GREMLIN Database
YJDF - Inner membrane protein YjdF
UniProt: P39270 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12463
Length: 209 (188)
Sequences: 595 (429)
Seq/√Len: 31.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
146_M153_W3.9421.00
135_L139_V3.8261.00
38_V76_G3.5791.00
102_K177_S3.5381.00
20_I70_I3.0921.00
71_I107_F3.0811.00
29_H82_K2.9641.00
44_V115_V2.9281.00
74_V83_V2.9071.00
35_L42_I2.8771.00
17_L66_F2.8691.00
36_M154_A2.8371.00
180_F184_L2.7151.00
141_L145_A2.6931.00
102_K171_D2.6191.00
134_F138_C2.3540.99
115_V143_I2.2520.99
82_K164_D2.2390.99
132_V136_V2.1150.98
20_I23_Y2.0190.98
141_L183_L2.0190.98
75_G100_Y1.9990.97
52_A62_Y1.9640.97
51_T62_Y1.8780.96
83_V152_W1.8540.96
137_C190_V1.8520.96
133_A190_V1.7800.95
14_A45_V1.7600.95
90_Q95_L1.7540.94
37_E166_L1.6810.93
64_L114_L1.6260.92
108_Q143_I1.6170.92
145_A149_L1.6040.91
40_P147_Y1.5460.90
139_V143_I1.5450.90
67_L71_I1.5440.90
106_F188_T1.5230.89
89_V103_L1.5070.88
32_L158_M1.4870.88
89_V93_L1.4780.87
120_L126_V1.4610.87
48_L51_T1.4580.87
34_W37_E1.4390.86
17_L73_M1.4160.85
95_L99_P1.3870.84
20_I74_V1.3850.84
120_L132_V1.3700.83
89_V95_L1.3590.83
52_A55_Y1.3230.81
99_P102_K1.3060.80
70_I74_V1.2930.79
152_W156_L1.2880.79
21_L25_G1.2780.78
71_I103_L1.2770.78
195_R198_C1.2730.78
38_V42_I1.2600.77
21_L38_V1.2570.77
129_R132_V1.2430.76
25_G31_K1.2310.76
75_G173_W1.2300.76
28_A31_K1.2290.76
21_L76_G1.2130.75
153_W156_L1.2060.74
20_I24_T1.1790.72
43_I47_L1.1780.72
79_T82_K1.1730.72
19_L39_T1.1720.72
126_V129_R1.1440.70
67_L107_F1.1300.69
78_Y150_I1.1270.69
132_V135_L1.1170.68
99_P171_D1.1080.68
64_L110_L1.1020.67
171_D177_S1.0960.67
92_W95_L1.0940.67
80_Y144_S1.0750.65
153_W157_A1.0740.65
73_M76_G1.0600.64
152_W177_S1.0530.64
61_L68_H1.0420.63
88_E92_W1.0200.61
85_V89_V1.0160.61
24_T77_Q1.0150.61
34_W166_L1.0140.61
108_Q144_S1.0100.60
113_A190_V1.0080.60
15_L150_I1.0070.60
22_I49_L1.0050.60
19_L22_I1.0040.60
68_H108_Q0.9990.59
87_F90_Q0.9990.59
50_A187_L0.9910.59
68_H72_L0.9880.59
72_L108_Q0.9830.58
155_A170_G0.9800.58
19_L96_S0.9760.58
19_L23_Y0.9650.57
67_L130_K0.9600.56
27_S31_K0.9550.56
138_C142_A0.9450.55
114_L197_H0.9440.55
54_R123_G0.9390.55
68_H102_K0.9380.55
30_D33_T0.9360.54
43_I46_Q0.9360.54
17_L20_I0.9350.54
44_V61_L0.9330.54
108_Q112_P0.9270.54
25_G28_A0.9210.53
136_V140_A0.9180.53
144_S182_A0.9100.52
13_S66_F0.9030.52
79_T166_L0.8970.51
87_F171_D0.8800.50
46_Q49_L0.8650.49
171_D181_C0.8550.48
74_V94_G0.8520.48
114_L193_L0.8450.47
40_P65_I0.8420.47
52_A56_P0.8380.47
75_G98_N0.8370.46
34_W79_T0.8350.46
136_V190_V0.8340.46
102_K125_Y0.8320.46
34_W118_E0.8290.46
81_A168_T0.8280.46
116_A126_V0.8130.45
33_T76_G0.8110.44
154_A158_M0.8090.44
154_A166_L0.7990.43
55_Y122_R0.7960.43
120_L135_L0.7930.43
37_E79_T0.7930.43
80_Y182_A0.7920.43
25_G34_W0.7900.43
37_E165_F0.7830.42
99_P181_C0.7830.42
104_G108_Q0.7820.42
47_L91_E0.7770.42
127_R188_T0.7750.42
36_M80_Y0.7670.41
100_Y176_Q0.7620.40
41_V46_Q0.7620.40
38_V73_M0.7610.40
120_L139_V0.7610.40
72_L112_P0.7560.40
86_G90_Q0.7480.39
41_V73_M0.7400.39
98_N173_W0.7400.39
110_L189_T0.7360.38
158_M161_G0.7350.38
28_A77_Q0.7340.38
16_T64_L0.7330.38
42_I187_L0.7320.38
116_A139_V0.7320.38
74_V77_Q0.7240.38
40_P76_G0.7240.38
64_L155_A0.7240.38
137_C187_L0.7210.37
31_K41_V0.7210.37
113_A117_R0.7190.37
68_H112_P0.7140.37
149_L183_L0.7120.37
137_C186_A0.7110.37
106_F181_C0.7100.37
93_L100_Y0.7080.36
42_I195_R0.7060.36
64_L107_F0.7060.36
42_I46_Q0.7040.36
46_Q60_L0.6990.36
40_P112_P0.6940.35
155_A162_A0.6930.35
124_M130_K0.6910.35
147_Y165_F0.6870.35
111_V186_A0.6860.35
155_A175_T0.6840.35
81_A166_L0.6810.34
37_E154_A0.6800.34
95_L132_V0.6780.34
165_F190_V0.6780.34
36_M44_V0.6770.34
85_V103_L0.6760.34
130_K133_A0.6760.34
20_I66_F0.6700.34
133_A136_V0.6700.34
102_K124_M0.6690.33
63_T96_S0.6680.33
16_T66_F0.6620.33
99_P152_W0.6610.33
45_V67_L0.6610.33
49_L123_G0.6580.33
154_A168_T0.6580.33
15_L121_V0.6570.33
86_G89_V0.6510.32
12_T63_T0.6350.31
12_T127_R0.6340.31
125_Y131_M0.6320.31
20_I27_S0.6290.31
46_Q192_F0.6280.31
82_K166_L0.6220.30
162_A166_L0.6190.30
142_A150_I0.6140.30
167_G170_G0.6120.29
187_L194_A0.6100.29
13_S49_L0.6060.29
15_L67_L0.6060.29
51_T55_Y0.6050.29
149_L179_M0.6050.29
149_L153_W0.6050.29
74_V90_Q0.6050.29
66_F77_Q0.6030.29
113_A140_A0.6030.29
50_A56_P0.6020.29
87_F160_Q0.5990.29
90_Q99_P0.5970.28
126_V132_V0.5960.28
124_M127_R0.5960.28
23_Y58_T0.5860.28
53_R103_L0.5850.28
83_V98_N0.5820.28
33_T162_A0.5790.27
147_Y167_G0.5750.27
81_A173_W0.5750.27
18_T196_F0.5740.27
126_V141_L0.5730.27
50_A191_I0.5720.27
48_L135_L0.5700.27
39_T181_C0.5690.27
37_E118_E0.5690.27
52_A167_G0.5680.27
153_W176_Q0.5680.27
17_L24_T0.5670.27
129_R133_A0.5660.26
124_M131_M0.5620.26
135_L138_C0.5600.26
88_E107_F0.5580.26
107_F111_V0.5560.26
122_R129_R0.5560.26
88_E91_E0.5540.26
117_R141_L0.5530.26
47_L191_I0.5530.26
14_A88_E0.5520.26
190_V194_A0.5520.26
133_A137_C0.5520.26
65_I115_V0.5510.26
33_T111_V0.5500.25
60_L193_L0.5490.25
103_L144_S0.5480.25
25_G41_V0.5480.25
61_L111_V0.5480.25
80_Y108_Q0.5460.25
111_V182_A0.5460.25
27_S42_I0.5450.25
28_A39_T0.5450.25
152_W180_F0.5370.25
26_I157_A0.5360.25
41_V77_Q0.5360.25
119_I123_G0.5340.25
14_A121_V0.5330.24
45_V135_L0.5310.24
164_D189_T0.5300.24
116_A136_V0.5290.24
117_R197_H0.5290.24
68_H175_T0.5280.24
72_L140_A0.5280.24
68_H144_S0.5270.24
37_E168_T0.5270.24
74_V85_V0.5260.24
17_L70_I0.5250.24
28_A34_W0.5230.24
130_K134_F0.5210.24
58_T96_S0.5180.24
124_M129_R0.5130.23
154_A180_F0.5120.23
25_G77_Q0.5100.23
26_I42_I0.5090.23
40_P62_Y0.5060.23
21_L42_I0.5060.23
105_H151_E0.5060.23
64_L111_V0.5040.23
98_N152_W0.5010.23
67_L94_G0.5000.23
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  
2ls2A 1 0.1196 8.9 0.97 Contact Map
2f95B 2 0.2488 5.3 0.973 Contact Map
2kluA 1 0.1866 2.4 0.977 Contact Map
3hd6A 3 0.8373 2.2 0.977 Contact Map
1m0kA 3 0.2057 1.8 0.979 Contact Map
3bz1X 1 0.1435 1.8 0.979 Contact Map
4tquM 1 0.4067 1.7 0.979 Contact Map
3wu2X 1 0.1483 1.7 0.979 Contact Map
2lcoA 1 0.0909 1.7 0.979 Contact Map
3vubA 2 0.1962 1.6 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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