YFII - BACSU - GREMLIN Contacts

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YFII - Uncharacterized oxidoreductase YfiI

UniProt:	P94437	Sequences: MMLNGERIISKPLRWAMVGGGRLSQVGYKHRIGALRDNTAFQLTAGAFDIDAERGKDFGVNLGVDAERCYPNYQTMFAEEAKRQDGIEVVSIATPNGTHYEICKAALEAGVHVICEKPLFFTSAEGQEIKALAEKKGKIVGVTYGFSGNQMLLQMRAMIEQGMIGDIRVVDLQYTHGFCATDEGEKISAAQKWRVDPAIAGPSFVLGDLSTHTYYMSQLIMPKMKIKELLCDRQSFVGSRAPLEDNAHVLMHYENGAVGTMWTSSINAGCMDGHRIRIVGSKASIEWWDSKPNELTYEVQGEPGQTLVRGMPYLDDVCNADERLGALHSEGLSEAWANIYLKFAIAIDAKNREDEEILNNLVYPDIDAGIEGIRWIENCVRSANQGSVWVEFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	393 (321)
Sequences:	24110 (17773)
Seq/√Len:	992.0

ECOLI - YCJS YGJR YDGJ YJHC YHHX YCEM
BACSU - YFII YRBE NTDC IOLX IOLW IOLG YULF YTET
SULSO - Q97UH0 Q97UJ6 Q97UK3 Q97UK0 Q97UJ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_Q	105_A	3.002	1.00
14_R	42_Q	2.797	1.00
104_K	132_L	2.793	1.00
147_S	215_Y	2.793	1.00
228_E	252_H	2.766	1.00
154_Q	157_A	2.703	1.00
127_Q	370_I	2.692	1.00
166_D	281_S	2.678	1.00
100_Y	128_E	2.671	1.00
52_A	56_K	2.671	1.00
108_E	132_L	2.509	1.00
227_K	254_E	2.491	1.00
156_R	160_E	2.407	1.00
104_K	128_E	2.346	1.00
16_A	76_M	2.324	1.00
100_Y	125_E	2.289	1.00
104_K	108_E	2.265	1.00
112_H	139_I	2.264	1.00
249_V	379_C	2.264	1.00
107_L	138_K	2.258	1.00
94_T	102_I	2.254	1.00
72_N	75_T	2.195	1.00
381_R	385_Q	2.160	1.00
131_A	135_K	2.131	1.00
45_A	70_Y	2.096	1.00
134_E	367_D	2.072	1.00
157_A	161_Q	2.070	1.00
12_P	42_Q	2.043	1.00
98_T	102_I	2.025	1.00
56_K	60_V	1.975	1.00
345_I	349_A	1.969	1.00
127_Q	374_R	1.959	1.00
40_A	348_D	1.944	1.00
89_V	343_F	1.925	1.00
127_Q	131_A	1.906	1.00
100_Y	104_K	1.896	1.00
103_C	115_C	1.886	1.00
107_L	133_A	1.885	1.00
154_Q	158_M	1.873	1.00
68_R	84_Q	1.869	1.00
164_I	280_G	1.830	1.00
132_L	136_K	1.806	1.00
16_A	87_I	1.776	1.00
94_T	98_T	1.770	1.00
101_E	105_A	1.761	1.00
37_D	40_A	1.732	1.00
112_H	138_K	1.703	1.00
51_D	54_R	1.696	1.00
108_E	136_K	1.694	1.00
71_P	75_T	1.689	1.00
34_A	91_S	1.680	1.00
123_S	377_E	1.679	1.00
15_W	89_V	1.678	1.00
87_I	111_V	1.673	1.00
253_Y	259_G	1.668	1.00
90_V	106_A	1.633	1.00
122_T	125_E	1.630	1.00
155_M	285_I	1.612	1.00
103_C	129_I	1.605	1.00
140_V	366_I	1.600	1.00
37_D	341_L	1.595	1.00
41_F	344_A	1.584	1.00
108_E	135_K	1.574	1.00
227_K	252_H	1.558	1.00
139_I	350_K	1.558	1.00
77_F	106_A	1.546	1.00
64_V	67_E	1.546	1.00
78_A	109_A	1.535	1.00
73_Y	105_A	1.467	1.00
371_E	374_R	1.462	1.00
158_M	163_M	1.460	1.00
225_K	371_E	1.446	1.00
233_R	383_A	1.446	1.00
57_D	61_N	1.443	1.00
143_T	339_I	1.441	1.00
130_K	370_I	1.441	1.00
121_F	125_E	1.440	1.00
130_K	366_I	1.440	1.00
156_R	219_L	1.437	1.00
218_Q	225_K	1.421	1.00
100_Y	129_I	1.418	1.00
168_R	281_S	1.416	1.00
225_K	254_E	1.413	1.00
28_Y	61_N	1.406	1.00
75_T	78_A	1.403	1.00
74_Q	78_A	1.381	1.00
55_G	69_C	1.366	1.00
171_D	277_R	1.355	1.00
221_M	257_A	1.349	1.00
70_Y	76_M	1.346	1.00
132_L	135_K	1.336	1.00
70_Y	84_Q	1.335	1.00
107_L	136_K	1.333	1.00
120_F	129_I	1.331	1.00
105_A	108_E	1.323	1.00
345_I	351_N	1.322	1.00
14_R	44_T	1.322	1.00
52_A	71_P	1.321	1.00
14_R	88_E	1.312	1.00
164_I	283_A	1.308	1.00
47_A	73_Y	1.304	1.00
167_I	278_I	1.301	1.00
126_G	370_I	1.296	1.00
20_G	46_G	1.293	1.00
342_K	346_A	1.285	1.00
105_A	109_A	1.285	1.00
226_I	253_Y	1.264	1.00
120_F	126_G	1.248	1.00
214_Y	375_W	1.235	1.00
218_Q	371_E	1.234	1.00
232_D	252_H	1.232	1.00
92_I	102_I	1.223	1.00
85_D	111_V	1.223	1.00
123_S	374_R	1.221	1.00
218_Q	253_Y	1.220	1.00
123_S	127_Q	1.218	1.00
128_E	131_A	1.211	1.00
47_A	76_M	1.209	1.00
277_R	286_E	1.201	1.00
106_A	113_V	1.199	1.00
342_K	363_Y	1.197	1.00
53_E	56_K	1.190	1.00
27_G	32_I	1.188	1.00
86_G	111_V	1.187	1.00
76_M	87_I	1.164	1.00
73_Y	102_I	1.162	1.00
381_R	384_N	1.161	1.00
92_I	103_C	1.154	1.00
365_D	368_A	1.146	1.00
158_M	161_Q	1.146	1.00
59_G	69_C	1.146	1.00
45_A	76_M	1.141	1.00
107_L	132_L	1.139	1.00
112_H	350_K	1.139	1.00
341_L	345_I	1.138	1.00
130_K	367_D	1.129	1.00
57_D	60_V	1.129	1.00
131_A	134_E	1.125	1.00
95_P	98_T	1.110	1.00
110_G	136_K	1.105	1.00
119_L	126_G	1.096	1.00
97_G	199_I	1.095	1.00
40_A	341_L	1.094	1.00
126_G	373_I	1.088	1.00
128_E	132_L	1.079	1.00
342_K	351_N	1.075	1.00
15_W	41_F	1.073	1.00
40_A	345_I	1.070	1.00
170_V	221_M	1.069	1.00
164_I	285_I	1.068	1.00
275_R	286_E	1.065	1.00
378_N	381_R	1.061	1.00
171_D	262_W	1.058	1.00
13_L	89_V	1.054	1.00
104_K	129_I	1.048	1.00
77_F	109_A	1.044	1.00
152_L	219_L	1.043	1.00
164_I	167_I	1.043	1.00
73_Y	77_F	1.043	1.00
377_E	381_R	1.035	1.00
218_Q	368_A	1.032	1.00
217_S	259_G	1.030	1.00
36_R	337_A	1.030	1.00
230_L	250_L	1.029	1.00
77_F	105_A	1.027	1.00
13_L	347_I	1.024	1.00
84_Q	111_V	1.022	1.00
196_D	199_I	1.017	1.00
18_V	102_I	1.016	1.00
125_E	128_E	1.015	1.00
30_H	91_S	1.011	1.00
344_A	348_D	1.004	1.00
63_G	67_E	1.002	1.00
157_A	160_E	1.001	1.00
45_A	87_I	0.996	1.00
112_H	347_I	0.994	1.00
170_V	259_G	0.986	1.00
226_I	251_M	0.986	1.00
148_G	342_K	0.985	1.00
167_I	221_M	0.982	1.00
32_I	61_N	0.976	1.00
129_I	140_V	0.975	1.00
55_G	71_P	0.975	1.00
115_C	140_V	0.973	1.00
124_A	127_Q	0.967	1.00
84_Q	87_I	0.965	1.00
120_F	125_E	0.965	1.00
147_S	368_A	0.956	1.00
114_I	143_T	0.956	1.00
361_L	365_D	0.948	1.00
153_L	363_Y	0.946	1.00
130_K	134_E	0.946	1.00
54_R	57_D	0.941	1.00
342_K	345_I	0.937	1.00
53_E	57_D	0.936	1.00
13_L	348_D	0.931	1.00
155_M	287_W	0.930	1.00
32_I	36_R	0.930	1.00
114_I	339_I	0.929	1.00
119_L	366_I	0.925	1.00
133_A	136_K	0.914	1.00
70_Y	75_T	0.913	1.00
102_I	105_A	0.913	1.00
56_K	69_C	0.913	1.00
124_A	128_E	0.911	1.00
12_P	40_A	0.910	1.00
337_A	341_L	0.908	1.00
103_C	113_V	0.908	1.00
167_I	280_G	0.908	1.00
46_G	58_F	0.908	1.00
170_V	278_I	0.899	1.00
338_N	341_L	0.899	1.00
123_S	370_I	0.898	1.00
145_G	335_A	0.891	1.00
20_G	49_D	0.879	1.00
107_L	113_V	0.878	1.00
119_L	140_V	0.877	1.00
52_A	55_G	0.875	1.00
345_I	350_K	0.874	1.00
232_D	258_V	0.873	1.00
75_T	84_Q	0.869	1.00
141_G	343_F	0.866	1.00
92_I	106_A	0.864	1.00
68_R	86_G	0.861	1.00
14_R	87_I	0.860	1.00
165_G	280_G	0.857	1.00
286_E	296_T	0.857	1.00
55_G	59_G	0.857	1.00
139_I	347_I	0.855	1.00
16_A	45_A	0.852	1.00
115_C	119_L	0.844	1.00
197_P	242_P	0.843	1.00
367_D	371_E	0.843	1.00
103_C	107_L	0.840	1.00
214_Y	376_I	0.840	1.00
15_W	34_A	0.839	1.00
34_A	41_F	0.839	1.00
100_Y	120_F	0.839	1.00
226_I	375_W	0.838	1.00
98_T	101_E	0.836	1.00
56_K	59_G	0.832	1.00
52_A	69_C	0.832	1.00
96_N	208_D	0.827	1.00
231_C	379_C	0.827	1.00
346_A	349_A	0.825	1.00
248_H	260_T	0.823	1.00
49_D	55_G	0.820	1.00
17_M	31_R	0.817	1.00
49_D	54_R	0.811	1.00
133_A	140_V	0.808	1.00
380_V	384_N	0.808	1.00
226_I	254_E	0.807	1.00
171_D	260_T	0.807	1.00
172_L	276_I	0.806	1.00
18_V	73_Y	0.806	1.00
44_T	68_R	0.803	1.00
196_D	242_P	0.803	1.00
230_L	382_S	0.802	1.00
127_Q	130_K	0.800	1.00
204_F	244_E	0.800	1.00
37_D	41_F	0.796	1.00
346_A	351_N	0.796	1.00
44_T	86_G	0.795	1.00
115_C	129_I	0.794	1.00
59_G	64_V	0.793	1.00
165_G	283_A	0.792	1.00
16_A	47_A	0.790	1.00
91_S	340_Y	0.790	1.00
173_Q	275_R	0.788	1.00
346_A	362_V	0.786	1.00
153_L	157_A	0.784	1.00
378_N	382_S	0.782	1.00
170_V	217_S	0.779	1.00
299_V	302_E	0.774	1.00
228_E	386_G	0.773	1.00
107_L	140_V	0.772	1.00
34_A	340_Y	0.770	1.00
351_N	361_L	0.768	1.00
133_A	366_I	0.766	1.00
277_R	284_S	0.760	1.00
64_V	68_R	0.759	1.00
159_I	280_G	0.755	1.00
44_T	87_I	0.754	1.00
141_G	346_A	0.753	1.00
133_A	138_K	0.752	1.00
26_V	32_I	0.750	1.00
217_S	253_Y	0.745	1.00
31_R	43_L	0.745	1.00
244_E	380_V	0.744	1.00
342_K	362_V	0.743	1.00
44_T	84_Q	0.743	1.00
30_H	340_Y	0.742	1.00
250_L	258_V	0.741	1.00
139_I	346_A	0.741	1.00
205_V	263_T	0.740	1.00
166_D	282_K	0.739	1.00
374_R	378_N	0.737	1.00
251_M	259_G	0.734	1.00
210_S	263_T	0.730	1.00
126_G	130_K	0.730	1.00
218_Q	372_G	0.728	1.00
115_C	142_V	0.727	1.00
100_Y	132_L	0.725	1.00
18_V	94_T	0.724	1.00
343_F	347_I	0.723	1.00
89_V	112_H	0.722	1.00
166_D	255_N	0.722	1.00
58_F	61_N	0.721	1.00
197_P	384_N	0.718	1.00
163_M	299_V	0.715	1.00
172_L	213_T	0.714	1.00
173_Q	262_W	0.711	1.00
228_E	232_D	0.708	1.00
336_W	339_I	0.708	1.00
373_I	377_E	0.706	1.00
211_T	372_G	0.705	1.00
370_I	374_R	0.704	1.00
275_R	288_W	0.703	1.00
221_M	253_Y	0.703	1.00
208_D	265_S	0.700	1.00
119_L	142_V	0.698	1.00
104_K	107_L	0.697	1.00
206_L	376_I	0.697	1.00
160_E	222_P	0.696	1.00
232_D	250_L	0.695	1.00
18_V	47_A	0.695	1.00
142_V	369_G	0.695	1.00
20_G	55_G	0.692	1.00
40_A	344_A	0.687	1.00
111_V	138_K	0.687	1.00
282_K	300_Q	0.686	1.00
159_I	278_I	0.685	1.00
16_A	90_V	0.680	1.00
51_D	56_K	0.680	1.00
139_I	361_L	0.679	1.00
175_T	262_W	0.678	1.00
144_Y	211_T	0.676	1.00
107_L	129_I	0.672	1.00
279_V	284_S	0.670	1.00
212_H	215_Y	0.668	1.00
101_E	128_E	0.665	1.00
169_V	258_V	0.663	1.00
147_S	219_L	0.663	1.00
220_I	278_I	0.662	1.00
299_V	303_P	0.660	1.00
70_Y	85_D	0.660	1.00
234_Q	252_H	0.659	1.00
42_Q	67_E	0.657	1.00
14_R	86_G	0.656	1.00
99_H	115_C	0.651	1.00
15_W	344_A	0.651	1.00
146_F	149_N	0.650	1.00
152_L	216_M	0.648	1.00
110_G	138_K	0.647	1.00
73_Y	106_A	0.646	1.00
366_I	369_G	0.646	1.00
26_V	30_H	0.643	1.00
253_Y	257_A	0.638	1.00
351_N	362_V	0.637	1.00
252_H	258_V	0.637	1.00
174_Y	209_L	0.635	1.00
245_D	266_I	0.635	1.00
20_G	58_F	0.634	1.00
218_Q	375_W	0.634	1.00
90_V	111_V	0.632	1.00
159_I	220_I	0.632	1.00
206_L	247_A	0.630	1.00
172_L	217_S	0.629	1.00
368_A	371_E	0.628	1.00
299_V	304_G	0.628	1.00
46_G	69_C	0.628	1.00
27_G	58_F	0.628	1.00
210_S	213_T	0.628	1.00
89_V	347_I	0.622	1.00
144_Y	215_Y	0.621	1.00
231_C	249_V	0.620	1.00
15_W	91_S	0.619	1.00
76_M	84_Q	0.615	1.00
114_I	141_G	0.615	1.00
215_Y	372_G	0.614	1.00
167_I	257_A	0.613	1.00
264_S	267_N	0.612	1.00
153_L	338_N	0.611	1.00
58_F	62_L	0.609	1.00
295_L	298_E	0.609	1.00
144_Y	372_G	0.609	1.00
31_R	58_F	0.608	1.00
236_F	245_D	0.607	1.00
121_F	200_A	0.607	1.00
225_K	374_R	0.606	1.00
145_G	336_W	0.605	1.00
231_C	247_A	0.605	1.00
193_W	196_D	0.604	1.00
27_G	31_R	0.601	1.00
215_Y	219_L	0.600	1.00
249_V	261_M	0.597	1.00
155_M	220_I	0.593	1.00
251_M	261_M	0.592	1.00
74_Q	101_E	0.591	1.00
156_R	220_I	0.584	1.00
91_S	114_I	0.583	1.00
372_G	376_I	0.583	1.00
381_R	387_S	0.581	1.00
214_Y	379_C	0.579	1.00
78_A	85_D	0.574	1.00
299_V	305_Q	0.573	1.00
59_G	67_E	0.572	1.00
41_F	89_V	0.571	1.00
103_C	140_V	0.569	1.00
141_G	342_K	0.568	1.00
108_E	128_E	0.566	1.00
117_K	212_H	0.566	1.00
28_Y	32_I	0.565	1.00
230_L	252_H	0.565	1.00
27_G	61_N	0.563	1.00
230_L	387_S	0.562	1.00
345_I	348_D	0.562	1.00
122_T	377_E	0.562	1.00
162_G	280_G	0.560	1.00
237_V	245_D	0.558	1.00
163_M	166_D	0.557	1.00
250_L	260_T	0.554	1.00
233_R	247_A	0.553	1.00
27_G	93_A	0.552	1.00
130_K	133_A	0.552	1.00
12_P	348_D	0.551	1.00
31_R	35_L	0.551	1.00
117_K	208_D	0.551	1.00
30_H	34_A	0.551	1.00
47_A	70_Y	0.549	1.00
162_G	166_D	0.548	1.00
139_I	343_F	0.546	1.00
116_E	143_T	0.546	1.00
124_A	377_E	0.544	1.00
37_D	337_A	0.543	1.00
46_G	55_G	0.542	1.00
119_L	129_I	0.541	1.00
246_N	264_S	0.541	1.00
141_G	339_I	0.540	1.00
101_E	104_K	0.540	1.00
103_C	133_A	0.540	1.00
207_G	377_E	0.539	1.00
229_L	375_W	0.539	1.00
206_L	249_V	0.538	1.00
302_E	305_Q	0.538	1.00
92_I	99_H	0.537	1.00
45_A	68_R	0.537	1.00
78_A	84_Q	0.537	1.00
148_G	364_P	0.537	1.00
217_S	261_M	0.535	1.00
376_I	380_V	0.533	1.00
142_V	212_H	0.533	1.00
30_H	93_A	0.531	1.00
169_V	279_V	0.530	1.00
17_M	43_L	0.529	1.00
251_M	375_W	0.528	1.00
104_K	136_K	0.528	1.00
18_V	92_I	0.528	1.00
50_I	94_T	0.528	1.00
26_V	93_A	0.527	1.00
37_D	344_A	0.526	1.00
139_I	362_V	0.523	1.00
13_L	344_A	0.519	1.00
18_V	90_V	0.519	1.00
38_N	41_F	0.518	1.00
362_V	365_D	0.518	1.00
176_H	209_L	0.517	1.00
21_G	93_A	0.517	1.00
169_V	260_T	0.517	1.00
88_E	348_D	0.515	1.00
231_C	383_A	0.514	1.00
97_G	121_F	0.511	1.00
92_I	113_V	0.510	1.00
194_R	208_D	0.510	1.00
169_V	246_N	0.509	1.00
170_V	276_I	0.509	1.00
146_F	215_Y	0.505	1.00
334_E	337_A	0.504	1.00
146_F	152_L	0.504	1.00
126_G	369_G	0.502	1.00
54_R	58_F	0.500	1.00
156_R	159_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
3dtyA	4	0.8957	100	0.18	Contact Map
3v5nA	4	0.8753	100	0.2	Contact Map
1h6dA	8	0.8753	100	0.222	Contact Map
2nvwA	3	0.8957	100	0.23	Contact Map
4gqaA	4	0.9008	100	0.242	Contact Map
1zh8A	2	0.8142	100	0.242	Contact Map
3btvA	2	0.8728	100	0.244	Contact Map
4fb5A	4	0.8906	100	0.252	Contact Map
3db2A	2	0.8677	100	0.254	Contact Map
3q2iA	4	0.8677	100	0.254	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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