LOCUS       NZ_CP097369             4072 bp    DNA     circular CON 16-JUN-2024
DEFINITION  Escherichia coli strain AGR6128 plasmid unnamed, complete sequence.
ACCESSION   NZ_CP097369
VERSION     NZ_CP097369.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28215601
            Assembly: GCF_023546845.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Burgess,S., Moinet,M., Brightwell,G. and Cookson,A.
  TITLE     Whole genome sequence analysis of ESBL-producing Escherichia coli
            recovered from New Zealand freshwater sites
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   Burgess,S., Moinet,M., Brightwell,G. and Cookson,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-MAY-2022) School of Veterinary Science, Massey
            University, Tennent Drive, Palmerston North 4474, New Zealand
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: NOV-2021
            Assembly Method                   :: Unicycler v. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 107x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023546845.1-RS_2024_06_16
            Annotation Date                   :: 06/16/2024 06:46:33
            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)                     :: 4,871
            CDSs (total)                      :: 4,755
            Genes (coding)                    :: 4,539
            CDSs (with protein)               :: 4,539
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 216
            CDSs (without protein)            :: 216
            Pseudo Genes (ambiguous residues) :: 0 of 216
            Pseudo Genes (frameshifted)       :: 76 of 216
            Pseudo Genes (incomplete)         :: 168 of 216
            Pseudo Genes (internal stop)      :: 44 of 216
            Pseudo Genes (multiple problems)  :: 59 of 216
            Pseudo Genes (short protein)      :: 1 of 216
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP097369.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AGR6128"
                     /isolation_source="water"
                     /db_xref="taxon:562"
                     /plasmid="unnamed"
                     /geo_loc_name="New Zealand: Tapuata Stream"
                     /collection_date="2021-02-23"
     gene            join(3073..4072,1..1148)
                     /gene="mobQ"
                     /locus_tag="M7747_RS24310"
                     /old_locus_tag="M7747_24310"
     CDS             join(3073..4072,1..1148)
                     /gene="mobQ"
                     /locus_tag="M7747_RS24310"
                     /old_locus_tag="M7747_24310"
                     /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_032495499.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGKSGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(1406..2107)
                     /locus_tag="M7747_RS24315"
                     /old_locus_tag="M7747_24315"
     CDS             complement(1406..2107)
                     /locus_tag="M7747_RS24315"
                     /old_locus_tag="M7747_24315"
                     /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(2640..2894)
                     /gene="mobC"
                     /locus_tag="M7747_RS24320"
                     /old_locus_tag="M7747_24320"
     CDS             complement(2640..2894)
                     /gene="mobC"
                     /locus_tag="M7747_RS24320"
                     /old_locus_tag="M7747_24320"
                     /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"
     Typing          complement(2896..3072)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3073..3431
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1407..2107)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..1145
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.545"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2987..4071
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.514"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttcccctgat gcaatgggcg gcaccggaat accgtagtga gcagggaaaa atccagtctc
       61 tgagccagca aatggaaaaa ttacgacagc attaccggaa ggtggagaaa caggacattc
      121 ccgcgagtca gatggcattt gaaaaacagt ggcagcagtg ggggaaatcc ggccttgcag
      181 ctctcagagc ccagttgctt aaacgtgaag aggaattgcg ccggaaggaa caggaagata
      241 ctgaacgtag tcgcgcggag cagctcagga aaaatgacaa tgccgttatg gattcagggg
      301 tgctgagagc agtcgttacg gggtatggcg aggctcccat gcctggtaac ggggaaatga
      361 cctgttacct tctgcttcac aaccggaacg gagaatatac gctctggggg aacgagctgg
      421 agaaataccg caccagaatc tttgagagtg ttgatttaat gcgtgacagg agtggttata
      481 tctgtgaccg aagcgaaatc ggccaacgtc cgccactgca acgtgtttat tcctctgcaa
      541 cctttgagca actgctgacg caggtttgcc agacatggcc gcaacatacc cgcaatctcc
      601 gccagccgaa gacatggccg gagtctttct gtcttggaga agaccgccag ccagccatgc
      661 catcaccagc ggcaaggaag gtggatttta tgcagggacg tctgccaccg acgctgatgc
      721 cggtcatgag ttctgtcgac cgggaaaccc gccagcttca gcttttgctg gtcatgggcg
      781 tggatgactc tctgggcggt gttatccggc ttaatggtac gctgtatccc gcgtttgccg
      841 ttccctcagc cgataacagg catctggtca tcagtgcgct gaccgataag gggttacggt
      901 atgcagggta tggtgttgcc gtaaatcacg atgcagacag ccacatatca cctgcaccag
      961 aactgatgca gtttcatctg aaaacccgtg aggcaccgct ttttgctgcc gtcaacacac
     1021 cagaaaaaca gccggatcat ctgttccgct cgctgggttt taatcgtacc tgggaggaat
     1081 ggcagcgcga ggaagatgca cgaacacaca ccaccgagag gagacatgat cgcggttggt
     1141 cacagtgaat gtgaacaata ttttgttttg tttaacatcg tgttatgttc gtcgatgttc
     1201 ttcgatgttc atcgacaggg atgaatgcaa gaagcacact cacataacgc aagcatagtt
     1261 ttgtttttcc gcccccaaaa attggggggt cttttttcgc tgcatcagag cgtttttgac
     1321 gcaatttttc acttcaatag taccttcgca ctactaacac aaaaaaaacg cagcagggag
     1381 cgttttaggt gccttaaaat cgattttaga tcgtcatctt gatctgtttg tcttccttga
     1441 agcgaaaatg cagggctaca accgtgcgcc cctttttgat cgtctcaaca gttacaacca
     1501 gatcgctttt ttcgttcagt tcggcgatgg ctggcttgat tatcatctta ttcaagtctt
     1561 tgaattgttg atatttatct tcaacggcaa gcatggttcg gaaatcatcg atagctatcg
     1621 ttctgtcacc ggtgctgcgg aactgctgga gcagctcgta aatgcggatg ctgtaggtgc
     1681 tggaaaggct ggagacgttc ttcacgacta cccgcgtaaa ctgccccttg agctgtgtca
     1741 gatacggcat gatggcatcg gagaaggtga tatctacttt cgcctcacct ttgaaatact
     1801 gcgcccggta ctgcacccag cggaactctt ctcgtttttc ctcgttcttg atgattactg
     1861 acctgtccca gaggcgatct atcgcttcct tgagcctagc ttcagcgtgc tgccgtccca
     1921 tgtcaggaaa ggcatcatga aactctgcag ccgtgatggt catggttttt tgttcatccg
     1981 gcgaagggga atcttctccg gattttaggc ggctgataca gaccagcagg aagcgctgtt
     2041 cctgcaaagt gagcttgtag cttgcctcga taagggcgtt tgatttgtaa gctatcagat
     2101 ctgacatttc gcttgctcgt tgctattggt ggcgtttttt tactgtacgc cacttatcat
     2161 atgggtggaa gttttttttt tgcaaccccc tttttctgtg gattacaccc ccaaaagctc
     2221 cacctttcac ccccaaaagc tccacctttc acccccaaaa gctccacctt tcacccccaa
     2281 aagctccact tatcttgcca gaacatcttt aaaatcatgg tgttacaaga cctaaaaagg
     2341 ttttaaaaaa aagatctaaa aataagatct taaaaactta acggcgagcc tgtggataac
     2401 ttggggtgct gaaaacaaaa aaccaataaa aacaatgcgt tgcaataaag cagaattgca
     2461 agtttcgaat acaccccctc caaccctgtg gaaacccagt attcatgcgg gttcagcgca
     2521 tatcacctgc cgaaaaaccg tgcgtatgtg ctcaacctgg cgactgattc acttccgctt
     2581 cctcgcccac tcgctcgcta acgctcggtc gctggggctg cggcgagcgg acgatacaat
     2641 cactgttctg gcagcgcctc cagctcgtta atcagcggca gtatgcgcgt cacatcagcc
     2701 tgtcgtgtca cctctgcctt caggaactgg agtaaccagg cacgcaactg cacctcctcc
     2761 ggctttctga cctttgccag caatgcagca cccacaacaa ccttctgcgc tgtgtccagg
     2821 ctccggctct tcgccttcag gcgctgtaat ctcgcctcag catcagcaat cttctgttcg
     2881 agcgttctgc tcatgatgta actccgtgcg cgatgaaaaa tcgcatttta gcgcgtcact
     2941 ggtagtttaa aaactgagct ggcataatgc acggcaaatc acgaagtgcg cacttataca
     3001 atctccactc cgtttcgatt gtgtgcgccc tgcggggctg aaagaaaact acaaaaaggc
     3061 attacggcag aaatggcgat ttatcatctc agcatgaaaa ttatctccag aagcagcggc
     3121 tacagcgccg tagcttccgc tgcctatcgt tccggttcac tgatgcttga tgagcgtacc
     3181 ggactgactc acgactacac ccgcaaaagc ggtgtggctg aggctgtgat tctgaccccc
     3241 gccaccgccc ctgcctggtg tacgaaccgt gccgaactct ggaatgccgt tgagaaggcc
     3301 gaacgccgga agaactcaca acttgcgcgg gaaattgaac tcgccatccc ccacgaactg
     3361 ccgcaggatg ccgcacggga aaccgttctc gcctttgtca gagaaaactt tgtcagtcag
     3421 ggcatgattg ctgatgtggc gttccatcac atggataaaa caaatcccca tgcgcacatc
     3481 atgctgacca cgagggctat cggacctgct gggttcagcg gaaaggtcag ggactggaac
     3541 gaccggacac atgccgagac gtggcgggca tcatgggctg accatgcaaa cagggcactg
     3601 gcgaacgccg gttatcagga agagatagac catcgttcat acgagcgaca ggggcttgag
     3661 aaaacgcctg gtattcacct cggaaagtct gcctgtgcga tggaaacacg cggtatcgaa
     3721 acagaacgcg gcgaacagaa tcgtctgatt aacaggctta acctggaaat acagatttcc
     3781 cgcaccgaac tcaggaacgg agggctgaca gagcctgccc gccgtgtggc tgaccttctg
     3841 aatatcgggc ttcctgacaa cgcaacttcg tacacactac gtgacattat cgaagcgttg
     3901 ccgaaggaca gtaactcggc atggaaactc accagtaatg ccatgtcgat gatggcagat
     3961 atgcaggcga cgcgcagacg ctgggaagag ctgaacaccg aacgaaagga agcgatgagc
     4021 catgctgcca gcctgaaaaa atcatcgccg ttttcgtccg gtttttcccg ta
//
