LOCUS       NZ_CP097362             5912 bp    DNA     circular CON 16-JUN-2024
DEFINITION  Escherichia coli strain AGR4587 plasmid unnamed, complete sequence.
ACCESSION   NZ_CP097362
VERSION     NZ_CP097362.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28215599
            Assembly: GCF_023546865.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5912)
  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  JOURNAL   Unpublished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 5912)
  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                   :: 78x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023546865.1-RS_2024_06_16
            Annotation Date                   :: 06/16/2024 05:48:48
            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)                     :: 5,105
            CDSs (total)                      :: 4,992
            Genes (coding)                    :: 4,748
            CDSs (with protein)               :: 4,748
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 244
            CDSs (without protein)            :: 244
            Pseudo Genes (ambiguous residues) :: 0 of 244
            Pseudo Genes (frameshifted)       :: 95 of 244
            Pseudo Genes (incomplete)         :: 183 of 244
            Pseudo Genes (internal stop)      :: 50 of 244
            Pseudo Genes (multiple problems)  :: 71 of 244
            Pseudo Genes (short protein)      :: 1 of 244
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP097362.1.
            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..5912
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AGR4587"
                     /isolation_source="water"
                     /db_xref="taxon:562"
                     /plasmid="unnamed"
                     /geo_loc_name="New Zealand: Tapuata Stream"
                     /collection_date="2020-03-02"
     gene            complement(join(5382..5912,1..1689))
                     /gene="vgrG"
                     /locus_tag="M7749_RS25470"
                     /old_locus_tag="M7749_25470"
     CDS             complement(join(5382..5912,1..1689))
                     /gene="vgrG"
                     /locus_tag="M7749_RS25470"
                     /old_locus_tag="M7749_25470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001574080.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type VI secretion system Vgr family protein"
                     /protein_id="WP_250011662.1"
                     /translation="MDVPVLNFDHSHHKLKIRGLQSPVDVLTFEGREQLSTPFRYDIQF
                     TSTDKAIAPESVLMQDGAFSLTAPPVQGMPVQTALRTLHGVITSFKHLSSSQDEARYEV
                     RLEPRMALLTRSRQNAIYQNLTVPQIVEKILRERHQMRGQDFVFNLKSAYPSREQVMQY
                     GEDDLTFVSRLLSEVGIWFRFATDARLKIEVVEFYDDQSGYERGLTLPLRHPSGLFDGE
                     TEAVWGLNTAYSVVEKNVTTRDYNYRTATAEMMTEQHDATGGDNTTYGEAYHYADNFLQ
                     KGDKEAAESGAFYARIRHERYLNEQAILKGQSTSSLLMPGLEIRVQGDDAPAVFRKGVL
                     ITGVTASAARDRSYELTFTAIPYSELYGYRPALIPCPVMAGTLPARVTSTVKNDIYAHI
                     DKDGRYRVNLDFDRDTWKPGYESLWVRQSRPYAGDTYGLHLPLLAGTEVSIAFEEGNPD
                     RPYIAGVKHDSAHTDHVTIQNYKRNVLRTPANNKIRLDDERGKEHIKVSTEYGGKSQLN
                     LGHLVDAGKQQRGEGFELRTDLWGAVRAKKGIFISADAQDKAQGQVVALITSRINDLTA
                     SVILMHAPKGVAVASGEHLQLAAVKNLQINAGNNADIGVVKNMFIGVGRALSVFVRKAG
                     IKLIANKGAVSVQAQHDLMELLAKKSIEIVSTEDEIRISAKKKITINGGGSYIRIEGSG
                     IEPGTPGDYNVKAVHYGRMGKAHEPVELQMLAEKVDEPPVKFFFS"
                     /name="vgrG"
     gene            complement(2153..3010)
                     /locus_tag="M7749_RS25475"
                     /old_locus_tag="M7749_25475"
     CDS             complement(2153..3010)
                     /locus_tag="M7749_RS25475"
                     /old_locus_tag="M7749_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001531916.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001531916.1"
                     /translation="MKKSFFLFLYFISLSAYPGDENAYIYGNDGTIEGIKYNYLDNVIK
                     FNIGDMSFDVFSKDNFFLKKCLLDNYSDSIDTGISFLTTDHEAIVFQSSGRFVLTKDVI
                     DICNSSEEKHAEVYPPVNIGMIADMNFRKNVALIYHPMGNISGKMVYQAELSKFVKKNY
                     RSSSFLTEVDPEKIQYLITGRFFYNGSYRDLEKKSYSGPFDLVSGVISPDAKYVDPFGL
                     GCDIDKVNHSIPHVYEISTAQRVAFKSDPALSAIINKEQIDKKCRQLLKASASLKDLGG
                     YLSQ"
                     /name="hypothetical protein"
     gene            complement(3007..5370)
                     /locus_tag="M7749_RS25480"
                     /old_locus_tag="M7749_25480"
     CDS             complement(3007..5370)
                     /locus_tag="M7749_RS25480"
                     /old_locus_tag="M7749_25480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000587242.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="M23 family metallopeptidase"
                     /protein_id="WP_000587242.1"
                     /translation="MIISPPFIRAKNNNENDAHWIERMMPVEPDRDYPINYGGSWHGGI
                     HVRHTNSDRQPEYVRAIADGVVVSIRNPSDQAACSLPPLNYNGSTDDGYVLLRHETEIG
                     TGEDGNIVYYSLYMHLEKIEEGISEGNKVYRKSSLGMPGHVDGDRGLHFQIFCDDDNLR
                     KITGRTTPEMDVSRHGRTDVVYGDIYFYLPPGTRFYRSAPENNAVDNTGEVFQSTEPLV
                     VTMCFDTGHCIMTTRRANPVIPSRYDIVGEVLTDADGTDYEYNLYSAALRLYPQSPSAG
                     FELLRFGRVINTEHETLIPANAPLWRTVSYPGGQGVINLAADVVTKFSDGDFPHWSGWR
                     LVDDDADSNSQCNSVILRGGGFTDFRQMICHFPLEWCNTGIEARYGWLKEGVIQERQEN
                     EANSDLSLGTDYYRPNNVEYNTTGDSHGESPQSAISEMPDLSYEQSNAYENAVRVLLLG
                     EEDWQTLVKHIKALCFDTSSIAEGRVWHFNPGEFIKHFRKCGWVDKAILKRIFASGTND
                     RDRAVIEQKVDIYGTAINIVMNKYIMNSPLRRAHFLGQGAVESSRLRSMQEKSQYQTVD
                     ENGRPVGGGIVPDSLRDENSDLGHWYGAIETEVDGYFSGVKYNSGGGRIAGSYDWILGN
                     CDTEDAQKFRGRGFKQLTGRSNYAEYWVYRAWIDTNSFTAKWWEDPLWRLHDRRRLTRI
                     PANIEEPHRVTRSEYNCIDTGGFFIVKTVDRRGTRSSITRAMDQDSEVIHLNNTTIDTT
                     DEQTIRSVSRAINGGENGLPDRITFTRAAKKVLI"
                     /name="M23 family metallopeptidase"
ORIGIN
        1 cacctgaccc tgcgccttgt cctgcgcgtc ggcgctgata aagatgcctt tctttgcccg
       61 tactgcaccc cacagatcgg tacgcagttc aaaaccttcc ccgcgctgct gtttcccggc
      121 atccaccaga tgaccgaggt tgagctggct cttgccgccg tactcggtac tgaccttgat
      181 atgctctttg ccgcgctcat cgtcgaggcg gattttgttg ttcgccgggg tgcgtagcac
      241 gttgcgcttg tagttctgaa tggtcacatg gtcagtgtgt gccgagtcgt gttttacgcc
      301 tgcaatataa ggtcggtccg ggttgccttc ctcaaaggcg atactgactt ccgttcccgc
      361 cagcagcggc aggtgcaggc cgtaggtgtc tcccgcatac gggcgcgact ggcgtaccca
      421 caggctttca taacccggtt tccacgtatc gcggtcaaag tcgaggttga cccggtagcg
      481 cccgtccttg tcgatatggg catagatatc gttcttcacc gtgctggtga cccgcgccgg
      541 aagcgtgccg gccatcacgg ggcaggggat aagcgccggg cggtagccgt agagctctga
      601 gtacgggatg gcggtaaacg tcagctcata gctgcggtca cgcgccgcgc tggccgtcac
      661 gccggtaatc agtacgccct tgcgaaatac cgcaggcgcg tcgtcgccct gaaccctgat
      721 ttccagcccc ggcatcagca gtgaactggt gctctggcct ttgagaatgg cctgttcatt
      781 caggtagcgt tcgtggcgga tacgggcata aaacgcgccg ctttccgctg cctccttgtc
      841 gcctttttgc aggaagttgt cagcgtagtg gtaggcttcg ccataggtgg tgttatcgcc
      901 cccggtggcg tcatgctgct ctgtcatcat ctctgctgtg gcggtgcggt agttgtagtc
      961 ccgcgtggtg acgtttttct ccaccacgct gtatgccgtg ttcagccccc atacggcttc
     1021 cgtttcacca tcaaacagcc ctgaaggatg gcgaagcggc agtgtcagcc cgcgctcgta
     1081 gccgctctgg tcgtcataaa actcgacaac ttcgattttc agccgggcgt cggtggcaaa
     1141 gcggaaccag atacccactt ccgacagcag gcgtgagaca aacgtcaggt cgtcctcacc
     1201 gtactgcatc acctgttcgc gggacgggta tgcgcttttg aggttaaaca cgaagtcctg
     1261 accgcgcatc tggtgccgct cgcgcaggat tttttcgacg atttgcggca ccgtcagatt
     1321 ctggtagatg gcgttctggc ggctgcgggt aagcagcgcc atacggggtt caaggcgcac
     1381 ttcgtaacgg gcttcgtcct gtgacgagga gaggtgttta aagctggtaa tgacgccgtg
     1441 cagggtgcgc agggcagtct gcaccggcat tccctgtacc ggtggtgccg tcaggctgaa
     1501 tgcgccgtcc tgcatcagca ccgactccgg cgcgatggct ttatcggtac tggtaaactg
     1561 aatgtcgtag cggaacgggg tactcagttg ttcgcggcct tcgaaggtca gcacatccac
     1621 cggactttgc aggccgcgaa ttttgagctt gtggtgtgag tggtcgaaat tcagaacagg
     1681 aacatccatt ttctttgtac tccttcattt atctaacaaa gaataacgag ccgttatttc
     1741 ttgttcggat acattctggg ataatgaatt attacattag agttataatt taaaatatga
     1801 caattcttct gtactgtcgt atagtttgat gaaacttcgt gaaaaatata tacgctctcc
     1861 tcctaaatat gctggtcagt gttgttcctg acgacctatc ataaaagaat gaagaaataa
     1921 aaaagctttt tgtgattttt ccgcatttat ggaaataatt tataaagtta cctgagataa
     1981 aatgccaaac ttatcctgca gcaataccat tggcattaaa aaatagcctc ttgaaattgt
     2041 tcaccaacgt cttcaagtct tcttcaacca ataataaaac tctggcaata tttgattgaa
     2101 aaaactcttc ttcgctatct cctatagcac agtagagtaa cggtgacata ttctactgac
     2161 ttaaatatcc acctaaatct ttcaaagatg cagatgcttt taataactgc cgacactttt
     2221 tatctatttg ttctttattt attatcgcag ataacgctgg atcgctttta aatgcaactc
     2281 gttgtgctgt ggatatttca tacacgtgtg gtatactatg attgacctta tcaatatcac
     2341 accccagacc gaaaggatct acatattttg catcaggaga gataacgcct gagacgagat
     2401 caaatgggcc tgaataactt tttttttcta aatctctgta actaccattg taaaaaaacc
     2461 tacccgttat caggtactgt attttttcag gatcaacctc cgttaagaag ctgcttgatc
     2521 tataattttt tttaacaaac tttgacaact cagcctgata taccattttt cctgaaatat
     2581 tacccattgg gtgatatata agagcaacat ttttcctgaa gttcatgtca gcaatcatcc
     2641 caatattgac aggtggataa acttccgcat gcttttcttc agaagaatta catatatcga
     2701 ttacatcttt tgttaaaaca aaccgacccg atgactgaaa aacaattgct tcatgatctg
     2761 ttgttaaaaa tgaaatgcct gtatctatac tgtcactgta gttatccaga agacatttct
     2821 ttaagaaaaa attatctttg ctgaaaacat caaaagacat atcaccaata ttgaacttta
     2881 ttacattatc gagataattg tatttaattc cttcaattgt tccatcgtta ccatatatgt
     2941 atgcattttc atctccagga tatgcactca gggatatgaa atataaaaat aaaaagaaac
     3001 tctttttcat attaaaacct tcttagctgc gcgtgtgaag gttatcctgt ctggcaaacc
     3061 attttcacca ccattaattg cacgggacac acttcttatt gtttgttcat ccgttgtatc
     3121 tatcgtggta ttgttcaaat gaataacttc actgtcttga tccatcgctc tggtaatact
     3181 tgaccgagta ccccgacgat caacggtctt aacaataaag aatccaccag tatcgataca
     3241 gttatattcg cttctggtaa ccctgtgagg ctcttcgata ttagccggta tgcgagttaa
     3301 acgacgacga tcatgtaagc gccacagagg gtcttcccac cacttagcgg taaaactatt
     3361 cgtatctatc caggcacgat agacccaata ttcggcataa tttgatcgac cagttaactg
     3421 cttaaaacct cgcccacgaa acttctgggc atcctcagtg tcgcagtttc ctagtatcca
     3481 gtcatatgag cctgcaattc gtcctccacc agaattatat ttaacaccag agaagtatcc
     3541 atcgacctca gtctcaattg caccatacca atgacccaag tccgaattct catcacgtaa
     3601 tgagtccgga acaatacctc cgccgactgg ccgaccattt tcatcaacag tttgatactg
     3661 gcttttttcc tgcatacttc ttaaacggga agattccact gccccttgcc ccagaaagtg
     3721 agcacgtctc agaggagaat tcattatata tttattcata acaatattta tagccgtacc
     3781 atatatatca actttttgtt caataaccgc tctatcacgg tcattagtac cagaggcaaa
     3841 aattcgcttc aatattgctt tgtcaaccca cccacacttc ctaaaatgct taataaactc
     3901 acccggatta aaatgccaaa cccgtccttc agcaatacta ctggtatcaa aacacagtgc
     3961 cttaatatgc ttcaccaacg tctgccagtc ttcttctccc agtaataaaa ctctgacggc
     4021 attttcataa gcatttgact gttcataaga caaatctggc atttctgata tagctgactg
     4081 aggagattct ccatggctat ctccagtcgt attatattcg acattatttg gcctgtagta
     4141 atccgtacct aatgataaat cgctgttagc ctcattttcc tgacgttcct gtattacccc
     4201 ttctttcaac cagccgtaac gcgcttctat tcccgtatta caccactcca gtgggaagtg
     4261 gcaaatcatc tgacgaaaat ccgtaaaacc accaccacgt aatattactg aattgcactg
     4321 actgttgctg tcagcgtcgt catctaccag tcgccagcca ctccagtgcg gaaaatcacc
     4381 gtcgctaaat tttgtcacaa catctgccgc cagatttatc actccttgcc caccgggata
     4441 gctcacggtt cgccacagtg gcgcattcgc gggtatcagt gtttcatgct cggtattgat
     4501 aacccgacca aagcgcagta actcaaaccc tgcgcttgga ctttgcggat aaagtctcag
     4561 tgcagcactg tacaagttgt attcataatc agtgccgtca gcatccgtca acacttctcc
     4621 cacaatgtca taacggcttg gtatcaccgg atttgctctg cgggtagtca tgatacaatg
     4681 gccagtatca aaacacatgg tgacaaccaa cggttccgtg ctctgaaaaa cttcacctgt
     4741 gttatctact gcgttgtttt ccggcgcact cctgtaaaag cgggtaccgg gcggcaggta
     4801 aaaatagata tccccgtaaa ccacgtcggt acgcccatga cggctcacat ccatctcagg
     4861 tgtagtgcgc ccggttattt ttctcagatt gtcatcatcg cagaaaattt ggaagtgcag
     4921 gccgcgatcc ccgtcgacat gccccggcat tcccagtgac gatttccggt agactttatt
     4981 tccttcactg ataccctctt caatcttttc caggtgcatg taaagagagt aataaacaat
     5041 attgccgtcc tcaccagtgc ctatttcagt ttcatgacga agcagaacat acccatcgtc
     5101 tgtgcttcca ttataattga gcggcggaag actacatgcc gcctggtcag agggattgcg
     5161 aatagatacc acgacaccat cagcaatggc acggacatat tctggttgcc tgtcactgtt
     5221 tgtatgtcta acgtggatgc ctccatgcca tgatccccca tagttgatgg gatagtcacg
     5281 gtcaggttca actggcatca tcctttcaat ccaatgagca tcgttttcat tgttattttt
     5341 cgctcgtata aatggcgggc taataatcat ttcttatatc cttaagaaaa gaaaaatttt
     5401 acgggtggct catctacttt ctctgccaac atttgtaact caacaggctc atgtgctttt
     5461 cccatacgcc cgtaatgcac cgctttgacg ttataatccc ccggcgttcc cggctcaatg
     5521 ccgctaccct caatccggat ataacttcca ccaccattaa tcgttatttt tttcttcgct
     5581 gaaatcctga tctcgtcctc agtactgacg atctctatcg acttcttcgc cagtaactcc
     5641 atcagatcgt gctgcgcctg taccgatact gcgcctttat tggcaatcag tttgataccc
     5701 gccttgcgca caaacacgct cagcgcccgc cctacgccga taaacatatt cttcaccacg
     5761 ccgatatcgg cgttgtttcc cgcatttatc tggaggtttt tcactgcggc cagttgcagg
     5821 tgctcgccgc tggcgaccgc cacacctttc ggcgcgtgca tcaaaatcac cgaggcggtc
     5881 aggtcattta tccggctggt tatcagcgcc ac
//
