PT-VENN - PFAM28P - GREMLIN Contacts

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PT-VENN - Pre-toxin domain with VENN motif

PFAM:	PF04829	Sequences: PSDLTEEEKQTISALSTLAAGLAGGLAGGSTADAVAGAQAGKNAVENNYLSD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	52 (50)
Sequences:	1100 (631)
Seq/√Len:	89.2
META:	0.535

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_G	33_D	2.878	1.00
20_A	41_G	2.834	1.00
42_K	46_E	2.834	1.00
3_D	8_E	2.560	1.00
5_T	8_E	2.473	1.00
21_G	38_A	2.109	1.00
20_A	37_G	1.928	1.00
11_T	14_A	1.865	1.00
16_S	19_A	1.775	1.00
30_S	33_D	1.720	1.00
6_E	10_Q	1.691	1.00
16_S	44_A	1.515	1.00
17_T	42_K	1.407	0.99
24_G	32_A	1.317	0.99
29_G	33_D	1.305	0.99
35_V	38_A	1.183	0.98
17_T	38_A	1.140	0.97
36_A	40_A	1.122	0.97
35_V	39_Q	1.086	0.96
39_Q	43_N	1.032	0.95
15_L	37_G	1.020	0.94
10_Q	14_A	1.019	0.94
20_A	49_Y	0.946	0.92
23_A	32_A	0.936	0.91
18_L	25_G	0.906	0.90
6_E	9_K	0.901	0.90
7_E	11_T	0.883	0.89
16_S	31_T	0.865	0.88
8_E	11_T	0.863	0.88
37_G	47_N	0.852	0.87
19_A	22_L	0.844	0.86
11_T	26_L	0.836	0.86
31_T	35_V	0.829	0.85
45_V	49_Y	0.823	0.85
13_S	17_T	0.820	0.85
16_S	20_A	0.809	0.84
5_T	11_T	0.795	0.83
25_G	34_A	0.784	0.82
19_A	40_A	0.765	0.81
43_N	47_N	0.759	0.80
36_A	39_Q	0.757	0.80
34_A	38_A	0.747	0.79
8_E	49_Y	0.723	0.77
31_T	43_N	0.721	0.77
11_T	15_L	0.703	0.75
13_S	42_K	0.699	0.74
12_I	21_G	0.698	0.74
18_L	21_G	0.695	0.74
14_A	17_T	0.694	0.74
22_L	26_L	0.685	0.73
24_G	41_G	0.685	0.73
17_T	22_L	0.680	0.72
9_K	42_K	0.676	0.72
4_L	34_A	0.673	0.71
11_T	35_V	0.667	0.71
18_L	27_A	0.656	0.70
9_K	34_A	0.629	0.66
13_S	16_S	0.628	0.66
4_L	43_N	0.621	0.65
3_D	7_E	0.614	0.64
44_A	49_Y	0.595	0.62
17_T	20_A	0.595	0.62
15_L	34_A	0.592	0.62
40_A	43_N	0.588	0.61
5_T	18_L	0.574	0.59
4_L	47_N	0.570	0.59
33_D	39_Q	0.568	0.59
27_A	33_D	0.567	0.58
19_A	35_V	0.566	0.58
30_S	36_A	0.537	0.54
13_S	50_L	0.525	0.53
32_A	35_V	0.519	0.52
17_T	44_A	0.516	0.51
13_S	44_A	0.506	0.50
17_T	34_A	0.500	0.49

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
3agxA	2	0.3462	30.1	0.801	Contact Map
3lz8A	2	0.5385	15.6	0.826	Contact Map
3anwB	1	0.5	15.3	0.826	Contact Map
3wolA	2	0.9231	15.1	0.826	Contact Map
4j80A	2	0.4231	9	0.843	Contact Map
3kdwA	2	0.9423	8.2	0.846	Contact Map
4y04A	2	0.9423	7.1	0.85	Contact Map
4b2nA	1	0.3654	5.9	0.856	Contact Map
1vzvA	2	0.9423	5.6	0.858	Contact Map
3e9lA	1	0.3462	5.4	0.858	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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