LOCUS       NZ_CP025336             3830 bp    DNA     circular CON 19-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain BL10
            plasmid p3.8k, complete sequence.
ACCESSION   NZ_CP025336
VERSION     NZ_CP025336.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07945789
            Assembly: GCF_002762135.3
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 3830)
  AUTHORS   Hong,Y.P., Wang,Y.W., Huang,I.H., Liao,Y.C., Kuo,H.C., Liu,Y.Y.,
            Tu,Y.H., Chen,B.H., Liao,Y.S. and Chiou,C.S.
  TITLE     Genetic Relationships among Multidrug-Resistant Salmonella enterica
            Serovar Typhimurium Strains from Humans and Animals
  JOURNAL   Antimicrob Agents Chemother 62 (5), e00213-18 (2018)
   PUBMED   29581119
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3830)
  AUTHORS   Hong,Y.P., Chiou,C.S. and Wang,Y.W.
  TITLE     Salmonella enterica subsp. enterica serovar Typhimurium strain BL10
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 3830)
  AUTHORS   Hong,Y.P., Chiou,C.S. and Wang,Y.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JUL-2018) Center for Diagnostics and Vaccine
            Development, Centers for Disease Control, R.O.C (Taiwan), No.20,
            Wenxin S. 3rd Rd., Nantun Dist., Taichung 408, Taiwan
  REMARK    Sequence update by submitter
REFERENCE   4  (bases 1 to 3830)
  AUTHORS   Hong,Y.P., Chiou,C.S. and Wang,Y.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-DEC-2017) Center for Diagnostics and Vaccine
            Development, Centers for Disease Control, R.O.C (Taiwan), No.20,
            Wenxin S. 3rd Rd., Nantun Dist., Taichung 408, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUL-2017
            Assembly Method                   :: CLC NGS Cell v. 10.1.1
            Genome Representation             :: Partial
            Expected Final Version            :: No
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002762135.3-RS_2024_03_19
            Annotation Date                   :: 03/19/2024 06:42:09
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,079
            CDSs (total)                      :: 4,957
            Genes (coding)                    :: 4,827
            CDSs (with protein)               :: 4,827
            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)              :: 130
            CDSs (without protein)            :: 130
            Pseudo Genes (ambiguous residues) :: 0 of 130
            Pseudo Genes (frameshifted)       :: 38 of 130
            Pseudo Genes (incomplete)         :: 96 of 130
            Pseudo Genes (internal stop)      :: 27 of 130
            Pseudo Genes (multiple problems)  :: 26 of 130
            Pseudo Genes (short protein)      :: 1 of 130
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP025336.1.
            Bacteria available from necropsy of sick pigs.
            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
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="BL10"
                     /serovar="Typhimurium"
                     /isolation_source="sick pig"
                     /host="Sus scrofa domesticus"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="p3.8k"
                     /geo_loc_name="Taiwan"
                     /lat_lon="23.29 N 120.27 E"
                     /collection_date="2011"
                     /collected_by="Hung-Chih Kuo"
     gene            605..871
                     /locus_tag="CTI29_RS24785"
                     /old_locus_tag="CTI29_25015"
     CDS             605..871
                     /locus_tag="CTI29_RS24785"
                     /old_locus_tag="CTI29_25015"
                     /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            complement(919..1107)
                     /locus_tag="CTI29_RS24790"
                     /old_locus_tag="CTI29_25020"
     CDS             complement(919..1107)
                     /locus_tag="CTI29_RS24790"
                     /old_locus_tag="CTI29_25020"
                     /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(1397..3301)
                     /locus_tag="CTI29_RS24795"
                     /old_locus_tag="CTI29_25025"
     CDS             complement(1397..3301)
                     /locus_tag="CTI29_RS24795"
                     /old_locus_tag="CTI29_25025"
                     /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"
     gene            complement(3607..3756)
                     /locus_tag="CTI29_RS27610"
                     /old_locus_tag="CTI29_25035"
     CDS             complement(3607..3756)
                     /locus_tag="CTI29_RS27610"
                     /old_locus_tag="CTI29_25035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /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_077464408.1"
                     /translation="MHEPPVQSDCCAFSGNYRLESNPERHEKSPLAAATGKQDVREMYR
                     EFLK"
                     /name="replication initiation protein"
     Typing          289..461
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          complement(2..182)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.604"
                     /coverage="84.0"
                     /evalue="1.99e-76"
     Typing          complement(3430..3830)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.434"
                     /coverage="99.0"
                     /evalue="8.489999999999997e-106"
ORIGIN
        1 agcggaatga caccggtaaa ccgaaaggca ggaacaggag agcgcacgag ggagctacca
       61 gggggaaacg cctgggatct ttatagtcct gtcgggtttc gccgccactg atttgagcgt
      121 cagatttcgt gatgcttgtc aggggggcgg agcctatgga aaaacggctt cgccgcggcc
      181 ttaccgtttc cctgttaagt ttcttcctgg catctcccag gaaatttccg ccccattcgt
      241 aatcccgcac cgctcgccgc agccgaacga ccgagcgcag cgagtcagtg agcgaggaag
      301 cggaatatct cctgtctcat atattccgct tacgctctgc tgctgcattt tcctcctgcc
      361 acatgaagca cttcactgat tcccgcaccc gtgcctacat aataagccag tatacactcc
      421 gctagcgcta cgtgactggt tcagggctgc gccccgacac ccgctaaaag cactgacgcg
      481 cctgcggctt gcccaacccc gcgccgtccg ggaaagaatt tcccgatcga cccgacgttt
      541 ctgtttacct gtgatgttaa cgtttggatc tttttcccgg gtttacctat tttaatgaag
      601 cgtaatgaag cgttcacagc tgacgttaat agatgggtgc ttcatgtttg gtttttcacc
      661 aggagaactt atgaaccttt gccccgatga acgtctgctc tttgtgcgga tgatttccgc
      721 tatgcttcgc cgttcgggcg gtgatgcggg tgctgttatg tttgaggcgt atcgccatat
      781 tgtgtccgat accaatcaag ctcgtcgttc ctgcatgctc gacctgctcg aaagcgtcag
      841 gcatgactat gtacacggtg gatatacata gttgccctgg atacgctttt cgtctaagtg
      901 agcgttcttt tcgtctcttt attcgccgtc ctgtataccg aagcgtgcgc tcagcttctg
      961 ataaagcgct tctgcctgtt cgtgcattcg ctcacagtcg gctgcctcgt catcaagatc
     1021 gagcacgtcg agtttttcga gcagcagcag cgactgcgcc cggataaatt ttgccatgtt
     1081 cagtgcggct gattcctgtt ttgtcatacg gctttttccc ggttttatgg tgatcgcaga
     1141 ctgaaatctt acttcattca cttgagtgca tagccatgca ggtacgcaga aatcatcagg
     1201 ggcgtttttt ctcgatatgg gcacagaaag gtgtatgttt caggtcggag tcctcagaaa
     1261 cgctctcaga gcctctcagg cggtgcacgc aacagatgtt atggtaaatc ctagttattt
     1321 gcaggcataa aaaagccgcc ttttaggcgg ttttttctga ttgtaagtta tcaagaccgg
     1381 atgctgaacg gcagtatcag acaataaagc gatcgaccag cgtggacatc gcttcagact
     1441 ggccgtccag catctggctg gcgctcgccg cctgagagac cagcgctgcg ttttgctgag
     1501 tgacctgctc cagctgattc agtgcctgat gcacctgcga cacgccaagc gactgctcat
     1561 tcgccgcacg ggcaatatcg ctcacgtact gtttcatccg cccggtattt tccgccgctg
     1621 ctttcagcgc ggtgccggac gcggtgactc gtgctacccc ttcgccaatc ttatccatat
     1681 tctggttaat cagctcacgg atctgactgg cttctcgtgc acagcgctgg gaaaggttac
     1741 gcacctccgt cgccactacc gcaaagcctt tgccaagctc accggcacgt gccgcttcaa
     1801 cggcggcgtt aagcgccagc aagttggtct ggaaagaaat ctcatcaatt gacgcaacaa
     1861 tctgggaaat ctgctcgctg gaagaacgaa tttccgccat gctctgactg gcctcgttag
     1921 agacgcgatt agcttccagt acgtcccgct ccatcgaatg tatcagacgc tccgcctcgc
     1981 tggcgttatc ggcggtctgg gtgatcgcag tagaaatctg ctccatgctg gcggccgttt
     2041 ccacaatcga tgccgcctgt tcatccgtac gctgggccag atcctgatta ccggcagcga
     2101 tatcactact ggcgctacgc aacaccaccg caccggactt aatttcttgc acgatatgct
     2161 gaatattctc aatcgcttgg ttataggcac ggttcagggc tgagagctcg tcgctgccgg
     2221 ggacgtcaag acgacgtgtc aggtcgccgt ccatctctgc gatggttttc agcgtaccgt
     2281 tcagttgctg ctggatactg cgtgccacca tcaccgcaaa ggcgatagca atcagtaggg
     2341 caaccaggct gattaccagg aaggactgcc agtcgacacg ggcattgtgg gcaagcagcg
     2401 cagcatgttc ctgcaaggca tccaccgcgc gattttccac cttttgcagc gtttcaatac
     2461 gctgggtctg aaggttaaac cagtcagtcg ggttgactcc aaatccgcct tcggcggctt
     2521 tattaaaagc cgtctcccgc agttcaagag cacgagttgc ttcagcggac tgaagagatt
     2581 tgtccagctc agccgcctgc acaggtgtgc taaagctgcg agctgccgtc agccaggcat
     2641 cctgctggcc taccacatcg ctaaacatgc tgaactggcc gtcgtcaaag cgatccatcg
     2701 agaagatatt ggacagcagc gcacgttcta caccagcctg ctccttcaaa ttcaagagac
     2761 tataataagc cgccagttcg ttcaccatcg agcctgaggt gcttaaatgc cccatcccgc
     2821 cgacaaactt cagcacgtca gagatggttt gggtatagaa ctgactcgct tttggtgaat
     2881 cgatagttaa ttcgctgatg gcggtacggg ttgagtcgag aaactgaata ctttcattaa
     2941 acgttttcag gggggcggca atatttccct ggagtaaatc cttattcgta tcggtcagca
     3001 accgcttaaa tgttgccagc accttgtcgg ttaactgccg ctgggcagct aagtcatcgc
     3061 gaaacttttg gccgcgcgcg ccgataaatc cagcgctcat tccacgttcg ctctggagtt
     3121 gatgcaccac atcacccgcg ctgcgggcga gcgtggtgag ctgtccaatg gtgttcatct
     3181 gctgttcggt attgatacgg ctgacaatac ccgaaccggc gaaccagacc aaggcaagca
     3241 gtagcgggaa taatgcaata aacaacttca tttgcattga aatacgataa gcccatgaca
     3301 tatcgatact ttccttactt tcttgaggga tcgcaggagt atcggtagat acatgcataa
     3361 actttatagt ttattgttgg gggaacgggc accacattcg gcagtggcgc tggtagcaat
     3421 ccataaagga tcttcttgag atcctttgac gatcgtcgta atctcttgct ctgtaaacga
     3481 aaaaaccacc cttgcaggtg gtttttcgaa ggttagataa tcctggcaga ttctctaacc
     3541 gtggtaacag tcttgtgcga gacatgtcac caaatttgtc cttctagtgt agcctcagtc
     3601 aggccactac ttcaagaact ctcgatacat ctctcgcaca tcctgtttac cagtggccgc
     3661 tgccagtggc gatttttcgt gtctttccgg gttggactca agacgatagt taccggaaaa
     3721 ggcgcagcag tcggactgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc
     3781 cttcccggaa ctgagtgtca ggcgtggaat gagataaacg cggccataac
//
