YUST - BACSU - GREMLIN Contacts

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YUST - Uncharacterized HTH-type transcriptional regulator YusT

UniProt:	O32186	Sequences: MESGDLRVFQMVAREGTITKAALQLGYVQSNVTARIQQLEAELGTTLFLRHNRGMTLSASGKLLLDYANKIIGLLDEASKALSSSAEPSGPLMIGCTQTTAAVRLPKLLASYYEEHPNVQLSLTTGHTQFLLDKVLRYELDGAFIGCECHHPELESYPAFEEEPVVVSAASVPDVEEAITKPILVYSTGCSYRETLEKWLRSVGVTQPVIMEFGTLEAIIGGVTAGLGISLLPRTVVQKHEAEGSIRLYPLPEALSQMKTEFIVRKDSFISSALRTFMDSFTPVKTAESQKSSLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	295 (278)
Sequences:	78958 (57205)
Seq/√Len:	3430.9

ECOLI - OXYR NAC ABGR CYNR YNEJ TDCA YFIE YBHD CYSB NHAR LYSR YEIE LEUO AAER CBL YAFC YBDO YDCI HCAR YFER TTDR DMLR YIDZ PGRR YCAN ILVY YIAU METR YHJC YNFL DSDC YDHB YGFI YAHB GCVA YBEF ALLS YEEY XAPR ICIA LRHA YJIE YHAJ PERR HDFR
BACSU - YUST GLTR CYSL YOFA YWBI ALSR YCGK GLTC CZCR YYBE CITR YTLI YWQM BSDA YVBU 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
70_K	74_L	3.632	1.00
15_E	24_Q	3.352	1.00
157_Y	282_T	2.626	1.00
67_Y	81_A	2.508	1.00
11_M	24_Q	2.483	1.00
95_G	140_L	2.475	1.00
158_P	259_K	2.290	1.00
172_V	181_K	2.239	1.00
158_P	161_E	2.206	1.00
161_E	259_K	2.206	1.00
91_P	122_S	2.195	1.00
45_T	60_S	2.186	1.00
223_V	230_S	2.151	1.00
111_S	284_V	2.147	1.00
10_Q	69_N	2.113	1.00
8_V	35_R	2.102	1.00
10_Q	14_R	2.057	1.00
91_P	120_Q	2.053	1.00
165_V	234_R	2.051	1.00
67_Y	74_L	2.040	1.00
163_E	234_R	2.020	1.00
111_S	280_S	1.989	1.00
161_E	257_Q	1.988	1.00
224_T	245_S	1.983	1.00
11_M	15_E	1.968	1.00
20_K	23_L	1.943	1.00
93_M	122_S	1.930	1.00
11_M	14_R	1.913	1.00
220_I	240_H	1.893	1.00
13_A	57_L	1.877	1.00
10_Q	65_L	1.871	1.00
174_D	177_E	1.860	1.00
168_S	249_Y	1.859	1.00
8_V	32_V	1.855	1.00
14_R	69_N	1.842	1.00
224_T	240_H	1.841	1.00
71_I	75_L	1.837	1.00
65_L	69_N	1.826	1.00
184_L	228_G	1.812	1.00
165_V	248_L	1.799	1.00
182_P	210_I	1.726	1.00
13_A	65_L	1.717	1.00
156_S	261_E	1.704	1.00
63_L	81_A	1.692	1.00
49_L	56_T	1.674	1.00
134_K	139_E	1.646	1.00
64_L	78_A	1.643	1.00
15_E	20_K	1.632	1.00
67_Y	70_K	1.584	1.00
155_E	266_K	1.559	1.00
18_I	36_I	1.554	1.00
10_Q	68_A	1.541	1.00
17_T	20_K	1.536	1.00
5_D	35_R	1.523	1.00
157_Y	264_V	1.523	1.00
14_R	24_Q	1.513	1.00
5_D	42_E	1.493	1.00
5_D	38_Q	1.492	1.00
278_M	282_T	1.449	1.00
28_V	31_N	1.439	1.00
112_Y	277_F	1.437	1.00
102_A	217_E	1.436	1.00
264_V	278_M	1.433	1.00
9_F	65_L	1.424	1.00
46_T	49_L	1.424	1.00
11_M	25_L	1.423	1.00
155_E	264_V	1.422	1.00
67_Y	77_E	1.422	1.00
51_H	56_T	1.420	1.00
145_I	263_I	1.413	1.00
8_V	27_Y	1.403	1.00
134_K	140_L	1.389	1.00
147_C	261_E	1.385	1.00
74_L	77_E	1.384	1.00
19_T	29_Q	1.384	1.00
115_E	280_S	1.377	1.00
112_Y	119_V	1.374	1.00
93_M	124_T	1.366	1.00
87_E	118_N	1.362	1.00
126_G	130_F	1.359	1.00
135_V	143_A	1.358	1.00
71_I	78_A	1.348	1.00
270_I	274_L	1.337	1.00
276_T	279_D	1.333	1.00
240_H	245_S	1.323	1.00
193_R	197_E	1.322	1.00
59_A	62_K	1.319	1.00
64_L	79_S	1.318	1.00
66_D	70_K	1.317	1.00
89_S	118_N	1.310	1.00
10_Q	72_I	1.301	1.00
111_S	115_E	1.301	1.00
262_F	278_M	1.301	1.00
162_E	235_T	1.296	1.00
168_S	172_V	1.293	1.00
219_I	230_S	1.293	1.00
136_L	153_E	1.280	1.00
221_G	224_T	1.275	1.00
67_Y	78_A	1.270	1.00
181_K	229_I	1.270	1.00
142_G	262_F	1.266	1.00
170_A	245_S	1.260	1.00
3_S	75_L	1.258	1.00
158_P	261_E	1.258	1.00
27_Y	31_N	1.249	1.00
170_A	247_R	1.247	1.00
168_S	229_I	1.236	1.00
113_Y	210_I	1.226	1.00
63_L	66_D	1.220	1.00
142_G	274_L	1.212	1.00
34_A	38_Q	1.211	1.00
110_A	225_A	1.207	1.00
234_R	248_L	1.205	1.00
42_E	79_S	1.199	1.00
9_F	48_F	1.186	1.00
173_P	181_K	1.185	1.00
110_A	114_E	1.181	1.00
9_F	13_A	1.165	1.00
63_L	67_Y	1.165	1.00
113_Y	182_P	1.157	1.00
156_S	263_I	1.157	1.00
126_G	134_K	1.135	1.00
107_K	225_A	1.130	1.00
248_L	251_L	1.112	1.00
234_R	238_Q	1.110	1.00
238_Q	242_A	1.102	1.00
34_A	37_Q	1.102	1.00
70_K	77_E	1.101	1.00
62_K	66_D	1.100	1.00
116_H	276_T	1.099	1.00
6_L	68_A	1.094	1.00
122_S	212_E	1.083	1.00
220_I	224_T	1.082	1.00
157_Y	278_M	1.081	1.00
11_M	21_A	1.078	1.00
280_S	284_V	1.071	1.00
182_P	208_P	1.071	1.00
101_A	125_T	1.065	1.00
167_V	248_L	1.064	1.00
37_Q	41_A	1.056	1.00
221_G	225_A	1.056	1.00
239_K	243_E	1.052	1.00
18_I	55_M	1.050	1.00
124_T	134_K	1.049	1.00
279_D	282_T	1.048	1.00
71_I	74_L	1.041	1.00
33_T	37_Q	1.032	1.00
79_S	83_S	1.029	1.00
9_F	47_L	1.024	1.00
111_S	114_E	1.023	1.00
35_R	38_Q	1.020	1.00
136_L	151_H	1.018	1.00
169_A	226_G	1.016	1.00
163_E	257_Q	1.015	1.00
12_V	21_A	1.011	1.00
280_S	283_P	1.010	1.00
275_R	279_D	1.010	1.00
108_L	281_F	1.004	1.00
265_R	268_S	1.000	1.00
73_G	77_E	0.999	1.00
112_Y	280_S	0.991	1.00
92_L	277_F	0.987	1.00
64_L	68_A	0.980	1.00
184_L	219_I	0.978	1.00
167_V	237_V	0.976	1.00
185_V	209_V	0.974	1.00
200_L	205_V	0.973	1.00
213_F	219_I	0.973	1.00
38_Q	41_A	0.967	1.00
12_V	18_I	0.965	1.00
4_G	7_R	0.964	1.00
21_A	32_V	0.959	1.00
57_L	61_G	0.951	1.00
112_Y	116_H	0.948	1.00
27_Y	32_V	0.947	1.00
8_V	25_L	0.945	1.00
13_A	48_F	0.931	1.00
76_D	79_S	0.930	1.00
194_E	197_E	0.930	1.00
7_R	76_D	0.929	1.00
20_K	24_Q	0.926	1.00
75_L	79_S	0.916	1.00
70_K	73_G	0.916	1.00
168_S	173_P	0.915	1.00
166_V	229_I	0.913	1.00
9_F	39_L	0.908	1.00
98_Q	215_T	0.906	1.00
9_F	57_L	0.906	1.00
213_F	222_G	0.900	1.00
175_V	253_E	0.896	1.00
115_E	283_P	0.895	1.00
134_K	137_R	0.894	1.00
76_D	80_K	0.892	1.00
45_T	82_L	0.890	1.00
16_G	56_T	0.888	1.00
271_S	274_L	0.887	1.00
147_C	259_K	0.881	1.00
95_G	143_A	0.880	1.00
108_L	280_S	0.867	1.00
48_F	55_M	0.866	1.00
240_H	243_E	0.860	1.00
155_E	158_P	0.858	1.00
60_S	63_L	0.853	1.00
110_A	227_L	0.847	1.00
66_D	69_N	0.847	1.00
182_P	209_V	0.844	1.00
199_W	203_V	0.843	1.00
108_L	284_V	0.842	1.00
60_S	82_L	0.841	1.00
77_E	81_A	0.840	1.00
140_L	143_A	0.836	1.00
19_T	23_L	0.835	1.00
95_G	145_I	0.835	1.00
120_Q	208_P	0.833	1.00
75_L	78_A	0.831	1.00
90_G	273_A	0.825	1.00
124_T	140_L	0.824	1.00
25_L	32_V	0.822	1.00
51_H	54_G	0.821	1.00
196_L	200_L	0.817	1.00
14_R	65_L	0.814	1.00
29_Q	33_T	0.813	1.00
272_S	276_T	0.811	1.00
94_I	142_G	0.811	1.00
174_D	252_P	0.810	1.00
74_L	78_A	0.808	1.00
113_Y	227_L	0.807	1.00
119_V	273_A	0.806	1.00
15_E	21_A	0.805	1.00
16_G	54_G	0.801	1.00
9_F	64_L	0.799	1.00
194_E	198_K	0.799	1.00
7_R	11_M	0.799	1.00
13_A	16_G	0.798	1.00
13_A	61_G	0.795	1.00
270_I	275_R	0.794	1.00
4_G	35_R	0.780	1.00
12_V	48_F	0.780	1.00
168_S	247_R	0.779	1.00
167_V	230_S	0.779	1.00
169_A	227_L	0.779	1.00
169_A	172_V	0.776	1.00
78_A	82_L	0.776	1.00
3_S	72_I	0.775	1.00
130_F	134_K	0.774	1.00
62_K	65_L	0.773	1.00
154_L	263_I	0.772	1.00
176_E	179_I	0.771	1.00
16_G	62_K	0.770	1.00
69_N	73_G	0.766	1.00
237_V	240_H	0.762	1.00
222_G	227_L	0.759	1.00
37_Q	46_T	0.755	1.00
5_D	8_V	0.754	1.00
163_E	250_P	0.753	1.00
68_A	71_I	0.751	1.00
279_D	283_P	0.749	1.00
12_V	32_V	0.747	1.00
90_G	119_V	0.743	1.00
215_T	218_A	0.741	1.00
138_Y	265_R	0.740	1.00
18_I	32_V	0.739	1.00
7_R	10_Q	0.739	1.00
49_L	58_S	0.738	1.00
96_C	101_A	0.733	1.00
167_V	232_L	0.733	1.00
276_T	280_S	0.730	1.00
172_V	182_P	0.730	1.00
12_V	36_I	0.723	1.00
199_W	202_S	0.720	1.00
142_G	277_F	0.720	1.00
112_Y	276_T	0.718	1.00
268_S	271_S	0.717	1.00
115_E	276_T	0.716	1.00
171_S	226_G	0.711	1.00
141_D	274_L	0.706	1.00
233_P	236_V	0.706	1.00
59_A	63_L	0.705	1.00
198_K	202_S	0.703	1.00
60_S	64_L	0.702	1.00
136_L	154_L	0.700	1.00
187_S	212_E	0.700	1.00
195_T	199_W	0.698	1.00
197_E	201_R	0.692	1.00
179_I	205_V	0.691	1.00
93_M	141_D	0.691	1.00
88_P	116_H	0.687	1.00
174_D	253_E	0.686	1.00
177_E	180_T	0.683	1.00
102_A	221_G	0.682	1.00
111_S	283_P	0.682	1.00
64_L	82_L	0.680	1.00
153_E	266_K	0.678	1.00
31_N	35_R	0.677	1.00
67_Y	71_I	0.677	1.00
93_M	140_L	0.672	1.00
57_L	62_K	0.672	1.00
196_L	199_W	0.663	1.00
166_V	231_L	0.662	1.00
176_E	203_V	0.660	1.00
198_K	201_R	0.660	1.00
107_K	110_A	0.657	1.00
9_F	61_G	0.655	1.00
195_T	198_K	0.655	1.00
23_L	26_G	0.655	1.00
56_T	62_K	0.653	1.00
49_L	54_G	0.649	1.00
7_R	72_I	0.647	1.00
77_E	80_K	0.639	1.00
186_Y	219_I	0.636	1.00
146_G	258_M	0.634	1.00
40_E	50_R	0.629	1.00
125_T	214_G	0.628	1.00
163_E	254_A	0.625	1.00
73_G	76_D	0.624	1.00
183_I	229_I	0.624	1.00
272_S	275_R	0.623	1.00
172_V	229_I	0.623	1.00
211_M	222_G	0.621	1.00
120_Q	212_E	0.621	1.00
170_A	244_G	0.620	1.00
239_K	242_A	0.619	1.00
183_I	207_Q	0.618	1.00
166_V	178_A	0.618	1.00
36_I	40_E	0.615	1.00
107_K	111_S	0.614	1.00
40_E	45_T	0.613	1.00
105_L	108_L	0.613	1.00
142_G	278_M	0.610	1.00
224_T	243_E	0.603	1.00
12_V	17_T	0.602	1.00
171_S	247_R	0.601	1.00
13_A	62_K	0.600	1.00
4_G	38_Q	0.599	1.00
72_I	76_D	0.598	1.00
80_K	84_S	0.597	1.00
180_T	208_P	0.595	1.00
4_G	8_V	0.594	1.00
43_L	64_L	0.591	1.00
96_C	105_L	0.588	1.00
193_R	212_E	0.587	1.00
68_A	72_I	0.582	1.00
92_L	273_A	0.579	1.00
116_H	119_V	0.578	1.00
187_S	214_G	0.578	1.00
194_E	199_W	0.578	1.00
92_L	142_G	0.577	1.00
135_V	154_L	0.576	1.00
264_V	275_R	0.574	1.00
45_T	49_L	0.574	1.00
21_A	25_L	0.573	1.00
213_F	218_A	0.572	1.00
45_T	85_S	0.567	1.00
89_S	120_Q	0.564	1.00
43_L	82_L	0.564	1.00
197_E	200_L	0.564	1.00
31_N	34_A	0.564	1.00
48_F	57_L	0.562	1.00
162_E	258_M	0.562	1.00
166_V	183_I	0.560	1.00
95_G	124_T	0.558	1.00
63_L	82_L	0.556	1.00
159_A	262_F	0.555	1.00
277_F	281_F	0.555	1.00
164_P	231_L	0.553	1.00
98_Q	127_H	0.553	1.00
95_G	126_G	0.553	1.00
30_S	34_A	0.544	1.00
28_V	34_A	0.542	1.00
18_I	29_Q	0.542	1.00
219_I	223_V	0.541	1.00
135_V	263_I	0.540	1.00
125_T	215_T	0.537	1.00
81_A	84_S	0.536	1.00
43_L	46_T	0.535	1.00
147_C	156_S	0.534	1.00
90_G	118_N	0.534	1.00
80_K	83_S	0.532	1.00
27_Y	35_R	0.532	1.00
104_R	108_L	0.532	1.00
200_L	207_Q	0.532	1.00
46_T	60_S	0.532	1.00
232_L	237_V	0.530	1.00
84_S	88_P	0.530	1.00
191_S	194_E	0.530	1.00
16_G	55_M	0.530	1.00
107_K	221_G	0.528	1.00
110_A	113_Y	0.524	1.00
100_T	104_R	0.524	1.00
106_P	110_A	0.524	1.00
57_L	65_L	0.522	1.00
193_R	199_W	0.522	1.00
160_F	260_T	0.521	1.00
192_Y	196_L	0.520	1.00
273_A	276_T	0.520	1.00
78_A	81_A	0.518	1.00
38_Q	42_E	0.516	1.00
102_A	215_T	0.516	1.00
245_S	248_L	0.516	1.00
155_E	267_D	0.515	1.00
216_L	233_P	0.514	1.00
136_L	139_E	0.514	1.00
96_C	123_L	0.514	1.00
222_G	228_G	0.512	1.00
120_Q	210_I	0.509	1.00
274_L	278_M	0.509	1.00
8_V	36_I	0.509	1.00
18_I	54_G	0.508	1.00
66_D	81_A	0.508	1.00
217_E	221_G	0.506	1.00
251_L	254_A	0.506	1.00
179_I	206_T	0.506	1.00
6_L	64_L	0.502	1.00
109_L	121_L	0.501	1.00
127_H	130_F	0.501	1.00
18_I	50_R	0.500	1.00
167_V	246_I	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
1uthA	2	0.7458	100	0.092	Contact Map
2esnA	3	0.9695	100	0.093	Contact Map
3fxqA	3	0.9695	100	0.099	Contact Map
3fzvA	4	0.9458	100	0.107	Contact Map
1ixcA	4	0.9627	100	0.108	Contact Map
2h98A	2	0.6915	100	0.11	Contact Map
1al3A	1	0.7085	100	0.112	Contact Map
4x6gA	4	1	100	0.114	Contact Map
2h9bA	2	0.6915	100	0.117	Contact Map
3szpA	3	0.9559	100	0.129	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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