GREMLIN Database
YGDQ - UPF0053 inner membrane protein YgdQ
UniProt: P67127 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13092
Length: 237 (212)
Sequences: 4433 (2386)
Seq/√Len: 163.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
96_G201_I3.7871.00
42_T45_R3.6941.00
61_L158_M3.5761.00
55_G133_M3.3241.00
59_M137_I3.3021.00
188_L225_E3.0701.00
18_L147_A2.5501.00
15_L159_A2.5181.00
103_A194_I2.5151.00
15_L163_I2.4851.00
46_A173_R2.2991.00
21_L150_L2.2791.00
43_A47_H2.1901.00
155_F159_A2.1711.00
61_L65_A2.1461.00
212_G216_F2.1351.00
104_S108_H2.1261.00
48_A132_I2.1221.00
173_R177_D2.1131.00
10_N14_A2.0251.00
51_L55_G1.9731.00
19_T163_I1.9641.00
9_P12_W1.9561.00
226_S230_I1.9191.00
191_S221_S1.9001.00
92_L203_E1.8961.00
44_Q47_H1.8721.00
65_A154_L1.8571.00
40_L128_A1.8401.00
105_K109_E1.8401.00
101_W105_K1.8221.00
227_L231_R1.7921.00
41_P44_Q1.7711.00
46_A50_R1.7611.00
55_G59_M1.7421.00
16_G20_L1.7361.00
93_L204_S1.7351.00
57_M162_V1.7291.00
202_L207_I1.7161.00
183_P232_N1.7101.00
105_K108_H1.6791.00
13_L17_T1.6771.00
159_A163_I1.5871.00
54_A58_V1.5791.00
214_I218_M1.5791.00
40_L48_A1.5761.00
109_E112_E1.5471.00
191_S224_V1.5391.00
22_E26_G1.5311.00
220_F224_V1.5061.00
213_Y216_F1.5021.00
58_V62_A1.5011.00
213_Y217_A1.5001.00
11_A156_I1.4761.00
11_A153_H1.4721.00
47_H51_L1.4551.00
225_E228_N1.4441.00
107_I187_M1.4421.00
224_V228_N1.4321.00
100_I197_G1.4231.00
59_M133_M1.3601.00
112_E115_E1.3411.00
70_V91_I1.3311.00
104_S194_I1.3261.00
230_I233_K1.3211.00
62_A66_S1.3031.00
64_L161_V1.2971.00
221_S224_V1.2921.00
130_V134_L1.2821.00
8_D11_A1.2801.00
222_I225_E1.2751.00
210_P213_Y1.2711.00
126_L130_V1.2611.00
47_H125_F1.2451.00
225_E229_L1.2431.00
181_R233_K1.2211.00
108_H112_E1.2131.00
50_R54_A1.2131.00
67_I137_I1.2131.00
151_S156_I1.1971.00
51_L129_I1.1861.00
10_N13_L1.1791.00
217_A221_S1.1791.00
177_D181_R1.1691.00
96_G197_G1.1661.00
38_A180_E1.1651.00
226_S229_L1.1491.00
221_S225_E1.1491.00
187_M191_S1.1461.00
217_A220_F1.1411.00
108_H184_S1.1331.00
195_L199_T1.1281.00
184_S232_N1.1191.00
45_R177_D1.1101.00
66_S70_V1.0750.99
227_L230_I1.0700.99
223_A227_L1.0590.99
129_I132_I1.0500.99
30_I33_L1.0480.99
211_K215_Y1.0450.99
14_A156_I1.0440.99
199_T203_E1.0300.99
218_M222_I1.0020.99
199_T214_I0.9800.99
123_S127_G0.9790.99
18_L156_I0.9750.99
7_T11_A0.9710.99
19_T23_I0.9700.99
59_M62_A0.9550.99
65_A69_W0.9420.99
198_F202_L0.9340.99
219_F223_A0.9340.99
22_E64_L0.9290.98
34_S176_G0.9260.98
30_I200_L0.9180.98
127_G130_V0.9170.98
148_V151_S0.9130.98
61_L161_V0.9100.98
151_S155_F0.9080.98
106_E190_L0.9080.98
215_Y225_E0.8970.98
228_N231_R0.8950.98
71_T144_V0.8940.98
72_R75_N0.8930.98
192_F221_S0.8910.98
179_V200_L0.8900.98
27_I30_I0.8870.98
109_E114_E0.8840.98
8_D12_W0.8820.98
11_A155_F0.8790.98
34_S129_I0.8740.98
68_A148_V0.8700.98
92_L196_V0.8690.98
98_F141_L0.8690.98
57_M165_V0.8570.97
205_F208_H0.8560.97
149_G196_V0.8540.97
12_W16_G0.8540.97
117_G120_T0.8540.97
112_E182_H0.8440.97
66_S69_W0.8380.97
184_S228_N0.8380.97
36_V132_I0.8370.97
34_S175_I0.8280.97
222_I226_S0.8220.97
57_M169_M0.8190.97
30_I175_I0.8190.97
195_L217_A0.8150.97
37_V176_G0.8140.97
11_A14_A0.8100.96
7_T12_W0.8100.96
17_T150_L0.8080.96
42_T46_A0.7970.96
11_A159_A0.7960.96
75_N93_L0.7930.96
18_L157_M0.7870.96
158_M162_V0.7870.96
137_I144_V0.7850.96
23_I166_G0.7830.96
53_L169_M0.7810.96
40_L44_Q0.7770.95
37_V173_R0.7760.95
122_V127_G0.7760.95
215_Y222_I0.7750.95
153_H156_I0.7720.95
147_A150_L0.7720.95
187_M227_L0.7680.95
185_V229_L0.7650.95
18_L151_S0.7620.95
167_V175_I0.7600.95
222_I229_L0.7600.95
48_A125_F0.7560.95
34_S179_V0.7530.95
15_L19_T0.7490.94
103_A193_L0.7490.94
128_A135_L0.7460.94
118_L121_R0.7430.94
126_L129_I0.7410.94
177_D180_E0.7380.94
147_A157_M0.7350.94
123_S128_A0.7330.94
216_F223_A0.7320.94
111_I115_E0.7300.94
161_V165_V0.7290.94
100_I104_S0.7270.94
216_F220_F0.7270.94
35_L186_K0.7270.94
210_P214_I0.7250.93
212_G220_F0.7190.93
26_G63_L0.7160.93
202_L205_F0.7150.93
119_K122_V0.7150.93
161_V164_A0.7140.93
36_V135_L0.7060.93
220_F227_L0.7020.92
183_P233_K0.7010.92
141_L144_V0.6990.92
192_F217_A0.6920.92
72_R152_D0.6900.92
91_I94_L0.6880.92
221_S226_S0.6860.91
37_V132_I0.6740.91
101_W104_S0.6740.91
182_H185_V0.6730.91
149_G203_E0.6730.91
103_A197_G0.6700.91
154_L158_M0.6700.91
96_G187_M0.6650.90
215_Y218_M0.6640.90
64_L196_V0.6640.90
221_S228_N0.6610.90
30_I189_A0.6600.90
179_V192_F0.6590.90
210_P221_S0.6570.90
37_V48_A0.6560.90
107_I190_L0.6560.90
49_R169_M0.6440.89
124_S127_G0.6430.89
63_L137_I0.6420.89
228_N232_N0.6420.89
220_F228_N0.6380.88
93_L201_I0.6370.88
22_E157_M0.6360.88
26_G168_M0.6300.88
111_I114_E0.6290.88
69_W72_R0.6280.87
214_I217_A0.6270.87
40_L129_I0.6230.87
17_T21_L0.6230.87
210_P225_E0.6220.87
211_K225_E0.6220.87
134_L138_I0.6190.87
60_R136_D0.6190.87
68_A72_R0.6160.86
134_L219_F0.6160.86
98_F102_K0.6150.86
22_E139_F0.6150.86
106_E186_K0.6130.86
179_V185_V0.6120.86
226_S233_K0.6120.86
184_S187_M0.6110.86
55_G129_I0.6110.86
47_H50_R0.6080.86
203_E207_I0.6050.86
95_G145_I0.6040.85
92_L200_L0.6030.85
26_G157_M0.6020.85
129_I133_M0.6000.85
8_D14_A0.6000.85
58_V65_A0.5980.85
56_A136_D0.5940.84
164_A176_G0.5910.84
45_R172_A0.5910.84
24_V196_V0.5910.84
94_L97_L0.5890.84
98_F197_G0.5830.83
145_I199_T0.5790.83
207_I220_F0.5780.83
41_P123_S0.5750.83
212_G224_V0.5750.83
190_L194_I0.5740.82
59_M63_L0.5710.82
31_I179_V0.5680.82
17_T22_E0.5680.82
209_V213_Y0.5670.82
218_M225_E0.5670.82
30_I160_A0.5600.81
35_L190_L0.5570.81
192_F196_V0.5570.81
209_V217_A0.5520.80
27_I160_A0.5510.80
67_I167_V0.5510.80
102_K106_E0.5500.80
40_L125_F0.5490.80
71_T92_L0.5470.79
117_G121_R0.5430.79
30_I34_S0.5420.79
118_L123_S0.5420.79
164_A175_I0.5420.79
104_S221_S0.5410.79
26_G141_L0.5390.78
198_F207_I0.5380.78
9_P13_L0.5380.78
107_I206_D0.5360.78
33_L36_V0.5350.78
51_L54_A0.5330.78
62_A65_A0.5310.77
64_L157_M0.5300.77
38_A45_R0.5290.77
36_V74_T0.5290.77
67_I148_V0.5280.77
40_L124_S0.5280.77
20_L55_G0.5280.77
36_V128_A0.5270.77
115_E223_A0.5270.77
161_V196_V0.5250.77
98_F101_W0.5240.76
145_I193_L0.5230.76
225_E232_N0.5230.76
122_V126_L0.5230.76
106_E187_M0.5210.76
69_W73_L0.5190.76
32_F200_L0.5190.76
45_R180_E0.5170.75
211_K214_I0.5160.75
65_A158_M0.5140.75
119_K124_S0.5140.75
36_V175_I0.5130.75
191_S195_L0.5110.75
67_I70_V0.5110.75
215_Y221_S0.5110.75
63_L140_S0.5100.74
214_I221_S0.5090.74
20_L24_V0.5080.74
49_R139_F0.5070.74
212_G215_Y0.5050.74
103_A175_I0.5040.74
93_L101_W0.5000.73
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  
4w6vA 1 0.443 38.4 0.944 Contact Map
2cfqA 1 0.4768 34.8 0.946 Contact Map
1pw4A 1 0.481 29.6 0.947 Contact Map
2gfpA 2 0.865 26.5 0.949 Contact Map
3wdoA 1 0.7637 14.1 0.955 Contact Map
3giaA 1 0.9451 10.5 0.957 Contact Map
3o7qA 1 0.4135 9.3 0.958 Contact Map
4dveA 3 0.4557 7.3 0.96 Contact Map
4ikvA 1 0.443 6.6 0.961 Contact Map
4xnjA 1 0.3924 5.7 0.962 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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