LOCUS       NZ_CP011432             5093 bp    DNA     circular CON 15-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain YU39
            isolate YUHS 05-78 plasmid pYU39_5.1, complete sequence.
ACCESSION   NZ_CP011432
VERSION     NZ_CP011432.1
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 5093)
  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 5093)
  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
            CP011432.1.
            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..5093
                     /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_5.1"
                     /geo_loc_name="Mexico: Yucatan"
                     /lat_lon="20.57 N 89.39 W"
                     /collection_date="2005"
                     /collected_by="Mussaret Zaidi"
                     /genotype="ST213"
     gene            join(4811..5093,1..209)
                     /locus_tag="SE14_RS25470"
     CDS             join(4811..5093,1..209)
                     /locus_tag="SE14_RS25470"
                     /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_032347463.1"
                     /translation="MAIGDDAIRDAFYLFTQQVAEMDNESLPKDVWGTPCFTYLMTRKQ
                     FNQMKVICQRNGWDVPTSPAIPITWSMFKHVLSARKSKDKLSWQECAEILATAFSVQSN
                     VYVSRDYSEQTIVLNASCRISVAGAGFFAMAIIDVSENNLAPVTAYHVTEAKCKAISRG
                     "
                     /name="hypothetical protein"
     gene            complement(742..1434)
                     /locus_tag="SE14_RS25475"
                     /old_locus_tag="SE14_05198"
     CDS             complement(742..1434)
                     /locus_tag="SE14_RS25475"
                     /old_locus_tag="SE14_05198"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_044716251.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYELLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCITELNKKSDLVVTVETIKKGRTVAALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1966..2220)
                     /locus_tag="SE14_RS25480"
                     /old_locus_tag="SE14_05199"
     CDS             complement(1966..2220)
                     /locus_tag="SE14_RS25480"
                     /old_locus_tag="SE14_05199"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032347465.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLPFLRREVTRQADLNRIQPLIDELEALPER"
                     /name="hypothetical protein"
     gene            2399..4558
                     /gene="mobQ"
                     /locus_tag="SE14_RS25485"
                     /old_locus_tag="SE14_05200"
     CDS             2399..4558
                     /gene="mobQ"
                     /locus_tag="SE14_RS25485"
                     /old_locus_tag="SE14_05200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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_032347464.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAEA
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVANLLNIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWAASGLAALRAQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNWEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPTADNSQLVINALTDKG
                     LRFAGYGEAVNHDADSPARPAPELMLFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWQREEYARTRVSDRKHERGWLL"
                     /name="mobQ"
     Typing          complement(2225..2398)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          2399..2757
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.611"
                     /coverage="100.0"
                     /evalue="1.82e-180"
     Typing          complement(743..1434)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2313..4549
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.381"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tggcaactgc tttttctgtg cagagtaatg tatacgttag cagagattat tcagagcaga
       61 cgattgtact taatgcttct tgtcgcatca gcgttgcagg ggcaggattt ttcgcaatgg
      121 cgattattga tgtctctgaa aataatttgg cccccgtaac tgcatatcat gtgacggagg
      181 ccaaatgtaa agctatatcg cgagggtgat aggaaggacg cccatttaag cagctctcct
      241 caatttaatg agaatgaacc ataacgccta aatatttccc ttcattgttt cctttcggat
      301 ctagcagcat cggcggtttt ctgctgtcta tcaaatcgct aattgttcag gaacatcaat
      361 gctcccactg ccgaacatta gaggatttct ccgtttatgg aatgttcttg cagtacattc
      421 aatctacatc aattgtggct atagtacaat atttattgag cgcagctaag gctaaactcc
      481 ccgcgaacag gggcttaaga tagggtgtgg aatgtcgcat tttgtgactt aggggcctca
      541 tctgcctcaa ttagttttat ccgattggta ctggttgtta gcgtagagta atgactatgg
      601 tccaactgga acccaaacgc taaagatgct ttaaagctct ctaaagttat ttttacgcag
      661 ttttcccctc tcttccatcg ccaccattac cagatgtaaa aaaatgcgcc agcgcgcgtt
      721 ttagatgcct taaaatcgat tttagatcgt catcttgatc tgcttgtctt ccttgaatcg
      781 aaaatgcagt gctgcaaccg tgcgcccctt cttgatcgtc tcaaccgtca caaccagatc
      841 gcttttttta ttcagttccg tgatacaggg ttttattagt atcttattta agtctctgaa
      901 ttgtttgtat ttattttcaa tacctaacat tgaacgaaag tcattaagag caataattct
      961 ctctcccgta ctgcggaatt gctggagaag ttcgtatatt cttatactgt aactgcttga
     1021 taaacctgat atgtttttta taacaacgcg cgtgaattgc cccttcagtt gcgtcagata
     1081 aggcattacc gcgtcagaga aggttattcg agccttggcc tcacctttag cgtactgtgc
     1141 gcgatactgg atccagcgga actcctcacg cttctcgtca tccttgagaa tgatcgacct
     1201 gtcccataaa cgatcgatcg cttcctgtaa ctgaacctcg gcatttttcc gccccatgtc
     1261 agggaatgaa tcaaaatatt ccgcggcggt aatggtcatt gttttttgca attcagcatc
     1321 agcaccagat ttcaatcgac tgatacacag caacagaaaa cgttgttcct gtagggtcag
     1381 tttgtagctg gcctcaacta gagcattcga cttgtaggca atcaagtccg acatacaaag
     1441 ctcccgttca aatgtggtga tactttaatg tgccccacaa ataagaaatg tggaatattt
     1501 ttttttatat cctcacattt ctgtgaataa caccttaaat tcctccacct ttaccttaaa
     1561 tccctccacc taaacacctt aaattcctcc acctttacct taaatccctc cacttataca
     1621 actgtaagcc attgatttta ataatgaatt tcacccctaa aacaagtatt aaaaacaaga
     1681 tcttaaaaac aagatctaaa aacttaacgg cgagcctgtg gaaaacttag gatgccaaaa
     1741 agaaaaactc agtaaaaaca atgcgttgca aaaaagcaga attgcaaatt ccgaatactc
     1801 cccctccagc cctgtggaaa tccagtattc atgcgggttc agcgcgtatc acctgccgaa
     1861 aaaccgtgcg tatgtgctca acctggctac gggttcactt ccgcttcctc gctcactcgc
     1921 tcgctaacgc ttggtcgctg gagctgcggc gagcggacgg tgtaatcacc gttctggcaa
     1981 tgcctccagc tcgtcaatca gtggctgtat cctgttcaag tcagcctgcc gtgtaacttc
     2041 tctccgcagg aacgggagca accaggcccg caactgcact tcctccggct ttctgacctt
     2101 tgccagcaat gctgcaccca caacgacctt ctgcgctgtg tccagactcc tgctcttcgc
     2161 cttcaggcgc tgcaatctgg cctcagcttc ggcaatcttc tgttcgagtg ttctgctcat
     2221 tccgtaactc cgtgcgcgat gaaaaatcgt attttatcgc gtcactggca gtttaaaaac
     2281 tgaactggca taatgcacgg cacatcacga agtgcgcact tatacaatct ccactccgtt
     2341 tcgattgtgt gcgccctgcg gggctgaaag aaaacgacaa aaaggcatta cggcagaaat
     2401 ggcgatttat catctcagca tgaaaatcat ctccagaaac agcggctaca gcgccgtcgc
     2461 ttctgctgcc tatcgttccg gttcactgat gcttgatgag cgtacaggac tgactcatga
     2521 ctacacccgc aaaagcggtg tggctgaagc tgtgattctg acccccgcga cagcccctgc
     2581 ctggtgtacg aaccgtgccg aactctggaa tgccgttgag aaggccgaac gccggaagaa
     2641 ctcacaactt gcgcgggaaa ttgaactcgc catcccccgc gaactgccgc aggatgccgc
     2701 acgggaaacc gttctcgcct ttgtcagaga aaactttgtc agtcagggca tgattgctga
     2761 tgtggcgttc catcacatgg ataaaacaaa tccccatgcg cacatcatgc tgaccacgag
     2821 ggctgtcgga cctgctggat tcggcggaaa ggtcagggac tggaacgacc ggacacatgc
     2881 tgaggcgtgg cgggcatcat gggctgacca tgcaaacagg gcactggcga acgccggtta
     2941 tcaggaagag atagaccatc gttcatacga gcgacagggg cttgagaaaa cgccgggtat
     3001 tcacctcgga aagtctgcct gtgcgatgga aacacgtggt atcgaaacag aacgcggcga
     3061 acagaatcgt ctgattaaca ggcttaacct ggaaatacag atttcccgca ccgaactcag
     3121 gaacggcggg ctgacagagc cagcccgccg tgtggctaac cttctgaata tcgggcttcc
     3181 tgacaacgca acttcgtaca cactacgtga catcatcgaa gcgttaccga aggacagtaa
     3241 tgcggcatgg aaactcacca gtaatgccat gtcgatgatg gcagatatgc aggcgacgcg
     3301 cagacgctgg gaagagctga acaccgaacg aaaggaagcg atgagccatg ctgccagcct
     3361 gaaaaaatca tcgccgtttt cgtccggttt ttcccgtatt cccctgatgc aatgggcggc
     3421 accggaatac cgtagtgagc agggaaaaat ccagtctctg agccagcaaa tggaaaaatt
     3481 gcgacagcat taccggaagg tggagaaaca ggacattccc gcgagtcaga cggcatttga
     3541 aaaacagtgg cagcagtggg ccgcatccgg ccttgcagct ctcagagccc agttgcttaa
     3601 acgtgaagag gaattacgca ggaaggagca ggaggataca gaacgtagtc gcgcggagcg
     3661 acgagcggaa cagctcagga aaaatgacaa tgccgttatg gattcagggg tactgagcgc
     3721 agtcgttacg gggtatggcg aggcccctat gcctggtaac tgggaaatga cctgttacct
     3781 tctgcttcac aaccggaacg gagaatatac gctctggggg aacgagttgg agaaataccg
     3841 caccaggatc tttgagcgtg ttgatttaat gcgtgacagg agtggttata tctgtgaccg
     3901 aagcgaaatc ggtcaacatc caccactgca acgtgtttat tcctctgcga cctttgagca
     3961 acttctgacg caggtttgcc agacatggcc gcaacatacc cgcaatctcc gccagccgaa
     4021 gacatggccg gagtcttttt gtcttggaga agaccgccag ccagccatgc catcactggc
     4081 agcaaggaag gtggatttta cgcagggacg tctgccaccg acgctgatgc cggtaatgag
     4141 ttctgtcgac cgggaaaccc gccagcttca gcttttgctg gtcatgggcg tggatgactc
     4201 tctgggcggt gttgtccggc ttaatggtac gctgtatcct gcgtttgccg tccccacagc
     4261 cgacaacagc cagctggtaa tcaatgctct gaccgacaaa ggtttacgat ttgccggtta
     4321 tggtgaagcg gtaaaccacg atgctgacag tccggcacgc cctgcgccag aacttatgct
     4381 gtttcatctg aaaacccgtg aggcaccgct ttttgctgcc gtcaatacac cagaaaaaca
     4441 gccggatcat ttgttccgct cgctgggttt taatcgcacc tgggacgaat ggcagcgcga
     4501 ggaatatgca cgaacacgcg tctccgacag gaaacatgag cgcggctggt tactttaaag
     4561 cactttccgc atacatattt tttatatggg cgaaaacaga ataattcgtt ttgagataga
     4621 aaatttcaac tctagtaggt agcgcaacga ccgtgattcg gcaaacggga gaaagaccgc
     4681 gcaatagccg tttcaggtat gataataaag cgattgctca gacattgaat tatgctgagc
     4741 tgtcggcagt ggaataacga cgcgtgaaga ccgtcataac taaaaaatgc cggataaata
     4801 aggaaaatca gtggctattg gcgatgatgc tatccgtgat gctttttatc tttttacaca
     4861 gcaagtcgct gaaatggata atgaatcact ccctaaagac gtctggggaa caccttgttt
     4921 cacttatttg atgactagaa aacaatttaa ccaaatgaag gtcatttgtc agaggaatgg
     4981 ttgggatgtg cccacatcac cggcgatacc tatcacttgg agtatgttca agcatgtgct
     5041 ctctgctcga aaatcgaagg ataaattaag ctggcaagaa tgcgcagaaa tct
//
