YFIE - ECOLI - GREMLIN Contacts

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YFIE - Uncharacterized HTH-type transcriptional regulator YfiE

UniProt:	P33634	Sequences: MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEQEFSVQLFEKIGRRMCLTREGKKLLPHIYELTRVMDTLREAAKKESDPDGELRVVSGETLLSYRMPQVLQRFRQRAPKVRLSLQSLNCYVIRDALLNDEADVGVFYRVGNDDALNRRELGEQSLVLVASPQIADVDFTEPGRHNACSFIINEPQCVFRQIFESTLRQRRITVENTIELISIESIKRCVAANIGVSYLPRFAVAKELECGELIELPFGEQSQTITAMCAHHAGKAVSPAMHTFIQCVEESFVAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11785
Length:	293 (283)
Sequences:	79611 (58113)
Seq/√Len:	3454.4

ECOLI - YFIE OXYR NAC TDCA CYNR ABGR YEIE LYSR CYSB LEUO YDCI YBHD YBDO NHAR AAER YNFL PGRR CBL HCAR DSDC ILVY YBEF METR YNEJ YAFC YFER YHJC TTDR DMLR YDHB XAPR YCAN YIDZ YEEY YAHB ALLS YIAU GCVA YGFI YHAJ ICIA PERR YJIE HDFR LRHA
BACSU - CYSL YWBI YCGK YWQM GLTR YOFA GLTC YYBE YUST CITR ALSR YTLI BSDA CZCR YVBU YXJO YRAN YKUM 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_E	74_V	3.736	1.00
15_E	24_K	3.451	1.00
157_R	287_E	2.681	1.00
67_H	81_A	2.567	1.00
11_T	24_K	2.556	1.00
95_V	140_A	2.525	1.00
158_E	264_T	2.331	1.00
91_E	122_S	2.262	1.00
158_E	161_E	2.259	1.00
45_V	60_E	2.255	1.00
161_E	264_T	2.240	1.00
228_V	235_S	2.200	1.00
10_K	69_Y	2.168	1.00
8_T	35_H	2.158	1.00
10_K	14_E	2.125	1.00
91_E	120_R	2.107	1.00
67_H	74_V	2.102	1.00
165_V	239_R	2.084	1.00
163_S	239_R	2.068	1.00
161_E	262_T	2.062	1.00
111_R	285_C	2.039	1.00
11_T	15_E	2.016	1.00
20_R	23_Q	1.996	1.00
93_R	122_S	1.989	1.00
179_E	182_R	1.971	1.00
11_T	14_E	1.952	1.00
13_V	57_L	1.930	1.00
10_K	65_L	1.925	1.00
8_T	32_V	1.898	1.00
229_A	250_E	1.892	1.00
71_L	75_M	1.889	1.00
14_E	69_Y	1.882	1.00
65_L	69_Y	1.875	1.00
168_A	254_L	1.873	1.00
189_I	233_G	1.866	1.00
165_V	253_E	1.838	1.00
187_S	215_T	1.798	1.00
13_V	65_L	1.756	1.00
156_R	266_M	1.748	1.00
63_K	81_A	1.717	1.00
49_E	56_C	1.716	1.00
134_A	139_E	1.699	1.00
64_L	78_L	1.687	1.00
15_E	20_R	1.676	1.00
67_H	70_E	1.630	1.00
155_N	271_A	1.591	1.00
18_F	36_I	1.588	1.00
10_K	68_I	1.581	1.00
17_S	20_R	1.572	1.00
157_R	269_H	1.565	1.00
14_E	24_K	1.545	1.00
5_R	35_H	1.541	1.00
5_R	42_E	1.535	1.00
133_D	137_N	1.508	1.00
5_R	38_Q	1.501	1.00
102_S	222_E	1.497	1.00
28_T	31_T	1.490	1.00
112_F	282_F	1.476	1.00
269_H	283_I	1.472	1.00
67_H	77_T	1.464	1.00
11_T	25_L	1.459	1.00
9_L	65_L	1.455	1.00
145_F	268_A	1.450	1.00
155_N	269_H	1.449	1.00
46_Q	49_E	1.446	1.00
51_I	56_C	1.444	1.00
283_I	287_E	1.436	1.00
74_V	77_T	1.429	1.00
8_T	27_C	1.424	1.00
19_L	29_Q	1.411	1.00
134_A	140_A	1.410	1.00
198_R	202_E	1.401	1.00
175_V	182_R	1.400	1.00
112_F	119_V	1.397	1.00
71_L	78_L	1.392	1.00
135_L	143_G	1.392	1.00
147_R	266_M	1.391	1.00
93_R	124_Q	1.389	1.00
115_R	285_C	1.386	1.00
87_D	118_K	1.382	1.00
186_C	234_V	1.377	1.00
275_V	279_M	1.362	1.00
281_T	284_Q	1.358	1.00
66_P	70_E	1.356	1.00
59_R	62_K	1.356	1.00
89_D	118_K	1.352	1.00
64_L	79_R	1.351	1.00
10_K	72_T	1.349	1.00
267_C	283_I	1.342	1.00
162_Q	240_F	1.322	1.00
224_I	235_S	1.320	1.00
136_L	153_A	1.305	1.00
142_V	267_C	1.304	1.00
67_H	78_L	1.299	1.00
226_R	229_A	1.292	1.00
111_R	115_R	1.281	1.00
27_C	31_T	1.279	1.00
158_E	266_M	1.275	1.00
113_R	215_T	1.265	1.00
142_V	279_M	1.256	1.00
63_K	66_P	1.254	1.00
170_P	250_E	1.253	1.00
113_R	187_S	1.252	1.00
170_P	252_I	1.248	1.00
239_R	253_E	1.240	1.00
34_F	38_Q	1.239	1.00
3_L	75_M	1.232	1.00
42_E	79_R	1.231	1.00
110_Q	230_A	1.229	1.00
110_Q	114_Q	1.214	1.00
9_L	48_F	1.212	1.00
63_K	67_H	1.209	1.00
9_L	13_V	1.199	1.00
168_A	234_V	1.190	1.00
156_R	268_A	1.180	1.00
239_R	243_A	1.171	1.00
177_F	257_G	1.167	1.00
107_Q	230_A	1.167	1.00
126_L	134_A	1.165	1.00
34_F	37_Q	1.149	1.00
253_E	256_F	1.145	1.00
70_E	77_T	1.142	1.00
62_K	66_P	1.137	1.00
176_D	252_I	1.123	1.00
187_S	213_E	1.119	1.00
122_S	217_E	1.116	1.00
6_F	68_I	1.115	1.00
116_A	281_T	1.109	1.00
178_T	182_R	1.109	1.00
11_T	21_A	1.108	1.00
226_R	230_A	1.108	1.00
157_R	283_I	1.104	1.00
37_Q	41_Q	1.095	1.00
243_A	247_E	1.083	1.00
71_L	74_V	1.076	1.00
101_L	125_S	1.075	1.00
18_F	55_M	1.074	1.00
167_V	253_E	1.073	1.00
136_L	151_D	1.069	1.00
35_H	38_Q	1.059	1.00
284_Q	287_E	1.059	1.00
33_T	37_Q	1.054	1.00
244_K	248_C	1.052	1.00
79_R	83_K	1.052	1.00
9_L	47_L	1.047	1.00
124_Q	134_A	1.045	1.00
112_F	285_C	1.036	1.00
280_H	284_Q	1.033	1.00
108_V	286_V	1.030	1.00
12_V	21_A	1.023	1.00
163_S	262_T	1.023	1.00
169_S	231_N	1.022	1.00
92_L	282_F	1.022	1.00
111_R	114_Q	1.020	1.00
73_R	77_T	1.017	1.00
64_L	68_I	1.007	1.00
189_I	224_I	1.007	1.00
12_V	18_F	1.005	1.00
270_H	273_K	1.004	1.00
218_L	224_I	1.000	1.00
4_R	7_I	1.000	1.00
199_Q	202_E	0.998	1.00
285_C	288_E	0.997	1.00
225_K	229_A	0.987	1.00
112_F	116_A	0.984	1.00
38_Q	41_Q	0.982	1.00
57_L	61_G	0.981	1.00
190_I	214_N	0.972	1.00
21_A	32_V	0.970	1.00
168_A	172_I	0.969	1.00
167_V	242_V	0.969	1.00
205_L	210_I	0.959	1.00
76_D	79_R	0.958	1.00
7_I	76_D	0.957	1.00
27_C	32_V	0.956	1.00
13_V	48_F	0.956	1.00
8_T	25_L	0.955	1.00
70_E	73_R	0.951	1.00
9_L	39_L	0.942	1.00
20_R	24_K	0.939	1.00
180_P	258_E	0.936	1.00
75_M	79_R	0.934	1.00
9_L	57_L	0.933	1.00
218_L	227_C	0.933	1.00
199_Q	203_S	0.930	1.00
134_A	137_N	0.930	1.00
98_E	220_S	0.924	1.00
166_L	234_V	0.917	1.00
276_S	279_M	0.909	1.00
76_D	80_E	0.907	1.00
115_R	288_E	0.902	1.00
108_V	285_C	0.901	1.00
16_G	56_C	0.901	1.00
95_V	143_G	0.898	1.00
45_V	82_A	0.894	1.00
48_F	55_M	0.887	1.00
204_T	208_R	0.885	1.00
188_F	212_V	0.885	1.00
155_N	158_E	0.881	1.00
51_I	54_R	0.879	1.00
60_E	63_K	0.879	1.00
110_Q	232_I	0.878	1.00
66_P	69_Y	0.874	1.00
60_E	82_A	0.866	1.00
19_L	23_Q	0.866	1.00
147_R	264_T	0.864	1.00
77_T	81_A	0.858	1.00
140_A	143_G	0.854	1.00
25_L	32_V	0.853	1.00
75_M	78_L	0.849	1.00
29_Q	33_T	0.847	1.00
90_G	278_A	0.846	1.00
277_P	281_T	0.837	1.00
113_R	232_I	0.836	1.00
187_S	214_N	0.834	1.00
119_V	278_A	0.831	1.00
14_E	65_L	0.830	1.00
15_E	21_A	0.829	1.00
95_V	145_F	0.829	1.00
7_I	11_T	0.824	1.00
94_V	142_V	0.824	1.00
120_R	213_E	0.822	1.00
9_L	64_L	0.819	1.00
74_V	78_L	0.818	1.00
16_G	54_R	0.818	1.00
124_Q	140_A	0.818	1.00
275_V	280_H	0.817	1.00
169_S	232_I	0.817	1.00
13_V	61_G	0.814	1.00
13_V	16_G	0.806	1.00
12_V	48_F	0.804	1.00
246_L	249_G	0.801	1.00
16_G	62_K	0.800	1.00
179_E	257_G	0.799	1.00
4_R	35_H	0.799	1.00
154_L	268_A	0.799	1.00
181_G	184_N	0.797	1.00
62_K	65_L	0.792	1.00
229_A	248_C	0.789	1.00
37_Q	46_Q	0.786	1.00
69_Y	73_R	0.785	1.00
182_R	185_A	0.784	1.00
167_V	235_S	0.781	1.00
78_L	82_A	0.780	1.00
163_S	260_S	0.777	1.00
227_C	232_I	0.776	1.00
68_I	71_L	0.776	1.00
132_R	136_L	0.773	1.00
5_R	8_T	0.769	1.00
12_V	32_V	0.768	1.00
96_S	101_L	0.767	1.00
201_F	205_L	0.765	1.00
49_E	58_T	0.764	1.00
18_F	32_V	0.762	1.00
90_G	119_V	0.762	1.00
204_T	207_Q	0.759	1.00
7_I	10_K	0.758	1.00
3_L	72_T	0.758	1.00
220_S	223_S	0.757	1.00
284_Q	288_E	0.754	1.00
12_V	36_I	0.753	1.00
138_D	270_H	0.752	1.00
168_A	252_I	0.749	1.00
112_F	281_T	0.746	1.00
163_S	255_P	0.746	1.00
167_V	237_L	0.744	1.00
200_I	204_T	0.743	1.00
171_Q	231_N	0.740	1.00
172_I	186_C	0.738	1.00
281_T	285_C	0.737	1.00
273_K	276_S	0.735	1.00
59_R	63_K	0.734	1.00
142_V	282_F	0.727	1.00
60_E	64_L	0.726	1.00
115_R	281_T	0.719	1.00
136_L	154_L	0.718	1.00
141_D	279_M	0.712	1.00
153_A	271_A	0.711	1.00
192_E	217_E	0.710	1.00
102_S	226_R	0.705	1.00
203_S	207_Q	0.703	1.00
93_R	141_D	0.700	1.00
167_V	246_L	0.700	1.00
238_P	241_A	0.694	1.00
177_F	255_P	0.693	1.00
88_P	116_A	0.693	1.00
31_T	35_H	0.692	1.00
67_H	71_L	0.690	1.00
64_L	82_A	0.690	1.00
184_N	210_I	0.689	1.00
57_L	62_K	0.682	1.00
93_R	140_A	0.682	1.00
179_E	258_E	0.679	1.00
191_N	224_I	0.676	1.00
202_E	206_R	0.675	1.00
56_C	62_K	0.673	1.00
49_E	54_R	0.673	1.00
107_Q	110_Q	0.673	1.00
7_I	72_T	0.671	1.00
244_K	247_E	0.668	1.00
181_G	208_R	0.667	1.00
242_V	246_L	0.666	1.00
9_L	61_G	0.665	1.00
23_Q	26_C	0.663	1.00
40_E	50_K	0.662	1.00
166_L	236_Y	0.661	1.00
188_F	234_V	0.660	1.00
80_E	84_K	0.658	1.00
246_L	253_E	0.655	1.00
125_S	219_I	0.654	1.00
77_T	80_E	0.653	1.00
200_I	203_S	0.645	1.00
216_I	227_C	0.639	1.00
277_P	280_H	0.637	1.00
4_R	38_Q	0.636	1.00
203_S	206_R	0.634	1.00
201_F	204_T	0.631	1.00
120_R	217_E	0.631	1.00
146_Y	263_I	0.629	1.00
36_I	40_E	0.626	1.00
73_R	76_D	0.621	1.00
105_M	108_V	0.618	1.00
166_L	183_H	0.617	1.00
72_T	76_D	0.617	1.00
12_V	17_S	0.616	1.00
43_F	64_L	0.616	1.00
142_V	283_I	0.616	1.00
172_I	176_D	0.614	1.00
197_F	201_F	0.611	1.00
198_R	217_E	0.610	1.00
192_E	219_I	0.610	1.00
13_V	62_K	0.608	1.00
40_E	45_V	0.607	1.00
96_S	105_M	0.604	1.00
111_R	288_E	0.603	1.00
4_R	8_T	0.603	1.00
92_L	142_V	0.601	1.00
45_V	49_E	0.597	1.00
218_L	223_S	0.596	1.00
107_Q	111_R	0.596	1.00
185_A	213_E	0.596	1.00
68_I	72_T	0.595	1.00
21_A	25_L	0.594	1.00
84_K	88_P	0.593	1.00
98_E	127_N	0.588	1.00
116_A	119_V	0.587	1.00
269_H	280_H	0.587	1.00
92_L	278_A	0.587	1.00
197_F	200_I	0.585	1.00
171_Q	252_I	0.585	1.00
170_P	249_G	0.584	1.00
282_F	286_V	0.583	1.00
89_D	120_R	0.582	1.00
135_L	154_L	0.579	1.00
199_Q	204_T	0.579	1.00
31_T	34_F	0.572	1.00
162_Q	263_I	0.572	1.00
63_K	82_A	0.570	1.00
48_F	57_L	0.570	1.00
95_V	124_Q	0.568	1.00
164_L	236_Y	0.568	1.00
18_F	29_Q	0.566	1.00
147_R	156_R	0.566	1.00
43_F	82_A	0.565	1.00
104_R	108_V	0.564	1.00
95_V	126_L	0.560	1.00
125_S	220_S	0.556	1.00
27_C	35_H	0.555	1.00
28_T	34_F	0.555	1.00
224_I	228_V	0.554	1.00
166_L	188_F	0.554	1.00
159_L	267_C	0.552	1.00
30_S	34_F	0.550	1.00
90_G	118_K	0.549	1.00
43_F	46_Q	0.548	1.00
80_E	83_K	0.548	1.00
160_G	265_A	0.547	1.00
173_A	252_I	0.547	1.00
100_L	104_R	0.546	1.00
45_V	85_E	0.543	1.00
175_V	178_T	0.541	1.00
16_G	55_M	0.541	1.00
110_Q	113_R	0.540	1.00
193_P	217_E	0.538	1.00
106_P	110_Q	0.538	1.00
221_I	238_P	0.536	1.00
181_G	210_I	0.536	1.00
107_Q	226_R	0.536	1.00
96_S	123_L	0.535	1.00
237_L	242_V	0.535	1.00
102_S	220_S	0.534	1.00
57_L	65_L	0.534	1.00
136_L	139_E	0.534	1.00
202_E	205_L	0.534	1.00
198_R	204_T	0.533	1.00
135_L	268_A	0.532	1.00
46_Q	60_E	0.532	1.00
78_L	81_A	0.531	1.00
222_E	226_R	0.529	1.00
278_A	281_T	0.528	1.00
6_F	64_L	0.528	1.00
227_C	233_G	0.527	1.00
205_L	212_V	0.527	1.00
8_T	36_I	0.526	1.00
250_E	253_E	0.524	1.00
18_F	50_K	0.523	1.00
269_H	275_V	0.518	1.00
196_V	199_Q	0.518	1.00
18_F	54_R	0.515	1.00
279_M	283_I	0.514	1.00
155_N	272_G	0.514	1.00
71_L	79_R	0.513	1.00
38_Q	42_E	0.513	1.00
43_F	79_R	0.511	1.00
191_N	221_I	0.511	1.00
8_T	21_A	0.510	1.00
30_S	33_T	0.510	1.00
120_R	215_T	0.509	1.00
109_L	121_L	0.508	1.00
198_R	201_F	0.508	1.00
10_K	76_D	0.507	1.00
66_P	81_A	0.507	1.00
280_H	283_I	0.501	1.00
144_V	286_V	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
3fxqA	3	0.9932	100	0.083	Contact Map
1uthA	2	0.7577	100	0.087	Contact Map
2esnA	3	0.9932	100	0.088	Contact Map
2h98A	2	0.6894	100	0.096	Contact Map
1ixcA	4	0.9863	100	0.099	Contact Map
4x6gA	4	1	100	0.1	Contact Map
2h9bA	2	0.6894	100	0.1	Contact Map
1al3A	1	0.7065	100	0.105	Contact Map
3fzvA	4	0.9693	100	0.106	Contact Map
3szpA	3	0.9795	100	0.123	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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