PDAA - BACSU - GREMLIN Contacts

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PDAA - Peptidoglycan-N-acetylmuramic acid deacetylase PdaA

UniProt:	O34928	Sequences: MKWMCSICCAAVLLAGGAAQAEAVPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRMSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHMIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLMFEKEMRLPSL	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

BACSU - PDAA PDAC YLXY YHEN PDAB YXKH

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_H	237_T	4.379	1.00
89_K	117_E	3.636	1.00
86_D	113_R	3.395	1.00
113_R	117_E	3.261	1.00
151_Y	157_Q	2.902	1.00
120_I	250_D	2.789	1.00
99_V	111_I	2.674	1.00
91_H	240_K	2.654	1.00
233_D	237_T	2.647	1.00
141_D	145_S	2.433	1.00
210_I	238_D	2.325	1.00
93_V	236_I	2.300	1.00
147_N	182_Y	2.176	1.00
130_D	168_V	2.038	1.00
167_G	187_W	2.011	1.00
90_K	233_D	2.007	1.00
115_S	156_K	1.986	1.00
192_V	195_K	1.978	1.00
206_Y	210_I	1.972	1.00
136_A	172_Y	1.957	1.00
206_Y	234_D	1.941	1.00
213_A	239_L	1.914	1.00
238_D	242_Q	1.835	1.00
126_F	145_S	1.809	1.00
132_T	168_V	1.772	1.00
135_T	138_Q	1.760	1.00
91_H	233_D	1.713	1.00
238_D	241_K	1.690	1.00
82_P	113_R	1.672	1.00
207_D	211_K	1.661	1.00
112_K	116_D	1.602	1.00
209_M	235_A	1.597	1.00
99_V	114_M	1.532	1.00
88_L	95_G	1.511	1.00
84_V	229_A	1.502	1.00
139_I	173_V	1.491	1.00
105_K	149_E	1.488	1.00
236_I	240_K	1.487	1.00
124_H	128_H	1.475	1.00
149_E	153_I	1.469	1.00
148_E	152_K	1.448	1.00
94_T	119_H	1.440	1.00
87_V	229_A	1.425	1.00
67_T	245_T	1.399	1.00
104_V	149_E	1.397	1.00
203_K	207_D	1.386	1.00
127_H	142_E	1.386	1.00
202_K	234_D	1.362	1.00
101_G	126_F	1.351	1.00
236_I	246_F	1.351	1.00
188_S	217_A	1.327	1.00
91_H	236_I	1.326	1.00
67_T	247_K	1.325	1.00
164_P	186_F	1.323	1.00
125_S	131_L	1.301	1.00
85_L	114_M	1.292	1.00
201_G	204_Y	1.287	1.00
84_V	232_L	1.283	1.00
104_V	111_I	1.282	1.00
203_K	234_D	1.278	1.00
111_I	153_I	1.270	1.00
144_D	148_E	1.253	1.00
226_R	230_E	1.245	1.00
202_K	206_Y	1.241	1.00
68_I	246_F	1.241	1.00
104_V	153_I	1.238	1.00
86_D	117_E	1.238	1.00
139_I	176_E	1.219	1.00
68_I	239_L	1.216	1.00
87_V	233_D	1.208	1.00
144_D	180_L	1.206	1.00
191_F	221_L	1.196	1.00
126_F	149_E	1.195	1.00
68_I	219_Y	1.190	1.00
93_V	246_F	1.189	1.00
87_V	232_L	1.187	1.00
185_V	249_I	1.175	1.00
232_L	236_I	1.175	1.00
130_D	166_R	1.172	1.00
74_N	223_T	1.171	1.00
175_K	179_R	1.164	1.00
82_P	110_L	1.159	1.00
96_T	120_I	1.152	1.00
83_K	230_E	1.149	1.00
134_K	138_Q	1.146	1.00
123_N	147_N	1.145	1.00
65_E	245_T	1.143	1.00
81_T	223_T	1.130	1.00
69_Y	247_K	1.127	1.00
149_E	152_K	1.126	1.00
83_K	87_V	1.122	1.00
66_K	244_Y	1.121	1.00
130_D	133_T	1.120	1.00
87_V	236_I	1.111	1.00
150_V	154_T	1.109	1.00
177_T	184_T	1.105	1.00
140_Q	180_L	1.099	1.00
136_A	179_R	1.092	1.00
140_Q	144_D	1.089	1.00
201_G	227_D	1.085	1.00
237_T	241_K	1.083	1.00
87_V	91_H	1.081	1.00
143_L	177_T	1.072	1.00
111_I	114_M	1.068	1.00
86_D	90_K	1.066	1.00
76_Y	223_T	1.061	1.00
72_F	232_L	1.029	0.99
85_L	113_R	0.994	0.99
136_A	176_E	0.990	0.99
138_Q	141_D	0.989	0.99
144_D	147_N	0.978	0.99
234_D	238_D	0.976	0.99
202_K	230_E	0.976	0.99
140_Q	176_E	0.966	0.99
237_T	240_K	0.966	0.99
115_S	154_T	0.965	0.99
129_P	142_E	0.959	0.99
140_Q	179_R	0.954	0.99
111_I	121_I	0.945	0.99
85_L	119_H	0.943	0.99
173_V	177_T	0.939	0.99
171_E	175_K	0.938	0.99
124_H	222_H	0.930	0.99
89_K	113_R	0.930	0.99
114_M	121_I	0.926	0.99
71_T	218_I	0.923	0.99
147_N	157_Q	0.922	0.99
72_F	84_V	0.919	0.99
190_A	194_W	0.909	0.98
189_V	217_A	0.902	0.98
206_Y	238_D	0.900	0.98
210_I	242_Q	0.899	0.98
93_V	240_K	0.899	0.98
100_T	125_S	0.889	0.98
231_A	235_A	0.881	0.98
136_A	140_Q	0.879	0.98
234_D	237_T	0.867	0.98
209_M	219_Y	0.863	0.98
68_I	213_A	0.862	0.98
80_Y	83_K	0.860	0.98
72_F	88_L	0.856	0.98
214_H	217_A	0.852	0.98
80_Y	229_A	0.838	0.97
105_K	126_F	0.828	0.97
218_I	249_I	0.827	0.97
66_K	243_G	0.826	0.97
205_A	231_A	0.825	0.97
131_L	162_L	0.824	0.97
113_R	116_D	0.818	0.97
89_K	94_T	0.811	0.97
85_L	117_E	0.791	0.96
123_N	143_L	0.790	0.96
247_K	251_D	0.785	0.96
172_Y	176_E	0.785	0.96
105_K	108_P	0.778	0.96
76_Y	81_T	0.773	0.96
82_P	86_D	0.773	0.96
203_K	206_Y	0.770	0.96
188_S	214_H	0.767	0.96
146_V	150_V	0.767	0.96
243_G	246_F	0.766	0.96
174_L	184_T	0.765	0.96
101_G	149_E	0.763	0.96
89_K	119_H	0.759	0.95
81_T	85_L	0.758	0.95
162_L	177_T	0.756	0.95
104_V	150_V	0.756	0.95
137_D	140_Q	0.754	0.95
187_W	220_L	0.752	0.95
127_H	145_S	0.751	0.95
196_I	200_K	0.750	0.95
125_S	129_P	0.750	0.95
94_T	248_S	0.746	0.95
148_E	157_Q	0.745	0.95
73_D	128_H	0.743	0.95
123_N	146_V	0.742	0.95
126_F	146_V	0.740	0.95
208_H	212_Q	0.737	0.95
128_H	222_H	0.731	0.94
137_D	141_D	0.729	0.94
76_Y	103_F	0.726	0.94
121_I	154_T	0.725	0.94
202_K	227_D	0.720	0.94
100_T	223_T	0.715	0.94
170_S	173_V	0.714	0.94
172_Y	175_K	0.710	0.94
75_G	81_T	0.705	0.93
104_V	108_P	0.705	0.93
143_L	162_L	0.696	0.93
74_N	124_H	0.690	0.93
206_Y	231_A	0.684	0.92
98_F	185_V	0.682	0.92
202_K	231_A	0.682	0.92
85_L	89_K	0.680	0.92
145_S	148_E	0.680	0.92
99_V	104_V	0.678	0.92
94_T	246_F	0.673	0.92
142_E	146_V	0.670	0.91
193_D	228_N	0.670	0.91
56_D	178_K	0.669	0.91
100_T	103_F	0.668	0.91
73_D	163_R	0.667	0.91
209_M	239_L	0.666	0.91
153_I	156_K	0.666	0.91
131_L	142_E	0.663	0.91
73_D	222_H	0.661	0.91
115_S	121_I	0.659	0.91
164_P	184_T	0.659	0.91
81_T	110_L	0.655	0.90
191_F	205_A	0.654	0.90
235_A	239_L	0.651	0.90
71_T	163_R	0.650	0.90
73_D	124_H	0.643	0.90
150_V	158_D	0.641	0.90
191_F	208_H	0.641	0.90
75_G	163_R	0.640	0.89
205_A	227_D	0.639	0.89
227_D	230_E	0.638	0.89
166_R	192_V	0.637	0.89
240_K	245_T	0.636	0.89
128_H	165_P	0.635	0.89
99_V	121_I	0.629	0.89
155_G	158_D	0.628	0.89
169_F	173_V	0.627	0.88
69_Y	249_I	0.625	0.88
72_F	95_G	0.623	0.88
169_F	174_L	0.622	0.88
62_N	65_E	0.619	0.88
83_K	86_D	0.619	0.88
158_D	182_Y	0.617	0.88
120_I	248_S	0.617	0.88
82_P	117_E	0.612	0.87
111_I	150_V	0.611	0.87
176_E	179_R	0.611	0.87
134_K	139_I	0.607	0.87
121_I	150_V	0.607	0.87
69_Y	96_T	0.604	0.87
109_Q	112_K	0.604	0.87
147_N	151_Y	0.602	0.86
247_K	252_L	0.601	0.86
196_I	201_G	0.596	0.86
74_N	100_T	0.593	0.86
171_E	174_L	0.592	0.85
190_A	195_K	0.590	0.85
176_E	180_L	0.589	0.85
96_T	249_I	0.589	0.85
248_S	251_D	0.587	0.85
71_T	249_I	0.582	0.85
74_N	103_F	0.572	0.84
54_K	57_A	0.570	0.83
200_K	227_D	0.570	0.83
138_Q	142_E	0.569	0.83
136_A	175_K	0.569	0.83
173_V	176_E	0.568	0.83
139_I	172_Y	0.563	0.83
146_V	149_E	0.560	0.82
58_F	61_G	0.560	0.82
78_N	224_V	0.560	0.82
89_K	92_R	0.558	0.82
102_H	106_D	0.557	0.82
206_Y	209_M	0.557	0.82
51_L	54_K	0.556	0.82
118_G	155_G	0.555	0.82
97_F	119_H	0.554	0.82
205_A	209_M	0.551	0.81
108_P	111_I	0.550	0.81
75_G	128_H	0.550	0.81
141_D	144_D	0.547	0.81
210_I	213_A	0.543	0.80
70_L	88_L	0.541	0.80
190_A	193_D	0.540	0.80
58_F	63_T	0.539	0.80
207_D	210_I	0.536	0.79
196_I	224_V	0.531	0.79
167_G	220_L	0.529	0.79
133_T	168_V	0.529	0.79
92_R	240_K	0.528	0.78
221_L	235_A	0.526	0.78
140_Q	143_L	0.526	0.78
108_P	152_K	0.523	0.78
69_Y	248_S	0.522	0.78
55_Y	58_F	0.519	0.77
159_N	183_Q	0.519	0.77
53_E	57_A	0.516	0.77
128_H	220_L	0.515	0.77
91_H	94_T	0.513	0.76
221_L	232_L	0.513	0.76
63_T	67_T	0.510	0.76
167_G	186_F	0.507	0.76
75_G	100_T	0.507	0.76
185_V	218_I	0.505	0.75
80_Y	225_S	0.504	0.75
70_L	236_I	0.503	0.75
147_N	158_D	0.503	0.75
204_Y	208_H	0.503	0.75
77_E	103_F	0.502	0.75
77_E	223_T	0.501	0.75
98_F	249_I	0.500	0.75

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

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

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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