LOCUS       NZ_CP069628             5514 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ESM1.4 plasmid pMUT2, complete sequence.
ACCESSION   NZ_CP069628
VERSION     NZ_CP069628.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17732898
            Assembly: GCF_023206635.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5514)
  AUTHORS   Kan,A., Emani,S., Daniel,B.P. and Joshi,N.S.
  TITLE     Directed evolution of an Escherichia coli secretor strain
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5514)
  AUTHORS   Kan,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-FEB-2021) Wyss Institute for Biologically Inspired
            Engineering, Harvard University, 3 Blackfan cir., Boston, MA 02115,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2021
            Assembly Method                   :: breseq v. 0.35.5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: GCA_003546975.1
            Genome Coverage                   :: 28.9x
            Sequencing Technology             :: Illumina HiSeq 4000
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023206635.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 04:11:34
            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)                     :: 4,860
            CDSs (total)                      :: 4,746
            Genes (coding)                    :: 4,525
            CDSs (with protein)               :: 4,525
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 221
            CDSs (without protein)            :: 221
            Pseudo Genes (ambiguous residues) :: 0 of 221
            Pseudo Genes (frameshifted)       :: 92 of 221
            Pseudo Genes (incomplete)         :: 140 of 221
            Pseudo Genes (internal stop)      :: 54 of 221
            Pseudo Genes (multiple problems)  :: 54 of 221
            Pseudo Genes (short protein)      :: 2 of 221
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069628.1.
            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..5514
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ESM1.4"
                     /isolation_source="laboratory evolution"
                     /db_xref="taxon:562"
                     /plasmid="pMUT2"
                     /geo_loc_name="USA: Boston, MA"
                     /collection_date="2019-05"
     gene            complement(join(5275..5514,1..408))
                     /gene="kwaA"
                     /locus_tag="JSQ89_RS24165"
                     /old_locus_tag="JSQ89_23920"
     CDS             complement(join(5275..5514,1..408))
                     /gene="kwaA"
                     /locus_tag="JSQ89_RS24165"
                     /old_locus_tag="JSQ89_23920"
                     /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="anti-phage protein KwaA"
                     /protein_id="WP_024199421.1"
                     /translation="MKIRMYLLSMLFLFIPITIYFSGIDNVWSVLDKAMSSCSGADGKF
                     QCVLDYSNSRLTFSVLRSVICGALILTCSYTYIWYRWVLKNLDSGAVSRKLKVVSCKKE
                     SGEYLSFLSTYIMPLVFTDLSKPSNIVNFLFVLIIVGFLHIKTKRIHCNPTLSLFNVSA
                     YKITYSVVANGREKTQDGELIVLSKDLIKENDFIRVINHDDYLTFAKKIIEE"
                     /name="kwaA"
     gene            complement(398..1294)
                     /locus_tag="JSQ89_RS24170"
                     /old_locus_tag="JSQ89_23925"
     CDS             complement(398..1294)
                     /locus_tag="JSQ89_RS24170"
                     /old_locus_tag="JSQ89_23925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674370.1"
                     /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_024199422.1"
                     /translation="MDNQALTLFNDRLPHKPYFSDDLQFGVRIAGKERALLAKYIQFNQ
                     PHAMYWLCFDVDRAGAAIDWADLGAPAPTLTIKNPENGHAHLLYALHTAVRTAPDGRAA
                     PLKYAAAIENALRKKLGADAGYSGLICKNPNHLHWQITVWQPELYTLDWLADYLDLGAA
                     NDREILPDYGLGRNCTLFDKTRKWAYRAIRQGWPQYDQWLQACIERAKAYNLQFSAPLD
                     ENEVMGIAKSVAKWTSKNLTELGFEEYVKQTHTSEIQRQRGKKSSGGGRPKVRDGEWIS
                     LGISRSTWYRKFYKNEN"
                     /name="replication initiation protein"
     gene            1559..1801
                     /locus_tag="JSQ89_RS24175"
                     /old_locus_tag="JSQ89_23930"
     CDS             1559..1801
                     /locus_tag="JSQ89_RS24175"
                     /old_locus_tag="JSQ89_23930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020301039.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
                     /protein_id="WP_001554710.1"
                     /translation="MATINIRIDDELKSRSYAALEKLGVTPSEVLRQTLEYVAQSGRLP
                     FQQVLLTEDDADLMAIVRDRLENPQAGVKVSLDEL"
                     /name="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
     gene            1791..2075
                     /locus_tag="JSQ89_RS24180"
                     /old_locus_tag="JSQ89_23935"
     CDS             1791..2075
                     /locus_tag="JSQ89_RS24180"
                     /old_locus_tag="JSQ89_23935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016149473.1"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_001554709.1"
                     /translation="MSYNLEFDPRALKEWRKLGDDVRLQFKKKLEQVLQHPRIDKNRLR
                     ELHDCYKIKLRASGYRLVYQVRDQTITVFVVAVGKRERSAAYDAADKRL"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(2120..2353)
                     /locus_tag="JSQ89_RS24185"
                     /old_locus_tag="JSQ89_23940"
     CDS             complement(2120..2353)
                     /locus_tag="JSQ89_RS24185"
                     /old_locus_tag="JSQ89_23940"
                     /inference="COORDINATES: protein motif:HMM:NF016769.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_001554708.1"
                     /translation="MTEMEQQLLSALESLQRHYEQQQQAWQDSYANLQRMFEVTSQELA
                     KNDRVCQALSMQVTGLAQQVESLNRTVRRLSN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(<2901..3587)
                     /locus_tag="JSQ89_RS24190"
                     /old_locus_tag="JSQ89_23945"
                     /pseudo=""
     CDS             complement(<2901..3587)
                     /locus_tag="JSQ89_RS24190"
                     /old_locus_tag="JSQ89_23945"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3577..3903)
                     /locus_tag="JSQ89_RS24195"
                     /old_locus_tag="JSQ89_23950"
     CDS             complement(3577..3903)
                     /locus_tag="JSQ89_RS24195"
                     /old_locus_tag="JSQ89_23950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001554615.1"
                     /translation="MEKRTKEIKIRLTEAEHQRLLERCDRKHLAEWLRAVGLGESRTAR
                     RRPLPTVDPTLLRQVSGIGNNLNQIARYLNQHGLPPQERVSLLAVLNSIDQHLAELLEQ
                     HRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(4130..5272)
                     /locus_tag="JSQ89_RS24200"
                     /old_locus_tag="JSQ89_23955"
     CDS             complement(4130..5272)
                     /locus_tag="JSQ89_RS24200"
                     /old_locus_tag="JSQ89_23955"
                     /inference="COORDINATES: protein motif:HMM:NF027488.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Kiwa anti-phage protein KwaB-like
                     domain-containing protein"
                     /protein_id="WP_001704287.1"
                     /translation="MSDDALDLDALEHNEEKAQELLELYKHFDCDINDVTLHTYFNFKN
                     KGKAGAKDSFSYKIAILKNDSELKQSIIDNVIKKTISDLENRVVIVSDVNTLSDRTNTI
                     SFLNDAEQYDNEQMKFLTGIVFDAGFGGDGNENIPIVDFDSVDLISKVDSIIFVLSKNN
                     DDNCITIYKKQYPVQNLSRKKNNFYGFSKKELSRVDQDMISIDGKASLVFAGDTVFIYD
                     QNVFERFFGYKAWIKNAATDFVNNMSTRFKGFVDLSKFIERVNKDSHDADAFSRKLAKA
                     YARSETKQTLQTITNEHLKSVLDENGYLAGVLKYKKGDATICIASHNQQDTFIAMVSEG
                     VLRSLITGIDYLSLGSKRKISSAASNTTTSTTSDSSSAAV"
                     /name="Kiwa anti-phage protein KwaB-like domain-containing
                     protein"
     Typing          complement(399..1432)
                     /name="rep_cluster_2486"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2074..3587)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.802"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aacaaacaaa aaattaacta tatttgatgg tttgcttaaa tcagtaaaga ccaacggcat
       61 tatgtacgtt gataaaaaag aaagatactc accggattct tttttacatg aaacgacctt
      121 taactttctt gacaccgcac cggagtctaa gtttttcaaa acccatcgat accaaatgta
      181 tgtataagaa caagttaaaa tcaaagcccc gcagatcact gacctcaata cagaaaatgt
      241 taatctgcta tttgaatagt cgagtacgca ttgaaatttt ccatccgcgc cagaacacga
      301 agacatggcc ttatctaaaa cagaccatac gttatcaata ccagaaaaat atattgttat
      361 cggtataaat aaaaacaaca ttgataagag atacattcta attttcattt ttgtaaaatt
      421 tcctgtacca cgttgatcta cttattccta aagaaatcca ttctccatct ctaactttcg
      481 gccttccacc accagagctt ttttttccac gttgacgctg aatttcagaa gtatgtgttt
      541 gtttaacata ctcttcaaag ccaagctctg taaggttctt acttgtccac ttagccacac
      601 ttttagcaat tcccatgact tcgttctcgt ctaaaggtgc ggagaactgc aggttgtagg
      661 ctttagcgcg ttcaatgcag gcttgtagcc attggtcata ctgcggccag ccttggcgga
      721 tagcgcggta agcccacttg cgggttttat cgaagagggt gcagttacgg cctaaaccgt
      781 agtccggcag gatttcgcgg tcattggctg cgccaaggtc gaggtaatcg gctaaccagt
      841 caagggtata gagctctggc tgccagacgg tgatctgcca gtgcaggtgg ttcggattct
      901 tgcaaattag ccctgaatac cccgcatctg cgcccaattt tttacgcagc gcattctcga
      961 tggcggcggc gtatttaagg ggggcagctc gaccatccgg cgcggtacgt accgccgtat
     1021 gcaaggcata caacaggtga gcatgtccgt tctcggggtt tttgatggtg agtgtgggcg
     1081 caggtgcccc cagatcggcc caatcaatcg cggctccggc tctgtccacg tcaaagcaaa
     1141 gccagtacat ggcgtgaggc tgattaaact ggatgtattt tgcgaggaga gcacgctctt
     1201 taccggcaat gcgaacacca aactgtaaat catcggagaa gtacggcttg tggggtaacc
     1261 ggtcgttaaa aagcgttaaa gcctgattat ccaaggctcc cagccttatg gcggggctgt
     1321 tgttttgcac gctgcatgtg ctaatatcct ttctaggttt cgacctagcc ctgaatgtca
     1381 tgtccgctcg ccaaagtaga gcatgatttc ggggctttgt tttttctgcc actaagttac
     1441 acctcaacaa cggtttttgt catccccgac aatccgttat tcctgcttgt tctcgcacgg
     1501 ctttacgctc atactacttc ttgtagatac acttgtcact acatcaagag gtgagatgat
     1561 ggccacgatt aatattcgga tcgatgacga gctgaaaagc cgctcttatg ccgcactgga
     1621 aaagctgggc gtaacgccgt ccgaggttct gcgccaaaca ctggaatatg tggcccaaag
     1681 cggacgtttg ccgttccagc aggttttgct gaccgaggat gatgccgatt tgatggctat
     1741 cgttcgggat cgtctggaaa acccacaggc gggcgtaaag gtgtcactgg atgagctata
     1801 accttgaatt tgatccccga gccctgaagg aatggcgcaa gctcggggat gatgtccgtc
     1861 tgcagttcaa gaaaaaactc gagcaggttc tacaacaccc gcggatcgat aaaaatcgcc
     1921 tgcgagagct gcatgactgc tacaaaatca agctccgtgc atccggttat cgcttggtct
     1981 atcaggttcg cgatcaaacc attacggtat tcgtggtggc ggtcggtaag cgcgagcgtt
     2041 ctgccgctta cgatgcggcc gataaacgct tataaactca tgccgtgacc gcgagaatac
     2101 cgctgttcgt gccgcttggc taattgctca agcggcgcac tgttctgttt aagctctcga
     2161 cttgctgcgc caagccggtg acttgcatgc tcaaggcctg acaaaccctg tcgtttttcg
     2221 ccaactcctg cgaggtaacc tcgaacatgc gctgtaagtt ggcgtagctg tcctgccacg
     2281 cttgctgctg ttgttcgtag tgcctctgta agctctctaa tgcgctcaga agctgctgct
     2341 ccatttcggt catgaatctc ttcaccctga tagataaaac cgcccagaat cgattctgtg
     2401 gcgtctgatg aggttatttg gcgctgtact tgatgacctg acgatgttga gcgttcttgt
     2461 actcgtcgat cttcttcgcc ccctgcggaa ggatcaggta atacacgctc ttgttcttgg
     2521 aatcgtgaat tatcgatacg ccggctccgg tctggctctt taagtcctgc aggatctggc
     2581 tctgctcgct gatttcgttc tggcgttcga ccacgatagt cccgagatac caagctactc
     2641 caatcaatat cgcaaacagg atcccactta atgccaggct gtacagccat gtcattccga
     2701 ctaagcggtg tatctgtttt agctggctgt cgttctcttc ttggatagcg gtctgtatgt
     2761 tccctgagct taatttcaag gcctcggtga tacgtttctc gtgcttctcg aatgcgttcg
     2821 cgacgctcgt tgcggtagtc ttggcttgct gcttcgattt gctctcgaac tcccgcgcta
     2881 aatttaaaat ctcgctcata cagcactcct tttaagcgaa tattcgggcc acctgccgga
     2941 tcagcaatac tgatactgga tttggtttcc cgtacgaccg acaatccggc atcggtaagg
     3001 tgggaaatca cccctttacg atccgtaatt tctccctgct caatcaagct gattagccct
     3061 ttggtaatgg cttccgctgc ctgctgtttg ttgcgaggaa ggtcattaga gggggttaat
     3121 gctcggcgat tagcagggtc attcgggtcg cgtaacccaa gccggtcatt ggtgagggtt
     3181 tgccatgcgt taacacgagg ccggtcagcc cgatcaaagt aaggttgtag ccgttttccg
     3241 ctctgcaatt cgatgttcgg gataacaaaa ttcaattcaa gacgcccttt gtcctgatgt
     3301 tgaacccaga ggcaggcata ctggtcttta tctagaccgg tcatcaatgt ctgctcccat
     3361 tcatccatca atcgctgctt ttcgccttcg ggtaaatcac tctcctgaaa agagagcacg
     3421 ccagaggtat aagttcgggc aaattcgcag ccatcaatca gctctttgac gtgctcaggg
     3481 ttaccccgta acaccgtcgc ttgttcgcgc tgacgatcag ggcccagaag gtaatcgaca
     3541 ggaccactcc cgccaccggc accacgacca tgaatcttaa cgatcacgat gttgctccag
     3601 cagttcggca agatgttggt caatgctatt gagcaccgct aacaacgaca cccgttcttg
     3661 cggcggtaag ccatgctgat tcaagtaacg ggctatttga ttgaggttat taccgatccc
     3721 gctgacctga cgtaacaagg tcgggtctac ggtaggtagc ggacgacgcc gagctgtacg
     3781 cgattcgcct aagccaacgg ctcgtaacca ctcggccaaa tgcttacggt cacagcgttc
     3841 aagtagccgc tgatgctccg cttcggtgag tctgattttg atctctttgg tgcgcttttc
     3901 catgagaatc cgctgagaaa gtttcgcacc caaagtgcga attttcgcag tggatgcaag
     3961 gggtttcggg gggcggcgag ccccctgaaa cagtcacaga cggcacctcg aagaggggac
     4021 gctgtgtgta ctggcttagt acagcatcta tcgtacatcg aggtcgcatc acgcacaaac
     4081 aaaaagcccc gcaaaagcag ggctgttatc tgatataggt tgttttgtct cacacggcag
     4141 cggaagagga atccgaagtg gtactggtag tagtattgga tgctgctgac gatattttcc
     4201 gctttgaccc aaggcttaaa taatcaatgc ctgtaatcaa cgatctcaat acgccttcgg
     4261 ataccatagc gataaacgta tcttgctggt tatggcttgc gatgcaaatc gtagcatcac
     4321 cttttttata ctttaaaaca cctgctaaat atccattttc atctagaaca ctcttaagat
     4381 gttcatttgt tattgtttgt agcgtttgct ttgtttcgct tcgagcatac gccttagcta
     4441 gcttccgaga aaaagcatcc gcatcatgac tatctttatt tactcgctca ataaatttgc
     4501 ttaagtcaac aaatccctta aaacgagtgg acatattgtt aacaaaatca gtggcagcat
     4561 tttttatcca tgctttatag ccaaaaaaac gctcgaaaac attttggtcg tagataaata
     4621 ccgtatcgcc agcaaaaaca agagatgcct taccatcaat agaaatcata tcttgatcta
     4681 ctcgagatag ttcttttttg ctaaacccat aaaaattatt tttctttctt gataagtttt
     4741 gaactggata ttgcttcttg tatatggtta tacaattgtc gtcattattc ttactcaaaa
     4801 cgaaaatgat tgagtcaact tttgatatta gatccacact gtcaaaatca acaattggga
     4861 tattttcatt gccatcacca ccaaacccag catcaaacac aatgccagtc agaaacttca
     4921 tttgctcatt atcatactgc tcagcatcat ttaaaaatga aatggtgttg gtgcggtcac
     4981 ttagtgtatt aacatctgat actatcacaa cccgattttc taaatcagat atagttttct
     5041 ttatcacatt atcaataatg gactgtttta gctcactgtc atttttaagg atggcaattt
     5101 tatagctaaa agagtcctta gcacccgctt tacctttatt tttaaagtta aagtaagtgt
     5161 gcaatgtaac atcgttaata tcacaatcaa aatgcttata cagttctaaa agctcttgtg
     5221 ctttttcttc attatgctcc aaagcatcaa gatctaaggc atcgtcactc atcatcattc
     5281 ctctatgatt tttttcgcga acgttaaata atcatcatga tttataactc tgataaaatc
     5341 attttctttt attaaatctt tagataaaac tatcaactca ccgtcttgcg ttttttccct
     5401 tccattagct accacactgt aagtaatctt ataggcagaa acattaaata atgacaatgt
     5461 tgggttgcag tgaattcttt ttgttttgat gtgcaaaaaa ccgacgataa tcaa
//
