PHINT_rpt - PFAM28P - GREMLIN Contacts

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PHINT_rpt - Phage-integrase repeat unit

PFAM:	PF14882	Sequences: EYKKRYKKDPRLPSNPDRVYKDEWKGWGDFLGTGRPRKYRTFEEARKAAQKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	52 (50)
Sequences:	2658 (2411)
Seq/√Len:	340.9
META:	0.882

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_R	8_K	4.324	1.00
42_F	46_R	2.815	1.00
25_K	29_D	2.794	1.00
28_G	33_T	2.404	1.00
46_R	50_Q	2.113	1.00
41_T	44_E	2.067	1.00
46_R	49_A	1.704	1.00
15_N	18_R	1.687	1.00
26_G	29_D	1.652	1.00
17_D	27_W	1.573	1.00
6_Y	9_D	1.548	1.00
27_W	31_L	1.502	1.00
21_K	24_W	1.392	1.00
13_P	19_V	1.351	1.00
28_G	34_G	1.342	1.00
28_G	36_P	1.339	1.00
12_L	30_F	1.278	1.00
9_D	12_L	1.252	1.00
40_R	48_A	1.249	1.00
24_W	27_W	1.240	1.00
12_L	48_A	1.193	1.00
6_Y	14_S	1.175	1.00
15_N	19_V	1.136	1.00
29_D	42_F	1.071	1.00
36_P	39_Y	1.069	1.00
47_K	51_K	0.971	1.00
2_Y	12_L	0.938	1.00
39_Y	48_A	0.912	1.00
4_K	47_K	0.856	1.00
3_K	15_N	0.839	1.00
22_D	25_K	0.809	1.00
27_W	30_F	0.805	1.00
47_K	50_Q	0.796	1.00
42_F	45_A	0.796	1.00
6_Y	12_L	0.777	1.00
48_A	51_K	0.767	1.00
37_R	40_R	0.761	1.00
12_L	39_Y	0.754	1.00
17_D	21_K	0.721	0.99
2_Y	5_R	0.720	0.99
25_K	42_F	0.713	0.99
26_G	35_R	0.693	0.99
8_K	11_R	0.693	0.99
34_G	47_K	0.681	0.99
6_Y	10_P	0.671	0.99
15_N	32_G	0.667	0.99
25_K	28_G	0.655	0.99
34_G	37_R	0.647	0.99
3_K	14_S	0.643	0.99
21_K	36_P	0.623	0.98
42_F	48_A	0.620	0.98
38_K	41_T	0.617	0.98
21_K	38_K	0.605	0.98
14_S	22_D	0.602	0.98
4_K	36_P	0.602	0.98
3_K	8_K	0.599	0.98
23_E	43_E	0.593	0.98
12_L	45_A	0.588	0.97
23_E	42_F	0.584	0.97
41_T	45_A	0.564	0.97
7_K	32_G	0.556	0.96
33_T	39_Y	0.555	0.96
4_K	43_E	0.552	0.96
20_Y	43_E	0.539	0.96
14_S	34_G	0.534	0.96
29_D	46_R	0.531	0.95
19_V	27_W	0.521	0.95
7_K	27_W	0.515	0.95
40_R	43_E	0.514	0.95
13_P	20_Y	0.512	0.94
42_F	49_A	0.507	0.94
3_K	17_D	0.504	0.94
23_E	27_W	0.503	0.94
37_R	43_E	0.503	0.94
24_W	31_L	0.500	0.94

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
1uw4B	1	0.9038	6.9	0.85	Contact Map
1yu0A	3	0.7885	5.3	0.858	Contact Map
2bpdA	2	0.6731	4.7	0.861	Contact Map
4do4A	2	0.7885	4.6	0.862	Contact Map
3wbzA	5	1	4.3	0.863	Contact Map
1gwmA	1	0.8846	4.2	0.864	Contact Map
3js8A	1	0.8269	4.2	0.864	Contact Map
1vquA	2	0.5385	4.1	0.865	Contact Map
1wcuA	1	0.8846	4	0.866	Contact Map
1dkiA	1	0.2885	3.7	0.867	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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