YAGI - ECOLI - GREMLIN Contacts

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YAGI - Uncharacterized HTH-type transcriptional regulator YagI

UniProt:	P77300	Sequences: MPIIQSVERALQILDLFNEQATELKITDISKLMGLSKSTLHSLLKTLQLHGYIDQNPENGKYRLGMKLVERGHFVVGSIDIRQKAKGWLTELSRRTGQTTHLGILDGREGVYIEKIEGKLAAIAYSRIGRRLPVHATAIGKVLIAWLGEAELNALLEGYQYTTFTPATLASREALMSALAQTREQGYALDSEENEQGVRCVAVPVWNHESRVIAALSLSTLTSRVDDAELANFREQLQQAGLALSRALGYPA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13349
Length:	252 (240)
Sequences:	12665 (9361)
Seq/√Len:	604.2

ECOLI - YAGI ALLR YIAJ ICLR KDGR MHPR RHMR YJHI
BACSU - KIPR
HALSA - Q9HHM8

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_V	10_A	3.205	1.00
95_R	236_Q	3.090	1.00
103_G	139_I	2.817	1.00
8_E	50_H	2.801	1.00
88_W	240_A	2.760	1.00
181_Q	185_Q	2.583	1.00
15_D	67_K	2.556	1.00
86_K	114_E	2.406	1.00
141_K	178_A	2.378	1.00
153_N	176_M	2.361	1.00
11_L	52_Y	2.329	1.00
141_K	193_E	2.254	1.00
109_E	131_R	2.201	1.00
98_Q	224_R	2.106	1.00
88_W	243_A	2.100	1.00
90_T	116_I	2.015	1.00
17_F	53_I	2.005	1.00
12_Q	50_H	1.978	1.00
147_L	151_E	1.975	1.00
146_W	206_W	1.923	1.00
190_D	200_C	1.923	1.00
105_L	134_V	1.896	1.00
203_V	237_L	1.845	1.00
191_S	199_R	1.820	1.00
56_N	59_N	1.819	1.00
203_V	241_G	1.809	1.00
88_W	247_A	1.807	1.00
199_R	222_T	1.773	1.00
91_E	243_A	1.757	1.00
15_D	50_H	1.734	1.00
54_D	63_R	1.704	1.00
234_R	238_Q	1.684	1.00
171_S	174_A	1.682	1.00
91_E	95_R	1.680	1.00
16_L	24_L	1.661	1.00
85_A	244_L	1.651	1.00
172_R	176_M	1.650	1.00
13_I	29_I	1.642	1.00
93_S	100_T	1.640	1.00
16_L	33_M	1.632	1.00
192_E	222_T	1.625	1.00
16_L	29_I	1.622	1.00
220_T	225_V	1.593	1.00
203_V	238_Q	1.591	1.00
44_L	53_I	1.584	1.00
16_L	32_L	1.581	1.00
218_L	233_F	1.568	1.00
44_L	62_Y	1.564	1.00
192_E	197_G	1.539	1.00
24_L	32_L	1.533	1.00
187_Y	234_R	1.511	1.00
25_K	28_D	1.509	1.00
178_A	181_Q	1.500	1.00
88_W	91_E	1.496	1.00
23_E	63_R	1.496	1.00
148_G	151_E	1.481	1.00
152_L	176_M	1.472	1.00
23_E	61_K	1.452	1.00
96_T	236_Q	1.451	1.00
117_E	123_I	1.446	1.00
236_Q	239_Q	1.445	1.00
35_L	40_L	1.430	1.00
182_T	188_A	1.422	1.00
153_N	172_R	1.416	1.00
29_I	40_L	1.410	1.00
165_T	168_T	1.409	1.00
110_G	143_L	1.402	1.00
206_W	245_S	1.400	1.00
229_E	232_N	1.383	1.00
67_K	70_E	1.376	1.00
93_S	116_I	1.376	1.00
110_G	134_V	1.350	1.00
82_R	114_E	1.346	1.00
48_Q	53_I	1.342	1.00
56_N	63_R	1.341	1.00
92_L	236_Q	1.339	1.00
17_F	24_L	1.338	1.00
17_F	23_E	1.314	1.00
85_A	102_L	1.309	1.00
15_D	52_Y	1.308	1.00
241_G	245_S	1.306	1.00
48_Q	55_Q	1.295	1.00
11_L	50_H	1.273	1.00
89_L	102_L	1.273	1.00
36_S	39_T	1.269	1.00
92_L	240_A	1.246	1.00
108_R	158_G	1.246	1.00
41_H	45_K	1.239	1.00
20_Q	24_L	1.232	1.00
149_E	176_M	1.230	1.00
157_E	172_R	1.227	1.00
20_Q	32_L	1.224	1.00
239_Q	243_A	1.223	1.00
149_E	153_N	1.214	1.00
30_S	40_L	1.208	1.00
86_K	90_T	1.196	1.00
29_I	44_L	1.194	1.00
169_L	178_A	1.176	1.00
206_W	212_V	1.165	1.00
146_W	204_P	1.161	1.00
179_L	182_T	1.153	1.00
145_A	182_T	1.153	1.00
26_I	41_H	1.133	1.00
96_T	233_F	1.126	1.00
136_A	164_F	1.123	1.00
238_Q	242_L	1.120	1.00
136_A	168_T	1.117	1.00
103_G	110_G	1.114	1.00
146_W	212_V	1.105	1.00
149_E	180_A	1.104	1.00
104_I	214_A	1.087	1.00
203_V	234_R	1.083	1.00
167_A	192_E	1.079	1.00
27_T	31_K	1.078	1.00
8_E	49_L	1.075	1.00
105_L	108_R	1.068	1.00
149_E	152_L	1.063	1.00
25_K	61_K	1.056	1.00
90_T	94_R	1.053	1.00
8_E	46_T	1.050	1.00
18_N	21_A	1.046	1.00
102_L	214_A	1.044	1.00
68_L	75_V	1.044	1.00
152_L	183_R	1.044	1.00
105_L	147_L	1.040	1.00
106_D	131_R	1.037	1.00
135_H	168_T	1.035	1.00
139_I	215_A	1.029	1.00
243_A	247_A	1.028	1.00
102_L	205_V	1.027	1.00
137_T	140_G	1.026	1.00
235_E	239_Q	1.022	1.00
207_N	211_R	1.018	1.00
96_T	218_L	1.018	1.00
153_N	157_E	1.011	1.00
52_Y	71_R	1.004	1.00
89_L	100_T	1.000	1.00
26_I	30_S	0.999	1.00
5_Q	9_R	0.994	1.00
28_D	31_K	0.991	1.00
156_L	172_R	0.985	1.00
216_L	244_L	0.983	1.00
91_E	240_A	0.977	1.00
164_F	168_T	0.977	1.00
151_E	154_A	0.971	1.00
166_P	196_Q	0.964	1.00
95_R	239_Q	0.956	1.00
242_L	246_R	0.951	1.00
86_K	116_I	0.945	1.00
163_T	170_A	0.940	1.00
103_G	112_Y	0.938	1.00
27_T	37_K	0.932	1.00
81_I	214_A	0.927	1.00
23_E	56_N	0.921	1.00
142_V	146_W	0.915	1.00
111_V	131_R	0.908	1.00
226_D	229_E	0.908	1.00
204_P	212_V	0.905	1.00
182_T	185_Q	0.904	1.00
138_A	200_C	0.904	1.00
14_L	68_L	0.890	1.00
177_S	180_A	0.889	1.00
84_K	247_A	0.886	1.00
89_L	114_E	0.886	1.00
100_T	218_L	0.885	1.00
177_S	181_Q	0.884	1.00
19_E	32_L	0.881	1.00
151_E	155_L	0.874	1.00
154_A	158_G	0.872	1.00
144_I	175_L	0.872	1.00
174_A	178_A	0.867	1.00
142_V	212_V	0.866	1.00
38_S	41_H	0.866	1.00
9_R	39_T	0.865	1.00
231_A	235_E	0.864	1.00
191_S	222_T	0.863	1.00
28_D	32_L	0.857	1.00
201_V	234_R	0.855	1.00
180_A	184_E	0.855	1.00
176_M	180_A	0.852	1.00
207_N	213_I	0.840	1.00
13_I	33_M	0.839	1.00
192_E	196_Q	0.834	1.00
142_V	182_T	0.832	1.00
82_R	86_K	0.831	1.00
13_I	43_L	0.822	1.00
101_H	219_S	0.820	1.00
202_A	217_S	0.815	1.00
185_Q	234_R	0.815	1.00
164_F	194_N	0.809	1.00
139_I	217_S	0.805	1.00
174_A	177_S	0.802	1.00
152_L	179_L	0.801	1.00
26_I	44_L	0.794	1.00
237_L	241_G	0.792	1.00
106_D	111_V	0.792	1.00
89_L	216_L	0.790	1.00
48_Q	62_Y	0.786	1.00
232_N	235_E	0.783	1.00
230_L	234_R	0.773	1.00
98_Q	120_L	0.771	1.00
240_A	243_A	0.770	1.00
33_M	40_L	0.770	1.00
181_Q	184_E	0.768	1.00
143_L	215_A	0.762	1.00
14_L	52_Y	0.758	1.00
221_L	224_R	0.757	1.00
200_C	219_S	0.756	1.00
178_A	182_T	0.754	1.00
138_A	202_A	0.753	1.00
178_A	185_Q	0.751	1.00
230_L	235_E	0.748	1.00
152_L	155_L	0.745	1.00
235_E	238_Q	0.744	1.00
17_F	22_T	0.741	1.00
101_H	115_K	0.738	1.00
64_L	68_L	0.734	1.00
136_A	194_N	0.733	1.00
88_W	244_L	0.733	1.00
169_L	174_A	0.730	1.00
6_S	10_A	0.728	1.00
145_A	179_L	0.727	1.00
189_L	230_L	0.726	1.00
169_L	175_L	0.723	1.00
89_L	116_I	0.722	1.00
55_Q	59_N	0.720	1.00
17_F	20_Q	0.720	1.00
200_C	217_S	0.719	1.00
105_L	151_E	0.718	1.00
81_I	85_A	0.716	1.00
35_L	39_T	0.716	1.00
55_Q	60_G	0.716	1.00
68_L	71_R	0.712	1.00
54_D	65_G	0.708	1.00
45_K	48_Q	0.705	1.00
101_H	126_S	0.704	1.00
45_K	49_L	0.702	1.00
80_D	83_Q	0.695	1.00
206_W	213_I	0.695	1.00
7_V	43_L	0.692	1.00
26_I	40_L	0.692	1.00
13_I	40_L	0.690	1.00
26_I	37_K	0.689	1.00
141_K	182_T	0.682	1.00
24_L	29_I	0.679	1.00
120_L	224_R	0.679	1.00
155_L	159_Y	0.679	1.00
68_L	72_G	0.673	1.00
239_Q	242_L	0.672	1.00
26_I	62_Y	0.670	1.00
240_A	244_L	0.670	1.00
201_V	230_L	0.665	1.00
191_S	227_D	0.662	1.00
105_L	143_L	0.662	1.00
54_D	66_M	0.659	1.00
242_L	245_S	0.659	1.00
30_S	33_M	0.658	1.00
108_R	155_L	0.657	1.00
165_T	169_L	0.654	1.00
147_L	152_L	0.648	1.00
104_I	113_I	0.647	1.00
91_E	94_R	0.644	1.00
180_A	183_R	0.637	1.00
152_L	180_A	0.635	1.00
152_L	156_L	0.634	1.00
216_L	241_G	0.629	1.00
93_S	118_G	0.628	1.00
238_Q	241_G	0.628	1.00
144_I	179_L	0.626	1.00
144_I	152_L	0.625	1.00
143_L	147_L	0.625	1.00
229_E	233_F	0.624	1.00
149_E	183_R	0.624	1.00
137_T	200_C	0.622	1.00
72_G	75_V	0.619	1.00
7_V	11_L	0.617	1.00
101_H	200_C	0.616	1.00
92_L	96_T	0.615	1.00
203_V	245_S	0.614	1.00
84_K	87_G	0.614	1.00
18_N	71_R	0.614	1.00
15_D	70_E	0.613	1.00
92_L	218_L	0.608	1.00
133_P	136_A	0.601	1.00
186_G	206_W	0.600	1.00
6_S	43_L	0.599	1.00
90_T	114_E	0.598	1.00
21_A	32_L	0.597	1.00
191_S	230_L	0.596	1.00
192_E	199_R	0.596	1.00
170_A	174_A	0.595	1.00
216_L	240_A	0.595	1.00
115_K	128_I	0.595	1.00
94_R	119_K	0.594	1.00
9_R	35_L	0.594	1.00
112_Y	126_S	0.593	1.00
55_Q	62_Y	0.592	1.00
28_D	61_K	0.588	1.00
135_H	161_Y	0.588	1.00
243_A	246_R	0.586	1.00
232_N	236_Q	0.585	1.00
12_Q	15_D	0.584	1.00
167_A	196_Q	0.582	1.00
117_E	127_R	0.582	1.00
17_F	21_A	0.577	1.00
92_L	100_T	0.574	1.00
161_Y	165_T	0.567	1.00
142_V	202_A	0.567	1.00
115_K	126_S	0.567	1.00
98_Q	220_T	0.566	1.00
7_V	46_T	0.566	1.00
23_E	59_N	0.565	1.00
205_V	214_A	0.564	1.00
216_L	237_L	0.563	1.00
142_V	204_P	0.563	1.00
18_N	64_L	0.563	1.00
52_Y	67_K	0.562	1.00
127_R	130_R	0.561	1.00
110_G	139_I	0.559	1.00
97_G	119_K	0.559	1.00
56_N	61_K	0.558	1.00
98_Q	218_L	0.557	1.00
45_K	55_Q	0.556	1.00
30_S	37_K	0.556	1.00
10_A	43_L	0.555	1.00
112_Y	139_I	0.554	0.99
122_A	223_S	0.553	0.99
73_H	76_V	0.552	0.99
228_A	232_N	0.551	0.99
236_Q	240_A	0.551	0.99
100_T	116_I	0.551	0.99
143_L	214_A	0.549	0.99
141_K	190_D	0.548	0.99
15_D	71_R	0.548	0.99
173_E	176_M	0.544	0.99
87_G	247_A	0.543	0.99
203_V	216_L	0.541	0.99
51_G	67_K	0.538	0.99
12_Q	16_L	0.537	0.99
110_G	132_L	0.537	0.99
41_H	55_Q	0.535	0.99
25_K	37_K	0.534	0.99
69_V	76_V	0.531	0.99
103_G	137_T	0.529	0.99
9_R	43_L	0.529	0.99
233_F	236_Q	0.529	0.99
126_S	130_R	0.525	0.99
187_Y	238_Q	0.524	0.99
101_H	217_S	0.522	0.99
175_L	179_L	0.518	0.99
16_L	20_Q	0.518	0.99
110_G	137_T	0.517	0.99
112_Y	132_L	0.514	0.99
85_A	89_L	0.512	0.99
114_E	128_I	0.511	0.99
206_W	214_A	0.509	0.99
99_T	115_K	0.508	0.99
142_V	188_A	0.506	0.99
173_E	177_S	0.502	0.99
139_I	200_C	0.500	0.99

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
3mq0A	2	0.9841	100	0.077	Contact Map
2ia2A	4	0.9841	100	0.077	Contact Map
2g7uA	6	0.9921	100	0.079	Contact Map
3r4kA	2	0.9881	100	0.08	Contact Map
1mkmA	4	0.9802	100	0.088	Contact Map
2xrnA	3	0.9563	100	0.102	Contact Map
2o0yA	4	0.9643	100	0.129	Contact Map
1ysqA	1	0.6905	100	0.397	Contact Map
1tf1A	1	0.7302	100	0.398	Contact Map
1yspA	1	0.6508	100	0.403	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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