GREMLIN Database
Phage_holin_5_2 - Phage holin family Hol44, in holin superfamily V
PFAM: PF16079 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 75 (74)
Sequences: 1843 (1420)
Seq/√Len: 165.0
META: 0.812

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
9_G27_L3.1721.00
16_P21_K2.7571.00
6_Y69_N2.3701.00
9_G23_I2.2091.00
70_Q74_Q2.1971.00
6_Y10_Y2.0121.00
63_L67_G1.8131.00
15_T25_L1.7261.00
7_L63_L1.7101.00
28_G67_G1.6701.00
5_C9_G1.6661.00
8_I30_L1.6241.00
28_G59_I1.5931.00
35_G54_A1.5891.00
27_L62_G1.5591.00
21_K25_L1.5571.00
31_G58_G1.5451.00
5_C27_L1.5411.00
12_L26_I1.5411.00
62_G67_G1.4981.00
32_I59_I1.4951.00
10_Y14_K1.4751.00
66_T70_Q1.3961.00
4_I56_L1.3451.00
18_I26_I1.3371.00
57_Q60_L1.3261.00
64_A67_G1.3251.00
27_L65_A1.3021.00
38_A42_M1.2721.00
1_I35_G1.2461.00
49_I52_F1.2381.00
7_L28_G1.2191.00
5_C62_G1.2191.00
6_Y68_L1.1711.00
6_Y65_A1.0791.00
48_D51_I1.0380.99
49_I53_G1.0340.99
27_L66_T1.0310.99
21_K74_Q1.0230.99
3_V64_A1.0140.99
1_I61_S1.0100.99
24_P31_G0.9930.99
22_Y26_I0.9820.99
31_G64_A0.9560.99
4_I59_I0.9290.99
6_Y72_V0.9200.98
35_G57_Q0.9180.98
3_V56_L0.9130.98
69_N74_Q0.9130.98
20_D23_I0.8840.98
28_G63_L0.8700.98
5_C31_G0.8400.97
15_T18_I0.8260.97
44_F48_D0.8080.96
38_A50_L0.8020.96
12_L15_T0.8000.96
26_I30_L0.7940.96
68_L72_V0.7930.96
28_G71_L0.7920.96
12_L18_I0.7680.95
23_I27_L0.7520.95
41_A49_I0.7480.95
19_P22_Y0.7430.94
47_T50_L0.7350.94
6_Y70_Q0.7180.93
39_V50_L0.7080.93
4_I34_L0.7050.93
34_L65_A0.7010.92
39_V43_D0.7010.92
57_Q61_S0.7010.92
1_I5_C0.7010.92
6_Y24_P0.7000.92
26_I29_V0.6870.92
33_V47_T0.6860.92
54_A57_Q0.6770.91
42_M45_P0.6660.90
11_I28_G0.6650.90
61_S65_A0.6600.90
49_I55_I0.6590.90
63_L68_L0.6470.89
68_L71_L0.6420.89
10_Y23_I0.6380.88
20_D70_Q0.6370.88
65_A68_L0.6350.88
9_G20_D0.6340.88
38_A45_P0.6270.88
32_I60_L0.6160.87
11_I25_L0.6040.86
6_Y66_T0.5950.85
69_N73_K0.5900.84
22_Y25_L0.5780.83
56_L60_L0.5780.83
46_A53_G0.5760.83
71_L74_Q0.5700.82
35_G61_S0.5690.82
23_I66_T0.5580.81
39_V42_M0.5540.80
13_K20_D0.5520.80
2_V64_A0.5520.80
31_G35_G0.5510.80
37_V40_F0.5460.79
4_I30_L0.5340.78
1_I34_L0.5320.78
29_V36_V0.5310.78
50_L53_G0.5300.77
32_I55_I0.5280.77
18_I22_Y0.5190.76
33_V52_F0.5120.75
36_V46_A0.5030.74
12_L27_L0.5030.74
43_D46_A0.5000.73
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  
4cz8A 2 0.9867 6.8 0.865 Contact Map
4czbA 2 1 6.7 0.866 Contact Map
3dh4A 3 0.8533 5 0.874 Contact Map
4pgrA 1 1 4.5 0.876 Contact Map
4bwzA 2 0.9867 4.2 0.878 Contact Map
1u7gA 3 0.88 4 0.88 Contact Map
2xq2A 2 0.8533 3.9 0.88 Contact Map
3hd6A 3 0.9733 3.7 0.881 Contact Map
2b2hA 3 0.8667 3.5 0.883 Contact Map
4ldsA 2 0.92 3.3 0.884 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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