LOCUS       NZ_CP129390             3205 bp    DNA     circular CON 19-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Infantis strain R13.1986
            plasmid pR13.1986_3k, complete sequence.
ACCESSION   NZ_CP129390
VERSION     NZ_CP129390.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10434137
            Assembly: GCF_030435995.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Infantis
  ORGANISM  Salmonella enterica subsp. enterica serovar Infantis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3205)
  AUTHORS   Chiou,C.-S., Chen,B.-H., Wang,Y.-W. and Teng,R.-H.
  TITLE     Salmonella enterica serovar Infantis
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3205)
  AUTHORS   Chiou,C.-S., Chen,B.-H., Wang,Y.-W. and Teng,R.-H.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JUL-2023) 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                     :: 29-JUN-2023
            Assembly Method :: flye v. 2.9.2; medaka v. 1.8.0; polypolish v.
            0.5.0; POLCA v. 4.1.0
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 683.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/14/2023 16:09:34
            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)                     :: 4,941
            CDSs (total)                      :: 4,819
            Genes (coding)                    :: 4,688
            CDSs (with protein)               :: 4,688
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 131
            CDSs (without protein)            :: 131
            Pseudo Genes (ambiguous residues) :: 0 of 131
            Pseudo Genes (frameshifted)       :: 51 of 131
            Pseudo Genes (incomplete)         :: 91 of 131
            Pseudo Genes (internal stop)      :: 28 of 131
            Pseudo Genes (multiple problems)  :: 35 of 131
            Pseudo Genes (short protein)      :: 1 of 131
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP129390.1.
            Bacteria and source DNA available from Chien-Shun Chiou (CDC,
            Taiwan).
            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..3205
                     /organism="Salmonella enterica subsp. enterica serovar
                     Infantis"
                     /mol_type="genomic DNA"
                     /strain="R13.1986"
                     /serovar="Infantis"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:595"
                     /plasmid="pR13.1986_3k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2013"
                     /collected_by="Centers for Disease Control, Taiwan"
                     /subtype="32"
     gene            1..195
                     /locus_tag="ETE97_RS24690"
                     /old_locus_tag="ETE97_24690"
     CDS             1..195
                     /locus_tag="ETE97_RS24690"
                     /old_locus_tag="ETE97_24690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_052923731.1"
                     /translation="MNKQQQTALNMARFIKSQSLALLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            860..973
                     /locus_tag="ETE97_RS24695"
                     /old_locus_tag="ETE97_24695"
     CDS             860..973
                     /locus_tag="ETE97_RS24695"
                     /old_locus_tag="ETE97_24695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071940873.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPQAAATGN"
                     /name="replication initiation protein"
     gene            complement(1222..1593)
                     /locus_tag="ETE97_RS24700"
                     /old_locus_tag="ETE97_24700"
     CDS             complement(1222..1593)
                     /locus_tag="ETE97_RS24700"
                     /old_locus_tag="ETE97_24700"
                     /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_064996074.1"
                     /translation="MSDSLDGFTEGDTQKEKQKVKQPKPFFNDVEESADRRHLRWTKSG
                     VTLAMTILVAVMNWMVISMLYHVLDEELSLIRSGFMRADERTVTTSVYLALIAGTVAEV
                     SALFLIIVKSVFKNNNNDI"
                     /name="hypothetical protein"
     gene            complement(1667..1915)
                     /locus_tag="ETE97_RS24705"
                     /old_locus_tag="ETE97_24705"
     CDS             complement(1667..1915)
                     /locus_tag="ETE97_RS24705"
                     /old_locus_tag="ETE97_24705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017096688.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_029793011.1"
                     /translation="MKNVRMQFDLPEDRLDELDSLMKKCGISTKKELFNYALTMLEWAV
                     DESESGHEIAAIDRDSKQFYALRMPILKRVNRTSTAN"
                     /name="hypothetical protein"
     Typing          complement(279..363)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(2692..2947)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.124"
                     /coverage="89.0"
                     /evalue="5.65e-115"
     Typing          complement(3072..3169)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.98"
                     /coverage="99.0"
                     /evalue="4.84e-41"
     Typing          386..932
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.718"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtgaacaaac agcaacaaac tgcgctgaat atggcgcgat ttatcaaaag ccagagcctg
       61 gcactgcttg aaaaactgga tgctctggat gccgacgaac aggcggccat gtgcgaacga
      121 ctgcacgaac tcgcggaaga actccagaac agcatccagg ttcgctttga ggccgaaagt
      181 gaaacaggaa cataacgaag ctgacggagg cgctcacggc ttgtccgcga gcgttttcgg
      241 cagcagacaa gcccgtcagg gcgcgtcagg gggttttagc gggtgtcggg gcgcagccat
      301 gacccagtca cgtagcgata gcggagtgta tactggctta actatgcggc atcagtgcgg
      361 attgtatgaa aagtgcacca tagccgatgt gaaatgccgc acagatgcgt aaggagaaaa
      421 tgcaacttcc gacactcttc cgcttcctcg ctcactgact cgctacgctc agtcgttcgg
      481 ctgcggcgag cggtgccggc acactcaaag gcggtaatac agttatccac agaatcaggg
      541 gataaggccg gaaagaacat gtgagcaaaa aggcaaaggc caacgaaagg ccgcgccgct
      601 ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaatcgac gctcaagtca
      661 gaggtggcga aacccgacag gactataaag ataccaggcg tttccccctg gaagctccct
      721 cgtgcgctct cctgttccga ccctgccgct taccggatac ctgtccgcct ttctcccttc
      781 gggaagcgtg gcgctttctc atagctcacg ctgttggtat ctcagttcgg tgtaggtcgt
      841 tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag cccgaccgct gcgccttatc
      901 cggtaactat cgtcttgagt ccaacccggt aagacacgac ttatcgccac aggcagcagc
      961 cactggtaac tgatttagag gagtttgtct tgaagtcatg cgcctgttaa ggctaaactg
     1021 aaagaacaga tttggtgact gtgctcctcc aagccagtga ccttggttca aagagcgcca
     1081 actcttagaa ccttcgaaaa aaccgcccgc caaggcggtt ttttcgtttc aacctcaaga
     1141 gattacattt tgattagagt gatctcaaga tagattgacc aaatacatgc gtaacttcac
     1201 cagaggtggc cgaagttaaa tctatatatc attgttatta ttcttaaaaa ctgactttac
     1261 aataatcaag aataaagctg acacctctgc tactgttcct gcaatcaaag ccaagtaaac
     1321 actagtagtt accgtccttt catccgcccg cataaagcca cttcttatga gcgaaagttc
     1381 ttcatcaaga acatgatata acatacttat gaccatccag ttcattactg cgaccaaaat
     1441 agtcatagct aaagtaacac cacttttagt ccatctaaga tgtcttctat cagcagactc
     1501 ctcgacgtca ttaaagaacg gtttgggctg ctttaccttt tgtttttctt tttgggtatc
     1561 gccctcagta aacccatcca ggctgtctga cacaatcaaa tcctcttgaa taaaaaaaag
     1621 aaggccagct taaactggcc ttctccttaa cacatcaagt gataagttaa tttgcagtag
     1681 atgtacggtt cactcgctta agaataggca ttcgtagagc ataaaattgc ttactgtctc
     1741 tatcgatagc tgcgatttcg tgaccacttt cggactcgtc cacagcccac tcaagcattg
     1801 ttaacgcgta gttgaacaac tcttttttag tacttatgcc gcacttcttc attaaagaat
     1861 cgagttcgtc caacctatct tcaggcagat cgaattgcat acgtacattt ttcataacta
     1921 atctccgagg ggccagcatg tcatccttac actctatgct gcacattctt cactattagg
     1981 gcctgtatta tttatatata tctacttata aataatttaa gtttcatatt tttatgatgc
     2041 tcctaattta gataagactt aaccttatct ctttttccgc aagcaggtta tccccaccat
     2101 ggaggaggtt gtgaatactc ctccatggtg gttattactc atcgacctca gtaaagactg
     2161 aaaaccaatc cttcaaagaa agctccttag gaggcagttc ttcaaagtcg gtacagtcct
     2221 cacttttccc ggaggtcgac gagcaggttt gagttaactt gctcacagat aaaatctcca
     2281 gtttacccac cacccaccgt gatgggttcc agattgtata ttacacctaa acacctcctt
     2341 tgtcgagtgt aacaggagca caaaacgagt atagaacgat agcggtcaaa aatacaacac
     2401 cagttgtaac aggatgagac aatcagccaa atctcaacct catttaccat aacgtcgcat
     2461 tacgcgcacc gctaaaacgc gctgaacgcg attctgccgc aaacaccgca aaaagagatg
     2521 tttcacccag tgaaaaccgg aaaaatgcgt caggatcgct ttcggctcac tgcatagcta
     2581 tgcatgaaag tgaatggcga tcggtttggg cgcatacagt gcccatgaga cacattttcg
     2641 gacattttca gttcgtgaat ccctgactca ttgctacata tctgaacaga cacccctagc
     2701 agcgccccca ggggcgtcct gtaaaaaaac acaccgcgcc gctagcagca cccctaatat
     2761 aagatgatgt tttttatgaa aatagtcagt accaccccta aaaagcggtg ttggcgcagc
     2821 tacaacaccg cgccgacacc gcttttttaa atatcacaaa gagagcaaga agaactaatt
     2881 tgtcataact ctctatttat aaagaaaaat cagcaaaaaa ttgtttttgc gtggggtgtg
     2941 ggcatttcag gcatgagaac agactcgcgt ttttccggag tatcagcgga attattgatt
     3001 aagaaacact cgacgcagag cgaaatttta tgcaacagcg gctgcactgc acagggatta
     3061 tttatcagtt gatatgctgt gccatgatac gtcctaaaga aacaggacag gatgtgcaat
     3121 tgtaataccg tcgcccgcaa cgtcttacaa ttaccaccgg gtcagggtct acccaacacc
     3181 cggtactgac ggagaacaac ggaag
//
