YGFI - ECOLI - GREMLIN Contacts

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YGFI - Uncharacterized HTH-type transcriptional regulator YgfI

UniProt:	P52044	Sequences: MDIFISKKMRNFILLAQTNNIARAAEKIHMTASPFGKSIAALEEQIGYTLFTRKDNNISLNKAGQELYQKLFPVYQRLSAIDNEIHNSGRRSREIVIGIDNTYPTIIFDQLISLGDKYEGVTAQPVEFSENGVIDNLFDRQLDFIISPQHVSARVQELENLTISELPPLRLGFLVSRRYEERQEQELLQELPWLQMRFQNRANFEAMIDANMRPCGINPTIIYRPYSFMAKISAVERGHFLTVIPHFAWRLVNPATLKYFDAPHRPMYMQEYLYSIRNHRYTATMLQHIAEDRDGTSH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12974
Length:	298 (279)
Sequences:	78911 (57705)
Seq/√Len:	3454.7

ECOLI - YGFI LYSR NHAR PGRR TDCA OXYR LEUO CYSB ILVY YNEJ YBHD NAC ABGR YIDZ HCAR XAPR CYNR YDCI CBL YBDO YFIE YNFL YFER YIAU YEIE TTDR DSDC YAFC DMLR YBEF YHJC YAHB ICIA AAER METR YCAN YDHB ALLS YEEY YHAJ GCVA YJIE LRHA HDFR PERR
BACSU - GLTR BSDA YWBI CYSL GLTC YOFA YYBE YCGK YUST YWQM CZCR CITR ALSR YVBU YTLI YKUM 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
73_P	77_R	3.599	1.00
18_T	27_K	3.406	1.00
164_S	293_R	2.561	1.00
98_G	142_L	2.540	1.00
70_K	84_E	2.434	1.00
235_V	242_T	2.307	1.00
14_L	27_K	2.263	1.00
179_Y	191_L	2.234	1.00
170_R	246_H	2.219	1.00
168_P	270_Q	2.204	1.00
165_E	168_P	2.203	1.00
94_E	124_Q	2.188	1.00
23_R	26_E	2.139	1.00
94_E	122_T	2.133	1.00
165_E	270_Q	2.107	1.00
17_Q	72_F	2.088	1.00
48_Y	63_A	2.049	1.00
11_N	38_S	2.041	1.00
96_V	124_Q	1.993	1.00
13_I	68_Y	1.982	1.00
236_E	256_T	1.977	1.00
70_K	77_R	1.970	1.00
168_P	268_Y	1.964	1.00
13_I	72_F	1.953	1.00
232_I	251_L	1.930	1.00
14_L	17_Q	1.922	1.00
194_L	240_F	1.908	1.00
13_I	17_Q	1.906	1.00
14_L	18_T	1.898	1.00
11_N	35_F	1.892	1.00
74_V	78_L	1.890	1.00
113_S	291_E	1.888	1.00
16_A	60_L	1.885	1.00
172_G	246_H	1.875	1.00
175_V	260_F	1.867	1.00
68_Y	72_F	1.836	1.00
21_I	39_I	1.821	1.00
133_V	145_I	1.785	1.00
52_T	59_S	1.739	1.00
236_E	251_L	1.714	1.00
67_L	81_I	1.710	1.00
192_P	222_I	1.705	1.00
66_E	84_E	1.676	1.00
163_I	272_Y	1.670	1.00
136_N	141_Q	1.648	1.00
172_G	259_Y	1.647	1.00
184_E	187_L	1.628	1.00
16_A	68_Y	1.620	1.00
17_Q	27_K	1.597	1.00
12_F	68_Y	1.581	1.00
18_T	23_R	1.574	1.00
114_L	288_H	1.561	1.00
13_I	71_L	1.558	1.00
162_T	277_R	1.550	1.00
11_N	30_M	1.536	1.00
135_D	139_D	1.536	1.00
114_L	121_V	1.516	1.00
8_K	38_S	1.515	1.00
22_A	32_A	1.512	1.00
62_K	65_Q	1.487	1.00
8_K	45_Q	1.476	1.00
31_T	34_P	1.455	1.00
164_S	275_S	1.450	1.00
49_T	52_T	1.445	1.00
70_K	73_P	1.445	1.00
287_Q	290_A	1.443	1.00
8_K	41_A	1.433	1.00
20_N	23_R	1.427	1.00
14_L	28_I	1.421	1.00
13_I	75_Y	1.414	1.00
91_R	120_G	1.409	1.00
5_I	8_K	1.397	1.00
70_K	80_A	1.394	1.00
162_T	275_S	1.386	1.00
147_S	274_Y	1.382	1.00
281_Y	285_M	1.377	1.00
74_V	81_I	1.376	1.00
205_E	209_D	1.375	1.00
149_Q	272_Y	1.372	1.00
104_P	229_M	1.353	1.00
6_S	78_L	1.348	1.00
177_R	256_T	1.346	1.00
96_V	126_V	1.325	1.00
137_L	145_I	1.318	1.00
136_N	142_L	1.304	1.00
144_F	285_M	1.302	1.00
138_F	160_N	1.301	1.00
169_L	247_F	1.294	1.00
54_K	59_S	1.286	1.00
67_L	82_D	1.280	1.00
231_K	242_T	1.280	1.00
144_F	273_L	1.275	1.00
175_V	241_L	1.272	1.00
45_Q	82_D	1.270	1.00
275_S	289_I	1.263	1.00
191_L	241_L	1.262	1.00
113_S	117_K	1.260	1.00
77_R	80_A	1.260	1.00
115_G	222_I	1.240	1.00
69_Q	73_P	1.229	1.00
246_H	250_R	1.229	1.00
70_K	81_I	1.206	1.00
233_S	236_E	1.206	1.00
273_L	289_I	1.203	1.00
65_Q	69_Q	1.195	1.00
177_R	258_K	1.195	1.00
40_A	44_E	1.193	1.00
66_E	69_Q	1.190	1.00
112_I	116_D	1.188	1.00
212_M	217_I	1.183	1.00
115_G	192_P	1.182	1.00
117_K	291_E	1.181	1.00
163_I	274_Y	1.180	1.00
165_E	272_Y	1.176	1.00
12_F	51_F	1.170	1.00
246_H	259_Y	1.160	1.00
180_E	191_L	1.157	1.00
250_R	253_N	1.152	1.00
12_F	16_A	1.144	1.00
113_S	116_D	1.143	1.00
37_K	40_A	1.137	1.00
12_F	50_L	1.133	1.00
30_M	34_P	1.132	1.00
112_I	237_R	1.107	1.00
37_K	41_A	1.105	1.00
251_L	256_T	1.105	1.00
194_L	231_K	1.101	1.00
124_Q	224_R	1.099	1.00
21_I	58_I	1.098	1.00
36_G	40_A	1.098	1.00
179_Y	182_R	1.095	1.00
192_P	220_T	1.091	1.00
114_L	291_E	1.089	1.00
276_I	279_H	1.089	1.00
286_L	290_A	1.088	1.00
73_P	80_A	1.084	1.00
95_I	288_H	1.083	1.00
174_L	259_Y	1.078	1.00
7_K	10_R	1.077	1.00
259_Y	262_A	1.077	1.00
74_V	77_R	1.076	1.00
15_L	24_A	1.071	1.00
9_M	71_L	1.070	1.00
14_L	24_A	1.067	1.00
10_R	79_S	1.063	1.00
225_P	231_K	1.063	1.00
176_S	238_G	1.047	1.00
289_I	293_R	1.044	1.00
38_S	41_A	1.042	1.00
118_Y	287_Q	1.042	1.00
109_D	237_R	1.038	1.00
138_F	158_L	1.032	1.00
60_L	64_G	1.032	1.00
66_E	70_K	1.030	1.00
290_A	293_R	1.020	1.00
232_I	236_E	1.019	1.00
175_V	179_Y	1.015	1.00
233_S	237_R	1.010	1.00
82_D	86_H	1.000	1.00
174_L	249_W	0.989	1.00
98_G	133_V	0.988	1.00
173_F	241_L	0.985	1.00
170_R	268_Y	0.985	1.00
185_Q	264_H	0.983	1.00
16_A	51_F	0.980	1.00
30_M	35_F	0.978	1.00
79_S	83_N	0.977	1.00
11_N	28_I	0.973	1.00
282_T	285_M	0.969	1.00
79_S	82_D	0.966	1.00
76_Q	80_A	0.966	1.00
12_F	60_L	0.963	1.00
225_P	234_A	0.961	1.00
206_A	209_D	0.954	1.00
195_Q	221_I	0.950	1.00
114_L	118_Y	0.944	1.00
15_L	21_I	0.943	1.00
110_Q	292_D	0.941	1.00
67_L	71_L	0.939	1.00
283_A	287_Q	0.938	1.00
126_V	136_N	0.933	1.00
179_Y	183_Q	0.931	1.00
136_N	139_D	0.928	1.00
110_Q	291_E	0.928	1.00
164_S	289_I	0.927	1.00
12_F	42_L	0.924	1.00
24_A	35_F	0.923	1.00
160_N	277_R	0.922	1.00
41_A	44_E	0.921	1.00
66_E	88_S	0.914	1.00
179_Y	192_P	0.912	1.00
51_F	58_I	0.910	1.00
48_Y	85_I	0.908	1.00
142_L	145_I	0.897	1.00
206_A	210_A	0.897	1.00
16_A	64_G	0.895	1.00
69_Q	72_F	0.886	1.00
23_R	27_K	0.884	1.00
187_L	190_E	0.878	1.00
98_G	147_S	0.875	1.00
101_N	227_S	0.871	1.00
19_N	59_S	0.868	1.00
122_T	220_T	0.868	1.00
175_V	180_E	0.862	1.00
149_Q	270_Q	0.859	1.00
181_E	191_L	0.857	1.00
121_V	284_T	0.848	1.00
73_P	76_Q	0.846	1.00
22_A	26_E	0.846	1.00
161_L	274_Y	0.842	1.00
54_K	57_N	0.841	1.00
193_W	219_P	0.840	1.00
28_I	35_F	0.834	1.00
162_T	165_E	0.834	1.00
192_P	221_I	0.834	1.00
174_L	242_T	0.834	1.00
183_Q	192_P	0.832	1.00
97_I	144_F	0.831	1.00
63_A	88_S	0.828	1.00
134_I	138_F	0.828	1.00
7_K	38_S	0.825	1.00
126_V	142_L	0.823	1.00
93_R	121_V	0.820	1.00
6_S	75_Y	0.809	1.00
98_G	145_I	0.807	1.00
19_N	65_Q	0.803	1.00
112_I	239_H	0.799	1.00
63_A	85_I	0.795	1.00
40_A	49_T	0.793	1.00
211_N	215_C	0.792	1.00
12_F	67_L	0.789	1.00
176_S	239_H	0.787	1.00
170_R	261_D	0.787	1.00
78_L	81_I	0.786	1.00
16_A	19_N	0.785	1.00
32_A	36_G	0.783	1.00
15_L	39_I	0.782	1.00
17_Q	68_Y	0.779	1.00
281_Y	286_L	0.777	1.00
252_V	255_A	0.775	1.00
186_E	189_Q	0.775	1.00
132_G	135_D	0.774	1.00
15_L	51_F	0.771	1.00
18_T	24_A	0.770	1.00
170_R	266_P	0.768	1.00
182_R	258_K	0.760	1.00
178_R	182_R	0.758	1.00
80_A	84_E	0.758	1.00
77_R	81_I	0.755	1.00
115_G	239_H	0.754	1.00
251_L	254_P	0.754	1.00
234_A	239_H	0.754	1.00
208_I	212_M	0.752	1.00
86_H	89_G	0.749	1.00
78_L	82_D	0.747	1.00
63_A	66_E	0.744	1.00
8_K	11_N	0.743	1.00
19_N	57_N	0.741	1.00
175_V	181_E	0.740	1.00
59_S	65_Q	0.731	1.00
138_F	161_L	0.728	1.00
245_P	248_A	0.728	1.00
96_V	142_L	0.724	1.00
81_I	85_I	0.722	1.00
71_L	74_V	0.721	1.00
93_R	284_T	0.721	1.00
180_E	183_Q	0.719	1.00
10_R	14_L	0.718	1.00
52_T	61_N	0.717	1.00
60_L	65_Q	0.717	1.00
174_L	244_I	0.716	1.00
52_T	57_N	0.713	1.00
211_N	214_P	0.712	1.00
21_I	35_F	0.712	1.00
175_V	258_K	0.709	1.00
15_L	35_F	0.702	1.00
186_E	215_C	0.701	1.00
114_L	287_Q	0.698	1.00
236_E	254_P	0.697	1.00
34_P	38_S	0.695	1.00
176_S	179_Y	0.691	1.00
72_F	76_Q	0.686	1.00
227_S	230_A	0.686	1.00
205_E	224_R	0.684	1.00
144_F	288_H	0.683	1.00
63_A	67_L	0.683	1.00
43_E	48_Y	0.683	1.00
180_E	184_E	0.682	1.00
95_I	284_T	0.680	1.00
279_H	282_T	0.679	1.00
283_A	286_L	0.677	1.00
181_E	184_E	0.676	1.00
210_A	214_P	0.675	1.00
189_Q	217_I	0.673	1.00
76_Q	79_S	0.673	1.00
223_Y	234_A	0.671	1.00
65_Q	68_Y	0.669	1.00
207_M	211_N	0.667	1.00
196_M	231_K	0.666	1.00
190_E	220_T	0.665	1.00
96_V	143_D	0.665	1.00
62_K	66_E	0.662	1.00
288_H	292_D	0.661	1.00
122_T	224_R	0.658	1.00
117_K	287_Q	0.658	1.00
140_R	276_I	0.658	1.00
71_L	75_Y	0.657	1.00
178_R	181_E	0.657	1.00
80_A	83_N	0.655	1.00
39_I	43_E	0.654	1.00
21_I	57_N	0.651	1.00
209_D	213_R	0.649	1.00
43_E	53_R	0.647	1.00
67_L	85_I	0.646	1.00
7_K	41_A	0.645	1.00
99_I	107_I	0.645	1.00
26_E	29_H	0.643	1.00
146_I	292_D	0.643	1.00
210_A	213_R	0.637	1.00
178_R	238_G	0.636	1.00
249_W	252_V	0.636	1.00
24_A	28_I	0.636	1.00
287_Q	291_E	0.635	1.00
10_R	13_I	0.634	1.00
178_R	258_K	0.634	1.00
212_M	219_P	0.630	1.00
137_L	274_Y	0.627	1.00
104_P	233_S	0.625	1.00
70_K	74_V	0.622	1.00
127_E	226_Y	0.621	1.00
92_S	118_Y	0.619	1.00
143_D	285_M	0.615	1.00
177_R	255_A	0.615	1.00
95_I	144_F	0.612	1.00
204_F	208_I	0.610	1.00
107_I	110_Q	0.608	1.00
173_F	243_V	0.608	1.00
15_L	20_N	0.606	1.00
179_Y	184_E	0.605	1.00
167_P	271_E	0.603	1.00
173_F	188_L	0.598	1.00
252_V	259_Y	0.596	1.00
193_W	241_L	0.595	1.00
132_G	136_N	0.595	1.00
127_E	227_S	0.594	1.00
285_M	289_I	0.592	1.00
83_N	87_N	0.590	1.00
173_F	193_W	0.588	1.00
66_E	85_I	0.588	1.00
174_L	252_V	0.588	1.00
87_N	92_S	0.586	1.00
162_T	278_N	0.585	1.00
234_A	240_F	0.584	1.00
207_M	210_A	0.583	1.00
231_K	235_V	0.582	1.00
208_I	211_N	0.580	1.00
60_L	68_Y	0.579	1.00
169_L	269_M	0.579	1.00
148_P	269_M	0.577	1.00
33_S	37_K	0.576	1.00
46_I	85_I	0.575	1.00
137_L	161_L	0.573	1.00
10_R	75_Y	0.572	1.00
34_P	37_K	0.567	1.00
133_V	140_R	0.567	1.00
51_F	60_L	0.566	1.00
275_S	286_L	0.566	1.00
175_V	182_R	0.565	1.00
200_N	224_R	0.565	1.00
46_I	67_L	0.563	1.00
225_P	230_A	0.562	1.00
92_S	120_G	0.562	1.00
48_Y	52_T	0.561	1.00
189_Q	218_N	0.558	1.00
7_K	11_N	0.558	1.00
171_L	243_V	0.556	1.00
109_D	112_I	0.556	1.00
109_D	113_S	0.556	1.00
284_T	287_Q	0.555	1.00
31_T	37_K	0.554	1.00
103_Y	106_I	0.550	1.00
144_F	289_I	0.550	1.00
93_R	120_G	0.548	1.00
93_R	118_Y	0.548	1.00
111_L	123_A	0.548	1.00
209_D	212_M	0.547	1.00
46_I	49_T	0.542	1.00
179_Y	241_L	0.541	1.00
69_Q	84_E	0.541	1.00
228_F	245_P	0.538	1.00
118_Y	121_V	0.535	1.00
75_Y	79_S	0.534	1.00
75_Y	78_L	0.534	1.00
98_G	126_V	0.534	1.00
244_I	249_W	0.532	1.00
11_N	39_I	0.531	1.00
70_K	85_I	0.527	1.00
166_L	273_L	0.525	1.00
104_P	227_S	0.524	1.00
12_F	64_G	0.523	1.00
146_I	273_L	0.522	1.00
135_D	141_Q	0.521	1.00
71_L	78_L	0.519	1.00
39_I	51_F	0.516	1.00
204_F	207_M	0.516	1.00
30_M	38_S	0.512	1.00
105_T	108_F	0.512	1.00
21_I	32_A	0.511	1.00
11_N	24_A	0.511	1.00
149_Q	163_I	0.510	1.00
100_D	103_Y	0.508	1.00
49_T	63_A	0.507	1.00
74_V	82_D	0.507	1.00
19_N	58_I	0.505	1.00
21_I	53_R	0.505	1.00
174_L	257_L	0.503	1.00
109_D	233_S	0.502	1.00
150_H	156_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
2esnA	3	0.9732	100	0.121	Contact Map
1uthA	2	0.7282	100	0.123	Contact Map
3fxqA	3	0.9732	100	0.129	Contact Map
2h98A	2	0.6711	100	0.131	Contact Map
2h9bA	2	0.6711	100	0.135	Contact Map
3fzvA	4	0.9463	100	0.135	Contact Map
1al3A	1	0.6846	100	0.136	Contact Map
1ixcA	4	0.9664	100	0.138	Contact Map
4x6gA	4	0.9698	100	0.147	Contact Map
3szpA	3	0.9497	100	0.172	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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