LOCUS       CP134928                5210 bp    DNA     circular BCT 27-SEP-2023
DEFINITION  Escherichia coli strain 284 plasmid pMB6980_5, complete sequence.
ACCESSION   CP134928
VERSION     CP134928.1
DBLINK      BioProject: PRJNA924946
            BioSample: SAMN32977818
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5210)
  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  JOURNAL   Unpublished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 5210)
  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..5210
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="284"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB6980_5"
                     /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            139..528
                     /locus_tag="RNP63_23930"
     CDS             139..528
                     /locus_tag="RNP63_23930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WNL98316.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(592..876)
                     /locus_tag="RNP63_23935"
     CDS             complement(592..876)
                     /locus_tag="RNP63_23935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WNL98317.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(894..1091)
                     /locus_tag="RNP63_23940"
     CDS             complement(894..1091)
                     /locus_tag="RNP63_23940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WNL98318.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            1303..1599
                     /locus_tag="RNP63_23945"
     CDS             1303..1599
                     /locus_tag="RNP63_23945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WNL98319.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            complement(2146..2379)
                     /locus_tag="RNP63_23950"
     CDS             complement(2146..2379)
                     /locus_tag="RNP63_23950"
                     /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="WNL98320.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMKLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2386..2904)
                     /locus_tag="RNP63_23955"
     CDS             complement(2386..2904)
                     /locus_tag="RNP63_23955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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="WNL98321.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSC
                     GTLWYLGGMIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPHQ
                     GKDWVQLME"
                     /name="MbeB family mobilization protein"
     gene            complement(2942..3640)
                     /locus_tag="RNP63_23960"
                     /pseudo=""
     CDS             complement(2942..3640)
                     /locus_tag="RNP63_23960"
                     /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(3582..3905)
                     /locus_tag="RNP63_23965"
     CDS             complement(3582..3905)
                     /locus_tag="RNP63_23965"
                     /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="WNL98322.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3970..4161
                     /locus_tag="RNP63_23970"
     CDS             3970..4161
                     /locus_tag="RNP63_23970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="WNL98314.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDSENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4829..4942
                     /locus_tag="RNP63_23975"
     CDS             4829..4942
                     /locus_tag="RNP63_23975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WNL98315.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="replication initiation protein"
     Typing          complement(4247..4334)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          4345..4901
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2043..3592)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.363"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tataattgcc ctctcttata tggaaccacc attcaatcac atcatgggga taatataagt
       61 gaaaacgttc gcattgttta tttttacgtg tatatgtatt tatagattgg aattttaaca
      121 aaataaaatg gagttaatat gttcaaatca tcagtaaagt caataacatc gagtactata
      181 ctgaccttac ttataggatg ttcaagtact gaaacaaaca aaaacattgt ttacaaagtt
      241 ggtggtgaca gcatcattct gaataaatat tgcatactta aaatgtaccc ttcccaatca
      301 gaaaaaaaca aaggcgtcat aatagaagta aacacagata gtttatgtaa gaaaaaacta
      361 aacgaaataa ctagtaaaaa tatagggaaa cccctgattt catattttga tggaaaagta
      421 atatcccaac ctgcaatcat tcattctgca ctaaatccaa cccattatta tcaacctgtg
      481 aacgatgaaa caacagtgat ggaaatcata aaagcatatt caaaataata ttaatagata
      541 taatcctgct taaggtatag cttaggcagg attatattta ttcagctctt attataaggt
      601 agtgtataca tgaataatct gccctgtccc actgacactt ttaaatttaa ttttatcaac
      661 accagcgccc ttgcaagaga tctgataaga tgctggacca ataacgttaa ctgttcttgg
      721 cccattaggg gcataccaga taaaagcaat aaatggaccg ggtacattag acaatgtatc
      781 aaaatagaca gtgtacgcga tatcaccagt atgattttca agttcaaccc aaggaccaaa
      841 aaagaaagga ggagcccaaa cattttgaga aatcatataa tctcctgatt agttcaatgc
      901 gaatgttctt cccattcact ctcgcaagaa acatctataa gctcaacatc tagcccacta
      961 acagaatcag agaaatactt ataaacatca tcccttgttc ccataaggtc tgccgaacat
     1021 gatagttcac aaccattctt attcctaact acaaataaga aacggtgaag caatactttt
     1081 tcttctttca ttttatccct ccctttattt acacagaata tactgtatat ataaatacta
     1141 gttttatata cagtataaat tacgccgcat tatttttcct gtcaatgata tgaattttca
     1201 tttttgtgat ctgaatcacc cttataaaaa tcaggaaggg aagattcgca gcagaaaaac
     1261 agcaccggat aacatcagga gaaaaaacag agaggagata acgtgagcaa aacaaaatct
     1321 ggtcgccacc gactgagcaa aacagacaaa cgcctgctgg ctgcacttat cgctgccgga
     1381 tacgaagagc ggacagcccg tgacctcatc cagaaacacg tttacacact gacacaggcc
     1441 gacctgcgcc atctggtcag tgaaatcagt aacggtgtgg gacagtcaca ggcctacgat
     1501 gcgatttacc aggcaagacg cattcgtctc gcccgtaaat tcctgaacgg aaaaaaaccg
     1561 gaagaagggc tgaacgcctg gaagggtgat ttaccataat cacttattgt acgcaccgcc
     1621 gaaacgcgtt cggtgcgatc acggcagcag acaggtaaaa atggcaacaa accacccgga
     1681 aaactgccgc gatcgcaccc ggtaaatttt aaccacatgc atacctatgc agccaggtga
     1741 atcacgcagg aattgccagt cagagaccgc tgaaacggat ttttttcata ctttcggaag
     1801 cgaagaagac ggggatttga gcaggaaaac agaagttcag gggaatgagc gcgatctggc
     1861 aatagaggca aaaacacgac tatgaaagac acaccagaat cgcgcccgta tgcgttttaa
     1921 cgcgttcctg tgttttcagc aaggtttatg actgaagcgc gttcccggtg ccccgaacca
     1981 accattatcc caaaaaatgc accggaaacg cgctgacaac attttagcct gtctctgatt
     2041 accatcccag cgaagggcca tccagtgtcc gttcctgtat ttccagctgg cgctcacgct
     2101 ccagggataa ctcatgttcg cgttcctgta tcagccgttc gtcccttatc tcctgttctc
     2161 gctgtataac tggctcaagc gttctgtccg ctcgctcaag tgctgcacct gctgactcaa
     2221 cttcatgacc cgctcgttca gcatcgcgtt gtcccgttgc gtaagcgaaa acattttctg
     2281 caattccacg aaggcgctct cccattcgtt cagccgctgc atatagtcct gttgcagttg
     2341 ctctaatgcg ttcagcaaat gtctttccag ctccgtcact ctgtgtcact ccatcagttg
     2401 tacccagtcc ttcccctgat ggggaatcac ctctgctgat ttcccgtacg gaaggaccag
     2461 aaatttcctg ttcccgtcct gtacgaactc cacgccccat gtcttcgcgt tcagtttctg
     2521 caatgtctct tcctgcttcc tgatatcttc caagttcgcc tgtatcatcc cgccaagata
     2581 ccagagcgtc ccgcaactca cggtaaacag gaaaatgacc atccccagta acatcatgcc
     2641 cgtattccct gccagcttta acacgtcctt cctgtgctgc atcatcgcct ctttcacccc
     2701 ttcccggtgc tttttcagtg attcctctgt cgaagctgtg aacagggcta tagcgtcttt
     2761 gattttcgtc tcgtttgatg tcacagcctt gcttacagat ttttcgagct tcctgaactc
     2821 gtcgttcagt attgtctctg tagattcggc tctctctttc agctttttct cgaactccgc
     2881 gcccgtctgt aaaagattgc tcataaaatg ctcctttcag cctgatattc ttcccaccgt
     2941 tcgggtctgc aatgctgata ctgcttcgcg tcaccctgac cacttcaagc cctgcctctg
     3001 tgagcgcctg aatcacatcc tgacggcctt ttatctcccc gacatgataa agagcgtcta
     3061 tcccgcgtgt gacgctctct gcaagcgcct gtttcgtttc cggcaggtta tcagagagag
     3121 tcagtatccg gcggttctcc ggggcgttgg ggtcatgcag cccgtaatgg tgattcacca
     3181 gcgtctgcca ggcatcaatt ctcggcctgt ctgcccggtc gtagtacggc tggaggcgtt
     3241 ttccggtctg tagctccatg ttcggaatga caaaattcag ctcaagccgt cccttgtcct
     3301 ggtgctccac ccacaggatg ctgtactgat ttttttcgag accgggcatc agtacacgct
     3361 caaagctcgc catcaccttt tcacgtcctc ccggtggcag ctccttctcc gcgaacgaca
     3421 gcacaccgga cgtgtatttc ttcgcaaatg gcgtggcatc gatgagttcc cgtacttctt
     3481 ccggattacc ctgaagcacc gttgcccctt cccggttacg ctcccttccc agcaggtaat
     3541 caaccggacc actgccacca ccttttcccc gggcatgaaa cttaactatc atcccgcgtc
     3601 ccctgttccc tgacggccag acgcaaccgg cgcagctcat ccccgatggc catcagtgcg
     3661 gccaccacct gaacccggtc gccggaagac cactgtccgc tgttcacctt acgggctgtc
     3721 tggttcaggt tattcccgat ggctgccagc tgacgcagta acggcggtgc cagtgtcggc
     3781 agcctcccgg aacgggcaac cggctcaccc aggcagaccc gccgcatcca taccgccagt
     3841 tgtttaccct cacagcgttc cagtaaccgg gcatgttcat catcagtaac ccgtatcgtg
     3901 agcatcctct cgcgtttcat cggtatcatt acccccatga acagaaatcc cccttacacg
     3961 gaggcatcag tgactaaaca ggaaaaaacc gcccttaaca tggcccgctt tatcagaagc
     4021 cagacattaa cgctgctgga gaagctcaac gaactggacg cggatgaaca ggcagatatc
     4081 tgtgaatcgc ttcacgacca cgccgatgag ctttaccgca gctgcctcgc gcgcttcggg
     4141 gatgacagtg aaaacctctg acatatgcag ctcccggaga cggtcacagc ttgcctgtga
     4201 gcggatgccg ggagcagaca agcccgccag ggcgcgtcag ggtgttttag cgggtttcgg
     4261 ggcgcagccc tgaaccagtc acgtagcgat agcggagtgt atactggctt aaccatgcgg
     4321 catcagtgcg gattgtatga aacgtgcgcc ataccgggtg tgaaatgccg cacagatgcg
     4381 taaggagaaa atgcacgtcc aggcgctttt ccgcttcctc gctcactgac tcgctacgct
     4441 cggtcgttcg gctgcggcga gcggtatcta ctcactcaaa aacgaaatgc tgttatccac
     4501 agaatcaggg gataacaccg gaaaaaacat gtgagcaaaa gaccaggaac aggaagaagg
     4561 ccgcgccgct ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaatcgac
     4621 gctcaagtca gaggtggcga aacccgacag gacttaaaga taccaggcgt ttccccccgg
     4681 aagctccctc gtgcgctctc ctgttccgac cttaccgttt accggatacc tgtccgcctt
     4741 tctcccttcg ggaagcgtgg cgctttctca tagctcacgc tgtaggtatc tcagttcggt
     4801 gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg
     4861 cgccttatcc ggtaactatc gtcttgagtc caacccggta agacacgact taacgccact
     4921 ggcagcagcc attggtaact aaaaagtgga tttagatacg cagaactctt gaagttgaag
     4981 ccttatagcg gctacactga aaggacatct tttggtatct gtgctccact taagccagct
     5041 acccggttag gtaatctgcc aggattagct aaccttcgaa aaaccacctg ccagggtggt
     5101 tttttcgttt acaggcagca gattacgcgc agaaaaaaag gatctcaaga agatcctttg
     5161 atcttttttt ctctaaactg caatcccatc agttcaggag agaaagatag
//
