GREMLIN Database
YKUD - Putative L,D-transpeptidase YkuD
UniProt: O34816 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 164 (149)
Sequences: 963 (619)
Seq/√Len: 50.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
79_Y149_E4.4241.00
99_N114_S4.1141.00
97_I113_L4.1011.00
112_W121_G4.0231.00
110_A148_I3.6201.00
95_F116_S3.1551.00
88_T137_K2.8531.00
114_S121_G2.6461.00
94_E159_R2.5201.00
87_L136_S2.3381.00
64_A68_T2.3011.00
61_S64_A2.3011.00
70_S75_V2.2391.00
17_A145_K2.1531.00
65_K134_A2.0891.00
108_F121_G2.0861.00
58_I154_V2.0801.00
17_A26_L1.9070.99
21_I46_P1.8710.99
102_R111_Y1.8230.99
111_Y147_V1.7980.99
149_E153_I1.7970.99
69_L77_K1.7860.99
100_R113_L1.7810.99
68_T75_V1.6970.99
155_P158_T1.6330.98
60_V140_I1.6290.98
21_I26_L1.5850.98
33_L41_Q1.5340.97
82_A136_S1.5330.97
66_T78_T1.4250.96
95_F117_K1.4160.95
142_M147_V1.4120.95
104_P107_P1.4120.95
85_K88_T1.3690.94
112_W147_V1.3640.94
61_S68_T1.3180.93
57_H70_S1.3010.93
77_K149_E1.2860.92
130_S135_V1.2810.92
82_A87_L1.2610.92
67_L122_I1.2500.91
16_A26_L1.2410.91
66_T131_I1.2310.91
126_N131_I1.2150.90
69_L150_L1.2100.90
66_T83_V1.2040.90
59_A70_S1.1860.89
45_I72_N1.1830.89
67_L81_I1.1770.89
69_L153_I1.1730.88
111_Y151_A1.1640.88
100_R151_A1.1570.88
100_R156_N1.1330.87
109_G125_T1.0960.85
113_L154_V1.0870.84
93_G128_P1.0800.84
115_L120_Y1.0790.84
103_N110_A1.0750.84
154_V158_T1.0730.83
111_Y152_S1.0710.83
94_E161_T1.0670.83
77_K153_I1.0590.83
125_T131_I1.0410.82
115_L122_I1.0230.80
23_T35_A1.0200.80
53_T70_S1.0160.80
26_L42_S0.9960.79
21_I27_L0.9890.78
17_A143_H0.9880.78
16_A23_T0.9790.77
68_T151_A0.9710.77
13_N17_A0.9660.76
38_T41_Q0.9540.76
104_P125_T0.9490.75
110_A144_N0.9480.75
31_P34_Q0.9460.75
84_G141_R0.9430.75
104_P109_G0.9410.75
98_I116_S0.9360.74
14_S18_D0.9330.74
23_T27_L0.9210.73
25_A28_Q0.9090.72
65_K136_S0.9070.72
56_Y71_L0.9000.71
80_P146_D0.8920.70
64_A154_V0.8890.70
130_S134_A0.8710.69
83_V134_A0.8680.68
17_A20_R0.8660.68
121_G124_G0.8610.68
19_F105_G0.8610.68
57_H76_M0.8580.67
60_V81_I0.8550.67
13_N143_H0.8530.67
99_N102_R0.8480.67
20_R143_H0.8300.65
115_L140_I0.8200.64
17_A144_N0.8180.64
15_I26_L0.8150.63
96_Y157_G0.8150.63
122_I128_P0.8080.63
13_N19_F0.8060.63
49_P78_T0.8050.62
18_D27_L0.7990.62
80_P107_P0.7900.61
113_L155_P0.7870.61
72_N94_E0.7810.60
22_S130_S0.7660.59
44_V152_S0.7650.59
74_R94_E0.7630.58
67_L115_L0.7610.58
88_T106_G0.7600.58
62_I83_V0.7600.58
72_N155_P0.7580.58
68_T132_G0.7450.57
24_A32_S0.7430.56
85_K143_H0.7430.56
40_G96_Y0.7420.56
142_M157_G0.7420.56
62_I92_T0.7270.55
94_E157_G0.7260.55
109_G141_R0.7260.55
86_I136_S0.7240.54
16_A143_H0.7210.54
102_R152_S0.7200.54
80_P109_G0.7180.54
50_D55_P0.7170.54
13_N32_S0.7120.53
26_L43_I0.7090.53
17_A142_M0.7050.52
58_I150_L0.7030.52
59_A68_T0.7010.52
21_I25_A0.7010.52
136_S139_C0.6990.52
91_P141_R0.6950.51
33_L37_L0.6880.51
52_Y152_S0.6870.51
96_Y116_S0.6850.50
27_L38_T0.6840.50
27_L35_A0.6810.50
85_K89_Q0.6790.50
87_L137_K0.6790.50
87_L90_T0.6790.50
96_Y156_N0.6780.50
65_K83_V0.6770.50
91_P109_G0.6730.49
61_S70_S0.6700.49
111_Y148_I0.6670.49
43_I98_I0.6560.47
61_S148_I0.6540.47
106_G131_I0.6520.47
68_T78_T0.6520.47
14_S22_S0.6510.47
15_I153_I0.6470.46
58_I132_G0.6450.46
104_P108_F0.6450.46
45_I154_V0.6450.46
131_I141_R0.6410.46
133_K143_H0.6340.45
116_S128_P0.6330.45
90_T140_I0.6310.45
61_S66_T0.6280.45
63_G70_S0.6270.44
113_L150_L0.6260.44
67_L130_S0.6200.44
113_L156_N0.6180.43
56_Y159_R0.6110.43
93_G117_K0.6110.43
56_Y83_V0.6100.43
33_L43_I0.6090.43
41_Q103_N0.6080.42
84_G139_C0.6060.42
106_G109_G0.6050.42
115_L160_V0.6050.42
66_T132_G0.6010.42
84_G90_T0.5920.41
70_S82_A0.5860.40
41_Q47_G0.5860.40
60_V67_L0.5830.40
17_A128_P0.5800.40
25_A78_T0.5800.40
123_H138_G0.5730.39
57_H133_K0.5700.39
46_P51_P0.5670.38
26_L129_A0.5670.38
142_M152_S0.5650.38
58_I97_I0.5650.38
33_L63_G0.5590.38
33_L36_G0.5590.38
128_P143_H0.5550.37
13_N23_T0.5550.37
50_D54_I0.5510.37
67_L148_I0.5460.36
127_N136_S0.5450.36
85_K145_K0.5440.36
21_I31_P0.5430.36
76_M129_A0.5420.36
51_P70_S0.5390.36
125_T128_P0.5370.36
128_P145_K0.5360.35
77_K110_A0.5330.35
39_A105_G0.5320.35
50_D57_H0.5300.35
46_P132_G0.5290.35
99_N116_S0.5280.35
82_A109_G0.5260.34
84_G111_Y0.5240.34
18_D47_G0.5240.34
113_L122_I0.5230.34
57_H159_R0.5230.34
150_L156_N0.5220.34
100_R155_P0.5190.34
16_A42_S0.5150.33
101_Q114_S0.5100.33
131_I135_V0.5100.33
82_A125_T0.5070.33
81_I130_S0.5070.33
25_A143_H0.5050.33
24_A76_M0.5050.33
22_S25_A0.5050.33
13_N28_Q0.5030.32
84_G95_F0.5020.32
84_G120_Y0.5000.32
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  
4a1kA 2 1 100 0.251 Contact Map
4lzhA 1 0.9573 100 0.269 Contact Map
4xvoA 1 0.9878 100 0.437 Contact Map
4jmnA 1 0.9939 100 0.449 Contact Map
1zatA 1 0.9817 100 0.48 Contact Map
4k73A 1 0.9695 100 0.505 Contact Map
3vypA 1 1 100 0.511 Contact Map
4qtfA 2 0.9878 100 0.513 Contact Map
5bmqA 3 0.9695 100 0.518 Contact Map
4xxtA 1 0.9634 99.9 0.535 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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