Minor_capsid_1 - PFAM28P - GREMLIN Contacts

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Minor_capsid_1 - Minor capsid protein

PFAM:	PF10665	Sequences: PKRLLIHSVTYKEYTGKDDWGKPTYAEPVTIKNVRFDPSTKYSGTSNGEQIVANAVLFVDAKNSTPLVDFKEGSKIVFDGKEYTVTKVIPLYPDSNKLHHYEVEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	105 (104)
Sequences:	516 (415)
Seq/√Len:	40.7
META:	0.715

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_D	22_K	3.122	1.00
75_K	82_E	2.814	1.00
87_K	104_E	2.719	1.00
60_D	100_H	2.710	1.00
13_E	26_A	2.656	1.00
9_V	31_I	2.541	1.00
9_V	57_L	2.482	1.00
60_D	99_H	2.382	1.00
45_T	50_Q	2.362	1.00
9_V	34_V	2.216	1.00
13_E	74_S	2.138	0.99
7_H	92_Y	2.080	0.99
6_I	92_Y	2.070	0.99
77_V	82_E	1.898	0.99
12_K	77_V	1.870	0.98
59_V	70_F	1.793	0.98
91_L	100_H	1.757	0.98
16_G	23_P	1.704	0.97
31_I	59_V	1.644	0.96
14_Y	73_G	1.638	0.96
5_L	63_N	1.623	0.96
60_D	63_N	1.578	0.95
66_P	70_F	1.577	0.95
90_P	101_Y	1.510	0.94
12_K	75_K	1.506	0.94
63_N	100_H	1.495	0.94
59_V	64_S	1.489	0.94
90_P	98_L	1.480	0.93
16_G	24_T	1.448	0.93
60_D	64_S	1.440	0.92
9_V	36_F	1.383	0.91
8_S	32_K	1.380	0.91
58_F	102_E	1.292	0.88
14_Y	74_S	1.276	0.87
72_E	81_K	1.266	0.86
57_L	103_V	1.233	0.85
11_Y	74_S	1.226	0.85
15_T	23_P	1.202	0.83
8_S	30_T	1.197	0.83
70_F	85_V	1.139	0.80
19_D	22_K	1.117	0.79
6_I	35_R	1.105	0.78
38_P	79_D	1.056	0.75
5_L	60_D	1.054	0.74
7_H	79_D	1.046	0.74
7_H	35_R	1.032	0.73
59_V	101_Y	1.030	0.73
71_K	74_S	1.030	0.73
32_K	95_S	1.021	0.72
56_V	104_E	1.019	0.72
64_S	100_H	1.010	0.71
34_V	64_S	1.010	0.71
2_K	33_N	0.987	0.69
15_T	22_K	0.985	0.69
97_K	103_V	0.983	0.69
19_D	48_G	0.980	0.69
89_I	93_P	0.966	0.68
40_T	53_A	0.959	0.67
85_V	88_V	0.958	0.67
7_H	78_F	0.955	0.67
63_N	99_H	0.952	0.67
4_L	37_D	0.952	0.67
53_A	104_E	0.940	0.66
7_H	38_P	0.939	0.66
44_G	49_E	0.912	0.63
38_P	102_E	0.891	0.61
25_Y	28_P	0.891	0.61
48_G	53_A	0.879	0.60
12_K	84_T	0.867	0.59
85_V	103_V	0.827	0.56
25_Y	30_T	0.826	0.56
67_L	70_F	0.812	0.54
31_I	57_L	0.811	0.54
4_L	35_R	0.808	0.54
67_L	76_I	0.806	0.54
44_G	50_Q	0.797	0.53
18_D	24_T	0.787	0.52
9_V	78_F	0.786	0.52
59_V	103_V	0.781	0.51
12_K	29_V	0.779	0.51
92_Y	95_S	0.779	0.51
78_F	92_Y	0.774	0.51
34_V	60_D	0.772	0.51
9_V	79_D	0.767	0.50
48_G	51_I	0.766	0.50
10_T	13_E	0.757	0.49
61_A	64_S	0.754	0.49
24_T	68_V	0.741	0.48
56_V	87_K	0.715	0.45
30_T	77_V	0.706	0.45
27_E	80_G	0.705	0.44
5_L	58_F	0.704	0.44
40_T	51_I	0.700	0.44
18_D	21_G	0.690	0.43
5_L	34_V	0.681	0.42
53_A	86_T	0.673	0.42
9_V	59_V	0.672	0.41
70_F	73_G	0.667	0.41
47_N	52_V	0.663	0.41
55_A	89_I	0.662	0.41
85_V	89_I	0.654	0.40
26_A	74_S	0.651	0.40
13_E	83_Y	0.650	0.39
73_G	84_T	0.649	0.39
35_R	92_Y	0.647	0.39
32_K	97_K	0.646	0.39
89_I	104_E	0.634	0.38
39_S	104_E	0.630	0.38
5_L	35_R	0.626	0.37
5_L	99_H	0.622	0.37
29_V	45_T	0.622	0.37
9_V	64_S	0.613	0.36
93_P	98_L	0.612	0.36
77_V	80_G	0.610	0.36
1_P	63_N	0.608	0.36
37_D	79_D	0.599	0.35
55_A	83_Y	0.599	0.35
25_Y	74_S	0.597	0.35
12_K	28_P	0.596	0.35
52_V	56_V	0.590	0.34
58_F	78_F	0.588	0.34
69_D	90_P	0.588	0.34
39_S	89_I	0.584	0.34
20_W	83_Y	0.576	0.33
12_K	33_N	0.574	0.33
59_V	63_N	0.573	0.33
25_Y	79_D	0.572	0.33
13_E	36_F	0.572	0.33
43_S	52_V	0.568	0.32
42_Y	53_A	0.565	0.32
23_P	27_E	0.565	0.32
7_H	94_D	0.563	0.32
47_N	50_Q	0.559	0.32
56_V	102_E	0.557	0.32
12_K	103_V	0.551	0.31
71_K	88_V	0.549	0.31
18_D	23_P	0.543	0.30
49_E	73_G	0.539	0.30
62_K	99_H	0.539	0.30
41_K	51_I	0.536	0.30
36_F	55_A	0.528	0.29
35_R	88_V	0.528	0.29
20_W	94_D	0.522	0.29
29_V	74_S	0.521	0.29
8_S	101_Y	0.520	0.29
56_V	86_T	0.520	0.29
73_G	103_V	0.520	0.29
64_S	99_H	0.520	0.29
15_T	26_A	0.518	0.29
3_R	15_T	0.515	0.28
8_S	26_A	0.514	0.28
55_A	78_F	0.512	0.28
14_Y	28_P	0.505	0.28
37_D	58_F	0.505	0.28
58_F	92_Y	0.504	0.28
69_D	95_S	0.500	0.27

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
3f3bA	1	0.9048	83.6	0.844	Contact Map
2kcaA	1	0.9619	38.2	0.887	Contact Map
2kz4A	1	0.9238	19.1	0.902	Contact Map
3bmbA	1	0.9429	18.7	0.903	Contact Map
1grjA	1	0.8476	13.2	0.909	Contact Map
3uv9A	3	0.5429	12.1	0.911	Contact Map
2f23A	1	0.8286	11.2	0.912	Contact Map
2eifA	1	0.4857	8.9	0.916	Contact Map
2pn0A	2	0.8476	8.4	0.917	Contact Map
4qt6A	1	0.4286	8.1	0.917	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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