LOCUS       CP101344                4710 bp    DNA     linear   BCT 15-AUG-2022
DEFINITION  Salmonella enterica strain s15D023 plasmid ps15D023_5.
ACCESSION   CP101344
VERSION     CP101344.1
DBLINK      BioProject: PRJNA850394
            BioSample: SAMN29636373
KEYWORDS    .
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4710)
  AUTHORS   Du,P., Liu,X., Liu,Y., Li,R., Lu,X., Cui,S., Wu,Y., Fanning,S. and
            Bai,L.
  TITLE     Dynamics of Antimicrobial Resistance and Genomic Epidemiology of
            Multidrug-Resistant Salmonella enterica Serovar Indiana ST17 from
            2006 to 2017 in China
  JOURNAL   mSystems, e0025322 (2022) In press
   PUBMED   35861536
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 4710)
  AUTHORS   Du,P., Liu,X., Liu,Y., Li,R., Lu,X., Cui,S., Wu,Y., Fanning,S. and
            Bai,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUL-2022) Institute of Infectious Diseases, Beijing
            Ditan Hospital, Capital Medical University, No.8 jingshundongjie,
            Beijing 100015, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 07/12/2022 17:12:05
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.1
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,880
            CDSs (total)                      :: 4,768
            Genes (coding)                    :: 4,619
            CDSs (with protein)               :: 4,619
            Genes (RNA)                       :: 112
            rRNAs                             :: 6, 6, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            partial rRNAs                     :: 1 (23S)
            tRNAs                             :: 81
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 149
            CDSs (without protein)            :: 149
            Pseudo Genes (ambiguous residues) :: 0 of 149
            Pseudo Genes (frameshifted)       :: 61 of 149
            Pseudo Genes (incomplete)         :: 110 of 149
            Pseudo Genes (internal stop)      :: 31 of 149
            Pseudo Genes (multiple problems)  :: 44 of 149
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..4710
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="s15D023"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="ps15D023_5"
                     /geo_loc_name="China:Henan"
                     /collection_date="2013"
                     /collected_by="State Key Laboratory of Infectious Disease
                     Prevention and Control"
     gene            complement(<1..716)
                     /locus_tag="NMV07_24345"
     CDS             complement(<1..716)
                     /locus_tag="NMV07_24345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001138014.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF4158 domain-containing protein"
                     /protein_id="UUX21719.1"
                     /translation="MPRRLILSATERDTLLALPESQDDLIRYYTFNDSDLSLIRQRRGD
                     ANRLGFAVQLCLLRYPGYALGTDSELPEPVILWVAKQVQAEPASWAKYGERDVTRREHA
                     QELRTYLQLAPFGLSDFRALVRELTELAQQTDKGLLLAGQALESLRQKRRILPALSVID
                     RACSEAIARANRRVYRALVEPLTDSHRAKLDELLKLKAGSSITWLTWLRQAPLKPNSRH
                     MLEHIERLKTFQLVDLP"
                     /name="DUF4158 domain-containing protein"
     gene            complement(720..1280)
                     /locus_tag="NMV07_24350"
     CDS             complement(720..1280)
                     /locus_tag="NMV07_24350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005220837.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="UUX21720.1"
                     /translation="MQGHRIGYVRVSSFDQNPERQLEQTQVSKVFTDKASGKDTQRPQL
                     EALLSFVREGDTVVVHSMDRLARNLDDLRRLVQKLTQRGVRIEFLKEGLVFTGEDSPMA
                     NLMLSVMGAFAEFERALIRERQREGIALAKQRGAYRGRKKALSDEQAATLRQRATAGEP
                     KAQLAREFNISRETLYQYLRTDD"
                     /name="recombinase family protein"
     gene            complement(1456..1806)
                     /locus_tag="NMV07_24355"
     CDS             complement(1456..1806)
                     /locus_tag="NMV07_24355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000454193.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3330 domain-containing protein"
                     /protein_id="UUX21721.1"
                     /translation="MEVVAEGVETPDCLAWLRQAGCDTVQGFLFARPMPAAAFVGFVNQ
                     WRNTTMNANEPSTSCCVCCKEIPLDAAFTPEGAEYVEHFCGLECYQRFQARASTATETS
                     VKPDACDSPPSG"
                     /name="DUF3330 domain-containing protein"
     gene            complement(2009..3022)
                     /gene="intI1"
                     /locus_tag="NMV07_24360"
     CDS             complement(2009..3022)
                     /gene="intI1"
                     /locus_tag="NMV07_24360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221021.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="class 1 integron integrase IntI1"
                     /protein_id="UUX21722.1"
                     /translation="MKTATAPLPPLRSVKVLDQLRERIRYLHYSLRTEQAYVHWVRAFI
                     RFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEI
                     GRPRPSRRLPVVLTPDEVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHG
                     TIIVREGKGSKDRALMLPESLAPSLREQLSRARAWWLKDQAEGRSGVALPDALERKYPR
                     AGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGITKPATPHTLRH
                     SFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDALPPLTSER"
                     /name="intI1"
     ARG             3055..3653
                     /name="dfrA17"
                     /gene="dfrA17"
                     /gene_name="trimethoprim resistant dihydrofolate reductase
                     dfr"
                     /tool="rgi"
                     /drug_class="diaminopyrimidine antibiotic"
                     /identity="99.36"
                     /coverage="126.75"
     ARG             3181..3650
                     /name="dfrA17"
                     /gene="dfrA17"
                     /gene_name="trimethoprim-resistant dihydrofolate reductase
                     DfrA17"
                     /tool="amrfinderplus"
                     /drug_class="TRIMETHOPRIM"
                     /identity="100.0"
                     /coverage="100.0"
     gene            3784..4572
                     /locus_tag="NMV07_24370"
     CDS             3784..4572
                     /locus_tag="NMV07_24370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000503573.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ANT(3'')-Ia family aminoglycoside
                     nucleotidyltransferase AadA5"
                     /protein_id="UUX21723.1"
                     /translation="MGEFFPAQVFKQLSHARAVIERHLAATLDTIHLFGSAIDGGLKPD
                     SDIDLLVTVSAAPNDSLRQALMLDLLKVSSPPGDGGTWRPLELTVVARSEVVPWRYPAR
                     RELQFGEWLRHDILSGTFEPAVLDHDLAILLTKARQHSLALLGPSAATFFEPVPKEHFS
                     KALFDTIAQWNAESDWKGDERNVVLALARIWYSASTGLIAPKDVAAAWVSERLPAEHRP
                     LICKARAAYLGSEDDDLAMRVEETAAFVRYAKATIERILR"
                     /name="ANT(3'')-Ia family aminoglycoside
                     nucleotidyltransferase AadA5"
     ARG             3785..4569
                     /name="aadA5"
                     /gene="aadA5"
                     /gene_name="ANT(3'')-Ia family aminoglycoside
                     nucleotidyltransferase AadA5"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
ORIGIN
        1 ggcaagtcca ccaactgaaa tgtcttcagc cgctcgatgt gttccagcat gtgccgagag
       61 ttgggtttca gcggtgcctg gcgcagccag gtcaaccagg tgatgctgct gccggccttg
      121 agcttcaaca gctcgtccag cttggcccga tgcgagtccg tgagtggttc gaccagggcg
      181 cggtagaccc gccgattggc tcgcgcaatg gcttccgagc aggcccggtc aatcacgctc
      241 agcgccggca ggatgcgtcg tttctgccgt aggctctcca gggcctgacc ggccagcagc
      301 aagcctttgt cggtctgctg ggccagctcg gttagctcgc gcaccagggc gcggaagtcg
      361 gacaggccga acggggccag ttgcaggtag gtgcgcagtt cctgggcatg ctcgcgacgg
      421 gtcacgtcgc gctcgccgta ctttgcccag ctcgccggct cggcctggac ttgcttcgcc
      481 acccacagga tgaccggctc gggcagctcg ctgtcggttc ccagcgcgta accggggtag
      541 cgcagcaggc agagctgcac ggcgaagccg aggcggttgg cgtcgccgcg tcgctggcgg
      601 atcagcgaca ggtcggagtc gttgaaggtg tagtagcgga tcaggtcatc ctggctttcc
      661 ggcagcgcaa gcagggtgtc ccgctccgtg gccgagagga tcaagcgacg cggcatgtgt
      721 cagtcgtccg tgcggaggta ctggtagagg gtttcccggc tgatgttgaa ctcgcgggca
      781 agctgcgcct tgggctcgcc ggccgtcgct cgctgccgca gggtagcagc ctgctcatcg
      841 gacagggctt tcttgcggcc ccggtacgcg ccacgctgct tggccaaggc gatgccctca
      901 cgctgccgct cgcggatcag ggcgcgctcg aactcagcga aggcccccat caccgacagc
      961 atcaggttgg ccatcggcga gtcctcgcca gtgaacacca ggccctcctt caggaactcg
     1021 atgcgcacgc cgcgctgagt cagcttctgt accaagcgac gcaggtcatc gaggttgcgg
     1081 gccagccgat ccatgctgtg caccaccact gtatcgcctt cgcggacgaa gctcagcagc
     1141 gcttcgagct gggggcgctg ggtgtccttg cccgatgcct tgtcggtgaa caccttgctc
     1201 acctgggttt gttccagctg gcgttccggg ttctggtcaa agctgctgac ccggacgtag
     1261 ccgatgcggt gcccctgcac gatgtctcct tggttgaagg cggcttaagt gcactttctg
     1321 ttccgttgtg cctcaaagcc catttctgtc aggctgaaat ctataacctt cgcgggcatg
     1381 tgtcaaaaaa tgggaaagca gactctattc tgacgaagcg gcgcggccct gcctgacatc
     1441 aagttagggt atgcctcaac ctgacggcgg cgaatcacaa gcgtccggtt tgacgctggt
     1501 ttcggtcgca gtgctggccc gcgcctggaa gcgctgatag cactccagcc cgcagaaatg
     1561 ctccacgtac tcggcccctt ccggcgtgaa ggcggcatcg agcgggattt ccttgcagca
     1621 cacgcagcaa ctggtgctcg gttcattggc gttcatggtg gtgttcctcc attggttgac
     1681 gaagccgacg aaggccgccg ccggcatcgg cctggcgaac aggaaaccct gcaccgtgtc
     1741 gcaacccgcc tgccgcaacc acgcaaggca gtcgggtgtt tccacaccct cggctaccac
     1801 ctccattgtc gttttcagaa gacggctgca ctgaacgtca gaagccgact gcactatagc
     1861 agcggagggg ttggatccat caggcaacga cgggctgctg ccggccatca gcggacgcag
     1921 ggaggacttt ccgcaaccgg ccgttcgatg cggcaccgat ggccttcgcg caggggtagt
     1981 gaatccgcca ggattgactt gcgctgccct acctctcact agtgaggggc ggcagcgcat
     2041 caagcggtga gcgcactccg gcaccgccaa ctttcagcac atgcgtgtaa atcatcgtcg
     2101 tagagacgtc ggaatggccg agcagatcct gcacggttcg aatgtcgtaa ccgctgcgga
     2161 gcaaggccgt cgcgaacgag tggcggaggg tgtgcggtgt ggcgggcttc gtgatgcctg
     2221 cttgttctac ggcacgtttg aaggcgcgct gaaaggtctg gtcatacatg tgatggcgac
     2281 gcacgacacc gctccgtgga tcggtcgaat gcgtgtgctg cgcaaaaacc cagaaccacg
     2341 gccaggaatg cccggcgcgc ggatacttcc gctcaagggc gtcgggaagc gcaacgccgc
     2401 tgcggccctc ggcctggtcc ttcagccacc atgcccgtgc acgcgacagc tgctcgcgca
     2461 ggctgggtgc caagctctcg ggtaacatca aggcccgatc cttggagccc ttgccctccc
     2521 gcacgatgat cgtgccgtga tcgaaatcca gatccttgac ccgcagttgc aaaccctcac
     2581 tgatccgcat gcccgttcca tacagaagct gggcgaacaa acgatgctcg ccttccagaa
     2641 aaccgaggat gcgaaccact tcatccgggg tcagcaccac cggcaagcgc cgcgacggcc
     2701 gaggtcttcc gatctcctga agccagggca gatccgtgca cagcaccttg ccgtagaaga
     2761 acagcaaggc cgccaatgcc tgacgatgcg tggagaccga aaccttgcgc tcgttcgcca
     2821 gccaggacag aaatgcctcg acttcgctgc tgcccaaggt tgccgggtga cgcacaccgt
     2881 ggaaacggat gaaggcacga acccagtgga cataagcctg ttcggttcgt aaactgtaat
     2941 gcaagtagcg tatgcgctca cgcaactggt ccagaacctt gaccgaacgc agcggtggta
     3001 acggcgcagt ggcggttttc atggcttgtt atgactgttt ttttgtacag tctatgcctc
     3061 gggcatccaa gcagcaagcg cgttacgccg tgggtcgatg tttgatgtta tggagcagca
     3121 acgatgttac gcagcagggc agtcgcccta aaacaaagtt agccattaag ggagttaaat
     3181 tgaaaatatc attgatttct gcagtgtcag aaaatggcgt aatcggtagt ggtcctgata
     3241 tcccgtggtc agtaaaaggt gagcaactac tctttaaagc gctcacatat aatcaatggc
     3301 tccttgtcgg aagaaaaaca tttgactcta tgggtgttct tccaaatcgc aaatatgcag
     3361 tagtgtcaaa gaacggaatt tcaagctcaa atgaaaacgt cctagttttt ccttcaatag
     3421 aaaatgcttt gaaagagcta tcaaaagtta cagatcatgt atatgtctct ggcgggggtc
     3481 aaatctataa tagccttatt gaaaaagcag atataattca tttgtctact gttcacgttg
     3541 aagtcgaagg tgatatcaaa ttccctataa tgcctgagaa tttcaatttg gtttttgaac
     3601 agttttttat gtctaatata aattatacat accagatttg gaaaaaaggc taacaatgcg
     3661 ttgcagcacc agtcgcttcg ctccttggac agcttttaag tcgcgtcttt gtggttttgc
     3721 tgcgcaaaag tattccacaa agccgcaact taaaagctgc cgctgaactt aacgttaggc
     3781 atcatgggtg aatttttccc tgcacaagtt ttcaagcagc tgtcccacgc tcgcgcggtg
     3841 atcgagcgcc atctggctgc gacactggac acaatccacc tgttcggatc tgcgatcgat
     3901 ggagggctga agccggacag cgacatagac ttgctcgtga ccgtcagcgc cgcacctaac
     3961 gattcgctcc ggcaggcgct aatgctcgat ttgctgaaag tctcatcacc gccaggcgat
     4021 ggcggaacat ggcgaccgct ggagctaact gttgtcgctc gaagcgaagt agtgccttgg
     4081 cgctatccgg cgcggcgtga gcttcagttc ggtgagtggc tccgccacga catcctttcc
     4141 ggaacgttcg agcctgccgt tctggatcac gatcttgcga ttttgctgac caaggcgagg
     4201 caacacagcc ttgcgcttct aggcccatcc gcagccacgt ttttcgagcc ggtgccgaag
     4261 gagcatttct ccaaggcgct tttcgacact attgcccagt ggaatgcaga gtcggattgg
     4321 aagggtgacg agcggaacgt cgttcttgct cttgctcgca tttggtacag cgcttcaact
     4381 ggtctcattg ctcctaagga cgttgctgcc gcatgggtat cggagcgttt gcctgccgag
     4441 catcggcccc tcatctgcaa ggcacgcgcg gcgtacctgg gtagcgagga cgacgaccta
     4501 gcaatgcgcg tcgaagagac ggccgcgttc gttcgatatg ccaaagcaac gattgagaga
     4561 atcttgcgtt gagcggcatg tgcgaaaagt gcatcgaccc gcgccgaggg catctgatgc
     4621 ctaactcggc gttcaagcgg acgggctgcg cccgccgctc aactatgcgt tagatgcact
     4681 aagcacataa ttgctcacag ccaaactatc
//
