LOCUS       CP123679                5310 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS11922684 plasmid pFSIS11922684-3, complete sequence.
ACCESSION   CP123679
VERSION     CP123679.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN12280429
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5310)
  AUTHORS   Ge,B., Mukherjee,S., Li,C., Harrison,L.B., Hsu,C.H., Tran,T.T.,
            Whichard,J.M., Dessai,U., Singh,R., Gilbert,J.M., Strain,E.A.,
            McDermott,P.F. and Zhao,S.
  TITLE     Genomic analysis of azithromycin-resistant Salmonella from food
            animals at slaughter and processing, and retail meats, 2011-2021,
            United States
  JOURNAL   Microbiol Spectr 12 (1), e0348523 (2024)
   PUBMED   37991374
REFERENCE   2  (bases 1 to 5310)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (16-JUL-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 5310)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-SEP-2021
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 424x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 10:48:06
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,021
            CDSs (total)                      :: 4,898
            Genes (coding)                    :: 4,762
            CDSs (with protein)               :: 4,762
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 48 of 136
            Pseudo Genes (incomplete)         :: 101 of 136
            Pseudo Genes (internal stop)      :: 19 of 136
            Pseudo Genes (multiple problems)  :: 31 of 136
            Pseudo Genes (short protein)      :: 1 of 136
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..5310
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="FSIS11922684"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pFSIS11922684-3"
                     /geo_loc_name="USA:MI"
                     /collection_date="2019"
                     /collected_by="USDA-FSIS"
     gene            complement(415..648)
                     /locus_tag="FOF40_25065"
     CDS             complement(415..648)
                     /locus_tag="FOF40_25065"
                     /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="WGN83554.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(655..1185)
                     /locus_tag="FOF40_25070"
     CDS             complement(655..1185)
                     /locus_tag="FOF40_25070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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="WGN83555.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(1223..1654)
                     /locus_tag="FOF40_25075"
                     /pseudo=""
     CDS             complement(1223..1654)
                     /locus_tag="FOF40_25075"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; 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(1863..2186)
                     /locus_tag="FOF40_25080"
     CDS             complement(1863..2186)
                     /locus_tag="FOF40_25080"
                     /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="WGN83558.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2251..2442
                     /locus_tag="FOF40_25085"
     CDS             2251..2442
                     /locus_tag="FOF40_25085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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="WGN83556.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2465..2785)
                     /locus_tag="FOF40_25090"
     CDS             complement(2465..2785)
                     /locus_tag="FOF40_25090"
                     /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="WGN83557.1"
                     /translation="MDNRVSVFEKGESARRSRTTERSESVSEEAEERLNWHFLLTHLCG
                     ISHRTWRTFHTIRTDAEWLSQYTLRYRYVTGSGLRPDTPKVNGLTRPGGLVCSRHPLTD
                     KL"
                     /name="hypothetical protein"
     gene            3627..3899
                     /locus_tag="FOF40_25095"
                     /pseudo=""
     CDS             3627..3899
                     /locus_tag="FOF40_25095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_021138877.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(3909..4724)
                     /locus_tag="FOF40_25100"
     CDS             complement(3909..4724)
                     /locus_tag="FOF40_25100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /protein_id="WGN83553.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(4870..4965)
                     /locus_tag="FOF40_25105"
                     /pseudo=""
     CDS             complement(4870..4965)
                     /locus_tag="FOF40_25105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013356662.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="amino acid ABC transporter substrate-binding
                     protein"
                     /name="amino acid ABC transporter substrate-binding
                     protein"
     ARG             complement(3913..4724)
                     /name="aph(3')-Ia"
                     /gene="aph(3')-Ia"
                     /gene_name="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2537..2618)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(3075..3262)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(312..1873)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgtaaaacga aataatttat tatcgttacc gatattttaa aaaaatcatt atttgcacag
       61 tgttcgagtt gttagtatca ctccttcctg aaaatccgct ccatttacca taacgtcgca
      121 ttgtacgcac cgccaaaacg cgttcggtgc gatcacggca gcagacaggt aaaaatggca
      181 acaaaccacc cgaaaaactg ccgcgatcgc acctgataaa ttttaaccgc atgaatacct
      241 atgcaaccag atgctacagg ccacattagc ccgccttaat ccactgaaca cgtcattttt
      301 catggtttca ccatcccagc gaagggccat ccagtgtccg ctcctggatt tccggctgac
      361 gctcccgctc cagagataac tcatgttcgc gttcctgcat cagccgttca tcccttatct
      421 cctgttctcg ctgtataact ggctcaagcg ttctgtccgc tcgctcaagt gctgcacctg
      481 ctgactcaac tgcatgactc gcccgttcag catcgcgttg tcccgttgcg taagcgaaaa
      541 cattttctgc aattccacga aggcgttctc ccattcgttc agccgctgca tatagtcctg
      601 ttgcagttgc tctaatgcgt tcagcaaatg tctttccagc tccgtcatgc tctgtcactc
      661 ctgcaccagt ctcactgcgt tcagtttgcc gttgtccttc gtccagttcg tttcggcttt
      721 catccccttc ggcaacacca gaaaacgtcc gttgctgtcc tcgtgataac gcacgcccca
      781 tgtcttcgcg ttcagcttct ccagactctc tttctgctcg cggagaatat tcatattcgc
      841 gtttatcttc atgccctggt accacagcag actcccggtc gtggcaaaca tcagtactga
      901 gacgataatc agccacagcc agcgtttcac gctcattttc agtacggttt tccagtgcgc
      961 gtccatcgta tcgacggtcg ttttctgata cctctccagc agttctttca gggctgttgt
     1021 atggtcgttg atagcgttcc tgattaaaga ttcgtttgag gtcagttccc tgtttacaga
     1081 ttcttcgagc ttcctgaact cgtcgttcag cattttctct gtagattcgg ctctctcttt
     1141 cagctttttc tcgaactccg cgcccgtctg taaaagattg ctcataaaac gctcctttca
     1201 gtctgatatt cctcccgccg ttcgggtctg caatgctgat actgcttcgc gtcaccctga
     1261 ccacttcaag ccccgcctct gtgagcgcct gaatcacatc ctgacggcct tttatctctc
     1321 cggcatggta aagcgcgtct atcccgcgtg tgacgccctc agcaagcgcc tgtttcgttt
     1381 ccggcaggtt atcaggaagg gtcagcgtcc ggcggttctc cggggcgttg gggtcatgca
     1441 gaccgtaatg gtgattcacc agcgtctgcc aggcatcaat tctcggcctg tctgcccggt
     1501 cgtagtacgg ctggaggcgt tttccggtct gtagctccat gttcggaatg acaaaattca
     1561 gctcaagccg tcccttgtcc tggtgctcca cccacaggat gctgtactga tttttctcga
     1621 gaccgggcat cagtacacgc tcaaagctcg ccatcacttt ttcacgccct ccaggcggca
     1681 gctccttctc cgcgaacgac agaacacctg acgtgtattt cttcgcaaat ggcgtggcat
     1741 cgatgagttc ccggacctct tccggattcc cctgaagcac cgttgcccct tcccggttac
     1801 gctcccttcc cagcaggtaa tcaaccggac cactgccacc accttttccc ctggcatgaa
     1861 acttaactat catcccgcgc cccctgttcc ctgaccgcca gacgcagccg gcgcagctca
     1921 tccccgatgg ccatcagtgc ggccaccacc tgaacccggt caccggaaga ccactgcccg
     1981 ctgttcacct tcctcgctgt ctggttaagg ttattcccga tggcggccag ctgacgcagt
     2041 aacggcggtg ccagtgtcgg cagcttcccg gaacgggcaa ccggctcacc caggcagacc
     2101 cgccgcatcc ataccgccag ttgtttaccc tcacagcgtt ccagtaaccg ggcatgttca
     2161 tcatcagtaa cccgtatcgt gagcatcctc tcgcgtttca tcggtatcat tacccccatg
     2221 aacagaaccc ccccttacac ggaggcatca gtgaccaaac aggaaaaaac cgcccttaac
     2281 atggcccgct tcatcagagg ccagacatta acgctgctgg agaagctcaa cgaactggac
     2341 gcggatgaac aggcagacat ctgtgaatcg cttcacgacc acgccgatga gctttaccgc
     2401 agttgcctcg cacgcttcgg ggatgacggt gaaaaccgct gacacatgca gctcccggag
     2461 acggtcacag cttgtctgtg agcggatgcc gggagcagac aagcccgcca gggcgcgtca
     2521 ggccgttgac ctttggggtg tcggggcgaa gccctgaccc agtcacgtag cgatagcgga
     2581 gtgtatactg gcttaaccat tcggcatcag tgcggattgt atgaaaagtg cgccatgtcc
     2641 ggtgtgaaat gccgcacaga tgcgtaagga gaaaatgcca gttcaggcgc tcttccgctt
     2701 cctcgctcac tgactcgcta cgctcggtcg ttcggctgcg gcgagcggac tctcctttct
     2761 caaaaacgct aaccctgtta tccacagaac ccggggataa accaggaaag aacatgtgcg
     2821 caaaaaacga aaccccggga aaggccgcgc cggaggcgct ttttccatag gctccgcccc
     2881 cctgacggac ttcacaaaac agacactttt tcggtgcatc tgtgggagcc ttgcggctca
     2941 accatgaaat ccgccagcgg tggcgaaacc cgacgtggct taaagatcat caccgtttcc
     3001 ggtgaatcgc tccctcctgc gcccccacgt tcccgccata tcgattaccg gatacctttt
     3061 ccgcctttct cccttacggg acacgtggcg ctttctcata gctcacgtct tctggtatct
     3121 cggggcgact taggcagttc gctccgggct gggctgtatg caggaacccc ccgttcagcc
     3181 cgactgctgc gccttctccg gtaactgttc tcttgggtcc aacccggaaa agacaccaca
     3241 aagcgccact ggcagcagcc attggtaaaa gtcatgtgcg agatatttag agagtacttg
     3301 aagtggctgc cggagtgcgg ctacactaga agaacaattt tggtgactcg tctcgcataa
     3361 gacagttacc tggttaagca gtctgcaagc tgacttaacc ttcgatcaaa ccgccctgca
     3421 aggcggtttt ttcgtttaca ggcagcagat tacgcgcaga aaaaaaggat ctcaagagga
     3481 tcctttgatc tttttgttac aaacgtctct atttgactcc cctgagagcg ttttagcgcg
     3541 cctctgaccc ccttggttac attccgacac cagaaacgct cccgtttttt acgtgcattt
     3601 ggcacggtat cgatggaggc tggggggcaa tcctcgaggc cgttatgccc tgggacacct
     3661 tcgccgccag cgtcaccgaa gcgcaaacat tggcgcggcc tgccgacttt gatttcctgc
     3721 accacatcgg tgaaagctat gccacgctac gccgctacgc gccgcagttc ctgggcgtgc
     3781 tcaaattgcg ggctgcgccc gccgccaagg gtgtgctcga tgccatcgac atgctgcgcg
     3841 gcatgaacag cgacagcgcg cgcaaggtgc ccgccgatgc gccaaccgca ttcattaaag
     3901 actaactatc agaaaaactc atcgagcatc aaatgaaact gcaatttatt catatcagga
     3961 ttatcaatac catatttttg aaaaagccgt ttctgtaatg aaggagaaaa ttcaccgagg
     4021 cagttccata gaatggcaag atcctggtat cggtctgcga ttccgactcg tccaacatca
     4081 atacaaccta ttaatttccc ctcgtcaaaa ataagattat caagtgagaa atcaccatga
     4141 gtgacgactg aatccggtga gaatggcaaa agcttatgca tttctttcca gacttgttca
     4201 acaggccagc cattacgctc atcatcaaaa tcactcgcat caaccaaacc gttattcatt
     4261 cgtgattgcg cctgagcgag acgaaatacg cgatcgctgt taaaaggaca attacaaaca
     4321 ggaatcgaat gcaaccggcg caggaacgct gccagcgcat caacaatatt ttcacctgaa
     4381 tcaggatatt cttctaatac ctggaatgct gttttcccgg ggatcgcagt ggtgagtaac
     4441 catgcatcat caggagtacg gataaaatgc ttgatggtcg gaagaggcat aaattccgtc
     4501 agccagttta gtctgaccat ctcatctgta acatcattgg caacgctacc tttgccatgt
     4561 ttcagaaaca actctggcgc atcgggcttc ccatacaatc gatagattgt cgcacctgat
     4621 tgcccgacat tatcgcgagc ccatttatac ccatataaat cagcatccag gttggaattt
     4681 aatcgctgcc tcgagcaaga cgtttcccgt tgaatatggc tcataacacc ccttgtatta
     4741 ctgtttatgt aagcagacag ttttattgtt catgatgata tatttttatc ttgtgcaatg
     4801 taacatcaga gattttgaga cacaacgtgg ttcccgccat atgaaaatcc ggccagacca
     4861 acatcattct ggcgctccga aagaagggat attcgccgcc gtgaccagcc tggagcgggt
     4921 cgcataatct ttggccgctt cgtagtcgag gaacatggca tgaactcttt cattacgcaa
     4981 aaaatcaaac aaatgaccat catcattata tagttggggg ctatttacaa tagataaatg
     5041 gaaatcaagc cctttaattt tcttgcttgc caatttacca aatacacagg gctgattgcc
     5101 tgacacccat tttcttagta aatcttcaat tttatcttta gaagtttcgt taaagataaa
     5161 tgaatgaata ttatcaatat cttttccaaa tgaaaaactg gatgataatt gtggtagttt
     5221 atttatacgt tgttgaagat tcatgaaagc tcccacaaga cacctcatat atttttttat
     5281 atactgaaac tacattatat ttattaccgg
//
