LOCUS       NZ_CP130094             2839 bp    DNA     circular CON 30-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Schwarzengrund strain
            SEMDH-29 plasmid unnamed1, complete sequence.
ACCESSION   NZ_CP130094
VERSION     NZ_CP130094.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361201
            Assembly: GCF_030505815.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Schwarzengrund
  ORGANISM  Salmonella enterica subsp. enterica serovar Schwarzengrund
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2839)
  AUTHORS   Sopovski,D., Commichaux,S., Zhao,S., Grim,C.J., Foley,S.L. and
            Khajanchi,B.K.
  TITLE     Complete genome sequences of 17 Salmonella enterica serovar
            Schwarzengrund strains carrying IncFIB-IncFIC (IncFII) fusion
            plasmid
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2839)
  AUTHORS   Sopovski,D., Commichaux,S., Zhao,S., Grim,C.J., Foley,S.L. and
            Khajanchi,B.K.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUN-2023) Office of Applied Research and Safety
            Assessment, CFSAN, U.S. Food and Drug Administration, 8301 Muirkirk
            Rd MOD1, Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Hybrid assembly using Unicyler v. unspecified
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 38.3x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/30/2023 12:04:17
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,973
            CDSs (total)                      :: 4,851
            Genes (coding)                    :: 4,682
            CDSs (with protein)               :: 4,682
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 169
            CDSs (without protein)            :: 169
            Pseudo Genes (ambiguous residues) :: 0 of 169
            Pseudo Genes (frameshifted)       :: 79 of 169
            Pseudo Genes (incomplete)         :: 114 of 169
            Pseudo Genes (internal stop)      :: 32 of 169
            Pseudo Genes (multiple problems)  :: 50 of 169
            Pseudo Genes (short protein)      :: 1 of 169
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130094.1.
            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..2839
                     /organism="Salmonella enterica subsp. enterica serovar
                     Schwarzengrund"
                     /mol_type="genomic DNA"
                     /strain="SEMDH-29"
                     /serovar="Schwarzengrund"
                     /isolation_source="urine"
                     /sub_species="enterica"
                     /db_xref="taxon:340190"
                     /plasmid="unnamed1"
                     /geo_loc_name="USA"
                     /lat_lon="37.0902 N 95.7129 W"
                     /collection_date="2017"
                     /collected_by="Minnesota Department of Health"
     gene            complement(join(2365..2839,1..497))
                     /locus_tag="QPJ60_RS24850"
                     /old_locus_tag="QPJ60_24850"
     CDS             complement(join(2365..2839,1..497))
                     /locus_tag="QPJ60_RS24850"
                     /old_locus_tag="QPJ60_24850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427687.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_045912058.1"
                     /translation="MERIDNKKIKVKYEKLSDRSEKDKPWDIHRHDCDLVADIYKQSFE
                     FERYFERMNECSGHLQYSEMLNRETGEIGIKLKSARFCRVRHCPVCQWRKSLMWKARFY
                     KALPDIEKQFKSARWMFLTLTVENCDVSEVREKIQWMNKSFIKMIQRKHFKNYNLGFVK
                     TTEITRSKDGKAHPHFHILLLMKPSYFKYGYLKTTDWAELWRDCLGVSYTPITDIRMVK
                     AKLNGEANKSAIAEAAAETLKYAVKPSDMVKDPEWFHELTRQVHKLRFVSTGGVLKDLF
                     KEDTSEKDLLLLSEEEDTDKELRILNYNWFKKDKNYKRKLED"
                     /name="protein rep"
     gene            complement(935..2194)
                     /locus_tag="QPJ60_RS24855"
                     /old_locus_tag="QPJ60_24855"
     CDS             complement(935..2194)
                     /locus_tag="QPJ60_RS24855"
                     /old_locus_tag="QPJ60_24855"
                     /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="plasmid recombination protein"
                     /protein_id="WP_171883928.1"
                     /translation="MSYQFIHIEDYGRVVSKKTKNNGSNDKYKKETKGRSVREIIAEAK
                     REKGNCPHVENPKDPILLFGVGLDEVEKLAYEYHDNTKITDKNGKEKKLRSDANILLAG
                     VVSLNKDNKDIWDDYKNDAIAYLSNKYGKKLVSVIEHTDEENPHFHFYIIQKPGLKFDL
                     IHDGKKALYENKDKKKHDQNIAYLDAMRGFQEDFFKVVSSNYGLTKDGPKRARLSRSDY
                     FKQSREVSLLDQVKLKATETGKKQGYSFAVDQFEKSSWWGKTKIAVSFKNSEFTALKAD
                     YKKLNRRKNHYKKKVDEVKEEISSEYENKLSEEYKKNKATSRNLYFTLNENQSLKEYKT
                     KYEDLNKSFNETLEEQKKPLLEENNTLKTENQNLKTENTENKKQLEKYQEFFTRVKKYY
                     GDRFSDFLEKIKPKTTIKPK"
                     /name="plasmid recombination protein"
ORIGIN
        1 tcagttgtct tcacaaaacc caagttatag tttttaaaat gctttctttg tatcattttt
       61 ataaatgatt tattcatcca ttggattttt tctcttactt cactgacatc acaattttca
      121 acggttaatg ttaaaaacat ccaacgagca cttttaaact gtttttctat atctggtaaa
      181 gccttataaa atcttgcttt ccacattagg cttttcctcc attgacaaac agggcaatgt
      241 cttactcggc aaaatcttgc cgatttaagt ttaataccta tttcacccgt ttcacgattt
      301 aacatttcag aatattgtaa atgaccagaa cattcgttca ttctttcaaa gtatctttca
      361 aactcgaacg attgtttata tatatcagca acaagatcac aatcgtgtct atgtatatcc
      421 cacggtttat ctttttcaga tctatcactt aatttttcat acttgacttt tattttttta
      481 ttatctattc tctccataga tataccgatc cccgtattat agtttttgac ttcgacactc
      541 aaaacttaac acggggattt tttttgtcaa tcattcgaca taaaacacct gctccaacac
      601 cacggaaacc cttacgggac aaggcttcaa gccactttta agcaccgttt ttcaaatcca
      661 cgttatccct attgtatcaa gtaaaggaaa tctgcccttt tcgggctgat tttaagaccc
      721 aaaaaccaac cccaaaacca ctactggaag aaaccctcca accataagcc aaaagccctg
      781 tatgggcttc tgagggcttc taacagcctt aaaaccggtt tatcaggttg aagcctcact
      841 tcgttctgct ccaaccataa caagggtatt tttatggtgt gtagtcaata acaatttcgg
      901 aaccccagag gggacccccc gaaattcttt ttgactattt aggcttaata gtcgttttag
      961 gttttatttt ttcaagaaaa tcagaaaaac gatcaccata atattttttc acacgagtaa
     1021 aaaactcctg atatttttca agttgttttt tattttcggt gttttctgtt tttaggtttt
     1081 ggttttcggt tttaagagtg ttgttttctt ccaaaagagg ttttttctgt tcttcgagtg
     1141 tttcattaaa tgatttattc aaatcctcat attttgtttt atattccttt aaagactgat
     1201 tttcatttaa tgtaaaatat agattccttg aagttgcctt attcttttta tattcttcag
     1261 aaagtttatt ttcatattca gagctgattt cttccttcac ctcatcaact ttctttttgt
     1321 aatggttctt tcttctgttc aacttcttat agtctgcttt aagtgctgta aactcactgt
     1381 ttttaaagga aactgcgatt ttggtttttc cccaccaaga cgatttttca aattgatcca
     1441 cggcaaaact ataaccctgt ttctttcctg tttctgttgc ttttaacttt acttgatcaa
     1501 gtaatgaaac ctcacgagat tgtttaaagt aatcactacg gctcaatctg gcccttttag
     1561 gaccatcttt cgttaaacca tagttagaac ttacaacttt aaaaaaatcc tcttgaaaac
     1621 ctctcatagc atctaaataa gcaatgtttt gatcgtgttt ctttttgtcc ttattttcat
     1681 ataatgcttt tttaccatcg tgtattaaat caaatttcaa tccgggtttt tgtattatat
     1741 aaaaatggaa gtgtggattt tcttcgtcgg tatgttctat tacagaaact aactttttac
     1801 cgtatttatt agacaaatag gcaatagcat catttttata atcatcccaa atatctttat
     1861 tgtctttatt taaacttaca accccagcca ataaaatatt agcatcagat cggagttttt
     1921 tttctttccc gtttttatcc gttatttttg tattgtcgtg atattcataa gcgagttttt
     1981 ccacttcatc caaaccaaca ccaaaaagca aaataggatc ttttggattt tcaacatgtg
     2041 gacagtttcc tttttctctt tttgcttctg caattatttc acgaaccgat ctaccttttg
     2101 tttctttttt atatttatca ttcgatccgt tattttttgt ttttttagat acaacccttc
     2161 cgtaatcttc aatatgtata aactgatagg acataatatt tacctctttt tttatcgtta
     2221 tatttaaata ataaatccgc agttttaaaa gtcaaataat atacataggg accgactatg
     2281 tttattcttc gaataaacgc cggcccctac ggggaaagtc aaaatcaaag gcataaaaaa
     2341 agcacctcag cggtgccttt tttactaatc ctcaagtttt cttttatagt ttttatcttt
     2401 tttaaaccag ttgtagttta gtattcttag ttctttatct gtatcttctt cttcacttaa
     2461 cagcaataaa tctttctcgg aagtatcttc cttaaataga tctttcaata ctccgccagt
     2521 tgatacaaac ctcaacttat ggacttgcct tgtcagttcg tggaaccatt caggatcttt
     2581 caccatatca gaaggcttca cagcatactt caaggtttca gccgcagcct cagctatggc
     2641 tgatttgttg gcttcaccgt tcagctttgc cttgaccata cgaatgtctg ttataggtgt
     2701 ataggaaaca cctaaacagt ctctccacaa ttcagcccaa tcagtagttt tcaaataacc
     2761 atatttaaaa taactcggct tcattaaaag caatatatga aaatgcggat gtgcttttcc
     2821 atctttcgat cttgttatt
//
