LOCUS       NZ_CP012684             4512 bp    DNA     circular CON 03-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain 33676
            plasmid p33676_4.5, complete sequence.
ACCESSION   NZ_CP012684
VERSION     NZ_CP012684.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03795193
            Assembly: GCF_001293505.1
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 4512)
  AUTHORS   Vinuesa,P., Silva,C. and Calva,E.
  TITLE     Complete genome sequencing of a multidrug-resistant and
            human-invasive Salmonella Typhimurium strain of the emerging
            sequence type 213 harboring a blaCMY-2-carrying IncF plasmid
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4512)
  AUTHORS   Vinuesa,P., Silva,C. and Calva,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-SEP-2015) Departamento de Microbiologia Molecular,
            Instituto de Biotecnologia, UNAM, Av. Universidad 3000, Cuernavaca,
            Morelos 62210, Mexico
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP2 v. 2.3.0.139497
            Assembly Name                     :: Senter_33676_1.0
            Long Assembly Name :: Salmonella enterica subsp. enterica serovar
            Typhimurium 33676 1.0
            Genome Coverage                   :: 119x
            Sequencing Technology             :: PacBio RS
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/03/2024 06:45:16
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,006
            CDSs (total)                      :: 4,885
            Genes (coding)                    :: 4,653
            CDSs (with protein)               :: 4,653
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 124 of 232
            Pseudo Genes (incomplete)         :: 116 of 232
            Pseudo Genes (internal stop)      :: 27 of 232
            Pseudo Genes (multiple problems)  :: 32 of 232
            Pseudo Genes (short protein)      :: 1 of 232
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP012684.1.
            Source DNA and bacteria are 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..4512
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="33676"
                     /serovar="Typhimurium"
                     /isolation_source="blood-culture"
                     /host="Homo sapiens; female"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="p33676_4.5"
                     /geo_loc_name="Mexico: Mexico City"
                     /lat_lon="19.43 N 99.13 W"
                     /collection_date="2011"
                     /collected_by="Juan J. Calva"
                     /genotype="ST213"
     gene            complement(253..444)
                     /locus_tag="SE15cs_RS24760"
                     /old_locus_tag="SE15cs_05072"
     CDS             complement(253..444)
                     /locus_tag="SE15cs_RS24760"
                     /old_locus_tag="SE15cs_05072"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            507..830
                     /locus_tag="SE15cs_RS24765"
                     /old_locus_tag="SE15cs_05073"
     CDS             507..830
                     /locus_tag="SE15cs_RS24765"
                     /old_locus_tag="SE15cs_05073"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1039..>1473
                     /locus_tag="SE15cs_RS28095"
                     /pseudo=""
     CDS             1039..>1473
                     /locus_tag="SE15cs_RS28095"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1508..2068
                     /locus_tag="SE15cs_RS27630"
                     /old_locus_tag="SE15cs_05074"
     CDS             1508..2068
                     /locus_tag="SE15cs_RS27630"
                     /old_locus_tag="SE15cs_05074"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2075..2308
                     /locus_tag="SE15cs_RS27635"
                     /old_locus_tag="SE15cs_05075"
     CDS             2075..2308
                     /locus_tag="SE15cs_RS27635"
                     /old_locus_tag="SE15cs_05075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2994..3833)
                     /locus_tag="SE15cs_RS24780"
                     /old_locus_tag="SE15cs_05076"
     CDS             complement(2994..3833)
                     /locus_tag="SE15cs_RS24780"
                     /old_locus_tag="SE15cs_05076"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(4025..4174)
                     /locus_tag="SE15cs_RS28220"
     CDS             complement(4025..4174)
                     /locus_tag="SE15cs_RS28220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     Typing          81..165
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          3833..4284
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          821..2406
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cggaagagcg cctgatgcgg cattttctcc ttacgcatct gtgcggtatt tcacaccgca
       61 tatggtgcac ttttcttata atccgcactg atgccacata gttaagccag tatacactcc
      121 gctatcgcta cgtgactggg tcagggctgc gccccgacac ccgctaaaac ccgctgacgc
      181 gccctgacgg gcttgtctgc tcccggcatc cgctcacagg caagctgtga acgtctccgg
      241 gagctgcatg tttcagttgc tttcaccgtc atcgccgaag cgtgcgaggc aactacggta
      301 gagttcgtcg gcgtggtcgt gaagtgattc gcagatgtct gcctgttcgt ccgcgtccag
      361 ctcgttgagt ttttccagca gggtcagcgt ctggcttctg ataaagcggg ccatgttaag
      421 ggctgttttt tcctgtttgg tcatggtctt aaggctcctt aataggggat tttttagggg
      481 gaatgatacc gatgaaacgc gagaagatgc tcacgatacg ggttagcgat gaggagcacg
      541 cccggttact ggaacgctgc gagggtaaac gactggcaga atggatgcgg cgggtctgtc
      601 tgggggagcc ggttgcgcgc acaggaaaac tgccgacact atcgccgcca ttgctgcggc
      661 atctggctgc catcgggaac aatctgaacc agacagcccg gaaggtgaac agcggccact
      721 ggtcttcgat tgaccgggtt catgtggtgg ccgctctgat ggccatcgag ggtgaattgc
      781 gccagttgcg gcaggctgtc agggaacagg ggggacggga tgatagttaa atttcatgcc
      841 agggggaaag gcggtggaag tggcccggtc gattacctgc tggggcggga gcgtaaccgc
      901 gaaggcgcaa cggtgctccg gggtaacccg gaagaaatcc gggaactcat tgatgccacg
      961 ccattttcga agaaatacac gtcaggcgtt ctgtcgttcg cggagaagga gttaccgccg
     1021 ggtgaacgcg aaagagtgat gacgagcttt gagcgtgttc ttatgcccgg tctcgaaaaa
     1081 gaccagtaca gcattctctg ggtggaacac caggataagg ggcggctcga actgaatttt
     1141 gtcattccga acatggaact acagagcggt aagcgcctcc agccgtacta cgaccgtgcg
     1201 gacaggccga ggataaatgc ctggcagacg ctggttaatc atcattacgg gctgcgtgac
     1261 ccgaacgcac cggagaacag acggacgctt gtcacaccga ataatctgcc aaaagcgaaa
     1321 caggaggccg cagaagcgat tacacggggt cttgaggcgc tttaccgtgc cggagcaata
     1381 aaaacgcgtc aggatgtcac tgaggcgctc acagcggcag gttttgaggt ggtgaggaca
     1441 accagaagca gtatcagtat tgccgacccg gagggggggc ggaatctcag gctaaagggg
     1501 gcgctgtatg agcaatcttt tacaaatggg aacggacttc gagaagaaac tgaaagagcg
     1561 agccgcttct accgagaaca tgctgaacag cgagttcagg aagctagaag agtctgtaga
     1621 caaggcactg agcttaaaca ggcagaaaat cagagacgct atcagcgaac atacaacatc
     1681 cgtgaaacag caactggata cgctgagcac caccgtgagc acgcagctca gcaccacaga
     1741 ggccgaactg tcccggcagc agaaaaacct gctctggcag gtgatcaaag ggcgggtact
     1801 gtttccggcg ctgaccgcgc tcagcgtcac gggcggcatt ttcctggggt gctgggggct
     1861 gattcagtgg caggaaagca ggattgcgaa aaatatcttg accatcagag agcaggaaaa
     1921 cacgctggcg aaactcgagg caaaaacctg gggggtgacg ttcgtcaatg gcgagaacgg
     1981 gaaatttctg gtgctgccgg acggggtgaa aggggaaaac acctggacgg tgggcgacaa
     2041 gaacgccgtg aggctggtca gggagtaaac gagtatgacg gaactggaag ggcatttgct
     2101 gaacgcctta gagcatttgc aacaggacta tatgcggcgg ctgaacgagt gggagagcgc
     2161 cttcgcagaa ttgcagaaga tgcacgcggt tacgcaacag aacaacgcga tactgaacga
     2221 gcgtgtcgtg aacttgagtc agcaggtgca gctattagcc ggacaagtcg accgcttgag
     2281 tcggttattt atcacgaaca acagataagg gatgaacagg agcgtcaggc gcaggagctt
     2341 gcccggcgct ggcatgaaga gcaggaaccc gaagcgcgga tctggcgtgg cccgtcaatg
     2401 gggatgtgac cggggtaccc ctgaaatcga gccagtttgt ggcacgccct acccggatgg
     2461 cgccaatgtt aatgtacgta cattagcatt aacaatatcc aaacctcccc attttgcccc
     2521 gttcgacggc tggaacgtgc gaaactgatc gtcattcagt ttcgcgcata actatgcatg
     2581 aggttaaaat ttaccaggcg cgatcgcggc agtttttcgg gtggtttgtt gctgttttta
     2641 cctgtctgct gccgtgatcg cgctgaacgc gtttaagcgg tacgcgcaat gcgacgttat
     2701 ggtaaatacg gagtatttta attgcgggcc tttgttgtat atctctgtcg tttgtccccg
     2761 ggggaagcat tactgctaac aagtcccgtg agaaaactgc gcaatcgtat tgcgcaccat
     2821 gaacctattc tcaaccgcaa tctggaggat gattttgcta cgataaagag aattatcgcg
     2881 tatcggtgtc agcattcatt ggagtggatg ctgaaaaacc aggtgttact ccctctactt
     2941 acacttaaac ctctctaaaa atataagtaa gtactatcga gggctatcat gaactatggt
     3001 gccctctgag catagctacc cattacttct tctatgtcat tgaataattc atttcttaac
     3061 tctaagtatt ctagtaactc catttctaat gactctgtcg tgaacttaaa tctagaagga
     3121 tctttgattg agtttactag tcttgataac gctctatatg ttttgagtga aggttgcatt
     3181 atagatggaa agtatttgaa aacctcttca tctctgttga aattaactaa aaacttgtag
     3241 tcatcattta taaatctcaa gcatacagcg tcaagcttat cgccttttct tattattatt
     3301 tctttatagg aaagatattt ttcagaagat aagtcccaca tcaagcgaaa atctctcttt
     3361 gcgaacgagt tcgcgtcatc attgaaaaga gatgatgtga tggctttgga tagaccttct
     3421 gtgtttatct ctttgttgga tgggtagtaa attttattaa ttgctttcat tctctcaaat
     3481 gatgaatata ggtcattatg ccaccttgtt gaaatcactc ctttagttat attctccttg
     3541 ctaaaattaa gccctgtatc aaaaataaat gcagccatca gtgaatatga tatgtttttt
     3601 attaactcag acttaaatgg ttccgctatg gagtagtaca gtgataaaat aactaaaaat
     3661 aaaaggtatt gtcttacctt tcccgatgag tatatgtaaa ggcgatattt atttattgat
     3721 agttttattt tgtatggaat gatctcattt ctgtcatatc ctcttcgtgg tggagcaaaa
     3781 caaaagaaac atgcagctat taataaaaca aaaaagatga acagtgtaag caagttcggc
     3841 tcctgtgtat gctcactatg catgattgtc ttgagatcta acgatcctga aggtagtctt
     3901 gtccgtaaac gaaaaaaccg cccagcaagg cggcttttcg aaggttctca gagcagcaac
     3961 tctttgaacc aaggtaactg gcttggagga gcacagccac caaatctgtc ctttcagttt
     4021 agccttaacc ggcgcataac ttcaagacta actcctctaa acggttacca atggctgctg
     4081 ccagtggcgt ttttacgtgt ctttccgggt tggactcaag acgatagtta ccggataagg
     4141 cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct
     4201 acaccgggcc gagataccaa cagcgtgagc tatgagaaag cgccacgctt cccgaaggga
     4261 gaaaggcgga caggtatccg gtaagcggca gggtcggaac aggagagcgc acgagggagc
     4321 ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctgacttg
     4381 agcatctgtt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gccagcggcg
     4441 cggccttctt cctgttcctg gccttttgct cacatgtttc ttttggcgtt atcccctgat
     4501 tctgtggata ac
//
