YUGG - BACSU - GREMLIN Contacts

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YUGG - Uncharacterized HTH-type transcriptional regulator YugG

UniProt:	O05236	Sequences: MKLTEKETEILEILDENSRADLETIAKMAGIPVNEVKTIIDKLEKEKVIIDYSAMIDWRKVDGHEGVTAMIDVKVTPKRGVGFDEVAERIYRFQEVESVYLMSGVYDLSVVIRGNSMSDVARFVSDKLSTLDSVVSTTTHFILKKYKHDGKVFETGDDDKRIVVSP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	166 (140)
Sequences:	13130 (8543)
Seq/√Len:	722.0

ECOLI - LRP ASNC YBAO
BACSU - YUGG AZLB LRPB YWRC LRPC YEZC LRPA
HALSA - Q9HNI1 Q9HQ13 Q9HQ33 Q9HQB6 Q9HP41 Q9HQG1 Q9HP70 Q9HNW8
SULSO - Q7LXS6 Q7LX67 Q97W90 Q97XP7 LYSM Q97X78 Q980P3 Q97VN7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_E	52_Y	2.949	1.00
13_I	28_M	2.910	1.00
74_K	136_S	2.586	1.00
105_V	138_T	2.581	1.00
98_S	111_V	2.567	1.00
22_L	40_I	2.334	1.00
115_N	119_D	2.301	1.00
13_I	20_A	2.127	1.00
59_R	118_S	2.110	1.00
50_I	57_D	2.080	1.00
7_E	39_I	2.043	1.00
42_K	46_E	2.041	1.00
76_T	135_V	1.969	1.00
70_M	100_Y	1.803	1.00
93_F	127_K	1.793	1.00
68_T	111_V	1.758	1.00
50_I	55_M	1.750	1.00
6_K	31_I	1.748	1.00
97_E	113_R	1.708	1.00
72_D	140_H	1.694	1.00
41_D	45_K	1.688	1.00
93_F	123_F	1.675	1.00
13_I	16_E	1.671	1.00
31_I	35_E	1.660	1.00
62_D	65_E	1.655	1.00
116_S	119_D	1.569	1.00
20_A	28_M	1.544	1.00
23_E	27_K	1.538	1.00
86_V	90_I	1.529	1.00
24_T	27_K	1.527	1.00
23_E	33_V	1.519	1.00
89_R	131_L	1.512	1.00
119_D	122_R	1.490	1.00
32_P	35_E	1.488	1.00
31_I	36_V	1.477	1.00
22_L	37_K	1.447	1.00
89_R	92_R	1.440	1.00
10_I	25_I	1.428	1.00
87_A	91_Y	1.394	1.00
122_R	126_D	1.392	1.00
73_V	110_V	1.378	1.00
29_A	36_V	1.374	1.00
95_E	119_D	1.371	1.00
19_R	52_Y	1.351	1.00
72_D	106_Y	1.339	1.00
20_A	25_I	1.335	1.00
71_I	112_I	1.309	1.00
145_K	148_H	1.306	1.00
5_E	9_E	1.302	1.00
74_K	135_V	1.292	1.00
14_L	40_I	1.280	1.00
74_K	105_V	1.268	1.00
84_D	88_E	1.262	1.00
79_R	85_E	1.231	1.00
95_E	127_K	1.227	1.00
121_A	144_K	1.220	1.00
24_T	28_M	1.215	1.00
41_D	44_E	1.201	1.00
65_E	115_N	1.193	1.00
87_A	144_K	1.186	1.00
67_V	117_M	1.184	1.00
21_D	24_T	1.182	1.00
4_T	39_I	1.172	1.00
17_N	28_M	1.163	1.00
16_E	28_M	1.162	1.00
75_V	86_V	1.156	1.00
13_I	25_I	1.155	1.00
6_K	9_E	1.134	1.00
6_K	29_A	1.106	1.00
72_D	138_T	1.090	1.00
68_T	113_R	1.076	1.00
87_A	108_L	1.058	1.00
20_A	24_T	1.053	1.00
51_D	55_M	1.048	1.00
9_E	12_E	1.048	1.00
22_L	26_A	1.024	1.00
99_V	110_V	1.024	1.00
9_E	13_I	0.997	1.00
85_E	89_R	0.974	1.00
96_V	112_I	0.973	1.00
19_R	44_E	0.960	1.00
88_E	91_Y	0.958	1.00
57_D	60_K	0.951	1.00
66_G	116_S	0.951	1.00
26_A	36_V	0.944	1.00
33_V	37_K	0.942	1.00
18_S	52_Y	0.942	1.00
114_G	119_D	0.936	1.00
70_M	109_S	0.935	1.00
114_G	120_V	0.931	1.00
22_L	33_V	0.924	1.00
102_M	109_S	0.920	1.00
12_E	16_E	0.917	1.00
9_E	29_A	0.899	1.00
100_Y	111_V	0.899	1.00
70_M	111_V	0.895	1.00
37_K	41_D	0.892	1.00
114_G	123_F	0.891	1.00
112_I	123_F	0.890	1.00
3_L	8_T	0.887	1.00
26_A	31_I	0.872	1.00
7_E	42_K	0.827	1.00
88_E	92_R	0.815	1.00
43_L	48_V	0.815	1.00
100_Y	142_I	0.814	1.00
96_V	99_V	0.809	1.00
23_E	37_K	0.805	1.00
58_W	113_R	0.802	1.00
18_S	24_T	0.795	1.00
90_I	99_V	0.791	1.00
70_M	142_I	0.781	1.00
73_V	86_V	0.778	1.00
61_V	65_E	0.777	1.00
25_I	36_V	0.770	1.00
100_Y	145_K	0.767	1.00
89_R	93_F	0.757	1.00
96_V	110_V	0.754	1.00
76_T	79_R	0.747	1.00
72_D	109_S	0.746	1.00
122_R	127_K	0.745	1.00
8_T	12_E	0.743	1.00
85_E	88_E	0.742	1.00
105_V	136_S	0.741	1.00
83_F	108_L	0.741	1.00
10_I	39_I	0.741	1.00
17_N	20_A	0.737	1.00
124_V	139_T	0.736	1.00
18_S	54_A	0.729	1.00
25_I	40_I	0.726	1.00
4_T	7_E	0.723	1.00
106_Y	138_T	0.719	1.00
72_D	105_V	0.715	1.00
48_V	60_K	0.707	1.00
84_D	87_A	0.702	1.00
34_N	38_T	0.698	1.00
10_I	36_V	0.696	1.00
129_S	137_T	0.695	1.00
117_M	141_F	0.694	1.00
87_A	146_Y	0.689	1.00
38_T	42_K	0.687	1.00
90_I	110_V	0.679	1.00
10_I	20_A	0.677	1.00
71_I	137_T	0.676	1.00
86_V	108_L	0.673	1.00
101_L	108_L	0.671	1.00
74_K	106_Y	0.671	1.00
69_A	120_V	0.664	1.00
26_A	33_V	0.658	1.00
103_S	141_F	0.652	1.00
76_T	133_S	0.643	1.00
5_E	8_T	0.642	1.00
95_E	123_F	0.634	1.00
71_I	110_V	0.633	1.00
13_I	17_N	0.630	1.00
85_E	133_S	0.629	1.00
124_V	137_T	0.628	1.00
10_I	13_I	0.625	1.00
68_T	145_K	0.619	1.00
118_S	121_A	0.619	1.00
34_N	37_K	0.615	1.00
38_T	41_D	0.615	1.00
18_S	51_D	0.614	1.00
118_S	122_R	0.610	1.00
57_D	61_V	0.608	1.00
11_L	43_L	0.607	1.00
47_K	50_I	0.606	1.00
68_T	142_I	0.603	1.00
39_I	43_L	0.603	1.00
119_D	123_F	0.598	1.00
69_A	141_F	0.595	1.00
22_L	36_V	0.589	1.00
3_L	48_V	0.588	1.00
7_E	43_L	0.586	1.00
123_F	127_K	0.583	1.00
49_I	52_Y	0.583	1.00
56_I	61_V	0.574	1.00
93_F	131_L	0.571	1.00
65_E	113_R	0.570	1.00
73_V	134_V	0.564	1.00
89_R	132_D	0.562	1.00
95_E	115_N	0.562	1.00
10_I	40_I	0.561	1.00
10_I	43_L	0.555	1.00
65_E	95_E	0.552	1.00
79_R	132_D	0.551	1.00
102_M	106_Y	0.547	1.00
68_T	100_Y	0.545	1.00
15_D	53_S	0.539	1.00
62_D	115_N	0.534	1.00
89_R	133_S	0.533	1.00
6_K	35_E	0.533	1.00
72_D	102_M	0.527	1.00
98_S	148_H	0.526	1.00
123_F	128_L	0.520	1.00
120_V	141_F	0.517	1.00
73_V	137_T	0.517	1.00
93_F	96_V	0.515	1.00
69_A	139_T	0.513	1.00
74_K	138_T	0.512	1.00
85_E	132_D	0.510	1.00
102_M	140_H	0.509	1.00
55_M	58_W	0.508	1.00
127_K	131_L	0.508	1.00
124_V	143_L	0.507	1.00
117_M	143_L	0.507	1.00
129_S	136_S	0.506	0.99
101_L	121_A	0.505	0.99
62_D	66_G	0.503	0.99
83_F	129_S	0.500	0.99
75_V	107_D	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
4ch7A	1	0.9217	100	0.172	Contact Map
4un1B	1	0.8976	100	0.208	Contact Map
4un1A	1	0.8554	100	0.224	Contact Map
2e1cA	1	0.8855	100	0.236	Contact Map
4pcqA	2	0.8976	100	0.238	Contact Map
2p5vA	5	0.9337	100	0.244	Contact Map
2ia0A	2	0.9157	100	0.256	Contact Map
3i4pA	5	0.9217	100	0.269	Contact Map
2cg4A	6	0.8916	100	0.273	Contact Map
2pn6A	5	0.8855	100	0.282	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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