LOCUS       NZ_CP100717             3988 bp    DNA     circular CON 23-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            R17.5474 plasmid pR17.5474_4.0k, complete sequence.
ACCESSION   NZ_CP100717
VERSION     NZ_CP100717.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21365146
            Assembly: GCF_024266445.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3988)
  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  JOURNAL   Unpublished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 3988)
  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                   :: 490x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/23/2023 02:07:40
            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)                     :: 5,198
            CDSs (total)                      :: 5,076
            Genes (coding)                    :: 4,943
            CDSs (with protein)               :: 4,943
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 35 of 133
            Pseudo Genes (incomplete)         :: 107 of 133
            Pseudo Genes (internal stop)      :: 17 of 133
            Pseudo Genes (multiple problems)  :: 25 of 133
            Pseudo Genes (short protein)      :: 1 of 133
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100717.1.
            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..3988
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="R17.5474"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pR17.5474_4.0k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="Centers for Disease Control, Taiwan"
     gene            join(3884..3988,1..216)
                     /locus_tag="NL730_RS25920"
                     /old_locus_tag="NL730_25920"
     CDS             join(3884..3988,1..216)
                     /locus_tag="NL730_RS25920"
                     /old_locus_tag="NL730_25920"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_045265547.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAVLETGGDD
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            425..>853
                     /locus_tag="NL730_RS25925"
                     /old_locus_tag="NL730_25925"
                     /pseudo=""
     CDS             425..>853
                     /locus_tag="NL730_RS25925"
                     /old_locus_tag="NL730_25925"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     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            894..1379
                     /locus_tag="NL730_RS25930"
                     /old_locus_tag="NL730_25930"
     CDS             894..1379
                     /locus_tag="NL730_RS25930"
                     /old_locus_tag="NL730_25930"
                     /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="WP_013631087.1"
                     /translation="MSSLLALAKDLEQQSKAQQQSTGEMLKAAFSEHEQSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEKKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            1383..1595
                     /locus_tag="NL730_RS25935"
                     /old_locus_tag="NL730_25935"
     CDS             1383..1595
                     /locus_tag="NL730_RS25935"
                     /old_locus_tag="NL730_25935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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="WP_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2175..2384
                     /locus_tag="NL730_RS25940"
                     /old_locus_tag="NL730_25940"
     CDS             2175..2384
                     /locus_tag="NL730_RS25940"
                     /old_locus_tag="NL730_25940"
                     /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_058679818.1"
                     /translation="MTKFEAFKDQITNAAKASFPEWVTFEYENDFPGYNESFVYESVCA
                     IKKTGELEVRNNADRYFSVKFISV"
                     /name="hypothetical protein"
     gene            complement(2440..2820)
                     /locus_tag="NL730_RS25945"
                     /old_locus_tag="NL730_25945"
     CDS             complement(2440..2820)
                     /locus_tag="NL730_RS25945"
                     /old_locus_tag="NL730_25945"
                     /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_032201349.1"
                     /translation="MKKITSLLLLGVFGLTGCAQNVSPQVAAQAQAPIYCENKQQCDAY
                     WTKAKAWIAMNSGWKIQMADETVIATYSPIGNSAILGYQVVKTPIGGERHEIVVQTACA
                     NMFGCIPNAIEQTAKLKNYIKN"
                     /name="hypothetical protein"
     Typing          3598..3770
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="84.659"
                     /coverage="100.0"
                     /evalue="9.74e-41"
     Typing          complement(3139..3651)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          207..1711
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.02"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccggcacgtg ccggcagact gccgtcgata tcgccggcgc tgctgcgcca gcttgccggt
       61 atgggtaaca acctgaacca gatcgcccgg aaagtgaatg ccggtggtgc cggtcatgat
      121 cgggtgcaga tcgtggccgc cctgatggca atcgacgcgg gactggagcg gctgcggcat
      181 gcggtgctgg aaacaggggg ggatgatgat cgttaaattc catccccggg ggcgtggtgg
      241 tggtgccggt ccggtggatt acctgctggg aaaagaccgg cagcgcgagg gggcgaccgt
      301 gctgcaggga aagccggagg aagtccggga gcttatcgat gcctcgccgt atgcgaaaaa
      361 gtacacctcc ggtgtgctgt cgttcgcgga ggctgaacta ccgcccgggc agcgggagca
      421 gatcatggcc agctttgagc gggttctgat gcccgggctc gataaagacc agtacagcat
      481 tctgtgggtg gagcacaccg acaaggggcg gctggagctg aatttcctga tccccaacac
      541 tgaactgctg accgggaaac gcctgcagcc gtactacgat cgcgccgacc ggccgcgcat
      601 cgatgcctgg cagaccgtgg tgaacggcag actggggctg catgatccaa acgccccgga
      661 gaaccggcgg ttactggtca cgccgtccgc actgccggaa acgaagctgg aagccgctca
      721 ggcgattaca cggggtttac tggccttagc ctcatccggg gagctcaaaa cgcgcgagga
      781 cgtcacaggg gcgctcatag cggcaggttt tgaggtggtc cgcaccacaa aaaacagtat
      841 cagcattgcc gacccggacg gggggcgaaa catccgactg aagggagcca tttatgagca
      901 gtcttttagc gctagcgaag gacttggagc agcaatcgaa agcgcagcag cagagtaccg
      961 gcgagatgct gaaagccgca ttcagcgagc acgagcagtc tgtaaaagcg gaactgagcg
     1021 caagcgcgaa gagaatcagc gacgccatca gcgcccacga gcagggtatg accgcggcga
     1081 tgcagtcgaa ccggctgagc gtgttgcgta tggttggccg gacgtggctg accatcaccc
     1141 tggtctcggt actgctgatc gccacgagcg ggagcattct gtggtggcag gggcagcaga
     1201 tcaccgggaa ttaccagact atccgggcgc aggagcggac gcaggccatg ctgtcggaga
     1261 agaaccacgg cgtgcagctg tcgctctgcg gggagaagaa actgtcctgc gtcaaagtga
     1321 acccgaaagc gggagcttac ggggaggaag ggaactggat ggtactggag aggaaatagc
     1381 ccatgacgga actggaaaaa cagttgctga ccgcattaga gcagttacat caggactact
     1441 cgcaaaggct ggacgagtgg gagagcgcct tcgcggaatg gcagaagatg tctggtctta
     1501 tgcaacggga gaacgcggcg ctgaacgagc gcgtcacgcg cttgagtcag caggtggcga
     1561 acttgagcag gcagttacag cgtttgagcc agtagtgcag cggcatgaaa tggcggtggc
     1621 cgccgaacgg gcatacgagc agaaacagca tgaaaaagag ctggctgaaa cccgttcccg
     1681 gcagcggagc tataacggtc cgacgctggg ctgactgcgc gcatccagtg acaaacccca
     1741 agaagaaggg ctcataaatt tcccgctaaa tacggtcgtg atgtttccat cacagcgtat
     1801 acaacggagg gattatgaga ctgtttaacg tgattgagac ggtgctgaac tgcctgtaca
     1861 tggcgctgga gatctgggac tggctggaga agcattttcc tgtttttaag gcgttcatcc
     1921 ggattctggc ctgaaatcag accgtatgca tctggctgca tgaccatgca gccgggtaaa
     1981 atttatctgt cacgaacggg gcggtgtatc gggtggtttg ttgccggttt tacctgactg
     2041 ccgccccgtt tgtggcgaac ctgtccggag cggtgcgggc aacggatgtt atggtaaatt
     2101 ggtgatctca tcatgctaat tctttctgtg gtaaaatctc tctgagccac ccggttctta
     2161 cataggatat atccatgacc aagtttgaag ctttcaaaga tcagataacg aatgccgcta
     2221 aagcatcttt tcctgagtgg gtaacgtttg aatatgaaaa tgattttcct ggatataatg
     2281 aatcctttgt ttatgaatcc gtctgtgcta ttaaaaaaac gggtgagtta gaagtaagaa
     2341 ataatgcgga cagatatttt agtgtgaagt ttatatcggt ctagcatgtt tgattgtttc
     2401 ggaaagcccg ctaaacgtgg gctttcatga atataatcat cagtttttta tgtagttttt
     2461 taattttgct gtttgttcga tggcattagg aatgcagcca aacatattgg cgcaggctgt
     2521 ttgaacgaca atttcgtgcc tttcccctcc aattggagtt tttaccactt gatatcctaa
     2581 aattgcacta ttaccaatag gtgagtacgt tgcaataacc gtttcatccg ccatttgtat
     2641 tttccagcct gagttcattg ctatccaagc ttttgcttta gtccagtaag catcacattg
     2701 ctgcttattt tcgcaatata taggcgcttg agcttgagct gctacttgtg ggctgacatt
     2761 ttgagcgcag ccggtcaagc caaagactcc gagtaataat agagaagtta tttttttcat
     2821 tttaagcctc tgttgtttat tgttttttat gtgctgattt taacattatc tatacgtagg
     2881 aaagaagaaa gtaggtgtgg ttaggttgca aaagaaaaat gatcttcttg agatcctttt
     2941 gagcagcgcg taatctcctg ctctgtaaac gaaaaaacca cctggggagg tggtttttcg
     3001 aaggttcagt aagttgggga acttctgaac cgtggtaaca gtcttgtgcg agacgtgtca
     3061 cccaatctgt ccttccagtg tagccgtagt aagggcacca cttcaagaac tctcacaata
     3121 tctctcgcac atcctgttta ccagtggccg ttgccaatgg cgattagtcg tgtctatccg
     3181 ggttggactc aagaagatag ttaccggaca aggcgcagcg gtcggactga acggggggtt
     3241 cgtgcataca gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa
     3301 tgagataaac gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga
     3361 gagcgcacga gggagccacc agggggaaac gcctggtatc tttatagtcc tgtcgggttt
     3421 cgccaccact gatttgagcg tcagatttcg tgatgtttgt caggggggcg gagcctatgg
     3481 aaaaacggca gcgccgcatc ctttttctgc cccgtttgtc atgccatatg cctttgctct
     3541 tctccgtgtg caggtaacgc ccgccgcagc cgaacggcag gagcgtccgc gactgagtga
     3601 gcgaggaggc gtcatatcct ctgaacttcc attttctgcc ttacgcccgc agctgcattt
     3661 tcctctgtca catgaagcac tttcctgatt accgcactca tgccaacata ataagccagt
     3721 atacactccg ctagcgctac gtgactggtt cagggctgcg ccccgaaacc cgctaaaagc
     3781 gactgacgcg cctgcggctt gtccaacacc gtgccgcccg ggaaaaattt cccgcccgtc
     3841 ccggtgttat caggaggcta ctctggcaga taaacgcaac aagatgctca cgatgtgggt
     3901 gacggaagac gaacaccggc ggctgctcga gcggtgcgac ggcaagcagc tggcggcgtg
     3961 gatgcgtcag acctgcctcg atgagaag
//
