Phage_P2_GpU - PFAM28P - GREMLIN Contacts

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Phage_P2_GpU - Phage P2 GpU

PFAM:	PF06995	Sequences: GDFVFEVSTLTFQELQRSTSARWAEHERIGGKPALQFTGPGLDTITLSGVLYPELVGPLAELDKLRAMADSGEPLPLVIGTGRVLGRWVITSISETQSYFDADGTPRKIEFTLTLKEYDD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (119)
Sequences:	3549 (2820)
Seq/√Len:	258.5
META:	0.734

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_E	116_K	2.488	1.00
91_T	116_K	2.484	1.00
35_L	89_V	2.288	1.00
21_A	69_A	2.239	1.00
68_M	75_L	2.095	1.00
92_S	114_T	2.048	1.00
14_E	48_S	2.006	1.00
28_R	34_A	1.996	1.00
16_Q	94_S	1.987	1.00
37_F	72_G	1.944	1.00
18_S	94_S	1.922	1.00
20_S	41_G	1.914	1.00
50_V	110_E	1.906	1.00
17_R	95_E	1.903	1.00
19_T	66_R	1.874	1.00
17_R	43_D	1.867	1.00
44_T	116_K	1.797	1.00
18_S	92_S	1.781	1.00
101_D	105_T	1.706	1.00
50_V	108_K	1.704	1.00
79_I	85_L	1.697	1.00
35_L	116_K	1.678	1.00
49_G	113_L	1.674	1.00
46_T	114_T	1.620	1.00
52_Y	108_K	1.611	1.00
35_L	42_L	1.604	1.00
32_K	117_E	1.595	1.00
48_S	112_T	1.588	1.00
94_S	112_T	1.564	1.00
62_L	109_I	1.563	1.00
49_G	111_F	1.557	1.00
20_S	92_S	1.510	1.00
19_T	43_D	1.447	1.00
25_E	42_L	1.422	1.00
106_P	109_I	1.412	1.00
23_W	89_V	1.396	1.00
16_Q	96_T	1.390	1.00
66_R	95_E	1.380	1.00
22_R	41_G	1.372	1.00
24_A	38_T	1.348	1.00
32_K	40_P	1.335	1.00
98_S	110_E	1.333	1.00
69_A	90_I	1.310	1.00
26_H	36_Q	1.309	1.00
76_P	87_R	1.224	1.00
25_E	35_L	1.218	1.00
19_T	69_A	1.218	1.00
25_E	41_G	1.183	1.00
18_S	44_T	1.182	1.00
44_T	114_T	1.171	1.00
79_I	83_R	1.112	1.00
21_A	37_F	1.095	1.00
46_T	112_T	1.074	1.00
40_P	70_D	1.071	1.00
89_V	116_K	1.063	1.00
47_L	115_L	1.058	1.00
27_E	33_P	1.029	1.00
22_R	27_E	1.021	1.00
35_L	91_T	1.014	1.00
91_T	114_T	1.010	1.00
48_S	110_E	0.998	1.00
96_T	112_T	0.996	1.00
12_F	15_L	0.993	1.00
22_R	39_G	0.987	1.00
65_L	93_I	0.985	1.00
17_R	66_R	0.972	1.00
45_I	88_W	0.961	1.00
37_F	40_P	0.952	1.00
71_S	75_L	0.944	1.00
62_L	95_E	0.937	1.00
14_E	96_T	0.936	1.00
51_L	111_F	0.927	1.00
43_D	70_D	0.925	1.00
21_A	70_D	0.923	1.00
28_R	31_G	0.915	1.00
98_S	108_K	0.908	1.00
61_E	64_K	0.901	1.00
3_F	68_M	0.897	1.00
57_G	60_A	0.890	1.00
97_Q	106_P	0.889	1.00
63_D	67_A	0.874	1.00
97_Q	100_F	0.864	1.00
25_E	33_P	0.862	1.00
8_S	11_T	0.862	1.00
20_S	91_T	0.851	0.99
63_D	66_R	0.847	0.99
23_W	35_L	0.837	0.99
65_L	111_F	0.835	0.99
69_A	93_I	0.834	0.99
59_L	106_P	0.833	0.99
93_I	113_L	0.828	0.99
66_R	70_D	0.823	0.99
22_R	38_T	0.811	0.99
76_P	84_V	0.807	0.99
44_T	91_T	0.802	0.99
25_E	91_T	0.800	0.99
15_L	45_I	0.792	0.99
74_P	89_V	0.782	0.99
53_P	57_G	0.775	0.99
59_L	105_T	0.774	0.99
16_Q	46_T	0.769	0.99
48_S	96_T	0.767	0.99
17_R	45_I	0.766	0.99
32_K	70_D	0.758	0.99
42_L	117_E	0.756	0.99
22_R	33_P	0.753	0.99
63_D	83_R	0.735	0.98
61_E	65_L	0.734	0.98
59_L	97_Q	0.733	0.98
2_D	68_M	0.728	0.98
10_L	51_L	0.726	0.98
68_M	71_S	0.722	0.98
21_A	93_I	0.717	0.98
15_L	97_Q	0.716	0.98
47_L	113_L	0.711	0.98
52_Y	58_P	0.711	0.98
96_T	110_E	0.710	0.98
67_A	71_S	0.709	0.98
51_L	61_E	0.707	0.98
3_F	65_L	0.702	0.98
12_F	100_F	0.700	0.98
100_F	106_P	0.692	0.98
65_L	90_I	0.691	0.98
90_I	93_I	0.680	0.97
83_R	87_R	0.679	0.97
82_G	86_G	0.674	0.97
56_V	61_E	0.673	0.97
10_L	61_E	0.670	0.97
80_G	104_G	0.668	0.97
43_D	66_R	0.668	0.97
65_L	68_M	0.660	0.97
54_E	107_R	0.659	0.97
6_E	9_T	0.655	0.97
59_L	63_D	0.651	0.97
66_R	93_I	0.649	0.97
25_E	89_V	0.640	0.96
62_L	111_F	0.632	0.96
14_E	98_S	0.630	0.96
32_K	119_D	0.628	0.96
60_A	63_D	0.627	0.96
35_L	118_Y	0.626	0.96
68_M	74_P	0.621	0.96
64_K	67_A	0.611	0.95
101_D	107_R	0.610	0.95
24_A	35_L	0.610	0.95
23_W	118_Y	0.608	0.95
32_K	42_L	0.607	0.95
7_V	11_T	0.605	0.95
53_P	107_R	0.601	0.95
29_I	36_Q	0.601	0.95
78_V	84_V	0.595	0.95
19_T	70_D	0.584	0.94
74_P	87_R	0.584	0.94
97_Q	109_I	0.577	0.94
81_T	105_T	0.576	0.94
60_A	64_K	0.569	0.93
58_P	109_I	0.567	0.93
40_P	72_G	0.565	0.93
42_L	89_V	0.564	0.93
12_F	47_L	0.564	0.93
74_P	118_Y	0.561	0.93
90_I	115_L	0.559	0.93
62_L	106_P	0.558	0.93
21_A	40_P	0.543	0.92
82_G	85_L	0.542	0.91
21_A	36_Q	0.541	0.91
99_Y	108_K	0.540	0.91
24_A	36_Q	0.534	0.91
16_Q	114_T	0.533	0.91
23_W	74_P	0.528	0.90
13_Q	50_V	0.526	0.90
53_P	58_P	0.522	0.90
37_F	69_A	0.519	0.90
19_T	93_I	0.517	0.89
51_L	65_L	0.514	0.89
26_H	34_A	0.514	0.89
3_F	10_L	0.509	0.89
88_W	115_L	0.500	0.88

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
2xwxA	2	0.8917	7.6	0.915	Contact Map
3ossC	1	0.5167	6.1	0.919	Contact Map
2pq0A	1	0.6833	5.8	0.919	Contact Map
2lnvA	1	0.7583	5.5	0.921	Contact Map
2zuvA	2	0.85	4.9	0.922	Contact Map
2zosA	1	0.675	4.6	0.923	Contact Map
1v54M	1	0.3583	4.3	0.924	Contact Map
3zx4A	2	0.6333	4.1	0.925	Contact Map
4csu9	1	0.9583	4	0.925	Contact Map
4divS	3	0.9083	4	0.925	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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