Phage_holin_4_1 - PFAM28P - GREMLIN Contacts

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Phage_holin_4_1 - Bacteriophage holin family

PFAM:	PF05105	Sequences: AFLGYLFGGWDGLLIALLILMVIDYITGVLAAIKNGKLSSRKGFKGIAKKVLYLLLVAVAHLLDKLLGGDGSYLRTAVIFFYIANEGISILENAGRLGVPIPKKLKKALEQLKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	114 (111)
Sequences:	7556 (5736)
Seq/√Len:	544.4
META:	0.857

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_A	96_R	3.987	1.00
60_A	78_V	2.978	1.00
27_T	93_N	2.637	1.00
40_S	92_E	2.520	1.00
28_G	32_A	2.500	1.00
21_M	54_L	2.481	1.00
43_G	85_N	2.469	1.00
35_N	96_R	2.320	1.00
20_L	83_I	2.284	1.00
16_A	62_L	2.224	1.00
25_Y	43_G	2.137	1.00
31_A	35_N	2.023	1.00
34_K	97_L	2.003	1.00
52_L	94_A	1.911	1.00
25_Y	46_G	1.898	1.00
94_A	99_V	1.882	1.00
38_L	88_I	1.879	1.00
46_G	50_K	1.850	1.00
34_K	45_K	1.811	1.00
61_H	65_K	1.807	1.00
17_L	82_Y	1.787	1.00
39_S	42_K	1.609	1.00
50_K	86_E	1.593	1.00
29_V	38_L	1.575	1.00
13_L	79_I	1.534	1.00
44_F	53_Y	1.513	1.00
103_K	107_K	1.484	1.00
53_Y	82_Y	1.471	1.00
30_L	48_A	1.452	1.00
24_D	89_S	1.294	1.00
104_K	107_K	1.265	1.00
59_V	87_G	1.257	1.00
33_I	108_A	1.245	1.00
11_D	75_R	1.240	1.00
84_A	88_I	1.223	1.00
19_I	62_L	1.215	1.00
6_L	58_A	1.208	1.00
95_G	106_K	1.205	1.00
15_I	19_I	1.203	1.00
51_V	56_L	1.200	1.00
3_L	7_F	1.176	1.00
87_G	109_L	1.156	1.00
61_H	75_R	1.141	1.00
62_L	65_K	1.127	1.00
87_G	91_L	1.127	1.00
28_G	89_S	1.115	1.00
56_L	94_A	1.102	1.00
12_G	15_I	1.098	1.00
57_V	79_I	1.098	1.00
33_I	38_L	1.093	1.00
11_D	15_I	1.089	1.00
17_L	57_V	1.088	1.00
103_K	106_K	1.087	1.00
23_I	55_L	1.076	1.00
23_I	90_I	1.071	1.00
30_L	97_L	1.042	1.00
80_F	84_A	1.024	1.00
21_M	53_Y	1.010	1.00
29_V	33_I	0.967	1.00
16_A	20_L	0.957	1.00
28_G	31_A	0.946	1.00
95_G	112_L	0.945	1.00
26_I	30_L	0.930	1.00
45_K	48_A	0.927	1.00
22_V	26_I	0.919	1.00
106_K	110_E	0.918	1.00
95_G	101_I	0.910	1.00
41_R	45_K	0.907	1.00
104_K	108_A	0.900	1.00
31_A	93_N	0.887	1.00
91_L	101_I	0.875	1.00
33_I	36_G	0.871	1.00
27_T	92_E	0.850	1.00
8_G	11_D	0.845	1.00
17_L	79_I	0.840	1.00
50_K	54_L	0.830	1.00
44_F	85_N	0.818	1.00
24_D	28_G	0.809	1.00
83_I	87_G	0.807	1.00
38_L	43_G	0.800	1.00
46_G	89_S	0.800	1.00
46_G	49_K	0.799	1.00
39_S	110_E	0.793	1.00
40_S	89_S	0.783	1.00
110_E	113_K	0.779	1.00
94_A	101_I	0.779	1.00
13_L	76_T	0.768	1.00
21_M	50_K	0.761	1.00
45_K	49_K	0.749	1.00
27_T	52_L	0.730	1.00
56_L	82_Y	0.722	1.00
48_A	52_L	0.719	1.00
25_Y	29_V	0.718	1.00
20_L	87_G	0.718	1.00
91_L	95_G	0.708	1.00
16_A	66_L	0.705	1.00
3_L	6_L	0.701	1.00
42_K	45_K	0.698	1.00
47_I	81_F	0.697	1.00
59_V	90_I	0.691	1.00
40_S	44_F	0.684	1.00
25_Y	47_I	0.680	1.00
52_L	97_L	0.677	1.00
27_T	31_A	0.671	1.00
53_Y	85_N	0.670	1.00
62_L	66_L	0.669	1.00
27_T	94_A	0.667	1.00
43_G	46_G	0.666	1.00
29_V	43_G	0.665	1.00
76_T	80_F	0.661	1.00
53_Y	86_E	0.659	1.00
30_L	33_I	0.658	1.00
31_A	97_L	0.657	1.00
32_A	37_K	0.654	1.00
43_G	47_I	0.646	1.00
44_F	49_K	0.642	1.00
13_L	80_F	0.637	1.00
43_G	88_I	0.636	1.00
34_K	48_A	0.634	1.00
66_L	83_I	0.623	1.00
55_L	59_V	0.622	1.00
32_A	38_L	0.622	1.00
23_I	59_V	0.619	1.00
107_K	111_Q	0.615	1.00
48_A	82_Y	0.612	1.00
14_L	79_I	0.610	1.00
95_G	98_G	0.609	1.00
47_I	85_N	0.606	1.00
19_I	23_I	0.605	1.00
37_K	110_E	0.599	1.00
27_T	90_I	0.586	1.00
88_I	91_L	0.584	0.99
84_A	109_L	0.582	0.99
64_D	75_R	0.579	0.99
63_L	87_G	0.578	0.99
63_L	67_L	0.578	0.99
64_D	68_G	0.577	0.99
24_D	86_E	0.572	0.99
88_I	92_E	0.572	0.99
8_G	75_R	0.571	0.99
68_G	71_G	0.570	0.99
70_D	73_Y	0.568	0.99
64_D	76_T	0.565	0.99
56_L	78_V	0.562	0.99
37_K	42_K	0.553	0.99
91_L	109_L	0.553	0.99
6_L	9_G	0.552	0.99
20_L	59_V	0.549	0.99
58_A	66_L	0.539	0.99
44_F	48_A	0.536	0.99
60_A	74_L	0.528	0.99
94_A	97_L	0.528	0.99
66_L	69_G	0.528	0.99
94_A	100_P	0.527	0.99
20_L	90_I	0.527	0.99
50_K	53_Y	0.523	0.99
40_S	46_G	0.521	0.99
64_D	79_I	0.512	0.99
85_N	88_I	0.511	0.99
101_I	106_K	0.511	0.99
49_K	53_Y	0.503	0.99
30_L	34_K	0.502	0.98
4_G	80_F	0.502	0.98
47_I	51_V	0.502	0.98
29_V	88_I	0.500	0.98
91_L	105_L	0.500	0.98

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
1iojA	1	0.2719	4.3	0.899	Contact Map
1ezeA	1	0.2719	3.6	0.902	Contact Map
2k5jA	2	0.2368	2.5	0.91	Contact Map
4p02B	1	0.3158	2.5	0.911	Contact Map
4k7jA	1	0.1754	2.4	0.911	Contact Map
4mndA	2	0.9211	2.4	0.911	Contact Map
3mz1A	2	0	2.2	0.913	Contact Map
3plaA	2	0.386	2.2	0.913	Contact Map
1yy3A	1	0.4298	2.2	0.913	Contact Map
3id6A	2	0.3947	2.1	0.914	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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