LOCUS       NZ_CP100700             3830 bp    DNA     circular CON 23-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Agona strain R18.2256
            plasmid pR18.2256_3.8k, complete sequence.
ACCESSION   NZ_CP100700
VERSION     NZ_CP100700.1
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 3830)
  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  JOURNAL   Unpublished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 3830)
  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
            CP100700.1.
            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..3830
                     /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_3.8k"
                     /collection_date="2018"
                     /collected_by="Centers of Disease Control, Taiwan"
                     /subtype="ST13"
     gene            168..356
                     /locus_tag="NL710_RS24150"
                     /old_locus_tag="NL710_24150"
     CDS             168..356
                     /locus_tag="NL710_RS24150"
                     /old_locus_tag="NL710_24150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(404..670)
                     /locus_tag="NL710_RS24155"
                     /old_locus_tag="NL710_24155"
     CDS             complement(404..670)
                     /locus_tag="NL710_RS24155"
                     /old_locus_tag="NL710_24155"
                     /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_213069224.1"
                     /translation="MKRSQLTLIDGCFMFGFSPGELMNLCPDERLLFVRMISAMLRRSG
                     GDAGAVMFEAYRHIVSDTNQARRSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            1804..3708
                     /locus_tag="NL710_RS24160"
                     /old_locus_tag="NL710_24160"
     CDS             1804..3708
                     /locus_tag="NL710_RS24160"
                     /old_locus_tag="NL710_24160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003839290.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="methyl-accepting chemotaxis protein"
                     /protein_id="WP_052895204.1"
                     /translation="MSWAYRISMQMKLFIALFPLLLALVWFAGSGIVSRINTEQQMNTI
                     GQLTTLARSAGDVVHQLQSERGMSAGFIGARGQKFRDDLAAQRQLTDKVLATFKRLLTD
                     TNKDLLQGNIAAPLKTFNESIQFLDSTRTAISELTIDSPKASQFYTQTISDVLKFVGGM
                     GHLSTSGSMVNELAAYYSLLNLKEQAGVERALLSNIFSMDRFDDGQFSMFSDVVGQQDA
                     WLTAARSFSTPVQAAELDKSLQSAEATRALELRETAFNKAAEGGFGVNPTDWFNLQTQR
                     IETLQKVENRAVDALQEHAALLAHNARVDWQSFLVISLVALLIAIAFAVMVARSIQQQL
                     NGTLKTIAEMDGDLTRRLDVPGSDELSALNRAYNQAIENIQHIVQEIKSGAVVLRSASS
                     DIAAGNQDLAQRTDEQAASIVETAASMEQISTAITQTADNASEAERLIHSMERDVLEAN
                     RVSNEASQSMAEIRSSSEQISQIVASIDEISFQTNLLALNAAVEAARAGELGKGFAVVA
                     TEVRNLSQRCAREASQIRELINQNMDKIGEGVARVTASGTALKAAAENTGRMKQYVSDI
                     ARAANEQSLGVSQVHQALNQLEQVTQQNAALVSQAASASQMLDGQSEAMSTLVDRFIV"
                     /name="methyl-accepting chemotaxis protein"
     Typing          complement(815..987)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          912..1496
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.54"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 aggctctgag agcgtttctg aggactccga cctgaaacat acacctttct gtgcccatat
       61 cgagaaaaaa cgcccctgat gatttctgcg tacctgcatg gctatgcact caagtgaatg
      121 aagtaagatt tcagtctgcg atcaccataa aaccgggaaa aagccgtatg acaaaacagg
      181 aatcagccgc actgaacatg gcaaaattta tccgggcgca gtcgctgctg ctgctcgaaa
      241 aactcgacgt gctcgatctt gatgacgagg cagccgactg tgagcgaatg cacgaacagg
      301 cagaagcgct ttatcagaag ctgagcgcac gcttcggtat acaggacggc gaataaagag
      361 acgaaaagaa cgctcactta gacgaaaagc gtatccaggg caactatgta tatccaccgt
      421 gtacatagtc atgcctgacg ctttcgagca ggtcgagcat gcaggaacga cgagcttgat
      481 tggtatcgga cacaatatgg cgatacgcct caaacataac agcacccgca tcaccgcccg
      541 aacggcgaag catagcggaa atcatccgca caaagagcag acgttcatcg gggcaaaggt
      601 tcataagttc tcctggtgaa aaaccaaaca tgaagcaccc atctattaac gtcagctgtg
      661 aacgcttcat tacgcttcat taaaataggt aaacccggga aaaagatcca aacgttaaca
      721 tcacaggtaa acagaaacgt cgggtcgatc gggaaattct ttcccggacg gcgcggggtt
      781 gggcaagccg caggcgcgtc agtgctttta gcgggtgtcg gggcgcagcc ctgaaccagt
      841 cacgtagcgc tagcggagtg tatactggct tattatgtag gcacgggtgc gggaatcagt
      901 gaagtgcttc atgtggcagg aggaaaatgc agcagcagag cgtaagcgga atatatgaga
      961 caggagatat tccgcttcct cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg
     1021 agcggtgcgg gattacgaat ggggcggaaa tttcctggga gatgccagga agaaacttaa
     1081 cagggaaacg gtaaggccgc ggcgaagccg tttttccata ggctccgccc ccctgacaag
     1141 catcacgaaa tctgacgctc aaatcagtgg cggcgaaacc cgacaggact ataaagatcc
     1201 caggcgtttc cccctggtag ctccctcgtg cgctctcctg ttcctacctt tcggtttacc
     1261 ggtgtcattc cgctgttatg gccgcgttta tctcattcca cgcctgacac tcagttccgg
     1321 gaaggcagtt cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgactgctg
     1381 cgccttttcc ggtaactatc gtcttgagtc caacccggaa agacacgaaa aatcgccact
     1441 ggcagcggcc actggtaaac aggatgtgcg agagatgtat cgagagttct tgaagtagtg
     1501 gcctgactga ggctacacta gaaggacaaa tttggtgaca tgtctcgcac aagactgtta
     1561 ccacggttag agaatctgcc aggattatct aaccttcgaa aaaccacctg caagggtggt
     1621 tttttcgttt acagagcaag agattacgac gatcgtcaaa ggatctcaag aagatccttt
     1681 atggattgct accagcgcca ctgccgaatg tggtgcccgt tcccccaaca ataaactata
     1741 aagtttatgc atgtatctac cgatactcct gcgatccctc aagaaagtaa ggaaagtatc
     1801 gatatgtcat gggcttatcg tatttcaatg caaatgaagt tgtttattgc attattcccg
     1861 ctactgcttg ccttggtctg gttcgccggt tcgggtattg tcagccgtat caataccgaa
     1921 cagcagatga acaccattgg acagctcacc acgctcgccc gcagcgcggg tgatgtggtg
     1981 catcaactcc agagcgaacg tggaatgagc gctggattta tcggcgcgcg cggccaaaag
     2041 tttcgcgatg acttagctgc ccagcggcag ttaaccgaca aggtgctggc aacatttaag
     2101 cggttgctga ccgatacgaa taaggattta ctccagggaa atattgccgc ccccctgaaa
     2161 acgtttaatg aaagtattca gtttctcgac tcaacccgta ccgccatcag cgaattaact
     2221 atcgattcac caaaagcgag tcagttctat acccaaacca tctctgacgt gctgaagttt
     2281 gtcggcggga tggggcattt aagcacctca ggctcgatgg tgaacgaact ggcggcttat
     2341 tatagtctct tgaatttgaa ggagcaggct ggtgtagaac gtgcgctgct gtccaatatc
     2401 ttctcgatgg atcgctttga cgacggccag ttcagcatgt ttagcgatgt ggtaggccag
     2461 caggatgcct ggctgacggc agctcgcagc tttagcacac ctgtgcaggc ggctgagctg
     2521 gacaaatctc ttcagtccgc tgaagcaact cgtgctcttg aactgcggga gacggctttt
     2581 aataaagccg ccgaaggcgg atttggagtc aacccgactg actggtttaa ccttcagacc
     2641 cagcgtattg aaacgctgca aaaggtggaa aatcgcgcgg tggatgcctt gcaggaacat
     2701 gctgcgctgc ttgcccacaa tgcccgtgtc gactggcagt ccttcctggt aatcagcctg
     2761 gttgccctac tgattgctat cgcctttgcg gtgatggtgg cacgcagtat ccagcagcaa
     2821 ctgaacggta cgctgaaaac catcgcagag atggacggcg acctgacacg tcgtcttgac
     2881 gtccccggca gcgacgagct ctcagccctg aaccgtgcct ataaccaagc gattgagaat
     2941 attcagcata tcgtgcaaga aattaagtcc ggtgcggtgg tgttgcgtag cgccagtagt
     3001 gatatcgctg ccggtaatca ggatctggcc cagcgtacgg atgaacaggc ggcatcgatt
     3061 gtggaaacgg ccgccagcat ggagcagatt tctactgcga tcacccagac cgccgataac
     3121 gccagcgagg cggagcgtct gatacattcg atggagcggg acgtactgga agctaatcgc
     3181 gtctctaacg aggccagtca gagcatggcg gaaattcgtt cttccagcga gcagatttcc
     3241 cagattgttg cgtcaattga tgagatttct ttccagacca acttgctggc gcttaacgcc
     3301 gccgttgaag cggcacgtgc cggtgagctt ggcaaaggct ttgcggtagt ggcgacggag
     3361 gtgcgtaacc tttcccagcg ctgtgcacga gaggccagtc agatccgtga gctgattaac
     3421 cagaatatgg ataagattgg cgaaggggta gcacgagtca ccgcgtccgg caccgcgctg
     3481 aaagcagcgg cggaaaatac cgggcggatg aaacagtacg tgagcgatat tgcccgtgcg
     3541 gcgaatgagc agtcgcttgg cgtgtcgcag gtgcatcagg cactgaatca gctggagcag
     3601 gtcactcagc aaaacgcagc gctggtctct caggcggcga gcgccagcca gatgctggac
     3661 ggccagtctg aagcgatgtc cacgctggtc gatcgcttta ttgtctgata ctgccgttca
     3721 gcatccggtc ttgataactt acaatcagaa aaaaccgcct aaaaggcggc ttttttatgc
     3781 ctgcaaataa ctaggattta ccataacatc tgttgcgtgc accgcctgag
//
