GREMLIN Database
YAFD - UPF0294 protein YafD
UniProt: P0A8U2 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11650
Length: 266 (231)
Sequences: 248 (199)
Seq/√Len: 13.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
232_V257_V6.8811.00
216_F255_L4.3141.00
234_Y259_F3.6640.99
45_R258_E3.1930.98
129_P170_Q3.0690.97
178_I231_F2.7510.94
134_A170_Q2.6910.94
239_V257_V2.6800.94
66_Y158_V2.5610.92
151_M181_H2.4560.90
214_V257_V2.3010.87
46_I74_L2.2770.86
62_V247_T2.2630.86
137_A174_I2.1870.84
59_W129_P2.0190.79
139_V177_Q1.9810.77
100_A133_L1.9180.75
211_L235_R1.9160.75
202_L216_F1.8990.74
39_S145_P1.8900.74
193_A231_F1.8590.72
48_V249_A1.8250.71
167_Y193_A1.7800.69
59_W170_Q1.7620.68
87_F93_L1.7600.68
108_S174_I1.7530.68
55_Q111_M1.7420.67
71_H115_A1.7080.66
114_S127_R1.7030.65
155_I257_V1.6770.64
42_E145_P1.6650.64
238_N260_S1.6640.64
138_L234_Y1.6630.64
55_Q224_A1.6540.63
67_G217_T1.6510.63
52_Y56_R1.6170.61
47_L70_A1.6080.61
120_Y158_V1.5590.58
178_I244_V1.5420.57
161_S205_F1.5310.57
216_F257_V1.5200.56
63_L122_C1.5050.56
54_Q100_A1.4910.55
74_L188_A1.4820.54
193_A233_F1.4660.54
36_E114_S1.4490.53
72_L152_V1.4320.52
97_Q136_S1.4220.51
36_E143_P1.4100.51
59_W101_F1.4070.50
175_G205_F1.4020.50
74_L152_V1.3810.49
63_L78_A1.3700.49
99_P202_L1.3590.48
178_I185_V1.3580.48
108_S133_L1.3460.47
58_E248_R1.3340.47
47_L195_S1.3290.46
171_L238_N1.3220.46
48_V136_S1.3160.46
129_P134_A1.3140.46
67_G158_V1.3140.46
123_P231_F1.3060.45
193_A224_A1.2950.45
158_V210_S1.2860.44
66_Y222_R1.2850.44
196_R207_R1.2840.44
254_P259_F1.2650.43
137_A151_M1.2620.43
137_A155_I1.2560.43
144_L178_I1.2520.42
65_N68_K1.2470.42
151_M249_A1.2450.42
100_A136_S1.2390.42
40_T44_I1.2320.41
122_C130_I1.2320.41
240_S260_S1.2240.41
39_S112_T1.2230.41
48_V74_L1.2090.40
214_V239_V1.2070.40
144_L147_T1.1910.39
136_S249_A1.1870.39
112_T140_T1.1820.39
170_Q221_R1.1780.39
129_P221_R1.1700.38
32_L158_V1.1680.38
217_T256_L1.1670.38
138_L193_A1.1570.38
114_S119_V1.1440.37
211_L236_G1.1420.37
97_Q100_A1.1400.37
144_L152_V1.1370.37
111_M224_A1.1190.36
176_D238_N1.1190.36
146_D238_N1.1130.35
129_P226_G1.1090.35
54_Q72_L1.1060.35
63_L100_A1.1060.35
151_M244_V1.1020.35
170_Q219_D1.1000.35
232_V256_L1.0980.35
64_K130_I1.0960.35
117_H178_I1.0900.34
216_F256_L1.0880.34
39_S42_E1.0840.34
157_A191_F1.0690.33
78_A242_A1.0670.33
144_L237_L1.0530.33
78_A253_N1.0510.33
181_H226_G1.0490.32
232_V255_L1.0400.32
200_N241_E1.0340.32
123_P144_L1.0320.32
122_C131_L1.0180.31
203_Y207_R1.0130.31
97_Q195_S1.0090.31
32_L35_G1.0090.31
212_R242_A0.9990.30
72_L184_P0.9970.30
64_K92_Y0.9920.30
46_I217_T0.9860.30
176_D180_H0.9840.30
42_E144_L0.9790.29
100_A221_R0.9770.29
170_Q226_G0.9770.29
100_A259_F0.9770.29
95_A113_L0.9750.29
37_P173_P0.9730.29
120_Y141_V0.9720.29
79_Q108_S0.9710.29
113_L167_Y0.9710.29
119_V178_I0.9630.29
162_L202_L0.9610.29
58_E249_A0.9580.28
187_M211_L0.9570.28
138_L155_I0.9470.28
94_A97_Q0.9460.28
100_A122_C0.9420.28
82_P228_P0.9410.28
112_T175_G0.9360.28
63_L219_D0.9310.27
117_H196_R0.9300.27
96_D118_P0.9290.27
30_Q35_G0.9290.27
100_A247_T0.9270.27
86_Q208_E0.9180.27
164_V195_S0.9170.27
72_L181_H0.9120.27
162_L171_L0.9100.26
122_C219_D0.9070.26
234_Y239_V0.9040.26
103_L111_M0.8990.26
200_N207_R0.8970.26
118_P221_R0.8970.26
155_I202_L0.8930.26
54_Q138_L0.8870.25
41_E112_T0.8850.25
105_Q126_E0.8830.25
207_R212_R0.8780.25
68_K182_S0.8750.25
59_W152_V0.8700.25
243_S248_R0.8670.25
54_Q226_G0.8600.24
89_T239_V0.8460.24
187_M222_R0.8450.24
104_P112_T0.8440.24
162_L167_Y0.8360.24
101_F170_Q0.8330.23
78_A198_R0.8290.23
118_P144_L0.8280.23
74_L167_Y0.8260.23
55_Q118_P0.8220.23
73_V239_V0.8210.23
170_Q249_A0.8190.23
84_L88_A0.8160.23
167_Y188_A0.8150.23
78_A152_V0.8150.23
100_A113_L0.8130.23
45_R233_F0.8130.23
230_D252_H0.8110.23
63_L163_G0.8070.22
182_S212_R0.8010.22
36_E204_R0.8000.22
242_A254_P0.7970.22
46_I196_R0.7970.22
47_L181_H0.7960.22
139_V225_F0.7910.22
54_Q234_Y0.7890.22
192_N251_D0.7890.22
157_A195_S0.7880.22
97_Q161_S0.7880.22
194_W198_R0.7780.21
55_Q244_V0.7750.21
51_I54_Q0.7720.21
54_Q247_T0.7720.21
169_K260_S0.7660.21
54_Q219_D0.7650.21
46_I68_K0.7650.21
223_R257_V0.7640.21
87_F140_T0.7620.21
185_V209_M0.7580.21
93_L244_V0.7570.21
217_T255_L0.7530.21
237_L259_F0.7520.21
143_P228_P0.7480.20
168_S238_N0.7470.20
100_A108_S0.7460.20
161_S166_V0.7450.20
52_Y226_G0.7450.20
56_R191_F0.7450.20
178_I238_N0.7420.20
164_V200_N0.7410.20
72_L116_A0.7410.20
232_V239_V0.7350.20
206_A227_R0.7310.20
115_A200_N0.7310.20
48_V66_Y0.7300.20
214_V258_E0.7280.20
97_Q164_V0.7250.20
201_A215_R0.7230.20
171_L195_S0.7230.20
125_R161_S0.7220.19
31_A158_V0.7210.19
84_L126_E0.7190.19
103_L258_E0.7190.19
118_P139_V0.7150.19
44_I173_P0.7120.19
101_F134_A0.7120.19
107_P206_A0.7110.19
39_S44_I0.7110.19
72_L237_L0.7080.19
63_L253_N0.7070.19
150_L171_L0.7060.19
100_A234_Y0.7050.19
75_L198_R0.7020.19
131_L163_G0.7020.19
173_P211_L0.7020.19
55_Q205_F0.7010.19
58_E178_I0.7010.19
146_D242_A0.6950.19
86_Q223_R0.6900.18
84_L132_R0.6900.18
87_F245_L0.6860.18
43_R199_M0.6860.18
59_W134_A0.6830.18
136_S234_Y0.6810.18
71_H139_V0.6810.18
32_L140_T0.6810.18
125_R227_R0.6760.18
117_H158_V0.6720.18
95_A162_L0.6710.18
188_A205_F0.6590.18
175_G208_E0.6580.17
185_V225_F0.6540.17
182_S204_R0.6530.17
101_F221_R0.6520.17
100_A249_A0.6470.17
48_V97_Q0.6440.17
174_I209_M0.6440.17
95_A98_V0.6420.17
214_V234_Y0.6420.17
69_D178_I0.6400.17
100_A219_D0.6390.17
46_I114_S0.6360.17
99_P216_F0.6360.17
136_S188_A0.6360.17
74_L124_L0.6350.17
54_Q62_V0.6320.17
230_D251_D0.6310.17
48_V137_A0.6300.17
100_A170_Q0.6290.17
230_D250_S0.6290.17
90_A239_V0.6280.17
45_R71_H0.6260.17
70_A256_L0.6230.16
51_I198_R0.6220.16
126_E253_N0.6190.16
202_L206_A0.6190.16
45_R69_D0.6170.16
60_L169_K0.6120.16
148_R212_R0.5980.16
82_P177_Q0.5960.16
86_Q89_T0.5950.16
196_R214_V0.5910.16
121_C244_V0.5890.15
172_L255_L0.5880.15
54_Q113_L0.5860.15
48_V188_A0.5840.15
120_Y185_V0.5820.15
133_L136_S0.5810.15
54_Q136_S0.5800.15
133_L167_Y0.5770.15
118_P213_Q0.5770.15
217_T241_E0.5700.15
145_P177_Q0.5700.15
32_L106_H0.5660.15
54_Q170_Q0.5640.15
70_A153_V0.5590.15
119_V199_M0.5580.15
111_M139_V0.5570.15
245_L256_L0.5550.15
41_E46_I0.5530.15
51_I118_P0.5530.15
63_L74_L0.5510.14
47_L150_L0.5510.14
70_A114_S0.5490.14
220_Q249_A0.5440.14
46_I93_L0.5400.14
228_P254_P0.5400.14
187_M206_A0.5380.14
132_R200_N0.5380.14
39_S144_L0.5370.14
99_P233_F0.5350.14
186_I259_F0.5330.14
40_T204_R0.5330.14
30_Q140_T0.5320.14
199_M236_G0.5300.14
80_T162_L0.5290.14
204_R207_R0.5280.14
97_Q118_P0.5260.14
182_S215_R0.5250.14
124_L140_T0.5250.14
69_D153_V0.5240.14
31_A232_V0.5230.14
72_L82_P0.5220.14
161_S195_S0.5220.14
170_Q216_F0.5210.14
89_T258_E0.5210.14
148_R182_S0.5200.14
94_A111_M0.5200.14
121_C140_T0.5160.14
92_Y116_A0.5150.14
78_A84_L0.5140.14
243_S260_S0.5130.14
72_L183_G0.5120.13
67_G188_A0.5110.13
158_V175_G0.5110.13
63_L162_L0.5110.13
101_F136_S0.5070.13
143_P197_R0.5070.13
185_V217_T0.5060.13
40_T182_S0.5060.13
102_V222_R0.5050.13
138_L172_L0.5050.13
140_T143_P0.5020.13
52_Y219_D0.5000.13
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  
4ruwA 1 0.8421 100 0.735 Contact Map
4k6lF 1 0.7857 99.9 0.753 Contact Map
3wcxA 1 0.8083 99.9 0.753 Contact Map
2ddrA 1 0.8271 99.9 0.755 Contact Map
3g6sA 1 0.8158 99.9 0.757 Contact Map
1sr4B 1 0.782 99.9 0.759 Contact Map
3mprA 4 0.8421 99.9 0.76 Contact Map
3tebA 1 0.812 99.9 0.76 Contact Map
2jc5A 1 0.8008 99.9 0.762 Contact Map
3l1wA 4 0.7895 99.9 0.763 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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