Phage_GP20 - PFAM28P - GREMLIN Contacts

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Phage_GP20 - Phage minor structural protein GP20

PFAM:	PF06810	Sequences: EQIDKIMKAENGKYIPKAKFDEVNEEKKTLKEQLKERDKQLEELKKSAGDNEELKKQIEELQAKNKTAKEEYEAKLADLKLDNALKLALTGAKAKNPKAVKALLDLDKLKLDEDGKVKGLDEQLKALKESDPYLFEEEEPGQTPNPKGF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	149 (137)
Sequences:	2624 (2186)
Seq/√Len:	186.7
META:	0.815

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_K	73_E	2.691	1.00
60_E	64_K	2.565	1.00
27_K	30_L	2.414	1.00
96_N	131_D	2.321	1.00
71_E	75_K	2.295	1.00
121_D	125_K	2.183	1.00
67_T	71_E	2.062	1.00
125_K	129_E	2.049	1.00
11_N	14_Y	1.995	1.00
56_K	60_E	1.982	1.00
63_A	67_T	1.955	1.00
59_E	62_Q	1.868	1.00
26_E	31_K	1.854	1.00
57_Q	60_E	1.818	1.00
110_K	118_K	1.813	1.00
42_E	45_K	1.790	1.00
66_K	70_E	1.750	1.00
20_F	23_V	1.729	1.00
23_V	27_K	1.694	1.00
9_A	12_G	1.675	1.00
57_Q	62_Q	1.671	1.00
112_D	116_K	1.655	1.00
17_K	21_D	1.648	1.00
27_K	31_K	1.621	1.00
50_D	53_E	1.600	1.00
59_E	63_A	1.590	1.00
79_L	83_N	1.518	1.00
70_E	74_A	1.508	1.00
105_D	108_K	1.481	1.00
93_K	136_E	1.468	1.00
7_M	12_G	1.466	1.00
78_D	82_D	1.462	1.00
29_T	33_Q	1.435	1.00
39_K	43_E	1.430	1.00
20_F	24_N	1.416	1.00
10_E	13_K	1.410	1.00
23_V	26_E	1.391	1.00
86_K	101_K	1.377	1.00
24_N	28_K	1.365	1.00
72_Y	75_K	1.353	1.00
32_E	36_E	1.349	1.00
34_L	37_R	1.327	1.00
62_Q	66_K	1.322	1.00
76_L	79_L	1.318	1.00
99_A	103_L	1.310	1.00
10_E	14_Y	1.305	1.00
94_A	100_V	1.271	1.00
119_G	122_E	1.271	1.00
19_K	22_E	1.261	1.00
19_K	24_N	1.260	1.00
74_A	78_D	1.229	1.00
52_E	55_K	1.220	1.00
35_K	39_K	1.210	1.00
21_D	24_N	1.190	1.00
99_A	102_A	1.189	1.00
42_E	46_K	1.180	1.00
36_E	40_Q	1.173	1.00
95_K	136_E	1.173	1.00
106_L	109_L	1.123	1.00
36_E	39_K	1.122	1.00
53_E	57_Q	1.121	1.00
32_E	35_K	1.119	1.00
48_A	51_N	1.111	1.00
67_T	70_E	1.106	1.00
64_K	68_A	1.106	1.00
89_L	94_A	1.105	1.00
77_A	81_L	1.104	1.00
126_A	129_E	1.091	1.00
55_K	59_E	1.086	1.00
73_E	77_A	1.084	1.00
7_M	11_N	1.065	1.00
58_I	61_L	1.065	1.00
40_Q	43_E	1.057	1.00
33_Q	36_E	1.056	1.00
88_A	91_G	1.053	1.00
30_L	33_Q	1.044	1.00
9_A	13_K	1.044	1.00
43_E	46_K	1.042	1.00
43_E	47_S	1.037	1.00
125_K	128_K	1.028	1.00
88_A	92_A	1.017	1.00
24_N	27_K	1.009	0.99
25_E	28_K	1.008	0.99
33_Q	38_D	1.004	0.99
37_R	40_Q	0.998	0.99
68_A	71_E	0.990	0.99
122_E	125_K	0.983	0.99
64_K	67_T	0.974	0.99
96_N	99_A	0.961	0.99
98_K	102_A	0.945	0.99
88_A	121_D	0.942	0.99
75_K	80_K	0.941	0.99
65_N	68_A	0.940	0.99
28_K	31_K	0.929	0.99
4_D	7_M	0.925	0.99
40_Q	45_K	0.924	0.99
60_E	63_A	0.920	0.99
126_A	130_S	0.916	0.99
34_L	38_D	0.909	0.99
7_M	14_Y	0.905	0.99
53_E	56_K	0.904	0.99
31_K	35_K	0.897	0.99
52_E	56_K	0.887	0.99
81_L	85_L	0.882	0.99
98_K	105_D	0.876	0.99
96_N	133_Y	0.876	0.99
11_N	16_P	0.869	0.98
98_K	103_L	0.864	0.98
112_D	118_K	0.862	0.98
17_K	20_F	0.860	0.98
29_T	32_E	0.838	0.98
56_K	59_E	0.835	0.98
7_M	10_E	0.831	0.98
18_A	22_E	0.826	0.98
92_A	124_L	0.821	0.98
99_A	131_D	0.813	0.98
96_N	103_L	0.802	0.97
63_A	66_K	0.790	0.97
47_S	50_D	0.786	0.97
127_L	131_D	0.778	0.97
72_Y	79_L	0.778	0.97
47_S	51_N	0.777	0.97
28_K	32_E	0.765	0.97
72_Y	76_L	0.756	0.96
69_K	72_Y	0.753	0.96
77_A	110_K	0.749	0.96
51_N	55_K	0.743	0.96
108_K	122_E	0.740	0.96
83_N	87_L	0.739	0.96
49_G	55_K	0.737	0.96
26_E	29_T	0.734	0.96
61_L	65_N	0.731	0.96
14_Y	20_F	0.720	0.95
13_K	16_P	0.717	0.95
16_P	19_K	0.714	0.95
19_K	23_V	0.705	0.95
4_D	10_E	0.704	0.95
11_N	15_I	0.702	0.95
10_E	16_P	0.694	0.94
40_Q	65_N	0.689	0.94
68_A	72_Y	0.688	0.94
100_V	103_L	0.683	0.94
88_A	120_L	0.679	0.94
21_D	25_E	0.678	0.94
117_V	120_L	0.669	0.93
66_K	69_K	0.669	0.93
9_A	14_Y	0.665	0.93
95_K	133_Y	0.663	0.93
86_K	98_K	0.660	0.93
111_L	117_V	0.658	0.92
123_Q	126_A	0.657	0.92
95_K	131_D	0.656	0.92
18_A	21_D	0.653	0.92
112_D	115_G	0.652	0.92
109_L	123_Q	0.647	0.92
82_D	101_K	0.647	0.92
26_E	30_L	0.636	0.91
14_Y	19_K	0.635	0.91
50_D	55_K	0.633	0.91
119_G	123_Q	0.630	0.91
37_R	41_L	0.616	0.90
95_K	99_A	0.610	0.89
58_I	65_N	0.604	0.89
54_L	58_I	0.602	0.89
11_N	21_D	0.595	0.88
81_L	109_L	0.595	0.88
81_L	106_L	0.592	0.88
47_S	55_K	0.590	0.88
51_N	54_L	0.589	0.88
99_A	133_Y	0.587	0.87
5_K	9_A	0.587	0.87
9_A	16_P	0.584	0.87
87_L	90_T	0.582	0.87
4_D	11_N	0.580	0.87
11_N	19_K	0.580	0.87
98_K	131_D	0.576	0.87
78_D	106_L	0.564	0.85
83_N	86_K	0.562	0.85
37_R	61_L	0.558	0.85
5_K	10_E	0.557	0.85
12_G	16_P	0.553	0.84
102_A	105_D	0.553	0.84
39_K	42_E	0.552	0.84
81_L	117_V	0.552	0.84
89_L	92_A	0.551	0.84
130_S	133_Y	0.550	0.84
84_A	117_V	0.546	0.83
77_A	80_K	0.543	0.83
54_L	57_Q	0.542	0.83
37_R	65_N	0.538	0.83
93_K	138_E	0.531	0.82
88_A	116_K	0.531	0.82
10_E	19_K	0.530	0.82
61_L	64_K	0.528	0.81
100_V	133_Y	0.521	0.81
57_Q	61_L	0.521	0.81
7_M	16_P	0.520	0.80
90_T	97_P	0.519	0.80
97_P	100_V	0.516	0.80
30_L	34_L	0.516	0.80
71_E	74_A	0.514	0.80
120_L	123_Q	0.510	0.79
35_K	38_D	0.507	0.79
38_D	65_N	0.505	0.79
80_K	84_A	0.502	0.78
42_E	62_Q	0.500	0.78

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
3c9iA	5	0.8121	70.6	0.86	Contact Map
3ojaB	1	0.5101	54.7	0.874	Contact Map
4q4gX	1	0	53.3	0.875	Contact Map
3q0xA	2	0.4094	48.8	0.878	Contact Map
4w7zA	3	0.4295	47.3	0.879	Contact Map
3mq9A	4	0.5101	40.5	0.884	Contact Map
4h5yA	1	0.9329	39.2	0.885	Contact Map
1deqA	1	0.7987	37.6	0.886	Contact Map
3vkgA	2	0.8591	36.1	0.887	Contact Map
4jzpA	2	0.349	35.6	0.887	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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