Virulence_fact - PFAM28P - GREMLIN Contacts

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Virulence_fact - Virulence factor

PFAM:	PF13769	Sequences: VYWRDIPAQVIAKDGRREAKRQLPERFQEAIDRAAMGSDAYLAEWRRGDPEERGGDLEEVADAVAAELEAEYDDERLKALV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	81 (79)
Sequences:	6600 (3382)
Seq/√Len:	380.5
META:	0.929

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_V	67_E	2.491	1.00
8_A	31_I	2.382	1.00
37_G	40_A	2.282	1.00
21_R	62_D	2.050	1.00
19_A	58_E	2.033	1.00
25_E	29_E	2.025	1.00
67_E	71_E	2.020	1.00
58_E	62_D	2.019	1.00
24_P	69_E	1.984	1.00
62_D	66_A	1.872	1.00
56_D	59_E	1.807	1.00
22_Q	28_Q	1.632	1.00
51_E	64_V	1.567	1.00
73_D	76_R	1.466	1.00
53_R	60_V	1.444	1.00
53_R	67_E	1.440	1.00
11_I	47_R	1.433	1.00
48_G	51_E	1.431	1.00
66_A	70_A	1.394	1.00
54_G	60_V	1.390	1.00
59_E	63_A	1.385	1.00
14_D	17_R	1.375	1.00
38_S	42_L	1.375	1.00
21_R	58_E	1.329	1.00
74_D	78_K	1.299	1.00
13_K	18_E	1.276	1.00
25_E	28_Q	1.265	1.00
72_Y	80_L	1.262	1.00
26_R	69_E	1.236	1.00
21_R	61_A	1.226	1.00
4_R	44_E	1.216	1.00
42_L	45_W	1.215	1.00
11_I	20_K	1.206	1.00
22_Q	25_E	1.205	1.00
72_Y	76_R	1.178	1.00
8_A	45_W	1.149	1.00
71_E	76_R	1.126	1.00
21_R	65_A	1.109	1.00
10_V	65_A	1.100	1.00
12_A	61_A	1.069	1.00
55_G	60_V	1.062	1.00
2_Y	46_R	1.041	1.00
53_R	63_A	1.032	1.00
2_Y	48_G	1.021	1.00
40_A	43_A	1.019	1.00
9_Q	22_Q	1.015	1.00
29_E	33_R	0.993	1.00
6_I	34_A	0.988	1.00
12_A	60_V	0.965	1.00
35_A	41_Y	0.960	1.00
13_K	16_R	0.936	1.00
63_A	67_E	0.929	1.00
32_D	35_A	0.916	1.00
12_A	19_A	0.897	1.00
33_R	36_M	0.890	1.00
51_E	60_V	0.886	1.00
26_R	30_A	0.886	1.00
24_P	65_A	0.884	1.00
57_L	60_V	0.876	1.00
60_V	63_A	0.870	1.00
30_A	34_A	0.857	1.00
76_R	79_A	0.848	1.00
66_A	69_E	0.838	1.00
75_E	79_A	0.836	1.00
5_D	34_A	0.822	1.00
61_A	65_A	0.815	1.00
65_A	69_E	0.794	1.00
37_G	44_E	0.791	1.00
11_I	18_E	0.784	1.00
33_R	78_K	0.782	1.00
75_E	78_K	0.781	1.00
8_A	22_Q	0.769	1.00
55_G	59_E	0.764	1.00
13_K	50_P	0.745	1.00
2_Y	5_D	0.740	1.00
31_I	45_W	0.736	1.00
32_D	36_M	0.735	1.00
60_V	64_V	0.723	1.00
19_A	61_A	0.714	1.00
19_A	57_L	0.713	1.00
17_R	58_E	0.708	1.00
32_D	41_Y	0.690	0.99
14_D	18_E	0.679	0.99
53_R	64_V	0.673	0.99
36_M	41_Y	0.665	0.99
8_A	41_Y	0.661	0.99
13_K	19_A	0.661	0.99
23_L	68_L	0.655	0.99
73_D	77_L	0.650	0.99
8_A	28_Q	0.648	0.99
9_Q	18_E	0.642	0.99
13_K	57_L	0.638	0.99
30_A	33_R	0.637	0.99
9_Q	42_L	0.632	0.99
76_R	80_L	0.628	0.99
10_V	64_V	0.625	0.99
13_K	20_K	0.615	0.99
6_I	9_Q	0.606	0.99
31_I	35_A	0.601	0.98
28_Q	45_W	0.596	0.98
3_W	35_A	0.585	0.98
24_P	77_L	0.581	0.98
23_L	65_A	0.579	0.98
20_K	47_R	0.566	0.98
5_D	46_R	0.565	0.98
64_V	71_E	0.565	0.98
62_D	65_A	0.559	0.98
14_D	57_L	0.552	0.97
25_E	39_D	0.539	0.97
10_V	68_L	0.533	0.97
29_E	74_D	0.524	0.96
17_R	21_R	0.519	0.96
53_R	56_D	0.506	0.96
11_I	30_A	0.503	0.95
28_Q	32_D	0.501	0.95
27_F	69_E	0.501	0.95
6_I	80_L	0.500	0.95
59_E	62_D	0.500	0.95

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
4faiA	1	0.4938	8.8	0.911	Contact Map
3hguA	2	0.3333	7.4	0.914	Contact Map
2i49A	1	0.8395	5.3	0.92	Contact Map
4artA	2	0.1728	5.1	0.92	Contact Map
4extA	1	0.679	4.9	0.921	Contact Map
4l7mA	1	0.5432	4.5	0.922	Contact Map
4hcwA	1	0.5556	4	0.925	Contact Map
2g29A	1	1	3.9	0.925	Contact Map
2bl8A	1	0.5926	3.8	0.925	Contact Map
4b46A	1	0.4198	3.6	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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