LOCUS       NZ_CP025247             2579 bp    DNA     circular CON 19-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Newport str. CDC
            2012K-0938 plasmid pSNE1-2012K-0938, complete sequence.
ACCESSION   NZ_CP025247
VERSION     NZ_CP025247.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02716906
            Assembly: GCF_004136175.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Newport str. CDC
            2012K-0938
  ORGANISM  Salmonella enterica subsp. enterica serovar Newport str. CDC 201...
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2579)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovenia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     Comparative Genomics of Salmonella Newport
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2579)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovenia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-DEC-2017) Meat Safety and Quality Research Unit,
            USDA-ARS-USMARC, State Spur 18D, Clay Center, NE 68933, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 195.6x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004136175.1-RS_2024_05_19
            Annotation Date                   :: 05/19/2024 03:44:29
            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)                     :: 4,694
            CDSs (total)                      :: 4,567
            Genes (coding)                    :: 4,455
            CDSs (with protein)               :: 4,455
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 18
            Pseudo Genes (total)              :: 112
            CDSs (without protein)            :: 112
            Pseudo Genes (ambiguous residues) :: 0 of 112
            Pseudo Genes (frameshifted)       :: 45 of 112
            Pseudo Genes (incomplete)         :: 75 of 112
            Pseudo Genes (internal stop)      :: 24 of 112
            Pseudo Genes (multiple problems)  :: 26 of 112
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP025247.1.
            Bacteria and source DNA available from USMARC.
            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..2579
                     /organism="Salmonella enterica subsp. enterica serovar
                     Newport str. CDC 2012K-0938"
                     /mol_type="genomic DNA"
                     /strain="CDC 2012K-0938"
                     /serovar="Newport"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:1454614"
                     /plasmid="pSNE1-2012K-0938"
                     /geo_loc_name="USA: BIFSCo Region 8"
                     /collection_date="2012-06"
                     /collected_by="CDC"
     gene            37..681
                     /locus_tag="AW48_RS24120"
                     /old_locus_tag="AW48_24655"
     CDS             37..681
                     /locus_tag="AW48_RS24120"
                     /old_locus_tag="AW48_24655"
                     /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"
     gene            complement(1063..1299)
                     /locus_tag="AW48_RS24125"
                     /old_locus_tag="AW48_24660"
     CDS             complement(1063..1299)
                     /locus_tag="AW48_RS24125"
                     /old_locus_tag="AW48_24660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012772745.1"
                     /translation="MARLTNLTPAEKKFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IELQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     gene            <2367..2522
                     /locus_tag="AW48_RS24150"
                     /old_locus_tag="AW48_24680"
                     /pseudo=""
     CDS             <2367..2522
                     /locus_tag="AW48_RS24150"
                     /old_locus_tag="AW48_24680"
                     /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"
     ARG             38..678
                     /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(1465..1638)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          1617..2108
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 atggcgtcat tactgtataa aaacacaggc atagatatga ctctggcatt agttggcgaa
       61 aaaattgaca gaaatcgctt caccggtgag aaagttgaaa atagtacatt ttttaactgc
      121 gatttttcag gtgccgacct gagcggcact gaatttatcg gctgccagtt ctatgatcgc
      181 gaaagtcaga aagggtgcaa ttttagtcgc gcaatgctga aagatgccat tttcaaaagc
      241 tgtgatttat caatggcaga tttccgcaac gtcagtgcct tgggcattga aattcgccac
      301 tgccgcgcac aaggcgcaga tttccgcggt gcaagcttta tgaatatgat caccacgcgc
      361 acctggtttt gcagcgcata tatcactaat actaatctaa gctacgccaa tttttcgaaa
      421 gtcgtgttgg aaaagtgtga gctgtgggaa aaccgctgga tggggactca ggtactgggt
      481 gcgacgttca gtggttcaga tctctccggc ggcgagtttt cgactttcga ctggcgagca
      541 gcaaacttca cacattgcga tctgaccaat tcggagttag gtgacttaga tattcggggt
      601 gttgatttac aaggcgttaa gttagacagc taccaggcat cgttgctcat ggagcggctt
      661 ggcatcgctg tgattggtta gttcagcgtt tacaccggga gatgcgtttg acgatttact
      721 tttacccgcg atcatcgcgt ttattgagtt tattatttat ctatgcgatt ccgatgaaaa
      781 attcgcacga aaatatggct aactcatagc aaaaaaaaag ccccctaagg gctttttttt
      841 gtacctgacg gtcagaccga ttaaacataa catcccttgc ccgcaccccc gcaggcgccc
      901 tcagcgcaat cctgctgcat cagggccgtt tccagcacct ttcctcacca gtatcccgga
      961 aaaacgcccc tgatgatttc tgcgcgactg catggctatg cacgcaggtg aatggcaggt
     1021 gatttcgcag cgtcagcacc actaaaccgc caaaagccaa aatcagcggc gcggcgcgcg
     1081 cggacgtgac caggcaaaat cggactgctg ccgctcatcc tcacgtaatg cacgctggcg
     1141 gtcggcgtaa cgctgcaact caatttgcgc acgcgctctg ttcaggacga tgtgccggtt
     1201 aggctgattt agctttttac ctgacgctct ttcagctgcg gcaacagcat catcaagaaa
     1261 ttttttctct gcaggcgtca agtttgtcag tctggccata acgttctcca gtcagaataa
     1321 atcagcacag tctgccagac acagtagaaa cgatgaagcg ccagcgacgg tgaaaggcag
     1381 tcagaaacgg tgaacgggag cggattttaa tccggtgccg tgaggcgttg gacaagccgc
     1441 aggcgcgtca ttagctttta gccggtttcg gggcgcagcc ctgaaccagt cacgtagcgc
     1501 tagcggagtg tatactggct gactatgttg gcacggatgt ggaaatcagt gaagtgcttc
     1561 atgtagcagg agaaaaaagg cggcaccagc gcgtcagcag gatatgtagt acaggatata
     1621 ttccgcttcc tcgctcactg actcgctgcg ctcggtcgtt cggctgcggc gagcggtgcc
     1681 ggcttacagg cggggcggaa atttcctggg agataccagg aaggagctta acagggaaga
     1741 gataaggccg cggcgaagcc gtttttccat aggctccgcc cccctgacaa acatcatgaa
     1801 atctgacgct caaatcagtg gtggcgaaac ccgatgcggc ttaaagatac caggcgtttc
     1861 cccctggtgg ctccctcgtg ctcccccgca ttcctgcctt tcggtttacc ggtgtcattc
     1921 cgctgttatg gccgcgttta tctcattcca cgcctgacac tcagttccgc gaaggcagtt
     1981 cgctcctgga tggactgtat gcacgaaccc cccgttcagt ccgactgctg cgccttatcc
     2041 ggtaactatc atcttgagtc caacccggaa agacacgact tatcgccact ggcagcagcc
     2101 actggtaact gatttagagg agttagtctt gaagttatgc gcctgttaag gctaaactga
     2161 aagaacagat ttggttactg cgctcctcgt aagccagtta ccacggttca aagagttgct
     2221 gctctgagaa ccttcgaaaa accgccttgc agggcggttt tttcgtttac agagcaagag
     2281 attacgacgc cacagaaagg atctcaagaa gatccttcac cgtaatggaa atctatccaa
     2341 tccgagcaca taggatacac atcgttataa cgctggatct gcgtgaattc cagcagcagc
     2401 aagagaaaga ctttctacaa accagcttac agcaggctaa atttaaccag aaaaaagccg
     2461 ctgaattact gggtctgact tatcatcagc tacgtgcctt gctgaagaaa caccagatct
     2521 aatacgcatt tgcaggtgtc atactggcgg gtttgacgca taacgtcata aggtttacc
//
