Phage_holin_1 - PFAM28P - GREMLIN Contacts

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Phage_holin_1 - Bacteriophage holin

PFAM:	PF04531	Sequences: INWKVRFKNKAFWLALIPAVLLLIQAVAGLFGYDLTSWALGDQLLAIVNAVFAVLAILGVVVDPTTKGISDSERALTYEKPK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	82 (82)
Sequences:	1080 (779)
Seq/√Len:	86.0
META:	0.734

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_R	82_K	5.369	1.00
5_V	12_F	2.728	1.00
28_A	33_Y	2.635	1.00
7_F	13_W	2.613	1.00
75_A	78_Y	2.594	1.00
42_D	46_A	2.494	1.00
18_P	52_F	2.365	1.00
2_N	5_V	2.048	1.00
19_A	56_A	2.037	1.00
72_S	75_A	1.826	1.00
25_Q	49_N	1.819	1.00
26_A	50_A	1.724	1.00
52_F	61_V	1.671	1.00
12_F	16_L	1.574	1.00
55_L	60_V	1.554	1.00
70_S	76_L	1.553	1.00
16_L	57_I	1.538	1.00
15_A	18_P	1.450	0.99
22_L	25_Q	1.413	0.99
17_I	48_V	1.407	0.99
39_A	43_Q	1.399	0.99
39_A	42_D	1.315	0.99
37_S	40_L	1.276	0.98
50_A	54_V	1.260	0.98
27_V	47_I	1.244	0.98
10_K	15_A	1.239	0.98
73_E	76_L	1.237	0.98
4_K	79_E	1.195	0.97
30_L	47_I	1.183	0.97
3_W	7_F	1.129	0.96
11_A	62_V	1.123	0.96
6_R	65_T	1.116	0.96
13_W	18_P	1.102	0.96
48_V	52_F	1.093	0.96
16_L	54_V	1.082	0.95
23_L	47_I	1.075	0.95
23_L	27_V	1.030	0.94
77_T	80_K	1.009	0.93
15_A	19_A	1.004	0.93
74_R	77_T	1.002	0.93
38_W	45_L	1.001	0.93
42_D	49_N	0.997	0.93
7_F	16_L	0.978	0.92
2_N	72_S	0.973	0.92
65_T	75_A	0.968	0.92
53_A	56_A	0.935	0.91
9_N	13_W	0.932	0.90
38_W	42_D	0.922	0.90
22_L	50_A	0.907	0.89
21_L	41_G	0.900	0.89
22_L	49_N	0.896	0.89
15_A	60_V	0.894	0.88
5_V	8_K	0.891	0.88
74_R	78_Y	0.881	0.88
7_F	76_L	0.876	0.87
34_D	38_W	0.874	0.87
5_V	65_T	0.844	0.85
73_E	77_T	0.841	0.85
25_Q	35_L	0.839	0.85
1_I	70_S	0.829	0.84
55_L	59_G	0.820	0.84
72_S	78_Y	0.818	0.84
70_S	77_T	0.813	0.83
69_I	79_E	0.808	0.83
14_L	49_N	0.798	0.82
41_G	44_L	0.796	0.82
70_S	73_E	0.793	0.82
67_K	70_S	0.788	0.81
7_F	80_K	0.783	0.81
21_L	44_L	0.768	0.80
3_W	61_V	0.754	0.78
6_R	64_P	0.741	0.77
68_G	71_D	0.739	0.77
17_I	52_F	0.730	0.76
67_K	77_T	0.727	0.76
23_L	26_A	0.722	0.75
30_L	44_L	0.710	0.74
19_A	50_A	0.707	0.74
63_D	72_S	0.697	0.73
19_A	22_L	0.695	0.72
24_I	44_L	0.669	0.70
22_L	53_A	0.652	0.68
10_K	63_D	0.635	0.66
1_I	6_R	0.619	0.64
6_R	9_N	0.617	0.63
69_I	77_T	0.609	0.62
27_V	43_Q	0.608	0.62
19_A	57_I	0.608	0.62
73_E	80_K	0.608	0.62
20_V	51_V	0.607	0.62
22_L	35_L	0.603	0.62
29_G	43_Q	0.603	0.62
78_Y	81_P	0.596	0.61
63_D	78_Y	0.583	0.59
65_T	78_Y	0.576	0.58
11_A	15_A	0.568	0.57
66_T	75_A	0.567	0.57
17_I	45_L	0.567	0.57
15_A	62_V	0.565	0.57
8_K	12_F	0.557	0.56
10_K	60_V	0.550	0.55
35_L	41_G	0.546	0.54
22_L	52_F	0.545	0.54
65_T	72_S	0.542	0.54
26_A	54_V	0.540	0.53
18_P	60_V	0.540	0.53
55_L	58_L	0.535	0.53
5_V	63_D	0.534	0.53
30_L	43_Q	0.533	0.52
5_V	72_S	0.527	0.52
14_L	70_S	0.526	0.51
15_A	59_G	0.524	0.51
26_A	49_N	0.522	0.51
30_L	35_L	0.521	0.51
62_V	67_K	0.515	0.50
73_E	79_E	0.515	0.50
19_A	60_V	0.515	0.50
3_W	65_T	0.515	0.50
29_G	34_D	0.512	0.50
23_L	28_A	0.508	0.49
74_R	81_P	0.504	0.49
10_K	13_W	0.503	0.48
8_K	80_K	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
2kogA	1	0.4024	16.4	0.899	Contact Map
1uf2A	7	0.8902	14.3	0.902	Contact Map
4o6yA	2	0.7561	10.4	0.907	Contact Map
3hd7A	1	0.3902	8.3	0.912	Contact Map
2wswA	3	0.9268	4.7	0.921	Contact Map
4wgvA	2	0.878	3.3	0.927	Contact Map
1f6yA	2	0.3415	3.1	0.928	Contact Map
4c7rA	3	0.9024	2.9	0.929	Contact Map
1lnqA	6	0.6707	2.7	0.93	Contact Map
4bgnA	3	0.7927	2.2	0.933	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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