NRPS - PFAM28P - GREMLIN Contacts

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NRPS - Nonribosomal peptide synthase

PFAM:	PF08415	Sequences: HRAVSGVEVLRELARRRGGAPAALMPVVFTSALEEGDALEWLGELVYGISQTPQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	54 (53)
Sequences:	4562 (3746)
Seq/√Len:	514.5
META:	0.703

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_V	12_E	5.210	1.00
13_L	17_R	3.152	1.00
4_V	8_E	3.051	1.00
12_E	15_R	2.927	1.00
4_V	9_V	2.580	1.00
30_T	50_S	2.359	1.00
8_E	12_E	1.876	1.00
45_L	48_G	1.859	1.00
10_L	25_M	1.779	1.00
12_E	16_R	1.695	1.00
7_V	11_R	1.656	1.00
19_G	22_A	1.573	1.00
30_T	33_L	1.524	1.00
39_L	43_G	1.433	1.00
37_D	41_W	1.328	1.00
5_S	8_E	1.203	1.00
37_D	40_E	1.179	1.00
38_A	41_W	1.148	1.00
48_G	51_Q	1.122	1.00
17_R	22_A	1.108	1.00
10_L	33_L	1.002	1.00
39_L	42_L	0.995	1.00
29_F	34_E	0.983	1.00
34_E	39_L	0.962	1.00
11_R	28_V	0.941	1.00
48_G	52_T	0.925	1.00
20_A	23_A	0.915	1.00
50_S	53_P	0.896	1.00
24_L	29_F	0.888	1.00
21_P	24_L	0.877	1.00
34_E	37_D	0.849	1.00
6_G	13_L	0.827	1.00
8_E	11_R	0.817	1.00
36_G	39_L	0.816	1.00
20_A	38_A	0.814	1.00
5_S	51_Q	0.785	1.00
32_A	48_G	0.752	1.00
16_R	21_P	0.747	1.00
18_G	22_A	0.728	1.00
6_G	16_R	0.721	1.00
36_G	40_E	0.719	1.00
40_E	43_G	0.715	1.00
10_L	14_A	0.673	1.00
40_E	44_E	0.673	1.00
10_L	23_A	0.663	1.00
14_A	32_A	0.661	1.00
39_L	44_E	0.645	1.00
20_A	24_L	0.642	1.00
39_L	45_L	0.635	1.00
20_A	44_E	0.628	1.00
14_A	23_A	0.620	1.00
13_L	25_M	0.615	1.00
9_V	51_Q	0.614	1.00
30_T	54_Q	0.601	0.99
36_G	43_G	0.597	0.99
10_L	32_A	0.590	0.99
24_L	30_T	0.577	0.99
9_V	13_L	0.571	0.99
25_M	32_A	0.564	0.99
19_G	23_A	0.562	0.99
6_G	9_V	0.556	0.99
16_R	42_L	0.547	0.99
5_S	52_T	0.545	0.99
7_V	54_Q	0.543	0.99
47_Y	51_Q	0.535	0.99
26_P	46_V	0.529	0.99
29_F	33_L	0.528	0.99
18_G	40_E	0.527	0.99
32_A	50_S	0.525	0.99
32_A	49_I	0.522	0.99
34_E	38_A	0.519	0.99
14_A	31_S	0.519	0.99
3_A	27_V	0.514	0.98
42_L	45_L	0.507	0.98
13_L	23_A	0.506	0.98
47_Y	53_P	0.504	0.98
6_G	19_G	0.504	0.98
41_W	44_E	0.503	0.98
9_V	26_P	0.501	0.98
23_A	26_P	0.500	0.98

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
4qicA	2	0.8704	8.2	0.856	Contact Map
2jgpA	1	0.9815	7.9	0.857	Contact Map
3j25A	1	0.9444	7.3	0.859	Contact Map
3n0rA	1	0.8704	7.1	0.86	Contact Map
3sy8A	6	0.9074	6.6	0.862	Contact Map
2h5eA	1	0.9815	6.6	0.862	Contact Map
1l5aA	2	0.9074	6.3	0.863	Contact Map
1dcfA	2	0.9815	5.5	0.867	Contact Map
3lteA	3	0.9444	5.1	0.869	Contact Map
4g97A	1	0.8704	5.1	0.869	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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