GREMLIN Database
Phage_holin_3_3 - LydA holin phage, holin superfamily III
PFAM: PF16083 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 80 (77)
Sequences: 2017 (1670)
Seq/√Len: 190.3
META: 0.824

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
51_C61_T2.9021.00
53_Y57_S2.9021.00
48_F62_A2.8611.00
53_Y60_L2.7791.00
61_T65_A2.2961.00
36_E74_R2.2671.00
15_V39_I2.1741.00
52_E59_L2.1101.00
9_A44_G2.0621.00
12_G42_F1.9391.00
46_L63_A1.8581.00
46_L66_G1.8331.00
16_R20_R1.8111.00
17_Y33_L1.7561.00
74_R77_D1.5261.00
62_A65_A1.4891.00
42_F66_G1.4851.00
15_V42_F1.4651.00
72_G75_A1.4391.00
50_L54_L1.4271.00
60_L63_A1.3991.00
41_G66_G1.3621.00
67_I70_H1.3541.00
51_C56_L1.3471.00
41_G67_I1.3381.00
43_A68_A1.3261.00
47_T68_A1.3191.00
39_I42_F1.3041.00
71_M75_A1.2671.00
68_A75_A1.2381.00
30_W34_I1.1131.00
70_H77_D1.0591.00
75_A79_L1.0471.00
17_Y28_F1.0221.00
41_G63_A1.0151.00
40_S73_A1.0121.00
51_C64_L0.9870.99
49_L62_A0.9850.99
70_H73_A0.9820.99
12_G16_R0.9810.99
26_R29_S0.9710.99
13_G44_G0.9630.99
28_F33_L0.9580.99
36_E70_H0.9500.99
17_Y36_E0.9460.99
11_L38_V0.9400.99
46_L67_I0.9290.99
57_S60_L0.9210.99
9_A69_G0.9210.99
15_V70_H0.9130.99
35_G39_I0.8870.99
45_L59_L0.8690.99
45_L49_L0.8680.99
20_R25_K0.8620.99
29_S32_E0.8510.98
44_G62_A0.8440.98
15_V35_G0.8360.98
18_L35_G0.8310.98
48_F52_E0.8150.98
8_L13_G0.8020.98
14_L37_L0.7950.97
13_G40_S0.7600.97
21_V24_G0.7580.97
47_T64_L0.7460.96
9_A13_G0.7150.95
44_G69_G0.7080.95
11_L18_L0.7010.95
14_L38_V0.6980.95
8_L45_L0.6910.94
22_K32_E0.6900.94
51_C59_L0.6880.94
13_G16_R0.6880.94
11_L15_V0.6790.94
43_A73_A0.6770.94
36_E48_F0.6700.93
19_R77_D0.6670.93
7_L55_G0.6640.93
73_A77_D0.6600.93
28_F32_E0.6550.93
16_R36_E0.6530.93
47_T51_C0.6520.92
11_L42_F0.6390.92
34_I38_V0.6190.90
14_L33_L0.6170.90
27_K31_R0.6120.90
54_L57_S0.6120.90
44_G66_G0.6090.90
44_G65_A0.6020.89
74_R78_L0.6010.89
47_T79_L0.6000.89
54_L64_L0.5970.89
60_L64_L0.5950.89
15_V18_L0.5940.89
8_L49_L0.5850.88
49_L59_L0.5810.87
49_L63_A0.5670.86
19_R23_K0.5660.86
16_R42_F0.5650.86
58_P62_A0.5510.85
25_K31_R0.5430.84
55_G58_P0.5400.83
11_L69_G0.5400.83
32_E47_T0.5390.83
6_L58_P0.5370.83
6_L45_L0.5360.83
37_L67_I0.5330.83
54_L78_L0.5320.83
36_E43_A0.5310.82
10_L37_L0.5310.82
19_R73_A0.5290.82
75_A78_L0.5280.82
6_L19_R0.5140.80
20_R24_G0.5130.80
40_S62_A0.5130.80
51_C65_A0.5020.79
52_E65_A0.5000.78
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  
2j69A 1 0.8375 12.5 0.826 Contact Map
2nqtA 4 0.3125 9.7 0.834 Contact Map
2hjsA 2 0.2875 8.4 0.839 Contact Map
3h9eO 4 0.275 7.9 0.841 Contact Map
1u7gA 3 0.925 7.6 0.843 Contact Map
2zy9A 2 0.9875 6.9 0.845 Contact Map
1vknA 4 0.3 6.7 0.846 Contact Map
3b9wA 3 0.925 6.1 0.849 Contact Map
1xygA 4 0.2875 6.1 0.849 Contact Map
3nd0A 2 0.8125 5.9 0.85 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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