LOCUS       NZ_CP042979             3990 bp    DNA     circular CON 09-JUL-2023
DEFINITION  Shigella flexneri Y strain PE577 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP042979
VERSION     NZ_CP042979.1
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 3990)
  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  JOURNAL   Unpublished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 3990)
  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
            CP042979.1.
            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..3990
                     /organism="Shigella flexneri Y"
                     /mol_type="genomic DNA"
                     /strain="PE577"
                     /serotype="Y"
                     /host="Homo sapiens"
                     /db_xref="taxon:424720"
                     /plasmid="unnamed1"
                     /geo_loc_name="Australia: Adelaide"
                     /collection_date="1990"
                     /note="clinical sample"
     gene            complement(255..446)
                     /locus_tag="FW259_RS00030"
                     /old_locus_tag="FW259_00030"
     CDS             complement(255..446)
                     /locus_tag="FW259_RS00030"
                     /old_locus_tag="FW259_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_149617738.1"
                     /translation="MTRQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLYDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            511..834
                     /locus_tag="FW259_RS00035"
                     /old_locus_tag="FW259_00035"
     CDS             511..834
                     /locus_tag="FW259_RS00035"
                     /old_locus_tag="FW259_00035"
                     /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            1043..>1474
                     /locus_tag="FW259_RS23975"
                     /old_locus_tag="FW259_00040"
                     /pseudo=""
     CDS             1043..>1474
                     /locus_tag="FW259_RS23975"
                     /old_locus_tag="FW259_00040"
                     /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            1512..2042
                     /locus_tag="FW259_RS00045"
                     /old_locus_tag="FW259_00045"
     CDS             1512..2042
                     /locus_tag="FW259_RS00045"
                     /old_locus_tag="FW259_00045"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_000067501.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLSDEFRKLEESVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNESLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLAQE"
                     /name="MbeB family mobilization protein"
     gene            2049..2282
                     /locus_tag="FW259_RS00050"
                     /old_locus_tag="FW259_00050"
     CDS             2049..2282
                     /locus_tag="FW259_RS00050"
                     /old_locus_tag="FW259_00050"
                     /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(2828..3220)
                     /locus_tag="FW259_RS00060"
                     /old_locus_tag="FW259_00060"
     CDS             complement(2828..3220)
                     /locus_tag="FW259_RS00060"
                     /old_locus_tag="FW259_00060"
                     /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"
     Typing          150..236
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(3587..3990)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.543"
                     /coverage="94.0"
                     /evalue="0.0"
     Typing          825..2386
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.505"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttttgagtg agtagatacc gctcgccgca gtcgaacgac cgagcgtagc gagtcagtga
       61 gcgaggaagc ggaaaagcgc ctggacgtgc attttctcct tacgcatctg tgcggcattt
      121 cacacccggt atggcgcact tttcatacaa tccgcactga tgccgcatgg ttaagccagt
      181 atacactccg ctatcgctac gtgactgggt catggctgcg ccccgacacc cgctaacacc
      241 cgctgacaag cccgtcagcg gttttcaccg tcatccccga agcgagcgag gcaactgcgg
      301 taaagctcat cggcgtggtc gtaaagcgat tcacagatgt ctgcctgttc atccgcgtcc
      361 agttcgttga gcttctccag cagcgttaat gtctggcttc tgataaagcg ggccatgtta
      421 agggcggttt tttcctgtct ggtcactgat gcctccgtgt aagggggatt tctgttcatg
      481 ggggtaatga taccgatgaa acgcgagagg atgctcacga tacgggttac tgatgatgaa
      541 catgcccggt tactggaacg ctgtgagggt aaacagctgg cggtatggat gcggcgggtc
      601 tgcctgggtg agccggttgc ccgttccggg aggctgccga cactggcacc gccgttactg
      661 cgtcagctgg ccgccatcgg gaataacctg aatcaggcag cgaggaaggt gaacagcggg
      721 cagtggtctt ccggtgaccg ggttcaggtg gtggccgcac tgatggccat cggggatgag
      781 ctgcgccggc tgcgtctggc cgtcagggaa caggggacgc gggatgatag ttaagtttca
      841 tgccagggga aaaggcggtg gcagtggtcc ggttgattac ctgctgggaa gggagcgtaa
      901 ccgggaaggg gcaacggtgc ttcagggtaa tccggaagaa gtccgggaac tcatcgatgc
      961 cacgccattt gcgaagaaat acacgtccgg tgttctctcg ttcgcggaga aggagctgcc
     1021 gccgggaggg cgtgaaaaag tgatggcgag ctttgagcgt gtactgatgc ccggtctcga
     1081 aaaaaatcag tacagcattc tgtgggtgga gcaccaggac aaggggcggc ttgagctgaa
     1141 ttttgtcatt ccgaacatgg agctacagac cggaaaacgc ctccagccgt actacgaccg
     1201 cgcagacagg ccgagaattg atgcctggca gacgctggtg aatcaccatt acgggctgca
     1261 tgacccgaac gccccggaga accgccggac gctgactctc cctgataacc tgccggaaac
     1321 gaaacaggcg cttgctgaga gcattacacg gtggatagac gctctttatc atgtcgggga
     1381 gataaaaggc cgtcaggatg tgattcaggc gctcacagag gcggggcttg aagtggtcag
     1441 ggtgacgcga agcagtatca gcattgcaga cccgaacggc gggaagaata tcagactgaa
     1501 aggagcattc tatgagcaat cttttacaga cgggcgcgga gttcgagaaa aagctgaaag
     1561 agagagccga atctacagag aaaatgctga gcgacgagtt caggaagctc gaagaatctg
     1621 taagcaaggc tgtgacatca aacgagacga aaatcaaaga cgctatagcc ctgttcacag
     1681 cttcgacaga ggaatcactg aaaaaacacc gggaaggggt gaaagaggcg atgatgcagc
     1741 acaggaagga cgtgttaaag ctggcaggga atacgggcat gatgttactg gggatggtca
     1801 ttttcctgtt taccgtgagt ggcgggacgc tctggtatct tggcgggatg atacaggcga
     1861 acctggaaga aatcaggaag cagaacgaga gtctggagaa gctgaacgcg aagacatggg
     1921 gcgtgcgtta tcacgagggg agcaacggac gttttctggt gttgcccgag gggatgaaag
     1981 ccgaaacgaa ctggacgatg gaaaacggga aacagaatgc cgtaaggctg gcacaggagt
     2041 gacagagcat gacggagctg gaaagccatt tgctgaacgc attagagcag ctgcaacagg
     2101 actatatgca gcggctgaac gaatgggaga gcgccttcgt ggaattgcag aaaatgtttt
     2161 cgcttacgca acgggacaac gcgatgctga acgagcgggt catgcagttg agtcagcagg
     2221 tgctgcactt gagcgagcag acagaacgct tgagccagtt atacagcgag aactggagat
     2281 aagagaggaa cggttgatac aggagcgcga acatgcgtta ttcctggaac gggaacgcca
     2341 gccggaaata caggaacgga cactggatgg cccttcgctg ggatggtaat cagagacagg
     2401 ctaaaatgtt gtcagcgcgt ttccggtgca ttttttggga taatggttgg ttcgggggca
     2461 ccgggaacgc gcttcagtca gaccttgctg aaaacacagg aacgagttaa aacgcatacg
     2521 ggcgcgattc tggtgtgtct tttgtcgctg tgttttgcct ctattgccag atcgcgctca
     2581 ttcccctgaa cttctgtttt cccgctcagg tccccgtctt cttcgcttcc gaaagcatga
     2641 ataaaatccg tttcagctgt ctctggctgg caattcctgc gtgattcaca tggctgcata
     2701 gctatgcatg tggttaaaat ttaccgggtg cgatcgcggc agtttttcgg gtggtttgtt
     2761 gccattttta cctgtctgct gccgtgatcg cgccgaacgc gtttcagcgg tgcgtacaat
     2821 taagatatta cgttaaattg tgagggaatg gtccccatat actgacttta tcatagggat
     2881 agggttggta gtgggtcgat tgggtttcgg cattgtttcc gttaatgcca attgcatttt
     2941 tgtatttgat gcaacagaag gcgtgagatt ctcctgggcc tggaaaggct aagtgtttag
     3001 aattgatggc aaaatatctt ccgtccgatt tttgaagtag ttgttgtttg gctgtctccc
     3061 aaagggtgct gttacaaact tcttgaattt gtagtttttg caggactctt attactgcgt
     3121 tgtcatgttc caattcttta ggggagtgta ttattctctc ttttaataag ctgtttacca
     3181 cagggtttag ttgttgtcta aagcacgcag ataatgccat tgctacacaa ttttgttccc
     3241 gaggaagcat gtttggcggg gtatgccgtg tttgatgtga tatgtctatt ctcatagaag
     3301 gtctctggct tatagcatca acaaatacgg ctataaaaca aaattttcat agagtgattc
     3361 aagatcttct tgagatcctt ttttgcggcg cgtaatctgc tgcctgcaaa caaaaaaacc
     3421 accgctacca acggtggttt gtttgccgga atctagagct accaactctt tcttccgaag
     3481 gtaactggct tggtggagca cagataccaa atgctgtcct tctagtgtag ccgcagttag
     3541 gccaccactt caagaactct taatatctca atccaccttg tccagttacc aatggctgct
     3601 gccagtggcg ttaagtcgtg tcttaccggg ttggactcaa gacgatagtt accggataag
     3661 gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc
     3721 tacaccgaac tgagatacca acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg
     3781 agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag
     3841 cttccagggg gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca cctctgactt
     3901 gagcgtcggt ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa cgccatcggc
     3961 gcggccttct tcctgttcct ggtcttttgc
//
