LOCUS       NZ_CP120565             5159 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Escherichia coli strain H22 plasmid pH22_5159, complete sequence.
ACCESSION   NZ_CP120565
VERSION     NZ_CP120565.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33748625
            Assembly: GCF_029536635.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5159)
  AUTHORS   Fedrova,P., Hrala,M., Micenkova,L., Tom,N., Bosak,J. and Smajs,D.
  TITLE     Complete genome sequences of five Escherichia coli strains with
            probiotic features
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5159)
  AUTHORS   Fedrova,P., Hrala,M., Micenkova,L., Tom,N., Bosak,J. and Smajs,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-MAR-2023) Department of Biology, Masaryk University,
            Kamenice 5, Brno 62500, Czech Republic
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 368x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029536635.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:38:59
            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)                     :: 5,062
            CDSs (total)                      :: 4,945
            Genes (coding)                    :: 4,743
            CDSs (with protein)               :: 4,743
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 202
            CDSs (without protein)            :: 202
            Pseudo Genes (ambiguous residues) :: 0 of 202
            Pseudo Genes (frameshifted)       :: 86 of 202
            Pseudo Genes (incomplete)         :: 125 of 202
            Pseudo Genes (internal stop)      :: 45 of 202
            Pseudo Genes (multiple problems)  :: 48 of 202
            Pseudo Genes (short protein)      :: 2 of 202
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP120565.1.
            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..5159
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="H22"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pH22_5159"
                     /geo_loc_name="Czech Republic"
                     /collection_date="1978"
     gene            join(4278..5159,1..690)
                     /locus_tag="P5708_RS25265"
                     /old_locus_tag="P5708_25265"
     CDS             join(4278..5159,1..690)
                     /locus_tag="P5708_RS25265"
                     /old_locus_tag="P5708_25265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_012882752.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGSGGGGGTGGS
                     KSESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEAL
                     RHNSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEK
                     EQAETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSS
                     SIHARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARA
                     GDEMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTAQTN
                     LLNSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKD
                     VLNKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDT
                     GDWKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTI
                     NEVLGI"
                     /name="colicin-like pore-forming protein"
     gene            1076..1213
                     /locus_tag="P5708_RS25270"
                     /old_locus_tag="P5708_25270"
     CDS             1076..1213
                     /locus_tag="P5708_RS25270"
                     /old_locus_tag="P5708_25270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001329514.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVAPSSSSKLTGISVQ
                     "
                     /name="colicin release lysis protein"
     gene            complement(2055..2249)
                     /locus_tag="P5708_RS25275"
                     /old_locus_tag="P5708_25275"
     CDS             complement(2055..2249)
                     /locus_tag="P5708_RS25275"
                     /old_locus_tag="P5708_25275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2533..2856
                     /gene="mobA"
                     /locus_tag="P5708_RS25280"
                     /old_locus_tag="P5708_25280"
     CDS             2533..2856
                     /gene="mobA"
                     /locus_tag="P5708_RS25280"
                     /old_locus_tag="P5708_25280"
                     /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            complement(3081..3500)
                     /locus_tag="P5708_RS25285"
                     /old_locus_tag="P5708_25285"
     CDS             complement(3081..3500)
                     /locus_tag="P5708_RS25285"
                     /old_locus_tag="P5708_25285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(3581..4018)
                     /locus_tag="P5708_RS25290"
                     /old_locus_tag="P5708_25290"
     CDS             complement(3581..4018)
                     /locus_tag="P5708_RS25290"
                     /old_locus_tag="P5708_25290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024247033.1"
                     /translation="MGHCNFMAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTQGHSEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERRRQEAERKQLQNEIAQLRQALEQEKKRGFWSRLSGH"
                     /name="hypothetical protein"
     Typing          2285..2524
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(1497..2026)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.776"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2534..2853
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.11e-62"
ORIGIN
        1 tcagaaacgc gtcttaacca gattagctct gagataaatg gaatccaaga ggctatttct
       61 caggctaata ataagcgaag tacagcagtt tcacgtattc atgatgctga agataatttg
      121 aaaacagcac agactaatct cctgaactcg cagattaagg atgctgtgga tgcaacagtt
      181 agcttttatc aaacgctatc tgaaaaatat ggtgaaaaat attcaaaaat ggcacaggaa
      241 cttgctgata aatctaaagg taagaaaatc agcaatgtga atgaagctct agctgctttt
      301 gagaaataca aggatgtatt aaataagaaa ttcagcaaag cagaccgtga tgcaattttc
      361 aatgcactgg aggcggttaa gtatgaagac tgggctaagc atttagatca gtttgccaag
      421 tacttgaaga ttacgggaca tgtttctttt ggatatgatg tggtatctga tatcctaaaa
      481 attaaggata caggtgactg gaagccgcta tttcttacat tagagaagaa agctgtagat
      541 gctggagtta gttatgttgt tgttttactt tttagtgtgc ttgctggaac tacattaggt
      601 atctggggga ttgctattgt tacaggcatt ctatgtgcct ttattgataa gaataaactt
      661 aatactataa atgaggtgtt gggtatttaa ttattcttta ttgatataaa cagtcctagc
      721 aatccaaatg ggattgctag gaccaaacaa agtagattgt atagcataaa taggtttaat
      781 tttgccacgg gggcattatt taggtttttt ctttttctga aaaaatcttt ctttatgaac
      841 ttaaaaaata tgtgttcaat agcatatttt gaatatgggc atagaatagt gcttatcact
      901 attgcgtata gcatcttatc tgacgctagg aaataatacc cttcgttgtt ttttgttata
      961 aggtatatat atataagtgc gcagtatagg ccaaacaaaa tattttttat gtagtatctt
     1021 aaactcataa attaaacctc gttatatatt cttttcattt tataaggatc gagttatgag
     1081 gaaaagattt tttgtgggaa tattcgctat aaacctcctt gttggatgtc aggctaacta
     1141 tatacgtgat gttcagggag ggactgtggc tccatcatct tcttctaaat tgacggggat
     1201 ctctgttcag tagaaaagat caaaggatct tcttgagatc ctttttttct gcgcgtaatc
     1261 tgctgcctgt aaacgaaaaa accgcctggg gaggcggttt gatcgaaggt taagtcagtt
     1321 ggggaactgc ttaaccgagg taactggctt cagcagagcg cagataccaa atactgtcct
     1381 tccagtgtag ccgtagtcgg gccactactt caagaactct gttgcaccat ttgcgccatc
     1441 atcgctctgc taaccaagtt accaacggct gctgccagtg gcgctaagtc gtgtcttacc
     1501 gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
     1561 tcgtgcacac agcccagctt ggagcgaacg acctacaccg agctgagata ccaacagcgt
     1621 gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaagc
     1681 ggcagggtcg gaacaggaga gcgcacgagg gagcttccag ggggaaacgc ctggtatctt
     1741 tatagtcctg tcgggtttcg ccacctctgg cttgagcgtc gatttttgtg atgctcgtca
     1801 ggggggcgga gcctatggaa aaacgcctgc ggcgctggct tcttccggtg ctttgctttt
     1861 tgctcacatg ttctttccgg ctttatcccc tgattctgtg gataaccgta ttaccgcttt
     1921 tgagtgagct gacaccgctc gccgcagtcg aacgtccgag cgtagcgagt cagtgagcga
     1981 ggaagcggaa gagcgcctta tgtgacattt tctccttacg ctctgttgtg ccgttcggca
     2041 tcctgtcctg agcgttatct ctctgtgcta ttttctactt caaagcgtgt ctggatgctg
     2101 ttctggagtt cttctgcgag ttcgtgcagc ttctcacaca tggtagcctg ttcgtcagca
     2161 tcgagtgcgt ccagcttttc gagcagcgtc aggctttggc tttttatgaa tcctgccatg
     2221 ttgagtacgg cttgctgctg cttgttcatc ttttcgtttt ctccgttctg tctgtcatct
     2281 gcgttgtgtg attatatcgc gtaccacttt tcgactgttt taccgccggt attctgccgt
     2341 ctgacgcttt gacgggtatt tctgcctgac aatactgtca ctgccaaaaa actgccgtgc
     2401 ctttgtcggt aattcgaact tgctgacagg acaggatgtg taattgttat accgcgcata
     2461 catgcacgct attacaatta ccctggtcag ggctttgccc cgacacccat gtcagatacg
     2521 gagccatgtt ttatgacaaa acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc
     2581 cctgttcgtc tgacggcaga agaagaccag gaaatcagaa aaagggctgc tgaatgcggc
     2641 aagaccgttt ccggtttttt acgggcggca gctctcggta agaaagttaa ctcactgact
     2701 gatgatcggg tactgaaaga agttatgaga ctgggggcgt tacagaaaaa actctttatc
     2761 gacggcaagc gtgtcgggga cagggagtat gcggaggtgc tgatcgctat tacggagtat
     2821 caccgtgccc tgttatccag gcttatggca gattagcttc ccggagagaa aactgtcgaa
     2881 aactgacggt atgaacaccg taagctccca aagtgatcac cattcgcttt catgcatagc
     2941 tatgcagaga gctgaaaacg atcctgacgc atccttcctg tttttccggg gtaaaacatc
     3001 tctttttgcg gtgtctgcgt cagaatcgcg ttcagcgcgt ttcagtggtg cgtacaatta
     3061 agggattatg gtaaatccac ttactgtctg ccctcgtagc catcgagata aaccgcagaa
     3121 atcgtgtcag ccagcagcct ggattttttc ggggtaaggt ctttgctgcg gtaatcagta
     3181 cccgcaaatt gagttgtgcc ccggagtgag tttaaaaatt cctggctgtg aaactgttga
     3241 atgcgttgtt gcacatcact ccgtgatttt cctgtcgctt tatctttagc tcccatatcc
     3301 cagaactgcc gaaaaaaagg caccatcatt cgtgttgtgt cggctttttg ggtggaaaag
     3361 ttgggatcaa aaccgtcatc agaagcatat acgtaatgcc gggtatgttg ttccacgctg
     3421 ccctttgggg tacaggctgt gagagctact gttgctgtta tcatggcgat aagacaaagt
     3481 ttgtttccgg tacgtctcat gagtgtctcc ctaccttaaa gtatttattc tcggtgagtt
     3541 attatccgaa gattatctta tcatcagttt ctgagcgcgt tcagtgaccg gacagcctgg
     3601 accagaatcc ccgtttcttt tcctgctcca gagcctgcct gagctgggct atctcattct
     3661 gtagctgttt ccgttctgct tcctggcgcc ggcgctccgt atcctgggct tgtttatcct
     3721 caagcatcag cgtcaggcat tgtttcagct cattcagttc ccggagaatg cgttctgtct
     3781 gctgatcatg aggtttttct gagtgtcctt gagtgtgcct ttctggtgtc tcattccgct
     3841 ttaattcgcc gtatgcccgg atcagttcac tggtttcaaa ctcccgtcgt ccgtcctggc
     3901 tggtacggta actgacaaga cctgagcgca tatcacggta aaactgtgaa cgcgatcttc
     3961 cagtcatttt cagtgcgtcc cggagtgtgt gccatgccat aaagttacag tgtcccatag
     4021 gtgtctcatc tcatggtttc agtaaaacat aatgaggtct gagaacggta atgtttgtgc
     4081 tggtttttgt ggcatcgggt ggaaatagca cgtggtgtgg gtggctgttt ttttgatcgt
     4141 tttcacaaaa atgaaaatcc acagggttga cagggaaaat gcagcggcgt aattttaaac
     4201 tgtatataaa accagtgatt atatatacag tatattgctt ttaactattt gtttttaatg
     4261 tcaaagagga ttttataatg gaaacagctg tagcgtacta taaagatggt gttccttatg
     4321 atgataaggg gcaggtaatc attactcttt tgaatggtaa tccagacggg agtggctctg
     4381 gctctggcgg tggtggtgga actggaggta gcaaaagtga aagttctgca gccattcatg
     4441 ccacagctaa atggtctact gctcaattga agaaaacgca ggcagaacag gctgcccgag
     4501 caaaagctgc cgcagaagca caggctaaag caaaagcaaa ccgggatgcg ctgactcaac
     4561 atctgaagga tattgtgaat gaggcgcttc gccataattc cactcatccg gaggttattg
     4621 acctggctca tgccaataat gcagcgatgc aggcagaagc agagcggttg cgccttgcaa
     4681 aagcagaaga aaaagcccgt aaagaagcgg aagctgcgga aaaggctttt caggaagcag
     4741 aacaacgacg taaagagata gagaaggagc aggctgaaac agaacgccaa ttgaaactgg
     4801 ctgaggatga agagaaacgc ctggcagcat tgagtgaaga ggcccgggct gtggaggtgg
     4861 cacaaaaaaa tcttgctgct gcacaatctg agctggcgaa agtggatgaa gagattaata
     4921 cgctcaatac ccgtttaagc tccagtattc atgcccgtga tgcagaaacg aatacgctgt
     4981 ccggaaaacg aaatgagttg gatcaggcat ctgctaaata taaagaactg gatgaaaggg
     5041 ttaaactttt atctcctagg gcgaatgatc cgcttcagag tcgtcctttt tttgaggcca
     5101 ccagactacg ggcgagagct ggtgatgaga tggaggaaaa acaaaagcag gtaacagca
//
