LOCUS       NZ_CP054982             5429 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain STIN_92 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP054982
VERSION     NZ_CP054982.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925548
            Assembly: GCF_022353685.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5429)
  AUTHORS   Che,Y., Xu,X., Yang,Y., Brinda,K., Hanage,W., Yang,C. and Zhang,T.
  TITLE     High-resolution genomic surveillance elucidates a multilayered
            hierarchical transfer of resistance between WWTP- and
            human/animal-associated bacteria
  JOURNAL   Microbiome 10 (1), 16 (2022)
   PUBMED   35078531
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5429)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: "Other" v. Unicycler
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology :: Illumina; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022353685.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:06:11
            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)                     :: 5,265
            CDSs (total)                      :: 5,144
            Genes (coding)                    :: 4,880
            CDSs (with protein)               :: 4,880
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 264
            CDSs (without protein)            :: 264
            Pseudo Genes (ambiguous residues) :: 0 of 264
            Pseudo Genes (frameshifted)       :: 85 of 264
            Pseudo Genes (incomplete)         :: 182 of 264
            Pseudo Genes (internal stop)      :: 46 of 264
            Pseudo Genes (multiple problems)  :: 47 of 264
            Pseudo Genes (short protein)      :: 4 of 264
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054982.1.
            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..5429
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STIN_92"
                     /isolation_source="Shatin WWTPs_92 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(join(5170..5429,1..304))
                     /locus_tag="HUZ60_RS26110"
                     /old_locus_tag="HUZ60_25760"
     CDS             complement(join(5170..5429,1..304))
                     /locus_tag="HUZ60_RS26110"
                     /old_locus_tag="HUZ60_25760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015959180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001749520.1"
                     /translation="MHALSILPSVARANLATKFSSHLKVIELFNTMQDSQVVVLSSLIE
                     GHHLTSSGNSVKADFEVTRLPAIIEMLEKKYFFPIRHLNVSVKSVTTGRMTGQTVYFIE
                     PEHIEQLLADPELVFANQERSLFFRSLEKEGKNLGKLIEKKGSVSQAVLSLLHHAYKDK
                     PLSDEMWKEIEDKFTHMLDELSAA"
                     /name="hypothetical protein"
     gene            complement(562..972)
                     /locus_tag="HUZ60_RS26115"
                     /old_locus_tag="HUZ60_25765"
     CDS             complement(562..972)
                     /locus_tag="HUZ60_RS26115"
                     /old_locus_tag="HUZ60_25765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000874179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000874179.1"
                     /translation="MAFISLSNLAAKTGRIIQSQCVTATQTKKSTGAVELGFRLSKSAM
                     DETGITIGDRVDILYDKEENQWMIKKISEGGFGVSGQKNKHGGYSSCAVRLTLRPGFPR
                     LSEDEEDNKKLLSDDSFTQLSEGVIVFRLDDE"
                     /name="hypothetical protein"
     gene            complement(1793..2005)
                     /locus_tag="HUZ60_RS26120"
                     /old_locus_tag="HUZ60_25770"
     CDS             complement(1793..2005)
                     /locus_tag="HUZ60_RS26120"
                     /old_locus_tag="HUZ60_25770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2009..2494)
                     /locus_tag="HUZ60_RS26125"
                     /old_locus_tag="HUZ60_25775"
     CDS             complement(2009..2494)
                     /locus_tag="HUZ60_RS26125"
                     /old_locus_tag="HUZ60_25775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749519.1"
                     /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_001749519.1"
                     /translation="MSSLLALAKDLEKQSKAQQQNTCEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEQKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            complement(<2529..3209)
                     /locus_tag="HUZ60_RS26425"
                     /old_locus_tag="HUZ60_25780"
                     /pseudo=""
     CDS             complement(<2529..3209)
                     /locus_tag="HUZ60_RS26425"
                     /old_locus_tag="HUZ60_25780"
                     /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            complement(3172..3492)
                     /locus_tag="HUZ60_RS26135"
                     /old_locus_tag="HUZ60_25785"
     CDS             complement(3172..3492)
                     /locus_tag="HUZ60_RS26135"
                     /old_locus_tag="HUZ60_25785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_000957082.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNTGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGND
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4130..4213
                     /locus_tag="HUZ60_RS26430"
     CDS             4130..4213
                     /locus_tag="HUZ60_RS26430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071532987.1"
                     /translation="MHEPPVQSDRCAFSGNYRLESNPERHD"
                     /name="replication initiation protein"
     gene            4515..5141
                     /locus_tag="HUZ60_RS26140"
                     /old_locus_tag="HUZ60_25790"
     CDS             4515..5141
                     /locus_tag="HUZ60_RS26140"
                     /old_locus_tag="HUZ60_25790"
                     /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_223149424.1"
                     /translation="MSPTLNKQASKERCAVEFATRKKSKTQRKKSKALSYRGLCFFCTL
                     VTGKCQWTSKMSKQDYIQLRTLTDQFYADNKGLQEALDGSNDGKVRGYGIVVIDLNGLV
                     FGIPLRSHLNHKFGFVSERSEGVKKGLDYTKALLIKKEEYVSRAYKIPTPEFTHINDNK
                     EKIQEDFNKFVNRYIEANVKKDENILRNYRYSTLKNYHKELGLED"
                     /name="hypothetical protein"
     Typing          complement(3601..3780)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.339"
                     /coverage="83.0"
                     /evalue="7.539999999999999e-48"
     Typing          3726..4239
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.217"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(1678..3182)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.426"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatagacagt ttgtccagtc atccttcctg tagttacaga tttaacagat acatttagat
       61 gacgaatagg gaaaaaatat tttttctcta acatctcgat aatcgccggt aagcgagtga
      121 cctcaaagtc ggctttgaca ctgttaccag aactggtgag gtgatggcct tcgatcagtg
      181 atgacaagac aacaacttgg gaatcctgca tcgtgttgaa gagctcgatc accttcaaat
      241 gagacgagaa tttagttgcc aggttagcgc gggcaactga aggtagtatt gataaagcgt
      301 gcatatgtat agcctcatat gtttttaaaa acataaactt aagagaccaa agccaatagc
      361 atcgcaccta tcagaataga aaatgtcgtg ttcacatccc tcaaaagaaa cgattttttc
      421 tttattagaa tgcaagttta tgaacataat gccgcccata acactccacc cttccaaagg
      481 tagtgatgtg ttgacaagaa ggcggagtta gtcgattgtt tggcgacgct cactaactct
      541 gcctttcctt tttggtcctt cctattcatc atccagcctg aagacgatta caccttcact
      601 tagctgagtg aatgaatcat cggaaagtag cttcttgttg tcctcttcat cctcagaaag
      661 gcgaggaaaa cctggtcgca aggtcaatct aacagcacac gatgagtaac cgccgtgctt
      721 gtttttttgc ccagacacac caaagccacc ttcactaatt ttcttaatca tccactggtt
      781 ttcttctttg tcgtaaagaa tgtcgacacg atccccaatg gtaataccag tctcgtccat
      841 agcgctcttg ctcaagcgga atcccagctc gacagcgccc gtgctttttt tcgtttgcgt
      901 ggccgtaaca cactgcgact ggattatcct tccagtcttc gctgccaagt tcgatagaga
      961 gataaaagcc ataatacaat ccgttttaga catcgatcag ttcttatacg gaagtgtacc
     1021 cagggagcga ggtggctttc aagatctttt gtattgattt ttctagagcc gcaaaaaacg
     1081 gcgataagaa accttaaata caaaaacaat tgctcgtatt gaacctcgtc aagatacaca
     1141 tccagatcga tctttatgta agtaaagggt atttttctat ggtgatttaa agtcgagcaa
     1201 cgtcagcgca tccaaaaaat caccaagtag gtgcaagaaa gccgcttata gaaactgatt
     1261 tttatgcctg tataggttgc cgatgagatg aatttaacat aagagttctt gcccgcaccg
     1321 cttcgggctg gttcggcgca aatacggtgc ctgtcgggtg aaacccctag caaagcaccc
     1381 ggtaaaccgc cccgtttacg ccagataaat ttcacttggc tgcatggtta tgcagccaga
     1441 tgaatgacag cagttttcgc gtataaatac ggtgtaaagc actaaaaagg ccactttccc
     1501 ccgaatcgct cccacagatc cattgccagt ttgacgcatt gcagtatcag actgagcgct
     1561 tttagtatct tcataaatcc ccctctcttg agccgtgatc ttttcatcac gaccgtattt
     1621 agcgggaaat ttatgagccc ttcttcttgg ggtttgtcac tggatgcgcg cagtcagccc
     1681 agcgtcggac cgttatagct ccgctgacgg aaacggggtt ctgccagctc tttttcatgc
     1741 tgtcgctgct cgtatgcccg ttcggcggcc accgccattt catgccgctg cactactggc
     1801 tcaaacgctg taactgcctg ctcaagttcg ccacctgctg actcaagcgc gtgacgcgct
     1861 cgttcagcgc cgcgttctcc cgttgcataa gaccagacat cttctgccat tccgcgaagg
     1921 cgctctccca ctcgtccagc ctttgcgagt agtcctgatg tagctgctct aatgcggtca
     1981 gcaactgttt ttccagttcc gtcatgggct atttcctctc cagtaccatc cagttccctt
     2041 cctccccgta agctcccgct ttcgggttca ctttgacgca ggacagtttc tgttccccac
     2101 agagcgacag ctgcacgccg tggttcttct ccgacagcat ggcctgcgtc cgctcctgcg
     2161 cccggatagt ctggtaattc ccggtgatct gctgcccctg ccaccacaga atgctcccgc
     2221 tcgtggcgat cagcagtact gagaccaggg tgatggtcag ccacgtccgg ccaaccatac
     2281 gcagcacgct cagccggttc gactgcatcg ccgcggtcat accctgctcg tgggcgctga
     2341 tggcgtcgct gattctcttc gcgcttgcgc tcagttccgc ttttacagac ttctcgtgct
     2401 cgctgaatgc ggctttcagc atctcgcagg tattctgctg ctgcgctttc gattgctttt
     2461 ccaagtcctt cgccagcgct aaaagactgc tcataaatgg ctcccttcag tcggatgttt
     2521 cgccccccgt ccgggtcggc aatgctgata ctgttctttg tggtgcggac cacctcaaaa
     2581 cctgccgcag tgagcgaccc tgtgacgtcc tcgcgcgttt tgagcgcccc ggatgaggct
     2641 aaggccagca aaccccgtgt aatcgcctga gcggcttcca gcttcgtttc cggcagtgcg
     2701 gacggcgtga ccagtaaccg ccggttcttc ggggcgtttg gatcatgcag ccccagtctg
     2761 ccgttcacca cggtctgcca ggcatcgatg cgcggccggt cggcgcgatc gtaatacggc
     2821 tgcaggcgtt tcccggtcag cagctctgtg ttggggatca ggaaattcag ctccagccgc
     2881 cccttgtcgg tgtgctccac ccacagaatg ctgtactggt ctttatcgag cccgggcatc
     2941 agaacccgct caaagctggc catgatctgc tcccgctgcc cgggcggcag ctcagcctcc
     3001 gcgaacgaca gtacgccgga ggtgtacttt ttcgcatacg gcgaggcatc gataagctcc
     3061 cggacttcct ccggctttcc ctgcagcacg gtcgccccct cgcgctgccg gtcttttccc
     3121 agcaggtaat ccaccggacc ggcaccacca ccgcgccccc ggggatggaa tttaacgatc
     3181 atcattcccc cctttttcca gcaccgcatg ccgcagccgc tccagtcccg cgtcgattgc
     3241 catcagggcg gccacgatct gcacccggtc atgaccggca ccaccggtat tcactttccg
     3301 ggcgatctgg ttcaggttat tacccatacc ggcaagctgg cgcagcagcg ccggcgatat
     3361 cgacggcagt ctgccggcac gcgccggctt ctcatcgagg caggtctgac gcatccacgc
     3421 cgccagctgc ttgccgtcgc accgctcgag cagccgccgg tgttcgtctt ccgtcaccca
     3481 catcgtgagc atcttgttgc gtttgtctgc cagagtagcc tcctgataac accgggacgg
     3541 gcgggaaatg tttcccggtc ggcacggtgt tggacaagcc gcaggcgcgt cagtggcttt
     3601 tagcgggttt cggggcgcag ccctgaacca gtcacgtagc gctagcggag tgtatactgg
     3661 cttaatatgt tacggcggag taacacttta taaaagtgct tcatgtggca ggggaaaatg
     3721 cagctgcagg gcgtacggga gaacatggag gttgcggtga tattacgcct cctcgctcac
     3781 tcggtcgctt ccgctcctgc cgttcggctg cggcgggcgt tacctgcaca cggataagag
     3841 caaaggcata cggcatgaca aacagggcaa gaaaaggatg cggcgctgcc gtttttccat
     3901 aggctccgcc cccctgacaa gcatcacgaa atctgacgct caaatcagtg gtggcgaaac
     3961 ccgacaggac tataaagata ccaggcgttt ccccctggtg gctccctcgt gcgctctcct
     4021 gttcctgcct ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt atctcattcc
     4081 acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc
     4141 ccccgttcag tccgaccgct gcgccttttc cggtaactat cgacttgagt ccaacccgga
     4201 aagacacgac taatcgccat tggcaacggc cactggtaaa catgatgtgc gagagatgta
     4261 ttgagagttc ttgaagtggt ggccttactg aggctacact ggaaggacgg atttggtgac
     4321 acgtctcgca caagactgtt accacggtta gataatctgc caggattaaa taaccttcga
     4381 aaaaccacct gccagggtgg ttttttcgtt tcaggagaag attacgctgg caaagtaagt
     4441 ccagtcaaga acagctacga aattgacttc acatataatt tttgatataa gtaaatctag
     4501 aagtggcggt aggaatgagc cccacgttaa acaaacaagc ttccaaagaa agatgtgcgg
     4561 tagagttcgc cacacgtaaa aaatccaaga ctcaacgaaa gaaaagcaaa gccctctctt
     4621 acagagggct ttgctttttt tgtacattgg ttacaggaaa atgccaatgg acatcaaaaa
     4681 tgagcaaaca ggattacata cagttaagaa cccttacaga ccagttttat gctgataaca
     4741 aaggcctaca agaggctctc gacggcagta atgatggaaa agtaagaggc tacggaatcg
     4801 tagttattga tctcaacgga ttggtgttcg ggataccctt acgaagccat ttaaaccata
     4861 aatttggatt cgtttcggag cgatcagaag gtgttaagaa aggactggat tacaccaaag
     4921 cgttgctaat taagaaagaa gagtatgtat cgcgagccta taagatacca actcctgaat
     4981 ttacccatat caatgataac aaagaaaaaa tacaagaaga tttcaacaaa ttcgtaaaca
     5041 gatacataga agcgaacgtc aagaaagatg aaaacatact cagaaactat cgttactcta
     5101 cgctgaaaaa ctatcacaaa gaattaggtt tagaagacta aaaaggcggt ctaacgaccg
     5161 cccttgcctt tacgccgcgc tcaattcatc cagcatatgg gtgaacttat cttctatctc
     5221 cttccacatc tcgtcagaaa gaggtttatc tttgtaggcg tgatgtagaa ggcttaagac
     5281 ggcttgagaa acactacctt ttttctcgat aagcttgccg agatttttcc cttctttttc
     5341 gagagaacga aagaagaggc tcctttcctg attagcaaac acaagctcag gatcagcgag
     5401 aagttgctcg atgtgttcag gctctatga
//
