LOCUS       NZ_CP103527             4074 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 2779 - blood draw same patient as MB9267
            plasmid pMB9272_6, complete sequence.
ACCESSION   NZ_CP103527
VERSION     NZ_CP103527.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174006
            Assembly: GCF_024918015.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4074)
  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 4074)
  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                   :: 91x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:46:45
            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)                     :: 5,256
            CDSs (total)                      :: 5,133
            Genes (coding)                    :: 4,930
            CDSs (with protein)               :: 4,930
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 65 of 203
            Pseudo Genes (incomplete)         :: 146 of 203
            Pseudo Genes (internal stop)      :: 38 of 203
            Pseudo Genes (multiple problems)  :: 43 of 203
            Pseudo Genes (short protein)      :: 4 of 203
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103527.1.
            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..4074
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2779 - blood draw same patient as MB9267"
                     /isolation_source="blood draw same patient as MB9267"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9272_6"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.706800 N 95.397100 W"
                     /collection_date="2019-10-28"
                     /collected_by="MDACC"
                     /genotype="ST405"
     gene            7..699
                     /locus_tag="M5S63_RS26150"
                     /old_locus_tag="M5S63_26150"
     CDS             7..699
                     /locus_tag="M5S63_RS26150"
                     /old_locus_tag="M5S63_26150"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(957..3116)
                     /gene="mobQ"
                     /locus_tag="M5S63_RS26155"
                     /old_locus_tag="M5S63_26155"
     CDS             complement(957..3116)
                     /gene="mobQ"
                     /locus_tag="M5S63_RS26155"
                     /old_locus_tag="M5S63_26155"
                     /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_016245161.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3295..3549
                     /gene="mobC"
                     /locus_tag="M5S63_RS26160"
                     /old_locus_tag="M5S63_26160"
     CDS             3295..3549
                     /gene="mobC"
                     /locus_tag="M5S63_RS26160"
                     /old_locus_tag="M5S63_26160"
                     /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_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(2759..3117)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          3118..3294
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          8..699
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(961..3203)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.332"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctttgtatgt cggacttgat tgcctacaag tcgaatgctt tggttgaggc cagctacaag
       61 ttgaccctac aggaacaacg ttttctgttg ctgtgtatca gtcgattgaa atctggtgct
      121 gatgctgaat tgcaaaagac aatgaccatt accgctgcgg aatattttga ttcattccct
      181 gacatggggc ggaaaaatgc cgaggttcag ttacaggaag cgatcgatcg tttatgggac
      241 aggtcgatca ttctcaagaa tgacgagaag cgtgaggagt tccgctggat ccagtatcgg
      301 gcacagtacg ctaaaggtga ggccaaggct cgaataacct tttctgacgc ggtaatgcct
      361 tatctgacgc aactgaaggg gcaattcacg cgcgttgtta taaaaaacat atcaggttta
      421 tcaagtagtt acagtataag aatatacgag ttcctccagc aattccgcag tacgggagag
      481 agaattattg ctcttaatga ctttcgttca atgttaggga ttgaaaataa atacaaacaa
      541 ttcagagact taaataaaat actaataaaa ccctgtgttg acgaactgaa caaaaaaagc
      601 gacctggctg taacggttga gacgatcaaa aaggggcgca cggttgtagc cctgcatttt
      661 cgcttcaagg aagacaaaca gatcaagatg acgatctaaa atcgatttta aggcacctaa
      721 aacgctccct gctgcgtttt ttttgtgtta gtagtgcgaa ggtactattg aagtgaaaaa
      781 ttgcgtcaaa aacgctctga tgcagcgaaa aaagaacccc caatttttgg gggcggaaaa
      841 acaaaactat gcttgcatta tgtgagtgtg cttcttgcat tcatccctgt cgatgaacat
      901 cgaagaacat cgacgaacat aacacgatgt taaacaaaac aaaatattgt tcacattcac
      961 tgtgaccaac cgcgatcatg tctcctctcg gtggtgtgtg ttcttgcatc ttcctcgcgc
     1021 cgccattcgt cccaggtacg attgaaaccc agcgagcgga acagatgatc cggctgtttt
     1081 tctggtgtgt tgacggcagc aaaaagcggt gcctcacggg ttttcagatg aaactccata
     1141 agttccggcg caggtgatat gtggctgtct gcatcgtgat ttacggcaac accataccct
     1201 gcataccgta accccttatc ggtcagtgca ctgatgacca gctggctgtt atcggctgag
     1261 ggaacggcaa acgcgggata cagcgtacca ttaagccgga caacaccgcc cagagagtca
     1321 tccacgccca tgaccagcaa aagctgaagc tggcgggttt cccggtcgac agaactcatt
     1381 accggcatca gcgtcggtgg cagacgtccc tgcgtaaaat ccaccttcct tgctgccagt
     1441 gatggcatgg ctggctggcg gtcttctcca agacagaaag actccggcca tgtcttcggc
     1501 tggcggagat tgcgggtata ttgcggccat gtctggcaaa cctgcgtcag aagttgctca
     1561 aaggtcgcag aggaataaac acgttgcagt ggtggatgtt gaccgatttc gcttcggtca
     1621 cagatataac cactcctgtc acgcattaaa tcaacacgct caaagattct ggtgcggtat
     1681 ttctccagct cgttccccca gagcgtgtat tctccgttcc ggttgtgaag cagaaggtaa
     1741 caggtcattt ccccgttacc aggcatgggg gcctcgccat accccgtaac gactgcgctc
     1801 agtacccctg aatccataac ggcattgtca tttttcctga gctgttccgc tcgtcgctcc
     1861 gcgcgactac gttctgtatc ctcctgctcc ttccggcgca attcctcttc acgtttaagc
     1921 aactggactc tgagagctgc aaggccggat gccccccact gctgccactg tttttcaaat
     1981 gccgtctgac tcgcgggaat gtcctgtttc tccaccttcc ggtaatgctg tcgcaatttt
     2041 tccatttgct ggctcagcga ctggattttt ccctgttcgc tacggtattc cggtgctgcc
     2101 cattgcatca ggggaatacg ggaaaaaccg gacgaaaacg gcgatgattt tttcaggctg
     2161 gcagcatggc tcatcgcttc ctttcgttcg gtgttcagct cttcccagcg tctgcgcgtc
     2221 gcctgcatat ctgccatcat cgacatggca ttactggtga gtttccatgc cgcattactg
     2281 tccttcggca acgcttcgat gatgtcacgt agtgtgtacg aagttgcgtt gtcaggaagc
     2341 acgatattca gaaggtcagc cacacggcgg gcaggctctg tcagcccgct gttcctgagt
     2401 tcagtgcggg aaatctgtat ttccaggtta agcctgttaa tcagacgatt ctgttcgccg
     2461 cgttctgttt cgataccgcg tgtttccatc gcacaggcag actttccgag gtgaatacca
     2521 ggcgttttct caagcccctg tcgctcgtat gaacgatggt ctatctcttc ctgataaccg
     2581 gcgttcgcca gtgctctgtt tgcatggtca gcccatgatg cacgccacgt ctcggcatgt
     2641 gtccggtcgt tccagtccct gacctttccg ccgaacccag caggtccgac agccctcgtg
     2701 gtcagcatga tgtgcgcatg gggatttgtt ttatccatgt gatggaacgc cacatcagca
     2761 atcatgccct gactgacaaa gttttctctg acaaaggcga gaacggtttc ccgtgcggca
     2821 tcctgcggca gttcacgggg gatagcgagt tcaatttccc gcgcaagttg tgagttcttc
     2881 cggcgttcgg ccttctcaac ggcattccag agttcggcac ggttcgtaca ccaggcaggg
     2941 gctgtcgcgg gggtcagaat cacagcttca gccacaccgc ttttgcgggt gtagtcgtga
     3001 gtcagtccgg tacgctcatc aagcattagt gaaccggaac gataggcagc ggaagctacg
     3061 gcgctgtagc cgctgcttct ggagataatt ttcatgctga gatgataaat cgccatttct
     3121 gccgtaatgc ctttttgtag ttttctttca gccccgcagg gcgcacacaa tcgaaacgga
     3181 gtggagattg tataagtgcg cacttcgtga tttgccgtgc attatgccag ctcagttttt
     3241 aaactaccag tgacgcgcta aaatgcgatt tttcatcgcg cacggagtta catcatgagc
     3301 agaacgctcg aacagaagat tgctgatgct gaggcgagat tacagcgcct gaaggcgaag
     3361 agccggagcc tggacacagc gcagaaggtt gttgtgggtg cagcattgct ggcaaaggtc
     3421 agaaagccgg aggaggtgca gttgcgtgcc tggttactcc agttcctgaa ggcagaggtg
     3481 acacgacagg ctgatgtgac gcgcatactg ccgctgatta acgagctgga ggcgctgcca
     3541 ggacagtgat tgtatcgtcc gctcgccgca gccccagcga ccgagcgtta gcgagcgagt
     3601 gggcgaggaa gcggaagtga atccgtcgcc aggttgagca catacgcacg gtttttcggc
     3661 aggtgatatg cgctgaaccc gcatgaatac tggatttcca cagggttgga aggggagtat
     3721 tcggaacttg caattctgct ttcttgcaac acattgtttt tattggtttt ttgttttcat
     3781 caccccaagt tatccacagg ctcgccgtta agtttttaga tcttgttttt aagatcttgt
     3841 ttttaatact tgttttaggg gtgaaattca ttaataaaat caatatgtta tagtggtatg
     3901 tgtggaggaa tttaaggtaa aggtggagga atttaaggtg tttaggtgga ggaatttaag
     3961 gtaaaggtgg aggaatttaa ggtgttattc acagaaatgt gaggatataa aaaaaaacat
     4021 tccacatttc ttatttgtgg ggcacattaa agcatcacca catttgaacg ggat
//
