AMPC - ECOLI - GREMLIN Contacts

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AMPC - Beta-lactamase

UniProt:	P00811	Sequences: MFKTTLCALLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAAWQILNALQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10040
Length:	377 (309)
Sequences:	14263 (11234)
Seq/√Len:	639.1

ECOLI - AMPC AMPH YFEW
BACSU - PBPE YBBE PBPX

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
184_L	192_T	3.697	1.00
96_R	193_R	3.471	1.00
191_Q	196_Q	3.336	1.00
51_Q	349_E	3.310	1.00
92_D	193_R	3.143	1.00
103_D	107_K	3.138	1.00
89_L	189_A	3.072	1.00
100_K	103_D	2.832	1.00
102_S	123_L	2.831	1.00
78_L	241_S	2.746	1.00
70_V	76_F	2.730	1.00
203_T	241_S	2.541	1.00
189_A	193_R	2.506	1.00
92_D	189_A	2.416	1.00
185_S	188_Q	2.410	1.00
103_D	108_Y	2.405	1.00
58_T	72_Q	2.343	1.00
47_A	247_A	2.281	1.00
176_A	180_K	2.233	1.00
88_V	249_W	2.233	1.00
63_D	66_K	2.219	1.00
178_A	189_A	2.182	1.00
182_S	189_A	2.181	1.00
57_F	244_E	2.100	1.00
84_T	249_W	2.074	1.00
62_A	68_Q	2.073	1.00
74_T	216_A	2.070	1.00
61_Y	67_K	2.038	1.00
92_D	96_R	2.002	1.00
176_A	179_V	1.950	1.00
89_L	190_M	1.936	1.00
250_V	342_V	1.924	1.00
90_G	174_F	1.872	1.00
184_L	189_A	1.863	1.00
250_V	351_G	1.844	1.00
345_I	348_K	1.829	1.00
200_L	203_T	1.825	1.00
80_S	83_K	1.805	1.00
190_M	195_F	1.764	1.00
192_T	196_Q	1.745	1.00
175_G	235_E	1.744	1.00
188_Q	192_T	1.739	1.00
158_W	163_Q	1.735	1.00
104_P	107_K	1.728	1.00
266_Q	269_Q	1.703	1.00
49_I	247_A	1.701	1.00
111_E	180_K	1.674	1.00
184_L	188_Q	1.669	1.00
121_T	124_H	1.658	1.00
94_I	101_L	1.610	1.00
33_T	37_E	1.608	1.00
143_S	146_D	1.605	1.00
90_G	99_I	1.598	1.00
79_G	335_T	1.594	1.00
184_L	193_R	1.594	1.00
45_A	243_I	1.580	1.00
85_F	239_V	1.553	1.00
49_I	351_G	1.546	1.00
47_A	243_I	1.544	1.00
327_S	347_E	1.541	1.00
186_F	235_E	1.533	1.00
202_H	214_N	1.515	1.00
93_A	178_A	1.506	1.00
72_Q	244_E	1.495	1.00
122_L	177_L	1.458	1.00
73_Q	244_E	1.454	1.00
29_H	59_W	1.450	1.00
95_A	260_N	1.437	1.00
124_H	161_G	1.436	1.00
34_P	38_Q	1.413	1.00
29_H	33_T	1.412	1.00
71_T	74_T	1.408	1.00
91_G	94_I	1.407	1.00
130_A	133_L	1.407	1.00
95_A	266_Q	1.406	1.00
93_A	182_S	1.397	1.00
130_A	170_S	1.379	1.00
85_F	249_W	1.372	1.00
50_Y	350_L	1.357	1.00
145_S	149_R	1.343	1.00
195_F	200_L	1.341	1.00
258_D	263_T	1.341	1.00
124_H	129_T	1.328	1.00
58_T	70_V	1.326	1.00
98_E	181_P	1.324	1.00
43_G	70_V	1.321	1.00
186_F	190_M	1.307	1.00
272_Q	275_Y	1.302	1.00
261_E	265_Q	1.298	1.00
61_Y	66_K	1.291	1.00
62_A	74_T	1.289	1.00
90_G	126_A	1.288	1.00
123_L	285_L	1.285	1.00
91_G	101_L	1.284	1.00
56_Y	59_W	1.282	1.00
81_V	246_M	1.270	1.00
260_N	263_T	1.269	1.00
87_G	126_A	1.267	1.00
45_A	70_V	1.262	1.00
83_K	166_Y	1.253	1.00
94_I	99_I	1.247	1.00
70_V	74_T	1.244	1.00
203_T	245_D	1.238	1.00
90_G	178_A	1.236	1.00
85_F	190_M	1.221	1.00
45_A	58_T	1.214	1.00
95_A	263_T	1.214	1.00
93_A	98_E	1.211	1.00
195_F	239_V	1.209	1.00
81_V	340_S	1.207	1.00
81_V	342_V	1.206	1.00
43_G	76_F	1.187	1.00
344_F	351_G	1.181	1.00
218_G	338_F	1.181	1.00
104_P	119_G	1.178	1.00
267_G	271_A	1.178	1.00
49_I	54_P	1.173	1.00
200_L	249_W	1.171	1.00
251_Q	254_L	1.162	1.00
29_H	56_Y	1.158	1.00
146_D	149_R	1.157	1.00
326_A	348_K	1.151	1.00
88_V	253_N	1.150	1.00
334_A	339_G	1.148	1.00
246_M	355_L	1.144	1.00
57_F	72_Q	1.143	1.00
30_R	34_P	1.141	1.00
167_A	170_S	1.140	1.00
124_H	127_T	1.140	1.00
87_G	171_I	1.139	1.00
158_W	165_L	1.132	1.00
89_L	193_R	1.126	1.00
205_I	239_V	1.124	1.00
47_A	54_P	1.120	1.00
86_T	186_F	1.116	1.00
158_W	162_T	1.114	1.00
119_G	159_A	1.111	1.00
198_L	252_S	1.104	1.00
284_G	289_M	1.103	1.00
254_L	344_F	1.101	1.00
200_L	245_D	1.096	1.00
265_Q	268_I	1.092	1.00
85_F	200_L	1.092	1.00
168_N	236_A	1.085	1.00
80_S	166_Y	1.078	1.00
108_Y	181_P	1.072	1.00
283_Q	288_E	1.072	1.00
343_A	352_I	1.071	1.00
82_S	239_V	1.068	1.00
75_L	214_N	1.064	1.00
243_I	355_L	1.061	1.00
159_A	162_T	1.059	1.00
265_Q	270_L	1.047	1.00
31_T	35_L	1.041	1.00
191_Q	195_F	1.038	1.00
329_V	344_F	1.036	1.00
106_T	118_N	1.035	1.00
195_F	203_T	1.029	1.00
148_L	176_A	1.029	1.00
33_T	36_I	1.027	1.00
36_I	59_W	1.026	1.00
63_D	68_Q	1.006	1.00
250_V	344_F	1.000	1.00
99_I	122_L	0.999	1.00
258_D	261_E	0.996	1.00
50_Y	53_K	0.994	1.00
78_L	82_S	0.991	1.00
61_Y	69_P	0.985	1.00
92_D	194_V	0.983	1.00
99_I	181_P	0.983	1.00
54_P	251_Q	0.982	1.00
45_A	76_F	0.980	1.00
54_P	57_F	0.976	1.00
75_L	240_K	0.973	1.00
77_E	240_K	0.968	1.00
103_D	122_L	0.960	1.00
85_F	246_M	0.955	1.00
332_T	341_Y	0.954	1.00
188_Q	191_Q	0.948	1.00
108_Y	177_L	0.947	1.00
105_T	125_L	0.946	1.00
264_L	267_G	0.941	1.00
164_R	283_Q	0.941	1.00
246_M	353_V	0.939	1.00
46_V	354_M	0.938	1.00
86_T	235_E	0.934	1.00
128_Y	170_S	0.933	1.00
33_T	59_W	0.932	1.00
75_L	202_H	0.931	1.00
251_Q	255_K	0.930	1.00
263_T	267_G	0.927	1.00
105_T	177_L	0.923	1.00
149_R	153_N	0.923	1.00
256_P	271_A	0.921	1.00
63_D	217_W	0.920	1.00
244_E	248_R	0.915	1.00
46_V	56_Y	0.915	1.00
47_A	353_V	0.914	1.00
89_L	182_S	0.908	1.00
200_L	241_S	0.907	1.00
50_Y	55_Y	0.906	1.00
328_W	345_I	0.904	1.00
248_R	259_I	0.904	1.00
226_H	230_G	0.900	1.00
171_I	174_F	0.899	1.00
49_I	251_Q	0.899	1.00
89_L	178_A	0.896	1.00
342_V	353_V	0.892	1.00
30_R	33_T	0.892	1.00
248_R	251_Q	0.886	1.00
87_G	286_G	0.885	1.00
199_K	248_R	0.884	1.00
77_E	335_T	0.882	1.00
202_H	245_D	0.882	1.00
89_L	194_V	0.878	1.00
32_I	44_M	0.874	1.00
252_S	257_L	0.873	1.00
123_L	127_T	0.871	1.00
75_L	204_W	0.866	1.00
126_A	174_F	0.865	1.00
289_M	327_S	0.863	1.00
267_G	270_L	0.861	1.00
144_S	176_A	0.851	1.00
177_L	181_P	0.850	1.00
93_A	96_R	0.846	1.00
64_I	219_Y	0.845	1.00
32_I	46_V	0.844	1.00
109_W	180_K	0.843	1.00
99_I	177_L	0.839	1.00
178_A	182_S	0.837	1.00
114_A	117_W	0.827	1.00
122_L	181_P	0.824	1.00
187_E	233_D	0.823	1.00
186_F	205_I	0.822	1.00
88_V	194_V	0.821	1.00
175_G	186_F	0.818	1.00
86_T	175_G	0.816	1.00
88_V	92_D	0.814	1.00
157_A	165_L	0.810	1.00
247_A	351_G	0.809	1.00
243_I	247_A	0.809	1.00
109_W	177_L	0.804	1.00
202_H	242_T	0.803	1.00
178_A	186_F	0.802	1.00
42_P	64_I	0.800	1.00
102_S	121_T	0.798	1.00
85_F	195_F	0.795	1.00
268_I	271_A	0.791	1.00
63_D	67_K	0.789	1.00
140_E	146_D	0.787	1.00
326_A	345_I	0.787	1.00
114_A	159_A	0.784	1.00
73_Q	202_H	0.783	1.00
200_L	248_R	0.778	1.00
44_M	354_M	0.775	1.00
124_H	160_P	0.775	1.00
179_V	185_S	0.772	1.00
179_V	182_S	0.771	1.00
254_L	351_G	0.766	1.00
172_G	236_A	0.765	1.00
92_D	95_A	0.764	1.00
46_V	59_W	0.761	1.00
44_M	356_A	0.760	1.00
242_T	245_D	0.759	1.00
226_H	229_P	0.757	1.00
129_T	161_G	0.756	1.00
288_E	331_K	0.755	1.00
283_Q	287_W	0.753	1.00
95_A	269_Q	0.752	1.00
329_V	346_P	0.751	1.00
57_F	243_I	0.746	1.00
128_Y	171_I	0.742	1.00
146_D	150_F	0.739	1.00
75_L	242_T	0.738	1.00
198_L	248_R	0.737	1.00
105_T	109_W	0.734	1.00
263_T	270_L	0.733	1.00
36_I	44_M	0.733	1.00
78_L	246_M	0.733	1.00
62_A	71_T	0.729	1.00
68_Q	74_T	0.727	1.00
94_I	100_K	0.727	1.00
48_V	352_I	0.727	1.00
122_L	174_F	0.725	1.00
253_N	274_R	0.721	1.00
187_E	191_Q	0.720	1.00
208_P	211_E	0.717	1.00
100_K	122_L	0.715	1.00
258_D	267_G	0.714	1.00
34_P	37_E	0.711	1.00
253_N	287_W	0.711	1.00
78_L	340_S	0.709	1.00
26_D	30_R	0.709	1.00
84_T	250_V	0.707	1.00
111_E	149_R	0.705	1.00
108_Y	122_L	0.704	1.00
182_S	185_S	0.703	1.00
250_V	353_V	0.701	1.00
47_A	351_G	0.699	1.00
26_D	29_H	0.698	1.00
81_V	84_T	0.695	1.00
61_Y	68_Q	0.692	1.00
100_K	108_Y	0.691	1.00
261_E	267_G	0.689	1.00
120_I	130_A	0.688	1.00
145_S	176_A	0.684	1.00
278_T	281_M	0.683	1.00
89_L	92_D	0.681	1.00
272_Q	277_Q	0.679	1.00
142_K	146_D	0.679	1.00
263_T	266_Q	0.678	1.00
32_I	36_I	0.678	1.00
84_T	342_V	0.675	1.00
27_I	30_R	0.673	1.00
61_Y	64_I	0.672	1.00
194_V	197_P	0.671	1.00
125_L	130_A	0.667	1.00
225_V	228_S	0.666	1.00
93_A	181_P	0.666	1.00
271_A	275_Y	0.665	1.00
35_L	41_I	0.665	1.00
261_E	264_L	0.663	1.00
116_Q	159_A	0.663	1.00
144_S	179_V	0.662	1.00
76_F	355_L	0.660	1.00
42_P	358_K	0.657	1.00
254_L	349_E	0.657	1.00
92_D	264_L	0.656	1.00
287_W	344_F	0.656	1.00
24_I	27_I	0.655	1.00
50_Y	349_E	0.654	1.00
247_A	353_V	0.652	1.00
271_A	274_R	0.652	1.00
265_Q	269_Q	0.650	1.00
171_I	286_G	0.650	1.00
100_K	123_L	0.649	1.00
326_A	347_E	0.649	1.00
182_S	193_R	0.648	1.00
61_Y	65_A	0.646	1.00
270_L	273_S	0.645	1.00
224_A	227_V	0.645	1.00
109_W	176_A	0.643	1.00
189_A	192_T	0.643	1.00
190_M	203_T	0.641	1.00
101_L	285_L	0.640	1.00
328_W	343_A	0.639	1.00
83_K	168_N	0.638	1.00
201_N	245_D	0.638	1.00
47_A	57_F	0.635	1.00
98_E	182_S	0.634	1.00
79_G	338_F	0.633	1.00
264_L	268_I	0.631	1.00
136_Q	169_S	0.629	1.00
282_Y	289_M	0.629	1.00
78_L	203_T	0.627	1.00
91_G	95_A	0.624	1.00
52_G	251_Q	0.624	1.00
190_M	194_V	0.618	1.00
106_T	113_T	0.615	1.00
104_P	121_T	0.614	1.00
247_A	251_Q	0.613	1.00
330_H	343_A	0.613	1.00
203_T	242_T	0.612	1.00
211_E	214_N	0.612	1.00
31_T	34_P	0.612	1.00
78_L	81_V	0.610	1.00
291_D	327_S	0.609	1.00
234_A	237_Y	0.607	1.00
256_P	267_G	0.607	1.00
32_I	59_W	0.607	1.00
105_T	112_L	0.602	1.00
79_G	237_Y	0.601	1.00
211_E	215_Y	0.600	1.00
267_G	273_S	0.600	1.00
144_S	148_L	0.599	1.00
330_H	334_A	0.597	1.00
149_R	152_Q	0.596	1.00
331_K	334_A	0.595	1.00
54_P	247_A	0.591	1.00
48_V	350_L	0.584	1.00
150_F	153_N	0.584	1.00
36_I	39_Q	0.583	1.00
120_I	133_L	0.582	1.00
204_W	208_P	0.581	1.00
144_S	147_L	0.578	1.00
123_L	277_Q	0.577	1.00
78_L	355_L	0.577	1.00
268_I	272_Q	0.577	1.00
241_S	246_M	0.577	1.00
126_A	171_I	0.576	1.00
225_V	230_G	0.575	1.00
205_I	234_A	0.574	1.00
80_S	168_N	0.571	1.00
94_I	103_D	0.570	1.00
217_W	224_A	0.569	1.00
130_A	167_A	0.569	1.00
71_T	214_N	0.569	1.00
120_I	124_H	0.567	1.00
112_L	120_I	0.566	1.00
283_Q	286_G	0.564	1.00
128_Y	331_K	0.564	1.00
190_M	205_I	0.563	1.00
274_R	329_V	0.563	1.00
84_T	287_W	0.562	1.00
106_T	119_G	0.560	1.00
243_I	353_V	0.560	1.00
265_Q	273_S	0.556	1.00
164_R	288_E	0.556	1.00
45_A	49_I	0.554	1.00
111_E	176_A	0.552	1.00
35_L	38_Q	0.549	1.00
43_G	357_N	0.548	1.00
190_M	239_V	0.548	1.00
113_T	117_W	0.547	1.00
245_D	248_R	0.546	1.00
340_S	355_L	0.545	1.00
252_S	264_L	0.544	1.00
78_L	85_F	0.543	1.00
82_S	238_G	0.541	1.00
212_E	215_Y	0.539	1.00
127_T	285_L	0.538	0.99
84_T	87_G	0.536	0.99
259_I	267_G	0.535	0.99
270_L	274_R	0.534	0.99
94_I	266_Q	0.534	0.99
248_R	252_S	0.529	0.99
127_T	271_A	0.528	0.99
289_M	292_W	0.528	0.99
216_A	219_Y	0.526	0.99
91_G	263_T	0.526	0.99
58_T	71_T	0.526	0.99
148_L	152_Q	0.523	0.99
268_I	273_S	0.522	0.99
45_A	57_F	0.520	0.99
225_V	229_P	0.520	0.99
247_A	250_V	0.518	0.99
120_I	160_P	0.518	0.99
105_T	108_Y	0.517	0.99
133_L	173_L	0.516	0.99
83_K	331_K	0.516	0.99
339_G	358_K	0.515	0.99
204_W	240_K	0.515	0.99
281_M	288_E	0.514	0.99
258_D	262_K	0.512	0.99
177_L	180_K	0.511	0.99
68_Q	71_T	0.510	0.99
234_A	238_G	0.510	0.99
41_I	356_A	0.509	0.99
116_Q	120_I	0.506	0.99
259_I	263_T	0.505	0.99
75_L	211_E	0.505	0.99
93_A	189_A	0.504	0.99
55_Y	350_L	0.503	0.99
227_V	230_G	0.503	0.99
85_F	203_T	0.502	0.99
330_H	341_Y	0.502	0.99
90_G	122_L	0.502	0.99
257_L	263_T	0.501	0.99
205_I	238_G	0.501	0.99
100_K	107_K	0.501	0.99
127_T	277_Q	0.500	0.99
142_K	150_F	0.500	0.99
105_T	173_L	0.500	0.99
123_L	266_Q	0.500	0.99

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
2ffyA	1	0.9496	100	0.201	Contact Map
4netA	1	0.9443	100	0.213	Contact Map
3wrzA	1	0.9443	100	0.217	Contact Map
2qz6A	1	0.9204	100	0.22	Contact Map
4wz4A	1	0.9496	100	0.225	Contact Map
3w8kA	1	0.9151	100	0.228	Contact Map
2qmiA	5	0.8541	100	0.248	Contact Map
1ei5A	2	0.8329	100	0.252	Contact Map
3rjuA	1	0.8647	100	0.252	Contact Map
4p6bA	5	0.8515	100	0.253	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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