LOCUS       NZ_CP011433             4800 bp    DNA     circular CON 15-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain YU39
            isolate YUHS 05-78 plasmid pYU39_4.8, complete sequence.
ACCESSION   NZ_CP011433
VERSION     NZ_CP011433.1
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 4800)
  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 4800)
  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
            CP011433.1.
            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..4800
                     /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_4.8"
                     /geo_loc_name="Mexico: Yucatan"
                     /lat_lon="20.57 N 89.39 W"
                     /collection_date="2005"
                     /collected_by="Mussaret Zaidi"
                     /genotype="ST213"
     gene            complement(266..499)
                     /locus_tag="SE14_RS28290"
                     /old_locus_tag="SE14_05201"
     CDS             complement(266..499)
                     /locus_tag="SE14_RS28290"
                     /old_locus_tag="SE14_05201"
                     /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(506..1066)
                     /locus_tag="SE14_RS28295"
                     /old_locus_tag="SE14_05202"
     CDS             complement(506..1066)
                     /locus_tag="SE14_RS28295"
                     /old_locus_tag="SE14_05202"
                     /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            complement(<1101..1754)
                     /locus_tag="SE14_RS28815"
                     /pseudo=""
     CDS             complement(<1101..1754)
                     /locus_tag="SE14_RS28815"
                     /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            complement(1744..2067)
                     /locus_tag="SE14_RS25500"
                     /old_locus_tag="SE14_05203"
     CDS             complement(1744..2067)
                     /locus_tag="SE14_RS25500"
                     /old_locus_tag="SE14_05203"
                     /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            2130..2321
                     /locus_tag="SE14_RS25505"
                     /old_locus_tag="SE14_05204"
     CDS             2130..2321
                     /locus_tag="SE14_RS25505"
                     /old_locus_tag="SE14_05204"
                     /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            2991..3140
                     /locus_tag="SE14_RS28960"
     CDS             2991..3140
                     /locus_tag="SE14_RS28960"
                     /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"
     gene            3332..4171
                     /locus_tag="SE14_RS25510"
                     /old_locus_tag="SE14_05206"
     CDS             3332..4171
                     /locus_tag="SE14_RS25510"
                     /old_locus_tag="SE14_05206"
                     /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"
     Typing          complement(2410..2494)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(2882..3333)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(169..1754)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttatgcgcg aaactgaatg acgatcagtt tcgcacgttc cagccgtcga acggggcaaa
       61 atggggaggt ttggatattg ttaatgctaa tgtacgtaca ttaacattgg cgccatccgg
      121 gtagggcgtg ccacaaactg gctcgatttc agggggtacc ccggtcacat ccccattgac
      181 gggccacgcc agatccgcgc ttcgggttcc tgctcttcat gccagcgccg ggcaagctcc
      241 tgcgcctgac gctcctgttc atcccttatc tgttgttcgt gataaataac cgactcaagc
      301 ggtcgacttg tccggctaat agctgcacct gctgactcaa gttcacgaca cgctcgttca
      361 gtatcgcgtt gttctgttgc gtaaccgcgt gcatcttctg caattctgcg aaggcgctct
      421 cccactcgtt cagccgccgc atatagtcct gttgcaaatg ctctaaggcg ttcagcaaat
      481 gcccttccag ttccgtcata ctcgtttact ccctgaccag cctcacggcg ttcttgtcgc
      541 ccaccgtcca ggtgttttcc cctttcaccc cgtccggcag caccagaaat ttcccgttct
      601 cgccattgac gaacgtcacc ccccaggttt ttgcctcgag tttcgccagc gtgttttcct
      661 gctctctgat ggtcaagata tttttcgcaa tcctgctttc ctgccactga atcagccccc
      721 agcaccccag gaaaatgccg cccgtgacgc tgagcgcggt cagcgccgga aacagtaccc
      781 gccctttgat cacctgccag agcaggtttt tctgctgccg ggacagttcg gcctctgtgg
      841 tgctgagctg cgtgctcacg gtggtgctca gcgtatccag ttgctgtttc acggatgttg
      901 tatgttcgct gatagcgtct ctgattttct gcctgtttaa gctcagtgcc ttgtctacag
      961 actcttctag cttcctgaac tcgctgttca gcatgttctc ggtagaagcg gctcgctctt
     1021 tcagtttctt ctcgaagtcc gttcccattt gtaaaagatt gctcatacag cgcccccttt
     1081 agcctgagat tccgcccccc ctccgggtcg gcaatactga tactgcttct ggttgtcctc
     1141 accacctcaa aacctgccgc tgtgagcgcc tcagtgacat cctgacgcgt ttttattgct
     1201 ccggcacggt aaagcgcctc aagaccccgt gtaatcgctt ctgcggcctc ctgtttcgct
     1261 tttggcagat tattcggtgt gacaagcgtc cgtctgttct ccggtgcgtt cgggtcacgc
     1321 agcccgtaat gatgattaac cagcgtctgc caggcattta tcctcggcct gtccgcacgg
     1381 tcgtagtacg gctggaggcg cttaccgctc tgtagttcca tgttcggaat gacaaaattc
     1441 agttcgagcc gccccttatc ctggtgttcc acccagagaa tgctgtactg gtctttttcg
     1501 agaccgggca taagaacacg ctcaaagctc gtcatcactc tttcgcgttc acccggcggt
     1561 aactccttct ccgcgaacga cagaacgcct gacgtgtatt tcttcgaaaa tggcgtggca
     1621 tcaatgagtt cccggatttc ttccgggtta ccccggagca ccgttgcgcc ttcgcggtta
     1681 cgctcccgcc ccagcaggta atcgaccggg ccacttccac cgcctttccc cctggcatga
     1741 aatttaacta tcatcccgtc ccccctgttc cctgacagcc tgccgcaact ggcgcaattc
     1801 accctcgatg gccatcagag cggccaccac atgaacccgg tcaatcgaag accagtggcc
     1861 gctgttcacc ttccgggctg tctggttcag attgttcccg atggcagcca gatgccgcag
     1921 caatggcggc gatagtgtcg gcagttttcc tgtgcgcgca accggctccc ccagacagac
     1981 ccgccgcatc cattctgcca gtcgtttacc ctcgcagcgt tccagtaacc gggcgtgctc
     2041 ctcatcgcta acccgtatcg tgagcatctt ctcgcgtttc atcggtatca ttccccctaa
     2101 aaaatcccct attaaggagc cttaagacca tgaccaaaca ggaaaaaaca gcccttaaca
     2161 tggcccgctt tatcagaagc cagacgctga ccctgctgga aaaactcaac gagctggacg
     2221 cggacgaaca ggcagacatc tgcgaatcac ttcacgacca cgccgacgaa ctctaccgta
     2281 gttgcctcgc acgcttcggc gatgacggtg aaagcaactg aaacatgcag ctcccggaga
     2341 cgttcacagc ttgcctgtga gcggatgccg ggagcagaca agcccgtcag ggcgcgtcag
     2401 cgggttttag cgggtgtcgg ggcgcagccc tgacccagtc acgtagcgat agcggagtgt
     2461 atactggctt aactatgtgg catcagtgcg gattataaga aaagtgcacc atatgcggtg
     2521 tgaaataccg cacagatgcg taaggagaaa atgccgcatc aggcgctctt ccgcttcctc
     2581 gctcactgac tcgctacgct cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa
     2641 gacggtgatg cggttatcca cagaatcagg ggataacgcc aaaagaaaca tgtgagcaaa
     2701 aggccaggaa caggaagaag gctgcgccgc tggcgttttt ccataggctc cgcccccctg
     2761 acgagcatca caaaaacaga tgctcaagtc agaggtggcg aaacccgaca ggactataaa
     2821 gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc
     2881 ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac
     2941 gctgttggta tctcggcccg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac
     3001 cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg
     3061 aaagacacgt aaaaacgcca ctggcagcag ccattggtaa ccgtttagag gagttagtct
     3121 tgaagttatg cgccggttaa ggctaaactg aaaggacaga tttggtggct gtgctcctcc
     3181 aagccagtta ccttggttca aagagttgct gctctgagaa ccttcgaaaa gccgccttgc
     3241 tgggcggttt tttcgtttac ggacaagact accttcagga tcgttagatc tcaagacaat
     3301 catgcatagt gagcatacac aggagccgaa cttgcttaca ctgttcatct tttttgtttt
     3361 attaatagct gcatgtttct tttgttttgc tccaccacga agaggatatg acagaaatga
     3421 gatcattcca tacaaaataa aactatcaat aaataaatat cgcctttaca tatactcatc
     3481 gggaaaggta agacaatacc ttttattttt agttatttta tcactgtact actccatagc
     3541 ggaaccattt aagtctgagt taataaaaaa catatcatat tcactgatgg ctgcatttat
     3601 ttttgataca gggcttaatt ttagcaagga gaatataact aaaggagtga tttcaacaag
     3661 gtggcataat gacctatatt catcatttga gagaatgaaa gcaattaata aaatttacta
     3721 cccatccaac aaagagataa acacagaagg tctatccaaa gccatcacat catctctttt
     3781 caatgatgac gcgaactcgt tcgcaaagag agattttcgc ttgatgtggg acttatcttc
     3841 tgaaaaatat ctttcctata aagaaataat aataagaaaa ggcgataagc ttgacgctgt
     3901 atgcttgaga tttataaatg atgactacaa gtttttagtt aatttcaaca gagatgaaga
     3961 ggttttcaaa tactttccat ctataatgca accttcactc aaaacatata gagcgttatc
     4021 aagactagta aactcaatca aagatccttc tagatttaag ttcacgacag agtcattaga
     4081 aatggagtta ctagaatact tagagttaag aaatgaatta ttcaatgaca tagaagaagt
     4141 aatgggtagc tatgctcaga gggcaccata gttcatgata gccctcgata gtacttactt
     4201 atatttttag agaggtttaa gtgtaagtag agggagtaac acctggtttt tcagcatcca
     4261 ctccaatgaa tgctgacacc gatacgcgat aattctcttt atcgtagcaa aatcatcctc
     4321 cagattgcgg ttgagaatag gttcatggtg cgcaatacga ttgcgcagtt ttctcacggg
     4381 acttgttagc agtaatgctt ccccccgggg acaaacgaca gagatataca acaaaggccc
     4441 gcaattaaaa tactccgtat ttaccataac gtcgcattgc gcgtaccgct taaacgcgtt
     4501 cagcgcgatc acggcagcag acaggtaaaa acagcaacaa accacccgaa aaactgccgc
     4561 gatcgcgcct ggtaaatttt aacctcatgc atagttatgc gcgaaactga atgacgatca
     4621 gtttcgcacg ttccagccgt cgaacggggc aaaatgggga ggtttggata ttgttaatgc
     4681 taatgtacgt acattaacat tggcgccatc cgggtagggc gtgccacaaa ctggctcgat
     4741 ttcagggggt accccggtca catccccatt gacgggccac gccagatccg cgcttcgggt
//
