LOCUS       NZ_CP087293             5463 bp    DNA     circular CON 27-MAR-2024
DEFINITION  Escherichia coli strain APEC 102026 plasmid p102026_3, complete
            sequence.
ACCESSION   NZ_CP087293
VERSION     NZ_CP087293.1
DBLINK      BioSample: SAMN23175190
            Assembly: GCF_028752695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5463)
  AUTHORS   Saliha,U., Tivendale,K.A., Noormohammadi,A.H. and Marenda,M.S.
  TITLE     Complete Genome sequence of avian pathogenic Escherichia coli field
            isolates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5463)
  AUTHORS   Saliha,U., Tivendale,K.A., Noormohammadi,A.H. and Marenda,M.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-NOV-2021) Veterinary Sciences, University of
            Melbourne, 250, Princes Highway, Werribee, VIC 3030, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 30-NOV-2020
            Assembly Method                   :: unicycler v. version 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: CP006834
            Genome Coverage                   :: 55.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_028752695.1-RS_2024_03_27
            Annotation Date                   :: 03/27/2024 02:21:49
            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)                     :: 5,337
            CDSs (total)                      :: 5,218
            Genes (coding)                    :: 4,928
            CDSs (with protein)               :: 4,928
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 290
            CDSs (without protein)            :: 290
            Pseudo Genes (ambiguous residues) :: 0 of 290
            Pseudo Genes (frameshifted)       :: 132 of 290
            Pseudo Genes (incomplete)         :: 173 of 290
            Pseudo Genes (internal stop)      :: 61 of 290
            Pseudo Genes (multiple problems)  :: 66 of 290
            Pseudo Genes (short protein)      :: 4 of 290
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP087293.1.
            Bacteria and source DNA available from Avian pathogenic E.coli.
            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..5463
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="APEC 102026"
                     /isolation_source="Tissue"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="p102026_3"
                     /geo_loc_name="Australia"
                     /lat_lon="37.8136 S 144.9631 E"
                     /collection_date="2019"
                     /collected_by="University of Melbourne"
     gene            join(5231..5463,1..892)
                     /locus_tag="LO741_RS26620"
                     /old_locus_tag="LO741_26565"
     CDS             join(5231..5463,1..892)
                     /locus_tag="LO741_RS26620"
                     /old_locus_tag="LO741_26565"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_021529456.1"
                     /translation="MSGGDGRGPGNTGLGHNGGKPSGNVNGSSGHGGPSSGGGYHYNPG
                     KGPASTVGPDGEVHINITGGMEKDPPGKHHGNGGSGNGHGAGNHNSNSGGNGKTTSIPG
                     WSPDSGKPGRYLPTNKDKLIKGLIQSIDDHSGTYTIHYTGGAVATVTVPNGDVNKMNVH
                     YNIGSGPSSGNKLTRDTIKSFLEFKAENEANAVNDAISKVNDFYKELASKYGDKLEKEA
                     KALADEAKGKKIRNANEAIKAFDRYKDVLNKKFSVSDREAIAKALESLNKDQMAKQLKI
                     FGKAFGVVGEAIQWGGFISGLVKGFRTGDWNEAFISGEKIAVGKVASVMVTVAFSAMAV
                     NPIGILGFAVIMAVTSALITDERLKQLNSFINGI"
                     /name="colicin-like pore-forming protein"
     gene            1693..2712
                     /locus_tag="LO741_RS26625"
                     /old_locus_tag="LO741_26570"
     CDS             1693..2712
                     /locus_tag="LO741_RS26625"
                     /old_locus_tag="LO741_26570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /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_001271364.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(2973..3371)
                     /locus_tag="LO741_RS26630"
                     /old_locus_tag="LO741_26575"
     CDS             complement(2973..3371)
                     /locus_tag="LO741_RS26630"
                     /old_locus_tag="LO741_26575"
                     /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_001222916.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            3548..4474
                     /locus_tag="LO741_RS26635"
                     /old_locus_tag="LO741_26580"
     CDS             3548..4474
                     /locus_tag="LO741_RS26635"
                     /old_locus_tag="LO741_26580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001736644.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIEGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     PTQQKEQLRELRKRWEVKHNEHMRKNGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIMEWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            4477..5010
                     /locus_tag="LO741_RS26640"
                     /old_locus_tag="LO741_26585"
     CDS             4477..5010
                     /locus_tag="LO741_RS26640"
                     /old_locus_tag="LO741_26585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168774.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQNLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVILED
                     KLAEKPVTGKNRKN"
                     /name="hypothetical protein"
     Typing          1694..2468
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          3549..4471
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggctcaggt aatggtcacg gtgctggaaa tcataacagc aattcaggcg gcaatggaaa
       61 aacaacgtct attcctggat ggagccctga ctctgggaaa cctggcagat atttaccgac
      121 aaataaagat aagttaatta agggacttat tcagtcaata gatgaccatt ctggaacgta
      181 cactatccat tatactggtg gtgcagtagc tacagtaact gtaccaaacg gtgatgtgaa
      241 taaaatgaat gttcactata atatcggtag tgggccgtca tcaggtaata aactgactcg
      301 tgatactata aaaagctttt tagaattcaa ggcagaaaat gaagctaatg ctgtaaatga
      361 tgcaataagc aaagttaatg acttttataa agagttagca tcaaaatacg gcgataagtt
      421 ggagaaagaa gccaaggcac tagccgatga agctaaaggg aaaaaaattc gcaatgctaa
      481 tgaggcgatt aaagcctttg ataggtacaa ggatgtgctt aataagaaat tcagcgtatc
      541 cgaccgagaa gcgattgcaa aagcactgga gtctcttaat aaagatcaaa tggctaaaca
      601 gttaaaaatt tttggtaagg cctttggtgt cgtaggtgag gctattcagt gggggggatt
      661 tatcagtggc ttagttaaag gattcagaac tggtgactgg aatgaggctt ttataagcgg
      721 ggaaaaaatc gcagtcggca aggtagcatc tgttatggtt acagtggcat ttagtgctat
      781 ggcagtaaat cctattggta ttttagggtt tgcagtaatt atggcagtga ctagtgcctt
      841 aattacagat gaaaggctga aacaactaaa cagctttatt aacggcattt aataaacaaa
      901 aggtcgtacc gtttgatatg gtatgacctt tattttgttt ttctatcgct ttttgttggt
      961 tataaagtaa tagactgtaa aaatcaatcc aaatggaggt agtgataata taatgcatat
     1021 tataaaaccc cagttaacga agttaaaagt tgtttttgtt agtaagggtg cttgcttatt
     1081 tattagtaat agacaaaaag ggtatgtgga cgatccaaaa agagatataa gtataaatat
     1141 aaataattct atacttgttg ggcttagatt caaacttgcg atgataaaag ataaaatgta
     1201 aaaggataag gcaaggataa aattccttaa atagaattcc atatctattt ttttcattta
     1261 taaaatcctc gttagttaaa tgtttataat attgccttac tttatccata aatctagaag
     1321 tagttatcac aaaagttact tttttgactc gttcgccctt ttgaacggtc gaaactgttt
     1381 gcgaatcgct ttcgtgcata gttatgcaac gccctgaaag tgattctgac gcatttttct
     1441 ggtttggcct ggtgtttcct tgtctttttg cgttttttgc gccagaaagc gactgagggc
     1501 gttttaaggg gtacgtacaa cgggagttat ggtaaatgga tcggttttgc gggaaggctc
     1561 gacaggtttt gttgttgggg gtagtgtaag cgactgaaaa acaaacgccc ctgaaattcg
     1621 tgtctctccg ccaagattgt cacgagaata caggggcgag gtcggtcgat aacctggaag
     1681 gaatcgtaac acatgagcgc cgcgcttcaa tacttcgaag aaaatttacc ccaccgcccc
     1741 tatcacacgg atgatctcgc tttcggcctt cgcatctccg gcaaagggcg tgcgcttctt
     1801 gcgcggtaca tccagcagaa ccagcctcat gcgcagttct ggctggtttt tgacgttgac
     1861 cgcgaggggg ctgcgattga ctggagcgac cggaacgccc ccgcgccgaa catcaccgtt
     1921 aaaaatcctg tgaacggaca cgctcacctg ctctacgcac tcaacatcgc cgtgagaacc
     1981 gcgcctgatg cctcggttaa ggcgctgaaa tatgccgcag cggttgaacg ttcgctgtgt
     2041 gagaaacttt gtgctgatgt gaactacagc ggcctgattt gcaaaaatcc gttccacctg
     2101 gaatggcagg tgatggagtg gcgcgaggac gcctataccc tcgatgaact ggcagattat
     2161 ctcgatttga gcgcctcaga gcgtcgtagc atcgataaac attacgggat ggggcgaaac
     2221 tgccacctgt tcgaaatgac gcgcaaatgg gcttacaggg cgattcgtca gggctggcca
     2281 gcgttctcac agtggcttga agcggtgatc cagcgtgtcg aaatgtacaa tgcatcgctt
     2341 cccgttccgc tttcactggc tgaatgtcgg gctattggca agagcattgc gaaatacacg
     2401 cacaggaact tcacgccgga aactttcgca cagtatgtgg ctgatacgca cacgccagaa
     2461 attcaggcag cacgcggtcg caagggcggg aaggccaatt cgtcagaaaa tcagtcggac
     2521 aaagggaaaa aaagcgccgc tgttcggtgg actgctaacg acgacaaacg tcgtagggcg
     2581 cttgatatgt atatcttggg agcgtcaacg gaagatattg cagtggcggt tggtgttagc
     2641 agccggacta ttcgacgctg gatggataat tctggagaat ggctaaccaa gaaacaaata
     2701 attaaatgtt agttaacaaa gaagcaacac taccccccgt tttttgttaa tgggatgtta
     2761 aattcgcgga catgaacaag cctatatcag ataacagcgc ctttcggcgt ctttttgagc
     2821 agcgggcttt ccggcggttt tctcctctca gcccagcaat ggtgcggctt accgcatgat
     2881 tgaggtggtc gtgctcgccg cagtctcatg accgagcgta gcgagcgaat gagcgaggaa
     2941 gcaccaggga accggaacac ggatggaggc acttacgcgt ctgggtttgg ggatgtctcc
     3001 agatcgtact taatttcctt aagtgcctgt aatatcctgt cttttttata gcatagctcg
     3061 cctgtttttg tgtctaccag tcctgcttcg atcagtagcc cagccgcgag aaagagtcgg
     3121 tgattgcgtt ctcgtcgttg tttttttccc tcgattcgtt tttggaccgc ctgttttcgt
     3181 tcgctctcct gtgcctgtaa gtcgtttttt tccgctgttg ccagtacgtg gaggagtttg
     3241 cgttcctgtt ctgtgagtcc tgcttcgttg tcgagcaggt caataatctg tctctgtcgt
     3301 gcggtctgtt ctccgagctt cctgatgaat ccgatccgtt tcttcagcca ttcgatgttg
     3361 ctgatgcgca tgttcgtggt gctccctggt gtttttttgc ggtgtgttgt ggtcgtgcag
     3421 tatatcgctt gcggtcggcg ggtgcagggg gtatcttccg tgctaattcg taaaattaga
     3481 aggaagcgca cttatatgtt tctctccttc gtcgagaaac agtgcgctcc tgcggagggc
     3541 tgaaaccgtg gcgacctatc acctcagcgt taagtttggt ggcaagggac aggctgcaaa
     3601 ccatgccgat tacatcgagc gcaaagagaa ataccgcgac cgtcaagatt tggaatattc
     3661 cgcacacgga aacatgccgg aatgggcgcg agataatccc tcccatttct ggcaggcggc
     3721 tgaccagttt gaacgtgcaa acggttcgac ttatcgggaa ctggagatag cgctgccccg
     3781 tgaactgaca ccggaacagc gccttgaact ggtgcaggat tttgtacgtc aggaagctgg
     3841 cgaacggcat gcatggagtt ttgccattca caatccgaaa gcgagcattg agggaggcga
     3901 acagcctcat gcgcatatca tgatgagtca gcgtgtgaat gatggcattg aacgtacacc
     3961 ggaacagtat ttccggcgct ataacgccag gtatcccgag cggggaggtg cgaaaaagga
     4021 ttcaggaagc ctgactccca ctcagcaaaa agagcagttg cgggaattgc gaaaacgctg
     4081 ggaggtgaag cacaacgaac atatgagaaa aaatggcttt gaaaggggct tcattgactg
     4141 tcggacgctg aaagaacagg gcattgaacg acgtcccgaa gtgcatctgg gttttgaagc
     4201 tgccggacgg cttgatgatg cccagcgtca tgacatcatg caaaaacggt ctgaaccgga
     4261 ctattcccgc catcttgaac aggcgcgaac ggtcgggcat gacatcatgg aatggctgga
     4321 cactccggtt aagcaacatg aactggtcag aaggctgcaa catgatgttg cgcgggagca
     4381 tggctttgac atgagagaca gagtgagcag acaggaccga actgaacctg aacgggttaa
     4441 atcaccgtca cgtggatttt ctatgggatt ctgaacatgg ccagcacaga agaaaaatta
     4501 ctcacgctcc tgttatcggt ggagcatttg caacataccg caatggagca acagaaagct
     4561 gttgctgatt ctctggctgt ggcaagggaa acacttcgcg gatatcggga tatttctgac
     4621 ggtgtggcaa aacaggtcag ggatgaagtc agaaatgagg tgcagaatct ggacgtagca
     4681 gggctgatag gtgagcgcat cagccaggat tttcagcggc tggaagagtc agtcgcaaac
     4741 atgaaggcaa acgcggatgc cctgaacagg gatattgcga caattcacag caatatcgtg
     4801 caggaataca acacccttaa agggtatagc tggaaatggc tgggtggggt gtcagtggct
     4861 tttctagtta tgttctgtgt gctcggatgg ggaatgaaaa caatgctcga caggaactac
     4921 aacgccacag cggcggtgta tcagaaagtt gtgatactgg aagataaact ggcggaaaaa
     4981 cctgtcacgg gtaagaaccg gaaaaactga cgcgcttcgc ttgtccaacg cctcacggac
     5041 agcgaaagga tttcgcgttc cgttcaccgt tttcatgagt gattcctccg aactgccaaa
     5101 aaatatccct ccctgacttg acagaaaaaa taatggcgag tactttttga tctgtacata
     5161 aaaccagtgg ttttatgtac agtattaact atgtaattaa ttgttttaac gattaaaaga
     5221 gggaattttt atgagtggtg gagatggtcg tggccctggt aatacagggc ttggacataa
     5281 cggtggtaaa cccagtggaa acgtgaatgg ctcatctgga catggaggac catcatctgg
     5341 cggtgggtat cattacaatc cgggaaaagg tcctgcaagc actgtaggtc ctgacgggga
     5401 ggtgcatatc aacattaccg gtggtatgga aaaagatcct ccaggaaaac atcacggtaa
     5461 tgg
//
