GREMLIN Database
YKAA - UPF0111 protein YkaA
UniProt: O34454 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 205 (195)
Sequences: 1521 (1112)
Seq/√Len: 79.6

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_K147_E3.4311.00
152_C187_A3.3451.00
53_D84_D2.9751.00
149_E188_D2.9401.00
59_M80_T2.9221.00
49_E53_D2.8631.00
52_G87_L2.7791.00
19_N52_G2.6581.00
23_T87_L2.6561.00
49_E84_D2.5991.00
45_L94_S2.5251.00
34_N37_T2.4811.00
153_D188_D2.4351.00
115_Y148_Y2.3841.00
149_E153_D2.3601.00
19_N51_K2.2801.00
22_E51_K2.2581.00
15_E58_V2.2581.00
108_H162_N2.1901.00
25_E121_K2.1761.00
122_E141_H2.1681.00
101_S165_G2.1281.00
47_E50_T2.1141.00
145_I194_A2.1101.00
86_V123_I2.0831.00
32_V110_D1.9861.00
43_D47_E1.9531.00
116_I186_I1.9281.00
44_T47_E1.8911.00
37_T40_E1.8621.00
122_E144_K1.8281.00
162_N166_N1.8121.00
118_E151_S1.7581.00
18_K124_L1.7151.00
14_T131_A1.7021.00
111_K114_G1.6781.00
26_Y44_T1.6751.00
19_N22_E1.6581.00
151_S154_N1.6161.00
28_V114_G1.5831.00
57_H146_K1.5570.99
127_I130_L1.5470.99
31_K113_S1.5300.99
57_H143_I1.5200.99
74_E203_K1.5120.99
122_E125_I1.5080.99
119_C148_Y1.4860.99
21_D121_K1.4780.99
9_F76_I1.4670.99
21_D124_L1.4620.99
120_A190_C1.4460.99
146_K191_Q1.4390.99
49_E88_D1.4330.99
28_V117_R1.4240.99
16_I52_G1.4170.99
126_T197_L1.4100.99
95_A157_R1.4090.99
24_A90_I1.4080.99
17_A124_L1.3820.99
159_S180_Y1.3750.99
46_K91_E1.3480.99
53_D88_D1.3340.98
67_F72_E1.3280.98
85_D88_D1.3230.98
86_V193_V1.3040.98
134_R138_I1.2620.98
58_V62_E1.2500.98
75_D203_K1.2440.97
40_E44_T1.2320.97
184_E188_D1.2200.97
9_F69_T1.2140.97
106_D180_Y1.1780.97
169_D172_K1.1730.96
30_F94_S1.1590.96
26_Y41_F1.1520.96
84_D88_D1.1520.96
30_F38_L1.1350.96
14_T128_E1.1310.96
109_I176_Y1.1290.96
106_D176_Y1.1280.96
129_L137_D1.1110.95
47_E51_K1.1020.95
29_N44_T1.0920.95
21_D25_E1.0790.94
157_R177_R1.0650.94
146_K195_N1.0460.93
26_Y45_L1.0430.93
100_F175_Q1.0380.93
19_N48_Y1.0370.93
16_I80_T1.0350.93
118_E121_K1.0310.93
189_S192_S1.0160.92
17_A83_L1.0130.92
63_L76_I1.0120.92
25_E117_R0.9980.92
18_K22_E0.9840.91
117_R121_K0.9690.90
15_E18_K0.9650.90
26_Y48_Y0.9340.89
195_N198_E0.9330.89
111_K151_S0.9250.88
127_I131_A0.9230.88
44_T51_K0.9090.87
60_I196_N0.9060.87
110_D116_I0.8990.87
69_T76_I0.8940.86
37_T41_F0.8930.86
93_F186_I0.8860.86
40_E43_D0.8850.86
137_D140_P0.8840.86
124_L128_E0.8840.86
48_Y51_K0.8810.86
140_P144_K0.8750.85
121_K125_I0.8750.85
50_T54_N0.8720.85
176_Y180_Y0.8680.85
13_L76_I0.8670.85
41_F44_T0.8570.84
20_I87_L0.8520.84
69_T72_E0.8500.83
178_E181_E0.8490.83
121_K124_L0.8460.83
9_F67_F0.8340.82
84_D149_E0.8250.82
156_H184_E0.8230.81
192_S195_N0.8210.81
153_D184_E0.8130.81
79_L193_V0.8100.80
66_A69_T0.8060.80
172_K175_Q0.8060.80
82_S85_D0.8050.80
157_R164_F0.8000.80
20_I23_T0.7990.80
89_G189_S0.7930.79
109_I116_I0.7930.79
163_L180_Y0.7920.79
32_V114_G0.7900.79
143_I191_Q0.7860.78
82_S192_S0.7850.78
149_E184_E0.7840.78
158_K162_N0.7830.78
73_R76_I0.7820.78
62_E65_K0.7790.78
120_A124_L0.7740.77
118_E144_K0.7730.77
26_Y29_N0.7700.77
116_I120_A0.7690.77
57_H198_E0.7660.77
27_F90_I0.7660.77
112_F156_H0.7600.76
29_N41_F0.7530.75
156_H181_E0.7530.75
16_I186_I0.7510.75
163_L179_I0.7500.75
59_M133_N0.7460.75
136_K140_P0.7450.75
145_I166_N0.7400.74
45_L48_Y0.7350.74
57_H191_Q0.7330.73
86_V190_C0.7310.73
71_I74_E0.7310.73
25_E29_N0.7290.73
143_I150_H0.7230.72
28_V113_S0.7220.72
22_E32_V0.7220.72
126_T141_H0.7200.72
98_E161_K0.7200.72
99_I160_L0.7180.72
187_A199_T0.7140.71
144_K148_Y0.7100.71
111_K158_K0.7000.70
171_I175_Q0.6990.70
49_E149_E0.6960.70
99_I157_R0.6960.70
115_Y118_E0.6950.69
39_K43_D0.6950.69
38_L97_M0.6910.69
18_K128_E0.6890.69
148_Y152_C0.6830.68
12_L55_H0.6820.68
29_N32_V0.6810.68
8_K62_E0.6790.68
119_C187_A0.6780.68
35_Q38_L0.6750.67
155_L159_S0.6730.67
67_F76_I0.6700.67
93_F183_L0.6700.67
61_K198_E0.6690.66
67_F71_I0.6650.66
168_T171_I0.6650.66
39_K98_E0.6580.65
133_N198_E0.6480.64
54_N58_V0.6460.64
24_A120_A0.6460.64
66_A71_I0.6460.64
16_I19_N0.6450.64
51_K54_N0.6390.63
22_E29_N0.6380.63
160_L177_R0.6370.63
143_I146_K0.6360.63
25_E28_V0.6350.62
163_L176_Y0.6340.62
112_F119_C0.6330.62
118_E148_Y0.6320.62
22_E47_E0.6310.62
48_Y94_S0.6310.62
150_H154_N0.6280.62
167_E173_V0.6280.62
113_S117_R0.6260.61
181_E185_E0.6220.61
57_H150_H0.6200.61
83_L86_V0.6180.60
31_K97_M0.6150.60
148_Y187_A0.6130.60
67_F70_P0.6120.60
63_L167_E0.6070.59
16_I20_I0.6030.58
103_T172_K0.6010.58
46_K50_T0.6000.58
95_A99_I0.5990.58
67_F73_R0.5960.58
35_Q55_H0.5960.58
37_T44_T0.5960.58
79_L200_I0.5930.57
20_I27_F0.5930.57
80_T196_N0.5900.57
56_V80_T0.5890.57
125_I141_H0.5880.57
42_A157_R0.5880.57
89_G182_T0.5820.56
115_Y152_C0.5820.56
92_H119_C0.5800.56
70_P73_R0.5800.56
56_V59_M0.5780.55
117_R120_A0.5780.55
29_N39_K0.5760.55
27_F31_K0.5760.55
51_K93_F0.5740.55
115_Y122_E0.5740.55
40_E103_T0.5730.55
13_L23_T0.5730.55
63_L70_P0.5720.55
59_M76_I0.5710.54
164_F177_R0.5710.54
123_I185_E0.5700.54
114_G118_E0.5690.54
88_D146_K0.5660.54
92_H182_T0.5660.54
130_L157_R0.5610.53
10_S174_I0.5590.53
156_H182_T0.5560.52
59_M89_G0.5520.52
56_V84_D0.5500.52
38_L200_I0.5450.51
64_N203_K0.5440.51
116_I122_E0.5420.51
92_H96_M0.5420.51
123_I127_I0.5400.50
36_T110_D0.5390.50
46_K94_S0.5390.50
80_T83_L0.5380.50
30_F45_L0.5370.50
32_V117_R0.5370.50
12_L15_E0.5340.50
27_F93_F0.5330.50
177_R181_E0.5330.50
93_F182_T0.5320.49
32_V113_S0.5320.49
159_S190_C0.5290.49
11_L138_I0.5280.49
11_L131_A0.5240.48
23_T123_I0.5230.48
10_S191_Q0.5220.48
166_N202_M0.5210.48
173_V177_R0.5210.48
88_D149_E0.5190.48
13_L200_I0.5190.48
149_E191_Q0.5170.47
45_L90_I0.5170.47
60_I77_L0.5170.47
69_T100_F0.5160.47
112_F155_L0.5160.47
193_V196_N0.5130.47
102_I194_A0.5120.47
24_A184_E0.5100.47
52_G90_I0.5090.46
97_M112_F0.5080.46
56_V60_I0.5070.46
43_D162_N0.5040.46
67_F184_E0.5020.46
108_H180_Y0.5000.45
49_E52_G0.5000.45
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  
3l39A 3 1 100 0.159 Contact Map
2oltA 5 0.9805 100 0.404 Contact Map
1t72A 5 0.961 98.4 0.794 Contact Map
2i0mA 2 0.9268 98.2 0.803 Contact Map
1xwmA 2 0.9512 98.2 0.805 Contact Map
1sumB 2 0.961 98.1 0.808 Contact Map
4q25A 2 0.9317 98 0.813 Contact Map
2w72C 2 0.361 21.1 0.937 Contact Map
2r80A 2 0.361 18.8 0.938 Contact Map
3wctB 3 0.3805 18.4 0.938 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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