LOCUS       NZ_CP087289             5269 bp    DNA     circular CON 27-MAR-2024
DEFINITION  Escherichia coli strain APEC 16-1068 plasmid p16_1058_2, complete
            sequence.
ACCESSION   NZ_CP087289
VERSION     NZ_CP087289.1
DBLINK      BioSample: SAMN23170097
            Assembly: GCF_028752675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5269)
  AUTHORS   Saliha,U.
  TITLE     Complete Genome sequence of avian pathogenic Escherichia coli field
            isolates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5269)
  AUTHORS   Saliha,U.
  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_028752675.1-RS_2024_03_27
            Annotation Date                   :: 03/27/2024 02:34:58
            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)                     :: 5,243
            CDSs (total)                      :: 5,117
            Genes (coding)                    :: 4,866
            CDSs (with protein)               :: 4,866
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 98
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 251
            CDSs (without protein)            :: 251
            Pseudo Genes (ambiguous residues) :: 1 of 251
            Pseudo Genes (frameshifted)       :: 116 of 251
            Pseudo Genes (incomplete)         :: 144 of 251
            Pseudo Genes (internal stop)      :: 49 of 251
            Pseudo Genes (multiple problems)  :: 53 of 251
            Pseudo Genes (short protein)      :: 4 of 251
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP087289.1.
            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..5269
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="APEC 16-1068"
                     /isolation_source="Tissue"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="p16_1058_2"
                     /geo_loc_name="Australia"
                     /lat_lon="37.8136 S 144.9631 E"
                     /collection_date="2016"
                     /collected_by="University of Melbourne"
     gene            complement(<2..478)
                     /locus_tag="LO742_RS26145"
                     /old_locus_tag="LO742_26120"
                     /pseudo=""
     CDS             complement(<2..478)
                     /locus_tag="LO742_RS26145"
                     /old_locus_tag="LO742_26120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000716853.1"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1972 domain-containing protein"
                     /name="DUF1972 domain-containing protein"
     gene            complement(488..1447)
                     /locus_tag="LO742_RS26150"
                     /old_locus_tag="LO742_26125"
     CDS             complement(488..1447)
                     /locus_tag="LO742_RS26150"
                     /old_locus_tag="LO742_26125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001099761.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="glycosyltransferase family 2 protein"
                     /protein_id="WP_001099761.1"
                     /translation="MNVAILLSTYNGEKYLEEQLDSLLLQSYQDFVVYIRDDGSSDRTV
                     NIINQYVMKDNRFINVGNSENLGCAASFINLLRNASADIYMFCDQDDYWLPNKLQRAVD
                     YFSAIDPLQPTLYHCDLSVVDEKLNIIQNSFLQHQKMSAYDSMRKNNLFIQNFVVGCSC
                     AVNASLAEFVLSRIGEQHVKMIAMHDWWLAVTAKLFGRIHFDNTQTILYRQHQGNVLGA
                     KSSGMMRFIRLGLNGQGISRVVSFRKKVCAQNKLLLDVYDKDLNLEQKKSIRLVIEGLK
                     ENSSIADLLKCFYHGSYMQGFKRNLALIYSVLYTKKRR"
                     /name="glycosyltransferase family 2 protein"
     gene            complement(1449..2458)
                     /gene="wzy"
                     /locus_tag="LO742_RS26155"
                     /old_locus_tag="LO742_26130"
                     /pseudo=""
     CDS             complement(1449..2458)
                     /gene="wzy"
                     /locus_tag="LO742_RS26155"
                     /old_locus_tag="LO742_26130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_158642100.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="O1 family O-antigen polymerase"
                     /name="wzy"
     gene            complement(3032..3577)
                     /locus_tag="LO742_RS26160"
                     /old_locus_tag="LO742_26135"
     CDS             complement(3032..3577)
                     /locus_tag="LO742_RS26160"
                     /old_locus_tag="LO742_26135"
                     /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_274431431.1"
                     /translation="MLLIIADYPNEMNMREGAMQRIDAIDSLIRDRKRVYLNISFKKHL
                     VRSNSSFNNVIVENLNAIIHRNIIKQYMQKSTTIYVHSVYNLLKVITLIDLKKTILDIH
                     GVVPEELLADNKKLLSKVYNMVEKKGVLGCKKLIHVSTEMQKHYEAKYGVNLAERSIVL
                     PIFEYKKYNPIAKQMDRK"
                     /name="hypothetical protein"
     gene            complement(3592..4719)
                     /gene="wecB"
                     /locus_tag="LO742_RS26165"
                     /old_locus_tag="LO742_26140"
     CDS             complement(3592..4719)
                     /gene="wecB"
                     /locus_tag="LO742_RS26165"
                     /old_locus_tag="LO742_26140"
                     /EC_number="5.1.3.14"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016243256.1"
                     /GO_function="GO:0008761 - UDP-N-acetylglucosamine
                     2-epimerase activity [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="UDP-N-acetylglucosamine 2-epimerase
                     (non-hydrolyzing)"
                     /protein_id="WP_000735124.1"
                     /translation="MKKLLLVFGTRPEAIKMASIIELLKKDCRFEYKICVTGQHKEMLD
                     QVMQVFDVKPDYNLRIMQPGQTLVSVATNILSRLSEVLIIEKPDIILVHGDTTTTLAAT
                     LAGYYHQIKVCHVEAGLRTGDIYSPWPEEGNRKVTGALACIHFAPTERSKDNLLREGVK
                     VNNIFVTGNTVIDSLFIAKDIIDNDPNIKNALHNKFNFLDKSRRVVLITGHRRENFGKG
                     FEDICFAIKELAFIYPNVDFIYPVHLNPNVMEPVHRILDNICNIYLIEPLDYLPFVYLM
                     NESYLILTDSGGIQEEAPSLGKPVLVMRDTTERPEAVEAGTVVLVGTSKIKIVNKVTEL
                     LNNADIYNAMSLLHNPYGDGTAAQKILNVLAQELI"
                     /name="wecB"
     gene            complement(4729..>5268)
                     /gene="wzx"
                     /locus_tag="LO742_RS26170"
                     /old_locus_tag="LO742_26145"
                     /pseudo=""
     CDS             complement(4729..>5268)
                     /gene="wzx"
                     /locus_tag="LO742_RS26170"
                     /old_locus_tag="LO742_26145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_157658977.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="O1 family O-antigen flippase"
                     /name="wzx"
ORIGIN
        1 cgttaaaaac gtactcagaa attgcctcat tatccgtaat aacgacatcc gaatattgaa
       61 ctgcgatttt ttctgaaaat tttaagaaac gtttcacttt tgaattccat ttatctcttc
      121 gccattccag gccatcaata ttagtaataa acttagcgcg tgttaagagt ttgaagaaag
      181 gcaaaaatga acaaccagaa acccctaaaa tcagaatcac atcaggcttc aaaaaaatag
      241 aatatgctaa cgaaattatg tcatacgcaa tgctctgcca tccattggct ttaagcggaa
      301 tataaattaa acgggcccca ttatgttttt tttggtggga tttgtagtga aacgatgaac
      361 aaaaaacatt atattcaact cccgaggaat tgtatcttgt taaattttca actaatgttt
      421 caaatccgcc atatgatgct ggtatgccaa cagtaccgat aatagcaatt tttttcataa
      481 ggatacacta tcttcttttt tttgtgtaaa gaactgaata tattaaggca agattacgtt
      541 taaaaccttg catatagcta ccatgataga aacattttaa aaggtcagca attgaagagt
      601 tctctttaag gccctcaatt acaagcctga tagatttttt ttgctcaaga tttaaatctt
      661 tatcatagac atctaaaaga agcttatttt gcgcacaaac tttttttcta aaagatacta
      721 ctcgcgaaat cccttgccca tttaatccta atcgaataaa acgcatcata cctgatgatt
      781 ttgcacctaa tacattgccc tgatgttgtc gataaagaat cgtttgagta ttatcaaaat
      841 ggattcgacc aaaaagtttt gcagtcacgg ctaaccacca gtcatgcata gctatcattt
      901 ttacatgctg ctctccaatt cgcgaaagaa caaattccgc aagtgaagca ttaacagcac
      961 atgaacaacc aacaacaaaa ttttgtatga aaagattatt ttttctcatt gaatcatacg
     1021 ctgacatttt ctgatgctgc aaaaatgaat tttgtataat attaagtttt tcatcaacaa
     1081 cgcttagatc gcaatgatac aaggtaggtt gtaaaggatc aatagccgaa aaataatcca
     1141 cagcacgctg taatttattc ggaagccaat aatcatcttg gtcacaaaac atataaatat
     1201 cggctgaagc atttcttaat aaattaataa acgaagcagc acaaccaaga ttttctgaat
     1261 tacccacgtt aataaatctg ttatctttca ttacgtattg gtttattata tttacagttc
     1321 tatcagatga tccgtcatca cggatataca ctacaaaatc ctgataactt tgaagcagca
     1381 atgaatccag ttgttcctct aaatattttt cgccattata cgtagacaac aaaatagcaa
     1441 cattcatttt ataatccttg accaactatt gatacagccc ttagtgttat aaacaacatt
     1501 aagcctgaaa ggataactat aatgactgca ataaaataac gcatattatt attttttata
     1561 tgcgaaagga ttaatactaa agccatcgga taaaatattc gcagcaactc tgcagttcga
     1621 taagcaatga ccgggactcc actagccaga aagaaaatac aaaaggctaa tattcctgaa
     1681 cattgcacat acttaataaa cttcgcctca ttatcattta attttatata tcggctaaga
     1741 taaaagatca aaataaatat tgataaaaac attatattat tcaggttgaa tattgccaaa
     1801 tcatttctat tgtctaatga tgatgaaata ctatataaat aatttactat tttttttcat
     1861 ttggcaaata tagtgcaatt gtatctgcat acacgtttaa aaagctcata catattacaa
     1921 accctataat tactattaat aacctcctat aactgtatat aaataatgac ataaataaaa
     1981 gcaaggcgct gtaatgaaac aaaatagcca acaccatcca tggcagtgca tgtttaatac
     2041 aatttttata aaagtaataa taaaccgaca catagcacat agtgactgca attgctatgc
     2101 gcaattgagt catttcatgc aaaaacacat aaaatgatac atatacatac aagaacaaat
     2161 atatataact atctttaatt atttttcttg catattttat tttccaactt aaacataagg
     2221 cacaaactaa cattgcaaaa aaaaatatat aggggaaatt taaataatga aacaaccgtg
     2281 ttaaatataa aaaggcaggc tcaatattat tgatttctcc gtatgtccca tcgtatattt
     2341 ctgtatatgg cagaaaatca gcaggaaagt agtcagattt gagtaaaact aagtagctca
     2401 aaatgaaaca taatagaaaa cataatatat aaccgttatc tttatatttg atacgcatac
     2461 aattacctga cccgcgatat gcttacataa ttttatatat gtaaaaaaat tcagcacagt
     2521 tgagcaataa gttctttctg tgccttgtag gttctcttct gataagaagt caaaatttgt
     2581 aaattatgtg cagccatttt ttcaagatcc aacaaactta tacttctgtt agccatttcc
     2641 tctgtagtaa tgtattgata tcccatcgaa taaaaatcac ctataagtgg ggagagcaca
     2701 actggaacga caccacactc taaatattca accaattttg tagggcacgc aactctgttt
     2761 actattatat catcgcgcaa tacaaaacca atatgacatt ctttttagaa agggaattac
     2821 ttcatcacgt gatagcgtag atgcattagc attgatatta tgtaatttta acgaatattt
     2881 atctataaac ccttccaagt tactctgtgg gatgaaaaag ttgaattcat acttacctgc
     2941 ttcattgttt atcactgtgt catcacaaac ttgaatcatt ttatcaatat tttgccatgt
     3001 ttgtaatcct ccaagataga tacttcgtat tttattttct gtccatttgt tttgcgattg
     3061 ggttatattt tttatattca aaaatcggga gcactattga cctttcagcc aagtttactc
     3121 catattttgc ttcatagtgt ttttgcattt ctgtactgac gtgtattaat tttttgcatc
     3181 caaggacacc ttttttttcc accatgttat atactttact aagtaatttt ttattatctg
     3241 ccaaaagttc ttccggtaca acaccatgta tatcaagaat tgtttttttt agatcaatga
     3301 gcgttataac ctttaataaa ttataaacag aatgaacata tatagttgtt gatttttgca
     3361 tgtactgttt tatgatgttt ctgtgaataa ttgcatttag attttcaact ataacattat
     3421 taaaggaact atttgagcga actagatgct ttttgaatga aatattcaaa tacactcgct
     3481 tgcgatctcg aatgagagag tctatcgcat ctattcgttg catagctccc tcgcgcatat
     3541 tcatttcgtt tggataatca gcaataatta ataacatatt tttagcttaa attaaattag
     3601 ctcttgggcg agcacattaa gaattttttg agcagctgtt ccatcgccat atggattatg
     3661 taacagagac atagcattgt agatatcagc attgtttaat agctccgtta ctttatttac
     3721 tatttttatc ttagaagtcc ccactaatac aacagtacca gcctcaaccg cctcagggcg
     3781 ttcagtagta tcacgcataa ccaaaaccgg tttacctaac gaaggcgctt cttcttgtat
     3841 cccccctgaa tcagtcaata ttaaatatga ctcattcatt aaataaacaa aaggcaaata
     3901 atccaagggc tcaataaggt aaatattaca tatattatct aatatacgat gtactggttc
     3961 cattacattg ggattaagat gcaccggata aataaaatct acattaggat aaatgaaagc
     4021 taattccttt attgcaaagc atatatcttc aaaacctttc ccgaaatttt ctcttcgatg
     4081 acctgttata agtactactc gtcggctttt atcaagaaaa ttaaatttat tatgtaaagc
     4141 gttctttata ttagggtcat tatctatgat atcttttgca ataaataaag agtcgatgac
     4201 ggtattaccc gttacaaata tattatttac tttgaccccc tccctcagga gattatcttt
     4261 tgatctctct gttggggcga aatgaataca tgctaatgcc cctgtaactt tacgattgcc
     4321 ctcttcaggc caaggagagt aaatatcccc tgttcttaat cctgcttcca catgacaaac
     4381 ttttatttgg tggtaatacc cagctaaagt agcagcaagg gtagtcgttg tatccccatg
     4441 cacaagtata atatctggct tttctataat taaaacttca cttaaccgtg agagtatatt
     4501 tgttgctaca gatactaatg tttgcccagg ctgcataatc cgtaaattat aatcaggttt
     4561 aacatcaaat acttgcataa cttgatcaag catctcttta tgttggcctg tcacacatat
     4621 tttatattcg aatctacaat ctttttttaa taattcaatg atagaggcca tctttattgc
     4681 ttcaggccta gtaccgaaca ctaataataa cttcttcata actattcctt aaattatttt
     4741 tttatatcgc ttaagtaaca atattgataa gaacatttca cccaataata ttgcacatgc
     4801 cactccagtg gcgttacaaa actgcaataa tagagtaatc aaaagtaatg ttataagcgc
     4861 tgatacgaat accatcctac tatatatttt acttcttcct gatgcactca atatctgaat
     4921 gccgaataca ttattaagaa caccaaaaaa gatccatgca cttaatattt gacctacaaa
     4981 aattgtttct tttggaaaat taagatagtc gattgcaaca ggtaaggtaa ttgcaacgat
     5041 aacagcagct ataaatgcta aaattataat tggtatacca gttttttttg ctgcctcaat
     5101 gccgtcaaat acggatagtg aaaacttacg acaattataa ggatatatag cttgcgtcag
     5161 tggtgtaaat agcgacaata cggccttgac tatcttttca gcggcggcat atacaccaac
     5221 aataacagga ttagtaaaaa tccctaatag aaaaatgcca ctattattg
//
