YBBH - BACSU - GREMLIN Contacts

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YBBH - Uncharacterized HTH-type transcriptional regulator YbbH

UniProt:	Q45581	Sequences: MATGGLAIIQSMKHKLPPSERKLADYILAHPHKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQDLKMRVAGDLAKPTFQGYRDIVPHEPLPSISEKTAGNAIQAIQDTSDLMDYKELERAVSLLLKAHTVHFIGLGASGIVAKDAQQKWLRIHKQATAFTDTHLVASLIANADKDDIVFAISFSGETQEIVELFAMAKEKGITTISLTQFSQTSVSALADVPLYTAHSNEALIRSAATSSRLAQLFIIDVLFLGMAAEQYETTTGYIDKTRAAIQSMRIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	283 (255)
Sequences:	8882 (6281)
Seq/√Len:	393.3

ECOLI - RPIR MURR YFHH HEXR
BACSU - YBBH GLVR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
131_H	178_D	4.676	1.00
209_S	222_A	3.795	1.00
198_A	221_L	2.949	1.00
13_K	25_D	2.751	1.00
183_A	197_F	2.710	1.00
189_E	217_S	2.705	1.00
126_L	206_T	2.701	1.00
135_F	145_A	2.670	1.00
131_H	176_D	2.464	1.00
40_N	59_S	2.403	1.00
123_A	208_I	2.368	1.00
62_L	71_R	2.341	1.00
12_M	15_K	2.324	1.00
106_Q	110_D	2.311	1.00
201_K	223_D	2.285	1.00
197_F	207_T	2.274	1.00
123_A	224_V	2.247	1.00
148_A	152_W	2.234	1.00
132_T	158_Q	2.177	1.00
131_H	179_D	2.150	1.00
124_V	257_G	2.042	1.00
240_A	243_S	2.008	1.00
175_A	205_I	2.008	1.00
199_M	202_E	2.006	1.00
30_H	33_K	2.004	1.00
181_V	200_A	1.993	1.00
176_D	179_D	1.988	1.00
125_S	261_E	1.920	1.00
105_I	109_Q	1.905	1.00
25_D	29_A	1.894	1.00
130_A	180_I	1.879	1.00
128_L	261_E	1.829	1.00
197_F	218_V	1.827	1.00
180_I	208_I	1.820	1.00
36_E	78_K	1.816	1.00
26_Y	30_H	1.813	1.00
11_S	15_K	1.812	1.00
116_D	119_E	1.792	1.00
206_T	223_D	1.780	1.00
183_A	193_I	1.769	1.00
132_T	160_T	1.766	1.00
135_F	148_A	1.747	1.00
126_L	224_V	1.734	1.00
184_I	251_I	1.707	1.00
145_A	184_I	1.674	1.00
184_I	210_L	1.666	1.00
152_W	258_M	1.659	1.00
200_A	205_I	1.633	1.00
135_F	182_F	1.632	1.00
185_S	218_V	1.625	1.00
37_S	41_E	1.610	1.00
24_A	56_L	1.571	1.00
57_C	68_L	1.559	1.00
70_M	73_A	1.543	1.00
42_I	55_R	1.520	1.00
206_T	224_V	1.520	1.00
37_S	45_L	1.518	1.00
119_E	122_R	1.518	1.00
207_T	222_A	1.517	1.00
20_E	59_S	1.506	1.00
226_L	250_I	1.500	1.00
11_S	14_H	1.497	1.00
148_A	251_I	1.480	1.00
108_I	249_F	1.463	1.00
262_Q	265_T	1.457	1.00
209_S	218_V	1.445	1.00
101_A	108_I	1.441	1.00
122_R	224_V	1.427	1.00
209_S	225_P	1.422	1.00
181_V	205_I	1.397	1.00
136_I	181_V	1.395	1.00
42_I	58_K	1.395	1.00
219_S	225_P	1.389	1.00
23_L	56_L	1.384	1.00
144_V	251_I	1.371	1.00
67_D	70_M	1.363	1.00
257_G	261_E	1.358	1.00
149_Q	160_T	1.358	1.00
183_A	207_T	1.350	1.00
125_S	129_K	1.340	1.00
13_K	21_R	1.339	1.00
126_L	180_I	1.332	1.00
42_I	59_S	1.302	1.00
65_F	69_K	1.271	1.00
128_L	258_M	1.262	1.00
201_K	221_L	1.254	1.00
57_C	75_D	1.248	1.00
21_R	25_D	1.243	1.00
111_T	229_A	1.237	1.00
63_K	67_D	1.229	1.00
128_L	262_Q	1.221	1.00
19_S	52_A	1.215	1.00
191_Q	195_E	1.193	1.00
182_F	210_L	1.190	1.00
69_K	73_A	1.179	1.00
132_T	179_D	1.177	1.00
19_S	22_K	1.173	1.00
53_V	79_P	1.166	1.00
183_A	200_A	1.164	1.00
195_E	198_A	1.156	1.00
146_K	163_T	1.151	1.00
92_P	95_S	1.145	1.00
228_T	247_Q	1.144	1.00
151_K	252_D	1.138	1.00
62_L	65_F	1.137	1.00
38_T	41_E	1.128	1.00
122_R	126_L	1.127	1.00
129_K	206_T	1.125	1.00
68_L	72_V	1.112	1.00
39_V	54_I	1.096	1.00
142_G	146_K	1.090	1.00
127_L	180_I	1.082	1.00
123_A	126_L	1.081	1.00
266_T	269_Y	1.080	1.00
33_K	45_L	1.076	1.00
149_Q	159_A	1.074	1.00
12_M	16_L	1.074	1.00
91_E	99_K	1.065	1.00
13_K	24_A	1.064	1.00
107_A	246_A	1.060	1.00
75_D	79_P	1.057	1.00
152_W	159_A	1.056	1.00
134_H	175_A	1.048	1.00
134_H	179_D	1.042	1.00
179_D	205_I	1.041	1.00
140_A	240_A	1.038	1.00
33_K	37_S	1.035	1.00
26_Y	46_A	1.033	1.00
135_F	152_W	1.030	1.00
175_A	181_V	1.015	1.00
175_A	179_D	1.014	1.00
148_A	182_F	1.005	1.00
111_T	228_T	0.993	1.00
257_G	260_A	0.992	1.00
84_Y	87_I	0.984	1.00
39_V	43_S	0.973	1.00
61_G	64_G	0.972	1.00
16_L	42_I	0.965	1.00
134_H	160_T	0.962	1.00
158_Q	162_F	0.962	1.00
152_W	255_F	0.961	1.00
22_K	54_I	0.960	1.00
64_G	67_D	0.953	1.00
127_L	258_M	0.947	1.00
199_M	203_K	0.940	1.00
143_I	146_K	0.938	1.00
71_R	74_G	0.938	1.00
147_D	151_K	0.938	1.00
133_V	180_I	0.938	1.00
119_E	224_V	0.936	1.00
23_L	46_A	0.935	1.00
31_P	35_I	0.930	1.00
76_L	79_P	0.928	1.00
62_L	68_L	0.928	1.00
110_D	113_D	0.916	1.00
26_Y	37_S	0.916	1.00
109_Q	113_D	0.914	1.00
127_L	182_F	0.907	1.00
27_I	68_L	0.893	1.00
149_Q	153_L	0.891	1.00
125_S	128_L	0.881	1.00
198_A	202_E	0.879	1.00
126_L	129_K	0.873	1.00
98_E	112_S	0.873	1.00
127_L	133_V	0.873	1.00
117_Y	121_E	0.867	1.00
219_S	227_Y	0.863	1.00
194_V	217_S	0.861	1.00
124_V	261_E	0.859	1.00
16_L	58_K	0.858	1.00
34_A	72_V	0.857	1.00
98_E	102_G	0.851	1.00
200_A	207_T	0.850	1.00
135_F	149_Q	0.850	1.00
106_Q	109_Q	0.844	1.00
17_P	20_E	0.843	1.00
111_T	246_A	0.842	1.00
105_I	108_I	0.842	1.00
121_E	261_E	0.837	1.00
51_A	54_I	0.835	1.00
185_S	188_G	0.835	1.00
147_D	244_R	0.833	1.00
162_F	170_S	0.832	1.00
94_P	98_E	0.830	1.00
97_S	117_Y	0.827	1.00
67_D	71_R	0.825	1.00
149_Q	161_A	0.823	1.00
211_T	219_S	0.819	1.00
42_I	53_V	0.816	1.00
26_Y	33_K	0.814	1.00
94_P	117_Y	0.803	1.00
144_V	184_I	0.801	1.00
129_K	178_D	0.800	1.00
134_H	181_V	0.799	1.00
40_N	50_D	0.796	1.00
154_R	171_L	0.793	1.00
130_A	179_D	0.791	1.00
123_A	226_L	0.787	1.00
54_I	64_G	0.786	1.00
42_I	65_F	0.785	1.00
35_I	38_T	0.781	1.00
127_L	130_A	0.781	1.00
122_R	125_S	0.779	1.00
83_G	86_D	0.779	1.00
142_G	163_T	0.773	1.00
194_V	198_A	0.770	1.00
124_V	128_L	0.768	1.00
26_Y	45_L	0.766	1.00
19_S	58_K	0.763	1.00
155_I	255_F	0.761	1.00
142_G	161_A	0.757	1.00
214_S	227_Y	0.755	1.00
123_A	254_L	0.755	1.00
65_F	68_L	0.754	1.00
23_L	52_A	0.753	1.00
180_I	206_T	0.749	1.00
133_V	182_F	0.748	1.00
64_G	68_L	0.747	1.00
166_H	192_E	0.743	1.00
93_L	102_G	0.743	1.00
52_A	55_R	0.741	1.00
131_H	158_Q	0.737	1.00
57_C	72_V	0.729	1.00
135_F	159_A	0.728	1.00
22_K	47_N	0.727	1.00
132_T	176_D	0.726	1.00
210_L	251_I	0.722	1.00
17_P	59_S	0.718	1.00
138_L	190_T	0.712	1.00
241_T	244_R	0.706	1.00
178_D	206_T	0.706	1.00
70_M	74_G	0.705	1.00
55_R	59_S	0.705	1.00
182_F	208_I	0.703	1.00
152_W	254_L	0.702	1.00
35_I	73_A	0.701	1.00
119_E	123_A	0.699	1.00
151_K	255_F	0.698	1.00
255_F	259_A	0.697	1.00
101_A	249_F	0.694	1.00
11_S	16_L	0.693	1.00
246_A	249_F	0.685	0.99
95_S	98_E	0.685	0.99
148_A	151_K	0.684	0.99
74_G	77_A	0.681	0.99
146_K	149_Q	0.678	0.99
238_S	241_T	0.674	0.99
93_L	121_E	0.674	0.99
118_K	121_E	0.673	0.99
56_L	60_L	0.672	0.99
189_E	212_Q	0.671	0.99
224_V	227_Y	0.671	0.99
173_A	199_M	0.670	0.99
162_F	171_L	0.670	0.99
137_G	141_S	0.669	0.99
57_C	64_G	0.668	0.99
27_I	56_L	0.666	0.99
41_E	44_A	0.666	0.99
14_H	21_R	0.666	0.99
111_T	114_L	0.661	0.99
183_A	196_L	0.659	0.99
82_Q	86_D	0.657	0.99
116_D	120_L	0.655	0.99
157_K	262_Q	0.652	0.99
96_I	99_K	0.648	0.99
66_Q	69_K	0.644	0.99
115_M	120_L	0.644	0.99
144_V	248_L	0.644	0.99
153_L	170_S	0.643	0.99
38_T	43_S	0.642	0.99
16_L	59_S	0.641	0.99
114_L	229_A	0.641	0.99
50_D	54_I	0.640	0.99
260_A	267_T	0.639	0.99
104_A	249_F	0.638	0.99
194_V	218_V	0.635	0.99
197_F	221_L	0.635	0.99
23_L	48_S	0.634	0.99
222_A	225_P	0.633	0.99
120_L	253_V	0.630	0.99
244_R	247_Q	0.626	0.99
31_P	34_A	0.626	0.99
244_R	248_L	0.623	0.99
217_S	221_L	0.619	0.99
62_L	67_D	0.618	0.99
34_A	37_S	0.618	0.99
101_A	104_A	0.616	0.99
55_R	58_K	0.614	0.99
121_E	257_G	0.612	0.99
211_T	216_T	0.611	0.99
24_A	28_L	0.608	0.99
168_V	195_E	0.608	0.99
22_K	53_V	0.608	0.99
23_L	53_V	0.605	0.99
249_F	252_D	0.603	0.99
110_D	114_L	0.602	0.99
146_K	161_A	0.599	0.99
22_K	50_D	0.597	0.99
61_G	74_G	0.596	0.99
144_V	247_Q	0.595	0.99
111_T	250_I	0.595	0.99
136_I	183_A	0.594	0.99
104_A	245_L	0.593	0.98
81_F	84_Y	0.590	0.98
208_I	224_V	0.587	0.98
20_E	68_L	0.586	0.98
17_P	42_I	0.585	0.98
102_G	106_Q	0.581	0.98
216_T	219_S	0.581	0.98
82_Q	85_R	0.580	0.98
83_G	87_I	0.574	0.98
177_K	204_G	0.570	0.98
136_I	175_A	0.568	0.98
237_R	240_A	0.567	0.98
183_A	209_S	0.564	0.98
195_E	199_M	0.563	0.98
141_S	247_Q	0.563	0.98
228_T	246_A	0.562	0.98
228_T	250_I	0.559	0.98
27_I	34_A	0.558	0.98
77_A	80_T	0.558	0.98
85_R	88_V	0.557	0.98
41_E	45_L	0.556	0.98
37_S	42_I	0.556	0.98
148_A	255_F	0.555	0.98
87_I	99_K	0.554	0.98
120_L	257_G	0.554	0.98
197_F	222_A	0.550	0.98
45_L	55_R	0.548	0.97
209_S	216_T	0.548	0.97
157_K	258_M	0.548	0.97
253_V	256_L	0.548	0.97
256_L	260_A	0.546	0.97
100_T	249_F	0.546	0.97
260_A	264_E	0.546	0.97
123_A	182_F	0.545	0.97
232_N	236_I	0.544	0.97
60_L	78_K	0.543	0.97
100_T	104_A	0.543	0.97
83_G	88_V	0.541	0.97
210_L	250_I	0.540	0.97
144_V	228_T	0.539	0.97
135_F	161_A	0.538	0.97
263_Y	266_T	0.538	0.97
150_Q	170_S	0.537	0.97
194_V	221_L	0.535	0.97
219_S	222_A	0.535	0.97
57_C	62_L	0.534	0.97
135_F	184_I	0.532	0.97
110_D	229_A	0.532	0.97
201_K	207_T	0.532	0.97
186_F	228_T	0.531	0.97
137_G	142_G	0.530	0.97
40_N	44_A	0.530	0.97
259_A	266_T	0.528	0.97
137_G	192_E	0.526	0.97
20_E	61_G	0.526	0.97
185_S	216_T	0.525	0.97
102_G	105_I	0.522	0.97
256_L	259_A	0.522	0.97
81_F	85_R	0.521	0.97
101_A	253_V	0.520	0.97
187_S	190_T	0.515	0.96
185_S	209_S	0.514	0.96
26_Y	34_A	0.514	0.96
124_V	258_M	0.513	0.96
46_A	53_V	0.512	0.96
237_R	243_S	0.512	0.96
138_L	192_E	0.512	0.96
254_L	258_M	0.511	0.96
264_E	267_T	0.511	0.96
66_Q	70_M	0.509	0.96
105_I	112_S	0.508	0.96
211_T	225_P	0.505	0.96
102_G	109_Q	0.504	0.96
96_I	100_T	0.504	0.96
126_L	130_A	0.503	0.96
166_H	169_A	0.502	0.96
131_H	177_K	0.501	0.96
71_R	75_D	0.501	0.96
226_L	254_L	0.501	0.96
262_Q	266_T	0.500	0.96

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
4ivnA	2	0.9329	100	0.184	Contact Map
3shoA	4	0.6572	100	0.508	Contact Map
2xhzA	4	0.6078	100	0.54	Contact Map
3fxaA	4	0.6643	100	0.548	Contact Map
3etnA	4	0.6537	100	0.553	Contact Map
2pocA	4	0.6678	100	0.558	Contact Map
3tbfA	2	0.6855	100	0.564	Contact Map
1moqA	2	0.6784	100	0.565	Contact Map
1m3sA	4	0.6325	99.9	0.568	Contact Map
1vimA	4	0.6537	99.9	0.571	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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