LOCUS       NZ_CP103631             4060 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 4012 plasmid pMB6206_5, complete sequence.
ACCESSION   NZ_CP103631
VERSION     NZ_CP103631.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174046
            Assembly: GCF_024918275.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4060)
  AUTHORS   Shropshire,W.C., Konovalova,A., McDaneld,P.M., Gohel,M., Strope,B.,
            Sahasrabhojane,P., Tran,C.N., Greenberg,D.E., Kim,J., Zhan,X.,
            Aitken,S.L., Bhatti,M., Tor,S., Treangen,T., Hanson,B.M., Arias,C.A.
            and Shelburne,S.A.
  TITLE     Systematic Analysis of Mobile Genetic Elements Mediating
            Beta-lactamase Gene Amplification in Non-Carbapenemase-Producing
            Carbapenem Resistant Enterobacterales Bloodstream Infections
  JOURNAL   mSystems (2022) In press
REFERENCE   2  (bases 1 to 4060)
  AUTHORS   Shropshire,W.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-AUG-2022) Infectious Diseases and Infection Control,
            University of Texas MD Anderson Cancer Center, South Campus Research
            Building 4, Houston, TX 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 273x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:21:21
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,007
            CDSs (total)                      :: 4,882
            Genes (coding)                    :: 4,698
            CDSs (with protein)               :: 4,698
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 184
            CDSs (without protein)            :: 184
            Pseudo Genes (ambiguous residues) :: 0 of 184
            Pseudo Genes (frameshifted)       :: 67 of 184
            Pseudo Genes (incomplete)         :: 116 of 184
            Pseudo Genes (internal stop)      :: 32 of 184
            Pseudo Genes (multiple problems)  :: 33 of 184
            Pseudo Genes (short protein)      :: 4 of 184
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103631.1.
            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..4060
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4012"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB6206_5"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-08-21"
                     /collected_by="MDACC"
                     /genotype="ST90"
     gene            join(3632..4060,1..273)
                     /locus_tag="M5S78_RS24895"
                     /old_locus_tag="M5S78_24895"
     CDS             join(3632..4060,1..273)
                     /locus_tag="M5S78_RS24895"
                     /old_locus_tag="M5S78_24895"
                     /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_015059933.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(519..2666)
                     /gene="mobQ"
                     /locus_tag="M5S78_RS24900"
                     /old_locus_tag="M5S78_24900"
     CDS             complement(519..2666)
                     /gene="mobQ"
                     /locus_tag="M5S78_RS24900"
                     /old_locus_tag="M5S78_24900"
                     /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_015059934.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKVAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQKWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRARIFERVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATVRRHDRGWSQ"
                     /name="mobQ"
     gene            2845..3099
                     /gene="mobC"
                     /locus_tag="M5S78_RS24905"
                     /old_locus_tag="M5S78_24905"
     CDS             2845..3099
                     /gene="mobC"
                     /locus_tag="M5S78_RS24905"
                     /old_locus_tag="M5S78_24905"
                     /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_000091744.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2309..2667)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2668..2844
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2..272
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.897"
                     /coverage="99.0"
                     /evalue="1.4199999999999998e-134"
     Typing          3763..3963
                     /name="Col8282"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.604"
                     /coverage="98.0"
                     /evalue="3.2100000000000004e-66"
     Typing          complement(523..2753)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.326"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agttacagta taaggatata cgaactcctc cagcagttcc gcagtactgg cgaacgtatt
       61 atcgctctcg atgattttcg ctcaatgctt gatatagagc ataaatatca aacatataaa
      121 tcacttaacc agcaattatt aagaccctgc attgacgaac tgaacaaaaa aagcgatctg
      181 gttgtaacgg ttgagacgat caaaaagggg cgcacggttg tagccctgca ttttcgcttc
      241 aaggaagaca aacagatcaa gatgacgatc tagaatcgat tttaaggcct ctaaaacgtt
      301 ctctggtgcg tttttttggt gtcaggtatg cgatggtact gctttggcaa taaattgcgt
      361 cagaattgat ttgagaggcc aaaaaagaac ccccaatttt gggggcggaa aaacaaaact
      421 atgtttgcgt tatgtgagtg tgcttcttgc attcatccct gtcgatgaac atcggcgaac
      481 ataacacgat gttacacaaa acaaaatatt gttcacattc actgtgacca accgcgatca
      541 tgtctcctca cggtggcgtg tgttcgtgca tcttcctcgc gccgccattc gtcccaggta
      601 cgattaaaac ccagcgagcg gaacagatga tccggctgtt tttctggtgt gttgacggca
      661 gcaaaaagcg gtgcctcacg ggttttcaga tgaaactgca tcagttctgg tgcaggtgat
      721 atgtggctgt ctgcatcgtg atttacggca acaccatacc ctgcataccg taacccctta
      781 tcggtcagtg cactgatgac cagctggctg ttatcggctg agggaacggc aaacgcggga
      841 tacagcgtac cattaagccg gacaacaccg cccagagagt catccacgcc catgaccagc
      901 aaaagctgaa gttgtcgggt ttcccggtct acagaactca ttaccggcat cagcgtcggt
      961 ggcagacgtc cctgcgtaaa atccaccttc cttgctgcca gtgatggcat ggctggctgg
     1021 cggtcttctc caagacagaa agactccggc catgtcttcg gctggcggag attgcgggta
     1081 tgttgcggcc atgtctggca aacctgcgtc agcagttgct caaaggtcgc agaggaataa
     1141 acacgttgca gtggcggacg ttggccgatt tcgcttcggt cacagatata accactcctg
     1201 tcacgcatta aatcaacacg ctcaaagatt ctggcgcggt atttctccag ttcgttcccc
     1261 cagagcgtat attctccgtt ccggttgtga agcagaaggt aacaggtcat ttccccgtta
     1321 ccaggcatgg gggcctcgcc ataccccgta acgactgcgc tcagtacccc tgaatccata
     1381 acggcattgt catttttcct gagctgctcc gcgcgactac gttcagtatc ttcctgttcc
     1441 ttccggcgca attcctcttc acgtttaagc aactgggctc tgagagctgc aaggccggat
     1501 tccccccact tctgccactg tttttcaaat gccatctgac tcgcgggaat gtcctgtttc
     1561 tccaccttcc ggtaatgctg tcgcaatttt tccatttgct ggctcagaga ctggattttt
     1621 ccctgctcac tacggtattc cggtgccgcc cattgcatca ggggaatacg ggaaaaaccg
     1681 gacgaaaacg gcgatgattt tttcaggctg gcagcatggc tcatcgctac ctttcgttcg
     1741 gtgttcagct cttcccagcg tctgcgcgtc gcctgcatat ctgccatcat cgacatggca
     1801 ttactggtga gtttccatgc cgagttactg tccttcggca acgcttcgat gatgtcacgt
     1861 agtgtgtacg aagttgcgtt gtcaggaagc ccgatattca gaaggtcagc cacacggcgg
     1921 gcaggctctg tcagccctcc gttcctgagt tcggtgcggg aaatctgtat ttccaggtta
     1981 agcctgttaa tcagacgatt ctgttcgccg cgttctgttt cgataccgcg tgtttccatc
     2041 gcacaggcag actttccgag gtgaatacca ggcgttttct caagcccctg tcgctcgtat
     2101 gaacgatggt ctatctcttc ctgataaccg gcgttcgcca gtgccctgtt tgcatggtca
     2161 gcccatgatg cccgccacgt ctcggcatgt gtccggtcgt tccagtccct gacctttcca
     2221 ccgaatccag caggtccgac agctctcgtg gtcagcatga tgtgcgcatg gggatttgtt
     2281 ttatccatgt gatggaacgc cacatcagca atcatgccct gactgacaaa gttttctctg
     2341 acaaaggcga gaacggtttc ccgtgcggca tcctgcggca gttcgtgggg gatggcgagt
     2401 tcaatttccc gcgcaagttg tgagttcttc cggcgttcgg ccttctcaac ggcattccag
     2461 agttcggcac ggttcgtaca ccaggcaggg gctgtcgcgg gagtcagaat cacagcttca
     2521 gccacaccgc ttttgcgggt gtagtcgtga gtcagtccgg tacgctcatc aagcatcagt
     2581 gaaccggaac gataggcagc agaagcaacg gcgctgtagc cgctgtttct ggagatgatt
     2641 ttcatgctga gatgataaat cgccatttct gccgtaatgc ctttttgtgg ttttctttca
     2701 gccccgcagg gcgcacacaa tcgaaacgga gtggagattg tataagtgcg cacttcgtga
     2761 tttgccgtgc attatgccag ctcagttttt aaactaccag tgacgcgcta aaatgcgatt
     2821 tttcatcgcg cacggagtta catcatgagc agaacactcg aacagaagat tgctgatgct
     2881 gaggccagat tacagcgcct gaaggcgaag agcaggagtc tggacacagc gcagaaggtc
     2941 attgtgggtg cagcattgct ggcaaaggtc agaaagccgg aggaggtgca gttgcgtgcc
     3001 tggttactcc agttcctgaa ggcagaggtg acacgacagg ctgatgtgac gcgcatactg
     3061 ccgctgatta acgagctgga agcgctgcca gaacagtgat tgtatcgtcc gctcgccgca
     3121 gtcccagcga ccgagcgtta gcgagcgagt gggcgaggaa gcggaagtga atccgtcgcc
     3181 tgattgagca catacgcacg gtttttcggg aggtgatatg cgctgaaccc gcatgaatac
     3241 tggatttcca cagggttgga gggggtgtat tcggaacttg caattctgct tttttgcaac
     3301 gcattgtttt tattggtttt ttgttttcag cactccaagt tatccacagg ctcgtcgtta
     3361 agtttttaga tcttgttttt aagatcttgt ttttaatact tgttttagtg ccaaaattcc
     3421 ttatagaaaa caaaatgtta caacgctata ggtaatatga tttaaggtaa aggtaatatg
     3481 atttaaggtg tttaggtaat atgatttaag gtaaaggtaa tatgatttaa ggtaatattc
     3541 acagaaaaag ggatattaaa ataaaaaggc attgcctttc gctgggggta tgtttatctt
     3601 ttattcatta ccttttgggg agggatgctc tatgtcggat ctaattgcct ataaatctaa
     3661 tgcgctggtt gaagccagtt ataaattgac cctacaggaa cagcgatttt tgttactttg
     3721 catcggtcga ttgaagtctg gggctgatgc agaatctcca aaattgcaaa agacaatgac
     3781 cattacagct gcggaatatt tcgattcatt ccctgacatg gggcggaaaa atgccgaggt
     3841 tcagttacag gaagcaattg atcgtttgtg ggacaggtca atcattctca aggatgacga
     3901 gaaacgtgag gagttccgct ggatccagta tcgggcacag tacgctaaag gcgaggccag
     3961 agcacaaata acattttctg acgcagtaat gccttatttg acacaactac aagggcaatt
     4021 tactagagtt gtaatcaaga atatatctag attatcaaga
//
