LOCUS       NZ_CP053757             5219 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain 506 plasmid pMHMC-006, complete sequence.
ACCESSION   NZ_CP053757
VERSION     NZ_CP053757.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07663113
            Assembly: GCF_013201485.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5219)
  AUTHORS   Hoffmann,M., Sanchez,M., Worley,J. and Bry,L.
  TITLE     clinical or host associated isolate for Shigella sonnei
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5219)
  AUTHORS   Hoffmann,M., Sanchez,M., Worley,J. and Bry,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-MAY-2020) CFSAN, US FDA, 5001 Campus Drive, College
            Park, MD 20740, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAR-2020
            Assembly Method                   :: HGAP v. 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 445.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013201485.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 06:48:10
            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)                     :: 5,497
            CDSs (total)                      :: 5,365
            Genes (coding)                    :: 4,629
            CDSs (with protein)               :: 4,629
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 736
            CDSs (without protein)            :: 736
            Pseudo Genes (ambiguous residues) :: 0 of 736
            Pseudo Genes (frameshifted)       :: 208 of 736
            Pseudo Genes (incomplete)         :: 523 of 736
            Pseudo Genes (internal stop)      :: 128 of 736
            Pseudo Genes (multiple problems)  :: 117 of 736
            Pseudo Genes (short protein)      :: 3 of 736
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053757.1.
            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..5219
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="506"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pMHMC-006"
                     /geo_loc_name="USA:Boston"
                     /collection_date="2017"
                     /collected_by="Brigham and Women's Hospital"
     gene            join(4907..5219,1..11)
                     /locus_tag="COO90_RS27225"
                     /old_locus_tag="COO90_27040"
     CDS             join(4907..5219,1..11)
                     /locus_tag="COO90_RS27225"
                     /old_locus_tag="COO90_27040"
                     /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_254103236.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGGPVARSGGVPAL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>651
                     /locus_tag="COO90_RS27230"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="COO90_RS27230"
                     /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            689..1219
                     /locus_tag="COO90_RS27235"
                     /old_locus_tag="COO90_27050"
     CDS             689..1219
                     /locus_tag="COO90_RS27235"
                     /old_locus_tag="COO90_27050"
                     /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_015386306.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNENLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            1226..1459
                     /locus_tag="COO90_RS27240"
                     /old_locus_tag="COO90_27055"
     CDS             1226..1459
                     /locus_tag="COO90_RS27240"
                     /old_locus_tag="COO90_27055"
                     /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_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2004..2300)
                     /locus_tag="COO90_RS27245"
                     /old_locus_tag="COO90_27060"
     CDS             complement(2004..2300)
                     /locus_tag="COO90_RS27245"
                     /old_locus_tag="COO90_27060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047647.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            2512..2709
                     /locus_tag="COO90_RS27250"
                     /old_locus_tag="COO90_27065"
     CDS             2512..2709
                     /locus_tag="COO90_RS27250"
                     /old_locus_tag="COO90_27065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            2727..3011
                     /locus_tag="COO90_RS27255"
                     /old_locus_tag="COO90_27070"
     CDS             2727..3011
                     /locus_tag="COO90_RS27255"
                     /old_locus_tag="COO90_27070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(3075..3464)
                     /locus_tag="COO90_RS27260"
                     /old_locus_tag="COO90_27075"
     CDS             complement(3075..3464)
                     /locus_tag="COO90_RS27260"
                     /old_locus_tag="COO90_27075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(3870..3983)
                     /locus_tag="COO90_RS27575"
     CDS             complement(3870..3983)
                     /locus_tag="COO90_RS27575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            complement(4651..4842)
                     /locus_tag="COO90_RS27265"
                     /old_locus_tag="COO90_27080"
     CDS             complement(4651..4842)
                     /locus_tag="COO90_RS27265"
                     /old_locus_tag="COO90_27080"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4479..4566
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          complement(3912..4465)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.099"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2..1563
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.616"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4875..5218
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.783"
                     /coverage="97.0"
                     /evalue="1.35e-64"
ORIGIN
        1 atgatagtta agtttcatgc ccggggaaaa ggtggtggca gtggtccggt tgattacctg
       61 ctgggaaggg agcgtaaccg ggaaggggca acggtgcttc agggtaatcc ggaagaagta
      121 cgggaactca tcgatgccac gccatttgcg aagaaataca cgtccggtgt gctgtcgttc
      181 gcggagaagg agctgccacc gggaggacgt gaaaaggtga tggcgagctt tgagcgtgta
      241 ctgatgcccg gtctcgaaaa aaatcagtac agcatcctgt gggtggagca ccaggacaag
      301 ggacggcttg agctgaattt tgtcattccg aacatggagc tacagaccgg aaaacgcctc
      361 cagccgtact acgaccgggc agacaggccg agaattgatg cctggcagac gctggtgaat
      421 caccattacg ggctgcatga ccccaacgcc ccggagaacc gccggatact gactctctct
      481 gataacctgc cggaaacgaa acaggcgctt gcagagagcg tcacacgcgg gatagacgct
      541 ctttatcatg tcggggagat aaaaggccgt caggatgtga ttcaggcgct cacagaggca
      601 gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggtggg
      661 aagaatatca ggctgaaagg agcattttat gagcaatctt ttacagacgg gcgcggagtt
      721 cgagaaaaag ctgaaagaga gagccgaatc tacagagaca atactgaacg acgagttcag
      781 gaagctcgaa aaatctgtaa gcaaggctgt gacatcaaac gagacgaaaa tcaaagacgc
      841 tatagccctg ttcacagctt cgacagagga atcactgaaa aaacaccggg aaggggtgaa
      901 agaggcgatg atgcagcaca ggaaggacgt gttaaagctg gcagggaata cgggcatgat
      961 gttactgggg atggtcattt tcctgtttac cgtgagtggc gggacgctct ggtatcttgg
     1021 cgggatgata caggcgaacc tggaagaaat caggaagcag aacgagaatc tggagaagct
     1081 gaacgcgaag acatggggcg tgcgttatca cgaggggagc aacggacgtt ttctggtgtt
     1141 gcccgagggg atgaaagccg aaacgaactg gacgatggaa aacgggaaac agaatgccgt
     1201 aaggctggta caggagtaac agagcatgac ggagctggaa agacatttgc tgaacgcatt
     1261 agagcaactg caacaggact atatgcagcg gctgaacgaa tgggagagcg ccttcgtgga
     1321 attgcagaaa atgttttcgc ttacgcaacg ggacaacgcg atgctgaacg agcgggtcat
     1381 gcagttgagt cagcaggtgc agcacttgag cgagcagaca gaacgcttga gccagttata
     1441 cagcgagaac aggagataag ggacgaacgg ctgatacagg aacgcgaaca tgcgttatcc
     1501 ctggagcgtg agcgccagct ggaaatacag gaacggacac tggatggccc ttcgctggga
     1561 tggtaatcag agacaggcta aaatgttgtc agcgcgtttc cggtgcattt tttgggataa
     1621 tggttggttc gggggcaccg ggaacgcgct tcagtcagac cttgctgaaa acacaggaac
     1681 gcgttaaaac gcatacgggc gcgattctgg tgtgtctttt gttgctgtgt tttgcctcta
     1741 ttgccagatc gcgctcattc ccctgaactt ctgttttccc gctccggtcc ccgtcttctt
     1801 cgcttccgaa agcatgaaaa aaatccgttt cagctgtctc tggctggcaa ttcctgcatg
     1861 attcacatag ctgcatagct atgcatgtgg ttaaaattta ccgggtacga tcgcggcagt
     1921 ttttcgggtg gtttgttgcc atttttacct gtctgctgcc gtgatcgcgc cgaacgcgtt
     1981 tcagcggtgc gtacaataag tgattatggt aaatcaccct tccaggcgtt cagcccttct
     2041 tccggttttt ttccgttcag gaatttacgg gcgagacgaa tgcgtcttgc ctggtaaatc
     2101 gcatcgtagg cctgtgactg tcccacaccg ttactgattt cactgaccag atggcgcagg
     2161 tcggcctgtg tcagtgtgta aacgtgtttc tggatgaggt cacgggctgt ccgctcttcg
     2221 tatccggcag cgataagtgc agccagcagg cgtttgtctg ttttgctcag tcggtggcga
     2281 ccagattttg ttttgctcac gttatctcct ctctgttttt tctcctgatg ttatccggtg
     2341 ctgtttttct gctgcgaatc ttcccttcct gatttttata agggtgattc agatcacaaa
     2401 aatgaaaatt catatcattg acaggaaaaa taatgcggcg taatttatac tgtatataaa
     2461 actagtgttt atatatacag tatattctgt gtaaataaag ggagggataa aatgaaagaa
     2521 gaaaaagtat tgcttcaccg tttcttattt gtagttagga ataagaatgg ttgtgaacta
     2581 tcatgttcgg cagaccttat gggaacaagg gatgatgttt ataagtattt ctctgattct
     2641 gttagtgggc tagatgttga gcttatagat gtttcttgcg agagtgaatg ggaagaacat
     2701 tcgcattgaa ctaatcagga gattatatga tttctcaaaa tgtttgggct cctcctttct
     2761 tttttggtcc ttgggttgaa cttgaaaatc atactggtga tatcgcgtac actgtctatt
     2821 ttgatacatt gtctaatgta cccggtccat ttattgcttt tatctggtat gcccctaatg
     2881 ggccaagaac agttaacgtt attggtccag catcttatca gatctcttgc aagggcgctg
     2941 gtgttgataa aattaaattt aaaagtgtca gtgggacagg gcagattatt catgtataca
     3001 ctaccttata ataagagctg aatagatata atcctgccta agctatacct taagcaggat
     3061 tatatctatt aatattattt tgaatatgct tttatgattt ccatcactgt tgtttcatcg
     3121 ttcacaggtt gataataatg ggttggattt agtgcagaat gaatgattgc aggttgggat
     3181 attacttttc catcaaaata tgaaatcagg ggtttcccta tatttttact agttatttcg
     3241 tttagttttt tcttacataa actatctgtg tttacttcta ttatgacgcc tttgtttttt
     3301 tctgattggg aagggtacat tttaagtatg caatatttat tcagaatgat gctgtcacca
     3361 ccaactttgt aaacaatgtt tttgtttgtt tcagtacttg aacatcctat aagtaaggtc
     3421 agtatagtac tcgatgttat tgactttact gatgatttga acatattaac tccattttat
     3481 tttgttaaaa ttccaatcta taaatacata tacacgtaaa aataaacaat gcgaacgttt
     3541 tcacttatat tattcccatg atgtgattga atggtggttc catataagag agggcaatta
     3601 tactatcttt ctctcctgaa ctgatgggat tgcagtttag agaaaaaaga tcaaaggatc
     3661 ttcttgagat cctttttttc tgcgcgtaat ctgctgcctg taaacgaaaa aaccaccctg
     3721 gcaggtggtt tttcgaaggt tagctaatcc tggcagatta cctaaccggg tagctggctt
     3781 aagtggagca cagataccaa aagatgtcct ttcagtgtag ccgctataag gcttcaactt
     3841 caagagttct gcgtatctaa atccactttt tagttaccaa tggctgctgc cagtggcgtt
     3901 aagtcgtgtc ttaccgggtt ggactcaaga cgatagttac cggataaggc gcagcggtcg
     3961 ggctgaacgg ggggttcgtg cacacagccc agcttggagc gaacgaccta caccgaactg
     4021 agatacctac agcgtgagct atgagaaagc gccacgcttc ccgaagggag aaaggcggac
     4081 aggtatccgg taagcggcag ggtcggaaca ggagagcgca cgagggagct tccgggggga
     4141 aacgcctggt atctttaagt cctgtcgggt ttcgccacct ctgacttgag cgtcgatttt
     4201 tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc cagcggcgcg gccttcttcc
     4261 tgttcctggt cttttgctca catgtttttt ccggtgttat cccctgattc tgtggataac
     4321 agcatttcgt ttttgagtga gtagataccg ctcgccgcag tcgaacgacc gagcgtagcg
     4381 agtcagtgag cgaggaagcg gaaaagcgcc tggacgtgca ttttctcctt acgcatctgt
     4441 gcggcatttc acacccggca tggcgtactt ttcatacaat ccgcactgat gccgcatggt
     4501 taagccagta tacactccgc tatcgctacg tgactgggtc agggctgcgc cccgacaccc
     4561 gctaaaacct gctgacgcgc cctgacgggc ttgtcagctc ccggcatccg ctcacagaca
     4621 agctgtgacc gtctccggga gctgcatgtg tcagaggttt tcaccgtcat ccccgaagcg
     4681 agcgaggcaa ctgcggtaaa gctcatcggc gtggtcgtga agcgattcac agatatctgc
     4741 ctgttcatcc gcgtccagtt cgttgagctt ctccagcagc gttaatgtct ggcttcttat
     4801 aaagcgggcc atgttaaggg cggttttttc ctgtttggtc actgatgcct ccgtgtaagg
     4861 gggatttctg ttcatgggga taatgatacc gatgaaacgc gagaggatgc tcacaatacg
     4921 ggttactgat gatgaacatg cccggttact tgaacgctgt gagggtaaac agctggcggt
     4981 atggatgcgg cgggtctgcc tgggggggcc ggttgcccgt tccggggggg tgccggcact
     5041 ggcaccgccg ttactgcgtc agctggccgc catcgggaat aacctgaatc agacagcgag
     5101 gaaggtgaac agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg ccgcactgat
     5161 ggccatcggg gatgagctgc gccggctgcg tctggccgtc agggaacagg ggacgcggg
//
