YBDZ - BACSU - GREMLIN Contacts

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YBDZ - Uncharacterized protein YbdZ

UniProt:	C0H3Q6	Sequences: MANPFENADGTYLVLVNEEGQYSLWPGFIDVPSGWTVVHEQKGREACLDYIQSHWSDMRPNSLKTVENV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	69 (63)
Sequences:	1299 (840)
Seq/√Len:	105.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_N	65_T	3.784	1.00
45_E	49_D	3.020	1.00
20_G	64_K	2.680	1.00
43_G	46_A	2.472	1.00
6_E	12_Y	2.379	1.00
42_K	46_A	2.335	1.00
19_E	62_S	1.847	1.00
20_G	61_N	1.841	1.00
49_D	53_S	1.812	1.00
39_H	42_K	1.740	1.00
11_T	41_Q	1.728	1.00
50_Y	54_H	1.695	1.00
13_L	37_V	1.630	1.00
27_G	41_Q	1.563	1.00
61_N	64_K	1.523	1.00
22_Y	58_M	1.502	1.00
18_E	36_T	1.468	1.00
42_K	47_C	1.444	1.00
15_L	24_L	1.420	1.00
16_V	36_T	1.336	0.99
38_V	50_Y	1.322	0.99
8_A	45_E	1.316	0.99
13_L	41_Q	1.313	0.99
31_V	37_V	1.309	0.99
15_L	23_S	1.290	0.99
39_H	47_C	1.203	0.99
59_R	63_L	1.136	0.98
16_V	22_Y	1.063	0.97
40_E	50_Y	1.056	0.97
14_V	51_I	1.032	0.97
13_L	31_V	1.014	0.96
16_V	38_V	1.005	0.96
49_D	52_Q	0.942	0.95
14_V	22_Y	0.941	0.95
10_G	28_F	0.907	0.93
14_V	47_C	0.870	0.92
11_T	27_G	0.859	0.91
13_L	27_G	0.858	0.91
24_L	44_R	0.849	0.91
15_L	48_L	0.822	0.90
58_M	63_L	0.808	0.89
30_D	33_S	0.808	0.89
18_E	61_N	0.785	0.87
13_L	40_E	0.784	0.87
59_R	62_S	0.781	0.87
8_A	44_R	0.768	0.86
44_R	48_L	0.762	0.86
20_G	36_T	0.759	0.86
13_L	47_C	0.757	0.85
7_N	26_P	0.745	0.84
36_T	65_T	0.730	0.83
40_E	46_A	0.728	0.83
14_V	50_Y	0.711	0.82
48_L	52_Q	0.701	0.81
5_F	15_L	0.696	0.80
17_N	21_Q	0.690	0.80
19_E	56_S	0.684	0.79
5_F	12_Y	0.672	0.78
46_A	49_D	0.656	0.76
4_P	28_F	0.655	0.76
23_S	51_I	0.648	0.75
22_Y	54_H	0.648	0.75
7_N	52_Q	0.645	0.75
21_Q	30_D	0.615	0.71
15_L	39_H	0.613	0.71
10_G	26_P	0.600	0.70
6_E	26_P	0.597	0.69
10_G	24_L	0.587	0.68
39_H	64_K	0.586	0.68
19_E	51_I	0.585	0.68
15_L	29_I	0.579	0.67
19_E	32_P	0.579	0.67
22_Y	38_V	0.578	0.67
24_L	48_L	0.570	0.66
13_L	39_H	0.567	0.65
56_S	64_K	0.558	0.64
53_S	56_S	0.556	0.64
12_Y	63_L	0.554	0.63
4_P	7_N	0.551	0.63
4_P	15_L	0.549	0.63
13_L	44_R	0.545	0.62
24_L	65_T	0.538	0.61
19_E	63_L	0.536	0.61
14_V	42_K	0.522	0.59
39_H	46_A	0.519	0.58
32_P	35_W	0.518	0.58
8_A	30_D	0.515	0.58
7_N	10_G	0.515	0.58
16_V	37_V	0.509	0.57
9_D	12_Y	0.508	0.57
3_N	6_E	0.503	0.56
49_D	56_S	0.502	0.56
40_E	58_M	0.501	0.56
35_W	55_W	0.500	0.56

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
2pstX	1	0.8841	100	0.089	Contact Map
2lpdA	1	1	100	0.092	Contact Map
2khrA	1	1	100	0.093	Contact Map
2myyA	1	1	100	0.098	Contact Map
4gr5A	1	1	99.7	0.496	Contact Map
2ikbA	2	0.8551	16.5	0.92	Contact Map
2nr7A	1	0.9275	13.7	0.923	Contact Map
1wr4A	1	0.5217	13.5	0.923	Contact Map
1jmqA	1	0.6377	10.9	0.926	Contact Map
1eg3A	1	0.7101	10.9	0.926	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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