LOCUS       NZ_CP085206             3179 bp    DNA     linear   CON 07-JUN-2024
DEFINITION  Shigella flexneri strain P099 plasmid p004.
ACCESSION   NZ_CP085206
VERSION     NZ_CP085206.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16710603
            Assembly: GCF_023204675.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3179)
  AUTHORS   Kim,S., Christine,S.-W. and Sims,L.
  TITLE     Genome announcement of Shigella flexneri in Macaca mulatta
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3179)
  AUTHORS   Kim,S., Christine,S.-W. and Sims,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-OCT-2021) Micro Surveillance, NCTR/FDA, 3900 NCTR Dr.,
            Jefferson, AR 72079, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: NOV-2020
            Assembly Method                   :: SPAdes v. Nov-2020
            Assembly Name                     :: NCTR_Sfle_1.1
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 167.0x
            Sequencing Technology             :: Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023204675.1-RS_2024_06_07
            Annotation Date                   :: 06/07/2024 02:55:54
            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)                     :: 4,986
            CDSs (total)                      :: 4,853
            Genes (coding)                    :: 4,114
            CDSs (with protein)               :: 4,114
            Genes (RNA)                       :: 133
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 104
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 739
            CDSs (without protein)            :: 739
            Pseudo Genes (ambiguous residues) :: 0 of 739
            Pseudo Genes (frameshifted)       :: 278 of 739
            Pseudo Genes (incomplete)         :: 417 of 739
            Pseudo Genes (internal stop)      :: 170 of 739
            Pseudo Genes (multiple problems)  :: 120 of 739
            Pseudo Genes (short protein)      :: 1 of 739
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP085206.1.
            Bacteria and source DNA available from Sung G Kim, NCTR/FDA, 3900
            NCTR Rd., Jefferson, AR 72079.
            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/
FEATURES             Location/Qualifiers
     source          1..3179
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="P099"
                     /isolation_source="Oral swab"
                     /host="Macaca mulatta"
                     /db_xref="taxon:623"
                     /plasmid="p004"
                     /geo_loc_name="USA"
                     /collection_date="2017-11-17"
     gene            506..640
                     /locus_tag="IUX27_RS25085"
     CDS             506..640
                     /locus_tag="IUX27_RS25085"
                     /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"
     gene            complement(885..1994)
                     /gene="wzz(fepE)"
                     /locus_tag="IUX27_RS24850"
                     /old_locus_tag="IUX27_24875"
     CDS             complement(885..1994)
                     /gene="wzz(fepE)"
                     /locus_tag="IUX27_RS24850"
                     /old_locus_tag="IUX27_24875"
                     /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            2869..3039
                     /locus_tag="IUX27_RS24855"
                     /old_locus_tag="IUX27_24880"
     CDS             2869..3039
                     /locus_tag="IUX27_RS24855"
                     /old_locus_tag="IUX27_24880"
                     /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_255625548.1"
                     /translation="MNMARCIKSQSLTLLEKLDALDADEQAAMCKRLHELAEELQNSIQ
                     IRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2326..2583)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(2708..2806)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          52..578
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 gcttaattat gaggcggcag agcagatggt gagagaacag cgacatatga ggtgtgaaat
       61 gctgcacaga tacgtaagga gaaaatgcag cttccggcgc tcttccgctt cctcgctcac
      121 tgactcgctg cgctcggtcg ttcggctgcg gcgagcggtg tctgctcacg caaagacgga
      181 tatacggtta tccacagaat caggggataa caccagaaaa aacatgtgag caaaaaagag
      241 gccccgaaaa aaggccgcgc cggtggcgtt tttccatagg ctccgccccc ctgacgagca
      301 tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactta aagataccag
      361 gcgtttcccc ctggtggctc cctcgtgcgc tctcctgttc ctgcctttcg gtttaccggt
      421 gtcattccgc tgttatggcc gcgttcgtct cattccacgc ctgacactca gttccgggta
      481 ggcagttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc
      541 cttatccggt aactatcgtc ttgagtccaa cccggtaaga cacgacttaa cgccattggc
      601 agcggccact ggtaaacagg atgtgcgaga gatgtattga gagttcttga agtggcagcc
      661 ttactgaggc tacactagaa ggacagattt ggtgacatgt ctcgcacaag actgttacca
      721 cggttcagaa gttccccaac ttactgaacc ttcgaaaaac cacctcccca ggtggttttt
      781 tcgttttcta gagtagaaga ctacggctgt aagggaatga tctcaagaag atcctttgaa
      841 ctttttataa aagttgctta taaaatgatg catcagcaca acttttactc aatcacactc
      901 atctttctgg cctccatggc atgacgtaaa agtatatagc cacatgcaag catccctcca
      961 atgacagaag aaagaattac aattatggca ttacttggcc catcctttct gaccggtaac
     1021 gttgggctca attgatactg aaatggcata aaatcaacat cccccacttt cgccacaacc
     1081 aattgattca caacatattg acgatttcgc aactccccac tcaattccga aacatccttg
     1141 attgattttt tgatgttcaa tttagttgct ataccatcag aaccgagagc cacaggaaaa
     1201 tctgggtcat ccttcataat ctgaccattg ctgtatacag gtttttttat tccagccgca
     1261 ttagcaacct ccagtgaata attgaggcgt cgaatatctg cattcagctg gtttctaatt
     1321 tttatctcat ccagtgcaag aatttctttt tcaacattag ttttaacttc tagtttattt
     1381 cttatatctt ccatcaaatc ccttacaaca agggaagaaa cataattaat atacccagac
     1441 aacacatcgt gagcttcttt acttgttgga gcagtaaaac tcagagtcca tgatacatac
     1501 aatgatgact tgtcgttttt cttactggca ttatcatcaa tcgacttcat atttttactc
     1561 aactcaacaa ttgcacgatg cagttcgaga gcgctaatgt tattcttttt aataatctcc
     1621 ataacataag gagatgatct catatactca ttcaacgaat taacggactg aaatttctta
     1681 ataaacagag caaatgcgct atcacgattg atatcaaaat ccactcccag aacatgaagc
     1741 ttggaaagct ccttatttaa ttcactccat tgaacagact cagcaggagt aaccacagca
     1801 gaactagtcc atttttgtgg caaaacaaaa gaaacaagaa agccaataca agcaaaaaat
     1861 agaatcaccc caacaatttt tatttttgct gcccataaaa cgctaatcaa gccaaaaagg
     1921 tcaatttctt cattaccatt cggcaacatg ttgtaattag aaaaatgttc gtcagagacc
     1981 tttgagattt tcattgaaaa aaacacaata tattaacata tggttttttt attctatcat
     2041 atgttaggaa aaaacctaaa aaccattcag cagacattta acataacatt ttattgcgcg
     2101 caccgctaaa acgcgctgaa cgcgattctg ccgcaaacac cgcaaaaaga gatgttttcc
     2161 ccggggtaaa ccggaaaaat gcgtcaggat cgctttcagc tcactgcata gctatgcatg
     2221 aaagtgaatg acgatcggtt tgggcgcata cagtgcccat gagacacatt ttcggacatt
     2281 ttcagttcgt gaatccctga ctcattgcta catatctgaa cagacacccc tagcagcgcc
     2341 cccaggggcg tcctgtaaaa aaacacaccg cgccgctagc agcaccccta atataagata
     2401 atgttttttt tatgaaaata gtcagtacca cccctaaaaa gcggtgttgg cgcagctaca
     2461 acaccgcgcc gacaccgctt ttttaaatat cacaaagaga gcaagaagaa ctaatttgtc
     2521 ataactctct atttataaag aaaaatcagc aaaaacttgt ttttgcgtgg ggtgtgggca
     2581 tttcaggcat gagaacagac tcgcgttttt ccggagtatc agcggaatta ttgattaaga
     2641 aacactcgac gcagagcgaa attttatgca acagcggctg cactgcacag ggattattta
     2701 tcagttgata tgctgtgcca tgatacgtcc taaagaaaca ggacaggatg tgcaattgta
     2761 ataccgtcgc ccgcaacgtc ttacaattac cacctgctca gggtcccccc cccgacaccc
     2821 ggaactgacg gagaacaacg gaaggtgaac aaataacaac aaactgcgct gaatatggcg
     2881 cgatgtatca aaagccagag cctgacactg cttgaaaaac tggatgctct ggatgccgac
     2941 gaacaggcgg ccatgtgcaa acgactgcac gaactcgcag aagaactcca gaacagcatc
     3001 cagattcgct ttgaggccga aagtgaaaca ggaacataac gaagctgacg gaggcggtca
     3061 cggctttccc gtgggcgttt tcgtcagcag acaagcccgt cagggcgcgt cagggggttt
     3121 tagcgggtgt cggggcgcag ccatgaccca gtcacgtagc gataacggag tgtatactg
//
