YIDZ - ECOLI - GREMLIN Contacts

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YIDZ - HTH-type transcriptional regulator YidZ

UniProt:	P31463	Sequences: MKKSITTLDLNLLLCLQLLMQERSVTKAAKRINVTPSAVSKSLAKLRAWFDDPLFVNSPLGLSPTPLMVSMEQNLAEWMQMSNLLLDKPHHQTPRGLKFELAAESPLMMIMLNALSKQIYQRYPQATIKLRNWDYDSLDAITRGEVDIGFSGRESHPRSRELLSSLPLAIDYEVLFSDVPCVWLRKDHPALHQTWNLDTFLRYPHISICWEQSDTWALDNVLQELGRERTIAMSLPEFEQSLFMAAQPDNLLLATAPRYCQYYNQLHQLPLVALPLPFDESQQKKLEVPFTLLWHKRNSHNPKIVWLRETIKNLYASMA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11721
Length:	319 (286)
Sequences:	78974 (56806)
Seq/√Len:	3359.0

ECOLI - YIDZ LEUO DSDC PGRR YDCI OXYR YBDO LYSR YBEF YBHD YEIE YAFC YCAN AAER NHAR DMLR TDCA NAC CYNR HCAR CYSB YFER YIAU TTDR YFIE ABGR YNFL YGFI METR YHJC CBL ILVY XAPR YEEY YNEJ GCVA ICIA YDHB YAHB ALLS YHAJ YJIE PERR LRHA HDFR
BACSU - CYSL YWBI YWQM YCGK GLTR YYBE GLTC YUST BSDA CITR ALSR YVBU YTLI YOFA CZCR YKUM YRAN 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
77_E	81_M	3.596	1.00
22_E	31_R	3.395	1.00
173_E	312_K	2.678	1.00
102_A	146_V	2.577	1.00
74_N	88_K	2.431	1.00
18_L	31_R	2.291	1.00
188_H	203_Y	2.237	1.00
245_A	254_A	2.211	1.00
98_K	129_K	2.197	1.00
177_S	289_P	2.195	1.00
174_V	177_S	2.184	1.00
179_V	258_R	2.166	1.00
174_V	289_P	2.125	1.00
98_K	127_T	2.092	1.00
27_K	30_K	2.086	1.00
52_D	67_L	2.049	1.00
196_N	199_T	2.046	1.00
15_C	42_S	2.044	1.00
21_Q	76_A	2.040	1.00
246_A	270_P	2.025	1.00
118_Q	310_T	1.991	1.00
74_N	81_M	1.990	1.00
242_L	265_Q	1.986	1.00
177_S	287_E	1.985	1.00
17_Q	72_E	1.978	1.00
17_Q	76_A	1.973	1.00
100_E	129_K	1.955	1.00
206_I	252_L	1.924	1.00
18_L	21_Q	1.922	1.00
17_Q	21_Q	1.920	1.00
18_L	22_E	1.897	1.00
181_C	258_R	1.892	1.00
20_M	64_P	1.881	1.00
15_C	39_V	1.879	1.00
78_W	82_S	1.854	1.00
72_E	76_A	1.816	1.00
184_L	274_L	1.812	1.00
25_V	43_L	1.801	1.00
246_A	265_Q	1.772	1.00
56_V	63_S	1.740	1.00
204_P	232_A	1.715	1.00
71_M	85_L	1.708	1.00
181_C	273_A	1.707	1.00
172_Y	291_T	1.687	1.00
70_S	88_K	1.670	1.00
140_A	145_E	1.649	1.00
20_M	72_E	1.616	1.00
139_D	143_R	1.613	1.00
119_I	307_L	1.605	1.00
22_E	27_K	1.596	1.00
21_Q	31_R	1.587	1.00
17_Q	75_L	1.564	1.00
171_D	296_K	1.560	1.00
16_L	72_E	1.541	1.00
15_C	34_V	1.513	1.00
12_L	42_S	1.492	1.00
119_I	126_A	1.490	1.00
215_T	219_D	1.487	1.00
12_L	49_W	1.483	1.00
173_E	294_W	1.480	1.00
26_T	36_P	1.463	1.00
66_P	69_V	1.460	1.00
74_N	77_E	1.450	1.00
24_S	27_K	1.446	1.00
35_T	38_A	1.437	1.00
53_P	56_V	1.432	1.00
18_L	32_I	1.425	1.00
9_D	12_L	1.419	1.00
12_L	45_K	1.413	1.00
17_Q	79_M	1.408	1.00
151_S	293_L	1.399	1.00
308_R	312_K	1.391	1.00
153_R	291_T	1.384	1.00
171_D	294_W	1.381	1.00
74_N	84_L	1.377	1.00
78_W	85_L	1.365	1.00
300_H	304_I	1.363	1.00
109_M	239_E	1.359	1.00
294_W	308_R	1.353	1.00
186_K	270_P	1.346	1.00
100_E	131_R	1.323	1.00
140_A	146_V	1.313	1.00
58_S	63_S	1.312	1.00
96_G	125_Q	1.311	1.00
306_W	309_E	1.300	1.00
292_L	308_R	1.298	1.00
10_L	82_S	1.298	1.00
148_I	304_I	1.295	1.00
118_Q	122_R	1.294	1.00
133_W	137_S	1.290	1.00
141_I	149_G	1.288	1.00
142_T	169_A	1.288	1.00
184_L	253_L	1.277	1.00
71_M	86_L	1.272	1.00
178_D	259_Y	1.268	1.00
120_Y	232_A	1.267	1.00
81_M	84_L	1.263	1.00
148_I	292_L	1.261	1.00
122_R	310_T	1.259	1.00
203_Y	253_L	1.246	1.00
248_P	252_L	1.245	1.00
265_Q	270_P	1.244	1.00
73_Q	77_E	1.232	1.00
74_N	85_L	1.217	1.00
258_R	273_A	1.217	1.00
186_K	272_V	1.207	1.00
243_F	246_A	1.206	1.00
241_S	254_A	1.204	1.00
174_V	291_T	1.199	1.00
120_Y	204_P	1.197	1.00
70_S	73_Q	1.187	1.00
69_V	73_Q	1.186	1.00
258_R	262_Y	1.183	1.00
44_A	48_A	1.183	1.00
117_K	121_Q	1.174	1.00
193_Q	272_V	1.170	1.00
16_L	55_F	1.169	1.00
34_V	38_A	1.161	1.00
189_P	203_Y	1.156	1.00
117_K	247_Q	1.156	1.00
172_Y	293_L	1.143	1.00
222_L	227_R	1.136	1.00
49_W	86_L	1.131	1.00
16_L	20_M	1.129	1.00
41_K	45_K	1.129	1.00
118_Q	121_Q	1.117	1.00
41_K	44_A	1.117	1.00
129_K	234_S	1.116	1.00
206_I	241_S	1.114	1.00
16_L	54_L	1.114	1.00
204_P	230_T	1.108	1.00
99_F	307_L	1.107	1.00
25_V	62_L	1.090	1.00
123_Y	306_W	1.089	1.00
133_W	140_A	1.087	1.00
40_S	44_A	1.082	1.00
194_T	277_P	1.082	1.00
183_W	273_A	1.081	1.00
185_R	248_P	1.079	1.00
119_I	310_T	1.079	1.00
11_N	14_L	1.078	1.00
77_E	84_L	1.078	1.00
262_Y	267_H	1.076	1.00
295_H	298_N	1.076	1.00
309_E	312_K	1.072	1.00
273_A	276_L	1.065	1.00
13_L	75_L	1.064	1.00
70_S	74_N	1.062	1.00
19_L	28_A	1.061	1.00
195_W	199_T	1.059	1.00
18_L	28_A	1.058	1.00
235_L	241_S	1.055	1.00
14_L	83_N	1.054	1.00
142_T	167_P	1.053	1.00
305_V	309_E	1.052	1.00
108_M	132_N	1.049	1.00
42_S	45_K	1.048	1.00
114_A	247_Q	1.047	1.00
78_W	81_M	1.041	1.00
243_F	247_Q	1.037	1.00
173_E	308_R	1.033	1.00
115_L	311_I	1.020	1.00
86_L	90_H	1.008	1.00
64_P	68_M	1.006	1.00
242_L	246_A	0.997	1.00
216_W	219_D	0.991	1.00
179_V	287_E	0.986	1.00
20_M	55_F	0.984	1.00
119_I	123_Y	0.983	1.00
34_V	39_V	0.981	1.00
182_V	253_L	0.974	1.00
183_W	261_Q	0.973	1.00
8_L	49_W	0.971	1.00
83_N	86_L	0.970	1.00
197_L	278_F	0.970	1.00
80_Q	84_L	0.966	1.00
184_L	188_H	0.964	1.00
188_H	191_L	0.957	1.00
15_C	32_I	0.957	1.00
131_R	140_A	0.956	1.00
83_N	87_D	0.952	1.00
235_L	244_M	0.952	1.00
19_L	25_V	0.950	1.00
71_M	75_L	0.943	1.00
140_A	143_R	0.940	1.00
122_R	313_N	0.940	1.00
16_L	64_P	0.939	1.00
207_S	231_I	0.933	1.00
310_T	313_N	0.929	1.00
28_A	39_V	0.926	1.00
45_K	48_A	0.926	1.00
115_L	310_T	0.915	1.00
70_S	92_Q	0.912	1.00
55_F	62_L	0.911	1.00
52_D	89_P	0.910	1.00
205_H	229_R	0.907	1.00
16_L	46_L	0.905	1.00
301_N	304_I	0.901	1.00
102_A	149_G	0.899	1.00
27_K	31_R	0.890	1.00
146_V	149_G	0.887	1.00
20_M	68_M	0.885	1.00
216_W	220_N	0.884	1.00
188_H	204_P	0.883	1.00
127_T	230_T	0.880	1.00
105_S	237_E	0.880	1.00
155_S	167_P	0.877	1.00
169_A	296_K	0.872	1.00
77_E	80_Q	0.872	1.00
23_R	63_S	0.869	1.00
126_A	303_K	0.866	1.00
73_Q	76_A	0.862	1.00
204_P	231_I	0.858	1.00
153_R	289_P	0.852	1.00
261_Q	265_Q	0.850	1.00
26_T	30_K	0.848	1.00
58_S	61_G	0.844	1.00
101_L	148_I	0.844	1.00
170_I	293_L	0.841	1.00
67_L	92_Q	0.838	1.00
190_A	203_Y	0.838	1.00
11_N	42_S	0.836	1.00
266_L	269_L	0.833	1.00
184_L	189_P	0.832	1.00
102_A	151_S	0.830	1.00
189_P	193_Q	0.826	1.00
171_D	174_V	0.823	1.00
32_I	39_V	0.823	1.00
309_E	313_N	0.819	1.00
192_H	204_P	0.818	1.00
188_H	192_H	0.817	1.00
20_M	23_R	0.813	1.00
221_V	225_L	0.811	1.00
67_L	89_P	0.811	1.00
131_R	146_V	0.810	1.00
97_L	126_A	0.810	1.00
183_W	254_A	0.809	1.00
97_L	303_K	0.808	1.00
300_H	305_V	0.805	1.00
23_R	69_V	0.804	1.00
44_A	53_P	0.800	1.00
196_N	277_P	0.799	1.00
10_L	79_M	0.797	1.00
16_L	71_M	0.796	1.00
198_D	201_L	0.795	1.00
199_T	202_R	0.791	1.00
19_L	43_L	0.788	1.00
82_S	85_L	0.787	1.00
82_S	86_L	0.783	1.00
179_V	275_P	0.780	1.00
84_L	88_K	0.780	1.00
19_L	55_F	0.777	1.00
21_Q	72_E	0.776	1.00
36_P	40_S	0.775	1.00
81_M	85_L	0.771	1.00
187_D	191_L	0.766	1.00
22_E	28_A	0.766	1.00
67_L	70_S	0.764	1.00
23_R	61_G	0.759	1.00
95_R	123_Y	0.759	1.00
265_Q	268_Q	0.759	1.00
148_I	307_L	0.756	1.00
302_P	306_W	0.753	1.00
183_W	256_A	0.749	1.00
246_A	268_Q	0.745	1.00
14_L	18_L	0.739	1.00
85_L	89_P	0.735	1.00
266_L	273_A	0.734	1.00
184_L	190_A	0.734	1.00
122_R	306_W	0.733	1.00
12_L	15_C	0.732	1.00
185_R	188_H	0.730	1.00
191_L	272_V	0.730	1.00
25_V	39_V	0.725	1.00
75_L	78_W	0.720	1.00
221_V	224_E	0.718	1.00
56_V	65_T	0.716	1.00
142_T	170_I	0.715	1.00
119_I	306_W	0.713	1.00
90_H	93_T	0.713	1.00
218_L	222_L	0.712	1.00
184_L	272_V	0.710	1.00
64_P	69_V	0.709	1.00
19_L	39_V	0.709	1.00
56_V	61_G	0.707	1.00
63_S	69_V	0.703	1.00
298_N	301_N	0.702	1.00
183_W	266_L	0.702	1.00
8_L	86_L	0.702	1.00
237_E	240_Q	0.702	1.00
100_E	146_V	0.699	1.00
261_Q	266_L	0.697	1.00
76_A	80_Q	0.697	1.00
103_A	108_M	0.696	1.00
137_S	140_A	0.694	1.00
215_T	234_S	0.691	1.00
69_V	72_E	0.691	1.00
38_A	42_S	0.690	1.00
147_D	304_I	0.686	1.00
179_V	279_D	0.684	1.00
220_N	223_Q	0.682	1.00
196_N	278_F	0.677	1.00
67_L	71_M	0.676	1.00
306_W	310_T	0.675	1.00
198_D	225_L	0.672	1.00
220_N	224_E	0.671	1.00
201_L	227_R	0.668	1.00
66_P	70_S	0.667	1.00
209_C	234_S	0.666	1.00
100_E	147_D	0.665	1.00
144_G	295_H	0.664	1.00
118_Q	313_N	0.663	1.00
187_D	248_P	0.661	1.00
257_P	260_C	0.661	1.00
84_L	87_D	0.661	1.00
47_R	52_D	0.659	1.00
233_M	244_M	0.658	1.00
80_Q	83_N	0.657	1.00
202_R	230_T	0.656	1.00
150_F	311_I	0.654	1.00
71_M	89_P	0.652	1.00
25_V	61_G	0.645	1.00
99_F	303_K	0.642	1.00
14_L	17_Q	0.641	1.00
74_N	78_W	0.639	1.00
208_I	241_S	0.637	1.00
187_D	190_A	0.637	1.00
75_L	79_M	0.636	1.00
109_M	243_F	0.635	1.00
30_K	33_N	0.633	1.00
187_D	272_V	0.630	1.00
47_R	57_N	0.628	1.00
103_A	112_L	0.627	1.00
127_T	234_S	0.626	1.00
11_N	45_K	0.626	1.00
182_V	200_F	0.626	1.00
217_A	221_V	0.624	1.00
19_L	24_S	0.624	1.00
205_H	253_L	0.619	1.00
28_A	32_I	0.616	1.00
43_L	47_R	0.615	1.00
302_P	305_V	0.612	1.00
141_I	293_L	0.612	1.00
216_W	221_V	0.609	1.00
244_M	252_L	0.609	1.00
219_D	223_Q	0.605	1.00
96_G	127_T	0.604	1.00
132_N	236_P	0.604	1.00
186_K	269_L	0.603	1.00
241_S	245_A	0.601	1.00
209_C	236_P	0.600	1.00
105_S	134_D	0.600	1.00
307_L	311_I	0.600	1.00
182_V	255_T	0.599	1.00
218_L	221_V	0.597	1.00
112_L	115_L	0.594	1.00
87_D	91_H	0.592	1.00
148_I	308_R	0.591	1.00
99_F	148_I	0.587	1.00
194_T	275_P	0.586	1.00
152_G	288_V	0.582	1.00
178_D	288_V	0.581	1.00
176_F	290_F	0.581	1.00
114_A	117_K	0.580	1.00
190_A	195_W	0.580	1.00
50_F	71_M	0.580	1.00
222_L	229_R	0.576	1.00
14_L	79_M	0.575	1.00
182_V	205_H	0.575	1.00
64_P	72_E	0.575	1.00
171_D	297_R	0.574	1.00
70_S	89_P	0.573	1.00
217_A	220_N	0.570	1.00
294_W	305_V	0.569	1.00
11_N	15_C	0.568	1.00
52_D	56_V	0.568	1.00
37_S	41_K	0.567	1.00
38_A	41_K	0.566	1.00
180_P	255_T	0.564	1.00
50_F	89_P	0.563	1.00
215_T	221_V	0.563	1.00
141_I	170_I	0.563	1.00
235_L	240_Q	0.561	1.00
116_S	128_I	0.560	1.00
276_L	279_D	0.560	1.00
55_F	64_P	0.559	1.00
132_N	237_E	0.559	1.00
102_A	131_R	0.558	1.00
102_A	133_W	0.558	1.00
194_T	199_T	0.556	1.00
123_Y	126_A	0.555	1.00
114_A	118_Q	0.554	1.00
97_L	125_Q	0.554	1.00
79_M	83_N	0.550	1.00
188_H	253_L	0.546	1.00
35_T	41_K	0.545	1.00
16_L	68_M	0.544	1.00
50_F	53_P	0.544	1.00
219_D	222_L	0.543	1.00
107_L	111_M	0.542	1.00
184_L	191_L	0.539	1.00
215_T	218_L	0.537	1.00
25_V	36_P	0.535	1.00
175_L	292_L	0.534	1.00
210_W	234_S	0.533	1.00
139_D	145_E	0.532	1.00
121_Q	191_L	0.526	1.00
15_C	43_L	0.525	1.00
266_L	270_P	0.524	1.00
91_H	95_R	0.523	1.00
109_M	237_E	0.523	1.00
189_P	192_H	0.520	1.00
73_Q	88_K	0.519	1.00
20_M	69_V	0.518	1.00
304_I	308_R	0.517	1.00
256_A	261_Q	0.515	1.00
15_C	28_A	0.514	1.00
183_W	271_L	0.513	1.00
97_L	123_Y	0.513	1.00
87_D	90_H	0.513	1.00
111_M	115_L	0.512	1.00
79_M	82_S	0.511	1.00
150_F	292_L	0.509	1.00
23_R	62_L	0.508	1.00
238_F	257_P	0.508	1.00
153_R	172_Y	0.507	1.00
53_P	67_L	0.507	1.00
25_V	57_N	0.506	1.00
43_L	55_F	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	0.931	100	0.094	Contact Map
1uthA	2	0.6991	100	0.118	Contact Map
3fzvA	4	0.8966	100	0.128	Contact Map
2h98A	2	0.6364	100	0.139	Contact Map
3fxqA	3	0.9185	100	0.14	Contact Map
2h9bA	2	0.6364	100	0.14	Contact Map
1ixcA	4	0.906	100	0.142	Contact Map
1al3A	1	0.6552	100	0.144	Contact Map
3szpA	3	0.9028	100	0.146	Contact Map
4x6gA	4	0.9342	100	0.147	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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