GREMLIN Database
Phage_T7_Capsid - Phage T7 capsid assembly protein
PFAM: PF05396 Sequences:
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_Y22_D3.3171.00
9_A13_K2.9441.00
2_E5_E2.8891.00
60_S63_E2.6791.00
55_W59_N2.5241.00
40_K46_E2.5021.00
26_A29_E2.4471.00
12_E18_K2.3671.00
39_V83_V2.3281.00
81_L85_G2.1661.00
69_K75_D2.1601.00
63_E89_R2.0601.00
85_G88_A2.0581.00
18_K22_D2.0450.99
27_G30_A2.0320.99
87_K91_E1.8350.99
33_E36_V1.6600.98
39_V76_L1.6510.98
86_L90_Y1.6510.98
82_A86_L1.6390.97
43_V87_K1.6140.97
48_A51_E1.5540.96
46_E50_N1.5510.96
9_A12_E1.5400.96
5_E9_A1.5330.96
36_V40_K1.5210.96
16_I20_L1.4720.95
47_E50_N1.4340.94
28_Q31_L1.4230.94
31_L34_Q1.3920.94
62_E77_E1.3660.93
52_M90_Y1.3370.92
6_E9_A1.2940.91
3_L25_I1.2840.90
56_A59_N1.2160.88
34_Q37_N1.1350.84
38_E80_K1.1090.83
82_A85_G1.1060.82
84_Q89_R1.0490.79
4_S7_S1.0410.78
54_E57_E1.0290.78
83_V86_L1.0290.78
17_P80_K1.0180.77
8_Y18_K1.0060.76
46_E54_E0.9880.75
65_D69_K0.9860.74
24_Y28_Q0.9770.74
8_Y21_V0.9740.74
33_E62_E0.9730.73
49_Y53_V0.9330.70
39_V79_I0.9290.70
27_G80_K0.9250.70
71_V79_I0.9100.68
50_N54_E0.9070.68
28_Q32_A0.9050.68
72_N97_E0.8920.67
65_D68_N0.8770.65
38_E41_S0.8760.65
80_K84_Q0.8740.65
11_L18_K0.8680.65
86_L89_R0.8670.65
19_E37_N0.8560.64
85_G95_G0.8540.63
74_G78_A0.8370.62
4_S24_Y0.8310.61
7_S28_Q0.8300.61
36_V46_E0.8240.61
11_L14_A0.8200.60
30_A34_Q0.8120.59
28_Q43_V0.8070.59
23_S28_Q0.7870.57
76_L80_K0.7760.56
25_I92_A0.7710.56
64_I68_N0.7700.55
29_E33_E0.7640.55
81_L86_L0.7640.55
81_L84_Q0.7560.54
16_I35_Q0.7530.54
53_V64_I0.7510.54
25_I39_V0.7470.53
33_E37_N0.7440.53
19_E41_S0.7410.53
41_S47_E0.7230.51
6_E10_A0.7140.50
3_L21_V0.7120.50
16_I78_A0.7110.50
56_A60_S0.7070.49
18_K65_D0.7000.49
90_Y95_G0.6990.48
17_P64_I0.6960.48
57_E61_P0.6860.47
64_I81_L0.6760.46
25_I36_V0.6760.46
43_V99_N0.6750.46
4_S20_L0.6720.46
26_A30_A0.6690.45
3_L7_S0.6630.45
74_G84_Q0.6540.44
18_K24_Y0.6460.43
60_S98_P0.6430.43
16_I21_V0.6400.43
6_E37_N0.6350.42
2_E19_E0.6310.42
67_F89_R0.6250.41
7_S10_A0.6210.41
46_E97_E0.6200.41
6_E84_Q0.6120.40
14_A95_G0.6010.39
61_P64_I0.6000.39
24_Y76_L0.5990.39
69_K78_A0.5980.39
37_N41_S0.5960.38
5_E18_K0.5890.38
55_W60_S0.5860.38
85_G90_Y0.5820.37
36_V62_E0.5790.37
49_Y67_F0.5790.37
67_F72_N0.5760.37
52_M66_A0.5740.36
91_E96_S0.5720.36
53_V71_V0.5690.36
12_E17_P0.5670.36
34_Q42_S0.5620.35
50_N61_P0.5620.35
4_S72_N0.5590.35
14_A40_K0.5530.35
75_D79_I0.5520.34
43_V49_Y0.5490.34
70_A92_A0.5450.34
87_K94_N0.5400.33
7_S25_I0.5390.33
20_L36_V0.5380.33
16_I49_Y0.5310.33
40_K81_L0.5300.33
20_L67_F0.5290.32
4_S34_Q0.5290.32
55_W86_L0.5270.32
52_M82_A0.5240.32
60_S64_I0.5230.32
48_A66_A0.5220.32
70_A73_S0.5220.32
14_A29_E0.5100.31
17_P20_L0.5070.31
69_K87_K0.5070.31
17_P96_S0.5040.30
47_E75_D0.5020.30
11_L15_G0.5000.30
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

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.

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