LOCUS       NZ_CP042978             3128 bp    DNA     circular CON 09-JUL-2023
DEFINITION  Shigella flexneri Y strain PE577 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP042978
VERSION     NZ_CP042978.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12588114
            Assembly: GCF_008370775.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri Y
  ORGANISM  Shigella flexneri Y
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3128)
  AUTHORS   Doore,S.M., Subramanian,S. and Parent,K.N.
  TITLE     Comparative genome analysis of the model bacteriophage host strain
            Shigella flexneri PE577
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3128)
  AUTHORS   Doore,S.M., Subramanian,S. and Parent,K.N.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-AUG-2019) Biochemistry and Molecular Biology, Michigan
            State University, 603 Wilson Rd, East Lansing, MI 48824, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: A5 pipeline v. v. 20160825
            Assembly Name                     :: MSU_PE577
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 30.0x
            Sequencing Technology             :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/09/2023 02:36:53
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,640
            CDSs (total)                      :: 4,510
            Genes (coding)                    :: 3,898
            CDSs (with protein)               :: 3,898
            Genes (RNA)                       :: 130
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 101
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 612
            CDSs (without protein)            :: 612
            Pseudo Genes (ambiguous residues) :: 0 of 612
            Pseudo Genes (frameshifted)       :: 214 of 612
            Pseudo Genes (incomplete)         :: 317 of 612
            Pseudo Genes (internal stop)      :: 154 of 612
            Pseudo Genes (multiple problems)  :: 75 of 612
            Pseudo Genes (short protein)      :: 5 of 612
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP042978.1.
            Bacteria and source DNA available from Kristin Parent, Department
            of Biochemistry and Molecular Biology, Michigan State University,
            603 Wilson Road Room 519, East Lansing, MI 48824 USA.
            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..3128
                     /organism="Shigella flexneri Y"
                     /mol_type="genomic DNA"
                     /strain="PE577"
                     /serotype="Y"
                     /host="Homo sapiens"
                     /db_xref="taxon:424720"
                     /plasmid="unnamed2"
                     /geo_loc_name="Australia: Adelaide"
                     /collection_date="1990"
                     /note="clinical sample"
     gene            complement(join(3110..3128,1..119))
                     /locus_tag="FW259_RS23970"
     CDS             complement(join(3110..3128,1..119))
                     /locus_tag="FW259_RS23970"
                     /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_168219890.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGKQDVEGQIW
                     "
                     /name="replication initiation protein"
     gene            complement(765..929)
                     /locus_tag="FW259_RS00015"
                     /old_locus_tag="FW259_00015"
     CDS             complement(765..929)
                     /locus_tag="FW259_RS00015"
                     /old_locus_tag="FW259_00015"
                     /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            1811..2920
                     /gene="wzz(fepE)"
                     /locus_tag="FW259_RS00020"
                     /old_locus_tag="FW259_00020"
     CDS             1811..2920
                     /gene="wzz(fepE)"
                     /locus_tag="FW259_RS00020"
                     /old_locus_tag="FW259_00020"
                     /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)"
     Typing          599..685
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          1000..1098
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="6.26e-40"
     Typing          1223..1480
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(48..574)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 acatcctgtt taccagtggc cgctgccaat ggcgttaagt cgtgtcttac cgggttggac
       61 tcaagacgat agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca
      121 cagcccagct tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg aatgagacga
      181 acgcggccat aacagcggaa tgacaccggt aaaccgaaag gcaggaacag gagagcgcac
      241 gagggagcca ccagggggaa acgcctggta tctttaagtc ctgtcgggtt tcgccacctc
      301 tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc
      361 accggcgcgg ccttttttcg gggcctcttt tttgctcaca tgttttttct ggtgttatcc
      421 cctgattctg tggataaccg tatatccgtc tttgcgtgag cagacaccgc tcgccgcagc
      481 cgaacgaccg agcgcagcga gtcagtgagc gaggaagcgg aagagcgccg gaagctgcat
      541 tttctcctta cgtatctgtg cagcatttca cacctcatat gtcgctgttc tctcaccatc
      601 tgctctgccg cctcataatt aagccagtat acactccgtt atcgctacgt gactgggtca
      661 tggctgcgcc ccgacacccg ctaaaacccc ctgacgcgcc ctgacgggct tgtctgctga
      721 cgaaaacgcc cacgggaaag ccgtgaccgc ctccgtcagc ttcgttatgt tcctgtttca
      781 ctttcggcct caaagcgaat ctggatgctg ttctggagtt cttctgcgag ttcgtgcagt
      841 cgtttgcaca tggccgcctg ttcgtcggca tccagagcat ccagtttttc aagcagtgtc
      901 aggctctggc ttttgataca tcgcgccata ttcagcgcag tttgttgtta tttgttcacc
      961 ttccgttgtt ctccgtcagt tccgggtgtc gggggggggg gccctgagca ggtggtaatt
     1021 gtaagacgtt gcgggcgacg gtattacaat tgcacatcct gtcctgtttc tttaggacgt
     1081 atcatggcac agcatatcaa ctgataaata atccctgtgc agtgcagccg ctgttgcata
     1141 aaatttcgct ctgcgtcgag tgtttcttaa tcaataattc cgctgatact ccggaaaaac
     1201 gcgagtctgt tctcatgcct gaaatgccca caccccacgc aaaaacaagt ttttgctgat
     1261 ttttctttat aaatagagag ttatgacaaa ttagttcttc ttgctctctt tgtgatattt
     1321 aaaaaagcgg tgtcggcgcg gtgttgtagc tgcgccaaca ccgcttttta ggggtggtac
     1381 tgactatttt cataaaaaaa acattatctt atattagggg tgctgctagc ggcgcggtgt
     1441 gtttttttac aggacgcccc tgggggcgct gctaggggtg tctgttcaga tatgtagcaa
     1501 tgagtcaggg attcacgaac tgaaaatgtc cgaaaatgtg tctcatgggc actgtatgcg
     1561 cccaaaccga tcgtcattca ctttcatgca tagctatgca gtgagctgaa agcgatcctg
     1621 acgcattttt ccggtttacc ccggggaaaa catctctttt tgcggtgttt gcggcagaat
     1681 cgcgttcagc gcgttttagc ggtgcgcgca ataaaatgtt atgttaaatg tctgctgaat
     1741 ggtttttagg ttttttccta acatatgata gaataaaaaa accatatgtt aatatattgt
     1801 gtttttttca atgaaaatct caaaggtctc tgacgaacat ttttctaatt acaacatgtt
     1861 gccgaatggt aatgaagaaa ttgacctttt tggcttgatt agcgttttat gggcagcaaa
     1921 aataaaaatt gttggggtga ttctattttt tgcttgtatt ggctttcttg tttcttttgt
     1981 tttgccacaa aaatggacta gttctgctgt ggttactcct gctgagtctg ttcaatggag
     2041 tgaattaaat aaggagcttt ccaagcttca tgttctggga gtggattttg atatcaatcg
     2101 tgatagcgca tttgctctgt ttattaagaa atttcagtcc gttaattcgt tgaatgagta
     2161 tatgagatca tctccttatg ttatggagat tattaaaaag aataacatta gcgctctcga
     2221 actgcatcgt gcaattgttg agttgagtaa aaatatgaag tcgattgatg ataatgccag
     2281 taagaaaaac gacaagtcat cattgtatgt atcatggact ctgagtttta ctgctccaac
     2341 aagtaaagaa gctcacgatg tgttgtctgg gtatattaat tatgtttctt cccttgttgt
     2401 aagggatttg atggaagata taagaaataa actagaagtt aaaactaatg ttgaaaaaga
     2461 aattcttgca ctggatgaga taaaaattag aaaccagctg aatgcagata ttcgacgcct
     2521 caattattca ctggaggttg ctaatgcggc tggaataaaa aaacctgtat acagcaatgg
     2581 tcagattatg aaggatgacc cagattttcc tgtggctctc ggttctgatg gtatagcaac
     2641 taaattgaac atcaaaaaat caatcaagga tgtttcggaa ttgagtgggg agttgcgaaa
     2701 tcgtcaatat gttgtgaatc aattggttgt ggcgaaagtg ggggatgttg attttatgcc
     2761 atttcagtat caattgagcc caacgttacc ggtcagaaag gatgggccaa gtaatgccat
     2821 aattgtaatt ctttcttctg tcattggagg gatgcttgca tgtggctata tacttttacg
     2881 tcatgccatg gaggccagaa agatgagtgt gattgagtaa aagttgtgct gatgcatcat
     2941 tttataagca acttttataa aaagttcaaa ggatcttctt gagatcattc ccttacagcc
     3001 gtagtcttct actctagaaa acgaaaaaac cacctgggga ggtggttttt cgaaggttca
     3061 gtaagttggg gaacttctga accgtggtaa cagtcttgtg cgagacatgt caccaaatct
     3121 gtccttct
//
