YTHB - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YTHB - Putative cytochrome bd menaquinol oxidase subunit II

UniProt:	O34505	Sequences: MEISTDALIAISIIWGFVFIYAVMATMDFGAGFWSMIYLNKEHMKATDIANRFLSPTWEVTNVFIVAIVVALFSFFPGATFVLGTVLLIPGSMILLLLAIRSGFLVFSNTAKERKTLRYISGISGFIIPAILILVLPVTHGGFIEKTDGIYNLNMSKIFSSPNAYSFIGFAILSTLFLSSLLLADFSNVAEEQDAYRAYRKSALITGPISLLFAVCIMVTMRNEANWLYSGMMNDFSWIIASFITFVIAGIALFLPNKSFGQNIGKPRLALVAIGIQYFLASYAYGRAHLPYMIYPDVTVMSGFTEPATFRALFATYIVAFIILFPGFFFFWKMFMRDKRYIRQEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	346 (322)
Sequences:	3256 (2065)
Seq/√Len:	115.1

ECOLI - CYDB APPB
BACSU - YTHB CYDB
HALSA - O54596

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_F	176_L	3.753	1.00
161_S	164_A	3.711	1.00
126_F	172_I	3.323	1.00
87_L	143_F	3.321	1.00
333_K	336_M	3.313	1.00
317_Y	321_F	3.143	1.00
23_V	275_G	2.819	1.00
130_A	172_I	2.804	1.00
130_A	168_I	2.782	1.00
307_P	311_R	2.773	1.00
176_L	202_S	2.637	1.00
48_D	52_R	2.557	1.00
33_F	172_I	2.481	1.00
12_S	16_G	2.433	1.00
129_P	171_A	2.387	1.00
108_S	118_R	2.384	1.00
154_N	157_K	2.347	1.00
163_N	217_I	2.346	1.00
326_P	329_F	2.331	1.00
93_M	131_I	2.277	1.00
31_A	50_A	2.227	1.00
169_G	173_L	2.187	1.00
46_A	194_D	2.165	1.00
18_V	72_L	2.158	1.00
197_R	201_K	2.158	1.00
16_G	20_I	2.124	1.00
137_P	167_F	2.064	1.00
188_N	340_R	2.051	1.00
315_A	319_V	2.033	1.00
266_K	269_L	2.032	1.00
134_L	168_I	2.026	1.00
122_G	126_F	2.011	1.00
9_I	314_F	1.990	1.00
7_A	304_F	1.980	1.00
75_F	313_L	1.974	1.00
116_T	119_Y	1.969	1.00
329_F	333_K	1.965	1.00
129_P	175_T	1.954	1.00
100_I	120_I	1.937	1.00
50_A	183_L	1.906	1.00
181_L	199_Y	1.902	1.00
165_Y	169_G	1.900	1.00
59_E	106_V	1.895	1.00
119_Y	123_I	1.893	1.00
173_L	209_I	1.887	1.00
124_S	128_I	1.886	1.00
141_G	161_S	1.842	1.00
49_I	339_K	1.748	1.00
292_Y	299_T	1.743	1.00
51_N	105_L	1.716	1.00
146_K	152_N	1.694	1.00
216_C	220_T	1.678	1.00
178_L	275_G	1.676	1.00
192_E	267_P	1.655	1.00
244_I	248_I	1.650	1.00
120_I	124_S	1.632	1.00
97_L	124_S	1.627	1.00
320_A	323_I	1.617	1.00
78_G	149_G	1.586	1.00
210_S	281_A	1.583	1.00
27_M	332_W	1.562	1.00
173_L	205_I	1.552	1.00
241_A	287_R	1.539	1.00
97_L	127_I	1.539	1.00
211_L	246_F	1.536	1.00
94_I	132_L	1.535	1.00
86_V	143_F	1.530	1.00
49_I	191_E	1.522	1.00
14_I	71_A	1.517	1.00
33_F	126_F	1.491	1.00
140_H	289_H	1.478	1.00
82_V	294_I	1.475	1.00
246_F	250_G	1.446	1.00
31_A	54_L	1.437	1.00
105_L	117_L	1.429	1.00
29_F	129_P	1.428	1.00
196_Y	200_R	1.428	1.00
255_L	273_A	1.422	1.00
311_R	315_A	1.421	1.00
131_I	160_S	1.410	1.00
185_D	268_R	1.408	1.00
7_A	310_F	1.399	1.00
27_M	57_T	1.393	1.00
47_T	118_R	1.377	1.00
181_L	270_A	1.377	1.00
180_S	199_Y	1.374	1.00
115_K	119_Y	1.373	1.00
27_M	271_L	1.367	1.00
87_L	138_V	1.362	1.00
258_K	266_K	1.360	1.00
91_G	135_V	1.355	1.00
138_V	164_A	1.344	1.00
36_M	122_G	1.337	1.00
130_A	134_L	1.336	1.00
131_I	134_L	1.335	1.00
314_F	318_I	1.334	1.00
255_L	258_K	1.329	1.00
87_L	90_P	1.300	1.00
32_G	125_G	1.292	0.99
218_M	233_M	1.290	0.99
31_A	183_L	1.286	0.99
10_A	75_F	1.286	0.99
207_G	211_L	1.279	0.99
174_S	278_Y	1.279	0.99
169_G	209_I	1.275	0.99
306_E	309_T	1.272	0.99
19_F	279_F	1.263	0.99
210_S	284_A	1.263	0.99
200_R	257_N	1.255	0.99
17_F	20_I	1.253	0.99
238_W	241_A	1.253	0.99
92_S	96_L	1.246	0.99
208_P	212_L	1.238	0.99
46_A	341_Y	1.235	0.99
20_I	325_F	1.235	0.99
249_A	253_L	1.231	0.99
249_A	277_Q	1.230	0.99
79_A	83_L	1.199	0.99
34_W	180_S	1.198	0.99
116_T	120_I	1.192	0.99
190_A	194_D	1.187	0.99
8_L	301_M	1.186	0.99
72_L	79_A	1.181	0.99
42_E	114_R	1.177	0.99
90_P	134_L	1.175	0.99
255_L	259_S	1.172	0.99
145_E	296_P	1.167	0.99
190_A	193_Q	1.155	0.99
17_F	67_A	1.151	0.99
307_P	310_F	1.151	0.99
171_A	175_T	1.146	0.99
38_Y	50_A	1.138	0.99
204_L	208_P	1.130	0.99
174_S	281_A	1.127	0.99
308_A	311_R	1.126	0.99
251_I	254_F	1.121	0.99
193_Q	196_Y	1.110	0.98
16_G	70_V	1.099	0.98
230_S	234_N	1.091	0.98
235_D	239_I	1.090	0.98
242_S	245_T	1.089	0.98
132_L	175_T	1.089	0.98
123_I	127_I	1.088	0.98
308_A	312_A	1.084	0.98
159_F	162_P	1.081	0.98
79_A	293_M	1.075	0.98
69_V	84_G	1.075	0.98
33_F	122_G	1.072	0.98
151_Y	157_K	1.067	0.98
39_L	46_A	1.065	0.98
127_I	131_I	1.062	0.98
139_T	294_I	1.062	0.98
49_I	187_S	1.043	0.98
242_S	284_A	1.039	0.98
250_G	254_F	1.037	0.98
35_S	51_N	1.036	0.98
235_D	238_W	1.034	0.98
35_S	122_G	1.033	0.98
82_V	145_E	1.030	0.97
49_I	52_R	1.027	0.97
177_F	181_L	1.024	0.97
19_F	282_S	1.023	0.97
57_T	182_L	1.022	0.97
13_I	16_G	1.020	0.97
193_Q	197_R	1.018	0.97
109_N	114_R	1.013	0.97
41_K	45_K	1.010	0.97
170_F	209_I	1.006	0.97
166_S	216_C	0.998	0.97
268_R	272_V	0.992	0.97
11_I	15_W	0.988	0.97
198_A	201_K	0.981	0.97
48_D	51_N	0.980	0.97
277_Q	281_A	0.973	0.96
83_L	143_F	0.972	0.96
48_D	109_N	0.964	0.96
126_F	130_A	0.959	0.96
87_L	294_I	0.959	0.96
143_F	294_I	0.955	0.96
245_T	248_I	0.954	0.96
189_V	193_Q	0.954	0.96
138_V	159_F	0.953	0.96
178_L	274_I	0.951	0.96
181_L	274_I	0.946	0.96
60_V	331_F	0.946	0.96
184_A	196_Y	0.945	0.96
184_A	192_E	0.940	0.96
254_F	258_K	0.936	0.96
252_A	256_P	0.934	0.96
214_A	284_A	0.932	0.95
279_F	283_Y	0.931	0.95
292_Y	297_D	0.931	0.95
215_V	219_V	0.930	0.95
69_V	80_T	0.927	0.95
25_A	29_F	0.922	0.95
13_I	70_V	0.921	0.95
97_L	128_I	0.915	0.95
84_G	91_G	0.908	0.95
41_K	341_Y	0.907	0.95
173_L	206_T	0.907	0.95
182_L	336_M	0.903	0.95
248_I	280_L	0.898	0.94
17_F	70_V	0.896	0.94
119_Y	122_G	0.895	0.94
177_F	199_Y	0.893	0.94
237_S	287_R	0.891	0.94
32_G	129_P	0.889	0.94
146_K	150_I	0.886	0.94
195_A	198_A	0.886	0.94
285_Y	289_H	0.880	0.94
305_T	309_T	0.879	0.94
22_A	328_F	0.875	0.94
312_A	316_T	0.872	0.94
134_L	165_Y	0.870	0.94
10_A	313_L	0.869	0.93
252_A	255_L	0.865	0.93
27_M	186_F	0.863	0.93
109_N	112_K	0.858	0.93
70_V	321_F	0.857	0.93
16_G	321_F	0.857	0.93
192_E	338_D	0.857	0.93
94_I	131_I	0.853	0.93
49_I	341_Y	0.851	0.93
136_L	285_Y	0.847	0.93
129_P	132_L	0.843	0.92
211_L	215_V	0.842	0.92
177_F	274_I	0.838	0.92
205_I	208_P	0.834	0.92
238_W	287_R	0.832	0.92
298_V	302_S	0.832	0.92
102_S	105_L	0.831	0.92
85_T	88_L	0.830	0.92
299_T	302_S	0.830	0.92
41_K	46_A	0.823	0.91
126_F	276_I	0.821	0.91
18_V	68_I	0.820	0.91
253_L	256_P	0.817	0.91
319_V	323_I	0.814	0.91
52_R	55_S	0.814	0.91
192_E	196_Y	0.810	0.91
117_L	120_I	0.807	0.91
22_A	132_L	0.805	0.91
114_R	118_R	0.803	0.90
256_P	259_S	0.802	0.90
228_L	231_G	0.801	0.90
126_F	129_P	0.797	0.90
227_W	230_S	0.797	0.90
79_A	82_V	0.796	0.90
45_K	49_I	0.795	0.90
145_E	294_I	0.788	0.90
93_M	127_I	0.785	0.89
185_D	271_L	0.784	0.89
73_F	80_T	0.782	0.89
290_L	310_F	0.771	0.89
15_W	286_G	0.770	0.89
33_F	125_G	0.770	0.89
198_A	202_S	0.770	0.89
39_L	42_E	0.769	0.88
177_F	202_S	0.769	0.88
298_V	303_G	0.766	0.88
69_V	160_S	0.765	0.88
180_S	184_A	0.765	0.88
170_F	210_S	0.764	0.88
19_F	23_V	0.759	0.88
25_A	186_F	0.753	0.87
22_A	282_S	0.748	0.87
243_F	246_F	0.748	0.87
240_I	243_F	0.747	0.87
144_I	157_K	0.746	0.87
113_E	116_T	0.745	0.87
52_R	110_T	0.744	0.87
130_A	165_Y	0.743	0.87
276_I	280_L	0.742	0.87
91_G	278_Y	0.741	0.87
199_Y	256_P	0.740	0.87
58_W	80_T	0.737	0.86
187_S	338_D	0.737	0.86
292_Y	296_P	0.735	0.86
238_W	245_T	0.733	0.86
120_I	123_I	0.732	0.86
330_F	334_M	0.731	0.86
39_L	50_A	0.731	0.86
210_S	214_A	0.729	0.86
246_F	249_A	0.729	0.86
226_N	229_Y	0.728	0.86
197_R	200_R	0.727	0.86
130_A	169_G	0.722	0.85
69_V	313_L	0.722	0.85
243_F	247_V	0.718	0.85
280_L	287_R	0.718	0.85
59_E	327_G	0.717	0.85
328_F	331_F	0.714	0.85
207_G	215_V	0.714	0.85
34_W	176_L	0.712	0.84
14_I	316_T	0.711	0.84
13_I	321_F	0.711	0.84
99_A	304_F	0.710	0.84
86_V	90_P	0.710	0.84
51_N	109_N	0.708	0.84
169_G	194_D	0.706	0.84
180_S	198_A	0.706	0.84
34_W	183_L	0.704	0.84
152_N	156_S	0.704	0.84
13_I	317_Y	0.703	0.84
78_G	303_G	0.700	0.83
57_T	331_F	0.698	0.83
29_F	102_S	0.697	0.83
50_A	191_E	0.696	0.83
71_A	74_S	0.696	0.83
52_R	109_N	0.695	0.83
237_S	243_F	0.693	0.83
22_A	175_T	0.692	0.83
196_Y	267_P	0.691	0.83
329_F	336_M	0.690	0.82
269_L	272_V	0.686	0.82
183_L	187_S	0.685	0.82
166_S	212_L	0.685	0.82
253_L	257_N	0.682	0.82
196_Y	199_Y	0.680	0.82
94_I	174_S	0.678	0.81
104_F	120_I	0.676	0.81
183_L	195_A	0.675	0.81
244_I	250_G	0.675	0.81
69_V	91_G	0.672	0.81
102_S	284_A	0.670	0.81
90_P	159_F	0.669	0.80
31_A	35_S	0.668	0.80
112_K	116_T	0.668	0.80
124_S	129_P	0.668	0.80
28_D	31_A	0.668	0.80
21_Y	29_F	0.666	0.80
194_D	198_A	0.664	0.80
38_Y	195_A	0.664	0.80
50_A	111_A	0.663	0.80
272_V	276_I	0.663	0.80
23_V	279_F	0.659	0.79
251_I	255_L	0.657	0.79
203_A	207_G	0.654	0.79
11_I	300_V	0.653	0.79
291_P	300_V	0.653	0.79
8_L	300_V	0.649	0.78
53_F	340_R	0.643	0.78
292_Y	295_Y	0.642	0.78
238_W	242_S	0.638	0.77
21_Y	335_F	0.635	0.77
67_A	71_A	0.632	0.77
217_I	220_T	0.632	0.77
14_I	79_A	0.630	0.76
187_S	271_L	0.628	0.76
19_F	275_G	0.628	0.76
326_P	331_F	0.624	0.76
241_A	252_A	0.621	0.75
29_F	98_L	0.619	0.75
53_F	182_L	0.619	0.75
130_A	137_P	0.619	0.75
191_E	195_A	0.618	0.75
280_L	284_A	0.618	0.75
241_A	244_I	0.617	0.75
282_S	285_Y	0.612	0.74
110_T	328_F	0.612	0.74
39_L	194_D	0.612	0.74
133_I	168_I	0.611	0.74
321_F	325_F	0.608	0.74
200_R	204_L	0.608	0.74
145_E	149_G	0.607	0.74
248_I	273_A	0.607	0.74
36_M	119_Y	0.605	0.73
102_S	107_F	0.604	0.73
99_A	104_F	0.603	0.73
29_F	32_G	0.603	0.73
84_G	313_L	0.602	0.73
244_I	247_V	0.600	0.73
138_V	162_P	0.600	0.73
45_K	341_Y	0.600	0.73
323_I	330_F	0.599	0.73
137_P	213_F	0.597	0.72
19_F	283_Y	0.597	0.72
228_L	288_A	0.597	0.72
89_I	93_M	0.596	0.72
59_E	62_N	0.593	0.72
247_V	250_G	0.593	0.72
148_D	152_N	0.593	0.72
11_I	81_F	0.592	0.72
297_D	302_S	0.592	0.72
204_L	210_S	0.591	0.72
17_F	313_L	0.591	0.72
321_F	326_P	0.590	0.72
50_A	190_A	0.589	0.71
67_A	316_T	0.589	0.71
244_I	257_N	0.589	0.71
56_P	317_Y	0.588	0.71
8_L	12_S	0.587	0.71
184_A	199_Y	0.586	0.71
7_A	307_P	0.585	0.71
251_I	273_A	0.583	0.71
137_P	164_A	0.583	0.71
58_W	101_R	0.582	0.71
17_F	71_A	0.582	0.71
200_R	256_P	0.580	0.70
314_F	338_D	0.580	0.70
242_S	246_F	0.578	0.70
14_I	286_G	0.577	0.70
215_V	218_M	0.577	0.70
145_E	298_V	0.577	0.70
278_Y	281_A	0.576	0.70
50_A	53_F	0.573	0.69
251_I	276_I	0.572	0.69
236_F	245_T	0.572	0.69
54_L	105_L	0.570	0.69
32_G	37_I	0.568	0.69
191_E	194_D	0.565	0.68
174_S	277_Q	0.563	0.68
129_P	172_I	0.563	0.68
248_I	287_R	0.562	0.68
7_A	301_M	0.559	0.68
241_A	284_A	0.556	0.67
111_A	114_R	0.556	0.67
314_F	317_Y	0.555	0.67
138_V	161_S	0.551	0.66
232_M	288_A	0.551	0.66
16_G	317_Y	0.551	0.66
160_S	164_A	0.550	0.66
207_G	214_A	0.550	0.66
84_G	88_L	0.550	0.66
177_F	203_A	0.549	0.66
200_R	203_A	0.547	0.66
283_Y	287_R	0.547	0.66
15_W	305_T	0.545	0.66
219_V	229_Y	0.544	0.65
21_Y	72_L	0.541	0.65
81_F	139_T	0.541	0.65
236_F	246_F	0.541	0.65
212_L	220_T	0.540	0.65
46_A	50_A	0.540	0.65
69_V	327_G	0.539	0.65
219_V	250_G	0.539	0.65
290_L	300_V	0.538	0.65
68_I	72_L	0.537	0.64
184_A	267_P	0.536	0.64
121_S	125_G	0.536	0.64
101_R	125_G	0.536	0.64
231_G	234_N	0.534	0.64
152_N	155_M	0.534	0.64
273_A	276_I	0.534	0.64
38_Y	41_K	0.530	0.63
170_F	213_F	0.530	0.63
234_N	237_S	0.529	0.63
177_F	206_T	0.529	0.63
129_P	139_T	0.528	0.63
184_A	270_A	0.527	0.63
269_L	273_A	0.525	0.63
11_I	313_L	0.525	0.63
163_N	288_A	0.524	0.63
53_F	65_I	0.524	0.63
153_L	157_K	0.523	0.62
267_P	270_A	0.522	0.62
281_A	320_A	0.521	0.62
74_S	85_T	0.520	0.62
198_A	209_I	0.519	0.62
176_L	180_S	0.518	0.62
9_I	12_S	0.515	0.61
56_P	98_L	0.515	0.61
140_H	285_Y	0.514	0.61
184_A	256_P	0.513	0.61
172_I	209_I	0.513	0.61
170_F	281_A	0.513	0.61
239_I	243_F	0.513	0.61
232_M	242_S	0.512	0.61
212_L	244_I	0.511	0.61
238_W	248_I	0.511	0.61
239_I	242_S	0.511	0.61
93_M	96_L	0.511	0.61
51_N	121_S	0.507	0.60
10_A	71_A	0.506	0.60
322_I	327_G	0.504	0.60
197_R	219_V	0.503	0.59
12_S	318_I	0.503	0.59
170_F	320_A	0.502	0.59
32_G	36_M	0.501	0.59
7_A	300_V	0.501	0.59
53_F	57_T	0.501	0.59
114_R	183_L	0.500	0.59
187_S	191_E	0.500	0.59

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
1zzaA	1	0.1474	31.1	0.966	Contact Map
2mfrA	1	0.1503	24.5	0.967	Contact Map
4wgvA	2	0.5578	19.9	0.969	Contact Map
2kncA	1	0.1387	19.7	0.969	Contact Map
2l8sA	1	0.1329	18.6	0.969	Contact Map
2yevB	1	0.1474	9.2	0.973	Contact Map
2m3eA	1	0.1387	8.5	0.973	Contact Map
4tphA	2	0.8237	8.3	0.974	Contact Map
4x5mA	2	0.2717	7.7	0.974	Contact Map
2m20A	2	0.1098	7.6	0.974	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.

Page generated in 0.0098 seconds.