LOCUS       NZ_CP117309             6047 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain RM004
            plasmid pRM004_2, complete sequence.
ACCESSION   NZ_CP117309
VERSION     NZ_CP117309.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32950809
            Assembly: GCF_028892975.1
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 6047)
  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 6047)
  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                   :: 539X
            Sequencing Technology :: illumina MiSeq + Nanopore Gridion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:17:33
            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)                     :: 4,726
            CDSs (total)                      :: 4,608
            Genes (coding)                    :: 4,467
            CDSs (with protein)               :: 4,467
            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)              :: 141
            CDSs (without protein)            :: 141
            Pseudo Genes (ambiguous residues) :: 0 of 141
            Pseudo Genes (frameshifted)       :: 64 of 141
            Pseudo Genes (incomplete)         :: 82 of 141
            Pseudo Genes (internal stop)      :: 28 of 141
            Pseudo Genes (multiple problems)  :: 30 of 141
            Pseudo Genes (short protein)      :: 1 of 141
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117309.1.
            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..6047
                     /organism="Salmonella enterica subsp. enterica serovar
                     Derby"
                     /mol_type="genomic DNA"
                     /strain="RM004"
                     /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="pRM004_2"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2000-10-30"
                     /collected_by="University of Nebraska-Lincoln"
     gene            complement(561..710)
                     /locus_tag="PQQ01_RS23565"
                     /old_locus_tag="PQQ01_23565"
     CDS             complement(561..710)
                     /locus_tag="PQQ01_RS23565"
                     /old_locus_tag="PQQ01_23565"
                     /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            1899..2714
                     /gene="sul2"
                     /locus_tag="PQQ01_RS23570"
                     /old_locus_tag="PQQ01_23570"
     ARG             1900..2711
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2801..>3043
                     /gene="glmM"
                     /locus_tag="PQQ01_RS23575"
                     /old_locus_tag="PQQ01_23575"
                     /pseudo=""
     CDS             2801..>3043
                     /gene="glmM"
                     /locus_tag="PQQ01_RS23575"
                     /old_locus_tag="PQQ01_23575"
                     /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(3279..4772)
                     /locus_tag="PQQ01_RS23580"
                     /old_locus_tag="PQQ01_23580"
     CDS             complement(3279..4772)
                     /locus_tag="PQQ01_RS23580"
                     /old_locus_tag="PQQ01_23580"
                     /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(4816..5205)
                     /locus_tag="PQQ01_RS23585"
                     /old_locus_tag="PQQ01_23585"
     CDS             complement(4816..5205)
                     /locus_tag="PQQ01_RS23585"
                     /old_locus_tag="PQQ01_23585"
                     /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            5423..5863
                     /locus_tag="PQQ01_RS23590"
                     /old_locus_tag="PQQ01_23590"
     CDS             5423..5863
                     /locus_tag="PQQ01_RS23590"
                     /old_locus_tag="PQQ01_23590"
                     /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"
     Typing          complement(746..919)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          843..1448
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acaccattca gccggggtaa gtcctgtttc cggcgttctt cccatccgaa aacggtgaac
       61 ggggacgcaa tttattgcgt ggccgtgaag cgttgccggc gcagccggaa aacccgctgt
      121 cagcacgttc aggaaggggg tgatgtacaa atggcacaga ggatgaaagt gacgtatgag
      181 ctgaaggaat gatgtaaaag tgatgtataa gtgatgtaaa agtgatgtat gaactgaagg
      241 agcgatgtaa ttctgtagtc aggaagaata acccgttcat gcaggcatga acgatacagt
      301 gaggaacgct ttttttgtca cgatctcccc ttaacctgcg taaatcaccc gccatggttg
      361 attatttttc aacctcaaaa tggtcataca cctaacgcag ccgcgatttt catcgcaact
      421 gcatgaagta aaagaaaaaa aaggaatatt tcgttttcac gagtaatacc cgggtattaa
      481 aaatccactg taattacatg aaaataaaga aataaaaggt aataccggag tattaccacg
      541 tacgcgggca agcgaaaaag ctataacgct tcccggccga caggcgaccc aaaatccaca
      601 ggggcatgca ggttctcttc agtaacctgc gccattaaat caaaaaggtc atattcgccg
      661 ggaagctgcg tatcagtcga atccagttgt tcatcatatt cagatggcat ggggtgatat
      721 ccagtagctg agaggttgtt agcgggtttc ggggcgcagc cctgaaccag tcatgtagcg
      781 ctagcggagt gtatactggc ttactatgtt gccacgattg cgaaaatcag tgaagtgctt
      841 catgtggcag gagaaaaaag gcagcaccgg cgcgtcagca gaatatgcga tacaggagat
      901 attccgcttc ctcgctcact gactcgctac gctcggtcgt tcggctgcgg cgagcggtac
      961 cggcttacgg acggggacgg aaatttcctg gaagatacca ggaagacact tagcaaagaa
     1021 gagataaggc cacggcgaag ccgtttttcc ataggctccg cccccctgac aagcatcgca
     1081 aaatctgacg ctcaaatcag tggtggcgaa acccgacagg actataaaga tcccaggcgt
     1141 ttccccctgg tagctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca
     1201 ttccgctgtt atggccgcgg tttctcattc cacgcctgac actcagttcc gtgaaggcag
     1261 ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgaccgc tgcgccttgt
     1321 ccggtaacta tcaacttgag tccaacccgg aaagacacga caaaacgcca ctggcagcag
     1381 ccattagtaa caggagtgca cgagaagata gattaagagg tcttgaagta gaggcctgac
     1441 tgcggctaca ctgaaagaac agttttggta atggcggtct cgtgaaccct gttaccgggt
     1501 taagcagttc cccaactgac ttaaccttcg aacaaaccgc ctccccaggc ggttttttcg
     1561 tttacagagc aagagattac gattcattga aaaggatctc aagaagatcc tttgtagatt
     1621 actatcaatt aatcttccga acatgacacc agtcactgtt gattacggtt aaaccgctcc
     1681 gtaacaggtt tccctcgtat tggtgacttg cagcaccaaa gaagcaaaaa agataaatat
     1741 atctacttat tgagagatga tatatttatt tccaaaatgc tacagataca tcatcatgaa
     1801 acggatcacc gcaaacaggt tactcgcctg gggattccct ttcgacccga gcatccgtat
     1861 gagactcatg ctcgattatt attattatag aagcccccat gaataaatcg ctcatcattt
     1921 tcggcatcgt caacataacc tcggacagtt tctccgatgg aggccggtat ctggcgccag
     1981 acgcagccat tgcgcaggcg cgtaagctga tggccgaggg ggcagatgtg atcgacctcg
     2041 gtccggcatc cagcaatccc gacgccgcgc ctgtttcgtc cgacacagaa atcgcgcgta
     2101 tcgcgccggt gctggacgcg ctcaaggcag atggcattcc cgtctcgctc gacagttatc
     2161 aacccgcgac gcaagcctat gccttgtcgc gtggtgtggc ctatctcaat gatattcgcg
     2221 gttttccaga cgctgcgttc tatccgcaat tggcgaaatc atctgccaaa ctcgtcgtta
     2281 tgcattcggt gcaagacggg caggcagatc ggcgcgaggc acccgctggc gacatcatgg
     2341 atcacattgc ggcgttcttt gacgcgcgca tcgcggcgct gacgggtgcc ggtatcaaac
     2401 gcaaccgcct tgtccttgat cccggcatgg ggttttttct gggggctgct cccgaaacct
     2461 cgctctcggt gctggcgcgg ttcgatgaat tgcggctgcg cttcgatttg ccggtgcttc
     2521 tgtctgtttc gcgcaaatcc tttctgcgcg cgctcacagg ccgtggtccg ggggatgtcg
     2581 gggccgcgac actcgctgca gagcttgccg ccgccgcagg tggagctgac ttcatccgca
     2641 cacacgagcc gcgccccttg cgcgacgggc tggcggtatt ggcggcgctg aaagaaaccg
     2701 caagaattcg ttaactgcac attcgggata tttctctata ttcgcggttc agcaggcatg
     2761 tcccctttga gggcgacccg acgacaggat aatcgacctt atggtgcgca aatatttcgg
     2821 cacagacggt attcgtggca aagccaacga aggcgcgatg acggcggaaa ccgccttgcg
     2881 cgtcggcatg gcggctggcc gtgtctttcg tcgcggtgac caccgccatc gtgtcgtgat
     2941 cggcaaggat acgcgcctgt cgggctatat gcttgaaccc gcgctcacag ccggtttcac
     3001 ctcgatgggc atggacgtat tcctttttgg cccgctgccg acaacgtata ggaagaataa
     3061 acgccctttt cacccaagtc caacagcttt ggaccacagt tgactctttc gacacccctg
     3121 cgatgcaacc caatccggct gacggggagc cagcaacgct gaaaatttac cctcctcttt
     3181 cccactagcg gctccttttc cgacaaccag cacggcggat ccctgccgcg gcgctgtgaa
     3241 cgcagcattt tgattggtat cgttggcctt caggctcgtc agtcaaacag acccaggagc
     3301 agctcagccg gtggcgcccg gctttcgggt aacgccctgg tcccgctggt ttcggctttg
     3361 tgcttcaggt gatcaaggat ctgcttgatc actatagggt cttcaatgca ggcgatgact
     3421 ttcatggcgc cgccgcagcc gctgcaggtc tcgatgtcga tattgaaaac acgcttgagc
     3481 cgttgcgccc atgtcatcga cgctcgccgt tgtgctggtg ttgccggttc atcagccacc
     3541 ctgaccttgt tgcccctgcc ccgttttgcc ggcgtgacca acgcccggtg ccgactgttg
     3601 ggtgcgaaca ccccgtggaa gcgggttagg ttgactctgg gcttcggtac cagggcggcc
     3661 agccttgcaa tgaaatccaa tggttcgaaa atgacgtgcg tggtgccgtc ccggtacggc
     3721 gtcttgagct ggtagcgcac gttgccgcct cgtgttaacg acagccgctt ctcggatacc
     3781 gccgggcggc tgatgtaccg gcacagccgt tcgagcttct tgcgttcatc ggccctggcc
     3841 gccacgccgg cgtgcaggct ggacccggct accttgccaa tcccgtcacc gaacggatca
     3901 ccactggtcg gcagagtttg caaagtgaac acctttcgcc ccgcctgtga accgacagcg
     3961 atacggtaag tgatcgagtg ccccagcagg ggtgtcatcg ggtcgtcatc caccgcatcc
     4021 gaggccagat agctgttttc gacatcccgt tccagcaggc cttgccgttc cagatagcga
     4081 cccacccggt gggcgatggt gtgcgtcagc tgggtgagct ctgggctggt cggcgccttg
     4141 acccagcgga aacgcgctga gccgtgggat tgctcgacat acacaccgtc gagaaacagc
     4201 atgtggaagt gaacattcag attgagcgcc gatccaaaac gctggatcag ggtgaccgcg
     4261 cccgtcttgg ccacttggtg ggtatggccc gctttcttga ccaggtgcgt ggcaatgacg
     4321 cggtaaacga tgcccagcac ccaccccatg atctcgggcc ggctggcaaa caggaaacgc
     4381 agctgaaacg ggaagctcaa cacccactga cgcatgggtt gttcaggcag tacttcatca
     4441 accagcaagg cggcactttc ggccatccgc cgcgccccac agctcgggca gaaaccgcga
     4501 cgcttacagc tgaaagcgac caggtgctcg gcgtggcaag actcgcagcg aacccgtaga
     4561 aagccatgct ccagccgccc gcattggaga aattcttcaa attcccgttg cacatagccc
     4621 ggcaattcct ttccctgctc tgccataagc gcagcgaatg ccgggtaata ctcgtcaacg
     4681 atctgataga gaagggtttg ctcgggtcgg tggctctggt aacgaccagt atcccgatcc
     4741 cggctggccg tcctggccgc cacatgaggc atgttccgcg tccttgcaat actgtgttta
     4801 catacagtct atcgcttagc ggaaagttct tttaccctca gccgaaatgc ctgccgttgc
     4861 tagacattgc cagccagtgc ccgtcactcc cactcttaca ttgttcgcag tatctaggta
     4921 catgttattg cgtgcacctt catgatgtat aatgttatta atgacagcag aaagatcgac
     4981 agaattaata ttcttcgtac ctgggacagt tatcgggtgt cggccagtga tgagaccaaa
     5041 ggatgcagta taagatgaac cactactatt atcatggcca ccattaccac caccgttaaa
     5101 actacctccc gaacttccag agccgctatg accatcattg taggggtcat ttggtcccat
     5161 gtgaccaaaa ccaccgacag taccgctatt taactctgta ctcataaaat tatcctcttt
     5221 gacttttaaa aacagcaaaa actgtattta taacaatgtg tttatataca gtattcgaaa
     5281 tactacgccc gtcaaaacca caccgtcaac aggttttttg tgtatttttc acgcctcacg
     5341 ggcagcctca gaccttttgt gttaaaacag taatatgttc tgctgttaca atacggtaca
     5401 cacaggagac actgtcactt ttatggcatg gcacacagtt caagagacac tgaaattaac
     5461 aggaaagtcg cgctcgcaat tatatcgtga catggctaaa ggccttgtca gctatcgcac
     5521 aggaaaaaat gatcgccggg agttcgagac cagtgaactg attcgggcct atggcgagct
     5581 gcgcacttct gagacaccaa aaaggcacaa ggagggacac tccaaatctg tcgttagcca
     5641 ggcggaaaat gctcagctag acgtcattca gcagaaactg gacgctctgc agcagactgt
     5701 taccctaatg cttgaagaca agatggcgcg ggaagcagaa aaccgcctgc gaaatgagga
     5761 gagggaacaa ctacaggccg aaattagccg tctggctgac gcgctggcac aggaaaaaaa
     5821 gcggggattc tggtcgcggc tgtttcgctc cggttcagag taacagtgca ggtgactctg
     5881 atttaccata acatctgtta tcagcaccgc ctgagaggcc ctcagggcgt ttctgacggg
     5941 aaaccggtaa aacaggcaac aaaccacccg aaaacccgcc agaaacgcgc aggctctgtt
     6001 tttacggcat gcatgagtat gcgcacaagt gcatagcgcg gaaattc
//
