LOCUS       CP128224                4110 bp    DNA     circular BCT 22-MAY-2024
DEFINITION  Shigella flexneri 1b strain sflex069 plasmid psflex069-C, complete
            sequence.
ACCESSION   CP128224
VERSION     CP128224.1
DBLINK      BioProject: PRJNA780545
            BioSample: SAMN35361188
KEYWORDS    .
SOURCE      Shigella flexneri 1b
  ORGANISM  Shigella flexneri 1b
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4110)
  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 emerging and increasing
            azithromycin-resistant Shigella flexneri 1b isolates in Ontario
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4110)
  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 (13-JUN-2023) Molecular Research, Public Health Ontario,
            661 University Ave, Toronto Ontario, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 31-MAR-2020
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: SF018-069
            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
            Annotation Date                   :: 06/15/2023 09:24:43
            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)                     :: 5,087
            CDSs (total)                      :: 4,955
            Genes (coding)                    :: 4,163
            CDSs (with protein)               :: 4,163
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 792
            CDSs (without protein)            :: 792
            Pseudo Genes (ambiguous residues) :: 0 of 792
            Pseudo Genes (frameshifted)       :: 305 of 792
            Pseudo Genes (incomplete)         :: 448 of 792
            Pseudo Genes (internal stop)      :: 173 of 792
            Pseudo Genes (multiple problems)  :: 131 of 792
            Pseudo Genes (short protein)      :: 5 of 792
            ##Genome-Annotation-Data-END##
            Bacteria and source DNA available from Shigella flexneri serotype
            1b.
            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/
FEATURES             Location/Qualifiers
     source          1..4110
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="sflex069"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="psflex069-C"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            complement(315..506)
                     /locus_tag="QS103_25360"
     CDS             complement(315..506)
                     /locus_tag="QS103_25360"
                     /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="XBA31295.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESFHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            570..893
                     /locus_tag="QS103_25365"
     CDS             570..893
                     /locus_tag="QS103_25365"
                     /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="XBA31299.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLCQLAAIGNNLNQTARKVNSGQWSSGNRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            883..1194
                     /locus_tag="QS103_25370"
     CDS             883..1194
                     /locus_tag="QS103_25370"
                     /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="XBA31296.1"
                     /translation="MIVKFHARGKGGGSGPVDYLLGRERNREGATVLQGNPEEVRELID
                     ATPFAKKYTSGVLSFAEKELPPGGREKVMASFERVLMPGLEKNQYSILWVDAPGQGTA"
                     /name="hypothetical protein"
     gene            1217..1531
                     /locus_tag="QS103_25375"
                     /pseudo=""
     CDS             1217..1531
                     /locus_tag="QS103_25375"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; 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            1572..1943
                     /locus_tag="QS103_25380"
     CDS             1572..1943
                     /locus_tag="QS103_25380"
                     /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="XBA31297.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTSALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILRE"
                     /name="MbeB family mobilization protein"
     gene            1983..2102
                     /locus_tag="QS103_25385"
     CDS             1983..2102
                     /locus_tag="QS103_25385"
                     /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="mbkB"
                     /protein_id="XBA31298.1"
                     /translation="MRYHEDSNGRFLVLPEGMKAETNWTMENGKQNAVRLVQE"
                     /name="mbkB"
     gene            2109..2342
                     /locus_tag="QS103_25390"
     CDS             2109..2342
                     /locus_tag="QS103_25390"
                     /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="XBA31293.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2888..3355)
                     /locus_tag="QS103_25395"
     CDS             complement(2888..3355)
                     /locus_tag="QS103_25395"
                     /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="XBA31294.1"
                     /translation="MRIDISHQTRHTPPNMLPREQNCVAMALSACFRQQLNPVVNSLLK
                     ERIIHSPKELEHDNAVIRVLQKLQIQEVCNNTLWETAKQQLLQKSDGRYFAINSKHLSF
                     PGPGESHAFCCIKYKNAIGINGNNAETQSTHYQPYPYDKVSIWGPFPHNLT"
                     /name="hypothetical protein"
     Typing          144..229
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          complement(3684..4110)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.43"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          544..890
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.552"
                     /coverage="98.0"
                     /evalue="7.739999999999999e-67"
     Typing          1158..2446
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.575"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgagtagata ccgctcgccg cagtcgaacg accgagcgta gcgagtcagt gagcgaggaa
       61 gcggaaaagc gcctggacgt gcattttctc cttacgcatc tgtgcggtat ttcatacccg
      121 gtatggcgca cttttcatac aatctgcact gatgccgcat ggttaagcca gtatacactc
      181 cgctatcgct acgtgactgg gtcatggctg cgccccgaca cccgctaaaa cctgctgatg
      241 cgccctgacg ggcttgtctg ctcccggcat ccgctcacag acaagctgtg agcggatgcc
      301 gggagcagca tatgtcagag gttttcaccg tcatccccga aacgtgcgag gcagctgcgg
      361 taaagctcat cggcgtggtc gtgaaacgat tcacagatat cagcctgttc atccgcgtcc
      421 agttcgttga gcttctccag cagcgttaat gtctggcttc tgataaagcg ggccatgtta
      481 agggcggttt tttcctgttt agtcactgat gcctccgtgt aagggggatt tctgttcagg
      541 aggtaatgat accgatgaaa cgcgagagga tgctcacgat acgggttact gatgatgaac
      601 atgcccggtt actggaacgc tgtgagggta aacagctggc ggtatggatg cggcgggtct
      661 gcctggggga gccggttgcc cgttccggga aactgccgac actggcaccg ccgttactgt
      721 gtcagctggc tgccatcggg aataacctga atcagacagc gaggaaggtg aacagcgggc
      781 agtggtcttc cggtaaccgg gttcaggtgg tggccgcact gatggccatc ggggacgagc
      841 tgcgccggct gcgtctggcc gtcagggaac aggggacgcg ggatgatagt taagtttcat
      901 gcccggggaa aaggtggtgg cagtggtccg gttgattacc tgctgggaag ggagcgtaac
      961 cgggaagggg caacggtgct tcagggtaat ccggaagaag tccgggaact catcgatgcc
     1021 acgccatttg cgaagaaata cacgtccggt gttctgtcgt tcgcggagaa ggagctgccg
     1081 ccgggaggac gtgaaaaagt gatggcgagc tttgagcgtg tactgatgcc cggtctcgaa
     1141 aaaaatcagt acagcatcct gtgggtggat gcaccaggac aagggacggc ttgagctgaa
     1201 ttttgtcatt ccgaacatgg agctacagac cggaaaacgc ctccagccgt actacgaccg
     1261 cgcagacagg cctagaattg atgcctggca gacgctggtt aatcactatt acgggctgca
     1321 tgacccgaac gccccggaga accgcaggac gctgacactc cctgataatc tgccggaaac
     1381 gaaacaggcg attgctgagg gcgttacacg cgggatagac gcgctttacc atgccggaga
     1441 gataaaaggc cgtcaggatg tgattcaggc tctcacagag gcagggattg acgtggttag
     1501 ggtgacgcga agcagtatca gcattgcaga cccgaacggc gggaagaata tcagactgaa
     1561 aggagcgttt tatgagcaat cttttacaga cgggtgcgga gttcgagaaa aagctgaaag
     1621 agagagccga atctacagag aaaatgctga acgacgagtt caggaagctc gaagaatctg
     1681 taaacaggga actgacctca aacgaatctt taatcaggaa cgctatcaac gaccatacat
     1741 cagccctgaa agaacttctg gagaggtatc agaaaacgac cgtcgatacg atggacgcac
     1801 actggaaaac cgtactgaaa atgagcgtga aacgctggct gtggctgatt atcgtctcag
     1861 tactgatgtt tgccacgacc gggagcctgc tgtggtacca gggcatgaag ataaacgcga
     1921 acatgaatat tctccgcgag tagaaagaga gtctggagaa gctgaacgcg aagacatggg
     1981 gcgtgcgtta tcacgaggac agcaacggac gttttctggt gttgcccgag gggatgaaag
     2041 ccgaaacgaa ctggacgatg gaaaacggga aacagaatgc cgtaaggctg gtacaggagt
     2101 aacagagcat gacggagctg gaaagacatt tgctgaacgc attagaacaa ctgcaacagg
     2161 actatatgca gcggctgaac gaatgggaga gcgccttcgt ggaattgcag aaaatgtttt
     2221 cgcttacgca acgggacaac gcgatgctga acgagcgggt catgcagttg agtcagcagg
     2281 tgcagcactt gagcgagcag acagaacgct tgagccagtt atacagcgag aacaggagat
     2341 aagggacgaa cggctgatac aggaatgcga acatgcgtta tccctggagc gtgagcacca
     2401 gctggaaata caggaacgga cactggatgg cccttcgctg ggatggtaat cagagacagg
     2461 ctaaaatgtt gtcagcgcgt ttccggtgca ttttttggga taatggttgg ttcgggggca
     2521 ccgggaacgc gcttcagtca gaccttgctg aaaacatagg aacgcgttaa aacgcatacg
     2581 ggcgcgattc tggtgtgtct tttgttgctg tgttttgcct ctattgccag atcgcgctca
     2641 ttcccctgaa cttctttttt cccgctcagg tccccgtctt cttcgcttcc gaaagcatga
     2701 aaaaaatccg tttcagctgt ctctggctgg caattcctgc gtgattcaca tggctgcata
     2761 gctatgcatg tggttaaaat ttaccgggtg cgatcgcggc agtttttcgg gtggtttgtt
     2821 gccattttta cctgtctgct gccgtgatcg cgccgaacgc gtttcagcgg tgcgtacaat
     2881 taagatatta cgttaaattg tgagggaatg gtccccatat actgacttta tcatagggat
     2941 agggttggta gtgggtcgat tgggtttcgg cattgtttcc gttaatgcca attgcatttt
     3001 tgtatttgat gcaacagaag gcgtgagatt ctcctgggcc tggaaaggat aagtgtttag
     3061 aattgatggc aaaatatctt ccatccgatt tttgaagtag ttgttgtttg gctgtctccc
     3121 aaagggtgtt gttacaaact tcttgaattt gtagtttttg caggactctt attactgcgt
     3181 tatcatgttc caattcttta ggggagtgta ttattctctc ttttaataag ctgtttacca
     3241 cagggtttag ttgttgtcta aagcacgcag ataatgccat tgctacacaa ttttgttccc
     3301 gaggaagcat gtttggcggg gtatgccgtg tttgatgtga tatgtctatt ctcatagaag
     3361 gtctctggct tatagcatca acaaatacgg ctataaaaca aaattttcat agagtgattc
     3421 aagatcttct tgagatcctt ttttgcggcg cgtaatctgc tgcctgcaaa caaaaaaacc
     3481 accgctacca acggtggttt gtttgccgga atctagagct accaactctt tcttccgaag
     3541 gtaactggct tggtggagca cagataccaa atgctgtcct tctagtgtag ccgcagttag
     3601 gccaccactt caagaactct taatatctca atccaccttg tccagttacc aatggctgct
     3661 gccagtggcg ttaagtcgtg tcttaccggg ttggactcaa gacgatagtt accggataag
     3721 gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc
     3781 tacaccgaac tgagatacca acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg
     3841 agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag
     3901 cttccagggg gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca cctctgactt
     3961 gagcgtcggt ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa cgccatcggc
     4021 gcggccttct tcctgtccct ggtcttttgc tcacatgttc tttccggcgt tatcccctga
     4081 ttctgtggat aacagcattt cgtttttgag
//
