LOCUS       NZ_CP117310             5919 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain RM004
            plasmid pRM004_3, complete sequence.
ACCESSION   NZ_CP117310
VERSION     NZ_CP117310.1
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 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                   :: 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
            CP117310.1.
            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="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_3"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2000-10-30"
                     /collected_by="University of Nebraska-Lincoln"
     gene            complement(<238..936)
                     /locus_tag="PQQ01_RS23595"
                     /old_locus_tag="PQQ01_23595"
                     /pseudo=""
     CDS             complement(<238..936)
                     /locus_tag="PQQ01_RS23595"
                     /old_locus_tag="PQQ01_23595"
                     /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(926..1249)
                     /locus_tag="PQQ01_RS23600"
                     /old_locus_tag="PQQ01_23600"
     CDS             complement(926..1249)
                     /locus_tag="PQQ01_RS23600"
                     /old_locus_tag="PQQ01_23600"
                     /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(2233..2637)
                     /locus_tag="PQQ01_RS23605"
                     /old_locus_tag="PQQ01_23605"
     CDS             complement(2233..2637)
                     /locus_tag="PQQ01_RS23605"
                     /old_locus_tag="PQQ01_23605"
                     /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(2707..2952)
                     /locus_tag="PQQ01_RS23610"
                     /old_locus_tag="PQQ01_23610"
     CDS             complement(2707..2952)
                     /locus_tag="PQQ01_RS23610"
                     /old_locus_tag="PQQ01_23610"
                     /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            3994..4428
                     /locus_tag="PQQ01_RS23615"
                     /old_locus_tag="PQQ01_23615"
     CDS             3994..4428
                     /locus_tag="PQQ01_RS23615"
                     /old_locus_tag="PQQ01_23615"
                     /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            4431..4883
                     /locus_tag="PQQ01_RS23620"
                     /old_locus_tag="PQQ01_23620"
     CDS             4431..4883
                     /locus_tag="PQQ01_RS23620"
                     /old_locus_tag="PQQ01_23620"
                     /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(5466..5678)
                     /locus_tag="PQQ01_RS23625"
                     /old_locus_tag="PQQ01_23625"
     CDS             complement(5466..5678)
                     /locus_tag="PQQ01_RS23625"
                     /old_locus_tag="PQQ01_23625"
                     /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"
     Typing          complement(1363..1535)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="1.98e-82"
     Typing          1460..2066
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.77"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(5..936)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.675"
                     /coverage="83.0"
                     /evalue="3.49e-178"
     Typing          complement(933..1249)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.396"
                     /coverage="99.0"
                     /evalue="1.97e-61"
     Typing          complement(5351..5919)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.895"
                     /coverage="100.0"
                     /evalue="1.02e-108"
ORIGIN
        1 agggtgatgg tcagccacgt ccggccgacc atacgcagca cgctcagccg gttcgactgc
       61 atcgccgcgg tcataccctg ctcgtgggcg ctgatggcgt cgctgattct cttcgcgctt
      121 gcgctcagtt ccgcttttac agacttctcg tgctcgctga atgcggcttt cagcatctcg
      181 ccggtactct gctgctgcgc tttcgattgc tgctccaagt ccttcgccag cgctaaaaga
      241 ctgctcataa atggctccct tcagtcggat gtttcgcccc ccgtccgggt cggcaatgct
      301 gatactgttt tttgtggtgc ggaccacctc aaaacctgcc gctgtgagcg cccctgtgac
      361 gtcctcgcgc gtttttagct ccccggatga ggctaaggcc agcaaccccc gtgtaatcgc
      421 ctgagcggct tccagcttcg ttttcggcag tgcggacggc gtgaccagta accgccggtt
      481 ctccggggcg tttggatcat gcagccccag tctgccgttc accacggtct gccaggcatc
      541 gatgcgcggc cggtcggcgc gatcgtagta cggctgcagg cgtttcccgg tcagcagttc
      601 agtgttgggg atcaggaaat tcagctccag ccgccccttg tcggtgtgct ccacccacag
      661 aatgctgtac tgatctttat cgagtccggg catcagaacc cgctcgaagc tggccatcag
      721 tttttcccgc tggccgggag ggagatcggc ctccgcaaac gacaggacgc cggaggtgta
      781 tttcttaacg taaggcgacg cgtcaatcag ctcccggact tcttccggct tcccctgcag
      841 gacggtggcg ccttcacgct gccggtcttt acccagcaga tagtccaccg gcccggcgcc
      901 accgccgcga ccgcgtggat gaaatttaac gatcatcgtc cgttcctttc tcaagaacgg
      961 cgtgccgcag ccgctcaagt ccggcatcga tggccatcag cgccgccaca atctgtaccc
     1021 tgtcatggcc ggtaccgccg ccggcgttaa cacggcgggc tatctggttc aggttattgc
     1081 ccatgccggc aagctggcgc agcagcgccg gcgagattga gggaagcttt ccggaacgtg
     1141 ccggcttttc gtccaggcag gtctgccgca tccacgctgc cagctgcctg ccgtcgcagc
     1201 gctcgagcag ccgccggtgc tcgtcctccg tcacccacat ggtgagcatc ttgttccgtt
     1261 tctctgacaa accggcctcc tgataacgcc gggacggacg ggaaaggctt tcccggtcgg
     1321 cgcggggttg gacaagccgc aggcgcgtca ggcttttggc gggtttcggg gcgcagccct
     1381 gaaccagtca cgtagcgcta gcggagtgta tactggctta ctatgttggc acggatgcga
     1441 atgtcagtga agtgcttcat gtggcaggag aaaaatgcag cagcggagcg tcagcagaat
     1501 atgtgataca ggatatattc cgcttcctcg ctcactgact cgctacgctc ggtcgttcgg
     1561 ctgcggcgag cggtaccggc ttacaggcgg ggcggaaatt tcctgggaga tgccaggaag
     1621 aagcttaaca gggaagcgat aaggccacgg cgaagccgtt tttccatagg ctccgccccc
     1681 ctgacaagca tcacgaaatc tgacgctcaa atcagtggtg gcgaaacccg acaggactat
     1741 aaagatacca ggcgtttccc cctggtggct ccctcgtgcg ctctcctgtt cctgcctttc
     1801 ggtttaccgg tgtcattccg ctgttatggc cgcgtttatc tcattccacg cctgacactc
     1861 ggttccggga aggcagttcg ctccaagctg gactgtatgc acgaaccccc cgttcagccc
     1921 gactgctgcg cctgttccgg taactttcaa cttgagtcca acccggaaag acacgacaaa
     1981 gcgccactgg cagcagccac tggtaagagg gtgtacaaga tattactgat gcagagttct
     2041 tgaagtatca gcccaactac ggctaaactg gaaggacgaa tttggtggca gcggtcttgt
     2101 acaccctgtt accacggttc agaagttccc caacttgctg aaccctcgaa aaaccacctc
     2161 cccaggtggt tttttcgttt atggacaaga gactacagcg gctaacttaa aatctcaata
     2221 cgtccgtcat gatcacgtcg aagtgctctc tgttacggcc gtatcttttg gctcattgct
     2281 actcttaaac attgatttca ctatgatgaa aaacaaagct gatacttcgg caaccgtacc
     2341 cgcaatcaga gccaaataca cgtcagtagt tactgttctg ttctccgccg gaagcactcc
     2401 catagaaatc atatgcatct cttgctgaac taccgtgcca agcatatcaa tgaccatcca
     2461 gttcattagc gcgacgacca cagtcatggc aaacgttacg cccgttttag accatcggag
     2521 atgccttctg tcagcccttt cttctgccgc cataatcgga ccaacaaagt cttttacgac
     2581 aagtaccttt ccgccggtag catctgaaaa tccgtctaaa tcattagggt cactcattaa
     2641 actactatcc tttaaataac aaaaaaggcc ggatcataga tctggccttt ttttttgttt
     2701 gctgcgttac tgagaggcag ttttcacctg gcgtttcagg attggcatac gtagggagta
     2761 gaactctttt ttcgctctat caatagcagc gatatcgtgg ccattttctg actcgtcaac
     2821 agcccactcg agcatagtta aggcgtaatt gaaaagctct ttcctagtac ttatgccgca
     2881 cttactcatc agagtgtcga gctcttgcag ccgatcttct ggaaggtcaa attgcatacg
     2941 tacgtttttc atgttgaatc tccgcaacta tctctccacg tccatgggtg atagccgaaa
     3001 cagtgtgaga ttattattgt tattatatca ataacttaat tgctaattgg tttattgctg
     3061 tctgtatttt gggtgcaagt gcacctatga ctaactaatg cgttggtcat gtgtaaatcg
     3121 ccagctatcg cgttgattag catgtagctc tcaccttggg gaaaaggcga tggcggtcat
     3181 ctttccccaa ggtgagtttc agtcatcttc ctctacagga tcgattaccc acgttttgag
     3241 aggtagttga aactctacct ctacgaaatc ggagcaatcc tcgctgtcct ccgaggacga
     3301 tgagctagct gaaatcaact tgctcacgat tagaatctcc atacatctac tgaaactttt
     3361 tcagtagctg atattaagac tactctaatt ttgtgtaaat gtcgagtaga atcggagggt
     3421 aaaatgagta tgcacagaga tgaccaaaaa aacaactaca gcaattgttt tatgcgtatt
     3481 tttttgtcat taagtgaaaa ctaataataa aattatttaa aaacaataga ttagaaaaac
     3541 aatcgggaag cgattttgta ggattgtctt ttgcgggaac aagcgactta ggggtcaaaa
     3601 aaacgtcgct cttacgaaga ttgatgatgc actaacaaaa aaagctgcct agggcagctt
     3661 tttttatgag tctgagtggc gtacgtgatg tccagttatc tagattcatc atccctcgca
     3721 atgaaggagc ccacccaagt ggctgctttc gcagggcgat ccactatcag cgcatgtcgc
     3781 ctcgccatca tatcgccatg acgggcaaat cgtcttctgt aagactcagt gcaagtatgg
     3841 tgacaatatg tcgctattta aaggtgacat attgtcatta catataaata tacatatata
     3901 aatatataca agcacagggc aacatcttat aaatataaga tgttgccctg tgcttgttgt
     3961 cacttctgaa gaaaaaaaat taactgaggt atcatgaaag ctaaaactga gccattggag
     4021 aagaagtggg gtgagcgaag catgcttatg ggatggacag ctattcctac gtctttcctg
     4081 tttcttcagg cagaactttc aatcacacct ttagggttta acattttgat aaacctagtt
     4141 tcccattggt gggaaaccaa agagcatcca tatccctctc aagagtcatt agctaaaaga
     4201 atgggtgtat ccaagcgctc gattcagagg gaggtaacga acttagttga gttggggctt
     4261 ataacgaagc aagctaacaa agccagtagc gctaagtaca agggaagaaa cacttacgat
     4321 cttactggct tagtcgaacg ccttaatgaa atggcaccag aaaagataac gagtatgcaa
     4381 cgacataaaa aagctccaga acagcctgat gagtcagggg aacaataaaa atgcccactt
     4441 ttacccagac cgggacaggg aaatatgact actggctgct cgatggagga aaaacgtttt
     4501 caaccatacc agcagacact cttccctcaa tatctacaga catgcccata cgtctacaga
     4561 ttggggatgg ctattttggg tccacacaca taacggcaag acatgggaag tggctcgagc
     4621 gttaccagcc tgatggatgc gtagctacat tcgttcataa gaaattaagc acttccggga
     4681 agatcctttt actggaggaa aaaaacaaga taggactggc tttaacgtta acccccaacg
     4741 cggctcttat cttaagaaat attggagatt tcttctccat aacaactctt tattacaaga
     4801 agagcggatt gggcggtgaa gaggttggga gatatacagg gtacaaatgg gcaacatcgc
     4861 catacataga aagacgccgc tagtttctaa aatcaggcag cgataaagac tggataatgc
     4921 cgatatcgaa taaactcact tccagcttta tatcaacgtt atttaccata acatccgttg
     4981 cccgcaccgc tccggacagg ttcgccacaa acgggacggc agtcaggtaa aaccggcaac
     5041 aaaccacccg atacaccgcc ccgtccgtga cagataaatt ttacccggct gcatggtcat
     5101 gcagccagat gcatacggtc tgatttcagg ccagaatccg gatgaacgcc ttaaaaacag
     5161 gaaaatgctt ctccagccag tcccagatct ccagcgccat gtacaggcag ttcagcatcg
     5221 tctcaatcac gttaaacagt ctcataatcc ctccgttgta tacgccgtga tgttttcatc
     5281 acgaccgtat ttagcgggaa atttatgagc ccttcttcgt gggggttgtc actggatgcc
     5341 actcagtcag cccagcgtcg gaccgttata gctccgctgg cgggaacggg cttccgccag
     5401 ctctttttcg tgctggcgct gctcgtatgc ccgttcggcg gccaccgcca tttcatgccg
     5461 ctgcactact ggctcaaacg ctgtaactgc ctgctcaagt tcgccacctg ctgactcaag
     5521 cgcgtgacgc gctcgttcag cgccgcgttc tcccgttgca taagaccaga catcttctgc
     5581 cattccgcga aggcgctctc ccactcgtcc agcctttgcg agtagtcctg atgtaactgc
     5641 tctaatgcgg tcagcaactg tttttccagt tccgtcatgg gctatttcct ctccagtacc
     5701 atccagttcc cttcctcccc gtaagctccc gctttcgggt tcactttgac gcaggacagt
     5761 ttcttctccc cgcagagcga cagctgcacg ccgtggttct tctccgacag catggcctgc
     5821 gtccgctcct gcgcccggat agtctggtaa ttcccggtga tctgctgccc ctgccaccac
     5881 agaatgctcc cgctcgtggc gatcagcagt accgagacc
//
