GREMLIN Database
YTRD - Probable ABC transporter permease YtrD
UniProt: O34953 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 325 (311)
Sequences: 584 (479)
Seq/√Len: 27.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
104_F248_G6.5551.00
111_G156_Y4.4411.00
10_E107_K4.2071.00
116_V149_I3.8901.00
108_F157_S3.8881.00
26_I122_G3.6121.00
240_M244_F3.6031.00
84_E255_M3.5151.00
274_Q315_Y3.4461.00
302_G306_G3.2631.00
85_R163_G3.2471.00
105_H245_Y3.1121.00
163_G172_Q3.0001.00
285_F302_G2.8331.00
150_I241_T2.7691.00
94_L252_F2.7511.00
90_F257_N2.6690.99
273_V279_I2.6370.99
101_G249_Y2.5020.99
80_Q156_Y2.4980.99
185_L279_I2.4700.99
94_L257_N2.3760.99
156_Y166_T2.3670.99
112_G116_V2.3530.99
101_G253_V2.3230.98
81_L160_M2.3060.98
121_I124_V2.1250.97
100_R103_I2.0840.97
178_T279_I2.0400.96
83_I118_P1.9900.96
282_I285_F1.9660.96
167_G261_G1.9480.95
9_K84_E1.9460.95
84_E107_K1.9420.95
178_T273_V1.9410.95
158_L186_L1.9250.95
83_I255_M1.9130.95
104_F166_T1.9090.95
19_V75_V1.8870.94
99_T253_V1.8840.94
281_G307_A1.8700.94
82_G172_Q1.8260.93
94_L103_I1.8100.93
277_V302_G1.7830.93
96_L103_I1.7360.92
77_A285_F1.7310.91
162_G166_T1.7280.91
84_E260_N1.7250.91
165_L175_V1.7020.91
21_T25_F1.6900.90
255_M260_N1.6780.90
85_R172_Q1.6320.89
68_L153_M1.6220.88
297_A301_I1.6150.88
7_L110_T1.5950.88
313_I317_A1.5800.87
247_I254_K1.5310.85
108_F156_Y1.5260.85
176_S183_P1.5130.85
255_M315_Y1.5080.84
215_Y218_P1.4920.84
115_I152_S1.4840.83
171_A197_L1.4840.83
12_R15_K1.4790.83
185_L189_L1.4650.83
22_I121_I1.4640.83
91_D95_S1.4500.82
306_G310_G1.4450.82
84_E163_G1.4420.82
92_F198_F1.4400.82
84_E93_T1.4190.81
165_L270_N1.4100.80
93_T255_M1.3770.79
81_L163_G1.3580.78
182_S186_L1.3500.77
9_K13_Q1.3450.77
177_F310_G1.3420.77
217_I220_I1.3400.77
91_D263_F1.3360.76
149_I238_A1.3250.76
94_L315_Y1.3160.75
84_E110_T1.3160.75
9_K93_T1.2990.74
197_L300_L1.2970.74
314_S318_I1.2840.73
6_L103_I1.2820.73
189_L284_G1.2760.73
279_I282_I1.2700.73
6_L85_R1.2600.72
157_S241_T1.2560.72
11_W19_V1.2500.71
178_T181_I1.2490.71
27_L31_L1.2420.71
279_I318_I1.2410.71
107_K110_T1.2410.71
26_I190_P1.2380.71
16_V111_G1.2370.71
234_L283_M1.2310.70
9_K260_N1.2250.70
70_W272_P1.2210.70
89_F93_T1.2170.69
284_G302_G1.2100.69
174_L178_T1.1980.68
200_G311_F1.1860.67
239_I246_I1.1830.67
113_M121_I1.1700.66
45_T238_A1.1700.66
112_G153_M1.1650.66
310_G314_S1.1610.66
85_R260_N1.1520.65
182_S279_I1.1480.65
94_L118_P1.1460.65
96_L255_M1.1440.64
216_F220_I1.1360.64
83_I94_L1.1320.64
12_R267_K1.1320.64
123_Y145_S1.1300.63
39_I242_I1.1290.63
161_A244_F1.1260.63
259_R270_N1.1210.63
83_I93_T1.1180.63
152_S165_L1.1070.62
82_G169_S1.1070.62
15_K18_L1.1050.62
92_F110_T1.1030.61
40_Y87_K1.0970.61
311_F320_K1.0960.61
113_M138_A1.0930.61
9_K14_N1.0860.60
171_A263_F1.0810.60
76_L115_I1.0760.60
298_G302_G1.0710.59
200_G316_F1.0690.59
92_F222_V1.0640.59
104_F218_P1.0420.57
6_L107_K1.0400.57
141_F144_Y1.0360.57
239_I243_I1.0310.56
146_L150_I1.0230.56
75_V184_F1.0200.55
5_G14_N1.0200.55
171_A261_G1.0180.55
125_L233_Y1.0080.54
130_I135_P1.0060.54
146_L242_I1.0030.54
24_V102_Q1.0030.54
103_I107_K0.9930.53
147_G234_L0.9870.53
84_E263_F0.9830.53
23_L256_S0.9790.52
13_Q91_D0.9760.52
6_L157_S0.9700.52
182_S320_K0.9660.51
300_L304_G0.9650.51
85_R255_M0.9640.51
318_I321_K0.9640.51
14_N80_Q0.9590.51
316_F320_K0.9540.50
16_V180_A0.9490.50
280_I284_G0.9460.50
162_G179_V0.9450.50
9_K91_D0.9410.49
309_I317_A0.9380.49
94_L97_P0.9360.49
48_E146_L0.9350.49
6_L93_T0.9270.48
133_L165_L0.9230.48
30_P310_G0.9220.48
103_I252_F0.9220.48
82_G85_R0.9200.48
111_G252_F0.9190.48
77_A159_V0.9170.48
98_Y234_L0.9140.47
90_F94_L0.9140.47
81_L85_R0.9130.47
255_M263_F0.9130.47
84_E89_F0.9120.47
165_L171_A0.9100.47
273_V277_V0.9100.47
77_A155_A0.9070.47
15_K91_D0.9010.46
23_L113_M0.9000.46
85_R277_V0.8990.46
178_T311_F0.8970.46
177_F305_T0.8900.46
125_L187_I0.8870.45
7_L11_W0.8850.45
10_E110_T0.8850.45
85_R98_Y0.8830.45
97_P287_Y0.8830.45
121_I228_E0.8830.45
260_N315_Y0.8810.45
107_K260_N0.8750.44
276_I310_G0.8750.44
24_V116_V0.8710.44
201_S304_G0.8670.44
27_L301_I0.8670.44
165_L251_S0.8590.43
161_A178_T0.8580.43
281_G287_Y0.8560.43
91_D255_M0.8530.43
182_S269_L0.8510.43
80_Q115_I0.8490.43
185_L284_G0.8430.42
87_K171_A0.8390.42
99_T249_Y0.8380.42
31_L138_A0.8370.42
119_Q145_S0.8360.42
152_S321_K0.8360.42
8_Y11_W0.8340.41
124_V242_I0.8300.41
167_G258_E0.8260.41
28_G57_S0.8250.41
100_R252_F0.8190.40
295_S300_L0.8190.40
98_Y305_T0.8190.40
42_G124_V0.8150.40
195_E278_I0.8140.40
87_K91_D0.8130.40
81_L164_A0.8110.40
178_T269_L0.8050.39
10_E84_E0.8050.39
146_L234_L0.8040.39
15_K180_A0.8040.39
132_L186_L0.8030.39
9_K263_F0.8030.39
161_A255_M0.8030.39
255_M265_L0.7970.39
11_W275_I0.7960.39
39_I251_S0.7940.39
253_V257_N0.7940.39
238_A293_S0.7900.38
190_P194_L0.7900.38
193_N197_L0.7870.38
133_L307_A0.7870.38
26_I292_A0.7840.38
256_S259_R0.7810.38
94_L255_M0.7790.37
234_L238_A0.7760.37
144_Y257_N0.7750.37
33_I276_I0.7710.37
316_F321_K0.7710.37
264_F270_N0.7600.36
92_F125_L0.7590.36
281_G288_F0.7590.36
270_N318_I0.7560.36
82_G108_F0.7510.36
165_L269_L0.7510.36
68_L170_F0.7500.35
73_G77_A0.7420.35
66_I139_V0.7410.35
122_G125_L0.7410.35
38_L170_F0.7390.35
72_W155_A0.7380.35
276_I280_I0.7330.34
289_G305_T0.7320.34
159_V176_S0.7320.34
37_Y242_I0.7310.34
116_V177_F0.7310.34
11_W134_K0.7300.34
17_A116_V0.7300.34
288_F302_G0.7290.34
200_G320_K0.7280.34
76_L104_F0.7260.34
33_I281_G0.7210.33
191_V205_I0.7180.33
186_L309_I0.7170.33
128_L235_V0.7160.33
80_Q88_S0.7160.33
203_D235_V0.7150.33
37_Y133_L0.7120.33
211_K304_G0.7110.33
21_T84_E0.7100.33
282_I311_F0.7050.32
91_D262_Y0.7040.32
70_W245_Y0.7000.32
310_G316_F0.6970.32
127_V304_G0.6950.32
174_L273_V0.6950.32
109_L239_I0.6920.32
161_A251_S0.6920.32
75_V228_E0.6910.31
55_V58_V0.6910.31
129_L231_P0.6840.31
104_F108_F0.6800.31
179_V185_L0.6790.31
71_I276_I0.6780.31
17_A165_L0.6780.31
160_M184_F0.6760.30
31_L133_L0.6750.30
259_R262_Y0.6750.30
90_F255_M0.6750.30
4_S34_L0.6740.30
119_Q137_Q0.6740.30
127_V242_I0.6730.30
240_M307_A0.6730.30
78_V85_R0.6720.30
142_H146_L0.6700.30
146_L297_A0.6640.30
30_P218_P0.6620.30
35_N300_L0.6600.29
189_L218_P0.6580.29
210_P293_S0.6560.29
123_Y141_F0.6500.29
81_L98_Y0.6490.29
62_N71_I0.6490.29
146_L247_I0.6490.29
134_K137_Q0.6460.29
73_G100_R0.6440.28
113_M238_A0.6410.28
99_T212_W0.6390.28
27_L305_T0.6380.28
46_G239_I0.6360.28
196_I256_S0.6340.28
183_P279_I0.6300.28
118_P121_I0.6300.28
99_T201_S0.6300.28
72_W195_E0.6290.28
97_P118_P0.6290.28
301_I317_A0.6270.27
200_G237_P0.6270.27
156_Y253_V0.6260.27
177_F273_V0.6260.27
84_E315_Y0.6240.27
148_M308_V0.6230.27
259_R264_F0.6230.27
103_I273_V0.6200.27
93_T107_K0.6170.27
162_G302_G0.6160.27
25_F119_Q0.6160.27
84_E168_N0.6160.27
61_L239_I0.6140.27
182_S273_V0.6120.27
193_N307_A0.6100.26
82_G86_S0.6090.26
80_Q183_P0.6040.26
93_T260_N0.6020.26
185_L271_R0.6020.26
159_V163_G0.6010.26
73_G255_M0.6010.26
170_F266_W0.6010.26
177_F219_I0.6000.26
264_F273_V0.5990.26
268_P313_I0.5990.26
199_G222_V0.5990.26
75_V113_M0.5960.26
26_I309_I0.5960.26
43_C248_G0.5940.26
108_F222_V0.5920.25
34_L234_L0.5900.25
236_I313_I0.5900.25
32_S117_V0.5900.25
131_M243_I0.5890.25
113_M227_A0.5890.25
66_I72_W0.5870.25
73_G162_G0.5870.25
70_W196_I0.5860.25
280_I283_M0.5850.25
18_L284_G0.5840.25
44_V77_A0.5830.25
177_F300_L0.5830.25
235_V308_V0.5820.25
80_Q311_F0.5820.25
285_F310_G0.5820.25
210_P243_I0.5770.25
80_Q107_K0.5760.24
97_P264_F0.5740.24
267_K296_F0.5730.24
26_I252_F0.5730.24
43_C128_L0.5690.24
165_L268_P0.5660.24
242_I254_K0.5660.24
277_V281_G0.5660.24
172_Q277_V0.5650.24
77_A108_F0.5640.24
16_V277_V0.5640.24
238_A307_A0.5610.24
163_G175_V0.5610.24
160_M164_A0.5600.24
54_C129_L0.5590.24
103_I321_K0.5590.24
109_L117_V0.5580.23
242_I253_V0.5580.23
301_I305_T0.5570.23
158_L274_Q0.5560.23
280_I310_G0.5550.23
240_M291_T0.5550.23
211_K225_K0.5530.23
126_S129_L0.5520.23
15_K262_Y0.5510.23
87_K132_L0.5500.23
74_V304_G0.5480.23
93_T161_A0.5480.23
81_L104_F0.5480.23
91_D97_P0.5460.23
63_S67_S0.5450.23
78_V111_G0.5440.23
42_G243_I0.5440.23
96_L273_V0.5430.23
124_V234_L0.5420.23
116_V139_V0.5410.23
4_S256_S0.5400.23
144_Y156_Y0.5390.22
89_F182_S0.5380.22
86_S281_G0.5380.22
42_G204_F0.5370.22
86_S173_L0.5340.22
182_S201_S0.5340.22
30_P126_S0.5330.22
264_F269_L0.5330.22
75_V192_I0.5320.22
6_L98_Y0.5320.22
59_D227_A0.5300.22
123_Y144_Y0.5290.22
85_R107_K0.5290.22
21_T30_P0.5290.22
238_A268_P0.5270.22
140_Y145_S0.5270.22
91_D257_N0.5260.22
25_F144_Y0.5260.22
47_K239_I0.5240.22
143_N246_I0.5240.22
183_P305_T0.5240.22
175_V311_F0.5240.22
157_S245_Y0.5220.22
174_L276_I0.5220.22
202_I214_Q0.5220.22
80_Q111_G0.5210.22
212_W225_K0.5190.21
303_M319_Y0.5190.21
67_S113_M0.5190.21
213_V235_V0.5180.21
85_R92_F0.5170.21
82_G299_Y0.5170.21
162_G165_L0.5170.21
177_F181_I0.5170.21
228_E232_Y0.5150.21
68_L276_I0.5140.21
279_I311_F0.5130.21
245_Y254_K0.5120.21
238_A287_Y0.5120.21
193_N301_I0.5120.21
194_L305_T0.5110.21
130_I141_F0.5100.21
99_T154_L0.5100.21
5_G9_K0.5100.21
178_T189_L0.5090.21
111_G168_N0.5090.21
294_E308_V0.5080.21
160_M180_A0.5080.21
6_L101_G0.5080.21
178_T280_I0.5080.21
117_V307_A0.5070.21
141_F243_I0.5070.21
65_F177_F0.5050.21
73_G163_G0.5040.21
59_D309_I0.5040.21
153_M241_T0.5040.21
83_I89_F0.5040.21
204_F247_I0.5040.21
161_A279_I0.5020.21
152_S200_G0.5020.21
101_G105_H0.5020.21
4_S85_R0.5010.21
24_V29_N0.5010.21
164_A252_F0.5000.20
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  
2xq2A 2 0.2462 58.2 0.936 Contact Map
2nwlA 3 0.6954 37.6 0.943 Contact Map
2mfrA 1 0.1569 26.8 0.948 Contact Map
4av3A 2 0.2769 16.5 0.953 Contact Map
3dh4A 3 0.1877 13.4 0.954 Contact Map
2cfqA 1 0.7723 7.6 0.959 Contact Map
4c7rA 3 0.6985 5.3 0.962 Contact Map
4a01A 2 0.3015 3.8 0.964 Contact Map
3hd7A 1 0.1046 3.7 0.965 Contact Map
4o9uB 2 0.2585 3.4 0.965 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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