YAGQ - ECOLI - GREMLIN Contacts

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YAGQ - Uncharacterized protein YagQ

UniProt:	P77183	Sequences: MSYPLFDKDEHWHKPEQAFLTDDHRTILRFAVEALMSGKGAVLVTLVEIRGGAARPLGAQMVVREDGRYCGFVSGGCVEAAAAFEALEMMGSGRDREIRYGEGSPWFDIVLPCGGGITLTLHKLRSAQPLLAVLNRLEQRKPVGLRYDPQAQSLVCLPTQTRTGWNLNGFEVGFRPCVRLMIYGRSLEAQATASLAAATGYDSHIFDLFPASASAQIDTDTAVILLCHDLNRELPVLQAAREAKPFYLGALGSYRTHTLRLQKLHELGWSREETTQIRAPVGIFPKARDAHTLALSVLAEVASVRLHQEEDSCLPPSS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13556
Length:	318 (282)
Sequences:	1626 (1320)
Seq/√Len:	78.6

ECOLI - YAGQ YQEB
BACSU - XDHA
SULSO - Q97UW4

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_V	121_L	4.467	1.00
265_H	271_R	3.883	1.00
182_I	193_A	3.514	1.00
40_G	65_E	3.394	1.00
295_L	302_A	3.250	1.00
270_S	273_E	3.198	1.00
99_R	118_T	3.120	1.00
223_V	240_A	3.097	1.00
44_V	119_L	3.001	1.00
249_G	281_V	2.979	1.00
201_Y	302_A	2.830	1.00
48_E	118_T	2.674	1.00
81_A	85_E	2.659	1.00
49_I	53_A	2.495	1.00
180_L	196_A	2.327	1.00
271_R	275_T	2.260	1.00
60_Q	172_V	2.247	1.00
196_A	298_L	2.128	1.00
247_Y	300_E	2.126	1.00
44_V	121_L	2.093	1.00
298_L	301_V	2.091	1.00
39_K	64_R	2.078	1.00
185_R	207_D	2.006	1.00
69_Y	83_A	2.006	1.00
261_L	274_T	2.005	1.00
278_R	300_E	2.003	1.00
243_A	276_Q	1.997	1.00
39_K	65_E	1.988	1.00
74_S	77_C	1.974	1.00
42_V	90_M	1.969	1.00
262_Q	266_E	1.961	1.00
180_L	222_A	1.950	1.00
238_Q	267_L	1.920	1.00
47_V	97_E	1.917	1.00
257_H	279_A	1.900	1.00
179_R	204_H	1.888	1.00
218_D	221_T	1.886	1.00
148_D	151_A	1.875	1.00
99_R	116_G	1.873	1.00
33_E	37_S	1.867	1.00
73_V	119_L	1.842	1.00
195_L	295_L	1.836	1.00
257_H	261_L	1.828	1.00
237_L	250_A	1.814	1.00
45_T	122_H	1.807	1.00
234_L	263_K	1.806	1.00
183_Y	236_V	1.782	1.00
245_P	276_Q	1.768	1.00
81_A	100_Y	1.761	1.00
195_L	198_A	1.731	1.00
245_P	248_L	1.727	1.00
78_V	117_I	1.714	1.00
64_R	68_R	1.692	1.00
217_I	221_T	1.687	1.00
303_S	307_H	1.671	1.00
36_M	131_L	1.647	1.00
199_T	298_L	1.643	1.00
287_A	292_T	1.638	1.00
52_G	75_G	1.631	1.00
255_R	259_L	1.620	1.00
42_V	89_M	1.592	1.00
225_L	240_A	1.573	1.00
192_T	224_I	1.560	0.99
132_A	136_R	1.543	0.99
85_E	98_I	1.542	0.99
44_V	82_A	1.534	0.99
180_L	301_V	1.513	0.99
285_P	293_L	1.498	0.99
194_S	198_A	1.497	0.99
223_V	245_P	1.467	0.99
54_A	188_E	1.458	0.99
178_V	305_R	1.434	0.99
261_L	277_I	1.406	0.99
32_V	36_M	1.398	0.99
195_L	298_L	1.393	0.99
30_F	34_A	1.374	0.99
289_D	292_T	1.350	0.98
136_R	141_K	1.346	0.98
100_Y	245_P	1.335	0.98
182_I	189_A	1.330	0.98
49_I	57_L	1.309	0.98
85_E	96_R	1.299	0.98
295_L	301_V	1.298	0.98
32_V	131_L	1.281	0.98
192_T	297_V	1.278	0.98
250_A	257_H	1.271	0.98
114_G	230_L	1.256	0.98
300_E	303_S	1.248	0.97
219_T	244_K	1.241	0.97
146_R	171_E	1.236	0.97
269_W	273_E	1.230	0.97
192_T	298_L	1.227	0.97
285_P	292_T	1.227	0.97
110_V	207_D	1.209	0.97
209_F	212_S	1.207	0.97
112_P	260_R	1.206	0.97
29_R	33_E	1.202	0.97
144_G	171_E	1.201	0.97
224_I	281_V	1.187	0.97
188_E	293_L	1.184	0.96
230_L	234_L	1.175	0.96
208_L	228_H	1.162	0.96
230_L	256_T	1.158	0.96
106_W	110_V	1.155	0.96
31_A	130_L	1.153	0.96
40_G	123_K	1.150	0.96
250_A	260_R	1.147	0.96
243_A	248_L	1.146	0.96
46_L	73_V	1.145	0.96
217_I	223_V	1.138	0.96
240_A	248_L	1.133	0.95
287_A	306_L	1.120	0.95
54_A	112_P	1.119	0.95
77_C	228_H	1.119	0.95
258_T	262_Q	1.119	0.95
92_S	96_R	1.118	0.95
242_E	269_W	1.116	0.95
199_T	295_L	1.116	0.95
89_M	123_K	1.114	0.95
97_E	118_T	1.110	0.95
45_T	60_Q	1.105	0.95
74_S	228_H	1.100	0.95
273_E	276_Q	1.093	0.94
89_M	92_S	1.090	0.94
86_A	90_M	1.073	0.94
55_R	290_A	1.057	0.93
146_R	169_G	1.052	0.93
170_F	251_L	1.040	0.93
248_L	277_I	1.037	0.93
177_C	200_G	1.004	0.92
201_Y	222_A	1.004	0.92
72_F	187_L	0.997	0.91
95_D	123_K	0.997	0.91
131_L	135_N	0.986	0.91
112_P	228_H	0.985	0.91
147_Y	154_L	0.984	0.91
181_M	204_H	0.982	0.91
54_A	253_S	0.980	0.91
112_P	188_E	0.976	0.90
227_C	233_E	0.971	0.90
250_A	279_A	0.967	0.90
52_G	233_E	0.966	0.90
240_A	245_P	0.966	0.90
191_A	291_H	0.964	0.90
150_Q	153_S	0.964	0.90
41_A	62_V	0.959	0.90
52_G	79_E	0.958	0.90
196_A	203_S	0.957	0.90
54_A	114_G	0.955	0.89
31_A	41_A	0.955	0.89
29_R	138_E	0.950	0.89
208_L	232_R	0.949	0.89
181_M	206_F	0.948	0.89
72_F	230_L	0.931	0.88
261_L	265_H	0.928	0.88
47_V	120_T	0.927	0.88
190_Q	194_S	0.925	0.88
104_S	108_D	0.921	0.88
201_Y	305_R	0.920	0.88
183_Y	223_V	0.920	0.88
188_E	253_S	0.918	0.87
75_G	79_E	0.911	0.87
244_K	273_E	0.905	0.87
300_E	304_V	0.900	0.86
112_P	256_T	0.899	0.86
189_A	224_I	0.899	0.86
208_L	229_D	0.894	0.86
209_F	227_C	0.888	0.86
44_V	63_V	0.876	0.85
230_L	260_R	0.869	0.84
77_C	81_A	0.868	0.84
133_V	143_V	0.867	0.84
150_Q	155_V	0.859	0.84
134_L	138_E	0.858	0.84
191_A	194_S	0.855	0.83
63_V	86_A	0.854	0.83
111_L	260_R	0.854	0.83
114_G	253_S	0.852	0.83
249_G	301_V	0.847	0.83
225_L	237_L	0.845	0.83
31_A	124_L	0.842	0.83
81_A	84_F	0.842	0.83
188_E	256_T	0.840	0.82
157_L	160_Q	0.839	0.82
74_S	81_A	0.839	0.82
30_F	33_E	0.836	0.82
148_D	153_S	0.834	0.82
304_V	307_H	0.829	0.82
247_Y	281_V	0.825	0.81
239_A	277_I	0.823	0.81
84_F	87_L	0.819	0.81
242_E	273_E	0.817	0.81
55_R	114_G	0.813	0.80
32_V	134_L	0.811	0.80
82_A	100_Y	0.811	0.80
103_G	116_G	0.804	0.80
229_D	232_R	0.804	0.80
89_M	95_D	0.803	0.79
180_L	224_I	0.801	0.79
226_L	253_S	0.800	0.79
136_R	143_V	0.800	0.79
188_E	251_L	0.798	0.79
248_L	269_W	0.797	0.79
105_P	108_D	0.794	0.79
74_S	251_L	0.794	0.79
87_L	91_G	0.791	0.78
101_G	260_R	0.786	0.78
257_H	277_I	0.785	0.78
102_E	107_F	0.781	0.78
53_A	259_L	0.780	0.77
114_G	260_R	0.777	0.77
235_P	239_A	0.776	0.77
90_M	295_L	0.771	0.77
54_A	233_E	0.769	0.76
140_R	176_P	0.768	0.76
82_A	119_L	0.768	0.76
82_A	121_L	0.767	0.76
196_A	224_I	0.767	0.76
55_R	59_A	0.766	0.76
283_I	286_K	0.765	0.76
111_L	229_D	0.764	0.76
256_T	260_R	0.763	0.76
179_R	202_D	0.762	0.76
42_V	86_A	0.761	0.76
193_A	205_I	0.760	0.76
224_I	301_V	0.754	0.75
182_I	244_K	0.754	0.75
234_L	267_L	0.753	0.75
292_T	306_L	0.750	0.75
77_C	101_G	0.750	0.75
77_C	111_L	0.744	0.74
34_A	41_A	0.744	0.74
148_D	152_Q	0.743	0.74
55_R	74_S	0.740	0.74
163_T	168_N	0.740	0.74
125_R	128_Q	0.738	0.73
283_I	300_E	0.736	0.73
85_E	100_Y	0.736	0.73
74_S	112_P	0.732	0.73
78_V	186_S	0.731	0.73
76_G	113_C	0.730	0.73
80_A	114_G	0.729	0.73
93_G	96_R	0.723	0.72
281_V	297_V	0.722	0.72
278_R	304_V	0.720	0.72
264_L	268_G	0.717	0.71
179_R	221_T	0.716	0.71
237_L	248_L	0.715	0.71
72_F	79_E	0.713	0.71
35_L	201_Y	0.712	0.71
182_I	192_T	0.712	0.71
188_E	226_L	0.709	0.70
30_F	70_C	0.708	0.70
141_K	158_P	0.708	0.70
82_A	187_L	0.705	0.70
155_V	158_P	0.702	0.70
53_A	117_I	0.700	0.69
301_V	305_R	0.697	0.69
112_P	253_S	0.697	0.69
78_V	192_T	0.695	0.69
73_V	187_L	0.689	0.68
151_A	158_P	0.689	0.68
43_L	296_S	0.683	0.68
272_E	275_T	0.683	0.68
222_A	305_R	0.681	0.67
102_E	110_V	0.680	0.67
51_G	58_G	0.679	0.67
150_Q	272_E	0.677	0.67
223_V	248_L	0.677	0.67
74_S	117_I	0.676	0.67
286_K	303_S	0.674	0.67
206_F	251_L	0.674	0.67
225_L	248_L	0.674	0.67
292_T	302_A	0.673	0.66
55_R	241_R	0.666	0.66
35_L	124_L	0.666	0.66
129_P	162_R	0.665	0.66
54_A	230_L	0.663	0.65
180_L	298_L	0.663	0.65
235_P	238_Q	0.662	0.65
135_N	138_E	0.662	0.65
54_A	227_C	0.661	0.65
87_L	90_M	0.661	0.65
250_A	256_T	0.660	0.65
256_T	293_L	0.660	0.65
77_C	113_C	0.659	0.65
40_G	90_M	0.655	0.64
73_V	241_R	0.655	0.64
217_I	245_P	0.655	0.64
209_F	285_P	0.653	0.64
112_P	229_D	0.653	0.64
181_M	217_I	0.653	0.64
82_A	256_T	0.651	0.64
180_L	203_S	0.648	0.64
74_S	230_L	0.646	0.63
185_R	209_F	0.645	0.63
75_G	207_D	0.641	0.63
207_D	227_C	0.638	0.62
229_D	260_R	0.638	0.62
146_R	266_E	0.637	0.62
209_F	213_A	0.635	0.62
295_L	299_A	0.633	0.62
77_C	100_Y	0.631	0.61
55_R	109_I	0.630	0.61
101_G	112_P	0.628	0.61
64_R	70_C	0.628	0.61
284_F	308_Q	0.627	0.61
87_L	164_G	0.625	0.61
230_L	263_K	0.625	0.61
78_V	100_Y	0.625	0.61
287_A	293_L	0.624	0.61
251_L	279_A	0.623	0.60
46_L	57_L	0.623	0.60
60_Q	174_F	0.622	0.60
181_M	221_T	0.621	0.60
39_K	66_D	0.621	0.60
222_A	246_F	0.620	0.60
89_M	121_L	0.619	0.60
55_R	73_V	0.619	0.60
191_A	195_L	0.618	0.60
256_T	268_G	0.617	0.60
104_S	107_F	0.615	0.60
162_R	165_W	0.615	0.60
153_S	205_I	0.615	0.60
59_A	148_D	0.614	0.59
73_V	82_A	0.609	0.59
82_A	186_S	0.608	0.59
183_Y	202_D	0.608	0.59
89_M	93_G	0.607	0.59
88_E	92_S	0.607	0.59
182_I	297_V	0.606	0.58
227_C	232_R	0.601	0.58
196_A	200_G	0.600	0.58
192_T	226_L	0.600	0.58
199_T	296_S	0.598	0.57
41_A	129_P	0.598	0.57
102_E	281_V	0.596	0.57
149_P	156_C	0.595	0.57
196_A	237_L	0.594	0.57
192_T	195_L	0.593	0.57
106_W	233_E	0.592	0.57
227_C	230_L	0.591	0.56
72_F	186_S	0.590	0.56
197_A	203_S	0.589	0.56
144_G	173_G	0.588	0.56
268_G	274_T	0.582	0.55
225_L	277_I	0.582	0.55
207_D	212_S	0.582	0.55
101_G	108_D	0.580	0.55
241_R	276_Q	0.579	0.55
186_S	230_L	0.579	0.55
98_I	101_G	0.578	0.55
227_C	293_L	0.578	0.55
41_A	124_L	0.577	0.55
74_S	111_L	0.576	0.55
208_L	236_V	0.575	0.54
54_A	75_G	0.569	0.54
93_G	123_K	0.569	0.54
86_A	162_R	0.568	0.54
73_V	109_I	0.568	0.54
78_V	102_E	0.568	0.54
201_Y	306_L	0.568	0.54
40_G	126_S	0.567	0.53
183_Y	225_L	0.567	0.53
96_R	103_G	0.566	0.53
193_A	203_S	0.566	0.53
112_P	226_L	0.566	0.53
140_R	218_D	0.565	0.53
34_A	39_K	0.565	0.53
75_G	233_E	0.563	0.53
56_P	288_R	0.563	0.53
120_T	147_Y	0.561	0.53
180_L	201_Y	0.560	0.53
90_M	121_L	0.560	0.53
73_V	232_R	0.558	0.52
179_R	290_A	0.558	0.52
74_S	256_T	0.557	0.52
229_D	288_R	0.557	0.52
102_E	251_L	0.556	0.52
135_N	166_N	0.553	0.52
229_D	240_A	0.553	0.52
287_A	296_S	0.551	0.51
73_V	122_H	0.551	0.51
109_I	117_I	0.549	0.51
149_P	157_L	0.548	0.51
132_A	135_N	0.548	0.51
232_R	236_V	0.548	0.51
185_R	213_A	0.548	0.51
150_Q	154_L	0.547	0.51
64_R	69_Y	0.547	0.51
134_L	147_Y	0.545	0.51
181_M	278_R	0.545	0.51
52_G	227_C	0.540	0.50
225_L	233_E	0.538	0.50
61_M	264_L	0.535	0.49
54_A	72_F	0.533	0.49
194_S	291_H	0.532	0.49
283_I	296_S	0.532	0.49
266_E	275_T	0.531	0.49
187_L	256_T	0.530	0.49
81_A	182_I	0.528	0.48
186_S	256_T	0.528	0.48
178_V	222_A	0.527	0.48
234_L	260_R	0.527	0.48
153_S	160_Q	0.526	0.48
52_G	115_G	0.525	0.48
148_D	169_G	0.523	0.48
54_A	79_E	0.518	0.47
50_R	118_T	0.514	0.47
81_A	98_I	0.513	0.47
130_L	134_L	0.513	0.47
45_T	55_R	0.513	0.47
46_L	233_E	0.510	0.46
45_T	247_Y	0.510	0.46
46_L	49_I	0.509	0.46
148_D	154_L	0.509	0.46
197_A	271_R	0.509	0.46
229_D	250_A	0.508	0.46
183_Y	227_C	0.503	0.45
33_E	62_V	0.503	0.45
265_H	269_W	0.503	0.45
59_A	225_L	0.501	0.45
187_L	208_L	0.500	0.45

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
2we8A	2	0.8616	100	0.171	Contact Map
3on5A	4	0.9119	100	0.236	Contact Map
2g1uA	2	0.4025	96.1	0.933	Contact Map
3l9wA	2	0.4088	96.1	0.933	Contact Map
3fwzA	2	0.3648	95.9	0.934	Contact Map
1id1A	2	0.4434	95.4	0.936	Contact Map
3llvA	2	0.3931	95.4	0.936	Contact Map
1lssA	3	0.3428	94.8	0.939	Contact Map
3q2oA	2	0.4182	94.4	0.94	Contact Map
1pjqA	2	0.4025	93.7	0.942	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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