LOCUS       NZ_CP095523             5632 bp    DNA     linear   CON 20-JAN-2024
DEFINITION  Escherichia coli strain GN04171 plasmid p4171-4.
ACCESSION   NZ_CP095523
VERSION     NZ_CP095523.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27361461
            Assembly: GCF_026651185.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5632)
  AUTHORS   Bethke,J.H., Ma,H.R., Tsoi,R., Cheng,L., Xiao,M. and You,L.
  TITLE     Vertical and horizontal gene transfer tradeoffs direct plasmid
            fitness
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5632)
  AUTHORS   Bethke,J.H., Ma,H.R., Tsoi,R., Cheng,L., Xiao,M. and You,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-APR-2022) Molecular Genetics and Microbiology, Duke
            University, CIEMAS Building 101 Science Drive, Durham, NC 27705, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 6.0.0.47841
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 259x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/20/2024 04:49:39
            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)                     :: 5,083
            CDSs (total)                      :: 4,970
            Genes (coding)                    :: 4,766
            CDSs (with protein)               :: 4,766
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 204
            CDSs (without protein)            :: 204
            Pseudo Genes (ambiguous residues) :: 0 of 204
            Pseudo Genes (frameshifted)       :: 73 of 204
            Pseudo Genes (incomplete)         :: 146 of 204
            Pseudo Genes (internal stop)      :: 34 of 204
            Pseudo Genes (multiple problems)  :: 43 of 204
            Pseudo Genes (short protein)      :: 3 of 204
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP095523.1.
            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/
FEATURES             Location/Qualifiers
     source          1..5632
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN04171"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4171-4"
                     /geo_loc_name="USA"
                     /lat_lon="36 N 78.9 W"
                     /collection_date="2011"
                     /collected_by="Vance G. Fowler Jr."
                     /genotype="131"
     gene            complement(<1..509)
                     /locus_tag="MW404_RS24840"
                     /old_locus_tag="MW404_24850"
                     /pseudo=""
     CDS             complement(<1..509)
                     /locus_tag="MW404_RS24840"
                     /old_locus_tag="MW404_24850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(990..1223)
                     /locus_tag="MW404_RS24845"
                     /old_locus_tag="MW404_24855"
     CDS             complement(990..1223)
                     /locus_tag="MW404_RS24845"
                     /old_locus_tag="MW404_24855"
                     /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_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1230..1760)
                     /locus_tag="MW404_RS24850"
                     /old_locus_tag="MW404_24860"
     CDS             complement(1230..1760)
                     /locus_tag="MW404_RS24850"
                     /old_locus_tag="MW404_24860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1798..2496)
                     /locus_tag="MW404_RS25485"
                     /pseudo=""
     CDS             complement(<1798..2496)
                     /locus_tag="MW404_RS25485"
                     /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(2438..2761)
                     /locus_tag="MW404_RS24860"
                     /old_locus_tag="MW404_24870"
     CDS             complement(2438..2761)
                     /locus_tag="MW404_RS24860"
                     /old_locus_tag="MW404_24870"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2826..3017
                     /locus_tag="MW404_RS24865"
                     /old_locus_tag="MW404_24875"
     CDS             2826..3017
                     /locus_tag="MW404_RS24865"
                     /old_locus_tag="MW404_24875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4220..5086)
                     /locus_tag="MW404_RS24870"
                     /old_locus_tag="MW404_24880"
     CDS             complement(4220..5086)
                     /locus_tag="MW404_RS24870"
                     /old_locus_tag="MW404_24880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(5088..>5632)
                     /locus_tag="MW404_RS24875"
                     /old_locus_tag="MW404_24885"
                     /pseudo=""
     CDS             complement(5088..>5632)
                     /locus_tag="MW404_RS24875"
                     /old_locus_tag="MW404_24885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=3
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          complement(3112..3193)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(3650..3837)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(887..2448)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttaacaccag ccttatatat ttttagccca tctttatcct gaaatggtac gctttcagta
       61 taaataacat cctcttttat tggatagcac tctggcatat gcagcgaaca aatatatttt
      121 tgtatgtcca ctaactcttc tgatggacga gcaaaggcaa gttgtggatg aataaaataa
      181 atgagatgcg cactgacctc tcctcttctt gcgcgttctt taaaacgaac tctttcatta
      241 cgcaaaaaat caaacaaatg accatcatca ttatatagtt gggggctatt tacaatagat
      301 aaatggaaat caagcccttt aattttcttg cttgccaatt taccaaatac acagggctga
      361 ttgcctgaca cccattttct tagtaaatct tcaattttat ctttagaagt ttcgttaaag
      421 ataaatgaat gaatattatc aatatctttt ccaaatgaaa aactggatga taattgtggt
      481 agtttattta tacgttgttg aagattcatg aaagctccca caagacacct catatatttt
      541 tttatatact gaaactacat tatatttatt accggcgtaa aacgaaataa tttattatcg
      601 ttaccgatat tttaaaaaaa tcattatttg cacagtgttc gagttgttag tatcactcct
      661 tcctgaaaat ccgctccatt taccataacg tcgcattgta cgcaccgcca aaacgcgttc
      721 ggtgcgatca cggcagcaga caggtaaaaa tggcaacaaa ccacccgaaa aactgccgcg
      781 atcgcacctg ataaatttta accgcatgaa tacctatgca accagatgct acaggccaca
      841 ttagcccgcc ttaatccact gaacacgtca tttttcatgg tttcaccatc ccagcgaagg
      901 gccatccagt gtccgctcct ggatttccgg ctgacgctcc cgctccagag ataactcatg
      961 ttcgcgttcc tgcatcagcc gttcatccct tatctcctgt tctcgctgta taactggctc
     1021 aagcgttctg tccgctcgct caagtgctgc acctgctgac tcaactgcat gactcgcccg
     1081 ttcagcatcg cgttgtcccg ttgcgtaagc gaaaacattt tctgcaattc cacgaaggcg
     1141 ttctcccatt cgttcagccg ctgcatatag tcctgttgca gttgctctaa tgcgttcagc
     1201 aaatgtcttt ccagctccgt catgctctgt cactcctgca ccagtctcac tgcgttcagt
     1261 ttgccgttgt ccttcgtcca gttcgtttcg gctttcatcc ccttcggcaa caccagaaaa
     1321 cgtccgttgc tgtcctcgtg ataacgcacg ccccatgtct tcgcgttcag cttctccaga
     1381 ctctctttct gctcgcggag aatattcata ttcgcgttta tcttcatgcc ctggtaccac
     1441 agcagactcc cggtcgtggc aaacatcagt actgagacga taatcagcca cagccagcgt
     1501 ttcacgctca ttttcagtac ggttttccag tgcgcgtcca tcgtatcgac ggtcgttttc
     1561 tgatacctct ccagcagttc tttcagggct gttgtatggt cgttgatagc gttcctgatt
     1621 aaagattcgt ttgaggtcag ttccctgttt acagattctt cgagcttcct gaactcgtcg
     1681 ttcagcattt tctctgtaga ttcggctctc tctttcagct ttttctcgaa ctccgcgccc
     1741 gtctgtaaaa gattgctcat aaaacgctcc tttcagtctg atattcctcc cgccgttcgg
     1801 gtctgcaatg ctgatactgc ttcgcgtcac cctgaccact tcaagccccg cctctgtgag
     1861 cgcctgaatc acatcctgac ggccttttat ctctccggca tggtaaagcg cgtctatccc
     1921 gcgtgtgacg ccctcagcaa gcgcctgttt cgtttccggc aggttatcag gaagggtcag
     1981 cgtccggcgg ttctccgggg cgttggggtc atgcagaccg taatggtgat tcaccagcgt
     2041 ctgccaggca tcaattctcg gcctgtctgc ccggtcgtag tacggctgga ggcgttttcc
     2101 ggtctgtagc tccatgttcg gaatgacaaa attcagctca agccgtccct tgtcctggtg
     2161 ctccacccac aggatgctgt actgattttt ctcgagaccg ggcatcagta cacgctcaaa
     2221 gctcgccatc actttttcac gccctccagg cggcagctcc ttctccgcga acgacagaac
     2281 acctgacgtg tatttcttcg caaatggcgt ggcatcgatg agttcccgga cctcttccgg
     2341 attcccctga agcaccgttg ccccttcccg gttacgctcc cttcccagca ggtaatcaac
     2401 cggaccactg ccaccacctt ttcccctggc atgaaactta actatcatcc cgcgccccct
     2461 gttccctgac cgccagacgc agccggcgca gctcatcccc gatggccatc agtgcggcca
     2521 ccacctgaac ccggtcaccg gaagaccact gcccgctgtt caccttcctc gctgtctggt
     2581 taaggttatt cccgatggcg gccagctgac gcagtaacgg cggtgccagt gtcggcagct
     2641 tcccggaacg ggcaaccggc tcacccaggc agacccgccg catccatacc gccagttgtt
     2701 taccctcaca gcgttccagt aaccgggcat gttcatcatc agtaacccgt atcgtgagca
     2761 tcctctcgcg tttcatcggt atcattaccc ccatgaacag aaccccccct tacacggagg
     2821 catcagtgac caaacaggaa aaaaccgccc ttaacatggc ccgcttcatc agaggccaga
     2881 cattaacgct gctggagaag ctcaacgaac tggacgcgga tgaacaggca gacatctgtg
     2941 aatcgcttca cgaccacgcc gatgagcttt accgcagttg cctcgcacgc ttcggggatg
     3001 acggtgaaaa ccgctgacac atgcagctcc cggagacggt cacagcttgt ctgtgagcgg
     3061 atgccgggag cagacaagcc cgccagggcg cgtcaggccg ttgacctttg gggtgtcggg
     3121 gcgaagccct gacccagtca cgtagcgata gcggagtgta tactggctta accattcggc
     3181 atcagtgcgg attgtatgaa aagtgcgcca tgtccggtgt gaaatgccgc acagatgcgt
     3241 aaggagaaaa tgccagttca ggcgctcttc cgcttcctcg ctcactgact cgctacgctc
     3301 ggtcgttcgg ctgcggcgag cggactctcc tttctcaaaa acgctaaccc tgttatccac
     3361 agaacccggg gataaaccag gaaagaacat gtgcgcaaaa aacgaaaccc cgggaaaggc
     3421 cgcgccggag gcgctttttc cataggctcc gcccccctga cggacttcac aaaacagaca
     3481 ctttttcggt gcatctgtgg gagccttgcg gctcaaccat gaaatccgcc agcggtggcg
     3541 aaacccgacg tggcttaaag atcatcaccg tttccggtga atcgctccct cctgcgcccc
     3601 cacgttcccg ccatatcgat taccggatac cttttccgcc tttctccctt acgggacacg
     3661 tggcgctttc tcatagctca cgtcttctgg tatctcgggg cgacttaggc agttcgctcc
     3721 gggctgggct gtatgcagga accccccgtt cagcccgact gctgcgcctt ctccggtaac
     3781 tgttctcttg ggtccaaccc ggaaaagaca ccacaaagcg ccactggcag cagccattgg
     3841 taaaagtcat gtgcgagata tttagagagt acttgaagtg gctgccggag tgcggctaca
     3901 ctagaagaac aattttggtg actcgtctcg cataagacag ttacctggtt aagcagtctg
     3961 caagctgact taaccttcga tcaaaccgcc ctgcaaggcg gttttttcgt ttacaggcag
     4021 cagattacgc gcagaaaaaa aggatctcaa gaggatcctt tgatcttttt gttacaaacg
     4081 tctctatttg actcccctga gagcgtttta gcgcgcctct gacccccttg gttacattcc
     4141 gacaccagaa acgctcccgt tttttacgtg catttggcac ggtatcgatg gaggccgggg
     4201 ggcaatcctg aacagaatgt tactcctctg agtattttct gttaagaaaa tatacactta
     4261 gcacagttac aataaatcct accccctgta agaatgtgaa ttgttcatcc aaaaacaacc
     4321 atgacaaaaa taatgcaact agcggaataa agtacaacat tatccctgcc aaatgaactg
     4381 ggagccaacg caaggagttc aagtaaaaac aaaaagctaa aaaatattgt aatattccag
     4441 atgaaaaaac aataatcacg gattccaacg gaagataaat tgatgattta gatataaaaa
     4501 taaagagcga tgacagtata agggagaatg tcaactgtcc gctcaataat gtgataggct
     4561 caaacgattt aataaggcga gacgatataa caacataaaa tgctgccgat aacacaccgg
     4621 caacaacaag acaatatcca acaatattat tcgatccatt actgatgtct ggcaaggcta
     4681 ccaaaatact gccaacaatt gcacctataa ggaacaatat aaaatattgc ggggaattaa
     4741 ttttaactga gcaaataaga acagacaaca ccaatataaa cactgattca agtgaaaaaa
     4801 taattgatgc gcttcctgct gaaataaaat aaagtccgta gagtgtaaaa gtatacgcta
     4861 agaatggttc aaaaacgcct gtcgcataag caagtatcgc ttttgagttt aatgggagtt
     4921 tttttctttt tataaaaaga actatccaag atagtattac tgcactacaa atctgccaga
     4981 aaaacacccc tccggcatct agttcttcaa ctcctttttt gctcattacg atagctgccc
     5041 cccatgagaa cgctgctaaa aaagcaaaaa gcattccttt aatcatatta atcatcctct
     5101 ttctcataaa ggggtttgtt ttcaaatttc cttggttgaa aggagttaaa aaacatagat
     5161 gcatcatcta caggaatacc aataaactct ccataataag gatcatctat aggaaactct
     5221 tctaatgaaa cataaaacaa tacattccag ttgaagatca ttggatcact attttctatt
     5281 tcatggagca atctttcatc cttagttaat tctcctggaa ttaatacatc agtatgataa
     5341 aaaccgctgt aataagaact attaccggtg tgcactgggc atccaaaacg atccaaatta
     5401 gattctgaat gccatgttgt agaaatccct tccggatgtg aatacccacc cttaccaaca
     5461 gactgaatag tcatgttacg aatatccgct aacgcttgtt cttgatcttt atagaaacct
     5521 ttttctatcg ccagcctcat aaaatgcccc ggggcattta cagaaataag tattccccct
     5581 ggtattcttc tatcatgatt tcttgttcta tgagcagaag agtaaaaaaa ca
//
