LOCUS       NZ_CP058593             4082 bp    DNA     circular CON 23-AUG-2023
DEFINITION  Shigella flexneri strain M2901 plasmid unnamed4, complete sequence.
ACCESSION   NZ_CP058593
VERSION     NZ_CP058593.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13753499
            Assembly: GCF_013402835.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4082)
  AUTHORS   Guglielmino,C.J.D., Kakkanat,A., Forde,B.M., Rubenach,S., Merone,L.,
            Stafford,R., Graham,R.M.A., Beatson,S.A. and Jennison,A.V.
  TITLE     Outbreak of multi-drug-resistant (MDR) Shigella flexneri in northern
            Australia due to an endemic regional clone acquiring an IncFII
            plasmid
  JOURNAL   Eur J Clin Microbiol Infect Dis 40 (2), 279-286 (2021)
   PUBMED   32888117
REFERENCE   2  (bases 1 to 4082)
  AUTHORS   Forde,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUL-2020) Public Health Microbiology, Queensland
            Health Forensic and Scientific Services, PO Box 594, Archerfield,
            QLD 4108, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2020
            Assembly Method                   :: Flye v. MAY-2020
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore
            PromethION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/23/2023 04:23:34
            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)                     :: 5,146
            CDSs (total)                      :: 5,014
            Genes (coding)                    :: 4,139
            CDSs (with protein)               :: 4,139
            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)              :: 875
            CDSs (without protein)            :: 875
            Pseudo Genes (ambiguous residues) :: 0 of 875
            Pseudo Genes (frameshifted)       :: 369 of 875
            Pseudo Genes (incomplete)         :: 457 of 875
            Pseudo Genes (internal stop)      :: 195 of 875
            Pseudo Genes (multiple problems)  :: 143 of 875
            Pseudo Genes (short protein)      :: 5 of 875
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058593.1.
            Bacteria and source DNA available from Queensland Health Forensic
            and Scientific Services.
            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..4082
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="M2901"
                     /serotype="2b"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Australia: Queensland"
                     /lat_lon="27 S 153 E"
                     /collection_date="2019"
                     /collected_by="Queensland Health"
     gene            complement(179..346)
                     /locus_tag="HXW98_RS25605"
                     /old_locus_tag="HXW98_25415"
     CDS             complement(179..346)
                     /locus_tag="HXW98_RS25605"
                     /old_locus_tag="HXW98_25415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_306284321.1"
                     /translation="MTELESHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MQNERAMQSS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(353..883)
                     /locus_tag="HXW98_RS25610"
                     /old_locus_tag="HXW98_25420"
     CDS             complement(353..883)
                     /locus_tag="HXW98_RS25610"
                     /old_locus_tag="HXW98_25420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067502.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLSDEFRKLEESVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNESLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<921..1619)
                     /locus_tag="HXW98_RS25800"
                     /old_locus_tag="HXW98_25425"
                     /pseudo=""
     CDS             complement(<921..1619)
                     /locus_tag="HXW98_RS25800"
                     /old_locus_tag="HXW98_25425"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1561..1884)
                     /locus_tag="HXW98_RS25620"
                     /old_locus_tag="HXW98_25430"
     CDS             complement(1561..1884)
                     /locus_tag="HXW98_RS25620"
                     /old_locus_tag="HXW98_25430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000956004.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQAARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1949..2140
                     /locus_tag="HXW98_RS25625"
                     /old_locus_tag="HXW98_25435"
     CDS             1949..2140
                     /locus_tag="HXW98_RS25625"
                     /old_locus_tag="HXW98_25435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165994.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLYDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2742..2900
                     /locus_tag="HXW98_RS25805"
     CDS             2742..2900
                     /locus_tag="HXW98_RS25805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005093880.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="hypothetical protein"
     gene            3142..3609
                     /locus_tag="HXW98_RS25630"
                     /old_locus_tag="HXW98_25440"
     CDS             3142..3609
                     /locus_tag="HXW98_RS25630"
                     /old_locus_tag="HXW98_25440"
                     /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_014526575.1"
                     /translation="MRIDISHQTRHTPPNMLPREQNCVAMALSACFRQQLNPVVNSLLK
                     ERIIHSPKELEHDNAVIRVLQKLQIQEVCNSTLWETAKQQLLQKSDGRYFAINSKHLAF
                     PGPGESHAFCCIKYKNAIGINGNNAETQSTHYQPYPYDKVSIWGPFPHNLT"
                     /name="hypothetical protein"
     Typing          complement(2160..2246)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          2257..2814
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.032"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(169..1571)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.009"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 atcccagcga agggccatcc agtgtccgtt cctgtatttc cggctggcgt tcccgttcca
       61 ggaataacgc atgttcgcgc tcctgtatca accgttcctc tcttatctcc acttctcgct
      121 tgcatttggc atcaaggcag cggatctgtc ttttcccatc agattggcgt ggcgcctctt
      181 aactcgactg catggcgcgc tcgttctgca tcgcgttgtc ccgttgcgta agcgaaaaca
      241 ttttctgcaa ttccacgaag gcgctctccc attcgttcag ccgctgcata tagtcctgtt
      301 gcagctgctc taatgcgttc agcaaatggc tttccagctc cgtcatgctc tgtcactcct
      361 gtaccagcct tacggcattc tgtttcccgt tttccatcgt ccagttcgtt tcggctttca
      421 tcccctcggg caacaccaga aaacgtccgt tgctcccctc gtgataacgc acgccccatg
      481 tcttcgcgtt cagcttctcc agactctcgt tctgcttcct gatttcttcc aggttcgcct
      541 gtatcatccc gccaagatac cagagcgtcc cgccactcac ggtaaacagg aaaatgacca
      601 tccccagtaa catcatgccc gtattccctg ccagctttaa cacgtccttc ctgtgctgca
      661 tcatcgcctc tttcacccct tcccgatgtt ttttcagtga ttcctctgtc gaagctgtga
      721 acagggctat agcgtctttg attttcgtct cgtttgatgt cacagccttg cttacagatt
      781 cttcgagctt cctgaactcg tcgctcagca ttttctctgt agattcggct ctctctttca
      841 gctttttctc gaactccgcg cccgtctgta aaagattgct catagaatgc tcctttcagt
      901 ctgatattct tcccgccgtt cgggtctgca atgctgatac tgcttcgcgt caccctgacc
      961 acttcaagcc ccgcctctgt gagcgcctga atcacatcct gacggccttt tatctccccg
     1021 acatgataaa gagcgtctat ccaccgtgta atgctctcag caagcgcctg tttcgtttcc
     1081 ggcaggttat cagggagagt cagcgtccgg cggttctccg gggcgttcgg gtcatgcagc
     1141 ccgtaatggt gattcaccag cgtctgccag gcatcaattc tcggcctgtc tgcgcggtcg
     1201 tagtacggct ggaggcgttt tccggtctgt agctccatgt tcggaatgac aaaattcagc
     1261 tcaagccgcc ccttgtcctg gtgctccacc cacagaatgc tgtactgatt tttttcgaga
     1321 ccgggcatca gtacacgctc aaagctcgcc atcacttttt cacgccctcc cggcggcagc
     1381 tccttctccg cgaacgagag aacaccggac gtgtatttct tcgcaaatgg cgtggcatcg
     1441 atgagttccc ggacttcttc cggattaccc tgaagcaccg ttgccccttc ccggttacgc
     1501 tcccttccca gcaggtaatc aaccggacca ctgccaccgc cttttcccct ggcatgaaac
     1561 ttaactatca tcccgcgtcc cctgttccct gacggccaga cgcagccggc gcagctcatc
     1621 cccgatggcc atcagtgcgg ccaccacctg aacccggtca ccggaagacc actgcccgct
     1681 gttcaccttc ctcgctgcct gattcaggtt attcccgatg gcggccagct gacgcagtaa
     1741 cggcggtgcc agtgtcggca gcctcccgga acgggcaacc ggctcaccca ggcagacccg
     1801 ccgcatccat accgccagct gtttaccctc acagcgttcc agtaaccggg catgttcatc
     1861 atcagtaacc cgtatcgtga gcatcctctc gcgtttcatc ggtatcatta cccccatgaa
     1921 cagaaatccc ccttacacgg aggcatcagt gaccaaacag gaaaaaaccg cccttaacat
     1981 ggcccgcttt atcagaagcc agacattaac gctgctggag aagctcaacg aactggacgc
     2041 ggatgaacag gcagacatct gtgaatcgct ttacgaccac gccgatgagc tttaccgcag
     2101 ttgcctcgct cgcttcgggg atgacggtga aaacctctga cgggcttgtc agcgggtgtt
     2161 agcgggtgtc ggggcgcagc catgacccag tcacgtagcg atagcggagt gtatactggc
     2221 ttaaccatgc ggcatcagtg cggattgtat gaaaagtgcg ccataccggg tgtgaaatgc
     2281 cgcacagatg cgtaaggaga aaatgcacgt ccaggcgctt ttccgcttcc tcgctcactg
     2341 actcgctacg ctcggtcgtt cgactgcggc gagcggtatc tactcactca aaaacgaaat
     2401 gctgttatcc acagaatcag gggataacgc cggaaagaac atgtgagcaa aagaccagga
     2461 acaggaagaa ggccgcgccg atggcgtttt tccataggct ccgcccccct gacgagcatc
     2521 acaaaaaccg acgctcaagt cagaggtggc gaaacccgac aggactataa agataccagg
     2581 cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg cttaccggat
     2641 acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca cgctgttggt
     2701 atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa ccccccgttc
     2761 agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg gtaagacacg
     2821 acttaacgcc actggcagca gccattggta actggacaag gtggattgag atattaagag
     2881 ttcttgaagt ggtggcctaa ctgcggctac actagaagga cagcatttgg tatctgtgct
     2941 ccaccaagcc agttaccttc ggaagaaaga gttggtagct ctagattccg gcaaacaaac
     3001 caccgttggt agcggtggtt tttttgtttg caggcagcag attacgcgcc gcaaaaaagg
     3061 atctcaagaa gatcttgaat cactctatga aaattttgtt ttatagccgt atttgttgat
     3121 gctataagcc agagaccttc tatgagaata gacatatcac atcaaacacg gcataccccg
     3181 ccaaacatgc ttcctcggga acaaaattgt gtagcaatgg cattatctgc gtgctttaga
     3241 caacaactaa accctgtggt aaacagctta ttaaaagaga gaataataca ctcccctaaa
     3301 gaattggaac atgacaacgc agtaataaga gtcctgcaaa aactacaaat tcaagaagtt
     3361 tgtaacagca ccctttggga gacagccaaa caacaactac ttcaaaaatc ggacggaaga
     3421 tattttgcca tcaattctaa acacttagcc tttccaggcc caggagaatc tcacgccttc
     3481 tgttgcatca aatacaaaaa tgcaattggc attaacggaa acaatgccga aacccaatcg
     3541 acccactacc aaccctatcc ctatgataaa gtcagtatat ggggaccatt ccctcacaat
     3601 ttaacgtaat atcttaattg tacgcaccgc tgaaacgcgt tcggcgcgat cacggcagca
     3661 gacaggtaaa aatggcaaca aaccacccga aaaactgccg cgatcgcacc cggtaaattt
     3721 taaccacatg catagctatg cagccatgtg aatcacgcag gaattgccag ccagagacag
     3781 ctgaaacgga ttttattcat gctttcggaa gcgaagaaga cggggacctg agcgggaaaa
     3841 cagaagttca ggggaatgag cgcgatctgg caatagaggc aaaacacagc gacaaaagac
     3901 acaccagaat cgcgcccgta tgcgttttaa ctcgttcctg tgttttcagc aaggtctgac
     3961 tgaagcgcgt tcccggtgcc cccgaaccaa ccattatccc aaaaaatgca ccggaaacgc
     4021 gctgacaaca ttttagcctg tctctgatta ccatcccagc gaagggccat ccagtgtccg
     4081 tt
//
