LOCUS       NZ_CP103649             4767 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 961 plasmid pMB5823_4, complete sequence.
ACCESSION   NZ_CP103649
VERSION     NZ_CP103649.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28173990
            Assembly: GCF_024918295.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4767)
  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 4767)
  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                   :: 61x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:24:23
            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)                     :: 5,145
            CDSs (total)                      :: 5,020
            Genes (coding)                    :: 4,743
            CDSs (with protein)               :: 4,743
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 277
            CDSs (without protein)            :: 277
            Pseudo Genes (ambiguous residues) :: 0 of 277
            Pseudo Genes (frameshifted)       :: 93 of 277
            Pseudo Genes (incomplete)         :: 197 of 277
            Pseudo Genes (internal stop)      :: 55 of 277
            Pseudo Genes (multiple problems)  :: 63 of 277
            Pseudo Genes (short protein)      :: 4 of 277
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103649.1.
            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..4767
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="961"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB5823_4"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-06-18"
                     /collected_by="MDACC"
                     /genotype="ST617"
     gene            1..192
                     /locus_tag="M5R18_RS25520"
                     /old_locus_tag="M5R18_25520"
     CDS             1..192
                     /locus_tag="M5R18_RS25520"
                     /old_locus_tag="M5R18_25520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            817..927
                     /locus_tag="M5R18_RS25525"
                     /old_locus_tag="M5R18_25525"
     CDS             817..927
                     /locus_tag="M5R18_RS25525"
                     /old_locus_tag="M5R18_25525"
                     /inference="COORDINATES: protein motif:HMM:NF033853.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="small membrane protein"
                     /protein_id="WP_259425790.1"
                     /translation="MDWISLAIAIALLVVAVYTGISYYKEKKTISRAFRR"
                     /name="small membrane protein"
     gene            complement(1137..1373)
                     /locus_tag="M5R18_RS25530"
                     /old_locus_tag="M5R18_25530"
     CDS             complement(1137..1373)
                     /locus_tag="M5R18_RS25530"
                     /old_locus_tag="M5R18_25530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016947370.1"
                     /translation="MKRLINLTPAEKRFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IESQRQAERQRSAREEERQQAEFTWSRPRAPRR"
                     /name="hypothetical protein"
     gene            2330..2443
                     /locus_tag="M5R18_RS25740"
     CDS             2330..2443
                     /locus_tag="M5R18_RS25740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071789001.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2928..3764)
                     /locus_tag="M5R18_RS25535"
                     /old_locus_tag="M5R18_25535"
     CDS             complement(2928..3764)
                     /locus_tag="M5R18_RS25535"
                     /old_locus_tag="M5R18_25535"
                     /inference="COORDINATES: protein motif:HMM:NF012307.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="reverse transcriptase domain-containing protein"
                     /protein_id="WP_087786174.1"
                     /translation="MSYLVKEVDSKDVFFFKKVLRKKNKSRVIYSVDDKSSSIYKDMEK
                     SISKRFICEISKKENFLIKKVPYAYYPGRSANQNAKAHQPFDFTLSMDIRDHFTSITPK
                     MVDWLLTPRELYLCFIDGSLPQGLSTSPVISNIAMMEVDRAILSELSNVVSNGSEPING
                     FVYRIKNFRYTRYSDDLVVSFNLHEPSMHLHRRIFLYIEALISKTIRQFGFEPNNNKVK
                     MQNEKSGFRVITGVSVSREIIKPTRKTKRKLRSAIHNANIDNAIGLYNWIKLVSRT"
                     /name="reverse transcriptase domain-containing protein"
     gene            complement(3761..4057)
                     /locus_tag="M5R18_RS25540"
                     /old_locus_tag="M5R18_25540"
     CDS             complement(3761..4057)
                     /locus_tag="M5R18_RS25540"
                     /old_locus_tag="M5R18_25540"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_071010377.1"
                     /translation="MDRSEFEKLISDLESKLKRAVLRVGLKKIEVQVFLLFPLGESQLG
                     TIHVEAYRRTDILNRKKPQPIYKIKSDCFKDIERGFLKWVIDYKSTIDKVAIK"
                     /name="hypothetical protein"
     Typing          complement(1798..1970)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.356"
                     /coverage="100.0"
                     /evalue="4.47e-49"
     Typing          1895..2439
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.364"
                     /coverage="90.0"
                     /evalue="0.0"
     Typing          complement(4427..4589)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.364"
                     /coverage="96.0"
                     /evalue="1.15e-69"
ORIGIN
        1 atgaacaaac aacaaaagac agccgttaac atggctaaat tcatccagga tcagtccctg
       61 cttcttctgg acaggcttaa tgagctggat ctggatcatg aggctgattt ctgcgagaaa
      121 ctccatgagg atgcggaacg cctttaccga agcctgtcag cgcgcctgaa tgagcagcag
      181 gacggtgcgt aatggctccg ttgtgggtat taccggagta ataccggcat cgccttaatt
      241 ttcattgtct tggcgcttaa tattattacc ccggtaatac ccagaatccc tttatttttt
      301 cttttttatt tatttttcat gaagttgcga tgaaaatcgc agctgcgtta ggtgtatgac
      361 catttaatga ttaaaaaatc atcatttttg gaagggcgct ctccgtaggt taagggttat
      421 ttggctaaaa agcgtcctgt tctttgatgg tcatgcaagc atgaccatct gggcaaccaa
      481 aaactacaga taaactacag ataaactaca aaaaacgttt tgcattagtg atggcagact
      541 acaaaaaaac tacaagaaaa ctacagataa actacaaagt aactgacctg ctccccgtga
      601 tttgttacat acccaccaca gggcattatt tttttttgat gatatgtaca aaatcagtga
      661 ttaggaataa tcttagccgc cttaacaaac acatacaaaa acagcggtta tgtttcatct
      721 caccacaata agtaacgaca gtatcatgct aaaaaaagat gatattatct ttatgaaatc
      781 ataacaggtt gtttttatta aattaatcag gcatttatgg actggatttc acttgctatc
      841 gccattgctc tacttgttgt agctgtctac acaggaatct catactacaa agaaaaaaaa
      901 acaatcagtc gtgcatttag gcgatagcgc cctatttacc ataatccctt cttacgcgca
      961 ccgcagaaac ggcctcaggg cgtttctgcg ccttcagcca caaaagagca cgtcttcccc
     1021 ccagaaaacc gcccggaatc gctctggtga gttttacggg ggtgaatgac tatgcaccgt
     1081 agtgaatacc acgctgtttc gccctgaact ccccacgaaa ccgacgaaag tggcaatcag
     1141 cgacgcggcg cccgcggacg cgaccaggta aattccgcct gctgccgctc ctcctcacgc
     1201 gcagatcgct gccgttctgc ctggcgctgc gattcgatct gtgcacgagc cctgttaagg
     1261 acaatgtgcc tgttgggctg attcagcttc ttgcctgacg ctctctcagc ggcggcaaca
     1321 gcatcgtcga gaaatctttt ctcggcgggc gtcaggttta tcagtcgttt catggcgatc
     1381 tccggtcaga ataactctgc acagtctgcc agacacggcg aacctcatga agaacctgca
     1441 gccgggaaca gccctgagat atcgttttgg tgccggcatc gtgatggcgg tactccaaaa
     1501 gggggcagtt tggatataga gaattattgt acggtaagcc tgttttttga acagacttac
     1561 ctatagcaat agggtgtact cccgcgctat acggcatttt cagaggtttg accttaatcg
     1621 gataacctaa atgcgatact gcaagagcga caacttaaaa gcgatagcca ctgacgcaat
     1681 atcaacccct tacgaaccaa gattggttaa ataatgcgct taacgtacaa aaatttccga
     1741 tctccaaact gacccccaaa aacacatctt gtcccgcttt cagtttctga atttgcgggt
     1801 tccgggcgca gcgccggacc agtcacgtag cgctagcgga gtgtatactg ccttagtatg
     1861 ttggcatgag tgcgataatc aggaaagcgc cttatgtggc aggagaaaaa tgctgcagca
     1921 gagcgtaagc agaatatgcg atacagaaga tattccgctt cctcgctcac tgactcgctt
     1981 cgctcggtcg ttcggctgcg gcgagcggta cagacttacg gaagggcgga gatttcctgg
     2041 aagatgccaa gaggatactt aacagggaag cgatagggcc gcggcgaagc cgtttttcca
     2101 taggctccgc ccccctgaca agcatcacaa aatctgacgc tcaaatcagt ggcggcgaaa
     2161 cccgacagga cttaaagata ccaggcgttt ccccctggtc gctccctcgt gcgctctcct
     2221 gttcctgcct ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt atctcattcc
     2281 acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc
     2341 ccccgttcag tccgactgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt
     2401 aagacatgca aaagcgccac tggcagcagc cactggtaac tgatttagag gagatagtct
     2461 tgaagtcatg cgccagttaa ggctaaacta aacgaacagt tttggtgact gcgctcctct
     2521 aactagccag ttacctcggt tcaaagagtt gctgctctga gaaccttcga gaaaaccgcc
     2581 ttgctgggcg gttttttcgt tttcagagca agagattacg acgagactga atgaatctca
     2641 agatttcatt tagcctgcca cccgatcatt caaagttttg gcgtagttct gacccgctcc
     2701 ccgtgatttt tacataccca ccacgggggc aataaggttt ctattgcgtt ttttcgataa
     2761 aacccgtagg ttttagaggt gattagctga gaggttccgc tccacaagag agatatagcg
     2821 agatgattcg tccgctgaat aatcctaaca tctagtaact tagcttacgc taaaccatgg
     2881 cccacagggc aatgtatgga ctagaacgta atcacacgtc gagaacatta tgttctcgac
     2941 actaatttga tccagttata cagcccgata gcattgtcta tgttggcgtt atgtattgct
     3001 gatctaagtt ttctttttgt tttccttgtt ggctttatga tttctcttga gacggataca
     3061 ccagtgataa ctctaaagcc agacttttca ttttgcattt taactttatt gttatttggt
     3121 tcaaaaccaa actgccttat ggttttactt attagggcct ctatatataa aaatatacgc
     3181 ctatgtaaat gcatagatgg ctcgtgcaaa ttaaagctta caactaaatc atcagaatac
     3241 cttgtgtatc ggaagttttt tattctgtat acaaaaccgt ttattggttc ggagccgtta
     3301 gatacaacat ttgataattc agataatatc gctctatcaa cctccatcat ggctatatta
     3361 gaaattactg ggctagtaga gagcccctga ggtaatgaac catctataaa acataggtat
     3421 aactcccttg gggtaagtaa ccaatctacc atcttaggcg ttatcgatgt gaagtgatct
     3481 cggatatcca tagataatgt aaaatcgaat ggctgatgag cttttgcgtt ttgattagcc
     3541 gaccttcccg gatagtaggc atatggtact ttttttatga ggaagttttc tttttttgat
     3601 atctcacaaa taaatctttt tgatattgat ttttccatat ctttataaat agaagaagac
     3661 ttgtcgtcaa ccgaatatat cactcttgat ttgtttttct tccttaaaac cttcttgaag
     3721 aaaaacacat ccttagagtc aacctccttt actaaataac tcatttaata gccaccttat
     3781 cgatagtcga tttataatca atgacccatt tcaaaaatcc cctttcgata tccttgaaac
     3841 aatcactttt tattttatat attggctgtg gttttttacg attcagtata tctgtacgtc
     3901 tatatgcttc gacatgaata gtacctagtt gcgattcacc gagtgggaat agtaggaata
     3961 cttgaacttc tatttttttc aggccaaccc tcaggactgc ccgtttcagt tttgactcca
     4021 gatctgatat tagtttttca aattcagatc tatccatacg ccctccctaa cttaaaatca
     4081 tattgggata atttaacata aggtcacatt gcccgcaccg cctcaggcgc cctcagagcg
     4141 tttctacgat ctcacctgca aaagaacaca ccctaccccc tgaaaaccgc ccaggatcgc
     4201 tcctgtaatt cacaggccat gaattgttat acccccaact gactgaccgg cagttccgcc
     4261 actggaaacc ggtgaaatcg ccaaaagtgg tggtgatcgg gtcacagaaa cggtgaacgg
     4321 gcgaataaat ttttttattc gtctgtgagg cgttcgcggg gtgtcggggg tcggccctga
     4381 cgggttttaa ctaaaaaatt ttgcggatca gaaaatattt taagggcgga atgacaccgg
     4441 taaaccgaaa ggcaggaaca ggagagcgca cgagggagcc atcaggggga aacgcctggt
     4501 atctttaagt cctgtcgggt ttcgccgcca ctgatttgag cgtcagattt cgtgatgctt
     4561 gtcagggggg cggagcctat ggaaaaacgc cccagcgggg cgtggccttt tcgcccttgt
     4621 ccttagcttt cgttatgctt accgttacgt tatctgctta gcctccctcc gctcgccgca
     4681 gactcatgac cgaacggagt gagcgaatga gcgaggaagc ggaaaacaat cagaacgtac
     4741 agtaagcact ttcgcgccgg ggccttc
//
