GREMLIN Database
PDAA - Peptidoglycan-N-acetylmuramic acid deacetylase PdaA
UniProt: O34928 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 263 (199)
Sequences: 2974 (2411)
Seq/√Len: 170.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
91_H237_T4.3791.00
89_K117_E3.6361.00
86_D113_R3.3951.00
113_R117_E3.2611.00
151_Y157_Q2.9021.00
120_I250_D2.7891.00
99_V111_I2.6741.00
91_H240_K2.6541.00
233_D237_T2.6471.00
141_D145_S2.4331.00
210_I238_D2.3251.00
93_V236_I2.3001.00
147_N182_Y2.1761.00
130_D168_V2.0381.00
167_G187_W2.0111.00
90_K233_D2.0071.00
115_S156_K1.9861.00
192_V195_K1.9781.00
206_Y210_I1.9721.00
136_A172_Y1.9571.00
206_Y234_D1.9411.00
213_A239_L1.9141.00
238_D242_Q1.8351.00
126_F145_S1.8091.00
132_T168_V1.7721.00
135_T138_Q1.7601.00
91_H233_D1.7131.00
238_D241_K1.6901.00
82_P113_R1.6721.00
207_D211_K1.6611.00
112_K116_D1.6021.00
209_M235_A1.5971.00
99_V114_M1.5321.00
88_L95_G1.5111.00
84_V229_A1.5021.00
139_I173_V1.4911.00
105_K149_E1.4881.00
236_I240_K1.4871.00
124_H128_H1.4751.00
149_E153_I1.4691.00
148_E152_K1.4481.00
94_T119_H1.4401.00
87_V229_A1.4251.00
67_T245_T1.3991.00
104_V149_E1.3971.00
203_K207_D1.3861.00
127_H142_E1.3861.00
202_K234_D1.3621.00
101_G126_F1.3511.00
236_I246_F1.3511.00
188_S217_A1.3271.00
91_H236_I1.3261.00
67_T247_K1.3251.00
164_P186_F1.3231.00
125_S131_L1.3011.00
85_L114_M1.2921.00
201_G204_Y1.2871.00
84_V232_L1.2831.00
104_V111_I1.2821.00
203_K234_D1.2781.00
111_I153_I1.2701.00
144_D148_E1.2531.00
226_R230_E1.2451.00
202_K206_Y1.2411.00
68_I246_F1.2411.00
104_V153_I1.2381.00
86_D117_E1.2381.00
139_I176_E1.2191.00
68_I239_L1.2161.00
87_V233_D1.2081.00
144_D180_L1.2061.00
191_F221_L1.1961.00
126_F149_E1.1951.00
68_I219_Y1.1901.00
93_V246_F1.1891.00
87_V232_L1.1871.00
185_V249_I1.1751.00
232_L236_I1.1751.00
130_D166_R1.1721.00
74_N223_T1.1711.00
175_K179_R1.1641.00
82_P110_L1.1591.00
96_T120_I1.1521.00
83_K230_E1.1491.00
134_K138_Q1.1461.00
123_N147_N1.1451.00
65_E245_T1.1431.00
81_T223_T1.1301.00
69_Y247_K1.1271.00
149_E152_K1.1261.00
83_K87_V1.1221.00
66_K244_Y1.1211.00
130_D133_T1.1201.00
87_V236_I1.1111.00
150_V154_T1.1091.00
177_T184_T1.1051.00
140_Q180_L1.0991.00
136_A179_R1.0921.00
140_Q144_D1.0891.00
201_G227_D1.0851.00
237_T241_K1.0831.00
87_V91_H1.0811.00
143_L177_T1.0721.00
111_I114_M1.0681.00
86_D90_K1.0661.00
76_Y223_T1.0611.00
72_F232_L1.0290.99
85_L113_R0.9940.99
136_A176_E0.9900.99
138_Q141_D0.9890.99
144_D147_N0.9780.99
234_D238_D0.9760.99
202_K230_E0.9760.99
140_Q176_E0.9660.99
237_T240_K0.9660.99
115_S154_T0.9650.99
129_P142_E0.9590.99
140_Q179_R0.9540.99
111_I121_I0.9450.99
85_L119_H0.9430.99
173_V177_T0.9390.99
171_E175_K0.9380.99
124_H222_H0.9300.99
89_K113_R0.9300.99
114_M121_I0.9260.99
71_T218_I0.9230.99
147_N157_Q0.9220.99
72_F84_V0.9190.99
190_A194_W0.9090.98
189_V217_A0.9020.98
206_Y238_D0.9000.98
210_I242_Q0.8990.98
93_V240_K0.8990.98
100_T125_S0.8890.98
231_A235_A0.8810.98
136_A140_Q0.8790.98
234_D237_T0.8670.98
209_M219_Y0.8630.98
68_I213_A0.8620.98
80_Y83_K0.8600.98
72_F88_L0.8560.98
214_H217_A0.8520.98
80_Y229_A0.8380.97
105_K126_F0.8280.97
218_I249_I0.8270.97
66_K243_G0.8260.97
205_A231_A0.8250.97
131_L162_L0.8240.97
113_R116_D0.8180.97
89_K94_T0.8110.97
85_L117_E0.7910.96
123_N143_L0.7900.96
247_K251_D0.7850.96
172_Y176_E0.7850.96
105_K108_P0.7780.96
76_Y81_T0.7730.96
82_P86_D0.7730.96
203_K206_Y0.7700.96
188_S214_H0.7670.96
146_V150_V0.7670.96
243_G246_F0.7660.96
174_L184_T0.7650.96
101_G149_E0.7630.96
89_K119_H0.7590.95
81_T85_L0.7580.95
162_L177_T0.7560.95
104_V150_V0.7560.95
137_D140_Q0.7540.95
187_W220_L0.7520.95
127_H145_S0.7510.95
196_I200_K0.7500.95
125_S129_P0.7500.95
94_T248_S0.7460.95
148_E157_Q0.7450.95
73_D128_H0.7430.95
123_N146_V0.7420.95
126_F146_V0.7400.95
208_H212_Q0.7370.95
128_H222_H0.7310.94
137_D141_D0.7290.94
76_Y103_F0.7260.94
121_I154_T0.7250.94
202_K227_D0.7200.94
100_T223_T0.7150.94
170_S173_V0.7140.94
172_Y175_K0.7100.94
75_G81_T0.7050.93
104_V108_P0.7050.93
143_L162_L0.6960.93
74_N124_H0.6900.93
206_Y231_A0.6840.92
98_F185_V0.6820.92
202_K231_A0.6820.92
85_L89_K0.6800.92
145_S148_E0.6800.92
99_V104_V0.6780.92
94_T246_F0.6730.92
142_E146_V0.6700.91
193_D228_N0.6700.91
56_D178_K0.6690.91
100_T103_F0.6680.91
73_D163_R0.6670.91
209_M239_L0.6660.91
153_I156_K0.6660.91
131_L142_E0.6630.91
73_D222_H0.6610.91
115_S121_I0.6590.91
164_P184_T0.6590.91
81_T110_L0.6550.90
191_F205_A0.6540.90
235_A239_L0.6510.90
71_T163_R0.6500.90
73_D124_H0.6430.90
150_V158_D0.6410.90
191_F208_H0.6410.90
75_G163_R0.6400.89
205_A227_D0.6390.89
227_D230_E0.6380.89
166_R192_V0.6370.89
240_K245_T0.6360.89
128_H165_P0.6350.89
99_V121_I0.6290.89
155_G158_D0.6280.89
169_F173_V0.6270.88
69_Y249_I0.6250.88
72_F95_G0.6230.88
169_F174_L0.6220.88
62_N65_E0.6190.88
83_K86_D0.6190.88
158_D182_Y0.6170.88
120_I248_S0.6170.88
82_P117_E0.6120.87
111_I150_V0.6110.87
176_E179_R0.6110.87
134_K139_I0.6070.87
121_I150_V0.6070.87
69_Y96_T0.6040.87
109_Q112_K0.6040.87
147_N151_Y0.6020.86
247_K252_L0.6010.86
196_I201_G0.5960.86
74_N100_T0.5930.86
171_E174_L0.5920.85
190_A195_K0.5900.85
176_E180_L0.5890.85
96_T249_I0.5890.85
248_S251_D0.5870.85
71_T249_I0.5820.85
74_N103_F0.5720.84
54_K57_A0.5700.83
200_K227_D0.5700.83
138_Q142_E0.5690.83
136_A175_K0.5690.83
173_V176_E0.5680.83
139_I172_Y0.5630.83
146_V149_E0.5600.82
58_F61_G0.5600.82
78_N224_V0.5600.82
89_K92_R0.5580.82
102_H106_D0.5570.82
206_Y209_M0.5570.82
51_L54_K0.5560.82
118_G155_G0.5550.82
97_F119_H0.5540.82
205_A209_M0.5510.81
108_P111_I0.5500.81
75_G128_H0.5500.81
141_D144_D0.5470.81
210_I213_A0.5430.80
70_L88_L0.5410.80
190_A193_D0.5400.80
58_F63_T0.5390.80
207_D210_I0.5360.79
196_I224_V0.5310.79
167_G220_L0.5290.79
133_T168_V0.5290.79
92_R240_K0.5280.78
221_L235_A0.5260.78
140_Q143_L0.5260.78
108_P152_K0.5230.78
69_Y248_S0.5220.78
55_Y58_F0.5190.77
159_N183_Q0.5190.77
53_E57_A0.5160.77
128_H220_L0.5150.77
91_H94_T0.5130.76
221_L232_L0.5130.76
63_T67_T0.5100.76
167_G186_F0.5070.76
75_G100_T0.5070.76
185_V218_I0.5050.75
80_Y225_S0.5040.75
70_L236_I0.5030.75
147_N158_D0.5030.75
204_Y208_H0.5030.75
77_E103_F0.5020.75
77_E223_T0.5010.75
98_F249_I0.5000.75
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  
1ny1A 1 0.8897 100 0.237 Contact Map
2j13A 1 0.7833 100 0.24 Contact Map
4m1bA 1 0.749 100 0.243 Contact Map
2iw0A 1 0.7833 100 0.255 Contact Map
2y8uA 1 0.7833 100 0.263 Contact Map
2cc0A 2 0.7338 100 0.269 Contact Map
2w3zA 1 0.7757 100 0.27 Contact Map
2vyoA 1 0.7605 100 0.278 Contact Map
4l1gA 1 0.7947 100 0.281 Contact Map
2c1iA 1 0.9087 100 0.283 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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