LOCUS       NZ_CP103630             4072 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 4012 plasmid pMB6206_4, complete sequence.
ACCESSION   NZ_CP103630
VERSION     NZ_CP103630.1
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 4072)
  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 4072)
  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
            CP103630.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4012"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB6206_4"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-08-21"
                     /collected_by="MDACC"
                     /genotype="ST90"
     gene            complement(join(3417..4072,1..46))
                     /locus_tag="M5S78_RS24880"
                     /old_locus_tag="M5S78_24880"
     CDS             complement(join(3417..4072,1..46))
                     /locus_tag="M5S78_RS24880"
                     /old_locus_tag="M5S78_24880"
                     /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(579..833)
                     /gene="mobC"
                     /locus_tag="M5S78_RS24885"
                     /old_locus_tag="M5S78_24885"
     CDS             complement(579..833)
                     /gene="mobC"
                     /locus_tag="M5S78_RS24885"
                     /old_locus_tag="M5S78_24885"
                     /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            1012..3159
                     /gene="mobQ"
                     /locus_tag="M5S78_RS24890"
                     /old_locus_tag="M5S78_24890"
     CDS             1012..3159
                     /gene="mobQ"
                     /locus_tag="M5S78_RS24890"
                     /old_locus_tag="M5S78_24890"
                     /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(835..1011)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1012..1370
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.722"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3418..4072)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.848"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          926..3156
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgcctcgat aagggcgttt gatttgtaag ctatcagatc tgacatttcg cttgctcgtt
       61 gctattggtg gcgttttttt actgtacgcc acttatcata tgggtggaag tttttttttt
      121 gcaaccccct ttttctgtgg attacacccc caaaagctcc acctttcacc cccaaaagct
      181 ccacctttca cccccaaaag ctccaccttt cacccccaaa agctccactt atcttgccag
      241 aacatcttta aaatcatggt gttacaagac ctaaaaaggt tttaaaaaaa agatctaaaa
      301 ataagatctt aaaaacttaa cggcgagcct gtggataact tggggtgctg aaaacaaaaa
      361 accaataaaa acaatgcgtt gaaataaagc agaattgcaa gtttcgaata caccccctcc
      421 aaccctgtgg aaacccagta ttcatgcggg ttcagcgcat atcacctgcc gaaaaaccgt
      481 gcgtatgtgc tcaacctggc gactgattca cttccgcttc ctcgcccact cgctcgctaa
      541 cgctcggtcg ctggggctgc ggcgagcgga cgatacaatc actgttctgg cagcgcctcc
      601 agctcgttaa tcagcggcag tatgcgcgtc acatcagcct gtcgtgtcac ctctgccttc
      661 aggaactgga gtaaccaggc acgcaactgc acctcctccg gctttctgac ctttgccagc
      721 aatgcagcac ccacaacaac cttctgcgct gtgtccaggc tccggctctt cgccttcagg
      781 cgctgtaatc tcgcctcagc atcagcaatc ttctgttcga gcgttctgct catgatgtaa
      841 ctccgtgcgc gatgaaaaat cgcattttag cgcgtcactg gtagtttaaa aactgagctg
      901 gcataatgca cggcaaatca cgaagtgcgc acttatacaa tctccactcc gtttcgattg
      961 tgtgcgccct gcggggctga aagaaaacta caaaaaggca ttacggcaga aatggcgatt
     1021 tatcatctca gcatgaaaat catctccaga agcagcggct acagcgccgt agcttccgct
     1081 gcctatcgtt ccggttcact gatgcttgat gagcgtaccg gactgactca cgactacacc
     1141 cgcaaaagcg gtgtggctga ggctgtgatt ctgacccccg ccaccgcccc tgcctggtgt
     1201 acgaaccgtg ccgaactctg gaatgccgtt gagaaggccg aacgccggaa gaactcacaa
     1261 cttgcgcggg aaattgaact cgccatcccc cacgaactgc cgcaggatgc cgcacgggaa
     1321 accgttctcg cctttgtcag agaaaacttt gtcagtcagg gcatgattgc tgatgtggcg
     1381 ttccatcaca tggataaaac aaatccccat gcgcacatca tgctgaccac gagggctatc
     1441 ggacctgctg ggttcagcgg aaaggtcagg gactggaacg accggacaca tgccgagacg
     1501 tggcgggcat catgggctga ccatgcaaac agggcactgg cgaacgccgg ttatcaggaa
     1561 gagatagacc atcgttcata cgagcgacag gggcttgaga aaacgcctgg tattcacctc
     1621 ggaaagtctg cctgtgcgat ggaaacacgc ggtatcgaaa cagaacgcgg cgaacagaat
     1681 cgtctgatta acaggcttaa cctggaaata cagatttccc gcaccgaact caggaacgga
     1741 gggctgacag agcctgcccg ccgtgtggct gaccttctga atatcgggct tcctgacaac
     1801 gcaacttcgt acacactacg tgacattatc gaagcgttgc cgaaggacag taactcggca
     1861 tggaaactca ccagtaatgc catgtcgatg atggcagata tgcaggcgac gcgcagacgc
     1921 tgggaagagc tgaacaccga acgaaaggaa gcgatgagcc atgctgccag cctgaaaaaa
     1981 tcatcgccgt tttcgtccgg tttttcccgt attcccctga tgcaatgggc ggcaccggaa
     2041 taccgtagtg agcagggaaa aatccagtct ctgagccagc aaatggaaaa attacgacag
     2101 cattaccgga aggtggagaa acaggacatt cccgcgagtc agatggcatt tgaaaaacag
     2161 tggcagcagt ggggggaatc cggccttgca gctctcagag cccagttgct taaacgtgaa
     2221 gaggaattgc gccggaagga acaggaagat actgaacgta gtcgcgcgga gcagctcagg
     2281 aaaaatgaca atgccgttat ggattcaggg gtgctgagag cagtcgttac ggggtatggc
     2341 gaggctccca tgcctggtaa cggggaaatg acctgttacc ttctgcttca caaccggaac
     2401 ggagaatata cgctctgggg gaacgagctg gagaaatacc gcaccagaat ctttgagagt
     2461 gttgatttaa tgcgtgacag gagtggttat atctgtgacc gaagcgaaat cggccaacgt
     2521 ccgccactgc aacgtgttta ttcctctgca acctttgagc aactgctgac gcaggtttgc
     2581 cagacatggc cgcaacatac ccgcaatctc cgccagccga agacatggcc ggagtctttc
     2641 tgtcttggag aagaccgcca gccagccatg ccatcaccag cggcaaggaa ggtggatttt
     2701 atgcagggac gtctgccacc gacgctgatg ccggtcatga gttctgtcga ccgggaaacc
     2761 cgccagcttc agcttttgct ggtcatgggc gtggatgact ctctgggcgg tgttatccgg
     2821 cttaatggta cgctgtatcc cgcgtttgcc gttccctcag ccgataacag gcatctggtc
     2881 atcagtgcgc tgaccgataa ggggttacgg tatgcagggt atggtgttgc cgtaaatcac
     2941 gatgcagaca gccacatatc acctgcacca gaactgatgc agtttcatct gaaaacccgt
     3001 gaggcaccgc tttttgctgc cgtcaacaca ccagaaaaac agccggatca tctgttccgc
     3061 tcgctgggtt ttaatcgtac ctgggaggaa tggcagcgcg aggaagatgc acgaacacac
     3121 accaccgaga ggagacatga tcgcggttgg tcacagtgaa tgtgaacaat attttgtttt
     3181 gtttaacatc gtgttatgtt cgtcgatgtt cttcgatgtt catcgacagg gatgaatgca
     3241 agaagcacac tcacataacg caagcatagt tttgtttttc cgcccccaaa aattgggggg
     3301 tcttttttcg ctgcatcaga gcgtttttga cgcaattttt cacttcaata gtaccttcgc
     3361 actactaaca caaaaaaaac gcagcaggga gcgttttagg tgccttaaaa tcgattttag
     3421 atcgtcatct tgatctgttt gtcttccttg aagcgaaaat gcagggctac aaccgtgcgc
     3481 ccctttttga tcgtctcaac agttacaacc agatcgcttt tttcgttcag ttcggcgatg
     3541 gctggcttga ttatcatctt attcaagtct ttgaattgtt gatatttatc ttcaacggca
     3601 agcatggttc ggaaatcatc gatagctatc gttctgtcac cggtgctgcg gaactgctgg
     3661 agcagctcgt aaatgcggat gctgtaggtg ctggaaaggc tggagacgtt cttcacgact
     3721 acccgcgtaa actgcccctt gagctgtgtc agatacggca tgatggcatc ggagaaggtg
     3781 atatctactt tcgcctcacc tttgaaatac tgcgcccggt actgcaccca gcggaactct
     3841 tctcgttttt cctcgttctt gatgattact gacctgtccc agaggcgatc tatcgcttcc
     3901 ttgagcctag cttcagcgtg ctgccgtccc atgtcaggaa aggcatcatg aaactctgca
     3961 gccgtgatgg tcatggtttt ttgttcatcc ggcgaagggg aatcttctcc ggatttcagg
     4021 cggctgatac agaccagcag gaagcgctgt tcctgcaaag tgagcttgta gc
//
