LOCUS       NZ_CP063299             3257 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            R17.1451 plasmid pR17.1451_p3.2k, complete sequence.
ACCESSION   NZ_CP063299
VERSION     NZ_CP063299.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16450741
            Assembly: GCF_015074905.1
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 3257)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W. and Chen,Y.-S.
  TITLE     Salmonella enterica subsp. enterica serovar Typhimurium strain
            R17.1451
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3257)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W. and Chen,Y.-S.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2020) Center for Diagnostics and Vaccine
            Development, Centers for Disease Control, Taiwan, No.20, Wenxin S.
            3rd Rd., Nantun Dist., Taichung City 408, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 16-OCT-2020
            Assembly Method                   :: Unicycler v. v0.4.6
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 11:51:36
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,024
            CDSs (total)                      :: 4,900
            Genes (coding)                    :: 4,776
            CDSs (with protein)               :: 4,776
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 40 of 124
            Pseudo Genes (incomplete)         :: 93 of 124
            Pseudo Genes (internal stop)      :: 22 of 124
            Pseudo Genes (multiple problems)  :: 28 of 124
            Pseudo Genes (short protein)      :: 1 of 124
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063299.1.
            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..3257
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="R17.1451"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pR17.1451_p3.2k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="Centers of Disease Control, Taiwan"
                     /subtype="ST19"
     gene            complement(531..725)
                     /locus_tag="IN819_RS24935"
                     /old_locus_tag="IN819_24970"
     CDS             complement(531..725)
                     /locus_tag="IN819_RS24935"
                     /old_locus_tag="IN819_24970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1869..2150)
                     /locus_tag="IN819_RS24940"
                     /old_locus_tag="IN819_24975"
     CDS             complement(1869..2150)
                     /locus_tag="IN819_RS24940"
                     /old_locus_tag="IN819_24975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000586174.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            2495..2791
                     /locus_tag="IN819_RS24945"
                     /old_locus_tag="IN819_24980"
     CDS             2495..2791
                     /locus_tag="IN819_RS24945"
                     /old_locus_tag="IN819_24980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_000609270.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antitoxin"
     gene            complement(3022..3134)
                     /locus_tag="IN819_RS25330"
                     /pseudo=""
     CDS             complement(3022..3134)
                     /locus_tag="IN819_RS25330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          376..458
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          762..860
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          985..1240
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.124"
                     /coverage="89.0"
                     /evalue="5.65e-115"
     Typing          complement(2..175)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.455"
                     /coverage="100.0"
                     /evalue="1.46e-72"
     Typing          complement(3063..3257)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.959"
                     /coverage="99.0"
                     /evalue="9.07e-91"
ORIGIN
        1 aacaggagag cgcacgaggg agccaccagg gggaaacgtc tggtatcttt aagtcctgtc
       61 gggtttcgcc acctctgact tgagcgtcga tttctgtgat gctcgtcagg ggggcggagc
      121 ctatggaaaa acgcctgcgg cgcggccttc ttcctgttcc tggtcttttg ctcacatgtt
      181 ctttccggcc ttatcccctg attctgtgga taactgtgtt accgtttttg tgtgagtcag
      241 taccgctcgc cgcagtcgaa cgaccgagcg tagcgagtca gtgagcgagg aagcggaaaa
      301 gcgcctggac gtgcattttc tccttacgca tctgtgcgga atttcacacc cggcatgggg
      361 cacttttcat acaatctgca ctgatgccgc atagttaagc cagtatacac tccgctatcg
      421 ctacgtgact gggtcagggc ttcgccccga cacccgctga cgcgccctgg cgggcttgtc
      481 tgctgccgaa aacgctcgcg gacaagccgt gagcgcctcc gtcagcttcg ttatgttcct
      541 gtttcacttt cggtctcaaa gcgaacctgg atgctgttct ggagttcttc cgcgagttcg
      601 tgcagtcgtt cgcacatggc cgcctgttcg tcggcatcca gagcatccag tttttcaagc
      661 agtgtcaggc tctggctttt gataaatcgc gccatattca gcgcagtttg ttgctgtttg
      721 ttcaccttcc gttgttctcc gtcagtaccg ggtgtcgggt ggaccctgac caggtggtaa
      781 ttgtaagacg ttgcgggcga cggtattaca attgcacatc ctgtcctgtt tttttaggac
      841 gtatcatggc acagcatatc aactgataaa taatccctgt gcagtgcagc cgctgttgca
      901 taaaatttcg ctctgcgtcg agtgtttctt aatcaataat tccgctgata ctccggaaaa
      961 acgcgagtct gttctcatgc ctgaaatgcc cacaccccac gcaaaaacaa ttttttgctg
     1021 atttttcttt ataaatagag agttatgaca aattagttct tcttgctctc tttgtgatat
     1081 ttaaaaaagc ggtgtcggcg cggtgttgta gctgcgccaa caccgctttt taggggtggt
     1141 actgactatt ttcataaaaa acatcatttt atattagggg tgctgctagc ggcgcggtgt
     1201 gtttttttac aagacgcccc tgggggcgct gctaggggtg tctgttcaga tatgtagcaa
     1261 tgagtcaggg attcacgaac tgaaaatgtc cgaaaatgtg tctcatgggc accgtatgcg
     1321 cccaaaccga tcgccattca ctttcatgca tagctatgca gtgagctgaa agcgatcctg
     1381 acgcattttt ccggttttcg cttggtaaaa catctctttt tgcggtgttc gcggcagaat
     1441 cgcgttcagc gcgttttagc ggtgcgtgta atgcgacgtt atggtaaatg ctgtgattta
     1501 cgggatggtt ttatctatgt ttagatcaat accacctcct atggaggtgg cttacaccga
     1561 tttttccttg ttgtctgttt cagaacagat agaggctttt ttggcaatta tccaaccact
     1621 attgatagtg tttattacta cttagataac tgagccttta ctgtatctgc ccctgcaagc
     1681 aggaacccaa cagttaagaa ccacccccag ccattgatac cttttagcgc tagaattgct
     1741 gcgctaatga tggctgctat agggactatc tggtacagaa aatacttcat ataacttacc
     1801 ccgaggtttt gcttttttat gagaccctaa agcatcgata ctgtcacttt gatgctttaa
     1861 ggaccttctt agtgataatc ctcgagatcc acgtcaaaga cgttaggttc ttcgagctta
     1921 aacactacgc gccagtttcc attgacctct aacgaatact ctccttgacg gtctcccttc
     1981 aatggatggc agcgcaatgc ctttaaatcc atcatatcct gcaagttcgt cgctgtgctt
     2041 aaggctgtta ggatcagctt cagacgttga gtaaactgtt gcggaattcc tgcgttgtta
     2101 cctgtttcgg caaacttacg caaaccttta tgcttgatat ttatgatcat taatcaccat
     2161 cccatatttg tttagataga aacatcgcag tttatttttc cggttcatcc gtatttccat
     2221 tgcaaacccc ttgctctatt tgaataaatg acgtaggttt tacttaacca agtcgcattt
     2281 taatctgttg acattggttt gatgcgctgt acaatgccgg ggccttgaat ttcacatcaa
     2341 gtacccacat cataaggaat gattagacgc accaatgtgc atcataatgt cattcttttt
     2401 tttagtcaac aatgagttgc gttatgcgca atgcgcaatc tgaaaacgca ataggcctat
     2461 ctttttaaaa ctaatatagg cttcagagga aggtatgatt aatcttgtcg atccagtaca
     2521 tccaggggtt tttatccgtg agatgtttat ggaaccgttt gaaatatcag ccgcggacct
     2581 gtctgaaaaa ctgcatgtat caccttccac tctaagtaga gtgctgaatg gaaaagctga
     2641 tttaagtgtt gagatggcat taaggctttc tcgagttctt ggtcgcagtg ccgagtcgtg
     2701 gataaacatg cagactcaat acagtcttaa cgcgagcagg aagtcaccta atgtcattaa
     2761 ggaattagat gaattggttc ctatattttg agaaaagaaa aggccgctat atgcggcctt
     2821 tttctgtctt gactctcagg caactggatc gtatcgtttc tcgtaaacga aaaaaccacc
     2881 cggcaaggtg gttttttcga aggttcagta accggcaagt ttctgaacca gggtaactgg
     2941 cttggaggag cgcagtcacc aaaacttgtt ctttcagttt agccttaact ggcgcataac
     3001 ttcaagacta actcctctaa atcagttacc agtggctgct gccaatggtg ttttgcatgt
     3061 ctttccgggt tggactcaag atgatagtta ccggataagg cgcagcggtc gggctgaacg
     3121 gggggttcgt gcacacagcc cagcttggag cgaacgacct acactgaacc gagataccta
     3181 cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg
     3241 gtaagcggca gggtcgg
//
