LOCUS       NZ_CP117314             6047 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain RM003
            plasmid pRM003_2, complete sequence.
ACCESSION   NZ_CP117314
VERSION     NZ_CP117314.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32950808
            Assembly: GCF_028892995.1
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                   :: 624X
            Sequencing Technology :: illumina MiSeq + Nanopore Gridion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:14:11
            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)                     :: 4,719
            CDSs (total)                      :: 4,601
            Genes (coding)                    :: 4,418
            CDSs (with protein)               :: 4,418
            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)              :: 183
            CDSs (without protein)            :: 183
            Pseudo Genes (ambiguous residues) :: 0 of 183
            Pseudo Genes (frameshifted)       :: 88 of 183
            Pseudo Genes (incomplete)         :: 84 of 183
            Pseudo Genes (internal stop)      :: 45 of 183
            Pseudo Genes (multiple problems)  :: 31 of 183
            Pseudo Genes (short protein)      :: 1 of 183
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117314.1.
            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="RM003"
                     /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="pRM003_2"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2000-10-30"
                     /collected_by="University of Nebraska-Lincoln"
     gene            126..275
                     /locus_tag="PQP99_RS23525"
                     /old_locus_tag="PQP99_23525"
     CDS             126..275
                     /locus_tag="PQP99_RS23525"
                     /old_locus_tag="PQP99_23525"
                     /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(1020..1460)
                     /locus_tag="PQP99_RS23530"
                     /old_locus_tag="PQP99_23530"
     CDS             complement(1020..1460)
                     /locus_tag="PQP99_RS23530"
                     /old_locus_tag="PQP99_23530"
                     /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            1678..2067
                     /locus_tag="PQP99_RS23535"
                     /old_locus_tag="PQP99_23535"
     CDS             1678..2067
                     /locus_tag="PQP99_RS23535"
                     /old_locus_tag="PQP99_23535"
                     /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            2111..3604
                     /locus_tag="PQP99_RS23540"
                     /old_locus_tag="PQP99_23540"
     CDS             2111..3604
                     /locus_tag="PQP99_RS23540"
                     /old_locus_tag="PQP99_23540"
                     /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(<3840..4082)
                     /gene="glmM"
                     /locus_tag="PQP99_RS23545"
                     /old_locus_tag="PQP99_23545"
                     /pseudo=""
     CDS             complement(<3840..4082)
                     /gene="glmM"
                     /locus_tag="PQP99_RS23545"
                     /old_locus_tag="PQP99_23545"
                     /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(4169..4984)
                     /gene="sul2"
                     /locus_tag="PQP99_RS23550"
                     /old_locus_tag="PQP99_23550"
     ARG             complement(4173..4984)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2..91
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.901"
                     /coverage="100.0"
                     /evalue="5.91e-38"
     Typing          5965..6047
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="9.88e-36"
     Typing          complement(5436..6041)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cttcactgat tttcgcaatc gtggcaacat agtaagccag tatacactcc gctagcgcta
       61 catgactggt tcagggctgc gccccgaaac ccgctaacaa cctctcagct actggatatc
      121 accccatgcc atctgaatat gatgaacaac tggattcgac tgatacgcag cttcccggcg
      181 aatatgacct ttttgattta atggcgcagg ttactgaaga gaacctgcat gcccctgtgg
      241 attttgggtc gcctgtcggc cgggaagcgt tatagctttt tcgcttgccc gcgtacgtgg
      301 taatactccg gtattacctt ttatttcttt attttcatgt aattacagtg gatttttaat
      361 acccgggtat tactcgtgaa aacgaaatat tccttttttt tcttttactt catgcagttg
      421 cgatgaaaat cgcggctgcg ttaggtgtat gaccattttg aggttgaaaa ataatcaacc
      481 atggcgggtg atttacgcag gttaagggga gatcgtgaca aaaaaagcgt tcctcactgt
      541 atcgttcatg cctgcatgaa cgggttattc ttcctgacta cagaattaca tcgctccttc
      601 agttcataca tcacttttac atcacttata catcactttt acatcattcc ttcagctcat
      661 acgtcacttt catcctctgt gccatttgta catcaccccc ttcctgaacg tgctgacagc
      721 gggttttccg gctgcgccgg caacgcttca cggccacgca ataaattgcg tccccgttca
      781 ccgttttcgg atgggaagaa cgccggaaac aggacttacc ccggctgaat ggtgtgaatt
      841 tccgcgctat gcacttgtgc gcatactcat gcatgccgta aaaacagagc ctgcgcgttt
      901 ctggcgggtt ttcgggtggt ttgttgcctg ttttaccggt ttcccgtcag aaacgccctg
      961 agggcctctc aggcggtgct gataacagat gttatggtaa atcagagtca cctgcactgt
     1021 tactctgaac cggagcgaaa cagccgcgac cagaatcccc gctttttttc ctgtgccagc
     1081 gcgtcagcca gacggctaat ttcggcctgt agttgttccc tctcctcatt tcgcaggcgg
     1141 ttttctgctt cccgcgccat cttgtcttca agcattaggg taacagtctg ctgcagagcg
     1201 tccagtttct gctgaatgac gtctagctga gcattttccg cctggctaac gacagatttg
     1261 gagtgtccct ccttgtgcct ttttggtgtc tcagaagtgc gcagctcgcc ataggcccga
     1321 atcagttcac tggtctcgaa ctcccggcga tcattttttc ctgtgcgata gctgacaagg
     1381 cctttagcca tgtcacgata taattgcgag cgcgactttc ctgttaattt cagtgtctct
     1441 tgaactgtgt gccatgccat aaaagtgaca gtgtctcctg tgtgtaccgt attgtaacag
     1501 cagaacatat tactgtttta acacaaaagg tctgaggctg cccgtgaggc gtgaaaaata
     1561 cacaaaaaac ctgttgacgg tgtggttttg acgggcgtag tatttcgaat actgtatata
     1621 aacacattgt tataaataca gtttttgctg tttttaaaag tcaaagagga taattttatg
     1681 agtacagagt taaatagcgg tactgtcggt ggttttggtc acatgggacc aaatgacccc
     1741 tacaatgatg gtcatagcgg ctctggaagt tcgggaggta gttttaacgg tggtggtaat
     1801 ggtggccatg ataatagtag tggttcatct tatactgcat cctttggtct catcactggc
     1861 cgacacccga taactgtccc aggtacgaag aatattaatt ctgtcgatct ttctgctgtc
     1921 attaataaca ttatacatca tgaaggtgca cgcaataaca tgtacctaga tactgcgaac
     1981 aatgtaagag tgggagtgac gggcactggc tggcaatgtc tagcaacggc aggcatttcg
     2041 gctgagggta aaagaacttt ccgctaagcg atagactgta tgtaaacaca gtattgcaag
     2101 gacgcggaac atgcctcatg tggcggccag gacggccagc cgggatcggg atactggtcg
     2161 ttaccagagc caccgacccg agcaaaccct tctctatcag atcgttgacg agtattaccc
     2221 ggcattcgct gcgcttatgg cagagcaggg aaaggaattg ccgggctatg tgcaacggga
     2281 atttgaagaa tttctccaat gcgggcggct ggagcatggc tttctacggg ttcgctgcga
     2341 gtcttgccac gccgagcacc tggtcgcttt cagctgtaag cgtcgcggtt tctgcccgag
     2401 ctgtggggcg cggcggatgg ccgaaagtgc cgccttgctg gttgatgaag tactgcctga
     2461 acaacccatg cgtcagtggg tgttgagctt cccgtttcag ctgcgtttcc tgtttgccag
     2521 ccggcccgag atcatggggt gggtgctggg catcgtttac cgcgtcattg ccacgcacct
     2581 ggtcaagaaa gcgggccata cccaccaagt ggccaagacg ggcgcggtca ccctgatcca
     2641 gcgttttgga tcggcgctca atctgaatgt tcacttccac atgctgtttc tcgacggtgt
     2701 gtatgtcgag caatcccacg gctcagcgcg tttccgctgg gtcaaggcgc cgaccagccc
     2761 agagctcacc cagctgacgc acaccatcgc ccaccgggtg ggtcgctatc tggaacggca
     2821 aggcctgctg gaacgggatg tcgaaaacag ctatctggcc tcggatgcgg tggatgacga
     2881 cccgatgaca cccctgctgg ggcactcgat cacttaccgt atcgctgtcg gttcacaggc
     2941 ggggcgaaag gtgttcactt tgcaaactct gccgaccagt ggtgatccgt tcggtgacgg
     3001 gattggcaag gtagccgggt ccagcctgca cgccggcgtg gcggccaggg ccgatgaacg
     3061 caagaagctc gaacggctgt gccggtacat cagccgcccg gcggtatccg agaagcggct
     3121 gtcgttaaca cgaggcggca acgtgcgcta ccagctcaag acgccgtacc gggacggcac
     3181 cacgcacgtc attttcgaac cattggattt cattgcaagg ctggccgccc tggtaccgaa
     3241 gcccagagtc aacctaaccc gcttccacgg ggtgttcgca cccaacagtc ggcaccgggc
     3301 gttggtcacg ccggcaaaac ggggcagggg caacaaggtc agggtggctg atgaaccggc
     3361 aacaccagca caacggcgag cgtcgatgac atgggcgcaa cggctcaagc gtgttttcaa
     3421 tatcgacatc gagacctgca gcggctgcgg cggcgccatg aaagtcatcg cctgcattga
     3481 agaccctata gtgatcaagc agatccttga tcacctgaag cacaaagccg aaaccagcgg
     3541 gaccagggcg ttacccgaaa gccgggcgcc accggctgag ctgctcctgg gtctgtttga
     3601 ctgacgagcc tgaaggccaa cgataccaat caaaatgctg cgttcacagc gccgcggcag
     3661 ggatccgccg tgctggttgt cggaaaagga gccgctagtg ggaaagagga gggtaaattt
     3721 tcagcgttgc tggctccccg tcagccggat tgggttgcat cgcaggggtg tcgaaagagt
     3781 caactgtggt ccaaagctgt tggacttggg tgaaaagggc gtttattctt cctatacgtt
     3841 gtcggcagcg ggccaaaaag gaatacgtcc atgcccatcg aggtgaaacc ggctgtgagc
     3901 gcgggttcaa gcatatagcc cgacaggcgc gtatccttgc cgatcacgac acgatggcgg
     3961 tggtcaccgc gacgaaagac acggccagcc gccatgccga cgcgcaaggc ggtttccgcc
     4021 gtcatcgcgc cttcgttggc tttgccacga ataccgtctg tgccgaaata tttgcgcacc
     4081 ataaggtcga ttatcctgtc gtcgggtcgc cctcagaggg gacatgcctg ctgagacgcg
     4141 aatatagaga aatatcccga atgtgcagtt aacgaattct tgcggtttct ttcagcgccg
     4201 ccaataccgc cagcccgtcg cgcaaggggc gcggctcgtg tgtgcggatg aagtcagctc
     4261 cacctgcggc ggcggcaagc tctgcagcga gtgtcgcggc cccgacatcc cccggaccac
     4321 ggcctgtgag cgcgcgcaga aaggatttgc gcgaaacaga cagaagcacc ggcaaatcga
     4381 agcgcagccg caattcatcg aaccgcgcca gcaccgagag cgaggtttcg ggagcagccc
     4441 ccagaaaaaa ccccatgccg ggatcaagga caaggcggtt gcgtttgata ccggcacccg
     4501 tcagcgccgc gatgcgcgcg tcaaagaacg ccgcaatgtg atccatgatg tcgccagcgg
     4561 gtgcctcgcg ccgatctgcc tgcccgtctt gcaccgaatg cataacgacg agtttggcag
     4621 atgatttcgc caattgcgga tagaacgcag cgtctggaaa accgcgaata tcattgagat
     4681 aggccacacc acgcgacaag gcataggctt gcgtcgcggg ttgataactg tcgagcgaga
     4741 cgggaatgcc atctgccttg agcgcgtcca gcaccggcgc gatacgcgcg atttctgtgt
     4801 cggacgaaac aggcgcggcg tcgggattgc tggatgccgg accgaggtcg atcacatctg
     4861 ccccctcggc catcagctta cgcgcctgcg caatggctgc gtctggcgcc agataccggc
     4921 ctccatcgga gaaactgtcc gaggttatgt tgacgatgcc gaaaatgatg agcgatttat
     4981 tcatgggggc ttctataata ataataatcg agcatgagtc tcatacggat gctcgggtcg
     5041 aaagggaatc cccaggcgag taacctgttt gcggtgatcc gtttcatgat gatgtatctg
     5101 tagcattttg gaaataaata tatcatctct caataagtag atatatttat cttttttgct
     5161 tctttggtgc tgcaagtcac caatacgagg gaaacctgtt acggagcggt ttaaccgtaa
     5221 tcaacagtga ctggtgtcat gttcggaaga ttaattgata gtaatctaca aaggatcttc
     5281 ttgagatcct tttcaatgaa tcgtaatctc ttgctctgta aacgaaaaaa ccgcctgggg
     5341 aggcggtttg ttcgaaggtt aagtcagttg gggaactgct taacccggta acagggttca
     5401 cgagaccgcc attaccaaaa ctgttctttc agtgtagccg cagtcaggcc tctacttcaa
     5461 gacctcttaa tctatcttct cgtgcactcc tgttactaat ggctgctgcc agtggcgttt
     5521 tgtcgtgtct ttccgggttg gactcaagtt gatagttacc ggacaaggcg cagcggtcgg
     5581 actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgccttc acggaactga
     5641 gtgtcaggcg tggaatgaga aaccgcggcc ataacagcgg aatgacaccg gtaaaccgaa
     5701 aggcaggaac aggagagcgc acgagggagc taccaggggg aaacgcctgg gatctttata
     5761 gtcctgtcgg gtttcgccac cactgatttg agcgtcagat tttgcgatgc ttgtcagggg
     5821 ggcggagcct atggaaaaac ggcttcgccg tggccttatc tcttctttgc taagtgtctt
     5881 cctggtatct tccaggaaat ttccgtcccc gtccgtaagc cggtaccgct cgccgcagcc
     5941 gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga atatctcctg tatcgcatat
     6001 tctgctgacg cgccggtgct gccttttttc tcctgccaca tgaagca
//
