Peptidase_S78_2 - PFAM28P - GREMLIN Contacts

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Peptidase_S78_2 - Putative phage serine protease XkdF

PFAM:	PF14550	Sequences: NVFKIAKVDEEKRIVYGPVLIPDRVDAQGDYFSKETIEKAAEKFMKNGRNVNLMHDGEKVGGGTVVESWIVDDKSKLGGLDVPKGTWMVGVKVDDDEVWEKVKSGELKGFSIEGYAKREE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (111)
Sequences:	6682 (4855)
Seq/√Len:	460.8
META:	0.974

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	90_G	3.163	1.00
11_E	103_K	3.100	1.00
101_K	106_E	2.816	1.00
19_V	89_V	2.605	1.00
91_V	110_F	2.422	1.00
100_E	104_S	2.255	1.00
17_G	110_F	2.210	1.00
13_R	96_D	2.188	1.00
13_R	99_W	2.139	1.00
12_K	38_E	2.079	1.00
14_I	90_G	2.010	1.00
68_S	87_W	1.920	1.00
18_P	21_I	1.858	1.00
52_N	113_E	1.793	1.00
34_K	84_K	1.754	1.00
64_T	94_D	1.739	1.00
72_D	75_S	1.689	1.00
51_V	91_V	1.679	1.00
53_L	107_L	1.638	1.00
23_D	34_K	1.631	1.00
72_D	76_K	1.564	1.00
43_K	47_N	1.561	1.00
14_I	92_K	1.504	1.00
26_D	30_D	1.468	1.00
65_V	91_V	1.468	1.00
41_A	68_S	1.443	1.00
46_K	94_D	1.409	1.00
38_E	42_E	1.401	1.00
46_K	64_T	1.392	1.00
65_V	89_V	1.381	1.00
33_S	36_T	1.330	1.00
71_V	88_M	1.302	1.00
20_L	32_F	1.293	1.00
14_I	66_V	1.270	1.00
46_K	92_K	1.268	1.00
22_P	86_T	1.252	1.00
24_R	27_A	1.237	1.00
96_D	100_E	1.198	1.00
101_K	104_S	1.181	1.00
25_V	31_Y	1.176	1.00
72_D	77_L	1.174	1.00
101_K	107_L	1.168	1.00
41_A	45_M	1.156	1.00
36_T	39_K	1.152	1.00
53_L	98_V	1.139	1.00
97_E	101_K	1.136	1.00
15_V	93_V	1.118	1.00
53_L	101_K	1.109	1.00
67_E	90_G	1.101	1.00
57_G	113_E	1.087	1.00
24_R	29_G	1.084	1.00
18_P	86_T	1.082	1.00
24_R	30_D	1.079	1.00
25_V	29_G	1.061	1.00
75_S	78_G	1.058	1.00
83_P	86_T	1.049	1.00
99_W	102_V	1.038	1.00
45_M	68_S	1.036	1.00
42_E	67_E	1.030	1.00
10_E	103_K	1.011	1.00
25_V	30_D	1.004	1.00
7_K	10_E	1.000	1.00
82_V	88_M	0.973	1.00
76_K	79_G	0.964	1.00
19_V	112_I	0.963	1.00
71_V	82_V	0.959	1.00
73_D	78_G	0.958	1.00
51_V	63_G	0.955	1.00
25_V	28_Q	0.951	1.00
20_L	112_I	0.944	1.00
63_G	98_V	0.935	1.00
21_I	83_P	0.928	1.00
82_V	86_T	0.923	1.00
73_D	76_K	0.914	1.00
21_I	86_T	0.912	1.00
52_N	56_D	0.899	1.00
62_G	95_D	0.891	1.00
44_F	65_V	0.889	1.00
42_E	92_K	0.880	1.00
69_W	88_M	0.858	1.00
41_A	70_I	0.851	1.00
42_E	66_V	0.849	1.00
11_E	99_W	0.848	1.00
15_V	102_V	0.840	1.00
16_Y	88_M	0.840	1.00
99_W	103_K	0.838	1.00
35_E	39_K	0.821	1.00
74_K	77_L	0.808	1.00
26_D	29_G	0.807	1.00
27_A	30_D	0.806	1.00
96_D	99_W	0.796	1.00
41_A	87_W	0.795	1.00
18_P	88_M	0.792	1.00
26_D	31_Y	0.753	1.00
52_N	57_G	0.747	1.00
21_I	24_R	0.741	1.00
24_R	31_Y	0.739	1.00
54_M	107_L	0.737	1.00
93_V	99_W	0.736	1.00
32_F	40_A	0.734	1.00
98_V	107_L	0.725	1.00
20_L	37_I	0.715	1.00
18_P	82_V	0.715	1.00
18_P	22_P	0.712	1.00
73_D	79_G	0.710	1.00
45_M	49_R	0.706	1.00
28_Q	31_Y	0.698	1.00
93_V	102_V	0.698	1.00
32_F	37_I	0.692	1.00
49_R	64_T	0.690	1.00
24_R	28_Q	0.687	1.00
63_G	93_V	0.685	1.00
74_K	78_G	0.679	1.00
40_A	43_K	0.673	1.00
34_K	37_I	0.671	1.00
71_V	75_S	0.667	1.00
76_K	81_D	0.667	1.00
9_D	12_K	0.662	1.00
73_D	77_L	0.656	1.00
71_V	84_K	0.651	1.00
16_Y	42_E	0.641	1.00
75_S	79_G	0.637	1.00
44_F	91_V	0.626	0.99
100_E	103_K	0.625	0.99
62_G	94_D	0.617	0.99
72_D	78_G	0.605	0.99
105_G	108_K	0.604	0.99
44_F	87_W	0.603	0.99
75_S	80_L	0.602	0.99
20_L	40_A	0.600	0.99
74_K	80_L	0.598	0.99
40_A	114_G	0.597	0.99
74_K	79_G	0.597	0.99
97_E	100_E	0.596	0.99
63_G	94_D	0.595	0.99
67_E	70_I	0.594	0.99
56_D	59_K	0.589	0.99
57_G	61_G	0.583	0.99
20_L	31_Y	0.577	0.99
38_E	70_I	0.574	0.99
14_I	42_E	0.574	0.99
16_Y	69_W	0.571	0.99
43_K	46_K	0.571	0.99
77_L	80_L	0.562	0.99
32_F	36_T	0.562	0.99
42_E	45_M	0.552	0.99
13_R	92_K	0.551	0.99
36_T	112_I	0.546	0.98
37_I	41_A	0.546	0.98
45_M	48_G	0.545	0.98
67_E	71_V	0.542	0.98
44_F	68_S	0.539	0.98
37_I	40_A	0.535	0.98
50_N	60_V	0.534	0.98
19_V	65_V	0.528	0.98
10_E	13_R	0.527	0.98
52_N	61_G	0.526	0.98
68_S	89_V	0.526	0.98
27_A	31_Y	0.523	0.98
75_S	82_V	0.518	0.98
12_K	35_E	0.516	0.98
45_M	64_T	0.514	0.98
45_M	65_V	0.513	0.98
102_V	107_L	0.513	0.98
32_F	112_I	0.507	0.98
18_P	83_P	0.500	0.97

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
2re7A	2	0.725	6.3	0.921	Contact Map
2ovcA	3	0.1083	5.9	0.922	Contact Map
2aq6A	2	0.6333	5.4	0.923	Contact Map
1vzvA	2	0.7667	5.2	0.924	Contact Map
4ehiA	2	0.4	5.1	0.924	Contact Map
3u1wA	3	0.7167	4.1	0.928	Contact Map
4w23R	1	0.6333	4.1	0.928	Contact Map
3zeyL	1	0.625	3.4	0.931	Contact Map
4h3wA	1	0.4083	3.3	0.931	Contact Map
4wyhA	1	0.775	3.2	0.932	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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