DHNA - ECOLI - GREMLIN Contacts

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DHNA - NADH dehydrogenase

UniProt:	P00393	Sequences: MTTPLKKIVIVGGGAGGLEMATQLGHKLGRKKKAKITLVDRNHSHLWKPLLHEVATGSLDEGVDALSYLAHARNHGFQFQLGSVIDIDREAKTITIAELRDEKGELLVPERKIAYDTLVMALGSTSNDFNTPGVKENCIFLDNPHQARRFHQEMLNLFLKYSANLGANGKVNIAIVGGGATGVELSAELHNAVKQLHSYGYKGLTNEALNVTLVEAGERILPALPPRISAAAHNELTKLGVRVLTQTMVTSADEGGLHTKDGEYIEADLMVWAAGIKAPDFLKDIGGLETNRINQLVVEPTLQTTRDPDIYAIGDCASCPRPEGGFVPPRAQAAHQMATCAMNNILAQMNGKPLKNYQYKDHGSLVSLSNFSTVGSLMGNLTRGSMMIEGRIARFVYISLYRMHQIALHGYFKTGLMMLVGSINRVIRPRLKLH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10649
Length:	434 (340)
Sequences:	16530 (11700)
Seq/√Len:	634.5

ECOLI - DHNA HCAD RCLA STHA NORW GSHR DLDH NIRB TRXB PRET AHPF
BACSU - YUMB YJLD YUTJ DLDH2 DLDH1 DLDH3 NASB YPDA NASD DHNA TRXB FENR1 FENR2 CZCO
HALSA - Q9HR27 Q9HP48 Q9HSN0 DLDH P82854
SULSO - Q97WG1 Q97VJ3 Q97WE3 Q97YT2 Q97VD9 Q97UP4 Q97U72 Q97ZB4 Q97XZ3 Q97UV0 Q97Y24 Q97Z19 Q97V69 Q97W27 Q97Z14 Q97VQ4 FENR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_R	83_S	4.350	1.00
174_A	267_A	4.166	1.00
7_K	35_K	3.787	1.00
299_E	303_Q	3.787	1.00
92_K	309_D	3.594	1.00
93_T	112_K	3.393	1.00
172_N	210_N	3.327	1.00
212_T	244_L	3.242	1.00
210_N	242_R	3.016	1.00
233_H	237_T	2.737	1.00
216_A	248_M	2.599	1.00
95_T	112_K	2.597	1.00
89_R	307_D	2.590	1.00
251_S	258_H	2.572	1.00
20_M	119_V	2.544	1.00
88_D	91_A	2.510	1.00
132_P	251_S	2.497	1.00
289_E	297_V	2.454	1.00
39_V	113_I	2.424	1.00
244_L	263_E	2.413	1.00
7_K	37_T	2.397	1.00
127_N	277_K	2.388	1.00
253_D	258_H	2.288	1.00
93_T	114_A	2.230	1.00
117_T	309_D	2.195	1.00
212_T	242_R	2.175	1.00
16_G	313_I	2.169	1.00
9_V	94_I	2.148	1.00
35_K	78_Q	2.138	1.00
37_T	80_Q	2.080	1.00
6_K	37_T	2.079	1.00
172_N	212_T	2.068	1.00
9_V	113_I	2.065	1.00
174_A	214_V	2.052	1.00
89_R	310_I	2.032	1.00
10_I	21_A	2.022	1.00
218_E	246_Q	2.019	1.00
258_H	264_Y	2.007	1.00
86_D	95_T	1.980	1.00
125_T	277_K	1.977	1.00
5_L	116_D	1.974	1.00
95_T	110_E	1.952	1.00
97_A	110_E	1.890	1.00
7_K	116_D	1.886	1.00
115_Y	118_L	1.869	1.00
248_M	260_K	1.865	1.00
88_D	93_T	1.860	1.00
247_T	261_D	1.856	1.00
83_S	97_A	1.847	1.00
8_I	24_L	1.822	1.00
341_A	345_I	1.811	1.00
119_V	345_I	1.804	1.00
219_R	229_S	1.799	1.00
291_N	295_Q	1.776	1.00
117_T	311_Y	1.734	1.00
85_I	97_A	1.729	1.00
174_A	257_L	1.725	1.00
122_L	316_C	1.723	1.00
5_L	114_A	1.689	1.00
6_K	117_T	1.687	1.00
125_T	279_P	1.687	1.00
250_T	260_K	1.662	1.00
9_V	39_V	1.662	1.00
85_I	95_T	1.641	1.00
172_N	268_D	1.632	1.00
8_I	34_A	1.628	1.00
244_L	247_T	1.616	1.00
291_N	318_S	1.615	1.00
226_P	373_T	1.606	1.00
11_V	84_V	1.591	1.00
289_E	306_R	1.587	1.00
247_T	263_E	1.556	1.00
6_K	78_Q	1.551	1.00
11_V	120_M	1.551	1.00
296_L	312_A	1.519	1.00
233_H	245_T	1.514	1.00
80_Q	111_R	1.509	1.00
226_P	230_A	1.506	1.00
340_C	344_N	1.484	1.00
11_V	122_L	1.476	1.00
214_V	265_I	1.468	1.00
139_I	153_E	1.467	1.00
9_V	37_T	1.453	1.00
311_Y	344_N	1.431	1.00
370_N	375_G	1.424	1.00
235_E	238_K	1.421	1.00
178_G	220_I	1.413	1.00
190_H	241_V	1.413	1.00
267_A	270_M	1.406	1.00
183_V	213_L	1.392	1.00
303_Q	308_P	1.391	1.00
234_N	237_T	1.388	1.00
250_T	258_H	1.375	1.00
347_A	352_K	1.370	1.00
313_I	341_A	1.360	1.00
143_N	146_Q	1.358	1.00
253_D	264_Y	1.351	1.00
307_D	310_I	1.351	1.00
172_N	266_E	1.344	1.00
39_V	96_I	1.328	1.00
125_T	280_D	1.327	1.00
169_G	209_L	1.321	1.00
96_I	113_I	1.310	1.00
37_T	113_I	1.295	1.00
252_A	270_M	1.289	1.00
23_Q	343_N	1.287	1.00
82_G	96_I	1.281	1.00
375_G	382_T	1.275	1.00
338_A	342_M	1.274	1.00
215_E	245_T	1.261	1.00
178_G	215_E	1.257	1.00
219_R	226_P	1.251	1.00
370_N	378_M	1.249	1.00
234_N	238_K	1.245	1.00
7_K	114_A	1.244	1.00
96_I	111_R	1.235	1.00
291_N	297_V	1.212	1.00
118_L	310_I	1.210	1.00
171_V	268_D	1.207	1.00
9_V	115_Y	1.198	1.00
8_I	119_V	1.197	1.00
142_D	146_Q	1.190	1.00
125_T	281_F	1.173	1.00
69_L	73_R	1.170	1.00
259_T	265_I	1.169	1.00
256_G	264_Y	1.165	1.00
173_I	189_L	1.163	1.00
91_A	112_K	1.147	1.00
88_D	92_K	1.146	1.00
244_L	265_I	1.143	1.00
373_T	377_L	1.139	1.00
5_L	35_K	1.136	1.00
138_C	252_A	1.136	1.00
302_L	317_A	1.135	1.00
146_Q	149_R	1.133	1.00
119_V	313_I	1.132	1.00
191_N	239_L	1.119	1.00
120_M	316_C	1.117	1.00
235_E	239_L	1.111	1.00
80_Q	113_I	1.110	1.00
253_D	256_G	1.101	1.00
298_V	312_A	1.100	1.00
372_S	376_S	1.096	1.00
115_Y	309_D	1.082	1.00
86_D	285_I	1.080	1.00
301_T	344_N	1.078	1.00
16_G	334_A	1.078	1.00
233_H	243_V	1.070	1.00
298_V	317_A	1.070	1.00
82_G	109_P	1.069	1.00
220_I	245_T	1.065	1.00
117_T	345_I	1.065	1.00
190_H	210_N	1.063	1.00
82_G	97_A	1.059	1.00
137_N	254_E	1.047	1.00
280_D	284_D	1.038	1.00
327_V	333_A	1.033	1.00
176_V	270_M	1.033	1.00
386_M	389_E	1.031	1.00
173_I	269_L	1.030	1.00
10_I	17_G	1.025	1.00
88_D	95_T	1.024	1.00
39_V	84_V	1.020	1.00
64_D	67_S	1.018	1.00
96_I	109_P	1.014	1.00
37_T	78_Q	1.011	1.00
230_A	233_H	1.008	1.00
303_Q	309_D	1.003	1.00
40_D	79_F	0.998	1.00
25_G	77_F	0.998	1.00
312_A	316_C	0.995	1.00
23_Q	342_M	0.989	1.00
13_G	40_D	0.987	1.00
121_A	313_I	0.986	1.00
372_S	382_T	0.979	1.00
342_M	346_L	0.975	1.00
24_L	342_M	0.974	1.00
212_T	265_I	0.973	1.00
68_Y	71_H	0.971	1.00
150_F	269_L	0.971	1.00
214_V	244_L	0.970	1.00
68_Y	72_A	0.963	1.00
61_E	65_A	0.957	1.00
142_D	150_F	0.954	1.00
39_V	80_Q	0.954	1.00
215_E	222_P	0.949	1.00
219_R	233_H	0.946	1.00
65_A	68_Y	0.946	1.00
231_A	234_N	0.945	1.00
6_K	35_K	0.945	1.00
186_S	211_V	0.939	1.00
302_L	341_A	0.938	1.00
231_A	235_E	0.937	1.00
145_H	148_R	0.936	1.00
173_I	209_L	0.933	1.00
67_S	70_A	0.933	1.00
304_T	312_A	0.924	1.00
247_T	260_K	0.921	1.00
20_M	338_A	0.910	1.00
20_M	342_M	0.910	1.00
43_H	81_L	0.910	1.00
13_G	38_L	0.909	1.00
214_V	247_T	0.908	1.00
10_I	20_M	0.908	1.00
247_T	259_T	0.900	1.00
20_M	341_A	0.895	1.00
312_A	317_A	0.891	1.00
20_M	313_I	0.888	1.00
281_F	285_I	0.888	1.00
19_E	338_A	0.886	1.00
17_G	121_A	0.882	1.00
341_A	344_N	0.880	1.00
16_G	121_A	0.876	1.00
38_L	72_A	0.869	1.00
190_H	239_L	0.865	1.00
255_G	266_E	0.864	1.00
21_A	77_F	0.861	1.00
311_Y	348_Q	0.855	1.00
171_V	210_N	0.854	1.00
387_M	391_R	0.850	1.00
280_D	283_K	0.849	1.00
259_T	263_E	0.849	1.00
131_T	134_V	0.848	1.00
389_E	392_I	0.844	1.00
122_L	281_F	0.842	1.00
97_A	109_P	0.841	1.00
217_G	222_P	0.836	1.00
213_L	243_V	0.835	1.00
117_T	348_Q	0.829	1.00
67_S	72_A	0.825	1.00
297_V	306_R	0.824	1.00
70_A	74_N	0.821	1.00
392_I	395_F	0.821	1.00
90_E	307_D	0.814	1.00
86_D	118_L	0.812	1.00
17_G	21_A	0.812	1.00
303_Q	307_D	0.811	1.00
303_Q	344_N	0.810	1.00
89_R	92_K	0.805	1.00
87_I	112_K	0.802	1.00
45_H	79_F	0.800	1.00
374_V	377_L	0.799	1.00
119_V	341_A	0.797	1.00
31_K	34_A	0.794	1.00
242_R	263_E	0.794	1.00
117_T	349_M	0.793	1.00
218_E	226_P	0.793	1.00
301_T	349_M	0.792	1.00
290_T	297_V	0.789	1.00
96_I	110_E	0.787	1.00
170_K	209_L	0.785	1.00
133_G	251_S	0.785	1.00
67_S	71_H	0.784	1.00
128_D	134_V	0.781	1.00
388_I	392_I	0.776	1.00
87_I	95_T	0.769	1.00
176_V	272_W	0.769	1.00
300_P	356_N	0.769	1.00
300_P	351_G	0.768	1.00
24_L	34_A	0.766	1.00
176_V	249_V	0.765	1.00
230_A	234_N	0.765	1.00
392_I	396_V	0.764	1.00
22_T	75_H	0.764	1.00
186_S	213_L	0.763	1.00
175_I	182_G	0.762	1.00
151_H	155_L	0.760	1.00
152_Q	155_L	0.759	1.00
89_R	287_G	0.751	1.00
42_N	145_H	0.751	1.00
376_S	382_T	0.748	1.00
72_A	77_F	0.748	1.00
371_F	374_V	0.747	1.00
393_A	396_V	0.746	1.00
374_V	378_M	0.744	1.00
225_P	376_S	0.739	1.00
304_T	307_D	0.736	1.00
390_G	393_A	0.736	1.00
7_K	113_I	0.736	1.00
172_N	267_A	0.734	1.00
386_M	390_G	0.734	1.00
132_P	135_K	0.731	1.00
219_R	373_T	0.730	1.00
302_L	340_C	0.728	1.00
86_D	284_D	0.723	1.00
6_K	80_Q	0.719	1.00
379_G	382_T	0.719	1.00
43_H	82_G	0.715	1.00
44_S	65_A	0.714	1.00
61_E	64_D	0.714	1.00
343_N	348_Q	0.714	1.00
220_I	229_S	0.712	1.00
303_Q	348_Q	0.711	1.00
174_A	265_I	0.711	1.00
386_M	392_I	0.710	1.00
140_F	146_Q	0.708	1.00
391_R	394_R	0.708	1.00
288_L	296_L	0.705	1.00
85_I	110_E	0.703	1.00
148_R	151_H	0.702	1.00
182_G	215_E	0.699	1.00
89_R	309_D	0.698	1.00
61_E	68_Y	0.697	1.00
141_L	147_A	0.697	1.00
50_L	53_E	0.694	1.00
290_T	296_L	0.693	1.00
34_A	116_D	0.692	1.00
172_N	209_L	0.692	1.00
186_S	241_V	0.690	1.00
384_G	388_I	0.689	1.00
24_L	36_I	0.687	1.00
25_G	76_G	0.687	1.00
214_V	259_T	0.683	1.00
387_M	393_A	0.682	1.00
219_R	230_A	0.681	1.00
359_Y	363_G	0.681	1.00
303_Q	311_Y	0.678	1.00
226_P	229_S	0.678	1.00
221_L	232_A	0.677	1.00
127_N	130_N	0.677	1.00
237_T	242_R	0.676	1.00
170_K	268_D	0.674	1.00
387_M	390_G	0.672	1.00
313_I	338_A	0.670	1.00
149_R	153_E	0.670	1.00
376_S	381_L	0.668	1.00
64_D	71_H	0.667	1.00
7_K	34_A	0.665	1.00
23_Q	339_T	0.664	1.00
391_R	396_V	0.661	1.00
134_V	272_W	0.659	1.00
89_R	285_I	0.659	1.00
144_P	148_R	0.659	1.00
60_D	63_V	0.658	1.00
176_V	274_A	0.657	1.00
146_Q	150_F	0.657	1.00
89_R	115_Y	0.656	1.00
18_L	38_L	0.653	1.00
296_L	316_C	0.652	1.00
389_E	393_A	0.651	1.00
65_A	69_L	0.650	1.00
128_D	135_K	0.650	1.00
24_L	345_I	0.648	1.00
295_Q	329_P	0.646	1.00
127_N	274_A	0.645	1.00
386_M	393_A	0.645	1.00
64_D	68_Y	0.644	1.00
232_A	365_L	0.644	1.00
144_P	147_A	0.644	1.00
185_L	271_V	0.642	1.00
142_D	147_A	0.641	1.00
259_T	262_G	0.640	1.00
218_E	245_T	0.639	1.00
334_A	338_A	0.639	1.00
124_S	276_I	0.638	1.00
42_N	52_H	0.638	1.00
11_V	94_I	0.636	1.00
183_V	361_D	0.636	1.00
224_L	367_S	0.635	1.00
236_L	241_V	0.634	1.00
61_E	67_S	0.633	1.00
175_I	186_S	0.632	1.00
36_I	77_F	0.631	1.00
46_L	51_L	0.631	1.00
39_V	94_I	0.629	1.00
20_M	24_L	0.624	1.00
183_V	236_L	0.622	1.00
15_A	335_H	0.620	1.00
66_L	70_A	0.617	1.00
151_H	192_A	0.615	1.00
288_L	307_D	0.615	1.00
348_Q	354_L	0.615	1.00
389_E	395_F	0.614	1.00
290_T	294_N	0.612	1.00
357_Y	367_S	0.612	1.00
385_S	389_E	0.611	1.00
35_K	116_D	0.611	1.00
8_I	36_I	0.611	1.00
126_S	129_F	0.610	1.00
388_I	393_A	0.609	1.00
148_R	152_Q	0.609	1.00
339_T	343_N	0.607	1.00
128_D	272_W	0.607	1.00
84_V	94_I	0.601	1.00
25_G	36_I	0.601	1.00
141_L	150_F	0.600	1.00
174_A	212_T	0.599	1.00
282_L	285_I	0.598	1.00
370_N	374_V	0.597	1.00
62_G	66_L	0.596	1.00
387_M	394_R	0.596	1.00
185_L	188_E	0.595	1.00
150_F	271_V	0.595	1.00
343_N	347_A	0.595	1.00
71_H	75_H	0.593	1.00
143_N	147_A	0.592	1.00
388_I	391_R	0.591	1.00
168_N	208_A	0.590	1.00
249_V	257_L	0.589	1.00
292_R	297_V	0.588	1.00
86_D	94_I	0.588	1.00
19_E	335_H	0.588	1.00
216_A	222_P	0.588	1.00
78_Q	111_R	0.587	1.00
296_L	304_T	0.586	1.00
229_S	233_H	0.585	1.00
130_N	134_V	0.584	1.00
311_Y	354_L	0.582	1.00
220_I	233_H	0.581	1.00
383_R	387_M	0.581	1.00
62_G	65_A	0.580	1.00
34_A	345_I	0.578	1.00
8_I	345_I	0.578	1.00
175_I	271_V	0.578	1.00
154_M	173_I	0.578	1.00
66_L	71_H	0.577	1.00
134_V	252_A	0.576	1.00
288_L	304_T	0.576	1.00
385_S	388_I	0.574	1.00
129_F	272_W	0.573	1.00
155_L	192_A	0.573	1.00
34_A	117_T	0.571	1.00
82_G	85_I	0.570	1.00
13_G	17_G	0.570	1.00
391_R	395_F	0.567	1.00
278_A	295_Q	0.566	1.00
34_A	346_L	0.566	1.00
66_L	69_L	0.566	1.00
385_S	390_G	0.565	1.00
137_N	140_F	0.565	1.00
54_V	148_R	0.564	1.00
56_T	188_E	0.563	1.00
147_A	189_L	0.563	1.00
295_Q	318_S	0.561	1.00
6_K	9_V	0.560	1.00
63_V	67_S	0.559	1.00
13_G	68_Y	0.559	1.00
236_L	243_V	0.557	1.00
302_L	344_N	0.553	1.00
183_V	221_L	0.552	1.00
124_S	329_P	0.552	1.00
147_A	150_F	0.551	1.00
61_E	148_R	0.547	1.00
179_G	182_G	0.546	1.00
224_L	357_Y	0.546	1.00
347_A	350_N	0.545	1.00
298_V	302_L	0.544	1.00
92_K	307_D	0.544	1.00
92_K	114_A	0.544	1.00
390_G	394_R	0.542	1.00
135_K	138_C	0.542	1.00
317_A	337_M	0.541	1.00
142_D	269_L	0.540	0.99
287_G	290_T	0.539	0.99
138_C	270_M	0.539	0.99
13_G	45_H	0.539	0.99
344_N	347_A	0.538	0.99
90_E	287_G	0.538	0.99
228_I	231_A	0.538	0.99
168_N	171_V	0.537	0.99
346_L	350_N	0.536	0.99
387_M	392_I	0.536	0.99
224_L	365_L	0.536	0.99
297_V	318_S	0.535	0.99
19_E	22_T	0.535	0.99
145_H	149_R	0.534	0.99
69_L	81_L	0.534	0.99
215_E	218_E	0.531	0.99
348_Q	351_G	0.528	0.99
289_E	304_T	0.528	0.99
9_V	118_L	0.526	0.99
311_Y	345_I	0.526	0.99
153_E	269_L	0.525	0.99
86_D	120_M	0.525	0.99
388_I	394_R	0.522	0.99
347_A	351_G	0.522	0.99
169_G	268_D	0.521	0.99
383_R	388_I	0.520	0.99
55_A	185_L	0.520	0.99
142_D	145_H	0.520	0.99
180_A	359_Y	0.519	0.99
19_E	339_T	0.519	0.99
21_A	38_L	0.517	0.99
386_M	391_R	0.517	0.99
182_G	273_A	0.517	0.99
384_G	387_M	0.516	0.99
354_L	359_Y	0.516	0.99
140_F	269_L	0.515	0.99
84_V	87_I	0.515	0.99
21_A	36_I	0.514	0.99
281_F	284_D	0.514	0.99
219_R	222_P	0.512	0.99
187_A	239_L	0.512	0.99
187_A	191_N	0.511	0.99
220_I	243_V	0.510	0.99
6_K	34_A	0.509	0.99
385_S	393_A	0.508	0.99
57_G	185_L	0.508	0.99
118_L	309_D	0.508	0.99
153_E	170_K	0.507	0.99
359_Y	362_H	0.507	0.99
250_T	262_G	0.505	0.99
17_G	38_L	0.505	0.99
15_A	331_A	0.503	0.99
8_I	117_T	0.503	0.99
141_L	144_P	0.503	0.99
361_D	364_S	0.502	0.99
285_I	290_T	0.502	0.99
344_N	348_Q	0.500	0.99
136_E	254_E	0.500	0.99

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
4g6hA	2	0.9562	100	0.279	Contact Map
4nwzA	2	0.9009	100	0.366	Contact Map
3sx6A	2	0.8986	100	0.409	Contact Map
3h8lA	2	0.7488	100	0.411	Contact Map
3hywA	4	0.9101	100	0.42	Contact Map
3kljA	1	0.8433	100	0.442	Contact Map
3icsA	2	0.9124	100	0.443	Contact Map
1xhcA	1	0.7857	100	0.444	Contact Map
3l8kA	3	0.8571	100	0.447	Contact Map
4fx9A	2	0.894	100	0.447	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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