LOCUS       NZ_CP128962             4073 bp    DNA     circular CON 07-JUL-2023
DEFINITION  Escherichia coli strain TUM2330 plasmid pMTY2330_Col8282, complete
            sequence.
ACCESSION   NZ_CP128962
VERSION     NZ_CP128962.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35768957
            Assembly: GCF_030389835.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4073)
  AUTHORS   Ikegaya,K., Aoki,K., Komori,K., Ishii,Y. and Tateda,K.
  TITLE     Analysis of the stepwise acquisition of blaCTX-M-2 and subsequent
            acquisition of either blaIMP-1 or blaIMP-6 in highly conserved
            IncN-pST5 plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4073)
  AUTHORS   Ikegaya,K., Aoki,K., Komori,K., Ishii,Y. and Tateda,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-JUN-2023) Department of Microbiology and Infectious
            Diseases, Toho University, 5-21-16, Omori-Nishi, Ota-Ku, Tokyo
            143-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 18-NOV-2021
            Assembly Method                   :: SPAdes v. v3.15.5
            Assembly Name                     :: Toho-u_TUM2330_Comp_v1.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: missing
            Genome Coverage                   :: 142x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/05/2023 07:45:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,989
            CDSs (total)                      :: 4,871
            Genes (coding)                    :: 4,738
            CDSs (with protein)               :: 4,738
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 59 of 133
            Pseudo Genes (incomplete)         :: 86 of 133
            Pseudo Genes (internal stop)      :: 34 of 133
            Pseudo Genes (multiple problems)  :: 41 of 133
            Pseudo Genes (short protein)      :: 4 of 133
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP128962.1.
            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="TUM2330"
                     /db_xref="taxon:562"
                     /plasmid="pMTY2330_Col8282"
                     /geo_loc_name="Japan"
                     /collection_date="2005"
                     /collected_by="Toho University School of Medicine"
     gene            complement(join(2502..4073,1..588))
                     /gene="mobQ"
                     /locus_tag="QVM93_RS24935"
                     /old_locus_tag="QVM93_24935"
     CDS             complement(join(2502..4073,1..588))
                     /gene="mobQ"
                     /locus_tag="QVM93_RS24935"
                     /old_locus_tag="QVM93_24935"
                     /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_137464071.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELGIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            767..1021
                     /gene="mobC"
                     /locus_tag="QVM93_RS24940"
                     /old_locus_tag="QVM93_24940"
     CDS             767..1021
                     /gene="mobC"
                     /locus_tag="QVM93_RS24940"
                     /old_locus_tag="QVM93_24940"
                     /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_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            1553..2254
                     /locus_tag="QVM93_RS24945"
                     /old_locus_tag="QVM93_24945"
     CDS             1553..2254
                     /locus_tag="QVM93_RS24945"
                     /old_locus_tag="QVM93_24945"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(231..589)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          590..766
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1554..2254
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.715"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..675)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.111"
                     /coverage="100.0"
                     /evalue="3.96e-146"
ORIGIN
        1 ctcaagcccc tgtcgctcgt atgaacgatg gtctatctct tcctgataac cggcgttcgc
       61 cagtgccctg ttcgcatggt cagcccatga tgcacgccac gtctcggcat gtgtccggtc
      121 gttccagtcc ctgacctttc caccgaatcc agcaggtccg acagctctcg tggtcagcat
      181 gatgtgcgca tggggatttg ttttatccat gtgatggaac gccacatcag caatcatgcc
      241 ctgactgaca aagttttctc tgacaaaggc gagaacggtt tcccgtgcgg catcctgcgg
      301 cagttcgcgg gggatgccga gttcaatttc ccgcgcaagt tgtgagttct tccggcgttc
      361 ggccttctca acggcattcc agagttcggc acggttcgta caccaggcag gggctgtcgc
      421 gggagtcaga atcacagctt cagccacacc gcttttgcgg gtgtagtcgt gagtcagtcc
      481 ggtacgctca tcaagcatca gtgaaccgga acgataggca gcagaagcaa cggcgctgta
      541 gccgctgttt ctggagatga ttttcatgct gagatgataa atcgccattt ctgccgtaat
      601 gcctttttgt ggttttcttt cagccccgca gggcgcacac aatcgaaacg gagtggagat
      661 tgtataagtg cgcacttcgt gattttccgt gcattatgcc agctcagttt ttaaactacc
      721 agtgacgcgc taaaatgcga tttttcatcg cgcacggagt tacatcatga gcagaacact
      781 cgaacagaag attgctgatg ctgaggccag attacagcgc ctgaaggcga agagcaggag
      841 tctggacaca gcgcagaagg tcattgtggg tgcagcattg ctggcaaagg tcagaaagcc
      901 ggaggaggtg cagttgcgtg cctggttact ccagttcctg aaggcagagg tgacacgaca
      961 ggctgatgtg acgcgcatac tgccgctgat taacgagctg gaagcgctgc caggacagtg
     1021 attgtatcgt ccgctcgccg cagtcccagc gaccgagcgt agcgagcgag tgggcgagga
     1081 agcggaagtg aatccgtcgc ctgattgagc acatacgcac ggtttttcgg gaggtgatat
     1141 gcgctgaacc cgcatgaata ctggatttcc acagggttgg agggggtgta ttcggaactt
     1201 gcaattctgc ttttttgcaa cgcattgttt ttattggttt tttgttttca tcactccaag
     1261 ttatccacag gctcgtcgtt aagtttttag atcttgtttt taagatcttg tttttaatac
     1321 ttgttttagc gccaaaattc cttatagaaa acaaaatgtt acaacgctat aggtaatatg
     1381 atttaaggta aaggtaatat gatttaaggt gtttaggtgg aggaatttaa ggtaaaggca
     1441 atatgattta aggtaatatt cacagaaaaa gggatattaa aataaaaagg cattgccttt
     1501 cgttgagggt atgtttatct tttattcatt accttttggg gagggatgct ctatgtcgga
     1561 tctaattgcc tataaatcca atgcgctggt tgaagccagt tataaattga ccctacagga
     1621 acagcgattt ttgttacttt gcatcggtcg attgaagtct ggggctgatg cagaatctcc
     1681 aaaattgcaa aagacaatga ccattacagc tgcggaatat ttcgattcat tccctgacat
     1741 ggggcggaaa aatgccgagg ttcagttaca ggaagcaatt gatcgtttgt gggacaggtc
     1801 aatcattctc aaggatgacg agaagcgtga ggagttccgc tggatccagt atcgggcaca
     1861 gtacgctaaa ggcgaggcca gagcacaaat aacattttct gacgcagtaa tgccttattt
     1921 gacacaacta caagggcaat ttactagagt tgtaatcaag aatatatcta gattatcaag
     1981 aagttacagt ataaggatat acgaactcct ccagcagttc cgcagtactg gcgaacgtat
     2041 tatcgctctc gatgattttc gctcaatgct tgatatagag cataaatatc aaacatataa
     2101 atcacttaac cagcaattat taagaccctg cattgacgaa ctgaacaaaa aaagcgacct
     2161 ggctgtaacg gttgagacga tcaaaaaggg gcgcacggtt gtagccctgc attttcgctt
     2221 caaggaagac aaacagatca agatgacgat ctaaaatcga ttttaaggca cctaaaacgc
     2281 tccctgctgc gttttttttg tgttagtagt gcgaaggtac tattgaagtg aaaaattgcg
     2341 tcaaaagcgc tctaatgcag cgaaaaaaga acccccaatt tttgggggcg gaaaaacaaa
     2401 actatgctgt gtgtgcttct tgcattcatc cctgtcgatg aacatcgaag aacatcgacg
     2461 aacataacac gatgttaaac aaaacaaaat attgttcaca ttcactgtga ccaaccgcga
     2521 tcatgtctcc tctcggtggc gtgtgttcgt gcatcttcct cgcgccgcca ttcgtcccag
     2581 gtacgattaa aacccagcga gcggaacaga tgatccggct gtttttctgg tgtgttgacg
     2641 gcagcaaaaa gcggtgcctc acgggttttc agatgaaact ccataagttc cggcgcaggt
     2701 gatatgtggc tgtctgcatc gtgatttacg gcaacaccat accctgcata ccgtaacccc
     2761 ttatcggtca gtgcactgat gaccagctgg ctgttatcgg ctgagggaac ggcaaacgcg
     2821 ggatacagcg taccattaag ccggacaaca ccgcccagag agtcatccac gcccatgacc
     2881 agcaaaagct gaagctggcg ggtttcccgg tcgacagaac tcattaccgg catcagcgtc
     2941 ggtagcagac gtccctgcgt aaaatccacc ttccttgctg ccagtgatgg catggctggc
     3001 tggcggtctt ctccaagaca gaaagactcc ggccatgtct tcggctggcg gagattgcgg
     3061 gtatattgcg gccatgtctg gcaaacctgc gtcagaagtt gctcaaaggt cgcagaggaa
     3121 taaacacgtt gcagtggtgg atgttgaccg atttcgcttc ggtcacagat ataaccactc
     3181 ctgtcacgca ttaaatcaac acgctcaaag attctggtgc ggtatttctc cagctcgttc
     3241 ccccagagcg tgtattctcc gttccggttg tgaagcagaa ggtaacaggt catttccccg
     3301 ttaccaggca tgggggcctc gccatacccc gtaacgactg cgctcagtac ccctgaatcc
     3361 ataacggcat tgtcattttt cctgagctgt tccgctcgtc gctccgcgcg actacgttct
     3421 gtatcctcct gctccttccg gcgcaattcc tcttcacgtt taagcaactg gactctgaga
     3481 gctgcaaggc cggatgcccc ccactgctgc cactgttttt caaatgccgt ctgactcgcg
     3541 ggaatgtcct gtttctccac cttccggtaa tgctgtcgca atttttccat ttgctggctc
     3601 agcgactgga tttttccctg ttcgctacgg tattccggtg ccgcccattg catcagggga
     3661 atacgggaaa aaccggacga aaacggcgat gattttttca ggctggcagc atggctcatc
     3721 gcttcctttc gttcggtgtt cagctcttcc cagcgtctgc gcgtcgcctg catatctgcc
     3781 atcatcgaca tggcattact ggtgagtttc catgccgcat tactgtcctt cggcaacgct
     3841 tcgatgatgt cacgtagtgt gtacgaagtt gcgttgtcag gaagcacgat attcagaagg
     3901 tcagccacac ggcgggcagg ctctgtcagc ccgctgtttc tgagttcggt acgggaaatc
     3961 tgtatttcca ggttaagtct gttaatcaga cgattctgtt cgccgcgttc tgtttcgata
     4021 ccgcgtgttt ccatcgcaca ggcagacttt ccgaggtgaa taccaggcgt ttt
//
