LOCUS       NZ_CP023837             5163 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain 4/2-1 plasmid p4_2_1.3, complete sequence.
ACCESSION   NZ_CP023837
VERSION     NZ_CP023837.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07760933
            Assembly: GCF_003856575.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5163)
  AUTHORS   Sandegren,L.
  TITLE     Dynamics of resistance plasmids in extended spectrum
            beta-lactamase-producing Enterobacteriaceae in the gut microflora of
            patients during 1 year post UTI
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5163)
  AUTHORS   Sandegren,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-OCT-2017) Medical Biochemistry and Microbiology,
            Uppsala University, Husargatan 3, Uppsala SE-75123, Sweden
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: CLC Genomics workbench v. 10
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 13x
            Sequencing Technology             :: Pacific bio + Miseq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003856575.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 02:15:03
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,805
            CDSs (total)                      :: 4,684
            Genes (coding)                    :: 4,447
            CDSs (with protein)               :: 4,447
            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)              :: 237
            CDSs (without protein)            :: 237
            Pseudo Genes (ambiguous residues) :: 0 of 237
            Pseudo Genes (frameshifted)       :: 86 of 237
            Pseudo Genes (incomplete)         :: 159 of 237
            Pseudo Genes (internal stop)      :: 46 of 237
            Pseudo Genes (multiple problems)  :: 50 of 237
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023837.1.
            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..5163
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4/2-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4_2_1.3"
                     /geo_loc_name="Sweden"
                     /collection_date="2009"
     gene            complement(join(4566..5163,1..329))
                     /locus_tag="CRT37_RS24070"
                     /old_locus_tag="CRT37_25455"
     CDS             complement(join(4566..5163,1..329))
                     /locus_tag="CRT37_RS24070"
                     /old_locus_tag="CRT37_25455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_019842150.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            506..904
                     /locus_tag="CRT37_RS24075"
                     /old_locus_tag="CRT37_25460"
     CDS             506..904
                     /locus_tag="CRT37_RS24075"
                     /old_locus_tag="CRT37_25460"
                     /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_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(1108..2022)
                     /locus_tag="CRT37_RS24080"
                     /old_locus_tag="CRT37_25465"
     CDS             complement(1108..2022)
                     /locus_tag="CRT37_RS24080"
                     /old_locus_tag="CRT37_25465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001271363.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            3755..3964
                     /locus_tag="CRT37_RS24090"
                     /old_locus_tag="CRT37_25470"
     CDS             3755..3964
                     /locus_tag="CRT37_RS24090"
                     /old_locus_tag="CRT37_25470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     gene            complement(4030..4563)
                     /locus_tag="CRT37_RS24095"
                     /old_locus_tag="CRT37_25475"
     CDS             complement(4030..4563)
                     /locus_tag="CRT37_RS24095"
                     /old_locus_tag="CRT37_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_029364822.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISHDFQRLEESVANMKVNADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     Typing          complement(1109..2022)
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.017"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..329)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.083"
                     /coverage="99.0"
                     /evalue="2.23e-65"
     Typing          complement(4570..5162)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.485"
                     /coverage="99.0"
                     /evalue="1.6799999999999998e-126"
ORIGIN
        1 ggattgtgaa tggcaaaact ccaggcgtgc cgttcgccag cttcctgacg tacaaaatcc
       61 tgcaccagtt caaggcgctg ttccggtgtc agttcacggg gtaatgcaat ttcaagttcc
      121 ctataggtcg aaccgttcgc acgttcaaac tggtcagccg cctgccagaa atgggaagga
      181 ttatccctgg cccattccgg catgtttccg tgtgcggaat attccaaatc ctgacggtcg
      241 cggtatttct ctttgcgctc gatgtaatcg gcgtggtttg cagcctgccc cttgccacca
      301 aatttaacgc tgaggtgata ggttgccacg gtttcagccc tctgcaggag cgcactgttt
      361 ctcgacgaag gagagaaaca tataagtgcg cttccttcta attttacgaa ttagcacgga
      421 agataccccc tgcacccgcc gaccgcaagc gatatactgc acgaccacaa cacaccgcaa
      481 aaaaacacca gggagcatca cgaacatgcg catcagcaac atcgaatggc tgaagaaacg
      541 gatcggattc atcaggaagc tcggagaaca gaccgcacga cagagacaga ttattgacct
      601 gatcgacaac gaagccggac tcacagaaca ggaacgcaaa cttctccacg tactggcaac
      661 agcggaaaaa aacgacttac aggcacagga gagcgaacga aaacaggcgg tccaaaaacg
      721 aatcgaggga aaaaaacaac gacgggaacg caatcaccgg ctctttctcg cggctgggct
      781 actgatcgaa gcaggactgg tagacacaaa aacaggcgag ctatgctata aaaaagacag
      841 gatattacaa gcacttaagg aacttaagta cgatctggag acatccccaa acccagacgc
      901 gtaagtgcct ccatccgtgt tccgattccc tggtgcttcc tcgctcattc gctcgctacg
      961 ctcggtcatg agactgcggc gagcactacc accacaatca cgcggaaagc cgcgccattg
     1021 cagggctgaa cgggggaaaa cggcaaaaaa cctgctgctc aaaaagacgc cagaaaggcg
     1081 ctgttatctg atataggctt atttggtcta ctctacgaga cctcgttttt tcagttggta
     1141 ataccaggcg cgactgatcc ctaatgcctc ccacggtttc agcgtgcgtg cagatgtagc
     1201 tactgtgcta cgcttagact tagaaccgcc cttgcgaccg cgtgcagcct gaatttctgg
     1261 cgtgtgcgta tcagccacat actgtgcgaa agtttccggc gtgaagttcc tgtgcgtgta
     1321 tttcgcaatg ctcttgccaa tagcccgaca ttcagccagt gaaagcggaa cgggaagcga
     1381 tgcattgtac atttcgacac gctggatcac cgcttcaagc cactgtgaga acgctggcca
     1441 gccctgacga atcgccctgt aagcccattt gcgcgtcatt tcgaacaggt ggcagtttcg
     1501 ccccatcccg taatgtttat cgatgctacg acgctctgag gcgctcaaat cgagataatc
     1561 agccagttca tcgagggtat aggcttcctc gcgccactcc atcaccagcc attccaggtg
     1621 gaacggattt ttgcaaatca ggccgctgta gttcacatcc gcacaaagtt tctcacacag
     1681 cgaacgttca accgctgcgg catatttcag cgccttaacc gaggcatcag gcgcggttct
     1741 cacggcgatg ttgagtgcgt agagcaggtg agcgtgtccg ttcacaggat ttttaacggt
     1801 gatgttcggc gcgggagcgt tccggtcgct ccagtcaatc gcagccccct cgcggtcaac
     1861 gtcaaaaacc agccagaact gtgcatgagg ctggttctgc tggatatacc gtgcaagaag
     1921 cgcgcgccct ttgccggaga tacgaaggcc gaaagcgaga tcatccgtgt gatagggacg
     1981 gtggggtaaa ttttcttcga agtattgaag cgcggcgctc atgtgttacg attccttcca
     2041 ggttatcgac cgacatcgcc cctgtatttt cgtgaaagtc ttggcggata gacacgaatt
     2101 tcaggggcgt ttgtttttca gtcgcttaca ctacccccaa cgacaaaacc tgtcgagcct
     2161 tcccgcaaat ccgatccatt taccataact cccgttgtac gtaccatgta aaacgccctc
     2221 aatcgctttc tggcgcaaaa aacgcaaaaa gacaagaaaa caccaggcca aaccagaaaa
     2281 acgcgtcaga atcgttttca gggcgttgca taactatgca cgaaagcgat gtgcgatcgg
     2341 tttcgtgcgt tctgaacacc gaacggctca aaacgacaag ttttctcccc tggtgcgtgg
     2401 cgctctgacg gggtttcctg tttccaaact tcacatctcg ccaggacaaa aaaaaccgac
     2461 ctggggtcgg tggcaagaat cagagtctat gggaaatatt ttagttatcg gatgctcaat
     2521 attcacaaac gcaaaaaatg cctcagtgat gccctaaaac aacctttcca gaaggagtcc
     2581 gcgctttacg atgcacggaa gagataaaaa accccacaaa agtggggaac caagagaaac
     2641 aacaattaca ggttgttggt tgtgttcgaa caacgatgaa gtagctacgc taaataataa
     2701 ttaccgtaca ggccctacat attcaacact aaatttaaga tcctgacgaa ggatttataa
     2761 atgcacgaaa acacatagac agacaaattc actaaattca tacacaaaaa caagtgtagt
     2821 tttctaagta aattagattc gacaaccaat tagtttatcc acatcgcatt ccactcttgc
     2881 tacaccaatc acatttcttg atatgtaata gcagaaaaaa taaaaccaga caccaataga
     2941 ccaaaaaaca aacattcaac aaaaaacatt ttgaacaata tcacaaaact gtcacaacca
     3001 tcatcagact attgaaaaaa actggttgct gttttataaa agcgactgta acaacctcca
     3061 ctctatagtt ccattagttt aaagtgtcac acaaactgag catccatttg ttttccttac
     3121 ttttgcccct gtattccaag gggttttttt ataacttaaa gattagcaca ccacacaaaa
     3181 acaataaaaa aaacgacaag ttatacaata aaaccagtac tatccataca gctaattaca
     3241 tataaatact attaaaccat ctggacatta aaaataaact cttataacat aaaattaatg
     3301 cggttccggt accatatgtc agggataatg tgcaaatgga ggtatcggaa ctgcatttca
     3361 gttcattatt aattaatggc aaaaaaaacc tctgcgagcg cagagggggt aaggaatgtt
     3421 cccggtcata atatgtcgat agtgtttata tacatacaga acaagaacaa caaccagcca
     3481 actaataaat attttatttt ttagagctga aaccttaaag ctcacttcca ttccatacat
     3541 tgttataaac cttatgttga aaactgaaag taagtacggc agacttatta agttgcgtgc
     3601 agtcttttca cgttatacaa acaagaacac ctgcgaagtt atttctcctt acatatcccc
     3661 ctatgccaac gggggatttt ttctggttca ctaacgcata aataatagtg acaccctatc
     3721 attcacaaac cgtgataata taaggattat catcatggca aaattaggtg aaaacacccc
     3781 acatattatc gatgctactg tagattttat ggcatcaagc caggcatttc gtgagtatct
     3841 gaaaaaactt ccccctgata acacaatacc gccagctctt actgatgagc acgtaccgtt
     3901 atatatacga aggctggaat actatcgtct gctttatcga ccaaagcaga cagaatcata
     3961 ttgaaaaaaa cggtgaacgg ttcgcgaaat cctttcgcgg gtcgtgaggc gttggacaag
     4021 cgaagcgcgt cagtttttcc ggctcttccc cgtgacaggt ttctccacca gtttatcttc
     4081 cagtgtcaca actttctgat acaccgccgc tgtggcgttg tagttcctgt cgagtattgt
     4141 tttcattccc catccgagca cacagaacat aaccagaaaa gccactgaca ccccacccag
     4201 ccatttccag ctataccctt taagggtgtt gtattcctgc acgatattgc tgtgaattgt
     4261 cgcaatatcc ctgttcaggg catccgcgtt taccttcatg tttgcgactg actcttccag
     4321 ccgctgaaaa tcatggctga tgcgctcacc tatcagccct gctacgtcca gcttctgcac
     4381 ctcgtttctg acttcatccc tgacctgttt tgccacaccg tcagaaatat cccgatatcc
     4441 gcgaagtgtt tcccttgcca cagccagaga atcagcaaca gctttctgtt gctccattgc
     4501 ggtatgttgc agatgctcca ccgataacag gagcgtgagt aatttttctt ctgtgctggc
     4561 catgttcaga atcccataga aaatccacgt gacggtgatt taacccgttc aggttcagtt
     4621 cggtcctgtc tgctcactct gtctctcatg tcaaagccat gctcccgcgc aacatcatgt
     4681 tgaagccttc tgaccagttc atgttgctta accggagtgt ccagccattc cctgatgtca
     4741 tgcccgaccg ttcgcgcctg ttcaagatgg cgggaatagt ccggttcaga ccgtttttgc
     4801 atgatgtcat gacgctgggc atcatcaagc cgtccggcag cttcaaaacc cagatgcact
     4861 tcgggacgtc gttcaatgcc ctgttctttc agcgtccggc agtcaatgaa gcccctttca
     4921 aagccatgct ttctcatatg ttcgttgtgc ttcacctccc agcgttttcg caattcccgc
     4981 aactgctctt tttgctgagt gagagtcagg cttccggaat cctttttcgc acctccccgc
     5041 tcgggatacc tggcgttata gcgccggaaa tactgttccg gtgtacgttc aatgccatca
     5101 ttcacacgct gactcatcat gatatgcgca tgaggctgtt cgccgccgtc aatgctcgct
     5161 ttc
//
