LOCUS       NZ_CP106860             3179 bp    DNA     circular CON 08-AUG-2023
DEFINITION  Shigella flexneri strain 2aT32 plasmid pT32S4, complete sequence.
ACCESSION   NZ_CP106860
VERSION     NZ_CP106860.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31018853
            Assembly: GCF_030582455.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3179)
  AUTHORS   Wang,Y. and Liu,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-SEP-2022) Department of Microbial Engineering, Beijing
            Institute of Biotechnology, Dongdajie, Beijing, Beijing 100071,
            China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 26-SEP-2000
            Assembly Method                   :: SOAPdenovo v. 09-2022
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Illumina HiSeq; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/02/2023 17:18:46
            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)                     :: 4,979
            CDSs (total)                      :: 4,851
            Genes (coding)                    :: 4,124
            CDSs (with protein)               :: 4,124
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 99
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 727
            CDSs (without protein)            :: 727
            Pseudo Genes (ambiguous residues) :: 0 of 727
            Pseudo Genes (frameshifted)       :: 258 of 727
            Pseudo Genes (incomplete)         :: 425 of 727
            Pseudo Genes (internal stop)      :: 168 of 727
            Pseudo Genes (multiple problems)  :: 122 of 727
            Pseudo Genes (short protein)      :: 5 of 727
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP106860.1.
            Bacteria and source DNA available from Chunjie Liu.
            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..3179
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="2aT32"
                     /db_xref="taxon:623"
                     /plasmid="pT32S4"
                     /geo_loc_name="Romania"
                     /collection_date="2000-10"
     gene            270..1379
                     /gene="wzz(fepE)"
                     /locus_tag="OBG40_RS23965"
                     /old_locus_tag="OBG40_23930"
     CDS             270..1379
                     /gene="wzz(fepE)"
                     /locus_tag="OBG40_RS23965"
                     /old_locus_tag="OBG40_23930"
                     /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            complement(2404..2568)
                     /locus_tag="OBG40_RS23970"
                     /old_locus_tag="OBG40_23935"
     CDS             complement(2404..2568)
                     /locus_tag="OBG40_RS23970"
                     /old_locus_tag="OBG40_23935"
                     /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"
     Typing          2238..2324
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          2638..2736
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2861..3118
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(1687..2213)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 ctcatgggca ctgtatgcgc ccaaaccgat cgtcattcac tttcatgcat agctatgcag
       61 tgagctgaaa gcgatcctga cgcatttttc cggtttaccc cggggaaaac atctcttttt
      121 gcggtgtttg cggcagaatc gcgttcagcg cgttttagcg gtgcgcgcaa taaaatgtta
      181 tgttaaatgt ctgctgaatg gtttttaggt tttttcctaa catatgatag aataaaaaaa
      241 ccatatgtta atatattgtg tttttttcaa tgaaaatctc aaaggtctct gacgaacatt
      301 tttctaatta caacatgttg ccgaatggta atgaagaaat tgaccttttt ggcttgatta
      361 gcgttttatg ggcagcaaaa ataaaaattg ttggggtgat tctatttttt gcttgtattg
      421 gctttcttgt ttcttttgtt ttgccacaaa aatggactag ttctgctgtg gttactcctg
      481 ctgagtctgt tcaatggagt gaattaaata aggagctttc caagcttcat gttctgggag
      541 tggattttga tatcaatcgt gatagcgcat ttgctctgtt tattaagaaa tttcagtccg
      601 ttaattcgtt gaatgagtat atgagatcat ctccttatgt tatggagatt attaaaaaga
      661 ataacattag cgctctcgaa ctgcatcgtg caattgttga gttgagtaaa aatatgaagt
      721 cgattgatga taatgccagt aagaaaaacg acaagtcatc attgtatgta tcatggactc
      781 tgagttttac tgctccaaca agtaaagaag ctcacgatgt gttgtctggg tatattaatt
      841 atgtttcttc ccttgttgta agggatttga tggaagatat aagaaataaa ctagaagtta
      901 aaactaatgt tgaaaaagaa attcttgcac tggatgagat aaaaattaga aaccagctga
      961 atgcagatat tcgacgcctc aattattcac tggaggttgc taatgcggct ggaataaaaa
     1021 aacctgtata cagcaatggt cagattatga aggatgaccc agattttcct gtggctctcg
     1081 gttctgatgg tatagcaact aaattgaaca tcaaaaaatc aatcaaggat gtttcggaat
     1141 tgagtgggga gttgcgaaat cgtcaatatg ttgtgaatca attggttgtg gcgaaagtgg
     1201 gggatgttga ttttatgcca tttcagtatc aattgagccc aacgttaccg gtcagaaagg
     1261 atgggccaag taatgccata attgtaattc tttcttctgt cattggaggg atgcttgcat
     1321 gtggctatat acttttacgt catgccatgg aggccagaaa gatgagtgtg attgagtaaa
     1381 agttgtgctg atgcatcatt ttataagcaa cttttataaa aagttcaaag gatcttcttg
     1441 agatcattcc cttacagccg tagtcttcta ctctagaaaa cgaaaaaacc acctggggag
     1501 gtggtttttc gaaggttcag taagttgggg aacttctgaa ccgtggtaac agtcttgtgc
     1561 gagacatgtc accaaatctg tccttctagt gtagcctcag taaggctgcc acttcaagaa
     1621 ctctcaatac atctctcgca catcctgttt accagtggcc gctgccaatg gcgttaagtc
     1681 gtgtcttacc gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg
     1741 aacggggggt tcgtgcacac agcccagctt ggagcgaact gcctacccgg aactgagtgt
     1801 caggcgtgga atgagacgaa cgcggccata acagcggaat gacaccggta aaccgaaagg
     1861 caggaacagg agagcgcacg agggagccac cagggggaaa cgcctggtat ctttaagtcc
     1921 tgtcgggttt cgccacctct gacttgagcg tcgatttttg tgatgctcgt caggggggcg
     1981 gagcctatgg aaaaacgcca ccggcgcggc cttttttcgg ggcctctttt ttgctcacat
     2041 gttttttctg gtgttatccc ctgattctgt ggataaccgt atatccgtct ttgcgtgagc
     2101 agacaccgct cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga
     2161 agagcgccgg aagctgcatt ttctccttac gtatctgtgc agcatttcac acctcatatg
     2221 tcgctgttct ctcaccatct gctctgccgc ctcataatta agccagtata cactccgtta
     2281 tcgctacgtg actgggtcat ggctgcgccc cgacacccgc taaaaccccc tgacgcgccc
     2341 tgacgggctt gtctgctgac gaaaacgccc acgggaaagc cgtgaccgcc tccgtcagct
     2401 tcgttatgtt cctgtttcac tttcggcctc aaagcgaatc tggatgctgt tctggagttc
     2461 ttctgcgagt tcgtgcagtc gtttgcacat ggccgcctgt tcgtcggcat ccagagcatc
     2521 cagtttttca agcagtgtca ggctctggct tttgatacat cgcgccatat tcagcgcagt
     2581 ttgttgttat ttgttcacct tccgttgttc tccgtcagtt ccgggtgtcg ggggggggac
     2641 cctgagcagg tggtaattgt aagacgttgc gggcgacggt attacaattg cacatcctgt
     2701 cctgtttctt taggacgtat catggcacag catatcaact gataaataat ccctgtgcag
     2761 tgcagccgct gttgcataaa atttcgctct gcgtcgagtg tttcttaatc aataattccg
     2821 ctgatactcc ggaaaaacgc gagtctgttc tcatgcctga aatgcccaca ccccacgcaa
     2881 aaacaagttt ttgctgattt ttctttataa atagagagtt atgacaaatt agttcttctt
     2941 gctctctttg tgatatttaa aaaagcggtg tcggcgcggt gttgtagctg cgccaacacc
     3001 gctttttagg ggtggtactg actattttca taaaaaaaac attatcttat attaggggtg
     3061 ctgctagcgg cgcggtgtgt ttttttacag gacgcccctg ggggcgctgc taggggtgtc
     3121 tgttcagata tgtagcaatg agtcagggat tcacgaactg aaaatgtccg aaaatgtgt
//
