GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ProRS-C_1 - Prolyl-tRNA synthetase C-terminal
Pfam: PF09180 (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: 767
Seq/Len: 11.28
HH_delta: 0.037 (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
24_C54_C0.880763.658
19_C24_C0.628862.612
1_Y31_E0.563892.342
21_D56_K0.563812.342
27_K31_E0.554842.304
1_Y5_K0.477331.983
19_C54_C0.468291.945
8_I14_V0.416811.731
25_E29_K0.414381.721
8_I34_A0.402251.671
4_F34_A0.400161.662
17_P58_A0.378381.572
27_K30_E0.372671.548
6_E10_K0.348251.446
36_I65_A0.344151.429
13_F37_R0.327851.362
5_K31_E0.325591.352
17_P61_W0.314471.306
16_V52_I0.310071.288
8_I32_T0.305161.267
27_K53_V0.300931.250
39_I62_V0.293821.220
6_E9_E0.287851.196
19_C51_C0.281221.168
47_E61_W0.280721.166
22_E26_E0.280151.164
37_R67_S0.270051.122
7_A14_V0.268571.115
15_L63_L0.267051.109
15_L61_W0.265461.103
16_V64_F0.264511.099
20_G62_V0.25861.074
35_T67_S0.250061.039
50_K57_P0.245321.019
1_Y4_F0.239950.997
25_E38_C0.228060.947
3_E6_E0.219840.913
28_I32_T0.217860.905
29_K37_R0.216950.901
18_W58_A0.216410.899
45_E60_K0.216340.899
36_I62_V0.207190.861
50_K56_K0.206250.857
31_E53_V0.202380.841
18_W60_K0.201950.839
2_E5_K0.200220.832
18_W36_I0.19490.810
25_E41_F0.192820.801
4_F28_I0.192190.798
4_F25_E0.191840.797
38_C67_S0.191440.795
20_G60_K0.18680.776
18_W59_K0.184140.765
3_E59_K0.183980.764
23_E55_G0.181950.756
23_E56_K0.181070.752
29_K38_C0.179440.745
58_A61_W0.176170.732
45_E48_G0.176030.731
42_D59_K0.175810.730
22_E27_K0.174690.726
9_E20_G0.174210.724
26_E66_R0.173960.723
35_T40_P0.173250.720
8_I36_I0.170140.707
50_K54_C0.168340.699
15_L45_E0.167590.696
13_F35_T0.166170.690
7_A10_K0.165150.686
46_P50_K0.163890.681
48_G59_K0.162890.677
17_P47_E0.161950.673
2_E10_K0.161530.671
12_G30_E0.160990.669
23_E32_T0.160970.669
57_P68_Y0.159920.664
65_A68_Y0.15970.663
5_K32_T0.15480.643
9_E50_K0.153860.639
18_W53_V0.153390.637
28_I64_F0.15320.636
17_P49_G0.152930.635
15_L38_C0.150760.626
21_D24_C0.150470.625
24_C51_C0.150440.625
10_K50_K0.148940.619
47_E52_I0.148880.618
15_L46_P0.147820.614
25_E64_F0.147680.613
53_V64_F0.147580.613
26_E29_K0.146290.608
46_P60_K0.146090.607
25_E40_P0.145060.602
1_Y32_T0.143550.596
33_G38_C0.141460.588
20_G24_C0.139470.579
4_F32_T0.137930.573
37_R63_L0.137720.572
25_E39_I0.137710.572
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
4hvcA199.80.037
3ialA199.80.041
1hc7A0.970699.80.061
1nj1A0.941299.80.093
1nj8A0.779499.50.292
3mp2A0.926556.60.852
1lkoA0.7206420.863
3tosA0.764724.30.878
3ttcA0.808819.30.884
3vthA0.720615.70.888

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