GREMLIN Database
YDFR - UPF0702 transmembrane protein YdfR
UniProt: P96696 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 225 (165)
Sequences: 206 (176)
Seq/√Len: 13.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
181_L186_L3.8341.00
125_E130_H3.3650.99
45_A89_L2.8900.96
72_I99_L2.6650.94
74_T91_A2.5170.92
129_L144_L2.4880.92
80_I123_V2.4220.91
178_A184_R2.3560.89
124_I159_V2.2760.88
65_Q77_V1.9580.78
40_L128_Q1.9130.76
192_P196_N1.8870.75
112_I134_L1.8850.75
160_K179_K1.8180.73
123_V137_M1.8170.73
35_F81_I1.8110.72
117_T143_Q1.7830.71
108_K142_D1.7810.71
136_K148_L1.7330.69
126_N135_K1.7280.69
186_L190_I1.7220.68
129_L181_L1.6910.67
36_T166_A1.6830.67
112_I135_K1.6590.65
74_T92_A1.6530.65
68_V154_T1.6410.64
55_R103_E1.6070.63
71_S74_T1.5870.62
43_I74_T1.5700.61
108_K120_A1.5540.60
70_I79_P1.5500.60
48_I186_L1.5400.59
123_V170_L1.5260.59
71_S91_A1.5150.58
48_I115_M1.5070.58
125_E133_N1.4900.57
153_V172_I1.4510.55
69_M73_G1.4340.54
72_I106_Q1.4080.52
92_A152_G1.3810.51
50_L103_E1.3800.51
139_L157_Q1.3620.50
55_R121_K1.3610.50
85_L197_K1.3470.49
38_E81_I1.3400.49
60_Q73_G1.3220.48
186_L195_I1.3190.48
101_V192_P1.2860.46
36_T52_I1.2800.46
58_I70_I1.2730.45
75_I82_E1.2680.45
156_I169_Q1.2610.45
128_Q176_D1.2600.44
85_L93_A1.2270.43
181_L185_D1.2140.42
94_I132_E1.2120.42
123_V147_Q1.1970.41
61_M117_T1.1840.40
102_M114_K1.1770.40
79_P88_T1.1720.40
191_H194_F1.1640.39
63_S109_S1.1640.39
79_P103_E1.1600.39
122_I197_K1.1540.39
40_L120_A1.1510.39
75_I95_F1.1500.39
101_V111_T1.1450.38
87_K93_A1.1440.38
76_I92_A1.1350.38
69_M77_V1.1320.38
173_E179_K1.1310.38
57_S69_M1.1290.38
102_M164_L1.1130.37
61_M80_I1.0970.36
65_Q117_T1.0940.36
61_M138_R1.0940.36
122_I128_Q1.0890.36
80_I154_T1.0850.35
60_Q158_D1.0820.35
74_T81_I1.0770.35
134_L177_D1.0730.35
179_K183_V1.0650.34
55_R167_N1.0650.34
88_T150_L1.0460.34
42_L153_V1.0450.34
183_V186_L1.0440.33
177_D187_K1.0440.33
40_L178_A1.0420.33
147_Q152_G1.0130.32
157_Q184_R1.0100.32
162_A170_L1.0090.32
75_I181_L0.9980.31
74_T77_V0.9850.31
130_H133_N0.9830.31
80_I92_A0.9750.30
71_S80_I0.9650.30
153_V188_K0.9630.30
56_K172_I0.9620.30
120_A163_T0.9580.30
104_W196_N0.9560.29
101_V133_N0.9480.29
145_E171_G0.9480.29
61_M173_E0.9470.29
99_L174_L0.9390.29
43_I98_T0.9380.29
68_V123_V0.9300.28
57_S146_M0.9250.28
81_I91_A0.9200.28
124_I153_V0.9150.28
132_E197_K0.9100.27
56_K95_F0.9020.27
63_S121_K0.8980.27
35_F71_S0.8970.27
94_I133_N0.8970.27
52_I187_K0.8940.27
92_A143_Q0.8940.27
187_K190_I0.8830.26
85_L188_K0.8780.26
60_Q79_P0.8710.26
41_V114_K0.8710.26
89_L132_E0.8650.26
50_L88_T0.8630.25
62_T75_I0.8590.25
124_I148_L0.8590.25
109_S112_I0.8560.25
41_V89_L0.8530.25
158_D178_A0.8480.25
80_I84_S0.8440.25
72_I157_Q0.8380.24
45_A107_M0.8330.24
188_K194_F0.8160.24
34_N38_E0.8090.23
41_V139_L0.8060.23
93_A109_S0.8050.23
154_T173_E0.7980.23
45_A93_A0.7950.23
124_I156_I0.7920.23
67_V136_K0.7920.23
102_M190_I0.7860.22
160_K176_D0.7740.22
79_P145_E0.7680.22
91_A143_Q0.7650.22
83_Y96_T0.7650.22
113_E120_A0.7600.21
34_N153_V0.7570.21
106_Q156_I0.7540.21
192_P195_I0.7530.21
75_I183_V0.7530.21
60_Q69_M0.7490.21
119_K147_Q0.7460.21
45_A170_L0.7430.21
131_I189_L0.7400.21
123_V161_I0.7370.21
70_I135_K0.7370.21
96_T107_M0.7350.21
141_A170_L0.7320.20
46_G88_T0.7290.20
76_I82_E0.7260.20
123_V173_E0.7240.20
139_L164_L0.7210.20
113_E145_E0.7180.20
109_S119_K0.7180.20
105_I179_K0.7170.20
102_M136_K0.7150.20
58_I68_V0.7110.20
48_I93_A0.7090.20
178_A181_L0.7080.20
36_T151_H0.7080.20
114_K119_K0.7060.20
192_P197_K0.7060.20
101_V176_D0.7020.19
83_Y126_N0.6970.19
160_K173_E0.6930.19
84_S146_M0.6880.19
136_K142_D0.6860.19
55_R66_T0.6850.19
62_T73_G0.6820.19
44_V101_V0.6770.19
53_S68_V0.6760.19
148_L153_V0.6730.19
121_K151_H0.6730.19
145_E158_D0.6720.18
33_M160_K0.6700.18
33_M94_I0.6700.18
99_L171_G0.6660.18
77_V88_T0.6640.18
105_I123_V0.6570.18
44_V90_I0.6560.18
65_Q103_E0.6520.18
77_V84_S0.6510.18
38_E84_S0.6510.18
163_T174_L0.6490.18
63_S115_M0.6490.18
50_L163_T0.6410.17
126_N174_L0.6390.17
183_V193_D0.6370.17
58_I142_D0.6340.17
62_T163_T0.6300.17
163_T171_G0.6270.17
50_L118_G0.6250.17
64_T143_Q0.6220.17
40_L155_A0.6140.17
47_V76_I0.6120.17
38_E76_I0.6110.17
85_L196_N0.6100.17
47_V52_I0.6090.17
128_Q170_L0.6080.16
92_A153_V0.6070.16
95_F183_V0.6050.16
71_S92_A0.6050.16
116_L123_V0.5960.16
75_I91_A0.5940.16
43_I71_S0.5930.16
52_I126_N0.5910.16
82_E193_D0.5890.16
49_L121_K0.5890.16
53_S134_L0.5890.16
177_D186_L0.5840.16
162_A172_I0.5830.16
46_G96_T0.5820.16
42_L80_I0.5800.16
56_K66_T0.5790.16
73_G78_Q0.5730.15
194_F197_K0.5710.15
148_L159_V0.5700.15
40_L176_D0.5680.15
151_H188_K0.5680.15
74_T155_A0.5600.15
36_T97_S0.5560.15
100_I197_K0.5560.15
178_A185_D0.5540.15
73_G150_L0.5500.15
44_V123_V0.5500.15
129_L196_N0.5460.15
134_L139_L0.5450.15
78_Q103_E0.5420.15
41_V91_A0.5400.15
39_S43_I0.5360.14
67_V86_F0.5350.14
58_I77_V0.5310.14
70_I170_L0.5290.14
48_I96_T0.5200.14
85_L169_Q0.5130.14
115_M125_E0.5110.14
67_V167_N0.5100.14
89_L151_H0.5100.14
173_E182_T0.5050.14
126_N187_K0.5000.14
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  
3c6fA 4 0.4711 99.9 0.676 Contact Map
3mxnA 1 0.5867 12.1 0.962 Contact Map
3okfA 3 0.7467 10.6 0.963 Contact Map
1nv8A 1 0.3867 7.8 0.965 Contact Map
4bpeO 1 0.4711 6.4 0.967 Contact Map
3gdeA 1 0.6533 6.1 0.967 Contact Map
1ujnA 2 0.7289 5.4 0.968 Contact Map
2l01A 2 0.3333 5.3 0.968 Contact Map
4dbgB 1 0.4267 5.1 0.968 Contact Map
4ujpO 1 0.4489 5.1 0.968 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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