HlyU - PFAM28P - GREMLIN Contacts

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HlyU - Transcriptional activator HlyU

PFAM:	PF10115	Sequences: SFLKKLFGGGGGAAAAKAAEPVEYKGFRIRPAPYKEGGQYQTAGVIEKEIDGEVKEHRFIRADTFASRDDAVEFSLRKAKQIIDEQGDRLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (90)
Sequences:	2404 (1694)
Seq/√Len:	178.6
META:	0.847

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_E	26_G	2.425	1.00
68_R	72_V	2.424	1.00
34_Y	41_Q	2.341	1.00
44_G	59_F	2.303	1.00
42_T	65_F	2.232	1.00
48_K	88_D	1.964	1.00
24_Y	84_D	1.957	1.00
36_E	41_Q	1.895	1.00
30_R	47_E	1.889	1.00
81_Q	85_E	1.882	1.00
59_F	82_I	1.794	1.00
67_S	70_D	1.787	1.00
47_E	56_E	1.785	1.00
70_D	73_E	1.749	1.00
69_D	73_E	1.644	1.00
25_K	84_D	1.640	1.00
21_P	30_R	1.623	1.00
65_F	74_F	1.606	1.00
41_Q	64_T	1.565	1.00
42_T	74_F	1.562	1.00
49_E	54_V	1.530	1.00
32_A	45_V	1.517	1.00
35_K	40_Y	1.491	1.00
28_R	47_E	1.471	1.00
31_P	76_L	1.448	1.00
40_Y	68_R	1.444	1.00
72_V	75_S	1.416	1.00
39_Q	64_T	1.381	1.00
30_R	45_V	1.378	1.00
39_Q	66_A	1.363	1.00
22_V	76_L	1.358	1.00
35_K	38_G	1.329	1.00
50_I	53_E	1.320	1.00
49_E	52_G	1.318	1.00
32_A	43_A	1.227	1.00
44_G	75_S	1.195	1.00
44_G	82_I	1.175	1.00
76_L	80_K	1.170	1.00
47_E	54_V	1.160	1.00
50_I	55_K	1.159	1.00
28_R	49_E	1.156	1.00
19_A	72_V	1.155	1.00
33_P	72_V	1.153	1.00
22_V	73_E	1.135	1.00
42_T	75_S	1.128	1.00
21_P	28_R	1.097	1.00
45_V	56_E	1.050	1.00
23_E	28_R	1.006	0.99
19_A	68_R	0.999	0.99
83_I	90_L	0.979	0.99
43_A	58_R	0.977	0.99
34_Y	60_I	0.964	0.99
29_I	83_I	0.927	0.99
27_F	88_D	0.925	0.99
86_Q	90_L	0.917	0.99
82_I	90_L	0.912	0.99
61_R	78_K	0.910	0.99
22_V	80_K	0.905	0.99
82_I	86_Q	0.894	0.99
7_F	10_G	0.883	0.98
65_F	75_S	0.882	0.98
9_G	12_G	0.880	0.98
2_F	5_K	0.859	0.98
73_E	77_R	0.857	0.98
86_Q	89_R	0.849	0.98
70_D	74_F	0.835	0.98
71_A	75_S	0.833	0.98
77_R	80_K	0.821	0.97
34_Y	40_Y	0.818	0.97
17_K	68_R	0.813	0.97
34_Y	58_R	0.803	0.97
76_L	83_I	0.799	0.97
18_A	21_P	0.789	0.97
36_E	39_Q	0.784	0.97
63_D	85_E	0.782	0.97
79_A	83_I	0.768	0.96
63_D	79_A	0.768	0.96
62_A	80_K	0.757	0.96
44_G	61_R	0.753	0.96
69_D	72_V	0.751	0.96
45_V	58_R	0.734	0.95
35_K	39_Q	0.727	0.95
34_Y	43_A	0.725	0.95
5_K	9_G	0.714	0.94
46_I	82_I	0.710	0.94
57_H	90_L	0.710	0.94
21_P	31_P	0.698	0.94
31_P	72_V	0.698	0.94
11_G	14_A	0.697	0.94
27_F	57_H	0.697	0.94
80_K	84_D	0.695	0.94
65_F	70_D	0.694	0.94
60_I	74_F	0.687	0.93
66_A	70_D	0.680	0.93
77_R	81_Q	0.675	0.93
44_G	78_K	0.670	0.92
27_F	91_F	0.661	0.92
27_F	48_K	0.660	0.92
74_F	77_R	0.655	0.91
2_F	8_G	0.650	0.91
27_F	50_I	0.643	0.91
4_K	7_F	0.639	0.90
13_A	16_A	0.630	0.90
28_R	54_V	0.629	0.90
75_S	82_I	0.628	0.90
63_D	78_K	0.622	0.89
24_Y	29_I	0.615	0.89
20_E	73_E	0.614	0.89
32_A	58_R	0.614	0.89
65_F	71_A	0.611	0.88
74_F	82_I	0.607	0.88
44_G	79_A	0.599	0.87
35_K	68_R	0.597	0.87
10_G	13_A	0.596	0.87
42_T	59_F	0.590	0.87
43_A	81_Q	0.589	0.86
70_D	77_R	0.586	0.86
34_Y	64_T	0.582	0.86
5_K	10_G	0.556	0.83
27_F	90_L	0.548	0.82
62_A	82_I	0.546	0.82
50_I	88_D	0.546	0.82
3_L	7_F	0.542	0.82
33_P	71_A	0.541	0.81
43_A	60_I	0.541	0.81
6_L	13_A	0.539	0.81
36_E	65_F	0.532	0.80
5_K	11_G	0.526	0.80
23_E	27_F	0.525	0.80
5_K	59_F	0.519	0.79
13_A	17_K	0.509	0.77
77_R	85_E	0.509	0.77
37_G	64_T	0.501	0.76
36_E	64_T	0.501	0.76
10_G	14_A	0.500	0.76

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
2konA	1	0.8022	75.5	0.866	Contact Map
1gtkA	1	0.7802	19.2	0.909	Contact Map
4htgA	2	0.7143	12.5	0.916	Contact Map
3lpzA	1	0.2198	11.1	0.918	Contact Map
4mlvA	1	0.7692	8.2	0.923	Contact Map
1iq8A	2	0.7802	6.7	0.926	Contact Map
4tndA	1	0	6.7	0.926	Contact Map
1eu1A	1	0.9341	4.3	0.932	Contact Map
3owaA	3	0.7802	4	0.933	Contact Map
1r2jA	1	0.9121	3.8	0.934	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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