LOCUS       NZ_CP091775             5969 bp    DNA     circular CON 20-DEC-2023
DEFINITION  Escherichia coli strain SWYH.B349aT plasmid pB349aT_2, complete
            sequence.
ACCESSION   NZ_CP091775
VERSION     NZ_CP091775.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25378667
            Assembly: GCF_022014695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5969)
  AUTHORS   Hui,S.W., Lai,G.K., Griffin,S.D. and Leung,F.C.
  TITLE     Complete genome sequence of Escherichia coli SWYH.B349aT isolated
            from feces of a Thoroughbred racehorse (Equus ferus caballus)
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5969)
  AUTHORS   Hui,S.W., Lai,G.K., Griffin,S.D. and Leung,F.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-JAN-2022) Shuyuan Molecular Biology Laboratory, The
            Independent Schools Foundation Academy, 1 Kong Sin Wan Road,
            Pokfulam, Hong Kong HK SAR, Hong Kong
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 26-JAN-2022
            Assembly Method                   :: Unicycler v. 0.4.8-beta
            Assembly Name                     :: Selina_Ecoli_SWYH.B349aT
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 70.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/20/2023 03:48:34
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,856
            CDSs (total)                      :: 4,736
            Genes (coding)                    :: 4,478
            CDSs (with protein)               :: 4,478
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 258
            CDSs (without protein)            :: 258
            Pseudo Genes (ambiguous residues) :: 0 of 258
            Pseudo Genes (frameshifted)       :: 82 of 258
            Pseudo Genes (incomplete)         :: 161 of 258
            Pseudo Genes (internal stop)      :: 48 of 258
            Pseudo Genes (multiple problems)  :: 34 of 258
            Pseudo Genes (short protein)      :: 5 of 258
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091775.1.
            Bacteria and source DNA available from Dr. Simon D. J. Griffin,
            Shuyuan Molecular Biology Laboratory, ISF Academy, 1 Kong Sin Road,
            Pokfulam, Hong Kong.
            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..5969
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SWYH.B349aT"
                     /isolation_source="feces"
                     /host="Equus ferus caballus (Thoroughbred)"
                     /db_xref="taxon:562"
                     /plasmid="pB349aT_2"
                     /geo_loc_name="Hong Kong: New Territories"
                     /lat_lon="22.514941 N 114.108267 E"
                     /collection_date="2020-03-21"
                     /collected_by="Simon D. J. Griffin"
     gene            join(5823..5969,1..87)
                     /locus_tag="L6V99_RS24120"
                     /old_locus_tag="L6V99_24120"
     CDS             join(5823..5969,1..87)
                     /locus_tag="L6V99_RS24120"
                     /old_locus_tag="L6V99_24120"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(815..1399)
                     /locus_tag="L6V99_RS24125"
                     /old_locus_tag="L6V99_24125"
     CDS             complement(815..1399)
                     /locus_tag="L6V99_RS24125"
                     /old_locus_tag="L6V99_24125"
                     /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_001708514.1"
                     /translation="MAAFIFDTGLNFSKENITKGVISTRWHNDLYSSFERMKAINKIYY
                     PSNKEINTEGLSKAITSSLFNDDANSFAKRDFRLMWDLSSEKYLSYKEIIIRKGDKLDA
                     VCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPSLKTYRALSRLVNSIKDPSRFKFTTES
                     LEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            1537..2765
                     /locus_tag="L6V99_RS24130"
                     /old_locus_tag="L6V99_24130"
     CDS             join(1537..1852,1852..2765)
                     /locus_tag="L6V99_RS24130"
                     /old_locus_tag="L6V99_24130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558215.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS3-like element IS2 family transposase"
                     /protein_id="WP_088895425.1"
                     /translation="MIDVLGPEKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQ
                     LFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKELQRLLGKKTMENELLKEAVEYG
                     RGKKVDSARALIARGWGVSLVSRCLRVSRAQLHVILRRTDDWMDGRRSRHTDDTDVLLR
                     IHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNALLLERKPAVPPSKR
                     AHTGRVAVKESNQRWCSDGFEFCCDNGERLRVTFALDCCDREALHWAVTTGGFNSETVQ
                     DVMLGAVERRFGNDLPSSPVEWLTDNGSCYRANETRQFARMLGLEPKNTAVRSPESNGI
                     AESFVKTIKRDYISIMPKPDGLTAAKNLAEAFEHYNEWHPHSALGYRSPREYLRQRACN
                     GLSDNRCLEI"
                     /name="IS3-like element IS2 family transposase"
     gene            complement(3182..3331)
                     /locus_tag="L6V99_RS24330"
     CDS             complement(3182..3331)
                     /locus_tag="L6V99_RS24330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     gene            complement(4001..4192)
                     /locus_tag="L6V99_RS24135"
                     /old_locus_tag="L6V99_24135"
     CDS             complement(4001..4192)
                     /locus_tag="L6V99_RS24135"
                     /old_locus_tag="L6V99_24135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4255..4578
                     /locus_tag="L6V99_RS24140"
                     /old_locus_tag="L6V99_24140"
     CDS             4255..4578
                     /locus_tag="L6V99_RS24140"
                     /old_locus_tag="L6V99_24140"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4787..>5227
                     /locus_tag="L6V99_RS24145"
                     /old_locus_tag="L6V99_24145"
                     /pseudo=""
     CDS             4787..>5227
                     /locus_tag="L6V99_RS24145"
                     /old_locus_tag="L6V99_24145"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            5256..5816
                     /locus_tag="L6V99_RS24150"
                     /old_locus_tag="L6V99_24150"
     CDS             5256..5816
                     /locus_tag="L6V99_RS24150"
                     /old_locus_tag="L6V99_24150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     Typing          3829..3913
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(3260..3818)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.761"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4569..5968
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.786"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgtgtcgtga acttgagtca gcaggtgcag ctattagccg gacaagtcga ccgcttgagt
       61 cggttattta tcacgaacaa cagataaggg atgaacagga gcgtcaggcg caggagcttg
      121 cccggcgctg gcatgaagag caggaacccg aagcgcggat ctggcgtggc ccgtcaatgg
      181 ggatgtgacc ggggtgcccc ctgaaatcga gccagtttgt ggcacgccct acccggatgg
      241 cgccaatgtt aatgtacgta cattagcatt aacaatatcc aaacctcccc attttgcccc
      301 gttcgacggc tggaacgtgc gaaactgatc gtcattcagt ttcgcgcata actatgcatg
      361 aggttaaaat ttaccaggcg cgatcgcggc agtttttcgg gtggtttgtt gctgttttta
      421 cctgtctgct gccgtgatcg cgctgaacgc gtttaagcgg tacgcgcaat gcgacgttat
      481 ggtaaatacg gagtatttta attgcgggaa ttaaaacaac aaaggcccgc tgtactctat
      541 acagcgggcc tttgttgtat atctctgtcg tttgtccccg gggggaagca ttactgctaa
      601 caagtcccgt gagaaaactg cgcaatcgta ttgcgcacca tgaacctatt ctcaaccgca
      661 atctggagga tgattttgct acgataaaga gaattatcgc gtatcggtgt cagcattcat
      721 tggagtggat gctgaaaaac caggtgttac tccctctact tacacttaaa cctctctaaa
      781 aatataagta agtactatcg agggctatca tgaactatgg tgccctctga gcatagctac
      841 ccattacttc ttctatgtca ttgaataatt catttcttaa ctctaagtat tctagtaact
      901 ccatttctaa tgactctgtc gtgaacttaa atctagaagg atctttgatt gagtttacta
      961 gtcttgataa cgctctatat gttttgagtg aaggttgcat tatagatgga aagtatttga
     1021 aaacctcttc atctctgttg aaattaacta aaaacttgta gtcatcattt ataaatctca
     1081 agcatacagc gtcaagctta tcgccttttc ttattattat ttctttatag gaaagatatt
     1141 tttcagaaga taagtcccac atcaagcgaa aatctctctt tgcgaacgag ttcgcgtcat
     1201 cattgaaaag agatgatgtg atggctttgg atagaccttc tgtgtttatc tctttgttgg
     1261 atgggtagta aattttatta attgctttca ttctctcaaa tgatgaatat aggtcattat
     1321 gccaccttgt tgaaatcacc cctttagtta tattctcctt gctaaaatta agccctgtat
     1381 caaaaataaa tgcagccatc agtgaatatg atatgttttt tattaactca gacttaaatg
     1441 gttcctagac tggccccctg aatctccaga caaccagtat cacttaaata agtgatagtc
     1501 ttaatactag tttttagact agtcattgga gaacagatga ttgatgtctt agggccggag
     1561 aaacgcagac ggcgtaccac acaggaaaag atcgcaattg ttcagcagag ctttgaaccg
     1621 gggatgacgg tctccctcgt tgcccggcaa catggtgtag cagccagcca gttatttctc
     1681 tggcgtaagc aataccagga aggaagtctt actgctgtcg ccgccggaga acaggttgtt
     1741 cctgcctctg aacttgctgc cgccatgaag cagattaaag aactccagcg cctgctcggc
     1801 aagaaaacga tggaaaatga actcctcaaa gaagccgttg aatatggacg ggcaaaaaag
     1861 tggatagcgc acgcgccctt attgcccggg gatggggagt aagcttagtc agccgttgtc
     1921 tccgggtgtc gcgtgcgcag ttgcacgtca ttctcagacg aaccgatgac tggatggatg
     1981 gccgccgcag tcgtcacact gatgatacgg atgtgcttct ccgtatacac catgttatcg
     2041 gagagctgcc cacgtatggt tatcgtcggg tatgggcgct gcttcgcaga caggcagaac
     2101 ttgatggtat gcctgcgatc aatgccaaac gtgtttaccg gatcatgcgc cagaatgcgc
     2161 tgttgcttga gcgaaaacct gctgtaccgc catcgaaacg ggcacataca ggcagagtgg
     2221 ccgtgaaaga aagcaatcag cgatggtgct ctgacgggtt cgagttctgc tgtgataacg
     2281 gagagagact gcgtgtcacg ttcgcgctgg actgctgtga tcgtgaggca ctgcactggg
     2341 cggtcactac cggcggcttc aacagtgaaa cagtacagga cgtcatgctg ggagcggtgg
     2401 aacgccgctt cggcaacgat cttccgtcgt ctccagtgga gtggctgacg gataatggtt
     2461 catgctaccg ggctaatgaa acacgccagt tcgcccggat gttgggactt gaaccgaaga
     2521 acacggcggt gcggagtccg gagagtaacg gaatagcaga gagcttcgtg aaaacgataa
     2581 agcgtgacta catcagtatc atgcccaaac cagacgggtt aacggcagca aagaaccttg
     2641 cagaggcgtt cgagcattat aacgaatggc atccgcatag tgcgctgggt tatcgctcgc
     2701 cacgggaata tctgcggcag cgggcttgta atgggttaag tgataacaga tgtctggaaa
     2761 tataggggca aatccagttc cgctatggag tagtacagtg ataaaataac taaaaataaa
     2821 aggtattgtc ttacctttcc cgatgagtat atgtaaaggc gatatttatt tattgatagt
     2881 tttattttgt atggaatgat ctcatttctg tcatatcctc ttcgtggtgg agcaaaacaa
     2941 aagaaacatg cagctattaa taaaacaaaa aagatgaaca gtgtaagcaa gttcggctcc
     3001 tgtgtatgct cactatgcat gattgtcttg agatctaacg atcctgaagg tagtcttgtc
     3061 cgtaaacgaa aaaaccgccc agcaaggcgg cttttcgaag gttctcagag cagcaactct
     3121 ttgaaccaag gtaactggct tggaggagca cagccaccaa atctgtcctt tcagtttagc
     3181 cttaaccggc gcataacttc aagactaact cctctaaacg gttaccaatg gctgctgcca
     3241 gtggcgtttt tacgtgtctt tccgggttgg actcaagacg atagttaccg gataaggcgc
     3301 agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca
     3361 ccgggccgag ataccaacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa
     3421 aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagcttc
     3481 cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc
     3541 gtctgttttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc agcggcgcgg
     3601 ccttcttcct gttcttggcc ttttgctcac atgtttcttt tggcgttatc ccctgattct
     3661 gtggataacc gcatcaccgt ctttgagtga gctgataccg ctcgccgcag ccgaacgacc
     3721 gagcgtagcg agtcagtgag cgaggaagcg gaagagcgcc tgatgcggca ttttctcctt
     3781 acgcatctgt gcggtatttc acaccgcata tggtgcactt ttcttataat ccgcactgat
     3841 gccacatagt taagccagta tacactccgc tatcgctacg tgactgggtc agggctgcgc
     3901 cccgacaccc gctaaaaccc gctgacgcgc cctgacgggc ttgtctgctc ccggcatccg
     3961 ctcacaggca agctgtgaac gtctccggga gctgcatgtt tcagttgctt tcaccgtcat
     4021 cgccgaagcg tgcgaggcaa ctacggtaga gttcgtcggc gtggtcgtga agtgattcgc
     4081 agatgtctgc ctgttcgtcc gcgtccagct cgttgagttt ttccagcagg gtcagcgtct
     4141 ggcttctgat aaagcgggcc atgttaaggg ctgttttttc ctgtttggtc atggtcttaa
     4201 ggctccttaa taggggattt tttaggggga atgataccga tgaaacgcga gaagatgctc
     4261 acgatacggg ttagcgatga ggagcacgcc cggttactgg aacgctgcga gggtaaacga
     4321 ctggcagaat ggatgcggcg ggtctgtctg ggggagccgg ttgcgcgcac aggaaaactg
     4381 ccgacactat cgccgccatt gctgcggcat ctggctgcca tcgggaacaa tctgaaccag
     4441 acagcccgga aggtgaacag cggccactgg tcttcgattg accgggttca tgtggtggcc
     4501 gcactgatgg ccatcgaggg tgaattgcgc cagttgcggc aggctgtcag ggaacagggg
     4561 ggacgggatg atagttaaat ttcatgccag ggggaaaggc ggtggaagtg gcccggtcga
     4621 ttacctgctg gggcgggagc gtaaccgcga aggcgcaacg gtgctccggg gtaacccgga
     4681 agaaatccgg gaactcattg atgccacgcc attttcgaag aaatacacgt caggcgttct
     4741 gtcgttcgcg gagaaggagt taccgccggg tgaacgcgaa agagtgatga cgagctttga
     4801 gcgtgttctt atgcccggtc tcgaaaaaga ccagtacagc attctctggg tggaacacca
     4861 ggataagggg cggctcgaac tgaattttgt cattccgaac atggaactac agagcggtaa
     4921 gcgcctccag ccgtactacg accgtgcgga caggccgagg ataaatgcct ggcagacgct
     4981 ggttaatcat cattacgggc tgcgtgaccc gaacgcaccg gagaacagac ggacgcttgt
     5041 cacaccgaat aatctgccaa aagcgaaaca ggaggccgca gaagcgatta cacggggtct
     5101 tgaggcgctt taccgtgccg gagcaataaa aacgcgtcag gatgtcactg aggcgctcac
     5161 agcggcaggt tttgaggtgg tgaggacaac cagaagcagt atcagtattg ccgacccgga
     5221 gggggggcgg aatctcaggc taaagggggc gctgtatgag caatctttta caaatgggaa
     5281 cagacttcga gaagaaactg aaagagcgag ccgcttctac cgagaacatg ctgaacagcg
     5341 agttcaggaa gctagaagag tctgtagaca aggcactgag cttaaacagg cagaaaatca
     5401 gagacgctat cagcgaacat acaacatccg tgaaacagca actggatacg ctgagcacca
     5461 ccgtgagcac gcagctcagc accacagagg ccgaactgtc ccggcagcag aaaaacctgc
     5521 tctggcaggt gatcaaaggg cgggtactgt ttccggcgct gaccgcgctc agcgtcacgg
     5581 gcggcatttt cctggggtgc tgggggctga ttcagtggca ggaaagcagg attgcgaaaa
     5641 atatcttgac catcagagag caggaaaaca cgctggcgaa actcgaggca aaaacctggg
     5701 gggtgacgtt cgtcaatggc gagaacggga aatttctggt gctgccggac ggggtgaaag
     5761 gggaaaacac ctggacggtg ggcgacaaga acgccgtgag gctggtcagg gagtaaacga
     5821 gtatgacgga actggaaggg catttgctga acgccttaga gcatttgcaa caggactata
     5881 tgcggcggct gaacgagtgg gagagcgcct tcgcagaatt gcagaagatg cacgcggtta
     5941 cgcaacagaa caacgcgata ctgaacgag
//
