LOCUS       NZ_CP128259             4082 bp    DNA     circular CON 28-JUN-2023
DEFINITION  Escherichia coli strain T309.Ta3 plasmid pT309.Ta3_4, complete
            sequence.
ACCESSION   NZ_CP128259
VERSION     NZ_CP128259.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35706290
            Assembly: GCF_030344975.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4082)
  AUTHORS   Lai,G.K.K., Leung,K.M., Leung,F.C.C. and Griffin,S.D.J.
  TITLE     Complete genome sequence of Escherichia coli T309.Ta3, an equine gut
            isolate
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4082)
  AUTHORS   Lai,G.K.K., Leung,K.M., Leung,F.C.C. and Griffin,S.D.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUN-2023) 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                     :: 09-MAY-2023
            Assembly Method                   :: Unicycler v. v0.4.8-beta
            Assembly Name :: SG_R102S22_Novo04_01_50Flow2_T309.Ta3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 277.0x
            Sequencing Technology :: Illumina NovaSeq; Illumina MiSeq; Oxford
            Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/26/2023 23:37:17
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,377
            CDSs (total)                      :: 5,257
            Genes (coding)                    :: 5,024
            CDSs (with protein)               :: 5,024
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 233
            CDSs (without protein)            :: 233
            Pseudo Genes (ambiguous residues) :: 0 of 233
            Pseudo Genes (frameshifted)       :: 88 of 233
            Pseudo Genes (incomplete)         :: 150 of 233
            Pseudo Genes (internal stop)      :: 59 of 233
            Pseudo Genes (multiple problems)  :: 56 of 233
            Pseudo Genes (short protein)      :: 4 of 233
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP128259.1.
            Bacteria and source DNA available from Dr. Simon D. J. Griffin,
            Shuyuan Molecular Biology Laboratory, The ISF Academy, 1 Kong Sin
            Wan 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..4082
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="T309.Ta3"
                     /isolation_source="feces"
                     /host="Equus ferus caballus"
                     /db_xref="taxon:562"
                     /plasmid="pT309.Ta3_4"
                     /geo_loc_name="Hong Kong: Ho Sheung Heung"
                     /lat_lon="22.514832 N 114.108248 E"
                     /collection_date="2021-03-21"
                     /collected_by="Simon D. J. Griffin"
     gene            complement(join(3788..4082,1..1865))
                     /gene="mobQ"
                     /locus_tag="QRX22_RS26875"
                     /old_locus_tag="QRX22_26875"
     CDS             complement(join(3788..4082,1..1865))
                     /gene="mobQ"
                     /locus_tag="QRX22_RS26875"
                     /old_locus_tag="QRX22_26875"
                     /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_062850896.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELDTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            2044..2298
                     /gene="mobC"
                     /locus_tag="QRX22_RS26880"
                     /old_locus_tag="QRX22_26880"
     CDS             2044..2298
                     /gene="mobC"
                     /locus_tag="QRX22_RS26880"
                     /old_locus_tag="QRX22_26880"
                     /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_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2831..3532
                     /locus_tag="QRX22_RS26885"
                     /old_locus_tag="QRX22_26885"
     CDS             2831..3532
                     /locus_tag="QRX22_RS26885"
                     /old_locus_tag="QRX22_26885"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1508..1866)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1867..2043
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2832..3532
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..1952)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.692"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tcggctgagg gaacggcaaa cgcgggatac agcgtaccat taagccggac aacaccgccc
       61 agagagtcat ccacgcccat gaccagcaaa agctgaagct ggcgggtttc ccggtcgaca
      121 gaactcatta ccggcatcag cgtcggtagc agacgtccct gcgtaaaatc caccttcctt
      181 gctgccagtg atggcatggc tggctggcgg tcttctccaa gacagaaaga ctccggccat
      241 gtcttcggct ggcggagatt gcgggtatat tgcggccatg tctggcaaac ctgcgtcaga
      301 agttgctcaa aggtcgcaga ggaataaaca cgttgcagtg gtggatgttg accgatttcg
      361 cttcggtcac agatataacc actcctgtca cgcattaaat caacacgctc aaagattctg
      421 gtgcggtatt tctccagctc gttcccccag agcgtgtatt ctccgttccg gttgtgaagc
      481 agaaggtaac aggtcatttc cccgttacca ggcatggggg cctcgccata ccccgtaacg
      541 actgcgctca gtacccctga atccataacg gcattgtcat ttttcctgag ctgttccgct
      601 cgtcgctccg cgcgactacg ttctgtatcc tcctgctcct tccggcgcaa ttcctcttca
      661 cgtttaagca actggactct gagagctgca aggccggatg ccccccactg ctgccactgt
      721 ttttcaaatg ccgtctgact cgcgggaatg tcctgtttct ccaccttccg gtaatgctgt
      781 cgcaattttt ccatttgctg gctcagcgac tggatttttc cctgttcgct acggtattcc
      841 ggtgccgccc attgcatcag gggaatacgg gaaaaaccgg acgaaaacgg cgatgatttt
      901 ttcaggctgg cagcatggct catcgcttcc tttcgttcgg tgtccagctc ttcccagcgt
      961 ctgcgcgtcg cctgcatatc tgccatcatc gacatggcat tactggtgag tttccatgcc
     1021 gcattactgt ccttcggcaa cgcttcgatg atgtcacgta gtgtgtacga agttgcgttg
     1081 tcaggaagca cgatattcag aaggtcagcc acacggcggg caggctctgt cagcccgctg
     1141 tttctgagtt cggtacggga aatctgtatt tccaggttaa gtctgttaat cagacgattc
     1201 tgttcgccgc gttctgtttc gataccgcgt gtttccatcg cacaggcaga ctttccgagg
     1261 tgaataccag gcgttttctc aagcccctgt cgctcgtatg aacgatggtc tatctcttcc
     1321 tgataaccgg cgttcgccag tgccctgttc gcatggtcag cccatgatgc acgccacgtc
     1381 tcggcatgtg tccggtcgtt ccagtccctg acctttccac cgaatccagc aggtccgaca
     1441 gctctcgtgg tcagcatgat gtgcgcatgg ggatttgttt tatccatgtg atggaacgcc
     1501 acatcagcaa tcatgccctg actgacaaag ttttctctga caaaggcgag aacggtttcc
     1561 cgtgcggcat cctgcggtag ttcgcggggg atggcgagtt caatttcccg cgcaagttgt
     1621 gagttcttcc ggcgttcggc cttctcaacg gcattccaga gttcggcacg gttcgtacac
     1681 caggcagggg ctgtcgcggg agtcagaatc acagcttcag ccacaccgct tttgcgggtg
     1741 tagtcgtgag tcagtccggt acgctcatca agcatcagtg aaccggaacg ataggcagca
     1801 gaagcaacgg cgctgtagcc gctgtttctg gagatgattt tcatgctgag atgataaatc
     1861 gccatttctg ccgtaatgcc tttttgtggt tttctttcag ccccgcaggg cgcacacaat
     1921 cgaaacggag tggagattgt ataagtgcgc acttcgtgat tttccgtgca ttatgccagc
     1981 tcagttttta aactaccagt gacgcgctaa aatgcgattt ttcatcgcgc acggagttac
     2041 atcatgagca gaacactcga acagaagatt gctgatgctg aggccagatt acagcgcctg
     2101 aaggcgaaga gcaggagtct ggacacagcg cagaaggtca ttgtgggtgc agcattgctg
     2161 gcaaaggtca gaaagccgga ggaggtgcag ttgcgtgcct ggttactcca gttcctgaag
     2221 gcagaggtga cacgacaggc tgatgtgacg cgcatactgc cgctgattaa cgagctggaa
     2281 gcgctgccag gacagtgatt gtatcgtccg ctcgccgcag tcccagcgac cgagcgttag
     2341 cgagcgagtg ggcgaggaag cggaagtgaa tccgtcgcct gattgagcac atacgcacgg
     2401 tttttcggga ggtgatatgc gctgaacccg catgaatact ggatttccac agggttggag
     2461 ggggtgtatt cggaacttgc aattctgctt ttttgcaacg cattgttttt attggttttt
     2521 tgttttcagc actccaagtt atccacaggc tcgtcgttaa gtttttagat cttgttttta
     2581 agatcttgtt tttaatactt gttttagcgc caaaattcct tatagaaaac aaaatgttac
     2641 aacgctatag gtaatatgat ttaaggtaaa ggtaatatga tttaaggtgt ttaggtggag
     2701 gaatttaagg taaaggcaat atgatttaag gtaatattca cagaaaaagg gatattaaaa
     2761 taaaaaggca ttgcctttcg ttgagggtat gtttatcttt tattcattac cttttgggga
     2821 gggatgctct atgtcggatc taattgccta taaatccaat gcgctggttg aagccagtta
     2881 taaattgacc ctacaggaac agcgattttt gttactttgc atcggtcgat tgaagtctgg
     2941 ggctgatgca gaatctccaa aattgcaaaa gacaatgacc attacagctg cggaatattt
     3001 cgattcattc cctgacatgg ggcggaaaaa tgccgaggtt cagttacagg aagcaattga
     3061 tcgtttgtgg gacaggtcaa tcattctcaa ggatgacgag aaacgtgagg agttccgctg
     3121 gatccagtat cgggcacagt acgctaaagg cgaggccaga gcacaaataa cattttctga
     3181 cgcagtaatg ccttatttga cacaactaca agggcaattt actagagttg taatcaagaa
     3241 tatatctaga ttatcaagaa gttacagtat aaggatatac gaactcctcc agcagttccg
     3301 cagtactggc gaacgtatta tcgctctcga tgattttcgc tcaatgcttg atatagagca
     3361 taaatatcaa acatataaat cacttaacca gcaattatta agaccctgca ttgacgaact
     3421 gaacaaaaaa agcgacctgg ctgtaacggt tgagacgatc aaaaaggggc gcacggttgt
     3481 agccctgcat tttcgcttca aggaagacaa acaaatcaag atgacgatct aaaatcgatt
     3541 ttaaggcacc taaaacgctc cctgctgcgt tttttttgtg ttagtagtgc gaaggtacta
     3601 ttgaagtgaa aaattgcgtc aaaagcgctc taatgcagcg aaaaaataac ccccaatttt
     3661 tgggggcgga aaaacaaaac tatgcttgca ttatgtgtgt gcttcttgca ttcatccctg
     3721 tcgatgaaca tcgaagaaca tcgacgaaca taacacgatg ttaaacaaaa caaaatattg
     3781 ttcacattca ctgtgaccaa ccgcgatcat gtctcctctc ggtggcgtgt gttcgtgcat
     3841 cttcctcgcg ccgccattcg tcccaggtac gattaaaacc cagcgagcgg aacagatgat
     3901 ccggctgttt ttctggtgtg ttgacggcag caaaaagcgg tgcctcacgg gttttcagat
     3961 gaaactccat aagttccggc gcaggtgata tgtggctgtc tgcatcgtga tttacggcaa
     4021 caccataccc tgcataccgt aaccccttat cggtcagtgc actgatgacc agctggctgt
     4081 ta
//
