LOCUS       NZ_CP023650             5153 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain CFSAN030807 plasmid pCFSAN030807_5, complete
            sequence.
ACCESSION   NZ_CP023650
VERSION     NZ_CP023650.1
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 5153)
  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  JOURNAL   Unpublished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 5153)
  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
            CP023650.1.
            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..5153
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="CFSAN030807"
                     /serovar="Serotype group D"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pCFSAN030807_5"
                     /geo_loc_name="Somalia"
     gene            9..332
                     /gene="mobA"
                     /locus_tag="AT852_RS27955"
                     /old_locus_tag="AT852_27955"
     CDS             9..332
                     /gene="mobA"
                     /locus_tag="AT852_RS27955"
                     /old_locus_tag="AT852_27955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(557..976)
                     /locus_tag="AT852_RS27960"
                     /old_locus_tag="AT852_27960"
     CDS             complement(557..976)
                     /locus_tag="AT852_RS27960"
                     /old_locus_tag="AT852_27960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(1057..1476)
                     /locus_tag="AT852_RS27965"
                     /old_locus_tag="AT852_27965"
     CDS             complement(1057..1476)
                     /locus_tag="AT852_RS27965"
                     /old_locus_tag="AT852_27965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001711305.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001329498.1"
                     /translation="MAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRREFETSE
                     LIRAYGELKRNETPERHTQGHSEKPHDQQTERILRELNELKQCLTLMLEDKQAQDTERR
                     RQEAERKQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="hypothetical protein"
     gene            1754..3319
                     /locus_tag="AT852_RS27970"
                     /old_locus_tag="AT852_27970"
     CDS             1754..3319
                     /locus_tag="AT852_RS27970"
                     /old_locus_tag="AT852_27970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_000447004.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTVQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            complement(3316..3657)
                     /locus_tag="AT852_RS27975"
                     /old_locus_tag="AT852_27975"
     CDS             complement(3316..3657)
                     /locus_tag="AT852_RS27975"
                     /old_locus_tag="AT852_27975"
                     /inference="COORDINATES: protein motif:HMM:NF015489.4"
                     /GO_function="GO:0015643 - toxic substance binding
                     [Evidence IEA]"
                     /GO_process="GO:0030153 - bacteriocin immunity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 family microcin immunity protein"
                     /protein_id="WP_000058755.1"
                     /translation="MSLRYYIKNILFGLYCALIYIYLITKNNEGYYFLASDKMLYAIVI
                     STILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLL
                     GLFISIKNN"
                     /name="colicin E1 family microcin immunity protein"
     gene            3705..3842
                     /locus_tag="AT852_RS27980"
                     /old_locus_tag="AT852_27980"
     CDS             3705..3842
                     /locus_tag="AT852_RS27980"
                     /old_locus_tag="AT852_27980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001329514.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVAPSSSSKLTGISVQ
                     "
                     /name="colicin release lysis protein"
     gene            complement(4684..4878)
                     /locus_tag="AT852_RS27990"
                     /old_locus_tag="AT852_27990"
     CDS             complement(4684..4878)
                     /locus_tag="AT852_RS27990"
                     /old_locus_tag="AT852_27990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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="WP_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4914..5153
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(4126..4655)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.59"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          10..329
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="4.45e-62"
ORIGIN
        1 catgttttat gacaaaacga agtggaagta atacgcgcag gcgggctatc agtcgccctg
       61 ttcgtctgac ggcagaagaa gaccaggaaa tcagaaaaag ggctgctgaa tgcggcaaga
      121 ccgtttccgg ttttttacgg gcggcagctc tcggtaagaa agttaactca ctgactgatg
      181 atcgggtact gaaagaagtt atgagactgg gggcgttaca gaaaaaactc tttatcgacg
      241 gcaagcgtgt cggggacagg gagtatgcgg aggtgctgat cgctattacg gagtatcacc
      301 gtgccctgtt atccaggctt atggcagatt agcttcccgg agagaaaact gtcgaaaact
      361 gacggtatga acaccgtaag ctcccaaagt gatcaccatt cgctttcatg catagctatg
      421 cagagagctg aaaacgatcc tgacgcatcc ttcctgtttt tccggggtaa aacatctctt
      481 tttgcggtgt ctgcgtcaga atcgcgttca gcgcgtttca gtggtgcgta caattaaggg
      541 attatggtaa atccacttac tgtctgccct cgtagccatc gagataaacc gcagaaatcg
      601 tgtcagccag cagcctggat tttttcgggg taaggtcttt gctgcggtaa tcagtacccg
      661 caaattgagt tgtgccccgg agtgagttta aaaattcctg gctgtgaaac tgttgaatgc
      721 gttgttgcac atcactccgt gattttcctg tcgctttatc tttagctccc atatcccaga
      781 actgccgaaa aaaaggcacc atcattcgtg ttgtgtcggc tttttgggtg gaaaagttgg
      841 gatcaaaacc gtcatcagaa gcatatacgt aatgccgggt atgttgttcc acgctgccct
      901 ttggggtaca ggctgtgaga gctactgttg ctgttatcat ggcgataaga caaagtttgt
      961 ttccggtacg tctcatgagt gtctccctac cttaaagtat ttattctcgg tgagttatta
     1021 tccgaagatt atcttatcat cagtttctga gcgcgttcag tgaccgaaca gcctggacca
     1081 gaatccccgt ttcttttcct gctccagagc ctgcctgagc tgggctatct cattctgtag
     1141 ctgtttccgt tctgcttcct ggcgccggcg ctccgtatcc tgggcttgtt tatcctcaag
     1201 catcagcgtc aggcattgtt tcagctcatt cagttcccgg agaatgcgtt ctgtctgctg
     1261 atcatgaggt ttttctgagt gtccttgagt gtgcctttct ggtgtctcat tccgctttaa
     1321 ttcgccgtat gcccggatca gttcactggt ttcaaactcc cgtcgtccgt cctggctggt
     1381 acggtaactg acaagacctg agcgcatatc acggtaaaac tgtgaacgcg atcttccagt
     1441 cattttcagt gcgtcccgga gtgtgtgcca tgccataaag ttacagtgtc ccataggtgt
     1501 ctcatctcat ggtttcagta aaacataatg aggtctgaga acggtaatgt ttgtgctggt
     1561 ttttgtggca tcgggtggaa atagcacgtg gtgtgggtgg ctgttttttt gatcgttttc
     1621 acaaaaatga aaatccacag ggttgacagg gaaaatgcag cggcgtaatt ttaaactgta
     1681 tataaaacca gtgattatat atacagtatg ttgcttttaa ctatttgttt ttaatgtcaa
     1741 agaggatttt ataatggaaa cagctgtagc gtactataaa gatggtgttc cttatgatga
     1801 taaggggcag gtaatcatta ctcttttgaa tggtaatcca gacgggagtg gctctggcgg
     1861 tggtggtgga actggaggta gcaaaagtga aagttctgca gccattcatg ccacagctaa
     1921 atggtctact gctcaattga agaaaacgca ggcagaacag gctgcccgag caaaagctgc
     1981 cgcagaagca caggctaaag caaaagcaaa ccgggatgcg ctgactcaac atctgaagga
     2041 tattgtgaat gaggcgcttc gccataattc cactcatccg gaggttattg acctggctca
     2101 tgccaataat gcagcgatgc aggcagaagc agagcggttg cgccttgcaa aagcagaaga
     2161 aaaagcccgt aaagaagcgg aagctgcgga aaaggctttt caggaagcag aacaacgacg
     2221 taaagagata gagaaggagc aggctgaaac agaacgccaa ttgaaactgg ctgaggatga
     2281 agagaaacgc ctggcagcat tgagtgaaga ggcccgggct gtggaggtgg cacaaaaaaa
     2341 tcttgctgct gcacaatctg agctggcgaa agtggatgaa gagattaata cgctcaatac
     2401 ccgtttaagc tccagtattc atgcccgtga tgcagaaacg aatacgctgt ccggaaaacg
     2461 aaatgagttg gatcaggcat ctgctaaata taaagaactg gatgaaaggg ttaaactttt
     2521 atctcctagg gcgaatgatc cgcttcagag tcgtcctttt tttgaggcca ccagactacg
     2581 ggcgagagct ggtgatgaga tggaggaaaa acaaaagcag gtaacagcat cagaaacgcg
     2641 tcttaaccag attagctctg agataaatgg aatccaagag gctatttctc aggctaataa
     2701 taagcgaagt acagcagttt cacgtattca tgatgctgaa gataatttga aaacagtaca
     2761 gactaatctc ctgaactcgc agattaagga tgctgtggat gcaacagtta gcttttatca
     2821 aacgctatct gaaaaatatg gtgaaaaata ttcaaaaatg gcacaggaac ttgctgataa
     2881 atctaaaggt aagaaaatca gcaatgtgaa tgaagctcta gctgcttttg agaaatacaa
     2941 ggatgtatta aataagaaat tcagcaaagc agaccgtgat gcaattttca atgcactgga
     3001 ggcggttaag tatgaagact gggctaagca tttagatcag tttgccaagt acttgaagat
     3061 tacgggacat gtttcttttg gatatgatgt ggtatctgat atcctaaaaa ttaaggatac
     3121 aggtgactgg aagccgctat ttcttacatt agagaagaaa gctgtagatg ctggagttag
     3181 ttatgttgtt gttttacttt ttagtgtgct tgctggaact acattaggta tctgggggat
     3241 tgctattgtt acaggcattc tatgtgcctt tattgataag aataaactta atactataaa
     3301 tgaggtgttg ggtatttaat tattctttat tgatataaac agtcctagca atccaaatgg
     3361 gattgctagg accaaacaaa gtagattgta tagcataaat aggtttaatt ttgccacggg
     3421 ggcattattt aggttttttc tttttctgaa aaaatctttc tttatgaact taaaaaatat
     3481 gtgttcaata gcatattttg aatatgggca tagaatagtg cttatcacta ttgcgtatag
     3541 catcttatct gacgctagga aataataccc ttcgttgttt tttgttataa ggtatatata
     3601 tataagtgcg cagtataggc caaacaaaat attttttatg tagtatctta aactcataaa
     3661 ttaaacctcg ttatatattc ttttcatttt ataaggatcg agttatgagg aaaagatttt
     3721 ttgtgggaat attcgctata aacctccttg ttggatgtca ggctaactat atacgtgatg
     3781 ttcagggagg gactgtggct ccatcatctt cttctaaatt gacggggatc tctgttcagt
     3841 agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct gctgcctgta
     3901 aacgaaaaaa ccgcctgggg aggcggtttg atcgaaggtt aagtcagttg gggaactgct
     3961 taaccgaggt aactggcttc agcagagcgc agataccaaa tactgtcctt ccagtgtagc
     4021 cgtagtcggg ccactacttc aagaactctg ttgcaccatt tgcgccatca tcgctctgct
     4081 aaccaagtta ccaacggctg ctgccagtgg cgctaagtcg tgtcttaccg ggttggactc
     4141 aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca
     4201 gcccagcttg gagcgaacga cctacaccga gccgagatac caacagcgtg agctatgaga
     4261 aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg
     4321 aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt atagtcctgt
     4381 cgggtttcgc cacctctggc ttgagcgtcg atttttgtga tgctcgtcag gggggcggag
     4441 cctatggaaa aacgcctgcg gcgctggctt cttccggtgc tttgcttttt gctcacatgt
     4501 tctttccggc tttatcccct gattctgtgg ataaccgtat taccgctttt gagtgagctg
     4561 acaccgctcg ccgcagtcga acgtccgagc gtagcgagtc agtgagcgag gaagcggaag
     4621 agcgccttat gtgacatttt ctccttacgc tctgttgtgc cgttcggcat cctgtcctga
     4681 gcgttatctc tctgtgctat tttctacttc aaagcgtgtc tggatgctgt tctggagttc
     4741 ttctgcgagt tcgtgcagct tctcacacat ggtagcctgt tcgtcagcat cgagtgcgtc
     4801 cagcttttcg agcagcgtca ggctttggct ttttatgaat cctgccatgt tgagtacggc
     4861 ttgctgctgc ttgttcatct tttcgttttc tccgttctgt ctgtcatctg cgttgtgtga
     4921 ttatatcgcg taccactttt caactgtttt accgccggta ttctgccgtc tgacgctttg
     4981 acgggtattt ctgcctgaca atactgtcac tgccaaaaaa ctgccgtgcc tttgtcggta
     5041 attcgaactt gctgacagga caggatgtgt aattgttata ccgcgcatac atgcacgcta
     5101 ttacaattac cctggtcagg gctttgcccc gacacccatg tcagatacgg agc
//
