LOCUS       NZ_CP060119             2101 bp    DNA     circular CON 16-APR-2024
DEFINITION  Shigella sonnei strain UKMCC_1015 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP060119
VERSION     NZ_CP060119.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15437744
            Assembly: GCF_014217935.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2101)
  AUTHORS   Wong,B.C., Md Zoqratt,M.Z.H. and Tan,H.S.
  TITLE     Complete genome of Shigella sonnei UKMCC1015
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2101)
  AUTHORS   Wong,B.C., Md Zoqratt,M.Z.H. and Tan,H.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-AUG-2020) School of Science, Monash University
            Malaysia, Jalan Lagoon Selatan, Subang Jaya, Selangor 47500,
            Malaysia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 10-AUG-2020
            Assembly Method                   :: Flye v. v 2.6; Pilon v. v 1.23
            Assembly Name                     :: UKMCC_1015
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 49.0x
            Sequencing Technology             :: Oxford Nanopore; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_014217935.1-RS_2024_04_16
            Annotation Date                   :: 04/16/2024 07:25:14
            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)                     :: 5,006
            CDSs (total)                      :: 4,870
            Genes (coding)                    :: 4,287
            CDSs (with protein)               :: 4,287
            Genes (RNA)                       :: 136
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 103
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 583
            CDSs (without protein)            :: 583
            Pseudo Genes (ambiguous residues) :: 0 of 583
            Pseudo Genes (frameshifted)       :: 173 of 583
            Pseudo Genes (incomplete)         :: 396 of 583
            Pseudo Genes (internal stop)      :: 86 of 583
            Pseudo Genes (multiple problems)  :: 71 of 583
            Pseudo Genes (short protein)      :: 3 of 583
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP060119.1.
            Bacteria and source DNA available from School of Science, Monash
            University Malaysia.
            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..2101
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="UKMCC_1015"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed2"
                     /geo_loc_name="Malaysia"
                     /lat_lon="2.9305 N 101.7787 E"
                     /collection_date="2018-06"
                     /collected_by="UKM culture collection"
     gene            complement(join(1416..2101,1..280))
                     /locus_tag="HYI41_RS24945"
                     /old_locus_tag="HYI41_24715"
     CDS             complement(join(1416..2101,1..280))
                     /locus_tag="HYI41_RS24945"
                     /old_locus_tag="HYI41_24715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            complement(1146..1412)
                     /locus_tag="HYI41_RS24950"
                     /old_locus_tag="HYI41_24720"
     CDS             complement(1146..1412)
                     /locus_tag="HYI41_RS24950"
                     /old_locus_tag="HYI41_24720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          complement(1757..1988)
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 aacgggcttg ccacatgagg gttcttctcc actggcagac agggcaatga cggacacggc
       61 aaaattgcgc actacgaagc cgtaggcgcg tttctccggt ttccatgatg gtagaccaac
      121 caaaacgtaa caaaccgcta caggaggcca tacggagtgc atagcgctcg aattcagcag
      181 cagtctggta gatacccccg acagaatcgg taagcgtgcg ctgggtatcc caaactgcat
      241 cacgggggct gtagtccgaa aggaatttat cttctgacat taagcctgct ccgatctggg
      301 caggctgtga tttgatgtgg tatattcatc acgtacctgt gcattgcgag ccagtacatg
      361 tcaccagagt ttgccgctga ggtgacacat tcgaaatgtt ggggagtgtt gacgcactcc
      421 ccaacgccga ttaaaaacgc ctcaattctg ctccattttc tttgacctgt caaaacccac
      481 tcaaagcctc gtcattactg ggctaaacca ctatttcata tccgccattt atcccttaag
      541 tataaataca aggatcacgc gcgagaattg cgcaaaaaat aaccacaatt ttaacccccc
      601 aaaacaagca cccccgaacg gcttacccca accttttcca cacacccgat caccaaaaca
      661 gggaataaaa acaaaaccct gtcttacagg tggatggcct cacttcgtga aaccatccac
      721 cccgcataag ttttttaatc ggtggtgtcg tcaatcacta aatcggaacc ccaaagggga
      781 cccccacgat ttagcatttg acgagattaa ctctcggaga tggcatcatg cttttaacgg
      841 actttaaaaa acggtgaacg gatgcggatt ttaatccgtg tctgtgaggc gttgagcaac
      901 gagcaaagcg aggcggtaga aagagagcca gcggcaggct caggacgata atccggggaa
      961 aatgtaccac tcgcagagtg ttaacatttg acatcggatt gtctatcctg cattggtgtc
     1021 gagttggcaa ggctgaggat aatgctgagg ataatgctga ggataatgca ggatagacag
     1081 agcactagag attgcatgca atctcgtacc tatcacctca gcctgccgct ggctcttttc
     1141 cagaactaag aatgcgttct taaaaatcca aacttgatac cgtttaaatc tattttcaca
     1201 aaaagagttt ttaccctctc gtttgttttc tgaatatata aaattaattc atcctcaaaa
     1261 ccttcgtgcg gatgaaaacc aaatgtgcca aaacttaatc catcaataag caaaataagg
     1321 tttttaaacc tgtcaggaat caccgcttca cttcttaaaa aaaataaacc aatagtctta
     1381 tttccattca ggtattcaat attaatattc atacgttaat ccgatttatc cttctcaggg
     1441 gcgcgtttgt aacgccgttt acctgaatcc cagacaaacg ccgtccgctt cccgtcatca
     1501 gtgccatccc ctacatcgtc ggcaatgaca agatcctcat tggtttctcg atccaactgg
     1561 aggacgtttt ttagcgcccc accggtcgag ataaaacggc gcttgtgaag ctgccgcgtc
     1621 agctcaagaa accactcagg atcgtttgcc atatcttccg gtttaacgga gtatttcagc
     1681 gtttcagcaa ccgcgctttg cagttgctcg gcaacgttgg ccacaacctc acctgtctta
     1741 gtttttactg cccgaatatc gatattcggc tcatagttca cccgcaagca atcgcgccag
     1801 agttctaccc aacgttcgtg cttaacgtag ttcttccctt taaaccaaga aggttgcacc
     1861 atcagcagac agtgaaaatg cggatgtgcg ctgccatcct tacctcgcgt cacctccgta
     1921 gccctgatcc acccctgaac aggtgatagc tcctttcgct tttccattcg cttaaacgcc
     1981 gcattcattg ctgtaaggac tgttccaagt tcacctatct cgcagttcct gacagttaac
     2041 gtcagaaaca accatcggga agacgggtaa tccacaacga ttttcggtag agcctgataa
     2101 a
//
