LOCUS       CP093143                3609 bp    DNA     circular BCT 06-MAY-2022
DEFINITION  Salmonella enterica strain 2015AM-0511 plasmid p2015AM-0511_3,
            complete sequence.
ACCESSION   CP093143
VERSION     CP093143.1
DBLINK      BioProject: PRJNA230403
            BioSample: SAMN07415498
KEYWORDS    .
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3609)
  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  JOURNAL   Unpublished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 3609)
  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 (26-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 3609)
  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                     :: 2015AM-0511_consensus
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 162x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/05/2022 15:41:39
            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)                     :: 4,674
            CDSs (total)                      :: 4,549
            Genes (coding)                    :: 4,437
            CDSs (with protein)               :: 4,437
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 19
            Pseudo Genes (total)              :: 112
            CDSs (without protein)            :: 112
            Pseudo Genes (ambiguous residues) :: 0 of 112
            Pseudo Genes (frameshifted)       :: 45 of 112
            Pseudo Genes (incomplete)         :: 84 of 112
            Pseudo Genes (internal stop)      :: 22 of 112
            Pseudo Genes (multiple problems)  :: 35 of 112
            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..3609
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="2015AM-0511"
                     /db_xref="taxon:28901"
                     /plasmid="p2015AM-0511_3"
                     /geo_loc_name="USA"
                     /collected_by="CDC"
     gene            join(3537..3609,1..1445)
                     /locus_tag="CHU58_23320"
     CDS             join(3537..3609,1..1445)
                     /locus_tag="CHU58_23320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000739598.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NERD domain-containing protein"
                     /protein_id="UPY43864.1"
                     /translation="MKKNIVRQVLESYGPCISSELAERIKRQNPSMSSDAIRKMISRST
                     DIGKLPFLRFSHNRRFIYLKDDFGSFKFWRALKKCMREANSAYSHAILSVINNGGYLKV
                     KDFGIVSGSPIKQAKHLSYESVLKNLLSAKILRSVYIDGIGDCVLINNNIANDISIFNM
                     ANCESFFDKPIFELIKAWLRNLGIVAFNQIKTKYDGENNPVVGSFEWDITAPSYVSPLA
                     EYSSDGLIPGFVVCDFALGFNRNEITTDAADTFIRKVQMTKSSRTNQRIMFVLFARRFE
                     KNAFNKLRSEGVLAITIANAFGNKVDESLARLSKVIQGTLSIERHPDELLQMVKDLESI
                     SGENGNLRGYIFELFVSSQICNFYGYGNVRINKEYKINGKHAEADVVLETNDDIYIVEC
                     KNVKTLPSMEVSLWMKTRVPIINSYYKSNNPDNKNIHHRLWVTGNIYPKDINRLDEFKC
                     NNKKIDVDYLFGQSLDDFFYQKKQVFNLYRKVISPDYKKGQIPDFDL"
                     /name="NERD domain-containing protein"
     gene            complement(1650..1808)
                     /locus_tag="CHU58_23325"
     CDS             complement(1650..1808)
                     /locus_tag="CHU58_23325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UPY43865.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPKRHDLSPLAAATGNWNSRAMIM
                     RSVLQSS"
                     /name="replication initiation protein"
     gene            complement(2304..2498)
                     /locus_tag="CHU58_23330"
     CDS             complement(2304..2498)
                     /locus_tag="CHU58_23330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="UPY43862.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2782..3105
                     /locus_tag="CHU58_23335"
     CDS             2782..3105
                     /locus_tag="CHU58_23335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="UPY43863.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     Typing          2534..2773
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(1741..2261)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.905"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          2783..3102
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.131"
                     /coverage="100.0"
                     /evalue="4.38e-62"
ORIGIN
        1 ttaagcgtca gaatccttct atgtcatctg atgcaatacg taaaatgatc tctcgaagca
       61 ctgatattgg taagttgcca tttttaagat ttagtcataa caggagattc atttatctaa
      121 aagatgactt tggtagcttc aaattttggc gggcgctcaa aaaatgtatg cgtgaggcaa
      181 attcggcgta ttctcacgct atactttccg taattaataa tggcggatac ttgaaggtaa
      241 aggatttcgg gattgtgtct ggctctccga taaagcaggc caagcattta agttatgaat
      301 ctgttctaaa aaatctgctt tcagctaaaa tacttagatc tgtgtatatt gatggtattg
      361 gtgattgtgt tttgataaat aataatatag ctaatgatat cagcatcttt aatatggcaa
      421 attgcgagtc tttttttgat aagccaatat ttgaactgat taaggcatgg ttgcgaaatt
      481 taggtattgt ggcttttaat caaataaaaa caaaatatga tggagagaac aatcctgtgg
      541 ttggttcttt cgagtgggat ataacagcgc caagttatgt gtcccctctt gctgaatatt
      601 ccagcgatgg actcatccca ggttttgttg tctgtgattt tgctctaggg tttaatcgaa
      661 atgaaattac caccgatgct gctgatacct tcataagaaa agttcagatg accaagtcct
      721 ctaggacaaa ccagaggatt atgtttgttc tttttgctag acgttttgag aagaatgcct
      781 tcaacaagct aaggagtgaa ggggttctgg ctataactat agctaatgcg tttggtaata
      841 aggtcgatga gagcttggcc agactatcga aggtgattca gggaacttta tctattgaaa
      901 gacatcctga tgagttactt caaatggtaa aagatctgga gtctatctct ggagagaatg
      961 gaaatttaag ggggtatatt tttgagcttt ttgtttcctc tcaaatttgt aatttctatg
     1021 gttatggaaa tgttcgtatt aataaagaat ataaaataaa cggtaaacat gccgaagctg
     1081 atgttgtatt ggaaactaac gatgatattt atatcgttga gtgcaaaaat gttaagactt
     1141 taccttcgat ggaggttagt ctttggatga aaacaagagt gccaattata aattcctact
     1201 acaaatcaaa taaccctgat aacaaaaata tacatcatcg tttgtgggtt acggggaata
     1261 tatatcctaa agatataaac cgattggacg agtttaaatg taataataag aagattgatg
     1321 ttgattattt atttggtcag tctttggatg attttttcta ccaaaaaaaa caagtgttta
     1381 atttatatag gaaagtcatt tcgccagatt ataaaaaagg gcaaataccc gattttgact
     1441 tatagaatga cgttttctag tctctgcatt tcttgacgat gacggcttga aaagcgtatc
     1501 ttcctccatg aaacgaaaaa accacccggc aaggtggttt ttcgaaggtt agttaatcct
     1561 ggcagattac ctaacctagg taactggctt cagcagagcg cagataccaa atcctgtcct
     1621 ttaagtgtag ccgtagttgg ggcatcactt caagaactct gtagtacgga ccgcattatc
     1681 atcgctctgc tattccagtt accagtggct gctgccagtg gcgataagtc gtgtcttttc
     1741 gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
     1801 tcgtgcacac agcccagctt ggagcgaacg acctacaccg ggccgagata ccaacagcgt
     1861 gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaaac
     1921 ggcagggtcg gaacaggaga gcgcacgagg gagcttccag ggggaaacgc ctggtatctt
     1981 tatagtcctg tcgggtttcg ccacctctgg cttgagcgtc gatttttgtg atgctcgtca
     2041 ggggggcgga gcctatggaa aaacgccacc ggcgcggcct ttttcgggtt cttgtttttt
     2101 gctcacatgt ttcttttggc tttatcccct gattctgtgg ataaccgcat taccgtcttt
     2161 gagtgagctg ataccgctcg ccgcagccga acgaccgagc gtagcgagtc agtgagcgag
     2221 gaagcggaag agcgccttat gtggcatttt ctccttacgc accggtatac cgttctgcat
     2281 cctgtctgga gcaggataca ctgttatacc ccggtgccac tttccgcttc aaagcgtgtc
     2341 tgtatgctgt tctggagttc ttccgcgagt tcgtgcagct tctcacacat ggcggcctgt
     2401 tcgtcggcat cgagtgcgtc cagcttttcg agcagcgtca ggctctggct ttttatgaat
     2461 cccgccatgt tgagtacggt ttgctgctgc ttgttcatct tttcgttttc tccgttctgt
     2521 ctgtcatctg cgttatgtga ttatatcgcg taccactttt cgactgtttt gctgccgcta
     2581 ttctgccgcc tggctttttg acgggcattt ctgtcagaca acactgtcac tgccaaaaaa
     2641 ctgccgtgcc tttgtcggta attcgagctt gctgacagga caggatgtgc aattgttata
     2701 ccgcgcatac atgcacgcta ttacaattac cctggtcagg gctttgcccc gacacccatg
     2761 tcagatacgg agccatgttt tatgacaaaa cgaagtggaa gtaatacgcg caggcgggct
     2821 atcagtcgcc ctgttcgtct gacggcagaa gaagaccagg aaatcagaaa aagggctgct
     2881 gaatgcggca agaccgtttc cggtttttta cgggcggcag ctctcggtaa gaaagttaac
     2941 tcactgactg atgatcgggt actgaaagaa gttatgagac tgggggcgtt acagaaaaaa
     3001 ctctttatcg acggcaagcg tatcggggac agggagtatg cggaggtgct gatcgctatt
     3061 acggagtatc accgtgccct gttatccagg cttatggcag attagcttcc cggggagaaa
     3121 actgttgaaa acagacggta tgaacaccgt aagctcccaa agtgatcacc attcgctttc
     3181 atgcataact atgcagcgag ctgaaaacga tcctgacgca tccttcctat ttttccgggg
     3241 taaaacatct ctttttgcgg tgtctgcgtc agaatcgcgt tcagcgcgtt tcagtggtgc
     3301 gtacaattaa gggattatgg taaatagggc ggttgatata tgatgatgaa atgtcacaag
     3361 cgtaacatct tgatttttaa ggataaatct cgcaggtgtg ttttttgtga tatgttgctt
     3421 ttgttaaatg tttgattttt atgatttttt tctttgtgtt tttttttggg atctatagat
     3481 attacacgta gtgtaatttt ataaatagcg tagtgtgaca aaaataagat gaatttatga
     3541 aaaaaaacat tgttagacaa gtgcttgaga gttatggtcc gtgcatatct tctgaacttg
     3601 ctgagagga
//
