GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pept_tRNA_hydro - Peptidyl-tRNA hydrolase
Pfam: PF01195 (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: 184
Sequences: 1958
Seq/Len: 10.64
HH_delta: -0.021 (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
92_L132_I0.817283.333
72_K76_S0.780353.182
117_I125_F0.777593.171
75_L85_I0.733712.992
43_S58_L0.723752.951
71_V116_I0.669262.729
25_D59_K0.659252.688
89_H113_L0.653352.664
15_T148_K0.653062.663
47_E54_K0.60792.479
66_L69_K0.607562.478
33_L46_S0.585192.386
111_N114_K0.580172.366
26_R29_S0.573842.340
58_L74_I0.509592.078
42_K69_K0.499122.035
3_V71_V0.497852.030
92_L141_V0.478671.952
10_P13_E0.463461.890
30_R166_E0.460651.878
33_L48_G0.457861.867
86_L128_L0.44031.795
28_A57_L0.437181.783
43_S70_A0.416951.700
107_S114_K0.416081.697
24_L57_L0.413091.685
30_R169_E0.411111.676
35_W46_S0.404961.651
24_L35_W0.394041.607
87_V116_I0.393141.603
58_L70_A0.392241.599
170_Q179_A0.392171.599
23_V161_I0.390731.593
115_S119_H0.389831.590
107_S117_I0.386211.575
21_F59_K0.383181.563
62_T70_A0.377151.538
1_L80_I0.368341.502
81_P84_N0.366881.496
175_G179_A0.363511.482
44_L61_Q0.360561.470
23_V88_I0.357041.456
72_K119_H0.354351.445
14_N22_M0.35041.429
19_V130_I0.340021.387
96_L160_V0.333491.360
23_V164_A0.331291.351
101_L128_L0.329821.345
26_R162_P0.327251.334
22_M149_F0.323321.318
142_A147_S0.319721.304
91_D108_G0.313911.280
103_K177_E0.31321.277
35_W59_K0.310361.266
75_L120_L0.309641.263
16_R153_E0.301641.230
134_R141_V0.301381.229
126_P176_F0.293591.197
113_L125_F0.29221.192
140_D143_D0.291181.187
136_P139_E0.289171.179
86_L171_I0.288611.177
82_P122_T0.286671.169
26_R165_A0.285841.166
170_Q183_F0.282631.153
96_L133_G0.27941.139
27_L168_L0.278641.136
154_R158_D0.278451.135
103_K126_P0.277781.133
170_Q174_G0.277691.132
175_G178_K0.275371.123
28_A33_L0.274521.119
135_P141_V0.272311.110
151_P155_E0.271861.109
178_K182_K0.271121.106
174_G178_K0.268781.096
156_L159_K0.267121.089
96_L157_L0.266961.089
64_M110_H0.265641.083
115_S118_Q0.265491.083
30_R165_A0.264631.079
155_E159_K0.264511.079
75_L80_I0.263221.073
2_I88_I0.262621.071
157_L161_I0.262521.071
167_A183_F0.252511.030
21_F60_P0.250881.023
152_E155_E0.250151.020
22_M157_L0.249111.016
130_I160_V0.248911.015
101_L176_F0.247641.010
26_R30_R0.24651.005
14_N154_R0.242080.987
21_F61_Q0.239820.978
128_L171_I0.239510.977
155_E158_D0.237570.969
180_M184_N0.235910.962
104_G124_D0.235130.959
170_Q175_G0.234860.958
23_V130_I0.233720.953
1_L58_L0.232910.950
23_V168_L0.232790.949
88_I168_L0.232560.948
49_S52_G0.231310.943
66_L115_S0.230830.941
31_L169_E0.22880.933
160_V164_A0.228290.931
55_V172_I0.227810.929
16_R147_S0.227780.929
157_L160_V0.227460.928
26_R161_I0.227440.927
53_E84_N0.225790.921
95_P98_K0.224670.916
107_S123_E0.223160.910
22_M154_R0.220110.898
150_S153_E0.219930.897
31_L48_G0.218770.892
93_D134_R0.218110.889
69_K119_H0.21710.885
19_V22_M0.216750.884
178_K181_N0.211990.864
89_H93_D0.211160.861
50_I55_V0.210990.860
96_L158_D0.210380.858
5_L64_M0.210040.857
94_L98_K0.209890.856
21_F25_D0.209880.856
91_D129_R0.209490.854
96_L156_L0.209170.853
99_I128_L0.209030.852
89_H104_G0.208380.850
76_S119_H0.208320.849
8_P61_Q0.207860.848
166_E182_K0.206160.841
139_E143_D0.204590.834
41_F78_Y0.204150.832
73_K76_S0.201110.820
132_I145_V0.200680.818
28_A46_S0.200080.816
133_G144_Y0.199990.816
43_S61_Q0.199290.813
168_L172_I0.198750.810
86_L168_L0.197630.806
62_T69_K0.197210.804
4_G20_G0.197030.803
51_K169_E0.196140.800
96_L149_F0.195740.798
105_G127_R0.194770.794
29_S34_S0.193790.790
83_E124_D0.193230.788
82_P120_L0.193010.787
3_V85_I0.192880.787
153_E156_L0.192240.784
179_A184_N0.189040.771
89_H102_K0.188030.767
69_K115_S0.187680.765
109_G145_V0.187480.765
12_Y15_T0.187160.763
28_A35_W0.186910.762
158_D162_P0.186150.759
110_H115_S0.185060.755
166_E169_E0.18460.753
177_E181_N0.181690.741
149_F157_L0.181140.739
161_I165_A0.180690.737
75_L82_P0.180370.736
2_I24_L0.179850.733
23_V165_A0.179640.733
169_E173_E0.178850.729
76_S79_K0.178420.728
6_G21_F0.176440.719
22_M161_I0.174750.713
86_L126_P0.174480.712
31_L50_I0.173390.707
44_L59_K0.172470.703
93_D129_R0.172190.702
41_F58_L0.172050.702
19_V157_L0.171740.700
89_H128_L0.170940.697
39_K77_F0.170090.694
93_D141_V0.169650.692
50_I172_I0.169560.691
114_K118_Q0.169060.689
101_L167_A0.168810.688
24_L31_L0.168720.688
159_K162_P0.167960.685
14_N148_K0.167920.685
1_L74_I0.167690.684
181_N184_N0.166830.680
113_L129_R0.166420.679
28_A48_G0.166340.678
102_K105_G0.166040.677
167_A179_A0.165780.676
35_W44_L0.165040.673
105_G113_L0.164960.673
110_H171_I0.164470.671
83_E103_K0.164070.669
94_L129_R0.164040.669
45_I74_I0.163170.665
91_D94_L0.162880.664
26_R158_D0.162340.662
165_A169_E0.162080.661
45_I78_Y0.161060.657
48_G55_V0.160490.654
92_L134_R0.16020.653
27_L31_L0.159880.652
4_G24_L0.159650.651
17_H65_N0.159030.649
24_L59_K0.15840.646
11_K63_Y0.157060.640
103_K124_D0.156460.638
156_L160_V0.15640.638
87_V125_F0.154640.631
12_Y18_N0.15450.630
35_W45_I0.153790.627
107_S113_L0.15370.627
106_S123_E0.153230.625
159_K163_Q0.153190.625
170_Q173_E0.152390.621
117_I123_E0.150680.614
41_F77_F0.149870.611
102_K106_S0.14970.610
95_P153_E0.148890.607
50_I169_E0.14860.606
42_K73_K0.147960.603
11_K148_K0.147570.602
136_P150_S0.147390.601
4_G21_F0.146680.598
34_S46_S0.146530.598
85_I120_L0.146430.597
179_A183_F0.146130.596
45_I56_I0.145630.594
163_Q182_K0.145390.593
30_R162_P0.145230.592
102_K113_L0.14470.590
101_L126_P0.144140.588
95_P133_G0.14360.586
176_F179_A0.14340.585
51_K173_E0.142760.582
174_G182_K0.142540.581
149_F160_V0.141610.577
36_K46_S0.141440.577
56_I84_N0.141160.576
91_D102_K0.141140.576
17_H90_D0.140220.572
9_G12_Y0.139860.570
2_I86_L0.139160.567
144_Y153_E0.139010.567
105_G109_G0.138980.567
19_V149_F0.138940.567
80_I84_N0.138110.563
109_G133_G0.136990.559
6_G59_K0.136780.558
41_F73_K0.13530.552
64_M67_S0.135240.551
136_P140_D0.13520.551
19_V160_V0.134760.550
89_H134_R0.134640.549
49_S54_K0.134450.548
93_D115_S0.134340.548
89_H129_R0.133340.544
109_G113_L0.133290.544
166_E170_Q0.133060.543
87_V122_T0.1330.542
18_N21_F0.132420.540
23_V27_L0.132210.539
134_R138_K0.132090.539
65_N90_D0.131540.536
2_I168_L0.130610.533
157_L176_F0.130610.533
41_F74_I0.130590.533
56_I79_K0.130350.532
93_D135_P0.130190.531
60_P114_K0.130170.531
94_L100_R0.129520.528
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
4fyjA1100-0.021
3v2iA1100-0.015
2z2iA1100-0.015
4fnoA1100-0.014
2pthA1100-0.013
4jx9A0.9946100-0.012
3neaA0.9946100-0.011
4hoyA0.9946100-0.006
1rybA0.9946100-0.004
2e85A0.7609850.936

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