LOCUS       NZ_CP045448             2989 bp    DNA     circular CON 18-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Schwarzengrund strain
            12888 plasmid p3_12888, complete sequence.
ACCESSION   NZ_CP045448
VERSION     NZ_CP045448.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13031564
            Assembly: GCF_009387895.1
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 2989)
  AUTHORS   Galetti,R., Penha Filho,R.A.C., Ferreira,J.C., Varani,A.M.,
            Sazinas,P., Jelsbak,L. and Darini,A.L.C.
  TITLE     The plasmidome of multidrug-resistant emergent Salmonella serovars
            isolated from poultry
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2989)
  AUTHORS   Galetti,R., Penha Filho,R.A.C., Ferreira,J.C., Varani,A.M.,
            Sazinas,P., Jelsbak,L. and Darini,A.L.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-OCT-2019) Biociencias Aplicadas a Farmacia, Faculdade
            de Ciencias Farmaceuticas de Ribeirao Preto, Avenida do Cafe, s/n,
            Ribeirao Preto, Sao Paulo 14040-903, Brazil
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 140x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/18/2023 02:32:10
            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)                     :: 4,791
            CDSs (total)                      :: 4,674
            Genes (coding)                    :: 4,546
            CDSs (with protein)               :: 4,546
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 81
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 128
            CDSs (without protein)            :: 128
            Pseudo Genes (ambiguous residues) :: 0 of 128
            Pseudo Genes (frameshifted)       :: 53 of 128
            Pseudo Genes (incomplete)         :: 91 of 128
            Pseudo Genes (internal stop)      :: 21 of 128
            Pseudo Genes (multiple problems)  :: 35 of 128
            Pseudo Genes (short protein)      :: 1 of 128
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP045448.1.
            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..2989
                     /organism="Salmonella enterica subsp. enterica serovar
                     Schwarzengrund"
                     /mol_type="genomic DNA"
                     /strain="12888"
                     /serovar="Schwarzengrund"
                     /isolation_source="cloacal swabs"
                     /host="poultry"
                     /sub_species="enterica"
                     /db_xref="taxon:340190"
                     /plasmid="p3_12888"
                     /geo_loc_name="Brazil"
                     /lat_lon="23.5475 S 46.63611 W"
                     /collection_date="2013"
                     /collected_by="JCF"
     gene            complement(778..927)
                     /locus_tag="GEO46_RS24220"
     CDS             complement(778..927)
                     /locus_tag="GEO46_RS24220"
                     /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_162846302.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMAKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            <1865..2020
                     /locus_tag="GEO46_RS22615"
                     /old_locus_tag="GEO46_22615"
                     /pseudo=""
     CDS             <1865..2020
                     /locus_tag="GEO46_RS22615"
                     /old_locus_tag="GEO46_22615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_707212.3"
                     /GO_function="GO:0043565 - sequence-specific DNA binding
                     [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     gene            2114..2758
                     /locus_tag="GEO46_RS22620"
                     /old_locus_tag="GEO46_22620"
     CDS             2114..2758
                     /locus_tag="GEO46_RS22620"
                     /old_locus_tag="GEO46_22620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="WP_012954666.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     ARG             2115..2755
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(963..1136)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          1115..1606
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ccttgcgtgc accgcctgag aggctctgag ggcgtttctg acgggaaacc ggtaaaacag
       61 gcaacaaacc acccgaaaac ccgccagaaa cgcgcaggct ctgtttttac ggcatgcatg
      121 agtatgcgcg caagtgcata gcgcggaaat tcacaccatt cagccagggg aagtcctgtt
      181 tccggcgttc ttcccatccg aaaacggtga acggggacgc aatttattgc gtggccgtga
      241 agcgttgccg gcgcagccgg aaaacccgct gtcagcacgt tcaggaaggg ggtgatgtac
      301 aaatggcaca gaggatgaaa gtgacgtatg agctgaagga atgatgtaaa agtgatgtat
      361 aaatgatgta aaagtgatgc aaaagtgttg taaaagtgat gtacaggccg aaggagtgtt
      421 gtaaaagtgt tgtaaaagtg atgtatgaac tgaaggagcg atgtaattct gtagtcagga
      481 agaataaccc gttcatgcag gcatgaacga tacagtgagg aacgcttttt tttgtcacga
      541 tctcccctta acctgcgtaa atcacccgcc atggttgatt atttttcaac ctcaaaatgg
      601 tcatacacct aacgcagccg cgattttcat cgcaactgca tgaattaaaa gaaaaaaaag
      661 taatgtttcg ttttcacgag taatacccag gtattaaaaa cccactgtaa ttacatgaaa
      721 ataaagaaat aaaaggtaat accggcgtat taccacgtac gcgggcaagc gaaaaagcta
      781 taacgcttcc cggccgacag gcggcccaga atccacaggg gcatgcagga tctcttcagt
      841 aaccttcgcc attaaatcaa aaaggtcata ttcgccggga agctgcgtat cagtcgaacc
      901 ccgttgttca tcatattcag atggcatggg gtgatatcca gtagcagaga ggttgttagc
      961 gggtttcggg gcgcagccct gaaccagtca cgtagcgcta gcggagtgta tactggctga
     1021 ctatgttggc acggatgtgg aaatcagtga agtgcttcat gtagcaggag aaaaaaggcg
     1081 gcaccagcgc gtcagcagga tatgtagtac aggatatatt ccgcttcctc gctcactgac
     1141 tcgctgcgct cggtcgttcg gctgcggcga gcggtgccgg cttacaggcg gggcggaaat
     1201 ttcctgggag ataccaggaa ggagcttaac agggaagaga taaggccgcg gcgaagccgt
     1261 ttttccatag gctccgcccc cctgacaaac atcatgaaat ctgacgctca aatcagtggt
     1321 ggcgaaaccc gatgcggctt aaagatacca ggcgtttccc cctggtggct ccctcgtgct
     1381 cccccgcatt cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcgtttatc
     1441 tcattccacg cctgacactc agttccgcga aggcagttcg ctcctggatg gactgtatgc
     1501 acgaaccccc cgttcagtcc gactgctgcg ccttatccgg taactatcat cttgagtcca
     1561 acccggaaag acacgactta tcgccactgg cagcagccac tggtaactga tttagaggag
     1621 ttagtcttga agttatgcgc ctgttaaggc taaactgaaa gaacagattt ggttactgcg
     1681 ctcctcgtaa gccagttacc acggttcaaa gagttgctgc tctgagaacc ttcgaaaaac
     1741 cgccttgcag ggcggttttt tcgtttacag agcaagagat tacgacgcca cagaaaggat
     1801 ctcaagaaga tccttcaccg taatggaaat ctatccaatc cgagcacata ggatacacat
     1861 cgttataacg ctggatctgc gtgaattcca gcagcagcaa gagaaagact ttctacaaac
     1921 cagcttacag caggctaaat ttaaccagaa aaaagccgct gaattactgg gtctgactta
     1981 tcatcagcta cgtgccttgc tgaagaaaca ccagatctaa tacgcatttg caggtgtcat
     2041 actggcgggt ttgacgcata acgtcataag gtttaccatg gcgtcattac tgtataaaaa
     2101 cacaggcata gatatgactc tggcattagt tggcgaaaaa attgacagaa atcgcttcac
     2161 cggtgagaaa gttgaaaata gtacattttt taactgcgat ttttcaggtg ccgacctgag
     2221 cggcactgaa tttatcggct gccagttcta tgatcgcgaa agtcagaaag ggtgcaattt
     2281 tagtcgcgca atgctgaaag atgccatttt caaaagctgt gatttatcaa tggcagattt
     2341 ccgcaacgtc agtgccttgg gcattgaaat tcgccactgc cgcgcacaag gcgcagattt
     2401 ccgcggtgca agctttatga atatgatcac cacgcgcacc tggttttgca gcgcatatat
     2461 cactaatact aatctaagct acgccaattt ttcgaaagtc gtgttggaaa agtgtgagct
     2521 gtgggaaaac cgctggatgg ggactcaggt actgggtgcg acgttcagtg gttcagatct
     2581 ctccggcggc gagttttcga ctttcgactg gcgagcagca aacttcacac attgcgatct
     2641 gaccaattcg gagttaggtg acttagatat tcggggtgtt gatttacaag gcgttaagtt
     2701 agacagctac caggcatcgt tgctcatgga gcggcttggc atcgctgtga ttggttagtt
     2761 cagcgtttac accgggagat gcgtttgacg atttactttt aaggggttcc tgtatctaat
     2821 tttttgctgg acattcatac ccgcgatcat cgcgtttatt gagtttatta tttatctatg
     2881 cgattccgat gaaaaattcg cacgaaaata tggctaactc atagcaaaaa aaaagccccc
     2941 taagggcttt tttttgtacc tgacggtcag accgattaaa cataacatc
//
