LOCUS       NC_017330               3180 bp    DNA     circular CON 03-DEC-2023
DEFINITION  Shigella flexneri 2002017 plasmid pSFxv_5, complete sequence.
ACCESSION   NC_017330
VERSION     NC_017330.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02603122
            Assembly: GCF_000022245.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri 2002017
  ORGANISM  Shigella flexneri 2002017
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3180)
  AUTHORS   Ye,C., Lan,R., Xia,S., Zhang,J., Sun,Q., Zhang,S., Jing,H., Wang,L.,
            Li,Z., Zhou,Z., Zhao,A., Cui,Z., Cao,J., Jin,D., Huang,L., Wang,Y.,
            Luo,X., Bai,X., Wang,Y., Wang,P., Xu,Q. and Xu,J.
  TITLE     Emergence of a new multidrug-resistant serotype X variant in an
            epidemic clone of Shigella flexneri
  JOURNAL   J Clin Microbiol 48 (2), 419-426 (2010)
   PUBMED   19955273
REFERENCE   2  (bases 1 to 3180)
  AUTHORS   Zhang,J., Xiong,Y., Ye,C., Zhou,Z. and Xu,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-JAN-2009) Chinese Center for Disease Control and
            Prevention, National Institute for Communicable Disease Control and
            Prevention, P.O. Box 5, Changping, Beijing 102206, P. R. China
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/03/2023 01:36:54
            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)                     :: 5,013
            CDSs (total)                      :: 4,882
            Genes (coding)                    :: 4,082
            CDSs (with protein)               :: 4,082
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 102
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 800
            CDSs (without protein)            :: 800
            Pseudo Genes (ambiguous residues) :: 0 of 800
            Pseudo Genes (frameshifted)       :: 319 of 800
            Pseudo Genes (incomplete)         :: 425 of 800
            Pseudo Genes (internal stop)      :: 180 of 800
            Pseudo Genes (multiple problems)  :: 121 of 800
            Pseudo Genes (short protein)      :: 5 of 800
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP001388.1.
            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..3180
                     /organism="Shigella flexneri 2002017"
                     /mol_type="genomic DNA"
                     /strain="2002017"
                     /serotype="Fxv"
                     /db_xref="taxon:591020"
                     /plasmid="pSFxv_5"
     gene            complement(169..333)
                     /locus_tag="SFXV_RS26640"
                     /old_locus_tag="SFxv_5155"
     CDS             complement(169..333)
                     /locus_tag="SFXV_RS26640"
                     /old_locus_tag="SFxv_5155"
                     /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_000090200.1"
                     /translation="MARCIKSQSLTLLEKLDALDADEQAAMCKRLHELAEELQNSIQIR
                     FEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1214..2323
                     /gene="wzz(fepE)"
                     /locus_tag="SFXV_RS26645"
                     /old_locus_tag="SFxv_5159"
     CDS             1214..2323
                     /gene="wzz(fepE)"
                     /locus_tag="SFXV_RS26645"
                     /old_locus_tag="SFxv_5159"
                     /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_005065596.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRAIVELSKNMKSIDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(2569..2703)
                     /locus_tag="SFXV_RS33010"
     CDS             complement(2569..2703)
                     /locus_tag="SFXV_RS33010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /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_071606675.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGKQDVREMY"
                     /name="replication initiation protein"
     Typing          3..89
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          403..501
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          626..883
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(2632..3158)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.591"
                     /coverage="98.0"
                     /evalue="4.9000000000000006e-173"
ORIGIN
        1 catctgctct gccgcctcat aattaagcca gtatacactc cgttatcgct acgtgactgg
       61 gtcatggctg cgccccgaca cccgctaaaa ccccctgacg cgccctgacg ggcttgtctg
      121 ctgacgaaaa cgcccacggg aaagccgtga ccgcctccgt cagcttcgtt atgttcctgt
      181 ttcactttcg gcctcaaagc gaatctggat gctgttctgg agttcttctg cgagttcgtg
      241 cagtcgtttg cacatggccg cctgttcgtc ggcatccaga gcatccagtt tttcaagcag
      301 tgtcaggctc tggcttttga tacatcgcgc catattcagc gcagtttgtt gttatttgtt
      361 caccttccgt tgttctccgt cagttccggg tgtcgggggg gggaccctga gcaggtggta
      421 attgtaagac gttgcgggcg acggtattac aattgcacat cctgtcctgt ttctttagga
      481 cgtatcatgg cacagcatat caactgataa ataatccctg tgcagtgcag ccgctgttgc
      541 ataaaatttc gctctgcgtc gagtgtttct taatcaataa ttccgctgat actccggaaa
      601 aacgcgagtc tgttctcatg cctgaaatgc ccacacccca cgcaaaaaca agtttttgct
      661 gatttttctt tataaataga gagttatgac aaattagttc ttcttgctct ctttgtgata
      721 tttaaaaaag cggtgtcggc gcggtgttgt agctgcgcca acaccgcttt ttaggggtgg
      781 tactgactat tttcataaaa aaaacattat cttatattag gggtgctgct agcggcgcgg
      841 tgtgtttttt tacaggacgc ccctgggggc gctgctaggg gtgtctgttc agatatgtag
      901 caatgagtca gggattcacg aactgaaaat gtccgaaaat gtgtctcatg ggcactgtat
      961 gcgcccaaac cgatcgtcat tcactttcat gcatagctat gcagtgagct gaaagcgatc
     1021 ctgacgcatt tttccggttt accccgggga aaacatctct ttttgcggtg tttgcggcag
     1081 aatcgcgttc agcgcgtttt agcggtgcgc gcaataaaat gttatgttaa atgtctgctg
     1141 aatggttttt aggttttttc ctaacatatg atagaataaa aaaaccatat gttaatatat
     1201 tgtgtttttt tcaatgaaaa tctcaaaggt ctctgacgaa catttttcta attacaacat
     1261 gttgccgaat ggtaatgaag aaattgacct ttttggcttg attagcgttt tatgggcagc
     1321 aaaaataaaa attgttgggg tgattctatt ttttgcttgt attggctttc ttgtttcttt
     1381 tgttttgcca caaaaatgga ctagttctgc tgtggttact cctgctgagt ctgttcaatg
     1441 gagtgaatta aataaggagc tttccaagct tcatgttctg ggagtggatt ttgatatcaa
     1501 tcgtgatagc gcatttgctc tgtttattaa gaaatttcag tccgttaatt cgttgaatga
     1561 gtatatgaga tcatctcctt atgttatgga gattattaaa aagaataaca ttagcgctct
     1621 cgaactgcat cgtgcaattg ttgagttgag taaaaatatg aagtcgattg atgataatgc
     1681 cagtaagaaa aacgacaagt catcattgta tgtatcatgg actctgagtt ttactgctcc
     1741 aacaagtaaa gaagctcacg atgtgttgtc tgggtatatt aattatgttt cttcccttgt
     1801 tgtaagggat ttgatggaag atataagaaa taaactagaa gttaaaacta atgttgaaaa
     1861 agaaattctt gcactggatg agataaaaat tagaaaccag ctgaatgcag atattcgacg
     1921 cctcaattat tcactggagg ttgctaatgc ggctggaata aaaaaacctg tatacagcaa
     1981 tggtcagatt atgaaggatg acccagattt tcctgtggct ctcggttctg atggtatagc
     2041 aactaaattg aacatcaaaa aatcaatcaa ggatgtttcg gaattgagtg gggagttgcg
     2101 aaatcgtcaa tatgttgtga atcaattggt tgtggcgaaa gtgggggatg ttgattttat
     2161 gccatttcag tatcaattga gcccaacgtt accggtcaga aaggatgggc caagtaatgc
     2221 cataattgta attctttctt ctgtcattgg agggatgctt gcatgtggct atatactttt
     2281 acgtcatgcc atggaggcca gaaagatgag tgtgattgag taaaagttgt gctgatgcat
     2341 cattttataa gcaactttta taaaaagttc aaaggatatt gttgagatca ttcccttaca
     2401 gccgtagtct tctactctag aaaacgaaaa aacccacctg gggaggtggt ttttcgaagg
     2461 ttcagtaagt tggggaactt ctgaaccgtg gtaacagtct tgtgcgagac atgtcaccaa
     2521 atctgtcctt ctagtgtagc ctcagtaagg ctgccacttc aagaactctc aatacatctc
     2581 tcgcacatcc tgtttaccag tggccgctgc caatggcgtt aagtcgtgtc ttaccgggtt
     2641 ggactcaaga cgatagttac cggataaagc gcagcggtcg ggctgaacgg ggggttcgtg
     2701 cacacagccc agattggagc gaactgccta cccggaactg agtgtcaggc gtggaatgag
     2761 acgaacgcgg ccataacagc ggaatgacac cggtaaaccg aaaggcagga acaggagagc
     2821 gcacgaggga gccgccaggg ggaaacgcct ggtatcttta agtcctgtcg ggtttcgcca
     2881 cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa
     2941 cgccaccggc gcggcctttt ttcggggcct cttttttgct cacatgtttt ttctggtgtt
     3001 atcccctgat tctgtggata accgtatatc cgtctttgcg tgagcagaca ccgctcgccg
     3061 cagccgaacg accgagcgca gcgagtcagt gagcgaggaa gcggaagagc gccggaagct
     3121 gcattttctc cttacgtatc tgtgcagcat ttcacacctc atatgtcgct gttctctcac
//
