LOCUS       NZ_CP149404             6863 bp    DNA     circular CON 05-APR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            Z1322HSL0036 plasmid pZ1322HSL0036-2, complete sequence.
ACCESSION   NZ_CP149404
VERSION     NZ_CP149404.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40439937
            Assembly: GCF_037888885.1
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  JOURNAL   Unpublished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                   :: 124X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037888885.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 21:19:55
            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)                     :: 4,731
            CDSs (total)                      :: 4,608
            Genes (coding)                    :: 4,501
            CDSs (with protein)               :: 4,501
            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)              :: 107
            CDSs (without protein)            :: 107
            Pseudo Genes (ambiguous residues) :: 0 of 107
            Pseudo Genes (frameshifted)       :: 35 of 107
            Pseudo Genes (incomplete)         :: 77 of 107
            Pseudo Genes (internal stop)      :: 21 of 107
            Pseudo Genes (multiple problems)  :: 24 of 107
            Pseudo Genes (short protein)      :: 1 of 107
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP149404.1.
            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="Z1322HSL0036"
                     /serovar="Typhimurium"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pZ1322HSL0036-2"
                     /geo_loc_name="South Korea"
                     /collection_date="2022-08-08"
     gene            541..732
                     /locus_tag="WI405_RS23605"
                     /old_locus_tag="WI405_23605"
     CDS             541..732
                     /locus_tag="WI405_RS23605"
                     /old_locus_tag="WI405_23605"
                     /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            1402..1515
                     /locus_tag="WI405_RS23610"
                     /old_locus_tag="WI405_23610"
     CDS             1402..1515
                     /locus_tag="WI405_RS23610"
                     /old_locus_tag="WI405_23610"
                     /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(1913..4549)
                     /locus_tag="WI405_RS23615"
                     /old_locus_tag="WI405_23615"
     CDS             complement(1913..4549)
                     /locus_tag="WI405_RS23615"
                     /old_locus_tag="WI405_23615"
                     /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(4554..6536)
                     /locus_tag="WI405_RS23620"
                     /old_locus_tag="WI405_23620"
     CDS             complement(4554..6536)
                     /locus_tag="WI405_RS23620"
                     /old_locus_tag="WI405_23620"
                     /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(408..505)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="2.25e-39"
     Typing          complement(827..907)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.73e-35"
     Typing          927..1474
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.128"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtgaattcca ggcatatctg agcagacacc cctaggggcg ctgctagggg tgtcctgtaa
       61 aaaaatgcga cgcgtcccta gggacgccca taccttaatt aactgttttt tataaagatt
      121 gtcagtactg accctaagta gggtcgccat agcgtcgcca tagggtcgtc aacgacgtgc
      181 ttttgcataa atctgaaaaa gaaaatacat ttttgaaacc ataacaacat gatttcaaaa
      241 gcaaatcagc aaaaaattag ttttgcgtgg ggtgtgggca tttcaggcat gagaacagac
      301 tcgcgttttt ccggggtatc tgcggaattt ttgataaaaa aaacctcgac gcagagcgaa
      361 attttatgca acagcggctg tacagcacag ggattattta tcagttgata tgctgtgcca
      421 tgatacctcc taaaaaacag gacaggatgt gcaattgtaa taccgtcgcg cgcaacgtct
      481 tacaattacc acctggtcag ggtccacccg acacccggta ctgacggaga acaaccgaag
      541 gtgaacaaac agcaacaaac tgcgctgaat atggcgcgat ttatcaaaag ccagacgcta
      601 accctgctag aaaaactcaa cgagctggac gcggacgaac aggcggacat ctgcgaatca
      661 cttcacgacc acgccgacga actctaccgc agttgcctcg ctcgcttcag tgatgatggt
      721 gaaaacctct gacacataca gctcccggag acggccacag cttgcctgtg agcggatgcc
      781 gggagcagac aagcccgtca gggcgcgtca ggccgtggac cttgcgggtg tcggggcgca
      841 gccatgaccc agtcacgtag cgatagcgga gtgtatactg gcttaactgt gcggaatcag
      901 tgcgattgta agaaaacagc ggcatatgcg gtgtgaaata tcgcatagat gcgtaaggag
      961 aacatgcctg ttcaggcact cttccgcttc ctcgctcact gactcgctac gctcggccgt
     1021 tcggctgcgg cgagcggtat cagcccactc aaaaacggta atgcggtgat ccacagaatc
     1081 aggggataaa gccaaaagga gcatgtgagc aaaaaacaag aaccaggaaa aggccgcgcc
     1141 gatggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag
     1201 tcagaggtgg cgaaacccga caggacttaa agataccagg agtttccccc tggtggctcc
     1261 ctcgtgcgct ctcctgttcc gaccctgccg attaccggat acctgtccgc ctttctccct
     1321 tcgggaagcg tggcgctttc tcatagctca cgctgttggt atctcagttc ggtgtaggtc
     1381 gttcgctcca agctgggctg tgtgcacgaa ccccccgttc agcccgaccg ctgcgcctta
     1441 tccggtaact atcgtcttga gtccaacccg gtaagacacg acttattgcc actggcagca
     1501 gccactggta actgatttag aggagtttgt cttgaagtta tgcacctgtt aaggctaaac
     1561 tgaaagaaca gattttggtg actgcgctcc tccaagccag ttacccggtt agataatctg
     1621 ccaggattag ctaaccttcg aaaaaccacc tgccagggtg gttttttcgt ttacaggcag
     1681 cagattacgc gcagaaaaaa aggatcacaa gaggatcctt gaatcttttc cccctcatcc
     1741 ccctaggcat aaacatagcg aacggttttt aaccacaatt caaaactaat gattcgcaac
     1801 agcaagaaca aacaatgcaa ccattacagg agcaatcatc aactcccggg gaggtggtta
     1861 gggataacaa taaaataacg gagcgtaatg ctccgttatt tattgtcgtg atttacagtg
     1921 gtagggaaag cgaggaggtt tcgagcgatt ctccatcatt cagcttgttc tgcatgtcgc
     1981 tgacaaaaac gtccatctgg ctgttggcaa agaatttaat cccaaccagt ctgacgtgct
     2041 cattttcatc aattacaatg cgctccctat cattcagggt ttcgagcatc cgttctttcc
     2101 atgcgtcatc cagcaaacga tcatccccct tcggttcaag gaacacctgc cagtaagtgt
     2161 tgtccgaatg gcgcgtcagt atcatgatga aatctggcat aaacccgcgc acgccgccga
     2221 actccgtgag cttaaagcgc gttgactgct cgtcgttacg cagtacgtaa atatcgtcat
     2281 aacgcgcttt tagcttcggc atgaatgctt ccagcgtttt aattaggcga tgctcaagct
     2341 gattcagtat cgcattatcg tacacgtacc attttttacc aatggtgggt acagcagtga
     2401 ttttctgatt aataactacc gacgggtcaa tgtgcaaact gtaatcttta ataacctctt
     2461 tcaccggctg gctgataaag cggtacgtgc cttttacctt ctgatcattg cggcgaacgt
     2521 tctctgagat acgcagcaga acggtttcca gtaggtgcag cttatctttt gccggtacgg
     2581 tggtgaaatc cagtgactgc ggtacgatga ctgtaatttt cagcttacca agataggcgt
     2641 cactgcggat gaactcacgg atgcctgtca gtttcgggaa gaaacgctgc aggttatcaa
     2701 gtgcgtaaaa gctgatcctt tgcatcgcct tgcggtaaaa acgctcgtcc agtaccagta
     2761 gttccggttt tgtgattcca gtctttgtgc ctgtcaggtt gtccagcgac tcctcgcaga
     2821 cggtctgata cggtatctca aagcgtgttt ccagcgagta ggtttcccag tttctgctgc
     2881 tgctctcaat ctcctccact tcgttgaagt acagcttacc cgcctgatac acggcggact
     2941 ttttaaaatc ttctttcagt ctggcgtgtt caatcgtacc gccgccatcc tgatgcacat
     3001 caatgtccgc ctgctccaaa gaggcatgca gtgttttgat gtacgccggt tcattgatgg
     3061 tgtgatagtg cagttgctcc agtacgctca aatccttcgt actgttatca aaacggcggg
     3121 tgaagcttcg ttgaccgtca taaatgaacg ggtagtaacg cgcgcctcgc ccgataagct
     3181 gcgcttcgct gtccgtgctg gttttgctgc tgctcgcctg ctcgctgatg cggacaatat
     3241 cgtagaggtt gagaacgtcc cagccttcat tcaccttcgc gacggcaaag acggctctca
     3301 ccggattatc gacttcttct agtgtattca gcaggacggg attctcttcc agcagatctg
     3361 acttgttgac gttcagcagg ttaaagtcgt taaagtcctc ctgaatttgc ccagtcaccg
     3421 tcactaaatc actgttagcg taacgctgaa tcactttatg ccagatactg gtgtcagagc
     3481 tgagctggag ttttttgtta gctagatgac gtctgacgct ctcaggtgtc atggcggcta
     3541 tcagttgcga aaactcctcc tgcttcgcct ttgatatcgc aatcttattc gacttgaaca
     3601 gaatgaccgg tttgaagccg gtgatgccgt gatctgctgc cgtcagttta cggtactggc
     3661 ttaaaagtac cgcatcaagc atcttgtcgc tgtcattctg gttggcttcc agcagcatga
     3721 ctttcttcga gtaaccgtct gacatgaact gtttcaggtc atactgatac accaccttac
     3781 cacggtattt ctgcccgata tctttgttcg caagatcaat ggtggcggtg aactcgaaca
     3841 ggcggttatc cggtcgcagg ttgaggatgt tctcaatcgt gcgttcccag gtctgctcct
     3901 cgttctccgg tgaggttttc gacttgcctc tagctttagt accggcgttg aaatgatgtg
     3961 cctcgtcacc aagcagcaca agggggattt cttttaaatc ctcgtaggtg atgctgttct
     4021 cacgatagct gttcagctcg tcgtgcatct tatggatagt agagagcttg aggtaaatcg
     4081 tgttacgttc cggtatggac gggaatgttt ctatcggttc gatggtgatt ttttccccgt
     4141 cgatttccag ctcctgactg aacaggtact tcggcgattg cggattaagc aagttctctc
     4201 gcgttttctg gataatcgcg tctgtatgca cgaagaaaat gaagttctga taccctaact
     4261 ctttaaacag ataaagtatc gttcctgcca tcaccatcgt tttccctgca ccggttgcca
     4321 tgtgaaacag caggtggcga taatgcagca gcgcatcatc ccgtttacgt tgcgtgtaat
     4381 gcaggtaacg cagtgcacca tgctgatagg ggcgcagggc atctttcagg ttttcctgaa
     4441 tatagtccgg cgtctgatag ttatcgtgga acagtcctgg ttcatcgaac tgcttcagcc
     4501 tgttaaacag tagcttctca ctgccgactg acttcggttt cttcgccatg ccgtcactcc
     4561 attccgtaga agctgcgggt aaaggcttta tcgctctccg aaatgctcag ttcgctgtcc
     4621 tccatatcag agacattcac gtagagttta tttttatcga ggatttcaat cagaagctgc
     4681 ttctgctcat gcagttccag ttcactgaaa gctaccttac ggaagatgcc atccacttcg
     4741 tactcagcgg acagcacatt ttccagctct acctgatagt tgagatgggc ctctgttttc
     4801 atcatggtaa agagtttttc gagttcttcc gtggactgcg ctttctgaat ttcatgcacg
     4861 aaataggcgt tcagctccat caattctgcg tagacaaagc tgcctccccc ctgccagtta
     4921 acgtcttttg agatcccccc ctgttcacct tcgatgactt ttttcaggcg aggtaccgta
     4981 atgtcgttga tgtactccat ctgctcaata ccgatatagc gacgccccat tttgtgagca
     5041 acagcagctg tagttccact accaagatta aagtctagaa ttaggtcatt tttagtagat
     5101 gttatttcga ttagcttagc caatagggtt tctggttttg tataatcaaa tatatttttc
     5161 cctaagaggg agctaatgtg ttttgtcgca ttgtcgttag aatacttgtt ttcagtaaac
     5221 tcaagtgttg acaatggctt tgttctatca aagtaggtta tgacataatc atttccgtcc
     5281 tttgatatct ttgcattttg atatgttttt gtatatatcc ttggcctttg gccgccattt
     5341 cttatttcaa taaacccatt ttcaaaccca aaatcgaata atttcctact ccatctccaa
     5401 gcccagtccg ccctgttatg cttgccattc attctatcat taaataaatt ttcatcacca
     5461 cctgggtaat atttctcacc attgatttct attatataat caagtgattt gctgtattga
     5521 aggctatcat aatccaaggt ttggttgagt ttgtagcttc ctctctcagc aaagtactca
     5581 tctttatatt tgaaattatc gtcgtcgtgc gaaactgcat acatacgctt gttttctaaa
     5641 cttctaacat aaagcagtat gtaatcatga ttctttgcga aaatgctggc ggatttccct
     5701 cctttctttg ttattcttgg gaatatagca atcctatttt ttcggccaaa aatatcatca
     5761 gccaacgagg ccaaataatt taattcatta tcatcaatac taattgcaat taacccgtca
     5821 tcgcacaaca aatcttttgc aacttcaagt ctgttcttca tgaaagtcag ccacgtagag
     5881 tgactaaatt tatcattata tttaaagcta tctgtatcag tattatatgg tggatctata
     5941 taaattaatt taactgactt ctcgtatata ttttttatac agtgcaacgc aattaggtta
     6001 tttcctctga taattaaatt atcattacgg ttaaatattc tttctttttt tactccttct
     6061 ttagagtaac gatttacttc tttgagaact ttcggtgaga acaaattatc tatttcatct
     6121 cgtgcgatga tttcattata gtaaacctct gattttcctt gatcttcttt cgacataccg
     6181 ccttcaagaa cacaatcctt gaaaggaaaa tccagcacca catcagaact gtaatcaagg
     6241 tatttacctt cgctagttaa tcccactttg ttccggtatt tagtgaagct attagcccaa
     6301 tattctttgt attttagaag accacataat ttgtcaaagt caaagataaa aatgccatca
     6361 atatccgcac cataaacaga gcggactttt tcattatcga ccaatgcctt gataaggtct
     6421 ggctgctttt gactgatagc gtcactcacc attgaacgtt gtaattcctc tccgttccag
     6481 aattgcggga atgcttttaa aaccttgtta agttctttta ttaattcggt ctgcatgtca
     6541 tggccttatg actgttaaat attggaatga ttgtaaggta tagcgttcgg tgctggaacc
     6601 cgacagctat gagttggatg cagttgcggg gaaatgcatc agaatgggtg gtatttaaca
     6661 taaacgctct tgcgcgcacc actaaaacgc gctgaacgcg attctgacgc aaacaccgca
     6721 aaaagagatg ttttaccagt gaaaaccaga aaaatgcgtc aggatcgttt tcagctcgat
     6781 gcatagctat gcatgaaagt gaatgacgat cggtttgagt gcattcggtg ccaataaggc
     6841 acattttcag acattttcag ttc
//
