YAIP - ECOLI - GREMLIN Contacts

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YAIP - Uncharacterized protein YaiP

UniProt:	Q47536	Sequences: MKTWIFICMSIAMLLWFLSTLRRKPSQKKGCIDAIIPAYNEGPCLAQSLDNLLRNPYFCRVICVNDGSTDNTEAVMAEVKRKWGDRFVAVTQKNTGKGGALMNGLNYATCDQVFLSDADTYVPPDQDGMGYMLAEIERGADAVGGIPSTALKGAGLLPHIRATVKLPMIVMKRTLQQLLGGAPFIISGACGMFRTDVLRKFGFSDRTKVEDLDLTWTLVANGYRIRQANRCIVYPQECNSPREEWRRWRRWIVGYAVCMRLHKRLLFSRFGIFSIFPMLLVVLYGVGIYLTTWFNEFITTGPHGVVLAMFPLIWVGVVCVIGAFSAWFHRCWLLVPLAPLSVVYVLLAYAIWIIYGLIAFFTGREPQRDKPTRYSALVEASTAYSQPSVTGTEKLSEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13298
Length:	398 (341)
Sequences:	11171 (8435)
Seq/√Len:	456.8

ECOLI - YAIP PGAC BCSA ARNC GTRB
BACSU - YDAM CSBB YKCC YKOT
HALSA - Q9HSB1 Q9HQQ6
SULSO - Q97YM4 Q97W52 Q97TY0 Q7LXY2 Q97UK7 Q97WK7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_G	71_N	5.153	1.00
56_P	130_G	4.775	1.00
195_T	199_R	4.365	1.00
33_D	110_C	3.727	1.00
114_F	192_M	3.284	1.00
33_D	60_R	3.191	1.00
71_N	74_A	3.089	1.00
65_N	91_T	3.058	1.00
112_Q	133_L	2.921	1.00
60_R	88_V	2.882	1.00
197_V	223_Y	2.868	1.00
64_V	104_G	2.851	1.00
46_A	78_E	2.802	1.00
112_Q	136_I	2.581	1.00
342_V	346_L	2.569	1.00
65_N	68_S	2.560	1.00
60_R	110_C	2.543	1.00
35_I	64_V	2.539	1.00
73_E	77_A	2.523	1.00
32_I	133_L	2.517	1.00
240_S	243_E	2.499	1.00
200_K	221_N	2.409	1.00
31_C	111_D	2.398	1.00
155_G	158_P	2.396	1.00
140_A	226_R	2.354	1.00
131_Y	230_R	2.336	1.00
46_A	50_D	2.298	1.00
74_A	78_E	2.290	1.00
135_E	228_A	2.231	1.00
32_I	129_M	2.187	1.00
141_D	223_Y	2.177	1.00
33_D	108_A	2.154	1.00
112_Q	192_M	2.122	1.00
136_I	192_M	2.118	1.00
31_C	109_T	2.096	1.00
125_D	131_Y	2.091	1.00
76_M	89_A	2.076	1.00
33_D	62_I	2.048	1.00
31_C	110_C	2.024	1.00
132_M	192_M	1.986	1.00
213_D	217_T	1.976	1.00
36_I	52_L	1.938	1.00
282_V	285_G	1.934	1.00
139_G	224_R	1.885	1.00
56_P	125_D	1.855	1.00
51_N	122_V	1.855	1.00
114_F	129_M	1.809	1.00
325_S	328_F	1.808	1.00
196_D	200_K	1.805	1.00
200_K	223_Y	1.799	1.00
186_I	191_G	1.797	1.00
40_N	68_S	1.795	1.00
63_C	76_M	1.769	1.00
281_V	285_G	1.709	1.00
50_D	79_V	1.698	1.00
46_A	75_V	1.667	1.00
105_L	113_V	1.648	1.00
197_V	218_L	1.628	1.00
49_L	79_V	1.627	1.00
271_G	274_S	1.619	1.00
356_G	359_A	1.605	1.00
97_K	101_L	1.601	1.00
41_E	118_A	1.598	1.00
57_Y	133_L	1.578	1.00
336_P	339_P	1.535	1.00
271_G	275_I	1.523	1.00
108_A	195_T	1.504	1.00
126_Q	190_C	1.504	1.00
64_V	100_A	1.503	1.00
142_A	225_I	1.491	1.00
247_R	251_W	1.486	1.00
137_E	224_R	1.478	1.00
355_Y	359_A	1.467	1.00
50_D	82_K	1.452	1.00
60_R	109_T	1.441	1.00
131_Y	134_A	1.440	1.00
278_M	281_V	1.420	1.00
30_G	57_Y	1.409	1.00
73_E	91_T	1.407	1.00
38_A	72_T	1.400	1.00
313_I	317_V	1.392	1.00
292_T	295_N	1.390	1.00
209_V	254_G	1.387	1.00
30_G	133_L	1.380	1.00
339_P	342_V	1.371	1.00
164_V	248_W	1.366	1.00
104_G	108_A	1.357	1.00
76_M	80_K	1.340	1.00
285_G	289_Y	1.327	1.00
147_P	189_A	1.327	1.00
77_A	91_T	1.322	1.00
112_Q	194_R	1.316	1.00
71_N	75_V	1.315	1.00
74_A	77_A	1.311	1.00
78_E	82_K	1.288	1.00
29_K	58_F	1.283	1.00
113_V	195_T	1.277	1.00
322_G	326_A	1.276	1.00
122_V	126_Q	1.268	1.00
31_C	60_R	1.260	1.00
302_P	307_L	1.260	1.00
344_Y	348_A	1.258	1.00
120_T	233_V	1.252	1.00
55_N	129_M	1.249	1.00
321_I	325_S	1.229	1.00
247_R	250_R	1.228	1.00
271_G	277_P	1.225	1.00
277_P	281_V	1.223	1.00
51_N	121_Y	1.218	1.00
141_D	194_R	1.214	1.00
75_V	79_V	1.212	1.00
54_R	124_P	1.211	1.00
116_S	122_V	1.207	1.00
90_V	107_Y	1.206	1.00
274_S	277_P	1.200	1.00
111_D	196_D	1.199	1.00
142_A	218_L	1.196	1.00
248_W	251_W	1.190	1.00
40_N	69_T	1.186	1.00
113_V	198_L	1.179	1.00
65_N	73_E	1.169	1.00
324_F	328_F	1.166	1.00
110_C	195_T	1.166	1.00
103_N	107_Y	1.156	1.00
258_C	262_H	1.156	1.00
314_W	318_V	1.154	1.00
281_V	284_Y	1.142	1.00
39_Y	94_N	1.141	1.00
56_P	124_P	1.136	1.00
60_R	108_A	1.124	1.00
161_R	165_K	1.122	1.00
321_I	326_A	1.122	1.00
244_E	248_W	1.113	1.00
77_A	80_K	1.109	1.00
101_L	115_L	1.109	1.00
342_V	345_V	1.106	1.00
34_A	114_F	1.106	1.00
59_C	129_M	1.102	1.00
77_A	81_R	1.101	1.00
173_R	176_Q	1.093	1.00
321_I	324_F	1.091	1.00
76_M	79_V	1.090	1.00
50_D	54_R	1.083	1.00
348_A	351_I	1.075	1.00
52_L	61_V	1.075	1.00
346_L	349_Y	1.070	1.00
35_I	104_G	1.063	1.00
277_P	285_G	1.063	1.00
353_I	356_G	1.062	1.00
282_V	286_V	1.062	1.00
33_D	195_T	1.060	1.00
324_F	327_W	1.056	1.00
315_V	319_C	1.043	1.00
62_I	88_V	1.039	1.00
341_S	345_V	1.037	1.00
316_G	321_I	1.033	1.00
309_M	317_V	1.031	1.00
47_Q	50_D	1.024	1.00
143_V	228_A	1.022	1.00
103_N	106_N	1.020	1.00
317_V	321_I	1.020	1.00
135_E	226_R	1.020	1.00
270_F	274_S	1.012	1.00
272_I	275_I	1.005	1.00
45_L	63_C	1.005	1.00
62_I	108_A	0.999	1.00
345_V	349_Y	0.999	1.00
285_G	288_I	0.998	1.00
314_W	317_V	0.998	1.00
291_T	295_N	0.997	1.00
343_V	346_L	0.997	1.00
149_T	237_E	0.995	1.00
26_S	29_K	0.992	1.00
79_V	82_K	0.975	1.00
311_P	315_V	0.974	1.00
52_L	122_V	0.973	1.00
345_V	348_A	0.967	1.00
279_L	285_G	0.965	1.00
278_M	282_V	0.964	1.00
280_L	284_Y	0.961	1.00
279_L	282_V	0.958	1.00
244_E	247_R	0.958	1.00
338_A	342_V	0.956	1.00
275_I	278_M	0.952	1.00
142_A	186_I	0.951	1.00
120_T	235_P	0.949	1.00
62_I	104_G	0.948	1.00
194_R	223_Y	0.948	1.00
123_P	234_Y	0.946	1.00
97_K	188_G	0.942	1.00
271_G	278_M	0.936	1.00
313_I	316_G	0.931	1.00
48_S	52_L	0.925	1.00
141_D	218_L	0.925	1.00
66_D	96_G	0.925	1.00
29_K	130_G	0.922	1.00
317_V	324_F	0.921	1.00
278_M	285_G	0.916	1.00
68_S	72_T	0.901	1.00
101_L	203_F	0.896	1.00
333_L	341_S	0.892	1.00
38_A	45_L	0.891	1.00
337_L	340_L	0.890	1.00
342_V	349_Y	0.890	1.00
88_V	107_Y	0.888	1.00
272_I	276_F	0.888	1.00
102_M	106_N	0.887	1.00
341_S	346_L	0.884	1.00
355_Y	358_I	0.883	1.00
340_L	345_V	0.883	1.00
201_F	218_L	0.881	1.00
66_D	94_N	0.875	1.00
274_S	278_M	0.872	1.00
275_I	285_G	0.872	1.00
235_P	238_C	0.869	1.00
48_S	53_L	0.868	1.00
341_S	348_A	0.867	1.00
75_V	78_E	0.865	1.00
93_K	96_G	0.864	1.00
218_L	223_Y	0.863	1.00
161_R	164_V	0.862	1.00
45_L	76_M	0.862	1.00
318_V	322_G	0.859	1.00
280_L	285_G	0.858	1.00
317_V	320_V	0.858	1.00
337_L	346_L	0.855	1.00
34_A	129_M	0.849	1.00
333_L	337_L	0.844	1.00
34_A	59_C	0.844	1.00
45_L	72_T	0.844	1.00
290_L	293_W	0.843	1.00
125_D	130_G	0.840	1.00
132_M	145_G	0.838	1.00
341_S	344_Y	0.836	1.00
274_S	281_V	0.836	1.00
329_H	332_W	0.835	1.00
322_G	325_S	0.831	1.00
90_V	103_N	0.831	1.00
105_L	198_L	0.825	1.00
337_L	344_Y	0.822	1.00
144_G	147_P	0.822	1.00
277_P	280_L	0.817	1.00
40_N	70_D	0.813	1.00
275_I	281_V	0.811	1.00
275_I	279_L	0.810	1.00
196_D	199_R	0.805	1.00
311_P	314_W	0.803	1.00
333_L	336_P	0.802	1.00
194_R	197_V	0.801	1.00
277_P	282_V	0.797	1.00
315_V	318_V	0.797	1.00
309_M	313_I	0.796	1.00
157_L	161_R	0.795	1.00
42_G	75_V	0.791	1.00
38_A	63_C	0.789	1.00
292_T	296_E	0.788	1.00
156_L	159_H	0.788	1.00
321_I	328_F	0.786	1.00
73_E	89_A	0.786	1.00
159_H	162_A	0.783	1.00
322_G	327_W	0.782	1.00
254_G	257_V	0.778	1.00
66_D	119_D	0.777	1.00
318_V	321_I	0.776	1.00
281_V	286_V	0.774	1.00
190_C	233_V	0.773	1.00
282_V	289_Y	0.772	1.00
315_V	322_G	0.768	1.00
78_E	81_R	0.767	1.00
169_I	173_R	0.766	1.00
151_L	158_P	0.766	1.00
158_P	161_R	0.765	1.00
82_K	85_D	0.760	1.00
98_G	210_E	0.757	1.00
317_V	325_S	0.755	1.00
80_K	87_F	0.754	1.00
320_V	328_F	0.750	1.00
323_A	327_W	0.749	1.00
98_G	102_M	0.748	1.00
135_E	143_V	0.748	1.00
90_V	104_G	0.745	1.00
210_E	213_D	0.743	1.00
337_L	341_S	0.742	1.00
96_G	119_D	0.738	1.00
275_I	282_V	0.738	1.00
282_V	288_I	0.737	1.00
36_I	48_S	0.736	1.00
320_V	327_W	0.735	1.00
340_L	344_Y	0.734	1.00
353_I	357_L	0.732	1.00
286_V	289_Y	0.732	1.00
319_C	322_G	0.731	1.00
105_L	108_A	0.731	1.00
38_A	118_A	0.730	1.00
203_F	206_R	0.728	1.00
334_L	344_Y	0.723	1.00
132_M	143_V	0.723	1.00
356_G	360_F	0.721	1.00
302_P	305_V	0.716	1.00
45_L	49_L	0.713	1.00
294_F	298_I	0.713	1.00
29_K	57_Y	0.712	1.00
274_S	280_L	0.709	1.00
320_V	325_S	0.707	1.00
274_S	284_Y	0.704	1.00
154_A	158_P	0.701	1.00
33_D	109_T	0.699	1.00
310_F	313_I	0.698	1.00
338_A	345_V	0.697	1.00
334_L	337_L	0.692	1.00
280_L	283_L	0.692	1.00
136_I	194_R	0.690	1.00
279_L	284_Y	0.689	1.00
345_V	351_I	0.689	1.00
258_C	261_L	0.688	1.00
244_E	251_W	0.688	1.00
145_G	190_C	0.683	1.00
92_Q	95_T	0.682	1.00
310_F	316_G	0.682	1.00
336_P	340_L	0.681	1.00
73_E	76_M	0.679	1.00
281_V	287_G	0.679	1.00
114_F	126_Q	0.678	1.00
160_I	163_T	0.678	1.00
53_L	86_R	0.675	1.00
48_S	51_N	0.673	1.00
344_Y	347_L	0.671	1.00
158_P	163_T	0.670	1.00
102_M	105_L	0.668	1.00
308_A	315_V	0.668	1.00
238_C	247_R	0.666	1.00
257_V	262_H	0.663	1.00
318_V	325_S	0.660	1.00
342_V	348_A	0.659	1.00
171_M	175_L	0.659	1.00
120_T	189_A	0.658	1.00
337_L	342_V	0.658	1.00
334_L	341_S	0.658	1.00
132_M	231_C	0.658	1.00
136_I	140_A	0.657	1.00
280_L	286_V	0.656	1.00
264_R	268_S	0.655	1.00
70_D	74_A	0.655	1.00
339_P	343_V	0.654	1.00
56_P	59_C	0.654	1.00
274_S	282_V	0.654	1.00
245_W	249_R	0.649	1.00
354_I	358_I	0.649	1.00
346_L	350_A	0.648	1.00
140_A	143_V	0.647	1.00
55_N	122_V	0.646	1.00
157_L	163_T	0.645	1.00
132_M	136_I	0.644	1.00
274_S	279_L	0.644	1.00
72_T	76_M	0.642	1.00
274_S	285_G	0.640	1.00
334_L	338_A	0.639	0.99
40_N	72_T	0.639	0.99
317_V	322_G	0.639	0.99
53_L	87_F	0.636	0.99
34_A	55_N	0.634	0.99
251_W	254_G	0.634	0.99
270_F	277_P	0.633	0.99
215_T	225_I	0.633	0.99
270_F	275_I	0.632	0.99
25_P	28_K	0.632	0.99
147_P	235_P	0.631	0.99
321_I	327_W	0.630	0.99
293_W	296_E	0.629	0.99
193_F	218_L	0.629	0.99
116_S	190_C	0.626	0.99
156_L	160_I	0.626	0.99
144_G	149_T	0.626	0.99
47_Q	121_Y	0.626	0.99
316_G	319_C	0.624	0.99
123_P	232_I	0.624	0.99
115_L	191_G	0.624	0.99
295_N	299_T	0.623	0.99
48_S	116_S	0.619	0.99
46_A	79_V	0.618	0.99
188_G	211_D	0.617	0.99
131_Y	228_A	0.616	0.99
49_L	76_M	0.615	0.99
46_A	82_K	0.614	0.99
337_L	345_V	0.614	0.99
265_L	269_R	0.610	0.99
310_F	314_W	0.608	0.99
61_V	87_F	0.606	0.99
100_A	104_G	0.605	0.99
311_P	322_G	0.605	0.99
278_M	284_Y	0.604	0.99
351_I	355_Y	0.603	0.99
274_S	286_V	0.602	0.99
121_Y	150_A	0.600	0.99
32_I	112_Q	0.599	0.99
141_D	197_V	0.599	0.99
238_C	251_W	0.599	0.99
172_K	175_L	0.598	0.99
36_I	63_C	0.596	0.99
271_G	276_F	0.596	0.99
209_V	212_L	0.596	0.99
36_I	116_S	0.596	0.99
271_G	281_V	0.595	0.99
210_E	254_G	0.595	0.99
174_T	229_N	0.595	0.99
273_F	277_P	0.591	0.99
160_I	164_V	0.590	0.99
197_V	200_K	0.590	0.99
21_L	24_K	0.590	0.99
114_F	132_M	0.589	0.99
146_I	227_Q	0.589	0.99
80_K	86_R	0.588	0.99
204_S	261_L	0.586	0.99
320_V	324_F	0.584	0.99
39_Y	67_G	0.584	0.99
168_M	172_K	0.582	0.99
364_R	367_Q	0.582	0.99
38_A	41_E	0.579	0.99
144_G	186_I	0.579	0.99
97_K	210_E	0.578	0.99
338_A	341_S	0.576	0.99
355_Y	360_F	0.576	0.99
336_P	341_S	0.573	0.99
236_Q	239_N	0.572	0.99
92_Q	103_N	0.570	0.99
284_Y	288_I	0.569	0.99
42_G	72_T	0.567	0.99
63_C	66_D	0.566	0.99
312_L	316_G	0.565	0.99
155_G	159_H	0.562	0.99
333_L	340_L	0.562	0.99
270_F	273_F	0.561	0.99
168_M	173_R	0.560	0.99
122_V	190_C	0.559	0.99
341_S	349_Y	0.559	0.99
102_M	203_F	0.557	0.99
265_L	268_S	0.555	0.99
317_V	328_F	0.555	0.99
237_E	247_R	0.554	0.99
263_K	266_L	0.554	0.99
207_T	213_D	0.554	0.99
129_M	192_M	0.553	0.99
314_W	322_G	0.552	0.99
318_V	326_A	0.552	0.99
158_P	162_A	0.550	0.98
208_K	254_G	0.549	0.98
165_K	169_I	0.549	0.98
247_R	254_G	0.548	0.98
323_A	326_A	0.548	0.98
98_G	101_L	0.547	0.98
282_V	287_G	0.547	0.98
37_P	100_A	0.547	0.98
95_T	99_G	0.545	0.98
188_G	210_E	0.545	0.98
219_V	225_I	0.544	0.98
111_D	194_R	0.544	0.98
259_M	262_H	0.544	0.98
354_I	359_A	0.544	0.98
335_V	340_L	0.544	0.98
165_K	187_S	0.542	0.98
319_C	324_F	0.542	0.98
284_Y	287_G	0.542	0.98
335_V	339_P	0.542	0.98
318_V	327_W	0.541	0.98
66_D	91_T	0.541	0.98
170_V	174_T	0.541	0.98
346_L	351_I	0.541	0.98
272_I	282_V	0.540	0.98
308_A	311_P	0.539	0.98
314_W	328_F	0.539	0.98
314_W	325_S	0.539	0.98
242_R	246_R	0.535	0.98
350_A	354_I	0.533	0.98
253_V	257_V	0.532	0.98
55_N	130_G	0.532	0.98
315_V	325_S	0.531	0.98
41_E	45_L	0.531	0.98
315_V	321_I	0.530	0.98
170_V	173_R	0.530	0.98
157_L	160_I	0.529	0.98
329_H	336_P	0.529	0.98
163_T	166_L	0.528	0.98
88_V	91_T	0.524	0.98
56_P	123_P	0.524	0.98
41_E	44_C	0.524	0.98
209_V	213_D	0.521	0.98
339_P	345_V	0.521	0.98
322_G	328_F	0.520	0.98
142_A	149_T	0.520	0.98
41_E	117_D	0.519	0.98
354_I	357_L	0.519	0.98
33_D	104_G	0.519	0.98
147_P	165_K	0.519	0.98
289_Y	295_N	0.518	0.98
316_G	327_W	0.517	0.98
342_V	347_L	0.517	0.98
257_V	261_L	0.516	0.98
339_P	344_Y	0.515	0.98
290_L	295_N	0.514	0.98
137_E	226_R	0.514	0.98
105_L	115_L	0.513	0.98
308_A	322_G	0.513	0.98
313_I	322_G	0.512	0.98
353_I	359_A	0.511	0.98
311_P	325_S	0.509	0.98
285_G	293_W	0.507	0.97
271_G	285_G	0.506	0.97
168_M	176_Q	0.504	0.97
340_L	346_L	0.504	0.97
347_L	351_I	0.501	0.97
119_D	235_P	0.501	0.97
189_A	247_R	0.500	0.97

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
4p02A	1	0.9372	100	0.385	Contact Map
2z86A	2	0.6834	100	0.544	Contact Map
3bcvA	2	0.4472	100	0.562	Contact Map
2bo4A	4	0.8291	100	0.575	Contact Map
1qg8A	1	0.5302	100	0.583	Contact Map
3l7iA	4	0.103	100	0.583	Contact Map
2d7iA	1	0.8719	100	0.587	Contact Map
4fixA	3	0.8794	100	0.588	Contact Map
3ckjA	2	0.6859	100	0.591	Contact Map
1xhbA	1	0.8719	100	0.598	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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