LOCUS       NZ_CP063298             4234 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            R17.1451 plasmid pR17.1451_p4.2k, complete sequence.
ACCESSION   NZ_CP063298
VERSION     NZ_CP063298.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16450741
            Assembly: GCF_015074905.1
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 4234)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W. and Chen,Y.-S.
  TITLE     Salmonella enterica subsp. enterica serovar Typhimurium strain
            R17.1451
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4234)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W. and Chen,Y.-S.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2020) 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 Date                     :: 16-OCT-2020
            Assembly Method                   :: Unicycler v. v0.4.6
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 11:51:36
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,024
            CDSs (total)                      :: 4,900
            Genes (coding)                    :: 4,776
            CDSs (with protein)               :: 4,776
            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)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 40 of 124
            Pseudo Genes (incomplete)         :: 93 of 124
            Pseudo Genes (internal stop)      :: 22 of 124
            Pseudo Genes (multiple problems)  :: 28 of 124
            Pseudo Genes (short protein)      :: 1 of 124
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063298.1.
            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..4234
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="R17.1451"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pR17.1451_p4.2k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="Centers of Disease Control, Taiwan"
                     /subtype="ST19"
     gene            complement(join(4169..4234,1..2154))
                     /gene="mobQ"
                     /locus_tag="IN819_RS24920"
                     /old_locus_tag="IN819_24955"
     CDS             complement(join(4169..4234,1..2154))
                     /gene="mobQ"
                     /locus_tag="IN819_RS24920"
                     /old_locus_tag="IN819_24955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_063106751.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLIHDYTRK
                     RGVDDAVILTPANAPSWCGDRSVLWNAVEKAEQRRNSQLAREIELAIPREISREAAREA
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLEKQIESLLRTYRAVKERDIPVRRQAFETQWNTWIS
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEYDARLKHHDNHRLSRETALAGVITELG
                     RAREPGTGRITRYMMLSNRAGEFTVWGDELAHYPQSVHDPVNVYLSPGGAVMVSDIREG
                     MPESHETMARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPAA
                     SPLPSAHRVDVTAYAAPEQLMPVVFSTERNSRTLNLLLCKGPEEMLVGFVRLEDELRPV
                     LALPSPDYSHLMVSIITENGIHLAGYGEAINRDADTPYPPEPKLMQFRLKGCQDTLFAA
                     INKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHYRGMSM"
                     /name="mobQ"
     gene            2333..2608
                     /locus_tag="IN819_RS24925"
                     /old_locus_tag="IN819_24960"
     CDS             2333..2608
                     /locus_tag="IN819_RS24925"
                     /old_locus_tag="IN819_24960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052995416.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRLQPLINELEKLPRPPAKPQNG"
                     /name="hypothetical protein"
     gene            complement(2814..3722)
                     /locus_tag="IN819_RS24930"
                     /old_locus_tag="IN819_24965"
     CDS             complement(2814..3722)
                     /locus_tag="IN819_RS24930"
                     /old_locus_tag="IN819_24965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_058657849.1"
                     /translation="MSAALQYFEENLPHRPYHTDDPAFGLRISGKGRALLARYIQQNQP
                     HAQHWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNLAVRTAPDASVKV
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSVDKHYGLGRNCHLFEITRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGLAKGEAYEDKRFMALCMLENGYSQ
                     KAIAAMLDVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     Typing          1797..2155
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2156..2326
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.093"
                     /coverage="97.0"
                     /evalue="2.65e-76"
     Typing          complement(2995..3722)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.376"
                     /coverage="94.0"
                     /evalue="0.0"
     Typing          complement(2..2154)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.036"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 ccattcatgc caggtctgat taaatccgag ttgacggaag agataatccg gcatctcttc
       61 cggtttgttg atggcagcaa aaagcgtgtc ctgacagccc ttaagcctga actgcatcag
      121 cttcggttcc ggtgggtacg gagtatcagc atcacggttt atggcctcac cgtagcctgc
      181 caggtgtatc ccgttctctg tgatgatgct taccatcaga tgactgtaat ccggcgacgg
      241 aagcgcaaga acgggacgca gctcgtcctc caggcgcaca aaaccgacaa gcatttcctc
      301 cggccctttg cacaacagca gattcagcgt cctgctgttt cgctctgtcg aaaagacaac
      361 gggcatgagt tgctccggtg ccgcataagc ggtgacgtcc acccggtgcg ctgacggcag
      421 cggagaggct gcgggcctgc ggtcgtcgct gaaataaaaa ttatccggcc agtgatgcgg
      481 cagcgccgga aaaccgtaag agggccaccc ctggcgcatc tgttccagta catgccggac
      541 cgtcgcaccg gaatacattc tcacacgctc aggccgcgcc atcgtctcat gagattctgg
      601 cattccctca cgtatatccg agaccatcac agccccgcct ggcgacaggt aaacattcac
      661 cgggtcatga acactctggg ggtaatgcgc cagctcatca ccccataccg tgaattctcc
      721 ggctctgtta ctcagcatca tgtagcgggt tatcctgccc gttcccggct ctctggcacg
      781 ccccagctcc gtaataaccc cggctaatgc cgtttctcgg ctcaggcgat ggttatcatg
      841 gtgtttcagc cgtgcgtcat attcctgttc cttccggcgc gcttccgctt cggcttcctc
      901 cctgcgccgc tccgcttccc gtgctgacag tttttctttc agctctgcca ttcccggcga
      961 aatccacgta ttccactgcg tttcaaaggc ctgacgacgg acgggaatgt cccgttcttt
     1021 cacggccctg taggtgcgga gaagagattc aatctgtttc tcgagtttcc agaagcggag
     1081 ttgtcttttg cggtattccg gttcagccca tgtcatcagg ggaagctctg acaggatgga
     1141 cgctaccgga cgggcttttc tgagtccggt catctctttt tcgagaatat cccgctcttt
     1201 caccagcgca ttcccctcac gtttgatgtc gtttgccttc ccgttcatcg ccacgaactc
     1261 cggtgtcatc tcccatgcgt tcccgcattc ctgcggcagt gtggcaatga attcccgcag
     1321 ggtatccgct gaggcattcg cggcgggaat ggtcagatta agggcttccg ctgcacgacg
     1381 tgcggcatcg ctgagttccc gtttccgcac gttctcctgt acctggatga ctgccagcct
     1441 tgtgcgggaa acctgtattt ccaggttaag gctgttaatc aggcggttct gctcaccgcg
     1501 ttctgtttcc atgccccgtt tttccatcgc acaggcagcc tttccgaggt gaaggcccgg
     1561 cgctttctcc agtccctgac gctcgtatga acgatggtct atctcttcct ggtagccggc
     1621 gttcgcaagc gctctgttcg catggtcagc ccatgatgcg cgccacgtct cggcgagtgc
     1681 ccggtcgttc cagtccctga cctttcctgc gaatcccgtt tccccgacag ctctcgtggt
     1741 cagcatgatg tgtgcatggg ggttggtccg gtccatatga tggaacgcca catcggcaat
     1801 catgccccga ctgacaaagt tttcccggac aaaagcgaga acggcctccc gtgcggcctc
     1861 gcgggaaatc tcacggggaa tggcgagttc aatctccctt gccagctggg agttccggcg
     1921 ctgttcggct ttctcgaccg cattccagag aacggaacgg tcaccacacc aggacggtgc
     1981 attcgcaggg gtgagaatga ccgcatcatc aacgccgcgt ttacgggtgt aatcgtggat
     2041 taatccggta cggtcatcgg gtatgacaga gccggaacgg taggcagcag aagcaacggc
     2101 actgtagccg ttttttcgcg aaatgatttt catgctgaga tgataaatcg ccatttctgc
     2161 cgtaatgcct ttttgccgtt ttctttcagc cccgcagggc gcacacaatc gaaacgaagt
     2221 gaagattgta taagtgcgca cttcgtgatg tgccgtgcat tatgccagct cagtttttaa
     2281 actaccagtg acgcgctaaa atgcgatttt tcaccgcgca aggagtcacg aaatgagcag
     2341 aacactcgaa cagaagattg ctgaagctga ggccagattg cagcgcctga aggcgaagag
     2401 ccggagcctg gacactgcgc aaaaagtcat tgtgggagca gccatgctgg cgagggtacg
     2461 gaggccggaa gaggcgcaac tgcgtgcgtt cctgctccag ttcctgcgaa aggaagtcac
     2521 aagacaggcc gatgtgaacc ggctacaacc actgattaac gagctggaga agctaccaag
     2581 accacctgcg aaaccgcaga acggataagc cccggcgcgt aagtgccaca tgcaccaccg
     2641 gacgcctttg cgcttcctcg cacattcgct cgctacgctc ggtcatgagg ctgcggcgag
     2701 cgctaccacc gcaatcacga ggaaaccagc gccattgctg ggcggaaccg gaaaaaccgc
     2761 aggaacgcca acagctcaaa aaagcgccga aaaggcgctg ttatctgata aggctatttg
     2821 tgcattgccc aattacggat cgtatttcga tgtacatcca gcatcgccgc aatagctttc
     2881 tgagaatatc cattctccag catacatagc gccatgaaac gcttgtcctc gtaggcttcg
     2941 cctttagcaa ggccaccttt ccggcctcga gcggcctgta cagcggaaaa gccttccggt
     3001 gagaattttc tgtgcgtgta tttcgcaatg ctcttgccaa tagcccggca ttcagccagt
     3061 gaaagaggaa cgggaagcga tgcgttgtac atttcgacac gctggatcac ggcatcaagc
     3121 cactgtgaga atgctggcca tccctgacga atcgctctgt aagcccattt acgcgttatt
     3181 tcgaacaggt ggcagtttcg ccccagcccg taatgtttat cgacgctacg acgctctgag
     3241 gcgctcaaat cgagataatc agccagttca tcgagggtat aggcttcctc gcgccactcc
     3301 atcacctgcc attccaggtg gaacggattt ttgcaaatca gtccgctgta gttcacatct
     3361 gcgtcaagtt tctcacacag cgcacgttca attgcagcgg cgtatttcag caccttaacc
     3421 gacgcatcag gcgcggttct cacggcaaga ttgagcgcgt atagcaggtg agcgtgccca
     3481 ttcacgggat tttttacggt gatgttcggc gcgggggcgt tccggtcgct ccagtcaatc
     3541 gcagccccct cgcggtcaac gtcaaaaacc agccagtgtt gcgcatgtgg ctggttctgc
     3601 tgaatgtacc gcgcaagaag cgcacgccct ttgccggaga tgcgaaggcc gaaagcggga
     3661 tcatccgtgt gatagggacg gtgaggtaaa ttttcttcga agtattgaag cgcggcgctc
     3721 atgtgttacg attccttcca ggttatcgac cgacatcgcc cctgtatctt cgtgaaagtc
     3781 ttggcggatc tacacgaatt tcaggggcgt ttgtttttca gtcgcttaca ctacacccaa
     3841 cggcaaatcc tgtcgatcct tcccgaaaaa ccgatccatt taccataact cctgttgtac
     3901 gtacccctta aaacgctctc agacgcgttc tgacgcaaaa aacacaaaaa gacaagaaaa
     3961 caccaggcca aaccagaaaa acgcgtcaga atcgttttca ggggtctgca taactattca
     4021 cgaaagcgat gcgcgatcgg tttcgaccgt tcagaagcgc gaacgggtca aaacggcaaa
     4081 ctttctcatc cagaaaacgc ctcacgggac gcggaatttt ttcgtgtccc gtgagacgtt
     4141 ggcggggttc ggggtgcagc cccggatatc acatactcat gccccggtaa tgtccggggc
     4201 gtcgttgttg ttgcctgtgc tgttcgtccc gctt
//
