LOCUS       NZ_CP058793             5128 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain STLIN_6 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP058793
VERSION     NZ_CP058793.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925576
            Assembly: GCF_022494435.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5128)
  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 5128)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUL-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. Unicycler 0.4.8
            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_022494435.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:11:09
            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)                     :: 4,890
            CDSs (total)                      :: 4,767
            Genes (coding)                    :: 4,558
            CDSs (with protein)               :: 4,558
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 209
            CDSs (without protein)            :: 209
            Pseudo Genes (ambiguous residues) :: 0 of 209
            Pseudo Genes (frameshifted)       :: 65 of 209
            Pseudo Genes (incomplete)         :: 135 of 209
            Pseudo Genes (internal stop)      :: 41 of 209
            Pseudo Genes (multiple problems)  :: 32 of 209
            Pseudo Genes (short protein)      :: 3 of 209
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058793.1.
            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..5128
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLIN_6"
                     /isolation_source="Stanley WWTPs_6 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            join(4765..5128,1..38)
                     /locus_tag="HZT08_RS24265"
                     /old_locus_tag="HZT08_24050"
     CDS             join(4765..5128,1..38)
                     /locus_tag="HZT08_RS24265"
                     /old_locus_tag="HZT08_24050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001505260.1"
                     /translation="MIDIQKLISWLGVEGAKAGLDKSEMTNAELIESFGNLLPKNPSKL
                     KRSDLVEEIILATRRMTHKSVEELMEMSKEDLYSYFHDQKYSRKELLDLLYTLEIRPGS
                     SAKKNLTEFTISEISDIGMYRRVAKGNHA"
                     /name="hypothetical protein"
     gene            complement(858..1091)
                     /locus_tag="HZT08_RS24270"
                     /old_locus_tag="HZT08_24060"
     CDS             complement(858..1091)
                     /locus_tag="HZT08_RS24270"
                     /old_locus_tag="HZT08_24060"
                     /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_000137441.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1098..1616)
                     /locus_tag="HZT08_RS24275"
                     /old_locus_tag="HZT08_24065"
     CDS             complement(1098..1616)
                     /locus_tag="HZT08_RS24275"
                     /old_locus_tag="HZT08_24065"
                     /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_000067503.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1654..2316)
                     /locus_tag="HZT08_RS24280"
                     /old_locus_tag="HZT08_24070"
                     /pseudo=""
     CDS             complement(<1654..2316)
                     /locus_tag="HZT08_RS24280"
                     /old_locus_tag="HZT08_24070"
                     /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(2294..2617)
                     /locus_tag="HZT08_RS24285"
                     /old_locus_tag="HZT08_24075"
     CDS             complement(2294..2617)
                     /locus_tag="HZT08_RS24285"
                     /old_locus_tag="HZT08_24075"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_000955995.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            2682..2873
                     /locus_tag="HZT08_RS24290"
                     /old_locus_tag="HZT08_24080"
     CDS             2682..2873
                     /locus_tag="HZT08_RS24290"
                     /old_locus_tag="HZT08_24080"
                     /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"
     gene            3504..3635
                     /locus_tag="HZT08_RS24295"
                     /old_locus_tag="HZT08_24085"
     CDS             3504..3635
                     /locus_tag="HZT08_RS24295"
                     /old_locus_tag="HZT08_24085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /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_096169391.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMGKGVYKIY"
                     /name="replication initiation protein"
     gene            3884..4768
                     /locus_tag="HZT08_RS24300"
                     /old_locus_tag="HZT08_24090"
     CDS             3884..4768
                     /locus_tag="HZT08_RS24300"
                     /old_locus_tag="HZT08_24090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505259.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_001505259.1"
                     /translation="MAVTVGFISEKGGVGKTTSCYHIAEGLSRFHEKRVLVIDADYQRG
                     GITGRFFPKLIENFGNQAPQGTTLFNKYQQLYSAAQQTTDIDIIKFNSGIDVIPADPRL
                     STVSTDKLPSTNNIRSNNAILLQHLKTISAVLSPIADNYDYILIDSHPEVSDVMRSIIY
                     ASDYCVSPVKLDRQSSIGVATVIGEINNVNEDIEMLRKALQVGDSYKDTVFAGAMGMMA
                     REYAEELKQTEQYEYNRLRQAGDIFKHYITEGDGLRVAAAERVSVYDVQISNAYKQASQ
                     FKNLTIEFMRTCR"
                     /name="ParA family protein"
     Typing          complement(2969..3142)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.571"
                     /coverage="100.0"
                     /evalue="1.23e-64"
     Typing          3066..3652
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.709"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(755..2304)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcatgtatcg tcgcgtagcg aaagggaatc atgcataaat aaaagccacc tgtgaggtgg
       61 ctttttatag gataaaaaaa tgccatttaa tataggcgat atagtttact taaagtcaga
      121 atcaaaagcg atgacggtca tcggatatgg atcgtctcaa aataacggtt acatagatct
      181 agctaattgt gcttggctag ataaagacaa ccgctattgc caaatactat tcttgtttca
      241 aacgatcgaa aaaagaatca gttaaaaact ggcttatctt cattgagcat accggacgaa
      301 cctatttacc ataacatccg ttgcccgcac cgcagaaacg cgttcggtgc gatcacggca
      361 gcagacaggt aaaaatggca acaaaccacc cgaaaaactg ccgcgatcgc acccggtaaa
      421 ttttaaccac atgcatagct atgcagccat gtgaatcacg caggaattgc cagccagaga
      481 cagctgaaac ggattttttt catgctttcg gaagcgaaga agacggggac cggagcggga
      541 aaacagaagt tcaggggaat gagcgcgatc tggcaataga ggcaaaacac agcaacaaaa
      601 gacacaccag aatcgcgccc gtatgcgttt taacgcgttc ctgtgttttc agcaaggtct
      661 gactgaagcg cgttcccggt gcccccgaac caaccattat cccaaaaaat gcaccggaaa
      721 cgcgctgaca acattttagc ctgtctctga ttaccatcca agcgaagggc catcctgtgt
      781 ccattcctgt atttccggct ggcgctcacg ctccagggat aactcatgtt cgcgctcctg
      841 tatcagccgt tcgtccctta tctcctgttc tcgctgtata actggctcaa gcgttctgtc
      901 cgctcgctca agtgctgcac ctgctgactc aactgcatga cctgctcgtt cagcatcgcg
      961 ttgtcccgtt gcgtaagcga aaacattttc tgcaattcca cgaaggcgct ctcccattcg
     1021 ctcagccgct gcatatagtc ctgttgcagt tgctctaagg cgttcagcaa atgtctttcc
     1081 agctccgtca ctctgtgtca ctccgtcagt tgtacccagt ccttctcctg atagggaatc
     1141 accgttgccg atttcccgta cggaaggacc agaaatttcc ttctcccgtc ctgcacaaac
     1201 tccacgcccc atgtcttcgc gttcagtttc tgcaatgttt cttcctgtat cctgatttct
     1261 tccaggttcg cctgtatccg cccgccaaga taccagagcg tcccgccact cacggtaaac
     1321 aggaaaagga ccatccccag taacatcatg cccgtattcc ctgccagctt taacacgtcc
     1381 ttcctgtgct gcatcatcgc ctctttcacc ccttcccggt gttttttcag tgattcctct
     1441 gtcgaagctg tgaacagggc tatagcgtct ttgattttcg tctcgtttga tgtcacagcc
     1501 ttgcttacag atttttcgag cttgctgaac tcgtcgttca gcattgtctc tgtagattcg
     1561 gctctctctt tcagcttttt ctcgaactcc gcgcccgtct gtaaaagatt gctcatagaa
     1621 tgctcctttc agtctgatat tcttcccgcc gttcgggtct gcaatgctga tactgcttcg
     1681 cgtcaccctg accacttcaa gccctgcctc tgtgagcgcc tgaatcacat cctgacggcc
     1741 ttttatctcc ccgacatgat aaagagcgtc tatcccgcgt gtgacgctct ctgcaagcgc
     1801 ctgtttcgtt tccggcaggt tatcagggag agtcagtatc cggcggttct ccggggcgtt
     1861 ggggtcatgc agcccgtaat ggtgattaac cagcgtctgc caggcatcaa ttctcggcct
     1921 gtctgcccgg tcgtagtacg gctggaggcg ttttccgctc tgtagctcca tgttcggaat
     1981 gacaaaattc agctcaagcc gtcccttgtc ctggtgctcc acccacagga tgctgtactg
     2041 atttttttcg agaccgggca tcagtacacg ctcaaagctc gccatcacct tttcacgtcc
     2101 tcccggcggc agctccttct ccgcgaacga cagaacacct gacgtgtatt tcttcgcaaa
     2161 tggcgtggca tcgatgagtt cccggacttc ttccggatta ccctgaagca ccgttgcccc
     2221 ttcccggtta cgctcccttc ccagcaggta atcaaccgga ccactgccac cgccttttcc
     2281 cctggcatga aacttaacta tcatcccgcg ctccatgttc cctgacgacc tgccgtaagc
     2341 tgcgcaactc tctctcgatg gccatcagtg cggccaccac ctgaacccgg tcaccggaag
     2401 accactgccc gctgttcacc ttcctcgccg tctgattcag attattcccg atggcagcca
     2461 gctggcgcag taacggcggt gccagtgtcg gcagcttccc ggaacgggca accggctcac
     2521 ccagacagac ccgccgcatc cataccgcca gctgtttacc ctcacagcgt tccagtaacc
     2581 gtgcatgttc atcatcagta acccgtatcg tgagcatcct ctcgcgtttc atcggtatca
     2641 ttaccccatg aacagaaatc cccccttaca cggaggcatc agtgactaaa caggaaaaaa
     2701 ccgcccttaa catggcccgc tttatcagaa gccagacatt aacgctgctg gaaaagctca
     2761 acgaactgga cgcggatgaa caggcagaca tctgtgaatc gcttcacgac cacgccgatg
     2821 agctttaccg cagctgcctc gcacgcttcg gggatgacgg tgaaaacctc tgacacatac
     2881 agctcccgga gacggtcaca gcttgtctgt gagcggatgc cgggagcaga caagcccgtc
     2941 agggcgcgtc aggccgttga ccttgcgggt gtcggggcgc agccatgacc cagtcacgta
     3001 gcgatagcgg agtgtatact ggcttactat gttggcatga gtgcgggtat caggaaagtg
     3061 cttcatgtgg caggagaaaa aaggcggcac cggagcgtca gcagaatatg tgatacagga
     3121 tatattccgc ttcctcgctc actgactcgc tacgctcggt cgttcgactg cggcgagcgg
     3181 aaatggctta cgaacggggc ggagatttcc tggaagatgc caggaagata cttaacaggg
     3241 aagcgatagg gtcgcggcga agccgttttt ccataggctc cgcccccctg acaagcatca
     3301 cgaaatctga cgctcaaatc agtggtggcg aaacccgaca ggactataaa gataccaggc
     3361 gtttccccct ggtggctccc tcgtgcgctc tcctgttcct gcctttcggt ttaccggtgt
     3421 cattccgctg ttatggccgc gtttatctca ttccacgcct gacactcagt tccgggtagg
     3481 cagttcgctc caagctggac tgtatgcacg aaccccccgt tcagtccgac tgctgcgcct
     3541 gttccggtaa ctatcgactt gagtccaacc cggaaagaca cgacaaagcg ccactggcag
     3601 cagccatggg taaaggggtg tacaagattt actgagtgag agttcttgaa gtatcagcct
     3661 tagagaggct aaactggaat aacagaattt ggtttcagcg gtcttgtaca ccctgttacc
     3721 acggttcaga agttccccaa cttactgaac cctcgaaaaa accgactccc cagtcggttt
     3781 ttttcgtttg atggctaaga gtacgctgac gttatactga acgtcaagga aagcgttgac
     3841 gctgttccct ctaccaaaaa aaagagattt gtaaggaata aaaatggctg tgacagttgg
     3901 gtttattagt gagaaaggtg gggttggtaa aacaacgtcc tgttatcaca ttgccgaagg
     3961 acttagtcgt tttcatgaaa aacgtgtttt agttatagat gcagattatc aacgcggggg
     4021 tataactgga agatttttcc ctaaactgat cgaaaacttt ggaaatcaag caccgcaagg
     4081 aacaacgtta tttaacaagt atcagcaatt atatagcgcg gcacaacaaa cgactgacat
     4141 agacataatt aaatttaata gtggtatcga tgtcattcca gccgaccctc gcttatcaac
     4201 cgtttcaact gataagctac ctagtacaaa caatataaga tcgaacaatg ccattctttt
     4261 acagcattta aaaaccataa gcgctgtatt atcacctatt gcagataatt atgactacat
     4321 attgattgat tcacaccccg aagtttctga tgtcatgcgc tctataatct acgcatcaga
     4381 ttattgtgta tcaccggtaa aactagacag gcaatcatct attggtgtgg ccacggtcat
     4441 aggtgagata aataatgtaa atgaagatat tgaaatgcta agaaaggcac tgcaagtcgg
     4501 cgattcatat aaggacacag ttttcgccgg agcaatggga atgatggcca gagaatatgc
     4561 agaagaactg aagcaaacag agcaatatga atacaacagg cttcggcaag caggtgacat
     4621 cttcaagcac tacataacgg aaggtgatgg gctaagagta gctgcagcag agcgcgtttc
     4681 agtgtatgat gtacagataa gtaacgctta caaacaagcg tcacagttta agaacttgac
     4741 gattgagttt atgaggactt gtcgatgata gatatccaaa aactgatatc ttggcttggc
     4801 gttgagggag ctaaagctgg cttggataaa agtgaaatga ctaatgccga gctaattgaa
     4861 tcctttggta atttacttcc aaagaaccca agcaaattaa aacgctccga tctcgttgag
     4921 gagattattt tagcaacaag gagaatgaca cataaatcag ttgaagaact gatggaaatg
     4981 tcaaaagaag atctgtattc atatttccac gatcagaaat atagcagaaa agaacttctt
     5041 gatttgttat atactcttga aatcagacct gggagctcag caaagaaaaa tctaaccgag
     5101 ttcacaataa gtgagataag tgatattg
//
