LOCUS       NZ_CP138851             3181 bp    DNA     circular CON 23-NOV-2023
DEFINITION  Shigella flexneri strain PNUSAE076676 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP138851
VERSION     NZ_CP138851.1
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 3181)
  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  JOURNAL   Unpublished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 3181)
  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
            CP138851.1.
            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..3181
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="PNUSAE076676"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA"
                     /collected_by="CDC"
     gene            join(3092..3181,1..45)
                     /locus_tag="SH220_RS25355"
                     /old_locus_tag="SH220_25355"
     CDS             join(3092..3181,1..45)
                     /locus_tag="SH220_RS25355"
                     /old_locus_tag="SH220_25355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /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_071606675.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGKQDVREMY"
                     /name="replication initiation protein"
     gene            complement(290..1399)
                     /gene="wzz(fepE)"
                     /locus_tag="SH220_RS25360"
                     /old_locus_tag="SH220_25360"
     CDS             complement(290..1399)
                     /gene="wzz(fepE)"
                     /locus_tag="SH220_RS25360"
                     /old_locus_tag="SH220_25360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_005065596.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRAIVELSKNMKSIDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            2282..2446
                     /locus_tag="SH220_RS25365"
                     /old_locus_tag="SH220_25365"
     CDS             2282..2446
                     /locus_tag="SH220_RS25365"
                     /old_locus_tag="SH220_25365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_000090200.1"
                     /translation="MARCIKSQSLTLLEKLDALDADEQAAMCKRLHELAEELQNSIQIR
                     FEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1731..1988)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(2113..2211)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2527..2613)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(11..112)
                     /name="rep_cluster_2392"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.262"
                     /coverage="80.0"
                     /evalue="4.260000000000001e-31"
     Typing          2638..3164
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 ttggcagcgg ccactggtaa acaggatgtg cgagagatgt attgagagtt cttgaagtgg
       61 cagccttact gaggctacac tagaaggaca gatttggtga catgtctcgc acaagactgt
      121 taccacggtt cagaagttcc ccaacttact gaaccttcga aaaaccacct ccccaggtgg
      181 ttttttcgtt ttctagagta gaagactacg gctgtaaggg aatgatctca agaagatcct
      241 ttgaactttt tataaaagtt gcttataaaa tgatgcatca gcacaacttt tactcaatca
      301 cactcatctt tctggcctcc atggcatgac gtaaaagtat atagccacat gcaagcatcc
      361 ctccaatgac agaagaaaga attacaatta tggcattact tggcccatcc tttctgaccg
      421 gtaacgttgg gctcaattga tactgaaatg gcataaaatc aacatccccc actttcgcca
      481 caaccaattg attcacaaca tattgacgat ttcgcaactc cccactcaat tccgaaacat
      541 ccttgattga ttttttgatg ttcaatttag ttgctatacc atcagaaccg agagccacag
      601 gaaaatctgg gtcatccttc ataatctgac cattgctgta tacaggtttt tttattccag
      661 ccgcattagc aacctccagt gaataattga ggcgtcgaat atctgcattc agctggtttc
      721 taatttttat ctcatccagt gcaagaattt ctttttcaac attagtttta acttctagtt
      781 tatttcttat atcttccatc aaatccctta caacaaggga agaaacataa ttaatatacc
      841 cagacaacac atcgtgagct tctttacttg ttggagcagt aaaactcaga gtccatgata
      901 catacaatga tgacttgtcg tttttcttac tggcattatc atcaatcgac ttcatatttt
      961 tactcaactc aacaattgca cgatgcagtt cgagagcgct aatgttattc tttttaataa
     1021 tctccataac ataaggagat gatctcatat actcattcaa cgaattaacg gactgaaatt
     1081 tcttaataaa cagagcaaat gcgctatcac gattgatatc aaaatccact cccagaacat
     1141 gaagcttgga aagctcctta tttaattcac tccattgaac agactcagca ggagtaacca
     1201 cagcagaact agtccatttt tgtggcaaaa caaaagaaac aagaaagcca atacaagcaa
     1261 aaaatagaat caccccaaca atttttattt ttgctgccca taaaacgcta atcaagccaa
     1321 aaaggtcaat ttcttcatta ccattcggca acatgttgta attagaaaaa tgttcgtcag
     1381 agacctttga gattttcatt gaaaaaaaca caatatatta acatatggtt tttttattct
     1441 atcatatgtt aggaaaaaac ctaaaaacca ttcagcagac atttaacata acattttatt
     1501 gcgcgcaccg ctaaaacgcg ctgaacgcga ttctgccgca aacaccgcaa aaagagatgt
     1561 tttccccggg gtaaaccgga aaaatgcgtc aggatcgctt tcagctcact gcatagctat
     1621 gcatgaaagt gaatgacgat cggtttgggc gcatacagtg cccatgagac acattttcgg
     1681 acattttcag ttcgtgaatc cctgactcat tgctacatat ctgaacagac acccctagca
     1741 gcgcccccag gggcgtcctg taaaaaaaca caccgcgccg ctagcagcac ccctaatata
     1801 agataatgtt ttttttatga aaatagtcag taccacccct aaaaagcggt gttggcgcag
     1861 ctacaacacc gcgccgacac cgctttttta aatatcacaa agagagcaag aagaactaat
     1921 ttgtcataac tctctattta taaagaaaaa tcagcaaaaa cttgtttttg cgtggggtgt
     1981 gggcatttca ggcatgagaa cagactcgcg tttttccgga gtatcagcgg aattattgat
     2041 taagaaacac tcgacgcaga gcgaaatttt atgcaacagc ggctgcactg cacagggatt
     2101 atttatcagt tgatatgctg tgccatgata cgtcctaaag aaacaggaca ggatgtgcaa
     2161 ttgtaatacc gtcgcccgca acgtcttaca attaccacct gctcagggtc cccccccccc
     2221 gacacccgga actgacggag aacaacggaa ggtgaacaaa taacaacaaa ctgcgctgaa
     2281 tatggcgcga tgtatcaaaa gccagagcct gacactgctt gaaaaactgg atgctctgga
     2341 tgccgacgaa caggcggcca tgtgcaaacg actgcacgaa ctcgcagaag aactccagaa
     2401 cagcatccag attcgctttg aggccgaaag tgaaacagga acataacgaa gctgacggag
     2461 gcggtcacgg ctttcccgtg ggcgttttcg tcagcagaca agcccgtcag ggcgcgtcag
     2521 ggggttttag cgggtgtcgg ggcgcagcca tgacccagtc acgtagcgat aacggagtgt
     2581 atactggctt aattatgagg cggcagagca gatggtgaga gaacagcgac atatgaggtg
     2641 tgaaatgctg cacagatacg taaggagaaa atgcagcttc cggcgctctt ccgcttcctc
     2701 gctcactgac tcgctgcgct cggtcgttcg gctgcggcga gcggtgtctg ctcacgcaaa
     2761 gacggatata cggttatcca cagaatcagg ggataacacc agaaaaaaca tgtgagcaaa
     2821 aaagaggccc cgaaaaaagg ccgcgccggt ggcgtttttc cataggctcc gcccccctga
     2881 cgagcatcac aaaaatcgac gctcaagtca gaggtggcga aacccgacag gacttaaaga
     2941 taccaggcgt ttccccctgg tggctccctc gtgcgctctc ctgttcctgc ctttcggttt
     3001 accggtgtca ttccgctgtt atggccgcgt tcgtctcatt ccacgcctga cactcagttc
     3061 cgggtaggca gttcgctcca agctgggctg tgtgcacgaa ccccccgttc agcccgaccg
     3121 ctgcgcctta tccggtaact atcgtcttga gtccaacccg gtaagacacg acttaacgcc
     3181 a
//
