Phage_holin_6_1 - PFAM28P - GREMLIN Contacts

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Phage_holin_6_1 - Bacteriophage holin of superfamily 6 (Holin_LLH)

PFAM:	PF09682	Sequences: INEILTPILVAIITLLAALLTKYLKPYLKAKTTAEQLEKIAEIAKIAVKAAEQLYKDGGKGEEKKEYALEKLKEFLKKKGIKITDEEIDALIEAAVKELKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	101 (95)
Sequences:	2477 (2137)
Seq/√Len:	219.2
META:	0.873

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_K	89_D	4.392	1.00
60_K	63_E	2.570	1.00
73_K	85_D	2.416	1.00
65_K	69_L	2.378	1.00
53_Q	93_E	2.193	1.00
51_A	67_Y	2.188	1.00
84_T	87_E	2.132	1.00
33_T	36_Q	2.053	1.00
22_K	26_P	1.914	1.00
50_A	54_L	1.874	1.00
47_A	68_A	1.873	1.00
7_P	10_V	1.810	1.00
34_A	38_E	1.799	1.00
75_F	78_K	1.749	1.00
72_L	88_I	1.706	1.00
22_K	25_K	1.672	1.00
47_A	71_K	1.647	1.00
31_K	35_E	1.532	1.00
69_L	89_D	1.519	1.00
75_F	79_K	1.491	1.00
47_A	51_A	1.483	1.00
57_D	60_K	1.420	1.00
69_L	73_K	1.404	1.00
23_Y	26_P	1.397	1.00
66_E	70_E	1.396	1.00
44_A	72_L	1.386	1.00
19_L	23_Y	1.382	1.00
93_E	96_V	1.373	1.00
73_K	77_K	1.346	1.00
45_K	49_K	1.323	1.00
52_E	96_V	1.322	1.00
44_A	91_L	1.317	1.00
38_E	41_A	1.313	1.00
67_Y	70_E	1.282	1.00
44_A	68_A	1.252	1.00
52_E	100_K	1.247	1.00
71_K	90_A	1.244	1.00
95_A	98_E	1.240	1.00
96_V	100_K	1.232	1.00
43_I	72_L	1.231	1.00
45_K	98_E	1.185	1.00
55_Y	59_G	1.155	1.00
71_K	75_F	1.155	1.00
48_V	53_Q	1.148	1.00
70_E	74_E	1.136	1.00
38_E	42_E	1.131	1.00
33_T	37_L	1.101	1.00
63_E	66_E	1.066	1.00
23_Y	27_Y	1.034	1.00
51_A	55_Y	1.034	1.00
18_A	22_K	0.984	1.00
35_E	39_K	0.972	1.00
53_Q	97_K	0.968	1.00
25_K	29_K	0.959	1.00
27_Y	31_K	0.942	1.00
74_E	78_K	0.935	1.00
10_V	14_T	0.928	0.99
56_K	60_K	0.927	0.99
76_L	88_I	0.905	0.99
71_K	74_E	0.880	0.99
76_L	81_I	0.866	0.99
44_A	48_V	0.865	0.99
39_K	42_E	0.860	0.99
50_A	53_Q	0.859	0.99
23_Y	29_K	0.846	0.99
7_P	14_T	0.838	0.99
37_L	40_I	0.831	0.99
32_T	36_Q	0.829	0.99
55_Y	61_G	0.827	0.99
77_K	82_K	0.823	0.99
40_I	91_L	0.808	0.99
51_A	59_G	0.807	0.99
69_L	88_I	0.805	0.99
14_T	18_A	0.798	0.98
53_Q	100_K	0.789	0.98
41_A	45_K	0.787	0.98
11_A	14_T	0.780	0.98
6_T	11_A	0.775	0.98
49_K	97_K	0.768	0.98
20_L	23_Y	0.767	0.98
47_A	72_L	0.766	0.98
65_K	93_E	0.754	0.98
92_I	96_V	0.752	0.98
76_L	79_K	0.723	0.97
63_E	67_Y	0.719	0.97
24_L	28_L	0.716	0.97
48_V	52_E	0.712	0.97
69_L	85_D	0.706	0.97
91_L	94_A	0.697	0.96
49_K	94_A	0.694	0.96
53_Q	96_V	0.692	0.96
48_V	95_A	0.676	0.96
50_A	67_Y	0.671	0.96
65_K	92_I	0.666	0.95
37_L	41_A	0.665	0.95
86_E	89_D	0.660	0.95
29_K	33_T	0.658	0.95
46_I	90_A	0.657	0.95
56_K	64_K	0.655	0.95
19_L	25_K	0.653	0.95
59_G	63_E	0.643	0.94
35_E	38_E	0.639	0.94
32_T	37_L	0.638	0.94
61_G	64_K	0.638	0.94
61_G	68_A	0.638	0.94
73_K	88_I	0.637	0.94
19_L	22_K	0.625	0.94
16_L	21_T	0.617	0.93
44_A	53_Q	0.609	0.93
52_E	61_G	0.609	0.93
76_L	84_T	0.601	0.92
52_E	64_K	0.597	0.92
51_A	68_A	0.596	0.92
7_P	11_A	0.591	0.92
62_E	66_E	0.590	0.91
65_K	96_V	0.585	0.91
76_L	80_G	0.583	0.91
96_V	99_L	0.582	0.91
72_L	76_L	0.581	0.91
30_A	33_T	0.576	0.90
43_I	75_F	0.573	0.90
89_D	96_V	0.567	0.90
59_G	67_Y	0.567	0.90
40_I	83_I	0.563	0.89
31_K	34_A	0.560	0.89
68_A	72_L	0.547	0.88
56_K	59_G	0.546	0.88
17_A	26_P	0.537	0.87
42_E	46_I	0.521	0.86
32_T	40_I	0.519	0.85
90_A	97_K	0.513	0.85
48_V	99_L	0.512	0.85
21_T	26_P	0.510	0.84
14_T	21_T	0.507	0.84
94_A	98_E	0.507	0.84
74_E	77_K	0.505	0.84
76_L	83_I	0.504	0.84
15_L	22_K	0.502	0.83
8_I	14_T	0.502	0.83
5_L	9_L	0.500	0.83
67_Y	71_K	0.500	0.83
12_I	16_L	0.500	0.83

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
2k19A	1	0.495	13.4	0.854	Contact Map
2m7gA	1	0.5842	11.8	0.858	Contact Map
4r3zC	1	0	11.1	0.86	Contact Map
4xlyA	2	0.8416	9.3	0.864	Contact Map
1qzmA	1	0.4455	9.1	0.865	Contact Map
4gitA	2	0.4356	9.1	0.865	Contact Map
1w26A	1	0.3663	7.8	0.869	Contact Map
2y0oA	2	0.3465	7.7	0.869	Contact Map
2kv5A	1	0.3267	7.1	0.871	Contact Map
2nscA	2	0.3663	6.6	0.873	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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