LOCUS       CP123657                5055 bp    DNA     circular BCT 14-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Reading strain CVM
            N58646 plasmid pN58646-2, complete sequence.
ACCESSION   CP123657
VERSION     CP123657.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN05416439
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Reading
  ORGANISM  Salmonella enterica subsp. enterica serovar Reading
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5055)
  AUTHORS   Ge,B.
  TITLE     Genomic Analysis of Azithromycin-Resistant Salmonella from Food
            Animals and Retail Meats, 2015-2021, United States
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5055)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 5055)
  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                   :: 632x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 10:10:26
            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)                     :: 4,686
            CDSs (total)                      :: 4,567
            Genes (coding)                    :: 4,457
            CDSs (with protein)               :: 4,457
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 52 of 110
            Pseudo Genes (incomplete)         :: 74 of 110
            Pseudo Genes (internal stop)      :: 17 of 110
            Pseudo Genes (multiple problems)  :: 30 of 110
            Pseudo Genes (short protein)      :: 1 of 110
            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..5055
                     /organism="Salmonella enterica subsp. enterica serovar
                     Reading"
                     /mol_type="genomic DNA"
                     /strain="CVM N58646"
                     /serovar="Reading"
                     /isolation_source="ground turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:165302"
                     /plasmid="pN58646-2"
                     /geo_loc_name="USA:MN"
                     /collection_date="2015"
                     /collected_by="FDA"
     gene            join(4929..5055,1..128)
                     /locus_tag="BCP20_23380"
     CDS             join(4929..5055,1..128)
                     /locus_tag="BCP20_23380"
                     /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="WGN09266.1"
                     /translation="MDSNNSQKNLQDKHADLLDKTYTLGWLDGYSEGYDDAIEDCQNAL
                     NKLENENELLNEIIENKDNVISEMASSVGRALQTVKKNK"
                     /name="hypothetical protein"
     gene            complement(158..1216)
                     /locus_tag="BCP20_23385"
     CDS             complement(158..1216)
                     /locus_tag="BCP20_23385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012508929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0005524 - ATP binding [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WGN09267.1"
                     /translation="MAIYAVWNNKGGVGKSYLTFQLASEYARQNPTKKVLVIDLCPQAN
                     SSSMLLGGMVNGENTLNQIHSATQRKTISGYIEDRIRSPYIPTNTGSNYVINVSTYNSR
                     IPDNLYLVTGDEQLELQASRVVGASFPGPHDAWRTVHLWINDLISDICNSWDNGDSCVF
                     IDCNPSFSIYTELALTAAERLLIPFSADGSSKRAVKAVLSLVYGERRHLNEPQSDFYLN
                     SNRYSMSLPQIYMYIGNRLTQMNNSSASAFKTVVTEIGDEIWKVWQTKPSLFCIHPNGS
                     STPNNKKSFRNMFQYEVNDANTASVVSGALGIPIATLTAGNKNVAGRTIKVNQTQLDKQ
                     VPNIVALAGMIE"
                     /name="ParA family protein"
     gene            complement(2381..2572)
                     /locus_tag="BCP20_23390"
     CDS             complement(2381..2572)
                     /locus_tag="BCP20_23390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="WGN09268.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2637..2960
                     /locus_tag="BCP20_23395"
     CDS             2637..2960
                     /locus_tag="BCP20_23395"
                     /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="WGN09269.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3169..3600
                     /locus_tag="BCP20_23400"
                     /pseudo=""
     CDS             3169..3600
                     /locus_tag="BCP20_23400"
                     /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            3638..4156
                     /locus_tag="BCP20_23405"
     CDS             3638..4156
                     /locus_tag="BCP20_23405"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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="WGN09263.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            4163..4396
                     /locus_tag="BCP20_23410"
     CDS             4163..4396
                     /locus_tag="BCP20_23410"
                     /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="WGN09264.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            4754..4939
                     /locus_tag="BCP20_23415"
     CDS             4754..4939
                     /locus_tag="BCP20_23415"
                     /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="WGN09265.1"
                     /translation="MTEDNVKNISDYRKNNDAVDANSSAISGKSAPAKLSEKLRNTVPS
                     GLRAQMRQQMRNKHGF"
                     /name="hypothetical protein"
     Typing          2211..2296
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          complement(1641..2189)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.595"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2951..4500
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.511"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgccttgaa taaactggaa aatgaaaacg aattgctcaa tgaaattatt gaaaacaaag
       61 ataatgtaat cagtgaaatg gcatctagtg tgggcagggc gttgcaaacg gtaaagaaaa
      121 ataaataaaa acaggccctt gaaaaagggc ctgtttttta ctcaatcata ccggcaagag
      181 cgacaatgtt gggcacttgc ttatcaagct gtgtctgatt tacctttatt gttcttcccg
      241 caacattctt atttcctgcg gttagtgtgg caattggaat accaagtgct cctgatacga
      301 cagatgctgt attggcatca tttacttcat actggaacat gttcctaaag gattttttat
      361 tattcggcgt tgagcttcca tttggatgaa tgcagaataa acttggtttt gtttgccaca
      421 ctttccaaat ctcatcgccg atctctgtta ccacagtttt gaatgcgcta gctgatgagt
      481 tgttcatttg agttaatctg tttccaatat acatgtatat ttgtggtaat gacatagaat
      541 aacgattgct gtttaaatag aaatctgact gtggttcgtt cagatgacgt cgctcgccat
      601 aaactaaaga aagaactgct ttaacagctc tttttgatga accatcagca gagaatggaa
      661 ttaataggcg ttcagctgcg gttaatgcta actcggtata aatagagaag ctgggattgc
      721 agtcgatgaa aacgcagctg tcgccattat cccatgagtt acaaatgtca ctaattagat
      781 cgttaatcca aagatgaaca gttctccatg cgtcatgagg tccagggaat gatgctccaa
      841 caactcttga tgcttgaagt tctaattgct catcgccagt aacaagatat agattatctg
      901 ggattctgct attgtatgta gatacgttga ttacgtagtt agaacctgta tttgtcggaa
      961 tatatggact tctaatccta tcctcaatat atccagaaat agtctttctt tgtgttgcag
     1021 aatgaatctg atttagcgta ttttcgccat taaccatccc gccaagtaac attgaggatg
     1081 agttagcttg tgggcataga tcaatcacca gaaccttttt tgtcgggttc tgtctggcgt
     1141 actcagaggc tagttgaaag gtaagataac ttttccccac tccgcctttg ttattccata
     1201 cggcatagat cgccatctat cactcctaat atagttttgt tgttagcttt aagtcagagt
     1261 actagagatt attgttctac tgttagtttc tttcagctaa ctgactgtgt ttcgagcggt
     1321 atggttagat gagggtgtcc gtattggcat gacctcttca gcatagtagg aacgtgattg
     1381 aaaggatttc ttgagatcct tattcgtggg atgtaatctt ctgcactgta aacgaaaaaa
     1441 ccacctgggg aggtggtttt tcgaaggatc agtaagttgg ggaacttctg aaccgtggta
     1501 acagggtgta caagaccact gccaccaaat ctgtcctttc agtttagctg tagttaggct
     1561 tcaacttcaa gaactctgcg ttagtaatat cttgtacatc ccttaccagt ggctgctgac
     1621 agtggcgtta agtcgtgtct taccgggttg gactcaagac gatagttacc ggataaggcg
     1681 cagcggtcgg gctgaacggg gggttcgtgc acacagccca gcttggagcg aacgacctac
     1741 accgaactga gataccaaca gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga
     1801 aaggcggaca ggtatccggt aagcggcagg gtcggaacag gagagcgcac gagggagctt
     1861 ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacct ctgacttgag
     1921 cgtcgatttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc caacagcgca
     1981 gccttttccg ggttctcgtt ttttgctcac atgtttcttt tggcgttatc ccctgattct
     2041 gtggataacc gcatctccgc ttttgagtga gccgacaccg ctcgccgcag ccgaacgacc
     2101 gagcgtagcg agtcagtgag cgaggaagcg gaagagcgcc ggaacgtgca ttttctcctt
     2161 acgcatctgt gcggcatttc acaccgcata tggcgctctt ttcttacaat ctgcactgat
     2221 gccgcatggt taagccagta tacactccgc tatcgctacg tgactgggtc atggctgcgc
     2281 cccgacaccc gctaaaacct gctgacgcgc cctgacgggc ttgtctgctc ccggcatccg
     2341 ctcacagaca agctgtgacc gtctccggga gctgcatgtg tcagaggttt tcaccgtcat
     2401 ccccgaaacg tgcgaggcag ctgcggtaaa gctcatcggc gtggtcgtga agcgattcac
     2461 agatgtctgc ctgttcatct gcgtccagtt cgttgagctt ctccagcagc gttaatgtct
     2521 ggcttctgat aaagcgggcc atgttaaggg cggttttttc ctgtttagtc actgatgcct
     2581 ccgtgtaagg gggtatttct gttcatgggg taatgatacc gatgaaacgc gagaggatgc
     2641 tcacgatacg ggttactgat gatgaacatg ccaggttact tgaacgctgt gagggtaaac
     2701 aactggcagt atggatgcgg cgggtctgcc tgggtgagcc ggttgcccgt tccgggaagc
     2761 tgccgacact ggcaccgccg ttactgcgtc agctggccgc catcgggaat aacctgaatc
     2821 agacagcgag gaaggtgaac agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg
     2881 ccgcactgat ggccatcggg gatgagctgc gccggctgcg tctggccgtc agggaacagg
     2941 gggcgcggga tgatagttaa atttcatgcc aggggaaaag gtggtggcag tggtccggtt
     3001 gattacctgc tggggaggga gcgtaaccgc gaaggcgcaa cggtgcttca gggtaatccg
     3061 gaagaagtcc gggaactcat cgatgccacg ccatttgcga agaaatacac gtccggtgtt
     3121 ctgtcgttcg cggagaagga gctgccgccg ggaggacgtg aaaaagtgat ggcgagcttt
     3181 gagcgtgtac tgatgcccgg tctcgaaaaa aatcagtaca gcatcctgtg ggtggagcac
     3241 caggacaagg gacggcttga gctgaatttt gtcattccga acatggagct acagaccgga
     3301 aaacgcctcc agccgtacta cgaccgcgca gacaggccta gaattgatgc ctggcagacg
     3361 ctggttaatc accattacgg gctgcatgac ccgaacgccc cggagaaccg caggacgctg
     3421 acactctctg ataatctgcc ggaaacgaaa caggcgattg ctgagggcgt tacacgcggg
     3481 atagacgcgc tttaccatgc cggagagata aaaggccgtc aggatgtgat tcaggcgctc
     3541 acagaggcgg ggcttgaagt ggtcagggtg acgcgaagca gtatcagcat tgcagacccg
     3601 aacggcggga ggaatatcag actgaaagga gcgttttatg agcaatcttt tacagacggg
     3661 cgcggagttc gagaaaaagc tgaaagagag agccgaatct acagagaaaa tgctgaacaa
     3721 cgagttcagg aagctcggcg agtctgtcag cgaggctgtg acctcaaacg agacgaaaat
     3781 cagagacgct atagccctgt tcacagcctc gacagagaaa tcgctggaaa aacaccggga
     3841 aggggtgaaa gaggcgatga tgcagcacag gaaggacgtg ttaaagctgg cagggaatac
     3901 gggcatgatg ttactgggga tagtctttct cctgtttacc gcgagtggcg ggacgctctg
     3961 gtatcttggc gggcggatac aggcgaacct ggaagaaatc aggatacagg aagaaacatt
     4021 gcagaaactg aacgcgaaga catggggcgt ggagtttgtg caggacggga gaaggaaatt
     4081 tctggtcctt ccgtacggga aatcggcaac ggtgattccc tatcagggga aggactgggt
     4141 acaactgacg gagtgacaca gagtgacgga gctggaaaga catttgctga acgcattaga
     4201 gcaactgcaa caggactata tgcagcggct gagcgaatgg gagagcgcct tcgtggaatt
     4261 gcagaagatg ttttcgctta cgcaacggga caacgcgatg ctgaacgagc gggtcatgca
     4321 gttgagtcag caggtgcagc acttgagcga gcagacagaa cgcttgagcc agttatacag
     4381 cgagaactgg agataagaga ggaacggctg atacaggagc gcgaacatgc gttatccctg
     4441 gaacgggagc gtcagccgga aatacaggaa cgcacgctgg atggtccttc gctgggatgg
     4501 tgaaaccatg aaaaatggca gcttcagtgg attaagaggg gttaatgtgg cctgtaccat
     4561 ctggttgcat aggtattcat gcggttaaaa tttatcaggc gcgatcgcgg cagtttttcg
     4621 ggtggtttgt tgccattttt acctgtctgc tgccgtgatc gcgctgaacg cgttttagcg
     4681 gtgcgcgtaa ggggtgttat gttcaattct ccagcgtata ttgggctgtt tacagcaata
     4741 ggtgtaatgt tctatgactg aagataacgt taagaatatt agcgactaca gaaagaataa
     4801 tgatgctgtt gatgctaata gtagtgctat ttcaggtaaa agcgctccag ctaagctgag
     4861 tgagaaactt agaaatacag ttccttctgg actgagggcc caaatgcgcc aacaaatgag
     4921 gaataaacat ggattctaat aacagtcaga aaaaccttca agataagcat gctgatcttc
     4981 tggataaaac ttatactctc ggctggttgg atgggtattc agaagggtat gatgatgcca
     5041 ttgaagattg tcaaa
//
