LOCUS       NZ_CP035551             3045 bp    DNA     circular CON 22-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            YU07-18 plasmid pYU07-18_3.0, complete sequence.
ACCESSION   NZ_CP035551
VERSION     NZ_CP035551.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10076457
            Assembly: GCF_011304815.1
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 3045)
  AUTHORS   Vinuesa,P., Silva,C., Calva,E. and Puente,J.L.
  TITLE     Evolutionary genomics of Salmonella Typhimurium ST213
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3045)
  AUTHORS   Vinuesa,P., Silva,C., Calva,E. and Puente,J.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-JAN-2019) Ingenieria Genomica, Centro de Ciencias
            Genomicas - UNAM, Avenida Universidad 2001, Cuernavaca, Mor. 62210,
            Mexico
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 06-AUG-2018
            Assembly Method                   :: unicycler v. 0.4.5
            Assembly Name                     :: YU07-18_hybrid_MinION_MiSeq
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 295x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_011304815.1-RS_2024_03_22
            Annotation Date                   :: 03/22/2024 04:05:46
            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)                     :: 5,046
            CDSs (total)                      :: 4,920
            Genes (coding)                    :: 4,717
            CDSs (with protein)               :: 4,717
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 118 of 203
            Pseudo Genes (incomplete)         :: 89 of 203
            Pseudo Genes (internal stop)      :: 30 of 203
            Pseudo Genes (multiple problems)  :: 31 of 203
            Pseudo Genes (short protein)      :: 1 of 203
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035551.1.
            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..3045
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="YU07-18"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pYU07-18_3.0"
                     /geo_loc_name="Mexico: Yucatan"
                     /lat_lon="20.40 N 89.13 W"
                     /collection_date="2007"
                     /collected_by="M. Zaidi"
                     /genotype="ST213"
     gene            complement(325..474)
                     /locus_tag="D6D39_RS25110"
     CDS             complement(325..474)
                     /locus_tag="D6D39_RS25110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023237787.1"
                     /translation="MPSEHDEQRDVADTQLPGEYDLFDLMAKVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(1387..1650)
                     /locus_tag="D6D39_RS25120"
                     /old_locus_tag="D6D39_25580"
     CDS             complement(1387..1650)
                     /locus_tag="D6D39_RS25120"
                     /old_locus_tag="D6D39_25580"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_023237785.1"
                     /translation="MISKVLWADKALSDRETIFESNDKVSGLSYAKSEDAKIKRAVSTI
                     KRNNKVGRNDLDERGYVYVLPKRYKILYRLTEEHIFIERVFY"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(1662..2057)
                     /locus_tag="D6D39_RS25125"
                     /old_locus_tag="D6D39_25585"
     CDS             complement(1662..2057)
                     /locus_tag="D6D39_RS25125"
                     /old_locus_tag="D6D39_25585"
                     /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_000896281.1"
                     /translation="MAFVSQVDKSRAASSRIGDSSIVVTQSYKASTKAQELSIRLKSLV
                     LSKGGMKIGDYVDVLYDKDSDRWMLRKMDGGLKITGKDDAPTGLIRYTLKDTHARFTED
                     KEHLPIRKSSIEDSLEIEDGQIVFKLD"
                     /name="hypothetical protein"
     gene            2292..2567
                     /locus_tag="D6D39_RS25130"
                     /old_locus_tag="D6D39_25590"
     CDS             2292..2567
                     /locus_tag="D6D39_RS25130"
                     /old_locus_tag="D6D39_25590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004099076.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
                     /protein_id="WP_023259899.1"
                     /translation="MQFRIESETKKMAKQALEKKGISLSDALRAFLDKLAATEKVMTKE
                     ETWLKEQIEETFSRVEKGEIRYYSEDEADERMNSFISKIEHQHETA"
                     /name="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
     Typing          complement(509..681)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.931"
                     /coverage="100.0"
                     /evalue="9.61e-51"
     Typing          648..1069
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.799"
                     /coverage="80.0"
                     /evalue="0.0"
ORIGIN
        1 agtctttttg tagtttacct gtagtcagga aaactactcc gttcatgcga gcatgaacgg
       61 agtagtgaag gacgcttttt tgtcatatca gcctcttaac ctgcgcagat ggcccagtca
      121 aaatgatgat tttttaaccc ttaaatggtc atacacctaa cgcagccgcg attttcatcg
      181 caactgcatg aattacataa aaaaaatggg atactccatt tgtcacggta atacgcaagg
      241 tattacaatc aactgtaaat acatgaaaat aaagaaataa gatgtaatac caccgtatta
      301 cacgtacgct tcccaacgaa aaagctataa cgcttcccgg ccgacaggtg gcccggaatc
      361 caccggggcg tgcaggttct cttcagtaac cttcgccatt aaatcaaaaa ggtcatactc
      421 gccgggaagc tgcgtatcag caacatcccg ttgttcatca tgttcagatg gcatggggtg
      481 atatccagta gctgagaggt tgttagcggg ttccgggcgc agcgccggac cagtcacgta
      541 gcgctagcgg agtgtatact ggcttagtat gttggcatga gtgcgataat caggaaagcg
      601 ccttatgtgg caggagaaaa atgctgcagc agagcgtaag cagaatatgc gatacagaag
      661 atattccgct tcctcgctca ctgactcgct gcgctcggtc gttcggctgc ggcgagcggt
      721 atcggcttac aggcggggcg gagatttcct ggaagatgcc aagaagaaac ttaacaggga
      781 agcgataagg ccacggcgga gccgtttttc cataggctcc gcccccctga caagcatcac
      841 agaatctgac actcaaatca gtggtggcga aacccgacag gactataaag ataccaggcg
      901 tttccccctg atggctccct cgtgcgctct cctgttcctg ccattcggtt taccggtgtc
      961 attccgctgt tatggccgcg tttgtctcat tccacgcctg acactcagtt ccgggtaggc
     1021 agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgacc cccacgacaa
     1081 acaagcaact cgactcttga atccaatctt gtttgactca aattatgaca atggtggaag
     1141 cctgtaataa ctgatttgcg gagcgtagaa agaaggtaag caaggatatc ttgaagtgag
     1201 cagtgaacta cggctacact gaaagaacaa gttttggtga ctgcgctccg cgaaagccag
     1261 ttaccacaag tccaatgagt tggtagctca aaggactacg aagaaaccac cgttggtagc
     1321 ggtggttttc ttcatcccaa gattaatagc taaagagacg cgtagtcaag aaaggtcgcc
     1381 aaaccatcag tagaaaacgc gctcaataaa aatatgctcc tcagtcagcc gatacaaaat
     1441 cttgtatctt ttaggtagaa catagacata acctcgctca tccaggtcat ttctgcctac
     1501 tttgttgttt cgttttatcg tagaaacagc acgtttaatt tttgcatctt ctgattttgc
     1561 atacgacaaa ccagaaacct tatcgttaga ctcaaagata gtctctcgat cagataatgc
     1621 cttatctgcc catagaacct tagagatcat caaacctccc gctagtcaag cttaaataca
     1681 atctgcccat cctcaatctc cagtgaatcc tcaatagagg atttacgaat agggaggtgc
     1741 tctttatcct cggtaaatct cgcatgtgta tccttcaggg tatatctaat caaccccgta
     1801 ggggcatcat ccttaccagt aatttttaaa cctccatcca tcttccttaa catccagcga
     1861 tcactatcct tgtcataaag aacatcaacg taatcaccaa ttttcatacc tcccttagat
     1921 aacactaacg attttaatct aatggatagc tcctgagcct tagttgaagc cttgtatgat
     1981 tgagtgacca ctatagacga atcaccaatc ctgctcgaag cagccctaga cttatcaacc
     2041 tgactaacaa atgccataaa acctcctgat agtttatttt catgttcata atacgatcgg
     2101 caaaaaatct tagcaacaca gaaccatgtt tttatctgat ctttatcctc tctcagaacc
     2161 cgaagaaaaa aagttacttt ttctaatcat aaatctaaga aaggaggcat tgactgtagg
     2221 gatcccagcg tctattgtga gcacaaacgt actcacaata gacgctggga tctatatcta
     2281 tggaaacaag ggtgcaattc agaattgaat ctgaaacaaa gaaaatggca aagcaagcac
     2341 ttgaaaaaaa aggcatttca cttagcgatg cgttaagagc gtttctcgat aagttagcag
     2401 caacggagaa ggttatgacg aaagaagaga catggctgaa agagcagata gaagagacat
     2461 tctcaagagt agaaaaagga gagatccgct attactcaga agatgaagct gacgaacgca
     2521 tgaactcctt catctctaaa atcgaacatc aacacgaaac cgcataaaaa aagccgccat
     2581 aaggcggctt tttttatgcc cttatttacc ataacaccct aattgtacgc accgccaaaa
     2641 cggcctcagg gcgtttctga caggaaacag gtaaaacaga caacaaacta tcagaaaatc
     2701 agccaaaaac acgttagttc tgttttcacg tcatgcatga gtatgcgcgc aagtgcatag
     2761 cgcggaaatt cacgccattc agccgtggta agtcctgttt ccgatgttct tcttacccga
     2821 aaacggtgaa cggggacgca atttattgcg tagccatgag gcattttgcc ggcacagccg
     2881 gaaaaaccat tttcagcacg tgcaggaaga ggggggcgga tgtacgaata gttcagaggt
     2941 cagatctgac gtaagaatga tgtaaaagtg atgtaattct gtagttgatt tgtagtttat
     3001 ctgtagttag ccctctgaaa ggcatgatta aacatcagct tttgt
//
