YBIH - ECOLI - GREMLIN Contacts

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YBIH - Uncharacterized HTH-type transcriptional regulator YbiH

UniProt:	P0ACU0	Sequences: MNNPAMTIKGEQAKKQLIAAALAQFGEYGMNATTREIAAQAGQNIAAITYYFGSKEDLYLACAQWIADFIGEQFRPHAEEAERLFAQPQPDRAAIRELILRACRNMIKLLTQDDTVNLSKFISREQLSPTAAYHLVHEQVISPLHSHLTRLIAAWTGCDANDTRMILHTHALIGEILAFRLGKETILLRTGWTAFDEEKTELINQTVTCHIDLILQGLSQRSL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12406
Length:	223 (181)
Sequences:	34661 (27305)
Seq/√Len:	2029.5

ECOLI - YBIH RUTR FABR BDCR BETI ACRR COMR ENVR UIDR NEMR SLMA YJDC RCDA
BACSU - YFIR YTTP FADR YHGD YVDT BSCR PKSA YVKB YVAF LMRA YCNC YDES YXAF YEZE YOBS YUXN YDGC YERO
HALSA - Q9HRF3
SULSO - Q97VV1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_R	45_I	3.906	1.00
28_Y	36_E	3.887	1.00
23_A	40_Q	3.585	1.00
53_G	57_D	2.677	1.00
25_F	32_A	2.416	1.00
54_S	57_D	2.274	1.00
149_T	166_I	2.257	1.00
24_Q	32_A	2.192	1.00
20_A	40_Q	2.126	1.00
24_Q	40_Q	2.116	1.00
13_A	16_Q	2.090	1.00
24_Q	36_E	2.075	1.00
24_Q	28_Y	2.034	1.00
15_K	65_W	2.017	1.00
27_E	40_Q	1.976	1.00
38_A	48_I	1.970	1.00
149_T	153_A	1.818	1.00
35_R	39_A	1.807	1.00
90_P	93_A	1.792	1.00
94_A	154_A	1.781	1.00
44_N	47_A	1.762	1.00
153_A	165_M	1.760	1.00
14_K	61_A	1.744	1.00
21_A	25_F	1.717	1.00
22_L	65_W	1.705	1.00
20_A	23_A	1.697	1.00
16_Q	20_A	1.695	1.00
15_K	19_A	1.672	1.00
29_G	32_A	1.587	1.00
34_T	49_T	1.578	1.00
18_I	61_A	1.562	1.00
36_E	40_Q	1.532	1.00
153_A	157_G	1.522	1.00
61_A	64_Q	1.505	1.00
34_T	45_I	1.503	1.00
22_L	62_C	1.493	1.00
36_E	39_A	1.462	1.00
23_A	27_E	1.457	1.00
156_T	162_D	1.456	1.00
32_A	37_I	1.434	1.00
65_W	69_F	1.420	1.00
171_A	175_E	1.413	1.00
22_L	66_I	1.411	1.00
12_Q	16_Q	1.383	1.00
21_A	58_L	1.378	1.00
75_R	147_H	1.377	1.00
60_L	64_Q	1.371	1.00
47_A	50_Y	1.362	1.00
153_A	156_T	1.361	1.00
64_Q	136_V	1.349	1.00
33_T	36_E	1.343	1.00
14_K	51_Y	1.341	1.00
155_W	160_A	1.332	1.00
34_T	48_I	1.331	1.00
52_F	61_A	1.302	1.00
49_T	54_S	1.299	1.00
20_A	24_Q	1.282	1.00
25_F	30_M	1.278	1.00
45_I	49_T	1.275	1.00
19_A	65_W	1.262	1.00
12_Q	15_K	1.247	1.00
93_A	97_E	1.243	1.00
156_T	163_T	1.218	1.00
43_Q	47_A	1.216	1.00
30_M	59_Y	1.202	1.00
57_D	61_A	1.192	1.00
145_H	170_H	1.186	1.00
18_I	52_F	1.181	1.00
164_R	167_L	1.177	1.00
21_A	62_C	1.161	1.00
60_L	136_V	1.157	1.00
145_H	149_T	1.156	1.00
73_Q	101_R	1.143	1.00
154_A	158_C	1.141	1.00
47_A	51_Y	1.138	1.00
96_R	100_L	1.129	1.00
23_A	117_N	1.116	1.00
18_I	62_C	1.107	1.00
56_E	60_L	1.105	1.00
20_A	41_A	1.102	1.00
174_G	178_A	1.101	1.00
122_I	125_E	1.095	1.00
57_D	60_L	1.092	1.00
156_T	159_D	1.089	1.00
22_L	26_G	1.082	1.00
13_A	51_Y	1.072	1.00
10_G	50_Y	1.072	1.00
90_P	160_A	1.068	1.00
48_I	58_L	1.044	1.00
163_T	168_H	1.043	1.00
142_S	146_S	1.039	1.00
151_L	155_W	1.038	1.00
117_N	120_K	1.032	1.00
94_A	151_L	1.025	1.00
46_A	50_Y	1.023	1.00
44_N	50_Y	1.016	1.00
28_Y	40_Q	1.012	1.00
150_R	154_A	1.007	1.00
37_I	58_L	1.004	1.00
65_W	68_D	1.003	1.00
64_Q	68_D	1.001	1.00
13_A	43_Q	1.000	1.00
147_H	150_R	1.000	1.00
89_Q	97_E	0.999	1.00
19_A	23_A	0.994	1.00
92_R	96_R	0.982	1.00
75_R	79_E	0.978	1.00
136_V	139_Q	0.977	1.00
97_E	100_L	0.973	1.00
145_H	166_I	0.971	1.00
56_E	130_T	0.961	1.00
73_Q	76_P	0.960	1.00
139_Q	143_P	0.957	1.00
149_T	165_M	0.956	1.00
61_A	65_W	0.930	1.00
45_I	50_Y	0.928	1.00
199_K	202_L	0.917	1.00
93_A	96_R	0.903	1.00
77_H	97_E	0.898	1.00
149_T	169_T	0.885	1.00
16_Q	19_A	0.885	1.00
156_T	165_M	0.880	1.00
71_G	143_P	0.879	1.00
56_E	132_A	0.875	1.00
11_E	15_K	0.873	1.00
77_H	101_R	0.868	1.00
113_D	116_V	0.868	1.00
161_N	164_R	0.865	1.00
151_L	154_A	0.865	1.00
166_I	170_H	0.862	1.00
183_K	186_I	0.861	1.00
39_A	45_I	0.856	1.00
150_R	153_A	0.853	1.00
68_D	72_E	0.846	1.00
8_I	12_Q	0.844	1.00
146_S	149_T	0.843	1.00
38_A	45_I	0.842	1.00
66_I	69_F	0.838	1.00
88_P	94_A	0.837	1.00
26_G	117_N	0.836	1.00
134_H	138_E	0.834	1.00
120_K	124_R	0.829	1.00
17_L	48_I	0.825	1.00
146_S	150_R	0.819	1.00
91_D	155_W	0.813	1.00
9_K	12_Q	0.806	1.00
135_L	139_Q	0.805	1.00
101_R	104_R	0.802	1.00
24_Q	27_E	0.800	1.00
118_L	121_F	0.796	1.00
99_I	172_L	0.794	1.00
18_I	22_L	0.787	1.00
69_F	72_E	0.786	1.00
100_L	104_R	0.782	1.00
105_N	115_T	0.773	1.00
143_P	146_S	0.772	1.00
28_Y	32_A	0.770	1.00
35_R	49_T	0.766	1.00
8_I	11_E	0.764	1.00
72_E	75_R	0.762	1.00
197_E	201_E	0.762	1.00
198_E	202_L	0.757	1.00
97_E	101_R	0.757	1.00
100_L	197_E	0.754	1.00
72_E	76_P	0.750	1.00
16_Q	41_A	0.744	1.00
138_E	142_S	0.742	1.00
195_F	198_E	0.740	1.00
196_D	199_K	0.740	1.00
154_A	157_G	0.737	1.00
115_T	118_L	0.737	1.00
89_Q	93_A	0.735	1.00
100_L	196_D	0.732	1.00
131_A	134_H	0.726	1.00
10_G	13_A	0.721	1.00
31_N	128_S	0.715	1.00
143_P	147_H	0.713	1.00
64_Q	140_V	0.711	1.00
119_S	122_I	0.708	1.00
71_G	75_R	0.706	1.00
167_L	202_L	0.704	1.00
101_R	105_N	0.702	1.00
167_L	171_A	0.701	1.00
91_D	158_C	0.696	1.00
102_A	106_M	0.693	1.00
64_Q	139_Q	0.690	1.00
164_R	168_H	0.690	1.00
136_V	140_V	0.689	1.00
19_A	22_L	0.687	1.00
71_G	147_H	0.686	1.00
78_A	147_H	0.685	1.00
124_R	128_S	0.685	1.00
41_A	44_N	0.684	1.00
18_I	65_W	0.682	1.00
9_K	13_A	0.681	1.00
120_K	123_S	0.680	1.00
116_V	119_S	0.675	1.00
30_M	56_E	0.670	1.00
38_A	43_Q	0.666	1.00
198_E	201_E	0.665	1.00
152_I	172_L	0.664	1.00
96_R	201_E	0.664	1.00
35_R	44_N	0.663	1.00
171_A	174_G	0.661	1.00
121_F	125_E	0.660	1.00
25_F	59_Y	0.658	1.00
96_R	99_I	0.652	1.00
17_L	41_A	0.651	1.00
99_I	102_A	0.643	1.00
13_A	47_A	0.641	1.00
34_T	38_A	0.638	1.00
13_A	44_N	0.637	1.00
121_F	124_R	0.635	1.00
34_T	55_K	0.631	1.00
156_T	161_N	0.629	1.00
174_G	177_L	0.629	1.00
177_L	181_L	0.626	1.00
27_E	36_E	0.624	1.00
182_G	185_T	0.623	1.00
88_P	93_A	0.621	1.00
30_M	55_K	0.620	1.00
10_G	51_Y	0.619	1.00
117_N	121_F	0.613	1.00
116_V	120_K	0.612	1.00
165_M	169_T	0.600	1.00
182_G	186_I	0.600	1.00
120_K	125_E	0.597	1.00
174_G	182_G	0.593	1.00
131_A	135_L	0.592	1.00
167_L	170_H	0.584	1.00
119_S	123_S	0.582	1.00
17_L	51_Y	0.581	1.00
196_D	200_T	0.580	1.00
91_D	94_A	0.579	1.00
129_P	132_A	0.575	1.00
90_P	94_A	0.575	1.00
94_A	155_W	0.574	1.00
79_E	87_Q	0.574	1.00
152_I	165_M	0.573	1.00
24_Q	33_T	0.573	1.00
76_P	101_R	0.563	1.00
41_A	45_I	0.563	1.00
31_N	125_E	0.558	1.00
135_L	138_E	0.557	1.00
152_I	156_T	0.556	1.00
168_H	171_A	0.555	1.00
69_F	73_Q	0.553	1.00
138_E	141_I	0.551	1.00
170_H	182_G	0.546	1.00
132_A	135_L	0.544	1.00
48_I	53_G	0.543	1.00
22_L	69_F	0.541	1.00
102_A	144_L	0.541	1.00
195_F	199_K	0.535	1.00
147_H	151_L	0.533	1.00
68_D	140_V	0.531	1.00
141_I	144_L	0.526	1.00
184_E	187_L	0.525	1.00
153_A	166_I	0.524	1.00
76_P	79_E	0.524	1.00
87_Q	97_E	0.516	1.00
88_P	97_E	0.511	1.00
183_K	187_L	0.511	1.00
155_W	158_C	0.508	1.00
116_V	121_F	0.507	1.00
194_A	198_E	0.506	1.00
175_E	179_F	0.504	1.00
98_L	102_A	0.504	1.00
16_Q	43_Q	0.503	1.00
69_F	115_T	0.501	1.00
38_A	41_A	0.501	1.00
129_P	133_Y	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
4jykA	2	0.8924	100	0.272	Contact Map
1t33A	2	0.9731	100	0.272	Contact Map
3npiA	2	0.9013	100	0.279	Contact Map
3nrgA	2	0.9238	100	0.284	Contact Map
3f0cA	2	0.8565	100	0.289	Contact Map
2qtqA	2	0.8969	100	0.294	Contact Map
2hyjA	2	0.8341	100	0.296	Contact Map
3on2A	1	0.861	100	0.297	Contact Map
1rktA	2	0.8879	100	0.3	Contact Map
3f1bA	2	0.8161	100	0.301	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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