LOCUS       NZ_CP087297             4630 bp    DNA     circular CON 27-MAR-2024
DEFINITION  Escherichia coli strain APEC E956 plasmid pE956_3, complete
            sequence.
ACCESSION   NZ_CP087297
VERSION     NZ_CP087297.1
DBLINK      BioSample: SAMN23175191
            Assembly: GCF_028752715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4630)
  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  JOURNAL   Unpublished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 4630)
  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_028752715.1-RS_2024_03_27
            Annotation Date                   :: 03/27/2024 02:32:16
            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)                     :: 4,902
            CDSs (total)                      :: 4,785
            Genes (coding)                    :: 4,546
            CDSs (with protein)               :: 4,546
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 108 of 239
            Pseudo Genes (incomplete)         :: 142 of 239
            Pseudo Genes (internal stop)      :: 53 of 239
            Pseudo Genes (multiple problems)  :: 58 of 239
            Pseudo Genes (short protein)      :: 4 of 239
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP087297.1.
            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..4630
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="APEC E956"
                     /isolation_source="Tissue"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pE956_3"
                     /geo_loc_name="Australia"
                     /lat_lon="37.8136 S 144.9631 E"
                     /collection_date="1998"
                     /collected_by="University of Melbourne"
     gene            complement(369..683)
                     /locus_tag="LO740_RS24460"
                     /old_locus_tag="LO740_24405"
     CDS             complement(369..683)
                     /locus_tag="LO740_RS24460"
                     /old_locus_tag="LO740_24405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001525991.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024139128.1"
                     /translation="MSNNYDLIAKAIKEKLQVTAYYQGFYREMCPHALGSKKGRKQALF
                     YQFGGESSKGTVTPGSTFNWRCIPIDGLTEVTLQSGQWYTAENHSQAQTCVDQIDIEVQ
                     "
                     /name="hypothetical protein"
     gene            complement(775..1077)
                     /locus_tag="LO740_RS24465"
                     /old_locus_tag="LO740_24410"
     CDS             complement(775..1077)
                     /locus_tag="LO740_RS24465"
                     /old_locus_tag="LO740_24410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001525992.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024139129.1"
                     /translation="MLKTVRSCLLSALLTHLFFGNIAVAKENLSDDKVKQAIIDESIAA
                     YPGTCACPFNSARNGSSCGRRSAWSKAGGYSPICYKKEVTKEMIKDWRASHSNNN"
                     /name="hypothetical protein"
     gene            complement(1177..1605)
                     /locus_tag="LO740_RS24470"
                     /old_locus_tag="LO740_24415"
     CDS             complement(1177..1605)
                     /locus_tag="LO740_RS24470"
                     /old_locus_tag="LO740_24415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000830439.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001749513.1"
                     /translation="MKRSGGTRYLYLISLITVAAALTACTPKGSVEQHTRHYVYASDDR
                     SDPNFYTNKADTTRMMIPFFQQFREMGEKDKAAGVSAETAQQRIKEFHSEKFLQSLRST
                     TTFAGRKYMNSDMPSPEKMKLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(1686..2123)
                     /locus_tag="LO740_RS24475"
                     /old_locus_tag="LO740_24420"
     CDS             complement(1686..2123)
                     /locus_tag="LO740_RS24475"
                     /old_locus_tag="LO740_24420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001749514.1"
                     /translation="MGHCNFMAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRR
                     EFETSELIRAYGELKQNETQERHTVGQAENPHDQQTERILRELNELKQYLTLMLEDKQA
                     QDMDRRHQEAEREQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="hypothetical protein"
     gene            2383..3546
                     /gene="cna"
                     /locus_tag="LO740_RS24480"
                     /old_locus_tag="LO740_24425"
     CDS             2383..3546
                     /gene="cna"
                     /locus_tag="LO740_RS24480"
                     /old_locus_tag="LO740_24425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032488335.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin colicin N"
                     /protein_id="WP_040089861.1"
                     /translation="MGSNGADNAHNNAFGGGKNPGIGNTSGAGSNGSASSNRGNSNGWS
                     WSNKPHKNDGFHSDGSYHITFHGDNNSKPKPGGNSGNRGNNGDGSSAKAGEITITPDNS
                     KPGRYISSNPEYSLLAKLIDAESIKGTEVYTFHTRKGQYVKVTVPDSNIDKMRVDYVNW
                     KGPKYNNKLVKRFVSQFLLFRKEEKEKNEKEALLKASELVSGMGDKLGEYLGEKYKNVA
                     KEVAGDIKNFHGRNIRSYNEAMASLNKVLANPKMKVNKSDKDAIVNAWKQVNAQDMANK
                     IGNLGKAFKVADLAIKVEKIREKSIEGYNTGNWGPLLLEVESWIIGGVVAGVAISLFGA
                     VLSFLPISGLAVTVLGVIGIMTISYLSSFIDANRVSNINNIISSVIR"
                     /name="cna"
     gene            complement(3555..4079)
                     /gene="cni"
                     /locus_tag="LO740_RS24485"
                     /old_locus_tag="LO740_24430"
     CDS             complement(3555..4079)
                     /gene="cni"
                     /locus_tag="LO740_RS24485"
                     /old_locus_tag="LO740_24430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_061352107.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin N immunity protein"
                     /protein_id="WP_040089860.1"
                     /translation="MDIKDRNKISKKISFSLLLLLSPFALIFFSYNNAPIPLLEKIIAY
                     LSLPGFHSSNNPPLSEAFNLYVHTAPLAAISLFIFTHKELELKPKSSSLRALKILTPFT
                     ILYISMIYCFLLTDTELTLSSKTFVLMSKNDLFLSFFYITLYIGIYIFTYLYLWFFIGT
                     YKLFTRGGILP"
                     /name="cni"
     gene            4107..4244
                     /locus_tag="LO740_RS24490"
                     /old_locus_tag="LO740_24435"
     CDS             4107..4244
                     /locus_tag="LO740_RS24490"
                     /old_locus_tag="LO740_24435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001329514.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_024139133.1"
                     /translation="MCGKILLILFFIMTLSACQVNHIRDVKGGTVAPSSSSRLTGVEIK
                     "
                     /name="colicin release lysis protein"
     gene            complement(4433..4594)
                     /locus_tag="LO740_RS24570"
     CDS             complement(4433..4594)
                     /locus_tag="LO740_RS24570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_071596883.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRARFI
                     QMLTEFLK"
                     /name="replication initiation protein"
     Typing          4526..4630
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.057"
                     /coverage="97.0"
                     /evalue="1.5e-46"
ORIGIN
        1 ttgatacagg agcgcgaaca tgtgttatcc ctggaacggg agcgtcagcc ggaaatacag
       61 gaacgcacgc tggatggccc ttcgctggga tggtgaaacc atgaaaaatg gcagcttcag
      121 tggattaagt ggggggaatg tggcctgtac catctggttg cataggtatt catacggtta
      181 aaatttatca ggcgcgatcg cggcagtttt tcgggtggtt tgttgccatt tttacctgtt
      241 tgctgccgtg atcgcgctga acgcgtttta gcggtgcgta caatcagggc tttatgttaa
      301 atgctgatgg ttgtcataaa cataaagctg ccactaatgg cagctttatg agggtacgaa
      361 tacaggcttt attgaacttc aatatcgatc tgatcaacac aagtctgtgc ttggctgtga
      421 ttttctgctg tgtaccactg gcctgattgt aaggtgacct cagttagacc atctatagga
      481 atgcagcgcc agttgaatgt ggaaccaggt gtcacagtac ctttactgct ttcaccgcca
      541 aactgataga aaagagcctg ttttcgtcct ttttttgaac ctagcgcatg agggcacatc
      601 tcgcggtaaa aaccttggta atatgctgtt acttgcaact tttctttgat tgccttggca
      661 attaaatcat aattattaga cacttagctt caatctccca gagtatgatt tcctgttgga
      721 aatatatgta tttatcagaa atgtaatgta aacagaaagt tataaaaata gaagtcagtt
      781 gttatttgag tgagaagctc gccaatcttt tatcatttct tttgttacct cttttttgta
      841 gcagattggc gaataacctc ctgctttgct ccaggcgctg cgcctgccgc acgagctgcc
      901 atttcttgcg ctgttaaacg gacatgcaca tgttccggga taggctgcta tcgactcgtc
      961 aataatcgcc tgctttactt tgtcatctga tagattttct ttcgccacag cgatattgcc
     1021 gaaaaaaaga tgtgtcagta aagctgataa cagacacgaa cgtactgtct taagcatttg
     1081 aatagtctcc gaggaataat cctaggagaa ttgcattttt gtacaaaaaa acaacttaaa
     1141 tcgcttcttg ttgttaaggg attatggtaa atccacttac tgtctgccct cgtagccatc
     1201 gagataaacc gcagaaatcg tgtcagccag cagcttcatt ttttccggtg atggcatatc
     1261 gctattcatg tattttctgc ccgcaaaggt agttgtgctt ctgagagact gaagaaattt
     1321 ttctgagtgg aattctttta tgcgttgctg tgccgtttct gctgatactc cggctgcttt
     1381 gtctttctcc cccatctccc tgaactgctg aaagaacgga atcatcatcc gtgtggtgtc
     1441 ggccttgttg gtgtagaagt tagggtcaga acggtcatcg gaagcgtaca cataatgtcg
     1501 ggtatgttgt tccacactgc ctttcggggt acaggccgtg agggctgcag ccacagttat
     1561 cagggatata agatacagat agcgtgtgcc accagaacgt ttcatacgtg tctccttacc
     1621 ttaaagtatt tattctcggt gagttattat ccgaagacta tcttatcatc agcctctgac
     1681 cgagttcagt gaccgaagag tctggaccag aatccccgtt tcttttcctg ttccagtgcc
     1741 tgcctgagct gggctatctc attctgtaac tgttcccgtt ctgcttcctg gtgcctgcga
     1801 tccatatcct gtgcctgttt atcctcaagc atcagcgtca ggtattgttt cagctcattc
     1861 agttcccgga gaatgcgttc tgtctgctga tcatgtggat tttctgcctg tcccacagtg
     1921 tgcctttctt gtgtctcatt ttgctttaat tcgccgtatg cccggatcag ttcactggtt
     1981 tcaaactccc ttcgtccgtc ctggctggta cggtaactga caagacctga gcgcatatca
     2041 cggtaaaact gtgaacgcga tcttccagtc attttcagtg cgtcccggag tgtgtgccat
     2101 gccataaagt tacagtgtcc cataggtgtc tcatctcatg gtttcagtaa aacataatga
     2161 ggtctgagaa cggtaatgtt tgcgccggtt tttgtggtat ccggcgggaa tagcgcgtgg
     2221 tgtgagagac tgtttttttg atcgttttca caaaaatgga agtccacagt cttgacaggg
     2281 aaaatgcagc ggcgtagctt ttatactgta cataaaacca gtggttatat gtacagtatt
     2341 tgtttttaat ggtttgtttt aaaagtcaaa gaggggttta ttatgggtag taatggcgca
     2401 gataacgcac ataacaatgc ttttggtgga gggaaaaatc cgggcattgg taataccagt
     2461 ggcgctggaa gtaatggtag cgcatcaagt aaccgaggaa attccaatgg atggtcatgg
     2521 agtaataagc ctcataaaaa tgatggcttc cacagtgatg gttcttacca tattacattt
     2581 catggggaca ataattcaaa gcctaaacct ggtgggaata gtggaaatag aggtaataat
     2641 ggtgatggat cgagtgctaa ggctggagag ataacaatta cacctgacaa ctcgaaacct
     2701 ggtcgttata tttcgtcaaa tccagaatat tcattgttag caaaattaat tgatgcggaa
     2761 tcaattaaag gtacagaggt atatactttt cacaccagaa aaggtcagta tgtcaaggtt
     2821 actgttccag atagtaatat tgataaaatg agagttgatt atgtgaactg gaagggaccg
     2881 aaatataaca ataaacttgt gaagaggttt gtgagccagt ttttattatt taggaaggaa
     2941 gaaaaagaaa aaaatgaaaa agaagccttg ctaaaggcta gtgaacttgt gtctggtatg
     3001 ggggataaac ttggcgagta tcttggagaa aaatataaaa atgtagctaa ggaagttgcc
     3061 ggtgatatta aaaactttca tggccgtaat attcgtagct ataatgaagc aatggcttca
     3121 ctgaataaag tgttagcaaa tccaaagatg aaagtaaaca aatctgataa ggatgccatt
     3181 gtgaatgcct ggaaacaggt taatgctcag gacatggcta ataagattgg taatcttggc
     3241 aaggcattta aggttgctga tttagctata aaggttgaga aaattaggga aaaaagcatt
     3301 gagggataca atactggcaa ctggggacct ctcctgctgg aggttgaatc atggatcatc
     3361 gggggcgttg ttgctggagt tgctattagt ttgtttgggg ctgtgttgag ttttctccca
     3421 atctcaggac ttgctgttac tgtgttgggg gtaataggaa taatgacgat tagttacttg
     3481 tcatctttca ttgatgcaaa tcgagtttcg aatataaata acattatatc tagtgttatt
     3541 cgatgacatg agtgtcaggg gagtatacct cccctggtaa atagtttata tgttcctata
     3601 aagaaccaaa ggtataaata tgtgaatata tatatcccaa tgtatagtgt tatatagaag
     3661 aaagacaaaa acaggtcatt ttttgacatt aatacaaatg tttttgatga caaggttagt
     3721 tctgtgtcag ttagcaagaa acagtatatc atggatatat aaagaatagt gaaaggagtt
     3781 aatatcttta gcgcccgcag agatgatgac tttggtttta actctaattc tttgtgtgtg
     3841 aatatgaata agctgattgc agctaaaggg gctgtatgaa catagagatt gaatgcttcg
     3901 cttaggggcg ggttgtttga tgaatgaaat cctggtaggg ataggtatgc gatgattttt
     3961 tcaaggagtg gtattggtgc attattataa ctgaaaaata ttaatgcgaa tggggaaagt
     4021 aagagcagaa gactgaatga tatttttttt gatatcttat ttctgtcttt tatatccatg
     4081 ttgctttctt tggatggttg gaaattatgt gtgggaaaat tctattgatc ttgtttttta
     4141 tcatgacact tagtgcatgt caggtcaatc acatccgtga tgtgaaagga gggactgttg
     4201 ctccatcatc atcatccaga ctaacaggag ttgaaattaa gtaaaagatc aaaggatcct
     4261 cttgagatcc tttttttctg cgcgtaatct gctgcctgta aacgaaaaaa ccgcctgggg
     4321 aggcggttta gtcgaaggtt aagtcagttg gggactgctt aaccgaggta actggcttca
     4381 gcagagcgca gataccaaat actgtccttt cagtgtagcc gcagttgggc catcacttca
     4441 agaactctgt aagcatctgg ataaatctcg ctctgctaat ccggttacca gtggctgctg
     4501 ccagtggcgt taaggcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg
     4561 cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct
     4621 acaccgggcc
//
