LOCUS       NZ_CP100738             3263 bp    DNA     circular CON 24-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Agona strain R18.1477
            plasmid pR18.1477_3.3k, complete sequence.
ACCESSION   NZ_CP100738
VERSION     NZ_CP100738.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29431227
            Assembly: GCF_024266785.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Agona
  ORGANISM  Salmonella enterica subsp. enterica serovar Agona
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3263)
  AUTHORS   Chiou,C.S., Chen,B.H., Wang,Y.W. and Teng,R.H.
  TITLE     28 Salmonella enterica strains that have azithromycin resistance
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3263)
  AUTHORS   Chiou,C.S., Chen,B.H., Wang,Y.W. and Teng,R.H.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUL-2022) Center for Diagnostics and Vaccine
            Development, Centers for Disease Control, Taiwan, No.20, Wenxin S.
            3rd Rd., Nantun Dist., Taichung City 408, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: flye v. 2.9; trycycler v. 0.5.3; medaka v. 1.6.0;
            homopolish v. 0.3.3; polca v. 4.0.5; polypolish v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 214x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/24/2023 04:36:00
            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)                     :: 4,929
            CDSs (total)                      :: 4,811
            Genes (coding)                    :: 4,687
            CDSs (with protein)               :: 4,687
            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)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 41 of 124
            Pseudo Genes (incomplete)         :: 94 of 124
            Pseudo Genes (internal stop)      :: 14 of 124
            Pseudo Genes (multiple problems)  :: 23 of 124
            Pseudo Genes (short protein)      :: 1 of 124
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100738.1.
            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..3263
                     /organism="Salmonella enterica subsp. enterica serovar
                     Agona"
                     /mol_type="genomic DNA"
                     /strain="R18.1477"
                     /serovar="Agona"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:58095"
                     /plasmid="pR18.1477_3.3k"
                     /geo_loc_name="Taiwan: Hsinchu County"
                     /collection_date="2018"
                     /collected_by="Centers of Disease Control, Taiwan"
                     /subtype="ST13"
     gene            complement(join(3223..3263,1..415))
                     /locus_tag="NL742_RS24600"
                     /old_locus_tag="NL742_24600"
     CDS             complement(join(3223..3263,1..415))
                     /locus_tag="NL742_RS24600"
                     /old_locus_tag="NL742_24600"
                     /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_039023474.1"
                     /translation="MTTKFNKFELHSAFRDGKLNEKYFVDLPYLKEEQRRALASFLGAI
                     TREEPLPGKNKPSWLDDNSIKISGTDAYEDGNYWHYHCGPYPEGVKLRSMTFNLGMNVA
                     GLTSAEVIHYQKLNDGTVFVVGFSPTHEPFPKSDAPHYNPLFTESDD"
                     /name="hypothetical protein"
     gene            812..1390
                     /locus_tag="NL742_RS24605"
                     /old_locus_tag="NL742_24605"
     CDS             812..1390
                     /locus_tag="NL742_RS24605"
                     /old_locus_tag="NL742_24605"
                     /inference="COORDINATES: protein motif:HMM:NF025107.2"
                     /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_052266651.1"
                     /translation="MKSEIELKKTEHSSVEIPERILAIWGRSILNSGWTSVPNELLKNQ
                     SKLGIGNTELVLLINLISFMHHPDARVYPSISLLCERMNQDRRTIQRNLNKLVEMDILR
                     IKIRSTGKNSKGMTNLYDITPLMLKLINLKIPSLNTPDEKHTCPKCGKIAISREEITKE
                     FGFRTDTNGKMRTQSWCKDCRGRKIADLP"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1382..1564)
                     /locus_tag="NL742_RS24610"
                     /old_locus_tag="NL742_24610"
     CDS             complement(1382..1564)
                     /locus_tag="NL742_RS24610"
                     /old_locus_tag="NL742_24610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001298668.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_139772311.1"
                     /translation="MNAVSPQTDRHSVSCIVMQRAENNPDAFFRFTPGKTSLFAVFAAE
                     SRSARFCGARNATLW"
                     /name="hypothetical protein"
     gene            complement(1598..1921)
                     /gene="mobA"
                     /locus_tag="NL742_RS24615"
                     /old_locus_tag="NL742_24615"
     CDS             complement(1598..1921)
                     /gene="mobA"
                     /locus_tag="NL742_RS24615"
                     /old_locus_tag="NL742_24615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2194..2388
                     /locus_tag="NL742_RS24620"
                     /old_locus_tag="NL742_24620"
     CDS             2194..2388
                     /locus_tag="NL742_RS24620"
                     /old_locus_tag="NL742_24620"
                     /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="WP_001041643.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1931..2157)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.797"
                     /coverage="99.0"
                     /evalue="6.34e-74"
     Typing          2418..2944
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.053"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          complement(1602..1921)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="9.72e-63"
ORIGIN
        1 catcagactt agggaagggc tcatgtgtag gggagaagcc tacgacaaac accgtgccat
       61 cgttgagttt ttgatagtgg atcacttcag cggaggttag ccccgcaacg ttcataccca
      121 agttaaaagt catcgatcta agtttgaccc cttctggata tggaccgcaa tgataatgcc
      181 agtagttccc gtcttcgtac gcatcagtac cggaaatttt aatggaatta tcatcaagcc
      241 atgaaggctt gtttttccct ggaagaggct cttcacgagt tatcgcaccc aagaaagagg
      301 ctaatgcccg gcgttgctct tctttgaggt agggtaaatc tacgaaatac ttttcattca
      361 gcttcccgtc tcggaaagcc gaatgaagct caaacttatt gaatttggtt gtcatcaaac
      421 actttccact taccttactg agtaagtaga tagcatatca aagatcgatt catcagactg
      481 cggagaatcg cattttaacg cttcatgtgc ctgattcttg tatgaacgcg agagcagcac
      541 ttcgtcagca cgagatttgt actgctgacg acgttctgta tcgcagctgt gattatcaaa
      601 tcgtacgttt gccaacatgt cagtcctatg tttgaagaag tctgggaaga taaaatctta
      661 ctcaattaga tggtaagaga ggtcctttcc cagtgctaga cattaggcct ttttggtcaa
      721 attaaagggc ggcattgatg ccgcccaaat aataaatcat aataacaata cctatatata
      781 taggtattgt tattatgatt ggtgacagaa attgaaatca gaaatcgaac tcaaaaaaac
      841 agaacactca tcagtagaga tcccagaaag gatcttagcc atatgggggc gcagcatttt
      901 aaactctggc tggacatccg tccccaatga actattaaaa aaccaatcta agctaggaat
      961 aggaaacaca gagcttgtac ttttgattaa tctgatatct ttcatgcatc atcctgacgc
     1021 aagagtgtac ccatcaattt cacttctatg cgaaagaatg aatcaggaca gacgaacaat
     1081 tcagagaaat ttaaacaagt tagtagaaat ggacattctg aggataaaaa tacgctccac
     1141 cggcaaaaac tctaaaggaa tgactaactt gtatgacata acccctttaa tgctgaagtt
     1201 aatcaaccta aaaataccat ctttaaatac gcccgatgaa aaacatacgt gtccaaaatg
     1261 cggaaaaata gccatatcaa gagaagaaat aacaaaggag tttggattca gaactgacac
     1321 taatgggaag atgagaacgc aaagttggtg caaggattgt cgaggtagga aaattgcgga
     1381 tttaccataa cgtcgcatta cgcgcaccgc agaaacgcgc tgaacgcgat tctgccgcaa
     1441 acaccgcaaa aagagatgtt ttccccgggg taaaccggaa aaatgcgtca ggattgtttt
     1501 cagcgcgttg catgactatg catgaaactg aatggcgatc ggtttggggg cttacggcgt
     1561 tcatatcgtc tgttttcgac agtttctctc cgggaagcta atcagccata agcctggata
     1621 acagggcacg gtgatactcc gtaatagcga tcagcacctc cgcatactcc ctgtccccga
     1681 cacgcttgcc gtcgataaag agttttttct gtaacgcccc cagtctcata acttctttca
     1741 gtacccggtc atcagtcagt gagttaactt tcttaccgag agctgccgcc cgtaaaaaac
     1801 cagaaacggt cttgccgcat tcagcagccc tttttctgat ttcctggtct tcttctgccg
     1861 tcagacgaac agggcgactg atagcccgcc tgcgcgtatt acttccactt cgttttgtca
     1921 taaaacatgg ctccgtatct gacatggggt gtcggggcga agccctgacc agggtaattg
     1981 taatagcgtg catgtatgcg cggtataaca attgcacatc ctgtcctgtc tgcaagttcg
     2041 aattaccaac aaagcactgc tgtttttttg gcagtgacag tgttgtctga ctgaaatgtc
     2101 cgtcggcaga ataccggcgg taagacggtc caaaagtggt gcgcgatata atcacacgac
     2161 gcagatgaca gacagaacgg agaaaacaga aagatgaaca agcagcagca aactgtactc
     2221 aacatggcgg gattcataaa aagccagagc ctgacgctgc tcgaaaaact ggacgcactc
     2281 gatgctgacg agcaggccgc catgtgtgag aagctgcacg aactcgcaga agaactccag
     2341 aacagcatac agacacgctt tgaagtagaa aatagcacag agatataacg ctcagggcag
     2401 gatgccgaac ggcacaacag agcgtaagga gaaaatgtca cataaggcgc tcttccgctt
     2461 cctcgctcac tgactcgcta cgctcggtcg ttcgactgcg gcgagcggtg tcagctcact
     2521 caaaggcggt aatacggtta tccacagaat caggggataa cgccggaaag aacatgtgag
     2581 caaaaagccg aagccaggga caaaggccgc gccgatggcg tttttccata ggctccgccc
     2641 cctgacgagc atcacaaaaa ccgacgctca agtcagaggt ggcgaaaccc gacaggacta
     2701 taaagatacc aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt tccgaccctg
     2761 ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc
     2821 tcacgctgtt ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac
     2881 gaaccccccg ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac
     2941 ccggaaagac acgacttatc gccattggct gcggccattg gtagacagga tgtgcgagag
     3001 atgtatcgag agttcttgaa gtgatggcct gactgcggct acactgaaag gacagatttg
     3061 gtgacatgtc tcgcacaaga ctgttaccac ggttcagaag ttccccaact tactgaacct
     3121 tcgaaaaacc acctccccag gtggtttttt cgtttcagga aaagagacta cagctgagag
     3181 aaaaaaatct caacatatcc ttaccagcca ctattcagat atttaatcat ctgattcagt
     3241 gaagagtggg ttgtaatgcg gcg
//
