LOCUS       NC_017321               4042 bp    DNA     circular CON 03-DEC-2023
DEFINITION  Shigella flexneri 2002017 plasmid pSFxv_4, complete sequence.
ACCESSION   NC_017321
VERSION     NC_017321.1
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 4042)
  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 4042)
  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
            CP001387.1.
            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..4042
                     /organism="Shigella flexneri 2002017"
                     /mol_type="genomic DNA"
                     /strain="2002017"
                     /serotype="Fxv"
                     /db_xref="taxon:591020"
                     /plasmid="pSFxv_4"
     gene            complement(314..505)
                     /locus_tag="SFXV_RS26615"
     CDS             complement(314..505)
                     /locus_tag="SFXV_RS26615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165994.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLYDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            570..893
                     /locus_tag="SFXV_RS26620"
     CDS             570..893
                     /locus_tag="SFXV_RS26620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000956004.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQAARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1102..>1533
                     /locus_tag="SFXV_RS32835"
                     /pseudo=""
     CDS             1102..>1533
                     /locus_tag="SFXV_RS32835"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1571..2101
                     /locus_tag="SFXV_RS31255"
     CDS             1571..2101
                     /locus_tag="SFXV_RS31255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067502.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLSDEFRKLEESVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNESLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            2108..2341
                     /locus_tag="SFXV_RS31260"
     CDS             2108..2341
                     /locus_tag="SFXV_RS31260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137443.1"
                     /translation="MTELESHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVLHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2887..3354)
                     /locus_tag="SFXV_RS30295"
                     /old_locus_tag="SFxv_5153"
     CDS             complement(2887..3354)
                     /locus_tag="SFXV_RS30295"
                     /old_locus_tag="SFxv_5153"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_014526575.1"
                     /translation="MRIDISHQTRHTPPNMLPREQNCVAMALSACFRQQLNPVVNSLLK
                     ERIIHSPKELEHDNAVIRVLQKLQIQEVCNSTLWETAKQQLLQKSDGRYFAINSKHLAF
                     PGPGESHAFCCIKYKNAIGINGNNAETQSTHYQPYPYDKVSIWGPFPHNLT"
                     /name="hypothetical protein"
     gene            complement(3596..3754)
                     /locus_tag="SFXV_RS33005"
     CDS             complement(3596..3754)
                     /locus_tag="SFXV_RS33005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005093880.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="hypothetical protein"
     Typing          209..295
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(2..198)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.485"
                     /coverage="100.0"
                     /evalue="1.52e-93"
     Typing          complement(3646..4042)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.98"
                     /coverage="92.0"
                     /evalue="0.0"
     Typing          884..2445
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.313"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cttttgctca catgttcttt ccggcgttat cccctgattc tgtggataac agcatttcgt
       61 ttttgagtga gtagataccg ctcgccgcag tcgaacgacc gagcgtagcg agtcagtgag
      121 cgaggaagcg gaaaagcgcc tggacgtgca ttttctcctt acgcatctgt gcggcatttc
      181 acacccggta tggcgcactt ttcatacaat ccgcactgat gccgcatggt taagccagta
      241 tacactccgc tatcgctacg tgactgggtc atggctgcgc cccgacaccc gctaacaccc
      301 gctgacaagc ccgtcagagg ttttcgccgt catccccgaa gcgagcgagg caactgcggt
      361 aaagctcatc ggcgtggtcg taaagcgatt cacagatgtc tgcctgttca tccgcgtcca
      421 gttcgttgag cttctccagc agcgttaatg tctggcttct gataaagcgg gccatgttaa
      481 gggcggtttt ttcctgtttg gtcactgatg cctccgtgta agggggattt ctgttcatgg
      541 gggtaatgat accgatgaaa cgcgagagga tgctcacgat acgggttact gatgatgaac
      601 atgcccggtt actggaacgc tgtgagggta aacagctggc ggtatggatg cggcgggtct
      661 gcctgggtga gccggttgcc cgttccggga ggctgccgac actggcaccg ccgttactgc
      721 gtcagctggc cgccatcggg aataacctga atcaggcagc gaggaaggtg aacagcgggc
      781 agtggtcttc cggtgaccgg gttcaggtgg tggccgcact gatggccatc ggggatgagc
      841 tgcgccggct gcgtctggcc gtcagggaac aggggacgcg ggatgatagt taagtttcat
      901 gccaggggaa aaggcggtgg cagtggtccg gttgattacc tgctgggaag ggagcgtaac
      961 cgggaagggg caacggtgct tcagggtaat ccggaagaag tccgggaact catcgatgcc
     1021 acgccatttg cgaagaaata cacgtccggt gttctctcgt tcgcggagaa ggagctgccg
     1081 ccgggagggc gtgaaaaagt gatggcgagc tttgagcgtg tactgatgcc cggtctcgaa
     1141 aaaaatcagt acagcattct gtgggtggag caccaggaca aggggcggct tgagctgaat
     1201 tttgtcattc cgaacatgga gctacagacc ggaaaacgcc tccagccgta ctacgaccgc
     1261 gcagacaggc cgagaattga tgcctggcag acgctggtga atcaccatta cgggctgcat
     1321 gacccgaacg ccccggagaa ccgccggacg ctgactctcc ctgataacct gccggaaacg
     1381 aaacaggcgc ttgctgagag cattacacgg tggatagacg ctctttatca tgtcggggag
     1441 ataaaaggcc gtcaggatgt gattcaggcg ctcacagagg cggggcttga agtggtcagg
     1501 gtgacgcgaa gcagtatcag cattgcagac ccgaacggcg ggaagaatat cagactgaaa
     1561 ggagcattct atgagcaatc ttttacagac gggcgcggag ttcgagaaaa agctgaaaga
     1621 gagagccgaa tctacagaga aaatgctgag cgacgagttc aggaagctcg aagaatctgt
     1681 aagcaaggct gtgacatcaa acgagacgaa aatcaaagac gctatagccc tgttcacagc
     1741 ttcgacagag gaatcactga aaaaacatcg ggaaggggtg aaagaggcga tgatgcagca
     1801 caggaaggac gtgttaaagc tggcagggaa tacgggcatg atgttactgg ggatggtcat
     1861 tttcctgttt accgtgagtg gcgggacgct ctggtatctt ggcgggatga tacaggcgaa
     1921 cctggaagaa atcaggaagc agaacgagag tctggagaag ctgaacgcga agacatgggg
     1981 cgtgcgttat cacgagggga gcaacggacg ttttctggtg ttgcccgagg ggatgaaagc
     2041 cgaaacgaac tggacgatgg aaaacgggaa acagaatgcc gtaaggctgg tacaggagtg
     2101 acagagcatg acggagctgg aaagccattt gctgaacgca ttagagcagc tgcaacagga
     2161 ctatatgcag cggctgaacg aatgggagag cgccttcgtg gaattgcaga aaatgttttc
     2221 gcttacgcaa cgggacaacg cgatgctgaa cgagcgggtc atgcagttga gtcagcaggt
     2281 gctgcacttg agcgagcaga cagaacgctt gagccagtta tacagcgaga actggagata
     2341 agagaggaac ggttgataca ggagcgcgaa catgcgttat tcctggaacg ggaacgccag
     2401 ccggaaatac aggaacggac actggatggc ccttcgctgg gatggtaatc agagacaggc
     2461 taaaatgttg tcagcgcgtt tccggtgcat tttttgggat aatggttggt tcgggggcac
     2521 cgggaacgcg cttcagtcag accttgctga aaacacagga acgagttaaa acgcatacgg
     2581 gcgcgattct ggtgtgtctt ttgtcgctgt gttttgcctc tattgccaga tcgcgctcat
     2641 tcccctgaac ttctgttttc ccgctcaggt ccccgtcttc ttcgcttccg aaagcatgaa
     2701 taaaatccgt ttcagctgtc tctggctggc aattcctgcg tgattcacat ggctgcatag
     2761 ctatgcatgt ggttaaaatt taccgggtgc gatcgcggca gtttttcggg tggtttgttg
     2821 ccatttttac ctgtctgctg ccgtgatcgc gccgaacgcg tttcagcggt gcgtacaatt
     2881 aagatattac gttaaattgt gagggaatgg tccccatata ctgactttat catagggata
     2941 gggttggtag tgggtcgatt gggtttcggc attgtttccg ttaatgccaa ttgcattttt
     3001 gtatttgatg caacagaagg cgtgagattc tcctgggcct ggaaaggcta agtgtttaga
     3061 attgatggca aaatatcttc cgtccgattt ttgaagtagt tgttgtttgg ctgtctccca
     3121 aagggtgctg ttacaaactt cttgaatttg tagtttttgc aggactctta ttactgcgtt
     3181 gtcatgttcc aattctttag gggagtgtat tattctctct tttaataagc tgtttaccac
     3241 agggtttagt tgttgtctaa agcacgcaga taatgccatt gctacacaat tttgttcccg
     3301 aggaagcatg tttggcgggg tatgccgtgt ttgatgtgat atgtctattc tcatagaagg
     3361 tctctggctt atagcatcaa caaatacggc tataaaacaa aattttcata gagtgattca
     3421 agatcttctt gagatccttt tttgcggcgc gtaatctgct gccggcaaac aaaaaaacca
     3481 ccgctaccaa cggtggtttg tttgccggaa tctagagcta ccaactcttt cttccgaagg
     3541 taactggctt ggtggagcac agataccaaa tgctgtcctt ctagtgtagc cgcagttagg
     3601 ccaccacttc aagaactctt aatatctcaa tccaccttgt ccagttacca atggctgctg
     3661 ccagtggcgt taagtcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg
     3721 cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct
     3781 agaccgaact gagataccaa cagcgtgagc tatgagaaag cgccgcgctt cccgaaggga
     3841 gaaaggcgga caggtatccg gtaagcggca gggtcggaac aggagagcgc acgagggagc
     3901 ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctgacttg
     3961 agcgtcggtt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gccatcggcg
     4021 cggccttctt cctgttcctg gt
//
