GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
tRNA_bind - Putative tRNA binding domain
Pfam: PF01588 (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: CL0021
Length: 95
Sequences: 3480
Seq/Len: 36.63
HH_delta: 0.038 (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
8_E22_K2.021253.978
5_K43_E1.217722.397
5_K92_P1.124452.213
7_L24_D1.069862.106
42_P85_V0.972911.915
15_S62_R0.931471.833
11_P37_K0.9261.823
1_I51_V0.922751.816
73_A84_L0.896351.764
10_E20_V0.896021.763
5_K49_K0.893221.758
22_K31_Q0.884591.741
41_E44_V0.853871.681
11_P19_Y0.831681.637
9_V19_Y0.824031.622
5_K24_D0.813761.602
12_H20_V0.789671.554
32_I68_G0.777231.530
77_G80_S0.759731.495
1_I45_L0.75841.493
91_P94_E0.75281.482
60_K65_E0.750941.478
32_I46_V0.738481.453
25_I30_R0.723051.423
31_Q64_V0.713081.403
33_V61_I0.713041.403
4_G23_V0.704581.387
20_V64_V0.699421.377
20_V31_Q0.695871.370
58_P65_E0.680171.339
58_P67_E0.657991.295
33_V64_V0.643511.267
10_E22_K0.628681.237
16_D62_R0.619991.220
74_S80_S0.618481.217
8_E46_V0.616611.214
4_G46_V0.602741.186
22_K29_E0.602061.185
19_Y42_P0.581011.144
40_Y85_V0.571011.124
9_V21_L0.560661.103
14_N64_V0.555741.094
1_I53_V0.547811.078
12_H15_S0.547391.077
21_L72_S0.541111.065
25_I52_V0.534621.052
47_G51_V0.533061.049
6_I50_V0.531981.047
51_V84_L0.524661.033
3_V90_A0.520691.025
4_G25_I0.51621.016
48_K85_V0.506280.996
75_E80_S0.503090.990
2_R48_K0.502690.989
6_I39_V0.496050.976
9_V42_P0.492350.969
7_L29_E0.491780.968
24_D92_P0.491280.967
14_N62_R0.488470.961
2_R54_A0.482060.949
45_L84_L0.474680.934
31_Q65_E0.467750.921
23_V70_L0.453970.893
30_R67_E0.446920.880
25_I46_V0.444390.875
85_V88_D0.43360.853
87_P90_A0.43250.851
32_I52_V0.430760.848
14_N63_G0.428520.843
6_I9_V0.427810.842
39_V42_P0.425430.837
75_E78_D0.420040.827
16_D38_N0.418660.824
19_Y34_S0.417490.822
25_I48_K0.415590.818
8_E41_E0.414760.816
21_L39_V0.413910.815
72_S83_L0.398590.784
38_N80_S0.39570.779
21_L70_L0.393290.774
23_V68_G0.393160.774
49_K89_D0.390010.768
19_Y37_K0.386210.760
74_S77_G0.386140.760
3_V43_E0.378140.744
45_L83_L0.37710.742
48_K51_V0.376880.742
31_Q67_E0.376320.741
74_S79_G0.374060.736
7_L22_K0.370830.730
35_G69_M0.365940.720
90_A94_E0.36420.717
56_L69_M0.360730.710
9_V41_E0.360630.710
12_H64_V0.360580.710
25_I28_E0.35940.707
51_V86_L0.355390.699
2_R25_I0.355190.699
25_I54_A0.354470.698
11_P15_S0.35420.697
1_I71_L0.354110.697
82_G88_D0.349830.689
23_V50_V0.348920.687
30_R49_K0.347290.684
82_G86_L0.346130.681
34_S72_S0.34530.680
15_S18_L0.344920.679
15_S19_Y0.342620.674
9_V39_V0.341960.673
11_P17_K0.337770.665
12_H62_R0.328590.647
4_G52_V0.327180.644
10_E64_V0.32690.643
43_E92_P0.3250.640
37_K42_P0.324560.639
51_V73_A0.321590.633
60_K63_G0.320990.632
21_L34_S0.318680.627
82_G87_P0.31820.626
12_H63_G0.316920.624
73_A79_G0.31240.615
43_E90_A0.310250.611
49_K59_R0.309360.609
20_V33_V0.307060.604
73_A77_G0.299670.590
43_E89_D0.299670.590
35_G61_I0.297750.586
74_S78_D0.297590.586
56_L59_R0.2970.585
15_S37_K0.293680.578
11_P42_P0.29340.577
9_V40_Y0.292140.575
53_V56_L0.291230.573
47_G71_L0.290450.572
34_S70_L0.290060.571
19_Y40_Y0.286760.564
3_V49_K0.285680.562
29_E67_E0.278050.547
34_S83_L0.274910.541
3_V94_E0.274220.540
27_E48_K0.271960.535
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
1pybA0.978999.90.038
2cwpA0.989599.90.039
1ntgA199.90.044
3pcoB199.90.048
3ersX199.90.049
3bu2A199.90.055
1rqgA0.957999.90.057
2nzhA0.989599.90.059
3g48A0.989599.90.065
1gd7A0.989599.90.068

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