LOCUS       NZ_CP149346             5310 bp    DNA     circular CON 05-APR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            Z1323SSL0001 plasmid pZ1323SSL0001-4, complete sequence.
ACCESSION   NZ_CP149346
VERSION     NZ_CP149346.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40439958
            Assembly: GCF_037866235.1
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 5310)
  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  JOURNAL   Unpublished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 5310)
  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                   :: 106X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037866235.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 21:21:47
            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)                     :: 5,012
            CDSs (total)                      :: 4,888
            Genes (coding)                    :: 4,756
            CDSs (with protein)               :: 4,756
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 132
            CDSs (without protein)            :: 132
            Pseudo Genes (ambiguous residues) :: 0 of 132
            Pseudo Genes (frameshifted)       :: 52 of 132
            Pseudo Genes (incomplete)         :: 90 of 132
            Pseudo Genes (internal stop)      :: 22 of 132
            Pseudo Genes (multiple problems)  :: 29 of 132
            Pseudo Genes (short protein)      :: 1 of 132
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP149346.1.
            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..5310
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="Z1323SSL0001"
                     /serovar="Typhimurium"
                     /host="Pig"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pZ1323SSL0001-4"
                     /geo_loc_name="South Korea"
                     /collection_date="2023-03-10"
     gene            39..854
                     /locus_tag="WI409_RS25020"
                     /old_locus_tag="WI409_25020"
     CDS             39..854
                     /locus_tag="WI409_RS25020"
                     /old_locus_tag="WI409_25020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /protein_id="WP_000018330.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(<864..>1136)
                     /locus_tag="WI409_RS25025"
                     /old_locus_tag="WI409_25025"
                     /pseudo=""
     CDS             complement(<864..>1136)
                     /locus_tag="WI409_RS25025"
                     /old_locus_tag="WI409_25025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_021138877.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            1978..2298
                     /locus_tag="WI409_RS25030"
                     /old_locus_tag="WI409_25030"
     CDS             1978..2298
                     /locus_tag="WI409_RS25030"
                     /old_locus_tag="WI409_25030"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_187655770.1"
                     /translation="MDNRVSVFEKGESARRSRTTERSESVSEEAEERLNWHFLLTHLCG
                     ISHRTWRTFHTIRTDAEWLSQYTLRYRYVTGSGLRPDTPKVNGLTRPGGLVCSRHPLTD
                     KL"
                     /name="hypothetical protein"
     gene            complement(2321..2512)
                     /locus_tag="WI409_RS25035"
                     /old_locus_tag="WI409_25035"
     CDS             complement(2321..2512)
                     /locus_tag="WI409_RS25035"
                     /old_locus_tag="WI409_25035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2577..2900
                     /locus_tag="WI409_RS25040"
                     /old_locus_tag="WI409_25040"
     CDS             2577..2900
                     /locus_tag="WI409_RS25040"
                     /old_locus_tag="WI409_25040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3109..>3540
                     /locus_tag="WI409_RS25045"
                     /old_locus_tag="WI409_25045"
                     /pseudo=""
     CDS             3109..>3540
                     /locus_tag="WI409_RS25045"
                     /old_locus_tag="WI409_25045"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3578..4108
                     /locus_tag="WI409_RS25050"
                     /old_locus_tag="WI409_25050"
     CDS             3578..4108
                     /locus_tag="WI409_RS25050"
                     /old_locus_tag="WI409_25050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_206353804.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDVHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            4115..4348
                     /locus_tag="WI409_RS25055"
                     /old_locus_tag="WI409_25055"
     CDS             4115..4348
                     /locus_tag="WI409_RS25055"
                     /old_locus_tag="WI409_25055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            <5108..>5203
                     /locus_tag="WI409_RS25060"
                     /old_locus_tag="WI409_25060"
                     /pseudo=""
     CDS             <5108..>5203
                     /locus_tag="WI409_RS25060"
                     /old_locus_tag="WI409_25060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013356662.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="amino acid ABC transporter substrate-binding
                     protein"
                     /name="amino acid ABC transporter substrate-binding
                     protein"
     ARG             40..851
                     /name="aph(3')-Ia"
                     /gene="aph(3')-Ia"
                     /gene_name="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             4..854
                     /name="APH(3')-Ia"
                     /gene="APH(3')-Ia"
                     /gene_name="APH(3')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="98.15"
                     /coverage="104.43"
     Typing          2146..2227
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          1502..1689
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          2891..4452
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aactgtctgc ttacataaac agtaatacaa ggggtgttat gagccatatt caacgggaaa
       61 cgtcttgctc gaggcagcga ttaaattcca acctggatgc tgatttatat gggtataaat
      121 gggctcgcga taatgtcggg caatcaggtg cgacaatcta tcgattgtat gggaagcccg
      181 atgcgccaga gttgtttctg aaacatggca aaggtagcgt tgccaatgat gttacagatg
      241 agatggtcag actaaactgg ctgacggaat ttatgcctct tccgaccatc aagcatttta
      301 tccgtactcc tgatgatgca tggttactca ccactgcgat ccccgggaaa acagcattcc
      361 aggtattaga agaatatcct gattcaggtg aaaatattgt tgatgcgctg gcagcgttcc
      421 tgcgccggtt gcattcgatt cctgtttgta attgtccttt taacagcgat cgcgtatttc
      481 gtctcgctca ggcgcaatca cgaatgaata acggtttggt tgatgcgagt gattttgatg
      541 atgagcgtaa tggctggcct gttgaacaag tctggaaaga aatgcataag cttttgccat
      601 tctcaccgga ttcagtcgtc actcatggtg atttctcact tgataatctt atttttgacg
      661 aggggaaatt aataggttgt attgatgttg gacgagtcgg aatcgcagac cgataccagg
      721 atcttgccat tctatggaac tgcctcggtg aattttctcc ttcattacag aaacggcttt
      781 ttcaaaaata tggtattgat aatcctgata tgaataaatt gcagtttcat ttgatgctcg
      841 atgagttttt ctgatagtta gtctttaatg aatgcggttg gcgcatcggc gggcaccttg
      901 cgcgcgctgt cgctgttcat gccgcgcagc atgtcgatgg catcgagcac acccttggcg
      961 gcgggcgcag cccgcaattt gagcacgccc aggaactgcg gcgcgtagcg gcgtagcgtg
     1021 gcatagcttt caccgatgtg gtgcaggaaa tcaaagtcgg caggccgcgc caatgtttgc
     1081 gcttcggtga cgctggcggc gaaggtgtcc cagggcataa cggcctcgag gattgccccc
     1141 cagcctccat cgataccgtg ccaaatgcac gtaaaaaacg ggagcgtttc tggtgtcgga
     1201 atgtaaccaa gggggtcaga ggcgcgctaa aacgctctca ggggagtcaa atagagacgt
     1261 ttgtaacaaa aagatcaaag gatcctcttg agatcctttt tttctgcgcg taatctgctg
     1321 cctgtaaacg aaaaaaccgc cttgcagggc ggtttgatcg aaggttaagt cagcttgcag
     1381 actgcttaac caggtaactg tcttatgcga gacgagtcac caaaattgtt cttctagtgt
     1441 agccgcactc cggcagccac ttcaagtact ctctaaatat ctcgcacatg acttttacca
     1501 atggctgctg ccagtggcgc tttgtggtgt cttttccggg ttggacccaa gagaacagtt
     1561 accggagaag gcgcagcagt cgggctgaac ggggggttcc tgcatacagc ccagcccgga
     1621 gcgaactgcc taagtcgccc cgagatacca gaagacgtga gctatgagaa agcgccacgt
     1681 gtcccgtaag ggagaaaggc ggaaaaggta tccggtaatc gatatggcgg gaacgtgggg
     1741 gcgcaggagg gagcgattca ccggaaacgg tgatgatctt taagccacgt cgggtttcgc
     1801 caccgctggc ggatttcatg gttgagccgc aaggctccca cagatgcacc gaaaaagtgt
     1861 ctgttttgtg aagtccgtca ggggggcgga gcctatggaa aaagcgcctc cggcgcggcc
     1921 tttcccgggg tttcgttttt tgcgcacatg ttctttcctg gtttatcccc gggttctgtg
     1981 gataacaggg ttagcgtttt tgagaaagga gagtccgctc gccgcagccg aacgaccgag
     2041 cgtagcgagt cagtgagcga ggaagcggaa gagcgcctga actggcattt tctccttacg
     2101 catctgtgcg gcatttcaca ccggacatgg cgcacttttc atacaatccg cactgatgcc
     2161 gaatggttaa gccagtatac actccgctat cgctacgtga ctgggtcagg gcttcgcccc
     2221 gacaccccaa aggtcaacgg cctgacgcgc cctggcgggc ttgtctgctc ccggcatccg
     2281 ctcacagaca agctgtgacc gtctccggga gctgcatgtg tcagcggttt tcaccgtcat
     2341 ccccgaagcg tgcgaggcaa ctgcggtaaa gctcatcggc gtggtcgtga agcgattcac
     2401 agatgtctgc ctgttcatcc gcgtccagtt cgttgagctt ctccagcagc gttaatgtct
     2461 ggcctctgat gaagcgggcc atgttaaggg cggttttttc ctgtttggtc actgatgcct
     2521 ccgtgtaagg gggggttctg ttcatggggg taatgatacc gatgaaacgc gagaggatgc
     2581 tcacgatacg ggttactgat gatgaacatg cccggttact ggaacgctgt gagggtaaac
     2641 aactggcggt atggatgcgg cgggtctgcc tgggtgagcc ggttgcccgt tccgggaagc
     2701 tgccgacact ggcaccgccg ttactgcgtc agctggccgc catcgggaat aaccttaacc
     2761 agacagcgag gaaggtgaac agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg
     2821 ccgcactgat ggccatcggg gatgagctgc gccggctgcg tctggcggtc agggaacagg
     2881 gggcgcggga tgatagttaa gtttcatgcc aggggaaaag gtggtggcag tggtccggtt
     2941 gattacctgc tgggaaggga gcgtaaccgg gaaggggcaa cggtgcttca ggggaatccg
     3001 gaagaggtcc gggaactcat cgatgccacg ccatttgcga agaaatacac gtcaggtgtt
     3061 ctgtcgttcg cggagaagga gctgccgcct ggagggcgtg aaaaagtgat ggcgagcttt
     3121 gagcgtgtac tgatgcccgg tctcgagaaa aatcagtaca gcatcctgtg ggtggagcac
     3181 caggacaagg gacggcttga gctgaatttt gtcattccga acatggagct acagaccgga
     3241 aaacgcctcc agccgtacta cgaccgggca gacaggccga gaattgatgc ctggcagacg
     3301 ctggtgaatc accattacgg tctgcatgac cccaacgccc cggagaaccg ccggacgctg
     3361 acccttcctg ataacctgcc ggaaacgaaa caggcgcttg ctgagggcgt cacacgcggg
     3421 atagacgcgc tttaccatgc cggagagata aaaggccgtc aggatgtgat tcaggcgctc
     3481 acagaggcgg ggcttgaagt ggtcagggtg acgcgaagca gtatcagcat tgcagacccg
     3541 aacggcggga ggaatatcag actgaaagga gcgttttatg agcaatcttt tacagacggg
     3601 cgcggagttc gagaaaaagc tgaaagagag agccgaatct acagagaaaa tgctgaacga
     3661 cgagttcagg aagctcgaag aatctgtaaa cagggaactg acctcaaacg aatctttaat
     3721 caggaacgct atcaacgacc atacaacagc cctgaaagaa ctgctggaga ggtatcagaa
     3781 aacgaccgtc gatacgatgg acgtgcactg gaaaaccgta ctgaaaatga gcgtgaaacg
     3841 ctggctgtgg ctgattatcg tctcagtact gatgtttgcc acgaccggga gtctgctgtg
     3901 gtaccagggc atgaagataa acgcgaatat gaatattctc cgcgagcaga aagagagtct
     3961 ggagaagctg aacgcgaaga catggggcgt gcgttatcac gaggacagca acggacgttt
     4021 tctggtgttg ccgaagggga tgaaagccga aacgaactgg acgaaggaca acggcaaact
     4081 gaacgcagtg agactggtgc aggagtgaca gagcatgacg gagctggaaa gacatttgct
     4141 gaacgcatta gagcaactgc aacaggacta tatgcagcgg ctgaacgaat gggagaacgc
     4201 cttcgtggaa ttgcagaaaa tgttttcgct tacgcaacgg gacaacgcga tgctgaacgg
     4261 gcgagtcatg cagttgagtc agcaggtgca gcacttgagc gagcggacag aacgcttgag
     4321 ccagttatac agcgagaaca ggagataagg gatgaacggc tgatgcagga acgcgaacat
     4381 gagttatctc tggagcggga gcgtcagccg gaaatccagg agcggacact ggatggccct
     4441 tcgctgggat ggtgaaacca tgaaaaatga cgtgttcagt ggattaaggc gggctaatgt
     4501 ggcctgtagc atctggttgc ataggtattc atgcggttaa aatttatcag gtgcgatcgc
     4561 ggcagttttt cgggtggttt gttgccattt ttacctgtct gctgccgtga tcgcaccgaa
     4621 cgcgttttgg cggtgcgtac aatgcgacgt tatggtaaat ggagcggatt ttcaggaagg
     4681 agtgatacta acaactcgaa cactgtgcaa ataatgattt ttttaaaata tcggtaacga
     4741 taataaatta tttcgtttta cgccggtaat aaatataatg tagtttcagt atataaaaaa
     4801 atatatgagg tgtcttgtgg gagctttcat gaatcttcaa caacgtataa ataaactacc
     4861 acaattatca tccagttttt catttggaaa agatattgat aatattcatt catttatctt
     4921 taacgaaact tctaaagata aaattgaaga tttactaaga aaatgggtgt caggcaatca
     4981 gccctgtgta tttggtaaat tggcaagcaa gaaaattaaa gggcttgatt tccatttatc
     5041 tattgtaaat agcccccaac tatataatga tgatggtcat ttgtttgatt ttttgcgtaa
     5101 tgaaagagtt catgccatgt tcctcgacta cgaagcggcc aaagattatg cgacccgctc
     5161 caggctggtc acggcggcga atatcccttc tttcggagcg ccagaatgat gttggtctgg
     5221 ccggattttc atatggcggg aaccacgttg tgtctcaaaa tctctgatgt tacattgcac
     5281 aagataaaaa tatatcatca tgaacaataa
//
