LOCUS       NZ_CP121089             4073 bp    DNA     circular CON 26-MAY-2024
DEFINITION  Escherichia coli strain ST3 plasmid p4kb, complete sequence.
ACCESSION   NZ_CP121089
VERSION     NZ_CP121089.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33902174
            Assembly: GCF_029623635.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4073)
  AUTHORS   Gaibani,P. and Amadesi,S.
  TITLE     Complete genome sequence of an Escherichia coli strain isolated from
            a neonatal intensive care unit in Northern Italy
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4073)
  AUTHORS   Gaibani,P. and Amadesi,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-MAR-2023) Microbiology, Policlinico
            Sant'Orsola-Malpighi, Via Massarenti 9, Bologna, BO 40138, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 13-MAR-2023
            Assembly Method                   :: Unicycler v. 0.5.0
            Assembly Name                     :: ecoli1455
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 160.0x
            Sequencing Technology :: Illumina iSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029623635.1-RS_2024_05_26
            Annotation Date                   :: 05/26/2024 06:40:51
            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)                     :: 4,980
            CDSs (total)                      :: 4,864
            Genes (coding)                    :: 4,712
            CDSs (with protein)               :: 4,712
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 152
            CDSs (without protein)            :: 152
            Pseudo Genes (ambiguous residues) :: 0 of 152
            Pseudo Genes (frameshifted)       :: 57 of 152
            Pseudo Genes (incomplete)         :: 109 of 152
            Pseudo Genes (internal stop)      :: 31 of 152
            Pseudo Genes (multiple problems)  :: 38 of 152
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP121089.1.
            Bacteria and source DNA available from Policlinico
            Sant'Orsola-Malpighi, Via Massarenti 9, 40138, Bologna (Italy).
            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..4073
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ST3"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4kb"
                     /geo_loc_name="Italy: Verona"
                     /lat_lon="45.45227 N 10.98564 E"
                     /collection_date="2022-12-06"
                     /collected_by="Azienda Ospedaliera Universitaria Integrata"
     gene            join(3822..4073,1..450)
                     /locus_tag="P5670_RS24870"
                     /old_locus_tag="P5670_24870"
     CDS             join(3822..4073,1..450)
                     /locus_tag="P5670_RS24870"
                     /old_locus_tag="P5670_24870"
                     /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"
     gene            complement(708..2855)
                     /gene="mobQ"
                     /locus_tag="P5670_RS24875"
                     /old_locus_tag="P5670_24875"
     CDS             complement(708..2855)
                     /gene="mobQ"
                     /locus_tag="P5670_RS24875"
                     /old_locus_tag="P5670_24875"
                     /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            3034..3288
                     /gene="mobC"
                     /locus_tag="P5670_RS24880"
                     /old_locus_tag="P5670_24880"
     CDS             3034..3288
                     /gene="mobC"
                     /locus_tag="P5670_RS24880"
                     /old_locus_tag="P5670_24880"
                     /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"
     Typing          complement(2498..2856)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2857..3033
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2..441
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.261"
                     /coverage="99.0"
                     /evalue="8.53e-132"
     Typing          3823..4073
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.85e-128"
     Typing          complement(712..2942)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atcatcaaga acgaggaaaa acgagaagag ttccgctggg tgcagtaccg ggcgcagtat
       61 ttcaaaggtg aggcgaaagt agatatcacc ttctccgatg ccatcatgcc gtatctgaca
      121 cagctcaagg ggcagtttac gcgggtagtc gtgaagaacg tctccagcct ttccagcacc
      181 tacagcatcc gcatttacga gctgctccag cagttccgca gcaccggtga cagaacgata
      241 gctatcgatg atttccgaac catgcttgcc gttgaagata aatatcaaca attcaaagac
      301 ttgaataaga tgataatcaa gccagccatc gccgaactga acgaaaaaag cgatctggtt
      361 gtaactgttg agacgatcaa aaaggggcgc acggttgtag ccctgcattt tcgcttcaag
      421 gaagacaaac agatcaagat gacgatctaa aatcgatttt aaggcaccta aaacgctccc
      481 tgctgcgttt tttttgtgtt agtagtgcga aggtactatt gaagtgaaaa attgcgtcaa
      541 aaacgctctg atgcagcgaa aaaagacccc ccaatttttg ggggcggaaa aacaaaacta
      601 tgcttgcgtt atgtgagtgt gcttcttgca ttcatccctg tcgatgaaca tcgaagaaca
      661 tcgacgaaca taacacgatg ttaaacaaaa caaaatattg ttcacattca ctgtgaccaa
      721 ccgcgatcat gtctcctctc ggtggtgtgt gttcgtgcat cttcctcgcg ctgccattcc
      781 tcccaggtac gattaaaacc cagcgagcgg aacagatgat ccggctgttt ttctggtgtg
      841 ttgacggcag caaaaagcgg tgcctcacgg gttttcagat gaaactgcat cagttctggt
      901 gcaggtgata tgtggctgtc tgcatcgtga tttacggcaa caccataccc tgcataccgt
      961 aaccccttat cggtcagcgc actgatgacc agatgcctgt tatcggctga gggaacggca
     1021 aacgcgggat acagcgtacc attaagccgg ataacaccgc ccagagagtc atccacgccc
     1081 atgaccagca aaagctgaag ctggcgggtt tcccggtcga cagaactcat gaccggcatc
     1141 agcgtcggtg gcagacgtcc ctgcataaaa tccaccttcc ttgccgctgg tgatggcatg
     1201 gctggctggc ggtcttctcc aagacagaaa gactccggcc atgtcttcgg ctggcggaga
     1261 ttgcgggtat gttgcggcca tgtctggcaa acctgcgtca gcagttgctc aaaggttgca
     1321 gaggaataaa cacgttgcag tggcggacgt tggccgattt cgcttcggtc acagatataa
     1381 ccactcctgt cacgcattaa atcaacactc tcaaagattc tggtgcggta tttctccagc
     1441 tcgttccccc agagcgtata ttctccgttc cggttgtgaa gcagaaggta acaggtcatt
     1501 tccccgttac caggcatggg agcctcgcca taccccgtaa cgactgctct cagcacccct
     1561 gaatccataa cggcattgtc atttttcctg agctgctccg cgcgactacg ttcagtatct
     1621 tcctgttcct tccggcgcaa ttcctcttca cgtttaagca actgggctct gagagctgca
     1681 aggccggatt ccccccactg ctgccactgt ttttcaaatg ccatctgact cgcgggaatg
     1741 tcctgtttct ccaccttccg gtaatgctgt cgtaattttt ccatttgctg gctcagagac
     1801 tggatttttc cctgctcact acggtattcc ggtgccgccc attgcatcag gggaatacgg
     1861 gaaaaaccgg acgaaaacgg cgatgatttt ttcaggctgg cagcatggct catcgcttcc
     1921 tttcgttcgg tgttcagctc ttcccagcgt ctgcgcgtcg cctgcatatc tgccatcatc
     1981 gacatggcat tactggtgag tttccatgcc gagttactgt ccttcggcaa cgcttcgata
     2041 atgtcacgta gtgtgtacga agttgcgttg tcaggaagcc cgatattcag aaggtcagcc
     2101 acacggcggg caggctctgt cagccctccg ttcctgagtt cggtgcggga aatctgtatt
     2161 tccaggttaa gcctgttaat cagacgattc tgttcgccgc gttctgtttc gataccgcgt
     2221 gtttccatcg cacaggcaga ctttccgagg tgaataccag gcgttttctc aagcccctgt
     2281 cgctcgtatg aacgatggtc tatctcttcc tgataaccgg cgttcgccag tgccctgttt
     2341 gcatggtcag cccatgatgc ccgccacgtc tcggcatgtg tccggtcgtt ccagtccctg
     2401 acctttccgc tgaacccagc aggtccgata gccctcgtgg tcagcatgat gtgcgcatgg
     2461 ggatttgttt tatccatgtg atggaacgcc acatcagcaa tcatgccctg actgacaaag
     2521 ttttctctga caaaggcgag aacggtttcc cgtgcggcat cctgcggcag ttcgtggggg
     2581 atggcgagtt caatttcccg cgcaagttgt gagttcttcc ggcgttcggc cttctcaacg
     2641 gcattccaga gttcggcacg gttcgtacac caggcagggg cggtggcggg ggtcagaatc
     2701 acagcctcag ccacaccgct tttgcgggtg tagtcgtgag tcagtccggt acgctcatca
     2761 agcatcagtg aaccggaacg ataggcagcg gaagctacgg cgctgtagcc gctgcttctg
     2821 gagataattt tcatgctgag atgataaatc gccatttctg ccgtaatgcc tttttgtagt
     2881 tttctttcag ccccgcaggg cgcacacaat cgaaacggag tggagattgt ataagtgcgc
     2941 acttcgtgat ttgccgtgca ttatgccagc tcagttttta aactaccagt gacgcgctaa
     3001 aatgcgattt ttcatcgcgc acggagttac atcatgagca gaacgctcga acagaagatt
     3061 gctgatgctg aggcgagatt acagcgcctg aaggcgaaga gccggagcct ggacacagcg
     3121 cagaaggttg ttgtgggtgc tgcattgctg gcaaaggtca gaaagccgga ggaggtgcag
     3181 ttgcgtgcct ggttactcca gttcctgaag gcagaggtga cacgacaggc tgatgtgacg
     3241 cgcatactgc cgctgattaa cgagctggag gcgctgccag aacagtgatt gtatcgtccg
     3301 ctcgccgcag ccccagcgac cgagcgttag cgagcgagtg ggcgaggaag cggaagtgaa
     3361 tcagtcgcca ggttgagcac atacgcacgg tttttcggca ggtgatatgc gctgaacccg
     3421 catgaatact gggtttccac agggttggag ggggtgtatt cgaaacttgc aattctgctt
     3481 tattgcaacg cattgttttt attggttttt tgttttcagc accccaagtt atccacaggc
     3541 tcgccgttaa gtttttaaga tcttattttt agatcttttt ttttaaaacc tttttaggtc
     3601 ttgtaacacc atgattttaa agatgttctg gcaagataag tggagctttt gggggtgaaa
     3661 ggtggagctt ttgggggtga aaggtggagc ttttgggggt gaaaggtgga gcttttgggg
     3721 gtgtaatcca cagaaaaagg gggttgcaaa aaaaaaactt ccacctatat gataagtggc
     3781 gtacagtaaa aaaacgccac caatagcaac gagcaagcga aatgtcagat ctgatagctt
     3841 acaaatcaaa cgcccttatc gaggcaagct acaagctcac tttgcaggaa cagcgcttcc
     3901 tgctggtctg tatcagccgc ctaaaatccg gagaagattc cccttcgccg gatgaacaaa
     3961 aaaccatgac catcacggct gcagagtttc atgatgcctt tcctgacatg ggacggcagc
     4021 acgctgaagc taggctcaag gaagcgatag atcgcctctg ggacaggtca gta
//
