LOCUS       NZ_CP149334             6863 bp    DNA     circular CON 05-APR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            Z1323SSL0011 plasmid pZ1323SSL0011-3, complete sequence.
ACCESSION   NZ_CP149334
VERSION     NZ_CP149334.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40439963
            Assembly: GCF_037860935.1
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  JOURNAL   Unpublished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                   :: 82X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037860935.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 21:19:02
            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)                     :: 4,893
            CDSs (total)                      :: 4,771
            Genes (coding)                    :: 4,637
            CDSs (with protein)               :: 4,637
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 43 of 134
            Pseudo Genes (incomplete)         :: 99 of 134
            Pseudo Genes (internal stop)      :: 23 of 134
            Pseudo Genes (multiple problems)  :: 29 of 134
            Pseudo Genes (short protein)      :: 1 of 134
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP149334.1.
            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="Z1323SSL0011"
                     /serovar="Typhimurium"
                     /host="Pig"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pZ1323SSL0011-3"
                     /geo_loc_name="South Korea"
                     /collection_date="2023-03-10"
     gene            142..333
                     /locus_tag="WI431_RS24450"
                     /old_locus_tag="WI431_24450"
     CDS             142..333
                     /locus_tag="WI431_RS24450"
                     /old_locus_tag="WI431_24450"
                     /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            1003..1116
                     /locus_tag="WI431_RS24455"
                     /old_locus_tag="WI431_24455"
     CDS             1003..1116
                     /locus_tag="WI431_RS24455"
                     /old_locus_tag="WI431_24455"
                     /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"
     gene            complement(1514..4150)
                     /locus_tag="WI431_RS24460"
                     /old_locus_tag="WI431_24460"
     CDS             complement(1514..4150)
                     /locus_tag="WI431_RS24460"
                     /old_locus_tag="WI431_24460"
                     /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(4155..6137)
                     /locus_tag="WI431_RS24465"
                     /old_locus_tag="WI431_24465"
     CDS             complement(4155..6137)
                     /locus_tag="WI431_RS24465"
                     /old_locus_tag="WI431_24465"
                     /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"
     Typing          complement(9..106)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="2.25e-39"
     Typing          complement(428..508)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.73e-35"
     Typing          528..1075
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.128"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atcagttgat atgctgtgcc atgatacctc ctaaaaaaca ggacaggatg tgcaattgta
       61 ataccgtcgc gcgcaacgtc ttacaattac cacctggtca gggtccaccc gacacccggt
      121 actgacggag aacaaccgaa ggtgaacaaa cagcaacaaa ctgcgctgaa tatggcgcga
      181 tttatcaaaa gccagacgct aaccctgcta gaaaaactca acgagctgga cgcggacgaa
      241 caggcggaca tctgcgaatc acttcacgac cacgccgacg aactctaccg cagttgcctc
      301 gctcgcttca gtgatgatgg tgaaaacctc tgacacatac agctcccgga gacggccaca
      361 gcttgcctgt gagcggatgc cgggagcaga caagcccgtc agggcgcgtc aggccgtgga
      421 ccttgcgggt gtcggggcgc agccatgacc cagtcacgta gcgatagcgg agtgtatact
      481 ggcttaactg tgcggaatca gtgcgattgt aagaaaacag cggcatatgc ggtgtgaaat
      541 atcgcataga tgcgtaagga gaacatgcct gttcaggcac tcttccgctt cctcgctcac
      601 tgactcgcta cgctcggccg ttcggctgcg gcgagcggta tcagcccact caaaaacggt
      661 aatgcggtga tccacagaat caggggataa agccaaaagg agcatgtgag caaaaaacaa
      721 gaaccaggaa aaggccgcgc cgatggcgtt tttccatagg ctccgccccc ctgacgagca
      781 tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactta aagataccag
      841 gagtttcccc ctggtggctc cctcgtgcgc tctcctgttc cgaccctgcc gattaccgga
      901 tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg
      961 tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt
     1021 cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac
     1081 gacttattgc cactggcagc agccactggt aactgattta gaggagtttg tcttgaagtt
     1141 atgcacctgt taaggctaaa ctgaaagaac agattttggt gactgcgctc ctccaagcca
     1201 gttacccggt tagataatct gccaggatta gctaaccttc gaaaaaccac ctgccagggt
     1261 ggttttttcg tttacaggca gcagattacg cgcagaaaaa aaggatcaca agaggatcct
     1321 tgaatctttt ccccctcatc cccctaggca taaacatagc gaacggtttt taaccacaat
     1381 tcaaaactaa tgattcgcaa cagcaagaac aaacaatgca accattacag gagcaatcat
     1441 caactcccgg ggaggtggtt agggataaca ataaaataac ggagcgtaat gctccgttat
     1501 ttattgtcgt gatttacagt ggtagggaaa gcgaggaggt ttcgagcgat tctccatcat
     1561 tcagcttgtt ctgcatgtcg ctgacaaaaa cgtccatctg gctgttggca aagaatttaa
     1621 tcccaaccag tctgacgtgc tcattttcat caattacaat gcgctcccta tcattcaggg
     1681 tttcgagcat ccgttctttc catgcgtcat ccagcaaacg atcatccccc ttcggttcaa
     1741 ggaacacctg ccagtaagtg ttgtccgaat ggcgcgtcag tatcatgatg aaatctggca
     1801 taaacccgcg cacgccgccg aactccgtga gcttaaagcg cgttgactgc tcgtcgttac
     1861 gcagtacgta aatatcgtca taacgcgctt ttagcttcgg catgaatgct tccagcgttt
     1921 taattaggcg atgctcaagc tgattcagta tcgcattatc gtacacgtac cattttttac
     1981 caatggtggg tacagcagtg attttctgat taataactac cgacgggtca atgtgcaaac
     2041 tgtaatcttt aataacctct ttcaccggct ggctgataaa gcggtacgtg ccttttacct
     2101 tctgatcatt gcggcgaacg ttctctgaga tacgcagcag aacggtttcc agtaggtgca
     2161 gcttatcttt tgccggtacg gtggtgaaat ccagtgactg cggtacgatg actgtaattt
     2221 tcagcttacc aagataggcg tcactgcgga tgaactcacg gatgcctgtc agtttcggga
     2281 agaaacgctg caggttatca agtgcgtaaa agctgatcct ttgcatcgcc ttgcggtaaa
     2341 aacgctcgtc cagtaccagt agttccggtt ttgtgattcc agtctttgtg cctgtcaggt
     2401 tgtccagcga ctcctcgcag acggtctgat acggtatctc aaagcgtgtt tccagcgagt
     2461 aggtttccca gtttctgctg ctgctctcaa tctcctccac ttcgttgaag tacagcttac
     2521 ccgcctgata cacggcggac tttttaaaat cttctttcag tctggcgtgt tcaatcgtac
     2581 cgccgccatc ctgatgcaca tcaatgtccg cctgctccaa agaggcatgc agtgttttga
     2641 tgtacgccgg ttcattgatg gtgtgatagt gcagttgctc cagtacgctc aaatccttcg
     2701 tactgttatc aaaacggcgg gtgaagcttc gttgaccgtc ataaatgaac gggtagtaac
     2761 gcgcgcctcg cccgataagc tgcgcttcgc tgtccgtgct ggttttgctg ctgctcgcct
     2821 gctcgctgat gcggacaata tcgtagaggt tgagaacgtc ccagccttca ttcaccttcg
     2881 cgacggcaaa gacggctctc accggattat cgacttcttc tagtgtattc agcaggacgg
     2941 gattctcttc cagcagatct gacttgttga cgttcagcag gttaaagtcg ttaaagtcct
     3001 cctgaatttg cccagtcacc gtcactaaat cactgttagc gtaacgctga atcactttat
     3061 gccagatact ggtgtcagag ctgagctgga gttttttgtt agctagatga cgtctgacgc
     3121 tctcaggtgt catggcggct atcagttgcg aaaactcctc ctgcttcgcc tttgatatcg
     3181 caatcttatt cgacttgaac agaatgaccg gtttgaagcc ggtgatgccg tgatctgctg
     3241 ccgtcagttt acggtactgg cttaaaagta ccgcatcaag catcttgtcg ctgtcattct
     3301 ggttggcttc cagcagcatg actttcttcg agtaaccgtc tgacatgaac tgtttcaggt
     3361 catactgata caccacctta ccacggtatt tctgcccgat atctttgttc gcaagatcaa
     3421 tggtggcggt gaactcgaac aggcggttat ccggtcgcag gttgaggatg ttctcaatcg
     3481 tgcgttccca ggtctgctcc tcgttctccg gtgaggtttt cgacttgcct ctagctttag
     3541 taccggcgtt gaaatgatgt gcctcgtcac caagcagcac aagggggatt tcttttaaat
     3601 cctcgtaggt gatgctgttc tcacgatagc tgttcagctc gtcgtgcatc ttatggatag
     3661 tagagagctt gaggtaaatc gtgttacgtt ccggtatgga cgggaatgtt tctatcggtt
     3721 cgatggtgat tttttccccg tcgatttcca gctcctgact gaacaggtac ttcggcgatt
     3781 gcggattaag caagttctct cgcgttttct ggataatcgc gtctgtatgc acgaagaaaa
     3841 tgaagttctg ataccctaac tctttaaaca gataaagtat cgttcctgcc atcaccatcg
     3901 ttttccctgc accggttgcc atgtgaaaca gcaggtggcg ataatgcagc agcgcatcat
     3961 cccgtttacg ttgcgtgtaa tgcaggtaac gcagtgcacc atgctgatag gggcgcaggg
     4021 catctttcag gttttcctga atatagtccg gcgtctgata gttatcgtgg aacagtcctg
     4081 gttcatcgaa ctgcttcagc ctgttaaaca gtagcttctc actgccgact gacttcggtt
     4141 tcttcgccat gccgtcactc cattccgtag aagctgcggg taaaggcttt atcgctctcc
     4201 gaaatgctca gttcgctgtc ctccatatca gagacattca cgtagagttt atttttatcg
     4261 aggatttcaa tcagaagctg cttctgctca tgcagttcca gttcactgaa agctacctta
     4321 cggaagatgc catccacttc gtactcagcg gacagcacat tttccagctc tacctgatag
     4381 ttgagatggg cctctgtttt catcatggta aagagttttt cgagttcttc cgtggactgc
     4441 gctttctgaa tttcatgcac gaaataggcg ttcagctcca tcaattctgc gtagacaaag
     4501 ctgcctcccc cctgccagtt aacgtctttt gagatccccc cctgttcacc ttcgatgact
     4561 tttttcaggc gaggtaccgt aatgtcgttg atgtactcca tctgctcaat accgatatag
     4621 cgacgcccca ttttgtgagc aacagcagct gtagttccac taccaagatt aaagtctaga
     4681 attaggtcat ttttagtaga tgttatttcg attagcttag ccaatagggt ttctggtttt
     4741 gtataatcaa atatattttt ccctaagagg gagctaatgt gttttgtcgc attgtcgtta
     4801 gaatacttgt tttcagtaaa ctcaagtgtt gacaatggct ttgttctatc aaagtaggtt
     4861 atgacataat catttccgtc ctttgatatc tttgcatttt gatatgtttt tgtatatatc
     4921 cttggccttt ggccgccatt tcttatttca ataaacccat tttcaaaccc aaaatcgaat
     4981 aatttcctac tccatctcca agcccagtcc gccctgttat gcttgccatt cattctatca
     5041 ttaaataaat tttcatcacc acctgggtaa tatttctcac cattgatttc tattatataa
     5101 tcaagtgatt tgctgtattg aaggctatca taatccaagg tttggttgag tttgtagctt
     5161 cctctctcag caaagtactc atctttatat ttgaaattat cgtcgtcgtg cgaaactgca
     5221 tacatacgct tgttttctaa acttctaaca taaagcagta tgtaatcatg attctttgcg
     5281 aaaatgctgg cggatttccc tcctttcttt gttattcttg ggaatatagc aatcctattt
     5341 tttcggccaa aaatatcatc agccaacgag gccaaataat ttaattcatt atcatcaata
     5401 ctaattgcaa ttaacccgtc atcgcacaac aaatcttttg caacttcaag tctgttcttc
     5461 atgaaagtca gccacgtaga gtgactaaat ttatcattat atttaaagct atctgtatca
     5521 gtattatatg gtggatctat ataaattaat ttaactgact tctcgtatat attttttata
     5581 cagtgcaacg caattaggtt atttcctctg ataattaaat tatcattacg gttaaatatt
     5641 ctttcttttt ttactccttc tttagagtaa cgatttactt ctttgagaac tttcggtgag
     5701 aacaaattat ctatttcatc tcgtgcgatg atttcattat agtaaacctc tgattttcct
     5761 tgatcttctt tcgacatacc gccttcaaga acacaatcct tgaaaggaaa atccagcacc
     5821 acatcagaac tgtaatcaag gtatttacct tcgctagtta atcccacttt gttccggtat
     5881 ttagtgaagc tattagccca atattctttg tattttagaa gaccacataa tttgtcaaag
     5941 tcaaagataa aaatgccatc aatatccgca ccataaacag agcggacttt ttcattatcg
     6001 accaatgcct tgataaggtc tggctgcttt tgactgatag cgtcactcac cattgaacgt
     6061 tgtaattcct ctccgttcca gaattgcggg aatgctttta aaaccttgtt aagttctttt
     6121 attaattcgg tctgcatgtc atggccttat gactgttaaa tattggaatg attgtaaggt
     6181 atagcgttcg gtgctggaac ccgacagcta tgagttggat gcagttgcgg ggaaatgcat
     6241 cagaatgggt ggtatttaac ataaacgctc ttgcgcgcac cactaaaacg cgctgaacgc
     6301 gattctgacg caaacaccgc aaaaagagat gttttaccag tgaaaaccag aaaaatgcgt
     6361 caggatcgtt ttcagctcga tgcatagcta tgcatgaaag tgaatgacga tcggtttgag
     6421 tgcattcggt gccaataagg cacattttca gacattttca gttcgtgaat tccaggcata
     6481 tctgagcaga cacccctagg ggcgctgcta ggggtgtcct gtaaaaaaat gcgacgcgtc
     6541 cctagggacg cccatacctt aattaactgt tttttataaa gattgtcagt actgacccta
     6601 agtagggtcg ccatagcgtc gccatagggt cgtcaacgac gtgcttttgc ataaatctga
     6661 aaaagaaaat acatttttga aaccataaca acatgatttc aaaagcaaat cagcaaaaaa
     6721 ttagttttgc gtggggtgtg ggcatttcag gcatgagaac agactcgcgt ttttccgggg
     6781 tatctgcgga atttttgata aaaaaaacct cgacgcagag cgaaatttta tgcaacagcg
     6841 gctgtacagc acagggatta ttt
//
