LOCUS       NZ_CP023848             5167 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain 4/1-1 plasmid p4_1_1.4, complete sequence.
ACCESSION   NZ_CP023848
VERSION     NZ_CP023848.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07760931
            Assembly: GCF_003856695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5167)
  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  JOURNAL   Unpublished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 5167)
  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                   :: 10x
            Sequencing Technology             :: Pacific bio + Miseq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003856695.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 02:15:24
            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)                     :: 5,342
            CDSs (total)                      :: 5,228
            Genes (coding)                    :: 5,004
            CDSs (with protein)               :: 5,004
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 224
            CDSs (without protein)            :: 224
            Pseudo Genes (ambiguous residues) :: 0 of 224
            Pseudo Genes (frameshifted)       :: 84 of 224
            Pseudo Genes (incomplete)         :: 161 of 224
            Pseudo Genes (internal stop)      :: 46 of 224
            Pseudo Genes (multiple problems)  :: 57 of 224
            Pseudo Genes (short protein)      :: 1 of 224
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023848.1.
            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..5167
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4/1-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4_1_1.4"
                     /geo_loc_name="Sweden"
                     /collection_date="2009"
     gene            complement(join(4570..5167,1..329))
                     /locus_tag="CRT35_RS27155"
                     /old_locus_tag="CRT35_28215"
     CDS             complement(join(4570..5167,1..329))
                     /locus_tag="CRT35_RS27155"
                     /old_locus_tag="CRT35_28215"
                     /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_001331297.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            506..904
                     /locus_tag="CRT35_RS27160"
                     /old_locus_tag="CRT35_28220"
     CDS             506..904
                     /locus_tag="CRT35_RS27160"
                     /old_locus_tag="CRT35_28220"
                     /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="CRT35_RS27165"
                     /old_locus_tag="CRT35_28225"
     CDS             complement(1108..2022)
                     /locus_tag="CRT35_RS27165"
                     /old_locus_tag="CRT35_28225"
                     /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_001271348.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            3759..3968
                     /locus_tag="CRT35_RS27175"
                     /old_locus_tag="CRT35_28230"
     CDS             3759..3968
                     /locus_tag="CRT35_RS27175"
                     /old_locus_tag="CRT35_28230"
                     /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(4034..4567)
                     /locus_tag="CRT35_RS27180"
                     /old_locus_tag="CRT35_28235"
     CDS             complement(4034..4567)
                     /locus_tag="CRT35_RS27180"
                     /old_locus_tag="CRT35_28235"
                     /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_000168770.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     Typing          complement(1248..2022)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /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(4574..5166)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.475"
                     /coverage="99.0"
                     /evalue="2.98e-125"
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 cggggaaaaa cggcaaaaaa cctgctgctc aaaaagacgc cagaaaggcg
     1081 ctgttatctg atataggctt atttggtcta ctctacgaga cctcgttttt tcagttggta
     1141 ataccaggcg cgactgatcc ctaatgcctc ccacggtttc agcgtgcgtg cagatgtagc
     1201 tactgtgctg 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 gcgcatgagg ctggttctgc tgtatgtacc gcgcaagaag
     1921 cgcacgccct ttgccggaga tgcgaagacc aaaagcgaga tcatccgtgt gatagggacg
     1981 atggggtaaa ttttcgtcga agtattgaag cgcggcgctc atgtgttacg attctctccg
     2041 ggttatgcga cctacacgcc ctctgtattt catgttgaat cttgccggat ctggacatga
     2101 tttcaggggc gtttgttttt cagtcgctta cactacaccc aacggcaaat cctgtcgaac
     2161 cttcccgaaa acccgatcca tttaccataa ctcccgttgt acgcccccct taaaacgccc
     2221 tcagtcgctt tctggcgcaa aaaacgcaaa aagacaagaa aacaccaggc caaaccagaa
     2281 aaacgcgtca gaatcgtttt cagggcgttg cataactatg cacgaaagcg atgtgcgatc
     2341 ggtttcgtgc gttctgaaca ccgaacggct caaaacgaca agttttctcc cctggtgcgt
     2401 ggcgctctga cggggtttcc tgtttccaaa cttcacatct cgccaggaca aaaaaaaacc
     2461 gacctggggt cggtggcaag aatcagagtc tatgggaaat attttagtta tcggatgctc
     2521 aatattcaca aacgcaaaaa atgcctcagt gatgccctaa aacaaccttt ccagaaggag
     2581 tccgcgcttt acgatgcacg gaagagataa aaaaccccac aaaagtgggg aaccaagaga
     2641 aacaacaatt acaggttgtt ggttgtgttc gaacaacgat gaagtagcta cgctaaataa
     2701 taattaccgt acaggcccta catattcaac actaaattta agatcctgac gaaggattta
     2761 taaatgcacg aaaacacata gacagacaaa ttcactaaat tcatacacaa aaacaagtgt
     2821 agttttctaa gtaaattaga ttcgacaacc aattagttta tccacatcgc attccactct
     2881 tgctacacca atcacatttc ttgatatgta atagcagaaa aaataaaacc agacaccaat
     2941 agaccaaaaa acaaacattc aacaagaaac attttgaaca atatcacaaa actgtcacaa
     3001 ccatcatcag actattgaaa aaaactggtt gctgttttat aaaagcgact gtaacaacct
     3061 ccactctata gttccattag tttaaagtgt cacacaaact gagcatccat ttgttttcct
     3121 tacttttgcc cctgtattcc aaggggtttt tttataactt aaagattagc acaccacaca
     3181 aaaacaataa aaaaaaacga caagttatac aataaaacca gtactatcca tacagctaat
     3241 tacatataaa tactattaaa ccatctggac attaaaaata aactcttata acataaaatt
     3301 aatgcggttc cggtaccata tgtcagggat aatgtgcaaa tggaggtatc ggaactgcat
     3361 ttcagttcat tattaattaa tgacaaaaaa aacctctgcg agcgcagagg gggtaaggaa
     3421 tgttcccggt cataatatgt cgatagtgtt tatatacata cagaacaaga acaacaacca
     3481 gccaactaat aaatatttta ttttttagag ctgaaacctt aaagctcact tccattccat
     3541 acattgttat aaaccttatg ttgaaaactg aaagtaagta cggcagactt attaagttgc
     3601 gtgcagtctt ttcacgttat acaaacaaga acacctgcga agttatttct ccttacatat
     3661 ccccctatgc caacggggga ttttttctgg ttcactaacg cataaataat agtgacaccc
     3721 tatcattcac aaaccgtgat aatataagga ttatcatcat ggcaaaatta ggtgaaaaca
     3781 ccccacatat tatcgatgct actgtagatt ttatggcatc aagccaggca tttcgtgagt
     3841 atctgaaaaa acttccccct gataacacaa taccgccagc tcttactgat gagcacgtac
     3901 cgttatatat acgaaggctg gaatactatc gtctgcttta tcgaccaaag cagacagaat
     3961 catattgaaa aaaacggtga acggttcgcg aaattctttc gcgggtcgtg aggcgttgga
     4021 caagcgaagc gcgtcagttt ttccggctct tccccgtgac aggtttctcc accagtttat
     4081 cttccagtgt cacaactttc tgatacaccg ccgctgtggc gttgtagttc ctgtcgagta
     4141 ttgttttcat tccccatccg agcacacaga acataaccag aaaagccact gacaccccac
     4201 ccagccattt ccagctatac cctttaaggg tgttgtattc ctgcacgata ttgctgtgaa
     4261 ttgtcgcaat atccctgttc agggcatccg cgtttgcctt catgtttgcg actgactctt
     4321 ccagccgctg aaaatcctgg ctgatgcgct cacctatcag tcctgccacg tccagcttct
     4381 gcacctcatt tctgacttca tccctgacct gttttgccac accgtcagaa atatcccgat
     4441 atccgcgaag agtttccctt gccacagcca gagaatcagc aacagctttc tgttgctcca
     4501 ttgcggtatg ttgcagatgc tccaccgata acaggagcgt aagtaatttt tcttctgtgc
     4561 tggccatgtt cagaatccca tagaaaatcc acgtgacggt gatttaaccc gttcaggtgc
     4621 agttcggttc tgtctgctca ctctgtctct catgtcaaag ccatgctccc gcgcaacatc
     4681 atgttgcagc cttctgacca gttcatgttg cttaaccgga gtgtccagcc attccctgat
     4741 gtcatgcccg accgttcgcg cctgttcaag atggcgggaa tagtccggtt cagaccgttt
     4801 ttgcatgatg tcatgacgct gggcatcatc aagccgtccg gcagcttcaa aacccagatg
     4861 cacttcggga cgtcgttcaa tgccctgttc tttcagcgtc cggcagtcaa tgaagcccct
     4921 ttcaaagcca tgctttctca tatgttcgtt gtgcttcacc tcccagcgtt ttcgcaattc
     4981 ccgcaactgc tctttttgct gagtgagagt caggcttccg gaatcctttt tcgcacctcc
     5041 ccgctcggga tacctggcgt tatagcgccg gaaatactgt tccggtgtac gttcaatgcc
     5101 atcattcaca cgctgactca tcatgatatg cgcatgaggc tgttcgccgc cgtcaatgct
     5161 cgctttc
//
