LOCUS       NZ_CP085205             4042 bp    DNA     linear   CON 07-JUN-2024
DEFINITION  Shigella flexneri strain P099 plasmid p003.
ACCESSION   NZ_CP085205
VERSION     NZ_CP085205.1
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 4042)
  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  JOURNAL   Unpublished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 4042)
  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
            CP085205.1.
            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..4042
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="P099"
                     /isolation_source="Oral swab"
                     /host="Macaca mulatta"
                     /db_xref="taxon:623"
                     /plasmid="p003"
                     /geo_loc_name="USA"
                     /collection_date="2017-11-17"
     gene            <1..133
                     /locus_tag="IUX27_RS24815"
                     /old_locus_tag="IUX27_24840"
                     /pseudo=""
     CDS             <1..133
                     /locus_tag="IUX27_RS24815"
                     /old_locus_tag="IUX27_24840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=2
                     /transl_table=11
                     /product="mobilization protein"
                     /name="mobilization protein"
     gene            140..373
                     /locus_tag="IUX27_RS24820"
                     /old_locus_tag="IUX27_24845"
     CDS             140..373
                     /locus_tag="IUX27_RS24820"
                     /old_locus_tag="IUX27_24845"
                     /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(919..1311)
                     /locus_tag="IUX27_RS24825"
                     /old_locus_tag="IUX27_24850"
     CDS             complement(919..1311)
                     /locus_tag="IUX27_RS24825"
                     /old_locus_tag="IUX27_24850"
                     /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(1628..1786)
                     /locus_tag="IUX27_RS25080"
     CDS             complement(1628..1786)
                     /locus_tag="IUX27_RS25080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005093880.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="hypothetical protein"
     gene            complement(2388..2579)
                     /locus_tag="IUX27_RS24830"
                     /old_locus_tag="IUX27_24855"
     CDS             complement(2388..2579)
                     /locus_tag="IUX27_RS24830"
                     /old_locus_tag="IUX27_24855"
                     /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            2644..2967
                     /locus_tag="IUX27_RS24835"
                     /old_locus_tag="IUX27_24860"
     CDS             2644..2967
                     /locus_tag="IUX27_RS24835"
                     /old_locus_tag="IUX27_24860"
                     /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            3176..>3607
                     /locus_tag="IUX27_RS24840"
                     /pseudo=""
     CDS             3176..>3607
                     /locus_tag="IUX27_RS24840"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            3645..>4042
                     /locus_tag="IUX27_RS24845"
                     /old_locus_tag="IUX27_24870"
     CDS             3645..>4042
                     /locus_tag="IUX27_RS24845"
                     /old_locus_tag="IUX27_24870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_248501244.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLSDEFRKLEESVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNESLEKLNA"
                     /name="MbeB family mobilization protein"
     Typing          2283..2369
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(1715..2272)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.853"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          5..477
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.203"
                     /coverage="98.0"
                     /evalue="6.24e-68"
     Typing          2958..4009
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.721"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 gaagacatgg ggcgtgcgtt atcacgaggg gagcaacgga cgttttctgg tgttgcccga
       61 ggggatgaaa gccgaaacga actggacgat ggaaaacggg aaacagaatg ccgtaaggct
      121 ggtacaggag tgacagagca tgacggagct ggaaagccat ttgctgaacg cattagagca
      181 gctgcaacag gactatatgc agcggctgaa cgaatgggag agcgccttcg tggaattgca
      241 gaaaatgttt tcgcttacgc aacgggacaa cgcgatgctg aacgagcggg tcatgcagtt
      301 gagtcagcag gtgctgcact tgagcgagca gacagaacgc ttgagccagt tatacagcga
      361 gaactggaga taagagagga acggttgata caggagcgcg aacatgcgtt attcctggaa
      421 cgggaacgcc agccggaaat acaggaacgg acactggatg gcccttcgct gggatggtaa
      481 tcagagacag gctaaaatgt tgtcagcgcg tttccggtgc attttttggg ataatggttg
      541 gctcgggggc accgggaacg cgcttcagtc agaccttgct gaaaacacag gaacgagtta
      601 aaacgcatac gggcgcgatt ctggtgtgtc ttttgtcgct gtgttttgcc tctattgcca
      661 gatcgcgctc attcccctga acttctgttt tcccgctcag gtccccgtct tcttcgcttc
      721 cgaaagcatg aataaaatcc gtttcagctg tctctggctg gcaattcctg cgtgattcac
      781 atggctgcat agctatgcat gtggttaaaa tttaccgggt gcgatcgcgg cagtttttcg
      841 ggtggtttgt tgccattttt acctgtctgc tgccgtgatc gcgccgaacg cgtttcagcg
      901 gtgcgtacaa ttaagatatt acgttaaatt gtgagggaat ggtccccata tactgacttt
      961 atcataggga tagggttggt agtgggtcga ttgggtttcg gcattgtttc cgttaatgcc
     1021 aattgcattt ttgtatttga tgcaacagaa ggcgtgagat tctcctgggc ctggaaaggc
     1081 taagtgttta gaattgatgg caaaatatct tccgtccgat ttttgaagta gttgttgttt
     1141 ggctgtctcc caaagggtgc tgttacaaac ttcttgaatt tgtagttttt gcaggactct
     1201 tattactgcg ttgtcatgtt ccaattcttt aggggagtgt attattctct cttttaataa
     1261 gctgtttacc acagggttta gttgttgtct aaagcacgca gataatgcca ttgctacaca
     1321 attttgttcc cgaggaagca tgtttggcgg ggtatgccgt gtttgatgtg atatgtctat
     1381 tctcatagaa ggtctctggc ttatagcatc aacaaatacg gctataaaac aaaattttca
     1441 tagagtgatt caagatcttc ttgagatcct tttttgcggc gcgtaatctg ctgcctgcaa
     1501 acaaaaaaac caccgctacc aacggtggtt tgtttgccgg aatctagagc taccaactct
     1561 ttcttccgaa ggtaactggc ttggtggagc acagatacca aatgctgtcc ttctagtgta
     1621 gccgcagtta ggccaccact tcaagaactc ttaatatctc aatccacctt gtccagttac
     1681 caatggctgc tgccagtggc gttaagtcgt gtcttaccgg gttggactca agacgatagt
     1741 taccggataa ggcgcagcgg tcgggctgaa cggggggttc gtgcacacag cccagcttgg
     1801 agcgaacgac ctacaccgaa ctgagatacc aacagcgtga gctatgagaa agcgccacgc
     1861 ttcccgaagg gagaaaggcg gacaggtatc cggtaagcgg cagggtcgga acaggagagc
     1921 gcacgaggga gcttccaggg ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc
     1981 acctctgact tgagcgtcgg tttttgtgat gctcgtcagg ggggcggagc ctatggaaaa
     2041 acgccatcgg cgtggccttc ttcctgttcc tggtcttttg ctcacatgtt ctttccggcg
     2101 ttatcccctg attctgtgga taacagcatt tcgtttttga gtgagtagat accgctcgcc
     2161 gcagtcgaac gaccgagcgt agcgagtcag tgagcgagga agcggaaaag cgcctggacg
     2221 tgcattttct ccttacgcat ctgtgcggca tttcacaccc ggtatggcgc acttttcata
     2281 caatccgcac tgatgccgca tggttaagcc agtatacact ccgctatcgc tacgtgactg
     2341 ggtcatggct gcgccccgac acccgctaac acccgctgac aagcccgtca gaggttttca
     2401 ccgtcatccc cgaagcgagc gaggcaactg cggtaaagct catcggcgtg gtcgtaaagc
     2461 gattcacaga tgtctgcctg ttcatccgcg tccagttcgt tgagcttctc cagcagcgtt
     2521 aatgtctggc ttctgataaa gcgggccatg ttaagggcgg ttttttcctg tttggtcact
     2581 gatgcctccg tgtaaggggg atttctgttc atgggggtaa tgataccgat gaaacgcgag
     2641 aggatgctca cgatacgggt tactgatgat gaacatgccc ggttactgga acgctgtgag
     2701 ggtaaacagc tggcggtatg gatgcggcgg gtctgcctgg gtgagccggt tgcccgttcc
     2761 gggaggctgc cgacactggc accgccgtta ctgcgtcagc tggccgccat cgggaataac
     2821 ctgaatcagg cagcgaggaa ggtgaacagc gggcagtggt cttccggtga ccgggttcag
     2881 gtggtggccg cactgatggc catcggggat gagctgcgcc ggctgcgtct ggccgtcagg
     2941 gaacagggga cgcgggatga tagttaagtt tcatgccagg ggaaaaggcg gtggcagtgg
     3001 tccggttgat tacctgctgg gaagggagcg taaccgggaa ggggcaacgg tgcttcaggg
     3061 taatccggaa gaagtccggg aactcatcga tgccacgcca tttgcgaaga aatacacgtc
     3121 cggtgttctc tcgttcgcgg agaaggagct gccgccggga gggcgtgaaa aagtgatggc
     3181 gagctttgag cgtgtactga tgcccggtct cgaaaaaaat cagtacagca ttctgtgggt
     3241 ggagcaccag gacaaggggc ggcttgagct gaattttgtc attccgaaca tggagctaca
     3301 gaccggaaaa cgcctccagc cgtactacga ccgcgcagac aggccgagaa ttgatgcctg
     3361 gcagacgctg gtgaatcacc attacgggct gcatgacccg aacgccccgg agaaccgccg
     3421 gacgctgact ctccctgata acctgccgga aacgaaacag gcgcttgctg agagcattac
     3481 acggtggata gacgctcttt atcatgtcgg ggagataaaa ggccgtcagg atgtgattca
     3541 ggcgctcaca gaggcggggc ttgaagtggt cagggtgacg cgaagcagta tcagcattgc
     3601 agacccgaac ggcgggaaga atatcagact gaaaggagca ttctatgagc aatcttttac
     3661 agacgggcgc ggagttcgag aaaaagctga aagagagagc cgaatctaca gagaaaatgc
     3721 tgagcgacga gttcaggaag ctcgaagaat ctgtaagcaa ggctgtgaca tcaaacgaga
     3781 cgaaaatcaa agacgctata gccctgttca cagcttcgac agaggaatca ctgaaaaaac
     3841 atcgggaagg ggtgaaagag gcgatgatgc agcacaggaa ggacgtgtta aagctggcag
     3901 ggaatacggg catgatgtta ctggggatgg tcattttcct gtttaccgtg agtggcggga
     3961 cgctctggta tcttggcggg atgatacagg cgaacctgga agaaatcagg aagcagaacg
     4021 agagtctgga gaagctgaac gc
//
