Phage_holin_3_7 - PFAM28P - GREMLIN Contacts

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Phage_holin_3_7 - Putative 3TM holin, Phage_holin_3

PFAM:	PF05449	Sequences: INALACLAIALRLLTYRRGGARHRPGVSWLAYLLIVATGSVAIRILFGLYPAVSWAEVLINLLLCVAVLRARGNVARLLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	80 (78)
Sequences:	565 (389)
Seq/√Len:	44.1
META:	0.481

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_Y	21_A	4.145	1.00
14_L	35_I	4.115	1.00
2_N	61_N	3.216	1.00
32_Y	36_V	3.069	1.00
9_I	38_T	2.867	1.00
8_A	69_L	2.501	1.00
37_A	59_L	2.106	0.99
8_A	65_C	1.936	0.99
12_R	16_Y	1.725	0.98
27_V	76_A	1.724	0.98
5_A	65_C	1.597	0.97
57_E	61_N	1.551	0.96
36_V	39_G	1.503	0.95
6_C	61_N	1.479	0.95
5_A	58_V	1.476	0.95
6_C	9_I	1.445	0.94
41_V	44_R	1.369	0.92
50_Y	57_E	1.339	0.91
42_A	57_E	1.338	0.91
28_S	69_L	1.335	0.91
28_S	31_A	1.325	0.91
44_R	54_S	1.322	0.91
5_A	62_L	1.255	0.88
54_S	57_E	1.250	0.88
10_A	13_L	1.169	0.84
34_L	37_A	1.162	0.84
11_L	62_L	1.123	0.82
22_R	76_A	1.117	0.81
72_R	75_V	1.085	0.79
75_V	79_L	1.066	0.78
13_L	35_I	1.041	0.77
54_S	76_A	1.036	0.76
37_A	43_I	1.032	0.76
25_P	29_W	1.029	0.76
46_L	59_L	1.023	0.75
27_V	63_L	1.019	0.75
3_A	29_W	1.012	0.74
10_A	38_T	1.012	0.74
7_L	42_A	1.012	0.74
37_A	57_E	1.006	0.74
40_S	54_S	0.993	0.73
12_R	15_T	0.975	0.72
28_S	76_A	0.959	0.70
12_R	35_I	0.959	0.70
38_T	64_L	0.950	0.70
67_A	78_L	0.942	0.69
16_Y	74_N	0.932	0.68
34_L	75_V	0.922	0.67
24_R	76_A	0.918	0.67
24_R	27_V	0.916	0.67
9_I	68_V	0.895	0.65
38_T	60_I	0.886	0.64
3_A	23_H	0.885	0.64
3_A	7_L	0.868	0.63
10_A	45_I	0.865	0.62
2_N	6_C	0.853	0.61
10_A	35_I	0.849	0.61
55_W	58_V	0.830	0.59
46_L	75_V	0.828	0.59
2_N	13_L	0.826	0.59
35_I	60_I	0.825	0.59
22_R	27_V	0.806	0.57
4_L	10_A	0.771	0.54
76_A	79_L	0.762	0.53
33_L	75_V	0.755	0.52
21_A	27_V	0.744	0.51
34_L	60_I	0.738	0.50
31_A	74_N	0.728	0.49
69_L	72_R	0.721	0.49
39_G	43_I	0.713	0.48
34_L	67_A	0.711	0.48
32_Y	39_G	0.706	0.47
24_R	64_L	0.699	0.47
18_R	40_S	0.689	0.46
63_L	78_L	0.684	0.45
10_A	36_V	0.675	0.44
53_V	71_A	0.674	0.44
6_C	10_A	0.674	0.44
22_R	56_A	0.658	0.43
26_G	37_A	0.651	0.42
7_L	48_G	0.640	0.41
41_V	50_Y	0.634	0.40
70_R	74_N	0.626	0.40
9_I	69_L	0.617	0.39
16_Y	23_H	0.612	0.38
14_L	23_H	0.608	0.38
40_S	44_R	0.606	0.38
36_V	47_F	0.596	0.37
49_L	60_I	0.590	0.36
41_V	54_S	0.589	0.36
25_P	70_R	0.581	0.36
5_A	24_R	0.580	0.36
64_L	78_L	0.579	0.35
58_V	61_N	0.567	0.34
10_A	32_Y	0.565	0.34
11_L	72_R	0.559	0.34
18_R	23_H	0.557	0.34
10_A	25_P	0.555	0.33
10_A	14_L	0.554	0.33
38_T	43_I	0.554	0.33
71_A	77_R	0.554	0.33
72_R	77_R	0.552	0.33
43_I	50_Y	0.550	0.33
24_R	72_R	0.548	0.33
54_S	63_L	0.539	0.32
17_R	33_L	0.528	0.31
38_T	45_I	0.522	0.31
13_L	66_V	0.521	0.31
11_L	79_L	0.517	0.30
9_I	60_I	0.511	0.30
41_V	75_V	0.510	0.30
32_Y	77_R	0.507	0.29
29_W	66_V	0.504	0.29
30_L	63_L	0.501	0.29
18_R	77_R	0.501	0.29
38_T	70_R	0.500	0.29
13_L	59_L	0.500	0.29

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
3wajA	1	0.95	2.8	0.908	Contact Map
2ks1B	1	0.325	2.2	0.914	Contact Map
2jwaA	2	0.3125	2.1	0.914	Contact Map
3rceA	1	0.9625	2	0.916	Contact Map
4wgvA	2	0.55	1.9	0.916	Contact Map
2l2tA	2	0.3375	1.8	0.918	Contact Map
4qncA	2	0.2125	1.7	0.918	Contact Map
4u9nA	2	0.8125	1.5	0.921	Contact Map
3lb6C	1	0	1.4	0.922	Contact Map
3l1lA	2	0.95	1.3	0.923	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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