LOCUS       NZ_CP103601             4786 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Escherichia coli strain 4848 plasmid pMB7536_5, complete sequence.
ACCESSION   NZ_CP103601
VERSION     NZ_CP103601.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174075
            Assembly: GCF_024917355.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4786)
  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 4786)
  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                   :: 58x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 05:49:14
            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)                     :: 4,926
            CDSs (total)                      :: 4,805
            Genes (coding)                    :: 4,551
            CDSs (with protein)               :: 4,551
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 254
            CDSs (without protein)            :: 254
            Pseudo Genes (ambiguous residues) :: 0 of 254
            Pseudo Genes (frameshifted)       :: 86 of 254
            Pseudo Genes (incomplete)         :: 167 of 254
            Pseudo Genes (internal stop)      :: 58 of 254
            Pseudo Genes (multiple problems)  :: 52 of 254
            Pseudo Genes (short protein)      :: 3 of 254
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103601.1.
            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..4786
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4848"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB7536_5"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-01-10"
                     /collected_by="MDACC"
                     /genotype="ST44"
     gene            join(4767..4786,1..259)
                     /locus_tag="M5T19_RS24445"
                     /old_locus_tag="M5T19_24445"
     CDS             join(4767..4786,1..259)
                     /locus_tag="M5T19_RS24445"
                     /old_locus_tag="M5T19_24445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013649743.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system YafQ family toxin"
                     /protein_id="WP_259384665.1"
                     /translation="MSIKREIEYSGQFQKDVKKAQKRHKDMSKLKTLMSLLINNNSPLP
                     QIYKDHPLQGNYKGYRDAHLEPDWILIYKITDDLLRFERTGTHSDLF"
                     /name="type II toxin-antitoxin system YafQ family toxin"
     gene            377..547
                     /locus_tag="M5T19_RS24450"
                     /old_locus_tag="M5T19_24450"
     CDS             377..547
                     /locus_tag="M5T19_RS24450"
                     /old_locus_tag="M5T19_24450"
                     /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_259384666.1"
                     /translation="MKEYKIEEHLKNEKEILMYLKEVLEDGDPTLIISALDDIKKRVMK
                     NNNQRLSNHRR"
                     /name="hypothetical protein"
     gene            complement(767..1822)
                     /locus_tag="M5T19_RS24455"
                     /old_locus_tag="M5T19_24455"
     CDS             complement(767..1822)
                     /locus_tag="M5T19_RS24455"
                     /old_locus_tag="M5T19_24455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000796671.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_259384667.1"
                     /translation="MSEHGDFFLYAKEKIITVLDNSLSGQMEGFSNTAYTFGRYGVTIY
                     ALWYAYTVLAGKQKSPVQDFIWNLTRLFVILMFVKNMDGWLNYALTGIDGLKETLSGNV
                     DVWTWLDQLWTKVQQVAAHLMAKDTSTYVKTDGAIGALFTYGGGVVALLAASIAFLMAE
                     ITLKMLAVTAPLFIFCLMFGFLRQMFNSWLQLIISSCLILLFGSLALRAGTSYLNVILS
                     LAVDTATQRNLIQVGATALVAGIFMAFVILQAKTYASQIASVGAEGAMQGAAAMGIATA
                     GFGAAKLGLGALKSGGRFGAGSFRGMRGKEGGFSESKGISGKTGNLVGQGAAAGYRKGK
                     EVTKWAKQRWG"
                     /name="type IV secretion system protein"
     gene            complement(1848..2105)
                     /locus_tag="M5T19_RS24460"
                     /old_locus_tag="M5T19_24460"
     CDS             complement(1848..2105)
                     /locus_tag="M5T19_RS24460"
                     /old_locus_tag="M5T19_24460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001228869.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_259384668.1"
                     /translation="MKKIIYLTGLCGVFLLSGCEETKSVEWWTEHHDEAVKKEAECKKS
                     GSDSQNCRNIKEANFRYQQLHAIEPSFRKYDKDLQKKSAK"
                     /name="EexN family lipoprotein"
     gene            complement(2123..2878)
                     /locus_tag="M5T19_RS24465"
                     /old_locus_tag="M5T19_24465"
     CDS             complement(2123..2878)
                     /locus_tag="M5T19_RS24465"
                     /old_locus_tag="M5T19_24465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000737859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_259384669.1"
                     /translation="MKKTLISTIIVGAGLLSSVSFTCTAAIPVTDAMSIAERAKQDMAT
                     AAQWVKEASQWTKELKAYQDELLSKTGIRDVQGLIQDAQSISNDLNTIYNEGESFYSDY
                     IENPQGVLSPKAQAILDKYQVGKTCINKGFSGDAIKGCEAKFLSDLATVEYGKKLETKL
                     KNDNSEMNSLINQVKNSKDPKQTADAANAVQLANLKFEKLKFQYEMYRDKQKDLAIYNK
                     ELNEANFRKQQLDAKEPSFKEADKKYNFD"
                     /name="type IV secretion system protein"
     gene            complement(3319..3807)
                     /locus_tag="M5T19_RS24470"
                     /old_locus_tag="M5T19_24470"
     CDS             complement(3319..3807)
                     /locus_tag="M5T19_RS24470"
                     /old_locus_tag="M5T19_24470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001565850.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_259384663.1"
                     /translation="MNTTESPMRKITKLHRQTYVDEAGLVKQDTTRETFSVPTEPPYIK
                     LYISDISAIHGLSKAQNDVLLQLAMLIGWDGIVSVSKSRFEKTIKPRIGIEYQSFKNIV
                     AKLVEKQLFFRSGRGELEANPFVFARGDWPSIYERRKRIELTITYDEKGRSVSSKVCD"
                     /name="hypothetical protein"
     gene            4500..4760
                     /locus_tag="M5T19_RS24475"
                     /old_locus_tag="M5T19_24475"
     CDS             4500..4760
                     /locus_tag="M5T19_RS24475"
                     /old_locus_tag="M5T19_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_414761.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
                     /protein_id="WP_259384664.1"
                     /translation="MAANAFVRARIDEALKNEAASVLAGMGLTVSDLVRITLTKVAREK
                     ALPFDMRIPNELTAKTITASEKGIDVHKAKDAGDIFNQLGI"
                     /name="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
ORIGIN
        1 cgaatactca ggccagtttc agaaggatgt gaagaaagct caaaagcggc ataaagatat
       61 gagcaaactt aaaactctta tgtcgctttt aattaacaat aattcaccac ttccacagat
      121 ttacaaagac catcctctgc aaggtaatta taaaggctac agggatgcac atctcgaacc
      181 tgactggata cttatctaca aaattacaga cgacttactg cgatttgagc gaacagggac
      241 gcattctgat ctgttttgat gtactaacaa acaataccga tgcaggatag gcaatgttgc
      301 caaaaaatgc tagcattctg ctatctattt ttggcaacat tgccgtgacc tacagtcggt
      361 tcttggaggg ggcaaattga aagaatataa aatagaagaa catttaaaaa atgaaaaaga
      421 aatactgatg tatcttaaag aagttttgga ggatggagat cctacattaa taatttccgc
      481 actggatgac ataaaaaaac gtgtaatgaa aaacaataat cagcgccttt caaatcatag
      541 acgctgatta tttaccttaa attactttta aggcattgcg ccccatttaa gcccccagaa
      601 aatcataagg aataaaactc cgtgtatgat taacttggtt tttttatcaa accttgataa
      661 aagtttcttt tctgtcttat caaacaatct aaaaagaagg tagcctaaat agcagataaa
      721 ggtaaataca aagatcaaca atatcgtagt tttgaacatg gaataatcac ccccatcttt
      781 gtttcgccca tttagtcact tccttccctt ttctgtatcc tgctgccgca ccctgaccga
      841 ctaaattccc cgtttttccg ctaatacctt tagactcaga aaacccacct tcttttccac
      901 gcattccacg aaaagagcca gcaccgaaac gcccaccgct ttttaatgcc ccaagaccga
      961 gtttagctgc accgaatccg gctgtagcta ttcccatcgc ggcggctccc tgcatggctc
     1021 cttctgcacc cacactggca atttgcgagg cgtaagtttt agcctgtaga ataacaaagg
     1081 ccataaatat tccagcaaca agtgcagttg cccccacctg tattagattt ctttgcgttg
     1141 ctgtatctac agccaaagat aaaataacat ttagataaga agtgccagcc cttaatgcca
     1201 gtgaaccaaa tagaaggatc aggcaggaac tgattatcag ttgtaaccag ctattgaaca
     1261 tctggcgcaa aaatccgaac atcaggcaga aaataaaaag cggggcagtg actgccagca
     1321 tttttaaagt gatttcagcc atcaggaaag caattgaagc agctaaaagc gctacaactc
     1381 caccgccata agtgaatagt gctcctattg ctccatcggt tttaacatag gttgatgtat
     1441 cttttgccat aaggtgtgca gcaacctgtt gcactttagt ccagagttga tccaaccatg
     1501 tccacacatc gacgttccct gacagggttt ctttcagacc atcaatccct gtcagggcgt
     1561 aattcagcca gccatccatg tttttaacaa acatcagaat gacgaacagg cgggtcaggt
     1621 tccagataaa gtcctgtaca ggggatttct gcttacctgc cagcactgta taggcatacc
     1681 acagtgcata gattgtcaca ccataacgcc caaaggtata agccgtattg ctaaatcctt
     1741 ccatctggcc tgaaagcgaa ttatcgagta cagttataat cttttcttta gcatataaga
     1801 aaaaatcacc atgctcagac atatatactc cttgttttca ttagttacta tttagctgac
     1861 tttttctgta gatctttgtc atatttccga aagctaggct ctatagcatg tagttgctga
     1921 taacggaaat tggcctcttt tatatttctg caattttgac tgtcactgcc tgacttttta
     1981 cattcagctt cttttttaac ggcttcgtcg tggtgttcag tccaccattc aacggatttt
     2041 gtttcctcac acccagaaag aagaaatacg ccacacagtc ccgttaaata aattatcttt
     2101 ttcatgaaaa tacctcactg tattaatcga aattatattt tttatcagct tctttaaatg
     2161 aaggttcttt tgcatccagt tgctgttttc tgaaattagc ctcatttaat tccttattgt
     2221 atatagccaa atccttttgc ttatcccgat acatttcata ctgaaatttt agcttttcaa
     2281 atttcaggtt ggctaattgt acggcgtttg ctgcatcagc cgtttgtttc gggtcttttg
     2341 aatttttgac ctgattaatc agagaattca tttcgctgtt atcatttttc agctttgttt
     2401 ccagcttttt accgtattca accgttgcca gatcggacag gaatttagcc tcgcaacctt
     2461 tgatagcatc gccgctgaat cctttgttaa tgcatgtttt accgacctga tacttatcca
     2521 gaatagcctg agcctttgga gataaaaccc cctgtgggtt ttcaatataa tctgaataga
     2581 aggactcccc ttcgttatag atggtgttca gatcattact gatagactgc gcgtcctgaa
     2641 tcagcccctg aacgtcacga atccctgttt ttgataacag ttcatcctga taggctttaa
     2701 gctcttttgt ccactgtgac gcctctttta cccactgcgc ggcagtagcc atatcttgtt
     2761 tagctcgttc agctatagac atagcatcag taacaggtat tgcagcagta caggtaaaac
     2821 tgactgaact taacaatcca gcccctacga tgatcgtact tattaacgtt tttttcattt
     2881 tcatcctctc ttaaaccttg ttagccagtt taaggtagct aaacagcaca atttttttaa
     2941 aaaaaacacc ctaaaatagg gtgtgcgctt tattcaaagt gtggtaaccg accatagaga
     3001 aaaccctgat cagggtgatg gtgcgcaggg aatggatgtt ggaacagtcc aggaactttt
     3061 ctgaggctga gtacagcgtt tttcttacgg tatcagggtg aagtcggcac aaggtggcta
     3121 tgtcactgaa tcccagccct atggcataca ggaacacaaa ccgcctttcg ttaccggata
     3181 acgacggttc agggaagatt tgctccagat acacatcact aatatcattg accacagtca
     3241 taataacctc tcttctaggt tgttgtgatt agcggtctgt aggaggtgcg aactcctaca
     3301 gaccgcgtta gaactttctt aatcgcaaac tttagatgat actgaacgac ctttctcatc
     3361 atatgtgatt gttaattcaa ttcttttcct tctctcatat attgaaggcc agtctcctct
     3421 agcaaaaaca aaaggatttg cttcaagctc tccccttcct gatctaaaga aaagttgttt
     3481 ctctaccagt ttggcaacaa tgtttttaaa tgattgatat tcaataccaa ttcttggttt
     3541 tatggttttc tcaaatctgc ttttagaaac agaaacgata ccatcccatc caattagcat
     3601 tgctaactgc aataatacgt cattttgagc cttagaaagg ccatgaattg ccgatatatc
     3661 agatatatac agctttatat aaggaggttc ggtagggaca gagaaggtct ctctcgtagt
     3721 gtcttgttta acaagaccag cttcatcaac gtaagtctgc cgatggagtt tagttatctt
     3781 tctcataggg ctttcagtgg tattcactat atctccaagg catccgataa atcatgtagt
     3841 actcgtattt aagtactaaa aagaacaaac ttcaagtact ttattcaaag tacgattagt
     3901 acttgaggtg agtacgatta gtacttgagg tgagtacgat tagtacttga ggtgagtacg
     3961 attagtactt gaggtgagta cgatattcgc ttctacacct tgctacgcct gattccttat
     4021 atctatatct atattttaag cagtactcat gagcggattt caggcaccaa aaattacttt
     4081 ttttatttca atgtgaacgt gcttttctgt cagatctgta gatattccgc ttcctcgctt
     4141 tggctgttcg ttcctcgtcg ctttgctcct gcggtacgcc tcagccaaag actgcggcga
     4201 gcggatagat ctctttcact ggtgcttttt cttgctctag ggattcacag gaggctctct
     4261 acgctgtttt aagggtacaa gatgcccgtc agggcatggg aggcgcgaaa aatgcttaca
     4321 gaggctctca ggcgttaaat cgcgccgatg ctgctaacta agatcggaca tattctgcgg
     4381 aacagcgcaa cgcgccccct gcaaagctgc tttttgctga ccgtacagcg atagtaattt
     4441 tgaagatgta gctcaattga gctacaatac cgatatgttt aatagctgag gatttgatca
     4501 tggcggcaaa cgcatttgtt cgtgcccgta tcgacgaggc actgaaaaac gaggcagctt
     4561 ctgttctagc tggaatgggt ttaactgtct ctgatttagt tcgtatcacc ctgaccaaag
     4621 ttgccagaga aaaagcgctg ccttttgata tgcgcattcc taatgaactg acagcgaaaa
     4681 cgataactgc cagtgaaaaa ggtattgatg ttcataaggc aaaagacgca ggcgatattt
     4741 ttaatcaact tggtatctga ttatttatga gcataaaaag ggaaat
//
