LOCUS       NZ_CP149296             5055 bp    DNA     circular CON 05-APR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            Z1323SSL0058 plasmid pZ1323SSL0058-3, complete sequence.
ACCESSION   NZ_CP149296
VERSION     NZ_CP149296.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40439974
            Assembly: GCF_037854785.1
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 5055)
  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  JOURNAL   Unpublished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 5055)
  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                   :: 113X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037854785.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 21:18:05
            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)                     :: 4,920
            CDSs (total)                      :: 4,797
            Genes (coding)                    :: 4,682
            CDSs (with protein)               :: 4,682
            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)              :: 115
            CDSs (without protein)            :: 115
            Pseudo Genes (ambiguous residues) :: 0 of 115
            Pseudo Genes (frameshifted)       :: 36 of 115
            Pseudo Genes (incomplete)         :: 85 of 115
            Pseudo Genes (internal stop)      :: 21 of 115
            Pseudo Genes (multiple problems)  :: 25 of 115
            Pseudo Genes (short protein)      :: 1 of 115
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP149296.1.
            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..5055
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="Z1323SSL0058"
                     /serovar="Typhimurium"
                     /host="Pig"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pZ1323SSL0058-3"
                     /geo_loc_name="South Korea"
                     /collection_date="2023-04-06"
     gene            complement(410..601)
                     /locus_tag="WI421_RS24530"
                     /old_locus_tag="WI421_24530"
     CDS             complement(410..601)
                     /locus_tag="WI421_RS24530"
                     /old_locus_tag="WI421_24530"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            666..989
                     /locus_tag="WI421_RS24535"
                     /old_locus_tag="WI421_24535"
     CDS             666..989
                     /locus_tag="WI421_RS24535"
                     /old_locus_tag="WI421_24535"
                     /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            1198..>1629
                     /locus_tag="WI421_RS24540"
                     /old_locus_tag="WI421_24540"
                     /pseudo=""
     CDS             1198..>1629
                     /locus_tag="WI421_RS24540"
                     /old_locus_tag="WI421_24540"
                     /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            1667..2185
                     /locus_tag="WI421_RS24545"
                     /old_locus_tag="WI421_24545"
     CDS             1667..2185
                     /locus_tag="WI421_RS24545"
                     /old_locus_tag="WI421_24545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_061672795.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            2192..2425
                     /locus_tag="WI421_RS24550"
                     /old_locus_tag="WI421_24550"
     CDS             2192..2425
                     /locus_tag="WI421_RS24550"
                     /old_locus_tag="WI421_24550"
                     /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_061672798.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2783..2968
                     /locus_tag="WI421_RS24555"
                     /old_locus_tag="WI421_24555"
     CDS             2783..2968
                     /locus_tag="WI421_RS24555"
                     /old_locus_tag="WI421_24555"
                     /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_074518866.1"
                     /translation="MTEDNVKNISDYRKNNDAVDANSSAISGKSAPAKLSEKLRNTVPS
                     GLRAQMRQQMRNKHGF"
                     /name="hypothetical protein"
     gene            2958..3212
                     /locus_tag="WI421_RS24560"
                     /old_locus_tag="WI421_24560"
     CDS             2958..3212
                     /locus_tag="WI421_RS24560"
                     /old_locus_tag="WI421_24560"
                     /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_023259653.1"
                     /translation="MDSNNSQKNLQDKHADLLDKTYTLGWLDGYSEGYDDAIEDCQNAL
                     NKLENENELLNEIIENKDNVISEMASSVGRALQTVKKNK"
                     /name="hypothetical protein"
     gene            complement(3242..4300)
                     /locus_tag="WI421_RS24565"
                     /old_locus_tag="WI421_24565"
     CDS             complement(3242..4300)
                     /locus_tag="WI421_RS24565"
                     /old_locus_tag="WI421_24565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012508929.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_023259654.1"
                     /translation="MAIYAVWNNKGGVGKSYLTFQLASEYARQNPTKKVLVIDLCPQAN
                     SSSMLLGGMVNGENTLNQIHSATQRKTISGYIEDRIRSPYIPTNTGSNYVINVSTYNSR
                     IPDNLYLVTGDEQLELQASRVVGASFPGPHDAWRTVHLWINDLISDICNSWDNGDSCVF
                     IDCNPSFSIYTELALTAAERLLIPFSADGSSKRAVKAVLSLVYGERRHLNEPQSDFYLN
                     SNRYSMSLPQIYMYIGNRLTQMNNSSASAFKTVVTEIGDEIWKVWQTKPSLFCIHPNGS
                     STPNNKKSFRNMFQYEVNDANTASVVSGALGIPIATLTAGNKNVAGRTIKVNQTQLDKQ
                     VPNIVALAGMIE"
                     /name="ParA family protein"
     gene            complement(4665..4796)
                     /locus_tag="WI421_RS24570"
                     /old_locus_tag="WI421_24570"
     CDS             complement(4665..4796)
                     /locus_tag="WI421_RS24570"
                     /old_locus_tag="WI421_24570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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_071787289.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLSAATGKGCTRYY"
                     /name="replication initiation protein"
     Typing          240..325
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          complement(6..225)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.189"
                     /coverage="99.0"
                     /evalue="2.62e-71"
     Typing          complement(4668..5055)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.154"
                     /coverage="90.0"
                     /evalue="7.969999999999999e-180"
     Typing          980..2529
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.511"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aacagcgcag ccttttccgg gttctcgttt tttgctcaca tgtttctttt ggcgttatcc
       61 cctgattctg tggataaccg catctccgct tttgagtgag ccgacaccgc tcgccgcagc
      121 cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg aagagcgccg gaacgtgcat
      181 tttctcctta cgcatctgtg cggcatttca caccgcatat ggcgctcttt tcttacaatc
      241 tgcactgatg ccgcatggtt aagccagtat acactccgct atcgctacgt gactgggtca
      301 tggctgcgcc ccgacacccg ctaaaacctg ctgacgcgcc ctgacgggct tgtctgctcc
      361 cggcatccgc tcacagacaa gctgtgaccg tctccgggag ctgcatgtgt cagaggtttt
      421 caccgtcatc cccgaaacgt gcgaggcagc tgcggtaaag ctcatcggcg tggtcgtgaa
      481 gcgattcaca gatgtctgcc tgttcatctg cgtccagttc gttgagcttc tccagcagcg
      541 ttaatgtctg gcttctgata aagcgggcca tgttaagggc ggttttttcc tgtttagtca
      601 ctgatgcctc cgtgtaaggg ggtatttctg ttcatggggt aatgataccg atgaaacgcg
      661 agaggatgct cacgatacgg gttactgatg atgaacatgc caggttactt gaacgctgtg
      721 agggtaaaca actggcagta tggatgcggc gggtctgcct gggtgagccg gttgcccgtt
      781 ccgggaagct gccgacactg gcaccgccgt tactgcgtca gctggccgcc atcgggaata
      841 acctgaatca gacagcgagg aaggtgaaca gcgggcagtg gtcttccggt gaccgggttc
      901 aggtggtggc cgcactgatg gccatcgggg atgagctgcg ccggctgcgt ctggccgtca
      961 gggaacaggg ggcgcgggat gatagttaaa tttcatgcca ggggaaaagg tggtggcagt
     1021 ggtccggttg attacctgct ggggagggag cgtaaccgcg aaggcgcaac ggtgcttcag
     1081 ggtaatccgg aagaagtccg ggaactcatc gatgccacgc catttgcgaa gaaatacacg
     1141 tccggtgttc tgtcgttcgc ggagaaggag ctgccgccgg gaggacgtga aaaagtgatg
     1201 gcgagctttg agcgtgtact gatgcccggt ctcgaaaaaa atcagtacag catcctgtgg
     1261 gtggagcacc aggacaaggg acggcttgag ctgaattttg tcattccgaa catggagcta
     1321 cagaccggaa aacgcctcca gccgtactac gaccgcgcag acaggcctag aattgatgcc
     1381 tggcagacgc tggttaatca ccattacggg ctgcatgacc cgaacgcccc ggagaaccgc
     1441 aggacgctga cactctctga taatctgccg gaaacgaaac aggcgattgc tgagggcgtt
     1501 acacgcggga tagacgcgct ttaccatgcc ggagagataa aaggccgtca ggatgtgatt
     1561 caggcgctca cagaggcggg gcttgaagtg gtcagggtga cgcgaagcag tatcagcatt
     1621 gcagacccga acggcgggag gaatatcaga ctgaaaggag cgttttatga gcaatctttt
     1681 acagacgggc gcggagttcg agaaaaagct gaaagagaga gccgaatcta cagagaaaat
     1741 gctgaacaac gagttcagga agctcggcga gtctgtcagc gaggctgtga cctcaaacga
     1801 gacgaaaatc agagacgcta tagccctgtt cacagcctcg acagagaaat cgctggaaaa
     1861 acaccgggaa ggggtgaaag aggcgatgat gcagcacagg aaggacgtgt taaagctggc
     1921 agggaatacg ggcatgatgt tactggggat agtctttctc ctgtttaccg cgagtggcgg
     1981 gacgctctgg tatcttggcg ggcggataca ggcgaacctg gaagaaatca ggatacagga
     2041 agaaacattg cagaaactga acgcgaagac atggggcgtg gagtttgtgc aggacgggag
     2101 aaggaaattt ctggtccttc cgtacgggaa atcggcaacg gtgattccct atcaggggaa
     2161 ggactgggta caactgacgg agtgacacag agtgacggag ctggaaagac atttgctgaa
     2221 cgcattagag caactgcaac aggactatat gcagcggctg agcgaatggg agagcgcctt
     2281 cgtggaattg cagaagatgt tttcgcttac gcaacgggac aacgcgatgc tgaacgagcg
     2341 ggtcatgcag ttgagtcagc aggtgcagca cttgagcgag cagacagaac gcttgagcca
     2401 gttatacagc gagaactgga gataagagag gaacggctga tacaggagcg cgaacatgcg
     2461 ttatccctgg aacgggagcg tcagcctgaa atacaggaac gcacgctgga tggtccttcg
     2521 ctgggatggt gaaaccatga aaaatggcag cttcagtgga ttaagagggg ttaatgtggc
     2581 ctgtaccatc tggttgcata ggtattcatg cggttaaaat ttatcaggcg cgatcgcggc
     2641 agtttttcgg gtggtttgtt gccattttta cctgtctgct gccgtgatcg cgctgaacgc
     2701 gttttagcgg tgcgcgtaag gggtgttatg ttcaattctc cagcgtatat tgggctgttt
     2761 acagcaatag gtgtaatgtt ctatgactga agataacgtt aagaatatta gcgactacag
     2821 aaagaataat gatgctgttg atgctaatag tagtgctatt tcaggtaaaa gcgctccagc
     2881 taagctgagt gagaaactta gaaatacagt tccttctgga ctgagggccc aaatgcgcca
     2941 acaaatgagg aataaacatg gattctaata acagtcagaa aaaccttcaa gataagcatg
     3001 ctgatcttct ggataaaact tatactctcg gctggttgga tgggtattca gaagggtatg
     3061 atgatgccat tgaagattgt caaaatgcct tgaataaact ggaaaatgaa aacgaattgc
     3121 tcaatgaaat tattgaaaac aaagataatg taatcagtga aatggcatct agtgtgggca
     3181 gggcgttgca aacggtaaag aaaaataaat aaaaacaggc ccttgaaaaa gggcctgttt
     3241 tttactcaat cataccggca agagcgacaa tgttgggcac ttgcttatca agctgtgtct
     3301 gatttacctt tattgttctt cccgcaacat tcttatttcc tgcggttagt gtggcaattg
     3361 gaataccaag tgctcctgat acgacagatg ctgtattggc atcatttact tcatactgga
     3421 acatgttcct aaaggatttt ttattattcg gcgttgagct tccatttgga tgaatgcaga
     3481 ataaacttgg ttttgtttgc cacactttcc aaatctcatc gccgatctct gttaccacag
     3541 ttttgaatgc gctagctgat gagttgttca tttgagttaa tctgtttcca atatacatgt
     3601 atatttgtgg taatgacata gaataacgat tgctgtttaa atagaaatct gactgtggtt
     3661 cgttcagatg acgtcgctcg ccataaacta aagaaagaac tgctttaaca gctctttttg
     3721 atgaaccatc agcagagaat ggaattaata ggcgttcagc tgcggttaat gctaactcgg
     3781 tataaataga gaagctggga ttgcagtcga tgaaaacgca gctgtcgcca ttatcccatg
     3841 agttacaaat gtcactaatt agatcgttaa tccaaagatg aacagttctc catgcgtcat
     3901 gaggtccagg gaatgatgct ccaacaactc ttgatgcttg aagttctaat tgctcatcgc
     3961 cagtaacaag atatagatta tctgggattc tgctattgta tgtagatacg ttgattacgt
     4021 agttagaacc tgtatttgtc ggaatatatg gacttctaat cctatcctca atatatccag
     4081 aaatagtctt tctttgtgtt gcagaatgaa tctgatttag cgtattttcg ccattaacca
     4141 tcccgccaag taacattgag gatgagttag cttgtgggca tagatcaatc accagaacct
     4201 tttttgtcgg gttctgtctg gcgtactcag aggctagttg aaaggtaaga taacttttcc
     4261 ccactccgcc tttgttattc catacggcat agatcgccat ctatcactcc taatatagtt
     4321 ttgttgttag ctttaagtca gagtactaga gattattgtt ctactgttag tttctttcag
     4381 ctaactgact gtgtttcgag cggtatggtt agatgagggt gtccgtattg gcatgacctc
     4441 ttcagcatag taggaacgtg attgaaagga tttcttgaga tccttattcg tgggatgtaa
     4501 tcttctgcac tgtaaacgaa aaaaccacct ggggaggtgg tttttcgaag gatcagtaag
     4561 ttggggaact tctgaaccgt ggtaacaggg tgtacaagac cactgccacc aaatctgtcc
     4621 tttcagttta gctgtagtta ggcttcaact tcaagaactc tgcgttagta atatcttgta
     4681 catcccttac cagtggctgc tgacagtggc gttaagtcgt gtcttaccgg gttggactca
     4741 agacgatagt taccggataa ggcgcagcgg tcgggctgaa cggggggttc gtgcacacag
     4801 cccagcttgg agcgaacgac ctacaccgaa ctgagatacc aacagcgtga gctatgagaa
     4861 agcgccacgc ttcccgaagg gagaaaggcg gacaggtatc cggtaagcgg cagggtcgga
     4921 acaggagagc gcacgaggga gcttccaggg ggaaacgcct ggtatcttta tagtcctgtc
     4981 gggtttcgcc acctctgact tgagcgtcga tttttgtgat gctcgtcagg ggggcggagc
     5041 ctatggaaaa acgcc
//
