YAGA - ECOLI - GREMLIN Contacts

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YAGA - Uncharacterized protein YagA

UniProt:	P37007	Sequences: MESLMPWDARDTMSLRTEFVLFASQDGANIRSLCRRFGISPATGYKWLQRWAQEGAAGLQDRPRIPHHSPNRSSDDITALLRMAHDRHERWGARKIKRWLEDQGHTMPAFSTVHNLMARHGLLPGASPGIPATGRFEHDAPNRLWQMDFKGHFPFGGGRCHPLTLLDDHSRFSLCLAHCTDERRETVQQQLVSVFERYGLPDRMTMDNGSPWGDTTGTWTALELWLMRLGIRVGHSRPYHPQTQGKLERFHRSLKAEVLQGKWFADSGELQRAFDHWRTVYNLERPHEALDMAVPGSRYQPSARQYSGNTTPPEYDEGVMVRKVDISGKLSVKGVSLSAGKAFRGERVGLKEMQEDGSYEVWWYSTKVGVIDLKKKSITMGKGC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12338
Length:	384 (334)
Sequences:	5010 (4249)
Seq/√Len:	232.5

ECOLI - YAGA INSD1 INSD2 INSD3 INSD4 INSD5 INSD6 INSK INSF1 INSF2 INSF3 INSF4 INSF5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
249_R	252_R	3.534	1.00
237_R	243_T	3.291	1.00
293_A	298_R	3.001	1.00
143_R	202_D	2.922	1.00
177_A	193_S	2.875	1.00
236_S	244_Q	2.754	1.00
226_L	231_I	2.730	1.00
252_R	256_A	2.678	1.00
142_N	145_W	2.654	1.00
145_W	194_V	2.538	1.00
182_E	211_P	2.434	1.00
164_T	247_L	2.422	1.00
293_A	301_P	2.271	1.00
181_D	186_T	2.270	1.00
161_H	182_E	2.261	1.00
168_D	246_K	2.256	1.00
110_F	114_H	2.246	1.00
321_V	347_R	2.222	1.00
164_T	251_H	2.189	1.00
32_S	36_R	2.184	1.00
147_M	206_M	2.181	1.00
112_T	115_N	2.106	1.00
144_L	203_R	2.100	1.00
332_V	352_E	2.090	1.00
97_K	101_E	2.063	1.00
171_R	287_H	2.061	1.00
283_L	296_G	1.977	1.00
54_E	58_G	1.968	1.00
34_C	44_G	1.948	1.00
140_A	202_D	1.936	1.00
150_K	255_K	1.922	1.00
296_G	300_Q	1.916	1.00
170_S	298_R	1.904	1.00
145_W	165_L	1.860	1.00
203_R	234_G	1.858	1.00
323_K	347_R	1.853	1.00
152_H	155_F	1.844	1.00
266_D	269_E	1.831	1.00
80_L	83_M	1.829	1.00
151_G	155_F	1.823	1.00
146_Q	245_G	1.768	1.00
96_I	100_L	1.749	1.00
146_Q	168_D	1.746	1.00
294_V	297_S	1.744	1.00
208_N	235_H	1.737	1.00
173_S	250_F	1.715	1.00
209_G	212_W	1.706	1.00
208_N	238_P	1.705	1.00
226_L	233_V	1.702	1.00
240_H	243_T	1.699	1.00
75_D	78_T	1.698	1.00
139_D	143_R	1.693	1.00
332_V	350_L	1.688	1.00
293_A	297_S	1.681	1.00
206_M	233_V	1.673	1.00
41_P	45_Y	1.659	1.00
174_L	177_A	1.615	1.00
165_L	194_V	1.598	1.00
271_Q	275_D	1.593	1.00
287_H	290_L	1.589	1.00
172_F	299_Y	1.585	1.00
140_A	143_R	1.571	1.00
165_L	190_Q	1.568	1.00
173_S	282_N	1.549	1.00
171_R	295_P	1.548	1.00
74_S	77_I	1.540	1.00
249_R	253_S	1.538	1.00
144_L	205_T	1.522	1.00
183_R	186_T	1.516	1.00
149_F	211_P	1.515	1.00
78_T	82_R	1.512	1.00
80_L	84_A	1.508	1.00
265_A	269_E	1.504	1.00
75_D	79_A	1.502	1.00
257_E	285_R	1.496	1.00
172_F	296_G	1.490	1.00
82_R	86_D	1.485	1.00
109_A	112_T	1.468	1.00
279_T	283_L	1.461	1.00
30_I	45_Y	1.454	1.00
147_M	212_W	1.445	1.00
178_H	274_F	1.412	1.00
43_T	47_W	1.407	1.00
78_T	116_L	1.377	1.00
146_Q	244_Q	1.375	1.00
144_L	168_D	1.368	1.00
188_Q	221_A	1.367	1.00
169_H	302_S	1.362	1.00
331_S	336_S	1.352	1.00
286_P	290_L	1.346	1.00
191_L	195_F	1.343	1.00
97_K	100_L	1.341	1.00
188_Q	225_W	1.339	1.00
205_T	243_T	1.335	1.00
211_P	214_D	1.334	1.00
147_M	165_L	1.327	1.00
109_A	115_N	1.325	1.00
77_I	85_H	1.325	1.00
146_Q	247_L	1.322	1.00
348_V	361_V	1.321	1.00
330_L	334_G	1.316	1.00
179_C	189_Q	1.302	1.00
173_S	278_R	1.293	1.00
213_G	235_H	1.289	1.00
303_A	307_S	1.286	1.00
151_G	154_P	1.284	1.00
175_C	278_R	1.283	1.00
149_F	163_L	1.277	1.00
33_L	37_F	1.272	1.00
99_W	102_D	1.260	1.00
191_L	206_M	1.259	1.00
257_E	277_W	1.243	1.00
81_L	84_A	1.240	1.00
171_R	246_K	1.230	1.00
324_V	348_V	1.227	1.00
111_S	115_N	1.220	1.00
331_S	334_G	1.218	1.00
191_L	222_L	1.218	1.00
32_S	35_R	1.203	1.00
30_I	48_L	1.201	1.00
193_S	197_R	1.194	1.00
179_C	190_Q	1.191	1.00
42_A	49_Q	1.189	1.00
178_H	271_Q	1.183	1.00
269_E	272_R	1.177	1.00
80_L	85_H	1.174	1.00
113_V	117_M	1.173	1.00
29_N	32_S	1.165	1.00
149_F	179_C	1.164	1.00
166_L	250_F	1.164	1.00
350_L	359_Y	1.160	1.00
187_V	222_L	1.154	1.00
99_W	103_Q	1.153	1.00
45_Y	49_Q	1.151	1.00
287_H	291_D	1.148	1.00
31_R	41_P	1.147	1.00
267_S	271_Q	1.146	1.00
116_L	119_R	1.143	1.00
174_L	193_S	1.143	1.00
154_P	157_G	1.141	1.00
100_L	104_G	1.140	1.00
28_A	36_R	1.137	1.00
256_A	260_Q	1.136	1.00
153_F	156_G	1.136	1.00
206_M	235_H	1.134	1.00
149_F	182_E	1.134	1.00
192_V	196_E	1.127	1.00
321_V	349_G	1.123	1.00
81_L	85_H	1.122	1.00
163_L	190_Q	1.120	1.00
330_L	350_L	1.114	1.00
93_A	96_I	1.109	1.00
236_S	239_Y	1.107	1.00
128_P	131_P	1.105	1.00
170_S	302_S	1.102	1.00
77_I	86_D	1.087	1.00
160_C	270_L	1.086	1.00
146_Q	246_K	1.086	1.00
150_K	251_H	1.077	1.00
172_F	282_N	1.071	1.00
42_A	45_Y	1.068	1.00
275_D	279_T	1.068	1.00
91_W	95_K	1.063	1.00
108_P	112_T	1.058	1.00
278_R	282_N	1.053	1.00
164_T	250_F	1.053	1.00
111_S	114_H	1.052	1.00
236_S	243_T	1.051	1.00
31_R	35_R	1.048	1.00
94_R	98_R	1.037	1.00
97_K	113_V	1.035	1.00
205_T	244_Q	1.027	1.00
171_R	290_L	1.012	1.00
322_R	350_L	1.011	1.00
28_A	32_S	1.010	1.00
57_A	60_Q	1.009	1.00
166_L	247_L	1.009	1.00
39_I	44_G	1.000	1.00
174_L	197_R	0.997	1.00
149_F	161_H	0.994	1.00
332_V	359_Y	0.993	1.00
203_R	232_R	0.991	1.00
49_Q	53_Q	0.989	1.00
93_A	117_M	0.989	1.00
81_L	116_L	0.987	1.00
81_L	96_I	0.985	1.00
237_R	240_H	0.984	1.00
163_L	187_V	0.983	1.00
65_I	69_S	0.980	1.00
224_L	228_R	0.978	1.00
152_H	156_G	0.977	1.00
247_L	251_H	0.976	1.00
191_L	204_M	0.975	1.00
253_S	281_Y	0.969	1.00
244_Q	247_L	0.966	1.00
184_R	188_Q	0.960	1.00
100_L	113_V	0.959	1.00
162_P	178_H	0.956	1.00
319_V	349_G	0.955	1.00
114_H	118_A	0.955	1.00
343_F	346_E	0.955	1.00
61_D	64_R	0.953	1.00
93_A	114_H	0.953	1.00
92_G	100_L	0.952	1.00
205_T	234_G	0.951	1.00
250_F	254_L	0.950	1.00
290_L	298_R	0.948	1.00
258_V	277_W	0.944	1.00
58_G	61_D	0.944	1.00
149_F	187_V	0.936	1.00
179_C	186_T	0.932	1.00
194_V	198_Y	0.932	1.00
302_S	306_Y	0.932	1.00
324_V	330_L	0.932	1.00
184_R	221_A	0.931	1.00
77_I	80_L	0.929	1.00
63_P	66_P	0.929	1.00
88_H	91_W	0.929	1.00
21_L	25_Q	0.928	1.00
200_L	229_L	0.926	1.00
249_R	256_A	0.923	1.00
174_L	194_V	0.923	1.00
82_R	85_H	0.923	1.00
70_P	73_S	0.921	1.00
220_T	224_L	0.919	1.00
187_V	212_W	0.917	1.00
95_K	98_R	0.916	1.00
334_G	337_L	0.911	1.00
220_T	223_E	0.909	1.00
93_A	97_K	0.909	1.00
273_A	276_H	0.907	1.00
141_P	169_H	0.902	0.99
141_P	170_S	0.902	0.99
138_H	144_L	0.902	0.99
30_I	34_C	0.900	0.99
124_P	127_S	0.900	0.99
290_L	295_P	0.895	0.99
117_M	120_H	0.885	0.99
189_Q	193_S	0.882	0.99
310_T	314_E	0.877	0.99
114_H	117_M	0.875	0.99
26_D	29_N	0.873	0.99
325_D	328_G	0.871	0.99
242_Q	245_G	0.865	0.99
200_L	231_I	0.864	0.99
79_A	83_M	0.864	0.99
163_L	212_W	0.862	0.99
204_M	231_I	0.861	0.99
33_L	36_R	0.860	0.99
81_L	113_V	0.857	0.99
96_I	113_V	0.850	0.99
333_K	337_L	0.848	0.99
222_L	226_L	0.848	0.99
40_S	43_T	0.847	0.99
258_V	274_F	0.842	0.99
324_V	328_G	0.842	0.99
94_R	97_K	0.836	0.99
142_N	299_Y	0.831	0.99
225_W	229_L	0.829	0.99
313_P	317_E	0.829	0.99
210_S	214_D	0.826	0.99
245_G	251_H	0.826	0.99
272_R	276_H	0.824	0.99
166_L	246_K	0.822	0.99
307_S	310_T	0.820	0.99
138_H	143_R	0.814	0.99
255_K	259_L	0.813	0.99
76_D	79_A	0.813	0.99
205_T	236_S	0.808	0.99
181_D	211_P	0.804	0.99
281_Y	287_H	0.804	0.99
180_T	267_S	0.803	0.99
190_Q	193_S	0.801	0.99
178_H	270_L	0.799	0.99
48_L	52_A	0.799	0.99
120_H	123_L	0.799	0.99
303_A	309_N	0.798	0.99
97_K	110_F	0.797	0.99
330_L	337_L	0.795	0.99
274_F	278_R	0.790	0.99
95_K	99_W	0.786	0.99
92_G	97_K	0.785	0.99
319_V	351_K	0.785	0.99
121_G	125_G	0.783	0.99
147_M	150_K	0.780	0.99
351_K	362_W	0.779	0.99
169_H	298_R	0.779	0.99
286_P	289_A	0.778	0.99
139_D	144_L	0.774	0.98
43_T	46_K	0.772	0.98
106_T	112_T	0.771	0.98
320_M	332_V	0.770	0.98
168_D	245_G	0.769	0.98
149_F	190_Q	0.758	0.98
37_F	44_G	0.758	0.98
145_W	201_P	0.758	0.98
112_T	116_L	0.758	0.98
346_E	363_W	0.756	0.98
22_F	25_Q	0.755	0.98
208_N	213_G	0.754	0.98
258_V	273_A	0.749	0.98
174_L	278_R	0.748	0.98
318_G	321_V	0.747	0.98
163_L	179_C	0.746	0.98
327_S	336_S	0.745	0.98
214_D	220_T	0.742	0.98
194_V	197_R	0.736	0.98
160_C	178_H	0.735	0.98
42_A	46_K	0.735	0.98
303_A	306_Y	0.735	0.98
154_P	158_G	0.734	0.98
135_R	144_L	0.734	0.98
151_G	157_G	0.733	0.98
205_T	235_H	0.729	0.98
162_P	274_F	0.729	0.98
177_A	189_Q	0.729	0.98
162_P	251_H	0.728	0.98
57_A	61_D	0.722	0.98
209_G	214_D	0.718	0.97
77_I	81_L	0.714	0.97
348_V	363_W	0.713	0.97
155_F	158_G	0.711	0.97
105_H	108_P	0.711	0.97
247_L	250_F	0.709	0.97
297_S	300_Q	0.707	0.97
303_A	310_T	0.706	0.97
221_A	225_W	0.706	0.97
115_N	118_A	0.705	0.97
193_S	196_E	0.704	0.97
90_R	97_K	0.702	0.97
110_F	113_V	0.701	0.97
91_W	96_I	0.700	0.97
214_D	222_L	0.697	0.97
191_L	225_W	0.697	0.97
138_H	168_D	0.692	0.97
143_R	203_R	0.692	0.97
165_L	191_L	0.692	0.97
270_L	274_F	0.691	0.97
109_A	113_V	0.690	0.97
175_C	193_S	0.686	0.97
94_R	110_F	0.681	0.97
140_A	169_H	0.680	0.97
295_P	299_Y	0.679	0.96
322_R	348_V	0.678	0.96
269_E	273_A	0.678	0.96
201_P	231_I	0.677	0.96
76_D	81_L	0.677	0.96
357_G	361_V	0.677	0.96
175_C	254_L	0.675	0.96
277_W	280_V	0.674	0.96
51_W	55_G	0.672	0.96
253_S	282_N	0.670	0.96
81_L	100_L	0.669	0.96
224_L	227_M	0.668	0.96
160_C	267_S	0.666	0.96
49_Q	52_A	0.665	0.96
322_R	330_L	0.664	0.96
77_I	84_A	0.661	0.96
92_G	95_K	0.660	0.96
141_P	302_S	0.660	0.96
313_P	316_D	0.659	0.96
59_L	63_P	0.659	0.96
197_R	279_T	0.659	0.96
93_A	100_L	0.652	0.96
310_T	315_Y	0.648	0.95
96_I	99_W	0.644	0.95
250_F	281_Y	0.642	0.95
108_P	113_V	0.641	0.95
146_Q	205_T	0.638	0.95
27_G	32_S	0.636	0.95
76_D	80_L	0.635	0.95
351_K	360_E	0.633	0.95
92_G	96_I	0.632	0.95
79_A	82_R	0.632	0.95
302_S	305_Q	0.631	0.95
95_K	257_E	0.631	0.95
130_I	133_T	0.629	0.95
171_R	289_A	0.629	0.95
79_A	86_D	0.628	0.95
349_G	362_W	0.627	0.95
78_T	120_H	0.627	0.95
342_A	346_E	0.625	0.94
161_H	211_P	0.624	0.94
187_V	209_G	0.622	0.94
306_Y	310_T	0.622	0.94
300_Q	304_R	0.622	0.94
341_K	344_R	0.619	0.94
184_R	187_V	0.619	0.94
50_R	53_Q	0.617	0.94
277_W	282_N	0.612	0.94
363_W	366_T	0.611	0.94
172_F	283_L	0.608	0.94
139_D	142_N	0.608	0.94
186_T	189_Q	0.607	0.94
102_D	280_V	0.606	0.94
335_V	339_A	0.605	0.93
302_S	308_G	0.604	0.93
314_E	317_E	0.604	0.93
254_L	258_V	0.603	0.93
73_S	77_I	0.603	0.93
182_E	212_W	0.602	0.93
82_R	120_H	0.602	0.93
111_S	118_A	0.601	0.93
29_N	35_R	0.601	0.93
64_R	67_H	0.598	0.93
185_E	221_A	0.596	0.93
304_R	307_S	0.596	0.93
138_H	169_H	0.595	0.93
31_R	42_A	0.594	0.93
251_H	255_K	0.593	0.93
306_Y	309_N	0.593	0.93
287_H	295_P	0.592	0.93
188_Q	222_L	0.592	0.93
358_S	362_W	0.591	0.93
192_V	225_W	0.590	0.93
40_S	46_K	0.589	0.93
186_T	211_P	0.586	0.92
163_L	177_A	0.584	0.92
142_N	150_K	0.583	0.92
147_M	204_M	0.582	0.92
172_F	279_T	0.581	0.92
174_L	198_Y	0.578	0.92
22_F	26_D	0.578	0.92
54_E	57_A	0.577	0.92
254_L	274_F	0.577	0.92
68_H	73_S	0.576	0.92
276_H	280_V	0.575	0.92
242_Q	251_H	0.574	0.92
330_L	361_V	0.574	0.92
268_G	271_Q	0.573	0.92
170_S	299_Y	0.572	0.91
153_F	157_G	0.572	0.91
24_S	48_L	0.572	0.91
123_L	126_A	0.572	0.91
162_P	175_C	0.570	0.91
66_P	71_N	0.569	0.91
147_M	191_L	0.567	0.91
353_M	359_Y	0.567	0.91
285_R	288_E	0.564	0.91
120_H	124_P	0.563	0.91
125_G	129_G	0.560	0.91
146_Q	236_S	0.560	0.91
286_P	291_D	0.558	0.90
206_M	212_W	0.557	0.90
301_P	304_R	0.553	0.90
198_Y	299_Y	0.551	0.90
171_R	253_S	0.551	0.90
148_D	248_E	0.550	0.90
311_T	314_E	0.548	0.90
339_A	361_V	0.547	0.90
307_S	311_T	0.546	0.89
253_S	257_E	0.545	0.89
175_C	274_F	0.545	0.89
299_Y	304_R	0.543	0.89
152_H	157_G	0.543	0.89
101_E	107_M	0.543	0.89
24_S	28_A	0.542	0.89
305_Q	309_N	0.537	0.89
142_N	199_G	0.537	0.89
184_R	211_P	0.535	0.89
54_E	62_R	0.534	0.88
123_L	127_S	0.534	0.88
82_R	116_L	0.534	0.88
145_W	299_Y	0.532	0.88
310_T	313_P	0.532	0.88
350_L	361_V	0.532	0.88
289_A	293_A	0.532	0.88
76_D	82_R	0.531	0.88
66_P	69_S	0.531	0.88
113_V	116_L	0.530	0.88
343_F	363_W	0.529	0.88
347_R	366_T	0.528	0.88
165_L	206_M	0.526	0.88
136_F	246_K	0.525	0.88
303_A	311_T	0.524	0.87
297_S	303_A	0.524	0.87
320_M	352_E	0.523	0.87
172_F	197_R	0.520	0.87
239_Y	244_Q	0.519	0.87
62_R	65_I	0.519	0.87
253_S	277_W	0.518	0.87
195_F	204_M	0.518	0.87
98_R	257_E	0.518	0.87
324_V	339_A	0.517	0.87
28_A	33_L	0.516	0.87
195_F	201_P	0.511	0.86
182_E	186_T	0.510	0.86
96_I	117_M	0.507	0.86
27_G	33_L	0.506	0.86
29_N	33_L	0.504	0.85
236_S	240_H	0.504	0.85
234_G	243_T	0.503	0.85
60_Q	63_P	0.503	0.85
333_K	352_E	0.503	0.85
149_F	209_G	0.503	0.85
110_F	118_A	0.503	0.85
149_F	212_W	0.502	0.85
94_R	101_E	0.502	0.85
357_G	366_T	0.501	0.85
73_S	78_T	0.500	0.85
69_S	73_S	0.500	0.85

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
4fcyA	4	0.9271	100	0.358	Contact Map
1bcoA	1	0.612	100	0.52	Contact Map
3oymA	3	0.8724	100	0.538	Contact Map
3f9kA	5	0.5391	100	0.595	Contact Map
4fw2A	2	0.5312	100	0.595	Contact Map
3hphA	3	0.5365	100	0.597	Contact Map
1k6yA	4	0.5052	100	0.598	Contact Map
2x78A	2	0.4792	100	0.609	Contact Map
4fw1A	2	0.5521	100	0.636	Contact Map
4u7bA	2	0.7266	100	0.637	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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