LOCUS       NZ_CP038599             3223 bp    DNA     circular CON 05-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Hadar strain 12-2388
            plasmid p12-2388.4, complete sequence.
ACCESSION   NZ_CP038599
VERSION     NZ_CP038599.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06030204
            Assembly: GCF_004768645.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Hadar
  ORGANISM  Salmonella enterica subsp. enterica serovar Hadar
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3223)
  AUTHORS   Robertson,J., Lin,J., Wren-Hedegus,A., Arya,G., Carrillo,C. and
            Nash,J.H.E.
  TITLE     Development of a multi-locus typing scheme for an Enterobacteriaceae
            linear plasmid that mediates inter-species transfer of flagella
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  AUTHORS   Robertson,J., Lin,J., Wren-Hedegus,A., Arya,G., Carrillo,C. and
            Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-APR-2019) Public Health Agency of Canada, National
            Microbiology Laboratory at Guelph, 110 Stone Road West, Guelph,
            Ontario N1G3W4, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 4.5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 60.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004768645.1-RS_2024_06_05
            Annotation Date                   :: 06/05/2024 01:02:17
            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)                     :: 4,555
            CDSs (total)                      :: 4,433
            Genes (coding)                    :: 4,299
            CDSs (with protein)               :: 4,299
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 70 of 134
            Pseudo Genes (incomplete)         :: 82 of 134
            Pseudo Genes (internal stop)      :: 25 of 134
            Pseudo Genes (multiple problems)  :: 40 of 134
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP038599.1.
            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..3223
                     /organism="Salmonella enterica subsp. enterica serovar
                     Hadar"
                     /mol_type="genomic DNA"
                     /strain="12-2388"
                     /serovar="Hadar"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:149385"
                     /plasmid="p12-2388.4"
                     /geo_loc_name="Canada"
                     /collected_by="NML"
     gene            join(2938..3223,1..38)
                     /locus_tag="CVJ63_RS23150"
                     /old_locus_tag="CVJ63_23150"
     CDS             join(2938..3223,1..38)
                     /locus_tag="CVJ63_RS23150"
                     /old_locus_tag="CVJ63_23150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_004193914.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            247..>681
                     /locus_tag="CVJ63_RS23680"
                     /pseudo=""
     CDS             247..>681
                     /locus_tag="CVJ63_RS23680"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            716..1201
                     /locus_tag="CVJ63_RS23325"
     CDS             716..1201
                     /locus_tag="CVJ63_RS23325"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_025367738.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1205..1420
                     /locus_tag="CVJ63_RS23330"
     CDS             1205..1420
                     /locus_tag="CVJ63_RS23330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_024195375.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1588..1920
                     /locus_tag="CVJ63_RS23160"
                     /old_locus_tag="CVJ63_23160"
     CDS             1588..1920
                     /locus_tag="CVJ63_RS23160"
                     /old_locus_tag="CVJ63_23160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="WP_001099531.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(2129..2299)
                     /locus_tag="CVJ63_RS23170"
                     /old_locus_tag="CVJ63_23170"
     CDS             complement(2129..2299)
                     /locus_tag="CVJ63_RS23170"
                     /old_locus_tag="CVJ63_23170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004193911.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="hypothetical protein"
     ARG             1589..1920
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          2651..2842
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          complement(2188..2668)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.867"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          29..1518
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.784"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2939..3222
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.842"
                     /coverage="89.0"
                     /evalue="1.64e-55"
ORIGIN
        1 atgccgtact ggaaaagggt gctgatgatg atcgttaagt ttcatcctcg ggggcgcggc
       61 ggcggcggcg ggccggtcga ttatctgctg ggtaaagatc gccagcgcga cggcgccagc
      121 gttctgcagg ggaagccgga tgaagtccgg gagcttatcg acgcctcgcc ctacgccaaa
      181 aagtacactt ccggcgttct gtcttttgcc gaacaggatt taccgcccgg ccagcgcgaa
      241 aagctgatgg cgagtttcga gcgggttctg atgcccggac tcgataaaga ccagtacagc
      301 gtgctgtggg ttgagcaccg ggacaagggg cggctggagc tgaacttcct gatcccgaac
      361 acggagcttc tgaccggcaa gcggctacag ccgtattacg accgcgccga ccgtccgcgc
      421 atcgatgcct ggcagaccat agtgaacggc aggctggggc tgcatgaccc gaacgcgccg
      481 gagaaccggc gggtgctggt ctcgccttcc gcgctgccgg aagcgaagca ggaagccgcc
      541 caggcgatta cgagcggcct gcttgccctt gcctcatccg gggagctgaa aacgcgtcag
      601 gacgtcactg aggcgctgga aagcgcaggt tttgaggtgg tgcgcaccac aaaaagcagc
      661 atcagcattg ccgacccgga cggggggcga aacatccgac tgaagggagc catctatgaa
      721 cagtctttta acgctggcga aggacttaga gcagaaatcg aaagcgcagc agcagactac
      781 cggcgagatg ctgaaagccg cattcagcga gcacgagaag tctgtcagag cggaactgag
      841 cgaaagcgag aagagaatca gcgccgccat cctcgaccac gaccggaagc tgtcctcagc
      901 catgagccag cgcacgaaag ggatgctgcg catggtcagc cagacgtggc tgaccatcgt
      961 tctggtctcc gcgctgctga tagcgtcgag cgcgggcatt ctgtggtggc aggggcagca
     1021 gatactcgag aactatacga ccatccggga gcagaagagc acgcaggcca tgctgtcaga
     1081 gaggaacagc ggcgtacagc tctcgacctg cggcgagcag agacgccgct gcgtgagggt
     1141 gaacccggaa gcgggacagt tcggagagga ctcgagctgg atgatactgg cggggaaata
     1201 gcacatgacg gagctggaaa aacagttgct gagcgcatta gagcagctac agcaggacta
     1261 ctcgaaaagg ctggacgagt gggagaacgc cttcgcggaa tggcggacga tgtctggtct
     1321 tattcaacgg gagaacgcgg cgctgaacga gcgcgtcacg gtcttgagca ggcaggtgca
     1381 gagtttgagc gagcagctgc gccggttgtc gaaaggctga acgcgataga aactcaccgg
     1441 cagcaggagc gggcggtgca gcaccagaaa gcgctggagc tggaacgatc gcagtggcag
     1501 catcatggtc cttcgctatg ataagccggg ttctattaat tagttgttat gtaaagatat
     1561 ttaaattttt caacatgagg tatttttatg aatacatata ttttcctggg aggggctatt
     1621 gtggctgaag tcataggcac cacctttatg aaatattcag aaggatttac acgcctgtgg
     1681 ccgtctgtag gaactgcaat aagttattgc gctgcctttt atctgctttc ccaaacattg
     1741 gaaaatatac ctaccggtat tgcttacgca atttggtctg gtgcgggaat tgtactaata
     1801 agcctagctg gttggttggt tagcggtcaa aaacttgatt ggcccgcaat tgcaggaatg
     1861 ttccttattt gcgttggagt tttggttatt aatatttttt caaaatcttc tgcgcattaa
     1921 ctttttaccg aagcatattg gccaaagcaa aaggatttcc ttgagatcct ttctttctgc
     1981 gcgtaatctt tttccctgta aacaaaaaaa ccaccgctac caacggtggt tcgtttgccg
     2041 gaattcagag ctaccaactc tttgttccga tggtaactgg ctttcacgga gcgcagatac
     2101 ctaaactgtc ctttcagtgt agccgcactc aggctttcac ttcaagaact ctgtaggcat
     2161 tctctacaat ctctgctccg tgaacccagt taccaatggc taccgccact ggcgatttgt
     2221 cgtgtctttc cgggttggac tcaagttgat agttaccgga acgggcgtgg tagtcggact
     2281 gaacgggggg ttcgtgcata cagtccatcc tggagcgaac tgcctacccg gaaccgagtt
     2341 tcaggcgtgg aatgagaaac cgcggccata acagcggaat gacaccggta aaccgaaagg
     2401 caggaatgcg ggggagcacg agggagccac cagggggaaa cgcctggtat ctttaagccg
     2461 catcgggttt cgccaccgct gatttgagcg tcattttcgt gatactcgtc aggggggcgg
     2521 agcctatgga aaaacggcaa ctccgcatcc ttttcttggc ctttcctgct tcgagcggca
     2581 tttgcttatc ccgtaatctg tgagctggta acgcccgccg cagtctcacg gcaggagcgt
     2641 agcgaccgag tgagcgagga ggcgtcattt catcaccacc tgcattttgc acttacgccc
     2701 ggcagccgca tttttcccct gtcacatgaa gcactttcat aaattgccac tccgtcataa
     2761 catgtttagc cagtatacac tccgctagcg ctacgtgact ggttcagggc tgcgccccga
     2821 aacccgctaa aaccactgcc gcgcctgcgg cttgtccaac accgtgccga ccgggaaaag
     2881 atttcccgtc cgtcccggcg ttatcaggag gccggattgg cagacaaacg cagcaaaatg
     2941 ctcaccatgt gggtgactga ggacgagcac cggcgtctgc tggagcgctg cgagggtaag
     3001 caactcgcgg cctggatgcg gcagacgtgc ctggacgaga agcccgcacg cgccggcaaa
     3061 cttccgtcga tctcgccggc gctgcttcgt cagcttgccg gcatggggaa caaccttaac
     3121 cagattgccc gccaggttaa cgccggtggt ggaagcggac acgaccgcgt gcagattgtc
     3181 gccgcgctga tggccatcga tgccggactc gagcggttgc ggc
//
