Cys_rich_VLP - PFAM28P - GREMLIN Contacts

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Cys_rich_VLP - Cysteine-rich VLP

PFAM:	PF14194	Sequences: TPAQRRAIRKLVRKLCANYDEGNCLLLDDGEECVCPQLISWYSLLCKYFRNAVLPLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	57 (56)
Sequences:	748 (383)
Seq/√Len:	51.2
META:	0.905

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_L	56_L	5.265	1.00
17_A	48_Y	3.821	1.00
48_Y	52_A	2.485	1.00
5_R	9_R	2.485	1.00
40_S	43_S	2.154	1.00
7_A	57_D	2.065	1.00
36_P	40_S	2.050	1.00
3_A	6_R	1.663	0.98
48_Y	56_L	1.638	0.98
5_R	41_W	1.532	0.97
34_V	38_L	1.347	0.94
15_L	50_R	1.331	0.94
17_A	52_A	1.313	0.93
2_P	10_K	1.221	0.90
20_D	25_L	1.219	0.90
2_P	5_R	1.192	0.89
30_G	35_C	1.189	0.89
11_L	49_F	1.158	0.88
16_C	19_Y	1.157	0.88
36_P	43_S	1.139	0.87
37_Q	40_S	1.117	0.86
36_P	45_L	1.098	0.85
27_L	37_Q	1.026	0.81
49_F	54_L	1.009	0.80
2_P	6_R	1.002	0.79
2_P	14_K	0.922	0.73
26_L	33_C	0.918	0.73
19_Y	38_L	0.917	0.73
42_Y	45_L	0.915	0.73
53_V	57_D	0.876	0.69
45_L	50_R	0.876	0.69
18_N	33_C	0.875	0.69
52_A	55_P	0.874	0.69
48_Y	53_V	0.874	0.69
37_Q	44_L	0.870	0.69
36_P	44_L	0.867	0.69
12_V	38_L	0.860	0.68
2_P	13_R	0.848	0.67
11_L	57_D	0.841	0.66
10_K	14_K	0.833	0.66
5_R	8_I	0.825	0.65
29_D	32_E	0.823	0.65
18_N	25_L	0.814	0.64
22_G	37_Q	0.813	0.64
34_V	42_Y	0.812	0.64
47_K	50_R	0.811	0.63
27_L	47_K	0.803	0.63
6_R	10_K	0.742	0.57
39_I	42_Y	0.739	0.56
5_R	51_N	0.736	0.56
14_K	21_E	0.726	0.55
14_K	51_N	0.721	0.54
18_N	26_L	0.720	0.54
35_C	47_K	0.675	0.50
3_A	14_K	0.659	0.48
15_L	48_Y	0.644	0.46
9_R	20_D	0.638	0.46
37_Q	50_R	0.634	0.45
34_V	39_I	0.633	0.45
14_K	56_L	0.632	0.45
26_L	36_P	0.625	0.45
5_R	12_V	0.625	0.45
3_A	7_A	0.625	0.45
27_L	30_G	0.624	0.44
2_P	7_A	0.617	0.44
29_D	33_C	0.609	0.43
10_K	13_R	0.594	0.41
27_L	36_P	0.592	0.41
6_R	41_W	0.591	0.41
5_R	42_Y	0.567	0.39
23_N	37_Q	0.559	0.38
4_Q	40_S	0.556	0.38
22_G	44_L	0.554	0.37
24_C	47_K	0.547	0.37
22_G	56_L	0.547	0.37
32_E	36_P	0.544	0.36
7_A	49_F	0.540	0.36
4_Q	37_Q	0.537	0.36
42_Y	47_K	0.535	0.36
22_G	47_K	0.528	0.35
6_R	13_R	0.524	0.35
50_R	53_V	0.515	0.34
30_G	33_C	0.508	0.33
52_A	56_L	0.500	0.32

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
1vw4R	1	0.6491	14.9	0.865	Contact Map
4o6iA	2	0.8421	11.8	0.871	Contact Map
1lbaA	1	0.9123	7.1	0.883	Contact Map
2e2dC	1	0.8421	5	0.891	Contact Map
1uapA	1	0.3684	4.9	0.891	Contact Map
3itfA	2	0.4561	4.5	0.894	Contact Map
4lu2A	2	0.8246	4.4	0.894	Contact Map
3ghgC	2	0.6667	4.3	0.894	Contact Map
3q7cA	1	0.8421	4	0.896	Contact Map
4k7eA	2	0.7193	3.9	0.897	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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