GREMLIN Database
Phage_holin_1 - Bacteriophage holin
PFAM: PF04531 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 82 (82)
Sequences: 1080 (779)
Seq/√Len: 86.0
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
74_R82_K5.3691.00
5_V12_F2.7281.00
28_A33_Y2.6351.00
7_F13_W2.6131.00
75_A78_Y2.5941.00
42_D46_A2.4941.00
18_P52_F2.3651.00
2_N5_V2.0481.00
19_A56_A2.0371.00
72_S75_A1.8261.00
25_Q49_N1.8191.00
26_A50_A1.7241.00
52_F61_V1.6711.00
12_F16_L1.5741.00
55_L60_V1.5541.00
70_S76_L1.5531.00
16_L57_I1.5381.00
15_A18_P1.4500.99
22_L25_Q1.4130.99
17_I48_V1.4070.99
39_A43_Q1.3990.99
39_A42_D1.3150.99
37_S40_L1.2760.98
50_A54_V1.2600.98
27_V47_I1.2440.98
10_K15_A1.2390.98
73_E76_L1.2370.98
4_K79_E1.1950.97
30_L47_I1.1830.97
3_W7_F1.1290.96
11_A62_V1.1230.96
6_R65_T1.1160.96
13_W18_P1.1020.96
48_V52_F1.0930.96
16_L54_V1.0820.95
23_L47_I1.0750.95
23_L27_V1.0300.94
77_T80_K1.0090.93
15_A19_A1.0040.93
74_R77_T1.0020.93
38_W45_L1.0010.93
42_D49_N0.9970.93
7_F16_L0.9780.92
2_N72_S0.9730.92
65_T75_A0.9680.92
53_A56_A0.9350.91
9_N13_W0.9320.90
38_W42_D0.9220.90
22_L50_A0.9070.89
21_L41_G0.9000.89
22_L49_N0.8960.89
15_A60_V0.8940.88
5_V8_K0.8910.88
74_R78_Y0.8810.88
7_F76_L0.8760.87
34_D38_W0.8740.87
5_V65_T0.8440.85
73_E77_T0.8410.85
25_Q35_L0.8390.85
1_I70_S0.8290.84
55_L59_G0.8200.84
72_S78_Y0.8180.84
70_S77_T0.8130.83
69_I79_E0.8080.83
14_L49_N0.7980.82
41_G44_L0.7960.82
70_S73_E0.7930.82
67_K70_S0.7880.81
7_F80_K0.7830.81
21_L44_L0.7680.80
3_W61_V0.7540.78
6_R64_P0.7410.77
68_G71_D0.7390.77
17_I52_F0.7300.76
67_K77_T0.7270.76
23_L26_A0.7220.75
30_L44_L0.7100.74
19_A50_A0.7070.74
63_D72_S0.6970.73
19_A22_L0.6950.72
24_I44_L0.6690.70
22_L53_A0.6520.68
10_K63_D0.6350.66
1_I6_R0.6190.64
6_R9_N0.6170.63
69_I77_T0.6090.62
27_V43_Q0.6080.62
19_A57_I0.6080.62
73_E80_K0.6080.62
20_V51_V0.6070.62
22_L35_L0.6030.62
29_G43_Q0.6030.62
78_Y81_P0.5960.61
63_D78_Y0.5830.59
65_T78_Y0.5760.58
11_A15_A0.5680.57
66_T75_A0.5670.57
17_I45_L0.5670.57
15_A62_V0.5650.57
8_K12_F0.5570.56
10_K60_V0.5500.55
35_L41_G0.5460.54
22_L52_F0.5450.54
65_T72_S0.5420.54
26_A54_V0.5400.53
18_P60_V0.5400.53
55_L58_L0.5350.53
5_V63_D0.5340.53
30_L43_Q0.5330.52
5_V72_S0.5270.52
14_L70_S0.5260.51
15_A59_G0.5240.51
26_A49_N0.5220.51
30_L35_L0.5210.51
62_V67_K0.5150.50
73_E79_E0.5150.50
19_A60_V0.5150.50
3_W65_T0.5150.50
29_G34_D0.5120.50
23_L28_A0.5080.49
74_R81_P0.5040.49
10_K13_W0.5030.48
8_K80_K0.5000.48
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  
2kogA 1 0.4024 16.4 0.899 Contact Map
1uf2A 7 0.8902 14.3 0.902 Contact Map
4o6yA 2 0.7561 10.4 0.907 Contact Map
3hd7A 1 0.3902 8.3 0.912 Contact Map
2wswA 3 0.9268 4.7 0.921 Contact Map
4wgvA 2 0.878 3.3 0.927 Contact Map
1f6yA 2 0.3415 3.1 0.928 Contact Map
4c7rA 3 0.9024 2.9 0.929 Contact Map
1lnqA 6 0.6707 2.7 0.93 Contact Map
4bgnA 3 0.7927 2.2 0.933 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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