YYZM - BACSU - GREMLIN Contacts

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YYZM - Uncharacterized protein YyzM

UniProt:	C0H3V8	Sequences: MADKDFGLNDIVEMKKPHPCGANSWKIIRMGMDIRIKCEGCSHSVMIPRREFERKLKKVLVKHEEPTS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	68 (59)
Sequences:	736 (425)
Seq/√Len:	55.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_A	40_G	3.266	1.00
35_R	44_S	2.890	1.00
51_E	55_K	2.579	1.00
13_E	23_N	2.107	1.00
13_E	58_K	2.096	1.00
9_N	26_K	1.964	1.00
6_F	53_E	1.860	0.99
26_K	37_K	1.795	0.99
12_V	52_F	1.758	0.99
24_S	39_E	1.529	0.98
26_K	39_E	1.519	0.98
28_I	35_R	1.476	0.97
13_E	57_K	1.447	0.97
24_S	61_V	1.446	0.97
35_R	46_M	1.441	0.97
6_F	27_I	1.418	0.96
28_I	44_S	1.407	0.96
30_M	34_I	1.404	0.96
17_P	23_N	1.398	0.96
21_G	43_H	1.385	0.96
52_F	56_L	1.356	0.95
19_P	40_G	1.349	0.95
7_G	62_K	1.330	0.95
25_W	36_I	1.304	0.94
48_P	51_E	1.298	0.94
6_F	52_F	1.257	0.93
11_I	61_V	1.180	0.91
24_S	60_L	1.138	0.89
14_M	55_K	1.108	0.88
11_I	39_E	1.080	0.86
12_V	27_I	1.067	0.86
8_L	30_M	1.060	0.85
7_G	27_I	1.053	0.85
53_E	56_L	1.040	0.84
14_M	52_F	1.023	0.83
43_H	55_K	0.999	0.82
40_G	43_H	0.952	0.79
25_W	45_V	0.934	0.77
36_I	52_F	0.912	0.76
29_R	46_M	0.841	0.69
7_G	61_V	0.837	0.69
34_I	53_E	0.792	0.65
24_S	45_V	0.788	0.64
6_F	56_L	0.777	0.63
28_I	34_I	0.754	0.61
19_P	53_E	0.739	0.59
19_P	48_P	0.737	0.59
39_E	61_V	0.720	0.57
51_E	54_R	0.716	0.57
22_A	39_E	0.705	0.56
37_K	42_S	0.688	0.54
43_H	48_P	0.685	0.54
6_F	59_V	0.683	0.53
14_M	46_M	0.683	0.53
47_I	52_F	0.660	0.51
13_E	60_L	0.655	0.50
34_I	56_L	0.650	0.50
9_N	50_R	0.645	0.49
21_G	47_I	0.634	0.48
56_L	59_V	0.633	0.48
30_M	56_L	0.611	0.46
11_I	24_S	0.609	0.45
5_D	8_L	0.600	0.45
27_I	30_M	0.593	0.44
14_M	59_V	0.577	0.42
19_P	22_A	0.575	0.42
37_K	44_S	0.571	0.41
7_G	10_D	0.570	0.41
13_E	62_K	0.569	0.41
42_S	46_M	0.558	0.40
12_V	56_L	0.556	0.40
47_I	51_E	0.552	0.39
24_S	42_S	0.550	0.39
14_M	36_I	0.547	0.39
14_M	51_E	0.543	0.39
36_I	40_G	0.542	0.38
6_F	12_V	0.541	0.38
36_I	45_V	0.537	0.38
14_M	57_K	0.530	0.37
32_M	50_R	0.526	0.37
28_I	55_K	0.519	0.36
14_M	44_S	0.516	0.36
24_S	32_M	0.515	0.36
30_M	52_F	0.513	0.36
29_R	33_D	0.513	0.36
39_E	43_H	0.513	0.36
35_R	50_R	0.506	0.35
23_N	60_L	0.500	0.34

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
3na7A	1	0.6912	47	0.89	Contact Map
1vq8Z	1	0.6324	16	0.913	Contact Map
4p1tA	1	0.6176	15.4	0.914	Contact Map
2yk0A	1	0.5882	14.8	0.915	Contact Map
4hw9A	3	0.9118	13.2	0.917	Contact Map
2e9hA	1	0.9559	11.9	0.918	Contact Map
3h2yA	1	0.0588	11.6	0.918	Contact Map
3sgiA	1	0.2794	10.8	0.92	Contact Map
4aybN	1	0.4853	10.8	0.92	Contact Map
5ajiA	3	0.8971	10.3	0.92	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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