LOCUS       NZ_CP035550             4593 bp    DNA     circular CON 22-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            YU07-18 plasmid pYU07-18_ColRNAI, complete sequence.
ACCESSION   NZ_CP035550
VERSION     NZ_CP035550.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10076457
            Assembly: GCF_011304815.1
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 4593)
  AUTHORS   Vinuesa,P., Silva,C., Calva,E. and Puente,J.L.
  TITLE     Evolutionary genomics of Salmonella Typhimurium ST213
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4593)
  AUTHORS   Vinuesa,P., Silva,C., Calva,E. and Puente,J.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-JAN-2019) Ingenieria Genomica, Centro de Ciencias
            Genomicas - UNAM, Avenida Universidad 2001, Cuernavaca, Mor. 62210,
            Mexico
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 06-AUG-2018
            Assembly Method                   :: unicycler v. 0.4.5
            Assembly Name                     :: YU07-18_hybrid_MinION_MiSeq
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 295x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_011304815.1-RS_2024_03_22
            Annotation Date                   :: 03/22/2024 04:05:46
            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)                     :: 5,046
            CDSs (total)                      :: 4,920
            Genes (coding)                    :: 4,717
            CDSs (with protein)               :: 4,717
            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)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 118 of 203
            Pseudo Genes (incomplete)         :: 89 of 203
            Pseudo Genes (internal stop)      :: 30 of 203
            Pseudo Genes (multiple problems)  :: 31 of 203
            Pseudo Genes (short protein)      :: 1 of 203
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035550.1.
            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..4593
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="YU07-18"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pYU07-18_ColRNAI"
                     /geo_loc_name="Mexico: Yucatan"
                     /lat_lon="20.40 N 89.13 W"
                     /collection_date="2007"
                     /collected_by="M. Zaidi"
                     /genotype="ST213"
     gene            complement(144..293)
                     /locus_tag="D6D39_RS25615"
     CDS             complement(144..293)
                     /locus_tag="D6D39_RS25615"
                     /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            complement(963..1154)
                     /locus_tag="D6D39_RS25080"
                     /old_locus_tag="D6D39_25540"
     CDS             complement(963..1154)
                     /locus_tag="D6D39_RS25080"
                     /old_locus_tag="D6D39_25540"
                     /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            1217..1540
                     /locus_tag="D6D39_RS25085"
                     /old_locus_tag="D6D39_25545"
     CDS             1217..1540
                     /locus_tag="D6D39_RS25085"
                     /old_locus_tag="D6D39_25545"
                     /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            1749..>2183
                     /locus_tag="D6D39_RS25490"
                     /pseudo=""
     CDS             1749..>2183
                     /locus_tag="D6D39_RS25490"
                     /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            2218..2778
                     /locus_tag="D6D39_RS25095"
                     /old_locus_tag="D6D39_25555"
     CDS             2218..2778
                     /locus_tag="D6D39_RS25095"
                     /old_locus_tag="D6D39_25555"
                     /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            2785..3018
                     /locus_tag="D6D39_RS25100"
                     /old_locus_tag="D6D39_25560"
     CDS             2785..3018
                     /locus_tag="D6D39_RS25100"
                     /old_locus_tag="D6D39_25560"
                     /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(3706..4545)
                     /locus_tag="D6D39_RS25105"
                     /old_locus_tag="D6D39_25570"
     CDS             complement(3706..4545)
                     /locus_tag="D6D39_RS25105"
                     /old_locus_tag="D6D39_25570"
                     /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          791..875
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(222..780)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.583"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1531..3116
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.811"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgatcctgaa ggtagtcttg tccgtaaacg aaaaaaccgc ccagcaaggc ggcttttcga
       61 aggttctcag agcagcaact ctttgaacca aggtaactgg cttggaggag cacagccacc
      121 aaatctgtcc tttcagttta gccttaaccg gcgcataact tcaagactaa ctcctctaaa
      181 cggttaccaa tggctgctgc cagtggcgtt tttacgtgtc tttccgggtt ggactcaaga
      241 cgatagttac cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc
      301 agcttggagc gaacgaccta caccgggccg agataccaac agcgtgagct atgagaaagc
      361 gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca
      421 ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag tcctgtcggg
      481 tttcgccacc tctgacttga gcatctgttt ttgtgatgct cgtcaggggg gcggagccta
      541 tggaaaaacg ccagcggcgc agccttcttc ctgttcctgg ccttttgctc acatgtttct
      601 tttggcgtta tcccctgatt ctgtggataa ccgcatcacc gtctttgagt gagctgatac
      661 cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg
      721 cctgatgcgg cattttctcc ttacgcatct gtgcggtatt tcacaccgca tatggtgcac
      781 ttttcttata atccgcactg atgccacata gttaagccag tatacactcc gctatcgcta
      841 cgtgactggg tcagggctgc gccccgacac ccgctaaaac ccgctgacgc gccctgacgg
      901 gcttgtctgc tcccggcatc cgctcacagg caagctgtga acgtctccgg gagctgcatg
      961 tttcagttgc tttcaccgtc atcgccgaag cgtgcgaggc aactacggta gagttcgtcg
     1021 gcgtggtcgt gaagtgattc gcagatgtct gcctgttcgt ccgcgtccag ctcgttgagt
     1081 ttttccagca gggtcagcgt ctggcttctg ataaagcggg ccatgttaag ggctgttttt
     1141 tcctgtttgg tcatggtctt aaggctcctt aataggggat tttttagggg gaatgatacc
     1201 gatgaaacgc gagaagatgc tcacgatacg ggttagcgat gaggagcacg cccggttact
     1261 ggaacgctgc gagggtaaac gactggcaga atggatgcgg cgggtctgtc tgggggagcc
     1321 ggttgcgcgc acaggaaaac tgccgacact atcgccgcca ttgctgcggc atctggctgc
     1381 catcgggaac aatctgaacc agacagcccg gaaggtgaac agcggccact ggtcttcgat
     1441 tgaccgggtt catgtggtgg ccgctctgat ggccatcgag ggtgaattgc gccagttgcg
     1501 gcaggctgtc agggaacagg ggggacggga tgatagttaa atttcatgcc agggggaaag
     1561 gcggtggaag tggcccggtc gattacctgc tggggcggga gcgtaaccgc gaaggcgcaa
     1621 cggtgctccg gggtaacccg gaagaaatcc gggaactcat tgatgccacg ccattttcga
     1681 agaaatacac gtcaggcgtt ctgtcgttcg cggagaagga gttaccgccg ggtgaacgcg
     1741 aaagagtgat gacgagcttt gagcgtgttc ttatgcccgg tctcgaaaaa gaccagtaca
     1801 gcattctctg ggtggaacac caggataagg ggcggctcga actgaatttt gtcattccga
     1861 acatggaact acagagcggt aagcgcctcc agccgtacta cgaccgtgcg gacaggccga
     1921 ggataaatgc ctggcagacg ctggttaatc atcattacgg gctgcgtgac ccgaacgcac
     1981 cggagaacag acggacgctt gtcacaccga ataatctgcc aaaagcgaaa caggaggccg
     2041 cagaagcgat tacacggggt cttgaggcgc tttaccgtgc cggagcaata aaaacgcgtc
     2101 aggatgtcac tgaggcgctc acagcggcag gttttgaggt ggtgaggaca accagaagca
     2161 gtatcagtat tgccgacccg gagggggggc ggaatctcag gctaaagggg gcgctgtatg
     2221 agcaatcttt tacaaatggg aacggacttc gagaagaaac tgaaagagcg agccgcttct
     2281 accgagaaca tgctgaacag cgagttcagg aagctagaag agtctgtaga caaggcactg
     2341 agcttaaaca ggcagaaaat cagagacgct atcagcgaac atacaacatc cgtgaaacag
     2401 caactggata cgctgagcac caccgtgagc acgcagctca gcaccacaga ggccgaactg
     2461 tcccggcagc agaaaaacct gctctggcag gtgatcaaag ggcgggtact gtttccggcg
     2521 ctgaccgcgc tcagcgtcac gggcggcatt ttcctggggt gctgggggct gattcagtgg
     2581 caggaaagca ggattgcgaa aaatatcttg accatcagag agcaggaaaa cacgctggcg
     2641 aaactcgagg caaaaacctg gggggtgacg ttcgtcaatg gcgagaacgg gaaatttctg
     2701 gtgctgccgg acggggtgaa aggggaaaat acctggacgg tgggcgacaa gaacgccgtg
     2761 aggctggtca gggagtaaac gagtatgacg gaactggaag ggcatttgct gaacgcctta
     2821 gagcatttgc aacaggacta tatgcggcgg ctgaacgagt gggagagcgc cttcgcagaa
     2881 ttgcagaaga tgcacgcggt tacgcaacag aacaacgcga tactgaacga gcgtgtcgtg
     2941 aacttgagtc agcaggtgca gctattagcc ggacaagtcg accgcttgag tcggttattt
     3001 atcacgaaca acagataagg gatgaacagg agcgtcaggc gcaggagctt gcccggcgct
     3061 ggcatgaaga gcaggaaccc gaagcgcgga tctggcgtgg cccgtcaatg gggatgtgac
     3121 cggggtaccc cctgaaatcg agccagtttg tggcacgccc tacccggatg gcgccaatgt
     3181 taatgtacgt acattagcat taacaatatc caaacctccc cattttgccc cgttcgacgg
     3241 ctggaacgtg cgaaactgat cgtcattcag tttcgcgcat aactatgcat gaggttaaaa
     3301 tttaccaggc gcgatcgcgg cagtttttcg ggtggtttgt tgctgttttt acctgtctgc
     3361 tgccgtgatc gcgctgaacg cgtttaagcg gtacgcgcaa tgcgacgtta tggtaaatac
     3421 ggagtatttt aattgcgggc ctttgttgta tatctctgtc gtttgtcccc ggggggaagc
     3481 attactgcta acaagtcccg tgagaaaact gcgcaatcgt attgcgcacc atgaacctat
     3541 tctcaaccgc aatctggagg atgattttgc tacgataaag agaattatcg cgtatcggtg
     3601 tcagcattca ttggagtgga tgctgaaaaa ccaggtgtta ctccctctac ttacacttaa
     3661 acctctctaa aaatataagt aagtactatc gagggctatc atgaactatg gtgccctctg
     3721 agcatagcta cccattactt cttctatgtc attgaataat tcatttctta actctaagta
     3781 ttctagtaac tccatttcta atgactctgt cgtgaactta aatctagaag gatctttgat
     3841 tgagtttact agtcttgata acgctctata tgttttgagt gaaggttgca ttatagatgg
     3901 aaagtatttg aaaacctctt catctctgtt gaaattaact aaaaacttgt agtcatcatt
     3961 tataaatctc aagcatacag cgtcaagctt atcgcctttt cttattatta tttctttata
     4021 ggaaagatat ttttcagaag ataagtccca catcaagcga aaatctctct ttgcgaacga
     4081 gttcgcgtca tcattgaaaa gagatgatgt gatggctttg gatagacctt ctgtgtttat
     4141 ctctttgttg gatgggtagt aaattttatt aattgctttc attctctcaa atgatgaata
     4201 taggtcatta tgccaccttg ttgaaatcac tcctttagtt atattctcct tgctaaaatt
     4261 aagccctgta tcaaaaataa atgcagccat cagtgaatat gatatgtttt ttattaactc
     4321 agacttaaat ggttccgcta tggagtagta cagtgataaa ataactaaaa ataaaaggta
     4381 ttgtcttacc tttcccgatg agtatatgta aaggcgatat ttatttattg atagttttat
     4441 tttgtatgga atgatctcat ttctgtcata tcctcttcgt ggtggagcaa aacaaaagaa
     4501 acatgcagct attaataaaa caaaaaagat gaacagtgta agcaagttcg gctcctgtgt
     4561 atgctcacta tgcatgattg tcttgagatc taa
//
