LOCUS       NZ_CP061529             3069 bp    DNA     circular CON 11-JAN-2024
DEFINITION  Shigella dysenteriae strain HNCMB 20080 plasmid pHNCMB20080_2,
            complete sequence.
ACCESSION   NZ_CP061529
VERSION     NZ_CP061529.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16094609
            Assembly: GCF_015475595.1
KEYWORDS    RefSeq.
SOURCE      Shigella dysenteriae
  ORGANISM  Shigella dysenteriae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3069)
  AUTHORS   Svab,D., Falgenhauer,L., Horvath,B., Maroti,G., Falgenhauer,J.,
            Chakraborty,T. and Toth,I.
  TITLE     Genomic analysis of a historical Shigella dysenteriae serotype 1
            strain carrying a genetically conserved but unstable Stx prophage
            region
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3069)
  AUTHORS   Svab,D., Falgenhauer,L., Horvath,B., Maroti,G., Falgenhauer,J.,
            Chakraborty,T. and Toth,I.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-SEP-2020) Institute of Hygiene and Environmental
            Medicine, Justus-Liebig-University Giessen, Schubertstrasse 81,
            Giessen 35392, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 170.0x
            Sequencing Technology             :: Illumina MiSeq; Nanopore Minion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/11/2024 05:01:16
            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)                     :: 4,745
            CDSs (total)                      :: 4,631
            Genes (coding)                    :: 3,631
            CDSs (with protein)               :: 3,631
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 1,000
            CDSs (without protein)            :: 1,000
            Pseudo Genes (ambiguous residues) :: 0 of 1,000
            Pseudo Genes (frameshifted)       :: 329 of 1,000
            Pseudo Genes (incomplete)         :: 616 of 1,000
            Pseudo Genes (internal stop)      :: 245 of 1,000
            Pseudo Genes (multiple problems)  :: 174 of 1,000
            Pseudo Genes (short protein)      :: 4 of 1,000
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP061529.1.
            Bacteria and source DNA available from Hungarian National
            Collection of Medical Bacteria, culture collection identifier HNCMB
            20080.
            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..3069
                     /organism="Shigella dysenteriae"
                     /mol_type="genomic DNA"
                     /strain="HNCMB 20080"
                     /host="Homo sapiens"
                     /db_xref="taxon:622"
                     /plasmid="pHNCMB20080_2"
                     /geo_loc_name="Hungary"
                     /collection_date="1954"
     gene            1..1110
                     /gene="wzz(fepE)"
                     /locus_tag="IC625_RS23285"
     CDS             1..1110
                     /gene="wzz(fepE)"
                     /locus_tag="IC625_RS23285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_000703379.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRVIVELSKNMKSVDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVMNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(2124..2318)
                     /locus_tag="IC625_RS23290"
     CDS             complement(2124..2318)
                     /locus_tag="IC625_RS23290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          1968..2054
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.591"
                     /coverage="100.0"
                     /evalue="2.44e-33"
     Typing          2355..2453
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(1417..1943)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.044"
                     /coverage="98.0"
                     /evalue="4.929999999999999e-168"
ORIGIN
        1 atgaaaatct caaaggtctc tgacgaacat ttttctaatt acaacatgtt gccgaatggt
       61 aatgaagaaa ttgacctttt tggcttgatt agcgttttat gggcagcaaa aataaaaatt
      121 gttggggtga ttctattttt tgcttgtatt ggctttcttg tttcttttgt tttgccacaa
      181 aaatggacta gttctgctgt ggttactcct gctgagtctg ttcaatggag tgaattaaat
      241 aaggagcttt ccaagcttca tgttctggga gtggattttg atatcaatcg tgatagcgca
      301 tttgctctgt ttattaagaa atttcagtcc gttaattcgt tgaatgagta tatgagatca
      361 tctccttatg ttatggagat tattaaaaag aataacatta gcgctctcga actgcatcgt
      421 gtaattgttg agttgagtaa aaatatgaag tcggttgatg ataatgccag caagaaaaac
      481 gacaagtcat cattgtatgt atcatggact ctgagtttta ctgctccaac aagtaaagaa
      541 gctcacgatg tgttgtctgg gtatattaat tatgtttctt cccttgttgt aagagatttg
      601 atggaagata taagaaataa actagaagtt aaaactaatg ttgaaaaaga aattcttgca
      661 ctggatgaga taaaaattag aaaccagcta aatgcagata ttcgacgcct caattattca
      721 ctggaggttg ctaatgcggc tggaataaaa aaacctgtat acagcaatgg tcagattatg
      781 aaggatgacc cagattttcc tgtggctctc ggttctgatg gtatagcaac taaattgaac
      841 atcaaaaaat caatcaagga tgtttcggaa ttgagtgggg agttgcgaaa tcgtcaatat
      901 gttatgaatc aattggttgt ggcgaaagtg ggggatgttg attttatgcc gtttcagtat
      961 caattgagcc caacgttacc ggtcagaaag gatgggccaa gtaatgccat aattgtaatt
     1021 ctttcttctg tcattggagg gatgcttgca tgtggctata tacttttacg tcatgccatg
     1081 gaggccagaa agatgagtgt gattgagtaa aagttgtgct gatgcatcat tttataagca
     1141 acttttataa aaagttcaaa ggatcttctt gagatcattc ccttacagcc gtactcttct
     1201 actctagaaa acgaaaaaac cacctgggga ggtggttttt cgaaggttca gtaagttggg
     1261 gacttctgaa ccgtggtaac agtcttgtgc gagacatgtc accaaatctg tccttctagt
     1321 gtagcctcag taaggctgcc acttcaagaa ctctcaatac atctctcgca catgctgttt
     1381 accagtggcc gctgccaatg gcgttaagtc gtgtcttacc gggttggact caagacgata
     1441 gttaccggat aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac agcccagctt
     1501 ggagcgaact gcctacccgg aactgagtgt caggcgtgga atgagacgaa cgcggccata
     1561 acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg agggagccac
     1621 cagggggaaa cgcctggtat ctttaagtcc tgtcgggttt cgccacctct gacttgagcg
     1681 tcggtttttg tgatgcttgt caggggggcg gagcctatgg aaaaacgcca ctggcgcggc
     1741 cttttttcgg ggcctctttt ttgctcacat gttttttccg gtgttatccc ctgattctgt
     1801 ggataaccgt atatccgtct ttgcgtgagc agacaccgct cgccgcagcc gaacgaccga
     1861 gcgcagcgag tcagtgagcg aggaagcgga agagagccgg aagctgcatt ttctccttac
     1921 gtctctgtgc agcatttaac acctcatatg tcgctgttct ctcaccatct gctctggcgc
     1981 cgcataatta agccagtata cactccgcta tcgctacgtg actgggtcat ggctgcgccc
     2041 cgacacccgc taaaaccccc tgacgggctt gtctgctgac gaaaacgccc acgggaaagc
     2101 cgtgaccgcc tccgtcagct tcgttatgtt cctgtttcac tttcggcctc aaagcgaatc
     2161 tggatgctgt tctggagttc ttctgcgagt tcgtgcagtc gttcgcacat ggccgcctgt
     2221 tcgtcggcat ccagagcatc cagtttttca agcagtgtca ggctctggct tttgataaat
     2281 cgcgccatat tcagcgcagt ttgttgttgt ttgttcatct tccgttgttc tccgtcagtt
     2341 ccgggtgtcg gggggaccct gagcaggtgg taattgtaag acgttgcggg cgacggtatt
     2401 acaattgcac atcctgtcct gtttctttag gacgtatcat ggcacagcat atcaactgat
     2461 aaataatccc tgtgcagtgc agccgctgtt gcataaaatt tcgctctgcg tcgagtgttt
     2521 cttaatcaat aattccgctg atactccgga aaaacgcgag tctgttctca tgcctgaaat
     2581 gcccacaccc cacgcaaaaa caggtttttg ctgatttttc tttataaata gagagttatg
     2641 acaaattagt tcttcttgct ctctttgtga tatttaaaaa agcggtgtcg gcgcggtgtg
     2701 tttttttaca ggacgcccct gggggcgctg ctaggggtgt ctgttcagat atgtagcaat
     2761 gagtcaggga ttcacgaacc gaaaatgtcc gaaaatgtgt ctcatgggca ctgtatgcgc
     2821 ccaaaccgat tgtcattcac tttcatgcat agctatgcag tgagctgaaa gcgatcctga
     2881 cgcatttttc cggtttaccc cggggaaaac atctcttttt gcggtgtttg cggcagaatc
     2941 gcgttcagcg cgttttagcg gtgcgcgcaa taaaatgtta tgttaaatgt ctactgaatg
     3001 gtttttaggt tttttcctaa catatgatag aataaaaaaa ccatatgtta atatattgtg
     3061 tttttttca
//
