YTBE - BACSU - GREMLIN Contacts

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YTBE - Uncharacterized oxidoreductase YtbE

UniProt:	O34678	Sequences: MTTHLQAKATLHNGVEMPWFGLGVFQVEEGSELVNAVKTAIVHGYRSIDTAAIYGNEAGVGEGIREGIEEAGISREDLFITSKVWNADLGYEETLAAFETSLSKLGLDYLDLYLIHWPVEGKYKEAWRALETLYKEGRIKAIGVSNFQIHHLEDLMTAAEIKPMINQVEFHPRLTQKELIRYCQNQGIQMEAWSPLMQGQLLDHPVLADIAQTYNKSVAQIILRWDLQHGIITIPKSTKEHRIKENASVFDFELTQDDMNRIDALNENLRVGPDPDNFDF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	280 (255)
Sequences:	32311 (20800)
Seq/√Len:	1302.5

ECOLI - YAJO YDHF YDJG TAS GPR DKGA YEAE DKGB YDBC
BACSU - YTBE GR YRPG GS69 YCSN IOLS YCCK YQKF
HALSA - Q9HS02 Q9HPH9 Q9HNN3 Q9HQU7 Q9HSE6 Q9HQT1
SULSO - Q97UG6 Q97UV9 Q97ZZ1 Q97UJ7 Q97V56 Q97U17

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_T	244_K	3.237	1.00
99_E	138_R	2.900	1.00
30_G	66_E	2.762	1.00
214_Y	258_D	2.753	1.00
255_T	258_D	2.563	1.00
95_L	132_T	2.477	1.00
39_T	43_H	2.380	1.00
98_F	133_L	2.379	1.00
95_L	136_E	2.315	1.00
69_E	106_G	2.312	1.00
131_E	135_K	2.119	1.00
109_Y	140_K	2.109	1.00
213_T	261_R	2.107	1.00
228_Q	259_M	2.095	1.00
182_Y	186_Q	2.075	1.00
39_T	240_E	2.050	1.00
240_E	244_K	2.046	1.00
100_T	104_K	2.045	1.00
132_T	136_E	2.044	1.00
183_C	190_M	1.968	1.00
213_T	258_D	1.955	1.00
208_A	212_Q	1.943	1.00
21_G	47_S	1.885	1.00
256_Q	260_N	1.853	1.00
43_H	244_K	1.851	1.00
91_Y	132_T	1.845	1.00
74_S	77_D	1.837	1.00
209_D	261_R	1.816	1.00
153_E	182_Y	1.716	1.00
216_K	252_F	1.698	1.00
229_H	263_D	1.692	1.00
40_A	45_Y	1.685	1.00
153_E	157_T	1.678	1.00
34_V	38_K	1.675	1.00
114_L	165_I	1.671	1.00
39_T	42_V	1.661	1.00
132_T	135_K	1.645	1.00
189_Q	232_I	1.644	1.00
84_V	113_Y	1.642	1.00
91_Y	95_L	1.640	1.00
43_H	247_A	1.636	1.00
34_V	66_E	1.630	1.00
95_L	99_E	1.630	1.00
217_S	245_E	1.599	1.00
58_A	62_E	1.598	1.00
129_A	132_T	1.589	1.00
260_N	264_A	1.582	1.00
82_S	110_L	1.581	1.00
82_S	101_S	1.578	1.00
30_G	34_V	1.577	1.00
9_A	16_E	1.576	1.00
248_S	251_D	1.567	1.00
206_V	209_D	1.556	1.00
80_I	107_L	1.552	1.00
224_R	252_F	1.539	1.00
98_F	113_Y	1.538	1.00
131_E	161_I	1.532	1.00
84_V	94_T	1.516	1.00
156_M	186_Q	1.486	1.00
10_T	16_E	1.485	1.00
41_I	78_L	1.477	1.00
96_A	100_T	1.477	1.00
24_V	48_I	1.456	1.00
15_V	141_A	1.456	1.00
81_T	114_L	1.452	1.00
148_Q	151_H	1.434	1.00
184_Q	230_G	1.431	1.00
99_E	103_S	1.427	1.00
181_R	185_N	1.426	1.00
134_Y	161_I	1.419	1.00
52_A	97_A	1.414	1.00
32_E	35_N	1.395	1.00
216_K	220_Q	1.386	1.00
35_N	39_T	1.383	1.00
168_V	190_M	1.382	1.00
178_E	181_R	1.380	1.00
29_E	32_E	1.373	1.00
114_L	191_E	1.356	1.00
224_R	228_Q	1.347	1.00
65_R	106_G	1.326	1.00
38_K	42_V	1.325	1.00
110_L	139_I	1.306	1.00
91_Y	128_R	1.302	1.00
244_K	248_S	1.301	1.00
180_I	184_Q	1.290	1.00
206_V	261_R	1.289	1.00
216_K	221_I	1.283	1.00
141_A	164_M	1.282	1.00
100_T	103_S	1.281	1.00
90_G	93_E	1.280	1.00
124_K	158_A	1.266	1.00
149_I	182_Y	1.256	1.00
15_V	79_F	1.256	1.00
105_L	110_L	1.254	1.00
95_L	129_A	1.253	1.00
208_A	218_V	1.252	1.00
156_M	182_Y	1.250	1.00
261_R	264_A	1.250	1.00
133_L	139_I	1.238	1.00
209_D	213_T	1.231	1.00
237_S	242_R	1.227	1.00
237_S	243_I	1.213	1.00
170_F	229_H	1.211	1.00
34_V	67_G	1.205	1.00
79_F	112_L	1.196	1.00
217_S	220_Q	1.193	1.00
118_P	151_H	1.174	1.00
139_I	142_I	1.173	1.00
47_S	81_T	1.170	1.00
91_Y	129_A	1.169	1.00
93_E	96_A	1.169	1.00
125_E	128_R	1.154	1.00
31_S	35_N	1.153	1.00
92_E	96_A	1.139	1.00
153_E	186_Q	1.132	1.00
75_R	107_L	1.131	1.00
37_V	67_G	1.130	1.00
134_Y	164_M	1.109	1.00
61_G	65_R	1.107	1.00
131_E	134_Y	1.106	1.00
112_L	165_I	1.094	1.00
35_N	240_E	1.092	1.00
65_R	69_E	1.090	1.00
135_K	160_E	1.084	1.00
226_D	233_T	1.079	1.00
241_H	244_K	1.079	1.00
133_L	138_R	1.075	1.00
169_E	174_L	1.074	1.00
47_S	191_E	1.072	1.00
99_E	136_E	1.067	1.00
130_L	142_I	1.062	1.00
75_R	109_Y	1.047	1.00
46_R	79_F	1.038	1.00
115_I	130_L	1.037	1.00
210_I	221_I	1.036	1.00
149_I	153_E	1.035	1.00
153_E	185_N	1.035	1.00
220_Q	248_S	1.027	1.00
175_T	266_N	1.026	1.00
154_D	158_A	1.025	1.00
48_I	64_I	1.020	1.00
209_D	212_Q	1.019	1.00
66_E	106_G	1.018	1.00
13_N	141_A	1.000	1.00
207_L	218_V	0.997	1.00
89_L	115_I	0.993	1.00
9_A	14_G	0.988	1.00
36_A	243_I	0.970	1.00
12_H	164_M	0.970	1.00
98_F	110_L	0.968	1.00
165_I	191_E	0.965	1.00
19_W	250_F	0.964	1.00
19_W	227_L	0.961	1.00
181_R	184_Q	0.961	1.00
220_Q	245_E	0.961	1.00
18_P	46_R	0.960	1.00
177_K	181_R	0.943	1.00
227_L	249_V	0.941	1.00
144_V	163_P	0.939	1.00
111_D	140_K	0.933	1.00
57_E	61_G	0.932	1.00
35_N	38_K	0.927	1.00
88_D	93_E	0.927	1.00
95_L	98_F	0.927	1.00
128_R	132_T	0.919	1.00
182_Y	185_N	0.915	1.00
239_K	242_R	0.915	1.00
133_L	136_E	0.913	1.00
96_A	99_E	0.912	1.00
129_A	133_L	0.910	1.00
58_A	104_K	0.906	1.00
172_P	222_I	0.901	1.00
172_P	262_I	0.900	1.00
62_E	66_E	0.897	1.00
245_E	248_S	0.895	1.00
37_V	48_I	0.893	1.00
124_K	154_D	0.892	1.00
24_V	64_I	0.890	1.00
144_V	152_L	0.884	1.00
62_E	104_K	0.877	1.00
128_R	131_E	0.875	1.00
241_H	245_E	0.874	1.00
228_Q	253_E	0.873	1.00
18_P	45_Y	0.867	1.00
257_D	261_R	0.865	1.00
91_Y	125_E	0.865	1.00
191_E	232_I	0.863	1.00
52_A	100_T	0.863	1.00
95_L	133_L	0.862	1.00
243_I	247_A	0.861	1.00
152_L	188_I	0.854	1.00
52_A	93_E	0.854	1.00
200_Q	203_D	0.854	1.00
260_N	263_D	0.849	1.00
142_I	163_P	0.844	1.00
52_A	88_D	0.841	1.00
210_I	214_Y	0.840	1.00
81_T	112_L	0.833	1.00
52_A	104_K	0.831	1.00
22_L	40_A	0.829	1.00
13_N	164_M	0.823	1.00
229_H	259_M	0.816	1.00
131_E	160_E	0.815	1.00
166_N	183_C	0.810	1.00
81_T	191_E	0.810	1.00
154_D	157_T	0.805	1.00
131_E	142_I	0.805	1.00
68_I	78_L	0.800	1.00
222_I	226_D	0.793	1.00
206_V	265_L	0.790	1.00
173_R	204_H	0.787	1.00
41_I	74_S	0.787	1.00
175_T	263_D	0.784	1.00
156_M	162_K	0.784	1.00
38_K	67_G	0.779	1.00
39_T	243_I	0.778	1.00
257_D	260_N	0.772	1.00
170_F	180_I	0.770	1.00
43_H	248_S	0.770	1.00
214_Y	255_T	0.766	1.00
223_L	249_V	0.764	1.00
179_L	183_C	0.764	1.00
149_I	179_L	0.763	1.00
213_T	255_T	0.762	1.00
45_Y	247_A	0.749	1.00
180_I	190_M	0.745	1.00
238_T	242_R	0.745	1.00
13_N	134_Y	0.740	1.00
41_I	48_I	0.739	1.00
219_A	245_E	0.735	1.00
34_V	63_G	0.734	1.00
224_R	249_V	0.730	1.00
149_I	178_E	0.725	1.00
228_Q	256_Q	0.724	1.00
180_I	229_H	0.722	1.00
34_V	62_E	0.720	1.00
102_L	138_R	0.717	1.00
98_F	138_R	0.710	1.00
102_L	107_L	0.710	1.00
97_A	100_T	0.708	1.00
203_D	208_A	0.707	1.00
82_S	113_Y	0.705	1.00
89_L	126_A	0.703	1.00
24_V	60_V	0.700	1.00
38_K	72_G	0.699	1.00
192_A	195_P	0.698	1.00
94_T	133_L	0.697	1.00
101_S	113_Y	0.695	1.00
31_S	34_V	0.695	1.00
20_F	227_L	0.695	1.00
127_W	142_I	0.694	1.00
146_N	193_W	0.690	1.00
114_L	143_G	0.686	1.00
30_G	63_G	0.684	1.00
38_K	74_S	0.683	1.00
144_V	147_F	0.683	1.00
57_E	104_K	0.681	1.00
202_L	205_P	0.680	1.00
50_T	64_I	0.679	1.00
38_K	73_I	0.679	1.00
225_W	263_D	0.678	1.00
195_P	235_P	0.677	1.00
61_G	101_S	0.675	1.00
10_T	13_N	0.673	1.00
192_A	233_T	0.672	1.00
64_I	68_I	0.667	1.00
117_W	146_N	0.666	1.00
9_A	19_W	0.666	1.00
127_W	155_L	0.666	1.00
183_C	188_I	0.663	1.00
46_R	77_D	0.662	1.00
170_F	226_D	0.659	1.00
211_A	221_I	0.659	1.00
17_M	232_I	0.658	1.00
36_A	240_E	0.656	1.00
212_Q	215_N	0.652	1.00
126_A	129_A	0.652	1.00
41_I	67_G	0.649	1.00
69_E	73_I	0.649	1.00
210_I	258_D	0.648	1.00
30_G	58_A	0.641	1.00
41_I	77_D	0.640	1.00
214_Y	221_I	0.636	1.00
94_T	126_A	0.636	1.00
127_W	163_P	0.633	1.00
195_P	226_D	0.633	1.00
76_E	109_Y	0.630	1.00
9_A	189_Q	0.628	1.00
110_L	113_Y	0.627	1.00
21_G	235_P	0.626	1.00
43_H	243_I	0.625	1.00
26_Q	198_Q	0.624	1.00
153_E	156_M	0.623	1.00
131_E	159_A	0.623	1.00
254_L	259_M	0.619	1.00
73_I	78_L	0.617	1.00
27_V	33_L	0.616	1.00
226_D	231_I	0.615	1.00
134_Y	139_I	0.615	1.00
242_R	245_E	0.615	1.00
15_V	140_K	0.614	1.00
221_I	254_L	0.614	1.00
57_E	60_V	0.614	1.00
124_K	128_R	0.614	1.00
12_H	187_G	0.614	1.00
94_T	129_A	0.613	1.00
144_V	166_N	0.612	1.00
22_L	27_V	0.611	1.00
170_F	231_I	0.611	1.00
42_V	240_E	0.609	1.00
216_K	248_S	0.608	1.00
207_L	222_I	0.604	1.00
170_F	190_M	0.598	1.00
194_S	198_Q	0.598	1.00
102_L	109_Y	0.597	1.00
41_I	46_R	0.596	1.00
123_Y	158_A	0.595	1.00
207_L	262_I	0.594	1.00
170_F	175_T	0.594	1.00
258_D	261_R	0.594	1.00
216_K	251_D	0.590	1.00
123_Y	126_A	0.588	1.00
201_L	222_I	0.584	1.00
221_I	262_I	0.584	1.00
32_E	240_E	0.584	1.00
95_L	138_R	0.584	1.00
90_G	126_A	0.584	1.00
130_L	134_Y	0.579	1.00
53_I	85_W	0.577	1.00
58_A	63_G	0.575	1.00
220_Q	252_F	0.571	1.00
49_D	167_Q	0.571	1.00
151_H	154_D	0.570	1.00
211_A	214_Y	0.568	1.00
135_K	161_I	0.568	1.00
113_Y	139_I	0.565	1.00
37_V	64_I	0.563	1.00
189_Q	231_I	0.563	1.00
237_S	246_N	0.561	1.00
33_L	63_G	0.560	1.00
221_I	258_D	0.560	1.00
22_L	36_A	0.559	1.00
102_L	110_L	0.559	1.00
211_A	218_V	0.558	1.00
12_H	162_K	0.557	1.00
62_E	103_S	0.556	1.00
227_L	233_T	0.556	1.00
25_F	194_S	0.554	1.00
102_L	108_D	0.554	1.00
123_Y	151_H	0.552	1.00
36_A	237_S	0.550	1.00
173_R	200_Q	0.549	1.00
98_F	102_L	0.548	1.00
91_Y	94_T	0.547	1.00
37_V	41_I	0.543	1.00
221_I	252_F	0.543	1.00
134_Y	141_A	0.541	1.00
74_S	78_L	0.537	1.00
84_V	97_A	0.536	1.00
259_M	263_D	0.535	1.00
115_I	126_A	0.534	1.00
210_I	261_R	0.534	1.00
254_L	258_D	0.530	1.00
123_Y	154_D	0.529	1.00
144_V	155_L	0.525	1.00
28_E	60_V	0.524	1.00
207_L	211_A	0.523	1.00
142_I	161_I	0.523	1.00
54_Y	116_H	0.520	1.00
192_A	226_D	0.519	1.00
84_V	89_L	0.518	1.00
27_V	36_A	0.517	1.00
156_M	188_I	0.516	1.00
67_G	72_G	0.512	1.00
101_S	104_K	0.511	1.00
68_I	74_S	0.510	1.00
20_F	250_F	0.508	1.00
113_Y	130_L	0.506	1.00
150_H	153_E	0.504	1.00
112_L	141_A	0.504	1.00
40_A	48_I	0.502	1.00
224_R	253_E	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
3b3dA	1	0.9786	100	0.116	Contact Map
3f7jA	1	0.9821	100	0.117	Contact Map
4f40A	1	0.9643	100	0.125	Contact Map
3v0sA	1	0.9	100	0.125	Contact Map
4otkA	1	0.975	100	0.126	Contact Map
2wzmA	1	0.9679	100	0.126	Contact Map
1pyfA	1	0.925	100	0.129	Contact Map
4r9oA	5	0.9464	100	0.13	Contact Map
3wbwA	1	0.9571	100	0.13	Contact Map
4q3mA	2	0.9607	100	0.13	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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