TABLE 3.
Characteristics of bacteriophage φE125 genes and gene products
| Gene | Orientationa | Start (position) | End (position) | Size of protein (kDa) | Protein function and homologs |
|---|---|---|---|---|---|
| 1 | R | 46 | 531 | 17.2 | Terminase (small subunit); phage GMSE-1 Orf16; 1e-12; AF311659; phage 7201 Orf21; 2e-09; AF145054 |
| 2 | R | 541 | 2253 | 64.2 | Terminase (large subunit); E. coli YmfN; 1e-162; NP_415667; phage D3 terminase; 1e-125; NP_061498 |
| 3 | R | 2250 | 2435 | 6.3 | |
| 4 | R | 2440 | 3699 | 46.4 | Portal protein; H. influenzae Orf25-like protein; 1e-40; AAF27362; CP-933C Z1849; 1e-40; NP_287334 |
| 5 | R | 3759 | 4664 | 31.7 | Capsid assembly protein/protease; phage WO Orf7; 8e-44; AB036665; prophage Gifsy-1 STM2605; 2e-34; AE008818 |
| 6 | R | 4767 | 6074 | 46.3 | Major capsid protein; CP-933N Z1804; 2e-09; NP_287292; CP-933M Z1360; 2e-09; NP_286882 |
| 7 | R | 6134 | 6319 | 6.4 | |
| 8 | R | 6326 | 6892 | 20.6 | |
| 9 | R | 6892 | 7218 | 12.1 | Phage HK022 gp9; 3e-08; AF069308 |
| 10 | R | 7211 | 7633 | 15.4 | Phage HK97 gp10; 4e-20; AF069529 |
| CP-933M Z1368; 1e-19; NP_286890 | |||||
| 11 | R | 7630 | 7977 | 12.1 | |
| 12 | R | 8039 | 8497 | 16.4 | Major tail subunit protein; phage HK97 gp12; 2e-20; NP_037706; E. coli ECs1800; 7e-17; NP_309827 |
| 13 | R | 8519 | 8989 | 17.4 | Tail assembly chaperone protein; phage HK97 gp13; 9e-06; NP_037708; phage HK97 gp14; 1e-05; NP_037707 |
| 14 | R | 8989 | 9273 | 10.0 | Phage HK97 gp14; 9e-07; NP_037707 |
| 15 | R | 9287 | 13351 | 143.0 | Tail length tape measure protein; CP-933P Z6034; 2e-25; NP_287971; E. coli ECs2240; 2e-25; NP_310267 |
| 16 | R | 13348 | 13686 | 12.5 | Minor tail protein; phage HK97 gp17; 1e-18; NP_037711; phage HK022 gp17; 3e-18; NP_037677 |
| 17 | R | 13695 | 15083 | 50.1 | |
| 18 | R | 15080 | 15763 | 25.2 | Minor tail protein; P. aeruginosa PA0638; 2e-62; G83565; phage N15 gp18; 3e-51; AF064539 |
| 19 | R | 15783 | 16565 | 28.6 | Tail component protein; P. aeruginosa PA0639; 1e-51; AE004499; phage HK97 gp19; 1e-43; AF069529 |
| 20 | R | 16562 | 17146 | 20.1 | Tail component protein; Y. pestis YPO2129; 3e-33; AJ414151; phage N15 gp20; 3e-28; AF064539 |
| 21 | R | 17143 | 20448 | 118.3 | Tail tip fiber protein; Y. pestis YPO2131; < 1e-119; AJ414151; phage N15 gp21; < 1e-119; AF064539 |
| 22 | R | 20445 | 20759 | 11.6 | |
| 23 | R | 20759 | 21493 | 27.6 | |
| 24 | R | 21536 | 21748 | 7.6 | Class II holin; phage PS119 gp13; 8e-04; AJ011581; phage PS34 gp13; 8e-04; AJ011580 |
| 25 | R | 21826 | 22230 | 14.7 | Lysozyme; X. fastidiosa XF0513; 2e-13; AE003900; phage PS119 gp19; 2e-11; AJ011581 |
| 26 | R | 22227 | 22775 | 18.6 | |
| 27 | R | 22918 | 23706 | 30.2 | DNA adenine methylase; phage GMSE-1 Orf10; 1e-40; AF311653; A. lwoffii AlwI methylase; 5e-19; AF431889 |
| 28 | R | 23815 | 24693 | 30.9 | |
| 29 | R | 24875 | 25435 | 19.1 | P. aeruginosa PA1508; 7e-07; AE004579; Y. pestis YPO0866; 8e-07; AE004579 |
| 30 | R | 25432 | 26166 | 26.3 | P. aeruginosa PA0822; 5e-23; AE004517; P. aeruginosa PA0823; 4e-09; AE004517 |
| 31 | R | 26194 | 27285 | 39.4 | P. aeruginosa PA0821; 1e-48; AE004517 |
| 32 | L | 28059 | 27418 | 25.0 | |
| 33 | R | 28145 | 28816 | 25.3 | Plasmid pFKN Orf11; 2e-17; AF359557; plasmid pNL1 Orf520; 3e-04; AF079317 |
| 29062 | 29014 | attP (3′ end of tRNA ProUGG) | |||
| 34 | L | 30292 | 29192 | 42.2 | Site-specific integrase; prophage XfP2 XF2530; 6e-09; AE004060; CP-933M Z1323; 1e-08; NP_286846 |
| 35 | L | 30609 | 30292 | 11.8 | |
| 36 | L | 31142 | 30642 | 19.3 | |
| 37 | L | 32131 | 31139 | 37.2 | M. tuberculosis Rv2734; 8e-32; NP_217250; N. punctiforme hypothetical protein; 4e-28; AAK68643 |
| 38 | L | 33180 | 32128 | 37.9 | |
| 39′ | L | 33314 | 33195 | ||
| tnpB | L | 34204 | 33350 | 32.6 | Transposase (IS3 family); IS868 ORF4; 1e-101; X55075; IS401 transposase subunit; 4e-99; L09108 |
| tnpA | L | 34539 | 34261 | 10.7 | Transposase (IS3 family); IS401 transposase subunit; 6e-29; L09108; IS868 Orf1; 9e-20; X55075 |
| ′39 | L | 34794 | 34636 | ||
| Gene | Orientationa | Start (position) | End (position) | Size of protein (kDa) | Protein function and homologs |
| 40 | L | 35195 | 34794 | 14.6 | Phage M×8 p77; 0.1; AF396866 |
| 41 | L | 35863 | 35192 | 25.1 | CP-9330 Z2097; 4e-05; AE005346; CP-933U Z3120; 2e-04; AE005422 |
| 42 | L | 36671 | 35877 | 29.8 | |
| 43 | L | 37670 | 36858 | 29.7 | Y. pestis YPMT1.49c; 1e-38; NC_003134; S. enterica HCM2.0006c; 2e-38; AL513384 |
| 44 | L | 37816 | 37667 | 5.5 | |
| 45 | R | 38065 | 38718 | 28.6 | |
| 46 | R | 38919 | 39173 | 9.1 | |
| 47 | L | 39586 | 39170 | 15.5 | |
| 48 | L | 39993 | 39862 | 4.7 | |
| 49 | L | 40278 | 40003 | 10.4 | |
| 50 | R | 40519 | 40662 | 5.0 | |
| 51 | R | 40747 | 40935 | 7.0 | |
| 52 | L | 41555 | 41163 | 14.4 | Repressor protein; X. fastidiosa XF0499; 9e-14; AE003899; prophage e14 protein b1145; 9e-04; F64859 |
| 53 | R | 42006 | 42338 | 11.8 | |
| 54 | L | 42821 | 42567 | 9.4 | |
| 55 | R | 43007 | 43447 | 15.8 | Phage phi CTX Orf33; 0.24; BAA36261 |
| 56 | R | 43452 | 44588 | 42.1 | DNA cytosine methylase; C. freundii Cfr9I methylase; 8e-45; X17022; P. alcaligenes Pac25I methylase; 1e-44; U88088 |
| 57 | R | 44585 | 45583 | 36.8 | PAPS reductase/sulfotransferase; phage 186 Orf84; 6e-55; U32222; A. pernix APE2075; 8e-07; F72512 |
| 58 | R | 45618 | 46439 | 29.9 | DNA partitioning protein; R. equi ParA; 1e-06; NP_066815; L. lactis ParA; 2e-05; NP_266252 |
| 59 | R | 46436 | 46696 | 9.5 | |
| 60 | R | 46850 | 47842 | 36.3 | CP-933R Z2397; 7e-06; NP_287824 |
| 61 | R | 48035 | 48388 | 13.9 | Prophage pi3 protein 45; 4e-05; AL596172; L. monocytogenes lmo2306; 6e-05; CAD00384 |
| 62 | R | 48385 | 48741 | 13.2 | |
| 63 | R | 48843 | 49181 | 12.6 | |
| 64 | R | 49172 | 49516 | 13.1 | |
| 65 | R | 49492 | 49752 | 9.8 | |
| 66 | R | 49761 | 50408 | 24.1 | |
| 67 | R | 50482 | 51876 | 51.3 | S. meliloti SMa0594; 6e-11; NP_435557 |
| 68 | L | 52603 | 52217 | 14.1 | Helix-turn-helix transcriptional regulator; S. meliloti SMc00089; 4e-10; NP_385047; A. tumefaciens AGR_C_1081p; 2e-04; NP_353634 |
| 69 | L | 52857 | 52600 | 9.3 | P. horikoshii PHS013; 1e-04; NP_142388; P. jensenii Orf10; 0.006; CAC38044 |
| 70 | R | 52916 | 53272 | 13.1 | Class I holin; X. nematophila prophage Orf7; 1e-16; CAB58450; H. influenzae holin-like protein; 4e-08; AF198256 |
a
R, right; L, left.