Holin_SPP1 - PFAM28P - GREMLIN Contacts

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Holin_SPP1 - SPP1 phage holin

PFAM:	PF04688	Sequences: KIDKGTIIRTIVLLLALINQILVAFGKSPLPIDEEQIYQAVSTVFTVVAALWAWWKNNSFTKKAKEADEVLKEH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (72)
Sequences:	961 (710)
Seq/√Len:	83.7
META:	0.693

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_S	68_D	5.040	1.00
20_Q	46_T	2.830	1.00
67_A	71_L	2.720	1.00
12_V	49_A	2.549	1.00
16_A	45_F	2.351	1.00
9_R	58_N	2.254	1.00
10_T	54_W	2.124	1.00
55_W	64_A	1.915	1.00
66_E	69_E	1.774	1.00
63_K	71_L	1.642	1.00
59_S	64_A	1.626	1.00
13_L	17_L	1.591	1.00
59_S	67_A	1.575	1.00
33_D	36_Q	1.573	1.00
21_I	25_F	1.544	1.00
4_K	8_I	1.527	1.00
63_K	67_A	1.520	0.99
49_A	53_A	1.516	0.99
57_N	68_D	1.434	0.99
37_I	41_V	1.429	0.99
28_S	33_D	1.426	0.99
67_A	70_V	1.330	0.99
38_Y	42_S	1.290	0.98
28_S	38_Y	1.288	0.98
32_I	40_A	1.177	0.97
22_L	29_P	1.174	0.97
48_V	52_W	1.155	0.97
24_A	39_Q	1.144	0.96
62_K	65_K	1.073	0.95
54_W	60_F	1.064	0.95
13_L	50_A	1.045	0.94
13_L	53_A	1.032	0.94
6_T	10_T	1.030	0.94
54_W	58_N	1.019	0.93
39_Q	43_T	0.975	0.92
45_F	49_A	0.973	0.92
10_T	60_F	0.949	0.91
23_V	29_P	0.946	0.90
32_I	37_I	0.943	0.90
42_S	46_T	0.940	0.90
23_V	28_S	0.936	0.90
68_D	71_L	0.928	0.90
4_K	45_F	0.925	0.89
13_L	20_Q	0.925	0.89
6_T	61_T	0.904	0.88
16_A	49_A	0.896	0.88
5_G	52_W	0.884	0.87
24_A	27_K	0.872	0.86
61_T	64_A	0.867	0.86
11_I	37_I	0.856	0.85
21_I	43_T	0.837	0.84
46_T	50_A	0.830	0.84
14_L	17_L	0.819	0.83
8_I	12_V	0.810	0.82
5_G	8_I	0.767	0.79
33_D	37_I	0.763	0.78
59_S	65_K	0.753	0.77
55_W	61_T	0.752	0.77
20_Q	23_V	0.717	0.74
42_S	45_F	0.713	0.73
60_F	67_A	0.709	0.73
66_E	70_V	0.708	0.73
9_R	19_N	0.707	0.73
19_N	30_L	0.703	0.72
39_Q	72_K	0.684	0.70
23_V	38_Y	0.679	0.70
24_A	43_T	0.674	0.69
53_A	56_K	0.674	0.69
55_W	59_S	0.668	0.68
31_P	54_W	0.665	0.68
15_L	20_Q	0.664	0.68
63_K	70_V	0.658	0.67
34_E	47_V	0.652	0.67
2_I	6_T	0.651	0.66
10_T	53_A	0.650	0.66
16_A	20_Q	0.649	0.66
7_I	10_T	0.648	0.66
16_A	46_T	0.643	0.65
64_A	67_A	0.629	0.64
46_T	49_A	0.609	0.61
11_I	49_A	0.609	0.61
34_E	38_Y	0.605	0.61
15_L	37_I	0.602	0.60
68_D	72_K	0.599	0.60
59_S	71_L	0.595	0.59
52_W	55_W	0.594	0.59
17_L	46_T	0.584	0.58
24_A	29_P	0.579	0.57
49_A	52_W	0.576	0.57
3_D	65_K	0.570	0.56
12_V	45_F	0.568	0.56
23_V	39_Q	0.565	0.56
22_L	27_K	0.559	0.55
65_K	72_K	0.555	0.54
59_S	63_K	0.554	0.54
64_A	68_D	0.552	0.54
35_E	38_Y	0.547	0.53
55_W	60_F	0.534	0.52
51_L	54_W	0.512	0.49
57_N	61_T	0.511	0.48
55_W	63_K	0.511	0.48
9_R	12_V	0.508	0.48
39_Q	42_S	0.507	0.48
20_Q	43_T	0.507	0.48
4_K	7_I	0.504	0.48
5_G	9_R	0.504	0.48
62_K	66_E	0.501	0.47
46_T	53_A	0.500	0.47

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
1pp7U	1	0.7162	9.6	0.889	Contact Map
4r9fA	1	0.4054	7.1	0.895	Contact Map
4i0uA	4	0.7838	6.6	0.897	Contact Map
4aurA	1	0.9324	5.8	0.9	Contact Map
4a4zA	1	0.7162	5.7	0.9	Contact Map
4u4cA	1	0.7162	3.9	0.908	Contact Map
3mktA	1	1	3.1	0.912	Contact Map
1v9dA	3	0.9189	3.1	0.912	Contact Map
1kwfA	1	0.6081	3	0.913	Contact Map
3j01B	1	0.8514	3	0.913	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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