LOCUS       NZ_CP023652             4238 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain CFSAN030807 plasmid pCFSAN030807_7, complete
            sequence.
ACCESSION   NZ_CP023652
VERSION     NZ_CP023652.1
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 4238)
  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  JOURNAL   Unpublished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 4238)
  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
            CP023652.1.
            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..4238
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="CFSAN030807"
                     /serovar="Serotype group D"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pCFSAN030807_7"
                     /geo_loc_name="Somalia"
     gene            join(4212..4238,1..687)
                     /locus_tag="AT852_RS28015"
                     /old_locus_tag="AT852_28015"
     CDS             join(4212..4238,1..687)
                     /locus_tag="AT852_RS28015"
                     /old_locus_tag="AT852_28015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001590713.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_001590713.1"
                     /translation="MNKKLIFSVLLCLFSFGSVAGIPVAIDASPEWAVEATRWTERLKQ
                     WSETARHYQSQIQAYKDQLATATGIRNIAAFTNELSNLQSELANIYKQGNSYISDFTSN
                     PEGALSSQAKNLFSKYGAFNMCSTGIESSDNLCKARIVSTAASIEQGNEINKQLSSAMS
                     QIQSLSNRIESSKDMKESQDLANALQAQSLKIQAIKMQYDVWDSKNRADAEMLKEQKYA
                     EYRLRQKNAKIPSFE"
                     /name="type IV secretion system protein"
     gene            689..991
                     /locus_tag="AT852_RS29165"
     CDS             689..991
                     /locus_tag="AT852_RS29165"
                     /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="WP_000593833.1"
                     /translation="MIKLNKLKEWVDNHWSRLNSTGSTPPPLLISLPIIVIVLSVELTL
                     KLVNALMYYGTLQFITDKIEKRFVPSGGIKERLLFTLKLFCILLLLLIVMRFSMK"
                     /name="hypothetical protein"
     gene            1875..2390
                     /locus_tag="AT852_RS28030"
                     /old_locus_tag="AT852_28030"
     CDS             1875..2390
                     /locus_tag="AT852_RS28030"
                     /old_locus_tag="AT852_28030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000097059.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            2454..2861
                     /locus_tag="AT852_RS28480"
     CDS             2454..2861
                     /locus_tag="AT852_RS28480"
                     /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="WP_133299398.1"
                     /translation="MSKNDVFACACRRLLEVVAGEQKWCFVRLLITTTWLEVFMTKHDA
                     IRISQLHQIFYDDDGLIDSEKNVTILYSIGFTVDEIAHFRNSTPNTVAGQLLNARVKLG
                     CASVSSLKPMILLRLLLNIKEIRFGFETDCK"
                     /name="hypothetical protein"
     gene            2949..3212
                     /locus_tag="AT852_RS28035"
                     /old_locus_tag="AT852_28035"
     CDS             2949..3212
                     /locus_tag="AT852_RS28035"
                     /old_locus_tag="AT852_28035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_000717655.1"
                     /translation="MKKICTLLMSIFILSACGEDTKSSDWWLNHPKEATEKYKECKKSG
                     EDSVNCQNVKKVAGIIGRTYGPMLEILKAESAEYDKQHGLNR"
                     /name="EexN family lipoprotein"
     gene            3217..4215
                     /locus_tag="AT852_RS28040"
                     /old_locus_tag="AT852_28040"
     CDS             3217..4215
                     /locus_tag="AT852_RS28040"
                     /old_locus_tag="AT852_28040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_000012467.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCYMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGAAGMAV
                     EKTRNQMKRGTRTAAEWAGEKGEQKRASIGALGMEARRRASLEKARARNSA"
                     /name="type IV secretion system protein"
     Typing          3218..4020
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.15e-160"
ORIGIN
        1 cttttgtgct tattttcatt tggttctgtc gcaggtattc cggttgctat tgatgccagt
       61 ccggaatggg ctgttgaagc cacaagatgg acagaacgac tcaaacaatg gtctgaaaca
      121 gcgcggcatt atcaaagtca gattcaggca tataaagacc agttagccac ggcaacaggt
      181 ataaggaata ttgcggcatt cacaaatgaa ctaagtaacc tacaatcaga gctggcaaac
      241 atttataagc aggggaacag ttatatttct gattttacca gtaatcctga aggtgcatta
      301 agtagtcagg cgaaaaatct gttcagcaag tatggtgctt ttaatatgtg ttctacaggc
      361 attgaaagtt ctgataacct ttgtaaggcc agaatagttt caacggccgc tagcattgaa
      421 cagggaaatg agataaataa gcagctatca agtgcaatgt ctcagattca gagtttaagt
      481 aaccgaattg agtcttcaaa ggatatgaaa gaatcccagg atttggctaa cgcattgcag
      541 gcgcagtcgt taaaaataca ggcaattaaa atgcagtatg atgtatggga tagtaaaaac
      601 agggctgatg cggaaatgtt gaaagagcaa aagtatgctg agtatcgcct gcgtcagaaa
      661 aatgcaaaga taccgagttt cgaatgatat gataaagcta aataagctaa aagaatgggt
      721 agataatcat tggtctagat tgaatagtac cggttctaca ccgccgccac tgttaatctc
      781 gctaccaatc atagttattg ttttaagtgt ggagcttacg ttaaagctgg ttaatgcttt
      841 aatgtattat ggtacattgc aatttatcac tgataaaatt gaaaagaggt ttgttcccag
      901 cggtggtata aaagaaagac tcctttttac gttaaagctg ttttgtattt tacttctgtt
      961 attaatagta atgcgatttt caatgaagta aaaaataaag gtcatcgaat agatggcctt
     1021 ttctattcta aattctaaat atagagcctg cggcaggcac aggcaaaaac atcgtttttg
     1081 gacaatcatg gataaaatgt taacattttg accatgattg tctatcctgc attgctcttt
     1141 tgccgacctc aaaaccccta gcgtgttttt gtttcccgat ctctagaacc accgagccgc
     1201 cacggttccg gcagcgcctt gagcgcaacc ggaaaccgtc tggggagaac cccagacccc
     1261 catcgctgta acatcgacgg tctacgacca cctaccaacc gtgtggctac ctgttccgtg
     1321 ctaatgggct ttgcaggggg ctggcgcggt tcttggcgac ctgaaagccc ctggttaggg
     1381 gtatcggcgc gcctgacctc ctgaaaccct ctgtaagcat ttttcgcgcc ttccatgccc
     1441 tgacgggcat ctaaagcccg tttcgtgcgt ctgagcgcgt tttaagagct aagacgacta
     1501 aaacattacc aacacctgaa aatcgcgttc tggtgctctg gatggcccac agaacgcatt
     1561 ttcgaacaga acagcaacgg catttctgac aacatgcgag aggtgatccc gctcgccgca
     1621 gccccagcga ccgaacgtag tgagcgagtg ggcgaggaag cggaagagaa ttgatagcca
     1681 taattgagca cctacgctcc ttagttaaga actaagaagg gaaattctcg gaacccgcat
     1741 gaatcctaga aagtggtgat caggatctgt accttgtaag ctcagatccg gtaccttgca
     1801 ggctcaaaaa ttgcttgatt ttgagcttat gaggatttat tgtgaatccc caaagcccaa
     1861 aaaaggatgc aataatgagc tcgctaagct tacagagata cgaaacaaac ccgtttttag
     1921 agcttatgac gatcccgatg aaagggaaac ggatacaagt atctcgtctt gggcgggatg
     1981 acaatgtttt ggttaatcaa aacacgggag aaaagtttgg aacacatgta accactttta
     2041 agcgtgtaga tagtgagcaa tttgttaagt tgtttactgc gaatattggg ttaacgtttg
     2101 atttatcatc ggcaggaatt aaagctttta atgttctttt atgggctgtt caaaaacaag
     2161 cctttgcaaa ggatcaggtt cttttggatt caagggctct tgatgacttt ttaaaaagct
     2221 atgatagctt aaaacttagt tatgctacgt taaagagagg aattaacgag ttagaaaaag
     2281 ctcagattat agcaaagaca atgcgtaaag gattttattt tataaacccc aattttgtat
     2341 ttaatggaga tcgaatagca tttacaaccc taattgagag ggattgttaa tcgatagaac
     2401 aatacaatgc aggatagaca atccactaga aattgcatgc aattttcagt ggattgtcca
     2461 aaaacgatgt ttttgcctgt gcctgccgca ggctactaga agtagtcgca ggcgaacaaa
     2521 agtggtgttt tgttcgcctg ctaatcacaa caacctggct agaggttttt atgactaaac
     2581 atgatgctat acgcatttct caacttcatc aaatttttta cgatgatgat ggattaattg
     2641 attcagaaaa gaacgtgact attttataca gtataggatt tacagttgat gaaatagctc
     2701 attttagaaa ttcaacacca aacacagttg cgggtcagct attaaatgca agggttaaat
     2761 taggttgcgc ctcggtttca tctttaaagc caatgatctt attaagattg cttttgaaca
     2821 taaaagagat tcgttttgga ttcgaaactg attgcaaata atatagttca ataggtattt
     2881 ttgctcttga ctagaattac aattgctgat tgtatcagca attgtaatgt ccatacgagg
     2941 aatcaaagat gaaaaaaatt tgtacgctct taatgtctat tttcattctt tccgcatgtg
     3001 gtgaagatac aaaatcatca gattggtggc ttaatcatcc caaagaagcg acggagaaat
     3061 ataaggagtg taaaaagtca ggggaagatt ctgttaattg tcaaaatgtt aaaaaagttg
     3121 ccggaattat tggtagaacc tatggcccta tgcttgaaat acttaaggct gagtcagctg
     3181 aatatgataa gcaacatgga ttgaacaggt gataacatgt ctggtttctt tgaaaagttt
     3241 aatagcgaag ttgttagtaa aatcgaagag atgaccaaac cacttcaaag tcaattaggt
     3301 caggatatgt tatctcttct aagtgcaggt attagcgttt atatcctctg ggttggctat
     3361 caaatattgg cagggaaacg ccagacccca ttacaagatc tcgtctggga tctatcaaaa
     3421 tttgccatta ttttaacatt cgtaagcaat gctgatggct atctgacggc agcaatggat
     3481 gctattaaat ctatgaagga tgggttcctt ggtaaacctg tatgggcaac gctagatacc
     3541 atgtggagta caactcagct tttggctgac aaagtttatg ctatggatca atccaaatat
     3601 gtgtcagttg aaggtggaat cgggtcaatg ttggtttggg gaggaagtat cctgattatg
     3661 tctgtagcgg ctgttattta catgcttgcc gatgtaacaa tgcagttagc tattcttgta
     3721 gctccgatat ttatcggttg ttatatgttt ggattcacta gagtaatgtt taataactgg
     3781 cttggtatat tattttctag tgtatttact gttatttttg ctggagttct cgtcaaaatt
     3841 ggtaccgagt ttcaaactga tatgcttagt cagatatcga gagatgctaa ctcaacaaat
     3901 attttaacaa tgggcgcaat ggcatttgta attggagttc tgattgctgt ctttgtctgg
     3961 aaatcatcga gtttcgcgca gcagcttgcc ggtgcaggtg ttgaaggtac tcttcaggga
     4021 atggctcttt tagggattgg ggctgctgga atggccgtag agaaaacgag aaaccagatg
     4081 aaacgtggaa cgcgaacagc cgccgaatgg gcaggtgaaa aaggggagca gaaacgggct
     4141 tcaataggcg cattgggaat ggaagcaaga agacgagcat ccctggaaaa agcacgtgcg
     4201 aggaattcag catgaacaaa aaactaattt tttcagta
//
