LOCUS       NZ_AP017616             4073 bp    DNA     circular CON 08-MAY-2024
DEFINITION  Escherichia coli strain 20Ec-P-124 plasmid pMRY16-002_6, complete
            sequence.
ACCESSION   NZ_AP017616
VERSION     NZ_AP017616.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00056130
            Sequence Read Archive: DRR065946, DRR065949
            Assembly: GCF_002357915.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Sekizuka,T., Kawanishi,M., Ohnishi,M., Shima,A., Kato,K.,
            Yamashita,A., Matsui,M., Suzuki,S. and Kuroda,M.
  TITLE     Elucidation of quantitative structural diversity of remarkable
            rearrangement regions, shufflons, in IncI2 plasmids
  JOURNAL   Sci Rep 7 (1), 928 (2017)
   PUBMED   28424528
  REMARK    DOI:10.1038/s41598-017-01082-y Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4073)
  AUTHORS   Sekizuka,T., Kawanishi,M., Ohnishi,M., Shima,A., Kato,K.,
            Yamashita,A., Matsui,M., Suzuki,S. and Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-JUL-2016) Contact:Tsuyoshi Sekizuka National Institute
            of Infectious Diseases, Pathogen Genomics Center; 1-23-1 Toyama,
            Shinjuku-ku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: HGAP Assembly v. 3.0; Celera Assembler v. 8.2
            Genome Coverage                   :: 200x
            Sequencing Technology             :: MiSeq; PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002357915.1-RS_2024_05_08
            Annotation Date                   :: 05/08/2024 03:26:50
            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)                     :: 5,320
            CDSs (total)                      :: 5,193
            Genes (coding)                    :: 4,966
            CDSs (with protein)               :: 4,966
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 227
            CDSs (without protein)            :: 227
            Pseudo Genes (ambiguous residues) :: 0 of 227
            Pseudo Genes (frameshifted)       :: 99 of 227
            Pseudo Genes (incomplete)         :: 141 of 227
            Pseudo Genes (internal stop)      :: 49 of 227
            Pseudo Genes (multiple problems)  :: 59 of 227
            Pseudo Genes (short protein)      :: 5 of 227
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP017616.1.
            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..4073
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="20Ec-P-124"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="pMRY16-002_6"
                     /geo_loc_name="Japan"
                     /collection_date="2008"
                     /note="strain coidentity: 20Ec-P-124 = MRY16-002"
     gene            48..302
                     /gene="mobC"
                     /locus_tag="CPZ02_RS28300"
                     /old_locus_tag="MRY16002_p60010"
     CDS             48..302
                     /gene="mobC"
                     /locus_tag="CPZ02_RS28300"
                     /old_locus_tag="MRY16002_p60010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            836..1537
                     /locus_tag="CPZ02_RS28310"
                     /old_locus_tag="MRY16002_p60020"
     CDS             836..1537
                     /locus_tag="CPZ02_RS28310"
                     /old_locus_tag="MRY16002_p60020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1795..3942)
                     /gene="mobQ"
                     /locus_tag="CPZ02_RS28315"
                     /old_locus_tag="MRY16002_p60030"
     CDS             complement(1795..3942)
                     /gene="mobQ"
                     /locus_tag="CPZ02_RS28315"
                     /old_locus_tag="MRY16002_p60030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     Typing          complement(3585..3943)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3944..4073
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.52e-62"
     Typing          837..1537
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1799..4029)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cagtgacgcg ctaaaatgcg atttttcatc gcgcacggag ttacatcatg agcagaacgc
       61 tcgaacagaa gattgctgat gctgaggcga gattacagcg cctgaaggcg aagagccgga
      121 gcctggacac agcgcagaag gttgttgtgg gtgctgcatt gctggcaaag gtcagaaagc
      181 cggaggaggt gcagttgcgt gcctggttac tccagttcct gaaggcagag gtgacacgac
      241 aggctgatgt gacgcgcata ctgccgctga ttaacgagct ggaggcgctg ccagaacagt
      301 gattgtatcg tccgctcgcc gcagccccag cgaccgagcg ttagcgagcg agtgggcgag
      361 gaagcggaag tgaatcagtc gccaggttga gcacatacgc acggtttttc ggcaggtgat
      421 atgcgctgaa cccgcatgaa tactgggttt ccacagggtt ggagggggtg tattcgaaac
      481 ttgcaattct gctttattgc aacgcattgt ttttattggt tttttgtttt cagcacccca
      541 agttatccac aggctcgccg ttaagttttt aagatcttat ttttagatct ttttttttaa
      601 aaccttttta ggtcttgtaa caccatgatt ttaaagatgt tctggcaaga taagtggagc
      661 ttttgggggt gaaaggtgga gcttttgggg gtgaaaggtg gagcttttgg gggtgaaagg
      721 tggagctttt gggggtgtaa tccacagaaa aagggggttg caaaaaaaaa acttccaccc
      781 atatgataag tggcgtacag taaaaaaacg ccaccaatag caacgagcaa gcgaaatgtc
      841 agatctgata gcttacaaat caaacgccct tatcgaggca agctacaagc tcactttgca
      901 ggaacagcgc ttcctgctgg tctgtatcag ccgcctaaaa tccggagaag attccccttc
      961 gccggatgaa caaaaaacca tgaccatcac ggctgcagag tttcatgatg cctttcctga
     1021 catgggacgg cagcacgctg aagctaggct caaggaagcg atagatcgcc tctgggacag
     1081 gtcagtaatc atcaagaacg aggaaaaacg agaagagttc cgctgggtgc agtaccgggc
     1141 gcagtatttc aaaggtgagg cgaaagtaga tatcaccttc tccgatgcca tcatgccgta
     1201 tctgacacag ctcaaggggc agtttacgcg ggtagtcgtg aagaacgtct ccagcctttc
     1261 cagcacctac agcatccgca tttacgagct gctccagcag ttccgcagca ccggtgacag
     1321 aacgatagct atcgatgatt tccgaaccat gcttgccgtt gaagataaat atcaacaatt
     1381 caaagacttg aataagatga taatcaagcc agccatcgcc gaactgaacg aaaaaagcga
     1441 tctggttgta actgttgaga cgatcaaaaa ggggcgcacg gttgtagccc tgcattttcg
     1501 cttcaaggaa gacaaacaga tcaagatgac gatctaaaat cgattttaag gcacctaaaa
     1561 cgctccctgc tgcgtttttt ttgtgttagt agtgcgaagg tactattgaa gtgaaaaatt
     1621 gcgtcaaaaa cgctctgatg cagcgaaaaa agacccccca atttttgggg gcggaaaaac
     1681 aaaactatgc ttgcgttatg tgagtgtgct tcttgcattc atccctgtcg atgaacatcg
     1741 aagaacatcg acgaacataa cacgatgtta aacaaaacaa aatattgttc acattcactg
     1801 tgaccaaccg cgatcatgtc tcctctcggt ggtgtgtgtt cgtgcatctt cctcgcgctg
     1861 ccattcctcc caggtacgat taaaacccag cgagcggaac agatgatccg gctgtttttc
     1921 tggtgtgttg acggcagcaa aaagcggtgc ctcacgggtt ttcagatgaa actgcatcag
     1981 ttctggtgca ggtgatatgt ggctgtctgc atcgtgattt acggcaacac cataccctgc
     2041 ataccgtaac cccttatcgg tcagcgcact gatgaccaga tgcctgttat cggctgaggg
     2101 aacggcaaac gcgggataca gcgtaccatt aagccggata acaccgccca gagagtcatc
     2161 cacgcccatg accagcaaaa gctgaagctg gcgggtttcc cggtcgacag aactcatgac
     2221 cggcatcagc gtcggtggca gacgtccctg cataaaatcc accttccttg ccgctggtga
     2281 tggcatggct ggctggcggt cttctccaag acagaaagac tccggccatg tcttcggctg
     2341 gcggagattg cgggtatgtt gcggccatgt ctggcaaacc tgcgtcagca gttgctcaaa
     2401 ggttgcagag gaataaacac gttgcagtgg cggacgttgg ccgatttcgc ttcggtcaca
     2461 gatataacca ctcctgtcac gcattaaatc aacactctca aagattctgg tgcggtattt
     2521 ctccagctcg ttcccccaga gcgtatattc tccgttccgg ttgtgaagca gaaggtaaca
     2581 ggtcatttcc ccgttaccag gcatgggagc ctcgccatac cccgtaacga ctgctctcag
     2641 cacccctgaa tccataacgg cattgtcatt tttcctgagc tgctccgcgc gactacgttc
     2701 agtatcttcc tgttccttcc ggcgcaattc ctcttcacgt ttaagcaact gggctctgag
     2761 agctgcaagg ccggattccc cccactgctg ccactgtttt tcaaatgcca tctgactcgc
     2821 gggaatgtcc tgtttctcca ccttccggta atgctgtcgt aatttttcca tttgctggct
     2881 cagagactgg atttttccct gctcactacg gtattccggt gccgcccatt gcatcagggg
     2941 aatacgggaa aaaccggacg aaaacggcga tgattttttc aggctggcag catggctcat
     3001 cgcttccttt cgttcggtgt tcagctcttc ccagcgtctg cgcgtcgcct gcatatctgc
     3061 catcatcgac atggcattac tggtgagttt ccatgccgag ttactgtcct tcggcaacgc
     3121 ttcgataatg tcacgtagtg tgtacgaagt tgcgttgtca ggaagcccga tattcagaag
     3181 gtcagccaca cggcgggcag gctctgtcag ccctccgttc ctgagttcgg tgcgggaaat
     3241 ctgtatttcc aggttaagcc tgttaatcag acgattctgt tcgccgcgtt ctgtttcgat
     3301 accgcgtgtt tccatcgcac aggcagactt tccgaggtga ataccaggcg ttttctcaag
     3361 cccctgtcgc tcgtatgaac gatggtctat ctcttcctga taaccggcgt tcgccagtgc
     3421 cctgtttgca tggtcagccc atgatgcccg ccacgtctcg gcatgtgtcc ggtcgttcca
     3481 gtccctgacc tttccgctga acccagcagg tccgatagcc ctcgtggtca gcatgatgtg
     3541 cgcatgggga tttgttttat ccatgtgatg gaacgccaca tcagcaatca tgccctgact
     3601 gacaaagttt tctctgacaa aggcgagaac ggtttcccgt gcggcatcct gcggcagttc
     3661 gtgggggatg gcgagttcaa tttcccgcgc aagttgtgag ttcttccggc gttcggcctt
     3721 ctcaacggca ttccagagtt cggcacggtt cgtacaccag gcaggggcgg tggcgggggt
     3781 cagaatcaca gcctcagcca caccgctttt gcgggtgtag tcgtgagtca gtccggtacg
     3841 ctcatcaagc atcagtgaac cggaacgata ggcagcggaa gctacggcgc tgtagccgct
     3901 gcttctggag ataattttca tgctgagatg ataaatcgcc atttctgccg taatgccttt
     3961 ttgtagtttt ctttcagccc cgcagggcgc acacaatcga aacggagtgg agattgtata
     4021 agtgcgcact tcgtgatttg ccgtgcatta tgccagctca gtttttaaac tac
//
