LOCUS       NZ_CP055027             6242 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain SWHEFF_67 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP055027
VERSION     NZ_CP055027.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925590
            Assembly: GCF_022353945.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 6242)
  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 6242)
  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_022353945.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:14:26
            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)                     :: 4,646
            CDSs (total)                      :: 4,527
            Genes (coding)                    :: 4,291
            CDSs (with protein)               :: 4,291
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 70 of 236
            Pseudo Genes (incomplete)         :: 148 of 236
            Pseudo Genes (internal stop)      :: 58 of 236
            Pseudo Genes (multiple problems)  :: 35 of 236
            Pseudo Genes (short protein)      :: 3 of 236
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055027.1.
            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..6242
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHEFF_67"
                     /isolation_source="Shek Wu Hui WWTPs_67 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            join(4667..6242,1..935)
                     /locus_tag="HUZ75_RS23035"
                     /old_locus_tag="HUZ75_22890"
     CDS             join(4667..6242,1..935)
                     /locus_tag="HUZ75_RS23035"
                     /old_locus_tag="HUZ75_22890"
                     /EC_number="2.3.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014754184.1"
                     /GO_function="GO:0016747 - acyltransferase activity,
                     transferring groups other than amino-acyl groups [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="acyltransferase family protein"
                     /protein_id="WP_219397942.1"
                     /translation="MQYKRIQEDQPQYFPFIDGLRALAVIAVIIYHLNAAWLPGGFVGV
                     DVFFVISGFVVSASITHFKGQGFWRFLAFFYARRIKRIFPALIVCLLITCYVSALFIPS
                     SWLSDVNQQTGLFAFVGLSNFILAANRRDYFAPTTEFNPFTHTWSLGVEEQFYLIFPIL
                     FVAWLHGQRGRKASAILFAVGLLISLIFSAWESQANPTNAYFLIPGRFWELASGVLLYQ
                     LVTLNSAEEKRRENRLSGPIALIALAGLFVAFAISTPDNFPMPGAVIAVISTLLLLFSL
                     YKQNSFPWLHRLLGNRYILFFGKTSYSLYLWHWPVFVLFRWTYGLETPLTKALAVALTL
                     VMATFSFYIVETPMRRSKMARQMPNPAIIAVGFCVIAISWWGASAMNARAGKISLSQVS
                     ADADLWYPDRGPATPDSPGCRADPQTIIQDGVEVMVFKPEGCVQEKASRYRVLHVIGDS
                     HTLAYAALYKQFAIRNNLEVDVYRNGGCPFISFQSERDIDNLQCREQAENSLHAIHQRI
                     QPGDVLFLASLRLPRFSDQWAYFGSKGHQQSFFSAQAEENRQRSVDYAIDKLRSFVDQG
                     VHVVFEAPKPIFSSPPFRCSDWFNRSNPICAKGMTMPQDLLQKYRALVLASYNKVIRAL
                     PAVAIWDPFPILCDGPECHAWKNGHSMFFDGDHLSAFGSMRLLPSFSEFMLPKLEKSAQ
                     SASSQIPAQGYQFNQPGVPDFLESFSGLSHAEDWGRWSDGNSAPAVVLSFIQPLPKGFT
                     LQIISKGYGPNIGHQARVIVDNEEQRLNLGEQATEDALHFANHAGAKRIEIIPPSPQSP
                     KDAGESTDGRKLGIGLLSIKIIAD"
                     /name="acyltransferase family protein"
     gene            complement(981..>1052)
                     /locus_tag="HUZ75_RS23040"
                     /old_locus_tag="HUZ75_22895"
                     /pseudo=""
     CDS             complement(981..>1052)
                     /locus_tag="HUZ75_RS23040"
                     /old_locus_tag="HUZ75_22895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005226751.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="4-carboxymuconolactone decarboxylase"
                     /name="4-carboxymuconolactone decarboxylase"
     gene            complement(1145..2029)
                     /locus_tag="HUZ75_RS23045"
                     /old_locus_tag="HUZ75_22900"
     CDS             complement(1145..2029)
                     /locus_tag="HUZ75_RS23045"
                     /old_locus_tag="HUZ75_22900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004088970.1"
                     /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_239617286.1"
                     /translation="MTNHALALFNERLPHKPYYSDDLQFGVRIAAKDRAILAKYIQFNQ
                     PHAQFWLGFDVDRQGAALDWSDRNAPAPTFTIMNPKNGHAHLLYGLETAIRTAPDGRIK
                     PLKYAAAVENALRKKLDADIGYSGLICQNPNHSHWKISVWQPELYTLDWLADSLELNAA
                     NDKEIVVDYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERASAYNLQFSFPLD
                     DKEVKGIANSISKWTFANFSDVAFREYVIKTHSPEIQSIRGRKSKGGGRPKMIGEPWKD
                     MGISRSTWYRKYR"
                     /name="replication initiation protein"
     gene            complement(2337..2591)
                     /locus_tag="HUZ75_RS23050"
                     /old_locus_tag="HUZ75_22905"
     CDS             complement(2337..2591)
                     /locus_tag="HUZ75_RS23050"
                     /old_locus_tag="HUZ75_22905"
                     /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_089075317.1"
                     /translation="MTEMEKQLLSALESLQHSYAQQQSEWQSSYASLQSMFDTTLNHYT
                     QNQHENARLSEQVTRLQQQVEDLSRQVISLSENLPLLLR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(<3184..3828)
                     /locus_tag="HUZ75_RS23055"
                     /old_locus_tag="HUZ75_22915"
                     /pseudo=""
     CDS             complement(<3184..3828)
                     /locus_tag="HUZ75_RS23055"
                     /old_locus_tag="HUZ75_22915"
                     /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(3818..4150)
                     /gene="mobC"
                     /locus_tag="HUZ75_RS23060"
                     /old_locus_tag="HUZ75_22920"
     CDS             complement(3818..4150)
                     /gene="mobC"
                     /locus_tag="HUZ75_RS23060"
                     /old_locus_tag="HUZ75_22920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006714101.1"
                     /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_089075320.1"
                     /translation="MEKRTKEIKIRLTEREHELLLERCEQSQLASWLRALGLGERRPRQ
                     RKLPTVDPALLRQISGMGNNLNQIARLLHQSPLFSPSERVQLLAVLTSMDHQLSVLLAE
                     HRCDDC"
                     /name="mobC"
ORIGIN
        1 cctcattgcg cctgcctcgc tttagcgacc agtgggccta ctttggttct aagggacatc
       61 aacaatcgtt ctttagcgcc caagccgagg aaaacaggca gcgctcagtt gattacgcca
      121 ttgataagct ccgtagcttt gtggaccagg gagttcatgt cgtttttgaa gcgccgaaac
      181 ccatcttctc ctcaccgcct ttccgctgtt cggactggtt caaccgtagc aaccctatct
      241 gcgcgaaagg tatgaccatg ccgcaagacc tgctgcaaaa gtatcgtgcg cttgttctgg
      301 caagctataa caaagttatc cgcgcgctgc ctgcggttgc tatctgggat cccttcccga
      361 tcctctgcga tggcccagag tgtcacgcct ggaaaaatgg tcactcgatg ttcttcgatg
      421 gcgatcatct cagcgcattt ggcagcatga ggctgctacc ctcttttagt gagttcatgc
      481 tgccaaagct cgaaaagtca gcgcagtcag cctcaagcca aatcccagca cagggttatc
      541 agtttaatca acctggcgtt cctgattttc tcgaaagttt ctccggatta tcccatgccg
      601 aagactgggg ccgctggagc gatggtaact cggcaccagc agtggtcctc tcctttatcc
      661 agcctttacc taaagggttt acgctgcaga taatcagtaa aggctacggc cctaatattg
      721 gtcatcaggc gcgggtaatt gttgataatg aagagcaacg tctcaatctc ggagagcagg
      781 cgacggaaga tgcattgcat ttcgctaacc atgcgggtgc aaaacgcatc gagattatcc
      841 cgccttcccc tcaaagccct aaagacgccg gtgagtccac cgatggcaga aaacttggta
      901 ttggcttgct gagtattaaa attattgccg attaaccggc acaggaggaa acgccagaga
      961 ttaacttggc gttgctgttt ctaaccctga ttcgcatcaa tctcatcaaa aacctgctgc
     1021 gccagatgca ttgtagcgtt ggcggcaggc aggcaggcag gcaggcaggc aggcaggcag
     1081 gcaggcaggc aggcagcagt agatcgcata aatcacattc taacctacaa cttataatca
     1141 taaatcacct gtatttccta taccatgttg accgactaat ccccatatcc ttccacggtt
     1201 caccaatcat cttaggtcgc cccccccctt tacttttcct tcctctaatt gattgtattt
     1261 ctggagagtg cgtttttatt acgtattctc taaacgctac atcagagaaa ttagcaaaag
     1321 tccatttaga tatgctgttt gcaatacctt taacttcttt atcgtccaat ggaaaagaaa
     1381 actgtaggtt ataggcacta gctcgttcat agcaggcttg cagccactgc tcatactcag
     1441 gccagccctg acggatggcg cgatatgccc actttcgtgt tttatcaaac agcgtgcaat
     1501 tacggcctaa accgtaatcg acgacaattt ctttgtcgtt cgcggcgttc agttcgagtg
     1561 agtcggctaa ccagtctagt gtgtagagtt caggctgcca tacggaaatt ttccagtgac
     1621 tgtggttagg attctgacaa atcagtcctg aataacctat gtctgcgtcg agttttttgc
     1681 gcagtgcatt ttcaactgct gccgcgtatt tgaggggttt tattcttccg tccggagcgg
     1741 tacgaatagc cgtttccagc ccgtaaagca gatgggcgtg cccgtttttc gggttcatga
     1801 tggtaaaagt aggggctggt gcgtttcggt cactccagtc taaggctgcc ccttgacggt
     1861 caacatcaaa tcccagccag aattgggcgt gaggttggtt aaactgaata tatttggcaa
     1921 gaatagcccg atctttggca gcaatacgca caccaaattg caaatcatcc gaataatacg
     1981 gtttatgagg gagacgttcg ttaaataacg ctaatgcgtg gttagtcaag actcccagcc
     2041 ttatggcggg gctgttgttt tacaccgttc atgtgctaat atctctctaa ggtttcgata
     2101 cctggccctg attgttcatg agaatccgcc aagattaacg catgaatatc ggggctttgt
     2161 tttttctgct gcggttaagt tacaccgaac agggttaatt tgtcatcttt gtccgctaat
     2221 ttcgtgtttt cacacccatt tttaaaatcc catcccaaaa ccattatcac ggctgcgcgt
     2281 tttttgtcgc tgttgctcta attcgtttcg ccgttgttct gcacgtttat gctcggctac
     2341 cgcaataaca ggggcagatt ttcgctcaaa ctgatgactt gcctgctcaa gtcctcgact
     2401 tgttgctgta agcgtgtcac ttgctcgctc agccgggcgt tttcgtgctg attttgcgtg
     2461 taatgattca aggtagtgtc gaacatgctc tgtaagctgg cgtaactgct ctgccattcg
     2521 ctctgctgtt gcgcgtaact gtgctgtaag ctctccagtg cgctcaggag ctgtttctcc
     2581 atttctgtca tgagaagaat tcctgcattg agaaaacgcc gctgtatcgt tgtcaggggc
     2641 gtttaaaggg gttatttggt ctgatatttg atgacggtat gaccgttctt gctctgatac
     2701 ggggcgccca cgttgtacgc cgatttcggt agaatcaggt aatactggtt tttcttcttg
     2761 tcgtccgtca ttaccgaaag ccctttccct gtgtattcgt tcatctccag cacgctctga
     2821 tctaacagct gaatttcctg ataacgatcg gctatcatct tgccctgata caccagaatg
     2881 ccggacagta tcgctatcag acaaagaccg gataacccga tccacagact gagtttgccc
     2941 atcatcgtaa ccaacagcca acgctgtcgt tggttctgct ctcggatagc gttgttgatg
     3001 ctctgctcgt ttgatttcaa ggcctgtctg atagcattct cgtgccgctg aaattcgatg
     3061 ctgacgctgg tttcggtagc ggcggcttgc tgcttcgata tcgtctcgaa ctgtttcgcc
     3121 aaatttaaaa tctcgctcat aaatcgcccc ttttaaacgg atatttcgcc cccctgacgg
     3181 atcagcaata ctgaggctgt tttttgtttc cctgaccacc tgaaaaccaa actgctcaag
     3241 gtgagacacc acatcctttc gttccctgat ttgaccaaca cgcatcagct ccgtcagtcc
     3301 cttggtgata ctttccgcag ccagctgttt gtcgcggggt aaatcactgg ccggcgttaa
     3361 cggacgccga taaatcgggt cattcgggtc gcgcaatcct aaacgctcat tcgttaacgt
     3421 ctgccacgca ttcactctcg ggcgatctgc gcggtcaaaa tagggctgaa gccgttttcc
     3481 gctctgtaac tccacattcg ggatcacaaa attcagctct aaacgacctt tatcctgatg
     3541 ctgaacccaa agacaggtgt actgatcttt atcaagaccg gtcatcaatg tattttccca
     3601 ttcatccatc agtcgggttt tctcatcggc aggtaaatcc cgctcctgaa aagaaagtac
     3661 accggaggtg tacgttcggg tgtattcact ggtatcaatc agctctttaa cccgctcagg
     3721 gtcgcctcgt agaacctccg cctgttcacg gtttcgatct ttacccagaa gataatcaac
     3781 ggggccacta ccggaacccg caccgcggga atgaatttta acaatcatcg caccgatgct
     3841 ccgctaataa gacactcaat tgatggtcca tgctggtgag aaccgccagt aactgaaccc
     3901 gttcagacgg tgaaaataac ggagactgat gcaaaagccg cgcaatttgg ttgagattat
     3961 tccccatgcc ggaaatttga cgaagcagtg ccggatcaac cgtaggtaat tttcgctgac
     4021 gagggcgacg ttcacccagt cccaatgccc gtaaccatga tgccagctga gattgctcac
     4081 accgttcaag caatagctca tgctcacgct cagtcagtct gatcttgatt tctttcgttc
     4141 gtttttccat agcgtccact gagaatgttt gcaccacagt gcgaatattc gcagtggata
     4201 catgggggtt tcgggggaat gtagttcccc tgaaccagtc actagtccac tcgatagagg
     4261 ggacttcgtg tgtactggct taaggtatat gtagtatgtc aaatcctatg ctggctgcat
     4321 agaagcagct ctctacaaaa gagggctgtt atctgatata ggttgttttg tctcagtaga
     4381 acagggcagc ctggcggccg caaattgaaa aaccgcgcca tcttcccgcc tctggttacc
     4441 ataacctgat gggataaaaa attttttccc cgtttatccc tccacatatt cttcacaatc
     4501 aaatatattg ctgcgacgaa tattttagat cacaaaacga aatacaaatt gttactgaat
     4561 ccacgtagct tcaagcgcgg aaaacacaga aagacagatt aatagtattg ctgattaggg
     4621 tcggctagct tgttgaataa gccaaccaga gcaggatatg gtgaatatgc agtacaaaag
     4681 aattcaagaa gatcagccgc agtattttcc cttcattgat ggattgcgcg ccctggcggt
     4741 tatcgcggtg attatatacc acctcaatgc cgcatggtta cccggaggat tcgttggcgt
     4801 cgatgtattc ttcgtaatat ccgggtttgt cgtcagcgcc tcaattaccc acttcaaagg
     4861 gcaaggtttc tggcgttttc tggcattctt ctatgcgcgc aggataaagc gtattttccc
     4921 tgccctcata gtctgtttac tgataacctg ctatgtctcc gcactcttta ttcctagctc
     4981 ctggctaagt gacgtcaacc aacaaactgg cttatttgcc tttgttggcc tgagtaactt
     5041 tattctggcg gctaacagac gcgactactt cgccccaact acagaattca acccctttac
     5101 ccatacctgg tccttaggcg ttgaagagca gttctatctg atattcccga tactatttgt
     5161 tgcgtggctg cacggccagc gcggtagaaa agcatcagca atactgttcg ccgtcgggct
     5221 gctgatatct ttgattttct cagcgtggga atcacaggcc aaccctacca acgcttattt
     5281 cctaatcccc ggacgcttct gggaactggc ttcaggcgta ctgctctatc agttggttac
     5341 gctgaatagc gcagaggaga aacggaggga aaaccggctt tccggcccta tcgcgctgat
     5401 tgcgctggca ggactttttg tcgcatttgc gatctcaacg cctgacaact tccctatgcc
     5461 gggagcagta atcgccgtta tctcaacgct gctattacta ttttcattgt ataaacagaa
     5521 cagtttccct tggctgcacc gcttgctggg aaatcgctac attctgtttt ttggcaaaac
     5581 atcctactca ttatatttat ggcattggcc tgtattcgtt ctctttcgct ggacgtatgg
     5641 cctcgagacg ccgttgacca aagcgcttgc tgtcgcgtta accctcgtga tggctacgtt
     5701 ctctttctat attgtcgaaa cccctatgcg gcgcagcaaa atggcaagac agatgcctaa
     5761 tcctgcaatc atcgccgtgg gattttgcgt tattgccatc agttggtggg gtgcttcggc
     5821 aatgaatgcg cgtgctggaa aaatttcctt gagccaagtt agcgccgatg ccgatttatg
     5881 gtatccggat cgcggccccg cgacgccaga ttcccctggt tgtcgtgccg atccgcaaac
     5941 catcattcaa gatggcgtcg aggtgatggt tttcaaaccg gaaggatgcg tgcaggaaaa
     6001 agcgtcaaga taccgggttc tgcacgttat cggcgattca catactctgg cctatgcggc
     6061 gttgtataag cagtttgcta tccgcaacaa tcttgaagtc gatgtatatc gcaacggcgg
     6121 ctgtccgttt attagtttcc agagcgaacg cgatatcgat aatctgcaat gtcgcgaaca
     6181 ggctgaaaac tcgctacacg caatacatca acgaatccag cccggcgacg tgcttttcct
     6241 cg
//
