YFIF - BACSU - GREMLIN Contacts

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YFIF - Uncharacterized HTH-type transcriptional regulator YfiF

UniProt:	P54722	Sequences: MELNHLVTGKIALNQYVHRLEQKDVSFYVHYWGAMTNHYNTLLHKHSFYEICYVVRGEGYYLEGDRTYPLREQTIFLSKPEHLHQIKSETGLFLFYVAFELSEDQSSAEWIKVMEEVKQSPFITMQLKDGEPPGLLWKTLMLQAAQPVNAFDKEILSHLSHALILSLIQTFLPYAQRPKQKQPIHTSSALLTEVKLHIKDNLSQPLKLTDVASHFHISGRHLSRLFAAELGVSYSEFVQNEKINKAAELLKSTNLSIKEIAEEIGFSVHYFTRVFSAKIGSSPGLFRSLYKDSKMTAFQINKPFQKIEQAKPHE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	314 (252)
Sequences:	26536 (22830)
Seq/√Len:	1438.2

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
247_A	279_I	3.304	1.00
232_V	240_N	3.229	1.00
199_K	241_E	3.163	1.00
255_L	263_E	3.149	1.00
243_I	279_I	3.089	1.00
209_T	219_G	2.840	1.00
245_K	248_E	2.832	1.00
201_N	204_Q	2.748	1.00
240_N	278_K	2.678	1.00
197_H	201_N	2.622	1.00
275_F	286_F	2.454	1.00
246_A	271_F	2.422	1.00
249_L	263_E	2.296	1.00
226_F	237_F	2.212	1.00
249_L	264_I	2.182	1.00
60_Y	67_T	2.174	1.00
281_S	289_L	2.143	1.00
194_V	222_L	2.090	1.00
207_K	210_D	2.083	1.00
198_I	238_V	2.002	1.00
255_L	259_E	1.924	1.00
235_S	239_Q	1.915	1.00
60_Y	69_P	1.898	1.00
194_V	215_F	1.895	1.00
62_L	67_T	1.869	1.00
249_L	255_L	1.861	1.00
202_L	241_E	1.848	1.00
197_H	214_H	1.836	1.00
191_L	230_L	1.824	1.00
243_I	278_K	1.801	1.00
195_K	230_L	1.785	1.00
250_L	257_I	1.781	1.00
159_L	162_A	1.752	1.00
247_A	286_F	1.739	1.00
211_V	234_Y	1.738	1.00
268_V	272_T	1.733	1.00
58_E	69_P	1.731	1.00
208_L	223_S	1.717	1.00
232_V	236_E	1.676	1.00
196_L	200_D	1.668	1.00
56_R	93_F	1.664	1.00
256_S	259_E	1.639	1.00
274_V	277_A	1.635	1.00
197_H	206_L	1.631	1.00
234_Y	238_V	1.607	1.00
221_H	225_L	1.599	1.00
248_E	252_S	1.598	1.00
55_V	95_F	1.595	1.00
222_L	234_Y	1.584	1.00
241_E	245_K	1.580	1.00
221_H	224_R	1.570	1.00
270_Y	274_V	1.565	1.00
199_K	237_F	1.551	1.00
58_E	71_R	1.539	1.00
259_E	263_E	1.527	1.00
258_K	268_V	1.499	1.00
284_G	288_S	1.489	1.00
210_D	214_H	1.477	1.00
258_K	262_E	1.470	1.00
134_G	138_K	1.467	1.00
203_S	263_E	1.457	1.00
245_K	249_L	1.456	1.00
202_L	245_K	1.443	1.00
64_G	82_H	1.436	1.00
281_S	285_L	1.435	1.00
246_A	264_I	1.431	1.00
198_I	241_E	1.426	1.00
217_I	221_H	1.424	1.00
266_F	274_V	1.422	1.00
209_T	213_S	1.407	1.00
188_S	229_E	1.407	1.00
245_K	264_I	1.404	1.00
220_R	224_R	1.397	1.00
162_A	166_S	1.397	1.00
60_Y	87_K	1.394	1.00
71_R	74_T	1.389	1.00
260_I	264_I	1.389	1.00
223_S	234_Y	1.388	1.00
259_E	262_E	1.385	1.00
195_K	199_K	1.370	1.00
62_L	85_Q	1.365	1.00
253_T	287_R	1.335	1.00
269_H	272_T	1.333	1.00
241_E	244_N	1.325	1.00
219_G	223_S	1.315	1.00
240_N	244_N	1.300	1.00
49_Y	80_P	1.294	1.00
217_I	222_L	1.293	1.00
272_T	282_S	1.290	1.00
204_Q	210_D	1.288	1.00
233_S	236_E	1.279	1.00
255_L	260_I	1.275	1.00
239_Q	274_V	1.268	1.00
56_R	72_E	1.262	1.00
147_P	152_D	1.240	1.00
218_S	221_H	1.240	1.00
158_H	165_L	1.237	1.00
190_L	217_I	1.230	1.00
158_H	161_H	1.200	1.00
272_T	284_G	1.197	1.00
285_L	288_S	1.188	1.00
79_K	82_H	1.187	1.00
158_H	162_A	1.185	1.00
194_V	211_V	1.178	1.00
138_K	142_L	1.157	1.00
44_H	84_H	1.150	1.00
247_A	251_K	1.138	1.00
273_R	277_A	1.134	1.00
135_L	139_T	1.121	1.00
189_A	193_E	1.110	1.00
50_E	84_H	1.107	1.00
208_L	234_Y	1.101	1.00
284_G	287_R	1.099	1.00
190_L	215_F	1.091	1.00
244_N	247_A	1.090	1.00
225_L	228_A	1.083	1.00
46_H	84_H	1.071	1.00
55_V	93_F	1.069	1.00
206_L	211_V	1.068	1.00
282_S	285_L	1.067	1.00
155_I	162_A	1.059	1.00
211_V	214_H	1.047	1.00
135_L	138_K	1.043	1.00
161_H	165_L	1.041	1.00
235_S	270_Y	1.039	1.00
251_K	290_Y	1.038	1.00
220_R	223_S	1.034	1.00
195_K	237_F	1.029	1.00
212_A	219_G	1.028	1.00
123_I	126_Q	1.024	1.00
197_H	215_F	1.015	1.00
155_I	159_L	1.014	1.00
257_I	260_I	1.010	1.00
203_S	245_K	1.008	1.00
210_D	213_S	1.002	1.00
243_I	274_V	0.990	1.00
193_E	214_H	0.987	1.00
225_L	229_E	0.984	1.00
208_L	219_G	0.982	1.00
192_T	196_L	0.980	1.00
285_L	289_L	0.979	1.00
270_Y	273_R	0.972	1.00
274_V	278_K	0.972	1.00
198_I	234_Y	0.963	1.00
272_T	276_S	0.962	1.00
239_Q	277_A	0.960	1.00
253_T	260_I	0.958	1.00
215_F	222_L	0.957	1.00
236_E	240_N	0.940	1.00
190_L	225_L	0.939	1.00
157_S	161_H	0.938	1.00
247_A	275_F	0.931	1.00
249_L	260_I	0.929	1.00
59_G	69_P	0.928	1.00
236_E	239_Q	0.924	1.00
59_G	70_L	0.924	1.00
62_L	87_K	0.923	1.00
54_V	59_G	0.922	1.00
132_P	166_S	0.922	1.00
43_L	83_L	0.921	1.00
193_E	215_F	0.920	1.00
112_K	115_E	0.902	1.00
202_L	238_V	0.897	1.00
53_Y	75_I	0.894	1.00
242_K	264_I	0.894	1.00
46_H	50_E	0.894	1.00
267_S	273_R	0.893	1.00
193_E	196_L	0.893	1.00
261_A	268_V	0.892	1.00
279_I	286_F	0.891	1.00
205_P	210_D	0.885	1.00
243_I	271_F	0.884	1.00
197_H	211_V	0.879	1.00
250_L	260_I	0.873	1.00
127_L	130_G	0.862	1.00
276_S	282_S	0.861	1.00
59_G	92_L	0.860	1.00
217_I	225_L	0.859	1.00
139_T	143_Q	0.858	1.00
239_Q	278_K	0.856	1.00
250_L	287_R	0.848	1.00
202_L	206_L	0.841	1.00
191_L	225_L	0.838	1.00
101_L	105_Q	0.830	1.00
194_V	226_F	0.830	1.00
281_S	286_F	0.830	1.00
123_I	127_L	0.828	1.00
132_P	135_L	0.821	1.00
139_T	162_A	0.820	1.00
194_V	197_H	0.819	1.00
191_L	194_V	0.817	1.00
226_F	230_L	0.815	1.00
154_E	157_S	0.812	1.00
61_Y	76_F	0.810	1.00
201_N	210_D	0.807	1.00
187_S	228_A	0.803	1.00
198_I	237_F	0.802	1.00
237_F	241_E	0.799	1.00
165_L	169_Q	0.798	1.00
246_A	249_L	0.794	1.00
43_L	85_Q	0.794	1.00
191_L	229_E	0.792	1.00
202_L	264_I	0.792	1.00
54_V	57_G	0.792	1.00
226_F	234_Y	0.788	1.00
49_Y	77_L	0.783	1.00
139_T	159_L	0.779	1.00
235_S	238_V	0.777	1.00
276_S	285_L	0.772	1.00
52_C	96_Y	0.770	1.00
132_P	136_L	0.764	1.00
130_G	134_G	0.760	1.00
131_E	135_L	0.760	1.00
131_E	134_G	0.753	1.00
223_S	227_A	0.751	1.00
50_E	98_A	0.749	1.00
211_V	222_L	0.743	1.00
201_N	214_H	0.741	1.00
260_I	287_R	0.740	1.00
223_S	233_S	0.738	1.00
188_S	192_T	0.731	1.00
194_V	234_Y	0.730	1.00
224_R	228_A	0.726	1.00
122_F	126_Q	0.725	1.00
236_E	278_K	0.723	1.00
154_E	161_H	0.723	1.00
269_H	282_S	0.720	1.00
63_E	66_R	0.709	1.00
199_K	245_K	0.706	1.00
206_L	242_K	0.706	1.00
192_T	195_K	0.702	1.00
139_T	142_L	0.701	1.00
155_I	158_H	0.699	1.00
267_S	270_Y	0.696	1.00
257_I	284_G	0.695	1.00
243_I	266_F	0.695	1.00
51_I	77_L	0.695	1.00
238_V	242_K	0.692	1.00
62_L	65_D	0.688	1.00
70_L	76_F	0.685	1.00
194_V	214_H	0.685	1.00
112_K	116_E	0.685	1.00
185_H	188_S	0.685	1.00
202_L	242_K	0.683	1.00
162_A	165_L	0.683	1.00
54_V	70_L	0.682	1.00
153_K	157_S	0.681	1.00
166_S	170_T	0.681	1.00
188_S	225_L	0.679	1.00
275_F	281_S	0.676	1.00
136_L	140_L	0.675	1.00
141_M	145_A	0.667	1.00
61_Y	86_I	0.666	1.00
136_L	159_L	0.660	1.00
246_A	260_I	0.659	1.00
156_L	159_L	0.659	1.00
206_L	210_D	0.656	1.00
155_I	165_L	0.656	1.00
132_P	139_T	0.653	1.00
59_G	86_I	0.647	1.00
187_S	190_L	0.639	1.00
256_S	260_I	0.639	1.00
267_S	277_A	0.639	1.00
122_F	125_M	0.639	1.00
56_R	91_G	0.638	1.00
269_H	273_R	0.638	1.00
74_T	124_T	0.637	1.00
244_N	278_K	0.636	1.00
136_L	139_T	0.633	1.00
126_Q	129_D	0.633	1.00
49_Y	52_C	0.632	1.00
52_C	76_F	0.631	1.00
223_S	235_S	0.630	1.00
142_L	146_Q	0.630	1.00
251_K	286_F	0.628	1.00
190_L	193_E	0.628	1.00
261_A	266_F	0.626	1.00
197_H	210_D	0.622	1.00
232_V	237_F	0.621	1.00
143_Q	169_Q	0.618	1.00
53_Y	137_W	0.618	1.00
52_C	61_Y	0.617	1.00
53_Y	130_G	0.617	1.00
227_A	233_S	0.616	1.00
208_L	235_S	0.614	1.00
211_V	215_F	0.614	1.00
248_E	251_K	0.614	1.00
114_M	117_V	0.611	1.00
254_N	260_I	0.609	1.00
154_E	158_H	0.608	1.00
271_F	283_P	0.607	1.00
152_D	156_L	0.605	1.00
238_V	241_E	0.605	1.00
135_L	142_L	0.599	1.00
121_P	124_T	0.599	1.00
115_E	119_Q	0.599	1.00
268_V	271_F	0.595	1.00
230_L	237_F	0.593	1.00
144_A	147_P	0.592	1.00
194_V	198_I	0.588	1.00
111_I	115_E	0.588	1.00
249_L	252_S	0.587	1.00
63_E	78_S	0.582	1.00
191_L	195_K	0.581	1.00
195_K	226_F	0.580	1.00
212_A	215_F	0.574	1.00
52_C	78_S	0.573	1.00
198_I	206_L	0.572	1.00
170_T	174_Y	0.572	1.00
40_N	87_K	0.570	1.00
244_N	279_I	0.568	1.00
262_E	268_V	0.566	1.00
45_K	83_L	0.565	1.00
247_A	281_S	0.563	1.00
78_S	84_H	0.561	1.00
196_L	199_K	0.560	1.00
97_V	101_L	0.559	1.00
51_I	75_I	0.557	1.00
215_F	219_G	0.557	1.00
208_L	220_R	0.556	1.00
266_F	270_Y	0.555	1.00
187_S	229_E	0.555	1.00
191_L	222_L	0.555	1.00
56_R	78_S	0.553	1.00
206_L	238_V	0.550	1.00
205_P	242_K	0.548	1.00
67_T	87_K	0.548	1.00
48_F	98_A	0.547	1.00
113_V	117_V	0.547	1.00
113_V	116_E	0.547	1.00
110_W	113_V	0.545	1.00
213_S	216_H	0.542	1.00
189_A	192_T	0.541	1.00
54_V	94_L	0.540	1.00
52_C	94_L	0.537	1.00
154_E	165_L	0.537	1.00
58_E	90_T	0.537	1.00
86_I	94_L	0.535	1.00
239_Q	270_Y	0.532	1.00
60_Y	63_E	0.532	1.00
254_N	287_R	0.531	1.00
143_Q	147_P	0.531	1.00
224_R	227_A	0.531	1.00
159_L	166_S	0.530	1.00
121_P	125_M	0.530	1.00
146_Q	149_N	0.529	1.00
244_N	248_E	0.529	1.00
54_V	92_L	0.528	1.00
191_L	215_F	0.526	1.00
50_E	78_S	0.525	1.00
53_Y	73_Q	0.525	1.00
271_F	275_F	0.525	1.00
61_Y	78_S	0.525	1.00
168_I	172_L	0.525	1.00
239_Q	243_I	0.524	1.00
194_V	225_L	0.523	1.00
101_L	104_D	0.522	1.00
149_N	152_D	0.521	1.00
190_L	194_V	0.520	1.00
191_L	226_F	0.519	1.00
125_M	129_D	0.519	1.00
136_L	166_S	0.518	1.00
74_T	126_Q	0.512	1.00
80_P	101_L	0.509	1.00
52_C	80_P	0.508	1.00
54_V	74_T	0.508	1.00
222_L	225_L	0.507	1.00
55_V	138_K	0.507	1.00
143_Q	155_I	0.505	1.00
78_S	92_L	0.504	1.00
159_L	164_I	0.504	1.00
52_C	86_I	0.504	1.00
171_F	175_A	0.504	1.00
222_L	230_L	0.503	1.00
246_A	275_F	0.502	1.00
64_G	83_L	0.502	1.00
171_F	174_Y	0.500	1.00
198_I	211_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
3gbgA	1	0.7962	100	0.32	Contact Map
3oouA	1	0.3312	100	0.538	Contact Map
1bl0A	1	0.3662	100	0.541	Contact Map
3oioA	1	0.3535	100	0.542	Contact Map
3mn2A	1	0.3344	100	0.546	Contact Map
3w6vA	1	0.3503	100	0.548	Contact Map
3mklA	1	0.3503	100	0.548	Contact Map
2k9sA	1	0.3344	99.9	0.551	Contact Map
3lsgA	2	0.3217	99.9	0.557	Contact Map
1d5yA	1	0.4045	99.9	0.574	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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