TABLE 1.

Description of bacteriophage AaΦ23 ORFs, gene products, and functional assignments

GeneStart positionStop positionSize (aa)aPotential function (gene name)Significant matches (source, accession no., e value)
orf1 111569348Integrase (int)Integrase (phage P22, P04890, 9e−66)
orf2 1336989115
orf3 16661352104Putative prophage protein (A. actinomycetemcomitans strain HK1651, 2e−55)
orf4 23771721218Putative prophage protein (A. actinomycetemcomitans strain HK1651, e−113)
orf5 29292444161Putative prophage protein (A. actinomycetemcomitans strain HK1651, 6e−48)
orf6 3144296260
orf7 37603137207
orf8 46503757297
orf9 4961466299
orf10 5218496484
orf11 5483520891
orf12 62265570218Putative prophage protein HI1422 (prophage φflu, P44193, 8e−10)
orf13 6670658783
orf14 71387662174Putative prophage protein (A. actinomycetemcomitans strain HK1651, 6e−78)
orf15 84918018157
orf16 93478460295
orf17 101219405250Repressor (cl)Repressor protein C1 (phage phi-80, P14819, e−44)
orf18 102311041968Repressor (cro)Hypothetical protein YdaS (E. coli strain K12, P76063, 7e−07); Cro protein (phage P22; P09964, 1.2)
orf19 1041010736108Putative prophage protein (A. actinomycetemcomitans strain HK1651, 3e−08)
orf20 1078811507239Antirepressor (antB)Putative prophage protein HI1422 (prophage φflu, E64029, 6e−24); AntB (phage N15, AAM53132.1, e−22)
orf21 115071166552
orf22 1166212444260DNA replication protein (o)Protein GP18 (phage P22, P03687, 6e−19)
orf23 1244413901485DNA Helicase (p)Replicative DNA helicase (phage P22, P03006, 2e−45)
orf24 1390414398163DNA adenine methylasePutative adenine-specific methylase (phage HP1, P51715, e−19)
orf25 1440514902165Recombination protein (ninB)Protein NinB (phage lambda, P03765, e−13)
orf26 148811512681
orf27 151261530559EF-Tu (Photorhabdus luminescens subsp. lumondii TTOI, NP_931892, 2e−07)
orf28 152801549571
orf29 1549516064189Recombination endonuclease (ninG)Protein NinG (phage lambda, P03770, 3e−18)
orf30 1606416435123Antitermination protein (q)Probable phage antitermination protein Q (Yersina pestis strain KIM, CAC90068.1, 7e−02)
orf31 1672517621298Antirepressor (ant)Antirepressor protein Ant (phage P22, P03037, 3e−26)
orf32 1778518231148
orf33 1822818596122Antiholin, holin 1?b
orf34 1850518870121Holin S, holin 2?b
orf35 1893919520193Lysin (R)Putative prophage protein HI1415 (prophage φflu, H64028, 2e−56)
Endolysin (bacteriophage epsilon15, NP_848233, 5e−29)
orf36 1952319855110Rz lytic protein (rz)Putative prophage protein HI1414 (prophage φflu, P44186, 7e−12)
Putative Rz lytic protein (phage SfV, AAL89453.1, e−3)
orf37 197672004893Rz1 lytic protein (rz1)Putative prophage protein HI1413 (prophage φflu, P44185, 3e−33)
orf38 200522031888
orf39 2047521035186Terminase small subunit (terS)Terminase small subunit (phage SF6, Q57374, 3e−11)
orf40 2098022443487Terminase large subunit (terL)Terminase large subunit (phage Beep781, AAN38019.1, e−50)
orf41 2244523758437Putative prophage protein HI1409 (prophage φflu, P44183, 0.0)
orf42 2367926081800Head proteinPutative prophage protein HI1407 (prophage φflu, B64122, e−109)
Minor prohead-head protein (bacteriophage SPP1, NP_690662, 3.5e−02)
orf43 260782629672
orf44 264302663066
orf45 2671327825370Putative prophage protein HI1405 (prophage φflu, AAC23055.1, e−171)
orf46 2783928288149
orf47 2830029214304Putative prophage proteins XF1577 and XF1682 (prophages XfP3 and XfP4, H82650, 7e−11)
orf48 2922529584119Putative prophage proteins XF1579 and XF1684 (prophages XfP3 and XfP4, A82665, 2e−14)
orf49 2958530031148Putative prophage proteins XF1580 and XF1685 (prophages XfP3 and XfP4, C82651, 7e−11)
orf50 3002830399123Putative prophage proteins XF1581 and XF1686 (prophages XfP3 and XfP4, C82665, e−17)
orf51 3018530826213Putative prophage proteins XF1582 and XF1687 (prophages XfP3 and XfP4, E82651, 9e−12)
orf52 3083132339502Putative prophage proteins XF1583 and XF1688 (prophages XfP3 and XfP4, F82651, e−123)
orf53 3238932820143Putative prophage proteins XF1584 and XF1689 (prophages XfP3 and XfP4, F82665, 9e−46)
orf54 3282033239139Putative prophage proteins XF1585 and XF1690 (prophages XfP3 and XfP4, H82651, 5e−20)
orf54-543282033403194Putative prophage proteins XF1585 and XF1690 (prophages XfP3 and XfP4, H82651, 1e−19)
orf55 3339035498702Tail-length tape measure proteinTail-length tape measure protein (Clostridium tetani strain E88, AAO35681, 8e−09)
orf56 3550236269255Putative prophage protein XF1591 (prophage XfP3, B82661, e−37)
orf57 3628036594104Hypothetical protein XF1628 (X. fastidiosa strain 9a5c, C82648, 2e−20)
orf58 3688137735284Putative prophage protein XF1593 (prophage XfP3, D82661, 4e−78)
orf59 3773238376214Baseplate proteinPutative baseplate protein (phage phi-CTX, BAA36243.1, 3e−06)
orf60 3837338732119Putative prophage protein XF1701 (prophage XfP4, F82648, 9e−26)
orf61 3876339905380Putative prophage protein XF1704 (prophage XfP4, A82649, 5e−96)
orf62 3990540486193Putative prophage protein HI1404 (prophage φflu, P44179, 5e−08)
orf63 4049741981494Tail fiber proteinPutative prophage protein HI1403 (prophage φflu, P44178, e−07)
Putative tail fiber protein H (phage 186, AAC34164.1, 2e−04)
orf64 4197242592206Tail fiber assembly proteinTail fiber assembly protein P37 (phage SfV, O22005.1, 2e−04)
orf65 425734283386Hypothetical protein NMB1120 (Neisseria meningitidis strain MC58, B81120, 4e−24)
  • a aa, amino acids.

  • b ?, assignment is speculative (see the text for a discussion).