GREMLIN Database
YBIA - Swarming motility protein YbiA
UniProt: P30176 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11579
Length: 160 (144)
Sequences: 1320 (980)
Seq/√Len: 81.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
98_R151_E3.5181.00
102_R155_Q2.9021.00
101_L148_L2.7741.00
46_T49_H2.7101.00
44_W53_A2.6541.00
50_Y100_A2.5431.00
101_L152_L2.3981.00
39_V103_A2.3631.00
86_R90_E2.3571.00
90_E93_K2.3101.00
51_F97_M2.2861.00
45_P49_H2.2471.00
93_K142_K2.1981.00
54_Q57_L2.1961.00
53_A62_R2.1831.00
49_H74_A2.1681.00
31_N101_L2.0631.00
61_Y77_M2.0511.00
28_D114_L1.9671.00
102_R152_L1.9271.00
109_A112_R1.7931.00
120_P157_A1.7571.00
98_R155_Q1.7561.00
72_M76_R1.7251.00
94_E98_R1.7021.00
57_L62_R1.6801.00
31_N97_M1.6671.00
38_K41_G1.6521.00
113_A117_A1.6511.00
16_I121_A1.5991.00
39_V50_Y1.5441.00
48_E52_Q1.5320.99
119_A157_A1.5310.99
50_Y103_A1.5230.99
48_E125_E1.5210.99
42_K63_E1.5080.99
31_N47_S1.5020.99
36_P43_T1.4990.99
17_I121_A1.4880.99
122_K147_Y1.4680.99
103_A106_E1.4270.99
46_T74_A1.3960.99
88_N92_V1.3720.99
54_Q96_V1.3640.99
94_E144_R1.3280.99
118_T123_L1.3200.98
60_K82_S1.3170.98
20_Y128_E1.2890.98
126_H135_D1.2360.98
53_A57_L1.2010.97
47_S100_A1.2000.97
94_E151_E1.1940.97
116_L157_A1.1640.97
149_L153_R1.1380.96
70_S73_V1.1310.96
45_P74_A1.1300.96
94_E132_Y1.1270.96
32_F125_E1.1150.96
112_R116_L1.1040.95
40_D99_K1.1020.95
114_L117_A1.0950.95
93_K144_R1.0940.95
73_V76_R1.0900.95
59_E62_R1.0710.94
44_W62_R1.0400.94
144_R147_Y1.0190.93
21_S24_D1.0150.93
132_Y144_R1.0010.92
35_W108_H1.0010.92
20_Y32_F0.9940.92
109_A113_A0.9910.92
64_E80_D0.9860.92
118_T153_R0.9850.92
28_D111_L0.9800.91
24_D33_A0.9710.91
86_R92_V0.9700.91
115_L118_T0.9510.90
115_L123_L0.9440.90
95_Q99_K0.9420.90
78_G81_R0.9380.89
98_R148_L0.9350.89
34_A45_P0.9320.89
32_F52_Q0.9300.89
92_V95_Q0.9280.89
131_A140_K0.9070.88
50_Y54_Q0.9040.88
15_T121_A0.8990.87
103_A107_Q0.8790.86
102_R106_E0.8710.86
32_F51_F0.8580.85
118_T150_M0.8460.84
127_T135_D0.8400.84
61_Y81_R0.8370.83
98_R102_R0.8320.83
105_F149_L0.8270.83
61_Y64_E0.8230.82
81_R84_P0.8220.82
99_K103_A0.8190.82
49_H66_R0.8180.82
143_N146_G0.8170.82
61_Y80_D0.8150.82
150_M153_R0.8080.81
92_V96_V0.8080.81
52_Q55_K0.8050.81
97_M133_W0.8050.81
31_N48_E0.8020.81
48_E55_K0.8020.81
69_S73_V0.7990.80
22_T27_G0.7980.80
54_Q99_K0.7950.80
36_P46_T0.7950.80
122_K150_M0.7840.79
33_A111_L0.7720.78
16_I122_K0.7700.78
42_K62_R0.7500.76
141_G146_G0.7440.75
65_I77_M0.7420.75
52_Q125_E0.7410.75
54_Q62_R0.7400.75
31_N51_F0.7390.75
55_K78_G0.7360.75
102_R154_E0.7350.75
55_K145_L0.7320.74
38_K43_T0.7310.74
30_S48_E0.7270.74
112_R156_L0.7270.74
31_N52_Q0.7260.74
39_V54_Q0.7230.73
118_T149_L0.6980.71
47_S97_M0.6960.71
115_L149_L0.6960.71
21_S30_S0.6950.70
39_V99_K0.6890.70
95_Q98_R0.6890.70
59_E73_V0.6880.70
106_E152_L0.6880.70
34_A117_A0.6880.70
20_Y65_I0.6870.70
111_L114_L0.6850.69
35_W46_T0.6820.69
75_A78_G0.6790.69
72_M80_D0.6670.67
59_E63_E0.6650.67
110_E113_A0.6640.67
71_P125_E0.6600.66
26_Y114_L0.6570.66
31_N125_E0.6550.66
79_R125_E0.6530.66
48_E130_D0.6500.65
50_Y96_V0.6470.65
70_S74_A0.6460.65
123_L150_M0.6440.65
48_E78_G0.6430.64
53_A66_R0.6370.64
16_I124_V0.6330.63
63_E67_R0.6320.63
148_L152_L0.6280.63
88_N96_V0.6250.62
31_N133_W0.6230.62
65_I74_A0.6230.62
115_L153_R0.6200.62
39_V44_W0.6170.61
30_S75_A0.6150.61
90_E119_A0.6110.61
105_F111_L0.6090.60
115_L150_M0.6080.60
44_W54_Q0.6070.60
94_E147_Y0.6040.60
49_H65_I0.6020.59
126_H137_G0.5990.59
68_V77_M0.5940.58
20_Y129_N0.5910.58
75_A81_R0.5910.58
123_L149_L0.5900.58
63_E69_S0.5890.58
28_D123_L0.5860.57
14_D122_K0.5850.57
32_F55_K0.5850.57
137_G140_K0.5850.57
107_Q135_D0.5850.57
27_G114_L0.5750.56
36_P45_P0.5730.56
98_R154_E0.5700.55
56_F81_R0.5700.55
76_R80_D0.5700.55
60_K64_E0.5690.55
30_S125_E0.5630.54
102_R156_L0.5610.54
90_E142_K0.5600.54
23_S27_G0.5600.54
116_L156_L0.5590.54
108_H111_L0.5570.54
94_E142_K0.5480.52
71_P74_A0.5480.52
20_Y31_N0.5470.52
103_A108_H0.5440.52
72_M129_N0.5390.51
50_Y99_K0.5390.51
105_F118_T0.5330.50
17_I26_Y0.5320.50
87_K91_S0.5320.50
75_A145_L0.5320.50
24_D155_Q0.5310.50
52_Q97_M0.5290.50
70_S121_A0.5250.49
21_S27_G0.5230.49
63_E66_R0.5180.49
48_E71_P0.5170.48
59_E87_K0.5150.48
55_K89_W0.5150.48
104_K108_H0.5120.48
22_T114_L0.5100.47
19_F89_W0.5080.47
58_D81_R0.5080.47
42_K66_R0.5060.47
77_M80_D0.5000.46
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  
2b3wA 1 1 100 0.049 Contact Map
1mtyG 1 0.6937 12.3 0.945 Contact Map
1mhyG 1 0.7125 7.2 0.951 Contact Map
1t35A 5 0.5062 5.1 0.954 Contact Map
2jzyA 1 0.5188 4.7 0.955 Contact Map
2zp1A 2 0.3563 4 0.956 Contact Map
3zq7A 1 0.5125 3.9 0.957 Contact Map
5ajtA 2 0.5563 3.5 0.957 Contact Map
3rjpA 1 0.4813 3.5 0.958 Contact Map
2zxjA 1 0.5 3.4 0.958 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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