GREMLIN Database
AMPD - 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD
UniProt: P13016 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10041
Length: 183 (148)
Sequences: 2036 (1248)
Seq/√Len: 102.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
76_C90_F3.7151.00
137_T174_F3.5591.00
48_I77_L3.5101.00
89_P92_K3.3271.00
76_C136_V3.3101.00
84_I132_Q3.0431.00
49_D87_Y3.0071.00
52_F152_T2.9831.00
127_D173_R2.9311.00
134_A177_L2.5161.00
31_L137_T2.4521.00
96_H114_G2.3951.00
130_Y170_D2.2571.00
117_L133_L2.2441.00
100_S157_I2.1721.00
79_R85_V2.1141.00
63_F67_I2.0581.00
90_F144_Y2.0221.00
125_Y168_A2.0121.00
90_F140_L2.0001.00
78_I133_L1.8671.00
172_A176_V1.8311.00
120_T123_L1.8141.00
51_L137_T1.7931.00
35_N121_D1.7631.00
79_R83_E1.7411.00
65_A68_A1.7361.00
93_R110_D1.7031.00
139_A143_C1.6931.00
127_D131_Q1.6821.00
88_V94_A1.6451.00
121_D163_T1.6361.00
54_G76_C1.6321.00
41_G120_T1.5541.00
78_I117_L1.5161.00
173_R177_L1.4931.00
46_P79_R1.4721.00
90_F136_V1.4631.00
58_P66_E1.4091.00
124_A168_A1.4051.00
58_P67_I1.4041.00
90_F143_C1.4041.00
101_Q104_G1.3811.00
63_F66_E1.3480.99
58_P62_P1.3210.99
101_Q106_E1.3010.99
40_P63_F1.2740.99
47_W50_A1.2710.99
50_A53_T1.2560.99
47_W64_F1.2520.99
36_I39_P1.2510.99
77_L87_Y1.2230.99
141_I147_I1.1990.99
46_P50_A1.1920.99
31_L174_F1.1830.99
58_P68_A1.1830.99
134_A138_R1.1630.98
66_E70_L1.1190.98
51_L141_I1.1020.98
97_A114_G1.0800.97
123_L168_A1.0730.97
153_G166_G1.0730.97
99_V107_R1.0710.97
103_Q150_N1.0660.97
35_N125_Y1.0490.97
55_T166_G1.0100.96
53_T137_T1.0050.96
91_D144_Y1.0000.96
71_R107_R0.9960.96
158_A161_R0.9840.95
61_H65_A0.9590.95
170_D173_R0.9590.95
128_A132_Q0.9530.94
37_S40_P0.9450.94
60_A79_R0.9320.94
46_P49_D0.9270.94
54_G87_Y0.9230.94
107_R110_D0.9030.93
64_F85_V0.8980.93
50_A55_T0.8910.92
140_L147_I0.8910.92
113_I140_L0.8830.92
132_Q135_A0.8820.92
73_S94_A0.8810.92
57_D60_A0.8790.92
141_I148_A0.8550.91
120_T168_A0.8530.91
67_I77_L0.8520.90
73_S95_W0.8340.90
64_F77_L0.8320.89
63_F77_L0.8250.89
59_Q62_P0.8240.89
122_T168_A0.8200.89
43_F123_L0.8180.89
134_A174_F0.8070.88
141_I146_D0.7910.87
56_I63_F0.7770.86
33_V37_S0.7760.86
51_L151_M0.7740.86
102_Y152_T0.7730.86
152_T155_C0.7720.86
108_C157_I0.7610.85
129_Q169_F0.7550.84
99_V105_R0.7550.84
62_P66_E0.7530.84
137_T141_I0.7490.84
42_E61_H0.7460.84
50_A112_S0.7440.83
103_Q149_K0.7350.83
105_R111_F0.7320.82
49_D111_F0.7320.82
96_H164_D0.7320.82
79_R118_E0.7310.82
34_H38_L0.7300.82
58_P63_F0.7190.81
78_I136_V0.7190.81
152_T156_D0.7150.81
122_T125_Y0.7050.80
82_G132_Q0.7020.80
64_F87_Y0.6960.79
152_T157_I0.6950.79
112_S115_I0.6940.79
80_R126_T0.6920.79
84_I136_V0.6860.78
108_C160_D0.6830.78
30_L112_S0.6820.78
141_I150_N0.6770.77
45_G93_R0.6770.77
58_P69_H0.6760.77
32_V157_I0.6760.77
134_A173_R0.6730.77
49_D83_E0.6700.76
119_G166_G0.6690.76
158_A162_K0.6640.76
146_D150_N0.6610.76
35_N163_T0.6590.75
131_Q149_K0.6560.75
49_D150_N0.6520.75
82_G86_Q0.6520.75
134_A137_T0.6520.75
77_L115_I0.6500.74
91_D143_C0.6420.73
173_R176_V0.6370.73
153_G156_D0.6370.73
114_G164_D0.6370.73
140_L144_Y0.6340.72
100_S152_T0.6340.72
33_V38_L0.6320.72
96_H112_S0.6230.71
97_A157_I0.6230.71
52_F108_C0.6220.71
81_D131_Q0.6210.71
30_L102_Y0.6210.71
74_A152_T0.6200.71
60_A85_V0.6180.71
155_C167_P0.6160.70
142_D172_A0.6150.70
44_G48_I0.6150.70
141_I145_P0.6100.70
52_F97_A0.6080.69
76_C84_I0.6050.69
77_L85_V0.6050.69
136_V143_C0.5980.68
48_I144_Y0.5970.68
45_G79_R0.5940.68
36_I40_P0.5940.68
156_D175_R0.5900.67
39_P43_F0.5880.67
40_P67_I0.5880.67
103_Q152_T0.5860.67
138_R146_D0.5820.66
125_Y164_D0.5790.66
53_T117_L0.5750.65
119_G130_Y0.5740.65
50_A108_C0.5620.63
51_L70_L0.5620.63
53_T77_L0.5610.63
142_D149_K0.5610.63
102_Y150_N0.5580.63
40_P43_F0.5560.62
48_I79_R0.5560.62
49_D54_G0.5540.62
59_Q63_F0.5530.62
101_Q142_D0.5490.62
77_L95_W0.5460.61
30_L33_V0.5460.61
140_L143_C0.5460.61
164_D169_F0.5430.61
122_T167_P0.5400.60
95_W110_D0.5400.60
108_C111_F0.5390.60
97_A164_D0.5370.60
172_A175_R0.5340.59
90_F146_D0.5330.59
67_I73_S0.5310.59
133_L174_F0.5310.59
106_E111_F0.5310.59
76_C89_P0.5300.59
136_V139_A0.5290.59
122_T174_F0.5280.59
82_G126_T0.5260.58
117_L169_F0.5260.58
48_I88_V0.5230.58
81_D101_Q0.5220.58
155_C160_D0.5220.58
147_I150_N0.5220.58
93_R107_R0.5210.58
31_L35_N0.5200.57
50_A60_A0.5200.57
171_W174_F0.5170.57
106_E138_R0.5160.57
131_Q143_C0.5140.57
76_C139_A0.5140.57
139_A144_Y0.5130.56
42_E45_G0.5120.56
131_Q135_A0.5120.56
35_N168_A0.5080.56
133_L171_W0.5050.55
104_G108_C0.5030.55
43_F111_F0.5020.55
45_G110_D0.5020.55
90_F139_A0.5000.55
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  
4bxjA 4 0.8415 100 0.341 Contact Map
3d2yA 3 0.8579 100 0.35 Contact Map
1j3gA 1 0.8907 100 0.356 Contact Map
4bolA 2 0.847 100 0.359 Contact Map
4ivvA 1 0.8033 100 0.39 Contact Map
4knkA 1 0.9016 100 0.44 Contact Map
4x36A 2 0.7923 100 0.455 Contact Map
1yb0A 3 0.8197 100 0.456 Contact Map
3rdrA 4 0.7869 100 0.457 Contact Map
4olsA 2 0.8142 100 0.473 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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