YFJR - BACSU - GREMLIN Contacts

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YFJR - Uncharacterized oxidoreductase YfjR

UniProt:	O34969	Sequences: MKIAVIGLGNMGQPIARNVLQAGYELTVYNRTKQKTEDLVTEGAQAADTPRLAAKSADIVITMLADDDSVSTVTFGEDGLLEGLAENGIHISMSTISVEFSEKLAAAHAEKGQFFLAAPVLGRPDAAAKAALRIITAGPAEAKQAAKPLLDSLSQQIFDVGEESKTANAAKISINFLLVSMLEALSESFLMMEKYGLEQKQFLEIASALFGSPVYQNYGTIMAEQKFEPAGFKMSLGLKDTNLALAAAKRVSANLPLAELAKSHFESGIEKGFGDLDWAALIKCIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	286 (275)
Sequences:	11491 (7540)
Seq/√Len:	454.6

ECOLI - GARR YGBJ GLXR SQUU 6PGD
BACSU - YFJR YKWC YQEC 6PGD 6PGDH
HALSA - Q9HMG5
SULSO - Q97XZ7 Q97ZE5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
147_K	151_D	3.603	1.00
71_S	103_K	3.305	1.00
140_A	144_Q	3.303	1.00
27_T	47_A	2.973	1.00
114_F	142_A	2.839	1.00
2_K	25_E	2.773	1.00
114_F	145_A	2.689	1.00
17_R	42_E	2.680	1.00
40_V	46_A	2.670	1.00
48_D	52_L	2.323	1.00
235_S	275_D	2.289	1.00
37_E	41_T	2.201	1.00
144_Q	147_K	2.184	1.00
36_T	46_A	2.154	1.00
108_H	113_Q	2.146	1.00
89_I	146_A	2.017	1.00
13_Q	38_D	1.995	1.00
211_G	216_Q	1.973	1.00
20_L	44_A	1.967	1.00
140_A	159_D	1.904	1.00
198_E	201_Q	1.899	1.00
24_Y	152_S	1.892	1.00
81_L	108_H	1.889	1.00
114_F	139_P	1.822	1.00
62_T	90_H	1.817	1.00
4_A	53_A	1.800	1.00
99_E	250_R	1.777	1.00
247_A	250_R	1.775	1.00
49_T	52_L	1.770	1.00
18_N	21_Q	1.766	1.00
85_A	88_G	1.728	1.00
22_A	152_S	1.727	1.00
32_T	35_K	1.723	1.00
34_Q	37_E	1.704	1.00
235_S	269_I	1.677	1.00
2_K	27_T	1.675	1.00
25_E	45_Q	1.675	1.00
109_A	139_P	1.675	1.00
105_A	163_E	1.670	1.00
33_K	37_E	1.653	1.00
106_A	110_E	1.650	1.00
51_R	55_K	1.639	1.00
192_M	202_F	1.628	1.00
139_P	142_A	1.620	1.00
134_I	153_L	1.619	1.00
74_T	90_H	1.609	1.00
63_M	93_M	1.594	1.00
273_F	276_L	1.577	1.00
107_A	110_E	1.576	1.00
89_I	142_A	1.563	1.00
116_L	138_G	1.552	1.00
84_L	88_G	1.551	1.00
134_I	154_S	1.542	1.00
118_A	134_I	1.524	1.00
143_K	147_K	1.519	1.00
28_V	44_A	1.518	1.00
103_K	107_A	1.493	1.00
18_N	130_A	1.489	1.00
105_A	109_A	1.471	1.00
116_L	146_A	1.461	1.00
61_I	93_M	1.435	1.00
200_K	204_E	1.424	1.00
143_K	159_D	1.422	1.00
37_E	40_V	1.419	1.00
66_D	69_S	1.408	1.00
51_R	83_G	1.402	1.00
124_P	128_A	1.399	1.00
53_A	57_A	1.394	1.00
220_T	224_E	1.382	1.00
180_S	184_A	1.373	1.00
27_T	45_Q	1.371	1.00
160_V	170_A	1.362	1.00
67_D	100_F	1.357	1.00
125_D	129_K	1.357	1.00
172_I	243_L	1.352	1.00
262_K	266_E	1.329	1.00
206_A	210_F	1.328	1.00
27_T	56_S	1.313	1.00
234_M	268_G	1.312	1.00
101_S	115_F	1.311	1.00
102_E	163_E	1.307	1.00
89_I	145_A	1.306	1.00
21_Q	42_E	1.303	1.00
193_E	199_Q	1.300	1.00
56_S	85_A	1.294	1.00
58_D	85_A	1.291	1.00
259_E	263_S	1.291	1.00
235_S	274_G	1.288	1.00
108_H	115_F	1.249	1.00
260_L	263_S	1.246	1.00
17_R	128_A	1.246	1.00
79_G	82_E	1.244	1.00
63_M	120_V	1.242	1.00
131_A	155_Q	1.236	1.00
207_S	216_Q	1.234	1.00
91_I	146_A	1.232	1.00
14_P	128_A	1.227	1.00
116_L	143_K	1.226	1.00
33_K	48_D	1.220	1.00
68_D	72_T	1.218	1.00
238_L	269_I	1.216	1.00
21_Q	128_A	1.202	1.00
59_I	89_I	1.197	1.00
249_K	259_E	1.193	1.00
4_A	57_A	1.191	1.00
146_A	150_L	1.186	1.00
190_L	194_K	1.175	1.00
139_P	162_E	1.172	1.00
16_A	26_L	1.171	1.00
88_G	113_Q	1.164	1.00
179_V	241_T	1.161	1.00
71_S	107_A	1.161	1.00
102_E	169_A	1.161	1.00
248_A	255_L	1.153	1.00
47_A	53_A	1.152	1.00
5_V	15_I	1.151	1.00
82_E	111_K	1.144	1.00
246_A	250_R	1.141	1.00
50_P	83_G	1.138	1.00
84_L	113_Q	1.136	1.00
81_L	111_K	1.135	1.00
59_I	149_L	1.134	1.00
93_M	134_I	1.129	1.00
179_V	237_G	1.122	1.00
39_L	44_A	1.122	1.00
97_S	100_F	1.119	1.00
5_V	16_A	1.114	1.00
195_Y	251_V	1.112	1.00
17_R	21_Q	1.109	1.00
254_N	259_E	1.108	1.00
5_V	61_I	1.094	1.00
38_D	41_T	1.094	1.00
64_L	73_V	1.092	1.00
10_N	124_P	1.069	1.00
245_L	259_E	1.061	1.00
263_S	266_E	1.061	1.00
102_E	106_A	1.049	1.00
90_H	108_H	1.045	1.00
71_S	100_F	1.043	1.00
52_L	55_K	1.041	1.00
107_A	111_K	1.036	1.00
136_T	143_K	1.034	1.00
67_D	97_S	1.030	1.00
238_L	266_E	1.030	1.00
162_E	166_T	1.029	1.00
105_A	139_P	1.026	1.00
93_M	153_L	1.026	1.00
27_T	57_A	1.025	1.00
30_N	35_K	1.024	1.00
106_A	109_A	1.022	1.00
242_N	262_K	1.021	1.00
61_I	149_L	1.019	1.00
84_L	90_H	1.009	1.00
54_A	83_G	0.989	1.00
159_D	162_E	0.989	1.00
206_A	209_L	0.988	1.00
246_A	249_K	0.988	1.00
78_D	107_A	0.987	1.00
38_D	42_E	0.969	1.00
116_L	136_T	0.960	1.00
173_S	192_M	0.957	1.00
189_F	203_L	0.953	1.00
8_L	39_L	0.953	1.00
266_E	270_E	0.951	1.00
234_M	269_I	0.949	1.00
151_D	157_I	0.942	1.00
177_L	188_S	0.941	1.00
232_F	236_L	0.939	1.00
207_S	215_Y	0.939	1.00
127_A	132_L	0.936	1.00
61_I	91_I	0.936	1.00
70_V	96_I	0.935	1.00
50_P	54_A	0.933	1.00
27_T	53_A	0.928	1.00
86_E	112_G	0.927	1.00
201_Q	204_E	0.921	1.00
121_L	174_I	0.921	1.00
69_S	72_T	0.916	1.00
31_R	69_S	0.912	1.00
180_S	257_L	0.911	1.00
173_S	188_S	0.911	1.00
78_D	82_E	0.910	1.00
74_T	108_H	0.906	1.00
242_N	246_A	0.905	1.00
121_L	135_I	0.903	1.00
47_A	52_L	0.902	1.00
20_L	43_G	0.902	1.00
34_Q	38_D	0.896	1.00
138_G	143_K	0.891	1.00
135_I	205_I	0.891	1.00
144_Q	159_D	0.886	1.00
100_F	103_K	0.885	1.00
51_R	79_G	0.885	1.00
160_V	166_T	0.883	1.00
18_N	153_L	0.882	1.00
213_P	217_N	0.878	1.00
13_Q	17_R	0.878	1.00
89_I	114_F	0.878	1.00
169_A	195_Y	0.877	1.00
74_T	80_L	0.875	1.00
5_V	26_L	0.873	1.00
59_I	145_A	0.871	1.00
33_K	46_A	0.870	1.00
97_S	246_A	0.867	1.00
71_S	104_L	0.864	1.00
203_L	219_G	0.863	1.00
194_K	253_A	0.857	1.00
269_I	274_G	0.855	1.00
50_P	53_A	0.853	1.00
101_S	168_N	0.852	1.00
35_K	38_D	0.851	1.00
169_A	247_A	0.850	1.00
91_I	118_A	0.847	1.00
160_V	205_I	0.846	1.00
238_L	262_K	0.843	1.00
96_I	100_F	0.840	1.00
15_I	153_L	0.839	1.00
181_M	212_S	0.834	1.00
19_V	61_I	0.834	1.00
117_A	164_S	0.831	1.00
8_L	28_V	0.829	1.00
186_S	281_L	0.828	1.00
203_L	207_S	0.826	1.00
170_A	197_L	0.825	1.00
268_G	280_A	0.821	1.00
103_K	106_A	0.820	1.00
242_N	266_E	0.815	1.00
142_A	145_A	0.812	1.00
200_K	224_E	0.808	1.00
65_A	69_S	0.803	1.00
183_E	257_L	0.802	1.00
276_L	280_A	0.798	1.00
192_M	197_L	0.797	1.00
117_A	167_A	0.796	1.00
62_T	70_V	0.796	1.00
2_K	58_D	0.795	1.00
46_A	49_T	0.794	1.00
148_P	151_D	0.784	1.00
114_F	141_E	0.783	1.00
267_S	270_E	0.781	1.00
257_L	261_A	0.781	1.00
228_E	276_L	0.781	1.00
6_I	50_P	0.779	1.00
60_V	80_L	0.768	1.00
28_V	36_T	0.768	1.00
233_K	236_L	0.768	1.00
99_E	102_E	0.767	1.00
140_A	162_E	0.766	1.00
13_Q	42_E	0.764	1.00
181_M	185_L	0.764	1.00
233_K	275_D	0.754	1.00
185_L	215_Y	0.751	1.00
176_F	258_A	0.750	1.00
194_K	251_V	0.750	1.00
263_S	267_S	0.749	1.00
92_S	115_F	0.748	1.00
142_A	146_A	0.747	1.00
81_L	113_Q	0.737	1.00
147_K	157_I	0.735	1.00
247_A	251_V	0.735	1.00
123_R	126_A	0.735	1.00
15_I	93_M	0.734	1.00
116_L	142_A	0.733	1.00
15_I	132_L	0.730	1.00
6_I	29_Y	0.729	1.00
19_V	26_L	0.728	1.00
95_T	243_L	0.727	1.00
234_M	280_A	0.726	1.00
177_L	185_L	0.725	1.00
137_A	167_A	0.723	1.00
64_L	69_S	0.723	1.00
59_I	91_I	0.721	1.00
20_L	42_E	0.720	1.00
176_F	244_A	0.716	1.00
24_Y	149_L	0.713	1.00
31_R	35_K	0.712	1.00
104_L	115_F	0.711	1.00
3_I	19_V	0.709	1.00
81_L	107_A	0.708	1.00
5_V	63_M	0.707	1.00
245_L	262_K	0.706	1.00
207_S	211_G	0.700	1.00
51_R	54_A	0.698	1.00
3_I	24_Y	0.697	1.00
158_F	205_I	0.694	1.00
62_T	74_T	0.691	1.00
15_I	63_M	0.685	1.00
207_S	210_F	0.683	1.00
219_G	222_M	0.682	1.00
3_I	149_L	0.676	1.00
141_E	144_Q	0.675	1.00
200_K	223_A	0.673	1.00
190_L	193_E	0.671	1.00
20_L	26_L	0.668	1.00
143_K	157_I	0.667	1.00
118_A	136_T	0.662	1.00
2_K	56_S	0.661	1.00
36_T	40_V	0.660	1.00
51_R	78_D	0.659	1.00
100_F	104_L	0.659	1.00
33_K	36_T	0.659	1.00
249_K	262_K	0.656	1.00
267_S	271_K	0.654	1.00
60_V	84_L	0.652	1.00
177_L	184_A	0.650	1.00
70_V	94_S	0.648	1.00
181_M	214_V	0.646	1.00
170_A	202_F	0.645	1.00
13_Q	39_L	0.643	1.00
70_V	100_F	0.640	0.99
64_L	70_V	0.639	0.99
150_L	157_I	0.639	0.99
172_I	244_A	0.635	0.99
173_S	191_M	0.635	0.99
80_L	84_L	0.634	0.99
177_L	181_M	0.631	0.99
182_L	278_W	0.629	0.99
136_T	150_L	0.628	0.99
197_L	202_F	0.628	0.99
16_A	28_V	0.628	0.99
219_G	223_A	0.624	0.99
147_K	159_D	0.623	0.99
137_A	159_D	0.623	0.99
126_A	131_A	0.622	0.99
150_L	154_S	0.622	0.99
96_I	168_N	0.615	0.99
156_Q	204_E	0.613	0.99
242_N	249_K	0.613	0.99
213_P	216_Q	0.611	0.99
169_A	197_L	0.611	0.99
191_M	255_L	0.609	0.99
115_F	163_E	0.608	0.99
73_V	79_G	0.606	0.99
97_S	243_L	0.605	0.99
57_A	60_V	0.604	0.99
238_L	242_N	0.604	0.99
268_G	273_F	0.603	0.99
137_A	164_S	0.603	0.99
96_I	101_S	0.603	0.99
30_N	33_K	0.602	0.99
11_M	15_I	0.602	0.99
221_I	226_K	0.601	0.99
118_A	150_L	0.600	0.99
180_S	261_A	0.599	0.99
203_L	223_A	0.598	0.99
177_L	206_A	0.598	0.99
68_D	71_S	0.598	0.99
72_T	78_D	0.597	0.99
46_A	50_P	0.595	0.99
72_T	79_G	0.593	0.99
53_A	56_S	0.587	0.99
245_L	249_K	0.586	0.99
86_E	111_K	0.585	0.99
9_G	65_A	0.583	0.99
14_P	124_P	0.581	0.99
70_V	92_S	0.581	0.99
208_A	211_G	0.580	0.99
30_N	69_S	0.578	0.99
52_L	56_S	0.578	0.99
62_T	92_S	0.576	0.99
164_S	167_A	0.575	0.99
190_L	253_A	0.573	0.99
55_K	83_G	0.572	0.99
136_T	157_I	0.571	0.99
85_A	113_Q	0.571	0.99
60_V	88_G	0.570	0.99
186_S	222_M	0.565	0.99
17_R	20_L	0.563	0.99
36_T	39_L	0.562	0.99
140_A	143_K	0.561	0.99
126_A	129_K	0.560	0.99
91_I	150_L	0.559	0.99
254_N	270_E	0.557	0.99
70_V	104_L	0.554	0.99
45_Q	56_S	0.552	0.99
218_Y	222_M	0.551	0.98
142_A	163_E	0.551	0.98
47_A	54_A	0.550	0.98
8_L	16_A	0.549	0.98
149_L	152_S	0.547	0.98
59_I	146_A	0.547	0.98
99_E	103_K	0.547	0.98
148_P	152_S	0.546	0.98
98_V	169_A	0.544	0.98
51_R	82_E	0.543	0.98
17_R	38_D	0.540	0.98
47_A	51_R	0.537	0.98
254_N	267_S	0.537	0.98
37_E	46_A	0.536	0.98
61_I	153_L	0.534	0.98
176_F	191_M	0.533	0.98
74_T	104_L	0.530	0.98
92_S	101_S	0.527	0.98
178_L	214_V	0.526	0.98
266_E	269_I	0.526	0.98
226_K	229_P	0.526	0.98
61_I	150_L	0.525	0.98
257_L	260_L	0.524	0.98
264_H	267_S	0.519	0.98
263_S	270_E	0.515	0.98
140_A	147_K	0.513	0.98
189_F	219_G	0.513	0.98
4_A	27_T	0.512	0.98
199_Q	223_A	0.510	0.98
58_D	88_G	0.509	0.97
122_G	132_L	0.509	0.97
166_T	169_A	0.508	0.97
14_P	130_A	0.508	0.97
18_N	22_A	0.505	0.97
101_S	163_E	0.503	0.97
84_L	87_N	0.501	0.97
30_N	36_T	0.500	0.97

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
3dojA	3	0.993	100	0.355	Contact Map
3pefA	5	0.993	100	0.356	Contact Map
3pduA	4	0.993	100	0.357	Contact Map
1vpdA	1	0.993	100	0.358	Contact Map
3ckyA	4	0.993	100	0.358	Contact Map
3obbA	4	0.9895	100	0.36	Contact Map
3zgyA	2	0.979	100	0.364	Contact Map
3g0oA	3	0.9825	100	0.367	Contact Map
2uyyA	3	0.993	100	0.369	Contact Map
1yb4A	4	0.9895	100	0.37	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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