ILVY - ECOLI - GREMLIN Contacts

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ILVY - HTH-type transcriptional regulator IlvY

UniProt:	P05827	Sequences: MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRHTIDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMEKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPCPVRNQVSVEKPDWSTVPFIMADQGPVRRRIELWFRRNKISNPMIYATVGGHEAMVSMVALGCGVALLPEVVLENSPEPVRNRVMILERSDEKTPFELGVCAQKKRLHEPLIEAFWKILPNHK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10503
Length:	297 (282)
Sequences:	79567 (58125)
Seq/√Len:	3461.3

ECOLI - ILVY OXYR LEUO CYSB LYSR YBHD PGRR CYNR XAPR AAER YNFL NAC CBL YFER YCAN YDCI YHJC YAHB YEEY YDHB TTDR ALLS TDCA DMLR HCAR YBDO YFIE ABGR YEIE YAFC METR YBEF YNEJ NHAR YGFI DSDC GCVA YHAJ YIDZ YIAU ICIA YJIE LRHA PERR HDFR
BACSU - BSDA CYSL YWBI GLTC CITR YCGK YYBE ALSR YWQM YTLI YVBU GLTR YOFA YUST YKUM YOAU YXJO CZCR YRAN

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_Q	3.717	1.00
15_S	24_A	3.502	1.00
96_F	141_A	2.616	1.00
67_F	81_T	2.505	1.00
233_V	240_A	2.364	1.00
11_H	24_A	2.339	1.00
92_E	123_K	2.254	1.00
20_R	23_R	2.170	1.00
184_E	187_D	2.158	1.00
92_E	121_E	2.156	1.00
14_E	69_Q	2.149	1.00
8_T	35_Q	2.106	1.00
45_Q	60_A	2.088	1.00
94_H	123_K	2.043	1.00
230_V	250_S	2.041	1.00
10_L	65_R	2.038	1.00
67_F	74_Q	2.025	1.00
10_L	69_Q	2.007	1.00
112_R	292_I	1.995	1.00
11_H	14_E	1.967	1.00
10_L	14_E	1.965	1.00
234_A	257_R	1.964	1.00
194_I	238_G	1.953	1.00
165_A	244_E	1.947	1.00
71_T	75_Y	1.945	1.00
11_H	15_S	1.937	1.00
13_A	57_L	1.933	1.00
8_T	32_L	1.928	1.00
163_N	271_E	1.898	1.00
18_F	36_I	1.893	1.00
234_A	250_S	1.893	1.00
65_R	69_Q	1.867	1.00
175_C	191_V	1.844	1.00
159_S	294_P	1.842	1.00
132_A	144_A	1.821	1.00
170_A	261_L	1.797	1.00
163_N	269_P	1.780	1.00
64_L	78_L	1.777	1.00
49_V	56_T	1.777	1.00
192_P	220_Y	1.756	1.00
160_M	271_E	1.728	1.00
63_E	81_T	1.723	1.00
135_K	140_E	1.687	1.00
160_M	163_N	1.678	1.00
13_A	65_R	1.656	1.00
113_F	289_F	1.645	1.00
14_E	24_A	1.640	1.00
9_F	65_R	1.626	1.00
15_S	20_R	1.616	1.00
10_L	68_A	1.599	1.00
8_T	27_V	1.596	1.00
5_D	35_Q	1.555	1.00
113_F	120_V	1.555	1.00
134_E	138_T	1.551	1.00
88_S	119_S	1.547	1.00
19_G	29_P	1.543	1.00
59_E	62_E	1.520	1.00
28_S	31_T	1.514	1.00
202_R	206_E	1.504	1.00
5_D	42_D	1.500	1.00
46_P	49_V	1.498	1.00
67_F	70_Q	1.480	1.00
17_H	20_R	1.478	1.00
5_D	38_R	1.476	1.00
11_H	25_M	1.456	1.00
157_A	278_K	1.448	1.00
10_L	72_L	1.446	1.00
146_A	275_C	1.440	1.00
158_F	273_G	1.424	1.00
67_F	77_Q	1.415	1.00
103_Y	227_E	1.414	1.00
71_T	78_L	1.413	1.00
148_K	273_G	1.405	1.00
282_H	286_I	1.400	1.00
90_S	119_S	1.390	1.00
172_A	257_R	1.364	1.00
143_L	286_I	1.358	1.00
167_V	244_E	1.355	1.00
274_V	290_W	1.354	1.00
94_H	125_T	1.351	1.00
135_K	141_A	1.339	1.00
276_A	290_W	1.335	1.00
64_L	79_R	1.335	1.00
3_L	75_Y	1.333	1.00
136_V	144_A	1.323	1.00
209_F	214_I	1.320	1.00
51_D	56_T	1.317	1.00
143_L	274_V	1.314	1.00
191_V	239_V	1.314	1.00
288_A	291_K	1.300	1.00
159_S	276_A	1.294	1.00
229_M	240_A	1.293	1.00
42_D	79_R	1.293	1.00
74_Q	77_Q	1.286	1.00
112_R	116_E	1.282	1.00
114_R	220_Y	1.280	1.00
250_S	257_R	1.279	1.00
66_V	70_Q	1.263	1.00
290_W	294_P	1.262	1.00
203_R	207_L	1.252	1.00
67_F	78_L	1.248	1.00
231_S	234_A	1.234	1.00
37_Q	41_E	1.227	1.00
62_E	66_V	1.221	1.00
181_V	259_M	1.215	1.00
63_E	66_V	1.214	1.00
9_F	48_F	1.214	1.00
114_R	192_P	1.211	1.00
157_A	276_A	1.210	1.00
244_E	248_E	1.206	1.00
111_D	115_A	1.203	1.00
170_A	239_V	1.199	1.00
27_V	31_T	1.186	1.00
112_R	115_A	1.169	1.00
167_V	260_I	1.168	1.00
9_F	13_A	1.152	1.00
244_E	260_I	1.149	1.00
194_I	229_M	1.148	1.00
93_L	289_F	1.148	1.00
9_F	47_L	1.147	1.00
111_D	235_L	1.146	1.00
34_R	38_R	1.144	1.00
34_R	37_Q	1.139	1.00
123_K	222_T	1.133	1.00
116_E	292_I	1.132	1.00
182_S	264_S	1.126	1.00
33_S	37_Q	1.124	1.00
277_Q	280_R	1.119	1.00
102_A	126_T	1.118	1.00
176_P	191_V	1.112	1.00
18_F	55_V	1.111	1.00
192_P	218_M	1.110	1.00
6_L	68_A	1.108	1.00
223_V	229_M	1.105	1.00
117_H	288_A	1.104	1.00
12_L	21_S	1.100	1.00
70_Q	77_Q	1.098	1.00
113_F	292_I	1.096	1.00
230_V	234_A	1.093	1.00
11_H	21_S	1.086	1.00
71_T	74_Q	1.085	1.00
164_L	245_V	1.082	1.00
7_K	76_Q	1.081	1.00
63_E	67_F	1.075	1.00
183_V	187_D	1.065	1.00
4_R	7_K	1.063	1.00
260_I	263_R	1.062	1.00
287_E	291_K	1.061	1.00
57_L	61_G	1.060	1.00
35_Q	38_R	1.056	1.00
108_P	235_L	1.051	1.00
185_K	265_D	1.050	1.00
231_S	235_L	1.041	1.00
172_A	259_M	1.022	1.00
251_P	256_N	1.021	1.00
249_N	255_R	1.018	1.00
169_I	260_I	1.013	1.00
203_R	206_E	1.011	1.00
178_R	192_P	1.009	1.00
27_V	32_L	1.009	1.00
8_T	25_M	1.007	1.00
79_R	83_D	1.006	1.00
76_Q	80_H	1.003	1.00
170_A	175_C	0.996	1.00
175_C	178_R	0.996	1.00
96_F	132_A	0.995	1.00
13_A	48_F	0.992	1.00
76_Q	79_R	0.987	1.00
113_F	117_H	0.986	1.00
291_K	294_P	0.986	1.00
64_L	68_A	0.985	1.00
223_V	232_M	0.979	1.00
193_F	217_P	0.972	1.00
12_L	18_F	0.969	1.00
73_L	77_Q	0.968	1.00
9_F	57_L	0.964	1.00
195_M	219_I	0.962	1.00
135_K	138_T	0.959	1.00
109_I	293_L	0.957	1.00
158_F	275_C	0.956	1.00
125_T	135_K	0.948	1.00
283_E	286_I	0.948	1.00
109_I	292_I	0.942	1.00
9_F	39_L	0.933	1.00
21_S	32_L	0.932	1.00
48_F	55_V	0.931	1.00
38_R	41_E	0.929	1.00
13_A	61_G	0.922	1.00
137_V	154_G	0.922	1.00
45_Q	82_I	0.918	1.00
63_E	85_Q	0.910	1.00
96_F	146_A	0.910	1.00
141_A	144_A	0.901	1.00
20_R	24_A	0.896	1.00
137_V	152_L	0.895	1.00
121_E	218_M	0.888	1.00
66_V	69_Q	0.888	1.00
99_V	225_G	0.881	1.00
192_P	219_I	0.881	1.00
19_G	23_R	0.876	1.00
160_M	273_G	0.875	1.00
120_V	285_L	0.873	1.00
16_R	56_T	0.863	1.00
148_K	271_E	0.860	1.00
207_L	211_R	0.857	1.00
133_M	137_V	0.856	1.00
25_M	32_L	0.853	1.00
70_Q	73_L	0.846	1.00
158_F	294_P	0.840	1.00
125_T	141_A	0.840	1.00
60_A	85_Q	0.833	1.00
95_I	143_L	0.827	1.00
165_A	269_P	0.826	1.00
51_D	54_T	0.824	1.00
187_D	190_T	0.821	1.00
29_P	33_S	0.821	1.00
184_E	264_S	0.817	1.00
96_F	144_A	0.817	1.00
111_D	237_C	0.817	1.00
91_G	285_L	0.814	1.00
282_H	287_E	0.813	1.00
208_W	212_N	0.812	1.00
175_C	181_V	0.810	1.00
60_A	82_I	0.810	1.00
9_F	64_L	0.809	1.00
37_Q	46_P	0.808	1.00
13_A	16_R	0.806	1.00
16_R	62_E	0.805	1.00
12_L	36_I	0.804	1.00
157_A	160_M	0.799	1.00
247_L	250_S	0.799	1.00
3_L	72_L	0.798	1.00
175_C	179_N	0.798	1.00
75_Y	78_L	0.797	1.00
74_Q	78_L	0.796	1.00
14_E	65_R	0.792	1.00
247_L	251_P	0.791	1.00
205_I	209_F	0.787	1.00
171_P	236_G	0.784	1.00
159_S	162_E	0.784	1.00
186_P	189_S	0.784	1.00
131_D	134_E	0.781	1.00
232_M	237_C	0.780	1.00
12_L	48_F	0.779	1.00
16_R	54_T	0.778	1.00
15_S	21_S	0.775	1.00
91_G	120_V	0.772	1.00
4_R	35_Q	0.772	1.00
177_V	191_V	0.771	1.00
171_P	237_C	0.770	1.00
89_L	117_H	0.769	1.00
77_Q	81_T	0.763	1.00
250_S	255_R	0.761	1.00
75_Y	79_R	0.761	1.00
143_L	289_F	0.761	1.00
114_R	237_C	0.759	1.00
60_A	63_E	0.756	1.00
159_S	290_W	0.755	1.00
284_P	288_A	0.750	1.00
5_D	8_T	0.749	1.00
205_I	208_W	0.746	1.00
165_A	262_E	0.745	1.00
208_W	211_R	0.742	1.00
243_P	246_V	0.740	1.00
68_A	71_T	0.738	1.00
7_K	11_H	0.736	1.00
49_V	58_T	0.734	1.00
18_F	32_L	0.732	1.00
113_F	288_A	0.728	1.00
204_R	208_W	0.727	1.00
78_L	82_I	0.725	1.00
83_D	86_G	0.723	1.00
137_V	156_V	0.721	1.00
57_L	62_E	0.721	1.00
31_T	35_Q	0.720	1.00
12_L	32_L	0.720	1.00
56_T	62_E	0.718	1.00
207_L	210_R	0.715	1.00
202_R	222_T	0.714	1.00
97_C	102_A	0.713	1.00
204_R	207_L	0.711	1.00
94_H	141_A	0.710	1.00
116_E	288_A	0.706	1.00
168_L	171_P	0.704	1.00
164_L	244_E	0.703	1.00
69_Q	73_L	0.703	1.00
168_L	239_V	0.702	1.00
169_I	247_L	0.698	1.00
196_A	229_M	0.698	1.00
40_E	45_Q	0.698	1.00
60_A	64_L	0.695	1.00
197_D	222_T	0.690	1.00
280_R	283_E	0.688	1.00
170_A	177_V	0.686	1.00
165_A	267_K	0.686	1.00
49_V	54_T	0.685	1.00
190_T	218_M	0.685	1.00
145_I	293_L	0.684	1.00
62_E	65_R	0.683	1.00
59_E	63_E	0.680	1.00
225_G	228_A	0.680	1.00
73_L	76_Q	0.670	1.00
139_G	277_Q	0.670	1.00
94_H	142_D	0.669	1.00
40_E	50_R	0.668	1.00
97_C	106_L	0.666	1.00
182_S	262_E	0.665	1.00
221_A	232_M	0.663	1.00
142_D	286_I	0.663	1.00
202_R	208_W	0.658	1.00
68_A	72_L	0.657	1.00
154_G	278_K	0.656	1.00
64_L	82_I	0.655	1.00
173_L	259_M	0.654	1.00
179_N	182_S	0.653	1.00
93_L	285_L	0.652	1.00
206_E	210_R	0.651	1.00
36_I	40_E	0.650	1.00
77_Q	80_H	0.650	1.00
178_R	259_M	0.649	1.00
184_E	265_D	0.648	1.00
126_T	224_G	0.647	1.00
23_R	26_H	0.645	1.00
203_R	208_W	0.643	1.00
121_E	222_T	0.643	1.00
251_P	260_I	0.641	1.00
18_F	54_T	0.641	1.00
7_K	10_L	0.641	1.00
156_V	275_C	0.640	1.00
193_F	239_V	0.636	1.00
103_Y	231_S	0.632	1.00
21_S	25_M	0.629	1.00
67_F	71_T	0.628	1.00
288_A	292_I	0.626	1.00
189_S	214_I	0.623	1.00
170_A	173_L	0.622	1.00
170_A	259_M	0.621	1.00
136_V	275_C	0.618	1.00
63_E	82_I	0.613	1.00
12_L	17_H	0.611	1.00
90_S	121_E	0.608	1.00
289_F	293_L	0.606	1.00
284_P	287_E	0.604	1.00
80_H	84_Q	0.603	1.00
143_L	290_W	0.602	1.00
106_L	109_I	0.598	1.00
126_T	225_G	0.596	1.00
93_L	143_L	0.593	1.00
197_D	224_G	0.591	1.00
131_D	135_K	0.590	1.00
162_E	272_L	0.589	1.00
206_E	209_F	0.588	1.00
4_R	38_R	0.587	1.00
57_L	65_R	0.586	1.00
147_G	270_F	0.585	1.00
4_R	8_T	0.581	1.00
30_S	34_R	0.581	1.00
232_M	238_G	0.581	1.00
132_A	139_G	0.579	1.00
48_F	57_L	0.578	1.00
229_M	233_V	0.573	1.00
169_I	242_L	0.573	1.00
108_P	111_D	0.572	1.00
276_A	287_E	0.572	1.00
7_K	72_L	0.571	1.00
43_L	64_L	0.570	1.00
110_L	122_I	0.569	1.00
223_V	228_A	0.568	1.00
43_L	82_I	0.567	1.00
28_S	34_R	0.566	1.00
45_Q	49_V	0.562	1.00
31_T	34_R	0.560	1.00
182_S	187_D	0.558	1.00
186_P	212_N	0.558	1.00
170_A	178_R	0.552	1.00
101_A	105_H	0.551	1.00
198_Q	222_T	0.549	1.00
108_P	112_R	0.545	1.00
172_A	256_N	0.544	1.00
214_I	217_P	0.543	1.00
91_G	119_S	0.541	1.00
242_L	247_L	0.540	1.00
43_L	46_P	0.540	1.00
203_R	209_F	0.538	1.00
72_L	76_Q	0.538	1.00
72_L	75_Y	0.536	1.00
9_F	61_G	0.535	1.00
8_T	36_I	0.535	1.00
177_V	183_V	0.534	1.00
18_F	29_P	0.533	1.00
169_I	240_A	0.530	1.00
66_V	81_T	0.529	1.00
96_F	125_T	0.529	1.00
201_V	205_I	0.528	1.00
117_H	120_V	0.527	1.00
226_H	243_P	0.527	1.00
173_L	178_R	0.525	1.00
36_I	48_F	0.525	1.00
103_Y	225_G	0.525	1.00
202_R	207_L	0.524	1.00
91_G	117_H	0.523	1.00
18_F	50_R	0.521	1.00
209_F	217_P	0.519	1.00
189_S	216_N	0.519	1.00
134_E	140_E	0.518	1.00
286_I	290_W	0.518	1.00
145_I	274_V	0.517	1.00
171_P	175_C	0.517	1.00
84_Q	89_L	0.517	1.00
68_A	75_Y	0.515	1.00
46_P	60_A	0.514	1.00
67_F	82_I	0.513	1.00
105_H	109_I	0.512	1.00
27_V	35_Q	0.510	1.00
196_A	226_H	0.508	1.00
148_K	152_L	0.508	1.00
8_T	21_S	0.507	1.00
71_T	79_R	0.507	1.00
16_R	55_V	0.506	1.00
210_R	213_K	0.503	1.00
6_L	64_L	0.502	1.00
209_F	212_N	0.501	1.00
257_R	260_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
3fzvA	4	0.9596	100	0.081	Contact Map
1ixcA	4	0.9731	100	0.083	Contact Map
1uthA	2	0.7407	100	0.083	Contact Map
2h98A	2	0.6734	100	0.083	Contact Map
1al3A	1	0.697	100	0.088	Contact Map
2h9bA	2	0.6734	100	0.088	Contact Map
3fxqA	3	0.9798	100	0.089	Contact Map
2esnA	3	0.9798	100	0.091	Contact Map
4x6gA	4	0.9865	100	0.097	Contact Map
3szpA	3	0.9731	100	0.106	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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