Table 2. Key genes and functional factors of the prophage regions predicted by PHASTEST (Prokka, Bakta annotation)

Region	PHASTEST	Prokka, Bakta	Start (bp)	Stop (bp)	Length (size; unit: bp)
Region 141,822 bp(589,962–631,783 bp)Intact	Attatchment_site	NA	589,962	589,975	14
	Integrase	xerC	590,128	591,330	1,203
	Phage-like_protein	NA	591,510	592,673	1,164
	Hypothentical_protein1)		592,872	592,997	126
	Hypothentical_protein1)		593,163	593,339	177
	Hypothentical_protein1)		593,481	594,527	1,047
	Hypothentical_protein1)		594,557	594,925	369
	Hypothentical_protein1)		594,998	595,414	417
	Phage-like_protein	lexA, xre	595,426	595,788	363
	Phage-like_protein	NA	595,961	596,191	231
	Hypothentical_protein	Prophage P1 protein 10	596,264	596,578	315
	Hypothentical_protein	DNA-binding helix-turn-helix protein	596,616	596,852	237
	Regulatory_protein	NA	596,999	597,199	201
	Hypothentical_protein1)		597,199	597,333	135
	Hypothentical_protein1)		597,358	597,540	183
	Hypothentical_protein	HTH cro/C1-type domain-containing protein	597,601	598,155	555
	Phage-like_protein	DNA-binding protein	598,161	598,445	285
	Hypothentical_protein1)		598,556	598,684	129
	Hypothentical_protein1)		598,817	599,203	387
	Phage-like_protein	NA	599,200	600,087	888
	Hypothentical_protein	DUF3799 domain-containing protein	600,119	600,871	753
	Phage-like_protein	NA	600,953	601,885	933
	Hypothentical_protein1)		601,882	602,169	288
	Hypothentical_protein	Glyco-hydro-42 domain-containing protein	602,693	603,226	531
	Phage-like_protein	Prophage P1 protein 24, holliday junction resolvase	603,237	603,638	402
	Hypothentical_protein1)		603,635	603,865	231
	Hypothentical_protein1)		603,868	603,999	132
	Hypothentical_protein	DUF2528 domain-containing protein	603,999	604,367	369
	Hypothentical_protein1)		604,367	604,474	108
	Hypothentical_protein1)		604,488	604,670	183
	Phage-like_protein	NA	604,663	605,010	348
	Hypothentical_protein1)		605,007	605,447	441
	Phage-like_protein	NA	605,444	605,611	168
	Regulatory_protein	arpU	605,742	606,200	459
	Hypothentical_protein1)		606,572	607,354	783
	Phage-like_protein	NA	607,427	607,606	180
	Terminase	NA	607,764	608,360	597
	Terminase	NA	608,344	609,630	1,287
	Portal_protein	NA	609,683	611,278	1,596
	Head_protein	Phage-Mu-F domain-containing protein	611,278	612,222	945
	Phage-like_protein	NA	612,330	612,977	648
	Head_protein	NA	612,991	614,061	1,071
	Head_protein	NA	614,076	614,441	366
	Hypothentical_protein1)		614,395	614,769	375
	phage tail protein[Lactiplantibacillus plantarum]	NA	614,759	615,313	555
	Hypothentical_protein	DUF3168 domain-containing protein	615,314	615,700	387
	phage tail protein[Lactiplantibacillus plantarum]	NA	615,712	616,299	588
	Hypothentical_protein1)		616,317	616,829	513
	Hypothentical_protein	SNF2 family protein	616,898	617,134	237
	Tail_protein	Prophage P2a protein 48 tape measure protein	617,134	621,138	4,005
	Hypothentical_protein	NA	621,138	621,869	732
	Phage-like_protein	Prophage-tail domain-containing protein	621,845	623,743	1,899
	Phage-like_protein	SGNH/GDSL hydrolase family protein	623,748	624,740	993
	Head_protein	BppU-N domain-containing protein	624,755	625,369	615
	Phage-like_protein	NA	625,375	626,115	741
	Hypothentical_protein1)		626,116	626,436	321
	Non_phage-like_protein	xkdX	626,436	626,612	177
	Phage-like_protein	NA	626,590	627,738	1,149
	Holin	Bacteriophage protein	627,739	628,035	297
	Holin	NA	628,022	628,381	360
	Attatchment_site	NA	631,770	631,783	14
Region 222,156 bp(1,083,498–1,105,644 bp)Incomplete	Phage-like_protein	Glucose-1-phosphate thymidylyltransferase (rfbA)	1,083,489	1,084,352	864
	Phage-like_protein	Cellulase domain-containing protein	1,084,375	1,085,664	1,290
	Phage-like_protein	dTDP-4-dehydrorhamnose 3,5-epimerase	1,085,724	1,086,305	582
	Phage-like_protein	dTDP-glucose 4,6-dehydratase	1,086,315	1,087,343	1,029
	Phage-like_protein	dTDP-4-dehydrorhamnose reductase	1,087,413	1,088,255	843
	Attatchment_site	NA	1,088,315	1,088,329	15
	Non_phage-like_protein1)		1,088,344	1,088,469	126
	Transposase	NA	1,088,478	1,088,963	486
	Non_phage-like_protein1)		1,089,006	1,089,233	228
	Transposase	NA	1,089,230	1,089,541	312
	Hypothentical_protein1)		1089676	1,089,903	228
	Integrase	Integrase/recombinase (xerC_3)	1,089,966	1,090,553	588
	Non_phage-like_protein	cpsC	1,090,910	1,091,680	771
	Non_phage-like_protein	cpsD / ywqD_1	1,091,692	1,092,420	729
	Non_phage-like_protein	Tyrosine-protein phosphatase / ywqE_1	1,092,407	1,093,180	774
	Phage-like_protein	Epimerase / wbgU_1	1,093,198	1,094,145	948
	Non_phage-like_protein	Priming glycosyltransferase / wecA_1	1,094,126	1,094,803	678
	Non_phage-like_protein	Glycosyltransferase, family 1 (GT1)	1,094,804	1,095,898	1,095
	Non_phage-like_protein	Exopolysaccharide phosphotransferase cps2G	1,095,914	1,096,912	999
	Non_phage-like_protein1)		1,096,950	1,098,089	1,140
	Hypothentical_protein1)		1,098,096	1,099,646	1,551
	Non_phage-like_protein	epsF_2	1,099,786	1,100,811	1,026
	Non_phage-like_protein1)		1,100,936	1,101,136	201
	Attatchment_site	NA	1,101,175	1,101,189	15
	Attatchment_site	NA	1,101,960	1,101,971	12
	Hypothentical_protein1)		1,102,296	1,102,964	669
	Hypothentical_protein1)		1,103,037	1,103,834	798
	Transposase	Integrase catalytic domain-containing protein / insK	1,104,022	1,104,639	618
	Attatchment_site	NA	1,105,633	1,105,644	12
Region 354,746 bp(2,163,794–2,218,539 bp)Intact	Attatchment_site	NA	2,163,794	2,163,805	12
		Holin2)	2,163,938	2,164,315	378
	Tail_protein	Prophage P2a protein 48 tape measure protein	2,171,852	2,175,925	4,074
	Hypothentical_protein	SNF2 family protein	2,175,925	2,176,161	237
	Hypothentical_protein	Phage protein	2,176,254	2,176,742	489
	phage tail protein[Lactiplantibacillus plantarum]	Phage protein	2,176,776	2,177,342	567
	Hypothentical_protein	DUF3168 domain-containing protein	2,177,354	2,177,740	387
	phage tail protein[Lactiplantibacillus plantarum]	Phage tail protein	2,177,742	2,178,296	555
	Hypothentical_protein	Prophage protein	2,178,286	2,178,660	375
	Head_protein	NA	2,178,614	2,178,979	366
	Head_protein	Phage capsid protein	2,178,994	2,180,052	1,059
	Phage-like_protein	DUF4355 domain-containing protein	2,180,069	2,180,716	648
	Head_protein	Phage-Mu-F domain-containing protein	2,180,823	2,181,767	945
	Portal_protein	Phage portal protein	2,181,770	2,183,422	1,653
	Terminase	NA	2,183,412	2,183,963	552
	Terminase	NA	2,184,052	2,184,711	660
	Hypothentical_protein1)		2,184,741	2,184,956	216
	Terminase	NA	2,184,916	2,185,425	510
	Hypothentical_protein1)		2,185,465	2,185,587	123
	Hypothentical_protein	Prophage Lp2 protein 33	2,185,623	2,185,886	264
	Phage-like_protein	Transposase	2,185,855	2,186,034	180
	Hypothentical_protein		2,186,631	2,186,861	231
		trnW / tRNA-Trp(cca)2)	2,186,914	2,186,985	72
		trnN / tRNA-Asn(gtt)2)	2,187,055	2,187,127	73
	Regulatory_protein	arpU	2,187,249	2,187,710	462
	Hypothentical_protein	Phage protein	2,187,789	2,187,989	201
	Hypothentical_protein1)		2,188,020	2,188,313	294
	Hypothentical_protein1)		2,188,383	2,188,514	132
	Hypothentical_protein	Phage protein	2,188,529	2,188,840	312
	Hypothentical_protein1)		2,188,913	2,189,362	450
	Hypothentical_protein1)		2,189,386	2,189,535	150
	Hypothentical_protein	Prophage Lp2 protein 25	2,189,538	2,189,705	168
	Phage-like_protein	Prophage Lp2 protein 24	2,189,698	2,190,078	381
	Hypothentical_protein	Prophage Lp1 protein 23	2,190,075	2,190,593	519
	Hypothentical_protein	Glyco-hydro-42 domain-containing protein	2,190,590	2,191,120	531
	Hypothentical_protein	Prophage protein	2,191,117	2,191,404	288
	Hypothentical_protein	DnaB-2 domain-containing protein	2,191,401	2,192,309	909
	Hypothentical_protein	DUF669 domain-containing protein	2,192,476	2,193,141	666
	Hypothentical_protein	Nucleotide-binding protein	2,193,144	2,193,806	663
	Hypothentical_protein	Phage major capsid protein	2,193,813	2,194,322	510
	Hypothentical_protein	Prophage protein	2,194,315	2,194,446	132
	Hypothentical_protein1)		2,194,579	2,194,707	129
	Non_phage-like_protein	DUF1508 domain-containing protein	2,194,762	2,194,941	180
	Regulatory_protein	XRE family transcriptional regulator	2,195,190	2,195,702	513
	Non_phage-like_protein1)		2,195,770	2,196,075	306
	Hypothentical_protein1)		2,196,117	2,196,257	141
	Repressor	HTH-type transcriptional regulator Xre	2,196,254	2,196,475	222
	Repressor	lexA	2,196,610	2,196,972	363
	Hypothentical_protein	Peptidase-M78 domain-containing protein	2,196,984	2,197,397	414
	Hypothentical_protein	Lipoprotein	2,197,424	2,197,759	336
	Hypothentical_protein	type I site-specific deoxyribonuclease	2,197,885	2,198,946	1,062
		tRNA-Xxx / tRNA-Ile(tat)2)	2,198,999	2,199,084	86
	Hypothentical_protein1)		2,199,110	2,199,286	177
		tRNA-Xxx / tRNA-Leu(taa)2)	2,199,329	2,199,412	84
	Hypothentical_protein1)		2,199,452	2,199,577	126
		tRNA-Xxx2)	2,199,590	2,199,682	93
		trnI / tRNA-Met(cat)2)	2,199,696	2,199,771	76
		trnG / tRNA-Gly(tcc)2)	2,199,776	2,199,846	71
	Non_phage-like_protein1)		2,199,894	2,201,642	1,749
	Phage-like_protein	site-specific DNA-methyltransferase (adenine-specific)	2,201,696	2,202,610	915
	Integrase	Tyr recombinase domain-containing protein	2,202,697	2,203,818	1,122
	Attatchment_site	NA	2,204,128	2,204,139	12
	Hypothentical_protein	Prophage Lp3 protein 24	2,204,169	2,204,375	207
	Attatchment_site	NA	2,204,682	2,204,703	22
Hypothentical_protein	TMhelix containing protein	2,204,795	2,205,100	306
Regulatory_protein	Prophage protein	2,205,183	2,205,563	381
Head_protein	Phage gp6-like head-tail connector protein	2,205,705	2,205,974	270
Head_protein	Phage major capsid protein	2,206,069	2,207,571	1,503
Portal_protein	Phage portal protein	2,207,593	2,208,693	1,101
Hypothentical_protein	ABC transporter permease	2,208,694	2,208,894	201
Hypothentical_protein	Terminase large subunit	2,208,848	2,210,551	1,704
Hypothentical_protein	Phage terminase small subunit P27 family	2,210,548	2,211,021	474
Endonuclease	Endonuclease	2,211,804	2,212,193	390
Head_protein	Phage tail protein	2,212,186	2,212,530	345
Hypothentical_protein	Phage protein	2,212,511	2,212,702	192
Hypothentical_protein	Phage protein	2,212,724	2,213,197	474
Phage-like_protein	Virulence protein	2,213,343	2,214,737	1,395
Hypothentical_protein	Replication protein	2,214,737	2,215,537	801
Hypothentical_protein	Phage protein	2,215,534	2,215,788	255
Hypothentical_protein1)		2,215,755	2,215,898	144
Hypothentical_protein1)		2,215,909	2,216,016	108
Phage-like_protein	DNA-binding protein	2,216,059	2,216,247	189
Hypothentical_protein1)		2,216,228	2,216,431	204
Hypothentical_protein1)		2,216,564	2,217,130	567
Integrase	Tyr recombinase domain-containing protein (xerC_6)	2,217,183	2,218,340	1,158
Attatchment_site	NA	2,218,518	2,218,539	22

Means genes commonly predicted as hypothetical proteins by PHASTEST, Prokka, and Bakta analyses.
Means genes or factors identified only by either Prokka or Bakta.
PHASTEST, phage search tool with enhanced sequence translation; NA, not applicable; xerC, integrase; arpU, antirepressor; SGNH, serine, glycine, asparagine, histidine; GDSL, Gly-Asp-Ser-Leu; tRNA, Trp, Asn, Ile, Leu, Met, Gly.