LOCUS       NZ_CP121364             5128 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain rl0044 plasmid pVP446, complete sequence.
ACCESSION   NZ_CP121364
VERSION     NZ_CP121364.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN34068129
            Assembly: GCF_029674645.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5128)
  AUTHORS   Perreten,V., Rossano,A. and Fernandez,J.E.
  TITLE     Complete genome of pathogenic Escherichia coli rl0044 from pig
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5128)
  AUTHORS   Perreten,V., Rossano,A. and Fernandez,J.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-APR-2023) Institute of Veterinary Bacteriology,
            University of Bern, Laenggassstrasse 122, Bern 3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 10-MAR-2023
            Assembly Method                   :: trycycler v. v0.5.3
            Assembly Name                     :: rl0044
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 142.36x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029674645.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 05:17:07
            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)                     :: 5,963
            CDSs (total)                      :: 5,832
            Genes (coding)                    :: 5,510
            CDSs (with protein)               :: 5,510
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 98
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 322
            CDSs (without protein)            :: 322
            Pseudo Genes (ambiguous residues) :: 0 of 322
            Pseudo Genes (frameshifted)       :: 124 of 322
            Pseudo Genes (incomplete)         :: 207 of 322
            Pseudo Genes (internal stop)      :: 67 of 322
            Pseudo Genes (multiple problems)  :: 68 of 322
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP121364.1.
            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..5128
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="rl0044"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pVP446"
                     /geo_loc_name="Switzerland"
                     /collection_date="2000-08-25"
                     /collected_by="Roland Lanz and Patrick Boerlin"
                     /identified_by="Roland Lanz and Patrick Boerlin"
     gene            5..136
                     /locus_tag="P9060_RS29730"
                     /old_locus_tag="P9060_29730"
     CDS             5..136
                     /locus_tag="P9060_RS29730"
                     /old_locus_tag="P9060_29730"
                     /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_001505258.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMSKGVYKIY"
                     /name="hypothetical protein"
     gene            385..1269
                     /locus_tag="P9060_RS29735"
                     /old_locus_tag="P9060_29735"
     CDS             385..1269
                     /locus_tag="P9060_RS29735"
                     /old_locus_tag="P9060_29735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505259.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_001505259.1"
                     /translation="MAVTVGFISEKGGVGKTTSCYHIAEGLSRFHEKRVLVIDADYQRG
                     GITGRFFPKLIENFGNQAPQGTTLFNKYQQLYSAAQQTTDIDIIKFNSGIDVIPADPRL
                     STVSTDKLPSTNNIRSNNAILLQHLKTISAVLSPIADNYDYILIDSHPEVSDVMRSIIY
                     ASDYCVSPVKLDRQSSIGVATVIGEINNVNEDIEMLRKALQVGDSYKDTVFAGAMGMMA
                     REYAEELKQTEQYEYNRLRQAGDIFKHYITEGDGLRVAAAERVSVYDVQISNAYKQASQ
                     FKNLTIEFMRTCR"
                     /name="ParA family protein"
     gene            1266..1667
                     /locus_tag="P9060_RS29740"
                     /old_locus_tag="P9060_29740"
     CDS             1266..1667
                     /locus_tag="P9060_RS29740"
                     /old_locus_tag="P9060_29740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001505260.1"
                     /translation="MIDIQKLISWLGVEGAKAGLDKSEMTNAELIESFGNLLPKNPSKL
                     KRSDLVEEIILATRRMTHKSVEELMEMSKEDLYSYFHDQKYSRKELLDLLYTLEIRPGS
                     SAKKNLTEFTISEISDIGMYRRVAKGNHA"
                     /name="hypothetical protein"
     gene            complement(2487..2720)
                     /locus_tag="P9060_RS29745"
                     /old_locus_tag="P9060_29745"
     CDS             complement(2487..2720)
                     /locus_tag="P9060_RS29745"
                     /old_locus_tag="P9060_29745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137441.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2727..3245)
                     /locus_tag="P9060_RS29750"
                     /old_locus_tag="P9060_29750"
     CDS             complement(2727..3245)
                     /locus_tag="P9060_RS29750"
                     /old_locus_tag="P9060_29750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067503.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3283..3945)
                     /locus_tag="P9060_RS29755"
                     /old_locus_tag="P9060_29755"
                     /pseudo=""
     CDS             complement(<3283..3945)
                     /locus_tag="P9060_RS29755"
                     /old_locus_tag="P9060_29755"
                     /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(3923..4246)
                     /locus_tag="P9060_RS29760"
                     /old_locus_tag="P9060_29760"
     CDS             complement(3923..4246)
                     /locus_tag="P9060_RS29760"
                     /old_locus_tag="P9060_29760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_000955995.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            4311..4502
                     /locus_tag="P9060_RS29765"
                     /old_locus_tag="P9060_29765"
     CDS             4311..4502
                     /locus_tag="P9060_RS29765"
                     /old_locus_tag="P9060_29765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4598..4771)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.571"
                     /coverage="100.0"
                     /evalue="1.23e-64"
     Typing          6..155
                     /name="rep_cluster_2406"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.928"
                     /coverage="95.0"
                     /evalue="1.13e-39"
     Typing          4738..5128
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.408"
                     /coverage="98.0"
                     /evalue="2.14e-176"
     Typing          complement(2384..3933)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctgtatgcac gaaccccccg ttcagtccga ctgctgcgcc tgttccggta actatcgact
       61 tgagtccaac ccggaaagac acgacaaagc gccactggca gcagccatga gtaaaggggt
      121 gtacaagatt tactgagtga gagttcttga agtatcagcc ttagagaggc taaactggaa
      181 taacagaatt tggtttcagc ggtcttgtac accctgttac cacggttcag aagttcccca
      241 acttactgaa ccctcgaaaa aaccgactcc ccagtcggtt tttttcgttt gatggctaag
      301 agtacgctga cgttatactg aacgtcaagg aaagcgttga cgctgttccc tctaccaaaa
      361 aaaagagatt tgtaaggaat aaaaatggct gtgacagttg ggtttattag tgagaaaggt
      421 ggggttggta aaacaacgtc ctgttatcac attgccgaag gacttagtcg ttttcatgaa
      481 aaacgtgttt tagttataga tgcagattat caacgcgggg gtataactgg aagatttttc
      541 cctaaactga tcgaaaactt tggaaatcaa gcaccgcaag gaacaacgtt atttaacaag
      601 tatcagcaat tatatagcgc ggcacaacaa acgactgaca tagacataat taaatttaat
      661 agtggtatcg atgtcattcc agccgaccct cgcttatcaa ccgtttcaac tgataagcta
      721 cctagtacaa acaatataag atcgaacaat gccattcttt tacagcattt aaaaaccata
      781 agcgctgtat tatcacctat tgcagataat tatgactaca tattgattga ttcacacccc
      841 gaagtttctg atgtcatgcg ctctataatc tacgcatcag attattgtgt atcaccggta
      901 aaactagaca ggcaatcatc tattggtgtg gccacggtca taggtgagat aaataatgta
      961 aatgaagata ttgaaatgct aagaaaggca ctgcaagtcg gcgattcata taaggacaca
     1021 gttttcgccg gagcaatggg aatgatggcc agagaatatg cagaagaact gaagcaaaca
     1081 gagcaatatg aatacaacag gcttcggcaa gcaggtgaca tcttcaagca ctacataacg
     1141 gaaggtgatg ggctaagagt agctgcagca gagcgcgttt cagtgtatga tgtacagata
     1201 agtaacgctt acaaacaagc gtcacagttt aagaacttga cgattgagtt tatgaggact
     1261 tgtcgatgat agatatccaa aaactgatat cttggcttgg cgttgaggga gctaaagctg
     1321 gcttggataa aagtgaaatg actaatgccg agctaattga atcctttggt aatttacttc
     1381 caaagaaccc aagcaaatta aaacgctccg atctcgttga ggagattatt ttagcaacaa
     1441 ggagaatgac acataaatca gttgaagaac tgatggaaat gtcaaaagaa gatctgtatt
     1501 catatttcca cgatcagaaa tatagcagaa aagaacttct tgatttgtta tatactcttg
     1561 aaatcagacc tgggagctca gcaaagaaaa atctaaccga gttcacaata agtgagataa
     1621 gtgatattgg catgtatcgt cgcgtagcga aagggaatca tgcataaata aaagccacct
     1681 gtgaggtggc tttttatagg ataaaaaaat gccatttaat ataggcgata tagtttactt
     1741 aaagtcagaa tcaaaagcga tgacggtcat cggatatgga tcgtctcaaa ataacggtta
     1801 catagatcta gctaattgtg cttggctaga taaagacaac cgctattgcc aaatactatt
     1861 cttgtttcaa acgatcgaaa aaagaatcag ttaaaaactg gcttatcttc attgagcata
     1921 ccggacgaac ctatttacca taacatccgt tgcccgcacc gcagaaacgc gttcggtgcg
     1981 atcacggcag cagacaggta aaaatggcaa caaaccaccc gaaaaactgc cgcgatcgca
     2041 cccggtaaat tttaaccaca tgcatagcta tgcagccatg tgaatcacgc aggaattgcc
     2101 agccagagac agctgaaacg gatttttttc atgctttcgg aagcgaagaa gacggggacc
     2161 ggagcgggaa aacagaagtt caggggaatg agcgcgatct ggcaatagag gcaaaacaca
     2221 gcaacaaaag acacaccaga atcgcgcccg tatgcgtttt aacgcgttcc tgtgttttca
     2281 gcaaggtctg actgaagcgc gttcccggtg cccccgaacc aaccattatc ccaaaaaatg
     2341 caccggaaac gcgctgacaa cattttagcc tgtctctgat taccatccaa gcgaagggcc
     2401 atcctgtgtc cattcctgta tttccggctg gcgctcacgc tccagggata actcatgttc
     2461 gcgctcctgt atcagccgtt cgtcccttat ctcctgttct cgctgtataa ctggctcaag
     2521 cgttctgtcc gctcgctcaa gtgctgcacc tgctgactca actgcatgac ctgctcgttc
     2581 agcatcgcgt tgtcccgttg cgtaagcgaa aacattttct gcaattccac gaaggcgctc
     2641 tcccattcgc tcagccgctg catatagtcc tgttgcagtt gctctaaggc gttcagcaaa
     2701 tgtctttcca gctccgtcac tctgtgtcac tccgtcagtt gtacccagtc cttctcctga
     2761 tagggaatca ccgttgccga tttcccgtac ggaaggacca gaaatttcct tctcccgtcc
     2821 tgcacaaact ccacgcccca tgtcttcgcg ttcagtttct gcaatgtttc ttcctgtatc
     2881 ctgatttctt ccaggttcgc ctgtatccgc ccgccaagat accagagcgt cccgccactc
     2941 acggtaaaca ggaaaaggac catccccagt aacatcatgc ccgtattccc tgccagcttt
     3001 aacacgtcct tcctgtgctg catcatcgcc tctttcaccc cttcccggtg ttttttcagt
     3061 gattcctctg tcgaagctgt gaacagggct atagcgtctt tgattttcgt ctcgtttgat
     3121 gtcacagcct tgcttacaga tttttcgagc ttgctgaact cgtcgttcag cattgtctct
     3181 gtagattcgg ctctctcttt cagctttttc tcgaactccg cgcccgtctg taaaagattg
     3241 ctcatagaat gctcctttca gtctgatatt cttcccgccg ttcgggtctg caatgctgat
     3301 actgcttcgc gtcaccctga ccacttcaag ccctgcctct gtgagcgcct gaatcacatc
     3361 ctgacggcct tttatctccc cgacatgata aagagcgtct atcccgcgtg tgacgctctc
     3421 tgcaagcgcc tgtttcgttt ccggcaggtt atcagggaga gtcagtatcc ggcggttctc
     3481 cggggcgttg gggtcatgca gcccgtaatg gtgattaacc agcgtctgcc aggcatcaat
     3541 tctcggcctg tctgcccggt cgtagtacgg ctggaggcgt tttccgctct gtagctccat
     3601 gttcggaatg acaaaattca gctcaagccg tcccttgtcc tggtgctcca cccacaggat
     3661 gctgtactga tttttttcga gaccgggcat cagtacacgc tcaaagctcg ccatcacctt
     3721 ttcacgtcct cccggcggca gctccttctc cgcgaacgac agaacacctg acgtgtattt
     3781 cttcgcaaat ggcgtggcat cgatgagttc ccggacttct tccggattac cctgaagcac
     3841 cgttgcccct tcccggttac gctcccttcc cagcaggtaa tcaaccggac cactgccacc
     3901 gccttttccc ctggcatgaa acttaactat catcccgcgc tccatgttcc ctgacgacct
     3961 gccgtaagct gcgcaactct ctctcgatgg ccatcagtgc ggccaccacc tgaacccggt
     4021 caccggaaga ccactgcccg ctgttcacct tcctcgccgt ctgattcaga ttattcccga
     4081 tggcagccag ctggcgcagt aacggcggtg ccagtgtcgg cagcttcccg gaacgggcaa
     4141 ccggctcacc cagacagacc cgccgcatcc ataccgccag ctgtttaccc tcacagcgtt
     4201 ccagtaaccg tgcatgttca tcatcagtaa cccgtatcgt gagcatcctc tcgcgtttca
     4261 tcggtatcat taccccatga acagaaatcc ccccttacac ggaggcatca gtgactaaac
     4321 aggaaaaaac cgcccttaac atggcccgct ttatcagaag ccagacatta acgctgctgg
     4381 aaaagctcaa cgaactggac gcggatgaac aggcagacat ctgtgaatcg cttcacgacc
     4441 acgccgatga gctttaccgc agctgcctcg cacgcttcgg ggatgacggt gaaaacctct
     4501 gacacataca gctcccggag acggtcacag cttgtctgtg agcggatgcc gggagcagac
     4561 aagcccgtca gggcgcgtca ggccgttgac cttgcgggtg tcggggcgca gccatgaccc
     4621 agtcacgtag cgatagcgga gtgtatactg gcttactatg ttggcatgag tgcgggtatc
     4681 aggaaagtgc ttcatgtggc aggagaaaaa aggcggcacc ggagcgtcag cagaatatgt
     4741 gatacaggat atattccgct tcctcgctca ctgactcgct acgctcggtc gttcgactgc
     4801 ggcgagcgga aatggcttac gaacggggcg gagatttcct ggaagatgcc aggaagatac
     4861 ttaacaggga agcgataggg tcgcggcgaa gccgtttttc cataggctcc gcccccctga
     4921 caagcatcac gaaatctgac gctcaaatca gtggtggcga aacccgacag gactataaag
     4981 ataccaggcg tttccccctg gtggctccct cgtgcgctct cctgttcctg cctttcggtt
     5041 taccggtgtc attccgctgt tatggccgcg tttatctcat tccacgcctg acactcagtt
     5101 ccgggtaggc agttcgctcc aagctgga
//
