GREMLIN Database
RFAY - Lipopolysaccharide core heptose(II) kinase RfaY
UniProt: P27240 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11425
Length: 232 (188)
Sequences: 414 (303)
Seq/√Len: 22.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
144_I173_V3.9111.00
58_I124_Y3.5921.00
127_G130_L3.1581.00
109_R117_T3.0411.00
213_L216_R2.9490.99
83_E87_E2.7170.99
158_S161_P2.6180.99
161_P166_F2.5800.98
157_V184_S2.5720.98
59_L121_I2.4560.98
150_A154_H2.3640.97
125_I174_R2.3490.97
55_G123_E2.3210.97
82_Y103_F2.2140.96
81_Y179_S2.0940.94
91_K95_E1.9950.93
29_L32_N1.9000.91
30_S33_I1.8760.90
151_L175_I1.8550.90
209_G213_L1.7970.88
89_T99_T1.7920.88
158_S166_F1.7890.88
57_L104_Y1.7560.87
186_Q190_K1.7540.87
52_T57_L1.7270.86
62_F120_M1.7090.86
212_L216_R1.6730.84
62_F179_S1.6680.84
76_L114_F1.6190.82
85_L120_M1.6030.82
85_L178_L1.5990.81
62_F81_Y1.5950.81
88_Q192_R1.5850.81
152_H195_L1.5380.79
51_D56_K1.5360.79
33_I106_L1.4930.77
132_D150_A1.4840.76
45_T81_Y1.4830.76
148_I161_P1.4800.76
160_D177_D1.4610.75
82_Y118_Y1.4430.74
45_T179_S1.4360.74
45_T164_G1.4230.73
96_G176_I1.4130.72
134_P138_D1.4120.72
207_D214_V1.4010.72
148_I192_R1.3850.71
44_D162_H1.3830.71
103_F118_Y1.3750.70
87_E126_D1.3430.69
209_G216_R1.3360.68
45_T173_V1.3300.68
62_F164_G1.3200.67
80_D108_E1.2880.65
211_Y214_V1.2880.65
115_V118_Y1.2850.65
147_S173_V1.2730.64
92_V156_M1.2670.64
82_Y85_L1.2570.63
206_R214_V1.2480.63
85_L167_I1.2440.62
152_H167_I1.2380.62
49_L56_K1.2320.62
158_S176_I1.2310.62
110_K115_V1.2290.61
130_L195_L1.2160.61
165_N177_D1.2080.60
73_F97_L1.2060.60
208_L212_L1.2020.60
89_T120_M1.2010.60
204_E214_V1.1780.58
162_H191_D1.1780.58
89_T178_L1.1710.58
84_R168_I1.1350.55
60_K177_D1.1270.55
208_L214_V1.1250.55
166_F175_I1.1220.54
50_I119_I1.1220.54
52_T55_G1.1170.54
162_H178_L1.1140.54
45_T180_G1.1130.54
103_F175_I1.0660.51
126_D186_Q1.0500.49
164_G179_S1.0480.49
206_R211_Y1.0470.49
208_L216_R1.0470.49
65_K166_F1.0440.49
53_D212_L1.0400.49
145_Q188_K1.0340.48
64_P151_L1.0330.48
47_V159_G1.0290.48
25_L104_Y1.0260.48
81_Y162_H1.0210.47
142_N146_Q1.0160.47
149_N153_Q1.0140.47
85_L89_T1.0130.47
29_L34_N1.0100.47
39_F47_V1.0070.47
102_D123_E1.0060.46
160_D165_N1.0050.46
30_S34_N1.0010.46
44_D152_H0.9920.46
208_L213_L0.9910.45
134_P137_D0.9880.45
32_N36_I0.9880.45
207_D210_Y0.9830.45
44_D179_S0.9770.45
67_K104_Y0.9670.44
38_V41_S0.9570.43
27_D34_N0.9550.43
149_N168_I0.9510.43
84_R100_L0.9510.43
26_N30_S0.9500.43
152_H173_V0.9490.43
173_V183_A0.9400.42
86_F162_H0.9330.42
47_V58_I0.9300.41
85_L179_S0.9280.41
27_D121_I0.9220.41
91_K106_L0.9190.41
65_K159_G0.9140.40
155_G166_F0.9120.40
191_D196_E0.9090.40
90_Q195_L0.9060.40
191_D194_D0.9040.40
60_K108_E0.9030.40
146_Q186_Q0.9030.40
185_A189_A0.9000.39
60_K160_D0.8970.39
45_T162_H0.8890.39
128_I132_D0.8840.38
81_Y164_G0.8780.38
210_Y215_Y0.8750.38
208_L215_Y0.8740.38
39_F51_D0.8730.38
47_V144_I0.8640.37
121_I170_N0.8570.37
88_Q196_E0.8540.36
92_V103_F0.8520.36
131_C134_P0.8520.36
161_P176_I0.8450.36
97_L147_S0.8450.36
88_Q191_D0.8400.36
111_T195_L0.8350.35
210_Y214_V0.8350.35
168_I191_D0.8310.35
209_G212_L0.8290.35
62_F180_G0.8290.35
104_Y121_I0.8270.35
144_I174_R0.8270.35
144_I147_S0.8210.34
204_E208_L0.8160.34
182_R187_R0.8120.34
65_K69_N0.8040.33
203_N207_D0.7990.33
65_K148_I0.7980.33
161_P192_R0.7900.33
99_T178_L0.7860.32
169_K174_R0.7750.32
192_R195_L0.7660.31
149_N158_S0.7620.31
179_S194_D0.7570.31
149_N188_K0.7470.30
100_L105_L0.7460.30
97_L175_I0.7430.30
45_T74_K0.7420.30
210_Y216_R0.7390.30
45_T65_K0.7390.30
209_G215_Y0.7380.29
27_D30_S0.7370.29
58_I181_K0.7340.29
107_A121_I0.7310.29
65_K147_S0.7180.28
162_H179_S0.7130.28
105_L193_I0.7100.28
77_L186_Q0.7080.28
95_E109_R0.7070.28
87_E146_Q0.7060.28
63_S82_Y0.7030.28
69_N179_S0.6980.27
44_D74_K0.6960.27
74_K180_G0.6950.27
51_D126_D0.6940.27
67_K103_F0.6900.27
151_L194_D0.6890.27
112_L126_D0.6890.27
42_I47_V0.6870.27
50_I125_I0.6790.26
123_E215_Y0.6780.26
60_K119_I0.6750.26
27_D31_Y0.6740.26
74_K152_H0.6740.26
56_K210_Y0.6730.26
83_E112_L0.6650.26
127_G171_G0.6570.25
121_I139_A0.6560.25
111_T116_H0.6560.25
80_D100_L0.6560.25
212_L215_Y0.6530.25
45_T70_E0.6490.25
74_K144_I0.6450.24
85_L158_S0.6430.24
29_L35_I0.6400.24
51_D110_K0.6390.24
82_Y89_T0.6390.24
65_K179_S0.6390.24
56_K86_F0.6380.24
88_Q181_K0.6350.24
31_Y34_N0.6330.24
121_I171_G0.6330.24
81_Y173_V0.6280.24
47_V156_M0.6270.24
113_R129_E0.6260.24
34_N116_H0.6260.24
125_I150_A0.6250.23
110_K113_R0.6250.23
151_L192_R0.6240.23
96_G150_A0.6230.23
152_H155_G0.6180.23
138_D142_N0.6180.23
157_V182_R0.6160.23
53_D139_A0.6160.23
31_Y53_D0.6100.23
91_K94_N0.6100.23
97_L144_I0.6090.23
143_K146_Q0.6050.23
80_D156_M0.6010.22
77_L141_K0.5980.22
35_I50_I0.5950.22
86_F191_D0.5930.22
172_E204_E0.5850.22
73_F173_V0.5850.22
87_E95_E0.5850.22
66_V181_K0.5820.21
31_Y134_P0.5820.21
69_N115_V0.5790.21
38_V126_D0.5790.21
90_Q141_K0.5780.21
97_L170_N0.5740.21
81_Y180_G0.5730.21
81_Y158_S0.5730.21
43_D143_K0.5720.21
40_R159_G0.5690.21
115_V143_K0.5660.21
75_S102_D0.5650.21
73_F121_I0.5560.20
81_Y178_L0.5530.20
60_K165_N0.5520.20
130_L151_L0.5500.20
210_Y213_L0.5490.20
84_R119_I0.5470.20
135_D139_A0.5450.20
82_Y194_D0.5420.20
171_G182_R0.5420.20
84_R189_A0.5410.20
211_Y215_Y0.5400.20
44_D167_I0.5400.20
201_I215_Y0.5390.20
144_I161_P0.5390.20
50_I114_F0.5390.20
78_K181_K0.5370.19
50_I59_L0.5370.19
60_K78_K0.5360.19
81_Y118_Y0.5340.19
147_S183_A0.5320.19
84_R183_A0.5280.19
94_N155_G0.5280.19
37_K96_G0.5240.19
40_R46_K0.5210.19
171_G204_E0.5150.19
122_I127_G0.5130.18
144_I175_I0.5110.18
128_I131_C0.5090.18
75_S162_H0.5090.18
93_R146_Q0.5080.18
53_D127_G0.5070.18
80_D118_Y0.5060.18
51_D214_V0.5060.18
145_Q158_S0.5060.18
149_N191_D0.5040.18
205_I208_L0.5040.18
55_G91_K0.5000.18
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  
4gyiA 1 0.8966 99.6 0.733 Contact Map
1zarA 1 0.8319 99.5 0.741 Contact Map
3tm0A 1 0.8362 99.5 0.746 Contact Map
3atsA 1 0.8707 99.5 0.747 Contact Map
2olcA 3 0.8707 99.5 0.75 Contact Map
1zthA 1 0.8319 99.5 0.75 Contact Map
4h05A 1 0.8448 99.5 0.752 Contact Map
3dxpA 2 0.8405 99.4 0.756 Contact Map
3w0oA 1 0.8233 99.4 0.759 Contact Map
2pywA 2 0.9138 99.4 0.761 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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