LOCUS       CP134908                3596 bp    DNA     circular BCT 27-SEP-2023
DEFINITION  Escherichia coli strain 3320 plasmid pMB3134_3, complete sequence.
ACCESSION   CP134908
VERSION     CP134908.1
DBLINK      BioProject: PRJNA924946
            BioSample: SAMN32977729
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3596)
  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  JOURNAL   Unpublished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 3596)
  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                   :: 407x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/21/2023 12:37:51
            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)                     :: 4,879
            CDSs (total)                      :: 4,767
            Genes (coding)                    :: 4,605
            CDSs (with protein)               :: 4,605
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 162
            CDSs (without protein)            :: 162
            Pseudo Genes (ambiguous residues) :: 0 of 162
            Pseudo Genes (frameshifted)       :: 62 of 162
            Pseudo Genes (incomplete)         :: 111 of 162
            Pseudo Genes (internal stop)      :: 32 of 162
            Pseudo Genes (multiple problems)  :: 38 of 162
            Pseudo Genes (short protein)      :: 3 of 162
            ##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..3596
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="3320"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB3134_3"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2017-01-08"
                     /collected_by="MDACC"
                     /note="genotype: ST91"
     gene            complement(join(3521..3596,1..83))
                     /locus_tag="RNQ06_24365"
     CDS             complement(join(3521..3596,1..83))
                     /locus_tag="RNQ06_24365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WNL80055.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPKRHDLSPLAAATGNWNSRAMIM
                     RSVLQSS"
                     /name="replication initiation protein"
     gene            complement(579..773)
                     /locus_tag="RNQ06_24370"
     CDS             complement(579..773)
                     /locus_tag="RNQ06_24370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="WNL80056.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1045..1368
                     /gene="mobA"
                     /locus_tag="RNQ06_24375"
     CDS             1045..1368
                     /gene="mobA"
                     /locus_tag="RNQ06_24375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_process:
                     GO:0006355 - regulation of DNA-templated transcription
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WNL80057.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            1799..3316
                     /locus_tag="RNQ06_24380"
     CDS             1799..3316
                     /locus_tag="RNQ06_24380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000739598.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NERD domain-containing protein"
                     /protein_id="WNL80054.1"
                     /translation="MKKNIVRQVLESYGPCISSELAERIKRQNPSMSSDAIRKMISRST
                     DIGKLPFLRFSHNRRFIYLKDDFGSFKFWRALKKCMREANSAYSHAILSVINNGGYLKV
                     KDFGIVSGSPIKQAKHLSYESVLKNLLSAKILRSVYIDGVGDCVLINNNIANDISIFNM
                     ANCESFFDKPIFELIKAWLRNLGIVAFNQIKTKYDGENNPVVGSFEWDITAPSYVSPLA
                     EYSSDGLIPGFVVCDFALGFNRNEITTDAADTFIRKVQMTKSSRTNQRIMFVLFARRFE
                     KNAFNKLRSEGVLAITIANAFGNKVDESLARLSKVIQGTLSIERHPDELLQMVKDLESI
                     SGENGNLRGYIFELFVSSQICNFYGYGNVRINKEYKINGKHAEADVVLETNDDIYIVEC
                     KNVKTLPSMEVSLWMKTRVPIINSYYKSNNPDNKNIHHRLWVTGNIYPKDINRLDEFKC
                     NNKKIDVDYLFGQSLDDFFYQKKQVFNLYRKVISPDYKKGQIPDFDL"
                     /name="NERD domain-containing protein"
     Typing          811..1036
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.167"
                     /coverage="99.0"
                     /evalue="4.9e-75"
     Typing          complement(16..536)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.524"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(3383..3594)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.822"
                     /coverage="89.0"
                     /evalue="2.61e-36"
     Typing          1046..1365
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="8.379999999999999e-60"
ORIGIN
        1 aagtcgtgtc ttttcgggtt ggactcaaga cgatagttac cggataaggc gcagcggtcg
       61 ggctgaacgg ggggttcgtg cacacagccc agcttggagc gaacgaccta caccgggccg
      121 agataccaac agcgtgagct atgagaaagc gccacgcttc ccgaagggag aaaggcggac
      181 aggtatccgg taaacggcag ggtcggaaca ggagagcgca cgagggagct tccaggggga
      241 aacgcctggt atctttatag tcctgtcggg tttcgccacc tctggcttga gcgtcaattt
      301 ttgtgatgct cgtcaggggg gcggagccta tggaaaaacg ccaccggcgc ggcctttttc
      361 gggttcttgt tttttgctca catgtttctt ttggctttat cccctgattc tgtggataac
      421 cgcattaccg tctttgagtg agctgatacc gctcgccgca gccgaacgac cgagcgtagc
      481 gagttagtga gcgaggaagc ggaagagcgc cttatgtggc attttctcct tacgcaccgg
      541 tataccgttc tgcatcctgt ctggagcagg atacactgtt ataccccggt gccactttcc
      601 gcttcaaagc gtgtctgtat gctgttctgg agttcttccg cgagttcgtg cagcttctca
      661 cacatggcgg cctgttcgtc ggcatcgagt gcgtccagct tttcgagcag cgtcaggctc
      721 tggcttttta tgaatcccgc catgttgagt acggtttgct gctgcttgtt catctttctg
      781 ttttctccgt tctgtctgtc ctctgcgtcg tgtgattata tcgcgtacca cttttcgacc
      841 gtcttaccgc cggtattctg ccgacggaca tttcagtcag acaacactgt cactgccaaa
      901 aaacagcagt gctttgttgg taattcgaac ttgcagacag gacaggatgt gcaattgtta
      961 taccgcgcat gcatgcacgc tattacaatt accctggtca gggcttcgcc ccgacacccc
     1021 gtgtcagata cggagccatg ttttatgaca aaacgaagtg gaagtaatac gcgcaggcgg
     1081 gctatcagtc gccctgttcg tctgacggca gaagaagacc aggaaatcag aaaaagggct
     1141 gctgaatgcg gcaagaccgt ttccggtttt ttacgggcgg cagctctcgg taagaaagtt
     1201 aactcactga ctgatgatcg ggtactgaaa gaagttatga gactgggggc gttacagaaa
     1261 aaactcttta tcgacggcaa gcgtgtcggg gacagggagt atgcggaggt gctgatcgct
     1321 attacggagt atcaccgtgc cctgttatcc aggcttatgg cagattagct tcccggagag
     1381 aaaactgtcg aaaacagacg gtatgaacac cgtaagcccc caaagtgatc accattcgct
     1441 ttcatgcata gctatgcagc gagctgaaaa cgatcctgac gcatttttcc ggttttcgct
     1501 tggtaacaca tctctttttg cggtgtctgc ggcagaatcc cgttcagcgc gtttctgcgg
     1561 tgcgtacaat taagggatta tggtaaatag ggcggttgat atatgatgat gaaatgtcac
     1621 aaacgtaaca tcttgatttt taaggataaa tgtcgcaggt gtgttttttg tgatatgttg
     1681 cttttgttaa atatttgatt tttatgattt ttttctttgt gttttttttg ggatctataa
     1741 atattacacg tagtgtaatt ttataaatag cgtagtgtga caaaaataag atgaatttat
     1801 gaaaaaaaac attgttagac aagtgcttga gagttatggt ccgtgcatat cttctgaact
     1861 tgctgagagg attaagcgtc agaatccttc tatgtcatct gatgcaatac gtaaaatgat
     1921 ctctcgaagc actgatattg gtaagttgcc atttttaaga tttagtcata acaggagatt
     1981 catttatcta aaagatgact ttggtagctt caaattttgg cgggcgctca aaaaatgtat
     2041 gcgtgaggca aattcggcgt attctcacgc tatactttcc gtaattaata atggcggata
     2101 cttgaaggta aaggatttcg ggattgtgtc tggctctccg ataaagcagg ccaagcattt
     2161 aagttatgaa tctgttctaa aaaatctgct ttcagctaaa atacttagat ctgtgtatat
     2221 tgatggtgtt ggtgattgtg ttttgataaa taataatata gctaatgata tcagcatctt
     2281 taatatggca aattgcgagt ctttttttga taagccaata tttgaactga ttaaggcatg
     2341 gttgcgaaat ttaggtattg tggcttttaa tcaaataaaa acaaaatatg atggagagaa
     2401 caatcctgtg gttggttctt tcgagtggga tataacagcg ccaagttatg tgtcccctct
     2461 tgctgaatat tccagcgatg gactcatccc aggttttgtt gtctgtgatt ttgctctagg
     2521 gtttaatcga aatgaaatta ccaccgatgc tgctgatacc ttcataagaa aagttcagat
     2581 gaccaagtcc tctaggacaa accagaggat tatgtttgtt ctttttgcta gacgttttga
     2641 gaagaatgcc ttcaacaagc taaggagtga aggggttctg gctataacta tagctaatgc
     2701 gtttggtaat aaggtcgatg agagcttggc cagactatcg aaggtgattc agggaacttt
     2761 atctattgaa agacatcctg atgagttact tcaaatggta aaagatctgg agtctatctc
     2821 tggagagaat ggaaatttaa gggggtatat ttttgagctt tttgtttcct ctcaaatttg
     2881 taatttctat ggttatggaa atgttcgtat taataaagaa tataaaataa acggtaaaca
     2941 tgccgaagct gatgttgtat tggaaactaa cgatgatatt tatatcgttg agtgcaaaaa
     3001 tgttaagact ttaccttcga tggaggttag tctttggatg aaaacaagag tgccaattat
     3061 aaattcctac tacaaatcaa ataaccctga taacaaaaat atacatcatc gtttgtgggt
     3121 tacggggaat atatatccta aagatataaa ccgattggac gagtttaaat gtaataataa
     3181 gaagattgat gttgattatt tatttggtca gtctttggat gattttttct accaaaaaaa
     3241 acaagtgttt aatttatata ggaaagtcat ttcgccagat tataaaaaag ggcaaatacc
     3301 cgattttgac ttatagaatg acgttttcta gtctctgcat ttcttgacga tgacggcttg
     3361 aaaagcgtat cttcctccat gaaacgaaaa aaccacccgg caaggtggtt tttcgaaggt
     3421 tagttaatcc tggcagatta cctaacctag gtaactggct tcagcagagc gcagatacca
     3481 aatcctgtcc tttaagtgta gccgtagttg gggcatcact tcaagaactc tgtagtacgg
     3541 accgcattat catcgctctg ctattccagt taccagtggc tgctgccagt ggcgat
//
