GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Intron_maturas2 - Type II intron maturase
Pfam: PF01348 (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: CL0359
Length: 146
Sequences: 804
Seq/Len: 5.51
HH_delta: 0.941 (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
48_N80_A0.393812.869
20_K26_K0.350462.553
48_N81_K0.334462.436
7_Y112_K0.300042.186
34_R48_N0.294642.146
65_S96_K0.286052.084
42_E115_K0.285712.081
34_R80_A0.266941.944
63_N115_K0.242261.765
40_D87_H0.231811.689
59_S80_A0.222381.620
38_L112_K0.218991.595
15_K42_E0.214411.562
41_L59_S0.214261.561
10_I96_K0.206941.507
20_K25_I0.19441.416
65_S103_D0.192451.402
7_Y12_K0.185131.349
36_I76_R0.184471.344
25_I80_A0.183491.337
4_I48_N0.178911.303
33_S36_I0.178681.302
25_I81_K0.178671.301
42_E82_T0.17761.294
51_I62_D0.174941.274
51_I65_S0.170631.243
18_R58_Y0.166571.213
42_E111_K0.16241.183
112_K115_K0.160381.168
26_K65_S0.16021.167
63_N84_A0.157531.147
110_F116_F0.155211.131
82_T115_K0.153641.119
58_Y115_K0.153311.117
24_K96_K0.153141.116
5_Q65_S0.151911.107
4_I116_F0.151471.103
68_N76_R0.149491.089
29_P73_Y0.145861.062
39_D42_E0.144981.056
21_G110_F0.143941.049
15_K54_L0.143091.042
21_G82_T0.142391.037
91_V94_V0.141781.033
10_I24_K0.14061.024
96_K103_D0.140331.022
66_R104_L0.139791.018
43_I82_T0.139371.015
24_K38_L0.139091.013
62_D102_K0.138951.012
52_R57_Y0.137481.001
93_K107_N0.13741.001
43_I58_Y0.137190.999
42_E84_A0.137080.999
58_Y116_F0.136470.994
83_L87_H0.136210.992
18_R103_D0.136190.992
78_S86_K0.136040.991
107_N113_K0.135960.990
84_A115_K0.135430.987
5_Q110_F0.135370.986
24_K41_L0.135180.985
41_L55_Y0.134610.981
35_L46_R0.133910.975
48_N55_Y0.133380.972
10_I103_D0.133150.970
42_E113_K0.132320.964
89_S96_K0.131680.959
48_N115_K0.131110.955
18_R65_S0.130150.948
15_K80_A0.130120.948
7_Y42_E0.128280.934
34_R59_S0.127840.931
20_K98_Y0.127520.929
50_E61_A0.127250.927
7_Y13_I0.127170.926
4_I20_K0.126780.924
70_R77_Y0.126470.921
41_L115_K0.12530.913
63_N98_Y0.124630.908
55_Y66_R0.124510.907
26_K80_A0.1240.903
4_I34_R0.12360.900
31_S85_R0.123440.899
26_K35_L0.123410.899
48_N56_N0.123090.897
36_I98_Y0.122710.894
55_Y95_F0.121950.888
4_I80_A0.121180.883
33_S112_K0.120830.880
4_I58_Y0.118620.864
40_D89_S0.118270.862
8_A11_E0.117850.858
104_L115_K0.116980.852
43_I83_L0.116550.849
38_L48_N0.116210.847
58_Y63_N0.115710.843
16_K76_R0.115220.839
52_R103_D0.114950.837
14_I23_C0.114170.832
7_Y30_I0.113540.827
14_I76_R0.113530.827
15_K34_R0.113270.825
32_R37_N0.113060.824
18_R82_T0.112570.820
108_E113_K0.111990.816
19_K64_R0.111760.814
23_C74_I0.111420.812
12_K66_R0.111350.811
51_I104_L0.110120.802
39_D97_K0.109740.799
59_S99_G0.10970.799
15_K115_K0.108910.793
38_L115_K0.108780.792
23_C27_G0.108760.792
48_N112_K0.108690.792
37_N62_D0.108490.790
41_L48_N0.107940.786
70_R80_A0.107640.784
26_K96_K0.107410.782
25_I44_I0.10670.777
79_C104_L0.106240.774
79_C83_L0.106020.772
33_S107_N0.105870.771
68_N73_Y0.105730.770
76_R98_Y0.105260.767
22_F46_R0.10450.761
25_I34_R0.104090.758
58_Y84_A0.103950.757
6_L77_Y0.103860.757
4_I55_Y0.103220.752
12_K54_L0.10280.749
44_I49_S0.102580.747
17_L75_L0.102460.746
6_L105_S0.1020.743
30_I45_N0.100980.736
41_L96_K0.100890.735
62_D65_S0.100570.733
70_R99_G0.100490.732
25_I48_N0.100430.732
28_K90_S0.100220.730
4_I54_L0.100120.729
82_T86_K0.099920.728
109_F114_K0.099890.728
14_I54_L0.099750.727
48_N116_F0.099610.726
18_R115_K0.099480.725
48_N51_I0.099410.724
11_E20_K0.09930.723
93_K105_S0.098720.719
52_R56_N0.098320.716
26_K44_I0.098180.715
58_Y95_F0.098160.715
58_Y110_F0.097720.712
84_A89_S0.09770.712
22_F75_L0.097680.712
3_R13_I0.097670.711
81_K115_K0.097580.711
55_Y85_R0.097580.711
38_L110_F0.09730.709
7_Y15_K0.097190.708
15_K59_S0.097010.707
11_E63_N0.096560.703
32_R50_E0.096470.703
21_G25_I0.096360.702
12_K103_D0.096340.702
20_K58_Y0.095630.697
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
1jr5A0.431520.50.941
3bboY0.486315.50.945
2dulA0.342513.20.946
2gnrA0.376712.60.947
1rr7A0.691811.10.948
2k3rA0.58911.10.948
3tlxA0.58910.60.948
2l8eA0.184910.40.948
3kdgA0.349310.30.948
3zf7o0.308210.20.949
If you are interested in a protein containing this domain,
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