LOCUS       NZ_CP117320             6045 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain RM002
            plasmid pRM002_3, complete sequence.
ACCESSION   NZ_CP117320
VERSION     NZ_CP117320.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32950807
            Assembly: GCF_028893015.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Derby
  ORGANISM  Salmonella enterica subsp. enterica serovar Derby
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 6045)
  AUTHORS   Lewis,G.L., Fenton,R.J., Moriyama,E.N., Loy,J.D. and Moxley,R.A.
  TITLE     Association of ISVsa3 with Multidrug Resistance in Salmonella
            enterica Isolates from Cattle (Bos taurus)
  JOURNAL   Microorganisms 11 (3), 631 (2023)
   PUBMED   36985205
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 6045)
  AUTHORS   Moxley,R.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-FEB-2023) School of Biological Sciences, University of
            Nebraska-Lincoln, 403 Manter Hall, Lincoln, NE 68588-0118, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 04-OCT-2021
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 510X
            Sequencing Technology :: illumina MiSeq + Nanopore Gridion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:33:58
            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)                     :: 4,807
            CDSs (total)                      :: 4,689
            Genes (coding)                    :: 4,517
            CDSs (with protein)               :: 4,517
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 172
            CDSs (without protein)            :: 172
            Pseudo Genes (ambiguous residues) :: 0 of 172
            Pseudo Genes (frameshifted)       :: 83 of 172
            Pseudo Genes (incomplete)         :: 82 of 172
            Pseudo Genes (internal stop)      :: 40 of 172
            Pseudo Genes (multiple problems)  :: 30 of 172
            Pseudo Genes (short protein)      :: 1 of 172
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117320.1.
            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..6045
                     /organism="Salmonella enterica subsp. enterica serovar
                     Derby"
                     /mol_type="genomic DNA"
                     /strain="RM002"
                     /serovar="Derby"
                     /isolation_source="Water from tanks in pens"
                     /host="Bos taurus"
                     /sub_species="enterica"
                     /db_xref="taxon:28144"
                     /plasmid="pRM002_3"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2000-09-19"
                     /collected_by="University of Nebraska-Lincoln"
     gene            complement(60..875)
                     /gene="sul2"
                     /locus_tag="PQQ14_RS24005"
                     /old_locus_tag="PQQ14_24005"
     ARG             complement(64..875)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2064..2213
                     /locus_tag="PQQ14_RS24010"
                     /old_locus_tag="PQQ14_24010"
     CDS             2064..2213
                     /locus_tag="PQQ14_RS24010"
                     /old_locus_tag="PQQ14_24010"
                     /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_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(2958..3398)
                     /locus_tag="PQQ14_RS24015"
                     /old_locus_tag="PQQ14_24015"
     CDS             complement(2958..3398)
                     /locus_tag="PQQ14_RS24015"
                     /old_locus_tag="PQQ14_24015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            3616..4005
                     /locus_tag="PQQ14_RS24020"
                     /old_locus_tag="PQQ14_24020"
     CDS             3616..4005
                     /locus_tag="PQQ14_RS24020"
                     /old_locus_tag="PQQ14_24020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4049..5542
                     /locus_tag="PQQ14_RS24025"
                     /old_locus_tag="PQQ14_24025"
     CDS             4049..5542
                     /locus_tag="PQQ14_RS24025"
                     /old_locus_tag="PQQ14_24025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91-like element ISVsa3 family transposase"
                     /protein_id="WP_001120888.1"
                     /translation="MPHVAARTASRDRDTGRYQSHRPEQTLLYQIVDEYYPAFAALMAE
                     QGKELPGYVQREFEEFLQCGRLEHGFLRVRCESCHAEHLVAFSCKRRGFCPSCGARRMA
                     ESAALLVDEVLPEQPMRQWVLSFPFQLRFLFASRPEIMGWVLGIVYRVIATHLVKKAGH
                     THQVAKTGAVTLIQRFGSALNLNVHFHMLFLDGVYVEQSHGSARFRWVKAPTSPELTQL
                     THTIAHRVGRYLERQGLLERDVENSYLASDAVDDDPMTPLLGHSITYRIAVGSQAGRKV
                     FTLQTLPTSGDPFGDGIGKVAGSSLHAGVAARADERKKLERLCRYISRPAVSEKRLSLT
                     RGGNVRYQLKTPYRDGTTHVIFEPLDFIARLAALVPKPRVNLTRFHGVFAPNSRHRALV
                     TPAKRGRGNKVRVADEPATPAQRRASMTWAQRLKRVFNIDIETCSGCGGAMKVIACIED
                     PIVIKQILDHLKHKAETSGTRALPESRAPPAELLLGLFD"
                     /name="IS91-like element ISVsa3 family transposase"
     gene            complement(<5778..6020)
                     /gene="glmM"
                     /locus_tag="PQQ14_RS24030"
                     /old_locus_tag="PQQ14_24030"
                     /pseudo=""
     CDS             complement(<5778..6020)
                     /gene="glmM"
                     /locus_tag="PQQ14_RS24030"
                     /old_locus_tag="PQQ14_24030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008891390.1"
                     /note="catalyzes the conversion of glucosamine-6-phosphate
                     to glucosamine-1-phosphate; 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="phosphoglucosamine mutase"
                     /name="glmM"
     Typing          1856..2029
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(1327..1932)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgctcaaagg ggacatgtct gctgcaccgc gaatatagag aaatatcccg aatgtgcagt
       61 taacgaattc ttgcggtttc tttcagcgcc gccaataccg ccagcccgtc gcgcaagggg
      121 cgcggctcgt gtgtgcggat gaagtcagct ccacctgcgg cggcggcaag ctctgcagcg
      181 agtgtcgcgg ccccgacatc ccccggacca cggcctgtga gcgcgcgcag aaaggatttg
      241 cgcgaaacag acagaagcac cggcaaatcg aagcgcagcc gcaattcatc gaaccgcgcc
      301 agcaccgaga gcgaggtttc gggagcagcc cccagaaaaa accccatgcc gggatcaagg
      361 acaaggcggt tgcgtttgat accggcaccc gtcagcgccg cgatgcgcgc gtcaaagaac
      421 gccgcaatgt gatccatgat gtcgccagcg ggtgcctcgc gccgatctgc ctgcccgtct
      481 tgcaccgaat gcataacgac gagtttggca gatgatttcg ccaattgcgg atagaacgca
      541 gcgtctggaa aaccgcgaat atcattgaga taggccacac cacgcgacaa ggcataggct
      601 tgcgtcgcgg gttgataact gtcgagcgag acgggaatgc catctgcctt gagcgcgtcc
      661 agcaccggcg cgatacgcgc gatttctgtg tcggacgaaa caggcgcggc gtcgggattg
      721 ctggatgccg gaccgaggtc gatcacatct gccccctcgg ccatcagctt acgcgcctgc
      781 gcaatggctg cgtctggcgc cagataccgg cctccatcgg agaaactgtc cgaggttatg
      841 ttgacgatgc cgaaaatgat gagcgattta ttcatggggg cttctataat aataataatc
      901 gagcatgagt ctcatacgga tgctcgggtc gaaagggaat ccccaggcga gtaacctgtt
      961 tgcggtgatc cgtttcatga tgatgtatct gtagcatttt ggaaataaat atatcatctc
     1021 tcaataagta gatatattta tcttttttgc ttctttggtg ctgcaagtca ccaatacgag
     1081 ggaaacctgt tacggagcgg tttaaccgta atcaacagtg actggtgtca tgttcggaag
     1141 attaattgat agtaatctac aaaggatctt cttgagatcc ttttcaatga atcgtaatct
     1201 cttgctctgt aaacgaaaaa accgcctggg gaggcggttt gttcgaaggt taagtcagtt
     1261 ggggaactgc ttaacccggt aacagggttc acgagaccgc cattaccaaa actgttcttt
     1321 cagtgtagcc gcagtcaggc ctctacttca agacctctta atctatcttc tcgtgcactc
     1381 ctgttactaa tggctgctgc cagtggcgtt ttgtcgtgtc tttccgggtt ggactcaagt
     1441 tgatagttac cggacaaggc gcagcggtcg gactgaacgg ggggttcgtg catacagtcc
     1501 agcttggagc gaactgcctt cacggaactg agtgtcaggc gtggaatgag aaaccgcggc
     1561 cataacagcg gaatgacacc ggtaaaccga aaggcaggaa caggagagcg cacgagggag
     1621 ctaccagggg gaaacgcctg ggatctttat agtcctgtcg ggtttcgcca ccactgattt
     1681 gagcgtcaga ttttgcgatg cttgtcaggg gggcggagcc tatggaaaaa cggcttcgcc
     1741 gtggccttat ctcttctttg ctaagtgtct tcctggtatc ttccaggaaa tttccgtccc
     1801 cgtccgtaag ccggtaccgc tcgccgcagc cgaacgaccg agcgtagcga gtcagtgagc
     1861 gaggaagcgg aatatctcct gtatcgcata ttctgctgac gcgccggtgc tgcctttttt
     1921 ctcctgccac atgaagcact tcactgattt tcgcaatcgt ggcaacatag taagccagta
     1981 tacactccgc tagcgctaca tgactggttc agggctgcgc cccgaaaccc gctaacaacc
     2041 tctcagctac tggatatcac cccatgccat ctgaatatga tgaacaactg gattcgactg
     2101 atacgcagct tcccggcgaa tatgaccttt ttgatttaat ggcgcaggtt actgaagaga
     2161 acctgcatgc ccctgtggat tttgggtcgc ctgtcggccg ggaagcgtta tagctttttc
     2221 gcttgcccgc gtacgtggta atactccggt attacctttt atttctttat tttcatgtaa
     2281 ttacagtgga tttttaatac ccgggtatta ctcgtgaaaa cgaaatattc cttttctttc
     2341 ttttaattca tgcagttgcg atgaaaatcg cggctgcgtt aggtgtatga ccattttgag
     2401 gttgaaaaat aatcaaccat ggcgggtgat ttacgcaggt taaggggaga tcgtgacaaa
     2461 aaaagcgttc ctcactgtat cgttcatgcc tgcatgaacg ggttattctt cctgactaca
     2521 gaattacatc gctccttcag ttcatacatc acttttacat cacttataca tcacttttac
     2581 atcattcctt cagctcatac gtcactttca tcctctgtgc catttgtaca tcaccccctt
     2641 cctgaacgtg ctgacagcgg gttttccggc tgcgccggca acgcttcacg gccacgcaat
     2701 aaattgcgtc cccgttcacc gttttcggat gggaagaacg ccggaaacag gacttacccc
     2761 ggctgaatgg tgtgaatttc cgcgctatgc acttgtgcgc atactcatgc atgccgtaaa
     2821 aacagagcct gcgcgtttct ggcgggtttt cgggtggttt gttgcctgtt ttaccggttt
     2881 cccgtcagaa acgccctgag ggcctctcag gcggtgctga taacagatgt tatggtaaat
     2941 cagagtcacc tgcactgtta ctctgaaccg gagcgaaaca gccgcgacca gaatccccgc
     3001 tttttttcct gtgccagcgc gtcagccaga cggctaattt cggcctgtag ttgttccctc
     3061 tcctcatttc gcaggcggtt ttctgcttcc cgcgccatct tgtcttcaag cattagggta
     3121 acagtctgct gcagagcgtc cagtttctgc tgaatgacgt ctagctgagc attttccgcc
     3181 tggctaacga cagatttgga gtgtccctcc ttgtgccttt ttggtgtctc agaagtgcgc
     3241 agctcgccat aggcccgaat cagttcactg gtctcgaact cccggcgatc attttttcct
     3301 gtgcgatagc tgacaaggcc tttagccatg tcacgatata attgcgagcg cgactttcct
     3361 gttaatttca gtgtctcttg aactgtgtgc catgccataa aagtgacagt gtctcctgtg
     3421 tgtaccgtat tgtaacagca gaacatatta ctgttttaac acaaaaggtc tgaggctgcc
     3481 cgtgaggcgt gaaaaataca caaaaaacct gttgacggtg tggttttgac gggcgtagta
     3541 tttcgaatac tgtatataaa cacattgtta taaatacagt ttttgctgtt tttaaaagtc
     3601 aaagaggata attttatgag tacagagtta aatagcggta ctgtcggtgg ttttggtcac
     3661 atgggaccaa atgaccccta caatgatggt catagcggct ctggaagttc gggaggtagt
     3721 tttaacggtg gtggtaatgg tggccatgat aatagtagtg gttcatctta tactgcatcc
     3781 tttggtctca tcactggccg acacccgata actgtcccag gtacgaagaa tattaattct
     3841 gtcgatcttt ctgctgtcat taataacatt atacatcatg aaggtgcacg caataacatg
     3901 tacctagata ctgcgaacaa tgtaagagtg ggagtgacgg gcactggctg gcaatgtcta
     3961 gcaacggcag gcatttcggc tgagggtaaa agaactttcc gctaagcgat agactgtatg
     4021 taaacacagt attgcaagga cgcggaacat gcctcatgtg gcggccagga cggccagccg
     4081 ggatcgggat actggtcgtt accagagcca ccgacccgag caaacccttc tctatcagat
     4141 cgttgacgag tattacccgg cattcgctgc gcttatggca gagcagggaa aggaattgcc
     4201 gggctatgtg caacgggaat ttgaagaatt tctccaatgc gggcggctgg agcatggctt
     4261 tctacgggtt cgctgcgagt cttgccacgc cgagcacctg gtcgctttca gctgtaagcg
     4321 tcgcggtttc tgcccgagct gtggggcgcg gcggatggcc gaaagtgccg ccttgctggt
     4381 tgatgaagta ctgcctgaac aacccatgcg tcagtgggtg ttgagcttcc cgtttcagct
     4441 gcgtttcctg tttgccagcc ggcccgagat catggggtgg gtgctgggca tcgtttaccg
     4501 cgtcattgcc acgcacctgg tcaagaaagc gggccatacc caccaagtgg ccaagacggg
     4561 cgcggtcacc ctgatccagc gttttggatc ggcgctcaat ctgaatgttc acttccacat
     4621 gctgtttctc gacggtgtgt atgtcgagca atcccacggc tcagcgcgtt tccgctgggt
     4681 caaggcgccg accagcccag agctcaccca gctgacgcac accatcgccc accgggtggg
     4741 tcgctatctg gaacggcaag gcctgctgga acgggatgtc gaaaacagct atctggcctc
     4801 ggatgcggtg gatgacgacc cgatgacacc cctgctgggg cactcgatca cttaccgtat
     4861 cgctgtcggt tcacaggcgg ggcgaaaggt gttcactttg caaactctgc cgaccagtgg
     4921 tgatccgttc ggtgacggga ttggcaaggt agccgggtcc agcctgcacg ccggcgtggc
     4981 ggccagggcc gatgaacgca agaagctcga acggctgtgc cggtacatca gccgcccggc
     5041 ggtatccgag aagcggctgt cgttaacacg aggcggcaac gtgcgctacc agctcaagac
     5101 gccgtaccgg gacggcacca cgcacgtcat tttcgaacca ttggatttca ttgcaaggct
     5161 ggccgccctg gtaccgaagc ccagagtcaa cctaacccgc ttccacgggg tgttcgcacc
     5221 caacagtcgg caccgggcgt tggtcacgcc ggcaaaacgg ggcaggggca acaaggtcag
     5281 ggtggctgat gaaccggcaa caccagcaca acggcgagcg tcgatgacat gggcgcaacg
     5341 gctcaagcgt gttttcaata tcgacatcga gacctgcagc ggctgcggcg gcgccatgaa
     5401 agtcatcgcc tgcattgaag accctatagt gatcaagcag atccttgatc acctgaagca
     5461 caaagccgaa accagcggga ccagggcgtt acccgaaagc cgggcgccac cggctgagct
     5521 gctcctgggt ctgtttgact gacgagcctg aaggccaacg ataccaatca aaatgctgcg
     5581 ttcacagcgc cgcggcaggg atccgccgtg ctggttgtcg gaaaaggagc cgctagtggg
     5641 aaagaggagg gtaaattttc agcgttgctg gctccccgtc agccggattg ggttgcatcg
     5701 caggggtgtc gaaagagtca actgtggtcc aaagctgttg gacttgggtg aaaagggcgt
     5761 ttattcttcc tatacgttgt cggcagcggg ccaaaaagga atacgtccat gcccatcgag
     5821 gtgaaaccgg ctgtgagcgc gggttcaagc atatagcccg acaggcgcgt atccttgccg
     5881 atcacgacac gatggcggtg gtcaccgcga cgaaagacac ggccagccgc catgccgacg
     5941 cgcaaggcgg tttccgccgt catcgcgcct tcgttggctt tgccacgaat accgtctgtg
     6001 ccgaaatatt tgcgcaccat aaggtcgatt atcctgtcgt cgggt
//
