YYBA - BACSU - GREMLIN Contacts

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YYBA - Uncharacterized HTH-type transcriptional regulator YybA

UniProt:	P37503	Sequences: MNDILREIGMIARALDSISNIEFKDLDLTRGQYLYLVRIYENPGIIQEKLAEMIKVDRTTAARAIKKLEMQGFIQKLPDEQNKKIKKLFPTEKGKKVYPLLRREGEHSTEVALSGFTSEEKETISALLHRVRKNIERDWEYVKKGNKRDY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	150 (131)
Sequences:	23486 (17163)
Seq/√Len:	1499.6

ECOLI - SLYA MPRA MARR
BACSU - YYBA YUSO YCGE YFIV YXAD MHQR YSMB YWAE YKOM YETL OHRR YDGG YPOP YWHA YDGJ YWOH YDCH YHJH YVMB YVNA YBFA
SULSO - Q97Z53 Q97YG9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_L	89_F	3.019	1.00
120_E	130_R	2.830	1.00
44_G	89_F	2.688	1.00
46_I	85_I	2.650	1.00
79_D	87_K	2.629	1.00
75_Q	89_F	2.506	1.00
123_T	127_L	2.358	1.00
117_T	120_E	2.261	1.00
78_P	86_K	2.153	1.00
123_T	126_A	2.115	1.00
40_Y	98_Y	2.039	1.00
46_I	49_K	1.995	1.00
32_Q	71_Q	1.960	1.00
40_Y	90_P	1.950	1.00
116_F	127_L	1.888	1.00
115_G	134_N	1.870	1.00
79_D	85_I	1.833	1.00
120_E	123_T	1.791	1.00
69_E	76_K	1.617	1.00
93_K	97_V	1.600	1.00
72_G	93_K	1.575	1.00
32_Q	67_K	1.538	1.00
7_E	129_H	1.506	1.00
47_Q	65_I	1.487	1.00
124_I	127_L	1.479	1.00
97_V	100_L	1.478	1.00
35_Y	64_A	1.453	1.00
66_K	70_M	1.442	1.00
42_N	53_M	1.404	1.00
65_I	88_L	1.400	1.00
120_E	126_A	1.396	1.00
29_T	32_Q	1.393	1.00
7_E	132_R	1.387	1.00
38_R	53_M	1.385	1.00
40_Y	95_K	1.358	1.00
93_K	96_K	1.342	1.00
22_E	104_E	1.317	1.00
127_L	130_R	1.275	1.00
44_G	87_K	1.269	1.00
26_L	104_E	1.265	1.00
76_K	86_K	1.253	1.00
7_E	125_S	1.240	1.00
26_L	100_L	1.204	1.00
120_E	127_L	1.179	1.00
66_K	83_K	1.160	1.00
48_E	58_R	1.153	1.00
47_Q	86_K	1.151	1.00
10_M	132_R	1.149	1.00
35_Y	61_A	1.146	1.00
49_K	52_E	1.144	1.00
56_V	60_T	1.144	1.00
57_D	60_T	1.125	1.00
48_E	52_E	1.122	1.00
20_N	24_K	1.114	1.00
126_A	130_R	1.113	1.00
125_S	129_H	1.112	1.00
42_N	45_I	1.105	1.00
59_T	62_A	1.102	1.00
104_E	107_H	1.093	1.00
11_I	132_R	1.083	1.00
47_Q	58_R	1.071	1.00
73_F	97_V	1.062	1.00
96_K	100_L	1.061	1.00
44_G	77_L	1.054	1.00
121_K	125_S	1.046	1.00
47_Q	61_A	1.033	1.00
22_E	107_H	1.013	1.00
47_Q	88_L	1.006	1.00
26_L	101_L	1.001	1.00
57_D	63_R	0.997	1.00
119_E	123_T	0.991	1.00
90_P	94_G	0.986	1.00
9_G	12_A	0.986	1.00
109_T	112_A	0.965	1.00
31_G	64_A	0.961	1.00
62_A	66_K	0.960	1.00
45_I	53_M	0.954	1.00
39_I	74_I	0.953	1.00
77_L	87_K	0.949	1.00
60_T	63_R	0.946	1.00
71_Q	97_V	0.943	1.00
11_I	128_L	0.913	1.00
56_V	61_A	0.904	1.00
43_P	95_K	0.896	1.00
73_F	93_K	0.896	1.00
92_E	95_K	0.894	1.00
66_K	69_E	0.888	1.00
12_A	16_D	0.886	1.00
40_Y	102_R	0.886	1.00
95_K	99_P	0.885	1.00
45_I	49_K	0.878	1.00
71_Q	93_K	0.873	1.00
49_K	53_M	0.871	1.00
22_E	111_V	0.868	1.00
75_Q	91_T	0.865	1.00
123_T	130_R	0.862	1.00
92_E	96_K	0.854	1.00
18_I	108_S	0.850	1.00
14_A	132_R	0.844	1.00
105_G	109_T	0.839	1.00
82_N	85_I	0.830	1.00
35_Y	50_L	0.827	1.00
25_D	104_E	0.824	1.00
36_L	98_Y	0.822	1.00
63_R	66_K	0.821	1.00
31_G	60_T	0.810	1.00
78_P	83_K	0.809	1.00
33_Y	101_L	0.809	1.00
103_R	107_H	0.805	1.00
27_D	71_Q	0.800	1.00
113_L	121_K	0.797	1.00
67_K	70_M	0.793	1.00
9_G	13_R	0.792	1.00
100_L	104_E	0.789	1.00
118_S	122_E	0.777	1.00
63_R	67_K	0.772	1.00
107_H	110_E	0.770	1.00
90_P	95_K	0.770	1.00
11_I	131_V	0.762	1.00
43_P	89_F	0.760	1.00
51_A	61_A	0.753	1.00
40_Y	99_P	0.750	1.00
111_V	114_S	0.748	1.00
38_R	54_I	0.744	1.00
42_N	49_K	0.743	1.00
129_H	133_K	0.738	1.00
65_I	74_I	0.736	1.00
79_D	82_N	0.732	1.00
117_T	121_K	0.730	1.00
19_S	22_E	0.729	1.00
51_A	58_R	0.727	1.00
13_R	17_S	0.725	1.00
122_E	125_S	0.720	1.00
38_R	42_N	0.713	1.00
8_I	12_A	0.710	1.00
69_E	75_Q	0.709	1.00
116_F	131_V	0.709	1.00
65_I	69_E	0.709	1.00
107_H	111_V	0.708	1.00
34_L	54_I	0.700	1.00
22_E	108_S	0.699	1.00
66_K	76_K	0.698	1.00
33_Y	105_G	0.692	1.00
80_E	87_K	0.690	1.00
69_E	74_I	0.689	1.00
22_E	25_D	0.688	1.00
47_Q	62_A	0.675	1.00
106_E	110_E	0.673	1.00
18_I	111_V	0.666	1.00
38_R	45_I	0.664	1.00
16_D	20_N	0.660	1.00
130_R	134_N	0.658	1.00
38_R	50_L	0.649	1.00
20_N	30_R	0.648	1.00
67_K	71_Q	0.645	1.00
61_A	65_I	0.635	1.00
96_K	99_P	0.632	1.00
76_K	88_L	0.624	1.00
35_Y	54_I	0.621	1.00
39_I	90_P	0.620	1.00
103_R	106_E	0.619	1.00
122_E	126_A	0.617	1.00
32_Q	64_A	0.613	1.00
31_G	56_V	0.612	1.00
116_F	121_K	0.612	1.00
119_E	122_E	0.607	1.00
48_E	51_A	0.599	1.00
100_L	103_R	0.592	1.00
37_V	41_E	0.589	1.00
7_E	10_M	0.582	1.00
8_I	11_I	0.575	1.00
33_Y	98_Y	0.570	1.00
127_L	134_N	0.570	1.00
102_R	106_E	0.556	1.00
68_L	73_F	0.551	1.00
19_S	105_G	0.551	1.00
34_L	38_R	0.550	1.00
108_S	111_V	0.550	1.00
105_G	108_S	0.546	1.00
116_F	130_R	0.540	1.00
39_I	45_I	0.539	1.00
37_V	102_R	0.532	1.00
113_L	117_T	0.531	1.00
126_A	129_H	0.531	1.00
48_E	85_I	0.523	1.00
99_P	103_R	0.522	1.00
98_Y	102_R	0.520	1.00
16_D	19_S	0.519	1.00
30_R	34_L	0.518	1.00
18_I	21_I	0.517	1.00
129_H	132_R	0.516	1.00
117_T	130_R	0.514	1.00
15_L	18_I	0.513	1.00
8_I	128_L	0.513	1.00
46_I	79_D	0.508	1.00
99_P	102_R	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
4mnuA	2	1	99.9	0.238	Contact Map
4rguA	4	0.94	99.9	0.269	Contact Map
1lj9A	2	0.96	99.9	0.27	Contact Map
3bj6A	2	0.9467	99.9	0.274	Contact Map
3deuA	2	0.8667	99.9	0.274	Contact Map
3cdhA	4	0.88	99.9	0.277	Contact Map
2fbkA	2	0.8667	99.9	0.278	Contact Map
3zplA	2	0.9867	99.9	0.279	Contact Map
4yifA	2	0.9267	99.9	0.279	Contact Map
3cjnA	2	0.92	99.9	0.279	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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