YNFL - ECOLI - GREMLIN Contacts

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YNFL - Uncharacterized HTH-type transcriptional regulator YnfL

UniProt:	P77559	Sequences: MNIELRHLRYFVAVAEELHFGRAAARLNISQPPLSQQIQALEQQIGARLLARTNRSVLLTAAGKQFLADSRQILSMVDDAAARAERLHQGEAGELRIGFTSSAPFIRAVSDTLSLFRRDYPDVHLQTREMNTREQIAPLIEGTLDMGLLRNTALPESLEHAVIVHEPLMAMIPHDHPLANNPNVTLAELAKEPFVFFDPHVGTGLYDDILGLMRRYHLTPVITQEVGEAMTIIGLVSAGLGVSILPASFKRVQLNEMRWVPIAEEDAVSEMWLVWPKHHEQSPAARNFRIHLLNALR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13850
Length:	297 (284)
Sequences:	79496 (58171)
Seq/√Len:	3451.8

ECOLI - YNFL YBHD YFER LYSR YEIE CYNR XAPR YAFC OXYR YCAN CYSB PGRR YEEY LEUO CBL HCAR NAC ILVY YDCI YFIE ICIA TTDR ABGR TDCA YBDO YHJC AAER NHAR YAHB DMLR YNEJ YBEF YIDZ METR YDHB DSDC GCVA ALLS YGFI YIAU YHAJ LRHA YJIE HDFR PERR
BACSU - YCGK CYSL ALSR YWBI YTLI GLTC YYBE BSDA CITR YOAU GLTR YWQM YVBU YUST YOFA YXJO YKUM 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
72_Q	76_M	3.809	1.00
17_E	26_R	3.459	1.00
13_A	26_R	2.790	1.00
69_D	83_R	2.655	1.00
161_A	293_L	2.582	1.00
162_V	270_E	2.538	1.00
47_A	62_A	2.414	1.00
12_V	71_R	2.385	1.00
98_G	144_L	2.322	1.00
169_M	247_A	2.300	1.00
12_V	16_E	2.282	1.00
94_E	126_Q	2.239	1.00
165_H	270_E	2.228	1.00
162_V	165_H	2.222	1.00
10_Y	37_Q	2.214	1.00
69_D	76_M	2.211	1.00
13_A	17_E	2.174	1.00
94_E	124_H	2.099	1.00
176_H	192_E	2.062	1.00
96_R	126_Q	2.044	1.00
236_V	243_S	1.990	1.00
15_A	59_L	1.984	1.00
165_H	268_V	1.972	1.00
167_P	247_A	1.947	1.00
115_L	291_H	1.943	1.00
73_I	77_V	1.920	1.00
67_L	71_R	1.913	1.00
10_Y	34_L	1.906	1.00
13_A	16_E	1.899	1.00
15_A	67_L	1.891	1.00
185_T	188_E	1.876	1.00
16_E	71_R	1.840	1.00
69_D	72_Q	1.821	1.00
12_V	67_L	1.800	1.00
22_R	25_A	1.787	1.00
193_P	223_T	1.786	1.00
160_H	272_W	1.757	1.00
195_V	241_G	1.749	1.00
65_Q	83_R	1.749	1.00
17_E	22_R	1.717	1.00
254_L	257_M	1.708	1.00
19_H	22_R	1.684	1.00
138_P	143_T	1.639	1.00
51_A	58_L	1.636	1.00
161_A	275_W	1.591	1.00
7_H	44_Q	1.562	1.00
66_F	80_A	1.552	1.00
76_M	79_D	1.551	1.00
7_H	40_A	1.548	1.00
105_F	230_M	1.547	1.00
53_T	58_L	1.536	1.00
12_V	70_S	1.531	1.00
159_E	277_K	1.530	1.00
135_Q	147_G	1.516	1.00
69_D	79_D	1.515	1.00
30_S	33_P	1.497	1.00
7_H	37_Q	1.492	1.00
275_W	289_R	1.480	1.00
20_F	38_I	1.474	1.00
138_P	144_L	1.474	1.00
16_E	26_R	1.462	1.00
159_E	275_W	1.451	1.00
13_A	27_L	1.448	1.00
137_A	141_E	1.446	1.00
237_S	253_Q	1.442	1.00
149_L	274_V	1.433	1.00
68_A	72_Q	1.431	1.00
169_M	261_P	1.425	1.00
119_D	291_H	1.414	1.00
96_R	128_R	1.412	1.00
73_I	80_A	1.389	1.00
289_R	293_L	1.381	1.00
233_I	253_Q	1.380	1.00
48_R	51_A	1.372	1.00
206_Y	210_L	1.371	1.00
162_V	272_W	1.358	1.00
281_Q	285_A	1.357	1.00
21_G	31_Q	1.348	1.00
69_D	80_A	1.343	1.00
116_F	123_V	1.343	1.00
5_L	77_V	1.341	1.00
166_E	248_S	1.335	1.00
273_L	289_R	1.335	1.00
151_N	272_W	1.335	1.00
232_I	243_S	1.333	1.00
65_Q	69_D	1.331	1.00
139_L	147_G	1.330	1.00
66_F	81_A	1.330	1.00
116_F	288_F	1.327	1.00
234_G	237_S	1.323	1.00
29_I	33_P	1.317	1.00
11_F	67_L	1.310	1.00
36_Q	40_A	1.306	1.00
4_E	7_H	1.291	1.00
92_A	122_D	1.281	1.00
114_S	238_A	1.280	1.00
146_M	273_L	1.275	1.00
12_V	74_L	1.263	1.00
287_N	290_I	1.262	1.00
140_I	157_S	1.261	1.00
181_N	188_E	1.256	1.00
192_E	242_V	1.255	1.00
172_I	242_V	1.242	1.00
10_Y	29_I	1.238	1.00
117_R	223_T	1.238	1.00
61_A	64_K	1.237	1.00
115_L	119_D	1.235	1.00
146_M	285_A	1.234	1.00
117_R	193_P	1.231	1.00
172_I	260_V	1.225	1.00
65_Q	68_A	1.225	1.00
177_P	192_E	1.218	1.00
72_Q	79_D	1.209	1.00
111_D	238_A	1.208	1.00
174_H	258_R	1.201	1.00
90_G	122_D	1.200	1.00
114_S	118_R	1.190	1.00
8_L	70_S	1.188	1.00
182_P	260_V	1.185	1.00
11_F	15_A	1.178	1.00
183_N	263_A	1.165	1.00
64_K	68_A	1.153	1.00
44_Q	81_A	1.148	1.00
128_R	138_P	1.146	1.00
13_A	23_A	1.138	1.00
160_H	274_V	1.132	1.00
11_F	50_L	1.130	1.00
234_G	238_A	1.129	1.00
36_Q	39_Q	1.128	1.00
161_A	289_R	1.128	1.00
247_A	251_R	1.123	1.00
77_V	81_A	1.123	1.00
184_V	188_E	1.117	1.00
73_I	76_M	1.113	1.00
120_Y	287_N	1.103	1.00
193_P	221_V	1.103	1.00
37_Q	40_A	1.084	1.00
233_I	237_S	1.067	1.00
39_Q	43_Q	1.067	1.00
196_F	222_I	1.062	1.00
20_F	57_V	1.061	1.00
75_S	79_D	1.043	1.00
237_S	258_R	1.042	1.00
174_H	256_E	1.038	1.00
173_P	239_G	1.037	1.00
62_A	65_Q	1.036	1.00
167_P	268_V	1.036	1.00
126_Q	225_E	1.036	1.00
81_A	85_E	1.028	1.00
95_L	288_F	1.020	1.00
286_R	290_I	1.019	1.00
140_I	155_P	1.019	1.00
237_S	256_E	1.015	1.00
66_F	70_S	1.000	1.00
35_S	39_Q	0.999	1.00
104_P	129_E	0.998	1.00
116_F	120_Y	0.985	1.00
72_Q	75_S	0.981	1.00
6_R	9_R	0.980	1.00
23_A	34_L	0.979	1.00
114_S	240_L	0.971	1.00
169_M	259_W	0.967	1.00
116_F	291_H	0.966	1.00
40_A	43_Q	0.962	1.00
14_V	23_A	0.960	1.00
115_L	118_R	0.958	1.00
59_L	63_G	0.951	1.00
18_L	58_L	0.941	1.00
171_M	250_K	0.936	1.00
207_D	210_L	0.935	1.00
159_E	162_V	0.933	1.00
207_D	211_G	0.932	1.00
14_V	20_F	0.931	1.00
247_A	261_P	0.930	1.00
112_T	292_L	0.927	1.00
9_R	78_D	0.926	1.00
22_R	26_R	0.924	1.00
195_V	232_I	0.923	1.00
77_V	80_A	0.923	1.00
11_F	49_L	0.920	1.00
65_Q	87_L	0.918	1.00
226_V	232_I	0.918	1.00
283_P	287_N	0.916	1.00
11_F	41_L	0.914	1.00
79_D	83_R	0.914	1.00
261_P	264_E	0.913	1.00
78_D	81_A	0.912	1.00
68_A	71_R	0.910	1.00
6_R	37_Q	0.905	1.00
290_I	293_L	0.903	1.00
17_E	23_A	0.901	1.00
212_L	216_Y	0.894	1.00
15_A	50_L	0.893	1.00
9_R	13_A	0.892	1.00
170_A	242_V	0.890	1.00
138_P	141_E	0.886	1.00
282_S	285_A	0.886	1.00
10_Y	27_L	0.885	1.00
172_I	176_H	0.882	1.00
9_R	12_V	0.881	1.00
253_Q	256_E	0.880	1.00
117_R	240_L	0.879	1.00
76_M	80_A	0.876	1.00
112_T	291_H	0.871	1.00
64_K	67_L	0.870	1.00
253_Q	258_R	0.870	1.00
18_L	56_S	0.869	1.00
101_S	228_E	0.868	1.00
16_E	67_L	0.867	1.00
175_D	239_G	0.864	1.00
136_I	140_I	0.863	1.00
226_V	235_L	0.860	1.00
29_I	34_L	0.858	1.00
53_T	56_S	0.855	1.00
252_V	256_E	0.852	1.00
11_F	59_L	0.852	1.00
47_A	84_A	0.851	1.00
15_A	18_L	0.851	1.00
21_G	25_A	0.844	1.00
151_N	270_E	0.833	1.00
14_V	50_L	0.832	1.00
128_R	144_L	0.830	1.00
93_G	284_A	0.829	1.00
185_T	263_A	0.826	1.00
31_Q	35_S	0.821	1.00
62_A	84_A	0.819	1.00
193_P	222_I	0.815	1.00
80_A	84_A	0.814	1.00
213_M	218_L	0.814	1.00
97_I	146_M	0.814	1.00
78_D	82_A	0.814	1.00
281_Q	286_R	0.805	1.00
276_P	279_H	0.799	1.00
71_R	75_S	0.798	1.00
228_E	231_T	0.793	1.00
50_L	57_V	0.793	1.00
144_L	147_G	0.792	1.00
70_S	73_I	0.792	1.00
178_L	192_E	0.790	1.00
235_L	240_L	0.789	1.00
180_N	193_P	0.789	1.00
27_L	34_L	0.788	1.00
98_G	149_L	0.781	1.00
9_R	74_L	0.780	1.00
167_P	266_D	0.778	1.00
172_I	177_P	0.778	1.00
116_F	287_N	0.776	1.00
167_P	261_P	0.775	1.00
176_H	179_A	0.775	1.00
98_G	135_Q	0.775	1.00
14_V	34_L	0.774	1.00
20_F	34_L	0.771	1.00
99_F	104_P	0.771	1.00
105_F	234_G	0.765	1.00
287_N	291_H	0.765	1.00
187_A	190_A	0.764	1.00
173_P	176_H	0.760	1.00
98_G	147_G	0.760	1.00
11_F	63_G	0.756	1.00
5_L	74_L	0.755	1.00
173_P	240_L	0.754	1.00
62_A	87_L	0.753	1.00
111_D	114_S	0.753	1.00
123_V	284_A	0.751	1.00
61_A	65_Q	0.751	1.00
142_G	276_P	0.750	1.00
253_Q	257_M	0.750	1.00
209_I	213_M	0.749	1.00
251_R	255_N	0.747	1.00
188_E	191_K	0.747	1.00
69_D	73_I	0.746	1.00
124_H	221_V	0.745	1.00
208_D	211_G	0.745	1.00
208_D	212_L	0.743	1.00
39_Q	48_R	0.739	1.00
212_L	215_R	0.738	1.00
14_V	38_I	0.735	1.00
59_L	64_K	0.734	1.00
51_A	60_T	0.731	1.00
134_E	138_P	0.730	1.00
198_D	225_E	0.728	1.00
15_A	64_K	0.728	1.00
171_M	259_W	0.726	1.00
134_E	137_A	0.724	1.00
257_M	261_P	0.724	1.00
140_I	158_L	0.722	1.00
145_D	285_A	0.720	1.00
170_A	244_I	0.720	1.00
171_M	245_L	0.717	1.00
7_H	10_Y	0.716	1.00
146_M	288_F	0.715	1.00
85_E	88_H	0.715	1.00
177_P	182_P	0.715	1.00
176_H	180_N	0.712	1.00
158_L	274_V	0.711	1.00
175_D	179_A	0.705	1.00
190_A	218_L	0.702	1.00
96_R	145_D	0.698	1.00
15_A	63_G	0.695	1.00
206_Y	212_L	0.691	1.00
11_F	66_F	0.690	1.00
210_L	214_R	0.688	1.00
6_R	40_A	0.686	1.00
18_L	64_K	0.683	1.00
237_S	254_L	0.682	1.00
25_A	28_N	0.681	1.00
211_G	215_R	0.680	1.00
279_H	282_S	0.677	1.00
33_P	37_Q	0.676	1.00
74_L	78_D	0.670	1.00
91_E	120_Y	0.669	1.00
197_F	232_I	0.666	1.00
258_R	261_P	0.664	1.00
129_E	227_G	0.662	1.00
157_S	277_K	0.656	1.00
150_R	269_S	0.655	1.00
194_F	220_P	0.655	1.00
93_G	123_V	0.654	1.00
194_F	242_V	0.652	1.00
58_L	64_K	0.651	1.00
109_V	112_T	0.650	1.00
171_M	243_S	0.649	1.00
62_A	66_F	0.647	1.00
283_P	286_R	0.644	1.00
124_H	225_E	0.643	1.00
119_D	287_N	0.640	1.00
66_F	84_A	0.638	1.00
45_I	66_F	0.637	1.00
246_P	249_F	0.635	1.00
79_D	82_A	0.625	1.00
224_Q	235_L	0.620	1.00
226_V	231_T	0.619	1.00
139_L	158_L	0.617	1.00
51_A	56_S	0.615	1.00
96_R	144_L	0.611	1.00
175_D	178_L	0.610	1.00
146_M	289_R	0.608	1.00
209_I	212_L	0.608	1.00
110_S	114_S	0.607	1.00
42_E	52_R	0.604	1.00
140_I	143_T	0.604	1.00
172_I	178_L	0.603	1.00
257_M	264_E	0.601	1.00
114_S	117_R	0.597	1.00
198_D	227_G	0.595	1.00
284_A	287_N	0.594	1.00
83_R	86_R	0.591	1.00
65_Q	84_A	0.589	1.00
206_Y	225_E	0.586	1.00
6_R	10_Y	0.586	1.00
168_L	244_I	0.584	1.00
20_F	31_Q	0.584	1.00
111_D	115_L	0.584	1.00
176_H	242_V	0.579	1.00
47_A	88_H	0.579	1.00
288_F	292_L	0.576	1.00
151_N	160_H	0.573	1.00
95_L	146_M	0.572	1.00
23_A	27_L	0.571	1.00
205_L	209_I	0.565	1.00
178_L	181_N	0.565	1.00
120_Y	123_V	0.561	1.00
92_A	124_H	0.560	1.00
75_S	78_D	0.559	1.00
108_A	112_T	0.559	1.00
205_L	208_D	0.555	1.00
45_I	48_R	0.554	1.00
14_V	19_H	0.554	1.00
213_M	220_P	0.553	1.00
197_F	229_A	0.551	1.00
98_G	128_R	0.549	1.00
40_A	44_Q	0.547	1.00
99_F	127_T	0.544	1.00
99_F	109_V	0.544	1.00
93_G	122_D	0.543	1.00
45_I	84_A	0.542	1.00
230_M	234_G	0.541	1.00
207_D	212_L	0.540	1.00
82_A	86_R	0.538	1.00
47_A	51_A	0.538	1.00
124_H	223_T	0.537	1.00
176_H	193_P	0.537	1.00
211_G	214_R	0.537	1.00
80_A	83_R	0.536	1.00
275_W	286_R	0.536	1.00
18_L	57_V	0.535	1.00
50_L	59_L	0.535	1.00
204_G	207_D	0.535	1.00
12_V	78_D	0.534	1.00
4_E	40_A	0.533	1.00
286_R	289_R	0.533	1.00
275_W	281_Q	0.531	1.00
177_P	181_N	0.531	1.00
210_L	213_M	0.530	1.00
163_I	273_L	0.530	1.00
139_L	274_V	0.530	1.00
48_R	62_A	0.529	1.00
170_A	189_L	0.527	1.00
82_A	85_E	0.527	1.00
166_E	269_S	0.526	1.00
285_A	289_R	0.524	1.00
100_T	103_A	0.524	1.00
111_D	234_G	0.519	1.00
178_L	184_V	0.518	1.00
45_I	81_A	0.518	1.00
33_P	36_Q	0.517	1.00
32_P	36_Q	0.515	1.00
124_H	222_I	0.513	1.00
105_F	228_E	0.511	1.00
133_R	137_A	0.511	1.00
8_L	66_F	0.511	1.00
172_I	179_A	0.510	1.00
32_P	35_S	0.509	1.00
118_R	240_L	0.508	1.00
232_I	236_V	0.508	1.00
148_L	292_L	0.508	1.00
166_E	246_P	0.508	1.00
29_I	37_Q	0.508	1.00
103_A	108_A	0.506	1.00
70_S	74_L	0.504	1.00
187_A	218_L	0.503	1.00
38_I	42_E	0.503	1.00
73_I	81_A	0.503	1.00
171_M	257_M	0.502	1.00
245_L	250_K	0.500	1.00
179_A	258_R	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
1ixcA	4	0.9865	100	0.069	Contact Map
2h98A	2	0.6869	100	0.075	Contact Map
2esnA	3	0.9832	100	0.076	Contact Map
3fzvA	4	0.963	100	0.078	Contact Map
2h9bA	2	0.6869	100	0.079	Contact Map
1uthA	2	0.7407	100	0.087	Contact Map
1al3A	1	0.697	100	0.089	Contact Map
3fxqA	3	0.9798	100	0.089	Contact Map
4x6gA	4	0.9832	100	0.094	Contact Map
3hhgA	3	0.9798	100	0.099	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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