TABLE 2.

ORF identification, position in the phage genome, putative function, and comparison with sequences available in public databases

ORFaStart positionStop positionORF size (aa)MMb (kDa)pIPutative RBS and start codoncPredicted functionBest-match BLASTp resultNo. of aa shared with best match/total no. of aa in best match (% identity)E valueSized (aa)Accession no.
1148116733939.18.2TGAGAGGAGATaaatATGIntegrase-recombinasePhage integrase (Staphylococcus epidermidis RP62A)92/329 (27)3.0E−18347YP_189166
21176350077488.19.0AGAAATAGAGGTaaaaATGExodeoxyribonucleaseExodeoxyribonuclease (Clostridium phage c-st)208/766 (27)4.0E−55746YP_398492
44264495923124.04.6CGAAAGGAAAActtatacaATGTransglycosylaseTransglycosylase (Lactococcus lactis MG1363)70/102 (68)1.0E−30199YP_001032097
65482582911513.85.3CTAAGGGGAATataacaaaATGPhage protein (Streptococcus phage)32/76 (42)6.0E−1193YP_596287
117089768519822.66.7AGAGAGGAAAGccaaaGTGThymidine kinaseThymidine kinase (Enterococcus faecium DO)105/192 (54)1.0E−50191ZP_00603785
1690489272748.69.4TTTATCGAGGAaaaataaATGgp121 (Lactococcus phage KSY1)29/72 (40)1.0E−0774YP_001469120
1995639724536.54.2AATATGGAGATgattaaATGe25 (Lactococcus phage bIL170)34/52 (65)4.0E−0953NP_047148
2198931040216919.24.8TGAAAGATGGAgcggtgATGORF23 (Lactococcus phage TP901-1)33/81 (40)1.0E−04116NP_112686
221039910644819.05.3GTGAAAGTGGTggaaggATGUnknown (Lactococcus phage P335)73/81 (90)2.0E−3681ABI54223
24110371175623928.45.4GTGAAAGAGGTaataacaATGORF27 (Lactococcus phage bIL286)83/222 (37)3.0E−22211NP_076661
27123101263310712.84.3ATTAAGGATATtaaATGProtein (Lactococcus phage P335 sensu lato)33/61 (54)4.0E−10116NP_839910
40185221901316319.19.2ATAAAAAAGGAgaagaacATGHNH endonucleaseHNH endonuclease (Lactococcus phage CB14)72/158 (45)3.0E−31166ACU46908
422031320516678.09.4ATAAAGGTAATagaaaATGHypothetical protein gp041 (Lactococcus phage 712)32/64 (50)2.0E−0770YP_764301
47219492232912614.86.2ATAAAGGAGAAcataaataATGProtein gp44 (Lactococcus phage P008)77/128 (60)6.0E−33126YP_762555
482240722547465.48.4AGAA*GGAGAAtacaaATGProtein ul36_22 (Lactococcus phage ul36)26/42 (61)3.0E−0850NP_663656
52234522406020223.55.0TGAAA*GAGGTgctaaATGNucleotidasePutative nucleotidase (Bacillus pumilus ATCC 7061)42/179 (23)1.0E−06192ZP_03056313
55252942632534337.46.5AGATAGGAGATtttaATGEndolysinEndolysin (Lactococcus phage KSY1)281/349 (80)5.0E−163347YP_001469072
57268492805140045.64.7TAAAAGGAG*TccaaagaaATGPhage-related protein (Clostridium acetobutylicum ATCC 824)88/377 (23)3.0E−09329AAK79153
58281013019469779.65.5AAATAGGAGAAaacaATGDnaB domain helicase (Nocardioidessp. JS614)120/395 (30)1.0E−36824YP_925839
59303013091820524.79.6AGAAATGGAGATggataaTTGHypothetical protein (Lactococcus lactis IL1403)32/55 (58)2.0E−06389NP_266805
60309283247251459.35.6TTATAAGAGGAaaatATGDNA helicasePhage DNA helicase (Clostridium phage c-st)124/502 (24)1.0E−30498YP_398488
61324833347533038.46.0TTAAAGGATAAaaaATGDNA primasePutative DNA primase (Clostridium phage c-st),91/319 (28)3.0E−15325YP_398489
62335403532159367.85.1ATAAATACGATttggagtgatgaaacATGssDNA exonucleasessDNA exonuclease (Lactococcus phage CB13)576/593 (97)0593ACU46843
643562135851769.44.6CATGAGGAGAAcataATGHypothetical protein (Lactococcus phage BK5-T)38/72 (52)3.0E−1576NP_116550
6535985362849911.26.1AGAAAGTAGAGgaactaaacATGHypothetical protein (Anaerotruncus colihominis DSM 17241),32/92 (34)8.0E−0896ZP_02444026
683702737200576.94.0TTTAAGGAGATtgaattATGProtein Q54_gp45 (Lactococcus phage Q54)38/57 (66)2.0E−1357YP_762614
703737237587718.87.5GGTGGGGAGGGattgaATGProtein p22 (Lactococcus phage phiLC3)20/22 (90)0.033106NP_996696
723779438000688.16.6ATTTTGGAGGAcaaccaATGUnknown (Lactococcus phage ul36.k1t1)56/65 (86)1.0E−2671ABD63723
7739198394949811.64.8TGTAGGGAGACtaatATGlwe1209 (Listeria welshimeri serovar 6b SLCC5334)28/71 (39)3.0E−0774YP_849406
82412974237335841.25.0GAAAAGGAGAAaacataATGEnvelope fusion protein (EFP) gp215 (Enterococcus phage phiEF24C)160/352 (45)1.0E−76363YP_001504324
88441314461916218.89.6GCAGAGGAA*TacacATGHNH endonucleaseHoming nuclease (Lactobacillus gasseri ATCC 33323)46/94 (48)6.0E−16243YP_814436
91477804889837243.610.0AAGAAGGAGGTaggataGTGTransposaseTransposase (Clostridium botulinum D strain 1873)153/361 (42)1.0E−61362ZP_04863298
93492344989021824.45AATAAGGAGAAtaaacacaATGPhage-related protein (Clostridium botulinum C)73/217 (33)4.0E−19212ZP_02621809
94503685233565573.45.2ATAACCGATTGaaaggaATGDNA gyrase subunit B topoisomeraseDNA topoisomerase (ATP-hydrolyzing) (Bacillus subtilis subsp. subtilis strain NCIB 3610)342/655 (52)0638ZP_03598261
95523375445170479.38.3CTAAAGAAGGGttagaataaaATGDNA gyrase subunit A topoisomeraseDNA gyrase/topoisomerase IV, subunit A (Bacillus subtilis subsp. subtilis strain NCIB 3610)290/679 (42)8.0E−153664ZP_03598260
96544705531228032.88.3AACAAGGAGAGtttacATGAdenine methyltransferaseMethyltransferase (Clostridium sp. 7_2_43FAA)145/280 (51)1.0E−69653ZP_05132801
99559835650117219.14.2TTAAAGGAGAAtaataATGDeoxyribosyltransferase2-Deoxyribosyltransferase (Enterococcus EC30)90/159 (56)1.0E−44161ZP_05645662
100564945715321924.99.8AGAAAAGGAAACaaATGNicotinamide mononucleotide transporterTransporter GCWU000282_00374 (Catonella morbi ATCC 51271)46/219 (21)8.0E−06278ZP_04449148
101572575851041748.05.6AGAAATGGGAGgaaatagATGAnaerobic ribonucleoside triphosphate reductaseAnaerobic ribonucleoside-triphosphate reductase (Mycoplasma penetrans HF-2)121/411 (29)2.0E−43713NP_757882
102588256107474986.35.9AGAAAATCATAactctaaacaaagtATGAnaerobic ribonucleoside reductase (large subunit)Ribonucleotide reductase of class III (anaerobic) large subunit (Vibrio furnissii CIP 102972)110/365 (30)1.0E−33706ZP_05879459
103610746167019822.95.6TGAAACAGGAGaataATGRibonucleoside reductase activator (small subunit)Putative anaerobic ribonucleoside-triphosphate reductase-activating protein (Reinekea sp. MED297)60/164 (36)7.0E−20172ZP_01114828
104617466247424228.69.4TGAAAAGAG*TgaataATGProtein, group I intronGroup I intron (Lactococcusphage Tuc2009), orf3869/193 (35)3.0E−24310NP_108715
1056252862726677.88.0AGAA*GGAGAAtaatATGProtein gp176 (Enterococcus phage phiEF24C)30/65 (46)8.0E−1265YP_001504285
1076306163300799.15.8AGAA*GGAGATataaaaATGRibonucleotide reductase, glutaredoxin subunitPutative glutaredoxin (Streptococcus pyogenes M1 GAS)28/73 (38)1.0E−0672NP_269480
108632936366412314.24.2TTAAAGGCTATacacATGRibonucleotide reductase stimulatory proteinRibonucleotide reductase stimulatory protein (Lactobacillus ruminis ATCC 25644)41/119 (34)1.0E−12127ZP_03958437
109636786517749955.45.8TAATAGGAGGTttcacTTGRibonucleotide reductase α subunitPutative ribonucleotide reductase (Enterococcus phage phiEF24C)128/218 (58)2.0E−68716YP_001504318
110652566593622626.16.2AGAAAGGAGAAcatgaaATGGuanylate kinaseGuanylate kinase (Sebaldella termitidis ATCC 33386)56/151 (37)5.0E−18181YP_003309720
111659146665724727.95.5GAAAAGGAATTgaataATGDeoxyUTP pyrophosphataseDeoxyUTP pyrophosphatase (Prosthecochloris aestuarii DSM 271)60/181 (33)2.0E−10164YP_002015340
112667546751525328.45.1AAAAAGGAGAAaataATGProteasePeptidase S8 and S53 subtilisin kexin sedolisin (Bacillus weihenstephanensis KBAB4)73/237 (30)1.0E−16298YP_001642665
114680676869921024.04.5AC*AAGGAGAAataaaATGHypothetical protein (Lactococcus lactis MG1363)110/212 (51)8.0E−54237YP_001033756
11669121734101,429165.96.6ATATAGGAGGAattgaATGDNA pol III subunit αDNA pol III α chain (Clostridium phage c-st),270/690 (39)1.0E−1321,032YP_398491
118737767410811013.14.2AATAAGGATAAaataacATGHypothetical protein (C. perfringens D strain JGS1721)29/69 (42)7.0E−04133ZP_02952724
123759387525822626.09.6GTTAAGGAGTTatttATGHolliday junction resolvaseCrossover junction endodeoxyribonuclease RuvC (Bacillus weihenstephanensis KBAB4)57/162 (35)5.0E−12166YP_001642769
124763997599213514.85.6CAAAAGGAGAAaataaataATGHolinN-Acetylmuramoyl-l-alanine amidase (Carnobacterium)36/112 (32)2.0E−06120ZP_02184646
127787227688761166.56.8ATGTAGGAGGAattacttaATGTail protein, host specificityProphage λSa1, minor structural protein (Streptococcus agalactiae CJB111)194/658 (29)3.0E−43618ZP_00787608
12884448787221,908214.34.9ATAGAGGAG*T aaatgctATGTail-host specificityTail-host specificity (Streptococcus phage Sfi21)133/248 (53)2.0E−731,276NP_049980
129853208455625428.85.1AGAAAGTTGGTaaaATGPhage tail componentProtein SERP1641 (S. epidermidis RP62A)46/145 (31)4.0E−10693YP_189206
13095202853723,276357.85.9TAAAAGGAGAGTgaaacTTGTail tape measure proteinTP901, tape measure protein (Clostridium beijerinckii 8052)149/500 (29)6.0E−401,889YP_001308504
131962129522033038.59.2GGACGGGTGGTaaacaATGRecombinase-integrasePhage integrase (Staphylococcus aureus TW20)118/340 (34)8.0E−41338CBI50038
132966919620916018.79.1GTTTTGGAGTGtaagaATGStructural proteinDNA polymerase III subunit alpha (Idiomarina loihiensis L2TR)27/89 (30)1.81,142YP_156071
136990389833423425.25.1TCCTAGGAGGAactaaataATGStructural proteinProtein A1723 (Clostridium botulinum C)83/254 (32)2.0E−25263ZP_02621789
137998209905925329.35.0AAAAGGGTGGTgataaagTTGCLOHYLEM_04418 (Clostridium hylemonae DSM 15053)63/260 (24)5.0E−06263ZP_03777366
1381004099980420123.05.5TGAAAGG*GGTggctggtaATGStructural proteinTcur_2861 (Thermomonospora curvata DSM 43183)23/68 (33)0.25258YP_003300444
13910116110040925028.65.6AAAATGGTGGActaatATGStructural proteinHypothetical protein (Blautia hansenii DSM 20583)60/236 (25)7.0E−06325ZP_05854124
14110189810145814616.95.1CGAAAGGAAGTagaatATGStructural proteinHypothetical protein (S. epidermidis RP62A)42/141 (29)1.0E−04144YP_189196
14210258110191922025.44.9AATAAGGAGATtacaaacaATGHypothetical protein (S. epidermidis RP62A)37/146 (25)2.0E−09183YP_189195
14310366310264433938.35.3ACCTAGGAGGAaaattttaATGStructural proteinHypothetical protein (S. epidermidis RP62A)118/335 (35)4.0E−47333YP_189194
14410422310370217318.75.4TAATAGGAGGAataattaATGStructural proteinUnnamed protein product (Tetraodon nigroviridis)20/68 (29)0.2316CAG01759
14510550510425241747.54.8AGTAAGGAGATaacaaATGStructural proteinPhage protein (S. aureus subsp. aureus TW20)68/201 (33)5.0E−18459CBI50026
14610705810551751358.15.9AGAAAGGAGATaggtTTGStructural proteinPhage protein (S. aureus subsp. aureus TW20)141/444 (31)8.0E−59520YP_189191
14710877910708256565.18.4GACGAGGAGAAttaaaaATGTerminase/ATPase subunitPutative prophage terminase, ATP subunit; phage SPbeta (Bacillus subtilis subsp. subtilis strain 168)140/547 (25)3.0E−37589NP_389994
14810981010878234239.74.7AGAAAGGATTTttaATGHypothetical protein (Clostridium phage D-1873)69/294 (23)6.0E−08304ZP_04863744
14911115610990941547.66.4TAGACGAGGGTtaatagaaataATGDNA polymerasePutative DNA polymerase (Lactococcus phage P087)169/426 (39)3.0E−80414YP_002875721
15011247811116543749.45.0AAATTTGAGGAtgaatATGPhosphate starvation-inducible PhoH/ATPaseNucleotide binding protein, PINc (Synechococcus sp. BL107)139/492 (28)7.0E−30463ZP_01468630
  • a ORFs in bold are those identified by mass spectrometry. Only the ORFs with significant hits to other proteins in databases are included in this table.

  • b MM, molecular mass.

  • c RBS, ribosome binding site. Underlined nucleotides correspond to bases identical to the L. lactis RBS consensus sequence. The uppercase letters represent the RBS sequence and the starting codon, whereas the lowercase letters represent the interspaced nucleotides between the RBS sequence and the starting codon. *, gap as compared to the RBS consensus sequence.

  • d Total size of the aligned protein.