GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GIIM - Group II intron maturase-specific domain
Pfam: PF08388 (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: 80
Sequences: 1371
Seq/Len: 17.14
HH_delta: 0.853 (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
12_T58_R0.654062.858
8_I55_V0.652332.850
7_K31_I0.490722.144
29_N33_R0.462162.019
5_R54_Y0.431631.886
23_E27_K0.391181.709
5_R51_L0.389451.702
12_T24_L0.386321.688
11_I31_I0.376531.645
25_I29_N0.37361.632
67_H70_K0.361511.580
5_R50_K0.360821.577
6_R10_E0.349831.529
52_D56_W0.339271.482
25_I59_L0.331451.448
60_R64_R0.296191.294
64_R67_H0.295651.292
30_P33_R0.294861.288
54_Y58_R0.291691.275
23_E26_K0.283491.239
3_R39_Y0.274681.200
54_Y57_R0.268991.175
16_N19_K0.264711.157
20_S23_E0.263571.152
24_L62_W0.261611.143
4_F31_I0.260841.140
62_W66_R0.249931.092
9_K54_Y0.249841.092
56_W60_R0.248381.085
35_W39_Y0.246631.078
21_L59_L0.243031.062
60_R67_H0.237821.039
5_R58_R0.230741.008
7_K10_E0.229411.002
46_K49_S0.226020.988
28_L32_L0.223570.977
26_K30_P0.222910.974
21_L62_W0.222470.972
14_R17_R0.217710.951
16_N24_L0.212640.929
17_R66_R0.210450.920
49_S53_H0.20850.911
35_W62_W0.207010.905
36_A44_S0.205930.900
44_S48_F0.20520.897
21_L63_L0.205180.897
34_G38_Y0.205170.896
35_W52_D0.204450.893
53_H56_W0.199020.870
29_N36_A0.198040.865
65_R68_K0.197710.864
11_I16_N0.197210.862
7_K26_K0.192760.842
19_K23_E0.192590.842
4_F7_K0.19230.840
16_N27_K0.191370.836
33_R37_N0.189910.830
14_R58_R0.189030.826
34_G37_N0.188330.823
41_I45_S0.187450.819
2_K6_R0.184830.808
36_A48_F0.183990.804
20_S25_I0.183320.801
64_R68_K0.182820.799
3_R6_R0.182660.798
10_E15_R0.181220.792
39_Y64_R0.17830.779
22_E26_K0.177320.775
35_W51_L0.177010.773
39_Y42_G0.17660.772
3_R17_R0.173390.758
9_K58_R0.172760.755
50_K54_Y0.172150.752
63_L66_R0.169320.740
6_R23_E0.169110.739
12_T59_L0.167990.734
45_S49_S0.165860.725
27_K69_R0.16480.720
66_R70_K0.164010.717
11_I58_R0.161490.706
8_I58_R0.159650.698
8_I28_L0.159540.697
50_K53_H0.159160.695
57_R60_R0.159040.695
2_K33_R0.157610.689
2_K10_E0.156490.684
31_I37_N0.155770.681
32_L51_L0.155690.680
15_R55_V0.154740.676
32_L55_V0.153670.671
40_R48_F0.153440.670
21_L25_I0.153410.670
19_K24_L0.151830.663
29_N32_L0.151680.663
7_K11_I0.151390.661
10_E17_R0.150860.659
53_H57_R0.150820.659
21_L51_L0.150160.656
21_L66_R0.150120.656
6_R11_I0.149660.654
29_N37_N0.149060.651
21_L24_L0.1480.647
4_F51_L0.147790.646
9_K63_L0.147140.643
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
4i43B0.987522.40.853
4jsnB0.487513.30.866
4jspB0.487513.30.866
2x5qA0.559.50.874
1jubA0.3758.60.876
1qp6A0.41258.30.877
3kv4A0.51257.90.879
3h4zA0.36256.70.882
2x96A0.756.30.884
3tjxA0.4755.90.885
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 0.0141 seconds.