GREMLIN Database
RFAS - Lipopolysaccharide core biosynthesis protein RfaS
UniProt: P27126 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11350
Length: 311 (297)
Sequences: 349 (327)
Seq/√Len: 19.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
118_D124_I9.6221.00
157_I220_N5.3801.00
155_Q218_N4.8651.00
134_Q235_L4.6291.00
27_K66_K3.4921.00
258_E294_K3.4091.00
244_N286_P3.3601.00
158_C223_V3.2851.00
233_W257_S3.1260.99
264_R284_V2.9970.99
98_R136_F2.9750.99
98_R300_M2.7370.98
70_I304_I2.7360.98
253_N256_G2.7360.98
124_I129_I2.4640.97
158_C178_L2.4030.96
258_E295_F2.3310.95
115_I130_K2.3170.95
67_D233_W2.2930.95
118_D129_I2.2580.94
134_Q234_T2.2130.94
261_S285_K2.1560.93
255_F267_I2.1390.92
137_P234_T2.0380.90
230_Q234_T2.0340.90
99_N114_D2.0290.90
263_S285_K2.0220.90
74_D99_N2.0180.90
118_D230_Q1.9960.89
132_I303_T1.9860.89
19_Y22_K1.9840.89
131_A257_S1.9800.89
110_A116_I1.9610.89
159_F215_R1.9500.88
100_T227_K1.9500.88
4_Y66_K1.9010.87
266_F276_L1.9000.87
96_L300_M1.8820.86
86_L93_K1.8750.86
257_S264_R1.8130.84
69_I93_K1.8080.84
134_Q164_D1.8060.84
261_S264_R1.7850.83
287_M294_K1.7400.82
259_I265_F1.7190.81
93_K113_F1.7190.81
246_K279_F1.7170.81
241_L287_M1.7120.81
17_I21_K1.6800.79
159_F212_N1.6400.78
134_Q238_L1.6350.77
99_N113_F1.6260.77
263_S282_S1.6240.77
99_N134_Q1.6050.76
99_N242_F1.5920.75
258_E291_S1.5780.75
157_I184_K1.5780.75
209_Y213_I1.5770.75
186_D215_R1.5370.73
100_T118_D1.5330.73
133_E234_T1.5280.72
70_I93_K1.5240.72
73_N99_N1.5220.72
5_F8_W1.5110.71
97_L116_I1.5070.71
240_A247_L1.4740.70
266_F269_G1.4430.68
158_C183_C1.4400.68
19_Y297_P1.4380.68
209_Y235_L1.4350.67
44_K75_S1.4110.66
165_K227_K1.4090.66
233_W259_I1.4040.66
261_S292_L1.3990.65
225_I268_I1.3960.65
98_R135_F1.3920.65
136_F296_S1.3880.65
121_H253_N1.3630.63
246_K264_R1.3320.61
37_W40_K1.3230.61
243_F247_L1.3170.61
179_T182_G1.2980.59
16_M96_L1.2940.59
234_T249_T1.2890.59
212_N216_T1.2720.58
276_L279_F1.2630.57
137_P297_P1.2500.56
67_D70_I1.2390.56
246_K249_T1.2380.56
100_T230_Q1.2350.55
281_N289_Y1.2320.55
170_I174_L1.2290.55
233_W295_F1.2250.55
121_H125_G1.2230.55
245_K254_V1.2040.54
276_L280_I1.1960.53
166_G270_H1.1870.52
12_Y135_F1.1830.52
112_Y269_G1.1800.52
250_N270_H1.1750.52
268_I273_W1.1710.51
174_L268_I1.1650.51
171_I179_T1.1570.51
233_W284_V1.1530.50
86_L121_H1.1480.50
233_W258_E1.1450.50
20_L305_V1.1390.49
260_Y279_F1.1300.49
132_I300_M1.1230.48
229_N234_T1.1180.48
119_F230_Q1.1110.48
154_S245_K1.1020.47
119_F162_G1.0940.47
232_G259_I1.0930.47
158_C248_I1.0890.46
93_K114_D1.0860.46
289_Y293_Y1.0770.46
187_F243_F1.0690.45
224_D246_K1.0660.45
54_R83_K1.0650.45
128_K152_N1.0520.44
240_A254_V1.0510.44
153_N220_N1.0440.43
98_R120_E1.0410.43
60_Y67_D1.0390.43
171_I225_I1.0380.43
135_F224_D1.0370.43
257_S284_V1.0370.43
99_N165_K1.0350.43
69_I230_Q1.0330.43
221_I240_A1.0320.43
293_Y298_D1.0300.43
98_R133_E1.0160.42
5_F72_I1.0080.41
218_N252_I1.0070.41
10_A226_T0.9950.40
232_G300_M0.9940.40
104_D235_L0.9800.40
291_S295_F0.9770.39
264_R283_S0.9760.39
82_N93_K0.9730.39
86_L114_D0.9700.39
136_F247_L0.9640.39
16_M300_M0.9610.38
264_R294_K0.9580.38
174_L223_V0.9510.38
241_L261_S0.9460.38
95_L234_T0.9450.37
133_E137_P0.9390.37
188_N207_I0.9370.37
96_L235_L0.9340.37
264_R291_S0.9300.37
124_I230_Q0.9270.36
95_L134_Q0.9230.36
219_A304_I0.9150.36
136_F300_M0.9140.36
248_I265_F0.9100.35
224_D237_I0.9060.35
264_R295_F0.9050.35
98_R137_P0.9050.35
250_N268_I0.9030.35
297_P300_M0.9000.35
129_I161_L0.8980.35
67_D257_S0.8960.35
224_D229_N0.8900.34
268_I272_D0.8890.34
97_L291_S0.8760.33
266_F275_K0.8740.33
134_Q237_I0.8720.33
8_W98_R0.8680.33
91_C134_Q0.8670.33
158_C238_L0.8630.33
246_K260_Y0.8630.33
72_I241_L0.8620.33
124_I127_E0.8610.33
118_D123_F0.8570.32
99_N166_G0.8540.32
145_N287_M0.8510.32
220_N283_S0.8480.32
119_F160_F0.8410.32
135_F189_V0.8410.32
259_I291_S0.8400.31
165_K209_Y0.8360.31
237_I240_A0.8330.31
133_E235_L0.8330.31
131_A234_T0.8320.31
12_Y118_D0.8220.31
45_I48_D0.8200.30
36_N74_D0.8180.30
240_A288_D0.8170.30
248_I268_I0.8140.30
111_N302_S0.8140.30
74_D234_T0.8120.30
4_Y160_F0.8110.30
178_L183_C0.8110.30
3_I29_I0.8100.30
258_E264_R0.8080.30
122_R254_V0.8060.30
248_I272_D0.8060.30
50_A54_R0.8030.30
235_L239_E0.8030.30
248_I266_F0.8020.29
71_I77_V0.8010.29
161_L215_R0.8010.29
222_I240_A0.7980.29
164_D230_Q0.7980.29
224_D249_T0.7970.29
120_E239_E0.7950.29
257_S300_M0.7950.29
72_I96_L0.7930.29
65_K222_I0.7900.29
174_L178_L0.7900.29
6_I230_Q0.7860.29
9_V13_E0.7830.28
73_N97_L0.7810.28
235_L238_L0.7810.28
134_Q242_F0.7800.28
198_T202_L0.7780.28
122_R126_N0.7780.28
116_I230_Q0.7760.28
131_A254_V0.7730.28
80_G283_S0.7720.28
277_E281_N0.7710.28
244_N292_L0.7690.28
248_I279_F0.7650.28
3_I70_I0.7630.27
103_E235_L0.7620.27
15_K209_Y0.7610.27
50_A87_K0.7590.27
240_A249_T0.7590.27
95_L116_I0.7560.27
97_L119_F0.7550.27
239_E259_I0.7550.27
97_L106_I0.7540.27
95_L235_L0.7500.27
32_P41_K0.7470.27
11_D182_G0.7450.27
44_K47_M0.7430.26
272_D291_S0.7310.26
294_K303_T0.7300.26
157_I183_C0.7280.26
47_M205_K0.7270.26
176_E180_T0.7240.26
70_I132_I0.7210.25
97_L100_T0.7210.25
7_N20_L0.7170.25
33_K40_K0.7170.25
283_S291_S0.7130.25
67_D123_F0.7130.25
267_I275_K0.7120.25
244_N289_Y0.7110.25
18_Q21_K0.7090.25
231_S254_V0.7080.25
209_Y240_A0.7070.25
260_Y287_M0.7060.25
236_R260_Y0.7030.25
38_I210_E0.7020.24
162_G171_I0.7010.24
3_I153_N0.6990.24
74_D95_L0.6970.24
66_K99_N0.6930.24
284_V287_M0.6920.24
10_A32_P0.6900.24
109_N202_L0.6840.24
266_F295_F0.6830.24
105_F120_E0.6830.24
128_K180_T0.6820.24
108_D158_C0.6820.24
67_D224_D0.6810.24
81_I254_V0.6810.24
265_F294_K0.6800.23
184_K218_N0.6790.23
100_T235_L0.6790.23
164_D192_D0.6730.23
249_T279_F0.6710.23
69_I118_D0.6700.23
220_N241_L0.6690.23
164_D235_L0.6690.23
207_I286_P0.6650.23
4_Y116_I0.6620.23
167_R236_R0.6610.23
38_I287_M0.6600.23
172_N229_N0.6600.23
170_I225_I0.6590.23
91_C235_L0.6580.22
235_L240_A0.6550.22
99_N164_D0.6540.22
67_D96_L0.6530.22
18_Q56_F0.6530.22
230_Q238_L0.6520.22
125_G128_K0.6510.22
179_T208_S0.6510.22
23_K302_S0.6510.22
162_G209_Y0.6500.22
8_W17_I0.6500.22
287_M304_I0.6490.22
94_V114_D0.6480.22
98_R134_Q0.6480.22
234_T246_K0.6470.22
217_L241_L0.6460.22
161_L250_N0.6450.22
134_Q165_K0.6430.22
96_L136_F0.6420.22
103_E227_K0.6400.22
266_F279_F0.6400.22
293_Y299_K0.6400.22
252_I255_F0.6360.22
29_I59_H0.6340.21
120_E230_Q0.6330.21
135_F232_G0.6320.21
184_K220_N0.6310.21
235_L243_F0.6310.21
111_N120_E0.6300.21
133_E300_M0.6280.21
14_L85_I0.6280.21
11_D30_T0.6250.21
222_I253_N0.6250.21
58_K223_V0.6210.21
12_Y19_Y0.6200.21
83_K207_I0.6200.21
176_E220_N0.6190.21
132_I299_K0.6190.21
98_R119_F0.6190.21
161_L207_I0.6180.21
120_E160_F0.6180.21
159_F296_S0.6170.21
77_V230_Q0.6170.21
138_I296_S0.6170.21
129_I242_F0.6170.21
18_Q128_K0.6160.21
155_Q179_T0.6160.21
70_I248_I0.6150.21
230_Q297_P0.6150.21
15_K77_V0.6130.21
82_N247_L0.6130.21
16_M98_R0.6100.20
173_E285_K0.6070.20
65_K241_L0.6070.20
259_I264_R0.6060.20
13_E234_T0.6050.20
117_Y132_I0.6030.20
22_K298_D0.6030.20
98_R162_G0.6010.20
15_K18_Q0.6000.20
104_D305_V0.6000.20
281_N302_S0.5990.20
82_N244_N0.5980.20
92_H126_N0.5970.20
103_E234_T0.5960.20
261_S265_F0.5940.20
100_T134_Q0.5940.20
272_D275_K0.5920.20
240_A245_K0.5920.20
117_Y130_K0.5910.20
130_K283_S0.5910.20
96_L115_I0.5900.20
176_E197_T0.5850.19
26_I99_N0.5840.19
42_I196_S0.5840.19
7_N17_I0.5830.19
169_Q211_E0.5810.19
12_Y132_I0.5800.19
143_I211_E0.5790.19
220_N261_S0.5780.19
296_S304_I0.5770.19
211_E214_R0.5740.19
87_K125_G0.5740.19
24_Y68_D0.5740.19
45_I118_D0.5730.19
157_I219_A0.5730.19
254_V285_K0.5730.19
95_L230_Q0.5690.19
8_W72_I0.5670.19
246_K251_N0.5640.19
44_K185_L0.5640.19
136_F162_G0.5630.19
18_Q23_K0.5620.19
89_I262_E0.5610.19
81_I117_Y0.5610.19
187_F223_V0.5600.18
99_N235_L0.5590.18
181_L305_V0.5590.18
103_E230_Q0.5570.18
156_P186_D0.5550.18
169_Q201_Y0.5550.18
72_I135_F0.5540.18
213_I301_M0.5540.18
137_P209_Y0.5540.18
121_H256_G0.5500.18
224_D233_W0.5500.18
63_D72_I0.5480.18
211_E290_D0.5470.18
243_F250_N0.5450.18
47_M304_I0.5450.18
16_M235_L0.5430.18
269_G284_V0.5430.18
100_T113_F0.5410.18
224_D234_T0.5390.18
6_I12_Y0.5390.18
96_L99_N0.5380.18
137_P212_N0.5380.18
171_I201_Y0.5370.18
121_H247_L0.5370.18
10_A164_D0.5370.18
299_K302_S0.5360.18
5_F93_K0.5350.18
135_F237_I0.5340.18
10_A23_K0.5340.18
7_N12_Y0.5340.18
119_F251_N0.5330.17
92_H105_F0.5310.17
14_L145_N0.5300.17
131_A233_W0.5290.17
107_L127_E0.5280.17
77_V174_L0.5270.17
117_Y304_I0.5270.17
35_Y44_K0.5270.17
135_F230_Q0.5260.17
127_E207_I0.5260.17
155_Q210_E0.5260.17
159_F171_I0.5240.17
269_G273_W0.5240.17
99_N304_I0.5240.17
44_K48_D0.5230.17
37_W41_K0.5220.17
9_V23_K0.5210.17
173_E177_R0.5210.17
187_F244_N0.5200.17
10_A13_E0.5180.17
73_N297_P0.5170.17
90_N234_T0.5160.17
160_F165_K0.5150.17
172_N287_M0.5150.17
33_K75_S0.5140.17
249_T254_V0.5110.17
256_G301_M0.5100.17
85_I93_K0.5050.16
36_N42_I0.5050.16
252_I269_G0.5040.16
91_C234_T0.5030.16
40_K56_F0.5020.16
58_K62_N0.5010.16
249_T260_Y0.5010.16
98_R297_P0.5000.16
264_R279_F0.5000.16
237_I247_L0.5000.16
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  
3c48A 2 0.9775 98.8 0.863 Contact Map
3froA 3 0.9775 98.7 0.865 Contact Map
2hy7A 1 0.955 98.6 0.87 Contact Map
3oy2A 2 0.9775 98.6 0.871 Contact Map
3okpA 1 0.9775 98.5 0.874 Contact Map
4w6qA 4 0.9035 98.4 0.877 Contact Map
3rhzA 4 0.9068 98.4 0.879 Contact Map
2r60A 1 0.9775 98.3 0.879 Contact Map
3ot5A 2 0.9614 98.2 0.883 Contact Map
2x0dA 2 0.9486 98.2 0.884 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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