LOCUS       NC_017320               6850 bp    DNA     circular CON 03-DEC-2023
DEFINITION  Shigella flexneri 2002017 plasmid pSFxv_2, complete sequence.
ACCESSION   NC_017320
VERSION     NC_017320.1
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 6850)
  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 6850)
  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
            CP001385.1.
            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..6850
                     /organism="Shigella flexneri 2002017"
                     /mol_type="genomic DNA"
                     /strain="2002017"
                     /serotype="Fxv"
                     /db_xref="taxon:591020"
                     /plasmid="pSFxv_2"
     gene            32..>112
                     /locus_tag="SFXV_RS33000"
                     /pseudo=""
     CDS             32..>112
                     /locus_tag="SFXV_RS33000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            340..576
                     /locus_tag="SFXV_RS26560"
     CDS             340..576
                     /locus_tag="SFXV_RS26560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674368.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000138111.1"
                     /translation="MTEMERQLLSALESLQTSYEQQQQAWQDSYSSLQRMFETTSQALE
                     RNGRVCLNLSNQVNALHEQVERLSSDLSRLTRS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            <638..1454
                     /locus_tag="SFXV_RS26565"
                     /old_locus_tag="SFxv_5134"
                     /pseudo=""
     CDS             <638..1454
                     /locus_tag="SFXV_RS26565"
                     /old_locus_tag="SFxv_5134"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004088970.1"
                     /note="frameshifted; internal stop; incomplete; partial in
                     the middle of a contig; missing N-terminus; Derived by
                     automated computational analysis using gene prediction
                     method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(1523..3043)
                     /locus_tag="SFXV_RS26800"
                     /old_locus_tag="SFxv_5135"
     CDS             complement(1523..3043)
                     /locus_tag="SFXV_RS26800"
                     /old_locus_tag="SFxv_5135"
                     /inference="COORDINATES: protein motif:HMM:NF013080.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LTA synthase family protein"
                     /protein_id="WP_000478744.1"
                     /translation="MFLISIIQMFSVMIIMLNIKIKDAFRAIILLLLLLLSMVISIEIS
                     SIISIGEYIPTLALANISETNSVGWKIKLLPFLVFLSFMIASLILKRLIKEKKIRNIMV
                     VVFLLSLLIPISPINAFFSSSYEVYSEAKEYNMSPHEISDIKSKYTKEIVTNDSYSHEI
                     INGNGKNILVIFIEGMSSLVISKELTPNLYEFRKKSISFNNYYNHTAATFRGLRGQLTS
                     SYQMTGGYYKDNSGLGQASKAEIEHKLNTYNYITKLPIILEENGYHTYFQASNSIDAPL
                     SLMLSTLKFNHIYGREDYNKKSGELTDKESFDLLFKKLNEAKQPFFYGVYTVGTHLGLD
                     SPDVKFYDGRNEYLNHFHQLDHWFGDFISHFNKTSLSKDTIVIITSDHASYPSEDYKKT
                     FKTDNTFFVDQIPLIIWSNGVEFKDINAHGLNSLSLTPTILDILGIKESHNMFIGESLF
                     EKEKNKNELNCTSAIGDLYVKTCNGKMEIEKRKEKIELIKQLQLFGDR"
                     /name="LTA synthase family protein"
     gene            3336..4027
                     /locus_tag="SFXV_RS26575"
     CDS             join(3336..3585,3585..4027)
                     /locus_tag="SFXV_RS26575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558260.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_227804375.1"
                     /translation="MASISISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRATAHFIGVGLNTIFRHFKKLRPQSVTSRIQPGRDVIV
                     CAEMDEQWSYVGAKSRQRWLFYAYDRLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLRQHLARPGRKSLSFSKSVELHDKVIGH
                     YLNIKHYQ"
                     /name="IS1 family transposase"
     gene            4272..4421
                     /locus_tag="SFXV_RS32040"
                     /old_locus_tag="SFxv_5137"
     CDS             4272..4421
                     /locus_tag="SFXV_RS32040"
                     /old_locus_tag="SFxv_5137"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138851.1"
                     /translation="MPSEHDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFRPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            4806..5174
                     /locus_tag="SFXV_RS26580"
                     /old_locus_tag="SFxv_5138"
     CDS             4806..5174
                     /locus_tag="SFXV_RS26580"
                     /old_locus_tag="SFxv_5138"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880027.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001273383.1"
                     /translation="MANFNPGPRTAIAAVRDSKNDIETWKKNGIRREEIVTVLNERYGL
                     NISLVAFDKALYRLRKSTDEPSLAGVDSVSVSETNFSEASGPDNGFFLSGNDFMRAEEE
                     SQRVVESFRDSLSRKKGF"
                     /name="hypothetical protein"
     gene            complement(5571..5888)
                     /locus_tag="SFXV_RS26585"
                     /old_locus_tag="SFxv_5140"
     CDS             complement(5571..5888)
                     /locus_tag="SFXV_RS26585"
                     /old_locus_tag="SFxv_5140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000718044.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000718045.1"
                     /translation="MKKIFILSAALIMAGCATKQYPQAANVTGPESSAMDCKAVALEIA
                     KTRSVQQEIEETGEFDGRTVLGFLGDFGIGNGMAKGEARKKAANRLNQLEALKAAKCAD
                     Q"
                     /name="hypothetical protein"
     Typing          complement(6290..6836)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.455"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 cagtggtgcg aattttttct cagcggtgcc tatggaaaag cgaacgaaag aaatcaaaat
       61 ccgcatgacc gagactgagc atcagcgtct gcttgaacgg tgtgaccgta cagccagcaa
      121 ctggagagcc tgaaagccca gagcggcgca ggggtagcga tttacaagga cgacaagcag
      181 aagaacacct atctggtggt actgccgaag aaagcgcatg gcaccgagac ctatacatcg
      241 acagccggaa acaccgtgat gaagtacacc tcgaaataac cccgtcagag cccacagaaa
      301 agccacagca cgtttttatc actgaggaca ggcaaaacca tgaccgagat ggaaaggcag
      361 cttctgagcg ccttagaaag cttacaaaca agttatgaac aacagcaaca ggcgtggcag
      421 gacagttaca gcagcttgca acgcatgttc gagactacct cacaggcact ggagcgcaac
      481 ggcagggtat gtctgaactt gagcaatcag gtgaacgcct tgcacgaaca ggtcgaacgc
      541 ttgagcagcg atctgagccg attaacacgc tcgtaaagca gcaggaacgg cagttacagc
      601 aggagaagca agcaacccgc tatcgaggtc agtccatgta ccacacaagc cgtacttctc
      661 ggatgatttg cactttggtg tgcgcatcgt agggaaagaa cgcgctattc tggcgaaata
      721 catccagttc aatcagcctc acgccatgtt ctggctggga tttgatgttg accgcatcgg
      781 cgcagccatt gactggagcg accgcaacgc tcccgcacct acgctgacca tcaccaaccc
      841 cgaaaacgga cacgcgcacc tgctttatgc gctggaaacc tctatacgca cagcacctga
      901 cggaaaaatg aaaccgttac gctacgcagc tgccgtagag aatgcgctac gtagaaaatt
      961 gggagctgac acgggatatt cggggctaat ttgcaagaat ccgaaccaca gtcactggaa
     1021 aattgccgcc gattatggtt taggccgtaa ctgcactctg ttcgacaaaa cccgcaagtg
     1081 ggcatatcgt gccatccgtc aggggtggcc tgagtatgag cagtggttac aagcctgcta
     1141 tgaacgagcc tgtgcctaca atttacaatt cgtatcacca ttaagtgaaa atgaagttct
     1201 tggaatatca aaaagcatct caaaatggac agcgaataat ttttaagagg atcgttttat
     1261 tgagtatgta aaaaatacgc accgttcaga aattcaaaga aagagagggg gtaaaggagg
     1321 aaagctaagc aattcaggag gacggcctaa aggtagtttt aatattaatt cctataactt
     1381 taaaaaaaga atgggagtct ttaggtgtta gtcgagccac attctacagg cggctcaaga
     1441 atgaaaaaaa gtaagtttta ttatcatttt aaaataaccc cacgtggact aataatcaac
     1501 atggggtaaa accgcctttt aattatctat caccaaaaag ttgcaattgt tttattaatt
     1561 ctattttttc ttttcttttc tcgatttcca ttttcccatt acacgttttc acatacaggt
     1621 cacctattgc agatgtacag ttgagttcat ttttattttt ttctttttca aatagagact
     1681 cacctatgaa catgttgtgt gactccttga tcccaagaat atctagtatt gttggcgtta
     1741 aagatagtga atttaaaccg tgtgcattaa tgtctttgaa ctcaacacca ttactccata
     1801 ttattaatgg aatctgatca acaaaaaaag tattatcagt tttgaatgtt tttttgtaat
     1861 cttctgatgg gtaacttgca tggtcacttg tgattatgac aattgtatct ttcgataagc
     1921 ttgtcttatt aaaatgagat ataaaatcac caaaccaatg gtctaattga tgaaagtgat
     1981 ttaaatattc atttctccca tcataaaact ttacatcagg gctatctaag ccaaggtgtg
     2041 tacctacagt ataaacacca tagaagaaag gttgtttagc ctcatttaat tttttaaata
     2101 ataaatcgaa agactctttg tctgtgagtt cacctgactt tttgttatag tcctcccttc
     2161 cgtatatatg attaaacttt aaagttgata gcattaaact caatggggca tctattgaat
     2221 tagatgcttg aaaatatgta tggtaaccat tttcctcaag tatgattggt agttttgtta
     2281 tgtaattgta agtatttagt ttatgttcga tctctgcttt agatgcttgg ccaaggccag
     2341 aattatcttt atagtaacca ccggtcattt gatatgatga ggttaactgt cctcttaaac
     2401 ctctaaatgt agctgcggta tggttgtaat agttgttaaa tgatattgat ttttttctaa
     2461 attcatataa attcggggtt agctccttag atattaccaa tgaagacata ccttcaataa
     2521 atattactaa aatatttttt ccgtttccat ttattatttc atgtgagtaa ctgtcgtttg
     2581 ttactatttc ttttgtgtat tttgacttta tatcacttat ttcatgtggt gacatattgt
     2641 attcttttgc ttccgaataa acttcatatg atgaagaaaa aaaagcattt attggagata
     2701 ttggtattaa caatgataat aaaaaaacaa caaccattat atttcttatt tttttttctt
     2761 ttatcaatct tttcaaaatc aatgatgcaa tcataaatga taagaacaca agaaaaggta
     2821 gtagttttat tttccagcca acactatttg tctctgatat atttgctagt gcaagtgtgg
     2881 gtatgtactc acctattgat ataatgctgc ttatttcaat agatataacc atggatagta
     2941 atagaagtaa aagcagaata attgctctaa atgcatcttt tatttttata ttaagcatta
     3001 taatcataac cgagaacatt tgaataattg aaattaaaaa catttataaa aacctttttt
     3061 tttggggggc gttgttgaat aaatagatat tatgctgtgg atctacaaaa atgtcggtct
     3121 tcctcaacct aaaatcagta agttaagttt agactcggga gcttatcaca atattgataa
     3181 gcgcatttga ctaaataaga catagaaaac agcataattc tccattattc aacaaatctg
     3241 gagatgtatt atactttttt aattaactgt ctgctagtgc ggtgatgctt ccaacttact
     3301 gatttagtgg atgacggtgc ttttgaggtg ctccggtggc ttccatttcc atcagctgtc
     3361 cctcctgttc cgctactgac ggcgttgtgc gtaacggtaa aagtactgcc ggacatcagc
     3421 gctatctctg ctctcactgc cgtaaaacat ggcagctaca gttcacttac accgcctctc
     3481 aacccggtac acaccagaaa atcattgata tggccatgaa tggcgtcgga tgccgggcaa
     3541 ccgcccactt tattggcgtt ggcctcaaca cgattttccg ccatttaaaa aactcaggcc
     3601 gcagtcggta acctcgcgca tacagccggg cagggacgtc atcgtctgcg cggaaatgga
     3661 cgaacagtgg agctacgtcg gggctaaatc acgccagcgc tggctgtttt acgcgtatga
     3721 caggctccgg aagacggttg ttgcgcacgt attcggtgaa cgcactatgg cgacgctggg
     3781 gcgtcttatg agtctgctgt caccctttga cgtggtgata tggatgacgg atggctggcc
     3841 gctgtatgaa tcccgcctga agggaaagct gcacgttatc agcaagcgat atacgcagcg
     3901 aattgagcgg cataatctga ggcagcatct ggcaaggccg ggacggaagt cactgtcgtt
     3961 ctcaaaatcg gtggagctgc atgacaaagt catcgggcat tatctaaaca taaaacacta
     4021 tcagtaagtt ggattcatta tcctacctac ctcttggcag gaaaaagcgc tcgcaaaaac
     4081 ggtgagaaaa aaacaagcct atatcagata acagccctct cctagacagg gctgttactt
     4141 tgccgtaacc acagaatctg tcatactaca ctaccgccta agtcagtata cactccgcta
     4201 gcgctacgtg actggtttag ggctgcgccc cgaaacccgc taaccacctc tcagctactg
     4261 gatatcaccc catgccatct gaacatgatg aacaactgga ttcgactgat acgcagcttc
     4321 ccggcgaata tgaccttttt gatttaatgg cgcaggttac tgaagagaac ctgcacgccc
     4381 cggtggattt taggccgcct gtcggccggg aagcgttata gctttttcgc ttacccgcgt
     4441 acgtggtaat acgccggtat tacatcttat ttctttattt tcatgtaatt acaggtggtt
     4501 gtaatacgtt gcgtattaca taaataaacg gggacttcag tttttacctt ttaattcatg
     4561 caattgcgat gaaaatcgcg gttgcgtatg gtgtatgacc atttaaggga taatgtaacc
     4621 tgacttttaa agaatgaatc tatctttggc tgcgcatgag atcgataaaa agcgttccac
     4681 atcaggcggt tcatggatac atgaaccgga aaggacaaca ataagacaat tgtaagacat
     4741 ttttttgcgt ttcaatctta tttttggact attatgagac aaatttaaga cattatgggc
     4801 ggtatatggc gaattttaac cctggtccaa gaacagccat tgcggctgtc agggattcca
     4861 agaacgatat agaaacctgg aagaaaaatg gtatccgtag ggaagagatt gtgactgtgc
     4921 tgaatgaacg ttacggcctg aatatctcac tggttgcgtt tgataaggct ctttacagat
     4981 tgagaaaaag tacagatgaa ccgtctcttg ctggtgtgga ttctgtgtct gtttcagaaa
     5041 cgaatttctc tgaagccagt gggcctgaca atggtttttt tctgtccggg aatgacttca
     5101 tgcgagcaga agaagaatct caaagagtgg ttgagtcatt cagagatagc cttagcagga
     5161 agaaaggatt ctgattttga attctaagta gtgaaatagt ggatcctcta ctcgaaattg
     5221 tcggatacct gcaattacct accgtgcctt acggcttggt caatgcctca cggccacgca
     5281 ataaattgcg tccccgttca ccgttttcgg atgggaagaa tgccggaaac aggacttacc
     5341 ctggctgaat ggggtgaatt ttcgcgctat gcacttgcgt gcatactcat gcatgccgta
     5401 aaaacagagc ctgcgcgttt ctggcgggtt ttcgggtggt ttgttgcctg ttttgccggt
     5461 ttcccgtcag aaacgccctg agggcctctc aggcggtgca cgcaacggat gttatggtaa
     5521 atccagctga ttggcaggta caaaaaagcc ccgcagggct tttttgtacc ttattgatct
     5581 gcacactttg cagccttcag ggcttccagc tgatttagcc ggttagctgc ttttttgcgg
     5641 gcttcgcctt ttgccatgcc atttcctatc ccaaaatcac ccaggaaacc taatacggtg
     5701 cgcccgtcaa attcgccggt ttcctcaatt tcttgttgta cactgcgcgt tttggcgatt
     5761 tccagagcta ccgctttgca atccattgcg gaagattctg gaccggtgac gttcgcggcc
     5821 tgtggatatt gctttgttgc gcatcctgcc atgattagcg ctgccgatag gatgaatatt
     5881 tttttcaaaa ttatccttat ttaggcatag ttaagagata cccattttat cggcaggaaa
     5941 tgagggtttt ttagttgaat tttgggaggg gcaaggttcc atattggtcg aggattctgg
     6001 agctgaccgg caacggccag cgcggctatg agccatgcgg tggttgagca tataaaggat
     6061 cttcttgagt tccttttttt ctacgcgtaa tctcttgctc tgaaaacgaa aaaaccacct
     6121 ggggaggtgg tttttcgaag gttaagtcag ttggggaact gcttaacctg gtaactggct
     6181 tcagcagagc gcagatacca aatactgtcc ttccagtgta gccgtagtta ggccaccact
     6241 tcaagaactc tatagcacca cctacattaa ctcgctctgc taatcctgtt accagtggct
     6301 gctgccagtg gcgctttgtc gtgtctttcc gggttggact caagacgata gttaccggat
     6361 aaggcgcagc agtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact
     6421 gccttcccgg aactgagtgt caggcgtgga atgagacaaa cgcggccata acagcggaac
     6481 gacaccggca aaccgaacgg caggaacagg agagcgcacg cgggagccac cagggggaaa
     6541 cgcctggtat ctttaagtcc tgtcgggttt cgccaccact gatttgagcg tcagatttcg
     6601 tgatgcttgt caggggggcg gagcctatgg aaaaacggct ttgccgcggc cctatcgctt
     6661 ccctgttaac tattttcctg gcatcttcca ggaaatctcc gccccgttcg taagccattt
     6721 ccgctcgccg cagtcgaacg accgagcgta gcgagtcagt gagcgaggaa gcggaatata
     6781 taatgtatca catattctgc tgacgcactg gtgccgcctt ttttgtcctg ccacatgaag
     6841 cactttctca
//
