LOCUS       NZ_CP149305             6863 bp    DNA     circular CON 05-APR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            Z1323SSL0045 plasmid pZ1323SSL0045-3, complete sequence.
ACCESSION   NZ_CP149305
VERSION     NZ_CP149305.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40439971
            Assembly: GCF_037855395.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 6863)
  AUTHORS   Chae,J.-C., Oh,J.Y., Jeong,J.H. and Kwak,S.M.
  TITLE     Complete genome sequence of Salmonella enterica subsp. enterica
            serovar Typhimurium isolated from humans and pigs
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6863)
  AUTHORS   Chae,J.-C., Oh,J.Y., Jeong,J.H. and Kwak,S.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-MAR-2024) Division of biotechnology, Jeonbuk National
            University, kobongro, Iksan 54596, South Korea
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 102X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037855395.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 21:24:13
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,858
            CDSs (total)                      :: 4,735
            Genes (coding)                    :: 4,599
            CDSs (with protein)               :: 4,599
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 44 of 136
            Pseudo Genes (incomplete)         :: 99 of 136
            Pseudo Genes (internal stop)      :: 22 of 136
            Pseudo Genes (multiple problems)  :: 27 of 136
            Pseudo Genes (short protein)      :: 1 of 136
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP149305.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..6863
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="Z1323SSL0045"
                     /serovar="Typhimurium"
                     /host="Pig"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pZ1323SSL0045-3"
                     /geo_loc_name="South Korea"
                     /collection_date="2023-04-06"
     gene            complement(461..652)
                     /locus_tag="WI427_RS24240"
                     /old_locus_tag="WI427_24240"
     CDS             complement(461..652)
                     /locus_tag="WI427_RS24240"
                     /old_locus_tag="WI427_24240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_048228005.1"
                     /translation="MNKQQQTALNMARFIKSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFSDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1520..3502
                     /locus_tag="WI427_RS24245"
                     /old_locus_tag="WI427_24245"
     CDS             1520..3502
                     /locus_tag="WI427_RS24245"
                     /old_locus_tag="WI427_24245"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015966094.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_080069401.1"
                     /translation="MQTELIKELNKVLKAFPQFWNGEELQRSMVSDAISQKQPDLIKAL
                     VDNEKVRSVYGADIDGIFIFDFDKLCGLLKYKEYWANSFTKYRNKVGLTSEGKYLDYSS
                     DVVLDFPFKDCVLEGGMSKEDQGKSEVYYNEIIARDEIDNLFSPKVLKEVNRYSKEGVK
                     KERIFNRNDNLIIRGNNLIALHCIKNIYEKSVKLIYIDPPYNTDTDSFKYNDKFSHSTW
                     LTFMKNRLEVAKDLLCDDGLIAISIDDNELNYLASLADDIFGRKNRIAIFPRITKKGGK
                     SASIFAKNHDYILLYVRSLENKRMYAVSHDDDNFKYKDEYFAERGSYKLNQTLDYDSLQ
                     YSKSLDYIIEINGEKYYPGGDENLFNDRMNGKHNRADWAWRWSRKLFDFGFENGFIEIR
                     NGGQRPRIYTKTYQNAKISKDGNDYVITYFDRTKPLSTLEFTENKYSNDNATKHISSLL
                     GKNIFDYTKPETLLAKLIEITSTKNDLILDFNLGSGTTAAVAHKMGRRYIGIEQMEYIN
                     DITVPRLKKVIEGEQGGISKDVNWQGGGSFVYAELMELNAYFVHEIQKAQSTEELEKLF
                     TMMKTEAHLNYQVELENVLSAEYEVDGIFRKVAFSELELHEQKQLLIEILDKNKLYVNV
                     SDMEDSELSISESDKAFTRSFYGME"
                     /name="site-specific DNA-methyltransferase"
     gene            3507..6143
                     /locus_tag="WI427_RS24250"
                     /old_locus_tag="WI427_24250"
     CDS             3507..6143
                     /locus_tag="WI427_RS24250"
                     /old_locus_tag="WI427_24250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012443154.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 -
                     hydrolase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase family protein"
                     /protein_id="WP_088365282.1"
                     /translation="MAKKPKSVGSEKLLFNRLKQFDEPGLFHDNYQTPDYIQENLKDAL
                     RPYQHGALRYLHYTQRKRDDALLHYRHLLFHMATGAGKTMVMAGTILYLFKELGYQNFI
                     FFVHTDAIIQKTRENLLNPQSPKYLFSQELEIDGEKITIEPIETFPSIPERNTIYLKLS
                     TIHKMHDELNSYRENSITYEDLKEIPLVLLGDEAHHFNAGTKARGKSKTSPENEEQTWE
                     RTIENILNLRPDNRLFEFTATIDLANKDIGQKYRGKVVYQYDLKQFMSDGYSKKVMLLE
                     ANQNDSDKMLDAVLLSQYRKLTAADHGITGFKPVILFKSNKIAISKAKQEEFSQLIAAM
                     TPESVRRHLANKKLQLSSDTSIWHKVIQRYANSDLVTVTGQIQEDFNDFNLLNVNKSDL
                     LEENPVLLNTLEEVDNPVRAVFAVAKVNEGWDVLNLYDIVRISEQASSSKTSTDSEAQL
                     IGRGARYYPFIYDGQRSFTRRFDNSTKDLSVLEQLHYHTINEPAYIKTLHASLEQADID
                     VHQDGGGTIEHARLKEDFKKSAVYQAGKLYFNEVEEIESSSRNWETYSLETRFEIPYQT
                     VCEESLDNLTGTKTGITKPELLVLDERFYRKAMQRISFYALDNLQRFFPKLTGIREFIR
                     SDAYLGKLKITVIVPQSLDFTTVPAKDKLHLLETVLLRISENVRRNDQKVKGTYRFISQ
                     PVKEVIKDYSLHIDPSVVINQKITAVPTIGKKWYVYDNAILNQLEHRLIKTLEAFMPKL
                     KARYDDIYVLRNDEQSTRFKLTEFGGVRGFMPDFIMILTRHSDNTYWQVFLEPKGDDRL
                     LDDAWKERMLETLNDRERIVIDENEHVRLVGIKFFANSQMDVFVSDMQNKLNDGESLET
                     SSLSLPL"
                     /name="DEAD/DEAH box helicase family protein"
     gene            complement(6541..6654)
                     /locus_tag="WI427_RS24255"
                     /old_locus_tag="WI427_24255"
     CDS             complement(6541..6654)
                     /locus_tag="WI427_RS24255"
                     /old_locus_tag="WI427_24255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072071404.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLLPLAAATGN"
                     /name="replication initiation protein"
     Typing          287..367
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.73e-35"
     Typing          689..786
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="2.25e-39"
     Typing          complement(2..263)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.636"
                     /coverage="98.0"
                     /evalue="1.2e-84"
     Typing          complement(6505..6863)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.075"
                     /coverage="100.0"
                     /evalue="5.23e-147"
ORIGIN
        1 tcgatttttg tgatgctcgt caggggggcg gagcctatgg aaaaacgcca tcggcgcggc
       61 cttttcctgg ttcttgtttt ttgctcacat gctccttttg gctttatccc ctgattctgt
      121 ggatcaccgc attaccgttt ttgagtgggc tgataccgct cgccgcagcc gaacggccga
      181 gcgtagcgag tcagtgagcg aggaagcgga agagtgcctg aacaggcatg ttctccttac
      241 gcatctatgc gatatttcac accgcatatg ccgctgtttt cttacaatcg cactgattcc
      301 gcacagttaa gccagtatac actccgctat cgctacgtga ctgggtcatg gctgcgcccc
      361 gacacccgca aggtccacgg cctgacgcgc cctgacgggc ttgtctgctc ccggcatccg
      421 ctcacaggca agctgtggcc gtctccggga gctgtatgtg tcagaggttt tcaccatcat
      481 cactgaagcg agcgaggcaa ctgcggtaga gttcgtcggc gtggtcgtga agtgattcgc
      541 agatgtccgc ctgttcgtcc gcgtccagct cgttgagttt ttctagcagg gttagcgtct
      601 ggcttttgat aaatcgcgcc atattcagcg cagtttgttg ctgtttgttc accttcggtt
      661 gttctccgtc agtaccgggt gtcgggtgga ccctgaccag gtggtaattg taagacgttg
      721 cgcgcgacgg tattacaatt gcacatcctg tcctgttttt taggaggtat catggcacag
      781 catatcaact gataaataat ccctgtgctg tacagccgct gttgcataaa atttcgctct
      841 gcgtcgaggt tttttttatc aaaaattccg cagatacccc ggaaaaacgc gagtctgttc
      901 tcatgcctga aatgcccaca ccccacgcaa aactaatttt ttgctgattt gcttttgaaa
      961 tcatgttgtt atggtttcaa aaatgtattt tctttttcag atttatgcaa aagcacgtcg
     1021 ttgacgaccc tatggcgacg ctatggcgac cctacttagg gtcagtactg acaatcttta
     1081 taaaaaacag ttaattaagg tatgggcgtc cctagggacg cgtcgcattt ttttacagga
     1141 cacccctagc agcgccccta ggggtgtctg ctcagatatg cctggaattc acgaactgaa
     1201 aatgtctgaa aatgtgcctt attggcaccg aatgcactca aaccgatcgt cattcacttt
     1261 catgcatagc tatgcatcga gctgaaaacg atcctgacgc atttttctgg ttttcactgg
     1321 taaaacatct ctttttgcgg tgtttgcgtc agaatcgcgt tcagcgcgtt ttagtggtgc
     1381 gcgcaagagc gtttatgtta aataccaccc attctgatgc atttccccgc aactgcatcc
     1441 aactcatagc tgtcgggttc cagcaccgaa cgctatacct tacaatcatt ccaatattta
     1501 acagtcataa ggccatgaca tgcagaccga attaataaaa gaacttaaca aggttttaaa
     1561 agcattcccg caattctgga acggagagga attacaacgt tcaatggtga gtgacgctat
     1621 cagtcaaaag cagccagacc ttatcaaggc attggtcgat aatgaaaaag tccgctctgt
     1681 ttatggtgcg gatattgatg gcatttttat ctttgacttt gacaaattat gtggtcttct
     1741 aaaatacaaa gaatattggg ctaatagctt cactaaatac cggaacaaag tgggattaac
     1801 tagcgaaggt aaataccttg attacagttc tgatgtggtg ctggattttc ctttcaagga
     1861 ttgtgttctt gaaggcggta tgtcgaaaga agatcaagga aaatcagagg tttactataa
     1921 tgaaatcatc gcacgagatg aaatagataa tttgttctca ccgaaagttc tcaaagaagt
     1981 aaatcgttac tctaaagaag gagtaaaaaa agaaagaata tttaaccgta atgataattt
     2041 aattatcaga ggaaataacc taattgcgtt gcactgtata aaaaatatat acgagaagtc
     2101 agttaaatta atttatatag atccaccata taatactgat acagatagct ttaaatataa
     2161 tgataaattt agtcactcta cgtggctgac tttcatgaag aacagacttg aagttgcaaa
     2221 agatttgttg tgcgatgacg ggttaattgc aattagtatt gatgataatg aattaaatta
     2281 tttggcctcg ttggctgatg atatttttgg ccgaaaaaat aggattgcta tattcccaag
     2341 aataacaaag aaaggaggga aatccgccag cattttcgca aagaatcatg attacatact
     2401 gctttatgtt agaagtttag aaaacaagcg tatgtatgca gtttcgcacg acgacgataa
     2461 tttcaaatat aaagatgagt actttgctga gagaggaagc tacaaactca accaaacctt
     2521 ggattatgat agccttcaat acagcaaatc acttgattat ataatagaaa tcaatggtga
     2581 gaaatattac ccaggtggtg atgaaaattt atttaatgat agaatgaatg gcaagcataa
     2641 cagggcggac tgggcttgga gatggagtag gaaattattc gattttgggt ttgaaaatgg
     2701 gtttattgaa ataagaaatg gcggccaaag gccaaggata tatacaaaaa catatcaaaa
     2761 tgcaaagata tcaaaggacg gaaatgatta tgtcataacc tactttgata gaacaaagcc
     2821 attgtcaaca cttgagttta ctgaaaacaa gtattctaac gacaatgcga caaaacacat
     2881 tagctccctc ttagggaaaa atatatttga ttatacaaaa ccagaaaccc tattggctaa
     2941 gctaatcgaa ataacatcta ctaaaaatga cctaattcta gactttaatc ttggtagtgg
     3001 aactacagct gctgttgctc acaaaatggg gcgtcgctat atcggtattg agcagatgga
     3061 gtacatcaac gacattacgg tacctcgcct gaaaaaagtc atcgaaggtg aacagggggg
     3121 gatctcaaaa gacgttaact ggcagggggg aggcagcttt gtctacgcag aattgatgga
     3181 gctgaacgcc tatttcgtgc atgaaattca gaaagcgcag tccacggaag aactcgaaaa
     3241 actctttacc atgatgaaaa cagaggccca tctcaactat caggtagagc tggaaaatgt
     3301 gctgtccgct gagtacgaag tggatggcat cttccgtaag gtagctttca gtgaactgga
     3361 actgcatgag cagaagcagc ttctgattga aatcctcgat aaaaataaac tctacgtgaa
     3421 tgtctctgat atggaggaca gcgaactgag catttcggag agcgataaag cctttacccg
     3481 cagcttctac ggaatggagt gacggcatgg cgaagaaacc gaagtcagtc ggcagtgaga
     3541 agctactgtt taacaggctg aagcagttcg atgaaccagg actgttccac gataactatc
     3601 agacgccgga ctatattcag gaaaacctga aagatgccct gcgcccctat cagcatggtg
     3661 cactgcgtta cctgcattac acgcaacgta aacgggatga tgcgctgctg cattatcgcc
     3721 acctgctgtt tcacatggca accggtgcag ggaaaacgat ggtgatggca ggaacgatac
     3781 tttatctgtt taaagagtta gggtatcaga acttcatttt cttcgtgcat acagacgcga
     3841 ttatccagaa aacgcgagag aacttgctta atccgcaatc gccgaagtac ctgttcagtc
     3901 aggagctgga aatcgacggg gaaaaaatca ccatcgaacc gatagaaaca ttcccgtcca
     3961 taccggaacg taacacgatt tacctcaagc tctctactat ccataagatg cacgacgagc
     4021 tgaacagcta tcgtgagaac agcatcacct acgaggattt aaaagaaatc ccccttgtgc
     4081 tgcttggtga cgaggcacat catttcaacg ccggtactaa agctagaggc aagtcgaaaa
     4141 cctcaccgga gaacgaggag cagacctggg aacgcacgat tgagaacatc ctcaacctgc
     4201 gaccggataa ccgcctgttc gagttcaccg ccaccattga tcttgcgaac aaagatatcg
     4261 ggcagaaata ccgtggtaag gtggtgtatc agtatgacct gaaacagttc atgtcagacg
     4321 gttactcgaa gaaagtcatg ctgctggaag ccaaccagaa tgacagcgac aagatgcttg
     4381 atgcggtact tttaagccag taccgtaaac tgacggcagc agatcacggc atcaccggct
     4441 tcaaaccggt cattctgttc aagtcgaata agattgcgat atcaaaggcg aagcaggagg
     4501 agttttcgca actgatagcc gccatgacac ctgagagcgt cagacgtcat ctagctaaca
     4561 aaaaactcca gctcagctct gacaccagta tctggcataa agtgattcag cgttacgcta
     4621 acagtgattt agtgacggtg actgggcaaa ttcaggagga ctttaacgac tttaacctgc
     4681 tgaacgtcaa caagtcagat ctgctggaag agaatcccgt cctgctgaat acactagaag
     4741 aagtcgataa tccggtgaga gccgtctttg ccgtcgcgaa ggtgaatgaa ggctgggacg
     4801 ttctcaacct ctacgatatt gtccgcatca gcgagcaggc gagcagcagc aaaaccagca
     4861 cggacagcga agcgcagctt atcgggcgag gcgcgcgtta ctacccgttc atttatgacg
     4921 gtcaacgaag cttcacccgc cgttttgata acagtacgaa ggatttgagc gtactggagc
     4981 aactgcacta tcacaccatc aatgaaccgg cgtacatcaa aacactgcat gcctctttgg
     5041 agcaggcgga cattgatgtg catcaggatg gcggcggtac gattgaacac gccagactga
     5101 aagaagattt taaaaagtcc gccgtgtatc aggcgggtaa gctgtacttc aacgaagtgg
     5161 aggagattga gagcagcagc agaaactggg aaacctactc gctggaaaca cgctttgaga
     5221 taccgtatca gaccgtctgc gaggagtcgc tggacaacct gacaggcaca aagactggaa
     5281 tcacaaaacc ggaactactg gtactggacg agcgttttta ccgcaaggcg atgcaaagga
     5341 tcagctttta cgcacttgat aacctgcagc gtttcttccc gaaactgaca ggcatccgtg
     5401 agttcatccg cagtgacgcc tatcttggta agctgaaaat tacagtcatc gtaccgcagt
     5461 cactggattt caccaccgta ccggcaaaag ataagctgca cctactggaa accgttctgc
     5521 tgcgtatctc agagaacgtt cgccgcaatg atcagaaggt aaaaggcacg taccgcttta
     5581 tcagccagcc ggtgaaagag gttattaaag attacagttt gcacattgac ccgtcggtag
     5641 ttattaatca gaaaatcact gctgtaccca ccattggtaa aaaatggtac gtgtacgata
     5701 atgcgatact gaatcagctt gagcatcgcc taattaaaac gctggaagca ttcatgccga
     5761 agctaaaagc gcgttatgac gatatttacg tactgcgtaa cgacgagcag tcaacgcgct
     5821 ttaagctcac ggagttcggc ggcgtgcgcg ggtttatgcc agatttcatc atgatactga
     5881 cgcgccattc ggacaacact tactggcagg tgttccttga accgaagggg gatgatcgtt
     5941 tgctggatga cgcatggaaa gaacggatgc tcgaaaccct gaatgatagg gagcgcattg
     6001 taattgatga aaatgagcac gtcagactgg ttgggattaa attctttgcc aacagccaga
     6061 tggacgtttt tgtcagcgac atgcagaaca agctgaatga tggagaatcg ctcgaaacct
     6121 cctcgctttc cctaccactg taaatcacga caataaataa cggagcatta cgctccgtta
     6181 ttttattgtt atccctaacc acctccccgg gagttgatga ttgctcctgt aatggttgca
     6241 ttgtttgttc ttgctgttgc gaatcattag ttttgaattg tggttaaaaa ccgttcgcta
     6301 tgtttatgcc tagggggatg agggggaaaa gattcaagga tcctcttgtg atcctttttt
     6361 tctgcgcgta atctgctgcc tgtaaacgaa aaaaccaccc tggcaggtgg tttttcgaag
     6421 gttagctaat cctggcagat tatctaaccg ggtaactggc ttggaggagc gcagtcacca
     6481 aaatctgttc tttcagttta gccttaacag gtgcataact tcaagacaaa ctcctctaaa
     6541 tcagttacca gtggctgctg ccagtggcaa taagtcgtgt cttaccgggt tggactcaag
     6601 acgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttcgt gcacacagcc
     6661 cagcttggag cgaacgacct acaccgaact gagataccaa cagcgtgagc tatgagaaag
     6721 cgccacgctt cccgaaggga gaaaggcgga caggtatccg gtaatcggca gggtcggaac
     6781 aggagagcgc acgagggagc caccaggggg aaactcctgg tatctttaag tcctgtcggg
     6841 tttcgccacc tctgacttga gcg
//
