YIAO - ECOLI - GREMLIN Contacts

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YIAO - 2,3-diketo-L-gulonate-binding periplasmic protein YiaO

UniProt:	P37676	Sequences: MKLRSVTYALFIAGLAAFSTSSLAAQSLRFGYETSQTDSQHIAAKKFNDLLQERTKGELKLKLFPDSTLGNAQAMISGVRGGTIDMEMSGSNNFAGLSPVMNLLDVPFLFRDTAHAHKTLDGKVGDDLKASLEGKGLKVLAYWENGWRDVTNSRAPVKTPADLKGLKIRTNNSPMNIAAFKVFGANPIPMPFAEVYTGLETRTIDAQEHPINVVWSAKFFEVQKFLSLTHHAYSPLLVVINKAKFDGLSPEFQQALVSSAQEAGNYQRKLVAEDQQKIIDGMKEAGVEVITDLDRKAFSDALGNQVRDMFVKDVPQGADLLKAVDEVQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12283
Length:	328 (313)
Sequences:	9373 (7085)
Seq/√Len:	400.4

ECOLI - YIAO
BACSU - DCTB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
250_P	253_Q	3.697	1.00
58_E	252_F	3.637	1.00
249_S	252_F	3.586	1.00
242_K	246_D	3.530	1.00
280_D	284_E	3.253	1.00
54_R	258_S	2.732	1.00
296_K	300_D	2.732	1.00
254_Q	258_S	2.682	1.00
138_K	242_K	2.673	1.00
318_A	322_K	2.547	1.00
52_Q	60_K	2.514	1.00
85_D	244_K	2.402	1.00
245_F	257_V	2.361	1.00
215_W	281_G	2.357	1.00
27_S	62_K	2.356	1.00
46_K	49_D	2.326	1.00
280_D	283_K	2.314	1.00
55_T	255_A	2.270	1.00
31_G	75_M	2.203	1.00
178_A	181_K	2.187	1.00
269_K	273_E	2.184	1.00
50_L	262_E	2.168	1.00
138_K	257_V	2.149	1.00
155_A	166_L	2.104	1.00
48_N	52_Q	2.088	1.00
49_D	53_E	2.035	1.00
149_D	230_H	2.008	1.00
244_K	247_G	2.006	1.00
50_L	54_R	1.983	1.00
27_S	60_K	1.959	1.00
178_A	309_M	1.907	1.00
46_K	50_L	1.876	1.00
45_K	49_D	1.858	1.00
281_G	285_A	1.852	1.00
50_L	53_E	1.833	1.00
127_D	323_A	1.792	1.00
46_K	266_Y	1.782	1.00
281_G	284_E	1.782	1.00
291_T	294_D	1.768	1.00
160_P	297_A	1.755	1.00
250_P	254_Q	1.751	1.00
133_E	242_K	1.738	1.00
161_A	164_K	1.724	1.00
273_E	277_K	1.706	1.00
100_V	131_S	1.701	1.00
279_I	283_K	1.694	1.00
129_K	139_V	1.637	1.00
54_R	255_A	1.636	1.00
28_L	244_K	1.627	1.00
111_R	115_H	1.625	1.00
311_V	318_A	1.613	1.00
26_Q	252_F	1.602	1.00
180_F	185_A	1.592	1.00
133_E	138_K	1.589	1.00
55_T	59_L	1.577	1.00
54_R	259_S	1.558	1.00
277_K	281_G	1.557	1.00
86_M	240_I	1.551	1.00
50_L	259_S	1.550	1.00
300_D	304_N	1.539	1.00
130_A	133_E	1.533	1.00
48_N	63_L	1.526	1.00
47_F	260_A	1.499	1.00
225_F	288_E	1.495	1.00
276_Q	280_D	1.484	1.00
18_F	21_S	1.483	1.00
274_D	277_K	1.462	1.00
294_D	297_A	1.456	1.00
123_K	126_D	1.452	1.00
49_D	52_Q	1.449	1.00
196_Y	222_V	1.445	1.00
296_K	299_S	1.440	1.00
182_V	305_Q	1.426	1.00
297_A	300_D	1.421	1.00
270_L	273_E	1.421	1.00
156_P	288_E	1.412	1.00
257_V	261_Q	1.412	1.00
121_D	268_R	1.411	1.00
220_F	285_A	1.407	1.00
266_Y	270_L	1.396	1.00
15_L	18_F	1.393	1.00
228_L	279_I	1.390	1.00
70_G	78_G	1.389	1.00
41_H	45_K	1.384	1.00
295_R	299_S	1.384	1.00
308_D	311_V	1.383	1.00
54_R	262_E	1.382	1.00
71_N	74_A	1.380	1.00
30_F	44_A	1.369	1.00
29_R	64_F	1.367	1.00
26_Q	59_L	1.360	1.00
51_L	255_A	1.360	1.00
304_N	308_D	1.349	1.00
32_Y	41_H	1.340	1.00
25_A	58_E	1.326	1.00
30_F	61_L	1.323	1.00
126_D	130_A	1.320	1.00
112_D	115_H	1.320	1.00
245_F	253_Q	1.319	1.00
26_Q	249_S	1.315	1.00
230_H	295_R	1.314	1.00
25_A	60_K	1.301	1.00
51_L	256_L	1.299	1.00
59_L	252_F	1.295	1.00
138_K	245_F	1.286	1.00
151_T	207_Q	1.271	1.00
58_E	251_E	1.271	1.00
28_L	85_D	1.268	1.00
47_F	51_L	1.265	1.00
51_L	61_L	1.259	1.00
181_K	187_P	1.252	1.00
117_H	272_A	1.250	1.00
161_A	297_A	1.250	1.00
211_I	279_I	1.249	1.00
190_M	204_I	1.245	1.00
195_V	204_I	1.235	1.00
258_S	262_E	1.234	1.00
308_D	312_K	1.224	1.00
218_K	221_E	1.223	1.00
290_I	294_D	1.220	1.00
75_M	87_E	1.217	1.00
29_R	62_K	1.217	1.00
190_M	198_G	1.213	1.00
240_I	244_K	1.208	1.00
253_Q	257_V	1.192	1.00
243_A	246_D	1.186	1.00
98_S	131_S	1.185	1.00
17_A	20_T	1.167	1.00
254_Q	257_V	1.163	1.00
305_Q	308_D	1.159	1.00
79_V	87_E	1.157	1.00
255_A	259_S	1.149	1.00
158_K	294_D	1.142	1.00
151_T	223_Q	1.141	1.00
159_T	162_D	1.132	1.00
14_G	17_A	1.130	1.00
158_K	162_D	1.121	1.00
114_A	118_K	1.120	1.00
259_S	262_E	1.120	1.00
211_I	228_L	1.116	1.00
13_A	16_A	1.114	1.00
168_I	206_A	1.108	1.00
79_V	241_N	1.104	1.00
156_P	225_F	1.103	1.00
48_N	61_L	1.102	1.00
64_F	69_L	1.095	1.00
215_W	278_I	1.090	1.00
31_G	84_I	1.086	1.00
36_Q	45_K	1.083	1.00
265_N	269_K	1.082	1.00
32_Y	63_L	1.081	1.00
125_G	129_K	1.076	1.00
59_L	256_L	1.072	1.00
130_A	134_G	1.065	1.00
266_Y	269_K	1.055	1.00
43_A	267_Q	1.049	1.00
259_S	263_A	1.048	1.00
143_W	263_A	1.043	1.00
278_I	281_G	1.043	1.00
28_L	86_M	1.043	1.00
182_V	309_M	1.043	1.00
50_L	266_Y	1.024	1.00
137_L	239_V	1.024	1.00
141_A	264_G	1.022	1.00
127_D	130_A	1.021	1.00
151_T	214_V	1.019	1.00
12_I	15_L	1.018	1.00
314_V	317_G	1.009	1.00
319_D	322_K	1.009	1.00
319_D	323_A	1.007	1.00
279_I	289_V	1.005	1.00
11_F	14_G	1.004	1.00
297_A	301_A	1.004	1.00
138_K	246_D	0.997	1.00
150_V	229_T	0.992	1.00
282_M	287_V	0.987	1.00
101_M	132_L	0.983	1.00
166_L	206_A	0.972	1.00
64_F	68_T	0.969	1.00
48_N	51_L	0.964	1.00
36_Q	66_D	0.963	1.00
292_D	296_K	0.962	1.00
211_I	226_L	0.953	1.00
140_L	260_A	0.953	1.00
224_K	288_E	0.951	1.00
160_P	298_F	0.948	1.00
240_I	245_F	0.944	1.00
150_V	180_F	0.939	1.00
117_H	121_D	0.935	1.00
77_S	97_L	0.934	1.00
178_A	182_V	0.929	1.00
196_Y	221_E	0.927	1.00
283_K	289_V	0.927	1.00
110_F	119_T	0.925	1.00
130_A	319_D	0.922	1.00
309_M	313_D	0.920	1.00
55_T	252_F	0.915	1.00
123_K	323_A	0.914	1.00
262_E	266_Y	0.913	1.00
149_D	228_L	0.911	1.00
29_R	85_D	0.907	1.00
115_H	118_K	0.907	1.00
51_L	59_L	0.902	1.00
82_G	85_D	0.896	1.00
131_S	134_G	0.895	1.00
277_K	280_D	0.894	1.00
272_A	276_Q	0.888	1.00
151_T	226_L	0.884	1.00
136_G	243_A	0.881	1.00
37_T	41_H	0.881	1.00
192_F	217_A	0.875	1.00
309_M	312_K	0.872	1.00
58_E	249_S	0.867	1.00
95_A	102_N	0.864	1.00
263_A	266_Y	0.863	1.00
307_R	311_V	0.862	1.00
197_T	201_T	0.860	1.00
22_S	25_A	0.858	1.00
42_I	45_K	0.853	1.00
129_K	133_E	0.848	1.00
163_L	185_A	0.847	1.00
126_D	129_K	0.847	1.00
28_L	256_L	0.846	1.00
77_S	81_G	0.839	1.00
302_L	305_Q	0.838	1.00
117_H	268_R	0.837	1.00
30_F	86_M	0.836	1.00
98_S	101_M	0.835	1.00
46_K	262_E	0.835	1.00
78_G	83_T	0.833	1.00
23_L	26_Q	0.833	1.00
301_A	305_Q	0.831	1.00
207_Q	223_Q	0.831	1.00
261_Q	265_N	0.829	1.00
154_R	224_K	0.827	1.00
293_L	297_A	0.819	1.00
123_K	127_D	0.818	1.00
45_K	63_L	0.818	1.00
167_K	186_N	0.816	1.00
48_N	60_K	0.812	1.00
47_F	61_L	0.805	1.00
47_F	256_L	0.804	1.00
183_F	302_L	0.803	1.00
243_A	247_G	0.801	1.00
293_L	296_K	0.799	1.00
32_Y	65_P	0.798	1.00
30_F	238_V	0.796	1.00
214_V	226_L	0.796	1.00
75_M	84_I	0.793	1.00
46_K	263_A	0.790	1.00
261_Q	264_G	0.789	1.00
111_R	299_S	0.788	1.00
238_V	260_A	0.787	1.00
16_A	19_S	0.787	1.00
276_Q	279_I	0.782	1.00
168_I	185_A	0.782	1.00
148_R	208_E	0.780	1.00
129_K	138_K	0.779	1.00
65_P	68_T	0.776	1.00
159_T	294_D	0.775	1.00
255_A	258_S	0.770	1.00
177_I	181_K	0.767	1.00
78_G	84_I	0.754	1.00
136_G	242_K	0.754	1.00
28_L	59_L	0.753	1.00
226_L	289_V	0.752	1.00
37_T	42_I	0.751	1.00
163_L	298_F	0.751	1.00
156_P	227_S	0.750	1.00
157_V	162_D	0.745	1.00
178_A	310_F	0.743	1.00
311_V	321_L	0.739	1.00
157_V	163_L	0.737	1.00
91_S	237_L	0.736	1.00
52_Q	55_T	0.736	1.00
52_Q	57_G	0.735	1.00
86_M	256_L	0.733	1.00
36_Q	41_H	0.730	1.00
59_L	255_A	0.730	1.00
122_G	125_G	0.729	1.00
73_Q	172_N	0.720	1.00
211_I	278_I	0.718	1.00
227_S	290_I	0.718	1.00
182_V	306_V	0.718	1.00
10_L	15_L	0.718	1.00
26_Q	247_G	0.715	1.00
7_T	10_L	0.715	1.00
17_A	21_S	0.714	1.00
90_G	234_S	0.713	1.00
183_F	301_A	0.712	1.00
149_D	226_L	0.712	1.00
244_K	248_L	0.712	1.00
99_P	313_D	0.709	1.00
28_L	240_I	0.709	1.00
76_I	137_L	0.707	1.00
194_E	197_T	0.704	1.00
42_I	270_L	0.703	1.00
164_K	184_G	0.698	1.00
79_V	137_L	0.693	1.00
139_V	237_L	0.691	1.00
142_Y	238_V	0.689	1.00
26_Q	244_K	0.687	1.00
148_R	232_A	0.686	1.00
199_L	223_Q	0.682	0.99
304_N	307_R	0.682	0.99
150_V	157_V	0.679	0.99
220_F	287_V	0.678	0.99
9_A	12_I	0.678	0.99
38_D	41_H	0.678	0.99
22_S	26_Q	0.677	0.99
311_V	322_K	0.673	0.99
252_F	255_A	0.671	0.99
47_F	263_A	0.670	0.99
18_F	22_S	0.670	0.99
42_I	274_D	0.668	0.99
262_E	265_N	0.667	0.99
224_K	287_V	0.666	0.99
299_S	304_N	0.664	0.99
127_D	319_D	0.664	0.99
51_L	259_S	0.663	0.99
197_T	200_E	0.659	0.99
242_K	245_F	0.657	0.99
192_F	213_V	0.657	0.99
52_Q	61_L	0.656	0.99
36_Q	65_P	0.653	0.99
168_I	180_F	0.652	0.99
133_E	246_D	0.651	0.99
70_G	75_M	0.651	0.99
153_S	206_A	0.648	0.99
103_L	324_V	0.648	0.99
59_L	248_L	0.646	0.99
31_G	70_G	0.645	0.99
41_H	65_P	0.645	0.99
141_A	260_A	0.642	0.99
251_E	254_Q	0.642	0.99
113_T	272_A	0.641	0.99
15_L	19_S	0.639	0.99
44_A	63_L	0.637	0.99
170_T	176_N	0.636	0.99
158_K	291_T	0.634	0.99
164_K	301_A	0.634	0.99
115_H	119_T	0.633	0.99
310_F	313_D	0.630	0.99
150_V	163_L	0.628	0.99
98_S	135_K	0.628	0.99
241_N	247_G	0.627	0.99
24_A	58_E	0.625	0.99
244_K	256_L	0.624	0.99
20_T	23_L	0.623	0.99
179_A	302_L	0.623	0.99
47_F	259_S	0.623	0.99
42_I	266_Y	0.622	0.99
61_L	256_L	0.622	0.99
114_A	117_H	0.621	0.99
179_A	306_V	0.620	0.99
150_V	168_I	0.620	0.99
132_L	139_V	0.620	0.99
300_D	305_Q	0.617	0.99
167_K	205_D	0.615	0.99
207_Q	219_F	0.614	0.99
273_E	276_Q	0.611	0.99
163_L	183_F	0.609	0.99
146_G	275_Q	0.605	0.99
92_N	171_N	0.604	0.99
180_F	208_E	0.604	0.99
170_T	177_I	0.603	0.99
28_L	61_L	0.602	0.99
69_L	84_I	0.602	0.99
58_E	255_A	0.602	0.99
274_D	278_I	0.601	0.99
16_A	20_T	0.600	0.99
192_F	195_V	0.600	0.99
79_V	239_V	0.599	0.99
170_T	180_F	0.598	0.99
161_A	301_A	0.597	0.99
215_W	220_F	0.597	0.99
122_G	126_D	0.597	0.99
61_L	86_M	0.596	0.99
73_Q	97_L	0.595	0.99
176_N	232_A	0.594	0.99
28_L	248_L	0.594	0.99
194_E	203_T	0.594	0.99
195_V	207_Q	0.593	0.99
302_L	307_R	0.593	0.99
208_E	231_H	0.591	0.99
113_T	117_H	0.587	0.98
19_S	23_L	0.585	0.98
8_Y	14_G	0.583	0.98
30_F	88_M	0.582	0.98
248_L	256_L	0.581	0.98
248_L	252_F	0.580	0.98
198_G	203_T	0.580	0.98
223_Q	287_V	0.579	0.98
8_Y	13_A	0.578	0.98
100_V	317_G	0.578	0.98
112_D	118_K	0.577	0.98
198_G	204_I	0.576	0.98
46_K	270_L	0.575	0.98
9_A	14_G	0.574	0.98
122_G	127_D	0.574	0.98
177_I	187_P	0.573	0.98
182_V	301_A	0.572	0.98
290_I	295_R	0.572	0.98
159_T	297_A	0.571	0.98
55_T	58_E	0.571	0.98
228_L	289_V	0.570	0.98
33_E	89_S	0.570	0.98
215_W	285_A	0.566	0.98
86_M	238_V	0.565	0.98
106_V	307_R	0.563	0.98
197_T	203_T	0.562	0.98
252_F	256_L	0.562	0.98
10_L	13_A	0.562	0.98
26_Q	58_E	0.561	0.98
15_L	20_T	0.561	0.98
117_H	144_E	0.559	0.98
42_I	46_K	0.557	0.98
143_W	264_G	0.554	0.98
174_P	178_A	0.554	0.98
258_S	261_Q	0.554	0.98
290_I	293_L	0.552	0.98
190_M	195_V	0.550	0.98
176_N	179_A	0.550	0.98
209_H	214_V	0.549	0.98
138_K	253_Q	0.549	0.98
154_R	205_D	0.547	0.98
188_I	204_I	0.542	0.97
41_H	63_L	0.541	0.97
79_V	86_M	0.541	0.97
215_W	282_M	0.540	0.97
114_A	272_A	0.539	0.97
150_V	290_I	0.538	0.97
153_S	223_Q	0.538	0.97
306_V	309_M	0.538	0.97
80_R	136_G	0.537	0.97
269_K	272_A	0.537	0.97
53_E	56_K	0.532	0.97
147_W	233_Y	0.532	0.97
25_A	62_K	0.531	0.97
43_A	263_A	0.531	0.97
56_K	251_E	0.530	0.97
73_Q	77_S	0.529	0.97
245_F	256_L	0.528	0.97
14_G	18_F	0.527	0.97
270_L	274_D	0.527	0.97
196_Y	200_E	0.527	0.97
227_S	293_L	0.525	0.97
144_E	233_Y	0.525	0.97
11_F	15_L	0.525	0.97
214_V	287_V	0.525	0.97
192_F	219_F	0.524	0.97
149_D	211_I	0.524	0.97
317_G	320_L	0.522	0.97
144_E	268_R	0.522	0.97
200_E	222_V	0.519	0.97
45_K	65_P	0.517	0.97
110_F	116_A	0.516	0.97
182_V	302_L	0.513	0.96
103_L	320_L	0.513	0.96
43_A	46_K	0.512	0.96
11_F	16_A	0.511	0.96
294_D	298_F	0.509	0.96
67_S	71_N	0.509	0.96
124_V	127_D	0.507	0.96
108_F	229_T	0.507	0.96
121_D	261_Q	0.506	0.96
320_L	324_V	0.505	0.96
19_S	22_S	0.502	0.96
127_D	131_S	0.502	0.96
174_P	313_D	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
3u65B	1	0.9116	100	0.172	Contact Map
2xwvA	1	0.9146	100	0.196	Contact Map
4xeqA	1	0.9146	100	0.199	Contact Map
4nguA	1	0.9207	100	0.199	Contact Map
4ovsA	1	0.9207	100	0.2	Contact Map
4ovqA	1	0.9207	100	0.202	Contact Map
4pddA	1	0.9146	100	0.203	Contact Map
4pakA	1	0.9238	100	0.204	Contact Map
4o94A	1	0.9177	100	0.205	Contact Map
4ovrA	1	0.9116	100	0.205	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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