LOCUS       NC_017329               6200 bp    DNA     circular CON 03-DEC-2023
DEFINITION  Shigella flexneri 2002017 plasmid pSFxv_3, complete sequence.
ACCESSION   NC_017329
VERSION     NC_017329.1
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 6200)
  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 6200)
  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
            CP001386.1.
            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..6200
                     /organism="Shigella flexneri 2002017"
                     /mol_type="genomic DNA"
                     /strain="2002017"
                     /serotype="Fxv"
                     /db_xref="taxon:591020"
                     /plasmid="pSFxv_3"
     gene            807..956
                     /locus_tag="SFXV_RS32045"
                     /old_locus_tag="SFxv_5144"
     CDS             807..956
                     /locus_tag="SFXV_RS32045"
                     /old_locus_tag="SFxv_5144"
                     /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_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(1701..2141)
                     /locus_tag="SFXV_RS26590"
                     /old_locus_tag="SFxv_5145"
     CDS             complement(1701..2141)
                     /locus_tag="SFXV_RS26590"
                     /old_locus_tag="SFxv_5145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            2359..2748
                     /locus_tag="SFXV_RS30270"
                     /old_locus_tag="SFxv_5146"
     CDS             2359..2748
                     /locus_tag="SFXV_RS30270"
                     /old_locus_tag="SFxv_5146"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            2792..>3196
                     /locus_tag="SFXV_RS26595"
                     /old_locus_tag="SFxv_5147"
                     /pseudo=""
     CDS             2792..>3196
                     /locus_tag="SFXV_RS26595"
                     /old_locus_tag="SFxv_5147"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /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="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(3303..4139)
                     /locus_tag="SFXV_RS26600"
                     /old_locus_tag="SFxv_5148"
     CDS             complement(3303..4139)
                     /locus_tag="SFXV_RS26600"
                     /old_locus_tag="SFxv_5148"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(4139..4942)
                     /gene="aph(3'')-Ib"
                     /locus_tag="SFXV_RS26605"
                     /old_locus_tag="SFxv_5149"
     ARG             complement(4143..4942)
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(5003..5818)
                     /gene="sul2"
                     /locus_tag="SFXV_RS26610"
                     /old_locus_tag="SFxv_5150"
     ARG             complement(5007..5818)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(3307..4139)
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          599..772
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(70..675)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.78"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gttggggaac tgcttaaccc ggtaacaggg ttcacgagac cgccgttacc aaaactgttc
       61 tttcagtgta gccgcagtca ggcctctact tcaagacctc ttaatctatc ttctcgtgca
      121 ctcctgttac tggtggctgc tgccggtggc gttttgtcgt gtctttccgg gttggactca
      181 agttgatagt taccggacaa ggcgcagcgg tcggactgaa cggggggttc gtgcatacag
      241 tccagcttgg agcgaactgc cttcacttaa atgagtgtca ggcgtggaat gagaaaccgc
      301 ggccataaca gcggaatgac accggtaaac cgaaaggcag gaacaggaga gcgcacgagg
      361 gagctaccag ggggaaacgc ctgggatctt tgtagtcctg tcgggtttcg ccaccactga
      421 tttgagcgtc agattttgcg atgcttgtca ggggggcgga gcctatggaa aaacggcttc
      481 gccgtggcct tatctcttct ttgctaagtg tcttcctggt atcttccagg aaatttccgt
      541 ccccgtccgt aagccggtac cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg
      601 agcgaggaag cggaatatct cctgtatcgc atattctgct gacgcgccgg tgctgccttt
      661 tttctcctgc cacatgaagc acttcactga ttttcgcaat cgttgcaaca tagtaagcca
      721 gtatacactc cgctagcgct acatgactgg ttcagggctg cgccccgaaa cccgctaaca
      781 acctctcagc tactggatat caccccatgc catctgaata tgatgaacaa ctggattcga
      841 ctgatacgca gcttcccggc gaatatgacc tttttgattt aatggcgcag gttactgaag
      901 agaacctgca tgcccctgtg gattttgggt cgcctgtcgg ccgggaagcg ttatagcttt
      961 ttcgcttgcc cgcgtacgtg gtaatactcc ggtattacct tttatttctt tattttcatg
     1021 taattacagt ggatttttaa tacccgggta ttactcgtga aaacgaaata ttcctttttt
     1081 ttcttttaat tcatgcagtt gcgatgaaaa tcgcggctgc gttaggtgta tgaccatttt
     1141 gaggttgaaa aataatcaac catggcgggt gatttacgca ggttaagggg agatcgtgac
     1201 aaaaaaagcg ttcctcactg tatcgttcat gcctgcatga acgggttatt cttcctgact
     1261 acagaattac atcgctcctt cagttcatac atcactttta catcacttat acatcacttt
     1321 tacatcattc cttcagctca tacgtcactt tcatcctctg tgccatttgt acatcacccc
     1381 cttcctgaac gtgctgacag cgggttttcc ggctgcgccg gcaacgcttc acggccacgc
     1441 aataaattgc gtccccgttc accgttttcg gatgggaaga acgccggaaa caggacttac
     1501 cccggctgaa tggtgtgaat ttccgcgcta tgcacttgtg cgcatactca tgcatgccgt
     1561 aaaaacagag cctgcgcgtt tctggcgggt tttcgggtgg tttgttgcct gttttaccgg
     1621 tttcccgtca gaaacgccct gagggcctct caggcggtgc tgataacaga tgttatggta
     1681 aatcagagtc acctgcactg ttactctgaa ccggagcgaa acagccgcga ccagaatccc
     1741 cgcttttttt cctgtgccag cgcgtcagcc agacggctaa tttcggcctg tagttgttcc
     1801 ctctcctcat ttcgcaggcg gttttctgct tcccgcgcca tcttgtcttc aagcattagg
     1861 gtaacagtct gctgcagagc gtccagtttc tgctgaatga cgtctagctg agcattttcc
     1921 gcctggctaa cgacagattt ggagtgtccc tccttgtgcc tttttggtgt ctcagaagtg
     1981 cgcagctcgc cataggcccg aatcagttca ctggtctcga actcccggcg atcatttttt
     2041 cctgtgcgat agctgacaag gcctttagcc atgtcacgat ataattgcga gcgcgacttt
     2101 cctgttaatt tcagtgtctc ttgaactgtg tgccatgcca taaaagtgac agtgtctcct
     2161 gtgtgtaccg tattgtaaca gcagaacata ttactgtttt aacacaaaag gtctgaggct
     2221 gcccgtgagg cgtgaaaaat acacaaaaaa cctgttgacg gtgtggtttt gacgggcgta
     2281 gtatttcgaa tactgtatat aaacacattg ttataaatac agtttttgct gtttttaaaa
     2341 gtcaaagagg ataattttat gagtacagag ttaaatagcg gtactgtcgg tggttttggt
     2401 cacatgggac caaatgaccc ctacaatgat ggtcatagcg gctctggaag ttcgggaggt
     2461 agttttaacg gtggtggtaa tggtggccat gataatagta gtggttcatc ttatactgca
     2521 tcctttggtc tcatcactgg ccgacacccg ataactgtcc caggtacgaa gaatattaat
     2581 tctgtcgatc tttctgctgt cattaataac attatacatc atgaaggtgc acgcaataac
     2641 atgtacctag atactgcgaa caatgtaaga gtgggagtga cgggcactgg ctggcaatgt
     2701 ctagcaacgg caggcatttc ggctgagggt aaaagaactt tccgctaagc gatagactgt
     2761 atgtaaacac agtattgcaa ggacgcggaa catgcctcat gtggcggcca ggacggccag
     2821 ccgggatcgg gatactggtc gttaccagag ccaccgaccc gagcaaaccc ttctctatca
     2881 gatcgttgac gagtattacc cggcattcgc tgcgcttatg gcagagcagg gaaaggaatt
     2941 gccgggctat gtgcaacggg aatttgaaga atttctccaa tgcgggcggc tggagcatgg
     3001 ctttctacgg gttcgctgcg agtcttgcca cgccgagcac ctggtcgctt tcagctgtaa
     3061 gcgtcgcggt ttctgcccga gctgtggggc gcggcggatg gccgaaagtg ccgccttgct
     3121 ggttgatgaa gtactgcctg aacaacccat gcgtcagtgg gtgttgagct tcccgtttca
     3181 gctgcgtttc ctgtttgggg tcgtttgcgg gaaggggcgg aatcctacgc taaggctttg
     3241 gccagcgata ttctccggtg agattgatgt gttcccaggg gataggagaa gtcgcttgat
     3301 atctagtatg acgtctgtcg cacctgcttg atcgcggccg cgatagctag atcgcgttgc
     3361 tcctcttctc catccgcgtt ccaagctgcg gaaaggcacc cataagcgta cgcctggtcg
     3421 agcaggcgac gcggatcgac gtccagcgca cgagagaatg cgtccgccat ctgtgcaatg
     3481 cgtctaggat cgagacaaag gtcgtctctg tcagccggat cgtagaacat attggcggcg
     3541 ccaaagccca cttcaccgac cagaccgacg ggatctatca ccagccagcc gcgactggag
     3601 aacatgatgt tttcatgatg cagatcgcca tgtagcccac gcagttccga ggcattgctc
     3661 atcatttgat cggctataat cgccgcgtgg acgtagtcag tttgacaacc tgcgttttga
     3721 tcatcgcgcg cccgctgaaa caaagctgca aagcgatccc ggatcgggag aagggcagaa
     3781 ggcaggggtt cctcagatgc ggcatacagc ttcgccatta gttccgctgc aatttcggtc
     3841 gcctggtagt cgccgtgctc ggcaacgatg tgagagagca ttcgctcccc ggcatattcg
     3901 agcaacatca gattgttctc acgaccgagc aaccggactg ctcccctccc attgcgccat
     3961 accagatagt cggccccgcg cagttcatca gcaatgtctt ctataggttt caatcccttg
     4021 acgattgcag gagtcccgtc tggcaatgaa actttccaaa cgaggctgga aaaggtgtcc
     4081 gcaatgagaa caggttgcga aacgtgccaa tgagcaggaa aaacaggcgg catgaacatc
     4141 aaccccaagt cagagggtcc aatcgcagat agaaggcaag gcgttcgcgg tcgggggctt
     4201 cgatccccaa tacattgaat aggacagcga aggcgcgctc tgcttcatct ggcgctgccc
     4261 agttctcttc ggcgttagca atcatgagtg ccaaatcggc atagcgatct gctgttccga
     4321 gccgcccaag gtcgatcaga cccgtgcatt gaagagtttt agggtccacc atgaagttcg
     4381 gcatgcaggg atcaccatgg caaacaacca tatcggtgcg ctcttggtcg agccgcaccg
     4441 gtagctctcg ttcgacacga gccaaaagat cgagctgcgg cgtactcttg tcctcgtccg
     4501 gtaagaagtc gggattgacg gcattgcggg acaccacatc aacggcgcgt ccgaacattc
     4561 gcgacagcct gcgctcaaac ggacattgat caaccgatag gctgtgaaca gcgccaagtt
     4621 gctgccccat tgacggccac gctttgagca aatccgctcc agacagatca gccgccggta
     4681 ctcccggaat tgccgttatc accaagcatg caccctcctg ttcctcctgc cagttgatga
     4741 cctcggggca agccacacct cgacctttga gccaaatgag gcggtcacgc tctccagcga
     4801 gctcaccgcg gcgggaagca ggtgcgattt tcgcgaaggc atgcccgtca ccacgtcgaa
     4861 aaacaaaatc accagattct ccgcctctga caggcaacca gtcagaatgc gattcaccaa
     4921 aaaaaatatt agttcgattc aatggaggtt ccttcagttt tctgatgaag cgcgaatata
     4981 gagaaatatc ccgaatgtgc agttaacgaa ttcttgcggt ttctttcagc gccgccaata
     5041 ccgccagccc gtcgcgcaag gggcgcggct cgtgtgtgcg gatgaagtca gctccacctg
     5101 cggcggcggc aagctctgca gcgagtgtcg cggccccgac atcccccgga ccacggcctg
     5161 tgagcgcgcg cagaaaggat ttgcgcgaaa cagacagaag caccggcaaa tcgaagcgca
     5221 gccgcaattc atcgaaccgc gccagcaccg agagcgaggt ttcgggagca gcccccagaa
     5281 aaaaccccat gccgggatca aggacaaggc ggttgcgttt gataccggca cccgtcagcg
     5341 ccgcgatgcg cgcgtcaaag aacgccgcaa tgtgatccat gatgtcgcca gcgggtgcct
     5401 cgcgccgatc tgcctgcccg tcttgcaccg aatgcataac gacgagtttg gcagatgatt
     5461 tcgccaattg cggatagaac gcagcgtctg gaaaaccgcg aatatcattg agataggcca
     5521 caccacgcga caaggcatag gcttgcgtcg cgggttgata actgtcgagc gagacgggaa
     5581 tgccatctgc cttgagcgcg tccagcaccg gcgcgatacg cgcgatttct gtgtcggacg
     5641 aaacaggcgc ggcgtcggga ttgctggatg ccggaccgag gtcgatcaca tctgccccct
     5701 cggccatcag cttacgcgcc tgcgcaatgg ctgcgtctgg cgccagatac cggcctccat
     5761 cggagaaact gtccgaggtt atgttgacga tgccgaaaat gatgagcgat ttattcatgg
     5821 gggcttctat aataataata atcgagcatg agtctcatac ggatgctcgg gtcgaaaggg
     5881 aatccccagg cgagtaacct gtttgcggtg atccgtttca tgatgatgta tctgtagcat
     5941 tttggaaata aatatatcat ctctcaataa gtagatatat ttatcttttt tgcttctttg
     6001 gtgctgcaag tcaccaatac gagggaaacc tgttacggag cggtttaacc gtaatcaaca
     6061 gtgactggtg tcatgttcgg aagattaatt gatagtaatc tacaaaggat cttcttgaga
     6121 tccttttcaa tgaatcgtaa tctcttgctc tgtaaacgaa aaaaccgcct ggggaggcgg
     6181 tttgttcgaa ggttaagtca
//
