YUMB - BACSU - GREMLIN Contacts

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YUMB - NADH dehydrogenase-like protein YumB

UniProt:	O05267	Sequences: MALNKPKIVILGAGYGGLMTVTRLTKYVGPNDADITLVNKHNYHYETTWMHEASAGTLHHDRCRYQIKDVINQSRVNFVQDTVKAIKIDEKKVVLANGELQYDYLVIGLGAVPETFGIKGLKEYAFPIANINTSRLLREHIELQFATYNTEAEKRPDRLTIVVGGAGFTGIEFLGELAARVPELCKEYDVDRSLVRIICVEAAPTVLPGFDPELVDYAVHYLEENGVEFKIGTAVQECTPEGVRVGKKDEEPEQIKSQTVVWAAGVRGHPIVEEAGFENMRGRVKVNPDLRAPGHDNVFILGDSSLFMNEDTERPYPPTAQIAMQQGITVAKNLGRLIKGGELEEFKPDIKGTVASLGEHNAVGVVYGRKLKGTPASFMKKVIDNRSLFMIGGLGLTLKKGKFKFF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	406 (325)
Sequences:	30715 (21659)
Seq/√Len:	1201.4

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_K	82_T	4.233	1.00
162_V	257_S	4.154	1.00
7_K	34_D	3.583	1.00
160_T	196_R	3.337	1.00
198_I	230_K	3.111	1.00
91_K	297_N	3.074	1.00
287_N	291_R	2.963	1.00
196_R	228_E	2.874	1.00
219_V	223_E	2.859	1.00
92_K	99_E	2.725	1.00
20_T	106_V	2.718	1.00
230_K	253_E	2.506	1.00
6_P	36_T	2.452	1.00
88_I	295_H	2.378	1.00
278_E	285_K	2.371	1.00
114_E	267_R	2.360	1.00
87_K	90_E	2.331	1.00
7_K	36_T	2.311	1.00
7_K	103_D	2.296	1.00
102_Y	105_L	2.284	1.00
202_A	234_A	2.280	1.00
119_K	237_E	2.277	1.00
36_T	79_V	2.251	1.00
38_V	100_L	2.240	1.00
8_I	24_L	2.134	1.00
104_Y	297_N	2.121	1.00
162_V	200_V	2.094	1.00
160_T	198_I	2.094	1.00
279_N	283_R	2.079	1.00
112_V	269_H	2.073	1.00
9_V	38_V	2.066	1.00
34_D	77_N	2.062	1.00
243_V	247_K	2.036	1.00
243_V	249_D	2.033	1.00
16_G	301_L	2.016	1.00
198_I	228_E	1.954	1.00
112_V	267_R	1.940	1.00
204_P	232_G	1.928	1.00
160_T	258_Q	1.917	1.00
94_V	99_E	1.910	1.00
106_V	334_L	1.887	1.00
9_V	100_L	1.879	1.00
271_I	274_E	1.782	1.00
157_D	195_V	1.720	1.00
205_T	215_V	1.710	1.00
359_E	364_G	1.705	1.00
9_V	93_V	1.702	1.00
109_L	304_S	1.698	1.00
88_I	298_V	1.695	1.00
330_V	334_L	1.694	1.00
299_F	333_N	1.664	1.00
104_Y	299_F	1.656	1.00
92_K	101_Q	1.618	1.00
10_I	21_V	1.614	1.00
59_H	62_R	1.604	1.00
212_P	362_A	1.598	1.00
278_E	294_G	1.593	1.00
130_N	133_T	1.567	1.00
85_A	94_V	1.564	1.00
91_K	95_L	1.563	1.00
95_L	98_G	1.553	1.00
233_T	251_E	1.531	1.00
200_V	255_I	1.524	1.00
291_R	296_D	1.511	1.00
237_E	248_K	1.509	1.00
84_K	94_V	1.495	1.00
161_I	177_L	1.495	1.00
212_P	216_D	1.492	1.00
329_T	333_N	1.486	1.00
162_V	247_K	1.481	1.00
178_A	196_R	1.476	1.00
9_V	36_T	1.471	1.00
171_I	199_C	1.465	1.00
106_V	301_L	1.462	1.00
230_K	233_T	1.454	1.00
359_E	367_Y	1.436	1.00
85_A	274_E	1.432	1.00
6_P	77_N	1.427	1.00
327_G	331_A	1.421	1.00
178_A	227_V	1.418	1.00
104_Y	334_L	1.414	1.00
13_A	39_N	1.412	1.00
8_I	33_A	1.409	1.00
166_A	201_E	1.403	1.00
219_V	231_I	1.371	1.00
284_V	300_I	1.370	1.00
159_L	258_Q	1.368	1.00
82_T	96_A	1.356	1.00
9_V	102_Y	1.346	1.00
49_W	52_E	1.345	1.00
11_L	83_V	1.344	1.00
133_T	136_L	1.336	1.00
95_L	100_L	1.336	1.00
239_T	248_K	1.333	1.00
331_A	335_G	1.330	1.00
23_R	332_K	1.330	1.00
201_E	231_I	1.319	1.00
126_F	140_H	1.317	1.00
160_T	256_K	1.313	1.00
221_Y	224_E	1.309	1.00
8_I	106_V	1.304	1.00
233_T	253_E	1.299	1.00
111_A	266_V	1.269	1.00
220_H	223_E	1.264	1.00
87_K	92_K	1.262	1.00
301_L	330_V	1.261	1.00
161_I	259_T	1.260	1.00
236_Q	248_K	1.257	1.00
161_I	195_V	1.257	1.00
11_L	109_L	1.252	1.00
16_G	323_A	1.249	1.00
362_A	366_V	1.229	1.00
205_T	212_P	1.224	1.00
361_N	365_V	1.208	1.00
290_L	330_V	1.207	1.00
221_Y	225_N	1.203	1.00
6_P	104_Y	1.189	1.00
132_N	135_R	1.181	1.00
179_A	225_N	1.181	1.00
289_D	333_N	1.178	1.00
364_G	371_L	1.176	1.00
69_D	73_Q	1.174	1.00
68_K	72_N	1.172	1.00
236_Q	252_P	1.172	1.00
36_T	100_L	1.170	1.00
246_G	254_Q	1.166	1.00
79_V	100_L	1.163	1.00
249_D	252_P	1.158	1.00
336_R	341_G	1.158	1.00
81_D	97_N	1.151	1.00
11_L	107_I	1.146	1.00
10_I	17_G	1.146	1.00
279_N	306_L	1.126	1.00
129_A	137_L	1.125	1.00
220_H	224_E	1.125	1.00
108_G	301_L	1.120	1.00
239_T	254_Q	1.115	1.00
219_V	229_F	1.097	1.00
107_I	304_S	1.096	1.00
129_A	133_T	1.093	1.00
84_K	96_A	1.089	1.00
244_R	254_Q	1.084	1.00
290_L	305_S	1.081	1.00
166_A	206_V	1.073	1.00
131_I	135_R	1.070	1.00
230_K	255_I	1.062	1.00
216_D	219_V	1.062	1.00
291_R	297_N	1.055	1.00
135_R	138_R	1.052	1.00
7_K	101_Q	1.050	1.00
70_V	74_S	1.048	1.00
59_H	66_Q	1.036	1.00
206_V	231_I	1.036	1.00
300_I	304_S	1.028	1.00
20_T	327_G	1.025	1.00
279_N	285_K	1.022	1.00
238_C	260_V	1.014	1.00
205_T	219_V	1.014	1.00
171_I	350_I	1.013	1.00
237_E	244_R	1.004	1.00
64_R	67_I	0.994	1.00
25_T	76_V	0.993	1.00
105_L	298_V	0.990	1.00
60_H	64_R	0.982	1.00
131_I	134_S	0.980	1.00
217_Y	221_Y	0.980	1.00
90_E	99_E	0.972	1.00
257_S	260_V	0.969	1.00
24_L	331_A	0.966	1.00
23_R	328_I	0.964	1.00
330_V	333_N	0.962	1.00
243_V	246_G	0.962	1.00
286_V	300_I	0.953	1.00
162_V	255_I	0.952	1.00
286_V	305_S	0.952	1.00
81_D	96_A	0.950	1.00
20_T	330_V	0.949	1.00
239_T	242_G	0.948	1.00
17_G	21_V	0.947	1.00
295_H	298_V	0.947	1.00
20_T	301_L	0.946	1.00
164_G	260_V	0.945	1.00
280_M	285_K	0.945	1.00
85_A	105_L	0.941	1.00
158_R	195_V	0.940	1.00
239_T	246_G	0.931	1.00
39_N	78_F	0.923	1.00
248_K	254_Q	0.919	1.00
178_A	225_N	0.917	1.00
233_T	250_E	0.915	1.00
21_V	76_V	0.914	1.00
38_V	79_V	0.914	1.00
292_A	300_I	0.913	1.00
66_Q	69_D	0.901	1.00
36_T	77_N	0.898	1.00
292_A	295_H	0.897	1.00
234_A	250_E	0.896	1.00
363_V	366_V	0.896	1.00
240_P	245_V	0.895	1.00
38_V	95_L	0.894	1.00
210_F	346_F	0.892	1.00
200_V	230_K	0.892	1.00
6_P	34_D	0.889	1.00
67_I	70_V	0.886	1.00
164_G	262_W	0.885	1.00
63_C	66_Q	0.880	1.00
129_A	134_S	0.879	1.00
125_A	238_C	0.877	1.00
42_N	80_Q	0.875	1.00
64_R	68_K	0.874	1.00
13_A	37_L	0.873	1.00
60_H	67_I	0.872	1.00
38_V	83_V	0.869	1.00
284_V	304_S	0.867	1.00
244_R	256_K	0.867	1.00
47_T	52_E	0.867	1.00
216_D	220_H	0.865	1.00
281_R	306_L	0.864	1.00
67_I	71_I	0.861	1.00
159_L	196_R	0.858	1.00
59_H	63_C	0.856	1.00
137_L	259_T	0.856	1.00
361_N	371_L	0.851	1.00
160_T	195_V	0.851	1.00
134_S	138_R	0.850	1.00
239_T	244_R	0.848	1.00
201_E	208_P	0.848	1.00
71_I	76_V	0.842	1.00
44_H	78_F	0.842	1.00
200_V	233_T	0.840	1.00
291_R	295_H	0.833	1.00
236_Q	250_E	0.833	1.00
66_Q	70_V	0.825	1.00
128_I	134_S	0.824	1.00
271_I	275_A	0.822	1.00
8_I	334_L	0.820	1.00
217_Y	220_H	0.819	1.00
20_T	331_A	0.817	1.00
363_V	367_Y	0.817	1.00
113_P	116_F	0.814	1.00
9_V	105_L	0.810	1.00
23_R	26_K	0.805	1.00
164_G	264_A	0.804	1.00
300_I	305_S	0.803	1.00
241_E	244_R	0.802	1.00
223_E	228_E	0.802	1.00
23_R	331_A	0.801	1.00
233_T	249_D	0.800	1.00
299_F	334_L	0.797	1.00
198_I	255_I	0.795	1.00
17_G	108_G	0.795	1.00
285_K	294_G	0.792	1.00
61_D	65_Y	0.790	1.00
106_V	330_V	0.789	1.00
203_A	208_P	0.788	1.00
102_Y	297_N	0.785	1.00
170_G	201_E	0.785	1.00
241_E	256_K	0.780	1.00
22_T	26_K	0.777	1.00
291_R	333_N	0.776	1.00
33_A	103_D	0.774	1.00
87_K	94_V	0.774	1.00
291_R	299_F	0.772	1.00
124_Y	240_P	0.771	1.00
365_V	371_L	0.770	1.00
290_L	329_T	0.769	1.00
332_K	337_L	0.767	1.00
118_I	121_L	0.760	1.00
10_I	20_T	0.757	1.00
160_T	257_S	0.754	1.00
175_G	179_A	0.752	1.00
94_V	97_N	0.751	1.00
299_F	330_V	0.750	1.00
19_M	324_M	0.750	1.00
19_M	327_G	0.749	1.00
7_K	33_A	0.744	1.00
83_V	93_V	0.741	1.00
117_G	121_L	0.741	1.00
346_F	356_S	0.740	1.00
87_K	91_K	0.738	1.00
270_P	273_E	0.737	1.00
60_H	66_Q	0.736	1.00
24_L	33_A	0.735	1.00
86_I	99_E	0.734	1.00
199_C	229_F	0.733	1.00
65_Y	68_K	0.731	1.00
360_H	363_V	0.729	1.00
174_L	199_C	0.729	1.00
299_F	337_L	0.727	1.00
130_N	134_S	0.727	1.00
6_P	79_V	0.725	1.00
198_I	257_S	0.722	1.00
60_H	63_C	0.721	1.00
250_E	253_E	0.720	1.00
16_G	108_G	0.719	1.00
328_I	332_K	0.718	1.00
289_D	338_I	0.718	1.00
83_V	86_I	0.717	1.00
133_T	137_L	0.717	1.00
249_D	255_I	0.717	1.00
60_H	135_R	0.713	1.00
6_P	9_V	0.711	1.00
69_D	72_N	0.705	1.00
159_L	195_V	0.704	1.00
200_V	249_D	0.703	1.00
134_S	177_L	0.702	1.00
163_V	174_L	0.702	1.00
205_T	216_D	0.701	1.00
222_L	229_F	0.701	1.00
206_V	215_V	0.700	1.00
130_N	135_R	0.700	1.00
210_F	356_S	0.699	1.00
17_G	37_L	0.698	1.00
66_Q	71_I	0.697	1.00
332_K	336_R	0.695	1.00
41_H	51_H	0.694	1.00
174_L	197_I	0.693	1.00
204_P	212_P	0.693	1.00
53_A	56_G	0.692	1.00
288_P	340_G	0.691	1.00
228_E	253_E	0.691	1.00
277_F	284_V	0.691	1.00
171_I	222_L	0.690	1.00
163_V	261_V	0.689	1.00
244_R	247_K	0.688	1.00
71_I	74_S	0.687	1.00
164_G	235_V	0.684	1.00
22_T	74_S	0.683	1.00
247_K	250_E	0.683	1.00
325_Q	328_I	0.679	1.00
24_L	334_L	0.678	1.00
68_K	80_Q	0.676	1.00
173_F	261_V	0.676	1.00
290_L	333_N	0.674	1.00
242_G	254_Q	0.673	1.00
364_G	369_R	0.672	1.00
272_V	275_A	0.670	1.00
283_R	318_P	0.670	1.00
173_F	176_E	0.669	1.00
167_G	170_G	0.667	1.00
322_I	326_Q	0.667	1.00
369_R	372_K	0.667	1.00
24_L	35_I	0.666	1.00
270_P	279_N	0.661	1.00
234_A	246_G	0.659	1.00
19_M	23_R	0.659	1.00
33_A	335_G	0.659	1.00
48_T	53_A	0.657	1.00
301_L	327_G	0.656	1.00
114_E	117_G	0.654	1.00
132_N	136_L	0.653	1.00
37_L	71_I	0.653	1.00
42_N	81_D	0.653	1.00
88_I	297_N	0.651	1.00
275_A	295_H	0.651	1.00
135_R	139_E	0.649	1.00
206_V	219_V	0.648	1.00
174_L	227_V	0.647	1.00
131_I	138_R	0.646	1.00
114_E	264_A	0.642	1.00
169_T	263_A	0.642	1.00
53_A	135_R	0.640	1.00
158_R	258_Q	0.640	1.00
59_H	67_I	0.634	1.00
65_Y	69_D	0.634	1.00
116_F	262_W	0.632	1.00
213_E	216_D	0.631	1.00
129_A	132_N	0.630	1.00
34_D	103_D	0.624	1.00
236_Q	246_G	0.623	1.00
246_G	252_P	0.622	1.00
104_Y	337_L	0.621	1.00
365_V	370_K	0.619	1.00
128_I	132_N	0.619	1.00
205_T	362_A	0.618	1.00
163_V	170_G	0.616	1.00
115_T	262_W	0.616	1.00
109_L	271_I	0.615	1.00
284_V	292_A	0.615	1.00
7_K	100_L	0.614	1.00
88_I	91_K	0.613	1.00
134_S	137_L	0.613	1.00
25_T	35_I	0.612	1.00
21_V	37_L	0.611	1.00
246_G	256_K	0.611	1.00
344_E	348_P	0.609	1.00
121_L	262_W	0.609	1.00
323_A	327_G	0.609	1.00
277_F	292_A	0.608	1.00
62_R	66_Q	0.608	1.00
161_I	261_V	0.608	1.00
240_P	243_V	0.607	1.00
90_E	101_Q	0.607	1.00
24_L	335_G	0.607	1.00
88_I	102_Y	0.605	1.00
268_G	283_R	0.604	1.00
19_M	328_I	0.603	1.00
120_G	237_E	0.603	1.00
359_E	363_V	0.603	1.00
172_E	175_G	0.603	1.00
245_V	249_D	0.601	1.00
243_V	248_K	0.601	1.00
47_T	50_M	0.598	1.00
173_F	177_L	0.598	1.00
215_V	219_V	0.597	1.00
61_D	64_R	0.596	1.00
249_D	253_E	0.594	1.00
283_R	306_L	0.594	1.00
171_I	229_F	0.593	1.00
119_K	122_K	0.593	1.00
19_M	22_T	0.592	1.00
71_I	78_F	0.591	1.00
136_L	140_H	0.590	1.00
345_E	348_P	0.584	1.00
85_A	91_K	0.582	1.00
82_T	85_A	0.582	1.00
77_N	80_Q	0.578	1.00
9_V	91_K	0.578	1.00
92_K	95_L	0.575	1.00
138_R	180_R	0.575	1.00
59_H	64_R	0.574	1.00
128_I	131_I	0.574	1.00
104_Y	338_I	0.573	1.00
40_K	269_H	0.572	1.00
33_A	104_Y	0.572	1.00
115_T	121_L	0.570	1.00
52_E	55_A	0.568	1.00
15_Y	320_A	0.566	1.00
176_E	180_R	0.565	1.00
353_T	356_S	0.556	1.00
307_F	317_P	0.555	1.00
136_L	139_E	0.553	1.00
115_T	122_K	0.552	1.00
31_N	335_G	0.552	1.00
25_T	75_R	0.552	1.00
48_T	52_E	0.552	1.00
206_V	229_F	0.550	1.00
8_I	104_Y	0.550	1.00
277_F	295_H	0.549	1.00
172_E	177_L	0.547	1.00
305_S	326_Q	0.546	1.00
18_L	37_L	0.545	1.00
70_V	73_Q	0.544	1.00
89_D	295_H	0.544	1.00
128_I	137_L	0.543	1.00
247_K	252_P	0.543	1.00
112_V	270_P	0.543	1.00
62_R	65_Y	0.542	1.00
336_R	339_K	0.541	1.00
83_V	87_K	0.541	1.00
37_L	76_V	0.541	1.00
340_G	343_L	0.539	1.00
292_A	298_V	0.539	1.00
52_E	57_T	0.538	1.00
244_R	249_D	0.536	1.00
31_N	332_K	0.535	1.00
162_V	260_V	0.534	1.00
117_G	122_K	0.534	1.00
207_L	218_A	0.534	1.00
123_E	240_P	0.534	1.00
85_A	275_A	0.532	1.00
168_F	348_P	0.529	1.00
222_L	227_V	0.528	1.00
47_T	51_H	0.528	1.00
212_P	215_V	0.527	1.00
86_I	271_I	0.525	1.00
48_T	54_S	0.524	1.00
168_F	172_E	0.522	1.00
241_E	246_G	0.521	1.00
270_P	304_S	0.521	1.00
347_K	350_I	0.519	1.00
17_G	39_N	0.519	1.00
137_L	177_L	0.519	1.00
56_G	173_F	0.518	1.00
286_V	290_L	0.518	1.00
171_I	206_V	0.517	1.00
162_V	198_I	0.515	1.00
81_D	95_L	0.515	1.00
275_A	298_V	0.514	1.00
13_A	44_H	0.513	1.00
201_E	204_P	0.512	1.00
84_K	87_K	0.511	1.00
43_Y	132_N	0.506	1.00
167_G	172_E	0.504	1.00
141_I	177_L	0.502	1.00
129_A	259_T	0.501	1.00
62_R	67_I	0.501	1.00
317_P	322_I	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
4g6hA	2	0.9729	100	0.268	Contact Map
4nwzA	2	0.9729	100	0.309	Contact Map
3sx6A	2	0.9507	100	0.378	Contact Map
3h8lA	2	0.7857	100	0.383	Contact Map
3hywA	4	0.9384	100	0.384	Contact Map
1xhcA	1	0.8374	100	0.399	Contact Map
3kljA	1	0.8424	100	0.411	Contact Map
3vrdB	1	0.9113	100	0.42	Contact Map
3l8kA	3	0.8744	100	0.423	Contact Map
1ojtA	2	0.8793	100	0.426	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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