AMIA - ECOLI - GREMLIN Contacts

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AMIA - N-acetylmuramoyl-L-alanine amidase AmiA

UniProt:	P36548	Sequences: MSTFKPLKTLTSRRQVLKAGLAALTLSGMSQAIAKDELLKTSNGHSKPKAKKSGGKRVVVLDPGHGGIDTGAIGRNGSKEKHVVLAIAKNVRSILRNHGIDARLTRSGDTFIPLYDRVEIAHKHGADLFMSIHADGFTNPKAAGASVFALSNRGASSAMAKYLSERENRADEVAGKKATDKDHLLQQVLFDLVQTDTIKNSLTLGSHILKKIKPVHKLHSRNTEQAAFVVLKSPSVPSVLVETSFITNPEEERLLGTAAFRQKIATAIAEGVISYFHWFDNQKAHSKKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11823
Length:	289 (237)
Sequences:	2036 (1305)
Seq/√Len:	84.8

ECOLI - AMIA AMIB AMIC
BACSU - YRVJ CWLC LYTC CWLD YQII

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
87_I	243_T	4.688	1.00
208_I	239_V	4.320	1.00
79_K	82_H	3.739	1.00
90_N	262_Q	3.360	1.00
92_R	104_L	3.232	1.00
86_A	261_R	3.186	1.00
58_V	101_D	3.127	1.00
92_R	96_R	2.994	1.00
96_R	102_A	2.913	1.00
63_P	88_A	2.878	1.00
78_S	252_E	2.829	1.00
74_G	252_E	2.760	1.00
94_I	266_T	2.623	1.00
130_M	272_V	2.593	1.00
61_L	88_A	2.570	1.00
78_S	256_G	2.464	1.00
88_A	132_I	2.340	1.00
90_N	261_R	2.326	1.00
103_R	120_I	2.305	1.00
135_D	146_S	2.305	1.00
241_V	268_I	2.273	1.00
204_L	239_V	2.239	1.00
116_D	119_E	2.190	1.00
72_A	246_I	2.164	1.00
86_A	90_N	2.104	1.00
95_L	100_I	2.059	1.00
90_N	258_A	2.037	1.00
76_N	252_E	2.031	1.00
209_L	220_S	2.027	1.00
113_P	116_D	1.929	1.00
147_V	209_L	1.888	1.00
63_P	105_T	1.888	1.00
60_V	105_T	1.793	1.00
73_I	79_K	1.777	1.00
84_V	134_A	1.772	1.00
95_L	102_A	1.709	1.00
171_D	176_K	1.696	1.00
171_D	174_A	1.692	1.00
137_F	142_A	1.672	1.00
58_V	103_R	1.661	1.00
103_R	124_H	1.657	1.00
164_S	168_N	1.656	1.00
93_S	96_R	1.654	1.00
60_V	126_A	1.628	1.00
227_A	232_K	1.623	1.00
100_I	273_I	1.610	1.00
88_A	104_L	1.601	1.00
94_I	269_A	1.575	1.00
132_I	243_T	1.565	1.00
93_S	97_N	1.564	1.00
91_V	268_I	1.559	1.00
95_L	269_A	1.520	1.00
94_I	262_Q	1.520	1.00
94_I	97_N	1.485	0.99
243_T	264_I	1.469	0.99
164_S	167_E	1.462	0.99
149_A	202_L	1.447	0.99
90_N	93_S	1.438	0.99
207_H	271_G	1.433	0.99
173_V	176_K	1.431	0.99
128_L	204_L	1.406	0.99
60_V	120_I	1.399	0.99
143_A	254_L	1.387	0.99
143_A	250_E	1.379	0.99
254_L	260_F	1.366	0.99
57_R	276_F	1.360	0.99
122_H	235_S	1.358	0.99
149_A	205_G	1.351	0.99
145_A	216_H	1.346	0.99
254_L	263_K	1.324	0.99
136_G	247_T	1.316	0.99
252_E	256_G	1.303	0.99
211_K	214_P	1.301	0.98
92_R	102_A	1.282	0.98
211_K	270_E	1.270	0.98
56_K	101_D	1.270	0.98
204_L	208_I	1.254	0.98
90_N	94_I	1.249	0.98
211_K	274_S	1.241	0.98
115_Y	229_V	1.240	0.98
257_T	260_F	1.238	0.98
116_D	123_K	1.229	0.98
120_I	124_H	1.227	0.98
135_D	145_A	1.222	0.98
153_R	227_A	1.190	0.97
118_V	233_S	1.182	0.97
148_F	245_F	1.176	0.97
128_L	272_V	1.159	0.97
171_D	175_G	1.154	0.97
87_I	132_I	1.143	0.97
184_L	188_V	1.142	0.97
145_A	212_I	1.138	0.96
114_L	229_V	1.137	0.96
87_I	264_I	1.135	0.96
112_I	116_D	1.135	0.96
81_K	109_D	1.135	0.96
91_V	269_A	1.134	0.96
63_P	84_V	1.126	0.96
251_E	260_F	1.125	0.96
111_F	114_L	1.119	0.96
202_L	225_Q	1.110	0.96
119_E	123_K	1.096	0.96
118_V	234_P	1.095	0.96
121_A	236_V	1.087	0.95
122_H	236_V	1.084	0.95
160_A	164_S	1.078	0.95
110_T	113_P	1.065	0.95
259_A	263_K	1.040	0.94
59_V	91_V	1.024	0.94
216_H	244_S	1.017	0.93
202_L	205_G	1.014	0.93
118_V	229_V	1.006	0.93
212_I	241_V	1.006	0.93
198_I	225_Q	1.006	0.93
92_R	107_S	1.002	0.93
156_S	164_S	0.995	0.93
70_T	73_I	0.985	0.92
172_E	176_K	0.981	0.92
68_I	111_F	0.978	0.92
209_L	218_L	0.970	0.92
122_H	234_P	0.967	0.92
95_L	272_V	0.959	0.91
207_H	278_W	0.956	0.91
61_L	95_L	0.956	0.91
61_L	102_A	0.953	0.91
211_K	271_G	0.945	0.91
56_K	99_G	0.929	0.90
89_K	108_G	0.924	0.90
262_Q	266_T	0.923	0.90
269_A	273_I	0.921	0.90
59_V	100_I	0.920	0.89
91_V	132_I	0.917	0.89
48_P	51_K	0.917	0.89
250_E	254_L	0.914	0.89
266_T	270_E	0.909	0.89
243_T	255_L	0.898	0.88
69_D	111_F	0.897	0.88
129_F	230_V	0.892	0.88
148_F	226_A	0.881	0.87
61_L	91_V	0.880	0.87
60_V	102_A	0.878	0.87
189_L	196_D	0.872	0.87
89_K	107_S	0.869	0.87
215_V	267_A	0.866	0.86
43_N	46_S	0.862	0.86
70_T	79_K	0.861	0.86
78_S	83_V	0.857	0.86
178_A	181_K	0.856	0.86
244_S	260_F	0.855	0.86
148_F	160_A	0.840	0.85
43_N	48_P	0.834	0.84
87_I	265_A	0.834	0.84
130_M	239_V	0.832	0.84
274_S	277_H	0.826	0.84
213_K	218_L	0.823	0.84
229_V	232_K	0.819	0.83
243_T	268_I	0.817	0.83
116_D	120_I	0.813	0.83
248_N	252_E	0.813	0.83
87_I	261_R	0.812	0.83
96_R	107_S	0.811	0.83
107_S	244_S	0.810	0.83
100_I	276_F	0.799	0.82
263_K	267_A	0.796	0.81
162_Y	165_E	0.789	0.81
158_A	161_K	0.789	0.81
254_L	257_T	0.789	0.81
156_S	160_A	0.787	0.81
122_H	233_S	0.782	0.80
146_S	260_F	0.782	0.80
260_F	264_I	0.779	0.80
139_N	142_A	0.776	0.80
157_S	224_E	0.773	0.80
59_V	128_L	0.770	0.79
194_Q	197_T	0.766	0.79
154_G	227_A	0.765	0.79
158_A	162_Y	0.756	0.78
178_A	186_Q	0.754	0.78
137_F	140_P	0.751	0.78
211_K	267_A	0.747	0.77
55_G	127_D	0.742	0.77
89_K	92_R	0.742	0.77
223_T	228_F	0.737	0.76
188_V	192_L	0.735	0.76
149_A	198_I	0.733	0.76
206_S	210_K	0.731	0.76
61_L	92_R	0.730	0.76
91_V	265_A	0.728	0.75
77_G	256_G	0.727	0.75
142_A	219_H	0.721	0.75
147_V	220_S	0.716	0.74
159_M	194_Q	0.715	0.74
134_A	246_I	0.709	0.73
177_K	180_D	0.708	0.73
145_A	238_S	0.708	0.73
54_G	250_E	0.703	0.73
160_A	168_N	0.703	0.73
43_N	50_A	0.702	0.73
84_V	132_I	0.701	0.73
91_V	272_V	0.700	0.72
100_I	269_A	0.698	0.72
59_V	95_L	0.697	0.72
88_A	91_V	0.693	0.72
232_K	236_V	0.692	0.72
114_L	228_F	0.690	0.71
172_E	178_A	0.689	0.71
143_A	251_E	0.689	0.71
209_L	213_K	0.688	0.71
146_S	245_F	0.686	0.71
45_H	49_K	0.685	0.71
63_P	92_R	0.684	0.71
207_H	274_S	0.680	0.70
48_P	54_G	0.678	0.70
203_T	278_W	0.673	0.69
185_L	189_L	0.673	0.69
74_G	83_V	0.669	0.69
76_N	249_P	0.666	0.69
115_Y	158_A	0.666	0.69
180_D	183_H	0.665	0.69
190_F	193_V	0.664	0.68
78_S	246_I	0.660	0.68
82_H	86_A	0.656	0.68
123_K	190_F	0.655	0.67
194_Q	198_I	0.654	0.67
154_G	157_S	0.652	0.67
129_F	168_N	0.648	0.67
183_H	187_Q	0.647	0.66
43_N	51_K	0.647	0.66
213_K	220_S	0.646	0.66
152_N	195_T	0.644	0.66
91_V	130_M	0.644	0.66
253_R	256_G	0.644	0.66
193_V	196_D	0.641	0.66
166_R	186_Q	0.636	0.65
135_D	222_N	0.636	0.65
114_L	230_V	0.633	0.65
160_A	167_E	0.633	0.65
149_A	223_T	0.630	0.64
215_V	270_E	0.628	0.64
65_H	242_E	0.627	0.64
64_G	242_E	0.627	0.64
197_T	234_P	0.627	0.64
181_K	186_Q	0.625	0.64
268_I	272_V	0.625	0.64
141_K	250_E	0.623	0.64
167_E	170_A	0.622	0.63
164_S	247_T	0.619	0.63
99_G	102_A	0.618	0.63
200_N	275_Y	0.617	0.63
148_F	228_F	0.616	0.63
195_T	202_L	0.615	0.63
49_K	52_K	0.614	0.62
193_V	197_T	0.614	0.62
129_F	228_F	0.614	0.62
64_G	133_H	0.612	0.62
65_H	133_H	0.612	0.62
156_S	168_N	0.610	0.62
126_A	238_S	0.608	0.62
218_L	251_E	0.607	0.62
250_E	253_R	0.607	0.62
147_V	241_V	0.605	0.61
145_A	260_F	0.605	0.61
67_G	71_G	0.604	0.61
83_V	256_G	0.603	0.61
74_G	78_S	0.600	0.61
204_L	271_G	0.598	0.60
83_V	195_T	0.597	0.60
137_F	219_H	0.597	0.60
210_K	274_S	0.596	0.60
194_Q	244_S	0.590	0.59
75_R	140_P	0.587	0.59
66_G	69_D	0.587	0.59
82_H	256_G	0.586	0.59
137_F	248_N	0.586	0.59
63_P	104_L	0.585	0.59
244_S	251_E	0.583	0.58
133_H	242_E	0.580	0.58
168_N	201_S	0.579	0.58
128_L	237_P	0.578	0.58
198_I	275_Y	0.576	0.58
56_K	100_I	0.576	0.58
78_S	104_L	0.576	0.58
83_V	134_A	0.575	0.57
89_K	104_L	0.572	0.57
63_P	120_I	0.572	0.57
187_Q	190_F	0.571	0.57
149_A	225_Q	0.569	0.57
190_F	194_Q	0.569	0.57
259_A	277_H	0.568	0.57
56_K	115_Y	0.567	0.56
219_H	246_I	0.566	0.56
45_H	48_P	0.565	0.56
249_P	270_E	0.565	0.56
148_F	163_L	0.565	0.56
148_F	224_E	0.564	0.56
185_L	188_V	0.562	0.56
154_G	232_K	0.558	0.55
192_L	196_D	0.556	0.55
258_A	262_Q	0.554	0.55
73_I	266_T	0.553	0.55
105_T	120_I	0.549	0.54
108_G	112_I	0.548	0.54
59_V	272_V	0.547	0.54
229_V	233_S	0.546	0.54
46_S	50_A	0.543	0.53
118_V	158_A	0.543	0.53
208_I	268_I	0.542	0.53
269_A	272_V	0.541	0.53
179_T	187_Q	0.541	0.53
208_I	241_V	0.539	0.53
58_V	99_G	0.538	0.53
44_G	48_P	0.537	0.52
118_V	236_V	0.537	0.52
68_I	175_G	0.537	0.52
145_A	244_S	0.537	0.52
43_N	47_K	0.536	0.52
47_K	277_H	0.536	0.52
258_A	261_R	0.536	0.52
168_N	171_D	0.535	0.52
150_L	238_S	0.534	0.52
94_I	265_A	0.533	0.52
161_K	195_T	0.532	0.52
75_R	83_V	0.530	0.51
233_S	238_S	0.530	0.51
162_Y	236_V	0.529	0.51
164_S	226_A	0.529	0.51
60_V	63_P	0.529	0.51
119_E	179_T	0.527	0.51
45_H	50_A	0.527	0.51
218_L	254_L	0.527	0.51
212_I	264_I	0.526	0.51
142_A	247_T	0.526	0.51
157_S	228_F	0.525	0.51
47_K	52_K	0.524	0.51
150_L	228_F	0.522	0.50
250_E	263_K	0.520	0.50
153_R	226_A	0.519	0.50
154_G	161_K	0.518	0.50
135_D	219_H	0.518	0.50
250_E	270_E	0.514	0.49
176_K	179_T	0.513	0.49
100_I	272_V	0.513	0.49
70_T	192_L	0.512	0.49
189_L	192_L	0.512	0.49
83_V	252_E	0.511	0.49
251_E	256_G	0.511	0.49
210_K	216_H	0.510	0.49
253_R	277_H	0.509	0.49
143_A	219_H	0.508	0.49
85_L	89_K	0.507	0.48
72_A	134_A	0.506	0.48
99_G	272_V	0.505	0.48
209_L	223_T	0.503	0.48
146_S	229_V	0.502	0.48
205_G	223_T	0.501	0.48
47_K	50_A	0.500	0.47

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
4binA	1	0.8651	100	0.205	Contact Map
3ne8A	2	0.7751	100	0.237	Contact Map
1jwqA	1	0.6125	100	0.324	Contact Map
4rn7A	1	0.6332	100	0.325	Contact Map
4lq6A	1	0.6367	100	0.336	Contact Map
1xovA	1	0.6401	100	0.351	Contact Map
3czxA	2	0.6055	100	0.366	Contact Map
3qayA	1	0.5917	100	0.388	Contact Map
4axvA	2	0.6644	27.6	0.96	Contact Map
2h9aB	1	0.4983	18.2	0.963	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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