LOCUS       NZ_CP138849             5250 bp    DNA     circular CON 23-NOV-2023
DEFINITION  Shigella flexneri strain PNUSAE076676 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP138849
VERSION     NZ_CP138849.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20175209
            Assembly: GCF_033870275.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5250)
  AUTHORS   Shrum Davis,S., Salazar-Hamm,P., Edge,K., Hannah,T., Houston,J.,
            Griego-Fisher,A., Lugo,F., Wenzel,N., Malone,D., Bradford,C.,
            Plymesser,K., Baker,M., Schwalm,K., Lathrop,S., Smelser,C.,
            Dinwiddie,D. and Domman,D.
  TITLE     Multidrug-resistant Shigella flexneri outbreak associated with a
            high-mortality spillover event into nonhuman primates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5250)
  AUTHORS   Shrum Davis,S., Salazar-Hamm,P., Edge,K., Hannah,T., Houston,J.,
            Griego-Fisher,A., Lugo,F., Wenzel,N., Malone,D., Bradford,C.,
            Plymesser,K., Baker,M., Schwalm,K., Lathrop,S., Smelser,C.,
            Dinwiddie,D. and Domman,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-NOV-2023) Internal Medicine, University of New Mexico
            Health Sciences Center, 915 Camino de Salud NE, Albuquerque, NM
            87131, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 21-SEP-2023
            Assembly Method                   :: Unicycler v. v.0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 36.5x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/22/2023 13:16:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,073
            CDSs (total)                      :: 4,941
            Genes (coding)                    :: 4,182
            CDSs (with protein)               :: 4,182
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 103
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 759
            CDSs (without protein)            :: 759
            Pseudo Genes (ambiguous residues) :: 0 of 759
            Pseudo Genes (frameshifted)       :: 264 of 759
            Pseudo Genes (incomplete)         :: 449 of 759
            Pseudo Genes (internal stop)      :: 172 of 759
            Pseudo Genes (multiple problems)  :: 124 of 759
            Pseudo Genes (short protein)      :: 5 of 759
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP138849.1.
            Bacteria and source DNA available from PNUSAE076676.
            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..5250
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="PNUSAE076676"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA"
                     /collected_by="CDC"
     gene            complement(join(5214..5250,1..167))
                     /locus_tag="SH220_RS25290"
                     /old_locus_tag="SH220_25290"
     CDS             complement(join(5214..5250,1..167))
                     /locus_tag="SH220_RS25290"
                     /old_locus_tag="SH220_25290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677232.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_047662947.1"
                     /translation="MSDINFGIFFIIAFGFITVGSFFIVLIRFLERAETILIGHLDLKS
                     KAIIHGLIILFIYWTLKFFAES"
                     /name="hypothetical protein"
     gene            complement(169..1245)
                     /locus_tag="SH220_RS25295"
                     /old_locus_tag="SH220_25295"
     CDS             complement(169..1245)
                     /locus_tag="SH220_RS25295"
                     /old_locus_tag="SH220_25295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000513453.1"
                     /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_052323655.1"
                     /translation="MATDNTYPVYDGNFFRATHDIILRAVEKSTSGMFDNYINIAYTLG
                     KYGVSLYILWYAFTVLARKQQTPVPDFIWNLCRFSIILMFVKNTGGWLDNANQAIDGLK
                     ETLAGGDPWLWMDQLWDKVITVGKKVWHLDTDTIPVVGVAAALLTYAGGILAMIVCAIV
                     FFSAEITLKILSITAPLFIMCLMFGFLRQMFNNWLQLIFSSLLIFMFAALALRAGMWQL
                     NGTLSSTLSSATAPNLFEAGATVLVSGIFMAWIIWQAKTYASQLAGVGVEGAMQGAAAM
                     GIGAGIFGASRMTRGALGMGRNAGIGAWKGLRRQEGGFGQSPGITGKAANLAGQGVNIG
                     AKKLRQAAIERAKKMYGG"
                     /name="type IV secretion system protein"
     gene            complement(1259..1528)
                     /locus_tag="SH220_RS25300"
                     /old_locus_tag="SH220_25300"
     CDS             complement(1259..1528)
                     /locus_tag="SH220_RS25300"
                     /old_locus_tag="SH220_25300"
                     /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_047662946.1"
                     /translation="MKYIVLVFLASLSFILTGCNEDTKSVDWWTNHPKEAVDKYKECKK
                     TGSDSDNCKNVRRAGLIIADTYPPMSEIYKQEARELDKKLGVSK"
                     /name="EexN family lipoprotein"
     gene            complement(1538..2296)
                     /locus_tag="SH220_RS25305"
                     /old_locus_tag="SH220_25305"
     CDS             complement(1538..2296)
                     /locus_tag="SH220_RS25305"
                     /old_locus_tag="SH220_25305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677228.1"
                     /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_047662945.1"
                     /translation="MKKRIISAVLASLSVISVAQAGIPVAIDANPEWAVEAGRWTERLK
                     QWAETVKHYENQINAYKQELLSKTGIRDVQGLVQSAQSVSQELMQIYDQGNAFIDDYIK
                     NPESALSEQAKSLLSDYRVTDTCQNLGYSGDQVRGCEATFLSQLASVEYGNKLESKLRQ
                     DNQTMKDLIEQVKNAKDTKATQDATNAVALEQLKFEKLKFQYQMYIDKQKQLSEYKKEM
                     AKASFRHEQINAKPIDYREAFSTQDFDLIK"
                     /name="type IV secretion system protein"
     gene            complement(2718..3449)
                     /locus_tag="SH220_RS25310"
                     /old_locus_tag="SH220_25310"
     CDS             complement(2718..3449)
                     /locus_tag="SH220_RS25310"
                     /old_locus_tag="SH220_25310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677229.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_021579673.1"
                     /translation="MTKKNVDQPMTMTVSLRGKNVVMSNAISRAAQSLSLAEKRIIFAA
                     IAQMGGKYAPVRITAQEYANTFGMPLKQAYSQLKEASENFFNRYIRFKLNEVSEIDVDV
                     WKIRWLGAYKYNDGEANVLLHFTPQVMPYLCELEDNFTKYQLSQACALRSVHSWRLLEL
                     FEQMNTNKENNGWLSISLEDFHHAMESPDSYKTTFGLLRKYMIEPAVKELTEKDHWMID
                     WKPIKKGRKVVRLEFWFRKEN"
                     /name="replication initiation protein"
     gene            complement(4557..5102)
                     /gene="ddp1"
                     /locus_tag="SH220_RS25315"
                     /old_locus_tag="SH220_25315"
     CDS             complement(4557..5102)
                     /gene="ddp1"
                     /locus_tag="SH220_RS25315"
                     /old_locus_tag="SH220_25315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000757693.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA distortion polypeptide 1"
                     /protein_id="WP_052972377.1"
                     /translation="MKQIKFRLDDAKHHDLLICLKSLYPDEPGLTVSKGMKLLANALLK
                     SKKTNQIQNDYADENNFIKTTLYLTGKQRADIEKAANRHGWTLSRECRYRIQTTLNNRL
                     DFFDQELLMMNRCRNTIDKIGRNFHYIIVNDQTRVLDKDGFYQDAERLKTEIFSLKNQF
                     ENYIMLCKGRTVSNKVDV"
                     /name="ddp1"
ORIGIN
        1 aataatataa ttaacccatg aataatggct ttagatttta aatctaaatg accaatcaat
       61 atggtttctg cacgttcaag aaaacggata agcacaataa aaaatgaacc aacagtaatg
      121 aagccaaatg cgattataaa aaagatacca aagttaatat cactcatatt aaccaccgta
      181 catttttttt gctctctcaa tagcggcctg acgaagtttt ttggcaccaa tattaacgcc
      241 ctgtccggcc aggttagcgg ctttgcccgt tattcccgga gactgtccga acccgccttc
      301 ctgacgacgc agacctttcc atgcaccaat accggcattt ctgcccatac caagtgcacc
      361 acgcgtcata cgggatgcac cgaaaatgcc agcaccaatc cccatagcgg ctgcgccctg
      421 catggcacct tcaacaccca cgccagcaag ctgtgaagca taggtttttg cctgccagat
      481 aatccatgcc ataaagatac ctgagacaag aactgtcgca cctgcttcaa ataaattagg
      541 agctgttgct gaagataaag tgctgcttaa tgttccattc aattgccaca tacctgcacg
      601 taacgccagt gctgcaaaca taaaaataag taatgaactg aaaataagct gtaaccagtt
      661 attaaacatc tgacgaagaa aaccgaacat cagacacata ataaataacg gtgctgtaat
      721 agaaaggatt tttaacgtaa tttctgctga aaaaaatact attgcacaca cgatcattgc
      781 taaaatgcct ccggcataag taagcaaggc cgctgcaaca cctacaacgg ggattgtatc
      841 tgtatcaaga tgccaaacct ttttaccaac agtaattact ttatcccaaa gttgatccat
      901 ccataaccaa ggatcaccac cggcgagagt ctcttttaag ccatctatag cttgattggc
      961 gttatcaagc catccccctg tatttttaac gaacattaaa attatcgaaa acctgcacaa
     1021 attccagata aaatctggaa caggagtttg ttgttttctt gctaagacag tgaatgcata
     1081 ccataagata tataaagaaa caccatattt acccagtgta taagcaatat tgatataatt
     1141 atcgaacatt cctgatgttg atttctcaac tgctcttaat attatatcat gagttgctct
     1201 aaagaaattt ccatcatata cgggataagt attatctgta gccatataac cccctcagtt
     1261 attttgaaac gcctaatttc ttatcaagtt ctctggcttc ttgcttgtat atttcactca
     1321 tcggaggata agtgtcagcg attataagtc ccgcacgtct tacgttttta caattatctg
     1381 agtcacttcc tgttttcttg cattctttat atttatcgac agcttctttc gggtgattag
     1441 tccaccaatc gacagatttt gtatcttcat tacatccggt aagaataaat gataaagatg
     1501 ctaaaaatac caagacgata tatttcataa aaacccctta tttgatcaaa tcaaagtctt
     1561 gtgttgaaaa tgcttctctg taatcaattg gttttgcatt aatttgttca tgacgaaaag
     1621 aagctttcgc catttccttt ttatattcag acagttgttt ttgtttatcg atgtacattt
     1681 gatactgaaa tttgagcttc tcaaacttca gttgttcaag tgcaacggcg tttgttgcat
     1741 cctgcgtggc tttcgtatcc ttcgcatttt taacctgctc gataaggtct ttcattgtct
     1801 gattgtcctg acgaagcttg ctctccagct tgttaccgta ttccacgctt gccagttgag
     1861 aaaggaacgt cgcttcacat ccccgtacct ggtcaccaga atatcccagg ttctggcagg
     1921 tatccgttac cctgtaatct gacaataacg atttggcctg ttccgataac gcactttcag
     1981 gatttttaat gtaatcgtca ataaaagcat tcccctgatc ataaatctgc atcagttcct
     2041 gactcactga ctgtgcggac tgcaccagtc cctgcacatc acggataccc gtttttgaca
     2101 gcagctcctg tttgtacgca tttatctgat tttcgtaatg tttcaccgtt tctgcccatt
     2161 gcttcagacg ttctgtccat cgtccggctt caaccgccca ttccggattg gcatcaatgg
     2221 caacaggtat ccccgcctga gcgacggaaa taaccgagag cgaagcgagc accgccgata
     2281 taatgcgttt cttcattatt gatctccact aaatataatc ctgataatta gccctctcct
     2341 ttaattaaag agagggctaa catcacttaa acataccgcg attgtattcc ttaagccaga
     2401 atttaaagtt acttacaata aacctcgtgc ccctgctagt aattcggaag cgacggatta
     2461 aatcactatt acgaatacct tcattacttg tgaacaaaag atataaagaa aaagagaaag
     2521 ggtctttctc aagggataaa ctaaatctcg agtttccttc tttcctctta ctatcaagat
     2581 aagcgtaaaa ttctttgcgg gtttttaact gatattcaga tatacttggg ccagccatac
     2641 agcctccgaa caggttgttg tggttagctg gtagtgaggg tggcagccct cattaccagc
     2701 gttaatcatt gatatgatta gttttctttc ctaaaccaga actcaagacg aacgactttt
     2761 ctccccttct taataggttt ccagtcgatc atccagtgat ctttctctgt taactccttt
     2821 accgccggtt caatcatata cttacgaagt aatccaaacg ttgttttata actatcgggt
     2881 gattccatag catgatgaaa atcttctaac gatatggata accatccatt attttccttg
     2941 ttcgtattca tttgttcaaa gagttctaac aaacgccatg aatgtactga acgcaatgcg
     3001 caagcttgag atagctgata cttcgtaaaa ttatcttcca gttcgcataa atatggcatt
     3061 acttgaggcg taaaatgtaa aagaacatta gcttcaccat cattatattt atacgcccct
     3121 aaccatctaa tcttccatac atcaacatca atctcactaa cttcatttaa tttaaagcga
     3181 atatatctat taaagaaatt ttccgaagcc tcttttaatt gtgaatatgc ttgctttaaa
     3241 ggcattccaa aggtgttagc atattcctgt gctgtaatcc ttactggcgc atatttccca
     3301 cccatctgag caatagctgc aaaaatgatg cgcttttcag ccaaagaaag gctttgcgcg
     3361 gcacgagata tagcattact catgacaaca tttttgccac gtaaactgac agtcatcgtc
     3421 attggttggt caacattctt cttggtcatt attcactcaa aagtaagatg tacagggcaa
     3481 gagtaagtac gtaaatcata cttacaaaaa atgaaaagta aaatcatttt ttactcttac
     3541 agttagctgt ggataatgcc cgaaaaaact tacttttaac ccgaaaaaac ttacttttaa
     3601 cccgaaaaaa cttactttta acccgaaaaa acttactttt aactctataa catcatgatt
     3661 ttaaaagagt tttggcgtct aaaaaggttt taaaaagaaa agataaaaag ggtttaaaaa
     3721 ggaatttgcc cccaaaatct gtggataacc atgctcaaac caagaggaca gatcacgtta
     3781 agctagagct acaataccta aaaacaatcc gctcgttttt taaccgctat gcgtatgtgc
     3841 tcaactcacc tacagactca cttccgcttc ctcgctcact cagtcgctac gctcctgccg
     3901 ttcgactgcg gcgagcggta ccacctctcg catgttgtcg gcgattccgt tgctgttctg
     3961 ttcgaaaatg cgttctgtga gccatccaga gcaccagaac gcgattttct ggtggtggta
     4021 atggttttct tcgtattggc ccttaaaacg cgctcagaag ctctcagacg cacgaaacag
     4081 gttttaaatg cccgtcaggg catggaaggc gcgaaaaacg attacagagc gtttcaggag
     4141 gtcaggcgcg ccgatacccc taaccagggg ctttcaggaa gcaggagacc gcgccagctc
     4201 cctgcaaagg ccgtttgcac aggaataaca acgatgatct cattactgga actgactaac
     4261 gtttagacgt gacaaaacac aagctaaccg tagttgctcg taataaatca catctctatg
     4321 gagagagatt ttttattatt gcgcaaagtt tatactataa acagtttaca gctatatcaa
     4381 gactgaaata gtaacaaatt tgccagtagt tccgtttcta ctagacgctc cttcgactcg
     4441 gatgaccccg aagcaaagaa aaaaacaaaa ggataaattc acatctcgca aagactctat
     4501 cagcaacatg tagtttattc aacaatacaa actagattta gttatcaatg tggacttcat
     4561 acatctacct tgtttgaaac tgttctcccc ttacataaca taatgtaatt ctcaaactga
     4621 tttttaagac taaaaatttc tgtcttaaga cgttccgcat cctgatagaa accatcttta
     4681 tcaagaaccc tggtctgatc attaacaatg atataatgaa agttacgacc aattttatct
     4741 atagtatttc ggcagcgatt catcatcagc agttcctggt cgaagaaatc aagcctatta
     4801 ttcagtgtgg tttgaatcct atatcgacat tcccgtgata atgtccaccc atgacggtta
     4861 gctgcttttt caatatcagc cctttgttta cctgttaagt aaagcgtggt tttgatgaaa
     4921 ttgttttcat cagcataatc attttgtatc tggttagttt ttttgctttt cagcaatgca
     4981 ttggcaagca gtttcatacc ttttgataca gtcaagcctg gttcatcagg ataaagagac
     5041 tttaggcaga tcagcaggtc atgatgctta gcatcatcaa gcctgaattt gatttgtttc
     5101 atatttgcac ttcctacagc acatgaatat ttactccgat gcaggatagg gcaaacgccg
     5161 caaaatggtt ccattttggc cgtttgcccg gtgacctaca gtcggttctt tgattaagat
     5221 tctgcaaaaa atttaagcgt ccagtatata
//
