GREMLIN Database
YDCF - Protein YdcF
UniProt: P34209 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12110
Length: 266 (207)
Sequences: 475 (348)
Seq/√Len: 24.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
16_A249_T8.6371.00
37_A148_I5.2411.00
100_T121_D3.6861.00
52_D105_I3.5171.00
96_R104_D3.2291.00
70_G123_S3.0471.00
128_E132_F3.0071.00
220_R244_I2.8230.99
39_C66_L2.6460.99
221_D236_H2.5730.99
41_I133_S2.5480.99
206_E210_S2.5320.99
19_V243_V2.4000.98
55_C59_R2.3740.98
45_N50_T2.2620.97
215_E234_I2.1880.97
136_L140_A2.0850.96
160_M235_V2.0830.96
54_A150_V2.0580.95
67_I106_A2.0090.95
219_L237_V2.0000.94
243_V246_A1.9260.93
221_D224_D1.8880.92
23_W237_V1.8550.92
122_Q132_F1.8210.91
156_Q207_R1.7690.90
45_N152_D1.7210.88
126_C159_T1.7190.88
56_K60_D1.6900.87
160_M164_R1.6530.86
162_T233_F1.6010.84
23_W239_F1.5990.84
122_Q139_Q1.5600.83
107_H114_H1.5580.83
219_L234_I1.5550.83
157_R161_A1.5380.82
39_C137_L1.5330.82
224_D236_H1.5080.81
128_E131_R1.4940.80
26_Q160_M1.4600.78
97_A100_T1.4470.78
74_S212_L1.4440.78
72_G155_M1.4280.77
151_Q155_M1.4250.77
46_A203_W1.3800.74
164_R235_V1.3770.74
73_H211_L1.3710.74
97_A101_I1.3700.74
17_I216_L1.3360.72
240_P243_V1.3360.72
47_V50_T1.3230.71
128_E162_T1.3170.71
127_G233_F1.2900.69
33_V56_K1.2840.69
122_Q135_A1.2810.68
103_A107_H1.2580.67
41_I147_A1.2500.67
54_A65_L1.2450.66
213_T254_A1.2440.66
96_R101_I1.2400.66
44_G67_I1.2390.66
42_L67_I1.2370.66
23_W219_L1.2260.65
151_Q163_F1.2230.65
42_L203_W1.2210.65
20_I216_L1.2090.64
244_I248_Q1.1950.63
142_E233_F1.1950.63
215_E219_L1.1920.63
126_C155_M1.1920.63
74_S207_R1.1860.62
74_S211_L1.1850.62
19_V246_A1.1850.62
71_I97_A1.1850.62
130_A163_F1.1850.62
134_I138_N1.1760.62
37_A187_G1.1740.62
115_E143_R1.1700.61
157_R162_T1.1610.61
105_I109_F1.1570.60
213_T251_K1.1530.60
66_L133_S1.1510.60
52_D135_A1.1500.60
129_N218_R1.1310.59
147_A170_N1.1270.58
105_I150_V1.1250.58
217_P250_L1.1220.58
102_L155_M1.1090.57
39_C142_E1.0930.56
72_G152_D1.0800.55
73_H203_W1.0710.54
152_D207_R1.0710.54
45_N153_P1.0630.54
155_M215_E1.0580.53
72_G216_L1.0560.53
13_T19_V1.0530.53
71_I123_S1.0400.52
72_G75_T1.0390.52
46_A74_S1.0320.52
39_C147_A1.0280.51
70_G124_T1.0250.51
155_M216_L1.0240.51
43_A156_Q1.0120.50
120_E129_N0.9950.49
40_V62_Q0.9700.47
122_Q235_V0.9640.47
118_W136_L0.9570.46
195_F199_L0.9560.46
140_A223_S0.9560.46
38_D145_H0.9450.45
118_W140_A0.9440.45
23_W197_N0.9320.45
191_D212_L0.9300.44
70_G155_M0.9270.44
43_A126_C0.9250.44
74_S208_Y0.9190.44
152_D155_M0.9140.43
162_T166_M0.9060.43
43_A58_A0.8930.42
14_I196_I0.8820.41
248_Q252_H0.8820.41
122_Q233_F0.8800.41
164_R219_L0.8730.40
38_D72_G0.8730.40
15_D142_E0.8700.40
220_R239_F0.8630.40
131_R135_A0.8620.40
58_A116_K0.8600.40
156_Q190_A0.8560.39
47_V222_D0.8550.39
18_N221_D0.8510.39
46_A211_L0.8500.39
194_I238_D0.8430.38
131_R204_P0.8400.38
130_A159_T0.8370.38
43_A153_P0.8320.38
56_K122_Q0.8310.38
15_D20_I0.8310.38
74_S155_M0.8300.37
13_T253_D0.8280.37
73_H234_I0.8260.37
72_G211_L0.8240.37
21_G217_P0.8110.36
43_A128_E0.8100.36
44_G156_Q0.8080.36
163_F220_R0.8080.36
66_L136_L0.8040.36
14_I205_V0.8010.36
219_L236_H0.8010.36
39_C250_L0.8010.36
18_N196_I0.7940.35
79_Y215_E0.7940.35
17_I223_S0.7900.35
97_A119_I0.7840.34
120_E218_R0.7810.34
67_I201_G0.7780.34
53_A189_N0.7760.34
189_N248_Q0.7690.34
152_D203_W0.7690.34
126_C154_T0.7680.33
72_G76_T0.7670.33
123_S203_W0.7650.33
74_S159_T0.7630.33
54_A68_S0.7590.33
136_L166_M0.7550.33
152_D234_I0.7490.32
189_N231_R0.7490.32
25_A207_R0.7450.32
105_I108_Q0.7430.32
44_G130_A0.7400.32
21_G154_T0.7400.32
147_A250_L0.7380.32
123_S151_Q0.7380.32
150_V157_R0.7320.31
132_F196_I0.7320.31
42_L74_S0.7320.31
36_Q135_A0.7220.31
70_G233_F0.7210.31
46_A202_L0.7210.31
113_P167_T0.7140.30
186_L205_V0.7100.30
38_D99_A0.7060.30
59_R109_F0.7030.29
73_H207_R0.7020.29
21_G47_V0.7020.29
19_V124_T0.7000.29
154_T198_Q0.7000.29
18_N22_Q0.6960.29
53_A150_V0.6870.29
125_N214_G0.6860.28
238_D242_E0.6850.28
53_A192_S0.6840.28
156_Q216_L0.6780.28
72_G163_F0.6740.28
74_S203_W0.6700.28
74_S163_F0.6660.27
155_M246_A0.6640.27
11_P143_R0.6590.27
131_R142_E0.6530.27
111_H209_L0.6480.26
219_L235_V0.6480.26
17_I191_D0.6480.26
185_Q245_H0.6480.26
215_E240_P0.6460.26
51_I102_L0.6450.26
70_G211_L0.6400.26
68_S132_F0.6390.26
53_A148_I0.6370.26
102_L130_A0.6360.26
134_I170_N0.6340.26
216_L239_F0.6320.25
43_A50_T0.6310.25
217_P251_K0.6270.25
163_F186_L0.6250.25
213_T250_L0.6230.25
154_T214_G0.6230.25
130_A195_F0.6230.25
125_N233_F0.6180.25
41_I199_L0.6180.25
24_L221_D0.6180.25
155_M219_L0.6170.25
104_D135_A0.6160.25
45_N117_I0.6150.25
48_M105_I0.6140.24
52_D108_Q0.6130.24
17_I244_I0.6110.24
220_R223_S0.6110.24
139_Q241_A0.6100.24
137_L154_T0.6080.24
125_N162_T0.6060.24
68_S112_I0.6060.24
58_A61_Q0.6050.24
61_Q209_L0.6050.24
73_H152_D0.6030.24
122_Q145_H0.5970.24
71_I76_T0.5960.24
133_S210_S0.5940.23
114_H142_E0.5930.23
141_V144_V0.5930.23
112_I116_K0.5900.23
65_L144_V0.5900.23
215_E221_D0.5900.23
152_D216_L0.5880.23
61_Q150_V0.5880.23
111_H157_R0.5870.23
45_N119_I0.5870.23
238_D243_V0.5850.23
245_H248_Q0.5840.23
40_V148_I0.5820.23
46_A247_W0.5820.23
42_L152_D0.5770.23
135_A138_N0.5750.22
152_D215_E0.5700.22
147_A205_V0.5690.22
23_W53_A0.5670.22
15_D19_V0.5660.22
44_G68_S0.5650.22
33_V59_R0.5630.22
43_A130_A0.5610.22
121_D149_V0.5610.22
221_D231_R0.5600.22
52_D221_D0.5600.22
144_V213_T0.5600.22
148_I204_P0.5590.22
68_S108_Q0.5580.22
61_Q255_V0.5580.22
39_C210_S0.5560.22
52_D205_V0.5560.22
25_A156_Q0.5550.21
241_A245_H0.5550.21
26_Q154_T0.5550.21
127_G152_D0.5530.21
14_I195_F0.5530.21
42_L54_A0.5520.21
206_E238_D0.5520.21
20_I205_V0.5510.21
97_A118_W0.5500.21
73_H154_T0.5430.21
207_R216_L0.5420.21
36_Q224_D0.5410.21
73_H78_L0.5380.21
10_S72_G0.5380.21
53_A65_L0.5380.21
60_D187_G0.5350.21
231_R236_H0.5330.20
104_D136_L0.5330.20
65_L124_T0.5310.20
17_I40_V0.5300.20
203_W207_R0.5290.20
42_L68_S0.5240.20
45_N208_Y0.5210.20
138_N144_V0.5190.20
36_Q209_L0.5180.20
18_N73_H0.5170.20
165_R232_D0.5150.20
46_A79_Y0.5150.20
20_I105_I0.5140.20
70_G152_D0.5130.20
124_T128_E0.5120.19
47_V102_L0.5110.19
162_T167_T0.5100.19
223_S231_R0.5080.19
42_L46_A0.5080.19
196_I245_H0.5070.19
76_T152_D0.5050.19
191_D234_I0.5030.19
140_A243_V0.5030.19
119_I149_V0.5030.19
113_P116_K0.5020.19
60_D235_V0.5000.19
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  
3ca8A 1 0.9812 100 0.337 Contact Map
1to6A 4 0.406 36 0.967 Contact Map
3cwcA 2 0.4248 35.6 0.967 Contact Map
3mb5A 3 0.485 32.9 0.967 Contact Map
3obeA 1 0.7669 27.4 0.969 Contact Map
1lehA 5 0.4887 26.4 0.969 Contact Map
2pr7A 1 0.4887 25.1 0.969 Contact Map
1o54A 4 0.485 22.9 0.97 Contact Map
4bgbA 1 0.4286 22.9 0.97 Contact Map
4qbgB 1 0.6955 22.6 0.97 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.

Page generated in 0.0084 seconds.