LOCUS       NZ_CP106859             4110 bp    DNA     circular CON 08-AUG-2023
DEFINITION  Shigella flexneri strain 2aT32 plasmid pT32SS, complete sequence.
ACCESSION   NZ_CP106859
VERSION     NZ_CP106859.1
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 4110)
  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
            CP106859.1.
            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..4110
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="2aT32"
                     /db_xref="taxon:623"
                     /plasmid="pT32SS"
                     /geo_loc_name="Romania"
                     /collection_date="2000-10"
     gene            complement(join(3909..4110,1..329))
                     /locus_tag="OBG40_RS23935"
                     /old_locus_tag="OBG40_23900"
     CDS             complement(join(3909..4110,1..329))
                     /locus_tag="OBG40_RS23935"
                     /old_locus_tag="OBG40_23900"
                     /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            complement(<367..798)
                     /locus_tag="OBG40_RS23940"
                     /old_locus_tag="OBG40_23905"
                     /pseudo=""
     CDS             complement(<367..798)
                     /locus_tag="OBG40_RS23940"
                     /old_locus_tag="OBG40_23905"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            complement(1007..1330)
                     /locus_tag="OBG40_RS23945"
                     /old_locus_tag="OBG40_23910"
     CDS             complement(1007..1330)
                     /locus_tag="OBG40_RS23945"
                     /old_locus_tag="OBG40_23910"
                     /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            1395..1586
                     /locus_tag="OBG40_RS23950"
                     /old_locus_tag="OBG40_23915"
     CDS             1395..1586
                     /locus_tag="OBG40_RS23950"
                     /old_locus_tag="OBG40_23915"
                     /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            2731..3123
                     /locus_tag="OBG40_RS23955"
                     /old_locus_tag="OBG40_23920"
     CDS             2731..3123
                     /locus_tag="OBG40_RS23955"
                     /old_locus_tag="OBG40_23920"
                     /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_128567429.1"
                     /translation="MALSACFRQQLNPVVNSLLKERIIHSPKELEHDNAVIRVLQKLQI
                     QEVCNSTLWETAKQQLLQKSDGRYFAINSKHLAFPGPGESHAFCCIKYKNAIGINGNNA
                     ETQSTHYQPYPYDKVSIWGPFPHNLT"
                     /name="hypothetical protein"
     gene            complement(3669..3902)
                     /locus_tag="OBG40_RS23960"
                     /old_locus_tag="OBG40_23925"
     CDS             complement(3669..3902)
                     /locus_tag="OBG40_RS23960"
                     /old_locus_tag="OBG40_23925"
                     /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"
     Typing          complement(1674..1760)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          1771..2328
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.032"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..1017)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.87"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3566..4110)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.703"
                     /coverage="100.0"
                     /evalue="6.22e-76"
ORIGIN
        1 agataccaga gcgtcccgcc actcacggta aacaggaaaa tgaccatccc cagtaacatc
       61 atgcccgtat tccctgccag ctttaacacg tccttcctgt gctgcatcat cgcctctttc
      121 accccttccc ggtgtttttt cagtgattcc tctgtcgaag ctgtgaacag ggctatagcg
      181 tctttgattt tcgtctcgtt tgatgtcaca gccttgctta cagattcttc gagcttcctg
      241 aactcgtcgc tcagcatttt ctctgtagat tcggctctct ctttcagctt tttctcgaac
      301 tccgcgcccg tctgtaaaag attgctcata gaatgctcct ttcagtctga tattcttccc
      361 gccgttcggg tctgcaatgc tgatactgct tcgcgtcacc ctgaccactt caagccccgc
      421 ctctgtgagc gcctgaatca catcctgacg gccttttatc tccccgacat gataaagagc
      481 gtctatccac cgtgtaatgc tctcagcaag cgcctgtttc gtttccggca ggttatcagg
      541 gagagtcagc gtccggcggt tctccggggc gttcgggtca tgcagcccgt aatggtgatt
      601 caccagcgtc tgccaggcat caattctcgg cctgtctgcg cggtcgtagt acggctggag
      661 gcgttttccg gtctgtagct ccatgttcgg aatgacaaaa ttcagctcaa gccgcccctt
      721 gtcctggtgc tccacccaca gaatgctgta ctgatttttt tcgagaccgg gcatcagtac
      781 acgctcaaag ctcgccatca ctttttcacg ccctcccggc ggcagctcct tctccgcgaa
      841 cgagagaaca ccggacgtgt atttcttcgc aaatggcgtg gcatcgatga gttcccggac
      901 ttcttccgga ttaccctgaa gcaccgttgc cccttcccgg ttacgctccc ttcccagcag
      961 gtaatcaacc ggaccactgc caccgccttt tcccctggca tgaaacttaa ctatcatccc
     1021 gcgtcccctg ttccctgacg gccagacgca gccggcgcag ctcatccccg atggccatca
     1081 gtgcggccac cacctgaacc cggtcaccgg aagaccactg cccgctgttc accttcctcg
     1141 ctgcctgatt caggttattc ccgatggcgg ccagctgacg cagtaacggc ggtgccagtg
     1201 tcggcagcct cccggaacgg gcaaccggct cacccaggca gacccgccgc atccataccg
     1261 ccagctgttt accctcacag cgttccagta accgggcatg ttcatcatca gtaacccgta
     1321 tcgtgagcat cctctcgcgt ttcatcggta tcattacccc catgaacaga aatccccctt
     1381 acacggaggc atcagtgacc aaacaggaaa aaaccgccct taacatggcc cgctttatca
     1441 gaagccagac attaacgctg ctggagaagc tcaacgaact ggacgcggat gaacaggcag
     1501 acatctgtga atcgctttac gaccacgccg atgagcttta ccgcagttgc ctcgctcgct
     1561 tcggggatga cggtgaaaac ctctgacgca tgcagctccc ggcatccgct cacagataag
     1621 ctgtgagcgg atgccgggag cagacaagcc cgtcagggcg cgtcagcggg tgttagcggg
     1681 tgtcggggcg cagccatgac ccagtcacgt agcgatagcg gagtgtatac tggcttaacc
     1741 atgcggcatc agtgcggatt gtatgaaaag tgcgccatac cgggtgtgaa atgccgcaca
     1801 gatgcgtaag gagaaaatgc acgtccaggc gcttttccgc ttcctcgctc actgactcgc
     1861 tacgctcggt cgttcgactg cggcgagcgg tatctactca ctcaaaaacg aaatgctgtt
     1921 atccacagaa tcaggggata acgccggaaa gaacatgtga gcaaaagacc aggaacagga
     1981 agaaggccgc gccgatggcg tttttccata ggctccgccc ccctgacgag catcacaaaa
     2041 accgacgctc aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc
     2101 cccctggaag ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt
     2161 ccgcctttct cccttcggga agcgtggcgc tttctcatag ctcacgctgt tggtatctca
     2221 gttcggtgta ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg
     2281 accgctgcgc cttatccggt aactatcgtc ttgagtccaa cccggtaaga cacgacttaa
     2341 cgccactggc agcagccatt ggtaactgga caaggtggat tgagatatta agagttcttg
     2401 aagtggtggc ctaactgcgg ctacactaga aggacagcat ttggtatctg tgctccacca
     2461 agccagttac cttcggaaga aagagttggt agctctagat tccggcaaac aaaccaccgt
     2521 tggtagcggt ggtttttttg tttgcaggca gcagattacg cgccgcaaaa aaggatctca
     2581 agaagatctt gaatcactct atgaaaattt tgttttatag ccgtatttgt tgatgctata
     2641 agccagagac cttctatgag aatagacata tcacatcaaa cacggcatac cccgccaaac
     2701 atgcttcctc gggaacaaaa ttgtgtagca atggcattat ctgcgtgctt tagacaacaa
     2761 ctaaaccctg tggtaaacag cttattaaaa gagagaataa tacactcccc taaagaattg
     2821 gaacatgaca acgcagtaat aagagtcctg caaaaactac aaattcaaga agtttgtaac
     2881 agcacccttt gggagacagc caaacaacaa ctacttcaaa aatcggacgg aagatatttt
     2941 gccatcaatt ctaaacactt agcctttcca ggcccaggag aatctcacgc cttctgttgc
     3001 atcaaataca aaaatgcaat tggcattaac ggaaacaatg ccgaaaccca atcgacccac
     3061 taccaaccct atccctatga taaagtcagt atatggggac cattccctca caatttaacg
     3121 taatatctta attgtacgca ccgctgaaac gcgttcggcg cgatcacggc agcagacagg
     3181 taaaaatggc aacaaaccac ccgaaaaact gccgcgatcg cacccggtaa attttaacca
     3241 catgcatagc tatgcagcca tgtgaatcac gcaggaattg ccagccagag acagctgaaa
     3301 cggattttat tcatgctttc tgaagcgaag aagacgggga cctgagcggg aaaacagaag
     3361 ttcaggggaa tgagcgcgat ctggcaatag aggcaaaaca cagcgacaaa agacacacca
     3421 gaatcgcgcc cgtatgcgtt ttaactcgtt cctgtgtttt cagcaaggtc tgactgaagc
     3481 gcgttcccgg tgcccccgaa ccaaccatta tcccaaaaaa tgcaccggaa acgcgctgac
     3541 aacattttag cctgtctctg attaccatcc cagcgaaggg ccatccagtg tccgttcctg
     3601 tatttccggc tggcgttccc gttccaggaa taacgcatgt tcgcgctcct gtatcaaccg
     3661 ttcctctctt atctccagtt ctcgctgtat aactggctca agcgttctgt ctgctcgctc
     3721 aagtgcagca cctgctgact caactgcatg acccgctcgt tcagcatcgc gttgtcccgt
     3781 tgcgtaagcg aaaacatttt ctgcaattcc acgaaggcgc tctcccattc gttcagccgc
     3841 tgcatatagt cctgttgcag ctgctctaat gcgttcagca aatggctttc cagctccgtc
     3901 atgctctgtc actcctgtac cagccttacg gcattctgtt tcccgttttc catcgtccag
     3961 ttcgtttcgg ctttcatccc ctcgggcaac accagaaaac gtccgttgct cccctcgtga
     4021 taacgcacgc cccatgtctt cgcgttcagc ttctccagac tctcgttctg cttcctgatt
     4081 tcttccaggt tcgcctgtat catcccgcca
//
