Phage_Gp19 - PFAM28P - GREMLIN Contacts

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Phage_Gp19 - Phage protein Gp19/Gp15/Gp42

PFAM:	PF09355	Sequences: LWRPLTPEEQERAEALLPDASDSLRVEAKKVGKDLDAMIAADPAYASVVKSVTVDVVARALMTSTDREPMTQESESAGGYSYSGTYLVPGGGLFIKKSELKRLGLRRQRYGVIDLY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	116 (111)
Sequences:	736 (605)
Seq/√Len:	57.4
META:	0.772

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_D	47_S	3.750	1.00
39_I	49_V	2.771	1.00
45_Y	49_V	2.759	1.00
73_E	82_Y	2.753	1.00
17_L	21_S	2.514	1.00
29_K	42_D	2.319	1.00
37_A	41_A	2.286	1.00
24_L	35_L	2.139	1.00
74_S	83_S	2.055	1.00
21_S	53_T	2.022	1.00
3_R	9_E	2.021	1.00
22_D	44_A	2.014	1.00
76_S	81_S	1.983	1.00
24_L	95_I	1.961	1.00
21_S	25_R	1.959	1.00
94_F	99_E	1.897	1.00
25_R	36_D	1.881	1.00
39_I	42_D	1.862	1.00
7_P	10_Q	1.845	1.00
33_K	38_M	1.827	0.99
56_V	95_I	1.748	0.99
59_R	99_E	1.702	0.99
64_S	68_E	1.697	0.99
17_L	53_T	1.631	0.99
75_E	82_Y	1.617	0.99
42_D	45_Y	1.575	0.98
27_E	30_K	1.546	0.98
19_D	51_S	1.461	0.97
5_L	9_E	1.449	0.97
72_Q	85_T	1.434	0.97
96_K	99_E	1.426	0.97
71_T	85_T	1.407	0.97
70_M	84_G	1.375	0.96
62_M	67_R	1.346	0.96
29_K	36_D	1.281	0.94
39_I	45_Y	1.275	0.94
23_S	27_E	1.269	0.94
13_A	61_L	1.260	0.94
26_V	42_D	1.243	0.93
77_A	80_Y	1.243	0.93
26_V	48_V	1.231	0.93
26_V	30_K	1.222	0.93
23_S	51_S	1.198	0.92
74_S	81_S	1.191	0.92
2_W	58_A	1.182	0.92
97_K	106_R	1.180	0.92
2_W	12_R	1.153	0.91
2_W	5_L	1.122	0.89
11_E	14_E	1.121	0.89
15_A	18_P	1.110	0.89
44_A	47_S	1.109	0.89
19_D	47_S	1.094	0.88
5_L	13_A	1.087	0.88
15_A	19_D	1.060	0.86
63_T	69_P	1.003	0.83
51_S	102_R	0.982	0.82
72_Q	83_S	0.981	0.82
26_V	44_A	0.956	0.80
4_P	11_E	0.953	0.80
89_P	92_G	0.942	0.79
48_V	51_S	0.936	0.79
57_V	60_A	0.916	0.77
20_A	56_V	0.908	0.77
51_S	55_D	0.900	0.76
58_A	61_L	0.887	0.75
39_I	46_A	0.887	0.75
46_A	50_K	0.884	0.75
20_A	55_D	0.879	0.74
4_P	7_P	0.868	0.73
62_M	65_T	0.868	0.73
17_L	20_A	0.854	0.72
36_D	39_I	0.846	0.71
62_M	66_D	0.840	0.71
34_D	37_A	0.837	0.71
63_T	99_E	0.835	0.70
8_E	11_E	0.832	0.70
28_A	35_L	0.821	0.69
60_A	93_L	0.820	0.69
6_T	18_P	0.818	0.69
37_A	49_V	0.816	0.69
58_A	62_M	0.794	0.66
14_E	18_P	0.789	0.66
65_T	68_E	0.781	0.65
79_G	84_G	0.780	0.65
88_V	92_G	0.766	0.64
95_I	100_L	0.761	0.63
11_E	110_Y	0.751	0.62
85_T	88_V	0.749	0.62
73_E	86_Y	0.744	0.61
47_S	50_K	0.744	0.61
63_T	93_L	0.743	0.61
25_R	28_A	0.721	0.59
29_K	44_A	0.720	0.59
20_A	23_S	0.717	0.59
97_K	101_K	0.716	0.58
27_E	31_V	0.700	0.57
96_K	100_L	0.695	0.56
78_G	81_S	0.694	0.56
40_A	46_A	0.688	0.55
75_E	80_Y	0.687	0.55
23_S	56_V	0.685	0.55
87_L	96_K	0.683	0.55
20_A	53_T	0.675	0.54
27_E	102_R	0.674	0.54
88_V	101_K	0.674	0.54
86_Y	89_P	0.673	0.54
10_Q	13_A	0.673	0.54
7_P	43_P	0.667	0.53
26_V	29_K	0.662	0.53
67_R	85_T	0.657	0.52
97_K	112_V	0.655	0.52
11_E	18_P	0.653	0.52
54_V	59_R	0.644	0.51
52_V	59_R	0.639	0.50
70_M	73_E	0.637	0.50
28_A	38_M	0.633	0.49
80_Y	84_G	0.621	0.48
3_R	13_A	0.618	0.48
53_T	95_I	0.616	0.48
68_E	71_T	0.611	0.47
54_V	61_L	0.610	0.47
82_Y	86_Y	0.609	0.47
19_D	23_S	0.607	0.47
23_S	102_R	0.606	0.46
77_A	82_Y	0.602	0.46
97_K	107_R	0.600	0.46
21_S	49_V	0.596	0.45
7_P	14_E	0.593	0.45
76_S	79_G	0.590	0.45
2_W	61_L	0.590	0.45
69_P	96_K	0.582	0.44
24_L	28_A	0.582	0.44
35_L	95_I	0.578	0.43
84_G	90_G	0.575	0.43
28_A	33_K	0.571	0.43
109_R	112_V	0.571	0.43
12_R	16_L	0.570	0.43
37_A	43_P	0.565	0.42
85_T	90_G	0.563	0.42
76_S	83_S	0.562	0.42
12_R	55_D	0.562	0.42
31_V	35_L	0.561	0.42
16_L	74_S	0.558	0.41
95_I	103_L	0.557	0.41
77_A	83_S	0.557	0.41
7_P	15_A	0.553	0.41
90_G	94_F	0.553	0.41
55_D	91_G	0.547	0.40
75_E	100_L	0.542	0.40
31_V	100_L	0.539	0.39
45_Y	48_V	0.539	0.39
88_V	94_F	0.537	0.39
59_R	80_Y	0.530	0.38
47_S	57_V	0.525	0.38
88_V	102_R	0.522	0.38
77_A	89_P	0.518	0.37
87_L	99_E	0.511	0.36
20_A	57_V	0.509	0.36
71_T	74_S	0.508	0.36
19_D	54_V	0.507	0.36
35_L	49_V	0.506	0.36
42_D	46_A	0.505	0.36
27_E	100_L	0.504	0.36
64_S	69_P	0.502	0.35
18_P	21_S	0.501	0.35
32_G	100_L	0.500	0.35

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
1xn8A	1	0.9224	65.4	0.885	Contact Map
5a21C	2	0.8103	58.1	0.89	Contact Map
4qolA	4	0.4655	12.3	0.923	Contact Map
4b7hA	4	0.4483	11	0.924	Contact Map
2eqzA	1	0.2759	9.1	0.927	Contact Map
1gweA	4	0.569	8.9	0.927	Contact Map
4qr9A	2	0.2845	8.9	0.928	Contact Map
3neaA	1	0.3362	8.4	0.928	Contact Map
2mrcA	1	0.319	8.1	0.929	Contact Map
4cabA	4	0.6207	7.2	0.931	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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