LOCUS       NZ_CP101942             3071 bp    DNA     circular CON 07-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica strain QA-1986 974 plasmid
            pSeFELIX702_3.2, complete sequence.
ACCESSION   NZ_CP101942
VERSION     NZ_CP101942.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29939568
            Assembly: GCF_024507995.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica
  ORGANISM  Salmonella enterica subsp. enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3071)
  AUTHORS   Wan,K.H., Park,S., Lawrence,Q., Eichenberger,J.P., Booth,B.W.,
            Piaggio,A.J., Chandler,J.C., Franklin,A.B. and Celniker,S.E.
  TITLE     FELIX
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3071)
  AUTHORS   Wan,K.H., Park,S., Lawrence,Q., Eichenberger,J.P., Booth,B.W.,
            Piaggio,A.J., Chandler,J.C., Franklin,A.B. and Celniker,S.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-JUL-2022) BDGP, Lawrence Berkeley National Laboratory,
            1 Cyclotron Road, Berkeley, CA 94720, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 143.95x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/06/2023 04:34:32
            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)                     :: 4,908
            CDSs (total)                      :: 4,784
            Genes (coding)                    :: 4,667
            CDSs (with protein)               :: 4,667
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 43 of 117
            Pseudo Genes (incomplete)         :: 87 of 117
            Pseudo Genes (internal stop)      :: 22 of 117
            Pseudo Genes (multiple problems)  :: 31 of 117
            Pseudo Genes (short protein)      :: 1 of 117
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP101942.1.
            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..3071
                     /organism="Salmonella enterica subsp. enterica"
                     /mol_type="genomic DNA"
                     /strain="QA-1986 974"
                     /isolation_source="cow"
                     /sub_species="enterica"
                     /db_xref="taxon:59201"
                     /plasmid="pSeFELIX702_3.2"
                     /geo_loc_name="USA: Colorado, CAFO C"
                     /collection_date="2012-08-29"
     gene            complement(join(2679..3071,1..252))
                     /locus_tag="NP448_RS24490"
                     /old_locus_tag="NP448_24495"
     CDS             complement(join(2679..3071,1..252))
                     /locus_tag="NP448_RS24490"
                     /old_locus_tag="NP448_24495"
                     /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(346..>501)
                     /locus_tag="NP448_RS24495"
                     /old_locus_tag="NP448_24500"
                     /pseudo=""
     CDS             complement(346..>501)
                     /locus_tag="NP448_RS24495"
                     /old_locus_tag="NP448_24500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /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            1439..1588
                     /locus_tag="NP448_RS24500"
                     /old_locus_tag="NP448_24505"
     CDS             1439..1588
                     /locus_tag="NP448_RS24500"
                     /old_locus_tag="NP448_24505"
                     /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"
     ARG             complement(2680..3071)
                     /name="QnrB19"
                     /gene="QnrB19"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="100.0"
                     /coverage="60.75"
     ARG             complement(2..252)
                     /name="QnrB68"
                     /gene="QnrB68"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="100.0"
                     /coverage="39.25"
     Typing          1231..1404
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(761..1252)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 aatgcccaag gcactgacgt tgcggaaatc tgccattgat aaatcacagc ttttgaaaat
       61 ggcatctttc agcattgcgc gactaaaatt gcaccctttc tgactttcgc gatcatagaa
      121 ctggcagccg ataaattcag tgccgctcag gtcggcacct gaaaaatcgc agttaaaaaa
      181 tgtactattt tcaactttct caccggtgaa gcgatttctg tcaatttttt cgccaactaa
      241 tgccagagtc atatctatgc ctgtgttttt atacagtaat gacgccatgg taaaccttat
      301 gacgttatgc gtcaaacccg ccagtatgac acctgcaaat acgtattaga tctggtgttt
      361 cttcagcaag gcacgtagct gatgataagt cagacccagt aattcagcgg cttttttctg
      421 gttaaattta gcctgctgta agctggtttg tagaaagtct ttctcttgct gctgctggaa
      481 ttcacgcaga tccagcgtta taacgatgtg tatcctatgt gctcggattg gatagatttc
      541 cattacggtg aaggatcttc ttgagatcct ttctgtggcg tcgtaatctc ttgctctgta
      601 aacgaaaaaa ccgccctgca aggcggtttt tcgaaggttc tcagagcagc aactctttga
      661 accgtggtaa ctggcttacg aggagcgcag taaccaaatc tgttctttca gtttagcctt
      721 aacaggcgca taacttcaag actaactcct ctaaatcagt taccagtggc tgctgccagt
      781 ggcgataagt cgtgtctttc cgggttggac tcaagatgat agttaccgga taaggcgcag
      841 cagtcggact gaacgggggg ttcgtgcata cagtccatcc aggagcgaac tgccttcgcg
      901 gaactgagtg tcaggcgtgg aatgagataa acgcggccat aacagcggaa tgacaccggt
      961 aaaccgaaag gcaggaatgc gggggagcac gagggagcca ccagggggaa acgcctggta
     1021 tctttaagcc gcatcgggtt tcgccaccac tgatttgagc gtcagatttc atgatgtttg
     1081 tcaggggggc ggagcctatg gaaaaacggc ttcgccgcgg ccttatctct tccctgttaa
     1141 gctccttcct ggtatctccc aggaaatttc cgccccgcct gtaagccggc accgctcgcc
     1201 gcagccgaac gaccgagcgc agcgagtcag tgagcgagga agcggaatat atcctgtact
     1261 acatatcctg ctgacgcgct ggtgccgcct tttttctcct gctacatgaa gcacttcact
     1321 gatttccaca tccgtgccaa catagtcagc cagtatacac tccgctagcg ctacgtgact
     1381 ggttcagggc tgcgccccga aacccgctaa caacctctct gctactggat atcaccccat
     1441 gccatctgaa tatgatgaac aacggggttc gactgatacg cagcttcccg gcgaatatga
     1501 cctttttgat ttaatggcga aggttactga agagatcctg catgcccctg tggattctgg
     1561 gccgcctgtc ggccgggaag cgttatagct ttttcgcttg cccgcgtacg tggtaatacg
     1621 ccggtattac cttttatttc tttattttca tgtaattaca gtgggttttt aatacctggg
     1681 tattactcgt gaaaacgaaa cattactttt ttttctttta attcatgcag ttgcgatgaa
     1741 aatcgcggct gcgttaggtg tatgaccatt ttgaggttga aaaataatca accatggcgg
     1801 gtgatttacg caggttaagg ggagatcgtg acaaaaaaaa gcgttcctca ctgtatcgtt
     1861 catgcaggca tgaacgggtt attcttcctg actacagaat tacatcgctc cttcagttca
     1921 tacatcactt ttacaacact tttacaacac tccttcggcc tgtacatcac ttttacaaca
     1981 cttttgcatc acttttacat catttataca tcacttttac atcattcctt cagctcatac
     2041 gtcactttca tcctctgtgc catttgtaca tcaccccctt cctgaacgtg ctgacagcgg
     2101 gttttccggc tgcgccggca acgcttcacg gccacgcaat aaattgcgtc cccgttcacc
     2161 gttttcggat gggaagaacg ccggaaacag gacttcccct ggctgaatgg tgtgaatttc
     2221 cgcgctatgc acttgcgcgc atactcatgc atgccgtaaa aacagagcct gcgcgtttct
     2281 ggcgggtttt cgggtggttt gttgcctgtt ttaccggttt cccgtcagaa acgccctcag
     2341 agcctctcag gcggtgcacg caagggatgt tatgtttaat cggtctgacc gtcaggtaca
     2401 aaaaaaagcc cttagggggc tttttttttg ctatgagtta gccatatttt cgttaagaca
     2461 tggcttcatg attcgggagt ggttattcgt tgttctcgcg aaaatgaatt ggttagatat
     2521 tcatcaaatt cctgtccaga atgcagcatt agatggcatg tcgttgatgc ggtaggtcag
     2581 gatattcgtc cactggagaa aacgtttcac aatgcttgcc aggagtcgta ctggttaaaa
     2641 gtaaatcgtc aaacgcatct cccggtgtaa acgctgaact aaccaatcac agcgatgcca
     2701 agccgctcca tgagcaacga tgcctggtag ctgtctaact taacgccttg taaatcaaca
     2761 ccccgaatat ctaagtcacc taactccgaa ttggtcagat cgcaatgtgt gaagtttgct
     2821 gctcgccagt cgaaagtcga aaactcgccg ccggagagat ctgaaccact gaacgtcgca
     2881 cccagtacct gagtccccat ccagcggttt tcccacagct cacacttttc caacacgact
     2941 ttcgaaaaat tggcgtagct tagattagta ttagtgatat atgcgctgca aaaccaggtg
     3001 cgcgtggtga tcatattcat aaagcttgca ccgcggaaat ctgcgccttg tgcgcggcag
     3061 tggcgaattt c
//
