LOCUS       NZ_CP117315             5919 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain RM003
            plasmid pRM003_3, complete sequence.
ACCESSION   NZ_CP117315
VERSION     NZ_CP117315.1
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 5919)
  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 5919)
  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
            CP117315.1.
            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..5919
                     /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_3"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2000-10-30"
                     /collected_by="University of Nebraska-Lincoln"
     gene            395..718
                     /locus_tag="PQP99_RS23555"
                     /old_locus_tag="PQP99_23555"
     CDS             395..718
                     /locus_tag="PQP99_RS23555"
                     /old_locus_tag="PQP99_23555"
                     /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_007772081.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            927..>1358
                     /locus_tag="PQP99_RS23560"
                     /old_locus_tag="PQP99_23560"
                     /pseudo=""
     CDS             927..>1358
                     /locus_tag="PQP99_RS23560"
                     /old_locus_tag="PQP99_23560"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            1396..1881
                     /locus_tag="PQP99_RS23565"
                     /old_locus_tag="PQP99_23565"
     CDS             1396..1881
                     /locus_tag="PQP99_RS23565"
                     /old_locus_tag="PQP99_23565"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_000096578.1"
                     /translation="MSSLLALAKDLEQQSKAQQQSTGEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEKKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            1885..2097
                     /locus_tag="PQP99_RS23570"
                     /old_locus_tag="PQP99_23570"
     CDS             1885..2097
                     /locus_tag="PQP99_RS23570"
                     /old_locus_tag="PQP99_23570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2680..3132)
                     /locus_tag="PQP99_RS23575"
                     /old_locus_tag="PQP99_23575"
     CDS             complement(2680..3132)
                     /locus_tag="PQP99_RS23575"
                     /old_locus_tag="PQP99_23575"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063054258.1"
                     /translation="MPTFTQTGTGKYDYWLLDGGKTFSTIPADTLPSISTDMPIRLQIG
                     DGYFGSTHITARHGKWLERYQPDGCVATFVHKKLSTSGKILLLEEKNKIGLALTLTPNA
                     ALILRNIGDFFSITTLYYKKSGLGGEEVGRYTGYKWATSPYIERRR"
                     /name="hypothetical protein"
     gene            complement(3135..3569)
                     /locus_tag="PQP99_RS23580"
                     /old_locus_tag="PQP99_23580"
     CDS             complement(3135..3569)
                     /locus_tag="PQP99_RS23580"
                     /old_locus_tag="PQP99_23580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283459.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_045332488.1"
                     /translation="MKAKTEPLEKKWGERSMLMGWTAIPTSFLFLQAELSITPLGFNIL
                     INLVSHWWETKEHPYPSQESLAKRMGVSKRSIQREVTNLVELGLITKQANKASSAKYKG
                     RNTYDLTGLVERLNEMAPEKITSMQRHKKAPEQPDESGEQ"
                     /name="helix-turn-helix domain-containing protein"
     gene            4611..4856
                     /locus_tag="PQP99_RS23585"
                     /old_locus_tag="PQP99_23585"
     CDS             4611..4856
                     /locus_tag="PQP99_RS23585"
                     /old_locus_tag="PQP99_23585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000800279.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_045332492.1"
                     /translation="MKNVRMQFDLPEDRLQELDTLMSKCGISTRKELFNYALTMLEWAV
                     DESENGHDIAAIDRAKKEFYSLRMPILKRQVKTASQ"
                     /name="hypothetical protein"
     gene            4926..5330
                     /locus_tag="PQP99_RS23590"
                     /old_locus_tag="PQP99_23590"
     CDS             4926..5330
                     /locus_tag="PQP99_RS23590"
                     /old_locus_tag="PQP99_23590"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_045332491.1"
                     /translation="MSDPNDLDGFSDATGGKVLVVKDFVGPIMAAEERADRRHLRWSKT
                     GVTFAMTVVVALMNWMVIDMLGTVVQQEMHMISMGVLPAENRTVTTDVYLALIAGTVAE
                     VSALFFIIVKSMFKSSNEPKDTAVTESTST"
                     /name="hypothetical protein"
     Typing          110..282
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="1.98e-82"
     Typing          complement(2..185)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.84"
                     /coverage="100.0"
                     /evalue="1.3500000000000006e-59"
     Typing          complement(5535..5919)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.855"
                     /coverage="100.0"
                     /evalue="7.69e-176"
     Typing          396..712
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.396"
                     /coverage="99.0"
                     /evalue="1.97e-61"
     Typing          709..2213
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.223"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cttatcgctt ccctgttaag cttcttcctg gcatctccca ggaaatttcc gccccgcctg
       61 taagccggta ccgctcgccg cagccgaacg accgagcgta gcgagtcagt gagcgaggaa
      121 gcggaatata tcctgtatca catattctgc tgacgctccg ctgctgcatt tttctcctgc
      181 cacatgaagc acttcactga cattcgcatc cgtgccaaca tagtaagcca gtatacactc
      241 cgctagcgct acgtgactgg ttcagggctg cgccccgaaa cccgccaaaa gcctgacgcg
      301 cctgcggctt gtccaacccc gcgccgaccg ggaaagcctt tcccgtccgt cccggcgtta
      361 tcaggaggcc ggtttgtcag agaaacggaa caagatgctc accatgtggg tgacggagga
      421 cgagcaccgg cggctgctcg agcgctgcga cggcaggcag ctggcagcgt ggatgcggca
      481 gacctgcctg gacgaaaagc cggcacgttc cggaaagctt ccctcaatct cgccggcgct
      541 gctgcgccag cttgccggca tgggcaataa cctgaaccag atagcccgcc gtgttaacgc
      601 cggcggcggt accggccatg acagggtaca gattgtggcg gcgctgatgg ccatcgatgc
      661 cggacttgag cggctgcggc acgccgttct tgagaaagga acggacgatg atcgttaaat
      721 ttcatccacg cggtcgcggc ggtggcgccg ggccggtgga ctatctgctg ggtaaagacc
      781 ggcagcgtga aggcgccacc gtcctgcagg ggaagccgga agaagtccgg gagctgattg
      841 acgcgtcgcc ttacgttaag aaatacacct ccggcgtcct gtcgtttgcg gaggccgatc
      901 tccctcccgg ccagcgggaa aaactgatgg ccagcttcga gcgggttctg atgcccggac
      961 tcgataaaga tcagtacagc attctgtggg tggagcacac cgacaagggg cggctggagc
     1021 tgaatttcct gatccccaac actgaactgc tgaccgggaa acgcctgcag ccgtactacg
     1081 atcgcgccga ccggccgcgc atcgatgcct ggcagaccgt ggtgaacggc agactggggc
     1141 tgcatgatcc aaacgccccg gagaaccggc ggttactggt cacgccgtcc gcactgccga
     1201 aaacgaagct ggaagccgct caggcgatta cacgggggtt gctggcctta gcctcatccg
     1261 gggagctaaa aacgcgcgag gacgtcacag gggcgctcac agcggcaggt tttgaggtgg
     1321 tccgcaccac aaaaaacagt atcagcattg ccgacccgga cggggggcga aacatccgac
     1381 tgaagggagc catttatgag cagtctttta gcgctggcga aggacttgga gcagcaatcg
     1441 aaagcgcagc agcagagtac cggcgagatg ctgaaagccg cattcagcga gcacgagaag
     1501 tctgtaaaag cggaactgag cgcaagcgcg aagagaatca gcgacgccat cagcgcccac
     1561 gagcagggta tgaccgcggc gatgcagtcg aaccggctga gcgtgctgcg tatggtcggc
     1621 cggacgtggc tgaccatcac cctggtctcg gtactgctga tcgccacgag cgggagcatt
     1681 ctgtggtggc aggggcagca gatcaccggg aattaccaga ctatccgggc gcaggagcgg
     1741 acgcaggcca tgctgtcgga gaagaaccac ggcgtgcagc tgtcgctctg cggggagaag
     1801 aaactgtcct gcgtcaaagt gaacccgaaa gcgggagctt acggggagga agggaactgg
     1861 atggtactgg agaggaaata gcccatgacg gaactggaaa aacagttgct gaccgcatta
     1921 gagcagttac atcaggacta ctcgcaaagg ctggacgagt gggagagcgc cttcgcggaa
     1981 tggcagaaga tgtctggtct tatgcaacgg gagaacgcgg cgctgaacga gcgcgtcacg
     2041 cgcttgagtc agcaggtggc gaacttgagc aggcagttac agcgtttgag ccagtagtgc
     2101 agcggcatga aatggcggtg gccgccgaac gggcatacga gcagcgccag cacgaaaaag
     2161 agctggcgga agcccgttcc cgccagcgga gctataacgg tccgacgctg ggctgactga
     2221 gtggcatcca gtgacaaccc ccacgaagaa gggctcataa atttcccgct aaatacggtc
     2281 gtgatgaaaa catcacggcg tatacaacgg agggattatg agactgttta acgtgattga
     2341 gacgatgctg aactgcctgt acatggcgct ggagatctgg gactggctgg agaagcattt
     2401 tcctgttttt aaggcgttca tccggattct ggcctgaaat cagaccgtat gcatctggct
     2461 gcatgaccat gcagccgggt aaaatttatc tgtcacggac ggggcggtgt atcgggtggt
     2521 ttgttgccgg ttttacctga ctgccgtccc gtttgtggcg aacctgtccg gagcggtgcg
     2581 ggcaacggat gttatggtaa ataacgttga tataaagctg gaagtgagtt tattcgatat
     2641 cggcattatc cagtctttat cgctgcctga ttttagaaac tagcggcgtc tttctatgta
     2701 tggcgatgtt gcccatttgt accctgtata tctcccaacc tcttcaccgc ccaatccgct
     2761 cttcttgtaa taaagagttg ttatggagaa gaaatctcca atatttctta agataagagc
     2821 cgcgttgggg gttaacgtta aagccagtcc tatcttgttt ttttcctcca gtaaaaggat
     2881 cttcccggaa gtgcttaatt tcttatgaac gaatgtagct acgcatccat caggctggta
     2941 acgctcgagc cacttcccat gtcttgccgt tatgtgtgtg gacccaaaat agccatcccc
     3001 aatctgtaga cgtatgggca tgtctgtaga tattgaggga agagtgtctg ctggtatggt
     3061 tgaaaacgtt tttcctccat cgagcagcca gtagtcatat ttccctgtcc cggtctgggt
     3121 aaaagtgggc atttttattg ttcccctgac tcatcaggct gttctggagc ttttttatgt
     3181 cgttgcatac tcgttatctt ttctggtgcc atttcattaa ggcgttcgac taagccagta
     3241 agatcgtaag tgtttcttcc cttgtactta gcgctactgg ctttgttagc ttgcttcgtt
     3301 ataagcccca actcaactaa gttcgttacc tccctctgaa tcgagcgctt ggatacaccc
     3361 attcttttag ctaatgactc ttgagaggga tatggatgct ctttggtttc ccaccaatgg
     3421 gaaactaggt ttatcaaaat gttaaaccct aaaggtgtga ttgaaagttc tgcctgaaga
     3481 aacaggaaag acgtaggaat agctgtccat cccataagca tgcttcgctc accccacttc
     3541 ttctccaatg gctcagtttt agctttcatg atacctcagt taattttttt tcttcagaag
     3601 tgacaacaag cacagggcaa catcttatat ttataagatg ttgccctgtg cttgtatata
     3661 tttatatatg tatatttata tgtaatgaca atatgtcacc tttaaatagc gacatattgt
     3721 caccatactt gcactgagtc ttacagaaga cgatttgccc gtcatggcga tatgatggcg
     3781 aggcgacatg cgctgatagt ggatcgccct gcgaaagcag ccacttgggt gggctccttc
     3841 attgcgaggg atgatgaatc tagataactg gacatcacgt acgccactca gactcataaa
     3901 aaaagctgcc ctaggcagct ttttttgtta gtgcatcatc aatcttcgta agagcgacgt
     3961 ttttttgacc cctaagtcgc ttgttcccgc aaaagacaat cctacaaaat cgcttcccga
     4021 ttgtttttct aatctattgt ttttaaataa ttttattatt agttttcact taatgacaaa
     4081 aaaatacgca taaaacaatt gctgtagttg tttttttggt catctctgtg catactcatt
     4141 ttaccctccg attctactcg acatttacac aaaattagag tagtcttaat atcagctact
     4201 gaaaaagttt cagtagatgt atggagattc taatcgtgag caagttgatt tcagctagct
     4261 catcgtcctc ggaggacagc gaggattgct ccgatttcgt agaggtagag tttcaactac
     4321 ctctcaaaac gtgggtaatc gatcctgtag aggaagatga ctgaaactca ccttggggaa
     4381 agatgaccgc catcgccttt tccccaaggt gagagctaca tgctaatcaa cgcgatagct
     4441 ggcgatttac acatgaccaa cgcattagtt agtcataggt gcacttgcac ccaaaataca
     4501 gacagcaata aaccaattag caattaagtt attgatataa taacaataat aatctcacac
     4561 tgtttcggct atcacccatg gacgtggaga gatagttgcg gagattcaac atgaaaaacg
     4621 tacgtatgca atttgacctt ccagaagatc ggctgcaaga gctcgacact ctgatgagta
     4681 agtgcggcat aagtactagg aaagagcttt tcaattacgc cttaactatg ctcgagtggg
     4741 ctgttgacga gtcagaaaat ggccacgata tcgctgctat tgatagagcg aaaaaagagt
     4801 tctactccct acgtatgcca atcctgaaac gccaggtgaa aactgcctct cagtaacgca
     4861 gcaaacaaaa aaaaaggcca gatctatgat ccggcctttt ttgttattta aaggatagta
     4921 gtttaatgag tgaccctaat gatttagacg gattttcaga tgctaccggc ggaaaggtac
     4981 ttgtcgtaaa agactttgtt ggtccgatta tggcggcaga agaaagggct gacagaaggc
     5041 atctccgatg gtctaaaacg ggcgtaacgt ttgccatgac tgtggtcgtc gcgctaatga
     5101 actggatggt cattgatatg cttggcacgg tagttcagca agagatgcat atgatttcta
     5161 tgggagtgct tccggcggag aacagaacag taactactga cgtgtatttg gctctgattg
     5221 cgggtacggt tgccgaagta tcagctttgt ttttcatcat agtgaaatca atgtttaaga
     5281 gtagcaatga gccaaaagat acggccgtaa cagagagcac ttcgacgtga tcatgacgga
     5341 cgtattgaga ttttaagtta gccgctgtag tctcttgtcc ataaacgaaa aaaccacctg
     5401 gggaggtggt ttttcgaggg ttcagcaagt tggggaactt ctgaaccgtg gtaacagggt
     5461 gtacaagacc gctgccacca aattcgtcct tccagtttag ccgtagttgg gctgatactt
     5521 caagaactct gcatcagtaa tatcttgtac accctcttac cagtggctgc tgccagtggc
     5581 gctttgtcgt gtctttccgg gttggactca agttgaaagt taccggaaca ggcgcagcag
     5641 tcgggctgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc cttcccggaa
     5701 ccgagtgtca ggcgtggaat gagataaacg cggccataac agcggaatga caccggtaaa
     5761 ccgaaaggca ggaacaggag agcgcacgag ggagccacca gggggaaacg cctggtatct
     5821 ttatagtcct gtcgggtttc gccaccactg atttgagcgt cagatttcgt gatgcttgtc
     5881 aggggggcgg agcctatgga aaaacggctt cgccgtggc
//
