YNEJ - ECOLI - GREMLIN Contacts

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YNEJ - Uncharacterized HTH-type transcriptional regulator YneJ

UniProt:	P77309	Sequences: MDLTQLEMFNAVAEAGSITQAAAKVHRVPSNLTTRLRQLETELGVDLFIRENQRLRLSPAGHNFLRYSQQILALVDEARSVVAGDEPQGLFSLGSLESTAAVRIPATLAEFNRRYPKIQFSLSTGPSGTMLDGVLEGKLNAAFIDGPINHTAIDGIPVYREELMIVTPQGYAPVTRASQVNGSNIYAFRANCSYRRHFESWFHADGAAPGTIHEMESYHGMLACVIAGAGIALIPRSMLESMPGHHQVEAWPLAEQWRWLTTWLVWRRGAKTRPLEAFIQLLDVPDSARQGYQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13818
Length:	293 (278)
Sequences:	79334 (57639)
Seq/√Len:	3456.9

ECOLI - YNEJ OXYR ABGR NAC NHAR DSDC YBDO CYSB CYNR HCAR LEUO YDHB YEIE YBHD CBL AAER YDCI TDCA YFIE PGRR YAHB LYSR ALLS YAFC YEEY ILVY TTDR YHJC METR YBEF DMLR YFER YGFI YCAN XAPR YNFL GCVA YHAJ YIDZ ICIA YIAU LRHA YJIE HDFR PERR
BACSU - GLTR GLTC CYSL YWBI YUST ALSR YOFA YKUM YYBE YCGK YWQM BSDA CITR YTLI YXJO YVBU CZCR 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_Q	74_L	3.652	1.00
15_A	24_K	3.384	1.00
156_I	283_D	2.654	1.00
67_Y	81_V	2.527	1.00
11_A	24_K	2.509	1.00
94_G	139_L	2.458	1.00
157_P	261_T	2.307	1.00
157_P	160_R	2.236	1.00
160_R	261_T	2.235	1.00
90_L	121_S	2.235	1.00
45_V	60_A	2.219	1.00
171_Y	183_S	2.212	1.00
225_V	232_A	2.169	1.00
10_N	69_Q	2.129	1.00
8_M	35_R	2.123	1.00
90_L	119_Q	2.084	1.00
10_N	14_E	2.075	1.00
164_M	236_R	2.057	1.00
67_Y	74_L	2.050	1.00
160_R	259_W	2.041	1.00
162_E	236_R	2.033	1.00
110_E	281_L	2.020	1.00
11_A	15_A	2.005	1.00
226_I	247_Q	1.977	1.00
92_S	121_S	1.960	1.00
20_Q	23_A	1.951	1.00
11_A	14_E	1.909	1.00
222_L	242_M	1.896	1.00
13_A	57_L	1.890	1.00
10_N	65_L	1.884	1.00
226_I	242_M	1.875	1.00
8_M	32_L	1.854	1.00
71_I	75_V	1.848	1.00
14_E	69_Q	1.844	1.00
164_M	250_A	1.839	1.00
186_Y	230_G	1.832	1.00
65_L	69_Q	1.830	1.00
167_T	251_W	1.814	1.00
184_N	212_I	1.742	1.00
13_A	65_L	1.723	1.00
155_G	263_W	1.713	1.00
49_I	56_R	1.686	1.00
63_N	81_V	1.679	1.00
133_G	138_K	1.657	1.00
64_F	78_A	1.645	1.00
15_A	20_Q	1.640	1.00
67_Y	70_Q	1.598	1.00
154_D	268_R	1.583	1.00
18_I	36_L	1.561	1.00
10_N	68_S	1.546	1.00
17_S	20_Q	1.543	1.00
156_I	266_W	1.526	1.00
14_E	24_K	1.521	1.00
5_Q	42_E	1.513	1.00
5_Q	35_R	1.503	1.00
266_W	279_I	1.490	1.00
5_Q	38_Q	1.489	1.00
132_D	136_E	1.474	1.00
111_F	278_F	1.456	1.00
101_A	219_H	1.456	1.00
154_D	266_W	1.455	1.00
28_V	31_N	1.453	1.00
11_A	25_V	1.444	1.00
67_Y	77_E	1.435	1.00
279_I	283_D	1.432	1.00
46_D	49_I	1.429	1.00
51_E	56_R	1.428	1.00
144_I	265_V	1.421	1.00
9_F	65_L	1.420	1.00
8_M	27_R	1.403	1.00
74_L	77_E	1.396	1.00
114_R	281_L	1.395	1.00
133_G	139_L	1.391	1.00
111_F	118_I	1.388	1.00
146_G	263_W	1.381	1.00
19_T	29_P	1.379	1.00
271_K	275_L	1.379	1.00
86_E	117_K	1.363	1.00
92_S	123_S	1.362	1.00
71_I	78_A	1.360	1.00
134_V	142_A	1.351	1.00
195_R	199_E	1.348	1.00
277_A	280_Q	1.337	1.00
64_F	79_R	1.336	1.00
242_M	247_Q	1.334	1.00
59_P	62_H	1.326	1.00
161_E	237_S	1.323	1.00
66_R	70_Q	1.320	1.00
88_Q	117_K	1.315	1.00
264_L	279_I	1.315	1.00
10_N	72_L	1.314	1.00
221_M	232_A	1.288	1.00
169_Q	247_Q	1.287	1.00
141_A	264_L	1.286	1.00
67_Y	78_A	1.284	1.00
135_L	152_A	1.283	1.00
223_A	226_I	1.276	1.00
110_E	114_R	1.269	1.00
169_Q	249_E	1.265	1.00
27_R	31_N	1.259	1.00
157_P	263_W	1.258	1.00
3_L	75_V	1.249	1.00
176_R	179_Q	1.248	1.00
167_T	231_I	1.234	1.00
112_N	212_I	1.233	1.00
183_S	231_I	1.223	1.00
63_N	66_R	1.222	1.00
109_A	227_A	1.210	1.00
42_E	79_R	1.210	1.00
34_T	38_Q	1.209	1.00
141_A	275_L	1.207	1.00
109_A	113_R	1.203	1.00
9_F	48_F	1.194	1.00
236_R	250_A	1.186	1.00
63_N	67_Y	1.173	1.00
9_F	13_A	1.168	1.00
112_N	184_N	1.165	1.00
155_G	265_V	1.151	1.00
125_G	133_G	1.147	1.00
106_A	227_A	1.137	1.00
250_A	253_L	1.137	1.00
34_T	37_R	1.124	1.00
115_Y	277_A	1.119	1.00
240_E	244_G	1.115	1.00
236_R	240_E	1.114	1.00
62_H	66_R	1.109	1.00
167_T	171_Y	1.108	1.00
156_I	279_I	1.103	1.00
6_L	68_S	1.101	1.00
70_Q	77_E	1.098	1.00
121_S	214_E	1.097	1.00
184_N	210_G	1.094	1.00
223_A	227_A	1.080	1.00
222_L	226_I	1.074	1.00
172_A	183_S	1.069	1.00
11_A	21_A	1.069	1.00
37_R	41_T	1.067	1.00
18_I	55_L	1.058	1.00
100_A	124_T	1.054	1.00
280_Q	283_D	1.053	1.00
166_V	250_A	1.053	1.00
71_I	74_L	1.051	1.00
171_Y	174_V	1.050	1.00
9_F	47_L	1.036	1.00
135_L	150_H	1.034	1.00
33_T	37_R	1.034	1.00
79_R	83_A	1.033	1.00
35_R	38_Q	1.029	1.00
241_S	245_H	1.027	1.00
276_E	280_Q	1.027	1.00
123_S	133_G	1.023	1.00
162_E	259_W	1.019	1.00
168_P	228_G	1.018	1.00
267_R	270_A	1.017	1.00
107_T	282_L	1.011	1.00
111_F	281_L	1.007	1.00
12_V	21_A	1.003	1.00
73_A	77_E	1.000	1.00
110_E	113_R	0.999	1.00
281_L	284_V	0.996	1.00
64_F	68_S	0.994	1.00
172_A	176_R	0.991	1.00
196_R	199_E	0.987	1.00
166_V	239_L	0.986	1.00
187_A	211_T	0.978	1.00
91_F	278_F	0.978	1.00
4_T	7_E	0.976	1.00
215_M	221_M	0.975	1.00
38_Q	41_T	0.970	1.00
186_Y	221_M	0.970	1.00
111_F	115_Y	0.970	1.00
12_V	18_I	0.969	1.00
57_L	61_G	0.959	1.00
177_A	255_E	0.958	1.00
21_A	32_L	0.958	1.00
202_F	207_A	0.951	1.00
27_R	32_L	0.940	1.00
13_A	48_F	0.939	1.00
7_E	76_D	0.936	1.00
70_Q	73_A	0.930	1.00
8_M	25_V	0.928	1.00
76_D	79_R	0.928	1.00
20_Q	24_K	0.924	1.00
165_I	231_I	0.924	1.00
9_F	39_L	0.921	1.00
75_V	79_R	0.914	1.00
9_F	57_L	0.913	1.00
133_G	136_E	0.912	1.00
215_M	224_C	0.905	1.00
107_T	281_L	0.904	1.00
76_D	80_S	0.897	1.00
16_G	56_R	0.894	1.00
272_T	275_L	0.892	1.00
114_R	284_V	0.889	1.00
45_V	82_V	0.887	1.00
146_G	261_T	0.886	1.00
242_M	245_H	0.884	1.00
97_E	217_S	0.880	1.00
94_G	142_A	0.876	1.00
196_R	200_S	0.871	1.00
89_G	274_P	0.867	1.00
201_W	205_D	0.864	1.00
109_A	229_A	0.859	1.00
154_D	157_P	0.859	1.00
48_F	55_L	0.857	1.00
66_R	69_Q	0.852	1.00
60_A	63_N	0.850	1.00
94_G	144_I	0.849	1.00
184_N	211_T	0.847	1.00
19_T	23_A	0.843	1.00
139_L	142_A	0.842	1.00
77_E	81_V	0.841	1.00
60_A	82_V	0.839	1.00
131_L	135_L	0.833	1.00
51_E	54_R	0.833	1.00
75_V	78_A	0.829	1.00
185_I	209_P	0.824	1.00
112_N	229_A	0.823	1.00
25_V	32_L	0.822	1.00
74_L	78_A	0.819	1.00
198_F	202_F	0.818	1.00
123_S	139_L	0.818	1.00
16_G	54_R	0.816	1.00
273_R	277_A	0.815	1.00
29_P	33_T	0.812	1.00
167_T	173_P	0.811	1.00
15_A	21_A	0.807	1.00
13_A	16_G	0.806	1.00
118_I	274_P	0.804	1.00
14_E	65_L	0.802	1.00
7_E	11_A	0.802	1.00
93_L	141_A	0.801	1.00
271_K	276_E	0.799	1.00
168_P	171_Y	0.798	1.00
9_F	64_F	0.797	1.00
153_I	265_V	0.790	1.00
4_T	35_R	0.787	1.00
119_Q	210_G	0.787	1.00
13_A	61_G	0.784	1.00
178_S	181_N	0.783	1.00
12_V	48_F	0.783	1.00
62_H	65_L	0.780	1.00
69_Q	73_A	0.777	1.00
16_G	62_H	0.775	1.00
179_Q	182_G	0.774	1.00
3_L	72_L	0.773	1.00
224_C	229_A	0.769	1.00
166_V	232_A	0.768	1.00
168_P	229_A	0.766	1.00
89_G	118_I	0.763	1.00
78_A	82_V	0.762	1.00
5_Q	8_M	0.760	1.00
37_R	46_D	0.759	1.00
162_E	252_P	0.759	1.00
174_V	249_E	0.753	1.00
137_G	267_R	0.751	1.00
95_S	100_A	0.750	1.00
49_I	58_S	0.750	1.00
277_A	281_L	0.749	1.00
68_S	71_I	0.748	1.00
12_V	32_L	0.748	1.00
18_I	32_L	0.746	1.00
171_Y	184_N	0.744	1.00
7_E	10_N	0.743	1.00
280_Q	284_V	0.741	1.00
166_V	234_I	0.736	1.00
111_F	277_A	0.736	1.00
239_L	242_M	0.734	1.00
12_V	36_L	0.731	1.00
173_P	183_S	0.729	1.00
141_A	278_F	0.726	1.00
201_W	204_A	0.724	1.00
172_A	175_T	0.723	1.00
217_S	220_G	0.722	1.00
189_R	214_E	0.721	1.00
197_H	201_W	0.718	1.00
198_F	201_W	0.718	1.00
170_G	228_G	0.717	1.00
114_R	277_A	0.717	1.00
135_L	153_I	0.714	1.00
167_T	249_E	0.713	1.00
162_E	257_W	0.713	1.00
60_A	64_F	0.705	1.00
200_S	204_A	0.703	1.00
59_P	63_N	0.702	1.00
101_A	223_A	0.697	1.00
140_N	275_L	0.693	1.00
181_N	207_A	0.690	1.00
87_P	115_Y	0.685	1.00
152_A	268_R	0.683	1.00
235_P	238_M	0.682	1.00
199_E	203_H	0.675	1.00
64_F	82_V	0.674	1.00
67_Y	71_I	0.674	1.00
31_N	35_R	0.674	1.00
173_P	176_R	0.673	1.00
57_L	62_H	0.671	1.00
92_S	140_N	0.666	1.00
200_S	203_H	0.664	1.00
197_H	200_S	0.663	1.00
56_R	62_H	0.659	1.00
106_A	109_A	0.659	1.00
77_E	80_S	0.653	1.00
92_S	139_L	0.653	1.00
23_A	26_H	0.647	1.00
7_E	72_L	0.646	1.00
165_I	233_L	0.646	1.00
49_I	54_R	0.643	1.00
185_I	231_I	0.643	1.00
9_F	61_G	0.640	1.00
188_F	221_M	0.640	1.00
145_D	260_L	0.640	1.00
40_E	50_R	0.637	1.00
196_R	201_W	0.636	1.00
124_T	216_E	0.633	1.00
119_Q	214_E	0.632	1.00
273_R	276_E	0.626	1.00
73_A	76_D	0.624	1.00
178_S	205_D	0.624	1.00
213_H	224_C	0.622	1.00
40_E	45_V	0.609	1.00
241_S	244_G	0.606	1.00
4_T	8_M	0.604	1.00
104_I	107_T	0.604	1.00
72_L	76_D	0.603	1.00
12_V	17_S	0.602	1.00
36_L	40_E	0.600	1.00
45_V	49_I	0.598	1.00
13_A	62_H	0.597	1.00
266_W	276_E	0.595	1.00
141_A	279_I	0.594	1.00
4_T	38_Q	0.592	1.00
110_E	284_V	0.592	1.00
80_S	84_G	0.590	1.00
182_G	210_G	0.590	1.00
169_Q	246_H	0.590	1.00
170_G	249_E	0.589	1.00
189_R	216_E	0.586	1.00
43_L	64_F	0.585	1.00
95_S	104_I	0.585	1.00
167_T	174_V	0.584	1.00
91_F	141_A	0.583	1.00
68_S	72_L	0.581	1.00
21_A	25_V	0.579	1.00
215_M	220_G	0.576	1.00
106_A	110_E	0.576	1.00
199_E	202_F	0.576	1.00
195_R	214_E	0.575	1.00
161_E	260_L	0.575	1.00
115_Y	118_I	0.575	1.00
91_F	274_P	0.572	1.00
63_N	82_V	0.571	1.00
226_I	245_H	0.570	1.00
103_R	107_T	0.568	1.00
88_Q	119_Q	0.568	1.00
165_I	180_V	0.564	1.00
97_E	126_P	0.564	1.00
158_V	264_L	0.561	1.00
48_F	57_L	0.560	1.00
89_G	117_K	0.559	1.00
171_Y	231_I	0.558	1.00
278_F	282_L	0.558	1.00
43_L	82_V	0.556	1.00
94_G	123_S	0.554	1.00
134_V	153_I	0.554	1.00
31_N	34_T	0.552	1.00
18_I	29_P	0.552	1.00
94_G	125_G	0.550	1.00
146_G	155_G	0.549	1.00
163_L	233_L	0.548	1.00
28_V	34_T	0.547	1.00
221_M	225_V	0.546	1.00
193_S	196_R	0.545	1.00
124_T	217_S	0.545	1.00
194_Y	198_F	0.544	1.00
170_G	174_V	0.544	1.00
43_L	46_D	0.544	1.00
84_G	87_P	0.542	1.00
195_R	201_W	0.541	1.00
234_I	239_L	0.538	1.00
30_S	34_T	0.537	1.00
165_I	185_I	0.537	1.00
105_P	109_A	0.535	1.00
16_G	55_L	0.535	1.00
134_V	265_V	0.535	1.00
95_S	122_L	0.533	1.00
27_R	35_R	0.531	1.00
194_Y	197_H	0.529	1.00
109_A	112_N	0.528	1.00
81_V	84_G	0.527	1.00
46_D	60_A	0.526	1.00
99_T	103_R	0.524	1.00
266_W	271_K	0.523	1.00
8_M	36_L	0.522	1.00
274_P	277_A	0.521	1.00
159_Y	262_T	0.519	1.00
154_D	269_G	0.518	1.00
57_L	65_L	0.518	1.00
202_F	209_P	0.517	1.00
106_A	223_A	0.517	1.00
178_S	207_A	0.515	1.00
275_L	279_I	0.514	1.00
135_L	138_K	0.514	1.00
218_Y	235_P	0.511	1.00
224_C	230_G	0.511	1.00
101_A	217_S	0.511	1.00
78_A	81_V	0.510	1.00
252_P	255_E	0.508	1.00
219_H	223_A	0.507	1.00
66_R	81_V	0.507	1.00
247_Q	250_A	0.506	1.00
80_S	83_A	0.506	1.00
6_L	64_F	0.505	1.00
195_R	198_F	0.504	1.00
18_I	50_R	0.502	1.00
71_I	79_R	0.502	1.00
18_I	54_R	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
2esnA	3	0.9829	100	0.098	Contact Map
3fxqA	3	0.9795	100	0.102	Contact Map
1uthA	2	0.7543	100	0.104	Contact Map
1ixcA	4	0.9761	100	0.109	Contact Map
2h98A	2	0.6928	100	0.112	Contact Map
2h9bA	2	0.6962	100	0.116	Contact Map
3fzvA	4	0.9556	100	0.12	Contact Map
1al3A	1	0.7065	100	0.122	Contact Map
4x6gA	4	1	100	0.124	Contact Map
3szpA	3	0.9659	100	0.135	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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