GREMLIN Database
YHDY - Inner membrane amino-acid ABC transporter permease protein YhdY
UniProt: P45768 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12836
Length: 367 (344)
Sequences: 927 (607)
Seq/√Len: 32.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
183_G195_S5.8851.00
53_L58_L5.3521.00
266_E275_T4.9601.00
54_N59_Q4.9241.00
89_Y101_N4.8101.00
30_S34_N4.7101.00
318_V334_G3.6991.00
161_L311_L3.2661.00
85_G97_R3.1781.00
165_I238_V3.1521.00
300_F345_F2.9681.00
23_W27_N2.7951.00
52_L56_A2.7791.00
43_W47_E2.6961.00
169_G299_L2.6681.00
32_W36_L2.6291.00
35_S39_I2.6131.00
262_Y280_I2.5961.00
159_L341_I2.5501.00
246_V292_L2.5291.00
286_K362_T2.5191.00
271_G274_K2.5141.00
306_V313_D2.3170.99
286_K364_R2.1950.99
329_G333_E2.1580.99
32_W35_S2.1360.99
347_F351_R2.1330.99
210_V237_G2.1040.98
314_L341_I2.1010.98
192_R196_V2.0260.98
221_F349_M2.0090.98
140_L143_G2.0080.98
235_L239_I1.9910.98
249_V295_T1.9790.98
23_W28_L1.9430.97
39_I43_W1.9310.97
256_A287_L1.9140.97
295_T298_A1.8820.97
230_K309_I1.8740.97
83_R324_D1.8540.96
37_L41_C1.8510.96
176_W240_L1.8420.96
301_K304_S1.8400.96
351_R354_Q1.8320.96
20_A24_V1.7970.96
43_W46_W1.7920.96
318_V338_A1.7650.95
293_V302_D1.7520.95
55_W333_E1.7490.95
264_A267_S1.7280.95
126_I130_A1.7100.94
33_S36_L1.7070.94
45_M50_P1.7060.94
86_Q317_S1.6930.94
180_L199_I1.6850.94
300_F349_M1.6730.94
29_F35_S1.6730.94
156_W219_P1.6700.94
42_I46_W1.6670.94
90_G99_R1.6520.93
242_Q298_A1.6450.93
84_F88_M1.6320.93
67_R71_T1.6310.93
64_G78_V1.6150.92
44_L47_E1.6040.92
222_M225_G1.5990.92
250_V285_L1.5880.92
166_A267_S1.5800.92
92_Y99_R1.5730.91
24_V29_F1.5580.91
65_S69_D1.5460.91
174_L246_V1.5350.90
67_R70_C1.5230.90
262_Y275_T1.5150.90
249_V294_N1.4730.88
64_G69_D1.4720.88
162_T314_L1.4570.88
178_I250_V1.4520.88
141_M156_W1.4420.87
79_F321_A1.4280.87
42_I176_W1.4160.86
61_N78_V1.4040.86
333_E356_L1.3840.85
89_Y100_I1.3840.85
293_V353_S1.3660.84
205_V213_M1.3630.84
139_W145_F1.3630.84
53_L57_F1.3630.84
87_F317_S1.3600.84
264_A274_K1.3460.83
294_N304_S1.3370.83
169_G313_D1.3200.82
352_Y355_Y1.3060.81
26_K39_I1.3060.81
20_A52_L1.3030.81
133_Y137_V1.3020.81
292_L299_L1.2870.81
20_A23_W1.2820.80
289_I353_S1.2800.80
272_Y352_Y1.2680.80
40_G48_L1.2630.79
161_L329_G1.2590.79
165_I306_V1.2420.78
159_L314_L1.2390.78
96_Q149_E1.2330.78
179_L294_N1.2310.77
31_S35_S1.2280.77
192_R325_P1.2260.77
199_I247_A1.2200.77
54_N58_L1.2200.77
237_G243_S1.2150.76
173_A242_Q1.2100.76
51_P54_N1.2090.76
304_S314_L1.2070.76
176_W243_S1.2070.76
41_C45_M1.2040.76
64_G71_T1.1980.75
114_M120_P1.1960.75
64_G79_F1.1910.75
155_Q280_I1.1820.74
176_W232_I1.1740.74
100_I160_T1.1730.74
265_A275_T1.1690.74
240_L285_L1.1640.73
118_I122_R1.1590.73
87_F141_M1.1580.73
36_L40_G1.1550.73
177_G246_V1.1550.73
168_V235_L1.1410.72
347_F354_Q1.1310.71
79_F334_G1.1260.71
105_L146_F1.1260.71
314_L338_A1.1230.71
124_R128_A1.1220.71
162_T342_Y1.1170.70
109_V358_K1.1130.70
198_F243_S1.1090.70
296_I302_D1.1080.70
225_G228_I1.1080.70
177_G250_V1.1050.69
142_Y150_R1.0940.69
79_F83_R1.0940.69
215_S230_K1.0930.68
27_N32_W1.0900.68
234_A309_I1.0890.68
205_V209_T1.0870.68
197_I201_F1.0790.67
92_Y98_W1.0770.67
96_Q99_R1.0670.67
193_I197_I1.0660.67
291_G294_N1.0540.66
37_L190_I1.0510.65
51_P59_Q1.0490.65
95_D149_E1.0480.65
168_V172_G1.0440.65
106_I354_Q1.0380.64
211_L305_L1.0380.64
87_F335_Y1.0340.64
322_T335_Y1.0340.64
198_F244_A1.0310.64
59_Q132_I1.0240.63
106_I133_Y1.0220.63
190_I194_L1.0190.63
22_V26_K1.0160.63
170_I299_L1.0120.62
141_M145_F1.0080.62
144_G148_L1.0070.62
159_L162_T0.9900.61
204_G302_D0.9890.61
274_K277_G0.9890.61
288_V304_S0.9830.60
30_S35_S0.9710.59
288_V291_G0.9630.59
249_V291_G0.9620.58
88_M104_L0.9610.58
173_A239_I0.9610.58
128_A132_I0.9580.58
97_R101_N0.9510.58
141_M164_I0.9480.57
153_T231_L0.9470.57
289_I313_D0.9400.57
41_C46_W0.9390.57
112_A116_W0.9360.56
153_T229_D0.9320.56
267_S274_K0.9320.56
170_I297_I0.9290.56
32_W38_T0.9280.56
228_I232_I0.9270.56
136_I140_L0.9220.55
272_Y276_Q0.9210.55
289_I356_L0.9200.55
308_I313_D0.9130.54
41_C50_P0.9120.54
230_K319_Q0.9080.54
213_M308_I0.9070.54
252_G301_K0.9000.53
169_G235_L0.8950.53
65_S68_A0.8910.53
103_A110_S0.8890.52
216_V335_Y0.8870.52
83_R174_L0.8810.52
293_V360_F0.8810.52
49_I53_L0.8740.51
140_L145_F0.8740.51
257_L280_I0.8720.51
161_L333_E0.8690.51
289_I293_V0.8680.51
26_K46_W0.8650.50
20_A26_K0.8590.50
354_Q358_K0.8490.49
128_A280_I0.8440.49
202_W210_V0.8380.48
169_G238_V0.8350.48
267_S311_L0.8340.48
230_K234_A0.8320.48
244_A305_L0.8320.48
302_D353_S0.8320.48
21_M24_V0.8310.48
79_F324_D0.8310.48
83_R86_Q0.8280.47
46_W50_P0.8210.47
219_P237_G0.8200.47
90_G93_P0.8190.47
40_G44_L0.8170.46
61_N72_K0.8170.46
242_Q309_I0.8170.46
91_L155_Q0.8160.46
34_N46_W0.8160.46
90_G98_W0.8150.46
270_L274_K0.8140.46
58_L65_S0.8090.46
93_P98_W0.8080.46
212_F252_G0.8000.45
285_L342_Y0.7980.45
297_I349_M0.7970.45
45_M56_A0.7940.45
273_W276_Q0.7910.44
156_W230_K0.7880.44
315_F335_Y0.7830.44
24_V41_C0.7790.43
201_F209_T0.7740.43
50_P54_N0.7740.43
30_S43_W0.7690.43
232_I257_L0.7680.42
47_E50_P0.7680.42
262_Y266_E0.7660.42
21_M25_R0.7660.42
142_Y145_F0.7630.42
22_V25_R0.7610.42
343_W347_F0.7610.42
110_S164_I0.7590.42
80_I171_A0.7590.42
77_W90_G0.7560.42
242_Q295_T0.7540.41
326_A348_S0.7540.41
196_V199_I0.7530.41
31_S345_F0.7530.41
64_G67_R0.7520.41
61_N73_A0.7510.41
33_S37_L0.7510.41
70_C301_K0.7510.41
118_I121_H0.7500.41
108_L112_A0.7480.41
307_I312_F0.7470.41
32_W179_L0.7450.41
23_W32_W0.7430.40
43_W202_W0.7420.40
316_S320_Q0.7390.40
39_I225_G0.7380.40
302_D305_L0.7370.40
130_A134_P0.7350.40
108_L225_G0.7340.40
95_D99_R0.7320.40
134_P143_G0.7310.40
361_N364_R0.7280.39
294_N354_Q0.7280.39
42_I50_P0.7280.39
36_L80_I0.7270.39
245_Y253_G0.7270.39
178_I281_L0.7260.39
60_A80_I0.7260.39
345_F349_M0.7260.39
114_M130_A0.7250.39
38_T45_M0.7240.39
125_Y130_A0.7230.39
248_E261_Q0.7230.39
293_V300_F0.7220.39
70_C76_C0.7200.39
45_M73_A0.7190.39
320_Q323_V0.7180.38
296_I345_F0.7180.38
325_P342_Y0.7160.38
267_S307_I0.7130.38
40_G149_E0.7130.38
207_L241_F0.7120.38
288_V301_K0.7120.38
26_K139_W0.7110.38
248_E251_R0.7110.38
180_L243_S0.7100.38
122_R195_S0.7060.38
172_G239_I0.7040.37
170_I270_L0.7040.37
249_V301_K0.7030.37
26_K30_S0.7000.37
219_P255_Q0.6990.37
31_S188_M0.6970.37
21_M48_L0.6970.37
264_A324_D0.6940.37
88_M100_I0.6910.36
87_F160_T0.6910.36
70_C78_V0.6910.36
208_I298_A0.6870.36
89_Y120_P0.6860.36
44_L49_I0.6830.36
175_P199_I0.6800.36
246_V295_T0.6780.35
71_T329_G0.6770.35
199_I255_Q0.6760.35
218_L229_D0.6750.35
40_G58_L0.6750.35
213_M299_L0.6750.35
77_W99_R0.6750.35
340_L344_I0.6750.35
185_R246_V0.6740.35
57_F362_T0.6730.35
249_V288_V0.6720.35
315_F324_D0.6710.35
214_S224_E0.6710.35
335_Y339_A0.6700.35
46_W326_A0.6690.35
40_G163_L0.6690.35
166_A339_A0.6650.34
227_S308_I0.6650.34
113_P125_Y0.6650.34
254_L284_A0.6630.34
26_K127_A0.6630.34
143_G148_L0.6620.34
132_I187_H0.6620.34
93_P222_M0.6620.34
232_I280_I0.6620.34
277_G343_W0.6590.34
188_M349_M0.6580.34
209_T236_V0.6560.34
292_L310_G0.6540.34
34_N196_V0.6520.33
196_V200_E0.6520.33
134_P140_L0.6510.33
171_A240_L0.6500.33
124_R257_L0.6490.33
38_T42_I0.6470.33
169_G296_I0.6450.33
314_L342_Y0.6400.33
22_V53_L0.6400.33
205_V221_F0.6400.33
193_I259_K0.6390.32
164_I257_L0.6390.32
43_W57_F0.6390.32
208_I302_D0.6380.32
304_S342_Y0.6380.32
44_L73_A0.6370.32
120_P160_T0.6370.32
279_V353_S0.6370.32
141_M160_T0.6360.32
271_G275_T0.6360.32
261_Q282_P0.6350.32
321_A334_G0.6310.32
43_W48_L0.6310.32
155_Q309_I0.6300.32
63_V68_A0.6290.32
242_Q299_L0.6290.32
168_V237_G0.6280.32
230_K299_L0.6280.32
110_S304_S0.6260.32
109_V129_W0.6260.32
62_W67_R0.6240.31
209_T213_M0.6240.31
127_A131_V0.6240.31
213_M216_V0.6220.31
328_L333_E0.6210.31
36_L348_S0.6170.31
276_Q309_I0.6150.31
234_A303_T0.6140.31
107_G165_I0.6140.31
310_G316_S0.6130.31
231_L324_D0.6090.30
83_R160_T0.6080.30
107_G133_Y0.6080.30
210_V219_P0.6070.30
244_A289_I0.6070.30
131_V135_L0.6020.30
228_I326_A0.6010.30
24_V36_L0.6010.30
350_S353_S0.6010.30
343_W357_E0.6000.30
45_M115_F0.5960.29
300_F337_F0.5930.29
54_N187_H0.5930.29
109_V238_V0.5930.29
130_A140_L0.5920.29
321_A356_L0.5910.29
169_G309_I0.5910.29
189_P193_I0.5890.29
160_T165_I0.5890.29
198_F304_S0.5880.29
114_M174_L0.5870.29
218_L358_K0.5850.29
41_C198_F0.5850.29
207_L302_D0.5850.29
214_S301_K0.5840.29
100_I277_G0.5840.29
87_F97_R0.5830.29
80_I148_L0.5800.28
78_V82_E0.5780.28
160_T209_T0.5780.28
173_A333_E0.5770.28
83_R91_L0.5770.28
105_L135_L0.5760.28
30_S267_S0.5760.28
195_S276_Q0.5750.28
103_A196_V0.5750.28
297_I353_S0.5740.28
30_S33_S0.5740.28
169_G242_Q0.5730.28
250_V284_A0.5720.28
49_I197_I0.5720.28
215_S327_W0.5700.28
26_K132_I0.5690.28
44_L58_L0.5680.28
40_G43_W0.5670.27
251_R261_Q0.5630.27
169_G197_I0.5620.27
154_R320_Q0.5620.27
133_Y326_A0.5620.27
21_M341_I0.5620.27
31_S34_N0.5620.27
124_R127_A0.5610.27
296_I299_L0.5610.27
284_A305_L0.5590.27
222_M265_A0.5590.27
81_H359_R0.5570.27
177_G278_L0.5540.27
165_I359_R0.5540.27
106_I137_V0.5520.27
260_G263_E0.5500.26
48_L336_V0.5490.26
309_I319_Q0.5480.26
103_A107_G0.5470.26
89_Y94_H0.5450.26
331_S335_Y0.5440.26
184_R200_E0.5400.26
289_I349_M0.5400.26
42_I68_A0.5390.26
209_T279_V0.5390.26
239_I324_D0.5380.26
136_I139_W0.5370.26
168_V340_L0.5370.26
162_T341_I0.5360.25
183_G189_P0.5360.25
106_I109_V0.5360.25
164_I354_Q0.5350.25
342_Y356_L0.5340.25
297_I305_L0.5340.25
278_L289_I0.5330.25
216_V230_K0.5320.25
300_F350_S0.5320.25
358_K363_G0.5320.25
31_S59_Q0.5310.25
168_V222_M0.5300.25
55_W311_L0.5290.25
169_G289_I0.5280.25
156_W159_L0.5270.25
24_V27_N0.5250.25
171_A286_K0.5240.25
154_R319_Q0.5240.25
207_L237_G0.5240.25
248_E282_P0.5230.25
156_W220_L0.5220.25
304_S340_L0.5220.25
108_L201_F0.5210.25
243_S315_F0.5210.25
45_M145_F0.5210.25
264_A333_E0.5210.25
34_N289_I0.5190.24
157_G233_R0.5180.24
88_M102_L0.5180.24
103_A128_A0.5180.24
164_I302_D0.5180.24
37_L67_R0.5170.24
167_S171_A0.5160.24
135_L279_V0.5160.24
315_F338_A0.5160.24
236_V276_Q0.5160.24
259_K266_E0.5150.24
196_V222_M0.5140.24
257_L287_L0.5140.24
38_T44_L0.5140.24
39_I326_A0.5130.24
214_S309_I0.5110.24
97_R104_L0.5090.24
279_V317_S0.5090.24
222_M279_V0.5090.24
112_A351_R0.5080.24
264_A294_N0.5080.24
90_G207_L0.5060.24
44_L48_L0.5060.24
91_L96_Q0.5050.24
52_L57_F0.5030.23
21_M68_A0.5030.23
40_G51_P0.5030.23
238_V313_D0.5030.23
319_Q322_T0.5010.23
191_V309_I0.5010.23
195_S313_D0.5010.23
347_F350_S0.5010.23
301_K319_Q0.5000.23
277_G280_I0.5000.23
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  
4ymuD 2 0.5858 100 0.762 Contact Map
3tuiA 2 0.5695 99.9 0.788 Contact Map
2onkC 2 0.6649 99.9 0.799 Contact Map
3d31C 2 0.6376 99.9 0.801 Contact Map
3rlfF 1 0.8665 99.9 0.813 Contact Map
3rlfG 1 0.6975 99.8 0.819 Contact Map
4tquM 1 0.7003 99.8 0.82 Contact Map
4tquN 1 0.7139 99.7 0.844 Contact Map
2m7cA 1 0.0545 7.4 0.978 Contact Map
3mktA 1 0.2262 6.3 0.979 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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