VirB3 - PFAM28P - GREMLIN Contacts

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VirB3 - Type IV secretory pathway, VirB3-like protein

PFAM:	PF05101	Sequences: ERDPVHRALTRPLLLLGVPRELFILNGTLAAALFLLGLSLWGLLLALVLHGVARLAAKRDPQFFDVLLLRLRTRRRVRNRRFWG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	84 (78)
Sequences:	7800 (4264)
Seq/√Len:	482.8
META:	0.887

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_N	50_H	3.665	1.00
22_L	53_A	3.367	1.00
18_V	23_F	3.231	1.00
56_A	63_F	2.329	1.00
26_N	49_L	2.290	1.00
19_P	64_F	2.258	1.00
21_E	65_D	2.082	1.00
62_Q	65_D	1.981	1.00
30_A	46_A	1.932	1.00
50_H	54_R	1.825	1.00
51_G	55_L	1.679	1.00
38_L	42_G	1.646	1.00
12_P	62_Q	1.623	1.00
60_D	66_V	1.510	1.00
18_V	50_H	1.495	1.00
28_T	32_A	1.486	1.00
22_L	64_F	1.475	1.00
23_F	50_H	1.474	1.00
39_S	42_G	1.408	1.00
5_V	10_T	1.402	1.00
68_L	72_R	1.399	1.00
15_L	23_F	1.344	1.00
7_R	11_R	1.321	1.00
18_V	26_N	1.319	1.00
7_R	10_T	1.302	1.00
70_R	73_T	1.282	1.00
36_L	39_S	1.238	1.00
37_G	40_L	1.201	1.00
49_L	53_A	1.159	1.00
18_V	54_R	1.098	1.00
69_L	73_T	1.080	1.00
18_V	53_A	1.074	1.00
19_P	57_A	1.058	1.00
38_L	41_W	1.046	1.00
53_A	57_A	1.045	1.00
54_R	58_K	1.039	1.00
74_R	77_V	1.033	1.00
21_E	25_L	1.030	1.00
56_A	59_R	1.010	1.00
76_R	79_N	1.000	1.00
14_L	57_A	0.994	1.00
44_L	48_V	0.988	1.00
18_V	57_A	0.984	1.00
19_P	65_D	0.983	1.00
70_R	74_R	0.978	1.00
37_G	42_G	0.976	1.00
57_A	63_F	0.971	1.00
14_L	19_P	0.903	1.00
26_N	46_A	0.892	1.00
75_R	79_N	0.888	1.00
43_L	47_L	0.886	1.00
77_V	80_R	0.877	1.00
26_N	53_A	0.875	1.00
45_L	49_L	0.870	1.00
55_L	59_R	0.864	1.00
75_R	78_R	0.863	1.00
74_R	80_R	0.854	1.00
51_G	54_R	0.854	1.00
32_A	35_L	0.852	1.00
3_D	6_H	0.839	1.00
76_R	80_R	0.831	1.00
30_A	49_L	0.830	1.00
3_D	7_R	0.829	1.00
52_V	56_A	0.826	1.00
38_L	43_L	0.811	1.00
74_R	78_R	0.800	1.00
22_L	26_N	0.794	1.00
20_R	24_I	0.777	1.00
26_N	30_A	0.747	1.00
43_L	46_A	0.737	1.00
44_L	47_L	0.734	1.00
13_L	20_R	0.722	1.00
71_L	75_R	0.716	1.00
41_W	44_L	0.712	1.00
42_G	46_A	0.706	1.00
41_W	46_A	0.690	1.00
8_A	13_L	0.660	1.00
62_Q	66_V	0.659	1.00
69_L	72_R	0.658	1.00
3_D	10_T	0.654	1.00
15_L	20_R	0.650	1.00
30_A	34_F	0.644	1.00
21_E	68_L	0.637	1.00
55_L	58_K	0.636	1.00
68_L	71_L	0.630	1.00
38_L	44_L	0.620	0.99
40_L	44_L	0.618	0.99
8_A	19_P	0.607	0.99
69_L	74_R	0.599	0.99
72_R	76_R	0.586	0.99
16_L	23_F	0.573	0.99
23_F	27_G	0.568	0.99
12_P	65_D	0.567	0.99
30_A	47_L	0.558	0.99
16_L	50_H	0.555	0.99
48_V	52_V	0.554	0.99
29_L	32_A	0.553	0.99
36_L	44_L	0.553	0.99
52_V	55_L	0.552	0.99
24_I	28_T	0.551	0.99
14_L	18_V	0.550	0.99
75_R	80_R	0.544	0.99
51_G	65_D	0.529	0.98
13_L	16_L	0.528	0.98
24_I	27_G	0.526	0.98
63_F	66_V	0.526	0.98
37_G	41_W	0.525	0.98
57_A	61_P	0.525	0.98
72_R	75_R	0.525	0.98
26_N	29_L	0.522	0.98
14_L	60_D	0.518	0.98
19_P	22_L	0.513	0.98
59_R	63_F	0.511	0.98
34_F	50_H	0.509	0.98
56_A	67_L	0.507	0.98
69_L	75_R	0.507	0.98
59_R	67_L	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
2w0cP	4	0.0357	3	0.894	Contact Map
2aq4A	1	0.3333	2.4	0.899	Contact Map
3ne5A	3	0.8452	1.6	0.909	Contact Map
3ujzA	2	0.5	1.3	0.913	Contact Map
1m8oB	1	0.2143	1.3	0.913	Contact Map
3hieA	2	0.3333	1.2	0.916	Contact Map
3wu2X	1	0.4524	1.2	0.916	Contact Map
2q2eA	2	0.9405	1.1	0.918	Contact Map
1efpA	1	0.3333	1	0.92	Contact Map
3j7y9	1	0.2143	1	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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