LOCUS       NZ_CP130066             4099 bp    DNA     circular CON 21-JUL-2023
DEFINITION  Shigella flexneri 1b strain A-10383 plasmid pA-10383B, complete
            sequence.
ACCESSION   NZ_CP130066
VERSION     NZ_CP130066.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361130
            Assembly: GCF_030506075.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri 1b
  ORGANISM  Shigella flexneri 1b
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4099)
  AUTHORS   Neemuchwala,A., Zittermann,S., Johnson,K., Middleton,D.,
            Stapleton,P.J., Ravirajan,V., Cronin,K., Allen,V.G. and Patel,S.N.
  TITLE     Genomic Characterization of Increased and Emerging
            Azithromycin-resistant Shigella flexneri 1b in Ontario
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4099)
  AUTHORS   Neemuchwala,A., Zittermann,S., Johnson,K., Middleton,D.,
            Stapleton,P.J., Ravirajan,V., Cronin,K., Allen,V.G. and Patel,S.N.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-JUN-2023) Molecular Research, Public Health Ontario,
            661 University Ave, Toronto Ontario, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-APR-2020
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: PHL-_18-A10383
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/19/2023 18:07:31
            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)                     :: 5,038
            CDSs (total)                      :: 4,907
            Genes (coding)                    :: 4,136
            CDSs (with protein)               :: 4,136
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 102
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 771
            CDSs (without protein)            :: 771
            Pseudo Genes (ambiguous residues) :: 0 of 771
            Pseudo Genes (frameshifted)       :: 272 of 771
            Pseudo Genes (incomplete)         :: 452 of 771
            Pseudo Genes (internal stop)      :: 173 of 771
            Pseudo Genes (multiple problems)  :: 123 of 771
            Pseudo Genes (short protein)      :: 5 of 771
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130066.1.
            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..4099
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="A-10383"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="pA-10383B"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            complement(join(3877..4099,1..89))
                     /locus_tag="QS169_RS25125"
                     /old_locus_tag="QS169_25125"
     CDS             complement(join(3877..4099,1..89))
                     /locus_tag="QS169_RS25125"
                     /old_locus_tag="QS169_25125"
                     /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_005065488.1"
                     /translation="MIVKFHARGKGGGSGPVDYLLGRERNREGATVLQGNPEEVRELID
                     ATPFAKKYTSGVLSFAEKELPPGGREKVMASFERVLMPGLEKNQYSILWVDAPGQGTA"
                     /name="hypothetical protein"
     gene            complement(79..402)
                     /locus_tag="QS169_RS25130"
                     /old_locus_tag="QS169_25130"
     CDS             complement(79..402)
                     /locus_tag="QS169_RS25130"
                     /old_locus_tag="QS169_25130"
                     /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_000955991.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLCQLAAIGNNLNQTARKVNSGQWSSGNRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            466..657
                     /locus_tag="QS169_RS25135"
                     /old_locus_tag="QS169_25135"
     CDS             466..657
                     /locus_tag="QS169_RS25135"
                     /old_locus_tag="QS169_25135"
                     /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_000165981.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESFHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1802..2194
                     /locus_tag="QS169_RS25140"
                     /old_locus_tag="QS169_25140"
     CDS             1802..2194
                     /locus_tag="QS169_RS25140"
                     /old_locus_tag="QS169_25140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014526575.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_134798933.1"
                     /translation="MALSACFRQQLNPVVNSLLKERIIHSPKELEHDNAVIRVLQKLQI
                     QEVCNNTLWETAKQQLLQKSDGRYFAINSKHLSFPGPGESHAFCCIKYKNAIGINGNNA
                     ETQSTHYQPYPYDKVSIWGPFPHNLT"
                     /name="hypothetical protein"
     gene            complement(2740..2973)
                     /locus_tag="QS169_RS25145"
                     /old_locus_tag="QS169_25145"
     CDS             complement(2740..2973)
                     /locus_tag="QS169_RS25145"
                     /old_locus_tag="QS169_25145"
                     /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(2980..3099)
                     /locus_tag="QS169_RS25150"
                     /old_locus_tag="QS169_25150"
     CDS             complement(2980..3099)
                     /locus_tag="QS169_RS25150"
                     /old_locus_tag="QS169_25150"
                     /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_005065476.1"
                     /translation="MRYHEDSNGRFLVLPEGMKAETNWTMENGKQNAVRLVQE"
                     /name="hypothetical protein"
     gene            complement(3139..3510)
                     /locus_tag="QS169_RS25155"
                     /old_locus_tag="QS169_25155"
     CDS             complement(3139..3510)
                     /locus_tag="QS169_RS25155"
                     /old_locus_tag="QS169_25155"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_000067494.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTSALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILRE"
                     /name="MbeB family mobilization protein"
     Typing          complement(744..829)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          842..1399
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.496"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(83..429)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.552"
                     /coverage="98.0"
                     /evalue="7.73e-67"
     Typing          complement(2637..3679)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.805"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3887..4098)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.958"
                     /coverage="99.0"
                     /evalue="5.93e-41"
ORIGIN
        1 gccccttccc ggttacgctc ccttcccagc aggtaatcaa ccggaccact gccaccacct
       61 tttccccggg catgaaactt aactatcatc ccgcgtcccc tgttccctga cggccagacg
      121 cagccggcgc agctcgtccc cgatggccat cagtgcggcc accacctgaa cccggttacc
      181 ggaagaccac tgcccgctgt tcaccttcct cgctgtctga ttcaggttat tcccgatggc
      241 agccagctga cacagtaacg gcggtgccag tgtcggcagt ttcccggaac gggcaaccgg
      301 ctcccccagg cagacccgcc gcatccatac cgccagctgt ttaccctcac agcgttccag
      361 taaccgggca tgttcatcat cagtaacccg tatcgtgagc atcctctcgc gtttcatcgg
      421 tatcattacc tcctgaacag aaatccccct tacacggagg catcagtgac taaacaggaa
      481 aaaaccgccc ttaacatggc ccgctttatc agaagccaga cattaacgct gctggagaag
      541 ctcaacgaac tggacgcgga tgaacaggct gatatctgtg aatcgtttca cgaccacgcc
      601 gatgagcttt accgcagctg cctcgcacgt ttcggggatg acggtgaaaa cctctgacat
      661 atgctgctcc cggcatccgc tcacagacaa gctgtgagcg gatgccggga gcagacaagc
      721 ccgtcagggc gcatcagcag gttttagcgg gtgtcggggc gcagccatga cccagtcacg
      781 tagcgatagc ggagtgtata ctggcttaac catgcggcat cagtgcagat tgtatgaaaa
      841 gtgcgccata ccgggtatga aataccgcac agatgcgtaa ggagaaaatg cacgtccagg
      901 cgcttttccg cttcctcgct cactgactcg ctacgctcgg tcgttcgact gcggcgagcg
      961 gtatctactc actcaaaaac gaaatgctgt tatccacaga atcaggggat aacgccggaa
     1021 agaacatgtg agcaaaagac cagggacagg aagaaggccg cgccgatggc gtttttccat
     1081 aggctccgcc cccctgacga gcatcacaaa aaccgacgct caagtcagag gtggcgaaac
     1141 ccgacaggac tataaagata ccaggcgttt ccccctggaa gctccctcgt gcgctctcct
     1201 gttccgaccc tgccgcttac cggatacctg tccgcctttc tcccttcggg aagcgtggcg
     1261 ctttctcata gctcacgctg ttggtatctc agttcggtgt aggtcgttcg ctccaagctg
     1321 ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg ccttatccgg taactatcgt
     1381 cttgagtcca acccggtaag acacgactta acgccactgg cagcagccat tggtaactgg
     1441 acaaggtgga ttgagatatt aagagttctt gaagtggtgg cctaactgcg gctacactag
     1501 aaggacagca tttggtatct gtgctccacc aagccagtta ccttcggaag aaagagttgg
     1561 tagctctaga ttccggcaaa caaaccaccg ttggtagcgg tggttttttt gtttgcaggc
     1621 agcagattac gcgccgcaaa aaaggatctc aagaagatct tgaatcactc tatgaaaatt
     1681 ttgttttata gccgtatttg ttgatgctat aagccagaga ccttctatga gaatagacat
     1741 atcacatcaa acacggcata ccccgccaaa catgcttcct cgggaacaaa attgtgtagc
     1801 aatggcatta tctgcgtgct ttagacaaca actaaaccct gtggtaaaca gcttattaaa
     1861 agagagaata atacactccc ctaaagaatt ggaacatgat aacgcagtaa taagagtcct
     1921 gcaaaaacta caaattcaag aagtttgtaa caacaccctt tgggagacag ccaaacaaca
     1981 actacttcaa aaatcggatg gaagatattt tgccatcaat tctaaacact tatcctttcc
     2041 aggcccagga gaatctcacg ccttctgttg catcaaatac aaaaatgcaa ttggcattaa
     2101 cggaaacaat gccgaaaccc aatcgaccca ctaccaaccc tatccctatg ataaagtcag
     2161 tatatgggga ccattccctc acaatttaac gtaatatctt aattgtacgc accgctgaaa
     2221 cgcgttcggc gcgatcacgg cagcagacag gtaaaaatgg caacaaacca cccgaaaaac
     2281 tgccgcgatc gcacccggta aattttaacc acatgcatag ctatgcagcc atgtgaatca
     2341 cgcaggaatt gccagccaga gacagctgaa acggattttt ttcatgcttt cggaagcgaa
     2401 gaagacgggg acctgagcgg gaaaaaagaa gttcagggga atgagcgcga tctggcaata
     2461 gaggcaaaac acagcaacaa aagacacacc agaatcgcgc ccgtatgcgt tttaacgcgt
     2521 tcctatgttt tcagcaaggt ctgactgaag cgcgttcccg gtgcccccga accaaccatt
     2581 atcccaaaaa atgcaccgga aacgcgctga caacatttta gcctgtctct gattaccatc
     2641 ccagcgaagg gccatccagt gtccgttcct gtatttccag ctggtgctca cgctccaggg
     2701 ataacgcatg ttcgcattcc tgtatcagcc gttcgtccct tatctcctgt tctcgctgta
     2761 taactggctc aagcgttctg tctgctcgct caagtgctgc acctgctgac tcaactgcat
     2821 gacccgctcg ttcagcatcg cgttgtcccg ttgcgtaagc gaaaacattt tctgcaattc
     2881 cacgaaggcg ctctcccatt cgttcagccg ctgcatatag tcctgttgca gttgttctaa
     2941 tgcgttcagc aaatgtcttt ccagctccgt catgctctgt tactcctgta ccagccttac
     3001 ggcattctgt ttcccgtttt ccatcgtcca gttcgtttcg gctttcatcc cctcgggcaa
     3061 caccagaaaa cgtccgttgc tgtcctcgtg ataacgcacg ccccatgtct tcgcgttcag
     3121 cttctccaga ctctctttct actcgcggag aatattcatg ttcgcgttta tcttcatgcc
     3181 ctggtaccac agcaggctcc cggtcgtggc aaacatcagt actgagacga taatcagcca
     3241 cagccagcgt ttcacgctca ttttcagtac ggttttccag tgtgcgtcca tcgtatcgac
     3301 ggtcgttttc tgatacctct ccagaagttc tttcagggct gatgtatggt cgttgatagc
     3361 gttcctgatt aaagattcgt ttgaggtcag ttccctgttt acagattctt cgagcttcct
     3421 gaactcgtcg ttcagcattt tctctgtaga ttcggctctc tctttcagct ttttctcgaa
     3481 ctccgcaccc gtctgtaaaa gattgctcat aaaacgctcc tttcagtctg atattcttcc
     3541 cgccgttcgg gtctgcaatg ctgatactgc ttcgcgtcac cctaaccacg tcaatccctg
     3601 cctctgtgag agcctgaatc acatcctgac ggccttttat ctctccggca tggtaaaccg
     3661 cgtgtaacgc cctcagcaat cgcctgtttc gtttccggca gattatcagg gagtgtcagc
     3721 gtcctgcggt tctccggggc gttcgggtca tgcagcccgt aatagtgatt aaccagcgtc
     3781 tgccaggcat caattctagg cctgtctgcg cggtcgtagt acggctggag gcgttttccg
     3841 gtctgtagct ccatgttcgg aatgacaaaa ttcagctcaa gccgtccctt gtcctggtgc
     3901 atccacccac aggatgctgt actgattttt ttcgagaccg ggcatcagta cacgctcaaa
     3961 gctcgccatc actttttcac gtcctcccgg cggcagctcc ttctccgcga acgacagaac
     4021 accggacgtg tatttcttcg caaatggcgt ggcatcgatg agttcccgga cttcttccgg
     4081 attaccctga agcaccgtt
//
