LOCUS       NZ_CP023651             5114 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain CFSAN030807 plasmid pCFSAN030807_6, complete
            sequence.
ACCESSION   NZ_CP023651
VERSION     NZ_CP023651.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03612247
            Assembly: GCF_002442535.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5114)
  AUTHORS   Hoffmann,M., Sanchez,M., Baugher,J. and Timme,R.
  TITLE     Whole genome sequencing of cultured foodborne pathogen
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5114)
  AUTHORS   Hoffmann,M., Sanchez,M., Baugher,J. and Timme,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-2017) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v.3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 700.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002442535.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 03:16:54
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,167
            CDSs (total)                      :: 5,037
            Genes (coding)                    :: 4,336
            CDSs (with protein)               :: 4,336
            Genes (RNA)                       :: 130
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 701
            CDSs (without protein)            :: 701
            Pseudo Genes (ambiguous residues) :: 0 of 701
            Pseudo Genes (frameshifted)       :: 197 of 701
            Pseudo Genes (incomplete)         :: 506 of 701
            Pseudo Genes (internal stop)      :: 123 of 701
            Pseudo Genes (multiple problems)  :: 117 of 701
            Pseudo Genes (short protein)      :: 3 of 701
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023651.1.
            Bacteria and source DNA available from Dwayne Roberson, US FDA.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5114
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="CFSAN030807"
                     /serovar="Serotype group D"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pCFSAN030807_6"
                     /geo_loc_name="Somalia"
     gene            complement(join(5097..5114,1..429))
                     /locus_tag="AT852_RS27995"
                     /old_locus_tag="AT852_27995"
     CDS             complement(join(5097..5114,1..429))
                     /locus_tag="AT852_RS27995"
                     /old_locus_tag="AT852_27995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_024235834.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPHNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            601..2151
                     /locus_tag="AT852_RS28000"
                     /old_locus_tag="AT852_28000"
     CDS             601..2151
                     /locus_tag="AT852_RS28000"
                     /old_locus_tag="AT852_28000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_039063720.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARHGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGELDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALCIQRSWARGVSRSNERDQDMER"
                     /name="MobA/MobL family protein"
     gene            complement(2347..3447)
                     /locus_tag="AT852_RS28005"
                     /old_locus_tag="AT852_28005"
     CDS             complement(2347..3447)
                     /locus_tag="AT852_RS28005"
                     /old_locus_tag="AT852_28005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001569522.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_252981440.1"
                     /translation="MNINFKHILPLLSSFFISGCDSDGISKVKSFVYYDIDDSMTVGKA
                     FDTRSDCINGTWSEKEDDRGRTIVTYTCDISESGLKIINSAIMQEPEDKAEYSIAQNNN
                     SIKSTNESLEEYKQKTPLVEKTKEVIIDHIRKLNSAFNEDPMIYSKLTISPYLDRMLYL
                     KDHNDNALNEICGGYEYIQSADSYSWRDVSEEYAKESCEKHIYKVYQSFKKNASPLITK
                     NSPGFYERVPPCENADECIKKTNIYFDDNFLNIYKRSQDRAPQIISDLKKHNIEIGEKL
                     NDCRKKLNISDVKLTYYWFVTDTGGVDYLDGVLTYNFQGKNRAENFHKQLLQYAYINYS
                     KNQIPRDFVTSIKNSIYYKIEDCTKF"
                     /name="hypothetical protein"
     gene            3968..4903
                     /locus_tag="AT852_RS28010"
                     /old_locus_tag="AT852_28010"
     CDS             3968..4903
                     /locus_tag="AT852_RS28010"
                     /old_locus_tag="AT852_28010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_024235833.1"
                     /translation="MSAALQYFEENLPHRPYHTDELAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDRVGAAIDWSDRNAPAPNITVKNPENGHAHLLYALNLAVRTAPDASVKA
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYALDELADYLDLRASE
                     RRSVDKHYGLGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPESFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLNVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     Typing          3969..4903
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          602..2148
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gagtagctct ttcccgcgtt tttcccattc ctgccatttt ggatggttgt gcggtagctc
       61 tgcgattcct gcgagtgcgc ctaccagttc ggcagcacta aactttggct ttccggtttt
      121 gctgtccacc agtcctgcca caatcatgag gcctgcggcc ttgtagagtt catgatcccg
      181 cgcctttcgt tccgcccttg cggctgcctt ccgttctgcc gctatgattg ccgttactct
      241 ggcttttgct gcggctgctt tctctgcggt tttttctgcc cgtatcagtg cggacaacgt
      301 tttttcatcc gtcgttgttc ggtttttttt ctctgccagt aacacaagta atctctgctg
      361 ctctgatggt gatttcagtc cgttgatgta ggcaattttt gcacttaacc actcttcacg
      421 atttgtcatt cttacctctg cacttttgcc gttaatgtga gttgttatta tgcataatat
      481 caccttgttt gcctgcgtgt gagaccgtaa aatcatccat gattaattca gggatgcgca
      541 cttagtagtt tctctccttc gtcgagaaac tgtgcgctcc tgcggagggc taaaaggcag
      601 atggcaagct accattgcac tgtcaaagct ggagcaaaag gcagtgcctt aaaacatgct
      661 gattacattt ccagatccgg cgaatataag agttacaaat cgcgggagga tctggaattt
      721 tcgtcatccg gtaacatgcc atcatgggcg aagaaaaatc ccgcagagct atggaaagcc
      781 gcagatgaat ttgaacgaaa aaacgggact gcataccgtg aaattgagat cgcgttaccg
      841 cgtgaactga cacgcgaaca acggatagaa cttgttgaag atttcgtgca aaaggaactt
      901 ggcgatcgcc atgcctacca gtacgcgatc cacaatccgc caggtgcaat cgacggaaag
      961 gaacagccac acgcgcatat catgttttgc gagcggatta atgatggtat tgaacgcgat
     1021 ccacagcaat tttttaaacg tgccaacagc aaatcaccag agcggggagg cgcaaaaaaa
     1081 gcgagtattc cccagacagc cggagagcga aaagccgccc ttgttgcgct gcgttcccgc
     1141 tgggcagatg tgcagaatga gcaccttgcg cgacacggtc acgagtcgcg cgtagatcat
     1201 cgttctctga aagaacaggg tatcaatcgc acgccggaag ttcatcttgg ccccgttcag
     1261 gccgccagtc tgaatgggga gcagattgtt gcaatccagg aacggaggaa tgccgagcgg
     1321 gaactcaaga ccgccagaga tgccgcaaat gccattcagc aggaacagga gcaaaagcaa
     1381 aaaatcaagg cagttgagcc tgttcgttca gcccgttcac cggagttatt gcttcagtac
     1441 cgcaaggtta tgaaaacggt cattcaggga gaggcaaggc ttgctcgttt aggggatgcc
     1501 aatcccaatg cgctcaaaga acataagctg cttcagaatg cgaaagctaa aaaagactct
     1561 ctttccgaat ggagtcgacg aatatatgaa ggggcacggt atttagacaa actggggcgt
     1621 aatgttgttt ccgcacaaag ggagctgcgg gagctacagg aacaacgcaa tgctttgaat
     1681 gggattcgtg gcctgtttcg gggggctgac aaaagggaga ttgatgcgcg tattctggag
     1741 caaaaaagtg tgctggaaac cgctgaacat gaaaggaatg aattcaggaa caagctacag
     1801 caagccgaat ccgagtggga caaagaaaac gctgctttta agcgtaccga gggatataag
     1861 tacgttgggg agctggacag gtacagagaa cgcgagattc tggcggcggc atctttagag
     1921 aacaccaggc aaaaggttgc tgaagaggta tccgttgccc gtagccagat gttatctctg
     1981 gagcctgaac tcagtatatc tggagatgaa aaagctcaaa tgcgacatga gttactggca
     2041 gaaatggcgc aggaacggca gcaacaggag gaaaaagcac tgtgtataca gcgatcctgg
     2101 gccagggggg tatcacgtag taacgaacgt gatcaagata tggagcgttg aaaatgtagc
     2161 aatatcggga ctgcgccccg aaccccgcca acgtttcacg gaacgcgaaa aaattccgcg
     2221 tcccgtgaaa cgttttctga atgagaaaaa ttgtcgtttt gatttactca cagttcagat
     2281 taatgaagtt aacaggtgtt aaatatttgc aggtggttat atgtgtaacc acctgtaagg
     2341 gaaggactaa aacttagtgc aatcttctat tttataataa atactatttt ttattgatgt
     2401 tacaaagtcc cgaggtattt gatttttgct gtagttaatg tatgcatatt gcaatagttg
     2461 tttatgaaag ttttcagctc tattctttcc ctgaaaatta tatgtcaaca ccccatctaa
     2521 ataatcaact cctccggtat ctgttacaaa ccagtaatag gttaatttga catctgagat
     2581 atttagtttt ttcctacaat catttaactt ttcacctatt tctatattgt gtttttttaa
     2641 atcagaaatt atttgaggtg ctctatcttg gcttcttttg tagatattta gaaagttatc
     2701 atcaaagtat atatttgttt tttttatgca ttcatctgcg ttctcacagg gggggacacg
     2761 ttcgtagaaa ccgggggagt ttttagttat taatggtgat gcatttttct taaacgattg
     2821 atatacttta tatatatgct tttcgcatga ttcttttgca tactcttcac ttacatcacg
     2881 ccaactgtaa ctatcggcag attgaatgta ttcgtaccca ccacaaattt catttagcgc
     2941 attgtcatta tggtccttta gatatagcat tctgtctaaa taagggctaa ttgtgagttt
     3001 gctatatatc attggatctt cattaaaagc actgtttagc tttcttatat gatctattat
     3061 gacctctttt gttttttcca ccagaggcgt tttctgtttg tattcctcta gtgattcatt
     3121 ggttgatttt atgctgttgt tattttgtgc tatagaatat tcagccttat cttcaggttc
     3181 ttgcataatg gctgaattta ttatttttag gccactttca ctaatatcac aggtatatgt
     3241 gacgatggtt cttcctcgat catcctcttt ttcactccat gtgccattga tgcaatcact
     3301 ccttgtatcg aaggctttac caacagtcat tgagtcgtca atgtcgtaat atacgaaaga
     3361 ctttaccttg cttattccat cagagtcgca tcctgaaata aaaaatgacg acaataaagg
     3421 aaggatatgt ttaaagttaa tattcatttt tcccattttt atttctaaca ataacgagga
     3481 aatattaata caggcgatat gttaatggaa tccatacata ccgataaacc gacttactat
     3541 gtttgtgctc aacgtcttac gcagttcgaa aagatttcgc accagttcac ctttttctgg
     3601 atgagaaagt ttgctgtttt gacctgttcg ctgttcaaaa cgagtgaaac cggacatgaa
     3661 tcgctttcgt gcatagttat gcagccccct gaaaacaatt ctggcgcgtt tttttggtct
     3721 ggcctgttgt ttccctgtct ttttgcgttt tttgcgacag aaagcgactg agggcgtttt
     3781 aaggggggcg cacaacggga gttatggtaa atggatcggg tttgcgggaa gactcgacag
     3841 gttttgtcgt tgggggtagt gtaagcgact gaaaaacaaa cgcccctgaa attcgtgtct
     3901 atccggcaag actttcacga agatacaggg gcgatgtcgg tcgataacct ggaaggaatc
     3961 gtaacacatg agcgccgcgc ttcaatactt cgaagaaaat ttacctcacc gtccctatca
     4021 cacggatgag ctcgctttcg gtcttcgtat ctccggcaaa gggcgtgcgc tgcttgctcg
     4081 ctacatccag caaaatcagc ctcatgcgca gttctggctg gtttttgacg ttgaccgcgt
     4141 aggagctgcg attgactgga gcgaccggaa cgcccccgcg ccgaacatca ccgtaaaaaa
     4201 tcccgagaac gggcacgctc acctgctcta cgcgctcaat cttgccgtga gaaccgcgcc
     4261 tgatgcgtcg gttaaggcgc tgaaatacgc cgctgcaatt gaacgtgcgc tgtgtgagaa
     4321 acttgacgca gatgtgaact acagcggact gatttgcaaa aatccgttcc acctggaatg
     4381 gcaggtgatg gagtggcgcg aggaagccta cgccctcgat gaactggctg attatctcga
     4441 tttgagagcc tcagagcgtc gtagcgtcga taaacattac gggctggggc gaaactgcca
     4501 tctgttcgaa atgacgcgca aatgggctta cagggcgatt cggcagggct ggccagcatt
     4561 ctcacagtgg cttgatgctg tgattcagcg tgtcgaaatg tacaacgcat cgcttcccgt
     4621 tccgctttct ccgcctgaat gtcgggctat tggcaagagc attgcgaaat acacgcacag
     4681 gaacttcacg ccggaaagtt tcgcacagta tgtggctgat acgcacacac cagaaataca
     4741 ggccaagaga ggccggaaag gtggcatcgc taaaggcgaa gcctacgatg acaagcgttt
     4801 catggcgcta tgtatgctgg agaatggata ttctcagaaa gctattgcgg cgatgctgaa
     4861 tgtacatcgt aatacgatcc gtaattgggc aatgcacaaa tagcctatat cagataacag
     4921 cgccttttcg gcgtcttttt gagcagcggg ctttccggcg gttttctcct ttcagcccag
     4981 caatggtgcg gcttaccgta tgattgaggt ggtcgtgctc gccgcagtct catgaccgag
     5041 cgtagcgagc gaatgagcga ggaagcacca gggaactgga acgtgaacgg aggctcttac
     5101 gcactgtctt tggt
//
