Q9HMA0 - HALSA - GREMLIN Contacts

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Q9HMA0 - Geranylgeranyl hydrogenase

UniProt:	Q9HMA0	Sequences: MMYDFVVVGVGPAGARFARRAAQQGYDVIAFEQGDLGTPLACSGHVSLDVWEFVPDEHHDALFQNDIRGARFHLGGADSSAHPFYKSTPISNAIDRVHLDEVLAEAARDAGADVREHHTVTDVTEHRNRVTVTARGPDDSIDVTAKMVAGSDGPRSRVRDALSLPEPDEFLHGALAFDPDPDHQDFVDVHLTVPGFFAWRIPRGDAGVEYGLAAAPGEDVAGRFDDLVADYGVDVEHRCSGLIPIGPPDTVTSHRGFLLGDAAGQTKPFTGGGIRYGMTAADAAARELDPDRPGTLAGYERAWRDALEREITLGHLVRAGYSMPTPIQSAGLRLFSGEIAVDMDKPTSLFSLDQARALLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	360 (316)
Sequences:	29843 (22733)
Seq/√Len:	1278.8

ECOLI - UBIH UBIF MHPA UBII FIXC YDIS CBRA YGCN
BACSU - YHJG YETM
HALSA - Q9HMA0 Q9HS24 Q9HS01 Q9HQE5
SULSO - Q97V18 Q97V59 Q97W89 Q97ZK8 Q97W83

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_I	115_R	3.927	1.00
33_Q	119_T	3.431	1.00
13_A	277_G	3.313	1.00
4_D	27_D	3.213	1.00
4_D	146_K	3.053	1.00
6_V	145_A	2.990	1.00
300_E	304_R	2.882	1.00
136_G	141_I	2.806	1.00
119_T	135_R	2.723	1.00
122_D	161_A	2.545	1.00
17_F	149_A	2.437	1.00
31_F	143_V	2.433	1.00
118_H	136_G	2.369	1.00
6_V	132_V	2.358	1.00
106_A	109_D	2.336	1.00
122_D	133_T	2.321	1.00
133_T	142_D	2.261	1.00
6_V	31_F	2.244	1.00
62_L	105_E	2.243	1.00
20_R	285_A	2.215	1.00
131_T	144_T	2.211	1.00
121_T	135_R	2.182	1.00
124_T	131_T	2.157	1.00
24_Q	289_D	2.156	1.00
131_T	142_D	2.051	1.00
101_E	105_E	2.023	1.00
118_H	134_A	2.000	1.00
27_D	113_D	1.982	1.00
16_R	278_M	1.978	1.00
220_V	223_R	1.970	1.00
13_A	259_L	1.917	1.00
221_A	225_D	1.916	1.00
134_A	143_V	1.915	1.00
225_D	229_A	1.898	1.00
124_T	133_T	1.876	1.00
150_G	158_V	1.857	1.00
115_R	118_H	1.850	1.00
5_F	26_Y	1.805	1.00
126_H	129_R	1.775	1.00
219_D	223_R	1.775	1.00
106_A	110_A	1.756	1.00
287_E	302_A	1.750	1.00
281_A	285_A	1.743	1.00
126_H	144_T	1.737	1.00
126_H	131_T	1.725	1.00
55_P	60_D	1.725	1.00
31_F	134_A	1.711	1.00
151_S	259_L	1.708	1.00
118_H	141_I	1.704	1.00
150_G	258_L	1.697	1.00
115_R	141_I	1.693	1.00
4_D	29_I	1.686	1.00
120_V	132_V	1.682	1.00
250_T	253_S	1.674	1.00
19_R	106_A	1.674	1.00
134_A	140_S	1.671	1.00
252_T	297_A	1.661	1.00
223_R	226_D	1.646	1.00
224_F	228_V	1.633	1.00
53_F	282_D	1.626	1.00
136_G	140_S	1.626	1.00
26_Y	289_D	1.609	1.00
304_R	308_E	1.600	1.00
5_F	21_A	1.591	1.00
135_R	140_S	1.586	1.00
6_V	143_V	1.571	1.00
287_E	298_G	1.568	1.00
23_Q	110_A	1.547	1.00
22_A	112_A	1.543	1.00
12_P	274_I	1.534	1.00
29_I	143_V	1.530	1.00
152_D	156_S	1.527	1.00
123_V	148_V	1.527	1.00
107_A	112_A	1.515	1.00
62_L	65_N	1.515	1.00
62_L	106_A	1.499	1.00
252_T	257_F	1.487	1.00
134_A	141_I	1.458	1.00
18_A	30_A	1.441	1.00
50_V	275_R	1.441	1.00
222_G	226_D	1.438	1.00
283_A	287_E	1.430	1.00
62_L	109_D	1.421	1.00
19_R	23_Q	1.420	1.00
56_D	282_D	1.408	1.00
222_G	225_D	1.403	1.00
125_E	253_S	1.403	1.00
17_F	281_A	1.399	1.00
77_A	80_S	1.396	1.00
147_M	296_L	1.396	1.00
224_F	227_L	1.385	1.00
124_T	142_D	1.378	1.00
35_D	117_H	1.369	1.00
61_A	65_N	1.364	1.00
257_F	284_A	1.363	1.00
157_R	161_A	1.358	1.00
104_A	116_E	1.348	1.00
7_V	17_F	1.346	1.00
279_T	306_A	1.341	1.00
286_R	302_A	1.314	1.00
60_D	64_Q	1.314	1.00
105_E	108_R	1.311	1.00
283_A	302_A	1.305	1.00
129_R	144_T	1.303	1.00
226_D	230_D	1.302	1.00
280_A	303_W	1.294	1.00
149_A	259_L	1.285	1.00
8_V	152_D	1.281	1.00
104_A	108_R	1.280	1.00
20_R	57_E	1.276	1.00
218_E	223_R	1.275	1.00
245_I	315_H	1.269	1.00
226_D	229_A	1.265	1.00
250_T	300_E	1.263	1.00
133_T	140_S	1.246	1.00
145_A	148_V	1.242	1.00
186_F	189_V	1.235	1.00
225_D	228_V	1.231	1.00
251_V	307_L	1.228	1.00
19_R	107_A	1.228	1.00
162_L	256_G	1.228	1.00
251_V	300_E	1.227	1.00
235_V	238_R	1.216	1.00
157_R	160_D	1.203	1.00
81_A	84_F	1.201	1.00
74_L	77_A	1.195	1.00
19_R	110_A	1.188	1.00
17_F	21_A	1.185	1.00
67_I	72_F	1.184	1.00
115_R	143_V	1.182	1.00
223_R	228_V	1.176	1.00
149_A	257_F	1.174	1.00
6_V	29_I	1.168	1.00
4_D	26_Y	1.163	1.00
121_T	140_S	1.162	1.00
187_V	190_H	1.160	1.00
264_G	280_A	1.147	1.00
219_D	222_G	1.142	1.00
8_V	120_V	1.141	1.00
120_V	158_V	1.139	1.00
165_P	249_D	1.139	1.00
50_V	278_M	1.139	1.00
74_L	78_D	1.126	1.00
287_E	295_T	1.105	1.00
176_A	179_P	1.096	1.00
120_V	123_V	1.096	1.00
29_I	113_D	1.091	1.00
125_E	255_R	1.085	1.00
121_T	133_T	1.083	1.00
10_V	15_A	1.067	1.00
252_T	300_E	1.055	1.00
22_A	110_A	1.050	1.00
219_D	228_V	1.049	1.00
8_V	158_V	1.042	1.00
41_A	44_G	1.037	1.00
44_G	274_I	1.037	1.00
23_Q	106_A	1.035	1.00
223_R	227_L	1.035	1.00
61_A	64_Q	1.035	1.00
186_F	190_H	1.031	1.00
287_E	290_P	1.029	1.00
173_G	176_A	1.023	1.00
130_V	255_R	1.013	1.00
37_G	116_E	1.006	1.00
16_R	20_R	1.001	1.00
22_A	111_G	1.000	1.00
31_F	115_R	0.997	1.00
123_V	161_A	0.992	1.00
7_V	18_A	0.990	1.00
298_G	301_R	0.986	1.00
31_F	118_H	0.985	1.00
98_H	101_E	0.980	1.00
218_E	222_G	0.978	1.00
221_A	228_V	0.972	1.00
67_I	70_A	0.972	1.00
164_L	248_P	0.971	1.00
253_S	256_G	0.971	1.00
173_G	178_D	0.966	1.00
28_V	112_A	0.955	1.00
132_V	145_A	0.952	1.00
258_L	262_A	0.951	1.00
59_H	106_A	0.951	1.00
104_A	114_V	0.950	1.00
252_T	293_P	0.945	1.00
30_A	114_V	0.936	1.00
218_E	228_V	0.935	1.00
95_D	98_H	0.930	1.00
8_V	148_V	0.929	1.00
154_P	265_Q	0.926	1.00
293_P	297_A	0.922	1.00
125_E	130_V	0.920	1.00
105_E	109_D	0.917	1.00
123_V	162_L	0.916	1.00
17_F	259_L	0.908	1.00
183_H	187_V	0.907	1.00
19_R	57_E	0.900	1.00
266_T	276_Y	0.899	1.00
171_L	175_L	0.895	1.00
16_R	57_E	0.892	1.00
188_D	191_L	0.889	1.00
169_E	173_G	0.886	1.00
56_D	286_R	0.883	1.00
183_H	186_F	0.883	1.00
172_H	176_A	0.882	1.00
171_L	176_A	0.880	1.00
62_L	102_V	0.876	1.00
7_V	28_V	0.873	1.00
130_V	148_V	0.871	1.00
125_E	254_H	0.871	1.00
283_A	286_R	0.869	1.00
209_E	213_A	0.869	1.00
297_A	301_R	0.867	1.00
180_D	183_H	0.867	1.00
49_D	279_T	0.863	1.00
266_T	311_I	0.862	1.00
308_E	312_T	0.849	1.00
290_P	298_G	0.848	1.00
175_L	178_D	0.848	1.00
96_R	100_D	0.843	1.00
18_A	28_V	0.842	1.00
120_V	157_R	0.841	1.00
220_V	224_F	0.839	1.00
199_W	211_G	0.839	1.00
120_V	161_A	0.832	1.00
184_Q	187_V	0.829	1.00
315_H	319_A	0.828	1.00
257_F	299_Y	0.822	1.00
59_H	102_V	0.821	1.00
108_R	113_D	0.821	1.00
147_M	257_F	0.820	1.00
102_V	106_A	0.817	1.00
232_G	235_V	0.814	1.00
15_A	107_A	0.813	1.00
51_W	60_D	0.811	1.00
156_S	159_R	0.809	1.00
22_A	107_A	0.808	1.00
4_D	145_A	0.808	1.00
167_P	249_D	0.801	1.00
52_E	55_P	0.799	1.00
219_D	224_F	0.799	1.00
21_A	26_Y	0.798	1.00
187_V	191_L	0.796	1.00
259_L	299_Y	0.794	1.00
15_A	104_A	0.794	1.00
218_E	224_F	0.792	1.00
108_R	111_G	0.791	1.00
18_A	112_A	0.786	1.00
42_C	96_R	0.785	1.00
218_E	225_D	0.782	1.00
150_G	256_G	0.782	1.00
44_G	96_R	0.778	1.00
252_T	296_L	0.778	1.00
132_V	148_V	0.777	1.00
10_V	32_E	0.777	1.00
25_G	28_V	0.775	1.00
298_G	302_A	0.774	1.00
51_W	92_N	0.771	1.00
63_F	102_V	0.769	1.00
169_E	172_H	0.767	1.00
285_A	289_D	0.766	1.00
248_P	258_L	0.765	1.00
221_A	224_F	0.764	1.00
248_P	251_V	0.762	1.00
149_A	284_A	0.762	1.00
107_A	111_G	0.755	1.00
49_D	272_G	0.753	1.00
20_R	24_Q	0.752	1.00
102_V	105_E	0.752	1.00
193_V	196_F	0.751	1.00
70_A	74_L	0.750	1.00
20_R	23_Q	0.750	1.00
15_A	100_D	0.748	1.00
184_Q	190_H	0.747	1.00
29_I	145_A	0.745	1.00
12_P	278_M	0.741	1.00
183_H	190_H	0.739	1.00
172_H	178_D	0.739	1.00
220_V	225_D	0.731	1.00
175_L	179_P	0.731	1.00
251_V	263_A	0.726	1.00
158_V	161_A	0.725	1.00
251_V	304_R	0.724	1.00
50_V	53_F	0.721	1.00
32_E	116_E	0.718	1.00
49_D	52_E	0.718	1.00
22_A	108_R	0.717	1.00
123_V	158_V	0.715	1.00
45_H	91_S	0.715	1.00
208_V	211_G	0.713	1.00
31_F	145_A	0.710	1.00
125_E	129_R	0.704	1.00
218_E	221_A	0.703	1.00
210_Y	213_A	0.703	1.00
270_T	314_G	0.701	1.00
70_A	75_G	0.699	1.00
174_A	177_F	0.699	1.00
37_G	104_A	0.698	1.00
21_A	288_L	0.697	1.00
258_L	263_A	0.696	1.00
150_G	156_S	0.693	1.00
282_D	286_R	0.693	1.00
95_D	204_G	0.691	1.00
302_A	305_D	0.687	1.00
45_H	93_A	0.686	1.00
54_V	278_M	0.684	1.00
94_I	99_L	0.684	1.00
174_A	178_D	0.682	1.00
21_A	285_A	0.679	1.00
265_Q	280_A	0.678	1.00
172_H	175_L	0.677	1.00
219_D	227_L	0.676	1.00
22_A	113_D	0.676	1.00
22_A	28_V	0.675	1.00
69_G	81_A	0.672	1.00
20_R	53_F	0.672	1.00
247_P	304_R	0.671	1.00
220_V	227_L	0.671	1.00
4_D	143_V	0.671	1.00
63_F	99_L	0.669	1.00
266_T	270_T	0.666	1.00
170_F	173_G	0.666	1.00
158_V	256_G	0.665	1.00
100_D	104_A	0.664	1.00
123_V	256_G	0.660	1.00
170_F	176_A	0.659	1.00
49_D	306_A	0.657	1.00
67_I	73_H	0.657	1.00
71_R	79_S	0.656	1.00
75_G	78_D	0.651	1.00
220_V	228_V	0.648	1.00
150_G	162_L	0.648	1.00
266_T	314_G	0.647	1.00
182_D	185_D	0.643	1.00
272_G	276_Y	0.643	1.00
171_L	315_H	0.639	1.00
18_A	107_A	0.638	1.00
73_H	79_S	0.637	1.00
181_P	184_Q	0.634	1.00
51_W	55_P	0.630	1.00
54_V	59_H	0.630	1.00
98_H	204_G	0.628	1.00
173_G	179_P	0.628	1.00
301_R	305_D	0.627	1.00
155_R	160_D	0.626	1.00
27_D	146_K	0.625	1.00
31_F	132_V	0.625	1.00
16_R	103_L	0.624	1.00
186_F	191_L	0.623	1.00
224_F	229_A	0.619	1.00
185_D	188_D	0.617	1.00
150_G	157_R	0.616	1.00
162_L	253_S	0.616	1.00
305_D	309_R	0.615	1.00
184_Q	188_D	0.614	1.00
219_D	225_D	0.613	1.00
148_V	256_G	0.613	1.00
60_D	63_F	0.612	1.00
54_V	99_L	0.604	1.00
164_L	253_S	0.602	1.00
182_D	186_F	0.601	1.00
36_L	40_L	0.599	1.00
231_Y	234_D	0.597	1.00
152_D	258_L	0.596	1.00
210_Y	214_A	0.596	1.00
227_L	230_D	0.594	1.00
247_P	308_E	0.594	1.00
168_D	171_L	0.594	1.00
307_L	311_I	0.594	1.00
159_R	162_L	0.593	1.00
171_L	177_F	0.592	1.00
15_A	114_V	0.588	1.00
317_V	320_G	0.586	1.00
246_G	249_D	0.586	1.00
279_T	283_A	0.584	1.00
119_T	157_R	0.583	1.00
19_R	22_A	0.582	1.00
269_F	318_R	0.582	1.00
34_G	40_L	0.581	1.00
36_L	116_E	0.580	1.00
254_H	293_P	0.578	1.00
53_F	57_E	0.577	1.00
19_R	112_A	0.575	1.00
167_P	176_A	0.575	1.00
294_G	298_G	0.568	1.00
170_F	175_L	0.568	1.00
71_R	80_S	0.568	1.00
222_G	228_V	0.567	1.00
17_F	288_L	0.563	1.00
124_T	127_R	0.563	1.00
238_R	242_L	0.562	1.00
159_R	258_L	0.562	1.00
277_G	281_A	0.561	1.00
218_E	227_L	0.561	1.00
55_P	64_Q	0.561	1.00
312_T	316_L	0.560	1.00
272_G	275_R	0.559	1.00
182_D	187_V	0.559	1.00
180_D	190_H	0.559	1.00
148_V	255_R	0.558	1.00
169_E	176_A	0.558	1.00
58_H	61_A	0.558	1.00
184_Q	189_V	0.558	1.00
173_G	177_F	0.556	1.00
73_H	78_D	0.556	1.00
15_A	30_A	0.555	1.00
46_V	50_V	0.554	1.00
120_V	134_A	0.553	1.00
183_H	188_D	0.553	1.00
234_D	238_R	0.551	1.00
66_D	70_A	0.550	1.00
185_D	189_V	0.550	1.00
279_T	303_W	0.550	1.00
76_G	79_S	0.549	1.00
259_L	277_G	0.547	1.00
180_D	184_Q	0.547	1.00
24_Q	285_A	0.546	1.00
180_D	185_D	0.546	1.00
37_G	100_D	0.546	1.00
225_D	230_D	0.545	1.00
261_D	273_G	0.545	1.00
259_L	281_A	0.545	1.00
47_S	275_R	0.544	1.00
20_R	281_A	0.544	1.00
118_H	135_R	0.544	1.00
274_I	277_G	0.544	1.00
270_T	317_V	0.543	1.00
17_F	20_R	0.540	1.00
284_A	288_L	0.538	1.00
247_P	251_V	0.538	1.00
71_R	74_L	0.538	1.00
28_V	111_G	0.537	1.00
264_G	303_W	0.537	1.00
17_F	285_A	0.535	1.00
171_L	174_A	0.533	1.00
274_I	278_M	0.532	1.00
74_L	80_S	0.531	1.00
182_D	189_V	0.531	1.00
257_F	296_L	0.530	1.00
246_G	251_V	0.530	1.00
209_E	214_A	0.530	1.00
183_H	189_V	0.530	1.00
5_F	147_M	0.528	1.00
20_R	282_D	0.528	1.00
73_H	76_G	0.527	1.00
276_Y	310_E	0.526	1.00
297_A	300_E	0.526	1.00
170_F	174_A	0.525	1.00
172_H	177_F	0.524	1.00
276_Y	307_L	0.523	1.00
180_D	189_V	0.523	1.00
152_D	158_V	0.521	1.00
209_E	212_L	0.521	1.00
199_W	203_R	0.520	1.00
148_V	158_V	0.519	1.00
159_R	164_L	0.518	1.00
66_D	69_G	0.517	1.00
45_H	271_G	0.516	1.00
294_G	297_A	0.516	1.00
147_M	288_L	0.515	1.00
197_F	201_I	0.514	1.00
149_A	288_L	0.512	1.00
185_D	191_L	0.511	1.00
181_P	185_D	0.510	1.00
107_A	114_V	0.510	1.00
28_V	107_A	0.510	1.00
123_V	130_V	0.508	1.00
5_F	17_F	0.508	1.00
174_A	179_P	0.507	1.00
169_E	178_D	0.507	1.00
34_G	38_T	0.506	1.00
10_V	30_A	0.506	1.00
267_K	270_T	0.504	1.00
17_F	284_A	0.501	1.00
16_R	54_V	0.500	1.00

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
2qa1A	2	0.9861	100	0.312	Contact Map
2qa2A	2	0.9889	100	0.316	Contact Map
4k5sA	2	0.9944	100	0.317	Contact Map
4n9xA	5	0.9278	100	0.327	Contact Map
4k2xA	2	0.975	100	0.334	Contact Map
1pn0A	3	0.9833	100	0.339	Contact Map
1k0iA	2	0.9944	100	0.35	Contact Map
2dkhA	2	0.9361	100	0.351	Contact Map
2x3nA	1	0.9028	100	0.353	Contact Map
4k22A	4	0.8833	100	0.362	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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