YBFI - BACSU - GREMLIN Contacts

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YBFI - Uncharacterized HTH-type transcriptional regulator YbfI

UniProt:	O31449	Sequences: MQNETRTLQLDPHLHIEAYRFKGIMQKFPNHFHDYYVIGFIEKGQRYLACQDQEYIINPGDLLLFNPRDTHSCEQIDGRTLDYRCINVMPDIMEKAVKEITGSGHLPYFSQHVLFRHELTASLQELHILISEEKQALRKEELFLHLLEELIRHYSDVTFLSSVPEPSDEVKMVCEFLEEHYAENVTLNDLSELTGWSKYHLLRSFTKQKGITPNSYMETIRINQAKKLLEQGVRPIDAAFQTGFSDQSHMTKFFKRQVGLTPKQYMKIFEKELHR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	275 (240)
Sequences:	32529 (27830)
Seq/√Len:	1796.4

ECOLI - CHBR YQHC YDIP RHAR RCLR YPDC MELR RHAS ARAC YIDL YEAM YBCM YIJO FEAR YDEO APPY ENVY GADX EUTR ADIY GADW MARA YKGA ROB SOXS XYLR
BACSU - YBFI YDEC YFIF YISR YOBQ BTR ADAA YTDP YESS YDEE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
226_K	258_V	3.202	1.00
222_I	258_V	2.996	1.00
233_V	241_Q	2.983	1.00
188_N	198_K	2.978	1.00
211_I	219_T	2.966	1.00
178_E	220_I	2.915	1.00
224_Q	227_K	2.788	1.00
176_F	180_H	2.774	1.00
180_H	183_E	2.718	1.00
219_T	257_Q	2.601	1.00
254_F	265_Y	2.578	1.00
228_L	241_Q	2.355	1.00
225_A	250_M	2.316	1.00
228_L	242_T	2.075	1.00
205_F	216_Y	2.072	1.00
173_V	201_L	2.068	1.00
186_T	189_D	2.059	1.00
47_Y	54_E	2.057	1.00
233_V	237_D	1.975	1.00
177_L	217_M	1.933	1.00
228_L	233_V	1.925	1.00
260_L	268_I	1.910	1.00
176_F	193_L	1.901	1.00
214_N	218_E	1.883	1.00
47_Y	56_I	1.870	1.00
234_R	237_D	1.834	1.00
222_I	257_Q	1.807	1.00
170_V	209_K	1.803	1.00
142_L	145_H	1.775	1.00
49_A	54_E	1.772	1.00
247_Q	251_T	1.752	1.00
187_L	202_L	1.739	1.00
181_Y	220_I	1.734	1.00
45_Q	56_I	1.703	1.00
226_K	265_Y	1.701	1.00
200_H	204_S	1.665	1.00
174_C	209_K	1.663	1.00
224_Q	228_L	1.658	1.00
253_F	256_R	1.657	1.00
145_H	149_E	1.630	1.00
173_V	194_T	1.629	1.00
58_N	61_D	1.620	1.00
236_I	247_Q	1.614	1.00
229_L	235_P	1.604	1.00
198_K	202_L	1.596	1.00
190_L	213_P	1.593	1.00
175_E	179_E	1.583	1.00
49_A	72_S	1.556	1.00
176_F	185_V	1.551	1.00
227_K	231_Q	1.551	1.00
200_H	203_R	1.539	1.00
43_K	82_D	1.535	1.00
42_E	84_R	1.534	1.00
211_I	215_S	1.519	1.00
237_D	241_Q	1.514	1.00
120_T	124_Q	1.496	1.00
36_Y	67_P	1.474	1.00
244_F	253_F	1.470	1.00
236_I	240_F	1.462	1.00
249_H	253_F	1.455	1.00
220_I	224_Q	1.447	1.00
201_L	213_P	1.447	1.00
196_W	200_H	1.446	1.00
260_L	264_Q	1.435	1.00
45_Q	58_N	1.434	1.00
237_D	240_F	1.432	1.00
47_Y	74_E	1.429	1.00
263_K	267_K	1.427	1.00
181_Y	224_Q	1.422	1.00
225_A	242_T	1.421	1.00
248_S	251_T	1.400	1.00
167_S	208_Q	1.398	1.00
213_P	217_M	1.396	1.00
238_A	242_T	1.395	1.00
178_E	216_Y	1.370	1.00
141_E	145_H	1.355	1.00
51_Q	69_D	1.345	1.00
224_Q	242_T	1.340	1.00
173_V	190_L	1.338	1.00
196_W	201_L	1.333	1.00
251_T	261_T	1.306	1.00
66_N	69_D	1.303	1.00
197_S	200_H	1.298	1.00
232_G	266_M	1.296	1.00
188_N	192_E	1.294	1.00
189_D	193_L	1.292	1.00
202_L	213_P	1.291	1.00
219_T	223_N	1.289	1.00
177_L	220_I	1.282	1.00
218_E	253_F	1.281	1.00
174_C	178_E	1.281	1.00
141_E	144_L	1.279	1.00
251_T	263_K	1.278	1.00
182_A	241_Q	1.276	1.00
212_T	215_S	1.258	1.00
199_Y	203_R	1.257	1.00
220_I	223_N	1.205	1.00
43_K	59_P	1.185	1.00
183_E	189_D	1.170	1.00
141_E	148_E	1.159	1.00
42_E	82_D	1.152	1.00
121_A	125_E	1.139	1.00
33_H	71_H	1.125	1.00
121_A	124_Q	1.124	1.00
226_K	230_E	1.121	1.00
191_S	198_K	1.116	1.00
31_H	71_H	1.113	1.00
169_E	204_S	1.107	1.00
148_E	152_R	1.089	1.00
138_R	142_L	1.085	1.00
252_K	256_R	1.084	1.00
204_S	207_K	1.077	1.00
37_V	71_H	1.070	1.00
113_V	116_R	1.069	1.00
149_E	153_H	1.068	1.00
215_S	218_E	1.066	1.00
185_V	190_L	1.062	1.00
264_Q	267_K	1.058	1.00
169_E	196_W	1.049	1.00
233_V	238_A	1.042	1.00
232_G	238_A	1.037	1.00
30_N	70_T	1.036	1.00
33_H	37_V	1.036	1.00
261_T	264_Q	1.033	1.00
235_P	238_A	1.019	1.00
182_A	224_Q	1.018	1.00
187_L	213_P	1.011	1.00
138_R	145_H	1.004	1.00
263_K	266_M	1.001	1.00
223_N	226_K	0.996	1.00
49_A	74_E	0.982	1.00
204_S	208_Q	0.981	1.00
246_D	252_K	0.977	1.00
189_D	192_E	0.977	1.00
187_L	198_K	0.976	1.00
168_D	172_M	0.966	1.00
251_T	255_K	0.964	1.00
171_K	175_E	0.962	1.00
199_Y	202_L	0.958	1.00
228_L	238_A	0.955	1.00
176_F	190_L	0.948	1.00
46_R	81_L	0.947	1.00
145_H	148_E	0.944	1.00
184_N	245_S	0.933	1.00
144_L	148_E	0.932	1.00
190_L	193_L	0.928	1.00
50_C	53_Q	0.920	1.00
140_E	144_L	0.918	1.00
174_C	216_Y	0.915	1.00
194_T	201_L	0.908	1.00
249_H	252_K	0.905	1.00
169_E	194_T	0.904	1.00
41_I	46_R	0.902	1.00
253_F	257_Q	0.898	1.00
124_Q	128_I	0.896	1.00
47_Y	76_I	0.887	1.00
214_N	249_H	0.880	1.00
41_I	44_G	0.878	1.00
176_F	194_T	0.875	1.00
226_K	254_F	0.874	1.00
181_Y	185_V	0.873	1.00
264_Q	268_I	0.869	1.00
172_M	193_L	0.865	1.00
170_V	173_V	0.857	1.00
45_Q	76_I	0.852	1.00
215_S	257_Q	0.844	1.00
218_E	256_R	0.844	1.00
118_E	121_A	0.840	1.00
218_E	257_Q	0.839	1.00
117_H	121_A	0.835	1.00
37_V	87_N	0.833	1.00
215_S	219_T	0.831	1.00
81_L	85_C	0.829	1.00
170_V	204_S	0.828	1.00
36_Y	64_L	0.825	1.00
222_I	250_M	0.823	1.00
205_F	209_K	0.822	1.00
177_L	213_P	0.821	1.00
221_R	242_T	0.818	1.00
258_V	265_Y	0.814	1.00
30_N	72_S	0.811	1.00
181_Y	217_M	0.805	1.00
173_V	176_F	0.796	1.00
214_N	217_M	0.795	1.00
184_N	189_D	0.789	1.00
222_I	253_F	0.788	1.00
255_K	261_T	0.785	1.00
190_L	201_L	0.782	1.00
125_E	142_L	0.779	1.00
117_H	120_T	0.776	1.00
196_W	204_S	0.774	1.00
39_G	85_C	0.772	1.00
46_R	57_I	0.767	1.00
229_L	266_M	0.764	1.00
260_L	265_Y	0.763	1.00
172_M	175_E	0.760	1.00
43_K	80_T	0.759	1.00
95_K	99_E	0.758	1.00
180_H	189_D	0.754	1.00
225_A	228_L	0.752	1.00
136_A	140_E	0.752	1.00
125_E	129_L	0.751	1.00
167_S	204_S	0.749	1.00
40_F	62_L	0.748	1.00
216_Y	220_I	0.746	1.00
105_H	108_Y	0.746	1.00
142_L	149_E	0.745	1.00
90_P	94_E	0.739	1.00
171_K	174_C	0.736	1.00
172_M	194_T	0.732	1.00
229_L	238_A	0.728	1.00
127_H	131_S	0.727	1.00
104_G	107_P	0.725	1.00
245_S	249_H	0.725	1.00
170_V	174_C	0.724	1.00
205_F	213_P	0.722	1.00
181_Y	242_T	0.721	1.00
166_P	207_K	0.720	1.00
240_F	245_S	0.719	1.00
185_V	189_D	0.719	1.00
94_E	98_K	0.718	1.00
255_K	264_Q	0.718	1.00
170_V	208_Q	0.717	1.00
239_A	247_Q	0.717	1.00
173_V	205_F	0.714	1.00
57_I	63_L	0.713	1.00
149_E	152_R	0.711	1.00
173_V	213_P	0.707	1.00
234_R	238_A	0.706	1.00
250_M	254_F	0.696	1.00
202_L	206_T	0.693	1.00
246_D	249_H	0.690	1.00
180_H	193_L	0.683	1.00
202_L	212_T	0.679	1.00
82_D	85_C	0.676	1.00
46_R	56_I	0.674	1.00
222_I	244_F	0.671	1.00
118_E	122_S	0.671	1.00
247_Q	250_M	0.670	1.00
138_R	148_E	0.668	1.00
135_Q	139_K	0.666	1.00
125_E	128_I	0.665	1.00
177_L	216_Y	0.660	1.00
49_A	52_D	0.659	1.00
125_E	145_H	0.656	1.00
206_T	212_T	0.656	1.00
137_L	141_E	0.653	1.00
238_A	266_M	0.652	1.00
137_L	144_L	0.651	1.00
118_E	125_E	0.646	1.00
202_L	214_N	0.642	1.00
218_E	249_H	0.641	1.00
118_E	149_E	0.641	1.00
230_E	265_Y	0.641	1.00
38_I	62_L	0.639	1.00
167_S	171_K	0.639	1.00
83_Y	86_I	0.638	1.00
116_R	120_T	0.637	1.00
96_A	99_E	0.636	1.00
39_G	65_F	0.632	1.00
48_L	63_L	0.631	1.00
128_I	132_E	0.629	1.00
169_E	172_M	0.628	1.00
129_L	133_E	0.624	1.00
95_K	98_K	0.624	1.00
138_R	141_E	0.622	1.00
178_E	224_Q	0.621	1.00
235_P	263_K	0.619	1.00
211_I	216_Y	0.617	1.00
85_C	88_V	0.616	1.00
41_I	57_I	0.614	1.00
138_R	152_R	0.613	1.00
150_L	154_Y	0.613	1.00
39_G	83_Y	0.613	1.00
228_L	231_Q	0.612	1.00
41_I	83_Y	0.612	1.00
65_F	71_H	0.610	1.00
187_L	214_N	0.608	1.00
97_V	100_I	0.603	1.00
51_Q	70_T	0.603	1.00
32_F	70_T	0.602	1.00
137_L	140_E	0.602	1.00
223_N	257_Q	0.602	1.00
239_A	244_F	0.601	1.00
191_S	194_T	0.600	1.00
115_F	118_E	0.599	1.00
46_R	73_C	0.597	1.00
122_S	125_E	0.597	1.00
121_A	128_I	0.595	1.00
89_M	92_I	0.593	1.00
122_S	126_L	0.593	1.00
217_M	221_R	0.592	1.00
38_I	64_L	0.590	1.00
185_V	221_R	0.588	1.00
203_R	207_K	0.588	1.00
209_K	216_Y	0.587	1.00
173_V	193_L	0.587	1.00
173_V	177_L	0.585	1.00
137_L	148_E	0.584	1.00
113_V	117_H	0.582	1.00
254_F	260_L	0.577	1.00
248_S	261_T	0.571	1.00
225_A	238_A	0.570	1.00
170_V	201_L	0.570	1.00
118_E	128_I	0.568	1.00
96_A	101_T	0.567	1.00
111_Q	115_F	0.567	1.00
223_N	258_V	0.567	1.00
97_V	101_T	0.563	1.00
40_F	123_L	0.562	1.00
250_M	262_P	0.562	1.00
190_L	194_T	0.561	1.00
143_F	150_L	0.561	1.00
166_P	169_E	0.561	1.00
146_L	149_E	0.559	1.00
244_F	249_H	0.557	1.00
217_M	220_I	0.555	1.00
45_Q	77_D	0.555	1.00
185_V	217_M	0.555	1.00
73_C	83_Y	0.554	1.00
177_L	185_V	0.551	1.00
127_H	130_I	0.547	1.00
164_P	167_S	0.546	1.00
126_L	129_L	0.545	1.00
96_A	100_I	0.543	1.00
254_F	258_V	0.541	1.00
194_T	198_K	0.540	1.00
166_P	200_H	0.538	1.00
61_D	110_S	0.535	1.00
181_Y	221_R	0.534	1.00
39_G	63_L	0.530	1.00
34_D	89_M	0.529	1.00
192_E	195_G	0.527	1.00
248_S	252_K	0.525	1.00
111_Q	114_L	0.524	1.00
54_E	74_E	0.524	1.00
152_R	156_D	0.523	1.00
143_F	147_L	0.522	1.00
176_F	189_D	0.520	1.00
41_I	81_L	0.520	1.00
139_K	142_L	0.519	1.00
174_C	205_F	0.518	1.00
180_H	185_V	0.517	1.00
146_L	150_L	0.517	1.00
84_R	87_N	0.516	1.00
138_R	149_E	0.515	1.00
155_S	159_F	0.514	1.00
175_E	178_E	0.513	1.00
147_L	150_L	0.511	1.00
201_L	204_S	0.508	1.00
34_D	68_R	0.508	1.00
145_H	152_R	0.507	1.00
206_T	209_K	0.507	1.00
39_G	48_L	0.507	1.00
122_S	142_L	0.505	1.00
35_Y	87_N	0.505	1.00
168_D	171_K	0.505	1.00
114_L	118_E	0.503	1.00
166_P	208_Q	0.502	1.00
103_S	106_L	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
3gbgA	1	0.8909	100	0.24	Contact Map
1bl0A	1	0.4	100	0.477	Contact Map
3oouA	1	0.3782	100	0.481	Contact Map
3mn2A	1	0.3818	100	0.482	Contact Map
3oioA	1	0.4036	100	0.484	Contact Map
3w6vA	1	0.3964	99.9	0.491	Contact Map
3mklA	1	0.4	99.9	0.492	Contact Map
2k9sA	1	0.3818	99.9	0.493	Contact Map
3lsgA	2	0.3673	99.9	0.502	Contact Map
1d5yA	1	0.4	99.9	0.509	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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