Phage_T7_Capsid - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

Phage_T7_Capsid - Phage T7 capsid assembly protein

PFAM:	PF05396	Sequences: GELSEESYAALEKAGIPKELVDSYIAGQEALAEQQVNEVKSSVGGEEAYNEMVEWAENNSPEEIDAFNKAVNSGDLEAIKLAVQGLKARYEAANGSEPNRLVTGKATPAAPQASKTEGFASQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	123 (98)
Sequences:	548 (459)
Seq/√Len:	46.4
META:	0.929

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_Y	22_D	3.317	1.00
9_A	13_K	2.944	1.00
2_E	5_E	2.889	1.00
60_S	63_E	2.679	1.00
55_W	59_N	2.524	1.00
40_K	46_E	2.502	1.00
26_A	29_E	2.447	1.00
12_E	18_K	2.367	1.00
39_V	83_V	2.328	1.00
81_L	85_G	2.166	1.00
69_K	75_D	2.160	1.00
63_E	89_R	2.060	1.00
85_G	88_A	2.058	1.00
18_K	22_D	2.045	0.99
27_G	30_A	2.032	0.99
87_K	91_E	1.835	0.99
33_E	36_V	1.660	0.98
39_V	76_L	1.651	0.98
86_L	90_Y	1.651	0.98
82_A	86_L	1.639	0.97
43_V	87_K	1.614	0.97
48_A	51_E	1.554	0.96
46_E	50_N	1.551	0.96
9_A	12_E	1.540	0.96
5_E	9_A	1.533	0.96
36_V	40_K	1.521	0.96
16_I	20_L	1.472	0.95
47_E	50_N	1.434	0.94
28_Q	31_L	1.423	0.94
31_L	34_Q	1.392	0.94
62_E	77_E	1.366	0.93
52_M	90_Y	1.337	0.92
6_E	9_A	1.294	0.91
3_L	25_I	1.284	0.90
56_A	59_N	1.216	0.88
34_Q	37_N	1.135	0.84
38_E	80_K	1.109	0.83
82_A	85_G	1.106	0.82
84_Q	89_R	1.049	0.79
4_S	7_S	1.041	0.78
54_E	57_E	1.029	0.78
83_V	86_L	1.029	0.78
17_P	80_K	1.018	0.77
8_Y	18_K	1.006	0.76
46_E	54_E	0.988	0.75
65_D	69_K	0.986	0.74
24_Y	28_Q	0.977	0.74
8_Y	21_V	0.974	0.74
33_E	62_E	0.973	0.73
49_Y	53_V	0.933	0.70
39_V	79_I	0.929	0.70
27_G	80_K	0.925	0.70
71_V	79_I	0.910	0.68
50_N	54_E	0.907	0.68
28_Q	32_A	0.905	0.68
72_N	97_E	0.892	0.67
65_D	68_N	0.877	0.65
38_E	41_S	0.876	0.65
80_K	84_Q	0.874	0.65
11_L	18_K	0.868	0.65
86_L	89_R	0.867	0.65
19_E	37_N	0.856	0.64
85_G	95_G	0.854	0.63
74_G	78_A	0.837	0.62
4_S	24_Y	0.831	0.61
7_S	28_Q	0.830	0.61
36_V	46_E	0.824	0.61
11_L	14_A	0.820	0.60
30_A	34_Q	0.812	0.59
28_Q	43_V	0.807	0.59
23_S	28_Q	0.787	0.57
76_L	80_K	0.776	0.56
25_I	92_A	0.771	0.56
64_I	68_N	0.770	0.55
29_E	33_E	0.764	0.55
81_L	86_L	0.764	0.55
81_L	84_Q	0.756	0.54
16_I	35_Q	0.753	0.54
53_V	64_I	0.751	0.54
25_I	39_V	0.747	0.53
33_E	37_N	0.744	0.53
19_E	41_S	0.741	0.53
41_S	47_E	0.723	0.51
6_E	10_A	0.714	0.50
3_L	21_V	0.712	0.50
16_I	78_A	0.711	0.50
56_A	60_S	0.707	0.49
18_K	65_D	0.700	0.49
90_Y	95_G	0.699	0.48
17_P	64_I	0.696	0.48
57_E	61_P	0.686	0.47
64_I	81_L	0.676	0.46
25_I	36_V	0.676	0.46
43_V	99_N	0.675	0.46
4_S	20_L	0.672	0.46
26_A	30_A	0.669	0.45
3_L	7_S	0.663	0.45
74_G	84_Q	0.654	0.44
18_K	24_Y	0.646	0.43
60_S	98_P	0.643	0.43
16_I	21_V	0.640	0.43
6_E	37_N	0.635	0.42
2_E	19_E	0.631	0.42
67_F	89_R	0.625	0.41
7_S	10_A	0.621	0.41
46_E	97_E	0.620	0.41
6_E	84_Q	0.612	0.40
14_A	95_G	0.601	0.39
61_P	64_I	0.600	0.39
24_Y	76_L	0.599	0.39
69_K	78_A	0.598	0.39
37_N	41_S	0.596	0.38
5_E	18_K	0.589	0.38
55_W	60_S	0.586	0.38
85_G	90_Y	0.582	0.37
36_V	62_E	0.579	0.37
49_Y	67_F	0.579	0.37
67_F	72_N	0.576	0.37
52_M	66_A	0.574	0.36
91_E	96_S	0.572	0.36
53_V	71_V	0.569	0.36
12_E	17_P	0.567	0.36
34_Q	42_S	0.562	0.35
50_N	61_P	0.562	0.35
4_S	72_N	0.559	0.35
14_A	40_K	0.553	0.35
75_D	79_I	0.552	0.34
43_V	49_Y	0.549	0.34
70_A	92_A	0.545	0.34
87_K	94_N	0.540	0.33
7_S	25_I	0.539	0.33
20_L	36_V	0.538	0.33
16_I	49_Y	0.531	0.33
40_K	81_L	0.530	0.33
20_L	67_F	0.529	0.32
4_S	34_Q	0.529	0.32
55_W	86_L	0.527	0.32
52_M	82_A	0.524	0.32
60_S	64_I	0.523	0.32
48_A	66_A	0.522	0.32
70_A	73_S	0.522	0.32
14_A	29_E	0.510	0.31
17_P	20_L	0.507	0.31
69_K	87_K	0.507	0.31
17_P	96_S	0.504	0.30
47_E	75_D	0.502	0.30
11_L	15_G	0.500	0.30

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
1ifyA	1	0.3659	20.2	0.923	Contact Map
4kqwA	2	0.439	13.8	0.928	Contact Map
2pfxA	3	0.439	13.1	0.929	Contact Map
1wgnA	1	0.3902	12.6	0.93	Contact Map
3c1lA	5	0.439	11.6	0.931	Contact Map
2mr9A	1	0.3415	10.7	0.932	Contact Map
2ekkA	1	0.3415	10.4	0.932	Contact Map
4p8bA	1	0.439	9.6	0.933	Contact Map
2lbcA	1	0.4146	9.3	0.934	Contact Map
2cpwA	1	0.3984	8.8	0.934	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.

Page generated in 0.0052 seconds.