LOCUS       NZ_CP025244             4593 bp    DNA     circular CON 24-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Newport str. CDC
            2012K-0663 isolate USDA-ARS-USMARC-1936 plasmid pSNE1-2012K-0663,
            complete sequence.
ACCESSION   NZ_CP025244
VERSION     NZ_CP025244.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02716905
            Assembly: GCF_004136115.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Newport str. CDC
            2012K-0663
  ORGANISM  Salmonella enterica subsp. enterica serovar Newport str. CDC 201...
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4593)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovenia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     Comparative Genomics of Salmonella Newport
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4593)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovenia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-DEC-2017) Meat Safety and Quality Research Unit,
            USDA-ARS-USMARC, State Spur 18D, Clay Center, NE 68933, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 165.52x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/24/2023 01:26:20
            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)                     :: 4,995
            CDSs (total)                      :: 4,871
            Genes (coding)                    :: 4,753
            CDSs (with protein)               :: 4,753
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 47 of 118
            Pseudo Genes (incomplete)         :: 86 of 118
            Pseudo Genes (internal stop)      :: 18 of 118
            Pseudo Genes (multiple problems)  :: 30 of 118
            Pseudo Genes (short protein)      :: 1 of 118
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP025244.1.
            Bacteria and source DNA available from USMARC.
            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..4593
                     /organism="Salmonella enterica subsp. enterica serovar
                     Newport str. CDC 2012K-0663"
                     /mol_type="genomic DNA"
                     /strain="CDC 2012K-0663"
                     /serovar="Newport"
                     /isolate="USDA-ARS-USMARC-1936"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:1454629"
                     /plasmid="pSNE1-2012K-0663"
                     /geo_loc_name="USA: BIFSCo Region 2"
                     /collection_date="2012"
                     /collected_by="CDC"
     gene            complement(163..396)
                     /locus_tag="AW92_RS25815"
     CDS             complement(163..396)
                     /locus_tag="AW92_RS25815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(403..963)
                     /locus_tag="AW92_RS25820"
     CDS             complement(403..963)
                     /locus_tag="AW92_RS25820"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<998..1432)
                     /locus_tag="AW92_RS26275"
                     /pseudo=""
     CDS             complement(<998..1432)
                     /locus_tag="AW92_RS26275"
                     /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(1641..1964)
                     /locus_tag="AW92_RS25005"
                     /old_locus_tag="AW92_25565"
     CDS             complement(1641..1964)
                     /locus_tag="AW92_RS25005"
                     /old_locus_tag="AW92_25565"
                     /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_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2027..2218
                     /locus_tag="AW92_RS25010"
                     /old_locus_tag="AW92_25570"
     CDS             2027..2218
                     /locus_tag="AW92_RS25010"
                     /old_locus_tag="AW92_25570"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3229..4068
                     /locus_tag="AW92_RS25025"
                     /old_locus_tag="AW92_25585"
     CDS             3229..4068
                     /locus_tag="AW92_RS25025"
                     /old_locus_tag="AW92_25585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     Typing          complement(2307..2391)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          2402..2957
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.907"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(66..1651)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acattggcgc catccgggta gggcgtgcca caaactggct cgatttcagg gggtaccccg
       61 gtcacatccc cattgacggg ccacgccaga tccgcgcttc gggttcctgc tcttcatgcc
      121 agcgccgggc aagctcctgc gcctgacgct cctgttcatc ccttatctgt tgttcgtgat
      181 aaataaccga ctcaagcggt cgacttgtcc ggctaatagc tgcacctgct gactcaagtt
      241 cacgacacgc tcgttcagta tcgcgttgtt ctgttgcgta accgcgtgca tcttctgcaa
      301 ttctgcgaag gcgctctccc actcgttcag ccgccgcata tagtcctgtt gcaaatgctc
      361 taaggcgttc agcaaatgcc cttccagttc cgtcatactc gtttactccc tgaccagcct
      421 cacggcgttc ttgtcgccca ccgtccaggt gttttcccct ttcaccccgt ccggcagcac
      481 cagaaatttc ccgttctcgc cattgacgaa cgtcaccccc caggtttttg cctcgagttt
      541 cgccagcgtg ttttcctgct ctctgatggt caagatattt ttcgcaatcc tgctttcctg
      601 ccactgaatc agcccccagc accccaggaa aatgccgccc gtgacgctga gcgcggtcag
      661 cgccggaaac agtacccgcc ctttgatcac ctgccagagc aggtttttct gctgccggga
      721 cagttcggcc tctgtggtgc tgagctgcgt gctcacggtg gtgctcagcg tatccagttg
      781 ctgtttcacg gatgttgtat gttcgctgat agcgtctctg attttctgcc tgtttaagct
      841 cagtgccttg tctacagact cttctagctt cctgaactcg ctgttcagca tgttctcggt
      901 agaagcggct cgctctttca gtttcttctc gaagtccgtt cccatttgta aaagattgct
      961 catacagcgc cccctttagc ctgagattcc gccccccctc cgggtcggca atactgatac
     1021 tgcttctggt tgtcctcacc acctcaaaac ctgccgctgt gagcgcctca gtgacatcct
     1081 gacgcgtttt tattgctccg gcacggtaaa gcgcctcaag accccgtgta atcgcttctg
     1141 cggcctcctg tttcgctttt ggcagattat tcggtgtgac aagcgtccgt ctgttctccg
     1201 gtgcgttcgg gtcacgcagc ccgtaatgat gattaaccag cgtctgccag gcatttatcc
     1261 tcggcctgtc cgcacggtcg tagtacggct ggaggcgctt accgctctgt agttccatgt
     1321 tcggaatgac aaaattcagt tcgagccgcc ccttatcctg gtgttccacc cagagaatgc
     1381 tgtactggtc tttttcgaga ccgggcataa gaacacgctc aaagctcgtc atcactcttt
     1441 cgcgttcacc cggcggtaac tccttctccg cgaacgacag aacgcctgat gtgtatttct
     1501 tcgaaaatgg cgtggcatca atgagttccc ggatttcttc cgggttaccc cggagcaccg
     1561 ttgcgccttc gcggttacgc tcccgcccca gcaggtaatc gaccgggcca cttccaccgc
     1621 ctttccccct ggcatgaaat ttaactatca tcccgtcccc cctgttccct gacagcctgc
     1681 cgcaactggc gcaattcacc ctcgatggcc atcagagcgg ccaccacatg aacccggtca
     1741 atcgaagacc agtggccgct gttcaccttc cgggctgtct ggttcagatt gttcccgatg
     1801 gcagccagat gccgcagcaa tggcggcgat agtgtcggca gttttcctgt gcgcgcaacc
     1861 ggctccccca gacagacccg ccgcatccat tctgccagtc gtttaccctc gcagcgttcc
     1921 agtaaccggg cgtgctcctc atcgctaacc cgtatcgtga gcatcttctc gcgtttcatc
     1981 ggtatcattc cccctaaaaa atcccctatt aaggagcctt aagaccatga ccaaacagga
     2041 aaaaacagcc cttaacatgg cccgctttat cagaagccag acgctgaccc tgctggaaaa
     2101 actcaacgag ctggacgcgg acgaacaggc agacatctgc gaatcacttc acgaccacgc
     2161 cgacgaactc taccgtagtt gcctcgcacg cttcggcgat gacggtgaaa gcaactgaaa
     2221 catgcagctc ccggagacgt tcacagcttg cctgtgagcg gatgccggga gcagacaagc
     2281 ccgtcagggc gcgtcagcgg gttttagcgg gtgtcggggc gcagccctga cccagtcacg
     2341 tagcgatagc ggagtgtata ctggcttaac tatgtggcat cagtgcggat tataagaaaa
     2401 gtgcaccata tgcggtgtga aataccgcac agatgcgtaa ggagaaaatg ccgcatcagg
     2461 cgctcttccg cttcctcgct cactgactcg ctacgctcgg tcgttcggct gcggcgagcg
     2521 gtatcagctc actcaaagac ggtgatgcgg ttatccacag aatcagggga taacgccaaa
     2581 agaaacatgt gagcaaaagg ccaggaacag gaagaaggcc gcgccgctgg cgtttttcca
     2641 taggctccgc ccccctgacg agcatcacaa aaacagatgc tcaagtcaga ggtggcgaaa
     2701 cccgacagga ctataaagat accaggcgtt tccccctgga agctccctcg tgcgctctcc
     2761 tgttccgacc ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc
     2821 gctttctcat agctcacgct gttggtatct cggcccggtg taggtcgttc gctccaagct
     2881 gggctgtgtg cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg
     2941 tcttgagtcc aacccggaaa gacacgtaaa aacgccactg gcagcagcca ttggtaaccg
     3001 tttagaggag ttagtcttga agttatgcgc cggttaaggc taaactgaaa ggacagattt
     3061 ggtggctgtg ctcctccaag ccagttacct tggttcaaag agttgctgct ctgagaacct
     3121 tcgaaaagcc gccttgctgg gcggtttttt cgtttacgga caagactacc ttcaggatcg
     3181 ttagatctca agacaatcat gcatagtgag catacacagg agccgaactt gcttacactg
     3241 ttcatctttt ttgttttatt aatagctgca tgtttctttt gttttgctcc accacgaaga
     3301 ggatatgaca gaaatgagat cattccatac aaaataaaac tatcaataaa taaatatcgc
     3361 ctttacatat actcatcggg aaaggtaaga caataccttt tatttttagt tattttatca
     3421 ctgtactact ccatagcgga accatttaag tctgagttaa taaaaaacat atcatattca
     3481 ctgatggctg catttatttt tgatacaggg cttaatttta gcaaggagaa tataactaaa
     3541 ggagtgattt caacaaggtg gcataatgac ctatattcat catttgagag aatgaaagca
     3601 attaataaaa tttactaccc atccaacaaa gagataaaca cagaaggtct atccaaagcc
     3661 atcacatcat ctcttttcaa tgatgacgcg aactcgttcg caaagagaga ttttcgcttg
     3721 atgtgggact tatcttctga aaaatatctt tcctataaag aaataataat aagaaaaggc
     3781 gataagcttg acgctgtatg cttgagattt ataaatgatg actacaagtt tttagttaat
     3841 ttcaacagag atgaagaggt tttcaaatac tttccatcta taatgcaacc ttcactcaaa
     3901 acatatagag cgttatcaag actagtaaac tcaatcaaag atccttctag atttaagttc
     3961 acgacagagt cattagaaat ggagttacta gaatacttag agttaagaaa tgaattattc
     4021 aatgacatag aagaagtaat gggtagctat gctcagaggg caccatagtt catgatagcc
     4081 ctcgatagta cttacttata tttttagaga ggtttaagtg taagtagagg gagtaacacc
     4141 tggtttttca gcatccactc caatgaatgc tgacaccgat acgcgataat tctctttatc
     4201 gtagcaaaat catcctccag attgcggttg agaataggtt catggtgcgc aatacgattg
     4261 cgcagttttc tcacgggact tgttagcagt aatgcttccc cccggggaca aacgacagag
     4321 atatacaaca aaggcccgca attaaaatac tccgtattta ccataacgtc gcattgcgcg
     4381 taccgcttaa acgcgttcag cgcgatcacg gcagcagaca ggtaaaaaca gcaacaaacc
     4441 acccgaaaaa ctgccgcgat cgcgcctggt aaattttaac ctcatgcata gttatgcgcg
     4501 aaactgaatg acgatcagtt tcgcacgttc cagccgtcga acggggcaaa atggggaggt
     4561 ttggatattg ttaatgctaa tgtacgtaca tta
//
