YGAV - ECOLI - GREMLIN Contacts

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YGAV - Probable HTH-type transcriptional regulator YgaV

UniProt:	P77295	Sequences: MTELAQLQASAEQAAALLKAMSHPKRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRDAQRILYSIKNEAVNAIIATLKNVYCP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13524
Length:	99 (83)
Sequences:	5270 (3360)
Seq/√Len:	368.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_G	71_Q	3.774	1.00
70_S	77_I	3.039	1.00
69_D	80_S	2.930	1.00
72_R	77_I	2.540	1.00
69_D	82_K	2.465	1.00
12_E	24_P	2.127	1.00
20_A	65_E	2.112	1.00
36_S	39_T	1.701	1.00
50_L	55_T	1.689	1.00
38_G	80_S	1.673	1.00
60_A	64_D	1.655	1.00
32_M	47_I	1.592	1.00
39_T	43_E	1.528	1.00
40_S	76_R	1.473	1.00
32_M	39_T	1.456	1.00
34_S	87_N	1.444	1.00
63_R	70_S	1.442	1.00
51_S	54_A	1.430	1.00
30_L	67_L	1.393	1.00
16_A	64_D	1.388	1.00
40_S	43_E	1.379	1.00
15_A	24_P	1.341	1.00
45_T	52_A	1.333	1.00
39_T	47_I	1.333	1.00
61_R	65_E	1.321	1.00
59_L	68_I	1.292	1.00
88_A	92_T	1.287	1.00
38_G	78_L	1.238	1.00
29_I	44_L	1.232	1.00
23_H	57_Q	1.209	1.00
30_L	81_I	1.208	1.00
50_L	54_A	1.206	1.00
84_E	87_N	1.185	1.00
11_A	28_L	1.182	1.00
10_S	13_Q	1.152	1.00
41_A	59_L	1.144	1.00
11_A	31_C	1.133	1.00
12_E	16_A	1.091	1.00
73_D	76_R	1.056	1.00
20_A	61_R	1.012	1.00
29_I	33_L	1.011	1.00
54_A	57_Q	0.996	1.00
38_G	73_D	0.982	1.00
40_S	78_L	0.969	1.00
25_K	50_L	0.967	1.00
34_S	91_A	0.960	1.00
45_T	55_T	0.952	1.00
25_K	55_T	0.940	1.00
43_E	46_R	0.937	1.00
61_R	64_D	0.926	1.00
66_G	82_K	0.918	1.00
87_N	91_A	0.913	1.00
88_A	91_A	0.900	1.00
33_L	39_T	0.900	1.00
59_L	63_R	0.895	1.00
44_L	55_T	0.879	1.00
54_A	58_H	0.874	1.00
15_A	27_L	0.873	1.00
57_Q	75_Q	0.857	1.00
41_A	63_R	0.856	1.00
63_R	77_I	0.851	1.00
33_L	68_I	0.849	1.00
42_G	76_R	0.834	1.00
33_L	36_S	0.826	1.00
48_T	55_T	0.810	1.00
57_Q	60_A	0.803	1.00
36_S	43_E	0.796	1.00
51_S	58_H	0.794	1.00
73_D	78_L	0.794	1.00
17_L	67_L	0.793	1.00
62_M	68_I	0.778	1.00
18_L	21_M	0.776	1.00
57_Q	61_R	0.771	1.00
25_K	28_L	0.769	1.00
18_L	89_I	0.767	1.00
18_L	22_S	0.766	1.00
89_I	93_L	0.756	1.00
45_T	49_G	0.747	1.00
17_L	89_I	0.735	1.00
13_Q	16_A	0.729	1.00
82_K	85_A	0.725	1.00
31_C	34_S	0.697	0.99
18_L	93_L	0.694	0.99
23_H	51_S	0.688	0.99
72_R	75_Q	0.684	0.99
60_A	63_R	0.684	0.99
59_L	79_Y	0.681	0.99
32_M	44_L	0.680	0.99
83_N	86_V	0.675	0.99
13_Q	85_A	0.665	0.99
43_E	47_I	0.659	0.99
28_L	32_M	0.653	0.99
35_G	39_T	0.645	0.99
51_S	75_Q	0.642	0.99
85_A	89_I	0.625	0.99
85_A	90_I	0.624	0.99
45_T	51_S	0.624	0.99
54_A	75_Q	0.621	0.99
39_T	44_L	0.616	0.99
53_S	74_A	0.612	0.98
20_A	67_L	0.607	0.98
21_M	89_I	0.606	0.98
84_E	88_A	0.605	0.98
14_A	93_L	0.600	0.98
85_A	88_A	0.596	0.98
50_L	53_S	0.588	0.98
21_M	30_L	0.586	0.98
28_L	31_C	0.586	0.98
29_I	55_T	0.584	0.98
25_K	58_H	0.582	0.98
11_A	15_A	0.580	0.98
42_G	46_R	0.568	0.98
31_C	90_I	0.547	0.97
71_Q	80_S	0.540	0.97
14_A	90_I	0.539	0.97
30_L	90_I	0.535	0.96
15_A	22_S	0.528	0.96
23_H	54_A	0.524	0.96
52_A	55_T	0.522	0.96
17_L	85_A	0.522	0.96
51_S	57_Q	0.514	0.96
85_A	92_T	0.513	0.96
23_H	45_T	0.503	0.95
19_K	22_S	0.500	0.95

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
3cuoA	2	0.9899	99.7	0.484	Contact Map
2kkoA	2	0.9899	99.7	0.497	Contact Map
3pqkA	2	0.9697	99.7	0.516	Contact Map
4k2eA	2	0.9596	99.7	0.521	Contact Map
1r1tA	2	0.9899	99.6	0.528	Contact Map
1u2wA	2	1	99.6	0.539	Contact Map
2jscA	2	0.8687	99.6	0.542	Contact Map
1r1uA	2	0.9495	99.6	0.544	Contact Map
2zkzA	2	0.899	99.6	0.545	Contact Map
3f6vA	2	0.8586	99.6	0.554	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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