LOCUS       NZ_CP006639             6222 bp    DNA     circular CON 07-MAY-2024
DEFINITION  Escherichia coli PCN061 plasmid PCN061p3, complete sequence.
ACCESSION   NZ_CP006639
VERSION     NZ_CP006639.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03765122
            Assembly: GCF_001029125.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli PCN061
  ORGANISM  Escherichia coli PCN061
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6222)
  AUTHORS   Liu,C., Zheng,H., Yang,M., Xu,Z., Wang,X., Wei,L., Tang,B., Liu,F.,
            Zhang,Y., Ding,Y., Tang,X., Wu,B., Johnson,T.J., Chen,H. and Tan,C.
  TITLE     Genome analysis and in vivo virulence of porcine extraintestinal
            pathogenic Escherichia coli strain PCN033
  JOURNAL   BMC Genomics 16 (1), 717 (2015)
   PUBMED   26391348
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 6222)
  AUTHORS   Liu,C., Tan,C., Xu,Z. and Chen,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-JUL-2013) Division of Animal Infectious
            Disease,College of Veterinary Medicine, Huazhong Agricultural
            University, Shizishan Street 1, Wuhan, Hubei 430070, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Newbler v. 2.3
            Genome Coverage                   :: 33X
            Sequencing Technology             :: 454
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001029125.1-RS_2024_05_07
            Annotation Date                   :: 05/07/2024 02:04:29
            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)                     :: 4,868
            CDSs (total)                      :: 4,751
            Genes (coding)                    :: 4,466
            CDSs (with protein)               :: 4,466
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 285
            CDSs (without protein)            :: 285
            Pseudo Genes (ambiguous residues) :: 0 of 285
            Pseudo Genes (frameshifted)       :: 81 of 285
            Pseudo Genes (incomplete)         :: 191 of 285
            Pseudo Genes (internal stop)      :: 53 of 285
            Pseudo Genes (multiple problems)  :: 40 of 285
            Pseudo Genes (short protein)      :: 5 of 285
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP006639.1.
            Source DNA is available from Chen Tan, email:
            tanchen@mail.hzau.edu.cn.
            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..6222
                     /organism="Escherichia coli PCN061"
                     /mol_type="genomic DNA"
                     /strain="PCN061"
                     /db_xref="taxon:1358422"
                     /plasmid="PCN061p3"
     gene            447..605
                     /locus_tag="PCN061_RS30085"
                     /old_locus_tag="PCN061_p302"
     CDS             447..605
                     /locus_tag="PCN061_RS30085"
                     /old_locus_tag="PCN061_p302"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     gene            1065..1880
                     /gene="sul2"
                     /locus_tag="PCN061_RS23205"
                     /old_locus_tag="PCN061_p305"
     ARG             1066..1877
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1941..2744
                     /gene="aph(3'')-Ib"
                     /locus_tag="PCN061_RS23210"
                     /old_locus_tag="PCN061_p306"
     ARG             1942..2741
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2744..3580
                     /locus_tag="PCN061_RS23215"
                     /old_locus_tag="PCN061_p307"
     CDS             2744..3580
                     /locus_tag="PCN061_RS23215"
                     /old_locus_tag="PCN061_p307"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(<3687..4091)
                     /locus_tag="PCN061_RS23220"
                     /old_locus_tag="PCN061_p308"
                     /pseudo=""
     CDS             complement(<3687..4091)
                     /locus_tag="PCN061_RS23220"
                     /old_locus_tag="PCN061_p308"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="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="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(4135..4524)
                     /locus_tag="PCN061_RS27095"
                     /old_locus_tag="PCN061_p309"
     CDS             complement(4135..4524)
                     /locus_tag="PCN061_RS27095"
                     /old_locus_tag="PCN061_p309"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4742..5182
                     /locus_tag="PCN061_RS23225"
                     /old_locus_tag="PCN061_p310"
     CDS             4742..5182
                     /locus_tag="PCN061_RS23225"
                     /old_locus_tag="PCN061_p310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            complement(5949..6098)
                     /locus_tag="PCN061_RS29495"
                     /old_locus_tag="PCN061_p314"
     CDS             complement(5949..6098)
                     /locus_tag="PCN061_RS29495"
                     /old_locus_tag="PCN061_p314"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             2745..3577
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2..85)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.75e-36"
     Typing          complement(6134..6222)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.889"
                     /coverage="100.0"
                     /evalue="2.12e-37"
     Typing          9..614
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtgcttcatg tggcaggaga aaaaaggcag caccggcgcg tcagcagaat atgcgataca
       61 ggagatattc cgcttcctcg ctcactgact cgctacgctc ggtcgttcgg ctgcggcgag
      121 cggtaccggc ttacggacgg ggacggaaat ttcctggaag ataccaggaa gacacttagc
      181 aaagaagaga taaggccacg gcgaagccgt ttttccatag gctccgcccc cctgacaagc
      241 atcgcaaaat ctgacgctca aatcagtggt ggcgaaaccc gacaggacta taaagatccc
      301 aggcgtttcc ccctggtagc tccctcgtgc gctctcctgt tcctgccttt cggtttaccg
      361 gtgtcattcc gctgttatgg ccgcggtttc tcattccacg cctgacactc agttccgtga
      421 aggcagttcg ctccaagctg gactgtatgc acgaaccccc cgttcagtcc gaccgctgcg
      481 ccttgtccgg taactatcaa cttgagtcca acccggaaag acacgacaaa acgccactgg
      541 cagcagccat tagtaacagg agtgcacgag aagatagatt aagaggtctt gaagtagagg
      601 cctgactgcg gctacactga aagaacagtt ttggtaatgg cggtctcgtg aaccctgtta
      661 ccgggttaag cagttcccca actgacttaa ccttcgaaca aaccgcctcc ccaggcggtt
      721 ttttcgttta cagagcaaga gattacgatt cattgaaaag gatctcaaga agatcctttg
      781 tagattacta tcaattaatc ttccgaacat gacaccagtc actgttgatt acggttaaac
      841 cgctccgtaa caggtttccc tcgtattggt gacttgcagc accaaagaag caaaaaagat
      901 aaatatatct acttattgag agatgatata tttatttcca aaatgctaca gatacatcat
      961 catgaaacgg atcaccgcaa acaggttact cgcctgggga ttccctttcg acccgagcat
     1021 ccgtatgaga ctcatgctcg attattatta ttatagaagc ccccatgaat aaatcgctca
     1081 tcattttcgg catcgtcaac ataacctcgg acagtttctc cgatggaggc cggtatctgg
     1141 cgccagacgc agccattgcg caggcgcgta agctgatggc cgagggggca gatgtgatcg
     1201 acctcggtcc ggcatccagc aatcccgacg ccgcgcctgt ttcgtccgac acagaaatcg
     1261 cgcgtatcgc gccggtgctg gacgcgctca aggcagatgg cattcccgtc tcgctcgaca
     1321 gttatcaacc cgcgacgcaa gcctatgcct tgtcgcgtgg tgtggcctat ctcaatgata
     1381 ttcgcggttt tccagacgct gcgttctatc cgcaattggc gaaatcatct gccaaactcg
     1441 tcgttatgca ttcggtgcaa gacgggcagg cagatcggcg cgaggcaccc gctggcgaca
     1501 tcatggatca cattgcggcg ttctttgacg cgcgcatcgc ggcgctgacg ggtgccggta
     1561 tcaaacgcaa ccgccttgtc cttgatcccg gcatggggtt ttttctgggg gctgctcccg
     1621 aaacctcgct ctcggtgctg gcgcggttcg atgaattgcg gctgcgcttc gatttgccgg
     1681 tgcttctgtc tgtttcgcgc aaatcctttc tgcgcgcgct cacaggccgt ggtccggggg
     1741 atgtcggggc cgcgacactc gctgcagagc ttgccgccgc cgcaggtgga gctgacttca
     1801 tccgcacaca cgagccgcgc cccttgcgcg acgggctggc ggtattggcg gcgctgaaag
     1861 aaaccgcaag aattcgttaa ctgcacattc gggatatttc tctatattcg cgcttcatca
     1921 gaaaactgaa ggaacctcca ttgaatcgaa ctaatatttt ttttggtgaa tcgcattctg
     1981 actggttgcc tgtcagaggc ggagaatctg gtgattttgt ttttcgacgt ggtgacgggc
     2041 atgccttcgc gaaaatcgca cctgcttccc gccgcggtga gctcgctgga gagcgtgacc
     2101 gcctcatttg gctcaaaggt cgaggtgtgg cttgccccga ggtcatcaac tggcaggagg
     2161 aacaggaggg tgcatgcttg gtgataacgg caattccggg agtaccggcg gctgatctgt
     2221 ctggagcgga tttgctcaaa gcgtggccgt caatggggca gcaacttggc gctgttcaca
     2281 gcctatcggt tgatcaatgt ccgtttgagc gcaggctgtc gcgaatgttc ggacgcgccg
     2341 ttgatgtggt gtcccgcaat gccgtcaatc ccgacttctt accggacgag gacaagagta
     2401 cgccgcagct cgatcttttg gctcgtgtcg aacgagagct accggtgcgg ctcgaccaag
     2461 agcgcaccga tatggttgtt tgccatggtg atccctgcat gccgaacttc atggtggacc
     2521 ctaaaactct tcaatgcacg ggtctgatcg accttgggcg gctcggaaca gcagatcgct
     2581 atgccgattt ggcactcatg attgctaacg ccgaagagaa ctgggcagcg ccagatgaag
     2641 cagagcgcgc cttcgctgtc ctattcaatg tattggggat cgaagccccc gaccgcgaac
     2701 gccttgcctt ctatctgcga ttggaccctc tgacttgggg ttgatgttca tgccgcctgt
     2761 ttttcctgct cattggcacg tttcgcaacc tgttctcatt gcggacacct tttccagcct
     2821 cgtttggaaa gtttcattgc cagacgggac tcctgcaatc gtcaagggat tgaaacctat
     2881 agaagacatt gctgatgaac tgcgcggggc cgactatctg gtatggcgca atgggagggg
     2941 agcagtccgg ttgctcggtc gtgagaacaa tctgatgttg ctcgaatatg ccggggagcg
     3001 aatgctctct cacatcgttg ccgagcacgg cgactaccag gcgaccgaaa ttgcagcgga
     3061 actaatggcg aagctgtatg ccgcatctga ggaacccctg ccttctgccc ttctcccgat
     3121 ccgggatcgc tttgcagctt tgtttcagcg ggcgcgcgat gatcaaaacg caggttgtca
     3181 aactgactac gtccacgcgg cgattatagc cgatcaaatg atgagcaatg cctcggaact
     3241 gcgtgggcta catggcgatc tgcatcatga aaacatcatg ttctccagtc gcggctggct
     3301 ggtgatagat cccgtcggtc tggtcggtga agtgggcttt ggcgccgcca atatgttcta
     3361 cgatccggct gacagagacg acctttgtct cgatcctaga cgcattgcac agatggcgga
     3421 cgcattctct cgtgcgctgg acgtcgatcc gcgtcgcctg ctcgaccagg cgtacgctta
     3481 tgggtgcctt tccgcagctt ggaacgcgga tggagaagag gagcaacgcg atctagctat
     3541 cgcggccgcg atcaagcagg tgcgacagac gtcatactag atatcaagcg acttctccta
     3601 tcccctggga acacatcaat ctcaccggag aatatcgctg gccaaagcct tagcgtagga
     3661 ttccgcccct tcccgcaaac gaccccaaac aggaaacgca gctgaaacgg gaagctcaac
     3721 acccactgac gcatgggttg ttcaggcagt acttcatcaa ccagcaaggc ggcactttcg
     3781 gccatccgcc gcgccccaca gctcgggcag aaaccgcgac gcttacagct gaaagcgacc
     3841 aggtgctcgg cgtggcaaga ctcgcagcga acccgtagaa agccatgctc cagccgcccg
     3901 cattggagaa attcttcaaa ttcccgttgc acatagcccg gcaattcctt tccctgctct
     3961 gccataagcg cagcgaatgc cgggtaatac tcgtcaacga tctgatagag aagggtttgc
     4021 tcgggtcggt ggctctggta acgaccagta tcccgatccc ggctggccgt cctggccgcc
     4081 acatgaggca tgttccgcgt ccttgcaata ctgtgtttac atacagtcta tcgcttagcg
     4141 gaaagttctt ttaccctcag ccgaaatgcc tgccgttgct agacattgcc agccagtgcc
     4201 cgtcactccc actcttacat tgttcgcagt atctaggtac atgttattgc gtgcaccttc
     4261 atgatgtata atgttattaa tgacagcaga aagatcgaca gaattaatat tcttcgtacc
     4321 tgggacagtt atcgggtgtc ggccagtgat gagaccaaag gatgcagtat aagatgaacc
     4381 actactatta tcatggccac cattaccacc accgttaaaa ctacctcccg aacttccaga
     4441 gccgctatga ccatcattgt aggggtcatt tggtcccatg tgaccaaaac caccgacagt
     4501 accgctattt aactctgtac tcataaaatt atcctctttg acttttaaaa acagcaaaaa
     4561 ctgtatttat aacaatgtgt ttatatacag tattcgaaat actacgcccg tcaaaaccac
     4621 accgtcaaca ggttttttgt gtatttttca cgcctcacgg gcagcctcag accttttgtg
     4681 ttaaaacagt aatatgttct gctgttacaa tacggtacac acaggagaca ctgtcacttt
     4741 tatggcatgg cacacagttc aagagacact gaaattaaca ggaaagtcgc gctcgcaatt
     4801 atatcgtgac atggctaaag gccttgtcag ctatcgcaca ggaaaaaatg atcgccggga
     4861 gttcgagacc agtgaactga ttcgggccta tggcgagctg cgcacttctg agacaccaaa
     4921 aaggcacaag gagggacact ccaaatctgt cgttagccag gcggaaaatg ctcagctaga
     4981 cgtcattcag cagaaactgg acgctctgca gcagactgtt accctaatgc ttgaagacaa
     5041 gatggcgcgg gaagcagaaa accgcctgcg aaatgaggag agggaacaac tacaggccga
     5101 aattagccgt ctggctgacg cgctggcaca ggaaaaaaag cggggattct ggtcgcggct
     5161 gtttcgctcc ggttcagagt aacagtgcag gtgactctga tttaccataa catctgttat
     5221 cagcaccgcc tgagaggccc tcagggcgtt tctgacggga aaccggtaaa acaggcaaca
     5281 aaccacccga aaacccgcca gaaacgcgca ggctctgttt ttacggcatg catgagtatg
     5341 cgcacaagtg catagcgcgg aaattcacac cattcagccg gggtaagtcc tgtttccggc
     5401 gttcttccca tccgaaaacg gtgaacgggg acgcaattta ttgcgtggcc gtgaagcgtt
     5461 gccggcgcag ccggaaaacc cgctgtcagc acgttcagga agggggtgat gtacaaatgg
     5521 cacagaggat gaaagtgacg tatgagctga aggaatgatg taaaagtgat gtataagtga
     5581 tgtaaaagtg atgtataagt gatgtaaaag tgatgtatga actgaaggag cgatgtaatt
     5641 ctgtagtcag gaagaataac ccgttcatgc aggcatgaac gatacagtga ggaacgcttt
     5701 ttttgtcacg atctcccctt aacctgcgta aatcacccgc catggttgat tatttttcaa
     5761 cctcaaaatg gtcatacacc taacgcagcc gcgattttca tcgcaactgc atgaattaaa
     5821 agaaaaaaaa ggaatatttc gttttcacga gtaatacccg ggtattaaaa atccactgta
     5881 attacatgaa aataaagaaa taaaaggtaa taccggagta ttaccacgta cgcgggcaag
     5941 cgaaaaagct ataacgcttc ccggccgaca ggcgacccaa aatccacagg ggcatgcagg
     6001 ttctcttcag taacctgcgc cattaaatca aaaaggtcat attcgccggg aagctgcgta
     6061 tcagtcgaat ccagttgttc atcatattca gatggcatgg ggtgatatcc agtagctgag
     6121 aggttgttag cgggtttcgg ggcgcagccc tgaaccagtc atgtagcgct agcggagtgt
     6181 atactggctt actatgttgc cacgattgcg aaaatcagtg aa
//
