LOCUS       NZ_CP103473             4063 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 4973 plasmid pMB9698_5, complete sequence.
ACCESSION   NZ_CP103473
VERSION     NZ_CP103473.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174076
            Assembly: GCF_024918135.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4063)
  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 4063)
  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                   :: 250x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:21:07
            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)                     :: 5,330
            CDSs (total)                      :: 5,209
            Genes (coding)                    :: 5,011
            CDSs (with protein)               :: 5,011
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 198
            CDSs (without protein)            :: 198
            Pseudo Genes (ambiguous residues) :: 0 of 198
            Pseudo Genes (frameshifted)       :: 68 of 198
            Pseudo Genes (incomplete)         :: 129 of 198
            Pseudo Genes (internal stop)      :: 42 of 198
            Pseudo Genes (multiple problems)  :: 38 of 198
            Pseudo Genes (short protein)      :: 5 of 198
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103473.1.
            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..4063
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4973"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9698_5"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2020-01-09"
                     /collected_by="MDACC"
                     /genotype="ST648"
     gene            complement(1..2148)
                     /gene="mobQ"
                     /locus_tag="M5S50_RS26480"
                     /old_locus_tag="M5S50_26485"
     CDS             complement(1..2148)
                     /gene="mobQ"
                     /locus_tag="M5S50_RS26480"
                     /old_locus_tag="M5S50_26485"
                     /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"
     gene            2327..2581
                     /gene="mobC"
                     /locus_tag="M5S50_RS26485"
                     /old_locus_tag="M5S50_26490"
     CDS             2327..2581
                     /gene="mobC"
                     /locus_tag="M5S50_RS26485"
                     /old_locus_tag="M5S50_26490"
                     /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            3115..3816
                     /locus_tag="M5S50_RS26490"
                     /old_locus_tag="M5S50_26495"
     CDS             3115..3816
                     /locus_tag="M5S50_RS26490"
                     /old_locus_tag="M5S50_26495"
                     /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"
     Typing          complement(1791..2149)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2150..2326
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3116..3816
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(5..2235)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcactgtgac caaccgcgat catgtctcct ctcggtggtg tgtgttcgtg catcttcctc
       61 gcgctgccat tcctcccagg tacgattaaa acccagcgag cggaacagat gatccggctg
      121 tttttctggt gtgttgacgg cagcaaaaag cggtgcctca cgggttttca gatgaaactg
      181 catcagttct ggtgcaggtg atatgtggct gtctgcatcg tgatttacgg caacaccata
      241 ccctgcatac cgtaacccct tatcggtcag cgcactgatg accagatgcc tgttatcggc
      301 tgagggaacg gcaaacgcgg gatacagcgt accattaagc cggataacac cgcccagaga
      361 gtcatccacg cccatgacca gcaaaagctg aagctggcgg gtttcccggt cgacagaact
      421 catgaccggc atcagcgtcg gtggcagacg tccctgcata aaatccacct tccttgccgc
      481 tggtgatggc atggctggct ggcggtcttc tccaagacag aaagactccg gccatgtctt
      541 cggctggcgg agattgcggg tatgttgcgg ccatgtctgg caaacctgcg tcagcagttg
      601 ctcaaaggtt gcagaggaat aaacacgttg cagtggcgga cgttggccga tttcgcttcg
      661 gtcacagata taaccactcc tgtcacgcat taaatcaaca ctctcaaaga ttctggtgcg
      721 gtatttctcc agctcgttcc cccagagcgt atattctccg ttccggttgt gaagcagaag
      781 gtaacaggtc atttccccgt taccaggcat gggagcctcg ccataccccg taacgactgc
      841 tctcagcacc cctgaatcca taacggcatt gtcatttttc ctgagctgct ccgcgcgact
      901 acgttcagta tcttcctgtt ccttccggcg caattcctct tcacgtttaa gcaactgggc
      961 tctgagagct gcaaggccgg attcccccca ctgctgccac tgtttttcaa atgccatctg
     1021 actcgcggga atgtcctgtt tctccacctt ccggtaatgc tgtcgtaatt tttccatttg
     1081 ctggctcaga gactggattt ttccctgctc actacggtat tccggtgccg cccattgcat
     1141 caggggaata cgggaaaaac cggacgaaaa cggcgatgat tttttcaggc tggcagcatg
     1201 gctcatcgct tcctttcgtt cggtgttcag ctcttcccag cgtctgcgcg tcgcctgcat
     1261 atctgccatc atcgacatgg cattactggt gagtttccat gccgagttac tgtccttcgg
     1321 caacgcttcg ataatgtcac gtagtgtgta cgaagttgcg ttgtcaggaa gcccgatatt
     1381 cagaaggtca gccacacggc gggcaggctc tgtcagccct ccgttcctga gttcggtgcg
     1441 ggaaatctgt atttccaggt taagcctgtt aatcagacga ttctgttcgc cgcgttctgt
     1501 ttcgataccg cgtgtttcca tcgcacaggc agactttccg aggtgaatac caggcgtttt
     1561 ctcaagcccc tgtcgctcgt atgaacgatg gtctatctct tcctgataac cggcgttcgc
     1621 cagtgccctg tttgcatggt cagcccatga tgcccgccac gtctcggcat gtgtccggtc
     1681 gttccagtcc ctgacctttc cgctgaaccc agcaggtccg atagccctcg tggtcagcat
     1741 gatgtgcgca tggggatttg ttttatccat gtgatggaac gccacatcag caatcatgcc
     1801 ctgactgaca aagttttctc tgacaaaggc gagaacggtt tcccgtgcgg catcctgcgg
     1861 cagttcgtgg gggatggcga gttcaatttc ccgcgcaagt tgtgagttct tccggcgttc
     1921 ggccttctca acggcattcc agagttcggc acggttcgta caccaggcag gggcggtggc
     1981 gggggtcaga atcacagcct cagccacacc gcttttgcgg gtgtagtcgt gagtcagtcc
     2041 ggtacgctca tcaagcatca gtgaaccgga acgataggca gcggaagcta cggcgctgta
     2101 gccgctgctt ctggagataa ttttcatgct gagatgataa atcgccattt ctgccgtaat
     2161 gcctttttgt agttttcttt cagccccgca gggcgcacac aatcgaaacg gagtggagat
     2221 tgtataagtg cgcacttcgt gatttgccgt gcattatgcc agctcagttt ttaaactacc
     2281 agtgacgcgc taaaatgcga tttttcatcg cgcacggagt tacatcatga gcagaacgct
     2341 cgaacagaag attgctgatg ctgaggcgag attacagcgc ctgaaggcga agagccggag
     2401 cctggacaca gcgcagaagg ttgttgtggg tgctgcattg ctggcaaagg tcagaaagcc
     2461 ggaggaggtg cagttgcgtg cctggttact ccagttcctg aaggcagagg tgacacgaca
     2521 ggctgatgtg acgcgcatac tgccgctgat taacgagctg gaggcgctgc cagaacagtg
     2581 attgtatcgt ccgctcgccg cagccccagc gaccgagcgt tagcgagcga gtgggcgagg
     2641 aagcggaagt gaatcagtcg ccaggttgag cacatacgca cggtttttcg gcaggtgata
     2701 tgcgctgaac ccgcatgaat actgggtttc cacagggttg gagggggtgt attcgaaact
     2761 tgcaattctg ctttattgca acgcattgtt tttattggtt ttttgttttc agcaccccaa
     2821 gttatccaca ggctcgccgt taagttttta agatcttatt tttagatctt tttttttaaa
     2881 acctttttag gtcttgtaac accatgattt taaagatgtt ctggcaagat aagtggagct
     2941 tttgggggtg aaaggtggag cttttggggg tgaaaggtgg agcttttggg ggtgaaaggt
     3001 ggagcttttg ggggtgtaat ccacagaaaa agggggttgc aaaaaaaaaa cttccaccca
     3061 tatgataagt ggcgtacagt aaaaaaacgc caccaatagc aacgagcaag cgaaatgtca
     3121 gatctgatag cttacaaatc aaacgccctt atcgaggcaa gctacaagct cactttgcag
     3181 gaacagcgct tcctgctggt ctgtatcagc cgcctaaaat ccggagaaga ttccccttcg
     3241 ccggatgaac aaaaaaccat gaccatcacg gctgcagagt ttcatgatgc ctttcctgac
     3301 atgggacggc agcacgctga agctaggctc aaggaagcga tagatcgcct ctgggacagg
     3361 tcagtaatca tcaagaacga ggaaaaacga gaagagttcc gctgggtgca gtaccgggcg
     3421 cagtatttca aaggtgaggc gaaagtagat atcaccttct ccgatgccat catgccgtat
     3481 ctgacacagc tcaaggggca gtttacgcgg gtagtcgtga agaacgtctc cagcctttcc
     3541 agcacctaca gcatccgcat ttacgagctg ctccagcagt tccgcagcac cggtgacaga
     3601 acgatagcta tcgatgattt ccgaaccatg cttgccgttg aagataaata tcaacaattc
     3661 aaagacttga ataagatgat aatcaagcca gccatcgccg aactgaacga aaaaagcgat
     3721 ctggttgtaa ctgttgagac gatcaaaaag gggcgcacgg ttgtagccct gcattttcgc
     3781 ttcaaggaag acaaacagat caagatgacg atctaaaatc gattttaagg cacctaaaac
     3841 gctccctgct gcgttttttt tgtgttagta gtgcgaaggt actattgaag tgaaaaattg
     3901 cgtcaaaagc gctctaatgc agcgaaaaaa gaacccccaa tttttggggg cggaaaaaca
     3961 aaactatgct tgcattatgt gtgtgtgctt cttgcattca tccctgtcga tgaacatcga
     4021 agaacataac acgatgttaa acaaaacaaa atattgttca cat
//
