LOCUS       NZ_CP011435             2677 bp    DNA     circular CON 15-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain YU39
            isolate YUHS 05-78 plasmid pYU39_2.7, complete sequence.
ACCESSION   NZ_CP011435
VERSION     NZ_CP011435.1
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 2677)
  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 2677)
  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
            CP011435.1.
            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..2677
                     /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_2.7"
                     /geo_loc_name="Mexico: Yucatan"
                     /lat_lon="20.57 N 89.39 W"
                     /collection_date="2005"
                     /collected_by="Mussaret Zaidi"
                     /genotype="ST213"
     gene            451..612
                     /locus_tag="SE14_RS28965"
     CDS             451..612
                     /locus_tag="SE14_RS28965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /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_071527578.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDLSPLAAATGNRIRGVSLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            complement(825..1229)
                     /locus_tag="SE14_RS25545"
                     /old_locus_tag="SE14_05213"
     CDS             complement(825..1229)
                     /locus_tag="SE14_RS25545"
                     /old_locus_tag="SE14_05213"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000014067.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_046891382.1"
                     /translation="MSGGNNFKMSQDYEIAQPKKKMAYPILVEEWDFLIGKIESISDDE
                     NIYHTISSIFLGVAGSALIAALTLDLPSDDGYMPRQILISWYVFWASLICGVLSMFFGR
                     KNKKINRTSAKDIVQQMRLIEKRYEQGSMD"
                     /name="hypothetical protein"
     gene            complement(1226..1498)
                     /locus_tag="SE14_RS25550"
                     /old_locus_tag="SE14_05214"
     CDS             complement(1226..1498)
                     /locus_tag="SE14_RS25550"
                     /old_locus_tag="SE14_05214"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001286144.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001286144.1"
                     /translation="MSDVKSDQIIKYLSEKWGGSKCPLCKKGRWNVSDKIFELREFHEG
                     NVVIGAGPIVPIIPVTCDNCGNVVLVNAIISGCLSADNKQDGGSK"
                     /name="hypothetical protein"
     gene            complement(1857..2180)
                     /gene="mobA"
                     /locus_tag="SE14_RS25555"
                     /old_locus_tag="SE14_05215"
     CDS             complement(1857..2180)
                     /gene="mobA"
                     /locus_tag="SE14_RS25555"
                     /old_locus_tag="SE14_05215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2464..2658
                     /locus_tag="SE14_RS25560"
                     /old_locus_tag="SE14_05216"
     CDS             2464..2658
                     /locus_tag="SE14_RS25560"
                     /old_locus_tag="SE14_05216"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041622.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALNADEQAAMCEKLHELA
                     EELQNSIQTRFEAENLTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2190..2426)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.49e-121"
     Typing          16..520
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.528"
                     /coverage="95.0"
                     /evalue="2.2999999999999997e-156"
     Typing          complement(1861..2180)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="9.47e-63"
ORIGIN
        1 aacggcatag aggagcgtaa ggagaaaatg tcacataagg cgctcttccg cttcctcgct
       61 cactgactcg ctacgctcgg tcgttcgact gcggcgagcg gtgtcagctc actcaaaggc
      121 ggtaatacgg ttatccacag aatcggggga taaaaccgga aagaacatgt gagcaaaaga
      181 caaagaccca gaagaagggc gcgcgggagg cgtttttcca taggctccgc ccccctgacg
      241 agcatcataa aaaccgacgc tcaagtcaga ggtggcgaaa cccgacagga ctataaagat
      301 accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttcctgcc tttcggttta
      361 ccaatgtcat tccgcagtta tggccgcgtt tatctcattc cacgcctgac actcagttcc
      421 gggtaggcag ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgaccgc
      481 tgcgccttat ccggtaacta tcgacttgaa tccaacccgg aaagacacga cttatcgcca
      541 ctggcagcag ccactggtaa ccgaattaga ggagttagcc ttgaagtcat gcgcctgtta
      601 aggctaaact gaaagaacaa gttttggtga ctgcgctcct ccaagccagt tacctcggct
      661 caaagagttg gtagctctga gaaccttcga aaaaccacct tgccgggtgg ttttttcgtt
      721 tcatagacaa gagactacga cgacaagaca aggatctcaa gaagatcctt acattatgcc
      781 ccccccttgg cacgccgtaa cctcgctaaa cgttcagcat ccagttaatc catactacct
      841 tgctcgtaac gtttctctat caatctcatt tgttgcacaa tatccttcgc agaagttcta
      901 ttaatctttt tattctttct accaaaaaac atagaaagca ctccacaaat aaggcttgcc
      961 caaaatacgt accatgaaat taatatctgc cttggcatat aaccatcatc tgatggcaaa
     1021 tctaaagtta atgctgctat caatgccgag ccagccacac ctaaaaatat agaactaatc
     1081 gtatggtata tattttcatc atcactaata ctttctattt tccctattaa aaaatcccat
     1141 tcttcaacaa gaatagggta agccattttc ttttttggtt gagcaatttc atagtcctga
     1201 gacattttaa aattattacc accactcact ttgagcctcc atcttgctta ttgtcagcag
     1261 ataagcaccc tgagataatg gcattaacaa gaacaacatt cccgcaatta tcacaagtta
     1321 caggaataat tgggactatc ggacctgccc caataacaac attaccttca tgaaattctc
     1381 ttagttcaaa aattttgtca gaaacattcc aacgcccttt tttacacaag ggacatttgc
     1441 tccctcccca cttttcagac aaatatttaa ttatttgatc tgacttaaca tcactcatat
     1501 tccctccaag cattccttat actcatatat ttattagcga acaatcacat cactcaataa
     1561 tttattgatc aagtaacttt atagagtaca tccatatctg ttttgtgcgc aaaaaaacat
     1621 aaatataaaa tcttacattt accataatac cagtattgta cgcaccgctg aaacgcgctg
     1681 aacgcgattc tgacgcagac accgcaaaaa gagatgtttt accccgggaa aacaggaagg
     1741 atgcgtcagg atcgttttca gctcgctgca tagctatgca tgaaagcgaa tggtgatcac
     1801 tttgggagct tacggtgttc ataccgtctg ttttcgacag ttttctctcc gggaagctaa
     1861 tctgccataa gtctggataa cagggcacgg tgatactccg taatagcgat cagcacctcc
     1921 gcatactccc tgtccccgac acgcttgccg tcgataaaga gttttttctg taacgccccc
     1981 agtctcataa cttctttcag tacccgatca tcagtcagtg agttaacttt cttaccgaga
     2041 gctgccgccc gtaaaaaacc ggaaacggtc ttgccgcatt cagcagccct ttttctgatt
     2101 tcctggtctt cttctgccgt cagacgaaca gggcgactga tagcccgcct gcgcgtatta
     2161 cttccacttc gttttgtcat aaaacatggc tccgtatctg acatgggtgt cggggcaaag
     2221 ccctgaccag ggcaattgta atagcgtgca tgtatgcgcg gtataacaat tgcacatcct
     2281 gtcctgtcag caagctcgaa ttaccgacaa aggcacggca gttttttggc agtgacagtg
     2341 ttgtctgaca gaaatgcccg tcaaaaagcc aagcggcaga atagcggcag caaaacagtc
     2401 gaaaagtggt acgcgatata atcacacaac gcagatgaca gacagaacgg agaaaacgaa
     2461 aagatgaaca agcagcagca agccgtactc aacatggcgg gattcataaa aagtcagagc
     2521 ctgacgctgc tcgaaaaact ggacgcactc aatgccgacg aacaggccgc catgtgtgag
     2581 aaactgcacg aactcgcaga agaactccag aacagcatac agacacgctt tgaagcggaa
     2641 aatcttaccg ggatataacg ctccagacag gatgcag
//
