LOCUS       CP123675                4175 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS12035116 plasmid pFSIS12035116-2, complete sequence.
ACCESSION   CP123675
VERSION     CP123675.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN16611448
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 4175)
  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 4175)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (30-OCT-2020) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4175)
  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                   :: 412x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 11:09:05
            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)                     :: 5,205
            CDSs (total)                      :: 5,082
            Genes (coding)                    :: 4,956
            CDSs (with protein)               :: 4,956
            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)              :: 126
            CDSs (without protein)            :: 126
            Pseudo Genes (ambiguous residues) :: 0 of 126
            Pseudo Genes (frameshifted)       :: 39 of 126
            Pseudo Genes (incomplete)         :: 98 of 126
            Pseudo Genes (internal stop)      :: 16 of 126
            Pseudo Genes (multiple problems)  :: 26 of 126
            Pseudo Genes (short protein)      :: 1 of 126
            CRISPR Arrays                     :: 3
            ##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..4175
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="FSIS12035116"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pFSIS12035116-2"
                     /geo_loc_name="USA:SD"
                     /collection_date="2020"
                     /collected_by="USDA-FSIS"
     gene            complement(join(4036..4175,1..55))
                     /locus_tag="IR414_26010"
     CDS             complement(join(4036..4175,1..55))
                     /locus_tag="IR414_26010"
                     /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="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WGN36839.1"
                     /translation="MNKQQQTALNMARFIKSPSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1154..1564
                     /locus_tag="IR414_26015"
     CDS             1154..1564
                     /locus_tag="IR414_26015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000874179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WGN36840.1"
                     /translation="MAFISLSNLAAKTGRIIQSQCVTATQTKKSTGAVELGFRLSKSAM
                     DETGITIGDRVDILYDKEENQWMIKKISEGGFGVSGQKNKHGGYSSCAVRLTLRPGFPR
                     LSEDEEDNKKLLSDDSFTQLSEGVIVFRLDDE"
                     /name="hypothetical protein"
     gene            1822..2385
                     /locus_tag="IR414_26020"
     CDS             1822..2385
                     /locus_tag="IR414_26020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015959180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WGN36841.1"
                     /translation="MHALSILPSVARANLATKFSSHLKVIELFNTMQDSQVVVLSSLIE
                     GHHLTSSGNSVKADFEVTRLPAIIEMLEKKYFFPIRHLNVSVKSVTTGRMTGQTVYFIE
                     PEHIEQLLADPELVFANQERSLFFRSLEKEGKNLGKLIEKKGSVSQAVLSLLHHAYKDK
                     PLSDEMWKEIEDKFTHMLDELSAA"
                     /name="hypothetical protein"
     gene            complement(2414..3040)
                     /locus_tag="IR414_26025"
     CDS             complement(2414..3040)
                     /locus_tag="IR414_26025"
                     /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="WGN36838.1"
                     /translation="MSPTLNKQASKERCAVEFATRKKSKTQRKKSKALSYRGLCFFCTL
                     VTGKCQWTSKMSKQDYIQLRTLTDQFYADNKGLQEALDGSNDGKVRGYGIVVIDLNGLV
                     FGIPLRSHLNHKFGFVSERSEGVKKGLDYTKALLIKKEEYVSRAYKIPTPEFTHINDNK
                     EKIQEDFNKFVNRYIEANVKKDENILRNYRYSTLKNYHKELGLED"
                     /name="hypothetical protein"
     Typing          81..156
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.25"
                     /coverage="87.0"
                     /evalue="2.07e-14"
     Typing          330..585
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.86"
                     /coverage="89.0"
                     /evalue="1.25e-96"
     Typing          complement(3317..3830)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tcgggctttt gataaatcgc gccatattca gcgcagtttg ttgttgtttg ttcaccttcc
       61 gttgttctcc gtcagttccg ggtgtcgggg ggaccctgag caggtggtaa ttgtaagacg
      121 ttgcgggcga cggtattaca attgcacatc ctgtcctgtc ctgtcctgtc ctgtttcttt
      181 aggacgtatc atggcacagc atatcaactg ataaataatc cctgtgcagt gcagccgctg
      241 ttgcataaaa tttcgctctg cgtcgagtgt ttcttaatca ataattccgc tgatactccg
      301 gaaaaacgcg agtctgttct catgcctgaa atgcccacac cccacgcaaa aacaagtttt
      361 tgctgatttt tctttataaa tagagagtta tgacaaatta gttcttcttg ctctctttgt
      421 gatatttaaa aaagcggtgt tggcgcagct acaacaccgc gccgacaccg ctttttaggg
      481 gtggtactga ctattttcat aaaaaacatc atcttatatt aggggtgctg ctagcggcgc
      541 ggtgtgtttt tttacaggac gcccctgggg gcgctgccag gggtgtctgt tcagatatgt
      601 agcaatgagt cagggattca cgaactgaaa atgtccgaaa atgtgtctca tgggtactgt
      661 atgcgcccaa accgatcgtc attcactttc atgcatagct atgcagtgag ctgaaatcga
      721 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtttgcggc
      781 agaatcgcgt tcagcgcgtt ttagcggtgc gcgcaagaac tcttatgtta aattcatctc
      841 atcggcaacc tatacaggca taaaaatcag tttctataag cggctttctt gcacctactt
      901 ggtgattttt ttggatgcgc tgacgttgct cgactttaaa tcaccataga aaaataccct
      961 ttacttacat aaagatcgat ctggatgtgt atcttgacga ggttcaatac gagcaattgt
     1021 ttttgtattt aaggtttctt atcgccgttt tttgcggctc tagaaaaatc aatacaaaag
     1081 atcttgaaag tcacctcgct ccctgggtac acttccgtat aagaactgat cgatgtctaa
     1141 aacggattgt attatggcct ttatctctct atcgaacttg gcagcgaaga ctggaaggat
     1201 aatccagtcg cagtgtgtta cggccacgca aacgaaaaaa agcacgggcg ctgtcgagct
     1261 gggattccgc ttgagcaaga gcgctatgga cgagactggt attaccattg gggatcgtgt
     1321 cgacattctt tacgacaaag aagaaaacca gtggatgatt aagaaaatta gtgaaggtgg
     1381 ctttggtgtg tctgggcaaa aaaacaagca cggcggttac tcatcgtgtg ctgttagatt
     1441 gaccttgcga ccaggttttc ctcgcctttc tgaggatgaa gaggacaaca agaagctact
     1501 ttccgatgat tcattcactc agctaagtga aggtgtaatc gtcttcaggc tggatgatga
     1561 ataggaagga ccaaaaagga aaggcagagt tagtgagcgt cgccaaacaa tcgactaact
     1621 ccgccttctg gtcaacacat cactaccttt ggaagggtgg agtgttatgg gcggcattat
     1681 gttcataaac ttgcattcta ataaagaaaa aatcgtttct tttgagggat gtgaacacga
     1741 cattttctat tctgataggt gcgatgctat tggctttggt ctcttaagtt tatgttttta
     1801 aaaacatatg aggctataca tatgcacgct ttatcaatac taccttcagt tgcccgcgct
     1861 aacctggcaa ctaaattctc gtctcatttg aaggtgatcg agctcttcaa cacgatgcag
     1921 gattcccaag ttgttgtctt gtcatcactg atcgaaggcc atcacctcac cagttctggt
     1981 aacagtgtca aagccgactt tgaggtcact cgcttaccgg cgattatcga gatgttagag
     2041 aaaaaatatt ttttccctat tcgtcatcta aatgtatctg ttaaatctgt aactacagga
     2101 aggatgactg gacaaactgt ctatttcata gagcctgaac acatcgagca acttctcgct
     2161 gatcctgagc ttgtgtttgc taatcaggaa aggagcctct tctttcgttc tctcgaaaaa
     2221 gaagggaaaa atctcggcaa gcttatcgag aaaaaaggta gtgtttctca agccgtctta
     2281 agccttctac atcacgccta caaagataaa cctctttctg acgagatgtg gaaggagata
     2341 gaagataagt tcacccatat gctggatgaa ttgagcgcgg cgtaaaggca agggcggtcg
     2401 ttagaccgcc tttttagtct tctaaaccta attctttgtg atagtttttc agcgtagagt
     2461 aacgatagtt tctgagtatg ttttcatctt tcttgacgtt cgcttctatg tatctgttta
     2521 cgaatttgtt gaaatcttct tgtatttttt ctttgttatc attgatatgg gtaaattcag
     2581 gagttggtat cttataggct cgcgatacat actcttcttt cttaattagc aacgctttgg
     2641 tgtaatccag tcctttctta acaccttctg atcgctccga aacgaatcca aatttatggt
     2701 ttaaatggct tcgtaagggt atcccgaaca ccaatccgtt gagatcaata actacgattc
     2761 cgtagcctct tacttttcca tcattactgc cgtcgagagc ctcttgtagg cctttgttat
     2821 cagcataaaa ctggtctgta agggttctta actgtatgta atcctgtttg ctcatttttg
     2881 atgtccattg gcattttcct gtaaccaatg tacaaaaaaa gcaaagccct ctgtaagaga
     2941 gggctttgct tttctttcgt tgagtcttgg attttttacg tgtggcgaac tctaccgcac
     3001 atctttcttt ggaagcttgt ttgtttaacg tggggctcat tcctaccgcc acttctagat
     3061 ttacttatat caaaaattat atgtgaagtc aatttcgtag ctgttcttga ctggacttac
     3121 tttgccagcg taatcttctc ctgaaacgaa aaaaccaccc tggcaggtgg tttttcgaag
     3181 gttatttaat cctggcagat tatctaaccg tggtaacagt cttgtgcgag acgtgtcacc
     3241 aaattcgtcc ttccagtgta gcctcagtaa ggccaccact tcaagaactc tcaatacatc
     3301 tctcgcacat catgtttacc agtggccgtt gccaatggcg attagtcgtg tctttccggg
     3361 ttggactcaa gtcgatagtt accggaaaag gcgcagcggt cggactgaac ggggggttcg
     3421 tgcatacagt ccagcttgga gcgaactgcc tacccggaac tgagtgtcag gcgtggaatg
     3481 agataaacgc ggccataaca gcggaatgac accggtaaac cgaaaggcag gaacaggaga
     3541 gcgcacgagg gagccaccag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg
     3601 ccaccactga tttgagcgtc agatttcgtg atgcttgtca ggggggcgga gcctatggaa
     3661 aaacggcagc gccgcatcct tttcttgccc tgtttgtcat gccgtatgcc tttgctctta
     3721 tccgtgtgca ggtaacgccc gccgcagccg aacggcagga gcggaagcga ccgagtgagc
     3781 gaggaggcgt aatgtcaccg caacctccat gttctcccgt acgccctgca gctgcatttt
     3841 cccctgccac atgaagcact tttataaagt gttactccgc cgtaacatat taagccagta
     3901 tacactccgc tatcgctacg tgactgggtc atggctgcgc cccgacaccc gctaaaaccc
     3961 cctgacgcgc cctgacgggc ttgtctgctg acgaaaacgc ccacgggaaa gccgtgaccg
     4021 cctccgtcag cttcgttatg ttcctgtttc actttcggcc tcaaagcgaa tctggatgct
     4081 gttctggagt tcttctgcga gttcgtgcag tcgttcgcac atggccgcct gttcgtcggc
     4141 atccagagca tccagttttt caagcagtgt caggc
//
