YQJA - BACSU - GREMLIN Contacts

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YQJA - Uncharacterized protein YqjA

UniProt:	P54538	Sequences: MFKIGYRTIKTALGTALAIYISQLLHLQNFASAGIITILCIQITQKRSLQASWARFSACCLAIAFSYLFFELIGYHPFVIGALLLIFIPITVLLKINEGIVTSSVIILHLYMSGGITPTFIWNEVQLITVGIGVALLMNLYMPSLDRKLIAYRKKIEDNFAVIFAEIERYLLTGEQDWSGKEIPETHQLITEAKNLAYRDVQNHILRYENLHYHYFKMREKQFEIIERLLPKVTSISITVDQGKMIAEFIHDLREAIHPGNTAYKFLKRLADMRKEFEEMPLPATREEFEARAALFHLLGEMEQYLVIKSYFKGIKAQKSLG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	322 (272)
Sequences:	7945 (6332)
Seq/√Len:	383.9

ECOLI - YCCS YHFK YEEA MDTO AAEB YDHK
BACSU - YQJA YGAE YVAC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_G	138_M	3.562	1.00
275_K	278_E	3.145	1.00
114_G	117_T	2.624	1.00
267_L	271_A	2.473	1.00
18_A	134_V	2.435	1.00
165_A	251_H	2.371	1.00
271_A	275_K	2.346	1.00
204_H	207_R	2.330	1.00
197_A	203_N	2.319	1.00
204_H	208_Y	2.226	1.00
106_I	109_H	2.167	1.00
87_F	91_T	2.132	1.00
58_A	62_A	2.088	1.00
200_D	203_N	2.061	1.00
109_H	113_S	2.061	1.00
108_L	112_M	2.060	1.00
10_K	139_N	2.050	1.00
247_A	251_H	2.027	1.00
219_R	222_Q	1.971	1.00
106_I	113_S	1.947	1.00
17_L	134_V	1.922	1.00
269_R	273_M	1.868	1.00
63_I	67_Y	1.835	1.00
36_I	128_I	1.818	1.00
101_V	104_S	1.761	1.00
102_T	105_V	1.757	1.00
274_R	278_E	1.756	1.00
229_L	232_K	1.755	1.00
122_W	126_Q	1.751	1.00
88_I	92_V	1.740	1.00
18_A	37_T	1.726	1.00
187_H	190_I	1.720	1.00
144_S	147_R	1.703	1.00
240_V	244_K	1.674	1.00
269_R	276_E	1.640	1.00
182_E	185_E	1.620	1.00
270_L	273_M	1.607	1.00
12_A	16_A	1.607	1.00
78_F	82_A	1.602	1.00
220_E	227_E	1.592	1.00
106_I	111_Y	1.592	1.00
21_I	25_L	1.582	1.00
272_D	276_E	1.563	1.00
14_G	37_T	1.527	1.00
227_E	230_L	1.508	1.00
228_R	232_K	1.501	1.00
109_H	112_M	1.500	1.00
184_P	187_H	1.491	1.00
251_H	255_E	1.489	1.00
89_P	92_V	1.488	1.00
21_I	134_V	1.480	1.00
265_K	269_R	1.480	1.00
239_T	243_G	1.471	1.00
269_R	274_R	1.466	1.00
119_T	123_N	1.460	1.00
64_A	68_L	1.459	1.00
270_L	274_R	1.442	1.00
20_Y	24_L	1.441	1.00
186_T	189_L	1.434	1.00
129_T	133_G	1.434	1.00
159_N	162_V	1.434	1.00
221_K	225_I	1.429	1.00
123_N	126_Q	1.426	1.00
213_Y	216_F	1.425	1.00
268_K	272_D	1.421	1.00
269_R	272_D	1.414	1.00
15_T	38_I	1.410	1.00
55_R	59_C	1.408	1.00
19_I	34_G	1.402	1.00
267_L	272_D	1.400	1.00
105_V	113_S	1.399	1.00
86_I	90_I	1.397	1.00
85_L	89_P	1.388	1.00
188_Q	192_E	1.384	1.00
59_C	128_I	1.358	1.00
76_H	79_V	1.354	1.00
267_L	270_L	1.351	1.00
161_A	254_R	1.344	1.00
267_L	274_R	1.342	1.00
254_R	258_H	1.341	1.00
224_E	228_R	1.332	1.00
245_M	248_E	1.307	1.00
255_E	259_P	1.306	1.00
55_R	58_A	1.305	1.00
199_R	202_Q	1.302	1.00
159_N	189_L	1.300	1.00
225_I	229_L	1.280	1.00
55_R	124_E	1.279	1.00
220_E	224_E	1.271	1.00
52_S	136_L	1.261	1.00
102_T	106_I	1.253	1.00
273_M	276_E	1.244	1.00
191_T	194_K	1.235	1.00
8_T	12_A	1.229	1.00
185_E	189_L	1.228	1.00
240_V	243_G	1.222	1.00
219_R	223_F	1.221	1.00
82_A	86_I	1.216	1.00
231_P	235_S	1.216	1.00
265_K	272_D	1.214	1.00
59_C	124_E	1.209	1.00
191_T	195_N	1.208	1.00
205_I	209_E	1.207	1.00
122_W	125_V	1.205	1.00
246_I	250_I	1.203	1.00
220_E	228_R	1.201	1.00
256_A	260_G	1.195	1.00
105_V	109_H	1.190	1.00
217_K	220_E	1.190	1.00
183_I	186_T	1.190	1.00
77_P	80_I	1.188	1.00
159_N	185_E	1.187	1.00
158_D	258_H	1.186	1.00
161_A	165_A	1.181	1.00
18_A	22_S	1.178	1.00
267_L	273_M	1.177	1.00
241_D	245_M	1.176	1.00
268_K	275_K	1.173	1.00
121_I	125_V	1.169	1.00
18_A	33_A	1.168	1.00
264_Y	268_K	1.167	1.00
13_L	138_M	1.159	1.00
225_I	228_R	1.159	1.00
230_L	233_V	1.158	1.00
197_A	201_V	1.156	1.00
201_V	205_I	1.153	1.00
162_V	165_A	1.145	1.00
50_Q	54_A	1.141	1.00
225_I	231_P	1.138	1.00
77_P	81_G	1.136	1.00
272_D	275_K	1.135	1.00
192_E	195_N	1.126	1.00
218_M	221_K	1.119	1.00
266_F	272_D	1.117	1.00
223_F	227_E	1.116	1.00
265_K	268_K	1.105	1.00
246_I	249_F	1.105	1.00
41_I	135_A	1.094	1.00
162_V	166_E	1.093	1.00
276_E	279_E	1.089	1.00
231_P	234_T	1.085	1.00
108_L	113_S	1.084	1.00
106_I	110_L	1.083	1.00
255_E	262_T	1.072	1.00
214_H	218_M	1.067	1.00
103_S	107_I	1.066	1.00
102_T	110_L	1.065	1.00
265_K	276_E	1.062	1.00
216_F	224_E	1.060	1.00
198_Y	201_V	1.059	1.00
251_H	254_R	1.057	1.00
61_L	64_A	1.056	1.00
198_Y	202_Q	1.035	1.00
227_E	234_T	1.029	1.00
267_L	278_E	1.027	1.00
266_F	274_R	1.027	1.00
227_E	231_P	1.025	1.00
242_Q	245_M	1.022	1.00
10_K	138_M	1.022	1.00
270_L	276_E	1.015	1.00
193_A	200_D	1.010	1.00
274_R	277_F	1.001	1.00
121_I	124_E	1.000	1.00
44_T	47_R	0.998	1.00
271_A	274_R	0.996	1.00
194_K	220_E	0.994	1.00
68_L	72_L	0.993	1.00
15_T	34_G	0.991	1.00
36_I	39_L	0.985	1.00
104_S	108_L	0.980	1.00
105_V	110_L	0.977	1.00
101_V	105_V	0.977	1.00
18_A	34_G	0.974	1.00
118_P	122_W	0.974	1.00
154_K	161_A	0.974	1.00
102_T	109_H	0.973	1.00
190_I	194_K	0.973	1.00
215_Y	219_R	0.967	1.00
199_R	203_N	0.956	1.00
159_N	182_E	0.951	1.00
100_I	103_S	0.951	1.00
32_S	59_C	0.949	1.00
124_E	128_I	0.942	1.00
248_E	252_D	0.930	1.00
83_L	87_F	0.929	1.00
100_I	104_S	0.927	1.00
62_A	124_E	0.926	1.00
215_Y	222_Q	0.925	1.00
105_V	112_M	0.924	1.00
107_I	110_L	0.922	1.00
110_L	113_S	0.918	1.00
51_A	124_E	0.913	1.00
22_S	33_A	0.905	1.00
252_D	256_A	0.904	1.00
213_Y	220_E	0.901	1.00
105_V	111_Y	0.898	1.00
250_I	254_R	0.895	1.00
225_I	233_V	0.895	1.00
197_A	200_D	0.892	1.00
214_H	219_R	0.892	1.00
266_F	269_R	0.891	1.00
154_K	158_D	0.886	1.00
151_A	155_K	0.882	1.00
190_I	193_A	0.879	1.00
205_I	208_Y	0.879	1.00
264_Y	273_M	0.877	1.00
56_F	132_I	0.874	1.00
103_S	109_H	0.874	1.00
14_G	134_V	0.867	1.00
33_A	37_T	0.867	1.00
104_S	107_I	0.864	1.00
264_Y	271_A	0.861	1.00
53_W	57_S	0.860	1.00
124_E	127_L	0.857	1.00
253_L	257_I	0.855	1.00
31_A	34_G	0.855	1.00
222_Q	225_I	0.852	1.00
39_L	42_Q	0.850	1.00
52_S	55_R	0.849	1.00
231_P	236_I	0.837	1.00
224_E	229_L	0.837	1.00
105_V	108_L	0.837	1.00
110_L	121_I	0.829	1.00
103_S	106_I	0.828	1.00
89_P	93_L	0.826	1.00
216_F	220_E	0.825	1.00
245_M	249_F	0.815	1.00
59_C	106_I	0.815	1.00
227_E	232_K	0.814	1.00
202_Q	205_I	0.813	1.00
193_A	203_N	0.810	1.00
213_Y	227_E	0.806	1.00
10_K	141_Y	0.801	1.00
194_K	203_N	0.801	1.00
129_T	132_I	0.800	1.00
248_E	251_H	0.799	1.00
239_T	246_I	0.797	1.00
36_I	40_C	0.796	1.00
200_D	204_H	0.795	1.00
239_T	245_M	0.794	1.00
44_T	48_S	0.786	1.00
22_S	127_L	0.783	1.00
235_S	238_I	0.783	1.00
185_E	188_Q	0.782	1.00
224_E	233_V	0.781	1.00
166_E	169_R	0.780	1.00
131_G	135_A	0.775	1.00
194_K	198_Y	0.771	1.00
266_F	270_L	0.770	1.00
32_S	55_R	0.765	1.00
15_T	19_I	0.763	1.00
219_R	232_K	0.762	1.00
232_K	235_S	0.762	1.00
220_E	223_F	0.760	1.00
55_R	128_I	0.757	1.00
215_Y	220_E	0.751	1.00
260_G	263_A	0.751	1.00
268_K	274_R	0.743	1.00
187_H	191_T	0.743	1.00
150_I	154_K	0.742	1.00
224_E	227_E	0.739	1.00
265_K	271_A	0.736	1.00
107_I	111_Y	0.730	1.00
79_V	82_A	0.730	1.00
134_V	138_M	0.729	1.00
56_F	129_T	0.726	1.00
239_T	242_Q	0.723	1.00
197_A	202_Q	0.723	1.00
249_F	254_R	0.722	1.00
229_L	233_V	0.718	1.00
66_S	121_I	0.718	1.00
264_Y	276_E	0.717	1.00
106_I	124_E	0.716	1.00
249_F	263_A	0.716	1.00
106_I	112_M	0.715	1.00
215_Y	226_I	0.713	1.00
63_I	125_V	0.709	1.00
35_I	39_L	0.707	1.00
69_F	73_I	0.707	1.00
207_R	210_N	0.701	1.00
98_E	101_V	0.698	0.99
269_R	277_F	0.694	0.99
242_Q	247_A	0.693	0.99
225_I	236_I	0.692	0.99
22_S	30_F	0.691	0.99
17_L	138_M	0.689	0.99
221_K	236_I	0.688	0.99
51_A	55_R	0.687	0.99
30_F	33_A	0.686	0.99
189_L	194_K	0.683	0.99
157_E	160_F	0.682	0.99
216_F	222_Q	0.680	0.99
266_F	273_M	0.678	0.99
60_C	125_V	0.674	0.99
221_K	227_E	0.674	0.99
107_I	113_S	0.673	0.99
225_I	230_L	0.673	0.99
267_L	276_E	0.670	0.99
52_S	58_A	0.665	0.99
154_K	254_R	0.662	0.99
256_A	263_A	0.658	0.99
202_Q	206_L	0.653	0.99
66_S	69_F	0.651	0.99
215_Y	221_K	0.649	0.99
247_A	250_I	0.646	0.99
227_E	233_V	0.646	0.99
103_S	110_L	0.646	0.99
213_Y	221_K	0.644	0.99
268_K	271_A	0.643	0.99
32_S	124_E	0.638	0.99
249_F	252_D	0.638	0.99
186_T	190_I	0.637	0.99
51_A	98_E	0.635	0.99
258_H	262_T	0.635	0.99
271_A	279_E	0.634	0.99
14_G	18_A	0.631	0.99
54_A	57_S	0.631	0.99
265_K	278_E	0.631	0.99
220_E	226_I	0.631	0.99
55_R	62_A	0.630	0.99
152_Y	192_E	0.629	0.99
221_K	224_E	0.624	0.99
100_I	108_L	0.623	0.99
87_F	90_I	0.621	0.99
101_V	106_I	0.619	0.99
219_R	226_I	0.618	0.99
275_K	279_E	0.616	0.99
133_G	137_L	0.611	0.99
222_Q	228_R	0.610	0.99
241_D	244_K	0.609	0.99
212_H	215_Y	0.605	0.99
108_L	111_Y	0.605	0.99
126_Q	130_V	0.604	0.99
59_C	66_S	0.603	0.99
273_M	277_F	0.602	0.99
49_L	52_S	0.599	0.98
40_C	63_I	0.599	0.98
222_Q	226_I	0.598	0.98
184_P	188_Q	0.596	0.98
183_I	187_H	0.596	0.98
240_V	248_E	0.595	0.98
203_N	207_R	0.595	0.98
186_T	194_K	0.590	0.98
100_I	105_V	0.583	0.98
229_L	236_I	0.583	0.98
166_E	182_E	0.582	0.98
22_S	25_L	0.582	0.98
153_R	156_I	0.582	0.98
92_V	95_K	0.578	0.98
234_T	237_S	0.577	0.98
205_I	210_N	0.577	0.98
91_T	96_I	0.575	0.98
225_I	232_K	0.575	0.98
109_H	124_E	0.575	0.98
135_A	139_N	0.571	0.98
218_M	229_L	0.570	0.98
239_T	260_G	0.570	0.98
140_L	143_P	0.568	0.98
40_C	135_A	0.564	0.98
222_Q	227_E	0.563	0.98
218_M	226_I	0.562	0.98
67_Y	71_E	0.561	0.98
16_A	20_Y	0.560	0.98
33_A	127_L	0.560	0.98
32_S	127_L	0.558	0.98
181_K	185_E	0.558	0.98
233_V	237_S	0.555	0.97
38_I	42_Q	0.554	0.97
267_L	275_K	0.552	0.97
215_Y	228_R	0.552	0.97
145_L	199_R	0.551	0.97
248_E	261_N	0.550	0.97
247_A	253_L	0.548	0.97
226_I	230_L	0.548	0.97
88_I	91_T	0.547	0.97
173_T	176_Q	0.539	0.97
227_E	237_S	0.537	0.97
32_S	128_I	0.537	0.97
171_L	178_W	0.537	0.97
190_I	203_N	0.536	0.97
102_T	111_Y	0.531	0.97
84_L	92_V	0.531	0.97
71_E	74_G	0.531	0.97
200_D	205_I	0.530	0.97
173_T	177_D	0.529	0.97
247_A	254_R	0.528	0.97
184_P	191_T	0.528	0.97
211_L	226_I	0.527	0.97
271_A	276_E	0.524	0.96
193_A	199_R	0.524	0.96
230_L	237_S	0.523	0.96
145_L	148_K	0.522	0.96
222_Q	229_L	0.518	0.96
162_V	182_E	0.514	0.96
264_Y	269_R	0.514	0.96
81_G	85_L	0.514	0.96
183_I	203_N	0.513	0.96
11_T	14_G	0.510	0.96
45_Q	48_S	0.509	0.96
101_V	112_M	0.507	0.96
214_H	229_L	0.506	0.96
48_S	128_I	0.506	0.96
257_I	260_G	0.505	0.96
80_I	87_F	0.504	0.96
155_K	189_L	0.503	0.96
60_C	64_A	0.503	0.96
243_G	247_A	0.502	0.96
215_Y	230_L	0.500	0.95

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
3kmiA	2	0.5311	98.4	0.781	Contact Map
4jkvA	2	0.2609	56.1	0.915	Contact Map
3effK	4	0.4317	42.5	0.922	Contact Map
4n78F	1	0.3416	32.9	0.926	Contact Map
4k0jA	3	0.4503	31.6	0.927	Contact Map
2oltA	5	0.5652	30.2	0.928	Contact Map
4q4gX	1	0	28.5	0.929	Contact Map
2d4yA	1	0.3727	28.5	0.929	Contact Map
3ne5A	3	0.4689	23.9	0.931	Contact Map
4cgkA	3	0.5	19.2	0.934	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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