LOCUS       NZ_CP055204             4791 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_3 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP055204
VERSION     NZ_CP055204.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925527
            Assembly: GCF_022354345.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4791)
  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 4791)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-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_022354345.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:20:11
            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)                     :: 5,236
            CDSs (total)                      :: 5,112
            Genes (coding)                    :: 4,860
            CDSs (with protein)               :: 4,860
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 252
            CDSs (without protein)            :: 252
            Pseudo Genes (ambiguous residues) :: 0 of 252
            Pseudo Genes (frameshifted)       :: 84 of 252
            Pseudo Genes (incomplete)         :: 172 of 252
            Pseudo Genes (internal stop)      :: 54 of 252
            Pseudo Genes (multiple problems)  :: 51 of 252
            Pseudo Genes (short protein)      :: 2 of 252
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055204.1.
            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..4791
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_3"
                     /isolation_source="Shatin WWTPs_3 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            join(4650..4791,1..182)
                     /locus_tag="HUZ39_RS25910"
                     /old_locus_tag="HUZ39_25780"
     CDS             join(4650..4791,1..182)
                     /locus_tag="HUZ39_RS25910"
                     /old_locus_tag="HUZ39_25780"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_052994485.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQMVREQRVQ
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            391..>822
                     /locus_tag="HUZ39_RS25915"
                     /pseudo=""
     CDS             391..>822
                     /locus_tag="HUZ39_RS25915"
                     /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            860..1378
                     /locus_tag="HUZ39_RS25920"
                     /old_locus_tag="HUZ39_25750"
     CDS             860..1378
                     /locus_tag="HUZ39_RS25920"
                     /old_locus_tag="HUZ39_25750"
                     /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_014640501.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGQIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVIPQGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            1385..1618
                     /locus_tag="HUZ39_RS25925"
                     /old_locus_tag="HUZ39_25755"
     CDS             1385..1618
                     /locus_tag="HUZ39_RS25925"
                     /old_locus_tag="HUZ39_25755"
                     /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_001565220.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQQDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1649..1810
                     /locus_tag="HUZ39_RS26225"
     CDS             1649..1810
                     /locus_tag="HUZ39_RS26225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001329495.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="WP_072060084.1"
                     /translation="MSYPWSVSASRKYRNAHWMVLHWDGETMKNGRLSGLRRANVVCTI
                     WLHRYSCG"
                     /name="mobilization protein"
     gene            complement(1817..2107)
                     /locus_tag="HUZ39_RS25930"
                     /old_locus_tag="HUZ39_25760"
     CDS             complement(1817..2107)
                     /locus_tag="HUZ39_RS25930"
                     /old_locus_tag="HUZ39_25760"
                     /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_239637987.1"
                     /translation="MNEASQCDKNHIHRYGQRTDLTSMITGKCIFAQTIYTHTIAISNK
                     TIEIQEDNFFTVVLIYHNVSLRAPLKRVQRDHGSRQVKMATNHPKNCRDRA"
                     /name="hypothetical protein"
     gene            2155..2847
                     /locus_tag="HUZ39_RS25935"
                     /old_locus_tag="HUZ39_25765"
     CDS             2155..2847
                     /locus_tag="HUZ39_RS25935"
                     /old_locus_tag="HUZ39_25765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000550475.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3800 domain-containing protein"
                     /protein_id="WP_000550474.1"
                     /translation="MHLLYVDESGTPSDPTLNHFVLSGISVFEKQTHWIEKEMNAIAAR
                     FNSDDPYEREFHGSPMRGGRDGWKKFSLNDRKQAIKDCLALLTQKHRDIRIFACVVPKG
                     SLDGKDVITESFYQISSRFDMYLSRLHHQGDTSRGVAIFDKSSTEKSIQSLARTFKDTG
                     YEYGKLRNFSEVPLFLDSKASRLIQLADLVSYSIFRKFELSDNEFYKIIENCFDYHNGK
                     VHGLYVAH"
                     /name="DUF3800 domain-containing protein"
     gene            complement(3020..3328)
                     /locus_tag="HUZ39_RS25940"
                     /old_locus_tag="HUZ39_25770"
     CDS             complement(3020..3328)
                     /locus_tag="HUZ39_RS25940"
                     /old_locus_tag="HUZ39_25770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001707532.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_058712689.1"
                     /translation="MTEKIQGTASVLNQTKTYEELVQKYSPEVANVLLARSINNALPNA
                     KITPNDVAGFCKVTTALRTGKVDLEKTVKEADADAKAVSANIIEGLKTKQKSTVEKE"
                     /name="hypothetical protein"
     gene            complement(3613..3726)
                     /locus_tag="HUZ39_RS26230"
     CDS             complement(3613..3726)
                     /locus_tag="HUZ39_RS26230"
                     /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="replication initiation protein"
                     /protein_id="WP_223149438.1"
                     /translation="MHEPPVQPDCCALSGNYRLESNPVRHDLTPLSAATGN"
                     /name="replication initiation protein"
     gene            complement(4394..4585)
                     /locus_tag="HUZ39_RS25945"
                     /old_locus_tag="HUZ39_25775"
     CDS             complement(4394..4585)
                     /locus_tag="HUZ39_RS25945"
                     /old_locus_tag="HUZ39_25775"
                     /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          4222..4303
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(3655..4198)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.967"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          173..1722
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.221"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4618..4790
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="2.16e-30"
ORIGIN
        1 cgttactgcg tcagctggcc gccatcggga ataacctgaa tcagactgcg aggaaggtga
       61 acagcgggca gtggtcttcc ggtgaccggg ttcaggtggt ggccgcactg atggccatcg
      121 agagagagtt gcgcagctta cggcagatgg tcagggaaca gagagtgcag gatgatagtt
      181 aagtttcatg ccaggggaaa aggtggtgga agtggtccgg ttgattacct gctgggaagg
      241 gagcgaaacc gggaaggggc aacggtgctt cagggtaatc cggaagaagt ccgggaactc
      301 atcgatgcca cgccatttgc gaagaaatac acgtcaggtg ttctgtcgtt cgcggagaag
      361 gagctgccgc cgggaggacg tgaaaaggtg atggcgagct ttgagcgtgt actgatgccc
      421 ggtctcgaaa agaatcagta cagcatcctg tgggtggagc accaggacaa gggacggctt
      481 gagctgaatt ttgtcattcc gaacatggag ctacagaccg gaaaacgcct ccagccgtac
      541 tacgaccggg cagacaggcc gagaattgat gcctggcaga cgctggttaa tcaccattac
      601 gggctgcatg accccaacgc cccggagaac cgccggacgc tgacccttcc tgataacctg
      661 ccggaaacga aacaggcgct tgcagagagc gtcacacgtg ggatagacgc tctttatcat
      721 gtcggggaga taaaaggccg tcaggatgtg attcaggcgc tcacagaggc agggcttgaa
      781 gtggtcaggg tgacgcgaag cagtatcagc attgcagacc cgaacggtgg gaagaatatc
      841 aggctgaaag gagcattcta tgagcaatct tttacagacg ggcgcggagt tcgagaaaaa
      901 gctgaaagag agagccgaat ctacagagac aatgctgaac gacgagttca gcaagctcga
      961 aaaatctgta agcaaggctg tgacatcaaa cgagacgaaa atcaaagacg ctatagccct
     1021 gttcacagct tcgacagagg aatcactgaa aaaacaccgg gaaggggtga aagaggcgat
     1081 gatgcagcac aggaaggacg tgttaaagct ggcagggaat acgggcatga tgttactggg
     1141 gatggtcatt ttcctgttta ccgtgagtgg cgggacgctc tggtatcttg gcgggcagat
     1201 acaggcgaac ctggaagaaa tcaggataca ggaagaaaca ttgcagaaac tgaacgcgaa
     1261 gacatggggc gtggagtttg tgcaggacgg gagaaggaaa tttctggtca tcccgcaggg
     1321 gaaatcggca acggtgattc cctatcaggg gaaggactgg gtacaactga cggagtgaca
     1381 cagagtgacg gagctggaaa gacatttgct gaacgcctta gagcaactgc aacaggacta
     1441 tatgcagcgg ctgaacgaat gggagagcgc cttcgtggaa ttgcagaaaa tgttttcgct
     1501 tacgcaacag gacaacgcga tgctgaacga gcaggtcatg cagttgagtc agcaggtgca
     1561 gcacttgagc gagcggacag aacgcttgag ccagttatac agcgagaaca ggagataagg
     1621 gacgaacggc tgatacagga gcgcgaacat gagttatccc tggagcgtga gcgccagccg
     1681 gaaatacagg aacgcacact ggatggtcct tcactgggat ggtgaaacta tgaaaaatgg
     1741 caggttaagt ggattaagac gggctaatgt ggtctgtacc atctggttgc ataggtattc
     1801 atgcggttaa aatttatcag gcgcgatcgc ggcagttttt cgggtggttt gttgccattt
     1861 ttacctgtct gctgccgtga tcgcgctgaa cgcgttttag cggtgcgcgt aatgagacgt
     1921 tatggtaaat aagaacaacg gtgaagaagt tatcttcttg aatttctatt gttttattgc
     1981 ttatggctat agtgtgtgta taaattgttt gggcaaatat gcacttgcct gttatcattg
     2041 atgttaagtc agttcgctgc ccatagcggt gtatgtgatt tttatcgcac tggcttgcct
     2101 cattcatgaa aatgccgcgc aaatgcgcgg tatttttcgt ttaaggagtc ttagatgcat
     2161 cttttatacg ttgatgagtc tggtacacca tcagatccta cccttaatca ttttgtcctt
     2221 tctggtatat cagtgtttga aaagcaaacg cactggatag agaaagagat gaatgcaatt
     2281 gcggctcgat ttaatagtga tgacccttat gaaagagaat ttcatggttc gccgatgaga
     2341 ggtggacgag atggctggaa aaagttttcc ctcaatgaca gaaagcaagc gatcaaagat
     2401 tgcctagcac tccttactca aaagcatcgg gatattcgca tatttgcatg cgttgtgccc
     2461 aagggctcct tagatggaaa ggatgtaata acagagtctt tttatcaaat atcgtctcgt
     2521 ttcgacatgt atttaagtcg attacatcac caaggtgata catctcgagg tgtagctatt
     2581 tttgataagt cgtcaacaga aaaaagtatt caatctcttg ctcgtacgtt taaagatact
     2641 ggatatgagt atggaaaact tcgcaacttc tctgaagtgc ctttattttt ggactctaag
     2701 gcgtcaagac tgattcagct tgctgatctt gtatcgtact caattttcag gaagtttgaa
     2761 ctcagtgata atgagttcta caaaattata gagaattgtt ttgactacca taatggtaaa
     2821 gttcacgggc tttacgtagc tcactaatgg aatggttgtt aatacgccac cataaataag
     2881 agctctttgt agctattgac tcgaagcttc tatgtaggct ttttcatgca tggcgtataa
     2941 aaccatatta tggtagtcct gcttgtttca ggtacaaaaa cgtcgcccta tagggcgacg
     3001 tttttgtacc tgcgggaaat cattcttttt caacagtgct tttttgtttg gtttttagac
     3061 cctcaatgat atttgctgaa acggctttcg catcggcatc ggcttctttc actgtttttt
     3121 ctagatcaac ttttcctgta cgcaaagctg tcgtcacttt gcagaatcca gcaacgtcat
     3181 ttggagttat ttttgcgtta ggtaaagcat tgttgataga ccttgccagt aagacgttag
     3241 ctacttctgg tgaatatttc tgaaccagct cttcataagt tttggtttga ttaagaacgc
     3301 tagctgttcc ttggattttc tctgtcatgt gaacctctag tctatagaat ttcaggtgta
     3361 gaacatgtat gccaatgcag aagcttaatc actggtaaac agtggatctt cttgtgatcc
     3421 ttttgttctc gtcgtaatct cactccctgt aaacaaaaaa accaccgcta ccaacggtgg
     3481 ttcgtttgcc ggaatcaaga gctaccaact ctttcttccg aaggtaactg gcttagagga
     3541 gctcagtcac caaagctgtc cttttagtgt agccgcatca cattaggaac ttcaagactc
     3601 tcctcctcta aatcaattac cagtggctgc tgacagtggc gttaagtcgt gtcttaccgg
     3661 gttggactca agacgatagt taccggataa ggcgcagcag tcgggctgaa cggggggttc
     3721 gtgcatacag cccagcttgg agcgaacgac ctacaccggg ccgagatacc tacagcgtga
     3781 gctatgagaa agcgccacgc ttcccgaagg gagaaaggcg gacaggtatc cggtaagcgg
     3841 cagggtcgga acaggagagc gcacgaggga gcttccaggg ggaaacgcct ggtatcttta
     3901 agtcctgtcg ggtttcgcca cctctgactt gagcgtcaat ttttgtgatg ctcgtcaggg
     3961 gggcggagcc tatggaaaaa cgccagcggc gtggcctttt ccgggttctt gttttttgct
     4021 cacatgtttc ttttggcgtt atcccctgat tctgtggata accgcattac cgtctttgag
     4081 tgagctgata ccgctcgccg cagccgaacg accgagcgta gcgagtcagt gagcgaggaa
     4141 gcggaagagc gcctgatgcg gcattttctc cttacgcatc tgtgcggtat ttcacaccgc
     4201 atatggtgct cttttcttat aatccgcact gatgccacat agttaagcca gtatacactc
     4261 cgctatcgct acgtgactgg gtcatggctg cgccccgaca cccgctaaaa cccgctgacg
     4321 cgccctgacg ggcttgtcta ctcccggtat ccgctcacag gcaagctgtg accgtctccg
     4381 ggagctgtat gtgtcagagg ttttcaccgt catccccgaa gcgtgcgagg cagctgcggt
     4441 aaagctcgtc ggcgtggtcg tgaagtgatt cacaaatatc ggcctgttca tctgcgtcca
     4501 gttcgttgag cttctccagc agcgttaatg tctggcttct tataaagcgg gccatgttaa
     4561 gggcggtttt ttcctgtttg gtcactgatg cctccgtgta agggggattt ctgttcatgg
     4621 gggtaatgat accgatgaaa cgcgagagga tgctcacaat acgggttact gatgatgaac
     4681 atgcccggtt acttgaacgc tgtgagggta aacagctggc ggtatggatg cggcgggtct
     4741 gtctgggtga gccggttgcc cgctccggga ggctgccgac actggcaccg c
//
