LOCUS       NZ_CP100701             3263 bp    DNA     circular CON 23-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Agona strain R18.2256
            plasmid pR18.2256_3.3k, complete sequence.
ACCESSION   NZ_CP100701
VERSION     NZ_CP100701.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29431230
            Assembly: GCF_024266385.1
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  JOURNAL   Unpublished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                   :: 521x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/23/2023 02:21:06
            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)                     :: 4,842
            CDSs (total)                      :: 4,724
            Genes (coding)                    :: 4,603
            CDSs (with protein)               :: 4,603
            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)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 43 of 121
            Pseudo Genes (incomplete)         :: 91 of 121
            Pseudo Genes (internal stop)      :: 13 of 121
            Pseudo Genes (multiple problems)  :: 24 of 121
            Pseudo Genes (short protein)      :: 1 of 121
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100701.1.
            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="R18.2256"
                     /serovar="Agona"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:58095"
                     /plasmid="pR18.2256_3.3k"
                     /collection_date="2018"
                     /collected_by="Centers of Disease Control, Taiwan"
                     /subtype="ST13"
     gene            272..850
                     /locus_tag="NL710_RS24165"
                     /old_locus_tag="NL710_24165"
     CDS             272..850
                     /locus_tag="NL710_RS24165"
                     /old_locus_tag="NL710_24165"
                     /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(842..1024)
                     /locus_tag="NL710_RS24170"
                     /old_locus_tag="NL710_24170"
     CDS             complement(842..1024)
                     /locus_tag="NL710_RS24170"
                     /old_locus_tag="NL710_24170"
                     /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(1058..1381)
                     /gene="mobA"
                     /locus_tag="NL710_RS24175"
                     /old_locus_tag="NL710_24175"
     CDS             complement(1058..1381)
                     /gene="mobA"
                     /locus_tag="NL710_RS24175"
                     /old_locus_tag="NL710_24175"
                     /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            1654..1848
                     /locus_tag="NL710_RS24180"
                     /old_locus_tag="NL710_24180"
     CDS             1654..1848
                     /locus_tag="NL710_RS24180"
                     /old_locus_tag="NL710_24180"
                     /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"
     gene            complement(2683..3138)
                     /locus_tag="NL710_RS24185"
                     /old_locus_tag="NL710_24185"
     CDS             complement(2683..3138)
                     /locus_tag="NL710_RS24185"
                     /old_locus_tag="NL710_24185"
                     /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"
     Typing          complement(1391..1617)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.797"
                     /coverage="99.0"
                     /evalue="6.34e-74"
     Typing          1878..2404
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.053"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          complement(1062..1381)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="9.72e-63"
ORIGIN
        1 ttcgtcagca cgagatttgt actgctgacg acgttctgta tcgcagctgt gattatcaaa
       61 tcgtacgttt gccaacatgt cagtcctatg tttgaagaag tctgggaaga taaaatctta
      121 ctcaattaga tggtaagaga ggtcctttcc cagtgctaga cattaggcct ttttggtcaa
      181 attaaagggc ggcattgatg ccgcccaaat aataaatcat aataacaata cctatatata
      241 taggtattgt tattatgatt ggtgacagaa attgaaatca gaaatcgaac tcaaaaaaac
      301 agaacactca tcagtagaga tcccagaaag gatcttagcc atatgggggc gcagcatttt
      361 aaactctggc tggacatccg tccccaatga actattaaaa aaccaatcta agctaggaat
      421 aggaaacaca gagcttgtac ttttgattaa tctgatatct ttcatgcatc atcctgacgc
      481 aagagtgtac ccatcaattt cacttctatg cgaaagaatg aatcaggaca gacgaacaat
      541 tcagagaaat ttaaacaagt tagtagaaat ggacattctg aggataaaaa tacgctccac
      601 cggcaaaaac tctaaaggaa tgactaactt gtatgacata acccctttaa tgctgaagtt
      661 aatcaaccta aaaataccat ctttaaatac gcccgatgaa aaacatacgt gtccaaaatg
      721 cggaaaaata gccatatcaa gagaagaaat aacaaaggag tttggattca gaactgacac
      781 taatgggaag atgagaacgc aaagttggtg caaggattgt cgaggtagga aaattgcgga
      841 tttaccataa cgtcgcatta cgcgcaccgc agaaacgcgc tgaacgcgat tctgccgcaa
      901 acaccgcaaa aagagatgtt ttccccgggg taaaccggaa aaatgcgtca ggattgtttt
      961 cagcgcgttg catgactatg catgaaactg aatggcgatc ggtttggggg cttacggcgt
     1021 tcatatcgtc tgttttcgac agtttctctc cgggaagcta atcagccata agcctggata
     1081 acagggcacg gtgatactcc gtaatagcga tcagcacctc cgcatactcc ctgtccccga
     1141 cacgcttgcc gtcgataaag agttttttct gtaacgcccc cagtctcata acttctttca
     1201 gtacccggtc atcagtcagt gagttaactt tcttaccgag agctgccgcc cgtaaaaaac
     1261 cagaaacggt cttgccgcat tcagcagccc tttttctgat ttcctggtct tcttctgccg
     1321 tcagacgaac agggcgactg atagcccgcc tgcgcgtatt acttccactt cgttttgtca
     1381 taaaacatgg ctccgtatct gacatggggt gtcggggcga agccctgacc agggtaattg
     1441 taatagcgtg catgtatgcg cggtataaca attgcacatc ctgtcctgtc tgcaagttcg
     1501 aattaccaac aaagcactgc tgtttttttg gcagtgacag tgttgtctga ctgaaatgtc
     1561 cgtcggcaga ataccggcgg taagacggtc caaaagtggt gcgcgatata atcacacgac
     1621 gcagatgaca gacagaacgg agaaaacaga aagatgaaca agcagcagca aactgtactc
     1681 aacatggcgg gattcataaa aagccagagc ctgacgctgc tcgaaaaact ggacgcactc
     1741 gatgctgacg agcaggccgc catgtgtgag aagctgcacg aactcgcaga agaactccag
     1801 aacagcatac agacacgctt tgaagtagaa aatagcacag agatataacg ctcagggcag
     1861 gatgccgaac ggcacaacag agcgtaagga gaaaatgtca cataaggcgc tcttccgctt
     1921 cctcgctcac tgactcgcta cgctcggtcg ttcgactgcg gcgagcggtg tcagctcact
     1981 caaaggcggt aatacggtta tccacagaat caggggataa cgccggaaag aacatgtgag
     2041 caaaaagccg aagccaggga caaaggccgc gccgatggcg tttttccata ggctccgccc
     2101 cctgacgagc atcacaaaaa ccgacgctca agtcagaggt ggcgaaaccc gacaggacta
     2161 taaagatacc aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt tccgaccctg
     2221 ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc
     2281 tcacgctgtt ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac
     2341 gaaccccccg ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac
     2401 ccggaaagac acgacttatc gccattggct gcggccattg gtagacagga tgtgcgagag
     2461 atgtatcgag agttcttgaa gtgatggcct gactgcggct acactgaaag gacagatttg
     2521 gtgacatgtc tcgcacaaga ctgttaccac ggttcagaag ttccccaact tactgaacct
     2581 tcgaaaaacc acctccccag gtggtttttt cgtttcagga aaagagacta cagctgagag
     2641 aaaaaaatct caacatatcc ttaccagcca ctattcagat atttaatcat ctgattcagt
     2701 gaagagtggg ttgtaatgcg gcgcatcaga cttagggaag ggctcatgtg taggggagaa
     2761 gcctacgaca aacaccgtgc catcgttgag tttttgatag tggatcactt cagcggaggt
     2821 tagccccgca acgttcatac ccaagttaaa agtcatcgat ctaagtttga ccccttctgg
     2881 atatggaccg caatgataat gccagtagtt cccgtcttcg tacgcatcag taccggaaat
     2941 tttaatggaa ttatcatcaa gccatgaagg cttgtttttc cctggaagag gctcttcacg
     3001 agttatcgca cccaagaaag aggctaatgc ccggcgttgc tcttctttga ggtagggtaa
     3061 atctacgaaa tacttttcat tcagcttccc gtctcggaaa gccgaatgaa gctcaaactt
     3121 attgaatttg gttgtcatca aacactttcc acttacctta ctgagtaagt agatagcata
     3181 tcaaagatcg attcatcaga ctgcggagaa tcgcatttta acgcttcatg tgcctgattc
     3241 ttgtatgaac gcgagagcag cac
//
