GREMLIN Database
Phage_holin_3_1 - Phage holin family (Lysis protein S)
PFAM: PF05106 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 99 (98)
Sequences: 684 (468)
Seq/√Len: 47.3
META: 0.466

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
30_I51_L3.8001.00
59_A80_I3.1651.00
2_K6_T3.0661.00
23_G56_T2.9111.00
34_R48_E2.8731.00
49_A83_L2.4631.00
86_E89_R2.4061.00
60_S74_V2.3181.00
58_A78_G2.2881.00
3_D6_T2.0681.00
53_G78_G2.0571.00
32_L49_A2.0431.00
53_G79_F1.9010.99
13_W17_H1.7380.98
62_G72_L1.7310.98
65_Y72_L1.7190.98
31_A34_R1.6870.98
64_E70_Q1.6840.98
57_L78_G1.6470.98
94_R97_N1.6080.97
91_L96_I1.5990.97
27_A56_T1.5730.97
45_R86_E1.5500.97
33_L50_L1.5450.97
52_C80_I1.5340.96
23_G77_G1.4870.96
56_T77_G1.3860.94
2_K5_D1.3690.93
69_P72_L1.3570.93
53_G75_F1.3490.93
79_F83_L1.3060.92
33_L47_L1.2790.91
87_K93_K1.2780.91
37_Y85_V1.2720.90
31_A49_A1.2450.90
77_G82_F1.2300.89
30_I35_V1.2300.89
83_L91_L1.1950.88
58_A77_G1.1160.84
52_C81_G1.0880.82
26_L57_L1.0820.82
65_Y69_P1.0530.80
31_A52_C1.0520.80
10_L13_W1.0200.78
49_A82_F0.9990.76
56_T78_G0.9920.76
62_G90_E0.9880.75
82_F88_I0.9810.75
21_I25_L0.9750.74
54_L61_S0.9570.73
51_L85_V0.9530.73
14_L29_V0.9460.72
68_L72_L0.9390.72
6_T10_L0.9220.70
57_L75_F0.9170.70
13_W18_W0.9060.69
38_D89_R0.9000.68
87_K91_L0.8830.67
32_L45_R0.8830.67
82_F89_R0.8670.65
47_L92_A0.8590.65
25_L97_N0.8570.65
4_P7_W0.8560.64
24_A73_A0.8520.64
34_R47_L0.8520.64
48_E69_P0.8360.63
11_L14_L0.8160.61
95_F99_K0.8120.60
35_V47_L0.7930.58
5_D10_L0.7840.58
54_L57_L0.7820.57
51_L76_I0.7790.57
37_Y44_R0.7740.57
83_L90_E0.7740.57
61_S78_G0.7700.56
27_A53_G0.7660.56
68_L71_S0.7660.56
24_A28_F0.7430.54
63_L88_I0.7310.52
2_K76_I0.7170.51
70_Q73_A0.7110.50
82_F93_K0.7110.50
26_L58_A0.7010.49
71_S96_I0.6980.49
19_P30_I0.6790.47
29_V42_W0.6770.47
56_T63_L0.6770.47
90_E98_R0.6590.45
25_L32_L0.6550.45
27_A93_K0.6480.44
39_G67_G0.6470.44
35_V85_V0.6460.44
12_A16_E0.6430.44
44_R48_E0.6390.43
28_F79_F0.6360.43
19_P92_A0.6340.43
35_V48_E0.6330.43
5_D11_L0.6330.43
54_L92_A0.6320.43
2_K8_A0.6310.42
46_L71_S0.6300.42
88_I96_I0.6300.42
62_G68_L0.6220.42
81_G91_L0.6200.41
13_W16_E0.6180.41
10_L68_L0.6170.41
24_A29_V0.6170.41
70_Q98_R0.6090.40
46_L83_L0.6030.40
74_V77_G0.6010.40
6_T9_A0.5980.39
56_T98_R0.5970.39
87_K95_F0.5960.39
15_S55_L0.5940.39
53_G57_L0.5930.39
17_H30_I0.5920.39
64_E71_S0.5880.38
59_A64_E0.5880.38
11_L15_S0.5810.38
46_L55_L0.5800.38
20_Q57_L0.5800.38
2_K9_A0.5750.37
26_L56_T0.5750.37
2_K12_A0.5740.37
76_I99_K0.5670.36
17_H54_L0.5630.36
55_L85_V0.5600.36
36_I47_L0.5470.35
62_G76_I0.5450.34
66_F72_L0.5430.34
75_F79_F0.5430.34
52_C63_L0.5360.34
61_S73_A0.5350.33
30_I54_L0.5340.33
5_D99_K0.5300.33
63_L80_I0.5260.33
34_R51_L0.5210.32
26_L59_A0.5190.32
39_G43_R0.5180.32
55_L81_G0.5180.32
87_K90_E0.5120.31
9_A12_A0.5110.31
31_A47_L0.5080.31
61_S76_I0.5020.31
6_T94_R0.5010.31
2_K11_L0.5010.31
22_Y40_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  
2j69A 1 0.7576 74.5 0.838 Contact Map
2b2hA 3 0.8283 27.1 0.88 Contact Map
4k0jA 3 0.9899 20.7 0.887 Contact Map
1u7gA 3 0.8485 17.3 0.891 Contact Map
4hw9A 3 0.8384 15.7 0.893 Contact Map
3b9wA 3 0.9293 14.9 0.894 Contact Map
4pd6A 3 0.9495 14.2 0.895 Contact Map
1ji6A 1 0.5051 12.6 0.897 Contact Map
2c9kA 1 0.5051 8.8 0.904 Contact Map
3w9iA 3 1 8.8 0.904 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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