NANA - ECOLI - GREMLIN Contacts

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NANA - N-acetylneuraminate lyase

UniProt:	P0A6L4	Sequences: MATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQERG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10637
Length:	297 (284)
Sequences:	10371 (6810)
Seq/√Len:	404.1

ECOLI - NANA DAPA YJHH YAGE
BACSU - DAPA KDGD
HALSA - DAPAL
SULSO - Q97UF0 Q97UI2 Q97WF2 KDGA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
228_D	231_T	3.751	1.00
32_Q	69_E	3.224	1.00
17_D	21_A	3.084	1.00
119_C	154_T	3.022	1.00
261_Y	286_K	2.935	1.00
28_R	69_E	2.768	1.00
24_K	61_Q	2.690	1.00
96_K	131_G	2.591	1.00
24_K	65_I	2.585	1.00
28_R	65_I	2.562	1.00
60_E	94_S	2.479	1.00
80_V	92_A	2.461	1.00
223_A	231_T	2.431	1.00
197_G	202_A	2.385	1.00
92_A	103_V	2.208	1.00
231_T	234_K	2.120	1.00
32_Q	73_K	2.018	1.00
223_A	228_D	2.008	1.00
218_Q	222_K	1.976	1.00
9_M	41_G	1.974	1.00
123_R	158_L	1.971	1.00
115_F	148_T	1.956	1.00
222_K	226_E	1.953	1.00
127_D	158_L	1.932	1.00
33_F	37_Q	1.931	1.00
198_L	224_L	1.906	1.00
115_F	151_Q	1.905	1.00
85_T	121_H	1.895	1.00
61_Q	64_E	1.871	1.00
257_T	282_L	1.860	1.00
123_R	127_D	1.860	1.00
40_D	222_K	1.850	1.00
23_D	26_S	1.843	1.00
116_E	120_D	1.825	1.00
56_L	87_E	1.802	1.00
146_K	173_Q	1.800	1.00
32_Q	36_Q	1.791	1.00
216_R	238_E	1.771	1.00
286_K	290_Q	1.768	1.00
116_E	154_T	1.767	1.00
28_R	68_E	1.759	1.00
37_Q	215_W	1.751	1.00
31_V	66_V	1.716	1.00
153_N	180_E	1.716	1.00
119_C	123_R	1.702	1.00
64_E	68_E	1.680	1.00
27_L	66_V	1.665	1.00
67_A	76_L	1.659	1.00
61_Q	65_I	1.649	1.00
135_V	163_A	1.646	1.00
10_A	210_Y	1.643	1.00
126_I	158_L	1.622	1.00
260_H	268_P	1.622	1.00
26_S	29_R	1.608	1.00
120_D	123_R	1.595	1.00
105_A	125_I	1.581	1.00
283_P	286_K	1.572	1.00
44_V	66_V	1.556	1.00
152_I	164_L	1.548	1.00
148_T	151_Q	1.520	1.00
65_I	69_E	1.516	1.00
129_A	132_L	1.510	1.00
63_L	78_A	1.507	1.00
92_A	129_A	1.497	1.00
58_E	271_R	1.494	1.00
234_K	238_E	1.483	1.00
35_I	74_I	1.443	1.00
154_T	157_T	1.443	1.00
27_L	62_V	1.421	1.00
15_P	27_L	1.410	1.00
96_K	129_A	1.399	1.00
88_S	125_I	1.379	1.00
219_G	223_A	1.379	1.00
96_K	132_L	1.351	1.00
13_L	259_L	1.348	1.00
120_D	124_A	1.340	1.00
283_P	287_A	1.339	1.00
248_K	284_E	1.338	1.00
279_E	283_P	1.334	1.00
279_E	282_L	1.333	1.00
40_D	218_Q	1.328	1.00
219_G	231_T	1.328	1.00
94_S	97_R	1.326	1.00
9_M	43_Y	1.298	1.00
65_I	68_E	1.296	1.00
123_R	157_T	1.290	1.00
82_C	88_S	1.280	1.00
257_T	261_Y	1.279	1.00
89_Q	124_A	1.271	1.00
278_D	281_Y	1.265	1.00
56_L	90_Q	1.263	1.00
6_R	225_K	1.258	1.00
60_E	90_Q	1.257	1.00
84_S	87_E	1.252	1.00
135_V	206_I	1.239	1.00
215_W	219_G	1.227	1.00
77_I	102_A	1.226	1.00
224_L	229_I	1.222	1.00
103_V	129_A	1.220	1.00
260_H	266_S	1.213	1.00
60_E	64_E	1.206	1.00
33_F	264_V	1.205	1.00
8_V	39_I	1.203	1.00
56_L	94_S	1.203	1.00
50_E	256_K	1.188	1.00
195_A	232_A	1.186	1.00
57_S	61_Q	1.182	1.00
178_R	186_L	1.182	1.00
35_I	73_K	1.168	1.00
31_V	70_A	1.160	1.00
124_A	272_K	1.158	1.00
229_I	233_Q	1.152	1.00
126_I	160_G	1.151	1.00
185_V	203_D	1.146	1.00
63_L	95_A	1.145	1.00
221_V	225_K	1.139	1.00
258_V	289_A	1.129	1.00
21_A	86_A	1.127	1.00
45_G	62_V	1.126	1.00
230_Q	233_Q	1.110	1.00
64_E	94_S	1.110	1.00
17_D	23_D	1.109	1.00
70_A	76_L	1.109	1.00
67_A	101_D	1.107	1.00
150_D	180_E	1.102	1.00
257_T	260_H	1.093	1.00
93_A	97_R	1.093	1.00
124_A	127_D	1.091	1.00
219_G	222_K	1.088	1.00
176_Q	180_E	1.086	1.00
93_A	128_S	1.074	1.00
24_K	28_R	1.073	1.00
25_A	28_R	1.067	1.00
60_E	97_R	1.062	1.00
64_E	98_Y	1.061	1.00
16_F	54_Q	1.059	1.00
124_A	128_S	1.058	1.00
77_I	135_V	1.042	1.00
18_Q	269_L	1.041	1.00
257_T	286_K	1.040	1.00
199_L	229_I	1.034	1.00
116_E	119_C	1.032	1.00
31_V	69_E	1.029	1.00
89_Q	93_A	1.018	1.00
103_V	132_L	1.013	1.00
287_A	290_Q	1.011	1.00
176_Q	244_D	1.011	1.00
26_S	267_V	1.003	1.00
80_V	95_A	1.003	1.00
116_E	278_D	1.003	1.00
6_R	203_D	1.002	1.00
78_A	100_F	0.999	1.00
277_V	285_L	0.998	1.00
94_S	98_Y	0.996	1.00
8_V	218_Q	0.994	1.00
103_V	134_M	0.986	1.00
10_A	34_N	0.984	1.00
231_T	235_L	0.980	1.00
155_L	161_V	0.977	1.00
282_L	286_K	0.973	1.00
284_E	287_A	0.969	1.00
281_Y	284_E	0.968	1.00
26_S	266_S	0.966	1.00
56_L	91_L	0.965	1.00
277_V	281_Y	0.962	1.00
245_L	288_L	0.960	1.00
28_R	32_Q	0.956	1.00
126_I	134_M	0.950	1.00
43_Y	104_S	0.948	1.00
10_A	39_I	0.947	1.00
199_L	233_Q	0.941	1.00
156_V	184_L	0.940	1.00
209_T	243_I	0.936	1.00
233_Q	237_T	0.936	1.00
223_A	235_L	0.933	1.00
90_Q	94_S	0.929	1.00
67_A	100_F	0.926	1.00
57_S	90_Q	0.926	1.00
119_C	151_Q	0.926	1.00
89_Q	128_S	0.923	1.00
260_H	282_L	0.921	1.00
30_L	259_L	0.921	1.00
107_T	145_V	0.920	1.00
136_V	152_I	0.919	1.00
35_I	70_A	0.916	1.00
81_G	106_V	0.912	1.00
40_D	221_V	0.910	1.00
80_V	103_V	0.910	1.00
118_H	145_V	0.910	1.00
20_Q	86_A	0.907	1.00
115_F	154_T	0.904	1.00
59_R	91_L	0.902	1.00
149_L	180_E	0.902	1.00
67_A	98_Y	0.900	1.00
12_L	34_N	0.900	1.00
82_C	87_E	0.895	1.00
174_M	197_G	0.894	1.00
90_Q	93_A	0.893	1.00
138_N	146_K	0.892	1.00
119_C	157_T	0.890	1.00
76_L	100_F	0.890	1.00
280_K	283_P	0.885	1.00
120_D	275_G	0.882	1.00
16_F	271_R	0.871	1.00
198_L	221_V	0.868	1.00
126_I	161_V	0.866	1.00
31_V	65_I	0.865	1.00
268_P	282_L	0.853	1.00
207_G	210_Y	0.851	1.00
220_I	235_L	0.849	1.00
44_V	62_V	0.849	1.00
230_Q	234_K	0.848	1.00
20_Q	272_K	0.847	1.00
39_I	214_G	0.838	1.00
8_V	221_V	0.836	1.00
194_F	205_G	0.832	1.00
93_A	96_K	0.831	1.00
261_Y	290_Q	0.830	1.00
213_M	242_V	0.830	1.00
12_L	42_L	0.830	1.00
149_L	176_Q	0.829	1.00
199_L	224_L	0.829	1.00
158_L	161_V	0.825	1.00
187_Y	204_G	0.823	1.00
188_N	197_G	0.822	1.00
105_A	134_M	0.821	1.00
280_K	284_E	0.815	1.00
227_G	230_Q	0.811	1.00
268_P	276_P	0.810	1.00
85_T	89_Q	0.809	1.00
261_Y	282_L	0.804	1.00
29_R	264_V	0.804	1.00
8_V	205_G	0.801	1.00
149_L	153_N	0.793	1.00
25_A	29_R	0.792	1.00
63_L	100_F	0.790	1.00
240_N	244_D	0.790	1.00
119_C	158_L	0.787	1.00
20_Q	269_L	0.785	1.00
57_S	60_E	0.785	1.00
95_A	100_F	0.780	1.00
18_Q	266_S	0.774	1.00
70_A	73_K	0.767	1.00
196_S	199_L	0.767	1.00
63_L	98_Y	0.767	1.00
45_G	78_A	0.765	1.00
236_Q	240_N	0.761	1.00
8_V	210_Y	0.760	1.00
54_Q	62_V	0.759	1.00
120_D	272_K	0.757	1.00
86_A	90_Q	0.749	1.00
213_M	216_R	0.749	1.00
47_S	110_Y	0.748	1.00
12_L	27_L	0.745	1.00
27_L	31_V	0.745	1.00
17_D	25_A	0.739	1.00
213_M	239_C	0.738	1.00
37_Q	214_G	0.737	1.00
219_G	235_L	0.736	1.00
42_L	70_A	0.730	1.00
99_G	132_L	0.728	1.00
260_H	267_V	0.728	1.00
41_G	77_I	0.726	1.00
88_S	105_A	0.724	1.00
137_Y	165_K	0.723	1.00
181_H	184_L	0.722	1.00
115_F	150_D	0.720	1.00
175_E	179_R	0.717	1.00
253_R	270_C	0.714	1.00
17_D	269_L	0.713	1.00
107_T	147_L	0.713	1.00
220_I	224_L	0.712	1.00
31_V	42_L	0.712	1.00
75_K	101_D	0.710	1.00
176_Q	179_R	0.710	1.00
248_K	281_Y	0.704	1.00
60_E	91_L	0.701	1.00
149_L	173_Q	0.700	1.00
80_V	105_A	0.697	1.00
269_L	276_P	0.696	1.00
147_L	152_I	0.696	1.00
216_R	219_G	0.695	1.00
270_C	274_F	0.694	1.00
123_R	154_T	0.694	1.00
22_L	27_L	0.693	1.00
146_K	170_D	0.692	1.00
174_M	178_R	0.691	1.00
139_I	143_S	0.688	1.00
196_S	200_A	0.685	1.00
215_W	262_M	0.682	1.00
56_L	60_E	0.679	0.99
45_G	54_Q	0.678	0.99
35_I	69_E	0.676	0.99
22_L	62_V	0.674	0.99
253_R	277_V	0.673	0.99
85_T	124_A	0.672	0.99
60_E	98_Y	0.671	0.99
51_A	79_H	0.670	0.99
34_N	39_I	0.670	0.99
195_A	224_L	0.670	0.99
226_E	231_T	0.668	0.99
259_L	262_M	0.667	0.99
117_E	275_G	0.667	0.99
259_L	264_V	0.666	0.99
136_V	147_L	0.662	0.99
70_A	74_I	0.661	0.99
18_Q	267_V	0.658	0.99
174_M	186_L	0.657	0.99
138_N	166_Q	0.656	0.99
12_L	66_V	0.656	0.99
152_I	177_I	0.654	0.99
283_P	290_Q	0.651	0.99
17_D	20_Q	0.651	0.99
114_S	253_R	0.648	0.99
249_T	281_Y	0.648	0.99
172_Y	192_E	0.647	0.99
63_L	67_A	0.646	0.99
223_A	226_E	0.643	0.99
30_L	34_N	0.642	0.99
55_S	86_A	0.640	0.99
9_M	77_I	0.638	0.99
194_F	220_I	0.636	0.99
277_V	282_L	0.635	0.99
261_Y	289_A	0.635	0.99
195_A	229_I	0.635	0.99
60_E	95_A	0.634	0.99
32_Q	35_I	0.633	0.99
135_V	162_G	0.632	0.99
52_F	111_Y	0.629	0.99
64_E	97_R	0.625	0.99
162_G	185_V	0.624	0.99
34_N	37_Q	0.622	0.99
33_F	262_M	0.621	0.99
284_E	288_L	0.621	0.99
87_E	90_Q	0.617	0.99
170_D	173_Q	0.617	0.99
150_D	176_Q	0.614	0.99
175_E	200_A	0.613	0.99
196_S	236_Q	0.611	0.99
44_V	76_L	0.611	0.99
153_N	181_H	0.605	0.99
131_G	160_G	0.604	0.99
72_G	101_D	0.602	0.99
150_D	153_N	0.601	0.99
114_S	117_E	0.601	0.99
179_R	237_T	0.600	0.99
16_F	58_E	0.596	0.99
250_G	254_G	0.594	0.99
166_Q	174_M	0.593	0.99
257_T	270_C	0.591	0.99
195_A	199_L	0.591	0.99
45_G	59_R	0.591	0.99
195_A	236_Q	0.588	0.99
107_T	122_Y	0.585	0.98
22_L	65_I	0.583	0.98
24_K	69_E	0.583	0.98
212_I	258_V	0.583	0.98
38_G	218_Q	0.582	0.98
147_L	151_Q	0.582	0.98
100_F	132_L	0.581	0.98
222_K	225_K	0.581	0.98
151_Q	154_T	0.580	0.98
173_Q	177_I	0.579	0.98
5_L	102_A	0.579	0.98
270_C	275_G	0.578	0.98
258_V	261_Y	0.573	0.98
163_A	185_V	0.573	0.98
175_E	236_Q	0.571	0.98
43_Y	77_I	0.568	0.98
135_V	185_V	0.565	0.98
77_I	104_S	0.564	0.98
57_S	94_S	0.561	0.98
223_A	232_A	0.560	0.98
234_K	237_T	0.560	0.98
68_E	71_K	0.560	0.98
39_I	218_Q	0.556	0.98
127_D	160_G	0.554	0.98
175_E	196_S	0.554	0.98
224_L	232_A	0.553	0.98
47_S	137_Y	0.553	0.98
258_V	285_L	0.552	0.98
13_L	255_L	0.551	0.98
23_D	266_S	0.551	0.98
155_L	158_L	0.551	0.98
194_F	217_Y	0.550	0.98
179_R	241_K	0.549	0.98
45_G	63_L	0.546	0.98
177_I	186_L	0.545	0.98
78_A	95_A	0.544	0.98
279_E	286_K	0.544	0.98
178_R	203_D	0.544	0.98
121_H	124_A	0.543	0.98
6_R	40_D	0.543	0.98
122_Y	161_V	0.542	0.98
171_L	193_I	0.540	0.97
105_A	122_Y	0.536	0.97
245_L	284_E	0.534	0.97
235_L	238_E	0.532	0.97
11_A	208_S	0.532	0.97
42_L	74_I	0.532	0.97
66_V	70_A	0.531	0.97
89_Q	125_I	0.530	0.97
212_I	259_L	0.530	0.97
212_I	255_L	0.529	0.97
21_A	61_Q	0.525	0.97
67_A	71_K	0.525	0.97
96_K	128_S	0.524	0.97
116_E	275_G	0.524	0.97
33_F	214_G	0.522	0.97
11_A	207_G	0.521	0.97
92_A	125_I	0.519	0.97
30_L	33_F	0.518	0.97
12_L	31_V	0.518	0.97
107_T	118_H	0.514	0.97
254_G	277_V	0.511	0.96
168_S	173_Q	0.508	0.96
86_A	124_A	0.508	0.96
163_A	184_L	0.507	0.96
91_L	95_A	0.507	0.96
53_V	85_T	0.506	0.96
209_T	217_Y	0.506	0.96
257_T	277_V	0.504	0.96
55_S	58_E	0.502	0.96
82_C	91_L	0.501	0.96
122_Y	136_V	0.501	0.96
198_L	225_K	0.500	0.96

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
2wkjA	3	0.9899	100	0.06	Contact Map
3na8A	3	0.9731	100	0.062	Contact Map
3eb2A	3	0.9764	100	0.062	Contact Map
4oe7A	3	0.9832	100	0.068	Contact Map
1f6kA	3	0.9798	100	0.072	Contact Map
3cprA	3	0.9798	100	0.074	Contact Map
3l21A	5	0.9832	100	0.074	Contact Map
4n4pA	3	0.9663	100	0.075	Contact Map
1xkyA	3	0.9798	100	0.075	Contact Map
3qzeA	2	0.9731	100	0.077	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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