GREMLIN Database
Phage_holin_3_7 - Putative 3TM holin, Phage_holin_3
PFAM: PF05449 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 80 (78)
Sequences: 565 (389)
Seq/√Len: 44.1
META: 0.481

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
16_Y21_A4.1451.00
14_L35_I4.1151.00
2_N61_N3.2161.00
32_Y36_V3.0691.00
9_I38_T2.8671.00
8_A69_L2.5011.00
37_A59_L2.1060.99
8_A65_C1.9360.99
12_R16_Y1.7250.98
27_V76_A1.7240.98
5_A65_C1.5970.97
57_E61_N1.5510.96
36_V39_G1.5030.95
6_C61_N1.4790.95
5_A58_V1.4760.95
6_C9_I1.4450.94
41_V44_R1.3690.92
50_Y57_E1.3390.91
42_A57_E1.3380.91
28_S69_L1.3350.91
28_S31_A1.3250.91
44_R54_S1.3220.91
5_A62_L1.2550.88
54_S57_E1.2500.88
10_A13_L1.1690.84
34_L37_A1.1620.84
11_L62_L1.1230.82
22_R76_A1.1170.81
72_R75_V1.0850.79
75_V79_L1.0660.78
13_L35_I1.0410.77
54_S76_A1.0360.76
37_A43_I1.0320.76
25_P29_W1.0290.76
46_L59_L1.0230.75
27_V63_L1.0190.75
3_A29_W1.0120.74
10_A38_T1.0120.74
7_L42_A1.0120.74
37_A57_E1.0060.74
40_S54_S0.9930.73
12_R15_T0.9750.72
28_S76_A0.9590.70
12_R35_I0.9590.70
38_T64_L0.9500.70
67_A78_L0.9420.69
16_Y74_N0.9320.68
34_L75_V0.9220.67
24_R76_A0.9180.67
24_R27_V0.9160.67
9_I68_V0.8950.65
38_T60_I0.8860.64
3_A23_H0.8850.64
3_A7_L0.8680.63
10_A45_I0.8650.62
2_N6_C0.8530.61
10_A35_I0.8490.61
55_W58_V0.8300.59
46_L75_V0.8280.59
2_N13_L0.8260.59
35_I60_I0.8250.59
22_R27_V0.8060.57
4_L10_A0.7710.54
76_A79_L0.7620.53
33_L75_V0.7550.52
21_A27_V0.7440.51
34_L60_I0.7380.50
31_A74_N0.7280.49
69_L72_R0.7210.49
39_G43_I0.7130.48
34_L67_A0.7110.48
32_Y39_G0.7060.47
24_R64_L0.6990.47
18_R40_S0.6890.46
63_L78_L0.6840.45
10_A36_V0.6750.44
53_V71_A0.6740.44
6_C10_A0.6740.44
22_R56_A0.6580.43
26_G37_A0.6510.42
7_L48_G0.6400.41
41_V50_Y0.6340.40
70_R74_N0.6260.40
9_I69_L0.6170.39
16_Y23_H0.6120.38
14_L23_H0.6080.38
40_S44_R0.6060.38
36_V47_F0.5960.37
49_L60_I0.5900.36
41_V54_S0.5890.36
25_P70_R0.5810.36
5_A24_R0.5800.36
64_L78_L0.5790.35
58_V61_N0.5670.34
10_A32_Y0.5650.34
11_L72_R0.5590.34
18_R23_H0.5570.34
10_A25_P0.5550.33
10_A14_L0.5540.33
38_T43_I0.5540.33
71_A77_R0.5540.33
72_R77_R0.5520.33
43_I50_Y0.5500.33
24_R72_R0.5480.33
54_S63_L0.5390.32
17_R33_L0.5280.31
38_T45_I0.5220.31
13_L66_V0.5210.31
11_L79_L0.5170.30
9_I60_I0.5110.30
41_V75_V0.5100.30
32_Y77_R0.5070.29
29_W66_V0.5040.29
30_L63_L0.5010.29
18_R77_R0.5010.29
38_T70_R0.5000.29
13_L59_L0.5000.29
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  
3wajA 1 0.95 2.8 0.908 Contact Map
2ks1B 1 0.325 2.2 0.914 Contact Map
2jwaA 2 0.3125 2.1 0.914 Contact Map
3rceA 1 0.9625 2 0.916 Contact Map
4wgvA 2 0.55 1.9 0.916 Contact Map
2l2tA 2 0.3375 1.8 0.918 Contact Map
4qncA 2 0.2125 1.7 0.918 Contact Map
4u9nA 2 0.8125 1.5 0.921 Contact Map
3lb6C 1 0 1.4 0.922 Contact Map
3l1lA 2 0.95 1.3 0.923 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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