YGZD - BACSU - GREMLIN Contacts

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YGZD - Uncharacterized HTH-type transcriptional regulator YgzD

UniProt:	C0H3X9	Sequences: MKNKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDVFWLEEEN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	66 (60)
Sequences:	1922 (1236)
Seq/√Len:	159.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_E	21_E	2.708	1.00
46_L	62_L	2.521	1.00
22_T	51_A	2.475	1.00
4_K	7_E	2.343	1.00
55_K	58_D	1.928	1.00
9_R	34_E	1.906	1.00
14_Y	51_A	1.881	1.00
46_L	56_M	1.846	1.00
54_M	58_D	1.604	1.00
8_L	59_V	1.587	1.00
6_K	10_A	1.577	1.00
8_L	54_M	1.572	1.00
7_E	10_A	1.570	1.00
7_E	13_G	1.436	1.00
18_K	22_T	1.408	1.00
15_S	18_K	1.405	1.00
25_V	30_V	1.393	1.00
23_V	51_A	1.375	1.00
7_E	11_R	1.346	1.00
48_I	59_V	1.336	1.00
43_L	47_K	1.311	1.00
31_A	35_K	1.299	1.00
49_C	56_M	1.243	1.00
33_I	38_Y	1.237	1.00
19_L	30_V	1.187	1.00
12_F	53_S	1.162	1.00
45_A	56_M	1.150	1.00
29_T	38_Y	1.109	1.00
14_Y	22_T	1.062	0.99
8_L	11_R	1.051	0.99
4_K	61_W	1.016	0.99
16_Q	30_V	1.011	0.99
10_A	13_G	0.999	0.99
39_V	42_L	0.987	0.99
18_K	21_E	0.971	0.99
43_L	62_L	0.957	0.99
23_V	52_F	0.946	0.99
14_Y	18_K	0.937	0.98
26_T	32_A	0.904	0.98
54_M	59_V	0.898	0.98
50_K	62_L	0.892	0.98
4_K	8_L	0.881	0.98
28_Q	32_A	0.876	0.98
6_K	13_G	0.874	0.98
47_K	62_L	0.872	0.98
39_V	62_L	0.869	0.97
15_S	31_A	0.846	0.97
11_R	54_M	0.818	0.96
19_L	52_F	0.808	0.96
12_F	22_T	0.806	0.96
39_V	43_L	0.805	0.96
37_D	42_L	0.790	0.96
38_Y	44_L	0.759	0.94
23_V	30_V	0.744	0.94
47_K	50_K	0.744	0.94
27_R	60_F	0.738	0.94
25_V	29_T	0.725	0.93
3_N	26_T	0.720	0.93
4_K	11_R	0.714	0.92
41_S	44_L	0.709	0.92
16_Q	27_R	0.706	0.92
3_N	45_A	0.700	0.92
25_V	33_I	0.698	0.92
5_V	61_W	0.693	0.91
48_I	54_M	0.663	0.89
8_L	12_F	0.649	0.88
5_V	48_I	0.647	0.88
5_V	62_L	0.638	0.88
4_K	55_K	0.620	0.86
19_L	23_V	0.614	0.86
17_E	27_R	0.601	0.84
3_N	60_F	0.575	0.82
23_V	44_L	0.567	0.81
33_I	42_L	0.565	0.81
19_L	51_A	0.556	0.79
40_P	44_L	0.550	0.79
50_K	53_S	0.547	0.78
32_A	37_D	0.546	0.78
55_K	61_W	0.546	0.78
44_L	47_K	0.539	0.77
46_L	50_K	0.538	0.77
33_I	44_L	0.532	0.76
4_K	22_T	0.520	0.75
6_K	35_K	0.515	0.74
3_N	28_Q	0.511	0.74
19_L	48_I	0.509	0.73
52_F	59_V	0.508	0.73
32_A	35_K	0.502	0.72
6_K	15_S	0.500	0.72
21_E	53_S	0.500	0.72

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
4yarA	2	1	99.5	0.228	Contact Map
3u3wA	2	0.9848	99.5	0.228	Contact Map
1y9qA	1	1	99.5	0.228	Contact Map
2p5tA	2	0.0606	99.5	0.231	Contact Map
4o8bA	2	1	99.4	0.243	Contact Map
4ichA	2	0	99.4	0.246	Contact Map
3mlfA	2	1	99.4	0.249	Contact Map
3tysA	2	0.9697	99.4	0.249	Contact Map
3ivpA	2	1	99.4	0.253	Contact Map
4ndwA	2	1	99.4	0.253	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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