GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ProRS-C_2 - Prolyl-tRNA synthetase C-terminal
Pfam: PF09181 (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. )
Length: 68
Sequences: 700
Seq/Len: 10.29
HH_delta: 0.301 (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
20_E24_E0.718272.821
15_I45_K0.663072.604
41_E45_K0.643872.529
14_L17_K0.535842.105
15_I19_K0.505441.985
18_I48_A0.477511.875
39_N43_E0.42481.668
19_K45_K0.422451.659
32_P61_Y0.407451.600
22_L29_I0.395191.552
22_L48_A0.384131.509
50_V65_A0.372871.464
41_E44_E0.372721.464
32_P58_G0.370481.455
30_L61_Y0.369271.450
35_E38_Y0.329741.295
30_L63_S0.324311.274
28_V51_L0.323491.271
14_L20_E0.313181.230
34_D62_I0.311681.224
36_S40_E0.307431.207
31_I64_I0.294631.157
22_L46_I0.28321.112
21_I25_K0.278231.093
49_S67_T0.272841.072
51_L67_T0.272451.070
33_Y50_V0.268991.056
33_Y58_G0.268551.055
53_E62_I0.263661.036
21_I29_I0.256331.007
16_E19_K0.248280.975
58_G61_Y0.246520.968
40_E66_R0.244810.962
56_Y64_I0.242320.952
15_I18_I0.229280.901
33_Y60_K0.227050.892
18_I39_N0.223540.878
22_L50_V0.223470.878
34_D60_K0.22320.877
38_Y57_E0.2170.852
21_I24_E0.211620.831
39_N52_G0.203260.798
57_E68_Y0.199140.782
36_S41_E0.197710.777
33_Y59_K0.196180.771
38_Y56_Y0.193060.758
50_V62_I0.191220.751
27_G44_E0.18940.744
14_L38_Y0.188850.742
20_E55_E0.185120.727
34_D38_Y0.182640.717
43_E51_L0.182250.716
52_G67_T0.179850.706
35_E57_E0.176560.693
27_G57_E0.174150.684
23_S66_R0.172890.679
15_I47_D0.168590.662
42_F64_I0.166980.656
38_Y50_V0.165530.650
20_E23_S0.164060.644
27_G37_I0.162170.637
42_F49_S0.161440.634
34_D45_K0.161110.633
39_N42_F0.158650.623
17_K21_I0.156050.613
29_I68_Y0.155640.611
30_L52_G0.154160.605
28_V49_S0.15140.595
30_L66_R0.15110.593
18_I29_I0.150890.593
65_A68_Y0.150370.591
16_E44_E0.148590.584
17_K59_K0.147220.578
53_E60_K0.147130.578
25_K30_L0.1470.577
24_E29_I0.146470.575
27_G30_L0.146380.575
48_A66_R0.14630.575
40_E52_G0.1460.573
42_F46_I0.145270.571
47_D50_V0.143460.563
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
1nj8A199.60.301
1nj1A199.50.335
3ialA199.40.371
4hvcA0.970699.40.375
1hc7A0.970699.40.38
3tosA0.9559380.873
2gmgA0.970616.20.893
3mtwA0.455912.90.897
1gh2A0.867611.80.899
3rhfA0.926511.70.899

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