Phage_holin_2_3 - PFAM28P - GREMLIN Contacts

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Phage_holin_2_3 - Bacteriophage holin family HP1

PFAM:	PF16080	Sequences: EKITSAASYGGSGATALFGALTLNEWAAIVGIVIGVATFLVNWYYKRKEYKLLKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (52)
Sequences:	822 (629)
Seq/√Len:	87.2
META:	0.616

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
49_E	53_L	4.011	1.00
46_K	49_E	3.492	1.00
41_V	45_Y	2.119	1.00
47_R	51_K	1.860	1.00
11_G	38_T	1.806	1.00
8_S	38_T	1.745	1.00
5_S	42_N	1.723	1.00
48_K	52_L	1.671	1.00
27_A	32_I	1.589	1.00
38_T	42_N	1.508	1.00
9_Y	38_T	1.486	0.99
23_L	26_W	1.455	0.99
34_I	39_F	1.432	0.99
15_T	31_G	1.404	0.99
6_A	10_G	1.380	0.99
9_Y	12_S	1.359	0.99
7_A	10_G	1.298	0.99
26_W	29_I	1.289	0.99
11_G	15_T	1.244	0.98
23_L	32_I	1.235	0.98
15_T	35_G	1.233	0.98
48_K	51_K	1.169	0.97
19_G	31_G	1.107	0.96
49_E	52_L	1.089	0.96
30_V	36_V	1.065	0.95
43_W	47_R	1.044	0.95
4_T	8_S	1.040	0.95
11_G	14_A	1.027	0.94
29_I	33_V	1.002	0.93
30_V	33_V	0.995	0.93
2_K	6_A	0.967	0.92
9_Y	42_N	0.964	0.92
19_G	27_A	0.956	0.92
28_A	32_I	0.943	0.91
23_L	27_A	0.940	0.91
12_S	15_T	0.888	0.88
39_F	43_W	0.884	0.88
3_I	6_A	0.848	0.86
17_L	21_L	0.796	0.82
30_V	34_I	0.786	0.82
44_Y	48_K	0.773	0.80
44_Y	49_E	0.771	0.80
46_K	50_Y	0.752	0.79
10_G	17_L	0.747	0.78
21_L	24_N	0.744	0.78
23_L	29_I	0.725	0.76
14_A	40_L	0.720	0.76
12_S	31_G	0.706	0.74
13_G	40_L	0.691	0.73
15_T	27_A	0.687	0.72
33_V	47_R	0.667	0.70
19_G	30_V	0.641	0.67
14_A	51_K	0.634	0.66
10_G	51_K	0.634	0.66
33_V	43_W	0.633	0.66
28_A	35_G	0.630	0.66
25_E	28_A	0.623	0.65
16_A	51_K	0.622	0.65
11_G	18_F	0.617	0.64
12_S	34_I	0.580	0.59
7_A	37_A	0.579	0.59
10_G	19_G	0.578	0.59
40_L	44_Y	0.570	0.58
15_T	24_N	0.568	0.58
15_T	40_L	0.559	0.56
17_L	25_E	0.553	0.56
3_I	13_G	0.530	0.53
26_W	30_V	0.527	0.52
13_G	33_V	0.524	0.52
22_T	29_I	0.521	0.51
20_A	23_L	0.518	0.51
15_T	28_A	0.516	0.51
17_L	20_A	0.505	0.49
4_T	10_G	0.504	0.49
50_Y	53_L	0.502	0.49
23_L	33_V	0.501	0.49
15_T	25_E	0.500	0.48
12_S	35_G	0.500	0.48

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
2kluA	1	0.6364	29.8	0.812	Contact Map
2l2tA	2	0.7818	25	0.819	Contact Map
4ry2A	2	1	24.6	0.82	Contact Map
4a82A	2	1	23.1	0.822	Contact Map
4q4hB	1	1	22.7	0.823	Contact Map
4um9B	2	0	22.3	0.823	Contact Map
4f4cA	1	1	21.6	0.825	Contact Map
3b5xA	2	1	17.4	0.832	Contact Map
2m20A	2	0.6545	16.5	0.834	Contact Map
4tllA	1	0.5818	15.7	0.835	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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