YDZF - BACSU - GREMLIN Contacts

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YDZF - Uncharacterized HTH-type transcriptional regulator YdzF

UniProt:	O31494	Sequences: MNSLCRSKQAPFEYTLSLIGGKWKMRILYELGCEKTMRYGELKRAMPFITHKMLSAQLKELQTDGLIHRSEVSHTPLKVEYSLSDRGRSLYPLIDEMCKWGMAQGGPHM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	109 (97)
Sequences:	8815 (5189)
Seq/√Len:	526.8

ECOLI - YTFH
BACSU - YDZF YVAP YODB YDEP HXLR YYBR YTCD YKVN
HALSA - Q9HRG9 Q9HPZ4
SULSO - Q97UU6 Q97U48

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
68_H	82_S	2.824	1.00
43_K	51_H	2.768	1.00
52_K	56_A	2.729	1.00
74_H	78_K	2.692	1.00
32_G	91_Y	2.512	1.00
89_S	103_A	2.491	1.00
70_S	82_S	2.444	1.00
68_H	84_S	2.285	1.00
30_E	45_A	1.981	1.00
72_V	80_E	1.962	1.00
31_L	67_I	1.935	1.00
93_L	96_E	1.809	1.00
72_V	78_K	1.726	1.00
86_R	104_Q	1.688	1.00
36_T	82_S	1.680	1.00
96_E	99_K	1.676	1.00
37_M	45_A	1.644	1.00
92_P	96_E	1.617	1.00
59_K	62_Q	1.584	1.00
53_M	56_A	1.584	1.00
36_T	80_E	1.577	1.00
27_I	57_Q	1.507	1.00
31_L	42_L	1.484	1.00
89_S	100_W	1.459	1.00
88_R	91_Y	1.401	1.00
85_D	88_R	1.367	1.00
24_K	60_E	1.366	1.00
24_K	57_Q	1.355	1.00
83_L	87_G	1.339	1.00
15_T	97_M	1.314	1.00
86_R	89_S	1.282	1.00
40_G	44_R	1.240	1.00
14_Y	105_G	1.226	1.00
15_T	101_G	1.219	1.00
51_H	55_S	1.214	1.00
37_M	41_E	1.207	1.00
66_L	87_G	1.174	1.00
21_G	57_Q	1.158	1.00
18_L	64_D	1.153	1.00
21_G	24_K	1.134	1.00
55_S	59_K	1.129	1.00
21_G	60_E	1.116	1.00
31_L	37_M	1.103	1.00
69_R	79_V	1.077	1.00
70_S	80_E	1.060	1.00
66_L	90_L	1.053	1.00
38_R	80_E	1.043	1.00
34_E	37_M	1.035	1.00
72_V	77_L	1.027	1.00
72_V	75_T	1.026	1.00
98_C	102_M	1.020	1.00
91_Y	95_D	1.019	1.00
82_S	88_R	1.005	1.00
28_L	83_L	0.999	1.00
39_Y	55_S	0.994	1.00
62_Q	67_I	0.981	1.00
27_I	46_M	0.968	1.00
49_I	54_L	0.963	1.00
24_K	61_L	0.959	1.00
99_K	103_A	0.949	1.00
71_E	76_P	0.942	1.00
18_L	66_L	0.941	1.00
53_M	57_Q	0.934	1.00
89_S	104_Q	0.925	1.00
24_K	64_D	0.913	1.00
25_M	94_I	0.902	1.00
72_V	76_P	0.871	1.00
46_M	49_I	0.869	1.00
41_E	44_R	0.868	1.00
30_E	42_L	0.860	1.00
92_P	99_K	0.856	1.00
95_D	99_K	0.844	1.00
27_I	49_I	0.842	1.00
13_E	17_S	0.840	1.00
39_Y	51_H	0.817	1.00
65_G	86_R	0.812	1.00
71_E	77_L	0.811	1.00
71_E	75_T	0.805	1.00
71_E	79_V	0.802	1.00
40_G	43_K	0.795	1.00
32_G	95_D	0.772	1.00
90_L	100_W	0.762	1.00
60_E	64_D	0.744	1.00
14_Y	104_Q	0.743	1.00
32_G	83_L	0.738	1.00
29_Y	98_C	0.738	1.00
23_W	49_I	0.736	1.00
8_K	14_Y	0.727	1.00
50_T	53_M	0.723	1.00
11_P	102_M	0.720	1.00
73_S	76_P	0.715	1.00
99_K	102_M	0.712	1.00
35_K	88_R	0.708	1.00
90_L	93_L	0.700	1.00
71_E	74_H	0.680	1.00
29_Y	32_G	0.678	1.00
37_M	42_L	0.678	1.00
8_K	17_S	0.675	1.00
95_D	98_C	0.671	1.00
38_R	41_E	0.669	1.00
8_K	13_E	0.668	1.00
74_H	80_E	0.658	1.00
16_L	97_M	0.650	1.00
93_L	97_M	0.649	1.00
31_L	36_T	0.627	1.00
75_T	79_V	0.626	1.00
74_H	77_L	0.623	1.00
30_E	34_E	0.623	1.00
49_I	79_V	0.623	1.00
101_G	105_G	0.620	1.00
12_F	105_G	0.614	1.00
51_H	57_Q	0.607	1.00
16_L	25_M	0.607	1.00
26_R	30_E	0.604	1.00
30_E	37_M	0.599	1.00
16_L	90_L	0.598	1.00
62_Q	71_E	0.587	0.99
62_Q	69_R	0.587	0.99
93_L	101_G	0.582	0.99
12_F	29_Y	0.578	0.99
26_R	46_M	0.576	0.99
92_P	95_D	0.571	0.99
61_L	66_L	0.571	0.99
39_Y	43_K	0.558	0.99
39_Y	54_L	0.548	0.99
55_S	69_R	0.547	0.99
70_S	73_S	0.547	0.99
31_L	83_L	0.546	0.99
102_M	105_G	0.542	0.99
28_L	90_L	0.538	0.99
40_G	79_V	0.537	0.99
47_P	53_M	0.530	0.99
28_L	61_L	0.529	0.99
92_P	103_A	0.527	0.99
13_E	47_P	0.524	0.99
74_H	79_V	0.519	0.99
10_A	39_Y	0.519	0.99
17_S	45_A	0.518	0.99
13_E	98_C	0.512	0.99
83_L	88_R	0.510	0.98
89_S	92_P	0.509	0.98
15_T	66_L	0.506	0.98
76_P	79_V	0.505	0.98
59_K	69_R	0.505	0.98
29_Y	39_Y	0.503	0.98
32_G	88_R	0.500	0.98

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
4gcvA	3	0.8991	99.8	0.39	Contact Map
4a5nA	2	0.9174	99.7	0.478	Contact Map
2fswA	2	0.945	99.7	0.488	Contact Map
1yyvA	2	0.9633	99.7	0.491	Contact Map
2hztA	2	0.8716	99.7	0.493	Contact Map
1z7uA	2	0.9633	99.6	0.501	Contact Map
2f2eA	4	0.9541	99.6	0.507	Contact Map
4hw0A	2	0.7982	99.5	0.539	Contact Map
3df8A	2	0.9358	99.5	0.551	Contact Map
4hqeA	2	0.9541	99.3	0.593	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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