LOCUS       CP134927                5631 bp    DNA     circular BCT 27-SEP-2023
DEFINITION  Escherichia coli strain 284 plasmid pMB6980_4, complete sequence.
ACCESSION   CP134927
VERSION     CP134927.1
DBLINK      BioProject: PRJNA924946
            BioSample: SAMN32977818
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  AUTHORS   Shropshire,W.C., Strope,B., Selvaraj Anand,S., Bremer,J.,
            McDaneld,P., Bhatti,M., Flores,A.R., Kalia,A. and Shelburne,S.A.
  TITLE     Temporal Dynamics of Genetically Heterogeneous Extended-Spectrum
            Cephalosporin Resistant Escherichia coli Bloodstream Infections
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5631)
  AUTHORS   Shropshire,W.C., Strope,B., Selvaraj Anand,S., Bremer,J.,
            McDaneld,P., Bhatti,M., Flores,A.R., Kalia,A. and Shelburne,S.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-JUN-2023) Infectious Diseases and Infection Control,
            University of Texas MD Anderson Cancer Center, South Campus Research
            Building 4, Houston, TEXAS 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.9.2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 67x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/21/2023 12:12:26
            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)                     :: 4,805
            CDSs (total)                      :: 4,684
            Genes (coding)                    :: 4,453
            CDSs (with protein)               :: 4,453
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 231
            CDSs (without protein)            :: 231
            Pseudo Genes (ambiguous residues) :: 0 of 231
            Pseudo Genes (frameshifted)       :: 68 of 231
            Pseudo Genes (incomplete)         :: 168 of 231
            Pseudo Genes (internal stop)      :: 35 of 231
            Pseudo Genes (multiple problems)  :: 40 of 231
            Pseudo Genes (short protein)      :: 4 of 231
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="284"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB6980_4"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-11-04"
                     /collected_by="MDACC"
                     /note="genotype: ST10"
     gene            complement(56..922)
                     /locus_tag="RNP63_23895"
     CDS             complement(56..922)
                     /locus_tag="RNP63_23895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0005215 - transporter activity [Evidence IEA];
                     GO_process: GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WNL98309.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(924..1976)
                     /locus_tag="RNP63_23900"
     CDS             complement(924..1976)
                     /locus_tag="RNP63_23900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WNL98310.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(2457..2690)
                     /locus_tag="RNP63_23905"
     CDS             complement(2457..2690)
                     /locus_tag="RNP63_23905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WNL98311.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2697..3227)
                     /locus_tag="RNP63_23910"
     CDS             complement(2697..3227)
                     /locus_tag="RNP63_23910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WNL98312.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(3265..3963)
                     /locus_tag="RNP63_23915"
                     /pseudo=""
     CDS             complement(3265..3963)
                     /locus_tag="RNP63_23915"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3905..4228)
                     /locus_tag="RNP63_23920"
     CDS             complement(3905..4228)
                     /locus_tag="RNP63_23920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WNL98313.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4293..4484
                     /locus_tag="RNP63_23925"
     CDS             4293..4484
                     /locus_tag="RNP63_23925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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="WNL98308.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4579..4660)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(5117..5304)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(2354..3915)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.232"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tacgtgcatt tggcacggta tcgatggagg ccggggggca atcctgaaca gaatgttact
       61 cctctgagta ttttctgtta agaaaatata cacttagcac agttacaata aatcctaccc
      121 cctgtaagaa tgtgaattgt tcatccaaaa acaaccatga caaaaataat gcaactagcg
      181 gaataaagta caacattatc cctgccaaat gaactgggag ccaacgcaag gagttcaagt
      241 aaaaacaaaa agctaaaaaa tattgtaata ttccagatga aaaaacaata atcacggatt
      301 ccaacggaag ataaattgat gatttagata taaaaataaa gagcgatgac agtataaggg
      361 agaatgtcaa ctgtccgctc aataatgtga taggctcaaa cgatttaata aggcgagacg
      421 atataacaac ataaaatgct gccgataaca caccggcaac aacaagacaa tatccaacaa
      481 tattattcga tccattactg atgtctggca aggctaccaa aatactgcca acaattgcac
      541 ctataaggaa caatataaaa tattgcgggg aattaatttt aactgagcaa ataagaacag
      601 acaacaccaa tataaacact gattcaagtg aaaaaataat tgatgcgctt cctgctgaaa
      661 taaaataaag tccgtagagt gtaaaagtat acgctaagaa tggttcaaaa acgcctgtcg
      721 cataagcaag tatcgctttt gagtttaatg ggagtttttt tctttttata aaaagaacta
      781 tccaagatag tattactgca ctacaaatct gccagaaaaa cacccctccg gcatctagtt
      841 cttcaactcc ttttttgctc attacgatag ctgcccccca tgagaacgct gctaaaaaag
      901 caaaaagcat tcctttaatc atattaatca tcctctttct cataaagggg tttgttttca
      961 aatttccttg gttgaaagga gttaaaaaac atagatgcat catctacagg aataccaata
     1021 aactctccat aataaggatc atctatagga aactcttcta atgaaacata aaacaataca
     1081 ttccagttga agatcattgg atcactattt tctatttcat ggagcaatct ttcatcctta
     1141 gttaattctc ctggaattaa tacatcagta tgataaaaac cgctgtaata agaactatta
     1201 ccggtgtgca ctgggcatcc aaaacgatcc aaattagatt ctgaatgcca tgttgtagaa
     1261 atcccttccg gatgtgaata cccaccctta ccaacagact gaatagtcat gttacgaata
     1321 tccgctaacg cttgttcttg atctttatag aaaccttttt ctatcgccag cctcataaaa
     1381 tgccccgggg catttacaga aataagtatt ccccctggta ttcttctatc atgatttctt
     1441 gttctatgag cagaagagta aaaaacatta acaccagcct tatatatttt tagcccatct
     1501 ttatcctgaa atggtacgct ttcagtataa ataacatcct cttttattgg atagcactct
     1561 ggcatatgca gcgaacaaat atatttttgt atgtccacta actcttctga tggacgagca
     1621 aaggcaagtt gtggatgaat aaaataaatg agatgcgcac tgacctctcc tcttcttgcg
     1681 cgttctttaa aacgaactct ttcattacgc aaaaaatcaa acaaatgacc atcatcatta
     1741 tatagttggg ggctatttac aatagataaa tggaaatcaa gccctttaat tttcttgctt
     1801 gccaatttac caaatacaca gggctgattg cctgacaccc attttcttag taaatcttca
     1861 attttatctt tagaagtttc gttaaagata aatgaatgaa tattatcaat atcttttcca
     1921 aatgaaaaac tggatgataa ttgtggtagc ttatttatac gttgttgaag attcatgaaa
     1981 gctcccacaa gacacctcat atattttttt atatactgaa actacattat atttattacc
     2041 ggcgtaaaac gaaataattt attatcgtta ccgatatttt aaaaaaatca ttatttgcac
     2101 agtgttcgag ttgttagtat cactccttcc tgaaaatccg ctccatttac cataacgtcg
     2161 cattgtacgc accgccaaaa cgcgttcggt gcgatcacgg cagcagacag gtaaaaatgg
     2221 caacaaacca cccgaaaaac tgccgcgatc gcacctgata aattttaacc gcatgaatac
     2281 ctatgcaacc agatgctaca ggccacatta gcccgcctta atccactgaa cacgtcattt
     2341 ttcatggttt caccatccca gcgaagggcc atccagtgtc cgctcctgga tttccggctg
     2401 acgctcccgc tccagagata actcatgttc gcgttcctgc atcagccgtt catcccttat
     2461 ctcctgttct cgctgtataa ctggctcaag cgttctgtcc gctcgctcaa gtgctgcacc
     2521 tgctgactca actgcatgac tcgcccgttc agcatcgcgt tgtcccgttg cgtaagcgaa
     2581 aacattttct gcaattccac gaaggcgttc tcccattcgt tcagccgctg catatagtcc
     2641 tgttgcagtt gctctaatgc gttcagcaaa tgtctttcca gctccgtcat gctctgtcac
     2701 tcctgcacca gtctcactgc gttcagtttg ccgttgtcct tcgtccagtt cgtttcggct
     2761 ttcatcccct tcggcaacac cagaaaacgt ccgttgctgt cctcgtgata acgcacgccc
     2821 catgtcttcg cgttcagctt ctccagactc tctttctgct cgcggagaat attcatattc
     2881 gcgtttatct tcatgccctg gtaccacagc agactcccgg tcgtggcaaa catcagtact
     2941 gagacgataa tcagccacag ccagcgtttc acgctcattt tcagtacggt tttccagtgc
     3001 gcgtccatcg tatcgacggt cgttttctga tacctctcca gcagttcttt cagggctgtt
     3061 gtatggtcgt tgatagcgtt cctgattaaa gattcgtttg aggtcagttc cctgtttaca
     3121 gattcttcga gcttcctgaa ctcgtcgttc agcattttct ctgtagattc ggctctctct
     3181 ttcagctttt tctcgaactc cgcgcccgtc tgtaaaagat tgctcataaa acgctccttt
     3241 cagtctgata ttcctcccgc cgttcgggtc tgcaatgctg atactgcttc gcgtcaccct
     3301 gaccacttca agccctgcct ctgtgagcgc ctgaatcaca tcctgacggc cttttatctc
     3361 cccgacatga taaagagcgt ctatcccgcg tgtgacgctc tctgcaagcg cctgtttcgt
     3421 ttccggcagg ttatcagaga gagtcagtat ccggcggttc tccggggcgt tggggtcatg
     3481 cagaccgtaa tggtgattca ccagcgtctg ccaggcatca attctcggcc tgtctgcccg
     3541 gtcgtagtac ggctggaggc gttttccggt ctgtagctcc atgttcggaa tgacaaaatt
     3601 cagctcaagc cgtcccttgt cctggtgctc cacccacagg atgctgtact gatttttctc
     3661 gagaccgggc atcagtacac gctcaaagct cgccatcact ttttcacgcc ctccaggcgg
     3721 cagctccttc tccgcgaacg acagaacacc tgacgtgtat ttcttcgcaa atggcgtggc
     3781 atcgatgagt tcccggacct cttccggatt cccctgaagc accgttgccc cttcccggtt
     3841 acgctccctt cccagcaggt aatcaaccgg accactgcca ccaccttttc ccctggcatg
     3901 aaacttaact atcatcccgc gccccctgtt ccctgaccgc cagacgcagc cggcgcagct
     3961 catccccgat ggccatcagt gcggccacca cctgaacccg gtcaccggaa gaccactgcc
     4021 cgctgttcac cttcctcgct gtctggttaa ggttattccc gatggcggcc agctgacgca
     4081 gtaacggcgg tgccagtgtc ggcagcttcc cggaacgggc aaccggctca cccaggcaga
     4141 cccgccgcat ccataccgcc agttgtttac cctcacagcg ttccagtaac cgggcatgtt
     4201 catcatcagt aacccgtatc gtgagcatcc tctcgcgttt catcggtatc attaccccca
     4261 tgaacagaac ccccccttac acggaggcat cagtgaccaa acaggaaaaa accgccctta
     4321 acatggcccg cttcatcaga ggccagacat taacgctgct ggagaagctc aacgaactgg
     4381 acgcggatga acaggcagac atctgtgaat cgcttcacga ccacgccgat gagctttacc
     4441 gcagttgcct cgcacgcttc ggggatgacg gtgaaaaccg ctgacacatg cagctcccgg
     4501 agacggtcac agcttgtctg tgagcggatg ccgggagcag acaagcccgc cagggcgcgt
     4561 caggccgttg acctttgggg tgtcggggcg aagccctgac ccagtcacgt agcgatagcg
     4621 gagtgtatac tggcttaacc attcggcatc agtgcggatt gtatgaaaag tgcgccatgt
     4681 ccggtgtgaa atgccgcaca gatgcgtaag gagaaaatgc cagttcaggc gctcttccgc
     4741 ttcctcgctc actgactcgc tacgctcggt cgttcggctg cggcgagcgg actctccttt
     4801 ctcaaaaacg ctaaccctgt tatccacaga acccggggat aaaccaggaa agaacatgtg
     4861 cgcaaaaaac gaaaccccgg gaaaggccgc gccggaggcg ctttttccat aggctccgcc
     4921 cccctgacgg acttcacaaa acagacactt tttcggtgca tctgtgggag ccttgcggct
     4981 caaccatgaa atccgccagc ggtggcgaaa cccgacgtgg cttaaagatc atcaccgttt
     5041 ccggtgaatc gctccctcct gcgcccccac gttcccgcca tatcgattac cggatacctt
     5101 ttccgccttt ctcccttacg ggacacgtgg cgctttctca tagctcacgt cttctggtat
     5161 ctcggggcga cttaggcagt tcgctccggg ctgggctgta tgcaggaacc ccccgttcag
     5221 cccgactgct gcgccttctc cggtaactgt tctcttgggt ccaacccgga aaagacacca
     5281 caaagcgcca ctggcagcag ccattggtaa aagtcatgtg cgagatattt agagagtact
     5341 tgaagtggct gccggagtgc ggctacacta gaagaacaat tttggtgact cgtctcgcat
     5401 aagacagtta cctggttaag cagtctgcaa gctgacttaa ccttcgatca aaccgccctg
     5461 caaggcggtt ttttcgttta caggcagcag attacgcgca gaaaaaaagg atctcaagag
     5521 gatcctttga tctttttgtt acaaacgtct ctatttgact cccctgagag cgttttagcg
     5581 cgcctctgac ccccttggtt acattccgac accagaaacg ctcccgtttt t
//
