DBH1 - BACSU - GREMLIN Contacts

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DBH1 - DNA-binding protein HU 1

UniProt:	P08821	Sequences: MNKTELINAVAEASELSKKDATKAVDSVFDTILDALKNGDKIQLIGFGNFEVRERSARKGRNPQTGEEIEIPASKVPAFKPGKALKDAVAGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	92 (90)
Sequences:	4799 (2718)
Seq/√Len:	286.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_R	78_A	3.318	1.00
59_K	68_E	2.755	1.00
35_A	40_D	2.693	1.00
22_T	26_D	2.497	1.00
54_E	75_K	2.399	1.00
57_A	70_E	2.367	1.00
61_R	66_G	2.253	1.00
59_K	70_E	2.166	1.00
52_V	75_K	2.071	1.00
60_G	71_I	2.050	1.00
8_N	18_K	2.022	1.00
20_D	23_K	1.953	1.00
83_K	87_D	1.891	1.00
10_V	25_V	1.845	1.00
61_R	68_E	1.844	1.00
19_K	23_K	1.773	1.00
54_E	73_A	1.716	1.00
28_V	32_I	1.625	1.00
36_L	85_L	1.578	1.00
51_E	80_K	1.568	1.00
41_K	49_N	1.554	1.00
36_L	52_V	1.525	1.00
55_R	76_V	1.477	1.00
41_K	51_E	1.413	1.00
17_S	20_D	1.391	1.00
33_L	85_L	1.371	1.00
10_V	28_V	1.354	1.00
45_I	82_G	1.324	1.00
9_A	13_A	1.321	1.00
21_A	24_A	1.277	1.00
6_L	44_L	1.253	1.00
57_A	73_A	1.186	1.00
9_A	31_T	1.171	1.00
16_L	21_A	1.166	1.00
74_S	90_A	1.164	1.00
16_L	24_A	1.136	1.00
3_K	26_D	1.133	1.00
32_I	42_I	1.095	1.00
13_A	34_D	1.088	1.00
48_G	79_F	1.082	1.00
33_L	88_A	1.056	1.00
13_A	31_T	1.048	1.00
34_D	38_N	1.024	1.00
39_G	75_K	1.023	1.00
29_F	47_F	1.004	1.00
30_D	33_L	0.998	1.00
9_A	12_E	0.996	1.00
43_Q	49_N	0.992	1.00
31_T	35_A	0.984	1.00
29_F	44_L	0.963	1.00
14_S	21_A	0.959	1.00
37_K	88_A	0.938	1.00
25_V	29_F	0.895	1.00
27_S	31_T	0.891	1.00
8_N	12_E	0.888	1.00
10_V	14_S	0.877	1.00
5_E	8_N	0.877	1.00
1_M	5_E	0.875	1.00
64_Q	67_E	0.870	1.00
51_E	78_A	0.861	1.00
16_L	20_D	0.848	1.00
74_S	86_K	0.840	1.00
62_N	67_E	0.823	1.00
47_F	50_F	0.821	1.00
28_V	31_T	0.816	1.00
58_R	76_V	0.809	0.99
47_F	82_G	0.797	0.99
55_R	74_S	0.795	0.99
34_D	37_K	0.780	0.99
36_L	77_P	0.776	0.99
13_A	30_D	0.770	0.99
77_P	89_V	0.768	0.99
2_N	5_E	0.758	0.99
10_V	24_A	0.751	0.99
61_R	64_Q	0.745	0.99
84_A	87_D	0.743	0.99
60_G	69_I	0.725	0.99
49_N	80_K	0.716	0.99
35_A	38_N	0.707	0.99
62_N	66_G	0.694	0.98
35_A	42_I	0.693	0.98
77_P	86_K	0.693	0.98
24_A	31_T	0.691	0.98
11_A	14_S	0.688	0.98
43_Q	58_R	0.684	0.98
77_P	85_L	0.676	0.98
31_T	34_D	0.673	0.98
23_K	27_S	0.673	0.98
50_F	79_F	0.667	0.98
7_I	22_T	0.667	0.98
4_T	8_N	0.661	0.98
33_L	37_K	0.661	0.98
13_A	27_S	0.653	0.98
45_I	84_A	0.652	0.98
57_A	72_P	0.651	0.98
30_D	34_D	0.650	0.98
38_N	54_E	0.648	0.98
60_G	68_E	0.641	0.97
22_T	41_K	0.631	0.97
26_D	30_D	0.630	0.97
17_S	21_A	0.625	0.97
15_E	23_K	0.624	0.97
55_R	58_R	0.621	0.97
49_N	82_G	0.614	0.97
53_R	76_V	0.609	0.96
39_G	54_E	0.608	0.96
29_F	33_L	0.597	0.96
34_D	54_E	0.591	0.96
19_K	22_T	0.580	0.95
10_V	21_A	0.576	0.95
27_S	30_D	0.572	0.95
2_N	45_I	0.571	0.95
32_I	50_F	0.564	0.95
15_E	21_A	0.559	0.94
32_I	47_F	0.556	0.94
15_E	20_D	0.554	0.94
7_I	25_V	0.548	0.94
9_A	35_A	0.548	0.94
3_K	22_T	0.537	0.93
9_A	38_N	0.531	0.93
59_K	69_I	0.531	0.93
52_V	85_L	0.530	0.93
38_N	70_E	0.529	0.93
62_N	65_T	0.529	0.93
43_Q	84_A	0.527	0.92
20_D	24_A	0.526	0.92
11_A	18_K	0.524	0.92
84_A	88_A	0.522	0.92
46_G	82_G	0.512	0.91
10_V	31_T	0.511	0.91
61_R	69_I	0.510	0.91
14_S	27_S	0.509	0.91
4_T	58_R	0.507	0.91
21_A	31_T	0.500	0.90
73_A	80_K	0.500	0.90

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
4qjuA	2	0.9783	100	0.149	Contact Map
2iieA	1	1	100	0.159	Contact Map
4p3vA	2	0.7826	100	0.159	Contact Map
1mulA	2	0.8261	100	0.163	Contact Map
1p71A	2	1	100	0.163	Contact Map
1b8zA	2	0.7283	100	0.164	Contact Map
1exeA	2	1	100	0.165	Contact Map
4pt4A	2	1	100	0.167	Contact Map
1owfB	1	1	100	0.168	Contact Map
1owfA	1	1	100	0.173	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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