YFER - ECOLI - GREMLIN Contacts

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YFER - Uncharacterized HTH-type transcriptional regulator YfeR

UniProt:	P0ACR7	Sequences: MNYSLKQLKVFVTVAQEKSFSRAGERIGLSQSAVSHSVKELENHTGVRLLDRTTREVVLTDAGQQLALRLERLLDELNSTLRDTGRMGQQLSGKVRVAASQTISAHLIPQCIAESHRRYPDIQFVLHDRPQQWVMESIRQGDVDFGIVIDPGPVGDLQCEAILSEPFFLLCHRDSALAVEDYVPWQALQGAKLVLQDYASGSRPLIDAALARNGIQANIVQEIGHPATLFPMVAAGIGISILPALALPLPEGSPLVVKRITPVVERQLMLVRRKNRSLSTAAEALWDVVRDQGNALMAGREGDPLYQI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14159
Length:	308 (286)
Sequences:	79729 (57780)
Seq/√Len:	3416.6

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_R	76_E	3.686	1.00
17_E	26_R	3.443	1.00
160_E	290_R	2.713	1.00
98_A	143_V	2.578	1.00
69_R	83_D	2.490	1.00
13_T	26_R	2.425	1.00
233_V	240_S	2.274	1.00
161_A	164_S	2.265	1.00
164_S	267_Q	2.261	1.00
94_K	125_V	2.242	1.00
114_E	292_Q	2.241	1.00
175_S	191_A	2.219	1.00
161_A	267_Q	2.215	1.00
47_V	62_A	2.152	1.00
166_P	244_A	2.131	1.00
94_K	123_Q	2.117	1.00
10_V	37_S	2.085	1.00
164_S	265_E	2.073	1.00
22_R	25_E	2.068	1.00
12_V	71_E	2.052	1.00
114_E	288_V	2.030	1.00
184_P	187_A	2.029	1.00
69_R	76_E	2.023	1.00
12_V	16_Q	2.007	1.00
96_R	125_V	1.978	1.00
168_F	244_A	1.973	1.00
16_Q	71_E	1.953	1.00
13_T	17_E	1.951	1.00
12_V	67_A	1.943	1.00
13_T	16_Q	1.924	1.00
194_V	238_G	1.901	1.00
10_V	34_V	1.897	1.00
15_A	59_L	1.882	1.00
73_L	77_L	1.866	1.00
67_A	71_E	1.837	1.00
234_A	250_P	1.805	1.00
230_F	250_P	1.804	1.00
192_K	220_V	1.763	1.00
51_D	58_V	1.731	1.00
66_L	80_T	1.705	1.00
65_Q	83_D	1.702	1.00
159_C	269_M	1.690	1.00
20_F	38_V	1.676	1.00
15_A	67_A	1.674	1.00
137_S	142_D	1.671	1.00
17_E	22_R	1.609	1.00
158_Q	274_K	1.590	1.00
180_E	187_A	1.583	1.00
12_V	70_L	1.564	1.00
16_Q	26_R	1.553	1.00
69_R	72_R	1.539	1.00
115_S	285_L	1.519	1.00
7_Q	37_S	1.519	1.00
136_E	140_Q	1.516	1.00
160_E	272_R	1.512	1.00
19_S	22_R	1.502	1.00
90_Q	121_D	1.497	1.00
11_F	67_A	1.495	1.00
7_Q	44_H	1.495	1.00
10_V	29_L	1.490	1.00
7_Q	40_E	1.455	1.00
115_S	122_I	1.454	1.00
234_A	255_L	1.449	1.00
30_S	33_A	1.446	1.00
286_W	290_R	1.446	1.00
21_S	31_Q	1.446	1.00
48_R	51_D	1.440	1.00
148_V	271_V	1.437	1.00
13_T	27_I	1.437	1.00
203_R	207_D	1.431	1.00
158_Q	272_R	1.427	1.00
69_R	79_S	1.411	1.00
105_A	227_A	1.404	1.00
61_D	64_Q	1.397	1.00
255_L	259_R	1.390	1.00
53_T	58_V	1.381	1.00
272_R	286_W	1.380	1.00
150_D	269_M	1.370	1.00
12_V	74_L	1.368	1.00
4_S	7_Q	1.365	1.00
92_S	121_D	1.361	1.00
278_L	282_A	1.359	1.00
138_I	146_G	1.356	1.00
137_S	143_V	1.351	1.00
284_A	287_D	1.346	1.00
96_R	127_H	1.344	1.00
73_L	80_T	1.343	1.00
76_E	79_S	1.339	1.00
114_E	118_R	1.335	1.00
118_R	288_V	1.333	1.00
165_E	245_L	1.323	1.00
5_L	77_L	1.322	1.00
139_R	156_D	1.311	1.00
270_L	286_W	1.306	1.00
66_L	81_L	1.305	1.00
68_L	72_R	1.282	1.00
171_C	239_I	1.274	1.00
145_F	270_L	1.272	1.00
116_H	220_V	1.270	1.00
229_L	240_S	1.255	1.00
191_A	239_I	1.252	1.00
69_R	80_T	1.247	1.00
231_P	234_A	1.244	1.00
145_F	282_A	1.238	1.00
44_H	81_L	1.236	1.00
116_H	192_K	1.223	1.00
65_Q	68_L	1.210	1.00
113_A	117_R	1.209	1.00
161_A	269_M	1.207	1.00
29_L	33_A	1.188	1.00
11_F	50_L	1.185	1.00
113_A	235_A	1.184	1.00
36_H	40_E	1.170	1.00
159_C	271_V	1.159	1.00
256_V	259_R	1.152	1.00
11_F	15_A	1.144	1.00
256_V	260_I	1.140	1.00
64_Q	68_L	1.139	1.00
39_K	43_N	1.137	1.00
248_P	252_G	1.135	1.00
244_A	248_P	1.134	1.00
176_A	191_A	1.134	1.00
125_V	222_E	1.133	1.00
129_R	137_S	1.123	1.00
168_F	258_K	1.121	1.00
119_Y	284_A	1.112	1.00
36_H	39_K	1.111	1.00
65_Q	69_R	1.109	1.00
114_E	117_R	1.099	1.00
72_R	79_S	1.095	1.00
192_K	218_N	1.094	1.00
288_V	292_Q	1.089	1.00
8_L	70_L	1.079	1.00
110_Q	235_A	1.078	1.00
104_S	128_D	1.076	1.00
287_D	290_R	1.074	1.00
250_P	255_L	1.069	1.00
160_E	286_W	1.065	1.00
183_V	187_A	1.060	1.00
20_F	57_V	1.059	1.00
11_F	49_L	1.059	1.00
35_S	39_K	1.058	1.00
230_F	234_A	1.056	1.00
13_T	23_A	1.054	1.00
73_L	76_E	1.053	1.00
194_V	229_L	1.053	1.00
210_L	215_I	1.051	1.00
231_P	235_A	1.050	1.00
283_E	287_D	1.049	1.00
139_R	154_V	1.045	1.00
6_K	9_K	1.044	1.00
37_S	40_E	1.044	1.00
115_S	288_V	1.043	1.00
273_R	276_R	1.039	1.00
223_I	229_L	1.033	1.00
171_C	258_K	1.029	1.00
95_V	285_L	1.028	1.00
14_V	23_A	1.025	1.00
172_H	236_G	1.025	1.00
111_C	289_V	1.024	1.00
166_P	265_E	1.011	1.00
181_D	257_V	1.009	1.00
81_L	85_G	1.008	1.00
204_P	207_D	1.001	1.00
75_D	79_S	0.990	1.00
9_K	78_N	0.987	1.00
249_L	253_S	0.987	1.00
288_V	291_D	0.980	1.00
173_R	254_P	0.977	1.00
127_H	137_S	0.970	1.00
170_L	247_L	0.969	1.00
29_L	34_V	0.966	1.00
66_L	70_L	0.964	1.00
59_L	63_G	0.963	1.00
195_L	219_I	0.963	1.00
15_A	50_L	0.957	1.00
14_V	20_F	0.956	1.00
10_V	27_I	0.950	1.00
169_L	239_I	0.950	1.00
204_P	208_A	0.949	1.00
40_E	43_N	0.948	1.00
78_N	81_L	0.947	1.00
223_I	232_M	0.946	1.00
115_S	119_Y	0.942	1.00
78_N	82_R	0.935	1.00
171_C	175_S	0.933	1.00
11_F	59_L	0.927	1.00
23_A	34_V	0.918	1.00
173_R	256_V	0.916	1.00
137_S	140_Q	0.916	1.00
22_R	26_R	0.907	1.00
65_Q	87_M	0.905	1.00
118_R	291_D	0.904	1.00
175_S	178_A	0.903	1.00
279_S	282_A	0.902	1.00
11_F	41_L	0.901	1.00
98_A	146_G	0.898	1.00
72_R	75_D	0.896	1.00
111_C	288_V	0.889	1.00
101_Q	225_H	0.880	1.00
50_L	57_V	0.872	1.00
68_L	71_E	0.869	1.00
18_K	58_V	0.866	1.00
47_V	84_T	0.860	1.00
6_K	37_S	0.856	1.00
123_Q	218_N	0.854	1.00
143_V	146_G	0.848	1.00
176_A	181_D	0.848	1.00
179_V	192_K	0.847	1.00
98_A	148_V	0.846	1.00
193_L	217_A	0.845	1.00
21_S	25_E	0.844	1.00
150_D	267_Q	0.842	1.00
27_I	34_V	0.840	1.00
15_A	63_G	0.839	1.00
53_T	56_E	0.838	1.00
171_C	176_A	0.837	1.00
97_V	145_F	0.834	1.00
158_Q	161_A	0.833	1.00
62_A	87_M	0.833	1.00
122_I	281_A	0.831	1.00
177_L	191_A	0.831	1.00
192_K	219_I	0.830	1.00
135_M	139_R	0.826	1.00
175_S	179_V	0.825	1.00
93_G	281_A	0.825	1.00
113_A	237_I	0.825	1.00
187_A	190_G	0.824	1.00
77_L	81_L	0.824	1.00
175_S	192_K	0.816	1.00
209_A	213_N	0.809	1.00
157_L	271_V	0.809	1.00
5_L	74_L	0.807	1.00
127_H	143_V	0.804	1.00
62_A	65_Q	0.804	1.00
15_A	18_K	0.803	1.00
116_H	237_I	0.800	1.00
234_A	254_P	0.799	1.00
31_Q	35_S	0.798	1.00
111_C	292_Q	0.796	1.00
79_S	83_D	0.794	1.00
244_A	258_K	0.793	1.00
287_D	291_D	0.792	1.00
18_K	64_Q	0.792	1.00
62_A	84_T	0.792	1.00
170_L	240_S	0.792	1.00
11_F	66_L	0.787	1.00
278_L	283_E	0.784	1.00
18_K	56_E	0.782	1.00
16_Q	67_A	0.778	1.00
77_L	80_T	0.775	1.00
17_E	23_A	0.775	1.00
280_T	284_A	0.772	1.00
186_Q	189_Q	0.772	1.00
172_H	237_I	0.771	1.00
166_P	263_V	0.769	1.00
39_K	48_R	0.768	1.00
76_E	80_T	0.763	1.00
156_D	274_K	0.763	1.00
14_V	50_L	0.763	1.00
166_P	259_R	0.761	1.00
9_K	13_T	0.753	1.00
7_Q	10_V	0.750	1.00
250_P	253_S	0.750	1.00
251_E	254_P	0.744	1.00
145_F	285_L	0.742	1.00
232_M	237_I	0.741	1.00
93_G	122_I	0.740	1.00
99_A	104_S	0.738	1.00
174_D	178_A	0.733	1.00
80_T	84_T	0.732	1.00
115_S	284_A	0.732	1.00
206_I	210_L	0.727	1.00
71_E	75_D	0.723	1.00
70_L	73_L	0.722	1.00
170_L	242_L	0.721	1.00
209_A	212_R	0.721	1.00
14_V	38_V	0.720	1.00
172_H	175_S	0.720	1.00
114_E	291_D	0.720	1.00
118_R	284_A	0.717	1.00
51_D	60_T	0.717	1.00
85_G	88_G	0.716	1.00
20_F	34_V	0.716	1.00
205_L	209_A	0.715	1.00
14_V	34_V	0.714	1.00
225_H	228_T	0.714	1.00
64_Q	67_A	0.713	1.00
185_W	261_T	0.710	1.00
91_L	119_Y	0.703	1.00
139_R	157_L	0.698	1.00
254_P	260_I	0.695	1.00
284_A	288_V	0.693	1.00
170_L	251_E	0.692	1.00
184_P	261_T	0.691	1.00
170_L	257_V	0.691	1.00
249_L	252_G	0.690	1.00
171_C	177_L	0.685	1.00
243_P	246_A	0.685	1.00
189_Q	215_I	0.685	1.00
174_D	236_G	0.685	1.00
208_A	212_R	0.682	1.00
58_V	64_Q	0.681	1.00
62_A	66_L	0.680	1.00
276_R	279_S	0.679	1.00
141_G	273_R	0.678	1.00
61_D	65_Q	0.677	1.00
96_R	143_V	0.677	1.00
9_K	12_V	0.672	1.00
33_A	37_S	0.670	1.00
59_L	64_Q	0.670	1.00
197_D	222_E	0.669	1.00
186_Q	213_N	0.668	1.00
144_D	282_A	0.667	1.00
96_R	144_D	0.666	1.00
51_D	56_E	0.655	1.00
171_C	259_R	0.652	1.00
105_A	231_P	0.652	1.00
66_L	84_T	0.650	1.00
193_L	239_I	0.649	1.00
174_D	177_L	0.648	1.00
196_Q	229_L	0.647	1.00
42_E	47_V	0.643	1.00
168_F	257_V	0.642	1.00
247_L	250_P	0.641	1.00
6_K	40_E	0.639	1.00
25_E	28_G	0.636	1.00
202_S	206_I	0.636	1.00
207_D	211_A	0.635	1.00
221_Q	232_M	0.634	1.00
79_S	82_R	0.633	1.00
205_L	208_A	0.633	1.00
69_R	73_L	0.633	1.00
203_R	222_E	0.632	1.00
206_I	209_A	0.630	1.00
123_Q	222_E	0.628	1.00
190_G	218_N	0.627	1.00
42_E	52_R	0.627	1.00
169_L	241_I	0.626	1.00
75_D	78_N	0.626	1.00
255_L	260_I	0.619	1.00
208_A	211_A	0.616	1.00
128_D	224_G	0.609	1.00
38_V	42_E	0.606	1.00
110_Q	113_A	0.605	1.00
99_A	108_I	0.604	1.00
169_L	188_L	0.604	1.00
280_T	283_E	0.604	1.00
110_Q	114_E	0.602	1.00
197_D	224_G	0.601	1.00
9_K	74_L	0.598	1.00
70_L	74_L	0.597	1.00
14_V	19_S	0.597	1.00
254_P	258_K	0.592	1.00
149_I	266_R	0.590	1.00
95_V	281_A	0.589	1.00
145_F	286_W	0.588	1.00
11_F	63_G	0.586	1.00
108_I	111_C	0.584	1.00
23_A	27_I	0.581	1.00
272_R	283_E	0.581	1.00
82_R	86_R	0.580	1.00
92_S	123_Q	0.579	1.00
6_K	10_V	0.578	1.00
177_L	183_V	0.573	1.00
65_Q	84_T	0.572	1.00
45_T	66_L	0.571	1.00
285_L	289_V	0.569	1.00
74_L	78_N	0.569	1.00
128_D	225_H	0.567	1.00
101_Q	130_P	0.567	1.00
251_E	255_L	0.567	1.00
98_A	129_R	0.566	1.00
229_L	233_V	0.564	1.00
147_I	289_V	0.564	1.00
95_V	145_F	0.562	1.00
138_I	157_L	0.558	1.00
45_T	84_T	0.557	1.00
223_I	228_T	0.557	1.00
50_L	59_L	0.556	1.00
47_V	51_D	0.556	1.00
210_L	217_A	0.554	1.00
33_A	36_H	0.553	1.00
20_F	56_E	0.552	1.00
167_F	241_I	0.550	1.00
98_A	127_H	0.549	1.00
204_P	209_A	0.548	1.00
119_Y	122_I	0.547	1.00
242_L	247_L	0.546	1.00
32_S	36_H	0.545	1.00
251_E	258_K	0.543	1.00
93_G	121_D	0.542	1.00
169_L	193_L	0.542	1.00
59_L	67_A	0.541	1.00
162_I	270_L	0.540	1.00
163_L	268_L	0.539	1.00
180_E	183_V	0.537	1.00
177_L	180_E	0.535	1.00
165_E	266_R	0.534	1.00
202_S	205_L	0.533	1.00
15_A	64_Q	0.532	1.00
198_Y	222_E	0.530	1.00
232_M	238_G	0.530	1.00
175_S	239_I	0.528	1.00
138_I	271_V	0.527	1.00
158_Q	275_N	0.526	1.00
150_D	159_C	0.526	1.00
30_S	36_H	0.525	1.00
45_T	48_R	0.522	1.00
176_A	179_V	0.519	1.00
176_A	180_E	0.519	1.00
20_F	31_Q	0.516	1.00
105_A	225_H	0.514	1.00
226_P	243_P	0.513	1.00
171_C	178_A	0.511	1.00
10_V	38_V	0.511	1.00
48_R	62_A	0.510	1.00
29_L	37_S	0.510	1.00
112_I	124_F	0.509	1.00
207_D	210_L	0.508	1.00
247_L	251_E	0.507	1.00
103_I	107_L	0.506	1.00
110_Q	231_P	0.506	1.00
82_R	85_G	0.505	1.00
86_R	91_L	0.505	1.00
107_L	111_C	0.504	1.00
86_R	89_Q	0.503	1.00
18_K	57_V	0.501	1.00
10_V	23_A	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
3fzvA	4	0.9318	100	0.108	Contact Map
2esnA	3	0.9513	100	0.115	Contact Map
1ixcA	4	0.9448	100	0.117	Contact Map
1uthA	2	0.7305	100	0.122	Contact Map
2h98A	2	0.6851	100	0.122	Contact Map
1al3A	1	0.7175	100	0.125	Contact Map
4x6gA	4	0.9773	100	0.127	Contact Map
3fxqA	3	0.9448	100	0.131	Contact Map
2h9bA	2	0.6883	100	0.133	Contact Map
3hhgA	3	0.9513	100	0.137	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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