LOCUS       CP123683                5310 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS11922707 plasmid pFSIS11922707-3, complete sequence.
ACCESSION   CP123683
VERSION     CP123683.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN12307539
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 (19-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                   :: 406x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 11:02:20
            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)                     :: 5,286
            CDSs (total)                      :: 5,159
            Genes (coding)                    :: 5,024
            CDSs (with protein)               :: 5,024
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 135
            CDSs (without protein)            :: 135
            Pseudo Genes (ambiguous residues) :: 0 of 135
            Pseudo Genes (frameshifted)       :: 44 of 135
            Pseudo Genes (incomplete)         :: 102 of 135
            Pseudo Genes (internal stop)      :: 17 of 135
            Pseudo Genes (multiple problems)  :: 27 of 135
            Pseudo Genes (short protein)      :: 1 of 135
            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="FSIS11922707"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pFSIS11922707-3"
                     /geo_loc_name="USA:NC"
                     /collection_date="2019"
                     /collected_by="USDA-FSIS"
     gene            join(5123..5310,1..133)
                     /locus_tag="FO395_26390"
     CDS             join(5123..5310,1..133)
                     /locus_tag="FO395_26390"
                     /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="WGN78792.1"
                     /translation="MDNRVSVFEKGESARRSRTTERSESVSEEAEERLNWHFLLTHLCG
                     ISHRTWRTFHTIRTDAEWLSQYTLRYRYVTGSGLRPDTPKVNGLTRPGGLVCSRHPLTD
                     KL"
                     /name="hypothetical protein"
     gene            complement(156..347)
                     /locus_tag="FO395_26395"
     CDS             complement(156..347)
                     /locus_tag="FO395_26395"
                     /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="WGN78793.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            412..735
                     /locus_tag="FO395_26400"
     CDS             412..735
                     /locus_tag="FO395_26400"
                     /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="WGN78796.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            944..1375
                     /locus_tag="FO395_26405"
                     /pseudo=""
     CDS             944..1375
                     /locus_tag="FO395_26405"
                     /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            1413..1943
                     /locus_tag="FO395_26410"
     CDS             1413..1943
                     /locus_tag="FO395_26410"
                     /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="WGN78794.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            1950..2183
                     /locus_tag="FO395_26415"
     CDS             1950..2183
                     /locus_tag="FO395_26415"
                     /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="WGN78795.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2943..3038
                     /locus_tag="FO395_26420"
                     /pseudo=""
     CDS             2943..3038
                     /locus_tag="FO395_26420"
                     /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"
     gene            3184..3999
                     /locus_tag="FO395_26425"
     CDS             3184..3999
                     /locus_tag="FO395_26425"
                     /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="WGN78791.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(4009..4281)
                     /locus_tag="FO395_26430"
                     /pseudo=""
     CDS             complement(4009..4281)
                     /locus_tag="FO395_26430"
                     /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"
     ARG             3185..3996
                     /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          4647..4834
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          726..2287
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttaagccag tatacactcc gctatcgcta cgtgactggg tcagggcttc gccccgacac
       61 cccaaaggtc aacggcctga cgcgccctgg cgggcttgtc tgctcccggc atccgctcac
      121 agacaagctg tgaccgtctc cgggagctgc atgtgtcagc ggttttcacc gtcatccccg
      181 aagcgtgcga ggcaactgcg gtaaagctca tcggcgtggt cgtgaagcga ttcacagatg
      241 tctgcctgtt catccgcgtc cagttcgttg agcttctcca gcagcgttaa tgtctggcct
      301 ctgatgaagc gggccatgtt aagggcggtt ttttcctgtt tggtcactga tgcctccgtg
      361 taaggggggg ttctgttcat gggggtaatg ataccgatga aacgcgagag gatgctcacg
      421 atacgggtta ctgatgatga acatgcccgg ttactggaac gctgtgaggg taaacaactg
      481 gcggtatgga tgcggcgggt ctgcctgggt gagccggttg cccgttccgg gaagctgccg
      541 acactggcac cgccgttact gcgtcagctg gccgccatcg ggaataacct taaccagaca
      601 gcgaggaagg tgaacagcgg gcagtggtct tccggtgacc gggttcaggt ggtggccgca
      661 ctgatggcca tcggggatga gctgcgccgg ctgcgtctgg cggtcaggga acagggggcg
      721 cgggatgata gttaagtttc atgccagggg aaaaggtggt ggcagtggtc cggttgatta
      781 cctgctggga agggagcgta accgggaagg ggcaacggtg cttcagggga atccggaaga
      841 ggtccgggaa ctcatcgatg ccacgccatt tgcgaagaaa tacacgtcag gtgttctgtc
      901 gttcgcggag aaggagctgc cgcctggagg gcgtgaaaaa gtgatggcga gctttgagcg
      961 tgtactgatg cccggtctcg agaaaaatca gtacagcatc ctgtgggtgg agcaccagga
     1021 caagggacgg cttgagctga attttgtcat tccgaacatg gagctacaga ccggaaaacg
     1081 cctccagccg tactacgacc gggcagacag gccgagaatt gatgcctggc agacgctggt
     1141 gaatcaccat tacggtctgc atgaccccaa cgccccggag aaccgccgga cgctgaccct
     1201 tcctgataac ctgccggaaa cgaaacaggc gcttgctgag ggcgtcacac gcgggataga
     1261 cgcgctttac catgccggag agataaaagg ccgtcaggat gtgattcagg cgctcacaga
     1321 ggcggggctt gaagtggtca gggtgacgcg aagcagtatc agcattgcag acccgaacgg
     1381 cgggaggaat atcagactga aaggagcgtt ttatgagcaa tcttttacag acgggcgcgg
     1441 agttcgagaa aaagctgaaa gagagagccg aatctacaga gaaaatgctg aacgacgagt
     1501 tcaggaagct cgaagaatct gtaaacaggg aactgacctc aaacgaatct ttaatcagga
     1561 acgctatcaa cgaccataca acagccctga aagaactgct ggagaggtat cagaaaacga
     1621 ccgtcgatac gatggacgcg cactggaaaa ccgtactgaa aatgagcgtg aaacgctggc
     1681 tgtggctgat tatcgtctca gtactgatgt ttgccacgac cgggagtctg ctgtggtacc
     1741 agggcatgaa gataaacgcg aatatgaata ttctccgcga gcagaaagag agtctggaga
     1801 agctgaacgc gaagacatgg ggcgtgcgtt atcacgagga cagcaacgga cgttttctgg
     1861 tgttgccgaa ggggatgaaa gccgaaacga actggacgaa ggacaacggc aaactgaacg
     1921 cagtgagact ggtgcaggag tgacagagca tgacggagct ggaaagacat ttgctgaacg
     1981 cattagagca actgcaacag gactatatgc agcggctgaa cgaatgggag aacgccttcg
     2041 tggaattgca gaaaatgttt tcgcttacgc aacgggacaa cgcgatgctg aacgggcgag
     2101 tcatgcagtt gagtcagcag gtgcagcact tgagcgagcg gacagaacgc ttgagccagt
     2161 tatacagcga gaacaggaga taagggatga acggctgatg caggaacgcg aacatgagtt
     2221 atctctggag cgggagcgtc agccggaaat ccaggagcgg acactggatg gcccttcgct
     2281 gggatggtga aaccatgaaa aatgacgtgt tcagtggatt aaggcgggct aatgtggcct
     2341 gtagcatctg gttgcatagg tattcatgcg gttaaaattt atcaggtgcg atcgcggcag
     2401 tttttcgggt ggtttgttgc catttttacc tgtctgctgc cgtgatcgca ccgaacgcgt
     2461 tttggcggtg cgtacaatgc gacgttatgg taaatggagc ggattttcag gaaggagtga
     2521 tactaacaac tcgaacactg tgcaaataat gattttttta aaatatcggt aacgataata
     2581 aattatttcg ttttacgccg gtaataaata taatgtagtt tcagtatata aaaaaatata
     2641 tgaggtgtct tgtgggagct ttcatgaatc ttcaacaacg tataaataaa ctaccacaat
     2701 tatcatccag tttttcattt ggaaaagata ttgataatat tcattcattt atctttaacg
     2761 aaacttctaa agataaaatt gaagatttac taagaaaatg ggtgtcaggc aatcagccct
     2821 gtgtatttgg taaattggca agcaagaaaa ttaaagggct tgatttccat ttatctattg
     2881 taaatagccc ccaactatat aatgatgatg gtcatttgtt tgattttttg cgtaatgaaa
     2941 gagttcatgc catgttcctc gactacgaag cggccaaaga ttatgcgacc cgctccaggc
     3001 tggtcacggc ggcgaatatc ccttctttcg gagcgccaga atgatgttgg tctggccgga
     3061 ttttcatatg gcgggaacca cgttgtgtct caaaatctct gatgttacat tgcacaagat
     3121 aaaaatatat catcatgaac aataaaactg tctgcttaca taaacagtaa tacaaggggt
     3181 gttatgagcc atattcaacg ggaaacgtct tgctcgaggc agcgattaaa ttccaacctg
     3241 gatgctgatt tatatgggta taaatgggct cgcgataatg tcgggcaatc aggtgcgaca
     3301 atctatcgat tgtatgggaa gcccgatgcg ccagagttgt ttctgaaaca tggcaaaggt
     3361 agcgttgcca atgatgttac agatgagatg gtcagactaa actggctgac ggaatttatg
     3421 cctcttccga ccatcaagca ttttatccgt actcctgatg atgcatggtt actcaccact
     3481 gcgatccccg ggaaaacagc attccaggta ttagaagaat atcctgattc aggtgaaaat
     3541 attgttgatg cgctggcagc gttcctgcgc cggttgcatt cgattcctgt ttgtaattgt
     3601 ccttttaaca gcgatcgcgt atttcgtctc gctcaggcgc aatcacgaat gaataacggt
     3661 ttggttgatg cgagtgattt tgatgatgag cgtaatggct ggcctgttga acaagtctgg
     3721 aaagaaatgc ataagctttt gccattctca ccggattcag tcgtcactca tggtgatttc
     3781 tcacttgata atcttatttt tgacgagggg aaattaatag gttgtattga tgttggacga
     3841 gtcggaatcg cagaccgata ccaggatctt gccattctat ggaactgcct cggtgaattt
     3901 tctccttcat tacagaaacg gctttttcaa aaatatggta ttgataatcc tgatatgaat
     3961 aaattgcagt ttcatttgat gctcgatgag tttttctgat agttagtctt taatgaatgc
     4021 ggttggcgca tcggcgggca ccttgcgcgc gctgtcgctg ttcatgccgc gcagcatgtc
     4081 gatggcatcg agcacaccct tggcggcggg cgcagcccgc aatttgagca cgcccaggaa
     4141 ctgcggcgcg tagcggcgta gcgtggcata gctttcaccg atgtggtgca ggaaatcaaa
     4201 gtcggcaggc cgcgccaatg tttgcgcttc ggtgacgctg gcggcgaagg tgtcccaggg
     4261 cataacggcc tcgaggattg ccccccagcc tccatcgata ccgtgccaaa tgcacgtaaa
     4321 aaacgggagc gtttctggtg tcggaatgta accaaggggg tcagaggcgc gctaaaacgc
     4381 tctcagggga gtcaaataga gacgtttgta acaaaaagat caaaggatcc tcttgagatc
     4441 ctttttttct gcgcgtaatc tgctgcctgt aaacgaaaaa accgccttgc agggcggttt
     4501 gatcgaaggt taagtcagct tgcagactgc ttaaccaggt aactgtctta tgcgagacga
     4561 gtcaccaaaa ttgttcttct agtgtagccg cactccggca gccacttcaa gtactctcta
     4621 aatatctcgc acatgacttt taccaatggc tgctgccagt ggcgctttgt ggtgtctttt
     4681 ccgggttgga cccaagagaa cagttaccgg agaaggcgca gcagtcgggc tgaacggggg
     4741 gttcctgcat acagcccagc ccggagcgaa ctgcctaagt cgccccgaga taccagaaga
     4801 cgtgagctat gagaaagcgc cacgtgtccc gtaagggaga aaggcggaaa aggtatccgg
     4861 taatcgatat ggcgggaacg tgggggcgca ggagggagcg attcaccgga aacggtgatg
     4921 atctttaagc cacgtcgggt ttcgccaccg ctggcggatt tcatggttga gccgcaaggc
     4981 tcccacagat gcaccgaaaa agtgtctgtt ttgtgaagtc cgtcaggggg gcggagccta
     5041 tggaaaaagc gcctccggcg cggcctttcc cggggtttcg ttttttgcgc acatgttctt
     5101 tcctggttta tccccgggtt ctgtggataa cagggttagc gtttttgaga aaggagagtc
     5161 cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg
     5221 cctgaactgg cattttctcc ttacgcatct gtgcggcatt tcacaccgga catggcgcac
     5281 ttttcataca atccgcactg atgccgaatg
//
