LOCUS       NZ_CP127084             4110 bp    DNA     circular CON 23-NOV-2023
DEFINITION  Shigella flexneri 1b strain SF-018-002 plasmid psflex002B, complete
            sequence.
ACCESSION   NZ_CP127084
VERSION     NZ_CP127084.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361129
            Assembly: GCF_033870415.1
KEYWORDS    RefSeq.
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     Whole genome sequencing of increased number of
            azithromycin-resistant Shigella flexneri 1b isolates in Ontario
  JOURNAL   Sci Rep 13 (1), 16582 (2023)
   PUBMED   37789081
  REMARK    Publication Status: Online-Only
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 (01-JUN-2023) Molecular Research, Public Health Ontario,
            661 University Ave, Toronto Ontario, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 30-MAR-2020
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: sflex002
            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                   :: 11/22/2023 13:22:32
            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)                     :: 4,929
            CDSs (total)                      :: 4,795
            Genes (coding)                    :: 4,061
            CDSs (with protein)               :: 4,061
            Genes (RNA)                       :: 134
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 105
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 734
            CDSs (without protein)            :: 734
            Pseudo Genes (ambiguous residues) :: 0 of 734
            Pseudo Genes (frameshifted)       :: 263 of 734
            Pseudo Genes (incomplete)         :: 418 of 734
            Pseudo Genes (internal stop)      :: 165 of 734
            Pseudo Genes (multiple problems)  :: 111 of 734
            Pseudo Genes (short protein)      :: 5 of 734
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP127084.1.
            Bacteria and source DNA available from Public health Ontario.
            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..4110
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="SF-018-002"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="psflex002B"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            complement(486..719)
                     /locus_tag="QQS68_RS24560"
                     /old_locus_tag="QQS68_24535"
     CDS             complement(486..719)
                     /locus_tag="QQS68_RS24560"
                     /old_locus_tag="QQS68_24535"
                     /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(726..1256)
                     /locus_tag="QQS68_RS24565"
                     /old_locus_tag="QQS68_24545"
                     /pseudo=""
     CDS             complement(726..1256)
                     /locus_tag="QQS68_RS24565"
                     /old_locus_tag="QQS68_24545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /name="MbeB family mobilization protein"
     gene            complement(<1297..1659)
                     /locus_tag="QQS68_RS24570"
                     /old_locus_tag="QQS68_24550"
                     /pseudo=""
     CDS             complement(<1297..1659)
                     /locus_tag="QQS68_RS24570"
                     /old_locus_tag="QQS68_24550"
                     /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(1634..1945)
                     /locus_tag="QQS68_RS24575"
                     /old_locus_tag="QQS68_24555"
     CDS             complement(1634..1945)
                     /locus_tag="QQS68_RS24575"
                     /old_locus_tag="QQS68_24555"
                     /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(1935..2258)
                     /locus_tag="QQS68_RS24580"
                     /old_locus_tag="QQS68_24560"
     CDS             complement(1935..2258)
                     /locus_tag="QQS68_RS24580"
                     /old_locus_tag="QQS68_24560"
                     /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            2322..2513
                     /locus_tag="QQS68_RS24585"
                     /old_locus_tag="QQS68_24565"
     CDS             2322..2513
                     /locus_tag="QQS68_RS24585"
                     /old_locus_tag="QQS68_24565"
                     /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            3658..4050
                     /locus_tag="QQS68_RS24590"
                     /old_locus_tag="QQS68_24570"
     CDS             3658..4050
                     /locus_tag="QQS68_RS24590"
                     /old_locus_tag="QQS68_24570"
                     /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"
     Typing          complement(2600..2685)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          2698..3255
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.496"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(383..1671)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.575"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1939..2285)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.552"
                     /coverage="98.0"
                     /evalue="7.739999999999999e-67"
ORIGIN
        1 aaatggcaac aaaccacccg aaaaactgcc gcgatcgcac ccggtaaatt ttaaccacat
       61 gcatagctat gcagccatgt gaatcacgca ggaattgcca gccagagaca gctgaaacgg
      121 atttttttca tgctttcgga agcgaagaag acggggacct gagcgggaaa aaagaagttc
      181 aggggaatga gcgcgatctg gcaatagagg caaaacacag caacaaaaga cacaccagaa
      241 tcgcgcccgt atgcgtttta acgcgttcct atgttttcag caaggtctga ctgaagcgcg
      301 ttcccggtgc ccccgaacca accattatcc caaaaaatgc accggaaacg cgctgacaac
      361 attttagcct gtctctgatt accatcccag cgaagggcca tccagtgtcc gttcctgtat
      421 ttccagctgg tgctcacgct ccagggataa cgcatgttcg cattcctgta tcagccgttc
      481 gtcccttatc tcctgttctc gctgtataac tggctcaagc gttctgtctg ctcgctcaag
      541 tgctgcacct gctgactcaa ctgcatgacc cgctcgttca gcatcgcgtt gtcccgttgc
      601 gtaagcgaaa acattttctg caattccacg aaggcgctct cccattcgtt cagccgctgc
      661 atatagtcct gttgcagttg ttctaatgcg ttcagcaaat gtctttccag ctccgtcatg
      721 ctctgttact cctgtaccag ccttacggca ttctgtttcc cgttttccat cgtccagttc
      781 gtttcggctt tcatcccctc gggcaacacc agaaaacgtc cgttgctgtc ctcgtgataa
      841 cgcacgcccc atgtcttcgc gttcagcttc tccagactct ctttctactc gcggagaata
      901 ttcatgttcg cgtttatctt catgccctgg taccacagca ggctcccggt cgtggcaaac
      961 atcagtactg agacgataat cagccacagc cagcgtttca cgctcatttt cagtacggtt
     1021 ttccagtgtg cgtccatcgt atcgacggtc gttttctgat acctctccag aagttctttc
     1081 agggctgatg tatggtcgtt gatagcgttc ctgattaaag attcgtttga ggtcagttcc
     1141 ctgtttacag attcttcgag cttcctgaac tcgtcgttca gcattttctc tgtagattcg
     1201 gctctctctt tcagcttttt ctcgaactcc gcacccgtct gtaaaagatt gctcataaaa
     1261 cgctcctttc agtctgatat tcttcccgcc gttcgggtct gcaatgctga tactgcttcg
     1321 cgtcacccta accacgtcaa tccctgcctc tgtgagagcc tgaatcacat cctgacggcc
     1381 ttttatctct ccggcatggt aaagcgcgtc tatcccgcgt gtaacgccct cagcaatcgc
     1441 ctgtttcgtt tccggcagat tatcagggag tgtcagcgtc ctgcggttct ccggggcgtt
     1501 cgggtcatgc agcccgtaat agtgattaac cagcgtctgc caggcatcaa ttctaggcct
     1561 gtctgcgcgg tcgtagtacg gctggaggcg ttttccggtc tgtagctcca tgttcggaat
     1621 gacaaaattc agctcaagcc gtcccttgtc ctggtgcatc cacccacagg atgctgtact
     1681 gatttttttc gagaccgggc atcagtacac gctcaaagct cgccatcact ttttcacgtc
     1741 ctcccggcgg cagctccttc tccgcgaacg acagaacacc ggacgtgtat ttcttcgcaa
     1801 atggcgtggc atcgatgagt tcccggactt cttccggatt accctgaagc accgttgccc
     1861 cttcccggtt acgctccctt cccagcaggt aatcaaccgg accactgcca ccaccttttc
     1921 cccgggcatg aaacttaact atcatcccgc gtcccctgtt ccctgacggc cagacgcagc
     1981 cggcgcagct cgtccccgat ggccatcagt gcggccacca cctgaacccg gttaccggaa
     2041 gaccactgcc cgctgttcac cttcctcgct gtctgattca ggttattccc gatggcagcc
     2101 agctgacaca gtaacggcgg tgccagtgtc ggcagtttcc cggaacgggc aaccggctcc
     2161 cccaggcaga cccgccgcat ccataccgcc agctgtttac cctcacagcg ttccagtaac
     2221 cgggcatgtt catcatcagt aacccgtatc gtgagcatcc tctcgcgttt catcggtatc
     2281 attacctcct gaacagaaat cccccttaca cggaggcatc agtgactaaa caggaaaaaa
     2341 ccgcccttaa catggcccgc tttatcagaa gccagacatt aacgctgctg gagaagctca
     2401 acgaactgga cgcggatgaa caggctgata tctgtgaatc gtttcacgac cacgccgatg
     2461 agctttaccg cagctgcctc gcacgtttcg gggatgacgg tgaaaacctc tgacatatgc
     2521 tgctcccggc atccgctcac agcttgtctg tgagcggatg ccgggagcag acaagcccgt
     2581 cagggcgcat cagcaggttt tagcgggtgt cggggcgcag ccatgaccca gtcacgtagc
     2641 gatagcggag tgtatactgg cttaaccatg cggcatcagt gcagattgta tgaaaagtgc
     2701 gccataccgg gtatgaaata ccgcacagat gcgtaaggag aaaatgcacg tccaggcgct
     2761 tttccgcttc ctcgctcact gactcgctac gctcggtcgt tcgactgcgg cgagcggtat
     2821 ctactcactc aaaaacgaaa tgctgttatc cacagaatca ggggataacg ccggaaagaa
     2881 catgtgagca aaagaccagg gacaggaaga aggccgcgcc gatggcgttt ttccataggc
     2941 tccgcccccc tgacgagcat cacaaaaacc gacgctcaag tcagaggtgg cgaaacccga
     3001 caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc
     3061 cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt
     3121 ctcatagctc acgctgttgg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct
     3181 gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg
     3241 agtccaaccc ggtaagacac gacttaacgc cactggcagc agccattggt aactggacaa
     3301 ggtggattga gatattaaga gttcttgaag tggtggccta actgcggcta cactagaagg
     3361 acagcatttg gtatctgtgc tccaccaagc cagttacctt cggaagaaag agttggtagc
     3421 tctagattcc ggcaaacaaa ccaccgttgg tagcggtggt ttttttgttt gcaggcagca
     3481 gattacgcgc cgcaaaaaag gatctcaaga agatcttgaa tcactctatg aaaattttgt
     3541 tttatagccg tatttgttga tgctataagc cagagacctt ctatgagaat agacatatca
     3601 catcaaacac ggcatacccc gccaaacatg cttcctcggg aacaaaattg tgtagcaatg
     3661 gcattatctg cgtgctttag acaacaacta aaccctgtgg taaacagctt attaaaagag
     3721 agaataatac actcccctaa agaattggaa catgataacg cagtaataag agtcctgcaa
     3781 aaactacaaa ttcaagaagt ttgtaacaac accctttggg agacagccaa acaacaacta
     3841 cttcaaaaat cggatggaag atattttgcc atcaattcta aacacttatc ctttccaggc
     3901 ccaggagaat ctcacgcctt ctgttgcatc aaatacaaaa atgcaattgg cattaacgga
     3961 aacaatgccg aaacccaatc gacccactac caaccctatc cctatgataa agtcagtata
     4021 tggggaccat tccctcacaa tttaacgtaa tatcttaatt gtacgcaccg ctgaaacgcg
     4081 ttcggcgcga tcacggcagc agacaggtaa
//
