LOCUS       NZ_CP100742             5892 bp    DNA     circular CON 23-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            R18.0292 plasmid pR18.0292_5.9k, complete sequence.
ACCESSION   NZ_CP100742
VERSION     NZ_CP100742.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21365150
            Assembly: GCF_024266225.1
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 5892)
  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  JOURNAL   Unpublished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 5892)
  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                   :: 329x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/23/2023 02:08:24
            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)                     :: 4,994
            CDSs (total)                      :: 4,870
            Genes (coding)                    :: 4,743
            CDSs (with protein)               :: 4,743
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 38 of 127
            Pseudo Genes (incomplete)         :: 95 of 127
            Pseudo Genes (internal stop)      :: 20 of 127
            Pseudo Genes (multiple problems)  :: 25 of 127
            Pseudo Genes (short protein)      :: 1 of 127
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100742.1.
            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..5892
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="R18.0292"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pR18.0292_5.9k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2018"
                     /collected_by="Centers for Disease Control, Taiwan"
     gene            complement(145..336)
                     /locus_tag="NL736_RS24900"
                     /old_locus_tag="NL736_24900"
     CDS             complement(145..336)
                     /locus_tag="NL736_RS24900"
                     /old_locus_tag="NL736_24900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165993.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHEHA
                     DELYRSCLSRFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            401..724
                     /locus_tag="NL736_RS24905"
                     /old_locus_tag="NL736_24905"
     CDS             401..724
                     /locus_tag="NL736_RS24905"
                     /old_locus_tag="NL736_24905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024242645.1"
                     /translation="MLTIRVTDDEHARLLERCDGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            933..>1364
                     /locus_tag="NL736_RS24910"
                     /old_locus_tag="NL736_24910"
                     /pseudo=""
     CDS             933..>1364
                     /locus_tag="NL736_RS24910"
                     /old_locus_tag="NL736_24910"
                     /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            1402..1920
                     /locus_tag="NL736_RS24915"
                     /old_locus_tag="NL736_24915"
     CDS             1402..1920
                     /locus_tag="NL736_RS24915"
                     /old_locus_tag="NL736_24915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_000067499.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTVSTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEMIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            1927..2160
                     /locus_tag="NL736_RS24920"
                     /old_locus_tag="NL736_24920"
     CDS             1927..2160
                     /locus_tag="NL736_RS24920"
                     /old_locus_tag="NL736_24920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2495..3379)
                     /locus_tag="NL736_RS24925"
                     /old_locus_tag="NL736_24925"
     CDS             complement(2495..3379)
                     /locus_tag="NL736_RS24925"
                     /old_locus_tag="NL736_24925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001439342.1"
                     /GO_function="GO:0005525 - GTP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GTPase"
                     /protein_id="WP_021551692.1"
                     /translation="MENNTQGIKLIKEAVDVLPKEIRKSVYNKIRNVINYEPVIGIMGK
                     TGAGKSSLCNSIFKGNVCAVSDVEACTRKVQELIISFGDRTIKIIDIPGVGENEAKDIE
                     YEELYKNLLPELDLVLWVVKGDDRAFSADEHFYKNVLKPVGGDEKVLFVLNQVDKIEPF
                     REWDEEKHQPSPSQQINIRKKEEYLIERFGFTKHPVISVSANEGYNISRLVEAIVRSLP
                     KEAQSGVVHQVKDEIKTKEIVETAKDGFADTVDRAIDDIIDTVLPKPIASVAKVAKKAI
                     VSVAKSVWGLLFG"
                     /name="GTPase"
     gene            complement(3415..3849)
                     /locus_tag="NL736_RS24930"
                     /old_locus_tag="NL736_24930"
     CDS             complement(3415..3849)
                     /locus_tag="NL736_RS24930"
                     /old_locus_tag="NL736_24930"
                     /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_021551691.1"
                     /translation="MGFWDSIKNAAIKAKCGVGIHGGNYKLIDGETCKYSKLCPDCNRT
                     IQKEQHKYGEESYKYDFKCTTVKKCIDCGAEQEGERHERFVEIAVDDYCNVKERCVRCF
                     TERVHGKRHNWYLSGSSDTYRHYKCSVCGEEKEERKTSFR"
                     /name="hypothetical protein"
     gene            complement(4077..4889)
                     /locus_tag="NL736_RS24935"
                     /old_locus_tag="NL736_24935"
     CDS             complement(4077..4889)
                     /locus_tag="NL736_RS24935"
                     /old_locus_tag="NL736_24935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000549943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EcsC family protein"
                     /protein_id="WP_000549944.1"
                     /translation="MHLEEGDLRALERAVELLEQDTITETLTQLVGTPIDYLMSKLPKG
                     AEEQIYSLVEKSLHKAADAALWSLDNEPNRIASTKTNKFFAAVSGAIGGAFGFSALAIE
                     LPVSTTIMLRSIADIARSEGFELDNIDTKLACLEVFSLGGPSDDDDAANTAYYATRSLT
                     AEIVQDLSKEISNIAVKNASSVQTGKWLASLIEKVATRFGIVITEKMAAQVVPVIGALT
                     GATLNTMFTDYYQDMARGHFIVKRLEKKYGNELIKAEYIKISSKLTNS"
                     /name="EcsC family protein"
     Typing          complement(5295..5838)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.505"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          715..2264
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.893"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agtatacact ccgctatcgc tacgtgactg ggtcatggct gcgccccgac acccgcaaaa
       61 acccgctgac gcgccctgac gggcttgtct gctcccggca tccgctcacc ggcaagctgt
      121 gaccgtctcc gggagctaca tgtgttacag gttttcaccg tcatccccga agcgtgagag
      181 gcagctgcgg taaagctcat cggcgtgctc gtgaagagat tcacagatgt ctgcctgttc
      241 atccgcgtcc agttcgttga gcttctccag tagcgttaat gtctggcttc tgataaagcg
      301 ggccatgtta agggcggttt tttcctgttt agtcactgat gcctccgtgt aagggggatt
      361 tctgttttat ggggtaatga taccgatgaa acgcgagagg atgctcacca tacgggttac
      421 tgatgatgaa catgcccggt tactggaacg ctgtgatggt aaacaactgg cggtatggat
      481 gcggcgggta tgcctgggtg agccggttgc ccgttccggg aagctgccga cactggcacc
      541 gccgttactg cgtcagctgg ctgccatcgg gaataacctg aatcagacgg cgaggaaggt
      601 gaacagcggg cagtggtctt ccggtgaccg ggttcaggtg gtggccgcac tgatggccat
      661 cgagagagag ttgcgcagct tacggcaggt cgtcagggaa cagggagcgc gggatgatag
      721 ttaaatttca tgccagggga aaaggcggtg gcagtggtcc ggttgattac ctgctgggaa
      781 gggagcgtaa ccgggaaggg gcaacggtgc ttcagggtaa tccggaagaa gtccgggaac
      841 tcatcgatgc cacgccattt gcgaagaaat acacgtcagg tgttctgtcg ttcgcggaga
      901 aggagctgcc gccgggagga cgtgaaaaag tgatggcgag ctttgagcgt gtactgatgc
      961 ccggtctcga aaaaaatcag tacagcatcc tgtgggttga gcaccaggac aagggacggc
     1021 ttgagctgaa ttttgtcatt ccgaacatgg agctacagag cggaaaacgc ctccagccgt
     1081 actatgaccg cgcagacagg ccgagaattg atgcctggca gacgctggtg aatcaccatt
     1141 acgggctgca tgacccgaat gccccggaga accgcaggac gctgacactc cctgataacc
     1201 tgccggaaac gaaacaggcg attgctgaga gcgttacacg ggggcttgat gtgctttacc
     1261 gtgccggaga gataaaagac cgtcaggatg tgattcaggc actcacagat gtgggagttg
     1321 aggttgtcag ggtgacgcga agcagtatca gcattgcaga cccgaacggc ggaaggaata
     1381 tcaggctgaa aggagcattt tatgagcaat cttttacaga cgggcgcgga gttcgagaaa
     1441 aagctgaaag agagagccga atctacagag aaaatgctga acgacgagtt caggaagctc
     1501 ggcgagtctg tcagcgaggc tgtgacatca aacgagacga aaatcagaga cgctatagcc
     1561 ctgttcacag tctcgacaga gaaatcgctg gaaaaacacc gggaaggggt gaaagaggcg
     1621 atgatgcagc acaggaagga cgtgttaaag ctggcaggga atacgggcat gatgttactg
     1681 gggatagtct ttcttctgtt taccgcgagt ggcgggacgc tctggtatct tggcggacgg
     1741 atacagacga acctggaaga aatcaggaag caggaagaga cattgcagaa actgaacgcg
     1801 aagacatggg gcgtggagtt tgtgcaggac gggaacagga aatttctggt ccttccgtac
     1861 gggaaatcag cagagatgat tccctttcag gggaaagagt gggtacatct gaaggagtga
     1921 cacagagtga cagagctgga aacacatttg ctgaacgcct tagagcagct gcaacaggac
     1981 tatatgcagc ggctgagcga atgggagagc gccttcgtgg aattgcagaa gatgttttcg
     2041 cttacgcaac gggacaacgc gatgctgaac gagcgggtca tgcagttgag tcagcaggtg
     2101 cagcacttga gcgagcagac agaacgcttg agccagttat acagcgagaa ctggagataa
     2161 gagaggaacg gttgatgcag gagcgcgaac atgcgttatc cctggaacgg gagcgtcagc
     2221 tggaaataca ggaacgcaca ctggatggcc cttcgctggg atggtgaaac catgaaaaat
     2281 ggcaggttca ttggattaag gcggactaat gtgctctgtg ccatctggtt gcataggtat
     2341 tcatacggtt aaaatttatc aggcgcgatc gtggcagttt ttcgggtggt ttgttgctat
     2401 ttttacctgt ctgctgccgt gatcgcgctg aacgcgtttt agcggtacgt acaaactgtt
     2461 gttatgttaa atactgatgg gctttcctgc ttgattatcc gaagagcaat ccccaaacac
     2521 ttttagctac agaaacaatg gctttcttgg cgactttagc cactgacgct attggtttag
     2581 gtagtacggt gtctattata tcatcaatag ctctatctac ggtgtctgcg aacccgtcct
     2641 ttgccgtttc tacaatttct tttgttttta tttcgtcttt tacttgatgc accactccgc
     2701 tctgtgcttc ctttgggagc gatcttacta ttgcctccac taaccttgaa atgttataac
     2761 cttcattcgc agatacagat ataacgggat gtttggtaaa accgaatcgt tctattaagt
     2821 attcttcctt ttttctaata tttatttgtt gtgagggtga tggttggtgt ttttcttcat
     2881 cccattcgcg gaatggctca atcttgtcga cttggtttaa aacaaacaac actttttcat
     2941 caccaccaac tggttttaaa acatttttat aaaagtgctc atcagctgaa aatgctcgat
     3001 catcaccttt aacaacccaa agcaccagat ctaattctgg gagaagattt ttatacaact
     3061 cttcatattc tatatcttta gcttcatttt cacctacacc tggtatatct attattttaa
     3121 ttgttctatc accaaatgaa attattaatt cctgaacctt tctcgtgcat gcttctacat
     3181 cactcactgc acatacatta cctttaaaga tagaattaca taggctggat ttaccagcgc
     3241 cggttttacc cataatccct attactggtt cgtaattaat aacatttcta attttgttat
     3301 agacagactt gcgaatctct ttaggtagaa catccacagc ttctttgatt aattttatac
     3361 cttgcgtatt gttttccata gttactattt tcctcatttt gttgttcata tgaattaacg
     3421 gaagcttgtt tttctttctt ctttttcttc cccgcataca gaacatttgt aatggcgata
     3481 ggtatcagaa ctcccactaa gataccaatt gtgtctttta ccatgaactc gctctgtaaa
     3541 acatctcacg catctttctt tcacattgca ataatcatcg actgcaattt caacaaatct
     3601 ttcatgcctt tcgccttctt gttcagcgcc acagtcgata cactttttta cagttgtgca
     3661 cttgaaatcg tatttataac tttcctctcc gtatttatgc tgttcttttt gtatagtgcg
     3721 attgcagtca gggcatagtt tagaatattt acaagtctca ccatcaataa gcttatagtt
     3781 tcctccgtgt atacctaccc cacacttagc cttgattgct gcatttttta tgctatccca
     3841 aaagcccatg gaaaaatctc cctacgatta gttgatataa gttgaacaat tcatcgacac
     3901 gattatacac gtatagtgtg tggatatata aaaatgagta tggatttatg ctctgtataa
     3961 tgtttttgtt atgttaaata tagcgctgaa aaagtggggg cactggataa acttcgtgtt
     4021 tttcccgcaa agatagtatt gaaaagtcat tgtctaattc atccaagata aatattttac
     4081 gaatttgtga gtttgcttga gatttttata tattcagcct ttattaactc attgccatat
     4141 tttttctcga gtcttttaac aatgaaatga cctcgagcca tatcttgata atagtcggta
     4201 aacattgtgt ttaatgtggc tccagttagt gctccaataa cgggaacgac ttgagctgcc
     4261 attttttccg taataactat accaaatctt gttgcaactt tttctattaa cgaagctaac
     4321 cattttcctg tttgtactga agatgcgttt ttgacagcaa tgttagaaat ttctttggat
     4381 aaatcttgta cgatctcggc agtcaaactt cttgttgcat agtatgcagt attagctgca
     4441 tcatcgtcat cagatggtcc tcccaaggaa aacacctcta agcaggccag tttggtatca
     4501 atattatcta gctcaaaacc ttcacttctt gctatgtcag caattgaacg aagcataatt
     4561 gtcgttgaaa ccggtaactc aattgctaat gcagaaaagc caaaagcgcc accaatggct
     4621 ccagatacgg ccgcaaagaa tttatttgtc ttagttgatg ctattcggtt aggttcattg
     4681 tctagactcc ataaggccgc atcagcagct ttgtggagcg atttttctac tagactataa
     4741 atttgctctt ctgccccttt gggaagttta ctcattaagt aatctattgg ggttccaact
     4801 aattgggtta atgtttcagt aattgtatct tgttctaata attctacggc cctttctaaa
     4861 gcccgcagat ctccttcttc aagatgcata taatgaatcc tttatgaatc aatcgatagt
     4921 ctacttttgt aagtgattcg tcttgggagc ttaccttgag cgagttcagt gattcaatag
     4981 gcgagatgcc gacatcattg ttgtctgtga agcaggagtg atgaaaagat caaaggatcc
     5041 tcttgtgatc ctttttttct gcgcgtaatc tgctgcctgt aaacaaaaaa accaccgcta
     5101 ccaacggtgg tttgtttgcc ggatcaagag ctaccaactc tttttccgaa ggtaactggc
     5161 ttggtggagc acagatacca aatactgtcc ttctagtgta gccgcagtta ggccaccact
     5221 tcaagaactc ttaatatctc aatccacctt gtccagttac cagtggctgc tgccagtggc
     5281 gctttgtcgt gtcttaccgg gttggactca agacgatagt taccggataa ggcgcagcgg
     5341 tcgggctgaa cggggggttc gtgcacacag cccagcttgg agcgaacgac ctacaccggg
     5401 ccgagatacc aacagcgtga gctatgagaa agcgctacgc ttcccgaagg gagaaaggcg
     5461 gacaggtatc cggtaaacgg cagggtcgga acaggagagc gcacgaggga gccaccaggg
     5521 ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc acctctgact tgagcgtcga
     5581 tttttgtgat gctcgtcagg ggggcggagc ctatggaaaa acgccagcgg cgcggccttt
     5641 cgttgccctt tgcctttttg ctcacatgtt ctttccggcc ttatcccctg attctgtgga
     5701 taaccgtatt accgcctttg agtgagccgg caccgctcgc cgcagccgaa cgaccgagcg
     5761 tagcgagtca gtgagcgagg aagcggaaga gcgcctgatg cggtattttc tccttacgca
     5821 tctgtgcggt atttcacatc gtatatggcg ctgttttctt acaatccgca ctaaatgccg
     5881 catagttaag cc
//
