Phage_r1t_holin - PFAM28P - GREMLIN Contacts

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Phage_r1t_holin - Putative lactococcus lactis phage r1t holin

PFAM:	PF16945	Sequences: TKKFWKAAGERAVKTFAQTALALIGAGAVGLLDVDWLQVLSVAALAAVLSLLTSIAGLPVGDPGSASLVPTR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	72 (62)
Sequences:	2791 (1984)
Seq/√Len:	252.0
META:	0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_F	47_A	3.981	1.00
14_K	53_T	3.015	1.00
15_T	18_Q	2.075	1.00
16_F	43_A	2.026	1.00
18_Q	53_T	1.727	1.00
14_K	57_G	1.698	1.00
50_S	54_S	1.623	1.00
21_L	56_A	1.602	1.00
20_A	39_V	1.568	1.00
2_K	6_K	1.512	1.00
30_G	41_S	1.497	1.00
8_A	54_S	1.480	1.00
8_A	51_L	1.465	1.00
20_A	52_L	1.433	1.00
12_A	51_L	1.407	1.00
15_T	19_T	1.397	1.00
19_T	46_A	1.395	1.00
4_F	8_A	1.337	1.00
12_A	54_S	1.310	1.00
20_A	43_A	1.276	1.00
43_A	47_A	1.247	1.00
38_Q	42_V	1.230	1.00
35_D	38_Q	1.194	1.00
17_A	52_L	1.189	1.00
53_T	57_G	1.141	1.00
25_G	29_V	1.140	1.00
34_V	45_L	1.126	1.00
25_G	49_L	1.102	1.00
22_A	46_A	1.074	1.00
21_L	49_L	1.065	1.00
7_A	57_G	1.043	1.00
37_L	40_L	1.032	1.00
25_G	28_A	1.012	1.00
6_K	9_G	1.005	1.00
30_G	33_D	1.001	1.00
4_F	57_G	0.978	1.00
34_V	39_V	0.970	1.00
15_T	46_A	0.962	1.00
12_A	50_S	0.936	1.00
19_T	23_L	0.918	1.00
16_F	40_L	0.898	1.00
32_L	41_S	0.887	1.00
18_Q	50_S	0.866	0.99
40_L	43_A	0.865	0.99
30_G	45_L	0.864	0.99
7_A	58_L	0.855	0.99
16_F	44_A	0.852	0.99
18_Q	49_L	0.838	0.99
22_A	26_A	0.832	0.99
7_A	11_R	0.832	0.99
40_L	44_A	0.821	0.99
39_V	43_A	0.821	0.99
22_A	42_V	0.819	0.99
9_G	51_L	0.816	0.99
11_R	15_T	0.800	0.99
3_K	7_A	0.796	0.99
41_S	45_L	0.789	0.99
19_T	43_A	0.765	0.99
23_L	42_V	0.763	0.99
4_F	58_L	0.745	0.98
14_K	18_Q	0.737	0.98
4_F	10_E	0.732	0.98
44_A	47_A	0.715	0.98
31_L	44_A	0.705	0.98
31_L	45_L	0.700	0.98
21_L	25_G	0.696	0.98
58_L	61_G	0.688	0.97
4_F	54_S	0.683	0.97
19_T	22_A	0.682	0.97
60_V	63_P	0.673	0.97
42_V	46_A	0.670	0.97
42_V	45_L	0.669	0.97
44_A	48_V	0.643	0.96
6_K	10_E	0.631	0.96
10_E	57_G	0.629	0.96
10_E	14_K	0.627	0.96
13_V	17_A	0.624	0.96
5_W	10_E	0.594	0.94
9_G	13_V	0.585	0.94
16_F	46_A	0.584	0.94
11_R	18_Q	0.580	0.93
8_A	55_I	0.579	0.93
12_A	47_A	0.569	0.93
53_T	56_A	0.566	0.93
31_L	42_V	0.565	0.93
17_A	56_A	0.539	0.91
28_A	31_L	0.537	0.91
3_K	6_K	0.527	0.90
37_L	44_A	0.525	0.90
41_S	48_V	0.519	0.89
8_A	50_S	0.511	0.88
14_K	50_S	0.503	0.88
26_A	45_L	0.500	0.87

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
2lo0A	2	0.3333	5	0.888	Contact Map
5aj3d	1	0	2.7	0.901	Contact Map
1iflA	10	0.7361	1.9	0.91	Contact Map
4grdA	5	0.9861	1.8	0.911	Contact Map
1o4vA	5	0.9861	1.7	0.911	Contact Map
4ay3A	2	0.9861	1.6	0.914	Contact Map
3bboD	1	0	1.4	0.916	Contact Map
4ja0A	6	0.9583	1.4	0.916	Contact Map
3orsA	5	0.9861	1.4	0.917	Contact Map
4rhpA	2	0.4167	1.4	0.917	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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