LOCUS       NZ_CP138850             4042 bp    DNA     circular CON 23-NOV-2023
DEFINITION  Shigella flexneri strain PNUSAE076676 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP138850
VERSION     NZ_CP138850.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20175209
            Assembly: GCF_033870275.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4042)
  AUTHORS   Shrum Davis,S., Salazar-Hamm,P., Edge,K., Hannah,T., Houston,J.,
            Griego-Fisher,A., Lugo,F., Wenzel,N., Malone,D., Bradford,C.,
            Plymesser,K., Baker,M., Schwalm,K., Lathrop,S., Smelser,C.,
            Dinwiddie,D. and Domman,D.
  TITLE     Multidrug-resistant Shigella flexneri outbreak associated with a
            high-mortality spillover event into nonhuman primates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4042)
  AUTHORS   Shrum Davis,S., Salazar-Hamm,P., Edge,K., Hannah,T., Houston,J.,
            Griego-Fisher,A., Lugo,F., Wenzel,N., Malone,D., Bradford,C.,
            Plymesser,K., Baker,M., Schwalm,K., Lathrop,S., Smelser,C.,
            Dinwiddie,D. and Domman,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-NOV-2023) Internal Medicine, University of New Mexico
            Health Sciences Center, 915 Camino de Salud NE, Albuquerque, NM
            87131, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 21-SEP-2023
            Assembly Method                   :: Unicycler v. v.0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 36.5x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/22/2023 13:16:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,073
            CDSs (total)                      :: 4,941
            Genes (coding)                    :: 4,182
            CDSs (with protein)               :: 4,182
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 103
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 759
            CDSs (without protein)            :: 759
            Pseudo Genes (ambiguous residues) :: 0 of 759
            Pseudo Genes (frameshifted)       :: 264 of 759
            Pseudo Genes (incomplete)         :: 449 of 759
            Pseudo Genes (internal stop)      :: 172 of 759
            Pseudo Genes (multiple problems)  :: 124 of 759
            Pseudo Genes (short protein)      :: 5 of 759
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP138850.1.
            Bacteria and source DNA available from PNUSAE076676.
            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..4042
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="PNUSAE076676"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA"
                     /collected_by="CDC"
     gene            join(3953..4042,1..69)
                     /locus_tag="SH220_RS25320"
                     /old_locus_tag="SH220_25320"
     CDS             join(3953..4042,1..69)
                     /locus_tag="SH220_RS25320"
                     /old_locus_tag="SH220_25320"
                     /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            386..778
                     /locus_tag="SH220_RS25325"
                     /old_locus_tag="SH220_25325"
     CDS             386..778
                     /locus_tag="SH220_RS25325"
                     /old_locus_tag="SH220_25325"
                     /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(1324..1557)
                     /locus_tag="SH220_RS25330"
                     /old_locus_tag="SH220_25330"
     CDS             complement(1324..1557)
                     /locus_tag="SH220_RS25330"
                     /old_locus_tag="SH220_25330"
                     /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(1564..2094)
                     /locus_tag="SH220_RS25335"
                     /old_locus_tag="SH220_25335"
     CDS             complement(1564..2094)
                     /locus_tag="SH220_RS25335"
                     /old_locus_tag="SH220_25335"
                     /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(<2132..2830)
                     /locus_tag="SH220_RS25340"
                     /old_locus_tag="SH220_25340"
                     /pseudo=""
     CDS             complement(<2132..2830)
                     /locus_tag="SH220_RS25340"
                     /old_locus_tag="SH220_25340"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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(2772..3095)
                     /locus_tag="SH220_RS25345"
                     /old_locus_tag="SH220_25345"
     CDS             complement(2772..3095)
                     /locus_tag="SH220_RS25345"
                     /old_locus_tag="SH220_25345"
                     /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            3160..3351
                     /locus_tag="SH220_RS25350"
                     /old_locus_tag="SH220_25350"
     CDS             3160..3351
                     /locus_tag="SH220_RS25350"
                     /old_locus_tag="SH220_25350"
                     /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"
     Typing          complement(3371..3457)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          3468..4025
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.032"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1221..2782)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.313"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctggcagcag ccattggtaa ctggacaagg tggattgaga tattaagagt tcttgaagtg
       61 gtggcctaac tgcggctaca ctagaaggac agcatttggt atctgtgctc caccaagcca
      121 gttaccttcg gaagaaagag ttggtagctc tagattccgg caaacaaacc accgttggta
      181 gcggtggttt ttttgtttgc aggcagcaga ttacgcgccg caaaaaagga tctcaagaag
      241 atcttgaatc actctatgaa aattttgttt tatagccgta tttgttgatg ctataagcca
      301 gagaccttct atgagaatag acatatcaca tcaaacacgg cataccccgc caaacatgct
      361 tcctcgggaa caaaattgtg tagcaatggc attatctgcg tgctttagac aacaactaaa
      421 ccctgtggta aacagcttat taaaagagag aataatacac tcccctaaag aattggaaca
      481 tgacaacgca gtaataagag tcctgcaaaa actacaaatt caagaagttt gtaacagcac
      541 cctttgggag acagccaaac aacaactact tcaaaaatcg gacggaagat attttgccat
      601 caattctaaa cacttagcct ttccaggccc aggagaatct cacgccttct gttgcatcaa
      661 atacaaaaat gcaattggca ttaacggaaa caatgccgaa acccaatcga cccactacca
      721 accctatccc tatgataaag tcagtatatg gggaccattc cctcacaatt taacgtaata
      781 tcttaattgt acgcaccgct gaaacgcgtt cggcgcgatc acggcagcag acaggtaaaa
      841 atggcaacaa accacccgaa aaactgccgc gatcgcaccc ggtaaatttt aaccacatgc
      901 atagctatgc agccatgtga atcacgcagg aattgccagc cagagacagc tgaaacggat
      961 tttattcatg ctttcggaag cgaagaagac ggggacctga gcgggaaaac agaagttcag
     1021 gggaatgagc gcgatctggc aatagaggca aaacacagcg acaaaagaca caccagaatc
     1081 gcgcccgtat gcgttttaac tcgttcctgt gttttcagca aggtctgact gaagcgcgtt
     1141 cccggtgccc ccgaaccaac cattatccca aaaaatgcac cggaaacgcg ctgacaacat
     1201 tttagcctgt ctctgattac catcccagcg aagggccatc cagtgtccgt tcctgtattt
     1261 ccggctggcg ttcccgttcc aggaataacg catgttcgcg ctcctgtatc aaccgttcct
     1321 ctcttatctc cagttctcgc tgtataactg gctcaagcgt tctgtctgct cgctcaagtg
     1381 cagcacctgc tgactcaact gcatgacccg ctcgttcagc atcgcgttgt cccgttgcgt
     1441 aagcgaaaac attttctgca attccacgaa ggcgctctcc cattcgttca gccgctgcat
     1501 atagtcctgt tgcagctgct ctaatgcgtt cagcaaatgg ctttccagct ccgtcatgct
     1561 ctgtcactcc tgtaccagcc ttacggcatt ctgtttcccg ttttccatcg tccagttcgt
     1621 ttcggctttc atcccctcgg gcaacaccag aaaacgtccg ttgctcccct cgtgataacg
     1681 cacgccccat gtcttcgcgt tcagcttctc cagactctcg ttctgcttcc tgatttcttc
     1741 caggttcgcc tgtatcatcc cgccaagata ccagagcgtc ccgccactca cggtaaacag
     1801 gaaaatgacc atccccagta acatcatgcc cgtattccct gccagcttta acacgtcctt
     1861 cctgtgctgc atcatcgcct ctttcacccc ttcccgatgt tttttcagtg attcctctgt
     1921 cgaagctgtg aacagggcta tagcgtcttt gattttcgtc tcgtttgatg tcacagcctt
     1981 gcttacagat tcttcgagct tcctgaactc gtcgctcagc attttctctg tagattcggc
     2041 tctctctttc agctttttct cgaactccgc gcccgtctgt aaaagattgc tcatagaatg
     2101 ctcctttcag tctgatattc ttcccgccgt tcgggtctgc aatgctgata ctgcttcgcg
     2161 tcaccctgac cacttcaagc cccgcctctg tgagcgcctg aatcacatcc tgacggcctt
     2221 ttatctcccc gacatgataa agagcgtcta tccaccgtgt aatgctctca gcaagcgcct
     2281 gtttcgtttc cggcaggtta tcagggagag tcagcgtccg gcggttctcc ggggcgttcg
     2341 ggtcatgcag cccgtaatgg tgattcacca gcgtctgcca ggcatcaatt ctcggcctgt
     2401 ctgcgcggtc gtagtacggc tggaggcgtt ttccggtctg tagctccatg ttcggaatga
     2461 caaaattcag ctcaagccgc cccttgtcct ggtgctccac ccacagaatg ctgtactgat
     2521 ttttttcgag accgggcatc agtacacgct caaagctcgc catcactttt tcacgccctc
     2581 ccggcggcag ctccttctcc gcgaacgaga gaacaccgga cgtgtatttc ttcgcaaatg
     2641 gcgtggcatc gatgagttcc cggacttctt ccggattacc ctgaagcacc gttgcccctt
     2701 cccggttacg ctcccttccc agcaggtaat caaccggacc actgccaccg ccttttcccc
     2761 tggcatgaaa cttaactatc atcccgcgtc ccctgttccc tgacggccag acgcagccgg
     2821 cgcagctcat ccccgatggc catcagtgcg gccaccacct gaacccggtc accggaagac
     2881 cactgcccgc tgttcacctt cctcgctgcc tgattcaggt tattcccgat ggcggccagc
     2941 tgacgcagta acggcggtgc cagtgtcggc agcctcccgg aacgggcaac cggctcaccc
     3001 aggcagaccc gccgcatcca taccgccagc tgtttaccct cacagcgttc cagtaaccgg
     3061 gcatgttcat catcagtaac ccgtatcgtg agcatcctct cgcgtttcat cggtatcatt
     3121 acccccatga acagaaatcc cccttacacg gaggcatcag tgaccaaaca ggaaaaaacc
     3181 gcccttaaca tggcccgctt tatcagaagc cagacattaa cgctgctgga gaagctcaac
     3241 gaactggacg cggatgaaca ggcagacatc tgtgaatcgc tttacgacca cgccgatgag
     3301 ctttaccgca gttgcctcgc tcgcttcggg gatgacggtg aaaacctctg acgggcttgt
     3361 cagcgggtgt tagcgggtgt cggggcgcag ccatgaccca gtcacgtagc gatagcggag
     3421 tgtatactgg cttaaccatg cggcatcagt gcggattgta tgaaaagtgc gccataccgg
     3481 gtgtgaaatg ccgcacagat gcgtaaggag aaaatgcacg tccaggcgct tttccgcttc
     3541 ctcgctcact gactcgctac gctcggtcgt tcgactgcgg cgagcggtat ctactcactc
     3601 aaaaacgaaa tgctgttatc cacagaatca ggggataacg ccggaaagaa catgtgagca
     3661 aaagaccagg aacaggaaga aggccgcgcc gatggcgttt ttccataggc tccgcccccc
     3721 tgacgagcat cacaaaaacc gacgctcaag tcagaggtgg cgaaacccga caggactata
     3781 aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc
     3841 gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc
     3901 acgctgttgg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga
     3961 accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc
     4021 ggtaagacac gacttaacgc ca
//
