YWZG - BACSU - GREMLIN Contacts

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YWZG - Putative DNA-binding protein YwzG

UniProt:	C0H3S6	Sequences: MLNRELVKGSTVILVLTLLNERPMYGYELVKEMGSRSGNELQMKEGTLYPSLHKLERQGYISSYWEKQEKGPDRKYYRITDEGKEVLAERTKEWSVFSAMMDRILKWSGQNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	112 (101)
Sequences:	3189 (2128)
Seq/√Len:	211.7

ECOLI - YQJI
BACSU - YWZG YIZB
SULSO - Q981A9 Q981A0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_P	64_Y	3.771	1.00
98_S	102_D	3.436	1.00
60_Y	86_V	2.791	1.00
62_S	78_R	2.778	1.00
20_N	84_K	2.629	1.00
25_Y	76_Y	2.236	1.00
59_G	82_E	2.178	1.00
23_P	78_R	2.010	1.00
12_V	54_K	1.940	1.00
86_V	89_E	1.868	1.00
18_L	24_M	1.851	1.00
14_L	101_M	1.829	1.00
64_Y	78_R	1.823	1.00
79_I	84_K	1.747	1.00
15_V	51_S	1.731	1.00
32_E	35_S	1.725	1.00
19_L	24_M	1.718	1.00
65_W	73_D	1.649	1.00
14_L	104_I	1.642	1.00
22_R	32_E	1.630	1.00
81_D	84_K	1.621	1.00
22_R	28_E	1.603	1.00
34_G	42_Q	1.585	1.00
24_M	32_E	1.572	1.00
13_I	90_R	1.541	1.00
46_G	50_P	1.497	1.00
26_G	52_L	1.488	1.00
23_P	66_E	1.465	1.00
17_T	105_L	1.441	1.00
91_T	105_L	1.414	1.00
24_M	28_E	1.397	1.00
82_E	85_E	1.387	1.00
5_E	8_K	1.363	1.00
32_E	36_R	1.319	1.00
13_I	105_L	1.316	1.00
28_E	32_E	1.294	1.00
20_N	87_L	1.244	1.00
14_L	33_M	1.236	1.00
17_T	91_T	1.217	1.00
88_A	92_K	1.191	1.00
12_V	51_S	1.148	1.00
85_E	89_E	1.137	1.00
55_L	60_Y	1.131	1.00
56_E	61_I	1.105	1.00
56_E	63_S	1.101	1.00
88_A	91_T	1.076	1.00
25_Y	28_E	1.067	1.00
60_Y	82_E	1.065	1.00
95_S	106_K	1.056	1.00
24_M	29_L	1.054	1.00
11_T	43_M	1.051	1.00
19_L	61_I	1.042	1.00
87_L	91_T	1.038	1.00
20_N	91_T	1.022	1.00
90_R	93_E	0.985	1.00
62_S	80_T	0.971	1.00
84_K	88_A	0.964	1.00
99_A	103_R	0.963	1.00
33_M	43_M	0.943	0.99
31_K	34_G	0.889	0.99
67_K	73_D	0.882	0.99
95_S	102_D	0.865	0.99
68_Q	72_P	0.861	0.99
91_T	95_S	0.855	0.99
92_K	96_V	0.852	0.99
96_V	99_A	0.851	0.99
95_S	98_S	0.848	0.99
86_V	90_R	0.847	0.99
53_H	61_I	0.844	0.99
12_V	58_Q	0.841	0.99
30_V	48_L	0.837	0.99
94_W	101_M	0.828	0.99
17_T	87_L	0.826	0.99
67_K	72_P	0.824	0.99
85_E	88_A	0.816	0.99
51_S	90_R	0.792	0.98
21_E	36_R	0.788	0.98
17_T	20_N	0.777	0.98
34_G	39_N	0.769	0.98
35_S	106_K	0.765	0.98
95_S	99_A	0.762	0.98
26_G	77_Y	0.750	0.97
66_E	69_E	0.748	0.97
30_V	44_K	0.735	0.97
94_W	98_S	0.733	0.97
40_E	100_M	0.726	0.97
85_E	99_A	0.726	0.97
7_V	90_R	0.723	0.97
82_E	86_V	0.716	0.97
10_S	101_M	0.715	0.97
99_A	106_K	0.713	0.97
71_G	74_R	0.709	0.96
40_E	96_V	0.685	0.96
64_Y	76_Y	0.680	0.95
97_F	105_L	0.665	0.95
81_D	85_E	0.661	0.95
94_W	102_D	0.661	0.95
53_H	57_R	0.657	0.95
46_G	53_H	0.656	0.94
21_E	32_E	0.654	0.94
50_P	75_K	0.652	0.94
21_E	35_S	0.651	0.94
85_E	92_K	0.648	0.94
92_K	106_K	0.646	0.94
6_L	10_S	0.633	0.93
58_Q	86_V	0.630	0.93
31_K	45_E	0.621	0.93
65_W	79_I	0.621	0.93
68_Q	73_D	0.617	0.92
17_T	21_E	0.612	0.92
13_I	43_M	0.611	0.92
35_S	89_E	0.607	0.92
59_G	99_A	0.599	0.91
6_L	97_F	0.599	0.91
21_E	106_K	0.597	0.91
41_L	75_K	0.593	0.91
30_V	52_L	0.592	0.91
15_V	29_L	0.592	0.91
61_I	77_Y	0.580	0.90
7_V	41_L	0.574	0.90
46_G	75_K	0.573	0.89
5_E	65_W	0.571	0.89
9_G	47_T	0.567	0.89
101_M	105_L	0.565	0.89
65_W	75_K	0.563	0.89
12_V	55_L	0.562	0.89
45_E	77_Y	0.561	0.88
26_G	63_S	0.556	0.88
11_T	52_L	0.551	0.88
44_K	48_L	0.549	0.87
91_T	106_K	0.548	0.87
35_S	85_E	0.548	0.87
18_L	22_R	0.542	0.87
39_N	42_Q	0.539	0.86
17_T	70_K	0.537	0.86
89_E	92_K	0.532	0.86
30_V	46_G	0.532	0.86
11_T	46_G	0.530	0.86
18_L	32_E	0.524	0.85
92_K	103_R	0.522	0.85
92_K	95_S	0.521	0.85
25_Y	47_T	0.520	0.84
6_L	104_I	0.519	0.84
89_E	93_E	0.515	0.84
53_H	90_R	0.511	0.83
14_L	97_F	0.509	0.83
10_S	15_V	0.509	0.83
100_M	104_I	0.508	0.83
68_Q	74_R	0.508	0.83
99_A	104_I	0.505	0.83
40_E	99_A	0.504	0.83
89_E	95_S	0.500	0.82

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
1bm9A	2	0.9375	99.9	0.329	Contact Map
1xmaA	2	0.9286	99.8	0.484	Contact Map
2zfwA	2	0.8839	99.8	0.492	Contact Map
2rkhA	2	0.8571	99.8	0.494	Contact Map
2e1nA	2	0.8839	99.8	0.506	Contact Map
3l9fA	2	0.9018	99.7	0.528	Contact Map
2dqlA	2	0.9107	99.7	0.528	Contact Map
3f8bA	2	0.9375	99.7	0.532	Contact Map
3hhhA	2	0.9286	99.7	0.543	Contact Map
2eshA	2	0.9375	99.7	0.56	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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