YIAU - ECOLI - GREMLIN Contacts

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YIAU - Uncharacterized HTH-type transcriptional regulator YiaU

UniProt:	P37682	Sequences: MTKLQLKYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNNFIADYKHEKRGRVTIYAPTGIITYLSKHVIDKIKDIGDITLSLKTCNLERNAFYEGVEFPDDCDVLISYAPPKDESLVASFITQYAVTAYASQRYLEKHPISRPDELEHHSCILIDSMMIDDANIWRFNVAGSKEVRDYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVPCFQQPYEWWLDLVAIFRKREYQPWRVQYVLDEMLREIRHQLAQSQQLRPEQAAESED	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12289
Length:	324 (286)
Sequences:	79324 (57258)
Seq/√Len:	3385.8

ECOLI - YIAU OXYR NAC TTDR CYSB AAER YBHD YAHB LEUO CYNR YDCI TDCA CBL NHAR YDHB GCVA LYSR DMLR YBDO DSDC YEEY YIDZ ALLS YAFC YFER METR YBEF YFIE PGRR YCAN ABGR YEIE ILVY YHJC YNFL XAPR YNEJ YGFI YHAJ HCAR ICIA PERR YJIE LRHA HDFR
BACSU - CYSL YCGK YWBI BSDA GLTR YTLI GLTC YYBE CITR ALSR YUST YOFA YWQM YVBU CZCR YXJO YRAN YKUM 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
75_D	79_R	3.556	1.00
20_S	29_V	3.383	1.00
165_S	301_L	2.667	1.00
101_Y	148_C	2.609	1.00
72_Y	86_F	2.423	1.00
16_V	29_V	2.276	1.00
242_A	249_V	2.268	1.00
180_Y	195_H	2.259	1.00
169_Q	278_D	2.193	1.00
166_F	169_Q	2.177	1.00
116_D	303_E	2.175	1.00
97_R	127_S	2.156	1.00
171_A	253_D	2.152	1.00
166_F	278_D	2.119	1.00
25_H	28_T	2.077	1.00
97_R	125_T	2.072	1.00
19_A	74_N	2.041	1.00
13_I	40_Y	2.033	1.00
50_L	65_F	2.033	1.00
188_R	191_E	2.005	1.00
169_Q	276_W	1.992	1.00
72_Y	79_R	1.969	1.00
15_S	74_N	1.959	1.00
239_L	259_D	1.957	1.00
243_R	264_T	1.953	1.00
15_S	70_L	1.949	1.00
99_T	127_S	1.944	1.00
116_D	299_E	1.944	1.00
16_V	19_A	1.917	1.00
15_S	19_A	1.911	1.00
16_V	20_S	1.907	1.00
198_I	247_G	1.893	1.00
13_I	37_V	1.889	1.00
176_A	268_C	1.887	1.00
18_A	62_L	1.886	1.00
173_T	253_D	1.878	1.00
76_M	80_N	1.861	1.00
70_L	74_N	1.811	1.00
243_R	259_D	1.811	1.00
23_I	41_L	1.791	1.00
54_D	61_M	1.725	1.00
196_S	229_N	1.716	1.00
69_L	83_L	1.715	1.00
173_T	267_P	1.701	1.00
164_A	280_V	1.689	1.00
68_A	86_F	1.674	1.00
18_A	70_L	1.619	1.00
117_K	296_V	1.595	1.00
19_A	29_V	1.592	1.00
20_S	25_H	1.580	1.00
15_S	73_I	1.571	1.00
163_V	285_K	1.551	1.00
208_A	212_R	1.545	1.00
14_I	70_L	1.540	1.00
13_I	32_I	1.530	1.00
10_E	40_Y	1.518	1.00
117_K	124_I	1.494	1.00
24_S	34_Q	1.486	1.00
10_E	47_K	1.481	1.00
165_S	283_F	1.481	1.00
93_E	123_D	1.476	1.00
33_A	36_N	1.457	1.00
72_Y	75_D	1.457	1.00
22_N	25_H	1.456	1.00
64_P	67_T	1.456	1.00
51_K	54_D	1.447	1.00
10_E	43_D	1.446	1.00
184_H	191_E	1.427	1.00
153_S	282_I	1.417	1.00
297_L	301_L	1.416	1.00
16_V	30_L	1.414	1.00
7_K	10_E	1.406	1.00
15_S	77_L	1.395	1.00
163_V	283_F	1.392	1.00
289_Q	293_V	1.385	1.00
76_M	83_L	1.384	1.00
72_Y	82_Q	1.383	1.00
107_I	236_Q	1.376	1.00
155_A	280_V	1.374	1.00
139_Y	145_P	1.368	1.00
283_F	297_L	1.360	1.00
144_F	161_S	1.343	1.00
99_T	129_K	1.335	1.00
95_R	123_D	1.334	1.00
281_A	297_L	1.319	1.00
56_T	61_M	1.316	1.00
295_Y	298_D	1.313	1.00
116_D	120_D	1.311	1.00
178_Q	264_T	1.311	1.00
131_C	135_R	1.311	1.00
8_Y	80_N	1.309	1.00
170_Y	254_K	1.291	1.00
238_A	249_V	1.286	1.00
79_R	82_Q	1.285	1.00
176_A	248_I	1.284	1.00
150_V	293_V	1.277	1.00
150_V	281_A	1.274	1.00
195_H	248_I	1.271	1.00
120_D	299_E	1.264	1.00
69_L	84_N	1.264	1.00
118_I	229_N	1.261	1.00
259_D	264_T	1.257	1.00
47_K	84_N	1.252	1.00
71_P	75_D	1.241	1.00
240_E	243_R	1.224	1.00
253_D	267_P	1.223	1.00
72_Y	83_L	1.220	1.00
178_Q	266_V	1.216	1.00
253_D	257_Q	1.210	1.00
166_F	280_V	1.208	1.00
68_A	71_P	1.202	1.00
209_N	213_F	1.202	1.00
118_I	196_S	1.197	1.00
14_I	53_F	1.193	1.00
257_Q	261_Q	1.192	1.00
67_T	71_P	1.186	1.00
115_I	119_K	1.175	1.00
42_A	46_S	1.172	1.00
176_A	180_Y	1.169	1.00
32_I	36_N	1.167	1.00
164_A	282_I	1.153	1.00
39_K	43_D	1.150	1.00
14_I	18_A	1.146	1.00
127_S	231_V	1.141	1.00
14_I	52_V	1.138	1.00
39_K	42_A	1.133	1.00
198_I	238_A	1.132	1.00
116_D	119_K	1.128	1.00
115_I	244_N	1.119	1.00
98_V	296_V	1.107	1.00
17_I	26_A	1.101	1.00
196_S	227_K	1.097	1.00
38_S	42_A	1.097	1.00
121_I	295_Y	1.096	1.00
75_D	82_Q	1.092	1.00
23_I	60_L	1.091	1.00
117_K	299_E	1.088	1.00
175_Y	267_P	1.084	1.00
9_R	12_K	1.082	1.00
16_V	26_A	1.082	1.00
68_A	72_Y	1.079	1.00
284_R	287_E	1.075	1.00
232_C	238_A	1.070	1.00
112_K	244_N	1.069	1.00
267_P	270_Q	1.066	1.00
40_Y	43_D	1.065	1.00
298_D	301_L	1.064	1.00
11_L	73_I	1.064	1.00
76_M	79_R	1.057	1.00
239_L	243_R	1.056	1.00
299_E	303_E	1.053	1.00
12_K	81_E	1.050	1.00
294_Q	298_D	1.045	1.00
113_H	300_M	1.036	1.00
177_S	245_H	1.035	1.00
165_S	297_L	1.033	1.00
144_F	159_D	1.032	1.00
62_L	66_G	1.028	1.00
240_E	244_N	1.024	1.00
84_N	88_A	1.020	1.00
189_P	272_P	1.014	1.00
171_A	276_W	0.987	1.00
209_N	212_R	0.985	1.00
175_Y	256_V	0.984	1.00
18_A	53_F	0.982	1.00
32_I	37_V	0.977	1.00
258_S	262_D	0.976	1.00
78_D	82_Q	0.972	1.00
17_I	23_I	0.969	1.00
13_I	30_L	0.968	1.00
117_K	121_I	0.967	1.00
174_A	248_I	0.967	1.00
120_D	302_R	0.964	1.00
81_E	84_N	0.962	1.00
81_E	85_N	0.959	1.00
215_V	224_Y	0.957	1.00
211_W	215_V	0.956	1.00
299_E	302_R	0.955	1.00
69_L	73_I	0.945	1.00
199_L	228_G	0.945	1.00
14_I	62_L	0.942	1.00
43_D	46_S	0.933	1.00
290_P	293_V	0.931	1.00
232_C	241_L	0.931	1.00
14_I	44_F	0.929	1.00
26_A	37_V	0.927	1.00
53_F	60_L	0.922	1.00
101_Y	151_L	0.917	1.00
113_H	299_E	0.907	1.00
50_L	87_I	0.907	1.00
180_Y	196_S	0.906	1.00
176_A	181_L	0.902	1.00
68_A	90_Y	0.901	1.00
18_A	66_G	0.900	1.00
104_T	234_N	0.897	1.00
186_I	266_V	0.896	1.00
25_H	29_V	0.887	1.00
148_C	151_L	0.880	1.00
155_A	278_D	0.876	1.00
101_Y	153_S	0.876	1.00
75_D	78_D	0.875	1.00
71_P	74_N	0.868	1.00
213_F	217_G	0.868	1.00
125_T	227_K	0.867	1.00
21_E	61_M	0.863	1.00
24_S	28_T	0.856	1.00
100_I	150_V	0.854	1.00
191_E	194_H	0.848	1.00
9_R	40_Y	0.843	1.00
175_Y	249_V	0.842	1.00
129_K	148_C	0.842	1.00
56_T	59_Q	0.841	1.00
161_S	285_K	0.840	1.00
30_L	37_V	0.840	1.00
124_I	292_R	0.835	1.00
162_L	282_I	0.835	1.00
196_S	228_G	0.834	1.00
65_F	90_Y	0.832	1.00
298_D	302_R	0.826	1.00
96_G	292_R	0.825	1.00
163_V	166_F	0.823	1.00
65_F	87_I	0.820	1.00
256_V	259_D	0.819	1.00
259_D	262_D	0.813	1.00
115_I	246_L	0.812	1.00
21_E	67_T	0.812	1.00
14_I	69_L	0.811	1.00
17_I	41_L	0.810	1.00
289_Q	294_Q	0.810	1.00
8_Y	77_L	0.808	1.00
34_Q	38_S	0.807	1.00
177_S	246_L	0.807	1.00
18_A	21_E	0.805	1.00
42_A	51_K	0.804	1.00
17_I	53_F	0.798	1.00
80_N	83_L	0.795	1.00
197_C	226_V	0.795	1.00
80_N	84_N	0.794	1.00
143_E	151_L	0.792	1.00
190_D	193_E	0.789	1.00
20_S	26_A	0.787	1.00
79_R	83_L	0.787	1.00
19_A	70_L	0.784	1.00
186_I	271_Q	0.783	1.00
188_R	272_P	0.781	1.00
171_A	269_F	0.780	1.00
180_Y	184_H	0.777	1.00
291_W	295_Y	0.777	1.00
21_E	59_Q	0.776	1.00
94_K	121_I	0.774	1.00
82_Q	86_F	0.774	1.00
118_I	246_L	0.772	1.00
113_H	303_E	0.771	1.00
177_S	180_Y	0.770	1.00
10_E	13_I	0.770	1.00
96_G	124_I	0.770	1.00
190_D	222_R	0.763	1.00
193_E	224_Y	0.762	1.00
65_F	68_A	0.762	1.00
150_V	296_V	0.759	1.00
23_I	37_V	0.749	1.00
241_L	246_L	0.748	1.00
175_Y	251_A	0.746	1.00
176_A	266_V	0.746	1.00
120_D	295_Y	0.745	1.00
135_R	139_Y	0.744	1.00
144_F	162_L	0.742	1.00
116_D	302_R	0.741	1.00
83_L	87_I	0.740	1.00
17_I	37_V	0.738	1.00
256_V	260_L	0.738	1.00
12_K	16_V	0.737	1.00
181_L	184_H	0.736	1.00
73_I	76_M	0.734	1.00
179_R	182_E	0.731	1.00
171_A	274_E	0.728	1.00
54_D	63_T	0.727	1.00
88_A	91_K	0.726	1.00
182_E	266_V	0.723	1.00
175_Y	260_L	0.722	1.00
208_A	231_V	0.721	1.00
213_F	216_A	0.719	1.00
54_D	59_Q	0.717	1.00
117_K	295_Y	0.715	1.00
74_N	78_D	0.715	1.00
234_N	237_S	0.715	1.00
61_M	67_T	0.711	1.00
62_L	67_T	0.711	1.00
260_L	263_G	0.709	1.00
252_P	255_S	0.708	1.00
184_H	196_S	0.705	1.00
36_N	40_Y	0.703	1.00
149_D	293_V	0.703	1.00
99_T	148_C	0.702	1.00
260_L	267_P	0.698	1.00
287_E	290_P	0.697	1.00
201_D	231_V	0.693	1.00
211_W	214_N	0.692	1.00
67_T	70_L	0.691	1.00
99_T	149_D	0.690	1.00
210_I	214_N	0.689	1.00
210_I	213_F	0.681	1.00
64_P	68_A	0.680	1.00
65_F	69_L	0.680	1.00
146_D	284_R	0.679	1.00
78_D	81_E	0.678	1.00
295_Y	299_E	0.672	1.00
194_H	227_K	0.671	1.00
23_I	59_Q	0.670	1.00
69_L	87_I	0.670	1.00
179_R	245_H	0.669	1.00
45_E	50_L	0.668	1.00
258_S	261_Q	0.659	1.00
107_I	240_E	0.659	1.00
82_Q	85_N	0.659	1.00
230_Y	241_L	0.658	1.00
200_I	238_A	0.658	1.00
125_T	231_V	0.657	1.00
12_K	15_S	0.654	1.00
152_I	300_M	0.653	1.00
9_R	43_D	0.652	1.00
98_V	292_R	0.652	1.00
45_E	55_R	0.649	1.00
197_C	248_I	0.649	1.00
73_I	77_L	0.648	1.00
28_T	31_G	0.645	1.00
17_I	22_N	0.641	1.00
102_A	110_L	0.640	1.00
72_Y	76_M	0.636	1.00
174_A	250_F	0.636	1.00
179_R	266_V	0.636	1.00
130_T	233_D	0.635	1.00
104_T	132_N	0.632	1.00
201_D	233_D	0.632	1.00
212_R	216_A	0.631	1.00
26_A	30_L	0.630	1.00
41_L	45_E	0.629	1.00
174_A	192_L	0.626	1.00
168_T	279_L	0.625	1.00
178_Q	263_G	0.611	1.00
291_W	294_Q	0.610	1.00
68_A	87_I	0.609	1.00
139_Y	144_F	0.609	1.00
150_V	297_L	0.608	1.00
85_N	89_D	0.608	1.00
154_Y	277_L	0.607	1.00
110_L	113_H	0.606	1.00
112_K	116_D	0.605	1.00
181_L	186_I	0.599	1.00
170_Y	277_L	0.598	1.00
36_N	39_K	0.598	1.00
181_L	195_H	0.598	1.00
174_A	197_C	0.597	1.00
95_R	125_T	0.595	1.00
296_V	300_M	0.594	1.00
130_T	234_N	0.592	1.00
98_V	150_V	0.592	1.00
241_L	247_G	0.589	1.00
238_A	242_A	0.589	1.00
48_V	69_L	0.587	1.00
12_K	77_L	0.587	1.00
112_K	115_I	0.584	1.00
53_F	62_L	0.584	1.00
114_V	126_L	0.581	1.00
101_Y	131_C	0.581	1.00
214_N	217_G	0.581	1.00
48_V	87_I	0.580	1.00
33_A	39_K	0.579	1.00
232_C	237_S	0.579	1.00
9_R	13_I	0.579	1.00
62_L	70_L	0.578	1.00
50_L	54_D	0.578	1.00
35_A	39_K	0.573	1.00
186_I	269_F	0.571	1.00
180_Y	248_I	0.570	1.00
283_F	294_Q	0.570	1.00
172_V	250_F	0.569	1.00
217_G	222_R	0.566	1.00
208_A	211_W	0.566	1.00
163_V	286_R	0.562	1.00
212_R	215_V	0.561	1.00
48_V	51_K	0.558	1.00
101_Y	129_K	0.557	1.00
77_L	81_E	0.556	1.00
14_I	66_G	0.555	1.00
251_A	256_V	0.553	1.00
121_I	124_I	0.553	1.00
235_T	252_P	0.551	1.00
207_D	211_W	0.550	1.00
106_I	109_Y	0.550	1.00
243_R	262_D	0.549	1.00
193_E	225_R	0.549	1.00
202_S	231_V	0.546	1.00
188_R	271_Q	0.542	1.00
96_G	123_D	0.542	1.00
71_P	86_F	0.540	1.00
167_I	281_A	0.540	1.00
23_I	34_Q	0.539	1.00
13_I	41_L	0.538	1.00
107_I	234_N	0.537	1.00
77_L	80_N	0.537	1.00
96_G	121_I	0.534	1.00
155_A	164_A	0.533	1.00
13_I	26_A	0.533	1.00
18_A	67_T	0.531	1.00
293_V	297_L	0.531	1.00
108_T	111_S	0.530	1.00
214_N	222_R	0.529	1.00
103_P	106_I	0.527	1.00
270_Q	273_Y	0.527	1.00
51_K	65_F	0.524	1.00
85_N	88_A	0.523	1.00
190_D	224_Y	0.523	1.00
32_I	40_Y	0.522	1.00
112_K	240_E	0.518	1.00
102_A	128_L	0.518	1.00
89_D	94_K	0.518	1.00
21_E	60_L	0.517	1.00
152_I	281_A	0.516	1.00
23_I	55_R	0.515	1.00
41_L	53_F	0.514	1.00
76_M	84_N	0.510	1.00
184_H	187_S	0.509	1.00
72_Y	87_I	0.508	1.00
144_F	147_D	0.506	1.00
111_S	115_I	0.503	1.00
73_I	80_N	0.501	1.00
207_D	210_I	0.501	1.00
90_Y	94_K	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
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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	0.9136	100	0.118	Contact Map
1uthA	2	0.6975	100	0.121	Contact Map
3fzvA	4	0.8858	100	0.139	Contact Map
3fxqA	3	0.9012	100	0.14	Contact Map
1ixcA	4	0.8981	100	0.141	Contact Map
4x6gA	4	0.9475	100	0.143	Contact Map
1al3A	1	0.6914	100	0.143	Contact Map
3szpA	3	0.8889	100	0.151	Contact Map
2h98A	2	0.6512	100	0.161	Contact Map
2h9bA	2	0.6543	100	0.168	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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