PTR - PFAM28P - GREMLIN Contacts

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PTR - Phage tail repeat like

PFAM:	PF12789	Sequences: EKAATSHTHAISDVTGLQTALDGKADTSHTHTIADVTGLQTALDGKADTSHTHTISDITD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (57)
Sequences:	1415 (1127)
Seq/√Len:	149.3
META:	0.881

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_Q	22_D	2.767	1.00
25_A	28_S	2.498	1.00
40_Q	44_D	2.281	1.00
3_A	6_S	2.175	1.00
38_G	42_A	2.012	1.00
16_G	20_A	1.992	1.00
47_A	50_S	1.856	1.00
33_I	40_Q	1.825	1.00
32_T	35_D	1.573	1.00
33_I	42_A	1.518	1.00
55_I	58_I	1.513	1.00
9_H	13_D	1.477	1.00
11_I	18_Q	1.464	1.00
54_T	57_D	1.430	1.00
12_S	34_A	1.329	1.00
10_A	13_D	1.325	1.00
19_T	41_T	1.313	1.00
20_A	42_A	1.289	1.00
11_I	33_I	1.278	1.00
15_T	37_T	1.221	1.00
8_T	30_T	1.216	1.00
28_S	50_S	1.214	1.00
39_L	43_L	1.174	1.00
47_A	51_H	1.165	1.00
27_T	49_T	1.103	0.99
26_D	48_D	1.095	0.99
11_I	20_A	1.060	0.99
33_I	55_I	1.046	0.99
31_H	35_D	1.030	0.99
33_I	39_L	1.027	0.99
16_G	38_G	0.999	0.99
24_K	46_K	0.981	0.99
5_T	27_T	0.965	0.98
18_Q	40_Q	0.950	0.98
54_T	59_T	0.924	0.98
22_D	44_D	0.912	0.98
32_T	37_T	0.910	0.98
14_V	36_V	0.886	0.97
11_I	22_D	0.882	0.97
9_H	53_H	0.871	0.97
53_H	57_D	0.848	0.96
43_L	46_K	0.845	0.96
6_S	28_S	0.835	0.96
30_T	52_T	0.822	0.96
47_A	53_H	0.815	0.95
25_A	29_H	0.813	0.95
54_T	58_I	0.813	0.95
11_I	14_V	0.784	0.94
8_T	52_T	0.770	0.94
7_H	13_D	0.769	0.94
23_G	45_G	0.766	0.94
10_A	54_T	0.764	0.94
14_V	58_I	0.762	0.94
10_A	15_T	0.758	0.93
11_I	17_L	0.743	0.93
20_A	23_G	0.742	0.93
33_I	43_L	0.725	0.92
10_A	32_T	0.716	0.91
39_L	46_K	0.712	0.91
4_A	26_D	0.712	0.91
33_I	44_D	0.688	0.90
5_T	49_T	0.684	0.89
16_G	21_L	0.682	0.89
13_D	35_D	0.682	0.89
17_L	39_L	0.679	0.89
19_T	23_G	0.677	0.89
17_L	24_K	0.672	0.88
21_L	24_K	0.672	0.88
52_T	56_S	0.649	0.87
11_I	16_G	0.631	0.85
36_V	39_L	0.625	0.85
11_I	55_I	0.621	0.84
17_L	21_L	0.609	0.83
29_H	36_V	0.606	0.83
31_H	53_H	0.602	0.82
6_S	12_S	0.598	0.82
34_A	37_T	0.596	0.82
14_V	17_L	0.594	0.82
35_D	57_D	0.582	0.80
31_H	36_V	0.570	0.79
41_T	45_G	0.570	0.79
7_H	51_H	0.568	0.79
13_D	57_D	0.544	0.76
5_T	8_T	0.536	0.75
6_S	50_S	0.502	0.70
34_A	56_S	0.500	0.69

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
3cveA	4	0.6667	1.2	0.9	Contact Map
2r6fA	2	1	1	0.904	Contact Map
3zqjA	1	1	1	0.907	Contact Map
3pihA	2	0.9833	0.9	0.907	Contact Map
3v6bA	2	0.3	0.9	0.907	Contact Map
2makB	2	0.3833	0.9	0.908	Contact Map
4ecgA	1	0.9667	0.9	0.91	Contact Map
4bgoA	1	0.9833	0.8	0.91	Contact Map
3he1A	3	0.3667	0.8	0.911	Contact Map
3qh9A	2	0.5167	0.8	0.911	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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