YNCE - ECOLI - GREMLIN Contacts

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YNCE - Uncharacterized protein YncE

UniProt:	P76116	Sequences: MHLRHLFSSRLRGSLLLGSLLVVSSFSTQAAEEMLRKAVGKGAYEMAYSQQENALWLATSQSRKLDKGGVVYRLDPVTLEVTQAIHNDLKPFGATINNTTQTLWFGNTVNSAVTAIDAKTGEVKGRLVLDDRKRTEEVRPLQPRELVADDATNTVYISGIGKESVIWVVDGGNIKLKTAIQNTGKMSTGLALDSEGKRLYTTNADGELITIDTADNKILSRKKLLDDGKEHFFINISLDTARQRAFITDSKAAEVLVVDTRNGNILAKVAAPESLAVLFNPARNEAYVTHRQAGKVSVIDAKSYKVVKTFDTPTHPNSLALSADGKTLYVSVKQKSTKQQEATQPDDVIRIAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13775
Length:	353 (291)
Sequences:	3510 (3090)
Seq/√Len:	181.2

ECOLI - YNCE TOLB 6PGL BAMB
BACSU - YWHL YWHK YXAL 6PGL YVRE
HALSA - Q9HHP3
SULSO - Q97VC7 Q97UH7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
183_T	201_T	6.334	1.00
229_K	248_T	4.643	1.00
189_G	202_T	4.580	1.00
203_N	207_E	3.906	1.00
289_T	299_I	3.719	1.00
248_T	258_V	3.639	1.00
272_P	289_T	3.060	1.00
208_L	248_T	2.994	1.00
201_T	211_I	2.988	1.00
200_Y	238_L	2.979	1.00
255_V	289_T	2.953	1.00
235_N	249_D	2.928	1.00
166_I	201_T	2.702	1.00
247_I	279_F	2.649	1.00
290_H	294_G	2.402	1.00
163_E	167_W	2.369	1.00
256_L	268_K	2.368	1.00
288_V	321_L	2.367	1.00
249_D	274_S	2.354	1.00
276_A	290_H	2.318	1.00
139_R	163_E	2.292	1.00
139_R	158_S	2.273	1.00
209_I	221_R	2.267	1.00
183_T	203_N	2.249	1.00
139_R	169_V	2.228	1.00
190_L	201_T	2.202	1.00
145_E	159_G	2.189	1.00
188_T	204_A	2.121	1.00
160_I	163_E	2.109	1.00
147_V	191_A	2.023	1.00
182_N	209_I	2.005	1.00
290_H	316_P	1.985	1.00
138_V	169_V	1.944	1.00
200_Y	236_I	1.938	1.00
191_A	237_S	1.930	1.00
229_K	250_S	1.894	1.00
237_S	278_L	1.864	1.00
247_I	257_V	1.797	1.00
202_T	236_I	1.777	1.00
202_T	233_F	1.774	1.00
288_V	298_V	1.720	1.00
32_E	35_L	1.720	1.00
157_I	199_L	1.716	1.00
272_P	291_R	1.698	1.00
183_T	211_I	1.693	1.00
183_T	209_I	1.693	1.00
252_A	256_L	1.678	1.00
193_D	238_L	1.638	1.00
200_Y	210_T	1.631	1.00
201_T	205_D	1.629	1.00
247_I	286_A	1.622	1.00
248_T	256_L	1.589	1.00
167_W	176_L	1.589	1.00
157_I	160_I	1.582	1.00
205_D	209_I	1.559	1.00
293_A	297_S	1.550	1.00
44_Y	48_Y	1.547	1.00
167_W	179_A	1.544	1.00
183_T	205_D	1.540	1.00
183_T	187_S	1.516	1.00
190_L	199_L	1.511	1.00
47_A	50_Q	1.478	1.00
318_S	331_S	1.465	1.00
34_M	37_K	1.464	1.00
229_K	233_F	1.463	1.00
212_D	215_D	1.454	1.00
32_E	36_R	1.448	1.00
149_D	192_L	1.419	1.00
259_D	262_N	1.410	1.00
55_L	59_T	1.401	1.00
322_S	325_G	1.401	1.00
201_T	209_I	1.395	1.00
170_D	173_N	1.393	1.00
218_I	221_R	1.388	1.00
33_E	36_R	1.387	1.00
250_S	254_E	1.385	1.00
313_P	330_V	1.385	1.00
39_V	43_A	1.385	1.00
182_N	211_I	1.379	1.00
54_A	57_L	1.362	1.00
43_A	47_A	1.357	1.00
158_S	169_V	1.353	1.00
229_K	252_A	1.319	1.00
296_V	330_V	1.318	1.00
289_T	297_S	1.313	1.00
291_R	295_K	1.289	1.00
72_Y	75_D	1.280	1.00
194_S	242_R	1.279	1.00
157_I	192_L	1.277	1.00
160_I	165_V	1.273	1.00
42_G	46_M	1.272	1.00
166_I	190_L	1.268	1.00
288_V	319_L	1.252	1.00
209_I	218_I	1.247	1.00
93_G	107_N	1.246	1.00
40_G	44_Y	1.236	1.00
48_Y	51_Q	1.227	1.00
247_I	277_V	1.212	1.00
31_A	34_M	1.205	1.00
48_Y	52_E	1.195	1.00
31_A	35_L	1.188	1.00
78_T	82_T	1.182	1.00
38_A	41_K	1.174	1.00
322_S	327_T	1.147	1.00
36_R	39_V	1.146	1.00
46_M	49_S	1.139	1.00
322_S	326_K	1.134	1.00
38_A	45_E	1.129	1.00
157_I	168_V	1.128	1.00
250_S	256_L	1.127	1.00
42_G	47_A	1.124	1.00
54_A	58_A	1.121	1.00
110_N	114_T	1.120	1.00
180_I	199_L	1.117	1.00
194_S	238_L	1.101	1.00
35_L	39_V	1.098	1.00
53_N	56_W	1.093	1.00
272_P	299_I	1.086	1.00
306_V	309_T	1.085	1.00
139_R	160_I	1.085	1.00
40_G	45_E	1.068	1.00
57_L	60_S	1.059	1.00
271_A	289_T	1.054	1.00
63_R	67_K	1.047	1.00
234_I	251_K	1.042	1.00
249_D	277_V	1.039	1.00
150_D	196_G	1.032	1.00
97_N	100_T	1.031	1.00
45_E	52_E	1.025	0.99
280_N	283_R	1.017	0.99
55_L	58_A	1.016	0.99
156_Y	159_G	1.016	0.99
74_L	77_V	1.015	0.99
47_A	52_E	1.009	0.99
97_N	101_Q	1.008	0.99
35_L	38_A	1.006	0.99
33_E	37_K	1.000	0.99
297_S	309_T	0.997	0.99
42_G	50_Q	0.992	0.99
36_R	40_G	0.989	0.99
321_L	327_T	0.984	0.99
92_F	95_T	0.980	0.99
191_A	236_I	0.965	0.99
83_Q	87_N	0.962	0.99
299_I	306_V	0.961	0.99
80_E	87_N	0.960	0.99
203_N	206_G	0.952	0.99
237_S	277_V	0.946	0.99
183_T	207_E	0.945	0.99
37_K	41_K	0.945	0.99
39_V	44_Y	0.943	0.99
203_N	209_I	0.938	0.99
40_G	43_A	0.938	0.99
239_D	279_F	0.932	0.99
274_S	299_I	0.931	0.99
228_G	258_V	0.927	0.99
75_D	78_T	0.922	0.99
47_A	53_N	0.921	0.99
32_E	38_A	0.919	0.99
284_N	300_D	0.914	0.99
157_I	169_V	0.900	0.99
45_E	54_A	0.897	0.99
46_M	50_Q	0.896	0.99
241_A	244_R	0.886	0.99
48_Y	54_A	0.882	0.98
308_K	311_D	0.881	0.98
42_G	45_E	0.880	0.98
240_T	283_R	0.879	0.98
143_P	169_V	0.877	0.98
32_E	37_K	0.877	0.98
300_D	303_S	0.876	0.98
41_K	45_E	0.874	0.98
95_T	147_V	0.872	0.98
156_Y	192_L	0.872	0.98
278_L	288_V	0.868	0.98
51_Q	55_L	0.862	0.98
31_A	37_K	0.855	0.98
235_N	277_V	0.850	0.98
31_A	38_A	0.849	0.98
38_A	43_A	0.847	0.98
54_A	59_T	0.846	0.98
32_E	40_G	0.845	0.98
36_R	41_K	0.840	0.98
44_Y	56_W	0.838	0.98
284_N	302_K	0.836	0.98
139_R	167_W	0.836	0.98
250_S	253_A	0.836	0.98
308_K	313_P	0.834	0.98
248_T	252_A	0.832	0.98
146_L	155_V	0.832	0.98
34_M	39_V	0.827	0.98
31_A	39_V	0.824	0.98
49_S	53_N	0.822	0.98
104_W	107_N	0.821	0.98
96_I	116_I	0.820	0.98
229_K	258_V	0.817	0.98
35_L	40_G	0.817	0.98
242_R	245_A	0.803	0.97
32_E	39_V	0.803	0.97
44_Y	49_S	0.802	0.97
56_W	60_S	0.795	0.97
38_A	54_A	0.795	0.97
82_T	87_N	0.794	0.97
43_A	49_S	0.792	0.97
80_E	88_D	0.788	0.97
159_G	187_S	0.788	0.97
64_K	68_G	0.787	0.97
66_D	72_Y	0.787	0.97
307_V	310_F	0.786	0.97
177_K	181_Q	0.784	0.97
66_D	75_D	0.782	0.97
148_A	238_L	0.774	0.97
276_A	319_L	0.773	0.97
37_K	45_E	0.772	0.97
65_L	68_G	0.770	0.96
31_A	36_R	0.769	0.96
313_P	332_V	0.767	0.96
52_E	56_W	0.767	0.96
272_P	297_S	0.766	0.96
34_M	40_G	0.763	0.96
50_Q	53_N	0.763	0.96
59_T	62_S	0.759	0.96
125_G	128_V	0.759	0.96
249_D	253_A	0.759	0.96
229_K	256_L	0.757	0.96
35_L	41_K	0.757	0.96
52_E	55_L	0.757	0.96
83_Q	88_D	0.754	0.96
37_K	40_G	0.754	0.96
245_A	266_L	0.753	0.96
285_E	288_V	0.752	0.96
33_E	38_A	0.751	0.96
44_Y	47_A	0.750	0.96
272_P	293_A	0.749	0.96
138_V	167_W	0.748	0.96
84_A	87_N	0.745	0.96
53_N	57_L	0.744	0.96
150_D	192_L	0.741	0.96
193_D	200_Y	0.735	0.95
105_F	115_A	0.731	0.95
31_A	41_K	0.731	0.95
187_S	201_T	0.728	0.95
291_R	297_S	0.724	0.95
50_Q	56_W	0.724	0.95
66_D	70_V	0.723	0.95
320_A	329_Y	0.722	0.95
234_I	249_D	0.719	0.95
185_K	203_N	0.714	0.95
210_T	238_L	0.707	0.94
321_L	324_D	0.705	0.94
204_A	232_F	0.704	0.94
51_Q	56_W	0.703	0.94
40_G	47_A	0.700	0.94
159_G	190_L	0.699	0.94
47_A	62_S	0.699	0.94
265_I	269_V	0.699	0.94
53_N	59_T	0.699	0.94
49_S	58_A	0.698	0.94
312_T	330_V	0.697	0.94
239_D	242_R	0.697	0.94
107_N	143_P	0.692	0.94
85_I	88_D	0.691	0.94
76_P	88_D	0.690	0.94
55_L	60_S	0.689	0.94
233_F	248_T	0.688	0.93
73_R	78_T	0.686	0.93
304_Y	308_K	0.685	0.93
326_K	331_S	0.685	0.93
315_H	318_S	0.683	0.93
297_S	306_V	0.682	0.93
149_D	152_T	0.682	0.93
253_A	271_A	0.681	0.93
95_T	146_L	0.680	0.93
33_E	40_G	0.679	0.93
319_L	328_L	0.675	0.93
166_I	187_S	0.675	0.93
136_E	139_R	0.675	0.93
306_V	310_F	0.671	0.93
327_T	332_V	0.671	0.93
139_R	143_P	0.670	0.93
44_Y	52_E	0.670	0.93
229_K	254_E	0.669	0.93
33_E	41_K	0.669	0.93
40_G	46_M	0.666	0.92
41_K	44_Y	0.665	0.92
78_T	81_V	0.665	0.92
35_L	43_A	0.662	0.92
52_E	57_L	0.661	0.92
65_L	72_Y	0.661	0.92
322_S	332_V	0.661	0.92
182_N	201_T	0.661	0.92
315_H	330_V	0.660	0.92
58_A	61_Q	0.659	0.92
235_N	276_A	0.659	0.92
123_V	128_V	0.657	0.92
35_L	56_W	0.655	0.92
35_L	42_G	0.654	0.92
75_D	79_L	0.653	0.92
277_V	289_T	0.653	0.92
38_A	42_G	0.652	0.92
320_A	331_S	0.651	0.91
239_D	244_R	0.649	0.91
232_F	249_D	0.646	0.91
171_G	301_A	0.646	0.91
65_L	69_G	0.640	0.91
293_A	299_I	0.640	0.91
38_A	51_Q	0.640	0.91
31_A	45_E	0.639	0.91
62_S	66_D	0.637	0.91
91_P	94_A	0.633	0.90
62_S	67_K	0.632	0.90
314_T	332_V	0.631	0.90
124_K	128_V	0.630	0.90
154_T	168_V	0.628	0.90
316_P	330_V	0.628	0.90
50_Q	54_A	0.625	0.90
80_E	83_Q	0.625	0.90
46_M	56_W	0.624	0.90
77_V	88_D	0.624	0.90
40_G	52_E	0.624	0.90
280_N	284_N	0.622	0.90
168_V	213_T	0.621	0.89
81_V	84_A	0.620	0.89
51_Q	57_L	0.620	0.89
290_H	297_S	0.620	0.89
63_R	69_G	0.619	0.89
64_K	67_K	0.619	0.89
81_V	85_I	0.618	0.89
91_P	116_I	0.613	0.89
77_V	80_E	0.608	0.88
274_S	293_A	0.605	0.88
156_Y	199_L	0.604	0.88
203_N	233_F	0.603	0.88
258_V	279_F	0.600	0.88
73_R	83_Q	0.600	0.88
237_S	279_F	0.599	0.88
40_G	48_Y	0.599	0.88
298_V	310_F	0.598	0.88
324_D	328_L	0.596	0.87
66_D	69_G	0.595	0.87
208_L	233_F	0.593	0.87
63_R	66_D	0.592	0.87
54_A	62_S	0.591	0.87
37_K	43_A	0.590	0.87
169_V	176_L	0.590	0.87
75_D	88_D	0.590	0.87
200_Y	245_A	0.590	0.87
47_A	54_A	0.588	0.87
50_Q	55_L	0.587	0.87
192_L	199_L	0.587	0.87
82_T	86_H	0.585	0.86
316_P	319_L	0.584	0.86
76_P	86_H	0.584	0.86
208_L	236_I	0.580	0.86
76_P	80_E	0.580	0.86
124_K	127_L	0.579	0.86
176_L	179_A	0.579	0.86
198_R	210_T	0.575	0.86
37_K	53_N	0.575	0.86
265_I	268_K	0.575	0.86
36_R	46_M	0.575	0.86
326_K	330_V	0.574	0.85
139_R	157_I	0.573	0.85
65_L	77_V	0.572	0.85
147_V	190_L	0.570	0.85
38_A	46_M	0.568	0.85
157_I	190_L	0.567	0.85
40_G	59_T	0.566	0.85
189_G	235_N	0.565	0.85
122_E	125_G	0.565	0.85
105_F	146_L	0.564	0.84
117_D	121_G	0.563	0.84
45_E	50_Q	0.561	0.84
74_L	80_E	0.560	0.84
49_S	57_L	0.559	0.84
253_A	256_L	0.556	0.84
44_Y	51_Q	0.556	0.84
257_V	269_V	0.553	0.83
96_I	102_T	0.553	0.83
170_D	212_D	0.551	0.83
259_D	264_N	0.551	0.83
105_F	155_V	0.549	0.83
91_P	97_N	0.548	0.83
275_L	292_Q	0.547	0.83
282_A	285_E	0.546	0.83
35_L	48_Y	0.546	0.83
46_M	53_N	0.545	0.82
170_D	177_K	0.543	0.82
31_A	43_A	0.542	0.82
187_S	205_D	0.542	0.82
76_P	82_T	0.542	0.82
113_V	158_S	0.540	0.82
326_K	332_V	0.540	0.82
74_L	79_L	0.539	0.82
180_I	201_T	0.538	0.82
317_N	332_V	0.538	0.82
92_F	96_I	0.533	0.81
52_E	58_A	0.532	0.81
44_Y	54_A	0.532	0.81
39_V	47_A	0.527	0.80
95_T	98_N	0.527	0.80
238_L	260_T	0.526	0.80
47_A	51_Q	0.524	0.80
255_V	271_A	0.524	0.80
164_S	206_G	0.523	0.80
329_Y	332_V	0.523	0.80
303_S	306_V	0.522	0.80
49_S	55_L	0.522	0.80
72_Y	77_V	0.520	0.79
45_E	61_Q	0.520	0.79
160_I	167_W	0.519	0.79
46_M	52_E	0.518	0.79
56_W	61_Q	0.518	0.79
34_M	47_A	0.517	0.79
48_Y	53_N	0.515	0.79
289_T	293_A	0.514	0.79
210_T	260_T	0.513	0.79
277_V	286_A	0.513	0.79
45_E	51_Q	0.512	0.78
328_L	331_S	0.510	0.78
212_D	261_R	0.510	0.78
278_L	320_A	0.508	0.78
39_V	53_N	0.507	0.78
321_L	328_L	0.507	0.78
271_A	291_R	0.507	0.78
78_T	88_D	0.506	0.78
325_G	329_Y	0.505	0.77
70_V	75_D	0.504	0.77
305_K	308_K	0.504	0.77
40_G	53_N	0.504	0.77
216_N	219_L	0.501	0.77
41_K	48_Y	0.501	0.77
58_A	67_K	0.501	0.77
317_N	330_V	0.500	0.77
324_D	327_T	0.500	0.77
36_R	49_S	0.500	0.77

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
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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
1vyhC	1	0.7479	100	0.297	Contact Map
4j73A	1	0.7394	100	0.326	Contact Map
3j60g	1	0.898	100	0.331	Contact Map
1gotB	1	0.8499	100	0.334	Contact Map
4j87A	1	0.7309	100	0.337	Contact Map
4u1eI	1	0.7309	100	0.344	Contact Map
5a1uD	1	0.7422	100	0.346	Contact Map
3zey7	1	0.7677	100	0.346	Contact Map
3mkqA	2	0.7365	100	0.346	Contact Map
3j38g	1	0.7649	100	0.347	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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