YJHI - ECOLI - GREMLIN Contacts

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YJHI - Uncharacterized HTH-type transcriptional regulator YjhI

UniProt:	P39360	Sequences: MVRKGCNSLVRAEKILTHIAWVGMASYMELLNKFQYPKSSLLNLLNVMVDCGFLIKNKNGYYSLGIKNYELGCQALHRQNIFEVTKRPMQELSLKSGLVCHLGAMESISAIYLDKIESPDSVPTSKSWIGKKLELHITALGKALLAWKTREELDYFLEALTLTPHTRNTFTDKKLFLEELQKTRLRGWAIDNEESTYGAVCLSMPVFNMYNRVNYAISLSGDPVVYSGNKIDSYLELLRKCAEQISYGLGYRNENEHLRKGN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12551
Length:	262 (243)
Sequences:	12750 (9365)
Seq/√Len:	600.8

ECOLI - YJHI RHMR MHPR ALLR YIAJ KDGR ICLR YAGI
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
9_L	12_A	3.229	1.00
95_K	237_L	3.111	1.00
103_G	140_L	2.834	1.00
10_V	51_C	2.800	1.00
88_P	241_C	2.795	1.00
182_K	186_R	2.580	1.00
17_T	67_K	2.568	1.00
86_K	114_D	2.408	1.00
142_K	179_E	2.385	1.00
13_E	53_F	2.365	1.00
154_D	177_L	2.330	1.00
142_K	194_E	2.247	1.00
109_S	132_K	2.182	1.00
88_P	244_Q	2.124	1.00
98_L	225_V	2.103	1.00
19_I	54_L	2.075	1.00
148_K	152_E	2.024	1.00
90_Q	116_I	2.016	1.00
14_K	51_C	2.011	1.00
147_W	207_F	1.944	1.00
105_M	135_L	1.901	1.00
204_M	238_L	1.896	1.00
191_D	201_C	1.868	1.00
192_N	200_V	1.859	1.00
88_P	248_G	1.845	1.00
204_M	242_A	1.834	1.00
200_V	223_P	1.767	1.00
235_L	239_R	1.750	1.00
91_E	244_Q	1.745	1.00
55_I	63_S	1.743	1.00
17_T	51_C	1.737	1.00
15_I	30_L	1.717	1.00
91_E	95_K	1.702	1.00
18_H	34_F	1.687	1.00
172_D	175_L	1.686	1.00
173_K	177_L	1.685	1.00
85_T	245_I	1.681	1.00
93_S	100_C	1.675	1.00
18_H	25_A	1.654	1.00
18_H	30_L	1.634	1.00
18_H	33_K	1.632	1.00
45_L	54_L	1.631	1.00
204_M	239_R	1.606	1.00
193_E	223_P	1.600	1.00
221_G	226_Y	1.594	1.00
230_K	233_S	1.561	1.00
219_L	234_Y	1.556	1.00
25_A	33_K	1.543	1.00
45_L	62_Y	1.541	1.00
179_E	182_K	1.535	1.00
193_E	198_G	1.518	1.00
26_S	29_E	1.515	1.00
188_W	235_L	1.507	1.00
153_L	177_L	1.504	1.00
88_P	91_E	1.497	1.00
24_M	63_S	1.491	1.00
149_T	152_E	1.490	1.00
237_L	240_K	1.490	1.00
96_S	237_L	1.478	1.00
183_T	189_A	1.470	1.00
36_Y	41_L	1.458	1.00
30_L	41_L	1.451	1.00
24_M	61_Y	1.445	1.00
110_A	144_L	1.431	1.00
207_F	246_S	1.427	1.00
67_K	70_E	1.425	1.00
166_T	169_T	1.417	1.00
154_D	173_K	1.385	1.00
82_F	114_D	1.358	1.00
110_A	135_L	1.354	1.00
85_T	102_L	1.343	1.00
17_T	53_F	1.341	1.00
92_L	237_L	1.340	1.00
49_V	54_L	1.337	1.00
93_S	116_I	1.337	1.00
57_N	63_S	1.336	1.00
19_I	25_A	1.328	1.00
242_A	246_S	1.324	1.00
13_E	51_C	1.322	1.00
117_E	123_P	1.321	1.00
49_V	56_K	1.303	1.00
108_I	159_A	1.301	1.00
19_I	24_M	1.301	1.00
22_V	25_A	1.292	1.00
89_M	102_L	1.268	1.00
240_K	244_Q	1.260	1.00
150_R	177_L	1.251	1.00
37_P	40_S	1.243	1.00
22_V	33_K	1.240	1.00
92_L	241_C	1.226	1.00
86_K	90_Q	1.226	1.00
42_L	46_N	1.223	1.00
31_L	41_L	1.212	1.00
180_L	183_T	1.209	1.00
30_L	45_L	1.198	1.00
158_E	173_K	1.192	1.00
170_F	179_E	1.174	1.00
207_F	213_V	1.158	1.00
146_A	183_T	1.155	1.00
105_M	148_K	1.152	1.00
147_W	205_P	1.151	1.00
96_S	234_Y	1.132	1.00
150_R	154_D	1.129	1.00
137_I	169_T	1.122	1.00
103_G	110_A	1.119	1.00
239_R	243_E	1.115	1.00
204_M	235_L	1.112	1.00
27_Y	42_L	1.110	1.00
6_C	47_V	1.108	1.00
168_N	193_E	1.107	1.00
147_W	213_V	1.096	1.00
28_M	32_N	1.093	1.00
150_R	153_L	1.091	1.00
26_S	61_Y	1.087	1.00
10_V	50_D	1.083	1.00
153_L	184_R	1.081	1.00
137_I	165_H	1.080	1.00
10_V	47_V	1.077	1.00
90_Q	94_L	1.074	1.00
102_L	215_Y	1.062	1.00
68_N	75_A	1.058	1.00
105_M	108_I	1.056	1.00
96_S	219_L	1.054	1.00
104_A	215_Y	1.052	1.00
157_L	173_K	1.052	1.00
232_D	236_E	1.047	1.00
140_L	216_A	1.045	1.00
227_S	230_K	1.043	1.00
150_R	181_Q	1.042	1.00
136_H	169_T	1.039	1.00
236_E	240_K	1.035	1.00
217_I	245_I	1.031	1.00
27_Y	31_L	1.024	1.00
106_E	132_K	1.023	1.00
89_M	100_C	1.018	1.00
29_E	32_N	1.016	1.00
102_L	206_V	1.014	1.00
53_F	71_L	1.009	1.00
138_T	141_G	1.004	1.00
244_Q	248_G	1.004	1.00
154_D	158_E	0.988	1.00
95_K	240_K	0.982	1.00
164_P	171_T	0.973	1.00
91_E	241_C	0.973	1.00
243_E	247_Y	0.972	1.00
208_N	212_R	0.966	1.00
7_N	11_R	0.959	1.00
28_M	38_K	0.945	1.00
86_K	116_I	0.944	1.00
167_R	197_Y	0.943	1.00
205_P	213_V	0.940	1.00
103_G	112_Y	0.939	1.00
24_M	57_N	0.938	1.00
111_I	132_K	0.934	1.00
123_P	126_K	0.934	1.00
152_E	155_Y	0.928	1.00
139_A	201_C	0.921	1.00
183_T	186_R	0.920	1.00
81_I	215_Y	0.908	1.00
19_I	23_G	0.906	1.00
21_W	33_K	0.904	1.00
84_V	248_G	0.903	1.00
16_L	68_N	0.902	1.00
178_E	182_K	0.901	1.00
143_A	147_W	0.898	1.00
178_E	181_Q	0.887	1.00
152_E	156_F	0.885	1.00
29_E	33_K	0.883	1.00
82_F	86_K	0.875	1.00
165_H	169_T	0.874	1.00
15_I	34_F	0.870	1.00
155_Y	159_A	0.866	1.00
101_H	220_S	0.864	1.00
145_L	176_F	0.861	1.00
181_Q	185_L	0.860	1.00
202_L	235_L	0.860	1.00
177_L	181_Q	0.858	1.00
89_M	114_D	0.852	1.00
175_L	179_E	0.850	1.00
39_S	42_L	0.847	1.00
192_N	223_P	0.845	1.00
100_C	219_L	0.845	1.00
175_L	178_E	0.843	1.00
165_H	195_S	0.834	1.00
19_I	22_V	0.834	1.00
186_R	235_L	0.829	1.00
143_A	213_V	0.828	1.00
143_A	183_T	0.827	1.00
49_V	62_Y	0.827	1.00
153_L	180_L	0.826	1.00
11_R	40_S	0.826	1.00
203_S	218_S	0.822	1.00
140_L	218_S	0.820	1.00
208_N	214_N	0.817	1.00
238_L	242_A	0.807	1.00
193_E	197_Y	0.807	1.00
105_M	152_E	0.806	1.00
89_M	217_I	0.798	1.00
106_E	111_I	0.798	1.00
98_L	120_D	0.795	1.00
15_I	44_L	0.784	1.00
182_K	185_L	0.783	1.00
222_D	225_V	0.783	1.00
179_E	183_T	0.779	1.00
139_A	203_S	0.776	1.00
241_C	244_Q	0.775	1.00
170_F	175_L	0.774	1.00
179_E	186_R	0.773	1.00
88_P	245_I	0.771	1.00
34_F	41_L	0.769	1.00
8_S	12_A	0.766	1.00
233_S	237_L	0.765	1.00
27_Y	45_L	0.760	1.00
56_K	60_G	0.756	1.00
36_Y	40_S	0.750	1.00
201_C	220_S	0.749	1.00
46_N	49_V	0.749	1.00
146_A	180_L	0.746	1.00
16_L	53_F	0.744	1.00
64_L	68_N	0.738	1.00
236_E	239_R	0.733	1.00
144_L	216_A	0.729	1.00
137_I	195_S	0.729	1.00
101_H	115_K	0.727	1.00
46_N	50_D	0.726	1.00
55_I	65_G	0.722	1.00
89_M	116_I	0.721	1.00
201_C	218_S	0.720	1.00
81_I	85_T	0.718	1.00
68_N	71_L	0.715	1.00
68_N	72_G	0.712	1.00
153_L	156_F	0.711	1.00
101_H	127_S	0.706	1.00
25_A	30_L	0.698	1.00
27_Y	41_L	0.697	1.00
56_K	59_N	0.696	1.00
31_L	34_F	0.689	1.00
108_I	156_F	0.686	1.00
153_L	181_Q	0.682	1.00
9_L	44_L	0.679	1.00
27_Y	38_K	0.679	1.00
142_K	183_T	0.677	1.00
15_I	41_L	0.676	1.00
170_F	176_F	0.674	1.00
202_L	231_I	0.674	1.00
93_S	118_S	0.674	1.00
148_K	153_L	0.672	1.00
120_D	225_V	0.671	1.00
243_E	246_S	0.671	1.00
233_S	236_E	0.666	1.00
207_F	214_N	0.666	1.00
105_M	144_L	0.666	1.00
156_F	160_L	0.665	1.00
91_E	94_L	0.663	1.00
27_Y	62_Y	0.662	1.00
80_N	83_E	0.660	1.00
192_N	228_G	0.660	1.00
153_L	157_L	0.659	1.00
240_K	243_E	0.655	1.00
181_Q	184_R	0.654	1.00
231_I	236_E	0.653	1.00
104_A	113_L	0.652	1.00
166_T	170_F	0.652	1.00
193_E	200_V	0.649	1.00
55_I	66_I	0.648	1.00
144_L	148_K	0.646	1.00
231_I	235_L	0.641	1.00
157_L	161_T	0.641	1.00
150_R	184_R	0.641	1.00
230_K	234_Y	0.639	1.00
239_R	242_A	0.639	1.00
171_T	175_L	0.639	1.00
217_I	242_A	0.639	1.00
101_H	201_C	0.634	1.00
241_C	245_I	0.629	1.00
145_L	180_L	0.629	1.00
92_L	96_S	0.627	1.00
72_G	75_A	0.625	1.00
9_L	13_E	0.623	1.00
17_T	70_E	0.617	1.00
98_L	221_G	0.616	1.00
217_I	241_C	0.614	1.00
92_L	219_L	0.613	1.00
84_V	87_R	0.612	1.00
92_L	100_C	0.610	1.00
190_I	231_I	0.609	1.00
20_A	71_L	0.609	1.00
244_Q	247_Y	0.608	1.00
136_H	162_L	0.607	1.00
56_K	62_Y	0.604	1.00
204_M	246_S	0.604	1.00
6_C	44_L	0.603	1.00
145_L	153_L	0.600	1.00
138_T	201_C	0.596	1.00
53_F	67_K	0.595	1.00
187_G	207_F	0.595	1.00
8_S	44_L	0.593	1.00
128_W	131_K	0.590	1.00
112_Y	127_S	0.589	1.00
94_L	119_P	0.588	1.00
90_Q	114_D	0.586	1.00
46_N	56_K	0.585	1.00
29_E	61_Y	0.585	1.00
52_G	67_K	0.581	1.00
134_E	137_I	0.580	1.00
11_R	36_Y	0.579	1.00
14_K	17_T	0.579	1.00
87_R	248_G	0.574	1.00
143_A	205_P	0.573	1.00
237_L	241_C	0.570	1.00
143_A	203_S	0.566	1.00
112_Y	140_L	0.564	1.00
31_L	38_K	0.563	1.00
206_V	215_Y	0.562	1.00
217_I	238_L	0.561	1.00
117_E	128_W	0.561	1.00
14_K	18_H	0.560	1.00
115_K	127_S	0.559	1.00
24_M	59_N	0.558	1.00
85_T	89_M	0.556	0.99
101_H	218_S	0.555	0.99
100_C	116_I	0.554	0.99
110_A	140_L	0.554	0.99
168_N	197_Y	0.553	0.99
144_L	215_Y	0.551	0.99
16_L	71_L	0.551	0.99
142_K	191_D	0.550	0.99
17_T	71_L	0.549	0.99
188_W	239_R	0.549	0.99
12_A	44_L	0.549	0.99
115_K	129_I	0.546	0.99
234_Y	237_L	0.545	0.99
58_K	61_Y	0.545	0.99
110_A	138_T	0.545	0.99
99_V	115_K	0.542	0.99
9_L	47_V	0.542	0.99
98_L	219_L	0.540	0.99
204_M	217_I	0.540	0.99
18_H	22_V	0.540	0.99
26_S	38_K	0.538	0.99
110_A	133_L	0.537	0.99
73_C	76_L	0.537	0.99
97_G	119_P	0.537	0.99
206_V	246_S	0.536	0.99
20_A	64_L	0.535	0.99
11_R	44_L	0.534	0.99
69_Y	76_L	0.532	0.99
57_N	61_Y	0.531	0.99
174_K	177_L	0.530	0.99
164_P	167_R	0.524	0.99
103_G	138_T	0.521	0.99
42_L	56_K	0.516	0.99
206_V	245_I	0.514	0.99
162_L	166_T	0.511	0.99
207_F	215_Y	0.509	0.99
108_I	160_L	0.509	0.99
112_Y	138_T	0.507	0.99
147_W	184_R	0.506	0.99
143_A	189_A	0.506	0.99
174_K	178_E	0.505	0.99
176_F	180_L	0.504	0.99
87_R	91_E	0.502	0.99
7_N	47_V	0.502	0.99
13_E	47_V	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	0.9504	100	0.121	Contact Map
2ia2A	4	0.9466	100	0.122	Contact Map
2g7uA	6	0.9542	100	0.125	Contact Map
1mkmA	4	0.9389	100	0.127	Contact Map
3r4kA	2	0.9656	100	0.136	Contact Map
2xrnA	3	0.9122	100	0.154	Contact Map
2o0yA	4	0.9389	100	0.171	Contact Map
1ysqA	1	0.6794	100	0.418	Contact Map
1tf1A	1	0.7023	100	0.418	Contact Map
3obfA	1	0.6718	100	0.427	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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