GREMLIN Database
RFAZ - Lipopolysaccharide core biosynthesis protein RfaZ
UniProt: P27241 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11426
Length: 283 (233)
Sequences: 205 (173)
Seq/√Len: 11.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
45_D185_Y5.0091.00
67_V115_V3.7640.99
23_D187_R3.3940.98
37_P246_I2.8740.93
171_T174_F2.5440.88
66_Y224_F2.4520.86
51_G201_R2.3190.83
70_D73_F2.3120.83
157_G173_A2.3100.83
241_S244_T2.2830.82
67_V172_I2.2440.81
50_N66_Y2.2320.80
187_R236_N2.2090.80
167_C178_Q2.1680.78
50_N70_D2.1440.78
211_P214_L2.1200.77
25_I44_K2.0920.76
173_A193_L2.0820.75
225_F251_I2.0790.75
30_G192_G2.0510.74
174_F178_Q2.0140.73
24_V169_C1.9940.72
73_F204_D1.9850.72
101_A117_R1.9590.71
172_I176_A1.9530.70
165_G203_Y1.9470.70
73_F201_R1.9180.69
40_V230_D1.8930.68
65_I185_Y1.8860.68
212_S215_S1.8490.66
196_T252_P1.8470.66
66_Y158_F1.8330.65
48_A52_S1.7670.62
173_A225_F1.7450.61
23_D44_K1.7290.61
32_T194_D1.7290.61
171_T178_Q1.6920.59
159_C178_Q1.6710.58
29_S201_R1.6630.57
67_V179_I1.6440.57
101_A193_L1.6290.56
63_P111_Q1.6150.55
157_G225_F1.5850.54
171_T194_D1.5830.54
201_R241_S1.5660.53
25_I191_S1.5490.52
70_D165_G1.5440.52
193_L245_A1.5440.52
243_D253_F1.5240.51
171_T195_L1.5220.51
28_L174_F1.4980.49
51_G73_F1.4900.49
32_T192_G1.4740.48
203_Y244_T1.4530.47
29_S178_Q1.4440.47
240_L244_T1.4410.47
194_D241_S1.4410.47
29_S167_C1.4350.46
52_S214_L1.4300.46
51_G178_Q1.4290.46
70_D158_F1.4170.46
55_Y200_S1.3880.44
37_P232_V1.3850.44
167_C171_T1.3530.42
51_G70_D1.3240.41
50_N192_G1.3190.41
30_G50_N1.3190.41
73_F203_Y1.3120.40
37_P41_L1.3110.40
28_L173_A1.3090.40
33_S197_G1.3080.40
43_T187_R1.3070.40
157_G201_R1.3060.40
200_S204_D1.2940.40
49_V66_Y1.2820.39
178_Q201_R1.2810.39
161_D184_K1.2740.39
30_G239_N1.2690.38
192_G239_N1.2690.38
201_R214_L1.2470.37
94_N204_D1.2430.37
49_V172_I1.2350.37
66_Y70_D1.2160.36
22_D45_D1.2150.36
51_G157_G1.2140.36
140_H189_I1.2010.35
133_F177_I1.1890.35
189_I234_D1.1880.35
139_I256_L1.1880.35
119_F188_I1.1880.35
34_Q246_I1.1860.35
193_L218_L1.1840.35
47_I180_A1.1750.34
206_N216_R1.1730.34
30_G194_D1.1640.34
53_A80_D1.1620.34
52_S221_I1.1530.33
27_F46_I1.1470.33
39_S49_V1.1440.33
31_P192_G1.1430.33
65_I97_V1.1400.33
55_Y70_D1.1270.32
136_L140_H1.1270.32
72_R113_C1.0960.31
52_S240_L1.0960.31
86_Q198_S1.0670.30
232_V251_I1.0620.29
225_F241_S1.0470.29
51_G202_F1.0400.29
188_I235_I1.0340.28
82_Y257_Q1.0290.28
22_D185_Y1.0280.28
86_Q231_N1.0240.28
21_S143_L1.0220.28
26_I190_C1.0210.28
173_A203_Y1.0210.28
44_K237_I1.0210.28
105_D229_H1.0190.28
185_Y247_S1.0070.27
171_T241_S1.0020.27
151_K231_N1.0010.27
151_K209_P0.9940.27
157_G182_S0.9930.27
176_A203_Y0.9930.27
70_D244_T0.9870.27
224_F229_H0.9820.26
214_L223_P0.9790.26
26_I180_A0.9790.26
246_I250_V0.9740.26
172_I210_M0.9720.26
194_D202_F0.9700.26
43_T107_L0.9650.26
255_K258_D0.9600.26
215_S220_K0.9590.25
25_I184_K0.9570.25
183_L186_A0.9490.25
42_R60_N0.9480.25
29_S52_S0.9480.25
99_E104_E0.9470.25
180_A256_L0.9460.25
45_D78_R0.9430.25
197_G251_I0.9370.25
197_G200_S0.9360.25
27_F43_T0.9330.25
51_G195_L0.9300.24
161_D196_T0.9280.24
174_F181_Y0.9270.24
98_Y103_K0.9200.24
163_S196_T0.9120.24
51_G204_D0.9070.24
195_L225_F0.9060.24
70_D172_I0.9060.24
66_Y171_T0.9030.23
33_S46_I0.9000.23
85_S97_V0.8940.23
47_I176_A0.8810.23
68_L169_C0.8760.23
73_F158_F0.8690.22
203_Y206_N0.8660.22
28_L199_C0.8610.22
50_N169_C0.8560.22
110_L255_K0.8540.22
224_F228_M0.8510.22
31_P188_I0.8480.22
96_D103_K0.8450.21
22_D184_K0.8440.21
38_L191_S0.8420.21
48_A166_Y0.8400.21
157_G203_Y0.8360.21
171_T201_R0.8290.21
201_R204_D0.8290.21
53_A157_G0.8280.21
52_S201_R0.8260.21
178_Q221_I0.8230.21
27_F92_I0.8220.21
83_K198_S0.8220.21
39_S236_N0.8170.21
98_Y119_F0.8170.21
24_V243_D0.8160.21
200_S228_M0.8130.20
28_L244_T0.8090.20
33_S201_R0.8090.20
237_I244_T0.8080.20
201_R223_P0.8040.20
87_R109_I0.8040.20
157_G195_L0.8030.20
51_G176_A0.8020.20
36_T191_S0.7930.20
72_R179_I0.7900.20
219_F246_I0.7870.20
66_Y214_L0.7830.20
116_L143_L0.7820.19
159_C173_A0.7820.19
80_D113_C0.7800.19
203_Y214_L0.7770.19
232_V237_I0.7770.19
106_K113_C0.7760.19
58_S198_S0.7750.19
43_T138_Q0.7740.19
137_R141_K0.7670.19
70_D241_S0.7660.19
50_N241_S0.7630.19
177_I239_N0.7620.19
44_K90_Y0.7560.19
193_L246_I0.7510.19
205_E253_F0.7480.18
189_I259_I0.7470.18
50_N159_C0.7420.18
218_L221_I0.7410.18
51_G214_L0.7410.18
27_F174_F0.7360.18
48_A53_A0.7300.18
99_E113_C0.7270.18
173_A195_L0.7270.18
62_V137_R0.7260.18
190_C193_L0.7260.18
51_G66_Y0.7150.18
64_F181_Y0.7150.18
75_H137_R0.7120.17
43_T61_I0.7120.17
139_I226_R0.7100.17
63_P94_N0.7000.17
26_I47_I0.6970.17
38_L230_D0.6910.17
51_G158_F0.6900.17
60_N259_I0.6840.17
26_I87_R0.6840.17
140_H164_L0.6830.17
34_Q107_L0.6820.17
79_D211_P0.6760.16
183_L253_F0.6760.16
52_S244_T0.6740.16
128_I255_K0.6740.16
213_E216_R0.6740.16
186_A190_C0.6730.16
48_A63_P0.6720.16
222_L247_S0.6640.16
65_I191_S0.6630.16
122_R196_T0.6630.16
193_L199_C0.6610.16
178_Q194_D0.6600.16
31_P101_A0.6570.16
110_L149_L0.6560.16
84_F238_Y0.6540.16
161_D171_T0.6530.16
195_L201_R0.6520.16
143_L234_D0.6490.16
27_F53_A0.6490.16
38_L259_I0.6410.16
149_L190_C0.6390.15
177_I215_S0.6380.15
111_Q116_L0.6380.15
198_S238_Y0.6380.15
85_S101_A0.6360.15
195_L241_S0.6320.15
73_F244_T0.6250.15
21_S127_F0.6230.15
80_D201_R0.6230.15
34_Q121_R0.6210.15
161_D208_N0.6200.15
180_A193_L0.6190.15
33_S63_P0.6160.15
49_V213_E0.6140.15
206_N259_I0.6140.15
51_G241_S0.6140.15
173_A176_A0.6130.15
50_N158_F0.6130.15
50_N55_Y0.6130.15
56_L178_Q0.6100.15
196_T205_E0.6080.15
28_L113_C0.6080.15
37_P182_S0.6080.15
79_D205_E0.6060.15
28_L196_T0.6060.15
109_I119_F0.6020.15
61_I203_Y0.6020.15
151_K236_N0.5930.14
171_T211_P0.5920.14
174_F214_L0.5920.14
62_V177_I0.5910.14
70_D224_F0.5910.14
50_N221_I0.5900.14
47_I129_K0.5890.14
55_Y178_Q0.5880.14
155_L234_D0.5870.14
144_L179_I0.5850.14
107_L187_R0.5850.14
149_L238_Y0.5840.14
84_F124_K0.5830.14
24_V140_H0.5830.14
212_S251_I0.5790.14
24_V170_H0.5780.14
128_I237_I0.5770.14
115_V167_C0.5760.14
83_K110_L0.5760.14
67_V176_A0.5730.14
26_I253_F0.5710.14
29_S33_S0.5710.14
26_I167_C0.5700.14
99_E103_K0.5670.14
185_Y220_K0.5670.14
137_R227_F0.5630.14
158_F178_Q0.5610.14
75_H103_K0.5610.14
48_A111_Q0.5600.14
193_L201_R0.5600.14
63_P229_H0.5590.14
51_G203_Y0.5570.13
26_I90_Y0.5560.13
46_I61_I0.5540.13
162_I179_I0.5470.13
204_D214_L0.5450.13
202_F244_T0.5440.13
172_I192_G0.5430.13
30_G172_I0.5430.13
25_I185_Y0.5420.13
171_T193_L0.5410.13
28_L240_L0.5400.13
51_G55_Y0.5380.13
68_L166_Y0.5370.13
45_D156_V0.5340.13
20_I82_Y0.5330.13
22_D189_I0.5310.13
104_E183_L0.5310.13
61_I252_P0.5310.13
51_G159_C0.5290.13
201_R221_I0.5260.13
144_L206_N0.5250.13
77_R225_F0.5250.13
25_I180_A0.5230.13
95_V256_L0.5220.13
29_S166_Y0.5200.13
139_I234_D0.5170.13
55_Y73_F0.5170.13
72_R119_F0.5160.13
90_Y218_L0.5160.13
66_Y193_L0.5160.13
230_D259_I0.5130.13
31_P150_S0.5130.13
201_R212_S0.5120.13
78_R188_I0.5120.13
34_Q233_K0.5120.13
43_T131_I0.5100.12
44_K184_K0.5100.12
90_Y170_H0.5080.12
204_D212_S0.5070.12
52_S168_S0.5050.12
107_L196_T0.5030.12
32_T234_D0.5030.12
65_I184_K0.5000.12
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  
2p2vA 3 0.8693 99.9 0.693 Contact Map
1ro7A 3 0.8127 99.9 0.707 Contact Map
2wqqA 1 0.7915 99.9 0.726 Contact Map
3lm8A 2 0.6643 29.4 0.96 Contact Map
3l8mA 5 0.6502 23.4 0.962 Contact Map
3hrgA 1 0.4134 20.9 0.963 Contact Map
3melA 2 0.6678 18.7 0.964 Contact Map
3k94A 2 0.6643 13.8 0.966 Contact Map
3ihkA 3 0.6502 13.4 0.966 Contact Map
3cq9A 2 0.6643 10.9 0.967 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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