GREMLIN Database
YTPR - Putative tRNA-binding protein YtpR
UniProt: O34943 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 201 (196)
Sequences: 382 (284)
Seq/√Len: 20.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
159_E164_P4.9121.00
102_E119_N4.0331.00
30_K35_V3.5541.00
36_K45_T3.4281.00
138_Q188_V3.2121.00
99_G142_V2.8030.99
91_D95_K2.6310.98
103_S117_K2.6040.98
131_A186_I2.6010.98
12_D54_S2.5820.98
79_L82_N2.5160.98
129_C186_I2.4390.97
33_D52_N2.4160.97
38_F45_T2.3990.97
50_I75_V2.3620.96
106_K114_S2.3300.96
101_V134_V2.3230.96
173_K182_A2.2860.96
157_D166_S2.2740.95
129_C172_A2.1380.94
120_V125_L2.1290.94
132_P180_A2.1240.93
172_A187_L2.0670.92
135_D138_Q2.0310.92
69_E73_Q1.9820.91
135_D188_V1.9610.90
33_D56_Y1.9540.90
194_E197_D1.9140.89
129_C134_V1.8780.88
77_E81_R1.8750.88
131_A138_Q1.8030.86
132_P181_P1.7900.86
10_V15_L1.7150.83
142_V169_I1.7100.83
19_Q44_E1.6680.81
69_E92_L1.6680.81
193_Y197_D1.6240.79
139_K195_A1.5970.78
138_Q186_I1.5720.77
134_V186_I1.5120.74
114_S129_C1.5000.74
129_C138_Q1.4910.73
16_I50_I1.4770.72
104_K114_S1.4540.71
96_F147_A1.4270.70
30_K51_F1.4180.69
5_Y11_G1.4180.69
129_C170_C1.3800.67
172_A186_I1.3750.67
36_K86_E1.3680.66
39_N42_T1.3440.65
141_V199_F1.3250.64
31_H84_V1.3170.63
2_N148_V1.2910.62
5_Y12_D1.2860.61
134_V138_Q1.2750.61
141_V187_L1.2720.61
131_A184_K1.2710.61
109_N161_R1.2700.60
131_A172_A1.2560.60
141_V172_A1.2140.57
121_G144_K1.2110.57
8_E62_N1.1950.56
114_S184_K1.1940.56
91_D147_A1.1930.56
129_C141_V1.1810.55
79_L84_V1.1790.55
157_D164_P1.1570.53
75_V88_L1.1350.52
118_V156_K1.1190.51
131_A134_V1.1050.50
7_K29_E1.1020.50
4_F148_V1.1010.50
37_I47_G1.0790.48
125_L163_V1.0750.48
140_V169_I1.0690.47
33_D53_A1.0670.47
56_Y78_I1.0650.47
125_L144_K1.0650.47
99_G140_V1.0500.46
116_C156_K1.0480.46
134_V169_I1.0470.46
100_Y191_G1.0470.46
37_I95_K1.0450.46
118_V169_I1.0400.46
100_Y136_Q1.0320.45
153_L157_D1.0300.45
148_V154_V1.0270.45
170_C186_I1.0210.44
143_A149_M1.0170.44
137_G188_V1.0150.44
13_T20_D1.0090.44
107_H115_V0.9990.43
118_V134_V0.9870.42
28_Y35_V0.9850.42
98_V193_Y0.9850.42
158_A166_S0.9840.42
76_N79_L0.9810.42
23_R46_T0.9800.42
129_C169_I0.9760.41
145_V166_S0.9690.41
139_K191_G0.9590.40
114_S153_L0.9470.40
36_K48_F0.9460.40
2_N17_S0.9450.40
33_D55_S0.9360.39
39_N44_E0.9260.38
72_V91_D0.9230.38
3_A71_F0.9170.38
35_V145_V0.9130.38
187_L199_F0.9120.37
72_V90_V0.8990.37
41_E85_E0.8950.36
38_F43_K0.8930.36
129_C184_K0.8860.36
131_A188_V0.8770.35
108_P115_V0.8720.35
8_E59_I0.8690.35
4_F9_G0.8670.35
101_V140_V0.8640.35
8_E177_L0.8630.35
50_I78_I0.8620.34
96_F144_K0.8600.34
169_I172_A0.8590.34
107_H163_V0.8570.34
107_H110_A0.8340.33
70_T182_A0.8220.32
53_A78_I0.8220.32
139_K192_D0.8190.32
178_P181_P0.8180.32
52_N56_Y0.8180.32
131_A170_C0.8110.32
133_N174_E0.8100.31
38_F42_T0.8090.31
21_V46_T0.8060.31
36_K84_V0.8040.31
32_G82_N0.8010.31
110_A183_E0.7980.31
112_K183_E0.7970.31
129_C140_V0.7890.30
97_V144_K0.7820.30
39_N46_T0.7790.30
31_H83_G0.7780.30
98_V189_L0.7770.30
99_G169_I0.7750.30
15_L68_S0.7750.30
94_P179_D0.7710.29
104_K116_C0.7710.29
101_V169_I0.7660.29
51_F186_I0.7620.29
71_F156_K0.7600.29
140_V187_L0.7570.29
166_S188_V0.7570.29
116_C169_I0.7500.28
132_P184_K0.7460.28
3_A116_C0.7450.28
149_M160_L0.7420.28
27_G38_F0.7400.28
158_A177_L0.7380.28
31_H87_T0.7370.28
15_L136_Q0.7320.27
76_N112_K0.7310.27
102_E124_T0.7300.27
76_N84_V0.7300.27
34_V67_L0.7260.27
95_K144_K0.7240.27
109_N131_A0.7210.27
5_Y10_V0.7210.27
22_T41_E0.7190.27
2_N108_P0.7160.26
104_K134_V0.7140.26
99_G127_I0.7100.26
57_L74_D0.7100.26
71_F116_C0.7090.26
18_L60_D0.7080.26
118_V184_K0.7040.26
58_T124_T0.7040.26
104_K136_Q0.7030.26
130_G133_N0.7030.26
15_L47_G0.7000.26
132_P179_D0.6990.26
117_K125_L0.6970.25
191_G195_A0.6960.25
134_V170_C0.6940.25
3_A15_L0.6940.25
78_I81_R0.6930.25
117_K147_A0.6930.25
138_Q172_A0.6910.25
38_F41_E0.6890.25
51_F131_A0.6850.25
62_N87_T0.6790.25
138_Q184_K0.6790.25
13_T32_G0.6790.25
70_T80_N0.6760.24
62_N192_D0.6650.24
130_G174_E0.6650.24
172_A184_K0.6630.24
65_V173_K0.6580.24
114_S172_A0.6540.23
101_V144_K0.6530.23
71_F112_K0.6470.23
105_E163_V0.6440.23
93_S135_D0.6440.23
73_Q93_S0.6410.23
119_N195_A0.6410.23
114_S131_A0.6380.23
4_F151_S0.6350.23
55_S124_T0.6340.22
88_L91_D0.6330.22
151_S173_K0.6320.22
101_V156_K0.6270.22
141_V169_I0.6250.22
44_E65_V0.6240.22
2_N158_A0.6240.22
52_N77_E0.6230.22
3_A86_E0.6220.22
171_S176_D0.6210.22
109_N184_K0.6200.22
163_V166_S0.6160.22
97_V137_G0.6150.22
103_S136_Q0.6140.22
112_K184_K0.6130.22
27_G42_T0.6100.21
67_L71_F0.6080.21
60_D73_Q0.6080.21
79_L195_A0.6060.21
128_V185_G0.6040.21
55_S81_R0.6030.21
57_L80_N0.6020.21
143_A150_P0.6020.21
76_N89_V0.5980.21
91_D94_P0.5980.21
76_N86_E0.5960.21
4_F47_G0.5940.21
125_L140_V0.5930.21
106_K112_K0.5920.21
43_K61_E0.5890.21
17_S37_I0.5820.20
171_S186_I0.5770.20
4_F50_I0.5760.20
43_K122_E0.5760.20
114_S134_V0.5750.20
32_G164_P0.5720.20
95_K147_A0.5710.20
77_E85_E0.5700.20
73_Q85_E0.5690.20
37_I125_L0.5680.20
112_K156_K0.5680.20
41_E197_D0.5660.20
56_Y82_N0.5650.20
140_V153_L0.5640.19
32_G137_G0.5610.19
144_K147_A0.5600.19
45_T93_S0.5580.19
9_G159_E0.5570.19
121_G124_T0.5560.19
24_E125_L0.5540.19
42_T45_T0.5490.19
52_N81_R0.5490.19
27_G80_N0.5480.19
109_N177_L0.5470.19
19_Q116_C0.5460.19
138_Q187_L0.5450.19
33_D50_I0.5440.19
48_F86_E0.5430.19
3_A53_A0.5430.19
52_N74_D0.5420.19
116_C134_V0.5390.18
96_F159_E0.5390.18
22_T191_G0.5390.18
12_D149_M0.5370.18
58_T69_E0.5360.18
79_L108_P0.5360.18
118_V186_I0.5330.18
41_E137_G0.5330.18
159_E171_S0.5290.18
91_D144_K0.5280.18
104_K132_P0.5250.18
150_P162_G0.5230.18
153_L184_K0.5220.18
35_V51_F0.5220.18
76_N83_G0.5210.18
145_V173_K0.5200.18
45_T70_T0.5200.18
32_G78_I0.5190.18
153_L159_E0.5180.18
133_N150_P0.5170.18
114_S186_I0.5170.18
107_H181_P0.5130.17
116_C172_A0.5130.17
57_L93_S0.5090.17
131_A161_R0.5080.17
13_T120_V0.5000.17
179_D182_A0.5000.17
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  
3bu2A 3 0.9701 100 0.294 Contact Map
4p72A 2 0.7214 100 0.497 Contact Map
3pcoB 2 0.7214 100 0.501 Contact Map
1b7yB 2 0.7114 100 0.51 Contact Map
2rhqB 2 0.7114 100 0.515 Contact Map
4up7A 2 0.2139 100 0.651 Contact Map
1pybA 2 0.5323 100 0.675 Contact Map
1mkhA 2 0.5274 100 0.679 Contact Map
2e8gA 1 0.8756 99.9 0.682 Contact Map
2cwpA 2 0.5274 99.9 0.684 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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