LOCUS       NZ_CP045944             4692 bp    DNA     circular CON 09-JUL-2023
DEFINITION  Shigella flexneri 2a strain AUSMDU00010535 plasmid
            pAUSMDU00010535_03, complete sequence.
ACCESSION   NZ_CP045944
VERSION     NZ_CP045944.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13191650
            Assembly: GCF_009664535.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri 2a
  ORGANISM  Shigella flexneri 2a
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4692)
  AUTHORS   Baines,S.L., Goncalves da Silva,A., Carter,G.P., Jennison,A.V.,
            Rathnayake,I.U., Graham,R.M.A., Sintchenko,V., Wang,Q.,
            Rockett,R.J., Timms,V.J., Martinez,E., Ballard,S., Tomita,T.,
            Isles,N., Horan,K.A., Pitchers,W., Stinear,T.P., Williamson,D.A.,
            Howden,B.P. and Seemann,T.
  TITLE     Complete microbial genomes for public health in Australia and
            Southwest Pacific
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4692)
  AUTHORS   Baines,S.L., Goncalves da Silva,A., Carter,G.P., Jennison,A.V.,
            Rathnayake,I.U., Graham,R.M.A., Sintchenko,V., Wang,Q.,
            Rockett,R.J., Timms,V.J., Martinez,E., Ballard,S., Tomita,T.,
            Isles,N., Horan,K.A., Pitchers,W., Stinear,T.P., Williamson,D.A.,
            Howden,B.P. and Seemann,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-2019) University of Melbourne, Microbiological
            Diagnostics Unit, First Floor, Building 248, Parkville, Victoria
            3010, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 18-OCT-2019
            Assembly Method                   :: Unicycler v. 0.4.8b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 105x
            Sequencing Technology :: Oxford Nanopore GridIon, Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/09/2023 03:38:56
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,172
            CDSs (total)                      :: 5,040
            Genes (coding)                    :: 4,236
            CDSs (with protein)               :: 4,236
            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)              :: 804
            CDSs (without protein)            :: 804
            Pseudo Genes (ambiguous residues) :: 0 of 804
            Pseudo Genes (frameshifted)       :: 298 of 804
            Pseudo Genes (incomplete)         :: 478 of 804
            Pseudo Genes (internal stop)      :: 174 of 804
            Pseudo Genes (multiple problems)  :: 143 of 804
            Pseudo Genes (short protein)      :: 5 of 804
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP045944.1.
            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..4692
                     /organism="Shigella flexneri 2a"
                     /mol_type="genomic DNA"
                     /strain="AUSMDU00010535"
                     /serotype="2a"
                     /host="Homo sapiens"
                     /db_xref="taxon:42897"
                     /plasmid="pAUSMDU00010535_03"
                     /geo_loc_name="Australia"
                     /collection_date="2017"
     gene            1..894
                     /locus_tag="GJE14_RS25585"
                     /old_locus_tag="GJE14_25585"
     CDS             1..894
                     /locus_tag="GJE14_RS25585"
                     /old_locus_tag="GJE14_25585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016237866.1"
                     /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_001277133.1"
                     /translation="MSAVLQRFREKLPHKPYCTNDFAYGVRILPKNIAILARFIQQNQP
                     HALYWLPFDVDRTGASIDWSDRNCPAPNITVKNPRNGHAHLLYALALPVRTAPDASASA
                     LRYAAAIERALCEKLGADVNYSGLICKNPCHPEWQEVEWREEPYTLDELADYLDLSASA
                     RRSVDKNYGLGRNYHLFEKVRKWAYRAIRQGWPVFSQWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGTKSKRAAVPTSARSLKPWEALGIS
                     RATYYRKLKCDPDLAK"
                     /name="replication initiation protein"
     gene            complement(1110..1385)
                     /locus_tag="GJE14_RS25590"
                     /old_locus_tag="GJE14_25590"
     CDS             complement(1110..1385)
                     /locus_tag="GJE14_RS25590"
                     /old_locus_tag="GJE14_25590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000091752.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRLQPLINELEKLPRPPAKPQNH"
                     /name="hypothetical protein"
     gene            1564..3783
                     /gene="mobQ"
                     /locus_tag="GJE14_RS25595"
                     /old_locus_tag="GJE14_25595"
     CDS             1564..3783
                     /gene="mobQ"
                     /locus_tag="GJE14_RS25595"
                     /old_locus_tag="GJE14_25595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_154074701.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLTHDYTRK
                     RGVDDAVILTPVNAPSWCGDRSVLWNAVEKAEQRRNSQLAREIELAIPREISREAAREA
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLEKQIESLRRTYRAVKERDIPARRQAFETQWNTWIS
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEYDARLKHHDNHRLSRETALAGVITGLG
                     RAREPGTGMITRYMILSNRAGEFTVWGDELADYPQSVHDQVNVYLSPGGAVMVTDIHSG
                     LSESHETLARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPAA
                     SPLPSAHRVDVTAYAAPEQLMPVVFSTERNSRTLNLLLCKGPEEMLVGFVRLEDELRPV
                     LALPSPDYSHLMVSIITENGIHLAGYGEAINRDADTPYPPEPKLMQFRLKGCQDTLFAA
                     INKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHYRGMSM"
                     /name="mobQ"
     gene            4086..4361
                     /locus_tag="GJE14_RS25600"
                     /old_locus_tag="GJE14_25600"
     CDS             4086..4361
                     /locus_tag="GJE14_RS25600"
                     /old_locus_tag="GJE14_25600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001419705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052977602.1"
                     /translation="MAYDEHSIRVMSADEIEQRFDWLRLENLAKEHRLPVDWVRRGFEA
                     CWRLGIEPDYFIDRYIFKRDVPLVPEFEVVFREIVNENRYRDRMRF"
                     /name="hypothetical protein"
     Typing          complement(1390..1563)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.857"
                     /coverage="100.0"
                     /evalue="5.54e-83"
     Typing          complement(1564..1922)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..894
                     /name="rep_cluster_2150"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.275"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1565..3780
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.61"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcgccg tacttcaacg cttcagggaa aaattaccgc acaaaccgta ctgtacgaac
       61 gatttcgcgt acggcgttcg cattctgccg aaaaacattg ccattcttgc ccgtttcatc
      121 cagcagaacc agccacatgc actgtactgg cttccctttg acgtggaccg gacgggggca
      181 tcaatcgact ggagcgaccg gaattgtccg gccccgaaca tcaccgtaaa aaatccccgt
      241 aacgggcacg cgcatctgct ctacgcgctc gcccttcctg tgagaactgc gccggatgca
      301 tcggcttcgg cgctcagata cgctgccgct attgagcgtg cgttgtgtga aaaactgggc
      361 gcggatgtga attacagcgg cctgatctgc aaaaatccgt gccaccctga atggcaggaa
      421 gtggaatggc gcgaggaacc ctacactctc gacgaactgg ctgattatct cgatttgagc
      481 gcctcagcgc gccgtagcgt cgataaaaat tacgggctgg ggcgaaacta ccatctgttc
      541 gaaaaggtcc gtaaatgggc ctacagagcg attcgtcagg gctggcctgt attctcacaa
      601 tggcttgatg ccgtgatcca gcgtgtcgaa atgtacaacg catcgcttcc cgttccgctt
      661 tctccggctg aatgtcgggc tattggcaag agcattgcga aatatacaca caggaaattc
      721 tcaccagagg gattttccgc tgtacaggcc gctcgaggtc gcaagggcgg aactaaatct
      781 aagcgcgcag cagttcctac atcagcacgt tcgctgaagc cgtgggaggc attagggatc
      841 agtcgagcga cgtactaccg aaaattaaaa tgtgatccag atctcgcaaa atgagaccag
      901 ataagcctta tcagataaca gcgccctttt ggcgtctttt tgagcagtga tctttcttgc
      961 gatttcctcc gttttgcccc gtaatggcgt ggctttccgc atgattgagg tggtagcgct
     1021 cgccgcagtc tcatgaccga gcgtagcgag cgaatgagcg aggaagcgca aaggcgtccg
     1081 gtggtgcatg ggcacttacg cgccggggct tagtggttct gcggtttcgc cggtggtctg
     1141 ggtagcttct ccagctcgtt aatcagcggt tgtagtcggt tcacatccgc ctgtcttgtg
     1201 acttcctttc gcagaaactg gagcaggaac gcacgcagtt gcgcttcttc cggcctccgt
     1261 accctcgcca gcatggcagc ccccacaatg actttttgcg ccgtgtccag gctccggctc
     1321 ttcgccttca ggcgctgtaa tctggcctca gcttcggcaa tcttctgttc gagtgttctg
     1381 ctcatttcgt gactccgtgc gcggtgaaaa atcgtatttt agcgcgtcac tggtagttgc
     1441 aaaactgaac tggcataatg cacggcacat cacgaagtgc gcacttatac aatcttcact
     1501 tcgtttcgat tgtgtgcggt ctgcgacgct aaaagaaaac ggcaaaaagg cattacggca
     1561 gaaatggcga tttatcatct cagcatgaaa atcatttcgc gaaaaaacgg ctacagtgcc
     1621 gttgcttctg ctgcctaccg ttccggctct gtcatacccg atgaccgtac cggattaacc
     1681 cacgattaca cccgtaaacg cggcgttgat gatgcggtca ttctcacccc tgtgaatgca
     1741 ccgtcctggt gtggtgaccg ttccgttctc tggaatgcgg tcgagaaagc cgaacagcgc
     1801 cggaactccc agctggcaag ggagattgaa ctcgccattc cccgtgagat ttcccgcgag
     1861 gccgcacggg aggccgttct cgcttttgtc cgggaaaact ttgtcagtcg gggcatgatt
     1921 gccgatgtgg cgttccatca tatggaccgg accaaccccc atgcacacat catgctgacc
     1981 acgagagctg tcggggaaac gggattcgca ggaaaggtca gggactggaa cgaccgggca
     2041 ctcgccgaga cgtggcgcgc atcatgggct gaccatgcga acagagcgct tgcgaacgcc
     2101 ggctaccagg aagagataga ccatcgttca tacgagcgtc agggactgga gaaagcgccg
     2161 ggccttcacc tcggaaaggc tgcctgtgcg atggaaaaac ggggcatgga aacagaacgc
     2221 ggtgagcaga accgcctgat taacagcctt aacctggaaa tacaggtttc ccgcacaagg
     2281 ctggcagtca tccaggtaca ggagaacgtg cggaaacggg aactcagcga tgccgcacgt
     2341 cgtgcagcgg aagcccttaa tctgaccatt cccgccgcga atgcctcagc ggataccctg
     2401 cgggaattca ttgccacact gccgcaggaa tgcgggaacg catgggagat gacaccggag
     2461 ttcgtggcga tgaacgggaa ggcaaacgac atcaaacgtg aggggaatgc gctggtgaaa
     2521 gagcgggata ttctcgaaaa agagatgacc ggactcagaa aagcccgtcc ggtagcgtcc
     2581 atcctgtcag agcttcccct gatgacatgg gctgaaccgg aataccgcaa aagacaactc
     2641 cgcttctgga aactcgagaa acagattgaa tctcttcgcc gcacctacag ggccgtgaaa
     2701 gaacgggaca ttcccgcccg tcgtcaggcc tttgaaacgc agtggaatac gtggatttcg
     2761 ccgggaatgg cagagctgaa agaaaaactg tcagcacggg aagcggagcg gcgcagggag
     2821 gaagccgaag cggaagcgcg ccggaaggaa caggaatatg acgcacggct gaaacaccat
     2881 gataaccatc gcctgagccg tgaaacggca ttagccgggg ttattacggg gctggggcgt
     2941 gccagagagc cgggaacggg catgataacc cgctacatga tactgagtaa cagagccgga
     3001 gaattcacgg tatggggtga tgaactggcg gattatcccc agagtgttca tgaccaggtg
     3061 aatgtttatc tgtcgccagg tggggccgtg atggtcacgg atatacattc ggggctgtca
     3121 gaatctcatg agacgctggc ccggcctgag cgtgtgagaa tgtattccgg tgcgacggtc
     3181 cggcatgtac tggaacagat gcgccagggg tggccctctt acggttttcc ggcgctgccg
     3241 catcactggc cggataattt ttatttcagc gatgaccgca ggcccgcagc ctctccgctg
     3301 ccgtcagcgc accgggtgga cgtcaccgct tatgcggcac cggagcaact catgcccgtt
     3361 gtcttttcga cagagcgaaa cagcaggacg ctgaatctgc tgttgtgcaa agggccggag
     3421 gaaatgcttg tcggttttgt gcgcctggag gacgagctgc gtcccgttct tgcgcttccg
     3481 tcgccggatt acagtcatct gatggtaagc atcatcacag agaacgggat acacctggca
     3541 ggctacggtg aggccataaa ccgtgatgct gatactccgt acccaccgga accgaagctg
     3601 atgcagttca ggcttaaggg ctgtcaggac acgctttttg ctgccatcaa caaaccggaa
     3661 gagatgccgg attatctctt ccgtcaactc ggatttaatc agacctggca tgaatggaag
     3721 cgggacgaac agcacaggca acaacaacga cgccccggac attaccgggg catgagtatg
     3781 tgatatccgg ggctgcaccc cgaaccccgc caacgtctca cgggacacga aaaaattccg
     3841 cgtcccgtga ggcgttttct ggatgagaaa gtttgccgtt ttgacccgtt cgcgcttctg
     3901 aacggtcgaa accgatcgcg catcgctttc gtgaatagtt atgcagaccc ctaaaaacga
     3961 ttctgacgcg tttttctggt ttggcctggt gttttcttgt ctttttgtgt tttttgcgtc
     4021 agaacgcgtc tgagagcgtt ttaaggggta cgcacaacag gagttatggt aaatcggagg
     4081 tgtttatggc ttacgacgaa cattcgattc gcgtgatgtc tgctgacgag atcgagcaac
     4141 gttttgactg gttgcgcctg gagaacctgg cgaaggagca tcgcctaccc gttgactggg
     4201 tccgacgggg atttgaagcc tgctggcgac tgggtatcga gccggattat ttcatcgaca
     4261 ggtatatctt caaacgggat gtgccactgg tgccggagtt tgaggtcgtg ttcagggaga
     4321 tcgtgaacga aaaccgatac agggatcgga tgcgtttctg atatgcctct aaaaacgcct
     4381 gtaagcgatt ctgacgcgtt tttctgattt gggtgaggtt ttttacgtcc atatccactt
     4441 ttttgcgtca cagagcgatt gagagcgttt tagagggtac gtacaacggg agttatggta
     4501 aatggatcgg gttttcggga aggttcgaca ggatttgccg ttgggtgtag tgtaagcgac
     4561 tgaaaaacaa acgccccgta aatcgtgctc tcaccgccaa gattgatcac gaaattacag
     4621 ggcgccgggt tccgcgtttc ccgatgggaa agcgcggtta gttaaactgt gtaccgagag
     4681 aaatcgtatc ac
//
