Phage_holin_3_1 - PFAM28P - GREMLIN Contacts

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Phage_holin_3_1 - Phage holin family (Lysis protein S)

PFAM:	PF05106	Sequences: EKDPDTWAALLAWLSEHWPQIYGALLAFVIALLRVIYDGGSWRRRLLEALLCGLLTLAASSGLEYFGLPQSLAVFIGGFIGFLGVEKIRELAKRFINRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	99 (98)
Sequences:	684 (468)
Seq/√Len:	47.3
META:	0.466

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_I	51_L	3.800	1.00
59_A	80_I	3.165	1.00
2_K	6_T	3.066	1.00
23_G	56_T	2.911	1.00
34_R	48_E	2.873	1.00
49_A	83_L	2.463	1.00
86_E	89_R	2.406	1.00
60_S	74_V	2.318	1.00
58_A	78_G	2.288	1.00
3_D	6_T	2.068	1.00
53_G	78_G	2.057	1.00
32_L	49_A	2.043	1.00
53_G	79_F	1.901	0.99
13_W	17_H	1.738	0.98
62_G	72_L	1.731	0.98
65_Y	72_L	1.719	0.98
31_A	34_R	1.687	0.98
64_E	70_Q	1.684	0.98
57_L	78_G	1.647	0.98
94_R	97_N	1.608	0.97
91_L	96_I	1.599	0.97
27_A	56_T	1.573	0.97
45_R	86_E	1.550	0.97
33_L	50_L	1.545	0.97
52_C	80_I	1.534	0.96
23_G	77_G	1.487	0.96
56_T	77_G	1.386	0.94
2_K	5_D	1.369	0.93
69_P	72_L	1.357	0.93
53_G	75_F	1.349	0.93
79_F	83_L	1.306	0.92
33_L	47_L	1.279	0.91
87_K	93_K	1.278	0.91
37_Y	85_V	1.272	0.90
31_A	49_A	1.245	0.90
77_G	82_F	1.230	0.89
30_I	35_V	1.230	0.89
83_L	91_L	1.195	0.88
58_A	77_G	1.116	0.84
52_C	81_G	1.088	0.82
26_L	57_L	1.082	0.82
65_Y	69_P	1.053	0.80
31_A	52_C	1.052	0.80
10_L	13_W	1.020	0.78
49_A	82_F	0.999	0.76
56_T	78_G	0.992	0.76
62_G	90_E	0.988	0.75
82_F	88_I	0.981	0.75
21_I	25_L	0.975	0.74
54_L	61_S	0.957	0.73
51_L	85_V	0.953	0.73
14_L	29_V	0.946	0.72
68_L	72_L	0.939	0.72
6_T	10_L	0.922	0.70
57_L	75_F	0.917	0.70
13_W	18_W	0.906	0.69
38_D	89_R	0.900	0.68
87_K	91_L	0.883	0.67
32_L	45_R	0.883	0.67
82_F	89_R	0.867	0.65
47_L	92_A	0.859	0.65
25_L	97_N	0.857	0.65
4_P	7_W	0.856	0.64
24_A	73_A	0.852	0.64
34_R	47_L	0.852	0.64
48_E	69_P	0.836	0.63
11_L	14_L	0.816	0.61
95_F	99_K	0.812	0.60
35_V	47_L	0.793	0.58
5_D	10_L	0.784	0.58
54_L	57_L	0.782	0.57
51_L	76_I	0.779	0.57
37_Y	44_R	0.774	0.57
83_L	90_E	0.774	0.57
61_S	78_G	0.770	0.56
27_A	53_G	0.766	0.56
68_L	71_S	0.766	0.56
24_A	28_F	0.743	0.54
63_L	88_I	0.731	0.52
2_K	76_I	0.717	0.51
70_Q	73_A	0.711	0.50
82_F	93_K	0.711	0.50
26_L	58_A	0.701	0.49
71_S	96_I	0.698	0.49
19_P	30_I	0.679	0.47
29_V	42_W	0.677	0.47
56_T	63_L	0.677	0.47
90_E	98_R	0.659	0.45
25_L	32_L	0.655	0.45
27_A	93_K	0.648	0.44
39_G	67_G	0.647	0.44
35_V	85_V	0.646	0.44
12_A	16_E	0.643	0.44
44_R	48_E	0.639	0.43
28_F	79_F	0.636	0.43
19_P	92_A	0.634	0.43
35_V	48_E	0.633	0.43
5_D	11_L	0.633	0.43
54_L	92_A	0.632	0.43
2_K	8_A	0.631	0.42
46_L	71_S	0.630	0.42
88_I	96_I	0.630	0.42
62_G	68_L	0.622	0.42
81_G	91_L	0.620	0.41
13_W	16_E	0.618	0.41
10_L	68_L	0.617	0.41
24_A	29_V	0.617	0.41
70_Q	98_R	0.609	0.40
46_L	83_L	0.603	0.40
74_V	77_G	0.601	0.40
6_T	9_A	0.598	0.39
56_T	98_R	0.597	0.39
87_K	95_F	0.596	0.39
15_S	55_L	0.594	0.39
53_G	57_L	0.593	0.39
17_H	30_I	0.592	0.39
64_E	71_S	0.588	0.38
59_A	64_E	0.588	0.38
11_L	15_S	0.581	0.38
46_L	55_L	0.580	0.38
20_Q	57_L	0.580	0.38
2_K	9_A	0.575	0.37
26_L	56_T	0.575	0.37
2_K	12_A	0.574	0.37
76_I	99_K	0.567	0.36
17_H	54_L	0.563	0.36
55_L	85_V	0.560	0.36
36_I	47_L	0.547	0.35
62_G	76_I	0.545	0.34
66_F	72_L	0.543	0.34
75_F	79_F	0.543	0.34
52_C	63_L	0.536	0.34
61_S	73_A	0.535	0.33
30_I	54_L	0.534	0.33
5_D	99_K	0.530	0.33
63_L	80_I	0.526	0.33
34_R	51_L	0.521	0.32
26_L	59_A	0.519	0.32
39_G	43_R	0.518	0.32
55_L	81_G	0.518	0.32
87_K	90_E	0.512	0.31
9_A	12_A	0.511	0.31
31_A	47_L	0.508	0.31
61_S	76_I	0.502	0.31
6_T	94_R	0.501	0.31
2_K	11_L	0.501	0.31
22_Y	40_G	0.500	0.30

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
2j69A	1	0.7576	74.5	0.838	Contact Map
2b2hA	3	0.8283	27.1	0.88	Contact Map
4k0jA	3	0.9899	20.7	0.887	Contact Map
1u7gA	3	0.8485	17.3	0.891	Contact Map
4hw9A	3	0.8384	15.7	0.893	Contact Map
3b9wA	3	0.9293	14.9	0.894	Contact Map
4pd6A	3	0.9495	14.2	0.895	Contact Map
1ji6A	1	0.5051	12.6	0.897	Contact Map
2c9kA	1	0.5051	8.8	0.904	Contact Map
3w9iA	3	1	8.8	0.904	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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