GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MULE - MULE transposase domain
Pfam: PF10551 (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: CL0219
Length: 93
Sequences: 2519
Seq/Len: 27.09
HH_delta: 0.836 (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
62_S81_H1.177184.218
39_E70_N0.841163.014
86_F90_R0.797672.858
43_E74_E0.694872.490
43_E47_E0.623592.235
39_E74_E0.545681.955
21_D27_F0.508171.821
64_F83_L0.473931.698
36_S41_S0.454781.630
60_I72_I0.444671.593
32_A45_F0.437231.567
21_D25_R0.423271.517
32_A48_K0.420441.507
57_P79_A0.395691.418
84_C87_H0.394561.414
62_S68_L0.38631.384
39_E43_E0.383191.373
47_E75_V0.376321.349
43_E75_V0.368151.319
65_D68_L0.357141.280
60_I76_F0.348821.250
62_S72_I0.345991.240
50_K76_F0.341361.223
63_D87_H0.338461.213
19_G29_V0.337151.208
60_I79_A0.32141.152
42_Y67_A0.31461.127
42_Y65_D0.306791.099
83_L88_I0.303611.088
88_I91_N0.297241.065
83_L91_N0.296811.064
43_E71_A0.296561.063
47_E50_K0.295631.059
42_Y45_F0.290411.041
59_V82_Q0.288871.035
50_K55_Q0.28431.019
28_P31_F0.280141.004
33_L42_Y0.271160.972
69_I83_L0.269010.964
49_L53_M0.26810.961
51_E55_Q0.26640.955
38_S41_S0.264320.947
20_I23_N0.264160.947
35_S41_S0.260960.935
47_E74_E0.253740.909
87_H91_N0.251560.901
20_I35_S0.249580.894
17_A45_F0.247610.887
46_L54_P0.24280.870
17_A32_A0.234570.841
37_E42_Y0.232630.834
68_L81_H0.23240.833
37_E84_C0.232080.832
32_A44_W0.230880.827
62_S69_I0.230170.825
70_N74_E0.229390.822
39_E66_K0.228690.819
17_A49_L0.228060.817
48_K51_E0.227310.815
42_Y68_L0.226710.812
71_A84_C0.22660.812
87_H90_R0.226370.811
51_E54_P0.224160.803
85_L89_L0.222960.799
67_A71_A0.222180.796
68_L72_I0.217960.781
50_K75_V0.216880.777
49_L54_P0.215690.773
73_K79_A0.213660.766
76_F79_A0.211030.756
35_S59_V0.210320.754
34_V41_S0.210.753
21_D30_A0.20890.749
37_E65_D0.208350.747
70_N73_K0.208010.745
29_V49_L0.205250.735
22_G74_E0.205120.735
57_P76_F0.202590.726
73_K81_H0.199510.715
22_G40_E0.198720.712
37_E64_F0.198040.710
61_I65_D0.196740.705
47_E51_E0.195370.700
64_F69_I0.191690.687
69_I81_H0.189820.680
45_F68_L0.189540.679
50_K53_M0.18950.679
45_F49_L0.188340.675
83_L86_F0.185720.666
40_E47_E0.185680.665
50_K56_K0.185640.665
44_W55_Q0.184270.660
44_W47_E0.181280.650
40_E44_W0.176240.632
27_F53_M0.175890.630
48_K70_N0.175380.628
35_S38_S0.175230.628
35_S66_K0.174990.627
37_E49_L0.173990.623
80_R83_L0.173840.623
21_D28_P0.170610.611
32_A41_S0.169450.607
35_S78_D0.16690.598
66_K69_I0.166810.598
24_G53_M0.166290.596
66_K70_N0.166150.595
81_H86_F0.16540.593
28_P68_L0.165310.592
56_K66_K0.165290.592
56_K78_D0.164590.590
53_M56_K0.163970.588
27_F45_F0.163960.588
41_S44_W0.163610.586
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
2qeeA0.967754.60.836
2phnA0.924737.40.851
1c0mA0.935535.20.853
2bw3A0.946232.40.855
2x78A0.91427.40.861
4fw2A0.935526.30.861
4fw1A0.935525.80.862
1cxqA0.935522.90.865
3hphA0.881721.70.867
3ttcA0.892518.90.87
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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