YVAP - BACSU - GREMLIN Contacts

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YVAP - Uncharacterized HTH-type transcriptional regulator YvaP

UniProt:	O32238	Sequences: MNQSEMCPRFEKAVDILSKRWVALIVFQLLNGSQRFSEIEAALPNLSGRVLSERLKELELEGVVKRDVIPETPVRIEYSLTDKGKALAPILGEISKWATEWIDPSFLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	108 (97)
Sequences:	9592 (5667)
Seq/√Len:	575.4

ECOLI - YTFH
BACSU - YVAP YDZF YODB YKVN YTCD YDEP YYBR HXLR
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
40_E	48_G	2.830	1.00
65_K	79_S	2.743	1.00
49_R	53_E	2.675	1.00
86_A	100_E	2.592	1.00
30_L	88_A	2.553	1.00
67_D	79_S	2.450	1.00
71_E	75_R	2.420	1.00
29_L	64_V	2.185	1.00
28_Q	42_A	2.155	1.00
65_K	81_T	2.118	1.00
69_I	77_E	1.855	1.00
83_K	101_W	1.785	1.00
90_I	93_E	1.724	1.00
69_I	75_R	1.690	1.00
29_L	39_I	1.687	1.00
89_P	93_E	1.673	1.00
25_I	54_R	1.637	1.00
93_E	96_K	1.630	1.00
56_K	59_E	1.603	1.00
33_S	77_E	1.575	1.00
33_S	79_S	1.538	1.00
50_V	53_E	1.521	1.00
80_L	84_G	1.515	1.00
34_Q	42_A	1.482	1.00
86_A	97_W	1.401	1.00
85_K	88_A	1.375	1.00
22_V	57_E	1.360	1.00
82_D	85_K	1.351	1.00
63_V	84_G	1.341	1.00
83_K	86_A	1.301	1.00
13_A	94_I	1.283	1.00
22_V	54_R	1.282	1.00
19_K	57_E	1.277	1.00
66_R	76_I	1.246	1.00
59_E	64_V	1.191	1.00
13_A	98_A	1.178	1.00
12_K	102_I	1.178	1.00
48_G	52_S	1.175	1.00
34_Q	38_E	1.174	1.00
37_S	41_A	1.158	1.00
16_I	61_E	1.139	1.00
29_L	34_Q	1.125	1.00
68_V	76_I	1.112	1.00
22_V	58_L	1.110	1.00
52_S	56_K	1.078	1.00
19_K	54_R	1.078	1.00
95_S	99_T	1.076	1.00
35_R	77_E	1.067	1.00
69_I	73_P	1.067	1.00
63_V	87_L	1.053	1.00
19_K	22_V	1.053	1.00
67_D	77_E	1.033	1.00
79_S	85_K	0.996	1.00
88_A	92_G	0.989	1.00
68_V	73_P	0.989	1.00
26_V	80_L	0.982	1.00
69_I	74_V	0.970	1.00
36_F	52_S	0.964	1.00
25_I	43_L	0.961	1.00
68_V	74_V	0.956	1.00
70_P	73_P	0.952	1.00
23_A	91_L	0.930	1.00
86_A	101_W	0.916	1.00
50_V	54_R	0.915	1.00
16_I	63_V	0.904	1.00
46_L	51_L	0.898	1.00
89_P	96_K	0.895	1.00
28_Q	39_I	0.892	1.00
38_E	41_A	0.889	1.00
96_K	100_E	0.887	1.00
31_N	34_Q	0.887	1.00
87_L	97_W	0.887	1.00
69_I	72_T	0.867	1.00
37_S	40_E	0.865	1.00
47_S	50_V	0.860	1.00
43_L	46_L	0.836	1.00
62_G	83_K	0.829	1.00
22_V	61_E	0.823	1.00
36_F	48_G	0.821	1.00
11_E	15_D	0.804	1.00
30_L	80_L	0.798	1.00
30_L	92_G	0.779	1.00
8_P	99_T	0.760	1.00
57_E	61_E	0.758	1.00
12_K	101_W	0.756	1.00
92_G	96_K	0.748	1.00
21_W	46_L	0.734	1.00
34_Q	39_I	0.730	1.00
25_I	46_L	0.719	1.00
72_T	76_I	0.716	1.00
27_F	30_L	0.715	1.00
68_V	72_T	0.714	1.00
90_I	94_I	0.713	1.00
96_K	99_T	0.710	1.00
27_F	95_S	0.710	1.00
68_V	71_E	0.701	1.00
98_A	102_I	0.682	1.00
28_Q	31_N	0.679	1.00
59_E	66_R	0.639	1.00
10_F	102_I	0.631	1.00
14_V	94_I	0.629	1.00
92_G	95_S	0.626	1.00
35_R	38_E	0.625	1.00
24_L	43_L	0.620	1.00
71_E	74_V	0.614	1.00
53_E	57_E	0.607	1.00
29_L	33_S	0.606	1.00
14_V	23_A	0.595	1.00
89_P	92_G	0.592	1.00
32_G	85_K	0.591	1.00
87_L	90_I	0.589	1.00
24_L	28_Q	0.589	1.00
35_R	69_I	0.581	1.00
37_S	48_G	0.576	1.00
28_Q	34_Q	0.564	0.99
26_V	87_L	0.558	0.99
10_F	27_F	0.554	0.99
11_E	23_A	0.553	0.99
58_L	63_V	0.551	0.99
46_L	76_I	0.551	0.99
71_E	77_E	0.551	0.99
99_T	102_I	0.550	0.99
36_F	40_E	0.549	0.99
73_P	76_I	0.547	0.99
31_N	42_A	0.545	0.99
33_S	39_I	0.540	0.99
29_L	59_E	0.538	0.99
40_E	51_L	0.537	0.99
100_E	103_D	0.534	0.99
7_C	36_F	0.527	0.99
13_A	63_V	0.526	0.99
71_E	76_I	0.524	0.99
59_E	68_V	0.519	0.99
48_G	54_R	0.516	0.99
6_M	12_K	0.514	0.99
33_S	67_D	0.513	0.99
85_K	89_P	0.510	0.99
86_A	89_P	0.509	0.99
79_S	82_D	0.509	0.99
98_A	101_W	0.505	0.99
12_K	27_F	0.504	0.99
83_K	102_I	0.503	0.99
90_I	98_A	0.503	0.99
29_L	80_L	0.502	0.99
56_K	66_R	0.500	0.99
12_K	15_D	0.500	0.99

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	0.9259	99.8	0.385	Contact Map
4a5nA	2	0.9444	99.7	0.468	Contact Map
1z7uA	2	0.9907	99.7	0.482	Contact Map
2hztA	2	0.8796	99.7	0.483	Contact Map
1yyvA	2	0.963	99.7	0.488	Contact Map
2fswA	2	0.9352	99.7	0.494	Contact Map
2f2eA	4	0.9722	99.6	0.503	Contact Map
4hw0A	2	0.8148	99.6	0.518	Contact Map
3df8A	2	0.9167	99.5	0.547	Contact Map
1xmaA	2	0.8796	99.3	0.602	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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