LOCUS       NZ_CP117303             6046 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain RM006
            plasmid pRM006_2, complete sequence.
ACCESSION   NZ_CP117303
VERSION     NZ_CP117303.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32950811
            Assembly: GCF_028892955.1
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 6046)
  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 6046)
  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                   :: 248X
            Sequencing Technology :: illumina MiSeq + Nanopore Gridion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:08:28
            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)                     :: 4,705
            CDSs (total)                      :: 4,587
            Genes (coding)                    :: 4,449
            CDSs (with protein)               :: 4,449
            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)              :: 138
            CDSs (without protein)            :: 138
            Pseudo Genes (ambiguous residues) :: 0 of 138
            Pseudo Genes (frameshifted)       :: 63 of 138
            Pseudo Genes (incomplete)         :: 78 of 138
            Pseudo Genes (internal stop)      :: 30 of 138
            Pseudo Genes (multiple problems)  :: 30 of 138
            Pseudo Genes (short protein)      :: 1 of 138
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117303.1.
            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..6046
                     /organism="Salmonella enterica subsp. enterica serovar
                     Derby"
                     /mol_type="genomic DNA"
                     /strain="RM006"
                     /serovar="Derby"
                     /isolation_source="Manila ropes placed above water tanks
                     and feed bunks used as sampling devices"
                     /host="Bos taurus"
                     /sub_species="enterica"
                     /db_xref="taxon:28144"
                     /plasmid="pRM006_2"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2000-10-30"
                     /collected_by="University of Nebraska-Lincoln"
     gene            663..812
                     /locus_tag="PQP83_RS23495"
                     /old_locus_tag="PQP83_23495"
     CDS             663..812
                     /locus_tag="PQP83_RS23495"
                     /old_locus_tag="PQP83_23495"
                     /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(1556..1996)
                     /locus_tag="PQP83_RS23500"
                     /old_locus_tag="PQP83_23500"
     CDS             complement(1556..1996)
                     /locus_tag="PQP83_RS23500"
                     /old_locus_tag="PQP83_23500"
                     /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            2214..2603
                     /locus_tag="PQP83_RS23505"
                     /old_locus_tag="PQP83_23505"
     CDS             2214..2603
                     /locus_tag="PQP83_RS23505"
                     /old_locus_tag="PQP83_23505"
                     /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            2647..4140
                     /locus_tag="PQP83_RS23510"
                     /old_locus_tag="PQP83_23510"
     CDS             2647..4140
                     /locus_tag="PQP83_RS23510"
                     /old_locus_tag="PQP83_23510"
                     /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(<4376..4618)
                     /gene="glmM"
                     /locus_tag="PQP83_RS23515"
                     /old_locus_tag="PQP83_23515"
                     /pseudo=""
     CDS             complement(<4376..4618)
                     /gene="glmM"
                     /locus_tag="PQP83_RS23515"
                     /old_locus_tag="PQP83_23515"
                     /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"
     gene            complement(4705..5520)
                     /gene="sul2"
                     /locus_tag="PQP83_RS23520"
                     /old_locus_tag="PQP83_23520"
     ARG             complement(4709..5520)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          455..628
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(2..531)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.948"
                     /coverage="87.0"
                     /evalue="0.0"
ORIGIN
        1 agtggcgttt tgtcgtgtct ttccgggttg gactcaagtt gatagttacc ggacaaggcg
       61 cagcggtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgccttc
      121 acggaactga gtgtcaggcg tggaatgaga aaccgcggcc ataacagcgg aatgacaccg
      181 gtaaaccgaa aggcaggaac aggagagcgc acgagggagc taccaggggg aaacgcctgg
      241 gatctttata gtcctgtcgg gtttcgccac cactgatttg agcgtcagat tttgcgatgc
      301 ttgtcagggg ggcggagcct atggaaaaac ggcttcgccg tggccttatc tcttctttgc
      361 taagtgtctt cctggtatct tccaggaaat ttccgtcccc gtccgtaagc cggtaccgct
      421 cgccgcagcc gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga atatctcctg
      481 tatcgcatat tctgctgacg cgccggtgct gccttttttc tcctgccaca tgaagcactt
      541 cactgatttt cgcaatcgtg gcaacatagt aagccagtat acactccgct agcgctacat
      601 gactggttca gggctgcgcc ccgaaacccg ctaacaacct ctcagctact ggatatcacc
      661 ccatgccatc tgaatatgat gaacaactgg attcgactga tacgcagctt cccggcgaat
      721 atgacctttt tgatttaatg gcgcaggtta ctgaagagaa cctgcatgcc cctgtggatt
      781 ttgggtcgcc tgtcggccgg gaagcgttat agctttttcg cttgcccgcg tacgtggtaa
      841 tactccggta ttacctttta tttctttatt ttcatgtaat tacagtggat ttttaatacc
      901 cgggtattac tcgtgaaaac gaaatattcc tttttttctt ttaattcatg cagttgcgat
      961 gaaaatcgcg gctgcgttag gtgtatgacc attttgaggt tgaaaaataa tcaaccatgg
     1021 cgggtgattt acgcaggtta aggggagatc gtgacaaaaa aagcgttcct cactgtatcg
     1081 ttcatgcctg catgaacggg ttattcttcc tgactacaga attacatcgc tccttcagtt
     1141 catacatcac ttttacatca cttatacatc acttttacat cattccttca gctcatacgt
     1201 cactttcatc ctctgtgcca tttgtacatc acccccttcc tgaacgtgct gacagcgggt
     1261 tttccggctg cgccggcaac gcttcacggc cacgcaataa attgcgtccc cgttcaccgt
     1321 tttcggatgg gaagaacgcc ggaaacagga cttaccccgg ctgaatggtg tgaatttccg
     1381 cgctatgcac ttgtgcgcat actcatgcat gccgtaaaaa cagagcctgc gcgtttctgg
     1441 cgggttttcg ggtggtttgt tgcctgtttt accggtttcc cgtcagaaac gccctgaggg
     1501 cctctcaggc ggtgctgata acagatgtta tggtaaatca gagtcacctg cactgttact
     1561 ctgaaccgga gcgaaacagc cgcgaccaga atccccgctt tttttcctgt gccagcgcgt
     1621 cagccagacg gctaatttcg gcctgtagtt gttccctctc ctcatttcgc aggcggtttt
     1681 ctgcttcccg cgccatcttg tcttcaagca ttagggtaac agtctgctgc agagcgtcca
     1741 gtttctgctg aatgacgtct agctgagcat tttccgcctg gctaacgaca gatttggagt
     1801 gtccctcctt gtgccttttt ggtgtctcag aagtgcgcag ctcgccatag gcccgaatca
     1861 gttcactggt ctcgaactcc cggcgatcat tttttcctgt gcgatagctg acaaggcctt
     1921 tagccatgtc acgatataat tgcgagcgcg actttcctgt taatttcagt gtctcttgaa
     1981 ctgtgtgcca tgccataaaa gtgacagtgt ctcctgtgtg taccgtattg taacagcaga
     2041 acatattact gttttaacac aaaaggtctg aggctgcccg tgaggcgtga aaaatacaca
     2101 aaaaacctgt tgacggtgtg gttttgacgg gcgtagtatt tcgaatactg tatataaaca
     2161 cattgttata aatacagttt ttgctgtttt taaaagtcaa agaggataat tttatgagta
     2221 cagagttaaa tagcggtact gtcggtggtt ttggtcacat gggaccaaat gacccctaca
     2281 atgatggtca tagcggctct ggaagttcgg gaggtagttt taacggtggt ggtaatggtg
     2341 gccatgataa tagtagtggt tcatcttata ctgcatcctt tggtctcatc actggccgac
     2401 acccgataac tgtcccaggt acgaagaata ttaattctgt cgatctttct gctgtcatta
     2461 ataacattat acatcatgaa ggtgcacgca ataacatgta cctagatact gcgaacaatg
     2521 taagagtggg agtgacgggc actggctggc aatgtctagc aacggcaggc atttcggctg
     2581 agggtaaaag aactttccgc taagcgatag actgtatgta aacacagtat tgcaaggacg
     2641 cggaacatgc ctcatgtggc ggccaggacg gccagccggg atcgggatac tggtcgttac
     2701 cagagccacc gacccgagca aacccttctc tatcagatcg ttgacgagta ttacccggca
     2761 ttcgctgcgc ttatggcaga gcagggaaag gaattgccgg gctatgtgca acgggaattt
     2821 gaagaatttc tccaatgcgg gcggctggag catggctttc tacgggttcg ctgcgagtct
     2881 tgccacgccg agcacctggt cgctttcagc tgtaagcgtc gcggtttctg cccgagctgt
     2941 ggggcgcggc ggatggccga aagtgccgcc ttgctggttg atgaagtact gcctgaacaa
     3001 cccatgcgtc agtgggtgtt gagcttcccg tttcagctgc gtttcctgtt tgccagccgg
     3061 cccgagatca tggggtgggt gctgggcatc gtttaccgcg tcattgccac gcacctggtc
     3121 aagaaagcgg gccataccca ccaagtggcc aagacgggcg cggtcaccct gatccagcgt
     3181 tttggatcgg cgctcaatct gaatgttcac ttccacatgc tgtttctcga cggtgtgtat
     3241 gtcgagcaat cccacggctc agcgcgtttc cgctgggtca aggcgccgac cagcccagag
     3301 ctcacccagc tgacgcacac catcgcccac cgggtgggtc gctatctgga acggcaaggc
     3361 ctgctggaac gggatgtcga aaacagctat ctggcctcgg atgcggtgga tgacgacccg
     3421 atgacacccc tgctggggca ctcgatcact taccgtatcg ctgtcggttc acaggcgggg
     3481 cgaaaggtgt tcactttgca aactctgccg accagtggtg atccgttcgg tgacgggatt
     3541 ggcaaggtag ccgggtccag cctgcacgcc ggcgtggcgg ccagggccga tgaacgcaag
     3601 aagctcgaac ggctgtgccg gtacatcagc cgcccggcgg tatccgagaa gcggctgtcg
     3661 ttaacacgag gcggcaacgt gcgctaccag ctcaagacgc cgtaccggga cggcaccacg
     3721 cacgtcattt tcgaaccatt ggatttcatt gcaaggctgg ccgccctggt accgaagccc
     3781 agagtcaacc taacccgctt ccacggggtg ttcgcaccca acagtcggca ccgggcgttg
     3841 gtcacgccgg caaaacgggg caggggcaac aaggtcaggg tggctgatga accggcaaca
     3901 ccagcacaac ggcgagcgtc gatgacatgg gcgcaacggc tcaagcgtgt tttcaatatc
     3961 gacatcgaga cctgcagcgg ctgcggcggc gccatgaaag tcatcgcctg cattgaagac
     4021 cctatagtga tcaagcagat ccttgatcac ctgaagcaca aagccgaaac cagcgggacc
     4081 agggcgttac ccgaaagccg ggcgccaccg gctgagctgc tcctgggtct gtttgactga
     4141 cgagcctgaa ggccaacgat accaatcaaa atgctgcgtt cacagcgccg cggcagggat
     4201 ccgccgtgct ggttgtcgga aaaggagccg ctagtgggaa agaggagggt aaattttcag
     4261 cgttgctggc tccccgtcag ccggattggg ttgcatcgca ggggtgtcga aagagtcaac
     4321 tgtggtccaa agctgttgga cttgggtgaa aagggcgttt attcttccta tacgttgtcg
     4381 gcagcgggcc aaaaaggaat acgtccatgc ccatcgaggt gaaaccggct gtgagcgcgg
     4441 gttcaagcat atagcccgac aggcgcgtat ccttgccgat cacgacacga tggcggtggt
     4501 caccgcgacg aaagacacgg ccagccgcca tgccgacgcg caaggcggtt tccgccgtca
     4561 tcgcgccttc gttggctttg ccacgaatac cgtctgtgcc gaaatatttg cgcaccataa
     4621 ggtcgattat cctgtcgtcg ggtcgccctc aaaggggaca tgcctgctga accgcgaata
     4681 tagagaaata tcccgaatgt gcagttaacg aattcttgcg gtttctttca gcgccgccaa
     4741 taccgccagc ccgtcgcgca aggggcgcgg ctcgtgtgtg cggatgaagt cagctccacc
     4801 tgcggcggcg gcaagctctg cagcgagtgt cgcggccccg acatcccccg gaccacggcc
     4861 tgtgagcgcg cgcagaaagg atttgcgcga aacagacaga agcaccggca aatcgaagcg
     4921 cagccgcaat tcatcgaacc gcgccagcac cgagagcgag gtttcgggag cagcccccag
     4981 aaaaaacccc atgccgggat caaggacaag gcggttgcgt ttgataccgg cacccgtcag
     5041 cgccgcgatg cgcgcgtcaa agaacgccgc aatgtgatcc atgatgtcgc cagcgggtgc
     5101 ctcgcgccga tctgcctgcc cgtcttgcac cgaatgcata acgacgagtt tggcagatga
     5161 tttcgccaat tgcggataga acgcagcgtc tggaaaaccg cgaatatcat tgagataggc
     5221 cacaccacgc gacaaggcat aggcttgcgt cgcgggttga taactgtcga gcgagacggg
     5281 aatgccatct gccttgagcg cgtccagcac cggcgcgata cgcgcgattt ctgtgtcgga
     5341 cgaaacaggc gcggcgtcgg gattgctgga tgccggaccg aggtcgatca catctgcccc
     5401 ctcggccatc agcttacgcg cctgcgcaat ggctgcgtct ggcgccagat accggcctcc
     5461 atcggagaaa ctgtccgagg ttatgttgac gatgccgaaa atgatgagcg atttattcat
     5521 gggggcttct ataataataa taatcgagca tgagtctcat acggatgctc gggtcgaaag
     5581 ggaatcccca ggcgagtaac ctgtttgcgg tgatccgttt catgatgatg tatctgtagc
     5641 attttggaaa taaatatatc atctctcaat aagtagatat atttatcttt tttgcttctt
     5701 tggtgctgca agtcaccaat acgagggaaa cctgttacgg agcggtttaa ccgtaatcaa
     5761 cagtgactgg tgtcatgttc ggaagattaa ttgatagtaa tctacaaagg atcttcttga
     5821 gatccttttc aatgaatcgt aatctcttgc tctgtaaacg aaaaaaccgc ctggggaggc
     5881 ggtttgttcg aaggttaagt cagttgggga actgcttaac ccggtaacag ggttcacgag
     5941 accgccatta ccaaaactgt tctttcagtg tagccgcagt caggcctcta cttcaagacc
     6001 tcttaatcta tcttctcgtg cactcctgtt actaatggct gctgcc
//
