GREMLIN Database
Kdo_hydroxy - 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase
PFAM: PF11004 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 274 (271)
Sequences: 2152 (1493)
Seq/√Len: 90.7
META: 0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
140_T225_T4.2661.00
18_F221_P4.0831.00
208_D212_N3.6341.00
150_V217_R3.0261.00
105_E147_E2.9021.00
203_M234_S2.8561.00
251_P254_A2.8041.00
75_F140_T2.7371.00
53_G73_R2.7321.00
95_R133_R2.7241.00
97_D249_L2.6201.00
152_R215_Q2.5661.00
152_R238_L2.4351.00
221_P224_S2.3921.00
160_L234_S2.3781.00
160_L203_M2.3351.00
155_E209_Y2.3221.00
158_E162_R2.3101.00
209_Y213_A2.2671.00
180_R188_R2.2631.00
142_V244_L2.2451.00
49_D98_R2.2341.00
80_T96_L2.1801.00
28_E31_R2.1111.00
197_L201_D2.1031.00
66_E69_R1.9911.00
215_Q238_L1.9761.00
113_W205_A1.9711.00
80_T248_F1.9611.00
131_R190_S1.9481.00
150_V219_E1.9311.00
83_V138_V1.9191.00
18_F224_S1.9121.00
33_F67_R1.9081.00
177_A181_A1.9031.00
39_L104_V1.8991.00
159_A162_R1.8981.00
80_T84_A1.8961.00
177_A183_G1.8801.00
138_V225_T1.8741.00
70_A74_R1.8441.00
13_A260_R1.8391.00
270_A273_P1.8381.00
264_R267_E1.8331.00
148_P219_E1.8331.00
47_S56_R1.7791.00
89_P256_V1.7581.00
58_A62_G1.7391.00
169_G198_Q1.7321.00
161_A269_L1.7061.00
76_S99_T1.6971.00
155_E163_R1.6761.00
114_R205_A1.6701.00
167_R202_R1.6581.00
257_D260_R1.6281.00
230_T243_A1.6261.00
150_V239_S1.6181.00
48_Y53_G1.5941.00
158_E268_R1.5931.00
84_A91_A1.5601.00
112_S115_K1.5481.00
10_A15_K1.5261.00
61_D64_D1.5161.00
83_V94_L1.5091.00
49_D52_T1.4891.00
29_E67_R1.4871.00
105_E109_R1.4741.00
79_A138_V1.4621.00
108_G118_D1.4320.99
119_R207_A1.4170.99
26_L34_L1.4110.99
84_A92_G1.4020.99
198_Q202_R1.3920.99
107_A147_E1.3830.99
168_A171_P1.3810.99
153_V218_V1.3700.99
195_L270_A1.3500.99
97_D128_R1.3460.99
252_V264_R1.3380.99
76_S96_L1.2990.99
75_F79_A1.2960.99
101_F242_Y1.2890.99
83_V227_I1.2870.99
73_R77_A1.2800.99
8_C89_P1.2800.99
71_M101_F1.2780.99
154_G213_A1.2580.98
58_A68_L1.2530.98
168_A202_R1.2480.98
39_L42_K1.2280.98
19_F82_L1.2250.98
58_A65_A1.2150.98
178_L182_L1.2110.98
32_R64_D1.2040.98
213_A234_S1.1980.98
161_A265_I1.1850.98
175_S183_G1.1830.98
167_R206_D1.1820.98
93_H253_E1.1770.98
106_E118_D1.1750.98
78_Q81_A1.1700.98
32_R67_R1.1660.98
93_H254_A1.1640.97
69_R73_R1.1510.97
156_P159_A1.1440.97
202_R206_D1.1360.97
147_E241_Q1.1340.97
143_N147_E1.1260.97
155_E159_A1.1230.97
7_A10_A1.1130.97
24_F138_V1.1120.97
261_S265_I1.1070.97
207_A211_R1.1060.97
177_A188_R1.1040.97
81_A85_R1.1000.96
168_A199_L1.0980.96
98_R128_R1.0890.96
252_V263_L1.0880.96
258_P264_R1.0760.96
252_V255_M1.0760.96
6_A10_A1.0740.96
199_L206_D1.0640.96
28_E32_R1.0630.96
169_G175_S1.0590.96
130_T133_R1.0560.96
143_N242_Y1.0530.95
124_A190_S1.0510.95
47_S100_S1.0450.95
19_F227_I1.0330.95
199_L203_M1.0230.95
49_D54_R1.0130.94
164_F202_R1.0120.94
84_A94_L1.0030.94
229_F232_Q0.9990.94
165_A168_A0.9970.94
77_A96_L0.9920.94
232_Q255_M0.9820.93
128_R228_V0.9810.93
101_F142_V0.9730.93
60_G65_A0.9720.93
4_Q7_A0.9590.93
263_L267_E0.9520.92
155_E213_A0.9500.92
100_S135_I0.9480.92
143_N241_Q0.9470.92
29_E32_R0.9470.92
208_D211_R0.9430.92
33_F38_L0.9380.92
39_L43_A0.9360.92
63_A67_R0.9290.91
53_G69_R0.9260.91
133_R251_P0.9230.91
113_W207_A0.9210.91
171_P175_S0.9170.91
6_A9_A0.9170.91
155_E214_P0.9170.91
22_L225_T0.9130.91
232_Q265_I0.9130.91
65_A69_R0.9080.90
75_F225_T0.9040.90
271_G274_L0.9030.90
66_E70_A0.9000.90
139_F230_T0.8940.90
255_M260_R0.8930.90
5_R9_A0.8910.90
114_R201_D0.8870.89
170_L195_L0.8830.89
4_Q8_C0.8810.89
30_E74_R0.8790.89
20_P23_P0.8780.89
31_R35_S0.8740.89
128_R135_I0.8730.89
77_A85_R0.8720.89
9_A257_D0.8710.89
254_A267_E0.8700.88
9_A13_A0.8670.88
44_K115_K0.8660.88
120_L255_M0.8650.88
101_F230_T0.8630.88
33_F68_L0.8600.88
34_L142_V0.8570.88
180_R187_S0.8540.88
33_F64_D0.8500.87
165_A270_A0.8490.87
260_R265_I0.8490.87
177_A180_R0.8460.87
11_L87_L0.8390.87
106_E111_L0.8350.86
134_R232_Q0.8300.86
152_R217_R0.8290.86
122_V237_A0.8210.85
165_A170_L0.8190.85
172_L175_S0.8180.85
67_R70_A0.8140.85
103_P237_A0.8130.85
15_K18_F0.8120.85
156_P232_Q0.8080.85
120_L236_A0.8050.84
178_L181_A0.8020.84
130_T228_V0.8010.84
111_L115_K0.8010.84
16_V153_V0.8000.84
163_R208_D0.7960.84
231_D235_H0.7960.84
8_C256_V0.7960.84
138_V227_I0.7940.83
154_G209_Y0.7910.83
220_F224_S0.7880.83
86_L227_I0.7860.83
47_S98_R0.7780.82
200_H204_K0.7770.82
106_E243_A0.7760.82
171_P174_G0.7750.82
163_R167_R0.7750.82
38_L43_A0.7710.82
44_K200_H0.7710.82
38_L41_G0.7660.81
115_K201_D0.7650.81
115_K130_T0.7640.81
140_T222_P0.7610.81
260_R264_R0.7580.81
217_R238_L0.7570.80
161_A165_A0.7570.80
104_V108_G0.7530.80
191_P195_L0.7500.80
261_S264_R0.7500.80
170_L191_P0.7460.79
162_R269_L0.7450.79
74_R78_Q0.7430.79
101_F122_V0.7420.79
49_D128_R0.7330.78
64_D68_L0.7310.78
232_Q260_R0.7310.78
56_R60_G0.7270.78
154_G215_Q0.7240.77
105_E108_G0.7220.77
140_T161_A0.7200.77
177_A182_L0.7200.77
45_N100_S0.7190.77
63_A66_E0.7180.77
19_F22_L0.7140.76
168_A194_H0.7140.76
30_E37_Q0.7110.76
105_E111_L0.7060.76
249_L252_V0.7040.75
252_V261_S0.7040.75
72_M219_E0.6980.75
67_R71_M0.6970.75
104_V111_L0.6970.75
127_S184_I0.6960.75
188_R191_P0.6950.75
11_L14_G0.6950.75
168_A195_L0.6850.73
153_V222_P0.6830.73
118_D195_L0.6780.73
168_A180_R0.6780.73
131_R188_R0.6740.72
228_V233_V0.6720.72
24_F30_E0.6700.72
165_A191_P0.6690.72
82_L86_L0.6690.72
38_L42_K0.6660.71
48_Y72_M0.6650.71
81_A208_D0.6630.71
172_L176_A0.6610.71
156_P209_Y0.6590.71
63_A73_R0.6560.70
112_S218_V0.6560.70
45_N200_H0.6540.70
30_E33_F0.6490.69
94_L250_L0.6490.69
203_M255_M0.6490.69
158_E260_R0.6470.69
77_A81_A0.6460.69
74_R77_A0.6440.69
237_A246_Q0.6430.69
259_E268_R0.6410.68
237_A251_P0.6380.68
189_R194_H0.6360.68
153_V216_Q0.6360.68
48_Y73_R0.6340.68
58_A61_D0.6320.67
221_P230_T0.6320.67
227_I255_M0.6310.67
175_S178_L0.6310.67
133_R249_L0.6310.67
49_D97_D0.6300.67
125_F245_E0.6300.67
168_A198_Q0.6300.67
33_F37_Q0.6300.67
263_L274_L0.6280.67
89_P92_G0.6240.66
87_L120_L0.6230.66
79_A83_V0.6210.66
242_Y270_A0.6200.66
130_T227_I0.6180.66
8_C88_P0.6160.65
96_L237_A0.6150.65
131_R187_S0.6150.65
127_S197_L0.6150.65
111_L203_M0.6110.65
33_F71_M0.6080.64
33_F41_G0.6070.64
115_K143_N0.6060.64
176_A188_R0.6050.64
167_R173_P0.6020.64
111_L118_D0.5990.63
112_S134_R0.5960.63
44_K47_S0.5960.63
114_R232_Q0.5950.63
109_R160_L0.5950.63
225_T243_A0.5940.63
49_D56_R0.5930.62
112_S234_S0.5930.62
72_M147_E0.5920.62
162_R268_R0.5910.62
160_L164_F0.5890.62
113_W119_R0.5880.62
115_K197_L0.5830.61
189_R197_L0.5790.61
35_S38_L0.5770.60
199_L202_R0.5770.60
83_V248_F0.5750.60
180_R183_G0.5740.60
176_A179_L0.5730.60
9_A256_V0.5730.60
148_P222_P0.5720.60
25_A31_R0.5720.60
44_K50_P0.5700.59
269_L274_L0.5680.59
120_L213_A0.5670.59
191_P272_R0.5660.59
106_E117_D0.5660.59
74_R120_L0.5650.59
5_R8_C0.5640.59
217_R239_S0.5620.58
39_L203_M0.5620.58
160_L199_L0.5610.58
203_M206_D0.5580.58
135_I251_P0.5560.58
109_R234_S0.5560.58
24_F74_R0.5550.57
25_A110_D0.5540.57
199_L232_Q0.5530.57
179_L183_G0.5520.57
127_S189_R0.5520.57
125_F200_H0.5500.57
155_E216_Q0.5490.57
166_P172_L0.5490.57
164_F167_R0.5480.56
106_E230_T0.5470.56
30_E35_S0.5470.56
159_A214_P0.5440.56
22_L75_F0.5440.56
55_L69_R0.5430.56
168_A203_M0.5410.56
125_F189_R0.5400.55
23_P32_R0.5370.55
130_T190_S0.5370.55
113_W228_V0.5360.55
226_W231_D0.5350.55
94_L227_I0.5330.54
105_E118_D0.5320.54
20_P36_P0.5320.54
154_G218_V0.5310.54
80_T242_Y0.5310.54
178_L250_L0.5300.54
58_A64_D0.5270.54
76_S80_T0.5270.54
48_Y106_E0.5270.54
78_Q85_R0.5250.53
113_W118_D0.5230.53
198_Q228_V0.5220.53
225_T228_V0.5210.53
16_V220_F0.5210.53
98_R126_P0.5200.53
64_D67_R0.5180.52
125_F196_M0.5180.52
102_R125_F0.5180.52
165_A269_L0.5160.52
112_S127_S0.5150.52
265_I269_L0.5150.52
97_D116_D0.5150.52
36_P39_L0.5150.52
134_R262_P0.5140.52
115_K174_G0.5120.52
218_V221_P0.5110.51
15_K221_P0.5100.51
103_P230_T0.5080.51
12_E16_V0.5080.51
173_P183_G0.5080.51
266_L274_L0.5080.51
257_D261_S0.5080.51
48_Y130_T0.5060.51
158_E232_Q0.5050.51
16_V218_V0.5050.51
119_R209_Y0.5040.50
262_P266_L0.5040.50
219_E243_A0.5040.50
45_N109_R0.5040.50
176_A191_P0.5030.50
47_S218_V0.5030.50
169_G172_L0.5010.50
257_D265_I0.5010.50
79_A99_T0.5010.50
205_A222_P0.5000.50
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  
3zytA 3 0.5584 22.6 0.973 Contact Map
4j25A 2 0.6606 18 0.974 Contact Map
4qu7A 1 0.2956 17.5 0.974 Contact Map
3d8cA 2 0.3248 15.6 0.975 Contact Map
2kxnB 1 0.3321 14.7 0.975 Contact Map
2qz6A 1 0.6058 14.5 0.975 Contact Map
1vrbA 2 0.3613 13.5 0.976 Contact Map
3fedA 2 0.3139 12.7 0.976 Contact Map
2mpuA 1 0.3212 12 0.976 Contact Map
4wkrA 1 0.2774 11.8 0.976 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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