OXYR - ECOLI - GREMLIN Contacts

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OXYR - Hydrogen peroxide-inducible genes activator

UniProt:	P0ACQ4	Sequences: MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGMLLVDQARTVLREVKVLKEMASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCVILALVKESEAFIEVPLFDEPMLLAIYEDHPWANRECVPMADLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPCIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHFDKVLKQAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10681
Length:	305 (286)
Sequences:	79831 (57868)
Seq/√Len:	3421.8

ECOLI - OXYR NAC CYSB CYNR YBHD LYSR CBL YAFC AAER TDCA TTDR YFER DMLR YCAN YHJC PGRR YDHB YAHB METR LEUO ABGR HCAR ALLS YEEY YDCI YFIE YBDO YEIE YNFL ILVY DSDC NHAR YIAU YBEF YNEJ GCVA ICIA XAPR YIDZ YGFI YHAJ YJIE LRHA PERR HDFR
BACSU - YWBI CYSL YCGK GLTR YTLI ALSR GLTC YYBE CITR BSDA YWQM YVBU YUST YOFA YKUM CZCR YXJO YRAN YOAU

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_T	74_E	3.536	1.00
15_H	24_S	3.369	1.00
158_V	290_R	2.683	1.00
96_G	141_L	2.524	1.00
67_Q	81_M	2.382	1.00
231_V	238_T	2.323	1.00
112_M	292_R	2.213	1.00
164_P	242_A	2.201	1.00
162_D	267_T	2.182	1.00
173_H	189_E	2.181	1.00
11_A	24_S	2.178	1.00
159_P	162_D	2.154	1.00
92_P	123_Y	2.142	1.00
20_R	23_D	2.120	1.00
14_E	69_R	2.103	1.00
92_P	121_E	2.085	1.00
159_P	267_T	2.052	1.00
182_P	185_D	2.015	1.00
45_V	60_A	2.004	1.00
8_Y	35_Q	1.994	1.00
10_V	65_V	1.989	1.00
228_R	248_E	1.981	1.00
94_H	123_Y	1.960	1.00
162_D	265_R	1.958	1.00
232_A	253_G	1.954	1.00
112_M	288_A	1.934	1.00
67_Q	74_E	1.921	1.00
192_L	236_G	1.898	1.00
169_I	257_L	1.895	1.00
10_V	69_R	1.888	1.00
11_A	14_E	1.885	1.00
8_Y	32_L	1.885	1.00
71_V	75_V	1.881	1.00
13_A	57_F	1.856	1.00
11_A	15_H	1.854	1.00
10_V	14_E	1.847	1.00
18_F	36_I	1.845	1.00
65_V	69_R	1.801	1.00
166_L	242_A	1.800	1.00
132_L	144_V	1.784	1.00
49_E	56_L	1.726	1.00
232_A	248_E	1.716	1.00
64_L	78_L	1.710	1.00
190_K	218_H	1.684	1.00
178_R	185_D	1.654	1.00
63_L	81_M	1.649	1.00
157_E	269_G	1.636	1.00
113_L	285_L	1.634	1.00
166_L	256_Y	1.625	1.00
135_Q	140_K	1.605	1.00
14_E	24_S	1.603	1.00
9_L	65_V	1.578	1.00
13_A	65_V	1.570	1.00
10_V	68_A	1.563	1.00
8_Y	27_V	1.557	1.00
15_H	20_R	1.553	1.00
156_I	274_P	1.527	1.00
113_L	120_L	1.521	1.00
19_R	29_Q	1.511	1.00
88_T	119_K	1.502	1.00
59_Q	62_M	1.500	1.00
134_A	138_S	1.490	1.00
5_D	35_Q	1.482	1.00
28_S	31_T	1.446	1.00
5_D	42_E	1.438	1.00
46_M	49_E	1.430	1.00
201_R	205_M	1.427	1.00
5_D	38_K	1.424	1.00
158_V	272_Y	1.424	1.00
10_V	72_L	1.417	1.00
17_H	20_R	1.417	1.00
67_Q	70_T	1.408	1.00
11_A	25_C	1.400	1.00
278_L	282_Y	1.396	1.00
286_A	290_R	1.392	1.00
146_L	271_V	1.382	1.00
156_I	272_Y	1.374	1.00
71_V	78_L	1.360	1.00
67_Q	77_V	1.353	1.00
148_L	269_G	1.350	1.00
171_E	253_G	1.347	1.00
90_S	119_K	1.335	1.00
103_P	225_E	1.334	1.00
112_M	116_T	1.332	1.00
137_D	154_A	1.326	1.00
272_Y	286_A	1.325	1.00
270_L	286_A	1.309	1.00
94_H	125_H	1.307	1.00
284_Q	287_E	1.296	1.00
143_C	282_Y	1.296	1.00
163_E	243_L	1.273	1.00
42_E	79_K	1.272	1.00
64_L	79_K	1.270	1.00
135_Q	141_L	1.269	1.00
136_L	144_V	1.258	1.00
3_I	75_V	1.257	1.00
51_T	56_L	1.256	1.00
227_L	238_T	1.254	1.00
169_I	237_I	1.253	1.00
143_C	270_L	1.251	1.00
114_H	218_H	1.251	1.00
189_E	237_I	1.246	1.00
74_E	77_V	1.223	1.00
242_A	246_P	1.213	1.00
208_C	213_A	1.212	1.00
116_T	288_A	1.212	1.00
62_M	66_D	1.212	1.00
37_R	41_D	1.202	1.00
242_A	256_Y	1.188	1.00
66_D	70_T	1.188	1.00
67_Q	78_L	1.187	1.00
248_E	253_G	1.187	1.00
229_N	232_A	1.184	1.00
114_H	190_K	1.180	1.00
171_E	255_V	1.175	1.00
179_E	255_V	1.171	1.00
63_L	66_D	1.170	1.00
9_L	48_L	1.168	1.00
112_M	115_Q	1.162	1.00
174_P	189_E	1.160	1.00
111_P	115_Q	1.157	1.00
192_L	227_L	1.144	1.00
157_E	271_V	1.141	1.00
159_P	269_G	1.139	1.00
127_A	131_Q	1.138	1.00
93_L	285_L	1.138	1.00
27_V	31_T	1.131	1.00
9_L	47_L	1.123	1.00
9_L	13_A	1.109	1.00
246_P	250_K	1.108	1.00
123_Y	220_R	1.102	1.00
33_S	37_R	1.101	1.00
34_G	37_R	1.099	1.00
7_E	76_K	1.096	1.00
34_G	38_K	1.093	1.00
111_P	233_A	1.092	1.00
287_E	290_R	1.086	1.00
113_L	288_A	1.086	1.00
190_K	216_D	1.079	1.00
12_L	21_A	1.078	1.00
18_F	55_V	1.075	1.00
273_R	276_S	1.075	1.00
221_A	227_L	1.075	1.00
117_F	284_Q	1.073	1.00
70_T	77_V	1.072	1.00
168_A	256_Y	1.069	1.00
102_G	126_E	1.063	1.00
6_L	68_A	1.050	1.00
11_A	21_A	1.050	1.00
71_V	74_E	1.049	1.00
127_A	135_Q	1.044	1.00
288_A	292_R	1.042	1.00
57_F	61_G	1.041	1.00
283_E	287_E	1.041	1.00
35_Q	38_K	1.025	1.00
109_I	289_I	1.023	1.00
170_Y	234_G	1.021	1.00
180_C	260_I	1.021	1.00
4_R	7_E	1.009	1.00
63_L	67_Q	1.008	1.00
181_V	185_D	1.003	1.00
108_H	233_A	1.001	1.00
228_R	232_A	1.001	1.00
256_Y	259_C	0.998	1.00
158_V	286_A	0.995	1.00
168_A	245_V	0.992	1.00
8_Y	25_C	0.989	1.00
137_D	152_S	0.988	1.00
167_L	237_I	0.982	1.00
79_K	83_S	0.981	1.00
229_N	233_A	0.981	1.00
76_K	80_E	0.977	1.00
27_V	32_L	0.969	1.00
13_A	48_L	0.967	1.00
76_K	79_K	0.964	1.00
116_T	291_A	0.959	1.00
96_G	132_L	0.958	1.00
127_A	132_L	0.954	1.00
193_M	217_T	0.950	1.00
64_L	68_A	0.949	1.00
164_P	265_R	0.947	1.00
12_L	18_F	0.946	1.00
169_I	173_H	0.941	1.00
113_L	117_F	0.935	1.00
73_R	77_V	0.935	1.00
9_L	57_F	0.932	1.00
135_Q	138_S	0.926	1.00
288_A	291_A	0.920	1.00
173_H	190_K	0.919	1.00
279_R	282_Y	0.911	1.00
125_H	135_Q	0.911	1.00
221_A	230_M	0.911	1.00
249_R	252_D	0.909	1.00
109_I	288_A	0.908	1.00
48_L	55_V	0.905	1.00
173_H	176_A	0.902	1.00
202_D	205_M	0.902	1.00
9_L	39_L	0.899	1.00
21_A	32_L	0.898	1.00
154_A	274_P	0.898	1.00
121_E	216_D	0.897	1.00
13_A	61_G	0.897	1.00
45_V	82_A	0.896	1.00
141_L	144_V	0.883	1.00
38_K	41_D	0.879	1.00
183_M	261_K	0.874	1.00
63_L	85_Q	0.872	1.00
96_G	146_L	0.866	1.00
177_N	190_K	0.865	1.00
66_D	69_R	0.864	1.00
20_R	24_S	0.858	1.00
190_K	217_T	0.856	1.00
174_P	179_E	0.856	1.00
120_L	281_R	0.855	1.00
245_V	248_E	0.855	1.00
155_F	271_V	0.854	1.00
99_P	223_S	0.853	1.00
169_I	174_P	0.849	1.00
185_D	188_G	0.843	1.00
19_R	23_D	0.842	1.00
16_R	56_L	0.841	1.00
287_E	291_A	0.841	1.00
51_T	54_K	0.840	1.00
95_I	143_C	0.838	1.00
148_L	267_T	0.837	1.00
168_A	238_T	0.835	1.00
133_L	137_D	0.829	1.00
70_T	73_R	0.819	1.00
25_C	32_L	0.818	1.00
12_L	36_I	0.808	1.00
60_A	85_Q	0.807	1.00
204_A	208_C	0.806	1.00
125_H	141_L	0.803	1.00
175_W	189_E	0.800	1.00
156_I	159_P	0.798	1.00
60_A	82_A	0.794	1.00
9_L	64_L	0.792	1.00
16_R	62_M	0.788	1.00
96_G	144_V	0.787	1.00
91_G	281_R	0.786	1.00
89_M	117_F	0.785	1.00
37_R	46_M	0.782	1.00
278_L	283_E	0.778	1.00
13_A	16_R	0.777	1.00
12_L	48_L	0.773	1.00
111_P	235_S	0.773	1.00
184_A	187_A	0.770	1.00
29_Q	33_S	0.767	1.00
14_E	65_V	0.766	1.00
202_D	206_G	0.765	1.00
91_G	120_L	0.765	1.00
170_Y	235_S	0.761	1.00
131_Q	134_A	0.757	1.00
74_E	78_L	0.757	1.00
75_V	78_L	0.755	1.00
4_R	35_Q	0.750	1.00
172_D	176_A	0.748	1.00
15_H	21_A	0.746	1.00
230_M	235_S	0.745	1.00
3_I	72_L	0.745	1.00
164_P	258_P	0.745	1.00
143_C	285_L	0.745	1.00
16_R	54_K	0.741	1.00
201_R	220_R	0.739	1.00
112_M	291_A	0.739	1.00
207_F	211_A	0.739	1.00
137_D	155_F	0.738	1.00
280_S	284_Q	0.736	1.00
116_T	284_Q	0.733	1.00
164_P	263_E	0.732	1.00
248_E	251_R	0.732	1.00
57_F	62_M	0.731	1.00
60_A	63_L	0.729	1.00
109_I	292_R	0.726	1.00
56_L	62_M	0.725	1.00
77_V	81_M	0.724	1.00
114_H	235_S	0.724	1.00
168_A	240_L	0.722	1.00
75_V	79_K	0.721	1.00
5_D	8_Y	0.720	1.00
31_T	35_Q	0.720	1.00
94_H	141_L	0.714	1.00
145_I	289_I	0.710	1.00
184_A	211_A	0.709	1.00
68_A	71_V	0.708	1.00
173_H	177_N	0.706	1.00
83_S	86_G	0.704	1.00
7_E	11_A	0.703	1.00
169_I	255_V	0.703	1.00
113_L	284_Q	0.700	1.00
18_F	32_L	0.699	1.00
78_L	82_A	0.699	1.00
97_L	102_G	0.698	1.00
182_P	260_I	0.696	1.00
180_C	258_P	0.695	1.00
12_L	32_L	0.693	1.00
241_P	244_A	0.692	1.00
49_E	58_T	0.688	1.00
187_A	213_A	0.688	1.00
232_A	251_R	0.685	1.00
170_Y	173_H	0.680	1.00
169_I	175_W	0.677	1.00
223_S	226_T	0.676	1.00
18_F	54_K	0.676	1.00
191_L	215_E	0.676	1.00
249_R	256_Y	0.674	1.00
49_E	54_K	0.674	1.00
60_A	64_L	0.673	1.00
188_G	216_D	0.673	1.00
40_E	45_V	0.672	1.00
206_G	210_E	0.672	1.00
176_A	255_V	0.670	1.00
94_H	142_D	0.667	1.00
69_R	73_R	0.666	1.00
97_L	106_L	0.665	1.00
142_D	282_Y	0.664	1.00
73_R	76_K	0.660	1.00
276_S	279_R	0.658	1.00
207_F	210_E	0.658	1.00
194_L	227_L	0.657	1.00
168_A	249_R	0.657	1.00
62_M	65_V	0.652	1.00
219_F	230_M	0.650	1.00
59_Q	63_L	0.650	1.00
195_E	220_R	0.649	1.00
68_A	72_L	0.648	1.00
77_V	80_E	0.643	1.00
93_L	281_R	0.641	1.00
121_E	220_R	0.641	1.00
172_D	175_W	0.638	1.00
40_E	50_R	0.636	1.00
206_G	209_F	0.636	1.00
205_M	209_F	0.636	1.00
284_Q	288_A	0.634	1.00
245_V	249_R	0.633	1.00
36_I	40_E	0.632	1.00
191_L	237_I	0.632	1.00
21_A	25_C	0.630	1.00
139_G	273_R	0.629	1.00
64_L	82_A	0.629	1.00
136_L	271_V	0.628	1.00
171_E	252_D	0.627	1.00
203_Q	207_F	0.623	1.00
172_D	255_V	0.623	1.00
23_D	26_H	0.619	1.00
126_E	222_T	0.617	1.00
167_L	186_L	0.616	1.00
7_E	10_V	0.612	1.00
172_D	234_G	0.610	1.00
90_S	121_E	0.608	1.00
12_L	17_H	0.607	1.00
161_F	268_I	0.606	1.00
208_C	215_E	0.601	1.00
67_Q	71_V	0.599	1.00
63_L	82_A	0.597	1.00
103_P	229_N	0.597	1.00
143_C	286_A	0.594	1.00
93_L	143_C	0.594	1.00
280_S	283_E	0.594	1.00
156_I	275_G	0.594	1.00
30_P	34_G	0.592	1.00
126_E	223_S	0.591	1.00
136_L	155_F	0.590	1.00
230_M	236_G	0.586	1.00
195_E	222_T	0.585	1.00
80_E	84_Q	0.585	1.00
106_L	109_I	0.585	1.00
4_R	38_K	0.585	1.00
57_F	65_V	0.585	1.00
285_L	289_I	0.583	1.00
227_L	231_V	0.582	1.00
175_W	178_R	0.581	1.00
167_L	191_L	0.579	1.00
204_A	207_F	0.579	1.00
163_E	266_R	0.574	1.00
110_I	122_M	0.573	1.00
167_L	239_L	0.572	1.00
175_W	181_V	0.571	1.00
205_M	208_C	0.568	1.00
174_P	178_R	0.567	1.00
43_L	82_A	0.567	1.00
131_Q	135_Q	0.564	1.00
31_T	34_G	0.564	1.00
165_M	239_L	0.563	1.00
108_H	112_M	0.563	1.00
182_P	261_K	0.558	1.00
132_L	139_G	0.558	1.00
196_D	220_R	0.557	1.00
147_A	266_R	0.557	1.00
28_S	34_G	0.556	1.00
221_A	226_T	0.556	1.00
4_R	8_Y	0.554	1.00
48_L	57_F	0.552	1.00
43_L	64_L	0.551	1.00
45_V	49_E	0.548	1.00
43_L	46_M	0.545	1.00
180_C	185_D	0.544	1.00
108_H	111_P	0.544	1.00
272_Y	283_E	0.543	1.00
7_E	72_L	0.541	1.00
36_I	48_L	0.537	1.00
101_V	105_L	0.535	1.00
72_L	75_V	0.534	1.00
240_L	245_V	0.531	1.00
91_G	119_K	0.531	1.00
66_D	81_M	0.530	1.00
200_L	204_A	0.528	1.00
68_A	75_V	0.524	1.00
8_Y	36_I	0.524	1.00
72_L	76_K	0.522	1.00
145_I	270_L	0.522	1.00
91_G	117_F	0.522	1.00
173_H	237_I	0.521	1.00
202_D	207_F	0.519	1.00
67_Q	82_A	0.516	1.00
117_F	120_L	0.513	1.00
282_Y	286_A	0.511	1.00
96_G	125_H	0.511	1.00
224_L	241_P	0.508	1.00
46_M	60_A	0.506	1.00
18_F	50_R	0.506	1.00
160_L	270_L	0.506	1.00
134_A	140_K	0.503	1.00
8_Y	21_A	0.503	1.00
148_L	157_E	0.502	1.00
96_G	127_A	0.501	1.00
9_L	61_G	0.501	1.00
168_A	254_V	0.501	1.00
18_F	29_Q	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
1uthA	2	0.7443	100	0.09	Contact Map
2esnA	3	0.9607	100	0.091	Contact Map
4x6gA	4	0.9934	100	0.094	Contact Map
1ixcA	4	0.9574	100	0.095	Contact Map
3fxqA	3	0.9574	100	0.096	Contact Map
3fzvA	4	0.941	100	0.096	Contact Map
1al3A	1	0.718	100	0.098	Contact Map
2h98A	2	0.6951	100	0.102	Contact Map
2h9bA	2	0.6984	100	0.112	Contact Map
3szpA	3	0.9508	100	0.114	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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