779
2m2eA0.718893.60.78
1gv2A0.593.60.78
1h8aC0.593.10.784
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0221 seconds.