LOCUS       NZ_CP117403             3370 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Give strain RM007
            plasmid pRM007_1, complete sequence.
ACCESSION   NZ_CP117403
VERSION     NZ_CP117403.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32950771
            Assembly: GCF_028892885.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Give
  ORGANISM  Salmonella enterica subsp. enterica serovar Give
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3370)
  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 3370)
  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                     :: 15-MAR-2021
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1016X
            Sequencing Technology :: illumina MiSeq + Nanopore Gridion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:00:09
            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)                     :: 4,520
            CDSs (total)                      :: 4,398
            Genes (coding)                    :: 4,292
            CDSs (with protein)               :: 4,292
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 106
            CDSs (without protein)            :: 106
            Pseudo Genes (ambiguous residues) :: 0 of 106
            Pseudo Genes (frameshifted)       :: 48 of 106
            Pseudo Genes (incomplete)         :: 76 of 106
            Pseudo Genes (internal stop)      :: 16 of 106
            Pseudo Genes (multiple problems)  :: 31 of 106
            Pseudo Genes (short protein)      :: 1 of 106
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117403.1.
            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..3370
                     /organism="Salmonella enterica subsp. enterica serovar
                     Give"
                     /mol_type="genomic DNA"
                     /strain="RM007"
                     /serovar="Give"
                     /isolation_source="Water from tanks in pens"
                     /host="Bos taurus"
                     /sub_species="enterica"
                     /db_xref="taxon:46626"
                     /plasmid="pRM007_1"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2001-09-17"
                     /collected_by="University of Nebraska-Lincoln"
     gene            complement(874..1107)
                     /locus_tag="PQQ13_RS22580"
                     /old_locus_tag="PQQ13_22580"
     CDS             complement(874..1107)
                     /locus_tag="PQQ13_RS22580"
                     /old_locus_tag="PQQ13_22580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1114..1674)
                     /locus_tag="PQQ13_RS22585"
                     /old_locus_tag="PQQ13_22585"
     CDS             complement(1114..1674)
                     /locus_tag="PQQ13_RS22585"
                     /old_locus_tag="PQQ13_22585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1703..2143)
                     /locus_tag="PQQ13_RS22590"
                     /old_locus_tag="PQQ13_22590"
                     /pseudo=""
     CDS             complement(<1703..2143)
                     /locus_tag="PQQ13_RS22590"
                     /old_locus_tag="PQQ13_22590"
                     /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(2352..2675)
                     /locus_tag="PQQ13_RS22595"
                     /old_locus_tag="PQQ13_22595"
     CDS             complement(2352..2675)
                     /locus_tag="PQQ13_RS22595"
                     /old_locus_tag="PQQ13_22595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2739..2930
                     /locus_tag="PQQ13_RS22600"
                     /old_locus_tag="PQQ13_22600"
     CDS             2739..2930
                     /locus_tag="PQQ13_RS22600"
                     /old_locus_tag="PQQ13_22600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3012..3092)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(792..2362)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggatggtgaa aggttggagg gaacggcaac aactcacccc tcccagtgaa gggacgggta
       61 gtttgccgct ctcgatatgc cggacggagc caaggccatc gatcacgggg cgcgtcagtg
      121 gaagaacccg cgcctgcgtg acgtatgcgt cttcgccgca ccatctcacc cgtcacgcca
      181 ccacataccg ggaactgccg ccaaggtcta actcaaccaa tctagccgcg ctacatacgg
      241 tttttgtggc aactcatcag gtgtccgctg tcgatgaaac tctctgcgcc ggtagcggaa
      301 ctctcacgcg tgcggtcgcc gtcgtcacag ctcccccaac cgcaaacgat tctcgcaaat
      361 acgcaagtat ctgcaaaaac aggttttttt cggggttcct gggagactgt gctgttgaaa
      421 aattcttgaa gaatacagaa ggctcatgca aactgaatga actggtttct gttgtggatc
      481 tcaacagttt ccacaggaac attgaggagg tcagagacct caatgaaccc gaaacagctc
      541 gccttcctgg cgagctgttt tcgttctacg cccgccgacg aaagatcgca agtgcaataa
      601 cgagattttt cacgtcttta cgctcaaaaa gtaaaaaaac catgttttcc cctggctgaa
      661 tccccaaaaa cgcgtgaaat gcgttttcag gatgttgcat agctatgcac aaatacggca
      721 cacgatttgt ttcgctcgcc ccagccgtcg aactggtcaa aatggcaaga tttcgtcact
      781 tccccggtca catctccatt gatggcccac tccgaacccg tgccgcgcgt tcctgtacct
      841 catgtctgta ccgggcacgc tcctgttcat cccttagctg ttgttcgcga taaataaccg
      901 actcaagcga tccacttgcc cggctaatct ctgcacctgc tgactcaata tcacgacgcg
      961 ctcgttcagt atcgcgttgt tccgttgcgt aacctcgtgc atcttctgca attccgcgaa
     1021 ggcgctctcc cactcgttca gccgccgcat atagtcctgt tgcaaatgct ctaaggcgtt
     1081 cagcaaatgc ccttccagtt ccgtcatact cgtttactcc ctgaccagcc tcacggcgtt
     1141 cttgtcgccc accgtccagg tgttttcccc tttcaccccg tccggcaaca ccagaaattt
     1201 cccgttctcg ccattgacga acgtcacccc ccaggttttt gcctcgagtt tcgccagcgt
     1261 gttttcctgc tctctgatag tcaggatatt tttcgcaatc ttgctttcct gccactccat
     1321 cagcccccag caccccagga aaatgccgcc cgtgacgctg agcgcggtca gcgccggaaa
     1381 cagtatccgc cctttgatca cccgccagag cagttttttc tgctgccggg acagttcggc
     1441 ctctgtggtg ctgaactgca tgctcacggt ggtgctcagc gtatccagtt gctttttcac
     1501 ggatgttgta tgttcgctga tagcgtctct gattttctgc ctgtttaagc tcaatgcctt
     1561 gtctacagac tcttcgagct tcctgaactc gctgttcagc atgttctcgg tagaagcggc
     1621 tcgctctttc agtttcttct cgaagtctgt tcccatttgt aaaagattgc tcatacagcg
     1681 ccccctttag cctgagattc cgccccccct ccgggtcggc aatactgatg ctgcttttgg
     1741 ttgtcctcac cacctcaaaa cctgccgctg taagcgcctc tgtgacatcc tgacgcgttt
     1801 ttattgctcc ggcatggtaa agagcctcaa gaccccgtgt aatcgcttct gcggcctcct
     1861 gtttcgcttt tggcagatta tttggcgtga caagcgtccg tctgttctcc ggtgcgttcg
     1921 ggtcacgcag cccgtaatga tgattaacca gcgtctgcca ggcatttatc ctcggcctgt
     1981 ccgcgcggtc gtagtacggc tggaggcgct taccgctctg tagctccatg ttcgggatga
     2041 caaaattcag ttcgagccgc cccttatcct ggtgttccac ccagagaatg ctgtactggt
     2101 ctttttcgag accgggcata agaacacgct caaagctcgt catcactctt tcgcgttcac
     2161 ccggcggtaa ctccttctcc gcgaacgaca gaacgcctga agtgtatttc ttcgagaatg
     2221 gcgtggaatc aatgagttcc cgcacttctt ccgggttacc ccggagcacc gttgcgcctt
     2281 cgcggttacg ctcccgcccc agcaggtaat cgaccgggcc acttccaccg cctttccccc
     2341 tggcatgaaa tttaactatc atcccgtacc ccctgttccc tgacagcctg ccgcaactgg
     2401 cgcaattcac cctcgatggc catcagtgcg gccaccacat gaacccggtc aatcgaagac
     2461 cactggccgc tgttcacctt ccgggctgtc tggttcaggt tgttcccgat ggcagccaga
     2521 tgccgcagca atggcggcga tagtgtcggc agttttcctg tgcgtgcaac cggctccccc
     2581 agacagaccc gccgcatcca ttccgccagt cgtttaccct cgcagcgttc cagtaaccgg
     2641 gcgtgctcct catcggtaac ccgtatcgtg agcatcttct cgcgtttcat cggtatcatt
     2701 ccccctaaca aatcccccat acaaggagcc ttaagaccat gaccaaacag gaaaaaacag
     2761 cccttaacat ggctcgcttt atcagaagcc agacgctaac cctgctggaa aaactcaacg
     2821 atctggacgc ggacgaacag gcagacatct gcgaatcact tcacgaccac gccgacgaac
     2881 tctaccgcag ttgcctcgca cgcttcggcg atgacggtga aagcaactga aacatgcagc
     2941 tcccggagac gttcacagct tgcctgtgag cggatgccgg gagcagacaa gcccgccagg
     3001 gcgcgtcagt gcgggtgtcg gggcgcagcc ctgacccagt tcacagagcg atagcgatgt
     3061 gtatactggc ttatctcatt ttgcatcggt gcagaatgga tgggaagtgc accatgtcag
     3121 gagtaaaaag ccgcacagat gtaaaaacag cgcacccgat aaacagcaca cacgcggaca
     3181 ctggcacagg cgcgtaagtg cacaatgctt gcatctgtga ctcttccgct tcctcgccca
     3241 ctcgctcact acgttcggtc gctggggctg cggcgagcgg tgggatcact ctcgttgtga
     3301 tgctgatccg tttttttttt gcactggagt tatcaggagt tgcggtgcac atgggatcgt
     3361 gcgatatgcc
//
