GREMLIN Database
tRNA-synt_2_TM - Transmembrane region of lysyl-tRNA synthetase
PFAM: PF16995 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 217 (209)
Sequences: 1295 (857)
Seq/√Len: 59.3
META: 0.542

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
13_V65_L5.6071.00
77_V117_L4.9151.00
154_G201_L4.2401.00
156_G160_L3.5651.00
174_A178_V3.1931.00
152_L156_G3.0271.00
208_A212_A3.0131.00
150_S208_A2.9801.00
183_G186_P2.8481.00
201_L205_G2.7741.00
181_L186_P2.4391.00
204_L208_A2.4001.00
11_W14_G2.3621.00
151_I175_L2.3561.00
170_R174_A2.2671.00
77_V121_L2.2121.00
84_A114_L2.1381.00
45_F48_P2.1221.00
181_L185_D2.1031.00
14_G62_A2.0821.00
173_Y177_R2.0481.00
170_R177_R2.0471.00
185_D189_F2.0161.00
41_P44_L1.9951.00
7_A11_W1.9481.00
197_V201_L1.9091.00
209_L212_A1.8961.00
159_E170_R1.8661.00
143_L212_A1.8551.00
170_R178_V1.8511.00
146_G150_S1.8231.00
150_S204_L1.7890.99
8_A11_W1.7750.99
181_L184_V1.7420.99
180_G183_G1.6870.99
17_G59_L1.6650.99
41_P48_P1.6040.99
84_A117_L1.5950.99
17_G55_A1.5950.99
197_V200_L1.5830.99
152_L155_W1.5720.99
6_P126_E1.5480.98
107_V111_V1.5360.98
118_V122_L1.4920.98
131_G135_S1.4680.98
78_V82_L1.4670.98
132_D135_S1.4590.98
65_L116_L1.4440.97
169_D174_A1.4270.97
19_L23_A1.4120.97
195_G199_F1.4110.97
182_A185_D1.4070.97
207_L211_A1.3990.97
104_V108_V1.3890.97
39_F44_L1.3860.97
30_R64_A1.3410.96
172_A176_N1.3350.96
73_W80_L1.3220.96
8_A12_L1.3180.96
53_A57_L1.2950.95
48_P51_S1.2890.95
10_G13_V1.2810.95
55_A73_W1.2770.95
53_A58_L1.2740.95
163_G167_G1.2700.95
111_V140_L1.2610.94
50_A69_K1.2530.94
70_R144_V1.2510.94
142_V215_V1.2460.94
201_L208_A1.2120.93
111_V148_A1.1910.93
182_A186_P1.1890.92
141_A145_G1.1880.92
210_L214_Y1.1760.92
82_L85_V1.1750.92
44_L48_P1.1750.92
162_P165_L1.1400.91
211_A214_Y1.1350.91
38_E41_P1.1280.90
67_R129_A1.1280.90
198_N202_G1.1140.90
157_L161_F1.1120.90
69_K120_L1.1030.89
149_V165_L1.0940.89
36_V41_P1.0930.89
14_G17_G1.0920.89
137_W141_A1.0900.89
81_A88_V1.0770.88
197_V208_A1.0770.88
80_L116_L1.0480.87
68_R128_Y1.0300.86
154_G205_G1.0300.86
171_L178_V1.0220.85
81_A84_A1.0200.85
58_L116_L1.0170.85
98_P101_R1.0160.85
189_F203_L1.0150.85
210_L213_A1.0100.85
15_L21_L1.0100.85
51_S54_S1.0070.84
13_V20_D1.0030.84
125_R172_A0.9960.84
69_K154_G0.9940.84
57_L75_L0.9920.84
66_R132_D0.9790.83
189_F195_G0.9740.82
161_F165_L0.9710.82
4_W9_A0.9550.81
90_A93_D0.9450.81
74_W213_A0.9440.80
178_V181_L0.9440.80
5_V123_A0.9330.80
6_P14_G0.9310.80
193_P205_G0.9210.79
19_L33_L0.9090.78
165_L173_Y0.9080.78
37_R41_P0.9040.77
195_G198_N0.8990.77
201_L209_L0.8970.77
33_L61_L0.8940.77
170_R173_Y0.8910.76
12_L19_L0.8900.76
7_A31_H0.8900.76
169_D177_R0.8760.75
10_G14_G0.8740.75
141_A146_G0.8690.75
88_V156_G0.8670.74
65_L76_L0.8590.74
208_A214_Y0.8590.74
173_Y193_P0.8520.73
25_V30_R0.8460.73
23_A26_S0.8460.73
143_L147_L0.8390.72
46_N53_A0.8280.71
102_E106_N0.8260.71
138_R150_S0.8240.71
184_V187_V0.8240.71
8_A146_G0.8210.70
39_F43_Y0.8200.70
151_I171_L0.8100.69
189_F213_A0.8080.69
49_A55_A0.8050.69
17_G21_L0.8030.69
23_A47_A0.8030.69
148_A152_L0.7960.68
35_P52_L0.7920.68
19_L22_L0.7880.67
15_L19_L0.7830.67
65_L69_K0.7820.67
73_W128_Y0.7790.66
7_A10_G0.7710.66
133_R137_W0.7670.65
205_G208_A0.7660.65
143_L215_V0.7650.65
141_A152_L0.7630.65
52_L140_L0.7610.64
84_A87_H0.7600.64
78_V203_L0.7570.64
100_V104_V0.7500.63
45_F49_A0.7470.63
52_L120_L0.7440.63
125_R128_Y0.7440.63
169_D176_N0.7400.62
137_W213_A0.7390.62
164_T167_G0.7380.62
173_Y176_N0.7380.62
44_L116_L0.7300.61
14_G18_L0.7290.61
122_L144_V0.7280.61
65_L129_A0.7260.61
34_H46_N0.7250.61
72_A135_S0.7240.61
192_R201_L0.7220.60
34_H44_L0.7190.60
174_A180_G0.7190.60
142_V155_W0.7180.60
38_E47_A0.7180.60
82_L149_V0.7130.59
80_L128_Y0.7120.59
30_R62_A0.7070.59
67_R72_A0.7050.59
12_L33_L0.7030.58
99_E104_V0.7020.58
147_L206_A0.7020.58
169_D173_Y0.7010.58
41_P46_N0.6990.58
6_P10_G0.6950.57
177_R181_L0.6930.57
9_A80_L0.6910.57
183_G188_R0.6890.57
61_L76_L0.6890.57
133_R155_W0.6890.57
111_V118_V0.6830.56
23_A29_L0.6810.56
15_L30_R0.6780.56
3_R8_A0.6760.55
100_V103_H0.6760.55
13_V24_A0.6750.55
75_L200_L0.6740.55
82_L86_L0.6730.55
179_V185_D0.6710.55
8_A15_L0.6640.54
134_G137_W0.6640.54
202_G208_A0.6630.54
58_L100_V0.6630.54
16_V20_D0.6610.54
15_L18_L0.6590.54
55_A154_G0.6570.53
203_L206_A0.6540.53
79_L155_W0.6540.53
60_L132_D0.6510.53
144_V147_L0.6410.52
176_N181_L0.6380.51
40_V81_A0.6370.51
125_R168_G0.6340.51
40_V43_Y0.6330.51
39_F46_N0.6310.50
55_A131_G0.6260.50
60_L213_A0.6250.50
181_L189_F0.6230.50
179_V182_A0.6210.49
34_H37_R0.6190.49
15_L28_P0.6180.49
153_L157_L0.6180.49
32_R36_V0.6180.49
55_A59_L0.6170.49
132_D136_R0.6110.48
10_G119_L0.6060.48
113_S143_L0.6040.47
62_A122_L0.6010.47
159_E171_L0.6010.47
136_R150_S0.6000.47
60_L70_R0.6000.47
11_W19_L0.5990.47
4_W7_A0.5990.47
147_L174_A0.5990.47
55_A79_L0.5980.47
166_A169_D0.5980.47
126_E146_G0.5960.47
78_V175_L0.5960.47
174_A177_R0.5950.46
126_E129_A0.5950.46
16_V21_L0.5940.46
58_L79_L0.5940.46
176_N179_V0.5940.46
63_A137_W0.5930.46
81_A200_L0.5910.46
98_P102_E0.5910.46
20_D51_S0.5890.46
7_A18_L0.5830.45
84_A89_L0.5820.45
192_R197_V0.5820.45
178_V182_A0.5800.45
131_G136_R0.5790.45
158_V173_Y0.5780.45
62_A76_L0.5750.44
150_S205_G0.5750.44
99_E102_E0.5750.44
86_L90_A0.5740.44
177_R198_N0.5740.44
62_A138_R0.5730.44
52_L146_G0.5660.43
13_V17_G0.5630.43
24_A30_R0.5620.43
200_L204_L0.5590.42
85_V92_A0.5590.42
104_V112_V0.5580.42
202_G206_A0.5570.42
45_F50_A0.5570.42
87_H91_L0.5570.42
163_G166_A0.5540.42
159_E174_A0.5530.42
62_A65_L0.5520.42
18_L25_V0.5510.42
25_V187_V0.5510.42
26_S29_L0.5490.41
120_L201_L0.5480.41
70_R130_R0.5480.41
51_S87_H0.5460.41
10_G66_R0.5460.41
107_V144_V0.5450.41
27_P73_W0.5430.41
171_L174_A0.5430.41
37_R42_G0.5380.40
27_P34_H0.5340.40
46_N68_R0.5330.40
104_V115_A0.5330.40
15_L119_L0.5330.40
14_G21_L0.5330.40
7_A44_L0.5300.39
150_S197_V0.5290.39
85_V93_D0.5280.39
71_R194_P0.5250.39
16_V24_A0.5240.39
81_A117_L0.5240.39
20_D32_R0.5230.39
17_G23_A0.5190.38
50_A54_S0.5180.38
21_L141_A0.5170.38
40_V44_L0.5160.38
12_L214_Y0.5150.38
3_R7_A0.5150.38
206_A213_A0.5140.38
58_L64_A0.5110.37
63_A148_A0.5090.37
18_L32_R0.5080.37
32_R41_P0.5070.37
169_D200_L0.5060.37
68_R157_L0.5050.37
126_E152_L0.5040.37
104_V107_V0.5030.36
145_G152_L0.5010.36
187_V190_D0.5010.36
129_A133_R0.5000.36
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
3effK 4 0.3871 26.9 0.929 Contact Map
2kluA 1 0.1382 10 0.942 Contact Map
2kncA 1 0.1567 5.3 0.949 Contact Map
2mofA 1 0.1935 5 0.949 Contact Map
2k1aA 1 0.1475 5 0.949 Contact Map
3u85B 1 0.0415 4.9 0.95 Contact Map
3pjsK 4 0.3871 4.6 0.95 Contact Map
3rkoN 1 0.7742 4.3 0.951 Contact Map
2l8sA 1 0.1429 4.3 0.951 Contact Map
1lnqA 6 0.3548 4.1 0.951 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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