GREMLIN Database
PDAD - Pyruvoyl-dependent arginine decarboxylase
UniProt: Q9HNQ0 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 160 (148)
Sequences: 267 (192)
Seq/√Len: 15.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
19_A144_A5.9971.00
29_V148_I3.8751.00
32_Y63_L3.6231.00
21_D121_R2.3950.93
127_E130_V2.2280.90
83_A114_I2.1570.89
108_D112_T2.1520.88
88_D124_D2.1400.88
72_T136_T2.0750.87
9_G27_A2.0530.86
19_A71_Q2.0520.86
107_A111_T2.0440.86
11_G87_R2.0390.86
85_A125_G2.0270.85
72_T137_A1.8300.79
36_R69_R1.8240.78
118_M125_G1.7660.76
11_G22_A1.7560.76
32_Y54_P1.7450.75
46_T125_G1.7290.74
79_S107_A1.7220.74
114_I126_V1.7200.74
20_Y67_E1.7160.74
80_A145_A1.7030.73
85_A118_M1.7020.73
6_I18_A1.6910.73
4_I149_A1.6780.72
111_T115_T1.5360.65
127_E137_A1.5090.64
81_G131_R1.5000.63
16_E44_D1.4710.62
28_N50_V1.4520.61
116_A119_D1.4450.60
75_P140_G1.4400.60
9_G48_S1.4090.58
79_S99_D1.3940.57
26_D29_V1.3850.57
20_Y65_V1.3680.56
125_G137_A1.3680.56
45_A67_E1.3500.55
45_A141_E1.3430.54
6_I87_R1.3310.54
94_F149_A1.2970.52
130_V133_E1.2870.51
99_D102_T1.2730.50
74_G77_Q1.2720.50
108_D111_T1.2530.49
103_P134_T1.2220.47
130_V135_V1.2130.47
47_V50_V1.1970.46
112_T116_A1.1850.45
122_D130_V1.1760.45
81_G132_T1.1720.45
22_A121_R1.1630.44
111_T130_V1.1410.43
41_I94_F1.1270.42
83_A110_V1.1230.42
63_L82_L1.1200.42
4_I47_V1.1120.41
112_T115_T1.1110.41
21_D31_N1.1040.41
127_E131_R1.1000.41
27_A37_V1.0980.40
71_Q144_A1.0970.40
14_P109_R1.0770.39
93_L150_A1.0700.39
15_T110_V1.0630.38
124_D127_E1.0490.38
36_R68_A1.0320.37
76_G139_A1.0280.37
90_A139_A1.0210.36
12_V70_G1.0130.36
13_A17_M1.0110.36
133_E137_A1.0100.36
127_E133_E0.9890.35
3_R52_T0.9870.34
140_G143_A0.9840.34
46_T124_D0.9830.34
74_G111_T0.9820.34
4_I41_I0.9800.34
124_D136_T0.9560.33
36_R67_E0.9530.33
107_A119_D0.9530.33
76_G137_A0.9480.32
8_W119_D0.9470.32
122_D129_S0.9460.32
28_N89_G0.9440.32
122_D133_E0.9380.32
15_T18_A0.9370.32
71_Q138_D0.9370.32
32_Y64_T0.9350.32
44_D139_A0.9290.31
79_S137_A0.9270.31
103_P107_A0.9180.31
111_T119_D0.9090.31
68_A133_E0.9040.30
117_G121_R0.9000.30
66_V146_V0.8870.29
66_V95_Y0.8840.29
26_D100_E0.8830.29
31_N121_R0.8820.29
30_H45_A0.8720.29
97_A114_I0.8630.28
69_R144_A0.8550.28
13_A22_A0.8500.28
95_Y113_G0.8470.28
130_V134_T0.8470.28
104_D140_G0.8450.27
135_V149_A0.8370.27
83_A144_A0.8370.27
6_I41_I0.8340.27
66_V150_A0.8300.27
66_V144_A0.8270.27
110_V117_G0.8260.27
72_T147_V0.8230.26
44_D56_L0.8180.26
30_H69_R0.8120.26
127_E132_T0.8020.26
104_D108_D0.8020.26
59_A91_P0.8010.26
79_S89_G0.8000.25
43_A95_Y0.7950.25
34_L146_V0.7890.25
35_I45_A0.7840.25
18_A109_R0.7800.25
105_D109_R0.7710.24
74_G100_E0.7700.24
82_L99_D0.7640.24
127_E136_T0.7470.23
78_A139_A0.7470.23
65_V117_G0.7460.23
95_Y142_H0.7450.23
22_A65_V0.7400.23
126_V132_T0.7370.23
57_G63_L0.7290.22
88_D136_T0.7290.22
54_P107_A0.7250.22
29_V52_T0.7140.22
70_G99_D0.7140.22
81_G118_M0.7120.22
58_P97_A0.7120.22
123_W127_E0.7010.21
48_S56_L0.6970.21
6_I103_P0.6940.21
83_A128_P0.6910.21
101_T111_T0.6840.21
66_V149_A0.6750.20
30_H117_G0.6750.20
40_V43_A0.6740.20
122_D137_A0.6720.20
125_G128_P0.6720.20
91_P120_V0.6700.20
31_N65_V0.6640.20
41_I59_A0.6630.20
6_I84_W0.6620.20
13_A93_L0.6610.20
12_V75_P0.6590.20
108_D119_D0.6580.20
14_P97_A0.6490.19
72_T143_A0.6480.19
81_G130_V0.6470.19
17_M20_Y0.6440.19
102_T106_V0.6430.19
85_A114_I0.6420.19
80_A88_D0.6410.19
45_A121_R0.6390.19
67_E98_A0.6370.19
90_A106_V0.6360.19
21_D25_A0.6280.19
11_G132_T0.6250.19
3_R49_P0.6230.19
29_V65_V0.6170.18
79_S82_L0.6160.18
49_P140_G0.6160.18
19_A35_I0.6140.18
22_A29_V0.6130.18
30_H151_Y0.6070.18
44_D129_S0.6060.18
93_L148_I0.6040.18
9_G146_V0.6040.18
65_V151_Y0.5990.18
37_V72_T0.5980.18
61_N148_I0.5940.18
144_A149_A0.5920.17
141_E145_A0.5860.17
16_E71_Q0.5800.17
57_G87_R0.5780.17
45_A87_R0.5770.17
6_I81_G0.5690.17
7_A93_L0.5660.17
82_L135_V0.5630.17
66_V140_G0.5600.16
135_V138_D0.5600.16
81_G117_G0.5580.16
45_A115_T0.5570.16
10_S103_P0.5490.16
31_N117_G0.5470.16
80_A146_V0.5460.16
36_R151_Y0.5450.16
40_V63_L0.5420.16
68_A143_A0.5400.16
68_A81_G0.5380.16
17_M85_A0.5360.16
15_T114_I0.5360.16
58_P106_V0.5320.16
28_N32_Y0.5320.16
123_W133_E0.5320.16
32_Y122_D0.5310.16
86_P90_A0.5280.15
81_G110_V0.5230.15
122_D126_V0.5230.15
126_V133_E0.5220.15
90_A123_W0.5210.15
63_L91_P0.5210.15
31_N106_V0.5210.15
143_A147_V0.5210.15
46_T119_D0.5150.15
29_V87_R0.5140.15
12_V135_V0.5120.15
21_D53_A0.5110.15
21_D93_L0.5080.15
20_Y62_T0.5000.15
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  
1n2mA 3 0.925 100 0.224 Contact Map
1n13B 3 0.6687 100 0.497 Contact Map
1n13A 3 0.2375 99.6 0.74 Contact Map
1pyaB 3 0.8875 54.2 0.938 Contact Map
2ozlB 2 0.675 29.1 0.947 Contact Map
3komA 2 0.675 23.2 0.95 Contact Map
3ju3A 4 0.65 21.6 0.951 Contact Map
3hq1A 2 0.5062 18 0.952 Contact Map
1umdB 2 0.6687 17.1 0.953 Contact Map
3uk1A 2 0.6687 14.6 0.954 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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