LOCUS       NZ_CP011434             4248 bp    DNA     circular CON 15-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain YU39
            isolate YUHS 05-78 plasmid pYU39_4.2, complete sequence.
ACCESSION   NZ_CP011434
VERSION     NZ_CP011434.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03653812
            Assembly: GCF_001006525.1
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 4248)
  AUTHORS   Calva,E., Silva,C., Zaidi,M.B., Sanchez-Flores,A., Estrada,K.,
            Silva,G.G., Soto-Jimenez,L.M., Wiesner,M., Fernandez-Mora,M.,
            Edwards,R.A. and Vinuesa,P.
  TITLE     Complete Genome Sequencing of a Multidrug-Resistant and
            Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the
            Emerging Sequence Type 213 Genotype
  JOURNAL   Genome Announc 3 (3), e00663-15 (2015)
   PUBMED   26089426
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4248)
  AUTHORS   Vinuesa,P., Silva,C. and Calva,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-MAY-2015) Departamento de Microbiologia Molecular,
            IBT-UNAM, Av. Universidad 2001 Col. Chamilpa, Cuernavaca, Morelos
            62210, Mexico
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP2 v. 2.2.0
            Assembly Name                     :: SentYU39_1.0
            Long Assembly Name :: Salmonella enterica serovar Typhimurium YU39
            1.0
            Genome Coverage                   :: 150x
            Sequencing Technology             :: PacBio; 454; Illumina GAIIx
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001006525.1-RS_2024_03_15
            Annotation Date                   :: 03/15/2024 03:06:50
            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)                     :: 5,142
            CDSs (total)                      :: 5,016
            Genes (coding)                    :: 4,885
            CDSs (with protein)               :: 4,885
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 131
            CDSs (without protein)            :: 131
            Pseudo Genes (ambiguous residues) :: 0 of 131
            Pseudo Genes (frameshifted)       :: 42 of 131
            Pseudo Genes (incomplete)         :: 96 of 131
            Pseudo Genes (internal stop)      :: 24 of 131
            Pseudo Genes (multiple problems)  :: 28 of 131
            Pseudo Genes (short protein)      :: 1 of 131
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP011434.1.
            Source DNA and bacteria available from Claudia Silva
            (csilvamex1@yahoo.com).
            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..4248
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="YU39"
                     /serovar="Typhimurium"
                     /isolate="YUHS 05-78"
                     /isolation_source="blood-culture"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pYU39_4.2"
                     /geo_loc_name="Mexico: Yucatan"
                     /lat_lon="20.57 N 89.39 W"
                     /collection_date="2005"
                     /collected_by="Mussaret Zaidi"
                     /genotype="ST213"
     gene            complement(127..444)
                     /locus_tag="SE14_RS25515"
                     /old_locus_tag="SE14_05207"
     CDS             complement(127..444)
                     /locus_tag="SE14_RS25515"
                     /old_locus_tag="SE14_05207"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000718044.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023224510.1"
                     /translation="MKKIFILSAALIMAGCATKQYPQAANVTGPESSAMDCKAVALEIA
                     KTRSVQQEIEATGEFDGRTVLGFLGDFGIGNGMAKGEARKKAANRLNQLEALKAAKCAD
                     Q"
                     /name="hypothetical protein"
     gene            1561..1710
                     /locus_tag="SE14_RS28530"
                     /old_locus_tag="SE14_05209"
     CDS             1561..1710
                     /locus_tag="SE14_RS28530"
                     /old_locus_tag="SE14_05209"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_200901907.1"
                     /translation="MPSEYDEQRDATDTQLPGEYDLFDLMAQVTEEDLHATVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            2094..2462
                     /locus_tag="SE14_RS25520"
     CDS             2094..2462
                     /locus_tag="SE14_RS25520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880027.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_046891378.1"
                     /translation="MANFNPGPRTAIAAVRDSKNDIETWKKNGIRREEIVTVLNERYGL
                     NISLVAFDKALYRLRKSTDEPSLADADSVSAAETNFSEASGPDNGFFLSGNDFMRAEEE
                     SQRVVESFRDSTGRKKGF"
                     /name="hypothetical protein"
     gene            <2788..3129
                     /locus_tag="SE14_RS25530"
                     /pseudo=""
     CDS             <2788..3129
                     /locus_tag="SE14_RS25530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611474.1"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="integrase core domain-containing protein"
                     /name="integrase core domain-containing protein"
     gene            3205..3609
                     /locus_tag="SE14_RS25535"
     CDS             3205..3609
                     /locus_tag="SE14_RS25535"
                     /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_046891379.1"
                     /translation="MIKKISSLFFFIFCCWGGVAHADENTNSNVTRVQILCKSNPSARI
                     ILNVNNVSKKIAAEFINNDSVAVFDQDDRSGQKIDDDLFVRDIYSENRKVVLGLVFSSR
                     DSQIKAAVLKPVEASQSMTMLKSCHQEVLH"
                     /name="hypothetical protein"
     gene            3886..4122
                     /locus_tag="SE14_RS25540"
                     /old_locus_tag="SE14_05211"
     CDS             3886..4122
                     /locus_tag="SE14_RS25540"
                     /old_locus_tag="SE14_05211"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230891.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_046891380.1"
                     /translation="MARLTDLTPAEKKFIDDAIAAAERAAGKKLNQPNRHIVLNRARAQ
                     IESQRLADRQRALRETERQQAEFTWSRPQAPRR"
                     /name="hypothetical protein"
     Typing          1353..1526
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.714"
                     /coverage="100.0"
                     /evalue="1.2e-79"
     Typing          complement(883..1429)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.727"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 tgttcttttg caggtgaggt cgtagaaacg ccctgagagc ctctcaggcg gtgcacgcaa
       61 cagatgttat ggtaaatcca gctgattggc aggtacaaaa aaagcccggc agggcttttt
      121 tgtaccttat tgatctgcac actttgcagc cttcagggct tccagctgat ttagccggtt
      181 agctgctttt ttgcgggctt cgccttttgc catgccattt cctatcccaa aatcacccag
      241 gaaacctaat acggtgcgcc cgtcaaattc gccggttgcc tcaatttctt gttgtacact
      301 gcgcgttttg gcgatttcca gagctaccgc tttgcaatcc attgcggaag attctggacc
      361 ggtgacgttc gcggcctgtg gatattgctt tgttgcgcat cctgccatga tcagcgctgc
      421 cgataggatg aatatttttt tcaaaattat ccttatttat ttaggcatag ttaagagata
      481 cccattttat catttaggca tagttaagag atacccattt tatcggcagg aaatgagggt
      541 tttttagttg aattttggga ggggcaaggt tccatattgg tcgaggattc tggagctgac
      601 cggcaacggc cagcgcggct atgggccatg cggtggttga gcatagaaag gatcttcttg
      661 agttcctttt tttctacgcg taatctcttg ctctgaaaac gaaaaaacca cctggggagg
      721 tggtttttcg aaggttaagt cagttgggga actgcttaac ctggtaactg gcttcagcag
      781 agcgcagata ccaaatactg tccttccagt gtagccgtag ttaggccacc acttcaagaa
      841 ctctatagca ccacctaaat taactcgctc tgctaatcct gttaccagtg gctgctgcca
      901 gtggcgcttt gtcgtgtctt tccgggttgg actcaagacg atagttaccg gataaggcgc
      961 agcagtcgga ctgaacgggg ggttcgtgca tacagtccag cttggagcga actgccttcc
     1021 cggaactgag tgtcaggcgt ggaatgagat aaacgcggcc ataacagcgg aatgacaccg
     1081 gtaaaccgaa aggcaggaac aggagagcgc acgagggagc caccaggggg aaacgcctgg
     1141 tatctttaag tcctgtcggg tttcgccacc actgatttga gcgtcagatt tcgtgatgct
     1201 tgtcaggggg gcggagccta tggaaaaacg gctttgccgc ggccctatcg cttccctgtt
     1261 aagtatcttc ctggcatctt ccaggaaatc tccgccccgt tcgtaagcca tttccgctcg
     1321 ccgcagtcga acgaccgagc gtagcgagtc agtgagcgag gaagcggaat atatcctgta
     1381 tcacatattc tgctgacgca ccggtgcagc cttttttctc ctgccacatg aagcacttca
     1441 ctgacaccct catcagtgcc aacatagtaa gccagtatac actccgctag cgctacgtga
     1501 ctggttcagg gctgcgcccc gaaacccgct aacaacccct tagctactgg atatcacccc
     1561 atgccatctg aatatgatga acaacgggat gcgactgata cgcagcttcc cggcgaatat
     1621 gacctttttg atttaatggc gcaggttact gaagaggacc tgcacgccac ggtggatttt
     1681 gggccgcctg tcggccggga agcgttatag ctttttcgct tacccccgta cgtgtaatac
     1741 gccggtatta catcttattt ctttattttc atgtgattac aggtggttgt aatacgttgc
     1801 gtattacata aataaacggg aacttcagtt tttacctttt aattcatgca attgcgatga
     1861 aaatcgcggt tgcgtatggt gtatgaccat ttaagggata atgtaacctg acttttaaag
     1921 aatgaatcta tctttggcag cgcatgagat cgataaaaag cgttccacat caggcggttc
     1981 atgtatccat gacccggaaa ggacaaaaat aagacaattg taagacattt ttttgcgttt
     2041 tactcttatt tttggactat tatgagacaa atgtaagaca ttatgggcgg tatatggcga
     2101 attttaaccc tggtccaaga acagccattg cagctgtcag ggattccaag aacgatatag
     2161 aaacctggaa gaaaaatggt atccgtaggg aagagattgt gactgtgctg aatgaacgtt
     2221 acggcctgaa tatctcactg gttgcgtttg ataaggctct ttacagattg agaaaaagta
     2281 cagatgaacc gtctcttgct gatgcggatt ctgtgtctgc tgcagaaacg aatttttctg
     2341 aagccagtgg gcctgacaat ggtttttttc tgtccgggaa tgacttcatg cgagcagaag
     2401 aagaatctca aagagtggtt gagtcattca gagatagcac tggcaggaag aaaggattct
     2461 gattttgaat tctaagtagt gaaatagtgg atcctctact cgaaattgtc ggatacctgc
     2521 aattacctac cgtgccttgc ggcttggtca atgcctcacg gctgcacagt aaactgcgca
     2581 gccgttcacc gttaatcagg tacagattta ccaattattc agtcgccttt acgcccgaaa
     2641 attcgctttt aacgtttgtg acctgctccc cgttgattag tacaccccga tgttagtaat
     2701 gtcttcataa gccacatgag gacatcccca tgaagaagcg tttttccgac gaacagatca
     2761 tcagtattct ccgcgaagcc gaagctgggg tatccggcga cgataagaac tgaccagggg
     2821 ccggagttca cttgccgtgc actggaacaa tgggcctttg agcatggtgt tgagttgcgc
     2881 ttaatccagc cgggcaagcc aacgcagaac ggatttattg agagctttaa cggacgattt
     2941 cgcgatgaat gtttgaatga gcactggttc agcgatatcg ttcatgccag gaaaattatt
     3001 aatgactggc ggcaggatta taacgaatgc cgcccgcact ccacgctgaa ttatcagaca
     3061 ccgtctgaat ttgcagcggg ctggagaaag ggtcattctg agaatgaaga ttccgacgtt
     3121 actaactgag tgttgtatct aatcgtgggg gcaggtcaaa cgaaccgtgg attgatatgg
     3181 gcattagccg gagaaaatat ttttatgata aaaaaaataa gtagtttatt tttttttatt
     3241 ttttgttgct ggggcggagt ggctcatgca gacgaaaata caaactctaa tgtaactaga
     3301 gttcagattt tatgcaaaag taatccatcc gcgaggatca tccttaatgt aaataatgta
     3361 agtaaaaaaa tagcagcaga gttcataaat aatgattctg tggctgtttt tgatcaggat
     3421 gataggagcg gacaaaaaat agatgatgat ttgtttgtgc gagacatata cagcgaaaac
     3481 aggaaggtcg ttttaggttt ggttttttca agtagagact ctcagattaa ggctgcggtg
     3541 ttgaagccgg tagaagcatc ccaaagcatg accatgttaa aatcctgcca tcaggaagtt
     3601 ttgcactaaa caacctatat cagataacag ccctcttgca gagggttgtt gcctgctaac
     3661 aggatagcat ttgacacacc gcagtgtatt ttaagtcagt atacactccg ctagcgctac
     3721 gtgactggtt cagggctgcg ccccgaaacc ccgccaacgt ttgactgaac cggattaaaa
     3781 tccgttcccg ttcaccgttt ctagaagctg tatccggttg cctgttcttc attaggttca
     3841 ctgcgtctgg cagactgtag ggagtattgt tatacggaga tccacatggc gcgactgaca
     3901 gacctgaccc ccgcagagaa aaagtttatc gacgacgcta tagccgctgc cgaacgtgcg
     3961 gccgggaaga agctcaatca gcctaacagg cacatcgttc tgaatagggc gcgtgcgcag
     4021 atcgaatcac agcgccttgc agaccggcag cgggcattgc gtgagacgga gcggcagcag
     4081 gcggaattta cctggtcgcg tccgcaggca ccacgccgct gaacgcgact tttgtcggtt
     4141 tcatggtatg ttcactccaa aacagcctgg cattcactcc tgtgcatagc catgcagacg
     4201 cgcagaaatc atcagcgcgt ttctgagcgg ttttcagggg gtaagatg
//
