LOCUS       NZ_CP117324             5919 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain RM001
            plasmid pRM001_2, complete sequence.
ACCESSION   NZ_CP117324
VERSION     NZ_CP117324.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32950806
            Assembly: GCF_028893035.1
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                   :: Raven v. 1.5.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 343X
            Sequencing Technology :: illumina MiSeq + Nanopore Gridion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:17:09
            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)                     :: 4,745
            CDSs (total)                      :: 4,627
            Genes (coding)                    :: 4,490
            CDSs (with protein)               :: 4,490
            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)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 65 of 137
            Pseudo Genes (incomplete)         :: 87 of 137
            Pseudo Genes (internal stop)      :: 19 of 137
            Pseudo Genes (multiple problems)  :: 31 of 137
            Pseudo Genes (short protein)      :: 1 of 137
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117324.1.
            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="RM001"
                     /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="pRM001_2"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2000-09-19"
                     /collected_by="University of Nebraska-Lincoln"
     gene            complement(join(5820..5919,1..92))
                     /locus_tag="PQP82_RS23680"
                     /old_locus_tag="PQP82_23680"
     CDS             complement(join(5820..5919,1..92))
                     /locus_tag="PQP82_RS23680"
                     /old_locus_tag="PQP82_23680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001323484.1"
                     /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_057193379.1"
                     /translation="MLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENAALNERVT
                     RLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(<55..141)
                     /locus_tag="PQP82_RS23685"
                     /old_locus_tag="PQP82_23685"
                     /pseudo=""
     CDS             complement(<55..141)
                     /locus_tag="PQP82_RS23685"
                     /old_locus_tag="PQP82_23685"
                     /inference="COORDINATES: protein motif:HMM:NF016769.2"
                     /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="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(117..602)
                     /locus_tag="PQP82_RS23690"
                     /old_locus_tag="PQP82_23690"
     CDS             complement(117..602)
                     /locus_tag="PQP82_RS23690"
                     /old_locus_tag="PQP82_23690"
                     /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            complement(<640..1071)
                     /locus_tag="PQP82_RS23695"
                     /old_locus_tag="PQP82_23695"
                     /pseudo=""
     CDS             complement(<640..1071)
                     /locus_tag="PQP82_RS23695"
                     /old_locus_tag="PQP82_23695"
                     /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            complement(1280..1603)
                     /locus_tag="PQP82_RS23700"
                     /old_locus_tag="PQP82_23700"
     CDS             complement(1280..1603)
                     /locus_tag="PQP82_RS23700"
                     /old_locus_tag="PQP82_23700"
                     /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            complement(2587..2991)
                     /locus_tag="PQP82_RS23705"
                     /old_locus_tag="PQP82_23705"
     CDS             complement(2587..2991)
                     /locus_tag="PQP82_RS23705"
                     /old_locus_tag="PQP82_23705"
                     /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"
     gene            complement(3061..3306)
                     /locus_tag="PQP82_RS23710"
                     /old_locus_tag="PQP82_23710"
     CDS             complement(3061..3306)
                     /locus_tag="PQP82_RS23710"
                     /old_locus_tag="PQP82_23710"
                     /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            4348..4782
                     /locus_tag="PQP82_RS23715"
                     /old_locus_tag="PQP82_23715"
     CDS             4348..4782
                     /locus_tag="PQP82_RS23715"
                     /old_locus_tag="PQP82_23715"
                     /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            4785..5237
                     /locus_tag="PQP82_RS23720"
                     /old_locus_tag="PQP82_23720"
     CDS             4785..5237
                     /locus_tag="PQP82_RS23720"
                     /old_locus_tag="PQP82_23720"
                     /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"
     Typing          complement(1717..1889)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="1.98e-82"
     Typing          1814..2420
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.77"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..1290)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.953"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1287..1603)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.396"
                     /coverage="99.0"
                     /evalue="1.97e-61"
ORIGIN
        1 ccagacatct tctgccattc cgcgaaggcg ctctcccact cgtccagcct ttgcgagtag
       61 tcctgatgta actgctctaa tgcggtcagc aactgttttt ccagttccgt catgggctat
      121 ttcctctcca gtaccatcca gttcccttcc tccccgtaag ctcccgcttt cgggttcact
      181 ttgacgcagg acagtttctt ctccccgcag agcgacagct gcacgccgtg gttcttctcc
      241 gacagcatgg cctgcgtccg ctcctgcgcc cggatagtct ggtaattccc ggtgatctgc
      301 tgcccctgcc accacagaat gctcccgctc gtggcgatca gcagtaccga gaccagggtg
      361 atggtcagcc acgtccggcc gaccatacgc agcacgctca gccggttcga ctgcatcgcc
      421 gcggtcatac cctgctcgtg ggcgctgatg gcgtcgctga ttctcttcgc gcttgcgctc
      481 agttccgctt ttacagactt ctcgtgctcg ctgaatgcgg ctttcagcat ctcgccggta
      541 ctctgctgct gcgctttcga ttgctgctcc aagtccttcg ccagcgctaa aagactgctc
      601 ataaatggct cccttcagtc ggatgtttcg ccccccgtcc gggtcggcaa tgctgatact
      661 gttttttgtg gtgcggacca cctcaaaacc tgccgctgtg agcgcccctg tgacgtcctc
      721 gcgcgttttt agctccccgg atgaggctaa ggccagcaac ccccgtgtaa tcgcctgagc
      781 ggcttccagc ttcgttttcg gcagtgcgga cggcgtgacc agtaaccgcc ggttctccgg
      841 ggcgtttgga tcatgcagcc ccagtctgcc gttcaccacg gtctgccagg catcgatgcg
      901 cggccggtcg gcgcgatcgt agtacggctg caggcgtttc ccggtcagca gttcagtgtt
      961 ggggatcagg aaattcagct ccagccgccc cttgtcggtg tgctccaccc acagaatgct
     1021 gtactgatct ttatcgagtc cgggcatcag aacccgctcg aagctggcca tcagtttttc
     1081 ccgctggccg ggagggagat cggcctccgc aaacgacagg acgccggagg tgtatttctt
     1141 aacgtaaggc gacgcgtcaa tcagctcccg gacttcttcc ggcttcccct gcaggacggt
     1201 ggcgccttca cgctgccggt ctttacccag cagatagtcc accggcccgg cgccaccgcc
     1261 gcgaccgcgt ggatgaaatt taacgatcat cgtccgttcc tttctcaaga acggcgtgcc
     1321 gcagccgctc aagtccggca tcgatggcca tcagcgccgc cacaatctgt accctgtcat
     1381 ggccggtacc gccgccggcg ttaacacggc gggctatctg gttcaggtta ttgcccatgc
     1441 cggcaagctg gcgcagcagc gccggcgaga ttgagggaag ctttccggaa cgtgccggct
     1501 tttcgtccag gcaggtctgc cgcatccacg ctgccagctg cctgccgtcg cagcgctcga
     1561 gcagccgccg gtgctcgtcc tccgtcaccc acatggtgag catcttgttc cgtttctctg
     1621 acaaaccggc ctcctgataa cgccgggacg gacgggaaag gctttcccgg tcggcgcggg
     1681 gttggacaag ccgcaggcgc gtcaggcttt tggcgggttt cggggcgcag ccctgaacca
     1741 gtcacgtagc gctagcggag tgtatactgg cttactatgt tggcacggat gcgaatgtca
     1801 gtgaagtgct tcatgtggca ggagaaaaat gcagcagcgg agcgtcagca gaatatgtga
     1861 tacaggatat attccgcttc ctcgctcact gactcgctac gctcggtcgt tcggctgcgg
     1921 cgagcggtac cggcttacag gcggggcgga aatttcctgg gagatgccag gaagaagctt
     1981 aacagggaag cgataaggcc acggcgaagc cgtttttcca taggctccgc ccccctgaca
     2041 agcatcacga aatctgacgc tcaaatcagt ggtggcgaaa cccgacagga ctataaagat
     2101 accaggcgtt tccccctggt ggctccctcg tgcgctctcc tgttcctgcc tttcggttta
     2161 ccggtgtcat tccgctgtta tggccgcgtt tatctcattc cacgcctgac actcggttcc
     2221 gggaaggcag ttcgctccaa gctggactgt atgcacgaac cccccgttca gcccgactgc
     2281 tgcgcctgtt ccggtaactt tcaacttgag tccaacccgg aaagacacga caaagcgcca
     2341 ctggcagcag ccactggtaa gagggtgtac aagatattac tgatgcagag ttcttgaagt
     2401 atcagcccaa ctacggctaa actggaagga cgaatttggt ggcagcggtc ttgtacaccc
     2461 tgttaccacg gttcagaagt tccccaactt gctgaaccct cgaaaaacca cctccccagg
     2521 tggttttttc gtttatggac aagagactac agcggctaac ttaaaatctc aatacgtccg
     2581 tcatgatcac gtcgaagtgc tctctgttac ggccgtatct tttggctcat tgctactctt
     2641 aaacattgat ttcactatga tgaaaaacaa agctgatact tcggcaaccg tacccgcaat
     2701 cagagccaaa tacacgtcag tagttactgt tctgttctcc gccggaagca ctcccataga
     2761 aatcatatgc atctcttgct gaactaccgt gccaagcata tcaatgacca tccagttcat
     2821 tagcgcgacg accacagtca tggcaaacgt tacgcccgtt ttagaccatc ggagatgcct
     2881 tctgtcagcc ctttcttctg ccgccataat cggaccaaca aagtctttta cgacaagtac
     2941 ctttccgccg gtagcatctg aaaatccgtc taaatcatta gggtcactca ttaaactact
     3001 atcctttaaa taacaaaaaa ggccggatca tagatctggc cttttttttt gtttgctgcg
     3061 ttactgagag gcagttttca cctggcgttt caggattggc atacgtaggg agtagaactc
     3121 ttttttcgct ctatcaatag cagcgatatc gtggccattt tctgactcgt caacagccca
     3181 ctcgagcata gttaaggcgt aattgaaaag ctctttccta gtacttatgc cgcacttact
     3241 catcagagtg tcgagctctt gcagccgatc ttctggaagg tcaaattgca tacgtacgtt
     3301 tttcatgttg aatctccgca actatctctc cacgtccatg ggtgatagcc gaaacagtgt
     3361 gagattatta ttgttattat atcaataact taattgctaa ttggtttatt gctgtctgta
     3421 ttttgggtgc aagtgcacct atgactaact aatgcgttgg tcatgtgtaa atcgccagct
     3481 atcgcgttga ttagcatgta gctctcacct tggggaaaag gcgatggcgg tcatctttcc
     3541 ccaaggtgag tttcagtcat cttcctctac aggatcgatt acccacgttt tgagaggtag
     3601 ttgaaactct acctctacga aatcggagca atcctcgctg tcctccgagg acgatgagct
     3661 agctgaaatc aacttgctca cgattagaat ctccatacat ctactgaaac tttttcagta
     3721 gctgatatta agactactct aattttgtgt aaatgtcgag tagaatcgga gggtaaaatg
     3781 agtatgcaca gagatgacca aaaaaacaac tacagcaatt gttttatgcg tatttttttg
     3841 tcattaagtg aaaactaata ataaaattat ttaaaaacaa tagattagaa aaacaatcgg
     3901 gaagcgattt tgtaggattg tcttttgcgg gaacaagcga cttaggggtc aaaaaaacgt
     3961 cgctcttacg aagattgatg atgcactaac aaaaaaagct gcctagggca gcttttttta
     4021 tgagtctgag tggcgtacgt gatgtccagt tatctagatt catcatccct cgcaatgaag
     4081 gagcccaccc aagtggctgc tttcgcaggg cgatccacta tcagcgcatg tcgcctcgcc
     4141 atcatatcgc catgacgggc aaatcgtctt ctgtaagact cagtgcaagt atggtgacaa
     4201 tatgtcgcta tttaaaggtg acatattgtc attacatata aatatacata tataaatata
     4261 tacaagcaca gggcaacatc ttataaatat aagatgttgc cctgtgcttg ttgtcacttc
     4321 tgaagaaaaa aaattaactg aggtatcatg aaagctaaaa ctgagccatt ggagaagaag
     4381 tggggtgagc gaagcatgct tatgggatgg acagctattc ctacgtcttt cctgtttctt
     4441 caggcagaac tttcaatcac acctttaggg tttaacattt tgataaacct agtttcccat
     4501 tggtgggaaa ccaaagagca tccatatccc tctcaagagt cattagctaa aagaatgggt
     4561 gtatccaagc gctcgattca gagggaggta acgaacttag ttgagttggg gcttataacg
     4621 aagcaagcta acaaagccag tagcgctaag tacaagggaa gaaacactta cgatcttact
     4681 ggcttagtcg aacgccttaa tgaaatggca ccagaaaaga taacgagtat gcaacgacat
     4741 aaaaaagctc cagaacagcc tgatgagtca ggggaacaat aaaaatgccc acttttaccc
     4801 agaccgggac agggaaatat gactactggc tgctcgatgg aggaaaaacg ttttcaacca
     4861 taccagcaga cactcttccc tcaatatcta cagacatgcc catacgtcta cagattgggg
     4921 atggctattt tgggtccaca cacataacgg caagacatgg gaagtggctc gagcgttacc
     4981 agcctgatgg atgcgtagct acattcgttc ataagaaatt aagcacttcc gggaagatcc
     5041 ttttactgga ggaaaaaaac aagataggac tggctttaac gttaaccccc aacgcggctc
     5101 ttatcttaag aaatattgga gatttcttct ccataacaac tctttattac aagaagagcg
     5161 gattgggcgg tgaagaggtt gggagatata cagggtacaa atgggcaaca tcgccataca
     5221 tagaaagacg ccgctagttt ctaaaatcag gcagcgataa agactggata atgccgatat
     5281 cgaataaact cacttccagc tttatatcaa cgttatttac cataacatcc gttgcccgca
     5341 ccgctccgga caggttcgcc acaaacggga cggcagtcag gtaaaaccgg caacaaacca
     5401 cccgatacac cgccccgtcc gtgacagata aattttaccc ggctgcatgg tcatgcagcc
     5461 agatgcatac ggtctgattt caggccagaa tccggatgaa cgccttaaaa acaggaaaat
     5521 gcttctccag ccagtcccag atctccagcg ccatgtacag gcagttcagc atcgtctcaa
     5581 tcacgttaaa cagtctcata atccctccgt tgtatacgcc gtgatgtttt catcacgacc
     5641 gtatttagcg ggaaatttat gagcccttct tcgtgggggt tgtcactgga tgccactcag
     5701 tcagcccagc gtcggaccgt tatagctccg ctggcgggaa cgggcttccg ccagctcttt
     5761 ttcgtgctgg cgctgctcgt atgcccgttc ggcggccacc gccatttcat gccgctgcac
     5821 tactggctca aacgctgtaa ctgcctgctc aagttcgcca cctgctgact caagcgcgtg
     5881 acgcgctcgt tcagcgccgc gttctcccgt tgcataaga
//
