LOCUS       CP093090                5466 bp    DNA     circular BCT 05-MAY-2022
DEFINITION  Salmonella enterica strain PNUSAS039582 plasmid pPNUSAS039582_2,
            complete sequence.
ACCESSION   CP093090
VERSION     CP093090.1
DBLINK      BioProject: PRJNA230403
            BioSample: SAMN09011259
KEYWORDS    .
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5466)
  AUTHORS   Webb,H.E., Kim,J.Y., Tagg,K.A., de la Cruz,F., Penil,A., Tolar,B.,
            Ellison,Z., Schwensohn,C., Brandenburg,J., Nichols,M. and
            Folster,J.P.
  TITLE     Twenty-one complete Salmonella enterica serotype Hadar genomes
            collected from patients in the United States
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5466)
  AUTHORS   Tarr,C.L., Trees,E., Katz,L.S., Carleton-Romer,H.A., Stroika,S.,
            Kucerova,Z., Roache,K.F., Sabol,A.L., Besser,J. and Gerner-Smidt,P.
  CONSRTM   PulseNet: The National Subtyping Network for Foodborne Disease
            Surveillance
  TITLE     Direct Submission
  JOURNAL   Submitted (28-JUL-2018) Enteric Diseases Laboratory Branch, Centers
            for Disease Control and Prevention, 1600 Clifton Rd., MS C03,
            Atlanta, GA 30333, USA
REFERENCE   3  (bases 1 to 5466)
  AUTHORS   Webb,H.E., Kim,J.Y., Tagg,K.A., de la Cruz,F., Penil,A., Tolar,B.,
            Ellison,Z., Schwensohn,C., Brandenburg,J., Nichols,M. and
            Folster,J.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-MAR-2022) EDLB, Centers for Disease Control and
            Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2022
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: PNUSAS039582_consensus
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 252x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/04/2022 09:54:59
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.1
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,790
            CDSs (total)                      :: 4,662
            Genes (coding)                    :: 4,539
            CDSs (with protein)               :: 4,539
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 19
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 49 of 123
            Pseudo Genes (incomplete)         :: 87 of 123
            Pseudo Genes (internal stop)      :: 25 of 123
            Pseudo Genes (multiple problems)  :: 34 of 123
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..5466
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="PNUSAS039582"
                     /db_xref="taxon:28901"
                     /plasmid="pPNUSAS039582_2"
                     /geo_loc_name="USA"
                     /collected_by="CDC"
     gene            13..204
                     /locus_tag="DEM16_23890"
     CDS             13..204
                     /locus_tag="DEM16_23890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="UPX71666.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1212..2021)
                     /locus_tag="DEM16_23895"
     CDS             complement(1212..2021)
                     /locus_tag="DEM16_23895"
                     /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="UPX71667.1"
                     /translation="MSKDKKGRSKNRYHQLVEKIFFDKYVDGDLEVLFERLEINSAAKD
                     LGIDLPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPAKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(2014..3264)
                     /locus_tag="DEM16_23900"
     CDS             complement(2014..3264)
                     /locus_tag="DEM16_23900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010222406.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="UPX71668.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELNPKYFIFENVKGLTVGKHKQFLVEIMDAFKNGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGITLPSYPEPLSIRTTVGDAIGDIPDAEKYPELWERDWVDAKFGEQ
                     SLYSSYLHGVRKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            complement(3655..3888)
                     /locus_tag="DEM16_23905"
     CDS             complement(3655..3888)
                     /locus_tag="DEM16_23905"
                     /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="UPX71664.1"
                     /translation="MTELETHLLSALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3895..4413)
                     /locus_tag="DEM16_23910"
     CDS             complement(3895..4413)
                     /locus_tag="DEM16_23910"
                     /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="UPX71665.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMRQHRRDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(4451..4882)
                     /locus_tag="DEM16_23915"
                     /pseudo=""
     CDS             complement(4451..4882)
                     /locus_tag="DEM16_23915"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; 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(5091..5414)
                     /locus_tag="DEM16_23920"
     CDS             complement(5091..5414)
                     /locus_tag="DEM16_23920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000955993.1"
                     /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="UPX71669.1"
                     /translation="MITIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQMAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGVR
                     DDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(290..378)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.222"
                     /coverage="100.0"
                     /evalue="3.2400000000000006e-27"
     Typing          389..926
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.634"
                     /coverage="99.0"
                     /evalue="1.75e-177"
     Typing          complement(3552..5101)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.466"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(5098..5447)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.453"
                     /coverage="99.0"
                     /evalue="7.13e-64"
ORIGIN
        1 acggaggcat cagtgactaa acaggaaaaa accgccctta acatggcccg ctttatcaga
       61 agccagacat taacgctgct ggagaaactc aacgaactgg acgcagatga acaggccgat
      121 atttgtgaat cacttcacga ccacgccgac gagctttacc gcagctgcct cgcacgtttc
      181 ggggatgacg gtgaaaacct ctgacacatg cagctcccgg agacggtcac agcttgtctg
      241 tgagcggatg ccgggagcag acaagcccgc cagggcgcgt cagcgggttt tagcgggtgt
      301 cggggcgcag ccctgaccca gtcacgtagc gatagcggag tgtatactgg cttatctcat
      361 tttgcatcgc tgcggattgt atgagaagtg caccatgtcc ggtgtgaaat gccgcacaga
      421 tgcgtaagga gaacataccg catcaggcgc tcttccgctt cctcgctcac tgactcgcta
      481 cgctcggtcg ttcggctgcg gcgagcggta tcagctcact caaagacggt gatgcggtta
      541 tccacagaat caggggataa caccggaaag aacatgtgag caaaaagcca gggacaggaa
      601 gaaggccgcg ccgctggcgt ttttccatag gctccgcccc cctgacgagc atcacaaaaa
      661 tcgatgctca agtcagaggt ggcgaaaccc gacaggactt aaagatacca ggcgtttccc
      721 cctggtggct ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccgg tgtcattccg
      781 ctgttatggc cgcgtttttc tcattccacg cctgacactc agttccgggt aggcagttcg
      841 ctccaagctg gactgtatgc acgaaccccc cgttcagtcc gaccgctgcg ccttttccgg
      901 taactatcga cttgagtcca acccggaaag acatgcaaaa gcgccaatgg caacggccac
      961 aggtaacgga ttcacggagc agagcggagt agagttatct acagagttct tgaagtggtg
     1021 gcctgactac ggctacacta aaaggacagt tttggtatct gcgctccgtg aaagccagtt
     1081 accttcggaa ggaagagttg gtagctctaa attccggcaa acgaaccacc gttggtagcg
     1141 gtggtttttt tgtttacagc ttaagagatt acggctagaa cgaaaggatc tcaagaagat
     1201 cctctcagaa atcatacaga catgcggtag tttgagatgt cagagctatc tagctctttt
     1261 gccggaacca gtttgtaatg cctttcctca atcaatttca cttgtccttc gtctatcttc
     1321 agctcaaaca gtgcaatcaa atcgctcgaa acaaactggg cggaaatagc tctacatcta
     1381 acatttgggt atttttgttc acaccacgct gtatcttgcg atgtttgcac cattgatatt
     1441 tgatcggttc caccttttgc ttggactggt attatataat ggcaaccgta tttatctatc
     1501 ccgacataaa gttcatcgat ctctatttga ccaattccct tcaccgtagt tcttaaatgg
     1561 ttctgtaaag aatatgtagt tatacctaga aatatatcta ttaatcggtt atacctcacc
     1621 ttcgccagca atgcctgttc gtcgtctaga gaataacctg tgattatctc cggggtatta
     1681 tctgggattt ttattgccac catatttgga tttggcaaaa tcctactaat agttaccaat
     1741 ctaaatcgat actttgacct acccgccagc tcaataatcc actccttacc ttctggttga
     1801 gtcaataaaa tactttctgg cataggtgtt ctaaatctga ttgaatatat aacatcacca
     1861 acattggaag ggagatctat acccaaatcc tttgcagcgc tgtttatctc taacctttca
     1921 aacaatacct ctaagtcacc atcaacatat ttatcgaaaa atatcttttc taccaactga
     1981 tggtatctat tttttgacct acctttttta tccttactca caaacaacct ccttgttact
     2041 attttttatt ctcttagcaa ttacatttga tgacacacca aacatagatg cagcatcgga
     2101 catagagata gcaaccaaac tttcatcacc gagtttgatt ttcttcgttg gtttttttgg
     2161 cgtaacgcca agaaccttca taatctgcaa gccaacactt ctagctagca tgggaggaac
     2221 actattaccg acctgtctaa atccatgcca cttagtcaca tgaaatctga accaatcagg
     2281 atatgaatgc agtcttgctg cctctctaac cgtaatgacc ctaggataga tcggatgtat
     2341 agggcgagga gatgtaaaag cacctctatc acttgctgtt cctgccctta aagtattaca
     2401 tagcccattc attgagagct ttttgaacct gctgattggt tctaccgtgt caggcaaagt
     2461 ttcaacaaac cgtcctctag aaatgtcaga gtgatctgtc agtaaagaac acgttaattt
     2521 atctttatta aaaattcttg ggtagctaaa atcacttggg tcttttctta cgccatgcaa
     2581 ataggatgag tataatgatt gctcaccaaa tttagcatca acccaatccc tctcccatag
     2641 ctcaggatat ttttctgcgt caggaatatc cccaatagcg tccccaaccg ttgttctaat
     2701 ggataatggt tctgggtatg atggcaaagt aattcctttc cttccaccca ttaagaaaag
     2761 acgacggcga tcttgaggga ccccataatc agctgcattt agcactttat aatcgcttac
     2821 aacgtcgtat ccgccatttt taaatgcatc cattatctct actaaaaact gcttatgctt
     2881 acctaccgtt aatcctttta cattttcaaa aatgaagtat ttagggttta gctcaagcac
     2941 cagccgtaca tagtgataga ccaatttgtt tctatcatca tcaagcgcgc gctttcctat
     3001 taatgaaaag ccttggcatg gagcgcctcc gatcactaca tcaatctctt tctcaccaat
     3061 acctgaaact tccctaacgt attctccggt aacatcaaca acacttctac atatcgtttt
     3121 gcacatagga aagttatatt tgtgagcaga gcaatgtatt ggatctattt caactgatgc
     3181 cattatatca aagccagctt gctcgaaacc gagactcagc ccacccgctc cagcaaataa
     3241 atcaacagca atcggtctag tcattcttta catccacgtt atataaaatc aacgtgatac
     3301 tatcagaaaa acgatcgatt taccgatcgt ttttctgatt ccgattgaac ataacatctc
     3361 ttgcccgcac cgcagaaacg cgttcggtgc gatcacggca gcagacaggt aaaaatggca
     3421 acaaaccacc cgaaaaactg ccgcgatcgc gcctgataaa ttttaaccgc atgaatacct
     3481 atgcaaccag atggtacagg ccacattaac ccctcttaat ccactgaagc tgccattttt
     3541 catggtttca ccatcccagc gaaggaccat ccagcgtgcg ttcctgtatt tccggctgac
     3601 gctcccgttc cagggataac gcatgttctc gctcctgtat cagccgttcc tctcttatct
     3661 ccagttctcg ctgtataact ggctcaagcg ttctgtctgc tcgctcaagt gctgcacctg
     3721 ctgactcaac tgcatgaccc gctcgttcag catcgcgttg tcccgttgcg taagcgaaaa
     3781 catcttctgc aattccacga aggcgctctc ccattcgctc agccgctgca tatagtcctg
     3841 ttgcagctgc tctaaggcgc tcagcaaatg tgtttccagc tctgtcactc tgtgtcactc
     3901 cgtcagttgt acccattcct tcccctgaaa ggaaatcacc tctgctgact tcccgtacgg
     3961 aaggaccaga aatttcctgt tcccgtcctg cacaaactcc acaccccatg tcttcgcgtt
     4021 cagtttctgc aatgtctctt cctgcttcct gatatcttcc aggttcgcct gtatccgccc
     4081 gccaagatac cagagcgtcc cgccactcgc ggtaaacagg agaaagacta tccccagtaa
     4141 catcatgccc gtattccctg ccagctttaa cacgtctctc ctgtgctgcc tcatcgcctc
     4201 tttcacccct tcccggtgtt tttccagcga ttcctctgtc gaggcggtga acagggctat
     4261 agcgtctctg attttcgtct cgtttgatgt cacagcctcg cttacagatt cgccgagcct
     4321 cctgaactcg ttgttcagca ttttctctgt agattcggct ctctctttca gctttttctc
     4381 gaactccgcg cccgtctgta aaagattgct cataaaatgc tcctttcagt ctgatattcc
     4441 tcccgccgtt cgggtctgca atgctgatac tgcttcgcgt caccctgacc acttccagcc
     4501 ccgcctccgt gagcgcctga atcacatcct gacggccttt tatctctccg gcatggtaaa
     4561 gtgcgtctat acctcgtgtg actccctcag caagcgcctg tttcttttcc ggcaggttat
     4621 cagggagagt cagtatccgg cggttctccg gggcgttggg gtcatgcagc ccgtaatggt
     4681 gattaaccag cgtctgccag gcatcaattc tcggtctgtc tgcgcggtcg tagtacggct
     4741 ggaggcgttt tccggtctcc agctccatgt tcggaatgac aaaattcagc tcaagccgcc
     4801 ccttgtcctg gtgctccacc cacagaatgc tgtactgatt tttttcaaga ccgggcatca
     4861 gtacacgctc aaagctcgcc atcacttttt cacgtcctcc aggcggcagt tctttctccg
     4921 caaacgacag aacaccggac gtgtatttct tcgcaaatgg cgtggcatcg atgagttccc
     4981 ggacttcttc cggattaccc tgaagcaccg ttgcgccttc ccggtttcgc tcccttccca
     5041 gcaggtaatc aaccggacca ctgccaccgc cttttcccct ggcatgaaat ttaacaatca
     5101 tcccgcactc cctgttccct gacgacctgc cgtaaactgc gcaactctct ctcgatggcc
     5161 atcagtgcgg ccaccacctg aacccggtca ccggaagacc actgcccgct gttcaccttc
     5221 ctcgctgtct gattcaggtt attcccgatg gcggccatct gacgcagtaa cggcggtgcc
     5281 agtgtcggca gcttcccgga acgggcaacc ggctcaccca ggcagacccg ccgcatccat
     5341 accgccagtt gtttaccctc acaacgttcc agcaaacggg catgttcatc atcagtaacc
     5401 cgtatcgtga tcatcctctc gcgtttcatc ggtatcatta cccccatgag cagaaatccc
     5461 ccttac
//
