LOCUS       CP123706                5310 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS11920112 plasmid pFSIS11920112-3, complete sequence.
ACCESSION   CP123706
VERSION     CP123706.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN11456655
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 (18-APR-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 (02-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                   :: 367x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/21/2023 09:07:41
            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)                     :: 5,288
            CDSs (total)                      :: 5,162
            Genes (coding)                    :: 5,028
            CDSs (with protein)               :: 5,028
            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)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 44 of 134
            Pseudo Genes (incomplete)         :: 102 of 134
            Pseudo Genes (internal stop)      :: 18 of 134
            Pseudo Genes (multiple problems)  :: 29 of 134
            Pseudo Genes (short protein)      :: 1 of 134
            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="FSIS11920112"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pFSIS11920112-3"
                     /geo_loc_name="USA:VA"
                     /collection_date="2019"
                     /collected_by="USDA-FSIS"
     gene            complement(join(5103..5310,1..608))
                     /locus_tag="FAD25_26400"
     CDS             complement(join(5103..5310,1..608))
                     /locus_tag="FAD25_26400"
                     /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="WGN46628.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(754..849)
                     /locus_tag="FAD25_26405"
                     /pseudo=""
     CDS             complement(754..849)
                     /locus_tag="FAD25_26405"
                     /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            complement(1609..1842)
                     /locus_tag="FAD25_26410"
     CDS             complement(1609..1842)
                     /locus_tag="FAD25_26410"
                     /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="WGN46629.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1849..2379)
                     /locus_tag="FAD25_26415"
     CDS             complement(1849..2379)
                     /locus_tag="FAD25_26415"
                     /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="WGN46630.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(2417..2848)
                     /locus_tag="FAD25_26420"
                     /pseudo=""
     CDS             complement(2417..2848)
                     /locus_tag="FAD25_26420"
                     /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(3057..3380)
                     /locus_tag="FAD25_26425"
     CDS             complement(3057..3380)
                     /locus_tag="FAD25_26425"
                     /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="WGN46631.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3445..3636
                     /locus_tag="FAD25_26430"
     CDS             3445..3636
                     /locus_tag="FAD25_26430"
                     /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="WGN46626.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3659..3979)
                     /locus_tag="FAD25_26435"
     CDS             complement(3659..3979)
                     /locus_tag="FAD25_26435"
                     /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="WGN46627.1"
                     /translation="MDNRVSVFEKGESARRSRTTERSESVSEEAEERLNWHFLLTHLCG
                     ISHRTWRTFHTIRTDAEWLSQYTLRYRYVTGSGLRPDTPKVNGLTRPGGLVCSRHPLTD
                     KL"
                     /name="hypothetical protein"
     gene            4821..5093
                     /locus_tag="FAD25_26440"
                     /pseudo=""
     CDS             4821..5093
                     /locus_tag="FAD25_26440"
                     /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             complement(5104..5309)
                     /name="APH(3')-Ia"
                     /gene="APH(3')-Ia"
                     /gene_name="APH(3')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="25.09"
     ARG             complement(4..608)
                     /name="APH(3')-Ia"
                     /gene="APH(3')-Ia"
                     /gene_name="APH(3')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="97.52"
                     /coverage="74.54"
     Typing          complement(3731..3812)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(4269..4456)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(1506..3067)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttatcaagtg agaaatcacc atgagtgacg actgaatccg gtgagaatgg caaaagctta
       61 tgcatttctt tccagacttg ttcaacaggc cagccattac gctcatcatc aaaatcactc
      121 gcatcaacca aaccgttatt cattcgtgat tgcgcctgag cgagacgaaa tacgcgatcg
      181 ctgttaaaag gacaattaca aacaggaatc gaatgcaacc ggcgcaggaa cgctgccagc
      241 gcatcaacaa tattttcacc tgaatcagga tattcttcta atacctggaa tgctgttttc
      301 ccggggatcg cagtggtgag taaccatgca tcatcaggag tacggataaa atgcttgatg
      361 gtcggaagag gcataaattc cgtcagccag tttagtctga ccatctcatc tgtaacatca
      421 ttggcaacgc tacctttgcc atgtttcaga aacaactctg gcgcatcggg cttcccatac
      481 aatcgataga ttgtcgcacc tgattgcccg acattatcgc gagcccattt atacccatat
      541 aaatcagcat ccaggttgga atttaatcgc tgcctcgagc aagacgtttc ccgttgaata
      601 tggctcataa caccccttgt attactgttt atgtaagcag acagttttat tgttcatgat
      661 gatatatttt tatcttgtgc aatgtaacat cagagatttt gagacacaac gtggttcccg
      721 ccatatgaaa atccggccag accaacatca ttctggcgct ccgaaagaag gaatattcgc
      781 cgccgtgacc agcctggagc gggtcgcata atctttggcc gcttcgtagt cgaggaacat
      841 ggcatgaact ctttcattac gcaaaaaatc aaacaaatga ccatcatcat tatatagttg
      901 ggggctattt acaatagata aatggaaatc aagcccttta attttcttgc ttgccaattt
      961 accaaataca cagggctgat tgcctgacac ccattttctt agtaaatctt caattttatc
     1021 tttagaagtt tcgttaaaga taaatgaatg aatattatca atatcttttc caaatgaaaa
     1081 actggatgat aattgtggta gtttatttat acgttgttga agattcatga aagctcccac
     1141 aagacacctc atatattttt ttatatactg aaactacatt atatttatta ccggcgtaaa
     1201 acgaaataat ttattatcgt taccgatatt ttaaaaaaat cattatttgc acagtgttcg
     1261 agttgttagt atcactcctt cctgaaaatc cgctccattt accataacgt cgcattgtac
     1321 gcaccgccaa aacgcgttcg gtgcgatcac ggcagcagac aggtaaaaat ggcaacaaac
     1381 cacccgaaaa actgccgcga tcgcacctga taaattttaa ccgcatgaat acctatgcaa
     1441 ccagatgcta caggccacat tagcccgcct taatccactg aacacgtcat ttttcatggt
     1501 ttcaccatcc cagcgaaggg ccatccagtg tccgctcctg gatttccggc tgacgctccc
     1561 gctccagaga taactcatgt tcgcgttcct gcatcagccg ttcatccctt atctcctgtt
     1621 ctcgctgtat aactggctca agcgttctgt ccgctcgctc aagtgctgca cctgctgact
     1681 caactgcatg actcgcccgt tcagcatcgc gttgtcccgt tgcgtaagcg aaaacatttt
     1741 ctgcaattcc acgaaggcgt tctcccattc gttcagccgc tgcatatagt cctgttgcag
     1801 ttgctctaat gcgttcagca aatgtctttc cagctccgtc atgctctgtc actcctgcac
     1861 cagtctcact gcgttcagtt tgccgttgtc cttcgtccag ttcgtttcgg ctttcatccc
     1921 cttcggcaac accagaaaac gtccgttgct gtcctcgtga taacgcacgc cccatgtctt
     1981 cgcgttcagc ttctccagac tctctttctg ctcgcggaga atattcatat tcgcgtttat
     2041 cttcatgccc tggtaccaca gcagactccc ggtcgtggca aacatcagta ctgagacgat
     2101 aatcagccac agccagcgtt tcacgctcat tttcagtacg gttttccagt gcgcgtccat
     2161 cgtatcgacg gtcgttttct gatacctctc cagcagttct ttcagggctg ttgtatggtc
     2221 gttgatagcg ttcctgatta aagattcgtt tgaggtcagt tccctgttta cagattcttc
     2281 gagcttcctg aactcgtcgt tcagcatttt ctctgtagat tcggctctct ctttcagctt
     2341 tttctcgaac tccgcgcccg tctgtaaaag attgctcata aaacgctcct ttcagtctga
     2401 tattcctccc gccgttcggg tctgcaatgc tgatactgct tcgcgtcacc ctgaccactt
     2461 caagccccgc ctctgtgagc gcctgaatca catcctgacg gccttttatc tctccggcat
     2521 ggtaaagcgc gtctatcccg cgtgtgacgc cctcagcaag cgcctgtttc gtttccggca
     2581 ggttatcagg aagggtcagc gtccggcggt tctccggggc gttggggtca tgcagaccgt
     2641 aatggtgatt caccagcgtc tgccaggcat caattctcgg cctgtctgcc cggtcgtagt
     2701 acggctggag gcgttttccg gtctgtagct ccatgttcgg aatgacaaaa ttcagctcaa
     2761 gccgtccctt gtcctggtgc tccacccaca ggatgctgta ctgatttttc tcgagaccgg
     2821 gcatcagtac acgctcaaag ctcgccatca ctttttcacg ccctccaggc ggcagctcct
     2881 tctccgcgaa cgacagaaca cctgacgtgt atttcttcgc aaatggcgtg gcatcgatga
     2941 gttcccggac ctcttccgga ttcccctgaa gcaccgttgc cccttcccgg ttacgctccc
     3001 ttcccagcag gtaatcaacc ggaccactgc caccaccttt tcccctggca tgaaacttaa
     3061 ctatcatccc gcgccccctg ttccctgacc gccagacgca gccggcgcag ctcatccccg
     3121 atggccatca gtgcggccac cacctgaacc cggtcaccgg aagaccactg cccgctgttc
     3181 accttcctcg ctgtctggtt aaggttattc ccgatggcgg ccagctgacg cagtaacggc
     3241 ggtgccagtg tcggcagctt cccggaacgg gcaaccggct cacccaggca gacccgccgc
     3301 atccataccg ccagttgttt accctcacag cgttccagta accgggcatg ttcatcatca
     3361 gtaacccgta tcgtgagcat cctctcgcgt ttcatcggta tcattacccc catgaacaga
     3421 accccccctt acacggaggc atcagtgacc aaacaggaaa aaaccgccct taacatggcc
     3481 cgcttcatca gaggccagac attaacgctg ctggagaagc tcaacgaact ggacgcggat
     3541 gaacaggcag acatctgtga atcgcttcac gaccacgccg atgagcttta ccgcagttgc
     3601 ctcgcacgct tcggggatga cggtgaaaac cgctgacaca tgcagctccc ggagacggtc
     3661 acagcttgtc tgtgagcgga tgccgggagc agacaagccc gccagggcgc gtcaggccgt
     3721 tgacctttgg ggtgtcgggg cgaagccctg acccagtcac gtagcgatag cggagtgtat
     3781 actggcttaa ccattcggca tcagtgcgga ttgtatgaaa agtgcgccat gtccggtgtg
     3841 aaatgccgca cagatgcgta aggagaaaat gccagttcag gcgctcttcc gcttcctcgc
     3901 tcactgactc gctacgctcg gtcgttcggc tgcggcgagc ggactctcct ttctcaaaaa
     3961 cgctaaccct gttatccaca gaacccgggg ataaaccagg aaagaacatg tgcgcaaaaa
     4021 acgaaacccc gggaaaggcc gcgccggagg cgctttttcc ataggctccg cccccctgac
     4081 ggacttcaca aaacagacac tttttcggtg catctgtggg agccttgcgg ctcaaccatg
     4141 aaatccgcca gcggtggcga aacccgacgt ggcttaaaga tcatcaccgt ttccggtgaa
     4201 tcgctccctc ctgcgccccc acgttcccgc catatcgatt accggatacc ttttccgcct
     4261 ttctccctta cgggacacgt ggcgctttct catagctcac gtcttctggt atctcggggc
     4321 gacttaggca gttcgctccg ggctgggctg tatgcaggaa ccccccgttc agcccgactg
     4381 ctgcgccttc tccggtaact gttctcttgg gtccaacccg gaaaagacac cacaaagcgc
     4441 cactggcagc agccattggt aaaagtcatg tgcgagatat ttagagagta cttgaagtgg
     4501 ctgccggagt gcggctacac tagaagaaca attttggtga ctcgtctcgc ataagacagt
     4561 tacctggtta agcagtctgc aagctgactt aaccttcgat caaaccgccc tgcaaggcgg
     4621 ttttttcgtt tacaggcagc agattacgcg cagaaaaaaa ggatctcaag aggatccttt
     4681 gatctttttg ttacaaacgt ctctatttga ctcccctgag agcgttttag cgcgcctctg
     4741 acccccttgg ttacattccg acaccagaaa cgctcccgtt ttttacgtgc atttggcacg
     4801 gtatcgatgg aggctggggg gcaatcctcg aggccgttat gccctgggac accttcgccg
     4861 ccagcgtcac cgaagcgcaa acattggcgc ggcctgccga ctttgatttc ctgcaccaca
     4921 tcggtgaaag ctatgccacg ctacgccgct acgcgccgca gttcctgggc gtgctcaaat
     4981 tgcgggctgc gcccgccgcc aagggtgtgc tcgatgccat cgacatgctg cgcggcatga
     5041 acagcgacag cgcgcgcaag gtgcccgccg atgcgccaac cgcattcatt aaagactaac
     5101 tatcagaaaa actcatcgag catcaaatga aactgcaatt tattcatatc aggattatca
     5161 ataccatatt tttgaaaaag ccgtttctgt aatgaaggag aaaattcacc gaggcagttc
     5221 catagaatgg caagatcctg gtatcggtct gcgattccga ctcgtccaac atcaatacaa
     5281 cctattaatt tcccctcgtc aaaaataaga
//
