LOCUS       NZ_CP149342             5310 bp    DNA     circular CON 05-APR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            Z1323SSL0002 plasmid pZ1323SSL0002-4, complete sequence.
ACCESSION   NZ_CP149342
VERSION     NZ_CP149342.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40439959
            Assembly: GCF_037864505.1
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  JOURNAL   Unpublished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                   :: 105X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037864505.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 21:12:48
            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)                     :: 5,013
            CDSs (total)                      :: 4,889
            Genes (coding)                    :: 4,760
            CDSs (with protein)               :: 4,760
            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)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 47 of 129
            Pseudo Genes (incomplete)         :: 91 of 129
            Pseudo Genes (internal stop)      :: 22 of 129
            Pseudo Genes (multiple problems)  :: 28 of 129
            Pseudo Genes (short protein)      :: 1 of 129
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP149342.1.
            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="Z1323SSL0002"
                     /serovar="Typhimurium"
                     /host="Pig"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pZ1323SSL0002-4"
                     /geo_loc_name="South Korea"
                     /collection_date="2023-03-10"
     gene            complement(<45..>140)
                     /locus_tag="WI444_RS25025"
                     /old_locus_tag="WI444_25025"
                     /pseudo=""
     CDS             complement(<45..>140)
                     /locus_tag="WI444_RS25025"
                     /old_locus_tag="WI444_25025"
                     /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"
     gene            complement(900..1133)
                     /locus_tag="WI444_RS25030"
                     /old_locus_tag="WI444_25030"
     CDS             complement(900..1133)
                     /locus_tag="WI444_RS25030"
                     /old_locus_tag="WI444_25030"
                     /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            complement(1140..1670)
                     /locus_tag="WI444_RS25035"
                     /old_locus_tag="WI444_25035"
     CDS             complement(1140..1670)
                     /locus_tag="WI444_RS25035"
                     /old_locus_tag="WI444_25035"
                     /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            complement(<1708..2406)
                     /locus_tag="WI444_RS25040"
                     /old_locus_tag="WI444_25040"
                     /pseudo=""
     CDS             complement(<1708..2406)
                     /locus_tag="WI444_RS25040"
                     /old_locus_tag="WI444_25040"
                     /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            complement(2348..2671)
                     /locus_tag="WI444_RS25045"
                     /old_locus_tag="WI444_25045"
     CDS             complement(2348..2671)
                     /locus_tag="WI444_RS25045"
                     /old_locus_tag="WI444_25045"
                     /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            2736..2927
                     /locus_tag="WI444_RS25050"
                     /old_locus_tag="WI444_25050"
     CDS             2736..2927
                     /locus_tag="WI444_RS25050"
                     /old_locus_tag="WI444_25050"
                     /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            complement(2950..3270)
                     /locus_tag="WI444_RS25055"
                     /old_locus_tag="WI444_25055"
     CDS             complement(2950..3270)
                     /locus_tag="WI444_RS25055"
                     /old_locus_tag="WI444_25055"
                     /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            <4112..>4384
                     /locus_tag="WI444_RS25060"
                     /old_locus_tag="WI444_25060"
                     /pseudo=""
     CDS             <4112..>4384
                     /locus_tag="WI444_RS25060"
                     /old_locus_tag="WI444_25060"
                     /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            complement(4394..5209)
                     /locus_tag="WI444_RS25065"
                     /old_locus_tag="WI444_25065"
     CDS             complement(4394..5209)
                     /locus_tag="WI444_RS25065"
                     /old_locus_tag="WI444_25065"
                     /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"
     ARG             complement(4398..5209)
                     /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"
     Typing          complement(3022..3103)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(3560..3747)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(797..2358)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgtggttccc gccatatgaa aatccggcca gaccaacatc attctggcgc tccgaaagaa
       61 gggatattcg ccgccgtgac cagcctggag cgggtcgcat aatctttggc cgcttcgtag
      121 tcgaggaaca tggcatgaac tctttcatta cgcaaaaaat caaacaaatg accatcatca
      181 ttatatagtt gggggctatt tacaatagat aaatggaaat caagcccttt aattttcttg
      241 cttgccaatt taccaaatac acagggctga ttgcctgaca cccattttct tagtaaatct
      301 tcaattttat ctttagaagt ttcgttaaag ataaatgaat gaatattatc aatatctttt
      361 ccaaatgaaa aactggatga taattgtggt agtttattta tacgttgttg aagattcatg
      421 aaagctccca caagacacct catatatttt tttatatact gaaactacat tatatttatt
      481 accggcgtaa aacgaaataa tttattatcg ttaccgatat tttaaaaaaa tcattatttg
      541 cacagtgttc gagttgttag tatcactcct tcctgaaaat ccgctccatt taccataacg
      601 tcgcattgta cgcaccgcca aaacgcgttc ggtgcgatca cggcagcaga caggtaaaaa
      661 tggcaacaaa ccacccgaaa aactgccgcg atcgcacctg ataaatttta accgcatgaa
      721 tacctatgca accagatgct acaggccaca ttagcccgcc ttaatccact gaacacgtca
      781 tttttcatgg tttcaccatc ccagcgaagg gccatccagt gtccgctcct ggatttccgg
      841 ctgacgctcc cgctccagag ataactcatg ttcgcgttcc tgcatcagcc gttcatccct
      901 tatctcctgt tctcgctgta taactggctc aagcgttctg tccgctcgct caagtgctgc
      961 acctgctgac tcaactgcat gactcgcccg ttcagcatcg cgttgtcccg ttgcgtaagc
     1021 gaaaacattt tctgcaattc cacgaaggcg ttctcccatt cgttcagccg ctgcatatag
     1081 tcctgttgca gttgctctaa tgcgttcagc aaatgtcttt ccagctccgt catgctctgt
     1141 cactcctgca ccagtctcac tgcgttcagt ttgccgttgt ccttcgtcca gttcgtttcg
     1201 gctttcatcc ccttcggcaa caccagaaaa cgtccgttgc tgtcctcgtg ataacgcacg
     1261 ccccatgtct tcgcgttcag cttctccaga ctctctttct gctcgcggag aatattcata
     1321 ttcgcgttta tcttcatgcc ctggtaccac agcagactcc cggtcgtggc aaacatcagt
     1381 actgagacga taatcagcca cagccagcgt ttcacgctca ttttcagtac ggttttccag
     1441 tgcacgtcca tcgtatcgac ggtcgttttc tgatacctct ccagcagttc tttcagggct
     1501 gttgtatggt cgttgatagc gttcctgatt aaagattcgt ttgaggtcag ttccctgttt
     1561 acagattctt cgagcttcct gaactcgtcg ttcagcattt tctctgtaga ttcggctctc
     1621 tctttcagct ttttctcgaa ctccgcgccc gtctgtaaaa gattgctcat aaaacgctcc
     1681 tttcagtctg atattcctcc cgccgttcgg gtctgcaatg ctgatactgc ttcgcgtcac
     1741 cctgaccact tcaagccccg cctctgtgag cgcctgaatc acatcctgac ggccttttat
     1801 ctctccggca tggtaaagcg cgtctatccc gcgtgtgacg ccctcagcaa gcgcctgttt
     1861 cgtttccggc aggttatcag gaagggtcag cgtccggcgg ttctccgggg cgttggggtc
     1921 atgcagaccg taatggtgat tcaccagcgt ctgccaggca tcaattctcg gcctgtctgc
     1981 ccggtcgtag tacggctgga ggcgttttcc ggtctgtagc tccatgttcg gaatgacaaa
     2041 attcagctca agccgtccct tgtcctggtg ctccacccac aggatgctgt actgattttt
     2101 ctcgagaccg ggcatcagta cacgctcaaa gctcgccatc actttttcac gccctccagg
     2161 cggcagctcc ttctccgcga acgacagaac acctgacgtg tatttcttcg caaatggcgt
     2221 ggcatcgatg agttcccgga cctcttccgg attcccctga agcaccgttg ccccttcccg
     2281 gttacgctcc cttcccagca ggtaatcaac cggaccactg ccaccacctt ttcccctggc
     2341 atgaaactta actatcatcc cgcgccccct gttccctgac cgccagacgc agccggcgca
     2401 gctcatcccc gatggccatc agtgcggcca ccacctgaac ccggtcaccg gaagaccact
     2461 gcccgctgtt caccttcctc gctgtctggt taaggttatt cccgatggcg gccagctgac
     2521 gcagtaacgg cggtgccagt gtcggcagct tcccggaacg ggcaaccggc tcacccaggc
     2581 agacccgccg catccatacc gccagttgtt taccctcaca gcgttccagt aaccgggcat
     2641 gttcatcatc agtaacccgt atcgtgagca tcctctcgcg tttcatcggt atcattaccc
     2701 ccatgaacag aaccccccct tacacggagg catcagtgac caaacaggaa aaaaccgccc
     2761 ttaacatggc ccgcttcatc agaggccaga cattaacgct gctggagaag ctcaacgaac
     2821 tggacgcgga tgaacaggca gacatctgtg aatcgcttca cgaccacgcc gatgagcttt
     2881 accgcagttg cctcgcacgc ttcggggatg acggtgaaaa ccgctgacac atgcagctcc
     2941 cggagacggt cacagcttgt ctgtgagcgg atgccgggag cagacaagcc cgccagggcg
     3001 cgtcaggccg ttgacctttg gggtgtcggg gcgaagccct gacccagtca cgtagcgata
     3061 gcggagtgta tactggctta accattcggc atcagtgcgg attgtatgaa aagtgcgcca
     3121 tgtccggtgt gaaatgccgc acagatgcgt aaggagaaaa tgccagttca ggcgctcttc
     3181 cgcttcctcg ctcactgact cgctacgctc ggtcgttcgg ctgcggcgag cggactctcc
     3241 tttctcaaaa acgctaaccc tgttatccac agaacccggg gataaaccag gaaagaacat
     3301 gtgcgcaaaa aacgaaaccc cgggaaaggc cgcgccggag gcgctttttc cataggctcc
     3361 gcccccctga cggacttcac aaaacagaca ctttttcggt gcatctgtgg gagccttgcg
     3421 gctcaaccat gaaatccgcc agcggtggcg aaacccgacg tggcttaaag atcatcaccg
     3481 tttccggtga atcgctccct cctgcgcccc cacgttcccg ccatatcgat taccggatac
     3541 cttttccgcc tttctccctt acgggacacg tggcgctttc tcatagctca cgtcttctgg
     3601 tatctcgggg cgacttaggc agttcgctcc gggctgggct gtatgcagga accccccgtt
     3661 cagcccgact gctgcgcctt ctccggtaac tgttctcttg ggtccaaccc ggaaaagaca
     3721 ccacaaagcg ccactggcag cagccattgg taaaagtcat gtgcgagata tttagagagt
     3781 acttgaagtg gctgccggag tgcggctaca ctagaagaac aattttggtg actcgtctcg
     3841 cataagacag ttacctggtt aagcagtctg caagctgact taaccttcga tcaaaccgcc
     3901 ctgcaaggcg gttttttcgt ttacaggcag cagattacgc gcagaaaaaa aggatctcaa
     3961 gaggatcctt tgatcttttt gttacaaacg tctctatttg actcccctga gagcgtttta
     4021 gcgcgcctct gacccccttg gttacattcc gacaccagaa acgctcccgt tttttacgtg
     4081 catttggcac ggtatcgatg gaggctgggg ggcaatcctc gaggccgtta tgccctggga
     4141 caccttcgcc gccagcgtca ccgaagcgca aacattggcg cggcctgccg actttgattt
     4201 cctgcaccac atcggtgaaa gctatgccac gctacgccgc tacgcgccgc agttcctggg
     4261 cgtgctcaaa ttgcgggctg cgcccgccgc caagggtgtg ctcgatgcca tcgacatgct
     4321 gcgcggcatg aacagcgaca gcgcgcgcaa ggtgcccgcc gatgcgccaa ccgcattcat
     4381 taaagactaa ctatcagaaa aactcatcga gcatcaaatg aaactgcaat ttattcatat
     4441 caggattatc aataccatat ttttgaaaaa gccgtttctg taatgaagga gaaaattcac
     4501 cgaggcagtt ccatagaatg gcaagatcct ggtatcggtc tgcgattccg actcgtccaa
     4561 catcaataca acctattaat ttcccctcgt caaaaataag attatcaagt gagaaatcac
     4621 catgagtgac gactgaatcc ggtgagaatg gcaaaagctt atgcatttct ttccagactt
     4681 gttcaacagg ccagccatta cgctcatcat caaaatcact cgcatcaacc aaaccgttat
     4741 tcattcgtga ttgcgcctga gcgagacgaa atacgcgatc gctgttaaaa ggacaattac
     4801 aaacaggaat cgaatgcaac cggcgcagga acgctgccag cgcatcaaca atattttcac
     4861 ctgaatcagg atattcttct aatacctgga atgctgtttt cccggggatc gcagtggtga
     4921 gtaaccatgc atcatcagga gtacggataa aatgcttgat ggtcggaaga ggcataaatt
     4981 ccgtcagcca gtttagtctg accatctcat ctgtaacatc attggcaacg ctacctttgc
     5041 catgtttcag aaacaactct ggcgcatcgg gcttcccata caatcgatag attgtcgcac
     5101 ctgattgccc gacattatcg cgagcccatt tatacccata taaatcagca tccaggttgg
     5161 aatttaatcg ctgcctcgag caagacgttt cccgttgaat atggctcata acaccccttg
     5221 tattactgtt tatgtaagca gacagtttta ttgttcatga tgatatattt ttatcttgtg
     5281 caatgtaaca tcagagattt tgagacacaa
//
