LOCUS       NZ_CP149847             4072 bp    DNA     circular CON 21-APR-2024
DEFINITION  Shigella sonnei strain 2024CK-00068 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP149847
VERSION     NZ_CP149847.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39595405
            Assembly: GCF_036080955.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     Pathogen: clinical or host-associated sample
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAR-2024) Utah Public Health Laboratory, Utah Public
            Health Laboratory Infectious Disease submission group, 4431 S 2700
            W, Salt Lake City, UT 84129, USA
REFERENCE   3  (bases 1 to 4072)
  CONSRTM   Clinical and Environmental Microbiology Branch: Whole genome
            sequencing antimicrobial resistance pathogens in the healthcare
            setting
  TITLE     Direct Submission
  JOURNAL   Submitted (24-JAN-2024) Division of Healthcare Quality Promotion, US
            Centers for Disease Control and Prevention, 1600 Clifton Rd,
            Atlanta, GA, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036080955.1-RS_2024_04_21
            Annotation Date                   :: 04/21/2024 15:24:51
            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)                     :: 4,777
            CDSs (total)                      :: 4,654
            Genes (coding)                    :: 4,418
            CDSs (with protein)               :: 4,418
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 79 of 236
            Pseudo Genes (incomplete)         :: 153 of 236
            Pseudo Genes (internal stop)      :: 46 of 236
            Pseudo Genes (multiple problems)  :: 42 of 236
            Pseudo Genes (short protein)      :: 4 of 236
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP149847.1.
            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..4072
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="2024CK-00068"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA"
                     /collection_date="2023-12-20"
     gene            complement(join(2794..4072,1..881))
                     /gene="mobQ"
                     /locus_tag="WKU68_RS23875"
                     /old_locus_tag="WKU68_23875"
     CDS             complement(join(2794..4072,1..881))
                     /gene="mobQ"
                     /locus_tag="WKU68_RS23875"
                     /old_locus_tag="WKU68_23875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            1060..1314
                     /gene="mobC"
                     /locus_tag="WKU68_RS23880"
                     /old_locus_tag="WKU68_23880"
     CDS             1060..1314
                     /gene="mobC"
                     /locus_tag="WKU68_RS23880"
                     /old_locus_tag="WKU68_23880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            1846..2538
                     /locus_tag="WKU68_RS23885"
                     /old_locus_tag="WKU68_23885"
     CDS             1846..2538
                     /locus_tag="WKU68_RS23885"
                     /old_locus_tag="WKU68_23885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(524..882)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          883..1059
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1847..2538
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..968)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.758"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2798..4071)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.765"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atcatcgaca tggcattact ggtgagtttc catgccgcat tactgtcctt cggcaacgct
       61 tcgatgatgt cacgtagtgt gtacgaagtt gcgttgtcag gaagcacgat attcagaagg
      121 tcagccacac ggcgggcagg ctctgtcagc ccgctgttcc tgagttcagt gcgggaaatc
      181 tgtatttcca ggttaagcct gttaatcaga cgattctgtt cgccgcgttc tgtttcgata
      241 ccgcgtgttt ccatcgcaca ggcagacttt ccgaggtgaa taccaggcgt tttctcaagc
      301 ccctgtcgct cgtatgaacg atggtctatc tcttcctgat aaccggcgtt cgccagtgct
      361 ctgtttgcat ggtcagccca tgatgcacgc cacgtctcgg catgtgtccg gtcgttccag
      421 tccctgacct ttccgccgaa cccagcaggt ccgacagccc tcgtggtcag catgatgtgc
      481 gcatggggat ttgttttatc catgtgatgg aacgccacat cagcaatcat gccctgactg
      541 acaaagtttt ctctgacaaa ggcgagaacg gtttcccgtg cggcatcctg cggcagttca
      601 cgggggatag cgagttcaat ttcccgcgca agttgtgagt tcttccggca ttcggccttc
      661 tcaacggcat tccagagttc ggcacggttc gtacaccagg caggggctgt cgcgggggtc
      721 agaatcacag cttcagccac accgcttttg cgggtgtagt cgtgagtcag tccggtacgc
      781 tcatcaagca tcagtgaacc ggaacgatag gcagcggaag ctacggcgct gtagccgctg
      841 cttctggaga taattttcat gctgagatga taaatcgcca tttctgccgt aatgcctttt
      901 tgtagttttc tttcagcccc gcagggcgca cacaatcgaa acggagtgga gattgtataa
      961 gtgcgcactt tgtgatttgt cgcgcattat gccagctcag tttttaaact accagtgacg
     1021 cgctaaaatg cgatttttca tcgcgcacgg agttacatca tgagcagaac gctcgaacag
     1081 aagattgctg atgctgaggc gagattacag cgcctgaagg cgaagagccg gagcctggac
     1141 acagcgcaga aggttgttgt gggtgcagca ttgctggcaa aggtcagaaa gccggaggag
     1201 gtgcagttgc gtgcctggtt actccagttc ctgaaggcag aggtgacacg acaggctgat
     1261 gtgacgcgca tactgccgct gattaacgag ctggaggcgc tgccaggaca gtgattgtat
     1321 cgtccgctcg ccgcagcccc agcgaccgag cgttagcgag cgagtgggcg aggaagcgga
     1381 agtgaatccg tcgccaggtt gagcacatac gcacggtttt tcggtaggtg atatgcgctg
     1441 aacccgcatg aatactggat ttccacaggg ttggaagggg agtattcgga acttgcaatt
     1501 ctgctttctt gcaacacatt gtttttattg gttttttgtt ttcagcgccc caagttatcc
     1561 acaggctcgc cgttaagttt ttagatcttg tttttaagat cttgttttta atacttgttt
     1621 tagggtcaaa attcattaat aaaatcaata tgttatagag gtatatgtgg aggaatttaa
     1681 ggtaaaggtg gaggaattta aggtgtttag gtggaggaat ttaaggtaaa ggtggaggaa
     1741 tttaaggtgt tattcacaga aatgtgagga tataaaaaaa aatattccac atttcttatt
     1801 tgtggggcac attaaagcat caccacattt gaacgggatc tttgtatgtc ggacttgatt
     1861 gcctacaagt cgaatgcttt ggttgaggcc agctacaagt tgaccctaca ggaacaacgt
     1921 tttctgttgc tgtgtatcag tcgattgaaa tctggtgctg atgctgaatt gcaaaagaca
     1981 atgaccatta ccgctgcgga atattttgat tcattccctg acatggggcg gaaaaatgcc
     2041 gaggttcagt tacaggaagc gatcgatcgt ttatgggaca ggtcgatcat tctcaagaat
     2101 gacgagaagc gtgaggagtt ccgctggatc cagtatcggg cacagtacgc taaaggtgag
     2161 gccaaggctc gaataacctt ttctgacgcg gtaatgcctt atctgacgca actgaagggg
     2221 caattcacgc gcgttgttat aaaaaacata tcaggtttat caagtagtta cagtataaga
     2281 atatacgagt tcctccagca attccgcagt acgggagaga gaattattgc tcttaatgac
     2341 tttcgttcaa tgttagggat tgaaaataaa tacaaacaat tcagagactt aaataaaata
     2401 ctaataaaac cctgtgttga cgaactgaac aaaaaaagcg acctggctgt aacggttgag
     2461 acgatcaaaa aggggcgcac ggttgtagcc ctgcattttc gcttcaagga agacaaacag
     2521 atcaagatga cgatctaaaa tcgattttaa ggcacctaaa acgctccctg ctgcgttttt
     2581 tttgtgttag tagtgcgaag gtactattga agtgaaaaat tgcgtcaaaa gcgctctaat
     2641 gcagcgaaaa aagaaccccc aatttttggg ggcggaaaaa caaaactatg cttgcattat
     2701 gtgtgtgctt cttgcattca tccctgtcga tgaacataga agaacatcga cgaacataac
     2761 acgatgttaa acaaaacaaa atattgttca cattcactgt gaccaaccgc gatcatgtct
     2821 cctctcggtg gtgtgtgttc ttgcatcttc ctcgcgccgc cattcatccc aggtacgatt
     2881 gaaacccaga gagcggaaca gatgatccgg ctgtttttct ggtgtgttga cggcagcaaa
     2941 aagcggtgcc tcacgggttt tcagatgaaa ctccataagt tccggcgcag gtgatatgtg
     3001 gctgtctgca tcgtgattta cggcaacacc ataccctgca taccgtaacc ccttatcggt
     3061 cagtgcactg atgaccagct ggctgttatc ggctgaggga acggcaaacg cgggatacag
     3121 cgtaccatta agccggacaa caccgcccag agagtcatcc acgcccatga ccagcaaaag
     3181 ctgaagctgg cgggtttccc ggtcgacaga actcattacc ggcatcagcg tcggtagcag
     3241 acgtccctgc gtaaaatcca ccttccttgc tgccagtgat ggcatggctg gctggcggtc
     3301 ttctccaaga cagaaagact ccggccatgt cttcggctgg cggagattgc gggtatattg
     3361 cggccatgtc tggcaaacct gcgtcagaag ttgctcaaag gtcgcagagg aataaacacg
     3421 ttgcagtggt ggatgttgac cgatttcgct tcggtcacag atataaccac tcctgtcacg
     3481 cattaaatca acacgctcaa agattctggt gcggtatttc tccagctcgt tcccccagag
     3541 cgtgtattct ccgttccggt tgtgaagcag aaggtaacag gtcatttccc cgttaccagg
     3601 catgggggcc tcgccatacc ccgtaacgac tgcgctcagt acccctgaat ccataacggc
     3661 attgtcattt ttcctgagct gttccgctcg tcgctccgcg cgactacgtt ctgtatcctc
     3721 ctgctccttc cggcgcaatt cctcttcacg tttaagcaac tggactctga gagctgcaag
     3781 gccggatgcc ccccactgct gccactgttt ttcaaatgcc gtctgactcg cgggaatgtc
     3841 ctgtttctcc accttccggt aatgctgtcg caatttttcc atttgctggc tcagcgactg
     3901 gatttttccc tgttcgctac ggtattccgg tgccgcccat tgcatcaggg gaatacggga
     3961 aaaaccggac gaaaacggcg atgatttttt caggctggca gcatggctca tcgcttcctt
     4021 tcgttcggtg ttcagctctt cccagcgtct gcgcgtcgcc tgcatatctg cc
//
