LOCUS       NZ_CP045937             5219 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain AUSMDU00010534 plasmid pAUSMDU00010534_05,
            complete sequence.
ACCESSION   NZ_CP045937
VERSION     NZ_CP045937.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13191651
            Assembly: GCF_009664515.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5219)
  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  JOURNAL   Unpublished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 5219)
  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                     :: 22-OCT-2019
            Assembly Method                   :: Unicycler v. 0.4.8b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 103x
            Sequencing Technology :: Oxford Nanopore GridIon, Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009664515.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 06:48:57
            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)                     :: 5,242
            CDSs (total)                      :: 5,108
            Genes (coding)                    :: 4,461
            CDSs (with protein)               :: 4,461
            Genes (RNA)                       :: 134
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 101
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 647
            CDSs (without protein)            :: 647
            Pseudo Genes (ambiguous residues) :: 0 of 647
            Pseudo Genes (frameshifted)       :: 177 of 647
            Pseudo Genes (incomplete)         :: 452 of 647
            Pseudo Genes (internal stop)      :: 106 of 647
            Pseudo Genes (multiple problems)  :: 86 of 647
            Pseudo Genes (short protein)      :: 3 of 647
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP045937.1.
            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..5219
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="AUSMDU00010534"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pAUSMDU00010534_05"
                     /geo_loc_name="Australia"
                     /collection_date="2017"
     gene            complement(108..341)
                     /locus_tag="GJE15_RS25605"
                     /old_locus_tag="GJE15_25605"
     CDS             complement(108..341)
                     /locus_tag="GJE15_RS25605"
                     /old_locus_tag="GJE15_25605"
                     /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_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(348..878)
                     /locus_tag="GJE15_RS25610"
                     /old_locus_tag="GJE15_25610"
     CDS             complement(348..878)
                     /locus_tag="GJE15_RS25610"
                     /old_locus_tag="GJE15_25610"
                     /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_015386306.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNENLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<916..1578)
                     /locus_tag="GJE15_RS25615"
                     /old_locus_tag="GJE15_25615"
                     /pseudo=""
     CDS             complement(<916..1578)
                     /locus_tag="GJE15_RS25615"
                     /old_locus_tag="GJE15_25615"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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(1556..1879)
                     /locus_tag="GJE15_RS25620"
                     /old_locus_tag="GJE15_25620"
     CDS             complement(1556..1879)
                     /locus_tag="GJE15_RS25620"
                     /old_locus_tag="GJE15_25620"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_000955995.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            1944..2135
                     /locus_tag="GJE15_RS25625"
                     /old_locus_tag="GJE15_25625"
     CDS             1944..2135
                     /locus_tag="GJE15_RS25625"
                     /old_locus_tag="GJE15_25625"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2803..2916
                     /locus_tag="GJE15_RS26565"
     CDS             2803..2916
                     /locus_tag="GJE15_RS26565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            3322..3711
                     /locus_tag="GJE15_RS25630"
                     /old_locus_tag="GJE15_25630"
     CDS             3322..3711
                     /locus_tag="GJE15_RS25630"
                     /old_locus_tag="GJE15_25630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(3775..4059)
                     /locus_tag="GJE15_RS25635"
                     /old_locus_tag="GJE15_25635"
     CDS             complement(3775..4059)
                     /locus_tag="GJE15_RS25635"
                     /old_locus_tag="GJE15_25635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(4077..4274)
                     /locus_tag="GJE15_RS25640"
                     /old_locus_tag="GJE15_25640"
     CDS             complement(4077..4274)
                     /locus_tag="GJE15_RS25640"
                     /old_locus_tag="GJE15_25640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            4486..4782
                     /locus_tag="GJE15_RS25645"
                     /old_locus_tag="GJE15_25645"
     CDS             4486..4782
                     /locus_tag="GJE15_RS25645"
                     /old_locus_tag="GJE15_25645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047647.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     Typing          complement(2221..2307)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="2.47e-38"
     Typing          2319..2875
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.642"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(5..1566)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttaccatccc agcgaagggc catccagtgt ccgttcctgt atttccagct ggcgctcacg
       61 ctccagggat aacgcatgtt cgcgttcctg tatcagccgt tcgtccctta tctcctgttc
      121 tcgctgtata actggctcaa gcgttctgtc tgctcgctca agtgctgcac ctgctgactc
      181 aactgcatga cccgctcgtt cagcatcgcg ttgtcccgtt gcgtaagcga aaacattttc
      241 tgcaattcca cgaaggcgct ctcccattcg ttcagccgct gcatatagtc ctgttgcagt
      301 tgctctaatg cgttcagcaa atgtctttcc agctccgtca tgctctgtta ctcctgtacc
      361 agccttacgg cattctgttt cccgttttcc atcgtccagt tcgtttcggc tttcatcccc
      421 tcgggcaaca ccagaaaacg tccgttgctc ccctcgtgat aacgcacgcc ccatgtcttc
      481 gcgttcagct tctccagatt ctcgttctgc ttcctgattt cttccaggtt cgcctgtatc
      541 atcccgccaa gataccagag cgtcccgcca ctcacggtaa acaggaaaat gaccatcccc
      601 agtaacatca tgcccgtatt ccctgccagc tttaacacgt ccttcctgtg ctgcatcatc
      661 gcctctttca ccccttcccg gtgttttttc agtgattcct ctgtcgaagc tgtgaacagg
      721 gctatagcgt ctttgatttt cgtctcgttt gatgtcacag ccttgcttac agatttttcg
      781 agcttcctga actcgtcgtt cagtattgtc tctgtagatt cggctctctc tttcagcttt
      841 ttctcgaact ccgcgcccgt ctgtaaaaga ttgctcataa aatgctcctt tcagcctgat
      901 attcttccca ccgttcgggt ctgcaatgct gatactgctt cgcgtcaccc tgaccacttc
      961 aagccctgcc tctgtgagcg cctgaatcac atcctgacgg ccttttatct ccccgacatg
     1021 ataaagagcg tctatcccgc gtgtgacgct ctctgcaagc gcctgtttcg tttccggcag
     1081 gttatcaggg agagtcagta tccggcggtt ctccggggcg ttggggtcat gcagcccgta
     1141 atggtgatta accagcgtct gccaggcatc aattctcggc ctgtctgccc ggtcgtagta
     1201 cggctggagg cgttttccgc tctgtagctc catgttcgga atgacaaaat tcagctcaag
     1261 ccgtcccttg tcctggtgct ccacccacag gatgctgtac tgattttttt cgagaccggg
     1321 catcagtaca cgctcaaagc tcgccatcac cttttcacgt cctcccggcg gcagctcctt
     1381 ctccgcgaac gacagaacac ctgacgtgta tttcttcgca aatggcgtgg catcgatgag
     1441 ttcccggact tcttccggat taccctgaag caccgttgcc ccttcccggt tacgctccct
     1501 tcccagcagg taatcaaccg gaccactgcc accgcctttt cccctggcat gaaacttaac
     1561 tatcatcccg cgctccatgt tccctgacga cctgccgtaa gctgcgcaac tctctctcga
     1621 tggccatcag tgcggccacc acctgaaccc ggtcaccgga agaccactgc ccgctgttca
     1681 ccttcctcgc cgtctgattc aggttattcc cgatggcagc cagctggcgc agtaacggcg
     1741 gtgccagtgt cggcagcttc ccggaacggg caaccggctc acccagacag acccgccgca
     1801 tccataccgc cagctgttta ccctcacagc gttcaagtaa ccgggcatgt tcatcatcag
     1861 taacccgtat tgtgagcatc ctctcgcgtt tcatcggtat cattatcccc atgaacagaa
     1921 atccccctta cacggaggca tcagtgacca aacaggaaaa aaccgccctt aacatggccc
     1981 gctttataag aagccagaca ttaacgctgc tggagaagct caacgaactg gacgcggatg
     2041 aacaggcaga tatctgtgaa tcgcttcacg accacgccga tgagctttac cgcagttgcc
     2101 tcgctcgctt cggggatgac ggtgaaaacc tctgacacat gcagctcccg gagacggtca
     2161 cagcttgtct gtgagcggat gccgggagct gacaagcccg tcagggcacg tcagcgggtt
     2221 ttagcgggtg tcggggcgca gccctgaccc agtcacgtag cgatagcgga gtgtatactg
     2281 gcttaaccat gcggcatcag tgcggatggt atgaaaagtg cgccataccg ggtgtgaaat
     2341 gccgcacaga tgcgtaagga gaaaatgcac gtccagccgc ttttccgctt cctcgctcac
     2401 tgactcgcta cgctcggtcg ttcgactgcg gcgagcggta tctactcact caaaaacgaa
     2461 atgctgttat ccacagaatc aggggataac accggaaaaa acatgtgagc aaaagaccag
     2521 gaacaggaag aaggccgcgc cgctggcgtt tttccatagg ctccgccccc ctgacgagca
     2581 tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactta aagataccag
     2641 gcgtttcccc ccggaagctc cctcgtgcgc tctcctgttc cgaccttacc gtttaccgga
     2701 tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgtagg
     2761 tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt
     2821 cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac
     2881 gacttaacgc cactggcagc agccattggt aactaaaaag tggatttaga tacgcagaac
     2941 tcttgaagtt gaagccttat agcggctaca ctgaaaggac atcttttggt atctgtgctc
     3001 cacttaagcc agctacccgg ttaggtaatc tgccaggatt agctaacctt cgaaaaacca
     3061 cctgccaggg tggttttttc gtttacaggc agcagattac gcgcagaaaa aaaggatctc
     3121 aagaagatcc tttgatcttt tttctctaaa ctgcaatccc atcagttcag gagagaaaga
     3181 tagtataatt gccctctctt atatggaacc accattcaat cacatcatgg gaataatata
     3241 agtgaaaacg ttcgcattgt ttatttttac gtgtatatgt atttatagat tggaatttta
     3301 acaaaataaa atggagttaa tatgttcaaa tcatcagtaa agtcaataac atcgagtact
     3361 atactgacct tacttatagg atgttcaagt actgaaacaa acaaaaacat tgtttacaaa
     3421 gttggtggtg acagcatcat tctgaataaa tattgcatac ttaaaatgta cccttcccaa
     3481 tcagaaaaaa acaaaggcgt cataatagaa gtaaacacag atagtttatg taagaaaaaa
     3541 ctaaacgaaa taactagtaa aaatataggg aaacccctga tttcatattt tgatggaaaa
     3601 gtaatatccc aacctgcaat cattcattct gcactaaatc caacccatta ttatcaacct
     3661 gtgaacgatg aaacaacagt gatggaaatc ataaaagcat attcaaaata atattaatag
     3721 atataatcct gcttaaggta tagcttaggc aggattatat ctattcagct cttattataa
     3781 ggtagtgtat acatgaataa tctgccctgt cccactgaca cttttaaatt taattttatc
     3841 aacaccagcg cccttgcaag agatctgata agatgctgga ccaataacgt taactgttct
     3901 tggcccatta ggggcatacc agataaaagc aataaatgga ccgggtacat tagacaatgt
     3961 atcaaaatag acagtgtacg cgatatcacc agtatgattt tcaagttcaa cccaaggacc
     4021 aaaaaagaaa ggaggagccc aaacattttg agaaatcata taatctcctg attagttcaa
     4081 tgcgaatgtt cttcccattc actctcgcaa gaaacatcta taagctcaac atctagccca
     4141 ctaacagaat cagagaaata cttataaaca tcatcccttg ttcccataag gtctgccgaa
     4201 catgatagtt cacaaccatt cttattccta actacaaata agaaacggtg aagcaatact
     4261 ttttcttctt tcattttatc cctcccttta tttacacaga atatactgta tatataaata
     4321 ctagttttat atacagtata aattacgccg cattattttt cctgtcaatg atatgaattt
     4381 tcatttttgt gatctgaatc acccttataa aaatcaggaa gggaagattc gcagcagaaa
     4441 aacagcaccg gataacatca agagaaaaaa cagagaggag ataacgtgag caaaacaaaa
     4501 tctggtcgcc accgactgag caaaacagac aaacgcctgc tggctgcact tatcgctgcc
     4561 ggatacgaag agcggacagc ccgtgacctc atccagaaac acgtttacac actgacacag
     4621 gccgacctgc gccatctggt cagtgaaatc agtaacggtg tgggacagtc acaggcctac
     4681 gatgcgattt accaggcaag acgcattcgt ctcgcccgta aattcctgaa cggaaaaaaa
     4741 ccggaagaag ggctgaacgc ctggaagggt gatttaccat aatcacttat tgtacgcacc
     4801 gctgaaacgc gttcggcgcg atcacggcag cagacaggta aaaatggcaa caaaccaccc
     4861 gaaaaactgc cgcgatcgta cccggtaaat tttaaccaca tgcatagcta tgcagctatg
     4921 tgaatcatgc aggaattgcc agccagagac agctgaaacg gatttttttc atgctttcgg
     4981 aagcgaagaa gacggggacc ggagcgggaa aacagaagtt caggggaatg agcgcgatct
     5041 ggcaatagag gcaaaacaca gcaacaaaag acacaccaga atcgcgcccg tatgcgtttt
     5101 aacgcgttcc tgtgttttca gcaaggtctg actgaagcgc gttcccggtg cccccgaacc
     5161 aaccattatc ccaaaaaatg caccggaaac gcgctgacaa cattttagcc tgtctctga
//
