Q9HQN6 - HALSA - GREMLIN Contacts

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Q9HQN6 - Menaquinone biosynthesis

UniProt:	Q9HQN6	Sequences: MTQTADVSRQRAWLMAARPHTLPAAAAPVVVGTALAVHTGVLAVWPAVAALVGAALIQIATNFANDYYDAVRGADTEDREGFTRVTAGGLIRPARVKQAMYVTFAAAILDGVYLVFVGGVPILVIGLASVASGITYTGGPYPLGYHGLGDAFVFLFFGVIAVTGTYYVQAAAHLAGAFPVAIPPGTVPLAAVVASLPVAAISTNIIVVNNIRDKDEDETTGKRTLAVRFGYRFSRLEYAGLLVVAYAAPLWFYATGYGASVFLPLVTLPLAVSVTKTVFERTEGAALNPALSRTGQLLAAYSALFAVGVAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	311 (273)
Sequences:	8792 (6342)
Seq/√Len:	383.9

ECOLI - MENA UBIA CYOE
BACSU - MENA COXX2 COXX1
HALSA - Q9HQN6 LYEL DGGGP COXX
SULSO - COXX DGGGP Q980Z2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_Y	93_P	3.574	1.00
70_A	93_P	3.468	1.00
60_A	104_F	2.995	1.00
94_A	98_Q	2.851	1.00
232_R	236_L	2.799	1.00
92_R	95_R	2.683	1.00
172_A	188_P	2.678	1.00
13_W	17_A	2.464	1.00
67_Y	97_K	2.461	1.00
273_S	277_T	2.249	1.00
79_R	82_F	2.214	1.00
214_K	218_E	2.183	1.00
294_T	298_L	2.149	1.00
233_F	236_L	2.099	1.00
12_A	90_L	2.081	1.00
33_T	47_A	2.073	1.00
293_R	297_L	2.073	1.00
120_V	124_V	2.043	1.00
215_D	218_E	2.036	1.00
291_L	294_T	2.002	1.00
63_F	103_T	1.992	1.00
293_R	296_Q	1.970	1.00
68_Y	138_G	1.888	1.00
72_R	222_K	1.866	1.00
22_L	55_A	1.866	1.00
101_Y	105_A	1.836	1.00
15_M	90_L	1.813	1.00
236_L	240_G	1.813	1.00
49_A	110_D	1.809	1.00
291_L	295_G	1.808	1.00
271_A	274_V	1.797	1.00
56_L	106_A	1.791	1.00
57_I	107_A	1.773	1.00
188_P	191_A	1.759	1.00
260_S	264_P	1.748	1.00
121_P	125_I	1.747	1.00
98_Q	102_V	1.741	1.00
276_K	280_E	1.734	1.00
298_L	302_S	1.727	1.00
261_V	265_L	1.715	1.00
292_S	296_Q	1.709	1.00
229_F	233_F	1.695	1.00
297_L	301_Y	1.679	1.00
283_E	286_A	1.677	1.00
14_L	17_A	1.637	1.00
11_R	15_M	1.623	1.00
49_A	113_Y	1.613	1.00
295_G	298_L	1.611	1.00
270_L	273_S	1.606	1.00
91_I	96_V	1.599	1.00
218_E	227_V	1.597	1.00
272_V	276_K	1.592	1.00
43_A	46_P	1.589	1.00
287_L	291_L	1.566	1.00
63_F	99_A	1.565	1.00
275_T	279_F	1.541	1.00
125_I	129_S	1.536	1.00
214_K	231_Y	1.526	1.00
272_V	275_T	1.520	1.00
13_W	95_R	1.507	1.00
294_T	297_L	1.449	1.00
268_L	271_A	1.440	1.00
246_Y	267_T	1.438	1.00
243_V	247_A	1.434	1.00
290_A	293_R	1.433	1.00
293_R	298_L	1.431	1.00
291_L	298_L	1.428	1.00
30_V	51_L	1.427	1.00
295_G	299_A	1.408	1.00
292_S	295_G	1.399	1.00
74_A	87_A	1.384	1.00
119_G	122_I	1.380	1.00
59_I	103_T	1.378	1.00
298_L	301_Y	1.367	1.00
296_Q	299_A	1.365	1.00
214_K	227_V	1.358	1.00
121_P	124_V	1.342	1.00
24_A	205_I	1.339	1.00
13_W	99_A	1.336	1.00
67_Y	96_V	1.331	1.00
264_P	267_T	1.330	1.00
56_L	103_T	1.322	1.00
226_A	234_S	1.320	1.00
147_G	228_R	1.315	1.00
163_T	195_S	1.308	1.00
56_L	107_A	1.304	1.00
93_P	97_K	1.298	1.00
274_V	277_T	1.289	1.00
143_L	146_H	1.274	1.00
269_P	273_S	1.268	1.00
166_Y	170_A	1.259	1.00
233_F	237_E	1.255	1.00
109_L	113_Y	1.250	1.00
271_A	275_T	1.246	1.00
75_D	220_T	1.245	1.00
290_A	294_T	1.241	1.00
121_P	129_S	1.237	1.00
64_A	100_M	1.232	1.00
33_T	169_Q	1.224	1.00
270_L	274_V	1.210	1.00
211_I	234_S	1.201	1.00
288_N	292_S	1.194	1.00
286_A	289_P	1.173	1.00
112_V	123_L	1.165	1.00
237_E	241_L	1.152	1.00
32_G	36_A	1.152	1.00
17_A	103_T	1.144	1.00
124_V	128_A	1.139	1.00
270_L	277_T	1.131	1.00
276_K	279_F	1.125	1.00
223_R	228_R	1.105	1.00
97_K	101_Y	1.103	1.00
94_A	97_K	1.096	1.00
261_V	264_P	1.087	1.00
294_T	302_S	1.087	1.00
144_G	222_K	1.073	1.00
294_T	301_Y	1.071	1.00
258_G	261_V	1.070	1.00
126_G	129_S	1.064	1.00
26_A	30_V	1.053	1.00
296_Q	302_S	1.049	1.00
260_S	263_L	1.048	1.00
63_F	100_M	1.044	1.00
200_A	241_L	1.042	1.00
17_A	63_F	1.038	1.00
52_V	110_D	1.038	1.00
291_L	297_L	1.038	1.00
99_A	103_T	1.034	1.00
274_V	279_F	1.033	1.00
296_Q	304_L	1.031	1.00
48_V	52_V	1.027	1.00
289_P	292_S	1.027	1.00
187_V	192_V	1.026	1.00
70_A	74_A	1.025	1.00
275_T	278_V	1.023	1.00
132_S	156_F	1.022	1.00
290_A	297_L	1.017	1.00
10_Q	14_L	1.014	1.00
53_G	110_D	1.009	1.00
262_F	265_L	1.008	1.00
297_L	300_A	1.008	1.00
260_S	267_T	1.002	1.00
111_G	114_L	0.997	1.00
241_L	245_A	0.995	1.00
17_A	59_I	0.995	1.00
236_L	239_A	0.992	1.00
197_P	248_A	0.991	1.00
166_Y	191_A	0.990	1.00
286_A	290_A	0.986	1.00
295_G	306_A	0.980	1.00
69_D	145_Y	0.978	1.00
16_A	96_V	0.975	1.00
76_T	216_E	0.973	1.00
290_A	301_Y	0.972	1.00
289_P	293_R	0.965	1.00
42_L	47_A	0.961	1.00
244_V	248_A	0.958	1.00
29_V	54_A	0.958	1.00
192_V	196_L	0.952	1.00
225_L	229_F	0.951	1.00
301_Y	306_A	0.951	1.00
238_Y	242_L	0.950	1.00
158_G	202_S	0.947	1.00
245_A	249_P	0.946	1.00
135_T	152_F	0.945	1.00
301_Y	304_L	0.945	1.00
189_L	192_V	0.944	1.00
123_L	127_L	0.943	1.00
297_L	304_L	0.942	1.00
290_A	296_Q	0.942	1.00
296_Q	300_A	0.939	1.00
290_A	298_L	0.939	1.00
112_V	120_V	0.939	1.00
297_L	302_S	0.938	1.00
143_L	152_F	0.936	1.00
45_W	49_A	0.933	1.00
295_G	302_S	0.925	1.00
294_T	300_A	0.923	1.00
86_T	96_V	0.922	1.00
285_A	289_P	0.921	1.00
284_G	287_L	0.920	1.00
295_G	301_Y	0.916	1.00
279_F	282_T	0.910	1.00
296_Q	301_Y	0.908	1.00
268_L	272_V	0.907	1.00
26_A	51_L	0.906	1.00
288_N	291_L	0.897	1.00
67_Y	100_M	0.897	1.00
213_D	217_D	0.893	1.00
239_A	243_V	0.891	1.00
122_I	125_I	0.887	1.00
258_G	262_F	0.887	1.00
215_D	219_T	0.879	1.00
214_K	226_A	0.877	1.00
69_D	72_R	0.876	1.00
187_V	191_A	0.868	1.00
70_A	86_T	0.867	1.00
120_V	123_L	0.865	1.00
240_G	244_V	0.865	1.00
284_G	288_N	0.864	1.00
248_A	252_F	0.864	1.00
207_V	237_E	0.863	1.00
273_S	276_K	0.862	1.00
231_Y	235_R	0.862	1.00
287_L	294_T	0.856	1.00
275_T	280_E	0.856	1.00
287_L	290_A	0.854	1.00
29_V	50_A	0.853	1.00
122_I	167_Y	0.851	1.00
104_F	130_V	0.849	1.00
278_V	281_R	0.848	1.00
95_R	98_Q	0.847	1.00
135_T	143_L	0.846	1.00
111_G	126_G	0.846	1.00
17_A	99_A	0.839	1.00
134_I	138_G	0.835	1.00
188_P	192_V	0.833	1.00
49_A	114_L	0.831	1.00
301_Y	305_F	0.830	1.00
16_A	63_F	0.828	1.00
143_L	147_G	0.825	1.00
237_E	240_G	0.822	1.00
292_S	298_L	0.821	1.00
283_E	287_L	0.819	1.00
105_A	109_L	0.812	1.00
272_V	279_F	0.800	1.00
71_V	75_D	0.799	1.00
263_L	267_T	0.794	1.00
108_I	112_V	0.794	1.00
110_D	114_L	0.792	1.00
266_V	269_P	0.790	1.00
81_G	84_R	0.789	1.00
297_L	303_A	0.788	1.00
210_N	226_A	0.786	1.00
172_A	190_A	0.783	1.00
292_S	299_A	0.782	1.00
232_R	235_R	0.781	1.00
127_L	131_A	0.778	1.00
235_R	238_Y	0.777	1.00
296_Q	303_A	0.772	1.00
294_T	299_A	0.772	1.00
241_L	244_V	0.771	1.00
63_F	91_I	0.768	1.00
211_I	233_F	0.768	1.00
274_V	278_V	0.768	1.00
63_F	96_V	0.765	1.00
44_V	48_V	0.765	1.00
61_T	133_G	0.762	1.00
91_I	99_A	0.761	1.00
215_D	231_Y	0.761	1.00
250_L	254_A	0.761	1.00
25_A	58_Q	0.760	1.00
13_W	16_A	0.760	1.00
204_N	241_L	0.756	1.00
286_A	293_R	0.752	1.00
34_A	306_A	0.749	1.00
153_V	206_I	0.745	1.00
137_T	145_Y	0.743	1.00
102_V	106_A	0.740	1.00
265_L	269_P	0.738	1.00
158_G	198_V	0.736	1.00
293_R	300_A	0.736	1.00
299_A	303_A	0.733	1.00
196_L	248_A	0.732	1.00
293_R	299_A	0.731	1.00
72_R	145_Y	0.729	1.00
64_A	68_Y	0.728	1.00
198_V	202_S	0.728	1.00
72_R	220_T	0.728	1.00
295_G	304_L	0.727	1.00
159_V	195_S	0.725	1.00
196_L	200_A	0.724	1.00
71_V	93_P	0.724	1.00
126_G	130_V	0.724	1.00
247_A	251_W	0.720	1.00
293_R	303_A	0.718	1.00
156_F	195_S	0.717	1.00
269_P	276_K	0.717	1.00
52_V	56_L	0.713	1.00
253_Y	262_F	0.713	1.00
131_A	135_T	0.707	1.00
211_I	231_Y	0.706	1.00
292_S	297_L	0.702	1.00
211_I	235_R	0.696	0.99
291_L	302_S	0.694	0.99
150_D	210_N	0.693	0.99
285_A	288_N	0.693	0.99
249_P	252_F	0.688	0.99
284_G	291_L	0.687	0.99
64_A	134_I	0.687	0.99
290_A	295_G	0.685	0.99
79_R	83_T	0.682	0.99
246_Y	249_P	0.678	0.99
289_P	297_L	0.676	0.99
14_L	19_P	0.675	0.99
111_G	123_L	0.674	0.99
150_D	224_T	0.674	0.99
295_G	305_F	0.672	0.99
24_A	28_P	0.672	0.99
45_W	48_V	0.671	0.99
205_I	209_N	0.668	0.99
95_R	99_A	0.667	0.99
297_L	305_F	0.666	0.99
234_S	238_Y	0.664	0.99
85_V	90_L	0.663	0.99
97_K	100_M	0.663	0.99
284_G	289_P	0.659	0.99
91_I	95_R	0.659	0.99
291_L	301_Y	0.658	0.99
264_P	268_L	0.658	0.99
242_L	245_A	0.657	0.99
235_R	239_A	0.656	0.99
299_A	302_S	0.654	0.99
144_G	150_D	0.654	0.99
165_T	168_V	0.650	0.99
13_W	18_R	0.650	0.99
270_L	276_K	0.649	0.99
154_F	159_V	0.649	0.99
56_L	110_D	0.646	0.99
271_A	278_V	0.646	0.99
267_T	270_L	0.638	0.99
148_L	229_F	0.635	0.99
157_F	202_S	0.634	0.99
269_P	272_V	0.633	0.99
69_D	137_T	0.633	0.99
300_A	305_F	0.630	0.99
296_Q	306_A	0.628	0.99
293_R	301_Y	0.627	0.99
100_M	104_F	0.623	0.99
84_R	87_A	0.622	0.99
272_V	277_T	0.621	0.99
282_T	285_A	0.621	0.99
283_E	291_L	0.620	0.99
271_A	276_K	0.617	0.99
163_T	191_A	0.616	0.99
204_N	242_L	0.616	0.99
250_L	253_Y	0.612	0.99
59_I	63_F	0.610	0.99
292_S	301_Y	0.609	0.99
190_A	255_T	0.607	0.99
201_I	245_A	0.603	0.99
289_P	294_T	0.602	0.99
287_L	295_G	0.600	0.98
60_A	103_T	0.600	0.98
67_Y	86_T	0.600	0.98
89_G	95_R	0.598	0.98
271_A	277_T	0.598	0.98
86_T	91_I	0.597	0.98
31_V	194_A	0.593	0.98
266_V	270_L	0.590	0.98
298_L	305_F	0.589	0.98
206_I	209_N	0.588	0.98
60_A	100_M	0.588	0.98
238_Y	245_A	0.588	0.98
84_R	89_G	0.587	0.98
68_Y	137_T	0.586	0.98
197_P	249_P	0.585	0.98
203_T	241_L	0.584	0.98
286_A	291_L	0.578	0.98
253_Y	256_G	0.577	0.98
12_A	17_A	0.574	0.98
46_P	114_L	0.573	0.98
261_V	267_T	0.571	0.98
291_L	299_A	0.570	0.98
35_L	166_Y	0.570	0.98
87_A	90_L	0.566	0.98
272_V	280_E	0.565	0.98
60_A	107_A	0.565	0.98
270_L	275_T	0.563	0.98
87_A	96_V	0.563	0.98
34_A	37_V	0.556	0.98
79_R	215_D	0.555	0.97
104_F	107_A	0.552	0.97
124_V	127_L	0.551	0.97
69_D	222_K	0.551	0.97
33_T	50_A	0.549	0.97
85_V	89_G	0.547	0.97
158_G	199_A	0.546	0.97
31_V	198_V	0.542	0.97
32_G	165_T	0.541	0.97
59_I	99_A	0.535	0.97
292_S	304_L	0.535	0.97
273_S	280_E	0.534	0.97
57_I	133_G	0.529	0.97
217_D	224_T	0.529	0.97
291_L	304_L	0.529	0.97
83_T	90_L	0.529	0.97
288_N	295_G	0.528	0.97
128_A	132_S	0.525	0.96
21_T	62_N	0.521	0.96
67_Y	70_A	0.516	0.96
281_R	286_A	0.515	0.96
125_I	128_A	0.514	0.96
58_Q	62_N	0.514	0.96
27_A	302_S	0.509	0.96
302_S	306_A	0.508	0.96
222_K	227_V	0.508	0.96
33_T	37_V	0.507	0.96
166_Y	188_P	0.506	0.96
33_T	42_L	0.506	0.96
50_A	169_Q	0.505	0.96
193_V	252_F	0.505	0.96
229_F	237_E	0.504	0.96
287_L	292_S	0.504	0.96
298_L	304_L	0.503	0.96
129_S	132_S	0.502	0.96
36_A	169_Q	0.501	0.95
108_I	123_L	0.501	0.95
45_W	113_Y	0.501	0.95
60_A	134_I	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
4od4A	1	0.8714	100	0.34	Contact Map
4tq3A	1	0.881	100	0.342	Contact Map
2onkC	2	0.2315	8.7	0.955	Contact Map
2xq2A	2	0.7524	6.3	0.958	Contact Map
3tx3A	2	0.5981	6.1	0.958	Contact Map
3o7qA	1	0.8135	4.9	0.96	Contact Map
2kogA	1	0.1286	4.4	0.961	Contact Map
2cfqA	1	0.4759	4.3	0.961	Contact Map
1pw4A	1	0.8296	3.4	0.963	Contact Map
1m56D	1	0.1158	2.9	0.964	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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