LOCUS       NZ_CP054234             4072 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain EcPF7 plasmid p2, complete sequence.
ACCESSION   NZ_CP054234
VERSION     NZ_CP054234.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15075993
            Assembly: GCF_013372405.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Sharon,B.M., Nguyen,A., Arute,A.P., Hulyalkar,N.V., Nguyen,V.H.,
            Zimmern,P.E. and De Nisco,N.J.
  TITLE     Complete Genome Sequences of Seven Uropathogenic Escherichia coli
            Strains Isolated from Postmenopausal Women Suffering from Recurrent
            Urinary Tract Infection
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   Sharon,B.M., Nguyen,A., Arute,A.P., Hulyalkar,N.V., Nguyen,V.H.,
            Zimmern,P.E. and De Nisco,N.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUN-2020) Biological Sciences, University of Texas at
            Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v.0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 74x, 122x
            Sequencing Technology             :: Illumina NextSeq, ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 02:33:00
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,067
            CDSs (total)                      :: 4,955
            Genes (coding)                    :: 4,748
            CDSs (with protein)               :: 4,748
            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)              :: 207
            CDSs (without protein)            :: 207
            Pseudo Genes (ambiguous residues) :: 0 of 207
            Pseudo Genes (frameshifted)       :: 78 of 207
            Pseudo Genes (incomplete)         :: 150 of 207
            Pseudo Genes (internal stop)      :: 32 of 207
            Pseudo Genes (multiple problems)  :: 49 of 207
            Pseudo Genes (short protein)      :: 3 of 207
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054234.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EcPF7"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p2"
                     /geo_loc_name="USA: Dallas, Texas"
                     /lat_lon="32.77 N 96.79 W"
                     /collection_date="2018-05"
                     /collected_by="UT Southwestern Medical Center/ UT Dallas"
     gene            complement(join(2709..4072,1..784))
                     /gene="mobQ"
                     /locus_tag="HR071_RS24980"
                     /old_locus_tag="HR071_24995"
     CDS             complement(join(2709..4072,1..784))
                     /gene="mobQ"
                     /locus_tag="HR071_RS24980"
                     /old_locus_tag="HR071_24995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            963..1217
                     /gene="mobC"
                     /locus_tag="HR071_RS24985"
                     /old_locus_tag="HR071_25000"
     CDS             963..1217
                     /gene="mobC"
                     /locus_tag="HR071_RS24985"
                     /old_locus_tag="HR071_25000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            1750..2451
                     /locus_tag="HR071_RS24990"
                     /old_locus_tag="HR071_25005"
     CDS             1750..2451
                     /locus_tag="HR071_RS24990"
                     /old_locus_tag="HR071_25005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(427..785)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          786..962
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1751..2451
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.858"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..871)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.241"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2713..4070)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.186"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 caggaagccc gatattcaga aggtcagcca cacggcgggc aggctctgtc agccctccgt
       61 tcctgagttc ggtgcgggaa atctgtattt ccaggttaag cctgttaatc agacgattct
      121 gttcgccgcg ttctgtttcg ataccgcgtg tttccatcgc acaggcagac tttccgaggt
      181 gaataccagg cgttttctca agcccctgtc gctcgtatga acgatggtct atctcttcct
      241 gataaccggc gttcgccagt gccctgtttg catggtcagc ccatgatgcc cgccacgtct
      301 cggcatgtgt ccggtcgttc cagtccctga cctttccgct gaacccagca ggtccgatag
      361 ccctcgtggt cagcatgatg tgcgcatggg gatttgtttt atccatgtga tggaacgcca
      421 catcagcaat catgccctga ctgacaaagt tttctctgac aaaggcgaga acggtttccc
      481 gtgcggcatc ctgcggcagt tcgtggggga tggcgagttc aatttcccgc gcaagttgtg
      541 agttcttccg gcgttcggcc ttctcaacgg cattccagag ttcggcacgg ttcgtacacc
      601 aggcaggggc ggtggcgggg gtcagaatca cagcctcagc cacaccgctt ttgcgggtgt
      661 agtcgtgagt cagtccggta cgctcatcaa gcatcagtga accggaacga taggcagcgg
      721 aagctacggc gctgtagccg ctgcttctgg agataatttt catgctgaga tgataaatcg
      781 ccatttctgc cgtaatgcct ttttgtagtt ttctttcagc cccgcagggc gcacacaatc
      841 gaaacggagt ggagattgta taagtgcgca cttcgtgatt tgccgtgcat tatgccagct
      901 cagtttttaa actaccagtg acgcgctaaa atgcgatttt tcatcgcgca cggagttaca
      961 tcatgagcag aacgctcgaa cagaagattg ctgatgctga ggcgagatta cagcgcctga
     1021 aggcgaagag ccggagcctg gacacagcgc agaaggttgt tgtgggtgct gcattgctgg
     1081 caaaggtcag aaagccggag gaggtgcagt tgcgtgcctg gttactccag ttcctgaagg
     1141 cagaggtgac acgacaggct gatgtgacgc gcatactgcc gctgattaac gagctggagg
     1201 cgctgccaga acagtgattg tatcgtccgc tcgccgcagc cccagcgacc gagcgttagc
     1261 gagcgagtgg gcgaggaagc ggaagtgaat cagtcgccag gttgagcaca tacgcacggt
     1321 ttttcggcag gtgatatgcg ctgaacccgc atgaatactg ggtttccaca gggttggagg
     1381 gggtgtattc gaaacttgca attctgcttt atttcaacgc attgttttta ttggtttttt
     1441 gttttcagca ccccaagtta tccacaggct cgccgttaag tttttaagat cttattttta
     1501 gatctttttt ttaaaacctt tttaggtctt gtaacaccat gattttaaag atgttctggc
     1561 aagataagtg gagcttttgg gggtgaaagg tggagctttt gggggtgaaa ggtggagctt
     1621 ttgggggtga aaggtggagc ttttgggggt gtaatccaca gaaaaagggg gttgcaaaaa
     1681 aaaaacttcc acccatatga taagtggcgt acagtaaaaa aacgccacca atagcaacga
     1741 gcaagcgaaa tgtcagatct gatagcttac aaatcaaacg cccttatcga ggcaagctac
     1801 aagctcactt tgcaggaaca gcgcttcctg ctggtctgta tcagccgcct gaaatccgga
     1861 gaagattccc cttcgccgga tgaacaaaaa accatgacca tcacggctgc agagtttcat
     1921 gatgcctttc ctgacatggg acggcagcac gctgaagcta ggctcaagga agcgatagat
     1981 cgcctctggg acaggtcagt aatcatcaag aacgaggaaa aacgagaaga gttccgctgg
     2041 gtgcagtacc gggcgcagta tttcaaaggt gaggcgaaag tagatatcac cttctccgat
     2101 gccatcatgc cgtatctgac acagctcaag gggcagttta cgcgggtagt cgtgaagaac
     2161 gtctccagcc tttccagcac ctacagcatc cgcatttacg agctgctcca gcagttccgc
     2221 agcaccggtg acagaacgat agctatcgat gatttccgaa ccatgcttgc cgttgaagat
     2281 aaatatcaac aattcaaaga cttgaataag atgataatca agccagccat cgccgaactg
     2341 aacgaaaaaa gcgatctggt tgtaactgtt gagacgatca aaaaggggcg cacggttgta
     2401 gccctgcatt ttcgcttcaa ggaagacaaa cagatcaaga tgacgatcta aaatcgattt
     2461 taaggcacct aaaacgctcc ctgctgcgtt ttttttgtgt tagtagtgcg aaggtactat
     2521 tgaagtgaaa aattgcgtca aaaacgctct gatgcagcga aaaaagaccc cccaattttt
     2581 gggggcggaa aaacaaaact atgcttgcgt tatgtgagtg tgcttcttgc attcatccct
     2641 gtcgatgaac atcgaagaac atcgacgaac ataacacgat gttaaacaaa acaaaatatt
     2701 gttcacattc actgtgacca accgcgatca tgtctcctct cggtggtgtg tgttcgtgca
     2761 tcttcctcgc gctgccattc ctcccaggta cgattaaaac ccagcgagcg gaacagatga
     2821 tccggctgtt tttctggtgt gttgacggca gcaaaaagcg gtgcctcacg ggttttcaga
     2881 tgaaactgca tcagttctgg tgcaggtgat atgtggctgt ctgcatcgtg atttacggca
     2941 acaccatacc ctgcataccg taacccctta tcggtcagcg cactgatgac cagatgcctg
     3001 ttatcggctg agggaacggc aaacgcggga tacagcgtac cattaagccg gataacaccg
     3061 cccagagagt catccacgcc catgaccagc aaaagctgaa gctggcgggt ttcccggtcg
     3121 acagaactca tgaccggcat cagcgtcggt ggcagacgtc cctgcataaa atccaccttc
     3181 cttgccgctg gtgatggcat ggctggctgg cggtcttctc caagacagaa agactccggc
     3241 catgtcttcg gctggcggag attgcgggta tgttgcggcc atgtctggca aacctgcgtc
     3301 agcagttgct caaaggttgc agaggaataa acacgttgca gtggcggacg ttggccgatt
     3361 tcgcttcggt cacagatata accactcctg tcacgcatta aatcaacact ctcaaagatt
     3421 ctggtgcggt atttctccag ctcgttcccc cagagcgtat attctccgtt ccggttgtga
     3481 agcagaaggt aacaggtcat ttccccgtta ccaggcatgg gagcctcgcc ataccccgta
     3541 acgactgctc tcagcacccc tgaatccata acggcattgt catttttcct gagctgctcc
     3601 gcgcgactac gttcagtatc ttcctgttcc ttccggcgca attcctcttc acgtttaagc
     3661 aactgggctc tgagagctgc aaggccggat tccccccact gctgccactg tttttcaaat
     3721 gccatctgac tcgcgggaat gtcctgtttc tccaccttcc ggtaatgctg tcgtaatttt
     3781 tccatttgct ggctcagaga ctggattttt ccctgctcac tacggtattc cggtgccgcc
     3841 cattgcatca ggggaatacg ggaaaaaccg gacgaaaacg gcgatgattt tttcaggctg
     3901 gcagcatggc tcatcgcttc ctttcgttcg gtgttcagct cttcccagcg tctgcgcgtc
     3961 gcctgcatat ctgccatcat cgacatggca ttactggtga gtttccatgc cgagttactg
     4021 tccttcggca acgcttcgat aatgtcacgt agtgtgtacg aagttgcgtt gt
//
