LOCUS       NZ_CP019692             6341 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain 75/02 plasmid p75-02_4, complete sequence.
ACCESSION   NZ_CP019692
VERSION     NZ_CP019692.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06286561
            Assembly: GCF_002150905.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 6341)
  AUTHORS   Svab,D., Balint,B., Maroti,G., Vasarhelyi,B., Horvath,B. and Toth,I.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-FEB-2017) NGS Platform, Seqomics Ltd., Vallakozok u.
            7., Morahalom 6782, Hungary
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: CLC Genomics Workbench v. 9.5; Geneious v. R9;
            SPAdes v. 3.0.5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 140.0x
            Sequencing Technology             :: Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002150905.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 03:20:21
            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)                     :: 5,359
            CDSs (total)                      :: 5,230
            Genes (coding)                    :: 4,495
            CDSs (with protein)               :: 4,495
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 735
            CDSs (without protein)            :: 735
            Pseudo Genes (ambiguous residues) :: 0 of 735
            Pseudo Genes (frameshifted)       :: 214 of 735
            Pseudo Genes (incomplete)         :: 524 of 735
            Pseudo Genes (internal stop)      :: 123 of 735
            Pseudo Genes (multiple problems)  :: 119 of 735
            Pseudo Genes (short protein)      :: 3 of 735
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP019692.1.
            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..6341
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="75/02"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="p75-02_4"
                     /geo_loc_name="Hungary: Halimba"
                     /lat_lon="47.0335 N 17.5364 E"
                     /collection_date="2002"
                     /collected_by="National Center for Epidemiology, Budapest,
                     Hungary"
     gene            complement(227..823)
                     /locus_tag="BZ172_RS27590"
                     /old_locus_tag="BZ172_29400"
     CDS             complement(227..823)
                     /locus_tag="BZ172_RS27590"
                     /old_locus_tag="BZ172_29400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000978013.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000977995.1"
                     /translation="MMKSDEKYQVPAWMRPLLPLLCNTGGNDPEELLNDTETTASANVV
                     RYVLIVAVRSQVDLLQLLYRKGLLRTEIPGGFSPEEAQALLDNLVRSHISKALSGERMA
                     ARDRNADLAWIGQQLVDAAWFVRATLEAHGMSVGNESPPAPPETMPDIQTRELVMLIKR
                     LASSLKAVKPDSCVVREAQDWLRDRKLVDITDILR"
                     /name="hypothetical protein"
     gene            complement(820..1539)
                     /locus_tag="BZ172_RS27595"
                     /old_locus_tag="BZ172_29405"
     CDS             complement(820..1539)
                     /locus_tag="BZ172_RS27595"
                     /old_locus_tag="BZ172_29405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001584594.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid SOS inhibition protein A"
                     /protein_id="WP_001276270.1"
                     /translation="MSARSRALIPLSAEQQAAMQAVAVTEQRRRQGRTLSAWPYATAFF
                     RCLNGSRRISLTDLRFFAPALTKEEFHGNRLLWLAAVDKLIESFGEVCVLPLPSDAGHR
                     LFPSVPFREGERRRQKTTLTEQKYSRQREREAERRELEYQTCFAQAQIDLAFHTPATVG
                     SWLSRWSGVVEEHDLETIFWGWCGRFPSLSSFDRFFWQEEPLWRLIFEAGEAGRGAPVQ
                     VRALEQWMIPNKLENVI"
                     /name="plasmid SOS inhibition protein A"
     gene            complement(1536..1970)
                     /gene="psiB"
                     /locus_tag="BZ172_RS27600"
                     /old_locus_tag="BZ172_29410"
     CDS             complement(1536..1970)
                     /gene="psiB"
                     /locus_tag="BZ172_RS27600"
                     /old_locus_tag="BZ172_29410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000845953.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugation system SOS inhibitor PsiB"
                     /protein_id="WP_001387500.1"
                     /translation="MNTELTLNALQSMNAQEYEEIRAAGSDMRRNLTHEVMRKVDAPAN
                     WMMNGEYGSEFGGFFPVQVRFTPAHERFHLALCSPGDVSQLWMLVLVNGGGQPFAVVQV
                     QHIFTPAAISHTLALAATLDAQGYSVNDIIHILMAEGGQA"
                     /name="psiB"
     gene            complement(2025..3983)
                     /locus_tag="BZ172_RS27605"
                     /old_locus_tag="BZ172_29415"
     CDS             complement(2025..3983)
                     /locus_tag="BZ172_RS27605"
                     /old_locus_tag="BZ172_29415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052657.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParB/RepB/Spo0J family partition protein"
                     /protein_id="WP_001145483.1"
                     /translation="MPVTKCEPETTRKASRKSVKTQETVLSALLAQTEEVSVPLASLIK
                     SPLNVRTVPYSAESVSELAESIKGVGLLQNLVVHTLPGDRYGVAAGGRRLAALNMLAER
                     GIIPADWPVRVKVIPQELATAASMTENGHRRDMHPAEQIAGFRAMAQEGKTPAQIGDLL
                     GYSPRHVQRMLKLADLAPVILDALAEDRITTEHCQALALENDTARQVQVFEAACQSGWG
                     GKPEVQTIRRLVTESEVAVAGNSKFRFVGADAFSPDELRTDLFSDDGDGYVDRVALDAA
                     LLEKLQAVAEHLREAEGWEWCAGRMEPVGECREDAGTYRCLPEPEAVLTEAEEERLNEL
                     MTRYDALENQCEESDLLEAEMKLIDCMAKVRAWTPEMRAGSGVVVSWRYGNVCVQRGVQ
                     LRSEDDATDDADRTEQVQEKASVEEISLPLLTKMSSERTLAVQAALMQQPDKSLALLAW
                     TLCLNVFDSGAYSKPAQISLECKHYSLTSDAPSGKEGAAFLALMAEKARLAALLPEGWS
                     RDMTTFLSLSQEVLLSLLSFCTACSLNGVQTRECGRTSRSPLDSLESAIGFHMRDWWQP
                     TKANFFGHLKKPQIIAALNDAGLSGAARDAEKMKKGDAAEHAEFHMKDNRWVPGWMCSP
                     RPQTDATERADNLADAA"
                     /name="ParB/RepB/Spo0J family partition protein"
     gene            complement(4042..4275)
                     /locus_tag="BZ172_RS27610"
                     /old_locus_tag="BZ172_29420"
     CDS             complement(4042..4275)
                     /locus_tag="BZ172_RS27610"
                     /old_locus_tag="BZ172_29420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000005972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF905 domain-containing protein"
                     /protein_id="WP_000006024.1"
                     /translation="MSEYFRILQGLPDGSFTREQAEAVAAQYRNVFIEDDQGTHFRLVV
                     RQDGTLIWRSWNFEDGAGYWMNQYIRDFGILK"
                     /name="DUF905 domain-containing protein"
     gene            complement(4333..4860)
                     /locus_tag="BZ172_RS27615"
                     /old_locus_tag="BZ172_29425"
     CDS             complement(4333..4860)
                     /locus_tag="BZ172_RS27615"
                     /old_locus_tag="BZ172_29425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001276102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="single-stranded DNA-binding protein"
                     /protein_id="WP_001276120.1"
                     /translation="MSARGINKVILVGRLGNDPEVRYIPNGGAVANLQVATSESWRDKQ
                     TGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIEGQLRTRSWEDNGITRYVTEILVK
                     TTGTVQMLGRAPQQNAQAQPKPQQNGQPQSADATKKGGAKTKGRGRKAAQPEPQPQPPE
                     GEDYGFSDDIPF"
                     /name="single-stranded DNA-binding protein"
     gene            complement(5606..6106)
                     /locus_tag="BZ172_RS29475"
                     /old_locus_tag="BZ172_29435"
     CDS             complement(5606..6106)
                     /locus_tag="BZ172_RS29475"
                     /old_locus_tag="BZ172_29435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000117633.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antirestriction protein ArdA"
                     /protein_id="WP_000117611.1"
                     /translation="MSVVAPAVYVGTWHKYNCGSIAGRWFDLTTFDDERDFFAACRALH
                     QDEADPELMFQDYEGFPGNMASECHINWAWVEGFRLARDEGCEEAYRLWVEDTGETDFD
                     TFRDAWWGEADSEEAFAVEFASDTGLLADVPETVALYFDYEAYARDLFLDSFTFIDGHV
                     FRR"
                     /name="antirestriction protein ArdA"
ORIGIN
        1 ctgccagccc ggctaagatg gaggcacggc acagcccgca cacgacgctg aggccacaga
       61 gctgaaaacc cacaaggcca tgccccgcat ggccgggtaa aagcggagcc gccggcgact
      121 tccttattcc ggcgagtgca gaggacacgc cgcatgacct ccagaccacc cctgatatga
      181 aacgatcatg atcggcgtgt ccctgcgtaa aatatacatg cctggttcac cggagaatat
      241 ctgtgatatc cacaagtttt ctgtcgcgca gccagtcctg cgcttcacgc accacacaac
      301 tgtccggttt caccgctttc agcgatgatg ccagtcgctt gatcaacatc accagttccc
      361 gtgtctgtat gtccggcatt gtctccggcg gagcaggggg actctcattt ccgacgctca
      421 tcccatgcgc ttccagtgtg gcacggacaa accaggcggc atcgaccagt tgctgtccaa
      481 tccaggccag atcggcattt ctgtcacggg ctgccattcg ctcgcccgac agcgccttgc
      541 tgatatggct gcgcaccaga ttatccagga gtgcctgcgc ttcttccggt gaaaagccac
      601 ctggtatctc tgtgcgcaac agccctttcc tgtacagaag ctgcagcaga tcaacctgcg
      661 accgcacagc aactatcagt acataacgga caacattcgc actggcagtg gtttctgtat
      721 cattcagcag ttcttccgga tcgttccccc cggtgttgca gagcaacggc aacagaggtc
      781 gcatccacgc gggaacctgg tatttttcgt ctgatttcat catattacgt tctccagctt
      841 gttcgggatc atccactgct caagtgcacg tacctgtacc ggtgcaccac gaccggcctc
      901 accggcttca aaaatcagcc gccagagtgg ttcctcctgc cagaaaaacc ggtcaaatga
      961 tgacagtgat ggaaaacgcc cgcaccaccc ccagaaaatc gtttccagat catgctcctc
     1021 aacaacacca gaccagcggg acaaccagct tccgaccgtg gcgggagtat gaaacgcaag
     1081 gtcaatctgc gcctgagcaa aacatgtctg gtattccagt tcccgtcgtt ctgcctcacg
     1141 ttcccgctgg cggctgtatt tctgctctgt cagcgtggtt ttctgacgac gacgctcacc
     1201 ttcacgaaaa ggcacggacg ggaacagacg gtgccccgca tcggatggca ggggaagaac
     1261 acagacttcc ccaaaacttt caatcagttt atccacggca gccagccaca ggagacggtt
     1321 gccatgaaat tcctccttcg tcagcgcagg ggcaaaaaag cggagatcgg tcagcgaaat
     1381 ccggcgactg ccattcaggc agcgaaagaa agcggtggca taaggccatg ctgaaagtgt
     1441 gcgtccctga cgacgacgtt gttctgtgac agccaccgcc tgcatggcgg cctgttgttc
     1501 tgcgctgagg gggatcagtg cccgtgaacg tgcgctcatg cctgacctcc ttctgccatc
     1561 aggatatgga tgatgtcgtt aacactgtat ccctgcgcat ccagtgtcgc ggcaagcgcc
     1621 agcgtgtgac tgatcgcggc aggcgtgaag atatgttgca cctgaacgac ggcgaaaggc
     1681 tgtccaccac cattcaccag aaccagcatc cagagctgag agacgtctcc cggcgaacat
     1741 aatgccaggt ggaaacgttc gtgggctggc gtgaaacgaa cctggacggg gaaaaagccc
     1801 ccgaactcgc tgccatactc tccgttcatc atccagttag ccggtgcgtc cactttacgc
     1861 atcacctcgt gagtgagatt acggcgcata tcgcttcccg cagcacggat ttcttcatat
     1921 tcctgggcat tcatggactg cagggcattc agtgtcagtt cggtattcat catcgtattt
     1981 ctccctctgc cgccccgtct ccggcggggc ggtgtggttg ttcatcaggc ggcatcagcc
     2041 aggttatcgg cgcgttcagt ggcatccgtc tgtggacgtg gtgaacacat ccagccaggc
     2101 acccagcggt tgtctttcat atggaactct gcatgttcag cggcatcgcc tttcttcatc
     2161 ttctctgcgt cccgtgcggc accggacagt ccggcatcat tcagggctgc gataatctgc
     2221 ggctttttca ggtgtccgaa gaagtttgct ttcgtcggct gccaccagtc gcgcatgtga
     2281 aaaccgatgg cgctctccag tgagtcaagc ggactgcgtg acgtgcgacc acactcgcgg
     2341 gtctggacac cgttaaggct gcatgcggtg cagaaactga gcagggataa cagcacctcc
     2401 tgactgagtg acaggaacgt cgtcatgtcc cgtgaccatc cctccggtaa cagggccgca
     2461 agacgggctt tttctgccat cagcgccagg aatgcggcac cttccttccc tgacggcgca
     2521 tcgctggtca gcgaataatg tttacattcc aggctgattt gtgctggttt actgtacgct
     2581 ccgctgtcaa acacattcag gcagagcgtc catgccagca gtgccagaga tttgtccggt
     2641 tgctgcatca gtgctgcctg gactgccagc gtgcgttcgg aagacatttt cgtcagcaac
     2701 ggcagactga tttcctccac tgacgctttc tcctgcacct gttccgtgcg gtcagcgtca
     2761 tcagtcgcgt catcttcact gcgcaactgc acaccacgct ggacacatac gtttccataa
     2821 cgccaggaca ccaccacgcc acttccggca cgcatctccg gcgtccacgc cctgaccttc
     2881 gccatgcagt caatcagctt catttctgct tccagcaggt cggattcctc acactggttt
     2941 tccagcgcgt cgtaacgcgt catcagttcg ttcaggcgtt cttcttctgc ctccgtcagc
     3001 accgcttccg gctccggcag acagcggtat gttccggcat cctcacggca ctcaccgaca
     3061 ggctccatgc gtccggcgca ccattcccag ccttcggctt cccgaaggtg ttcagcgaca
     3121 gcctggagtt tttccagcag ggcagcatcg agcgccacgc ggtcgacata accgtccccg
     3181 tcatcgctga acaaatcagt acgcagttcg tcaggtgaga aagcatcagc ccccacgaag
     3241 cggaatttac tgttacctgc caccgccact tcactttcgg tcaccagacg acgaatggtc
     3301 tgtacttccg gtttaccgcc ccatcccgac tggcaggcgg cttcaaacac ctgcacctga
     3361 cgcgcggtgt cgttctccag cgccagcgcc tgacagtgct ctgtggtgat gcggtcttct
     3421 gccagcgcat cgaggatgac aggcgcaagg tctgccagtt tcagcattcg ctgaacgtgg
     3481 cggggcgaat agcccagcaa atcaccgatt tgtgcaggcg ttttgccttc ctgcgccatc
     3541 gcacggaatc cggcaatctg ttcggcaggg tgcatatccc gacgatgacc gttttcagtc
     3601 attgatgcag ccgtcgccag ctcctgcgga ataaccttca cgcgtacagg ccagtcagcc
     3661 ggaatgatgc cacgctctgc cagcatgttg agtgcagcca gtcggcgacc acctgcggcg
     3721 acaccgtaac ggtcaccagg cagggtatgc acgaccagat tctgcagcag tccgacgccc
     3781 ttaatggact ccgccagttc gctgacggac tccgcagaat acggcaccgt gcgcacattc
     3841 agcggtgatt taatcagcga ggccagcggc acgctcactt cctccgtctg cgccagcagg
     3901 gcagacagga cagtttcctg cgtttttaca gatttacggc ttgctttgcg ggtggtttct
     3961 ggttcacact tcgttacagg cataatcatc cccttataat tgcttatgtc ctgccggacg
     4021 ttcgcgcgtc cggcacctct cttacttaag aatcccgaaa tccctgatgt actggttcat
     4081 ccagtacccg gcaccgtcct caaaattcca ggagcgccag atcaacgtgc catcctgacg
     4141 gacaaccagg cgaaaatgcg ttccctgatc atcctcgata aagacgttcc ggtactgtgc
     4201 ggcaacggct tccgcctgtt cgcgggtaaa ggagccgtcc ggcagtccct gaagtattct
     4261 gaaatattcg ctcatcctca tatctccggt gatgccccgc acagggcggg gcggttgtca
     4321 cagtcagccc gatcagaacg ggatgtcgtc tgaaaacccg taatcctccc cctccggcgg
     4381 ttgcggctga ggctctggct gcgcggcctt acgtccacgg cctttcgttt tcgcgccacc
     4441 ttttttcgtc gcgtcagcac tctgtggctg cccattctgc tgaggcttcg gttgcgcctg
     4501 agcgttctgc tgtggtgcac gtcccagcat ctgcacggtg cccgtggtct taacaagaat
     4561 ttcagtgacg taacgggtga taccgttatc ttcccagcta cgggtgcgaa gctgaccttc
     4621 gatgtagacc tgcgcaccct tgcgcagata ttcacctgcc acttccgcga gcttgccgaa
     4681 cagcaccacg cggtgccatt ccgtctgctc ccgcatctcc cccgtctgtt tgtcacgcca
     4741 gctttctgat gtggccacct gcaggtttgc cactgcgccc ccgttgggga tgtaacggac
     4801 ttccggatca ttgcccagac gcccgacgag gatgaccttg ttgataccac gtgcactcat
     4861 aagaacctcc tgactgaaag atgtgagata aaccggatac cggcgacggg acgttcatgt
     4921 gccccttcag aggagcgaaa gctcctcctg ccgtccactt cacaggggtt tctccccgca
     4981 gtggaccttt ccgatggggg cccgtttacc gcctcacggg acagctgtcc gggggcggac
     5041 gcaaaatttt tagccgggtt catggctaaa aattttgtgg ccggtgcatc tcaccctgga
     5101 cagatggaac gggagggggt tacgtctgcc ccccggaaag tccacagcgg gaaacaggcc
     5161 gcaggggtgg cggcaggagg gaagactgcg ccatcaggcg cagtggcctt acacaccgtc
     5221 aggtgtgcag ggagcgccgt ttccggcgcg acaggggcgg cgcgaccgga acggtcgctg
     5281 caagcctggt ttttcagaca tcggaccgta gcggcagccc gaaaccgcgc cagcgggttc
     5341 ggcggagact ggcgggtgcg ccagcagctg cctgtcggag tcgggcctga cgaccggatg
     5401 ccgccaggca gccgggagcc gaaggtgtcc ccgcctccgg aaatcagaac aacagaaacg
     5461 acataacaga aaaatgcctc acaccatgac gtgcaggaag ggcagcgccg caggcgcggc
     5521 cctcctgcat ttcaggcagg cgtaagcctg ccagggtttt ccggcggcct ggcaggccat
     5581 acccccgccg gagcggggga gtaaatcacc gacggaacac atgaccgtca ataaaggtga
     5641 aggagtccag gaataaatcc cgcgcatacg cctcatagtc aaaatagagc gccaccgtct
     5701 ccggcacgtc agccagcagg ccggtatcac tggcgaactc aaccgcaaaa gcctcctcac
     5761 tgtcagcctc gccccaccag gcatcgcgga aggtgtcaaa atccgtctca ccggtatcct
     5821 ccacccagag acgataagcc tcttcgcagc cttcatcccg tgccaggcgg aagccttcaa
     5881 cccaggccca gttgatatgg cattcagagg ccatattccc cgggaatccc tcataatcct
     5941 gaaacatcag ttcaggatcg gcttcatcct ggtgaagagc acggcaggcg gcgaaaaagt
     6001 cgcgctcatc atcaaacgtg gtcaggtcaa accagcgtcc ggcgatgctt ccacagttgt
     6061 atttgtgcca ggttccaacg tatacagcag gtgcaacaac agacattccc gaatcctcca
     6121 tagtcacatg ttctgcgaca ccgggcggtg ccgtgcctcc ataaaagccg ggcgataagg
     6181 cggggatgca ggggcgcaag ggaagccgca gcctgacgca cacggctgac gggagttgca
     6241 gggtgaggcc gcgaaacctg agcggacgaa cgcccggaaa atcacggcag acgggaagga
     6301 gggaccgggt gaccgcagcg gcgaagcgta cccttgcatc c
//
