LOCUS       NZ_CP055172             4073 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STEFF_22 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP055172
VERSION     NZ_CP055172.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925537
            Assembly: GCF_022353565.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4073)
  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 4073)
  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_022353565.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:09:50
            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)                     :: 4,815
            CDSs (total)                      :: 4,697
            Genes (coding)                    :: 4,552
            CDSs (with protein)               :: 4,552
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 145
            CDSs (without protein)            :: 145
            Pseudo Genes (ambiguous residues) :: 0 of 145
            Pseudo Genes (frameshifted)       :: 52 of 145
            Pseudo Genes (incomplete)         :: 85 of 145
            Pseudo Genes (internal stop)      :: 31 of 145
            Pseudo Genes (multiple problems)  :: 24 of 145
            Pseudo Genes (short protein)      :: 2 of 145
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055172.1.
            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..4073
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_22"
                     /isolation_source="Shatin WWTPs_22 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed2"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(join(3943..4073,1..571))
                     /locus_tag="HUZ49_RS23930"
                     /old_locus_tag="HUZ49_23795"
     CDS             complement(join(3943..4073,1..571))
                     /locus_tag="HUZ49_RS23930"
                     /old_locus_tag="HUZ49_23795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1105..1359)
                     /gene="mobC"
                     /locus_tag="HUZ49_RS23935"
                     /old_locus_tag="HUZ49_23800"
     CDS             complement(1105..1359)
                     /gene="mobC"
                     /locus_tag="HUZ49_RS23935"
                     /old_locus_tag="HUZ49_23800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            1538..3685
                     /gene="mobQ"
                     /locus_tag="HUZ49_RS23940"
                     /old_locus_tag="HUZ49_23805"
     CDS             1538..3685
                     /gene="mobQ"
                     /locus_tag="HUZ49_RS23940"
                     /old_locus_tag="HUZ49_23805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     Typing          complement(1361..1537)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1538..1896
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..571)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1452..3682
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgattatcat cttattcaag tctttgaatt gttgatattt atcttcaacg gcaagcatgg
       61 ttcggaaatc atcgatagct atcgttctgt caccggtgct gcggaactgc tggagcagct
      121 cgtaaatgcg gatgctgtag gtgctggaaa ggctggagac gttcttcacg actacccgcg
      181 taaactgccc cttgagctgt gtcagatacg gcatgatggc atcggagaag gtgatatcta
      241 ctttcgcctc acctttgaaa tactgcgccc ggtactgcac ccagcggaac tcttctcgtt
      301 tttcctcgtt cttgatgatt actgacctgt cccagaggcg atctatcgct tccttgagcc
      361 tagcttcagc gtgctgccgt cccatgtcag gaaaggcatc atgaaactct gcagccgtga
      421 tggtcatggt tttttgttca tccggcgaag gggaatcttc tccggatttt aggcggctga
      481 tacagaccag caggaagcgc tgttcctgca aagtgagctt gtagcttgcc tcgataaggg
      541 cgtttgattt gtaagctatc agatctgaca tttcgcttgc tcgttgctat tggtggcgtt
      601 tttttactgt acgccactta tcatatgggt ggaagttttt tttttgcaac cccctttttc
      661 tgtggattac acccccaaaa gctccacctt tcacccccaa aagctccacc tttcaccccc
      721 aaaagctcca cctttcaccc ccaaaagctc cacttatctt gccagaacat ctttaaaatc
      781 atggtgttac aagacctaaa aaggttttaa aaaaaaagat ctaaaaataa gatcttaaaa
      841 acttaacggc gagcctgtgg ataacttggg gtgctgaaaa caaaaaacca ataaaaacaa
      901 tgcgttgcaa taaagcagaa ttgcaagttt cgaatacacc ccctccaacc ctgtggaaac
      961 ccagtattca tgcgggttca gcgcatatca cctgccgaaa aaccgtgcgt atgtgctcaa
     1021 cctggcgact gattcacttc cgcttcctcg cccactcgct cgctaacgct cggtcgctgg
     1081 ggctgcggcg agcggacgat acaatcactg ttctggcagc gcctccagct cgttaatcag
     1141 cggcagtatg cgcgtcacat cagcctgtcg tgtcacctct gccttcagga actggagtaa
     1201 ccaggcacgc aactgcacct cctccggctt tctgaccttt gccagcaatg cagcacccac
     1261 aacaaccttc tgcgctgtgt ccaggctccg gctcttcgcc ttcaggcgct gtaatctcgc
     1321 ctcagcatca gcaatcttct gttcgagcgt tctgctcatg atgtaactcc gtgcgcgatg
     1381 aaaaatcgca ttttagcgcg tcactggtag tttaaaaact gagctggcat aatgcacggc
     1441 aaatcacgaa gtgcgcactt atacaatctc cactccgttt cgattgtgtg cgccctgcgg
     1501 ggctgaaaga aaactacaaa aaggcattac ggcagaaatg gcgatttatc atctcagcat
     1561 gaaaattatc tccagaagca gcggctacag cgccgtagct tccgctgcct atcgttccgg
     1621 ttcactgatg cttgatgagc gtaccggact gactcacgac tacacccgca aaagcggtgt
     1681 ggctgaggct gtgattctga cccccgccac cgcccctgcc tggtgtacga accgtgccga
     1741 actctggaat gccgttgaga aggccgaacg ccggaagaac tcacaacttg cgcgggaaat
     1801 tgaactcgcc atcccccacg aactgccgca ggatgccgca cgggaaaccg ttctcgcctt
     1861 tgtcagagaa aactttgtca gtcagggcat gattgctgat gtggcgttcc atcacatgga
     1921 taaaacaaat ccccatgcgc acatcatgct gaccacgagg gctatcggac ctgctgggtt
     1981 cagcggaaag gtcagggact ggaacgaccg gacacatgcc gagacgtggc gggcatcatg
     2041 ggctgaccat gcaaacaggg cactggcgaa cgccggttat caggaagaga tagaccatcg
     2101 ttcatacgag cgacaggggc ttgagaaaac gcctggtatt cacctcggaa agtctgcctg
     2161 tgcgatggaa acacgcggta tcgaaacaga acgcggcgaa cagaatcgtc tgattaacag
     2221 gcttaacctg gaaatacaga tttcccgcac cgaactcagg aacggagggc tgacagagcc
     2281 tgcccgccgt gtggctgacc ttctgaatat cgggcttcct gacaacgcaa cttcgtacac
     2341 actacgtgac attatcgaag cgttgccgaa ggacagtaac tcggcatgga aactcaccag
     2401 taatgccatg tcgatgatgg cagatatgca ggcgacgcgc agacgctggg aagagctgaa
     2461 caccgaacga aaggaagcga tgagccatgc tgccagcctg aaaaaatcat cgccgttttc
     2521 gtccggtttt tcccgtattc ccctgatgca atgggcggca ccggaatacc gtagtgagca
     2581 gggaaaaatc cagtctctga gccagcaaat ggaaaaatta cgacagcatt accggaaggt
     2641 ggagaaacag gacattcccg cgagtcagat ggcatttgaa aaacagtggc agcagtgggg
     2701 ggaatccggc cttgcagctc tcagagccca gttgcttaaa cgtgaagagg aattgcgccg
     2761 gaaggaacag gaagatactg aacgtagtcg cgcggagcag ctcaggaaaa atgacaatgc
     2821 cgttatggat tcaggggtgc tgagagcagt cgttacgggg tatggcgagg ctcccatgcc
     2881 tggtaacggg gaaatgacct gttaccttct gcttcacaac cggaacggag aatatacgct
     2941 ctgggggaac gagctggaga aataccgcac cagaatcttt gagagtgttg atttaatgcg
     3001 tgacaggagt ggttatatct gtgaccgaag cgaaatcggc caacgtccgc cactgcaacg
     3061 tgtttattcc tctgcaacct ttgagcaact gctgacgcag gtttgccaga catggccgca
     3121 acatacccgc aatctccgcc agccgaagac atggccggag tctttctgtc ttggagaaga
     3181 ccgccagcca gccatgccat caccagcggc aaggaaggtg gattttatgc agggacgtct
     3241 gccaccgacg ctgatgccgg tcatgagttc tgtcgaccgg gaaacccgcc agcttcagct
     3301 tttgctggtc atgggcgtgg atgactctct gggcggtgtt atccggctta atggtacgct
     3361 gtatcccgcg tttgccgttc cctcagccga taacaggcat ctggtcatca gtgcgctgac
     3421 cgataagggg ttacggtatg cagggtatgg tgttgccgta aatcacgatg cagacagcca
     3481 catatcacct gcaccagaac tgatgcagtt tcatctgaaa acccgtgagg caccgctttt
     3541 tgctgccgtc aacacaccag aaaaacagcc ggatcatctg ttccgctcgc tgggttttaa
     3601 tcgtacctgg gaggaatggc agcgcgagga agatgcacga acacacacca ccgagaggag
     3661 acatgatcgc ggttggtcac agtgaatgtg aacaatattt tgttttgttt aacatcgtgt
     3721 tatgttcgtc gatgttcttc gatgttcatc gacagggatg aatgcaagaa gcacactcac
     3781 ataacgcaag catagttttg tttttccgcc cccaaaaatt ggggggtctt ttttcgctgc
     3841 atcagagcgt ttttgacgca atttttcact tcaatagtac cttcgcacta ctaacacaaa
     3901 aaaaacgcag cagggagcgt tttaggtgcc ttaaaatcga ttttagatcg tcatcttgat
     3961 ctgtttgtct tccttgaagc gaaaatgcag ggctacaacc gtgcgcccct ttttgatcgt
     4021 ctcaacagtt acaaccagat cgcttttttc gttcagttcg gcgatggctg gct
//
