LOCUS       NZ_CP116156             5903 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P61 plasmid pDETEC40, complete
            sequence.
ACCESSION   NZ_CP116156
VERSION     NZ_CP116156.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988466
            Assembly: GCF_027944855.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5903)
  AUTHORS   Moran,R.A., Baomo,L., Doughty,E.L., Guo,Y., Ba,X., van Schaik,W.,
            Zhuo,C. and McNally,A.
  TITLE     Extended-spectrum beta-lactamase genes traverse the Escherichia coli
            populations of ICU patients, staff and environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5903)
  AUTHORS   Moran,R.A., Baomo,L., Doughty,E.L., Guo,Y., Ba,X., van Schaik,W.,
            Zhuo,C. and McNally,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JAN-2023) Institute of Microbiology and Infection,
            University of Birmingham, Institute of Microbiology and Infection,
            Birmingham B15 2TT, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 10x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/25/2024 01:59:19
            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)                     :: 4,937
            CDSs (total)                      :: 4,816
            Genes (coding)                    :: 4,535
            CDSs (with protein)               :: 4,535
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 281
            CDSs (without protein)            :: 281
            Pseudo Genes (ambiguous residues) :: 0 of 281
            Pseudo Genes (frameshifted)       :: 70 of 281
            Pseudo Genes (incomplete)         :: 207 of 281
            Pseudo Genes (internal stop)      :: 43 of 281
            Pseudo Genes (multiple problems)  :: 39 of 281
            Pseudo Genes (short protein)      :: 3 of 281
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116156.1.
            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..5903
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P61"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC40"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-08-01"
     gene            complement(317..475)
                     /locus_tag="PIC71_RS24715"
     CDS             complement(317..475)
                     /locus_tag="PIC71_RS24715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_205849009.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHDLSPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(972..1166)
                     /locus_tag="PIC71_RS24565"
                     /old_locus_tag="PIC71_24565"
     CDS             complement(972..1166)
                     /locus_tag="PIC71_RS24565"
                     /old_locus_tag="PIC71_24565"
                     /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="WP_271289858.1"
                     /translation="MNKQQQTVLNMAKFIKSQSLTLLEKLDSLDADAQAAMCEKLHELA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1438..1761
                     /gene="mobA"
                     /locus_tag="PIC71_RS24570"
                     /old_locus_tag="PIC71_24570"
     CDS             1438..1761
                     /gene="mobA"
                     /locus_tag="PIC71_RS24570"
                     /old_locus_tag="PIC71_24570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2144..4150
                     /locus_tag="PIC71_RS24575"
                     /old_locus_tag="PIC71_24575"
     CDS             2144..4150
                     /locus_tag="PIC71_RS24575"
                     /old_locus_tag="PIC71_24575"
                     /EC_number="2.3.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008322522.1"
                     /GO_function="GO:0016747 - acyltransferase activity,
                     transferring groups other than amino-acyl groups [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="acyltransferase family protein"
                     /protein_id="WP_096942834.1"
                     /translation="MKVTQSADSQPFNPPKAFRYDINGLRAWAVVAVVLYHFGVPGFAG
                     GFVGVDVFFVISGFLMTGIIITGLERGNFSLWGFYLARARRIIPALLVLCVSLLILGWF
                     WLPNADYRMLASHVGTAVVFISNVKFWREAGYFDAASHEKWLLHTWSLSVEWQFYILLP
                     LCCLLVWHWFGKRGVKLALVVAGLLSLALSIYVSERWPGAAFYLLPTRAWEMLAGGLVW
                     WGTRTQPMPRQWAALAELGGFVLIILAITTFDRGMLWPGYLALVPVVGAMLVLSANRQR
                     SWLTANFFASRLGASSYSIYLWHWPLVVLLTYIGEQSNSQWIVAGVFGSLLLGELSLRG
                     VENPARKGFAKLGIVAQGGLLAVMSGVVGLAVVSVFLGVKYSYPVFSQRLDAKVNIIAD
                     ESLNVKPRRDDCFVSSGVTSPACVYGGNKVKAILLGDSHADAVSSGLAASVLKNTDGIL
                     DLTYASCPTIFGLNVVSNDNSTKCKEFNSWAKEKISAYSSDIPLVIVNRTSVYAFGQHN
                     IKEQMNMPLSYFDIYNIKITDEFLNAYSDGLIESACELAKQRPVYIMRPIPEMMVDVPK
                     TMARALAFGKQSTEISISLEEYHARHKLVWDAQDVAAARCGVKILDPLPYLCHDGRCWG
                     SKNGRPIYYDDDHLSEYGNKLLVPMFKQVFVVQ"
                     /name="acyltransferase family protein"
     gene            4390..5898
                     /locus_tag="PIC71_RS24580"
                     /old_locus_tag="PIC71_24580"
     CDS             4390..5898
                     /locus_tag="PIC71_RS24580"
                     /old_locus_tag="PIC71_24580"
                     /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_074502197.1"
                     /translation="MLRDFLKEKEIGCIQYVFVYPNIPKNKVDNFSKYFSNGFLSQEKV
                     CLFLDDTVFGSGKEGVLFTENYLCRKRIFEPSLSLLISDIIRMECKGRSLYVNGDCFYK
                     FSTVSGKDLQHIVNVMNEWIGEEKAQKLPGSINNVSDIEMNCAPRKEDSDERQPIVADM
                     LIKFLSSNNSFIVEWISKNFKERILDYIDSDDALNKLTFVIYGKMPSALMPFVKPEDVR
                     NFIAKNKVDFLNAIGLCGETENRANVIAGQTAAIDVCKCDDNYSEENVENKKTKEIKRG
                     EPENYELAFSLLRDDDSSVNNVLRFITKISLRHMWDVFNSSPFPPVYRVKYKLAYDFYN
                     AISQMLCSIDIDETDEAFELQMAASLAIFPVMVFASVVHIKDNYPITNDVLDLFIENVE
                     VTLNACCCFYNNDSNREFFRQMSVSFVENALSRGNVLINEFIDAGVKGISITREDLDLL
                     CSEAIYATDEWIDAISKIELSENKGYIYGWRELLCTSPLDAFIG"
                     /name="hypothetical protein"
     Typing          1204..1429
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.583"
                     /coverage="99.0"
                     /evalue="1.05e-76"
     Typing          complement(404..929)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.925"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          1439..1758
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.37e-62"
ORIGIN
        1 actaagtaaa taataagctt gagaagcttt tcttttgctg ttatctcttc tttttaagaa
       61 aaaccgctag agtcggcggt ttttctggtt ttgttgacaa tcgttgtgtg acttaatcgt
      121 gagcgctctt ttagccaaaa aactaaagga tctcttgaga tccttttttt ctaagcgtaa
      181 tctgctgcct gtaaacgaaa aaaccaccct ggcaggtggt ttttcgaagg ttagctaatc
      241 ctggcagatt acctaaccgg gtaactggct tggtggagca cagataccaa atgctgtcct
      301 tctagtgtag cctcagttag gccaccactt caagaactct taatatctca atccaccttg
      361 tccagttacc aatggctgct gccagtggcg ataagtcgtg tctttccggg ttggactcaa
      421 gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg tgcacacagc
      481 ccagcttgga gcgaacgacc tacaccgaac tgagatacca acagcgtgag ctatgagaaa
      541 gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa
      601 caggagagcg cacgagggag cttccagggg gaaacgcctg gtatctttat agtcctgtcg
      661 ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc
      721 tatggaaaaa cgcctgcggt gctggcttct tccggtgctt tgctttttgc tcacatgttc
      781 tttccggctt tatcccctga ttctgtggat aaccgtatta ccgcctttga gtgagctgac
      841 accgctcgcc gcagtcgaac gaccgagcgt agcgagtcag tgagcgagga agcggaagag
      901 cgccttatgt gtcattttct ccttacgcac aggtataccg ttctgcatcc tgtctggtgc
      961 cggatatacc gttatacccc ggtgccactt tccgcttcaa agcgtgtctg tatgctgttc
     1021 tggagttctt ctgcgagttc gtgcagtttc tcacacatgg cggcctgtgc atcagcatcg
     1081 agtgagtcca gtttttcgag cagcgtcagg ctctggcttt ttatgaattt tgccatgttg
     1141 agtacagttt gctgctgctt gttcatcttt ctgctttctc cgttctgtct gtcatctgcg
     1201 tagtgtgatt atatcgcgca ccacttttcg accgtcttac cgccggtatt ctgccgacgg
     1261 acatttcagt cagacaacac tgtcactgcc aaaaaacagc agtgctttgt tggtaattcg
     1321 aacttgcaga caggacagga tgtgtaattg ttataccgcg catacatgca cgctattaca
     1381 attaccctgg tcagggcttc gccccgacac cccatgtcag atacggagcc atgttttatg
     1441 acaaaacgaa gtggaagtaa tacgcgcagg cgggctatca gtcgccctgt tcgtctgacg
     1501 gcagaagaag accaggaaat cagaaaaagg gctgctgaat gcggcaagac cgtttctggt
     1561 tttttacggg cggcagctct cggtaagaaa gttaactcac tgactgatga ccgggtgctg
     1621 aaagaagtta tgcgactggg ggcgttgcag aaaaaactct ttatcgacgg caagcgtgtc
     1681 ggggacagag agtatgcgga ggtgctgatc gctattacgg agtatcaccg tgccctgtta
     1741 tccaggctta tggcagatta gcttcccgga gagaaactgt cgaaaacaga cggtatgaac
     1801 gccgtaagcc cccaaaccga tcgccattca ctttcatgca tagctatgca gtgagctgaa
     1861 agcgatcctg acgcattttt ccggtttacc ccggagaaaa catctctttt tgcggtgtct
     1921 gcgtcagaat cgcgttcagc gcgttttggc ggtacgcgta atgtgacgtt atggtaaata
     1981 gtttgcttgt ttagctgcta aggataaaaa atggcgagca acatcaactt taatgcacgt
     2041 agaaagcaat tgaatcataa tgtggccctt tttttgcgct gtttgtcgac cattttgaca
     2101 aatctctgta gtaaatagtg gttatggaat gtcacttcat cctatgaaag taactcaatc
     2161 agctgattcc cagcctttta atccaccgaa ggcgtttcgc tacgacataa atggcctgcg
     2221 ggcttgggct gttgttgccg tggtacttta tcactttggc gtgcccgggt ttgccggtgg
     2281 ttttgttggg gttgatgtat tttttgttat ctctggcttt ttaatgactg ggattattat
     2341 caccggtctt gaacgtggaa acttttcgct gtgggggttt tatttagcgc gtgcgaggcg
     2401 gattattcca gcgctgttgg tgctctgcgt cagcttattg atattgggtt ggttctggtt
     2461 gcctaatgct gactacagga tgttggcatc ccatgttgga actgcggtag tgtttatttc
     2521 taatgtcaag ttctggcgtg aagctggcta ttttgatgct gcaagtcacg aaaaatggtt
     2581 attgcacact tggtcgctgt cggtggagtg gcaattttat attttattgc cgttgtgctg
     2641 tttattagtg tggcactggt ttggtaaacg cggtgtaaag ctggcgctag ttgttgctgg
     2701 attgctgtca ctggctttgt ctatctatgt cagtgagcgt tggcctgggg ctgcatttta
     2761 tctattaccg actcgtgcgt gggaaatgtt agccggtggt ttggtgtggt ggggcactcg
     2821 aactcaaccg atgccacgtc agtgggcggc attagctgaa ttgggcggtt ttgtgctgat
     2881 tatattggct attaccacct ttgaccgggg gatgctatgg cctggctatc ttgcgttagt
     2941 gccggtggtg ggtgctatgt tggtcttgtc cgctaatcga cagcgctcgt ggctaacagc
     3001 taactttttt gcgagtcgtc taggagctag ctcttactcg atctatctgt ggcattggcc
     3061 gttagtggta ttgctaactt atatcggtga gcaaagtaat tctcaatgga ttgtggctgg
     3121 ggtgtttggt tcgctgctat tgggtgaatt gtcgctgcgt ggggtagaaa atcctgctcg
     3181 taaaggtttt gccaaattag gtattgtggc gcaaggcggg ctattggctg tgatgtccgg
     3241 tgttgttggg ctggctgtag tgtcggtttt tctgggtgtt aaatattcat atccggtgtt
     3301 tagtcagcga ctggatgcaa aagttaatat tattgctgat gagtctctta atgtaaaacc
     3361 aagaagagat gattgttttg ttagctcggg tgttacgtct ccagcctgtg tttatggtgg
     3421 aaataaagtt aaagcaattt tacttggtga tagtcatgct gatgcggtat caagtggttt
     3481 ggcagcatct gtgttgaaaa atacagatgg aattcttgat ttaacatatg ctagttgccc
     3541 aactattttt gggttgaatg ttgtgagtaa tgataacagc accaagtgca aagagttcaa
     3601 ctcttgggca aaagaaaaaa tatcagcata tagctctgac attccattag tgattgtaaa
     3661 tagaacatct gtgtatgctt ttggtcagca caacatcaaa gaacagatga acatgccact
     3721 atcatatttt gatatttata atattaaaat aacagatgag tttttgaatg cgtattcgga
     3781 tgggttgatt gagagtgctt gtgaattagc taagcaaaga ccagtgtaca ttatgcgacc
     3841 tattcctgaa atgatggttg atgttcctaa aactatggct cgtgcactag cgtttggaaa
     3901 acaatccacg gaaatatcta tttcgctcga agagtatcat gctcgtcaca agttggtgtg
     3961 ggatgcacaa gatgtggctg cagctcggtg tggcgttaaa attcttgatc cactgccata
     4021 tttgtgccac gacggtcgct gctggggaag caaaaatggt cgaccaatct attacgatga
     4081 tgaccatttg agcgagtatg gaaataaact gcttgttccg atgttcaagc aggtatttgt
     4141 tgtgcagtag tggtttccaa ggcagccgct atggtggctg ccaatgttga tgggaaggct
     4201 atatttaact gcgtgtaatg cgacgttatg gtaaatatcc aagttttgcc gtatcgcatg
     4261 gaagtgcatg ctattgcaat gacacaatat tgttcgttgc taaaactggc ttttggaaga
     4321 tgatttgggt gatgctttat gtctttatgc aatagtcatt tatccacagt agattaagaa
     4381 ggtgatagga tgttaagaga ttttttaaaa gaaaaagaga ttggttgtat tcagtatgtg
     4441 tttgtatacc caaacattcc aaaaaataaa gtagataatt tttcaaaata tttttctaat
     4501 ggttttctat cgcaagaaaa agtctgtctc tttcttgatg acactgtatt tggtagtggg
     4561 aaagaaggag ttttatttac agagaactac ttatgtcgaa aaagaatatt cgaaccaagc
     4621 ttgtcgctgt taatttcaga tataataaga atggaatgca aaggacgttc tttatatgtt
     4681 aatggggatt gtttttataa gtttagtact gttagcggaa aagacttgca gcacattgtt
     4741 aatgtgatga atgaatggat tggcgaagaa aaagcgcaaa aattacccgg ttctattaac
     4801 aatgtaagtg acattgagat gaattgcgca cccagaaaag aagatagcga tgaacgccaa
     4861 cctattgtag ctgatatgtt gataaaattc ttatcatcaa ataatagttt tattgttgag
     4921 tggataagca agaattttaa agaaagaatt ttagattata ttgatagtga tgatgcgcta
     4981 aataaattaa cttttgttat ttatggtaag atgccatctg ctttgatgcc ttttgttaag
     5041 ccagaagatg ttagaaactt tattgcaaag aacaaagttg attttttaaa tgccattggt
     5101 ttatgcgggg agactgaaaa tcgagcaaat gttatagctg gtcaaactgc agcaattgat
     5161 gtctgtaaat gcgatgataa ttactcagaa gagaatgtgg aaaacaaaaa aacaaaagaa
     5221 ataaaaagag gggagccgga aaattatgag ttagcatttt ctttgttgcg tgatgatgac
     5281 tcctctgtta ataacgtatt acgttttatt acaaaaatat ctctaagaca tatgtgggat
     5341 gtttttaact cctctccatt ccctcctgtg tatagggtaa aatataagtt agcatatgac
     5401 ttctataacg caatatcaca aatgttgtgt tcgatagaca ttgatgaaac tgatgaagcc
     5461 tttgaattgc aaatggctgc tagtttggct attttcccag taatggtgtt cgcttctgtt
     5521 gttcatataa aagataacta tccaataact aatgatgttt tagacttatt tatagagaac
     5581 gtagaggtta cacttaatgc atgctgctgc ttttataata atgatagcaa tagagagttt
     5641 tttagacaaa tgtcagtgtc ttttgttgag aatgctttat cgcgtggaaa tgttttgatt
     5701 aacgagttta ttgatgctgg ggtcaaggga atatccatta cgagagaaga tctggattta
     5761 ttatgttcag aggcaatata tgcaactgat gagtggattg atgctatatc taaaatagaa
     5821 ttatcagaaa ataaaggtta tatctacgga tggagagaat tgctgtgcac atcgccatta
     5881 gatgcattta ttggataatt tat
//
