YOFA - BACSU - GREMLIN Contacts

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YOFA - HTH-type transcriptional regulator YofA

UniProt:	O34685	Sequences: MESGDLKIFQAVAREGSITKAAQMLNYVQSNVTARVHNLEEDLNIRLFHRTNRGMKLTAAGENLLQYADQVLSLLDQAEKSTRMSRQPKGPLRIGSLETMAVTHLPEHAASFLRRFPEVDLSVNTADTHHLIQQVLDHKVDGAFVYGPVEHAAVRQLHVSHDELVLISSREGTAEDMLQQPMLFFGAGCSHRDRVKRLLEEAGIHNQKIIEFGTLEAIIKGVSAGMGTALLPKSAVDGSEHRTNVWIHQLPPSYQDLEIVFIYRKDFFITSAFQTFLDEINEMKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	285 (275)
Sequences:	78541 (57150)
Seq/√Len:	3446.3

ECOLI - YFIE NAC OXYR ABGR NHAR YNEJ LEUO TDCA YDCI YBHD CYNR PGRR AAER CYSB YEIE ILVY YAFC HCAR LYSR CBL YNFL DSDC YGFI YBDO YHJC TTDR YFER YIAU YBEF YIDZ METR YDHB YCAN DMLR YEEY YAHB XAPR ALLS GCVA YJIE LRHA HDFR YHAJ PERR ICIA
BACSU - YOFA YUST CYSL GLTR YWBI YCGK YRAN CITR CZCR YYBE GLTC BSDA YWQM YKUM ALSR YTLI YVBU YXJO 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_Q	74_L	3.656	1.00
15_E	24_M	3.408	1.00
157_L	281_N	2.587	1.00
95_G	140_V	2.545	1.00
67_Y	81_S	2.513	1.00
11_A	24_M	2.437	1.00
172_G	180_Q	2.358	1.00
222_V	229_A	2.243	1.00
91_P	122_S	2.243	1.00
158_H	161_H	2.238	1.00
161_H	258_E	2.231	1.00
158_H	258_E	2.231	1.00
45_I	60_A	2.161	1.00
8_I	35_R	2.109	1.00
91_P	120_D	2.106	1.00
163_E	233_K	2.102	1.00
10_Q	69_D	2.073	1.00
67_Y	74_L	2.053	1.00
10_Q	14_R	2.029	1.00
20_K	23_Q	2.028	1.00
165_V	233_K	1.998	1.00
161_H	256_D	1.987	1.00
111_S	279_E	1.979	1.00
173_T	176_D	1.979	1.00
93_R	122_S	1.976	1.00
11_A	15_E	1.971	1.00
10_Q	65_L	1.944	1.00
11_A	14_R	1.935	1.00
14_R	69_D	1.935	1.00
168_S	248_H	1.931	1.00
13_A	57_L	1.897	1.00
223_S	244_N	1.885	1.00
8_I	32_V	1.881	1.00
71_V	75_L	1.867	1.00
183_L	227_G	1.847	1.00
65_L	69_D	1.840	1.00
165_V	247_I	1.757	1.00
181_P	209_I	1.744	1.00
49_H	56_K	1.716	1.00
156_Q	260_V	1.697	1.00
13_A	65_L	1.694	1.00
64_L	78_A	1.689	1.00
63_N	81_S	1.687	1.00
18_I	36_V	1.677	1.00
134_Q	139_K	1.668	1.00
15_E	20_K	1.652	1.00
155_R	265_K	1.587	1.00
10_Q	68_A	1.558	1.00
67_Y	70_Q	1.555	1.00
14_R	24_M	1.551	1.00
5_D	35_R	1.535	1.00
168_S	172_G	1.533	1.00
17_S	20_K	1.526	1.00
5_D	42_D	1.516	1.00
157_L	263_Y	1.508	1.00
5_D	38_N	1.506	1.00
133_Q	137_D	1.506	1.00
9_F	65_L	1.494	1.00
112_F	276_F	1.493	1.00
8_I	27_Y	1.457	1.00
11_A	25_L	1.455	1.00
28_V	31_N	1.455	1.00
46_R	49_H	1.441	1.00
19_T	29_Q	1.433	1.00
112_F	119_V	1.431	1.00
102_V	216_E	1.430	1.00
67_Y	77_Q	1.426	1.00
155_R	263_Y	1.421	1.00
87_Q	118_E	1.418	1.00
51_T	56_K	1.407	1.00
145_V	262_I	1.406	1.00
59_A	62_E	1.397	1.00
263_Y	277_L	1.397	1.00
147_G	260_V	1.393	1.00
71_V	78_A	1.381	1.00
134_Q	140_V	1.381	1.00
192_R	196_K	1.375	1.00
93_R	124_N	1.375	1.00
10_Q	72_L	1.365	1.00
74_L	77_Q	1.362	1.00
135_V	143_A	1.351	1.00
269_I	273_F	1.344	1.00
162_D	234_S	1.326	1.00
89_K	118_E	1.319	1.00
64_L	79_E	1.312	1.00
261_F	277_L	1.308	1.00
277_L	281_N	1.305	1.00
170_R	244_N	1.300	1.00
136_L	153_A	1.300	1.00
275_T	278_D	1.297	1.00
180_Q	228_T	1.296	1.00
218_I	229_A	1.294	1.00
66_Q	70_Q	1.293	1.00
142_G	261_F	1.290	1.00
3_S	75_L	1.274	1.00
142_G	273_F	1.271	1.00
220_K	223_S	1.263	1.00
67_Y	78_A	1.262	1.00
170_R	246_W	1.258	1.00
113_L	209_I	1.248	1.00
63_N	66_Q	1.243	1.00
42_D	79_E	1.241	1.00
115_R	279_E	1.238	1.00
158_H	260_V	1.237	1.00
168_S	228_T	1.236	1.00
27_Y	31_N	1.234	1.00
111_S	115_R	1.221	1.00
233_K	247_I	1.215	1.00
9_F	48_F	1.196	1.00
110_A	114_R	1.194	1.00
34_A	38_N	1.189	1.00
110_A	224_A	1.188	1.00
113_L	181_P	1.174	1.00
156_Q	262_I	1.170	1.00
9_F	13_A	1.165	1.00
233_K	237_D	1.158	1.00
126_A	134_Q	1.142	1.00
62_E	66_Q	1.140	1.00
63_N	67_Y	1.127	1.00
107_E	224_A	1.127	1.00
37_H	41_E	1.126	1.00
34_A	37_H	1.126	1.00
237_D	241_H	1.119	1.00
122_S	211_E	1.112	1.00
70_Q	77_Q	1.100	1.00
6_L	68_A	1.100	1.00
116_F	275_T	1.099	1.00
247_I	250_L	1.097	1.00
11_A	21_A	1.090	1.00
18_I	55_M	1.090	1.00
101_A	125_T	1.088	1.00
181_P	207_Q	1.074	1.00
9_F	47_L	1.072	1.00
33_T	37_H	1.068	1.00
220_K	224_A	1.059	1.00
167_I	247_I	1.055	1.00
71_V	74_L	1.046	1.00
111_S	114_R	1.042	1.00
12_V	21_A	1.039	1.00
264_R	267_F	1.038	1.00
157_L	277_L	1.036	1.00
238_G	242_R	1.034	1.00
274_Q	278_D	1.033	1.00
35_R	38_N	1.032	1.00
92_L	276_F	1.032	1.00
169_S	225_G	1.030	1.00
199_L	204_I	1.030	1.00
212_F	218_I	1.027	1.00
79_E	83_R	1.024	1.00
112_F	279_E	1.020	1.00
136_L	151_H	1.018	1.00
124_N	134_Q	1.010	1.00
183_L	218_I	1.007	1.00
4_G	7_K	1.006	1.00
57_L	61_G	0.994	1.00
163_E	256_D	0.994	1.00
73_S	77_Q	0.991	1.00
64_L	68_A	0.989	1.00
167_I	236_V	0.985	1.00
12_V	18_I	0.984	1.00
278_D	281_N	0.982	1.00
7_K	76_D	0.982	1.00
184_F	208_K	0.976	1.00
38_N	41_E	0.974	1.00
219_I	223_S	0.972	1.00
193_D	196_K	0.971	1.00
27_Y	32_V	0.970	1.00
8_I	25_L	0.969	1.00
112_F	116_F	0.969	1.00
108_H	280_I	0.969	1.00
21_A	32_V	0.955	1.00
13_A	48_F	0.953	1.00
76_D	79_E	0.949	1.00
166_L	228_T	0.944	1.00
174_A	252_P	0.939	1.00
134_Q	137_D	0.933	1.00
20_K	24_M	0.931	1.00
9_F	57_L	0.928	1.00
76_D	80_K	0.926	1.00
9_F	39_L	0.922	1.00
70_Q	73_S	0.922	1.00
212_F	221_G	0.920	1.00
108_H	279_E	0.920	1.00
270_T	273_F	0.916	1.00
98_E	214_T	0.902	1.00
45_I	82_T	0.894	1.00
48_F	55_M	0.891	1.00
95_G	143_A	0.890	1.00
140_V	143_A	0.883	1.00
16_G	56_K	0.883	1.00
240_E	243_T	0.882	1.00
95_G	145_V	0.881	1.00
75_L	79_E	0.876	1.00
147_G	258_E	0.875	1.00
169_S	172_G	0.871	1.00
195_V	199_L	0.866	1.00
19_T	23_Q	0.859	1.00
66_Q	69_D	0.858	1.00
63_N	84_M	0.851	1.00
51_T	54_G	0.849	1.00
132_I	136_L	0.848	1.00
25_L	32_V	0.847	1.00
110_A	226_M	0.847	1.00
193_D	197_R	0.842	1.00
90_G	272_A	0.842	1.00
155_R	158_H	0.841	1.00
198_L	202_A	0.839	1.00
120_D	207_Q	0.839	1.00
172_G	181_P	0.836	1.00
124_N	140_V	0.835	1.00
182_M	206_N	0.835	1.00
13_A	61_G	0.833	1.00
60_A	63_N	0.832	1.00
60_A	82_T	0.830	1.00
181_P	208_K	0.829	1.00
13_A	16_G	0.825	1.00
94_I	142_G	0.824	1.00
119_V	272_A	0.823	1.00
154_V	262_I	0.820	1.00
75_L	78_A	0.817	1.00
29_Q	33_T	0.815	1.00
9_F	64_L	0.815	1.00
175_E	178_L	0.813	1.00
77_Q	81_S	0.810	1.00
169_S	226_M	0.809	1.00
269_I	274_Q	0.806	1.00
14_R	65_L	0.805	1.00
168_S	246_W	0.804	1.00
3_S	72_L	0.803	1.00
113_L	226_M	0.803	1.00
271_S	275_T	0.803	1.00
173_T	251_P	0.802	1.00
16_G	62_E	0.802	1.00
167_I	229_A	0.801	1.00
15_E	21_A	0.797	1.00
74_L	78_A	0.796	1.00
16_G	54_G	0.794	1.00
37_H	46_R	0.785	1.00
7_K	11_A	0.782	1.00
4_G	35_R	0.781	1.00
12_V	48_F	0.772	1.00
5_D	8_I	0.767	1.00
221_G	226_M	0.765	1.00
90_G	119_V	0.764	1.00
78_A	82_T	0.764	1.00
153_A	265_K	0.759	1.00
163_E	249_Q	0.758	1.00
12_V	36_V	0.758	1.00
68_A	71_V	0.752	1.00
69_D	73_S	0.747	1.00
62_E	65_L	0.746	1.00
96_S	101_A	0.746	1.00
49_H	58_T	0.745	1.00
223_S	242_R	0.744	1.00
195_V	198_L	0.744	1.00
167_I	231_L	0.740	1.00
12_V	32_V	0.738	1.00
136_L	154_V	0.732	1.00
142_G	276_F	0.731	1.00
18_I	32_V	0.730	1.00
138_H	264_R	0.729	1.00
267_F	270_T	0.729	1.00
214_T	217_A	0.729	1.00
194_R	198_L	0.724	1.00
112_F	275_T	0.722	1.00
178_L	204_I	0.719	1.00
232_P	235_A	0.719	1.00
198_L	201_E	0.718	1.00
88_P	116_F	0.716	1.00
240_E	247_I	0.714	1.00
60_A	64_L	0.710	1.00
176_D	179_Q	0.708	1.00
196_K	200_E	0.707	1.00
197_R	201_E	0.703	1.00
7_K	10_Q	0.701	1.00
167_I	240_E	0.699	1.00
171_E	225_G	0.697	1.00
275_T	279_E	0.696	1.00
59_A	63_N	0.694	1.00
57_L	62_E	0.693	1.00
31_N	35_R	0.691	1.00
93_R	140_V	0.686	1.00
115_R	275_T	0.683	1.00
93_R	141_D	0.682	1.00
186_G	211_E	0.679	1.00
64_L	82_T	0.679	1.00
56_K	62_E	0.676	1.00
141_D	273_F	0.674	1.00
175_E	202_A	0.673	1.00
236_V	240_E	0.671	1.00
60_A	84_M	0.669	1.00
49_H	54_G	0.668	1.00
173_T	252_P	0.665	1.00
67_Y	71_V	0.662	1.00
102_V	220_K	0.658	1.00
40_E	50_R	0.656	1.00
197_R	200_E	0.655	1.00
172_G	228_T	0.654	1.00
171_E	246_W	0.653	1.00
23_Q	26_N	0.652	1.00
40_E	45_I	0.648	1.00
193_D	198_L	0.647	1.00
125_T	213_G	0.646	1.00
166_L	230_L	0.645	1.00
73_S	76_D	0.641	1.00
77_Q	80_K	0.639	1.00
238_G	241_H	0.637	1.00
107_E	110_A	0.635	1.00
36_V	40_E	0.634	1.00
179_Q	207_Q	0.634	1.00
7_K	72_L	0.633	1.00
120_D	211_E	0.632	1.00
196_K	199_L	0.631	1.00
4_G	38_N	0.631	1.00
194_R	197_R	0.630	1.00
210_I	221_G	0.630	1.00
192_R	211_E	0.629	1.00
96_S	105_L	0.626	1.00
271_S	274_Q	0.625	1.00
163_E	253_S	0.624	1.00
9_F	61_G	0.622	1.00
68_A	72_L	0.619	1.00
185_F	218_I	0.617	1.00
166_L	177_M	0.617	1.00
146_Y	257_L	0.616	1.00
182_M	228_T	0.616	1.00
105_L	108_H	0.614	1.00
12_V	17_S	0.612	1.00
92_L	272_A	0.599	1.00
142_G	277_L	0.598	1.00
43_L	64_L	0.597	1.00
92_L	142_G	0.597	1.00
170_R	243_T	0.595	1.00
72_L	76_D	0.594	1.00
4_G	8_I	0.593	1.00
21_A	25_L	0.592	1.00
199_L	206_N	0.587	1.00
212_F	217_A	0.586	1.00
191_H	195_V	0.585	1.00
162_D	257_L	0.585	1.00
98_E	127_D	0.582	1.00
135_V	262_I	0.581	1.00
43_L	82_T	0.578	1.00
107_E	111_S	0.577	1.00
276_F	280_I	0.576	1.00
63_N	82_T	0.573	1.00
89_K	120_D	0.573	1.00
186_G	213_G	0.572	1.00
160_S	259_I	0.572	1.00
45_I	49_H	0.572	1.00
48_F	57_L	0.572	1.00
116_F	119_V	0.570	1.00
13_A	62_E	0.569	1.00
90_G	118_E	0.569	1.00
95_G	124_N	0.568	1.00
31_N	34_A	0.568	1.00
135_V	154_V	0.568	1.00
218_I	222_V	0.565	1.00
263_Y	274_Q	0.563	1.00
95_G	126_A	0.561	1.00
166_L	182_M	0.559	1.00
125_T	214_T	0.557	1.00
28_V	34_A	0.557	1.00
164_L	230_L	0.556	1.00
159_V	261_F	0.554	1.00
30_S	34_A	0.553	1.00
84_M	87_Q	0.552	1.00
18_I	54_G	0.551	1.00
18_I	29_Q	0.549	1.00
144_F	280_I	0.549	1.00
221_G	227_G	0.548	1.00
104_H	108_H	0.547	1.00
57_L	65_L	0.544	1.00
100_M	104_H	0.544	1.00
43_L	46_R	0.542	1.00
155_R	266_D	0.539	1.00
8_I	36_V	0.537	1.00
66_Q	81_S	0.536	1.00
147_G	156_Q	0.535	1.00
27_Y	35_R	0.534	1.00
102_V	214_T	0.533	1.00
16_G	55_M	0.533	1.00
177_M	180_Q	0.532	1.00
46_R	60_A	0.532	1.00
250_L	253_S	0.524	1.00
175_E	204_I	0.522	1.00
107_E	220_K	0.522	1.00
272_A	275_T	0.520	1.00
215_L	232_P	0.519	1.00
45_I	85_S	0.517	1.00
106_P	110_A	0.516	1.00
231_L	236_V	0.516	1.00
78_A	81_S	0.516	1.00
96_S	123_V	0.515	1.00
80_K	83_R	0.514	1.00
273_F	277_L	0.513	1.00
109_A	121_L	0.512	1.00
136_L	139_K	0.512	1.00
8_I	21_A	0.510	1.00
190_S	193_D	0.508	1.00
43_L	79_E	0.508	1.00
187_A	211_E	0.508	1.00
191_H	194_R	0.507	1.00
244_N	247_I	0.507	1.00
110_A	113_L	0.507	1.00
192_R	198_L	0.506	1.00
163_E	254_Y	0.505	1.00
18_I	50_R	0.504	1.00
178_L	205_H	0.503	1.00
72_L	75_L	0.501	1.00
120_D	209_I	0.501	1.00
67_Y	82_T	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	1	100	0.092	Contact Map
1uthA	2	0.7509	100	0.092	Contact Map
2esnA	3	0.9965	100	0.093	Contact Map
1ixcA	4	0.9895	100	0.104	Contact Map
2h98A	2	0.6807	100	0.106	Contact Map
3fzvA	4	0.9719	100	0.108	Contact Map
4x6gA	4	1	100	0.109	Contact Map
2h9bA	2	0.6807	100	0.11	Contact Map
1al3A	1	0.6982	100	0.11	Contact Map
3szpA	3	0.986	100	0.128	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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