LOCUS       NZ_CP006638             5754 bp    DNA     circular CON 07-MAY-2024
DEFINITION  Escherichia coli PCN061 plasmid PCN061p2, complete sequence.
ACCESSION   NZ_CP006638
VERSION     NZ_CP006638.1
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 5754)
  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 5754)
  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
            CP006638.1.
            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..5754
                     /organism="Escherichia coli PCN061"
                     /mol_type="genomic DNA"
                     /strain="PCN061"
                     /db_xref="taxon:1358422"
                     /plasmid="PCN061p2"
     gene            join(5345..5754,1..109)
                     /locus_tag="PCN061_RS23170"
     CDS             join(5345..5754,1..109)
                     /locus_tag="PCN061_RS23170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310049.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001445155.1"
                     /translation="MSEKAKKVGRRSLSKRRESLIKELWGDELSELNIWNRKEHDGFTT
                     IPRTLNYINRIIDYLAGAGSPVSQTYLSLWCRVFDEGFVEIRDKDALAFESGFSGQRAV
                     TTWLGRMKKLRELGLISTKPGTSGEFHYVIMLNPLYVIKKSYESNGWARDERYNALFSR
                     MQEVGAEWE"
                     /name="hypothetical protein"
     gene            106..669
                     /locus_tag="PCN061_RS23175"
                     /old_locus_tag="PCN061_p201"
     CDS             106..669
                     /locus_tag="PCN061_RS23175"
                     /old_locus_tag="PCN061_p201"
                     /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_000999222.1"
                     /translation="MNDMKAVRHRYKQRYDFAASEVVGAFDELRSLDWSLEIASLSDVE
                     MSKRWIGAVDPNGVARLPPNGGWDWVKLYNGYLKNPSAFVCAIKSEGKLCALIGGGVSD
                     SKVVTKLHYLESAPYDTALSGYALDISVTYVVTVANAMGSEYSAIYEPNSKVREIAIND
                     YGFSEDNLFGTSKDFALYLPMSRI"
                     /name="hypothetical protein"
     gene            complement(679..831)
                     /locus_tag="PCN061_RS29195"
     CDS             complement(679..831)
                     /locus_tag="PCN061_RS29195"
                     /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_001341064.1"
                     /translation="MLAHAVELKKATEPCSSGTAGAFRQRVKARRAEQGRSNQQPEKLY
                     GVLVG"
                     /name="hypothetical protein"
     gene            complement(1127..1273)
                     /locus_tag="PCN061_RS29870"
                     /old_locus_tag="PCN061_p203"
     CDS             complement(1127..1273)
                     /locus_tag="PCN061_RS29870"
                     /old_locus_tag="PCN061_p203"
                     /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="hypothetical protein"
                     /protein_id="WP_050863271.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHAKAPLAAANGKRMYKRLLT
                     QSS"
                     /name="hypothetical protein"
     gene            1502..1705
                     /locus_tag="PCN061_RS29490"
                     /old_locus_tag="PCN061_p204"
     CDS             1502..1705
                     /locus_tag="PCN061_RS29490"
                     /old_locus_tag="PCN061_p204"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001347451.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000415556.1"
                     /translation="MEKRQRRILFQPFLISAKSLYPAIRELATPAAVSRQERSDRVSEE
                     ASYHRNLHFLLYALQLHFSPAT"
                     /name="hypothetical protein"
     gene            1914..2237
                     /locus_tag="PCN061_RS23185"
                     /old_locus_tag="PCN061_p205"
     CDS             1914..2237
                     /locus_tag="PCN061_RS23185"
                     /old_locus_tag="PCN061_p205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001445156.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2446..>2880
                     /locus_tag="PCN061_RS29875"
                     /pseudo=""
     CDS             2446..>2880
                     /locus_tag="PCN061_RS29875"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2915..3400
                     /locus_tag="PCN061_RS29095"
                     /old_locus_tag="PCN061_p207"
     CDS             2915..3400
                     /locus_tag="PCN061_RS29095"
                     /old_locus_tag="PCN061_p207"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_139244276.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTSEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3404..3619
                     /locus_tag="PCN061_RS29100"
                     /old_locus_tag="PCN061_p208"
     CDS             3404..3619
                     /locus_tag="PCN061_RS29100"
                     /old_locus_tag="PCN061_p208"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137421.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3818..4582)
                     /locus_tag="PCN061_RS23195"
                     /old_locus_tag="PCN061_p209"
     CDS             complement(3818..4582)
                     /locus_tag="PCN061_RS23195"
                     /old_locus_tag="PCN061_p209"
                     /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_228252686.1"
                     /translation="MQPREWLMLSMYILVQAPVLTGLSKNQTESLTTNNKRGRGCILSH
                     KKHLQHEFYRIDFIKNEIYSPIKVFYMKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDR
                     LNDADYLIAVRNRRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTP
                     KAWKMLTDGQRYPVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTE
                     KLSLNEAIERAKKDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     Typing          1626..1810
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.17"
                     /coverage="86.0"
                     /evalue="5.83e-49"
     Typing          complement(1165..1680)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.019"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2228..3723
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.984"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tccactttac gtaattaaaa agtcatatga atcaaatgga tgggcaaggg atgagcgtta
       61 caacgctcta ttttctagga tgcaggaagt gggggcggag tgggaatgaa cgacatgaaa
      121 gctgttcgtc accgatataa gcagagatat gattttgctg cgtcagaagt agtgggggcg
      181 tttgatgaac ttagaagttt ggattggagt ttagaaatcg catctttaag tgacgtggaa
      241 atgtcaaaga gatggattgg ggctgttgat cctaacggtg ttgcaagact accacctaac
      301 ggtggatggg actgggttaa gctctataac ggctatttga agaaccctag cgcattcgtc
      361 tgtgccatta aatcagaagg caagctatgc gctctgattg gtggcggggt ttctgatagt
      421 aaagtggtaa ctaagctgca ttaccttgaa tcagcccctt atgacacggc tctttcagga
      481 tatgcactgg atatttctgt tacgtatgtt gttactgtcg cgaatgcgat gggaagcgaa
      541 tactcagcca tctatgagcc aaatagcaaa gtcagagaga tagctataaa tgattatgga
      601 tttagcgagg acaacttgtt tgggacaagt aaagatttcg ctctgtatct accaatgagc
      661 cggatttaac cggctcattt atcctaccag tacgccgtag agtttttctg gctgttggtt
      721 tgatcggcct tgctctgctc gtcttgcttt cacgcgctgg cgaaatgctc cggctgtgcc
      781 agaagagcat ggttccgtcg cttttttaag ttcgaccgcg tgagctaaca tattatttcc
      841 gttttttcgt gagttagtac aaagcatatg aggtgacgga tacgtcaact tcatagtaac
      901 tgtactgtat tgtagaagag atgcgcaagt cgcagaatta atgcgaccct tcattgacga
      961 ggcgaagagt aaacgcgtat cttctttgaa aacgaaaaaa ccacccggca aggtggtttt
     1021 tcgaaggttc attaaaccgg caagtttatg aaccgtggta acagggtgta caagaccact
     1081 gccaccaaat tcgtccttcc agtttagccg tagttgggct gatacttcaa gaactctgcg
     1141 ttagtaatct cttgtacatc ctcttaccgt tggctgctgc cagtggcgct tttgcatgtc
     1201 tttccgggtt ggactcaaga tgatagttac cggataaggc gcagcagtcg gactgaacgg
     1261 ggggttcgtg catacagtcc agcttggagc gaactgccta cccggaactg agtgtcaggc
     1321 gtggaatgag aaaccgcggc cataacagcg gagtgacacc ggtaaaccga aaggcaggaa
     1381 caggagagcg cacgagggag ctaccagggg gaaacgcctg ggatctttat agtcctgtcg
     1441 ggtttcgccg cctctgattt gagcgtcaga tttcgtgatg cttgtcaggg gggcggagcc
     1501 tatggaaaaa cggcaacgcc gcatcctttt tcagcccttc ctgatttccg ctaagtctct
     1561 ttatccagcc attcgtgagc ttgcaacgcc cgccgcagtc tcacggcagg agcgcagcga
     1621 ccgagtgagc gaggaggcgt catatcaccg taacctccat tttctcctgt acgccctgca
     1681 gctgcatttt tcccctgcca catgaagcac tttcattaag tgttactccg ccataacata
     1741 ttgagccagt atacactccg ctagcgctac gtgactggtt cagggctgcg ccccgaaacc
     1801 tgctaaaacc actgacgcgc ctgcggcttg tccaacaccg cgccgaccgg gaaaagattt
     1861 cccgcccgtc ccggcgttat caggaggctg gattggcaga caaacgcagt aaaatgctca
     1921 cgatgtgggt gaccgaagat gagcaccgcc gtctgttgga acgctgcgac ggtaaacagc
     1981 ttgcagcctg gatgcgccag acgtgcctgg acgagaaacc cgcccgcgcc ggcaagcttc
     2041 cctcgatctc gccggcgctg cttcgtcagc ttgccggcat ggggaacaac ctcaaccaga
     2101 ttgcccggca ggttaacgcc ggtggtggca gcgggcacga ccgcgtgcag gtcgtcgccg
     2161 cgctgatggc catagatgcc ggactcgagc ggctgcggca tgctgtgctg gaaaagggtg
     2221 cagacgatga tcgttaagtt tcacccgcga gggcgcggcg gtggcgccgg tccggtggat
     2281 tatctgctgg ggaaagaccg acagcgcgac ggcgccaccg ttctgcaggg gaagccggaa
     2341 gaagtcaggg agcttatcga cgcctcgccc tacgcaaaaa agtacacatc cggcgtcctg
     2401 tcctttgccg aaaaggattt accgcccggg cagcgcgaaa agctgatggc gagctttgaa
     2461 cgggttctga tgcccggact cgataaagac cagtacagcg tgctgtgggt tgagcaccag
     2521 gataaggggc gactggagct gaacttcctg atcccgaaca tggagctgct gaccggcaag
     2581 cgtctccagc cgtattacga ccgcgccgac cgtccgcgca ttgatgcctg gcagaccatc
     2641 gtgaacggca ggctggggct gcatgacccg aacgcgcctg aaaaccggcg ggcgctggtc
     2701 acgccgtccg cgctgccgaa aacgaagcag gaagccgctc aggcaattac acggggttta
     2761 ctggccttag cctcatccgg ggagctgaaa acccgccagg acgtcactga ggcgctggaa
     2821 agcgcaggtt ttgaggtggt acgcaccaca aaaagcagca tcagcattgc cgacccggac
     2881 ggggggcgaa acatccgact gaagggagcc atctatgaac agtcttttaa cgctggcaaa
     2941 ggacttagag cagaaatcga aagcgcagca gcagagtacc agcgagatgc tgaaagccgc
     3001 attcagcgag cacgagaagt ctgtcagagc ggaactgagc gaaagcgaga agagaatcag
     3061 cgccgccatc ctcgaccacg accggaagct gtcctcagcc atgagccagc gcacgaaagg
     3121 catggtgcgt atggtcagcc agacgtggct gaccatcgtc ctggtgtctg cactgctgac
     3181 agcatcgggc gcaagcattc tgtggtggca ggggcagcag atactcgaca attacacgat
     3241 catccgggag cagaagagca cgcaggccat gctgtccgag aggaacagcg gcgtgcagct
     3301 ctcgacctgc ggagagcaga gacgccgctg cgtgagggtg aacccggaag cgggacggtt
     3361 cggagaggat tcgagctgga tgatactggc ggggaaatag cacatgacgg agctggaaaa
     3421 acagttgctg agcgcattag agcagctaca gcaggactac tcgaaaaggc tggacgagtg
     3481 ggagaacgcc ttcgcggaat ggcggacgat gtctggtctt atgcaacggg agaacgcggc
     3541 gctgagcgag cgcgtcacgg gcttgagcag gcaggtgcag agtttgagcg agcagctgcg
     3601 ccggttgtca caaggctgaa cgtgatagag gcacatcgtg agcaggaacg ggcggcgcag
     3661 catcagaaaa cgctggagct ggaacgatct cagcgacagc gaacgtacaa cggtccgtca
     3721 ctttgaatct gtgcgccgga aaagcatggg cttgctgttt ctggcgcaca ggttcagttc
     3781 tagaacatga ggctgctatc ttgttgttca cgcttcatca gatcttgatg cttattgtta
     3841 tggctgagct atcaatccct gttgcgttgc taatatcctt tttggctctt tcaattgcct
     3901 cgttaaggga gagtttttct gttttctctt cagccagacc aggaatcact gtattaggaa
     3961 ccgatgggga tgaaggatgg aatttcttcc attccagttg ttccggtgtt accccaatac
     4021 gtaaaaaagc ttcctgtgcg ctcaggtaag caaccggata gcgctgacca tcggttagca
     4081 ttttccatgc ttttggcgtg tgaatttctg cgtattcatc aaaggttatg acgttcctgt
     4141 cgtcgtaatc agggctttta aaacacccgg taattttggc gatcaggaat gctgtgccgt
     4201 gttccaggtc ttttactgcc cacgtttccc ttctgtttct tactgctatg aggtaatcgg
     4261 catcgttgag cctgtctgtt ctggcatgcc agtagcctga ccccccctca gttctcatta
     4321 tgttcaaatc cttcccggta aaaaccacaa cagctttcat atctttcata tagaaaacct
     4381 taataggtga gtaaatttca ttttttatga aatctatacg atagaattcg tgttgtaaat
     4441 gttttttatg cgataaaata cagcccctac ctcttttatt gttagtggta aggctttctg
     4501 tttggttttt tgataaaccg gttaaaacag gggcttggac gaggatatac attgaaagca
     4561 tgagccattc acgtggctgc atggctatgc agtcgcgtga aatttatcag gcgcagaatg
     4621 cgcggtttag cggggagttt actgccggtt ttaccgggct aacgccgctt tcacgctgaa
     4681 cccgtccgga gcggtgcggg caagggatgt tatggtaaat ggtttctgag gtgtaagcga
     4741 aaactcgagt tttgacgcca ttctgagtag gtaatttgca gacggaataa atactggcga
     4801 gcaataagct catcaacaaa aaatggagat cctaagatgg atagagaaac cctataccta
     4861 ctcaaaacgt tagaccataa caatgccttg cttgacgata ttatccgaag aaagatgggt
     4921 aggtactaca acacgaagat tttgcgtgat tcctgtgatg ctattgaagc cgaactacga
     4981 cgtcgaggaa tcatttaaaa agacgaagcc cgcttatgtg ggctttttca ttgcgcattc
     5041 agggcacccc ttcccccccc cttaaccccc ctaagaaccc cattcagcac agcgagcaca
     5101 acgattacat tagagtacat tgagaacagc gagtacaaaa tagcgcataa ctaattgaaa
     5161 aataaaaccg taattgtaaa aaatattaca tctcaatatt tgtattgaca aaaaaaaaga
     5221 atcatatcaa atgagatgtt ggttaatgat gtgcttggtt tttgtgttat tacacataac
     5281 tcattgaata taataggttt tttgttgata atattttcat gttgaattga cttttggggg
     5341 ataaatgtca gagaaggcaa aaaaagtagg taggcgctct ctatcaaaaa gaagagaaag
     5401 tctaataaaa gagctctggg gggatgagct ttccgaactt aatatatgga acaggaaaga
     5461 acacgatgga tttacaacaa tcccaagaac attgaattat atcaatagga taatcgatta
     5521 ccttgctggc gctggatctc ctgtgtcaca gacatacctc agtttatggt gtcgagtttt
     5581 tgacgaggga ttcgtcgaaa ttagggataa agatgctctg gcatttgagt cagggtttag
     5641 tgggcagcga gcggtgacta cttggctagg aagaatgaaa aagctacggg agctgggact
     5701 gatatcaacg aagcctggta cttctggcga gtttcattat gtaattatgt tgaa
//
