Phage_holin_4_2 - PFAM28P - GREMLIN Contacts

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Phage_holin_4_2 - Mycobacterial 4 TMS phage holin, superfamily IV

PFAM:	PF04020	Sequences: MRLLLRWLINALALLVAAYLVPGISVDGFGTALIAALVLGLLNALVRPILKLLTLPLTILTLGLFLLVINALMLWLAAWLVPGFHVDGFWAALLGALVISIVSWV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	105 (104)
Sequences:	37561 (24461)
Seq/√Len:	2398.6
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_L	95_G	2.976	1.00
58_T	66_L	2.778	1.00
26_V	32_A	2.320	1.00
51_K	66_L	2.267	1.00
75_W	79_W	2.245	1.00
88_G	91_A	2.150	1.00
71_A	93_L	2.145	1.00
15_L	19_Y	2.121	1.00
74_L	99_I	2.075	1.00
47_R	51_K	2.024	1.00
42_L	73_M	2.018	1.00
90_W	94_L	1.935	1.00
72_L	75_W	1.930	1.00
13_A	17_A	1.856	1.00
28_G	31_T	1.856	1.00
14_L	35_A	1.777	1.00
13_A	102_V	1.721	1.00
35_A	84_F	1.709	1.00
24_I	95_G	1.697	1.00
15_L	32_A	1.686	1.00
21_V	91_A	1.646	1.00
91_A	94_L	1.609	1.00
39_L	77_A	1.573	1.00
25_S	85_H	1.560	1.00
17_A	98_V	1.535	1.00
7_W	11_A	1.516	1.00
23_G	91_A	1.490	1.00
17_A	99_I	1.479	1.00
87_D	91_A	1.440	1.00
7_W	37_L	1.336	1.00
25_S	87_D	1.323	1.00
42_L	77_A	1.289	1.00
38_V	77_A	1.286	1.00
65_F	68_V	1.269	1.00
86_V	92_A	1.257	1.00
76_L	79_W	1.201	1.00
75_W	89_F	1.199	1.00
6_R	10_N	1.194	1.00
3_L	7_W	1.186	1.00
23_G	87_D	1.177	1.00
35_A	77_A	1.163	1.00
14_L	39_L	1.137	1.00
51_K	69_I	1.130	1.00
38_V	81_V	1.129	1.00
30_G	34_I	1.111	1.00
54_T	58_T	1.108	1.00
14_L	95_G	1.103	1.00
75_W	92_A	1.083	1.00
75_W	78_A	1.061	1.00
17_A	95_G	1.051	1.00
96_A	100_S	1.021	1.00
16_V	19_Y	1.015	1.00
18_A	22_P	1.008	1.00
51_K	54_T	1.008	1.00
7_W	10_N	0.995	1.00
43_N	70_N	0.987	1.00
21_V	94_L	0.986	1.00
55_L	58_T	0.965	1.00
98_V	102_V	0.953	1.00
51_K	58_T	0.948	1.00
14_L	99_I	0.931	1.00
31_T	81_V	0.929	1.00
91_A	95_G	0.926	1.00
11_A	36_A	0.925	1.00
17_A	21_V	0.918	1.00
61_T	65_F	0.917	1.00
89_F	93_L	0.909	1.00
45_L	48_P	0.908	1.00
10_N	14_L	0.889	1.00
7_W	36_A	0.887	1.00
54_T	65_F	0.883	1.00
92_A	96_A	0.873	1.00
72_L	76_L	0.861	1.00
27_D	31_T	0.856	1.00
12_L	16_V	0.845	1.00
50_L	73_M	0.842	1.00
27_D	85_H	0.826	1.00
18_A	26_V	0.824	1.00
78_A	86_V	0.820	1.00
21_V	98_V	0.817	1.00
71_A	92_A	0.817	1.00
29_F	33_L	0.812	1.00
35_A	39_L	0.799	1.00
36_A	40_G	0.799	1.00
26_V	31_T	0.797	1.00
67_L	93_L	0.767	1.00
11_A	33_L	0.767	1.00
58_T	69_I	0.760	1.00
79_W	82_P	0.760	1.00
99_I	103_S	0.759	1.00
39_L	43_N	0.753	1.00
95_G	99_I	0.749	1.00
40_G	44_A	0.746	1.00
50_L	69_I	0.740	1.00
58_T	65_F	0.736	1.00
64_L	68_V	0.733	1.00
16_V	20_L	0.726	1.00
42_L	76_L	0.721	1.00
73_M	76_L	0.713	1.00
66_L	70_N	0.710	1.00
56_P	60_L	0.707	1.00
24_I	86_V	0.693	1.00
34_I	81_V	0.690	1.00
18_A	32_A	0.688	1.00
78_A	84_F	0.686	1.00
82_P	85_H	0.683	1.00
52_L	55_L	0.682	1.00
31_T	83_G	0.681	1.00
61_T	64_L	0.671	1.00
67_L	100_S	0.671	1.00
7_W	33_L	0.668	1.00
17_A	20_L	0.657	1.00
55_L	59_I	0.656	1.00
67_L	97_L	0.651	1.00
71_A	75_W	0.649	1.00
3_L	37_L	0.645	1.00
24_I	74_L	0.642	1.00
52_L	56_P	0.639	1.00
10_N	99_I	0.637	1.00
78_A	82_P	0.634	1.00
70_N	100_S	0.634	1.00
8_L	12_L	0.632	1.00
11_A	32_A	0.626	1.00
41_L	44_A	0.622	1.00
48_P	52_L	0.597	1.00
51_K	55_L	0.592	1.00
47_R	73_M	0.589	1.00
57_L	65_F	0.589	1.00
47_R	69_I	0.586	1.00
2_R	6_R	0.584	1.00
21_V	24_I	0.583	1.00
27_D	83_G	0.581	1.00
78_A	92_A	0.572	1.00
4_L	8_L	0.571	1.00
31_T	34_I	0.569	1.00
19_Y	22_P	0.568	1.00
26_V	84_F	0.567	1.00
78_A	85_H	0.566	1.00
3_L	44_A	0.561	1.00
34_I	38_V	0.561	1.00
66_L	104_W	0.553	1.00
66_L	103_S	0.547	1.00
9_I	13_A	0.537	1.00
30_G	79_W	0.533	1.00
13_A	16_V	0.530	1.00
41_L	45_L	0.529	1.00
42_L	46_V	0.528	1.00
12_L	15_L	0.520	1.00
10_N	13_A	0.520	1.00
57_L	60_L	0.517	1.00
30_G	33_L	0.513	1.00
31_T	35_A	0.512	1.00
32_A	36_A	0.510	1.00
87_D	90_W	0.506	1.00
69_I	73_M	0.501	1.00
79_W	83_G	0.500	1.00

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
4czbA	2	0.981	3	0.892	Contact Map
4p6vD	1	0.8571	2.7	0.894	Contact Map
4cz8A	2	0.9619	2.4	0.896	Contact Map
4lz6A	1	0.9905	2	0.901	Contact Map
4humA	1	1	1.7	0.905	Contact Map
3w4tA	1	0.9905	1.6	0.907	Contact Map
3mktA	1	0.9905	1.4	0.909	Contact Map
4bwzA	2	0.9524	1.2	0.913	Contact Map
3hzqA	3	0.6381	1.2	0.914	Contact Map
1oedC	1	0.7429	1.2	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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