LOCUS       NC_011408               5366 bp    DNA     circular CON 01-JUN-2024
DEFINITION  Escherichia coli SE11 plasmid pSE11-5, complete sequence.
ACCESSION   NC_011408
VERSION     NC_011408.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00061087
            Assembly: GCF_000010385.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli SE11
  ORGANISM  Escherichia coli SE11
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Oshima,K., Toh,H., Ogura,Y., Sasamoto,H., Morita,H., Park,S.H.,
            Ooka,T., Iyoda,S., Taylor,T.D., Hayashi,T., Itoh,K. and Hattori,M.
  TITLE     Complete genome sequence and comparative analysis of the wild-type
            commensal Escherichia coli strain SE11 isolated from a healthy adult
  JOURNAL   DNA Res 15 (6), 375-386 (2008)
   PUBMED   18931093
REFERENCE   2  (bases 1 to 5366)
  AUTHORS   Hattori,M., Oshima,K., Toh,H., Sasamoto,H. and Shiba,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-OCT-2006) Contact:Masahira Hattori Graduate School of
            Frontier Sciences, University of Tokyo; 5-1-5 Kashiwanoha, Kashiwa,
            Chiba 277-8562, Japan URL :http://www.cb.k.u-tokyo.ac.jp/hattorilab/
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000010385.1-RS_2024_06_01
            Annotation Date                   :: 06/01/2024 01:28:55
            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)                     :: 5,106
            CDSs (total)                      :: 4,988
            Genes (coding)                    :: 4,817
            CDSs (with protein)               :: 4,817
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 171
            CDSs (without protein)            :: 171
            Pseudo Genes (ambiguous residues) :: 0 of 171
            Pseudo Genes (frameshifted)       :: 74 of 171
            Pseudo Genes (incomplete)         :: 107 of 171
            Pseudo Genes (internal stop)      :: 28 of 171
            Pseudo Genes (multiple problems)  :: 34 of 171
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP009245.1.
            This work was done in collaboration with Yoshitoshi Ogura, Tadasuke
            Ooka, and Tetsuya Hayashi (University of Miyazaki), Sang-Hee Park
            and Kikuji Itoh (University of Tokyo), and Hidetoshi Morita (Azabu
            University).
            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..5366
                     /organism="Escherichia coli SE11"
                     /mol_type="genomic DNA"
                     /strain="SE11"
                     /db_xref="taxon:409438"
                     /plasmid="pSE11-5"
     gene            join(5054..5366,1..11)
                     /locus_tag="ECSE_RS26000"
     CDS             join(5054..5366,1..11)
                     /locus_tag="ECSE_RS26000"
                     /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_001350082.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>651
                     /locus_tag="ECSE_RS29505"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="ECSE_RS29505"
                     /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            689..1207
                     /locus_tag="ECSE_RS28735"
                     /old_locus_tag="ECSE_P5-0002"
     CDS             689..1207
                     /locus_tag="ECSE_RS28735"
                     /old_locus_tag="ECSE_P5-0002"
                     /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_011182895.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNDEFSRLGESVSEAVTSNE
                     TKIKGAIAQFTASTEESLKKHREGVKEAMMQHRKDMLKLAGSSGMRLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRVQEETLRKLNAKTWGVEFVQGGGRKFLVIPQGMSAEVTHYQ
                     GKDWIQLTE"
                     /name="MbeB family mobilization protein"
     gene            1214..1447
                     /locus_tag="ECSE_RS28740"
     CDS             1214..1447
                     /locus_tag="ECSE_RS28740"
                     /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_010976343.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSERTEHLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1819..2799)
                     /locus_tag="ECSE_RS26010"
                     /old_locus_tag="ECSE_P5-0004"
     CDS             complement(1819..2799)
                     /locus_tag="ECSE_RS26010"
                     /old_locus_tag="ECSE_P5-0004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000369747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000369747.1"
                     /translation="MDNNFTSYFTNPKYVTNYNFNGKGLIYIENERDYVFWESIFNAHF
                     DGMYEIKASIKNDGRRGKDALLELIPTLNKNCLLAIDGDFDYISECDYRFGKFMSNAYV
                     LHTHSYSRESAVFSKSKIDEVVSKLRLTLPCTFDVNKPIQIISKRYFKALVGFLYLMKK
                     NRDLAINIDIHKPIKKCEFRKYINNDFTSNDKIIQEMTSLLEPIENEIYSYIDERSIEF
                     SSFVEQANRKGLKEDSAYRFISGHVLNDNILLPMLARIKFLMERQSLRSIASEDTSREN
                     KSNMISAIKNHYRDNCKVKTIITHLNLCANDEISKMIHSKVSAIH"
                     /name="hypothetical protein"
     gene            complement(2801..3808)
                     /locus_tag="ECSE_RS26015"
     CDS             complement(2801..3808)
                     /locus_tag="ECSE_RS26015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010359104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_000111649.1"
                     /translation="MSVKIKKLSIESLFDEHNVEWILDDVNVLVGKNGKGKSVILNIIH
                     SLLNKEESTEVNYCKKASIYLNDKRMISRRNDPSSSEFLKIIASQVLKGLSENKKEIKK
                     LAKIKNKEQEEKIKSEMELILEKLSSKDTDAPKGYFVEMGEKEKGKQEEKDKINTTYIS
                     TINMSANSTNEIKKSSGEKVMVLDFEIKEEKDAALKKIASGSRSSEEKKTLLDVLNGFF
                     KDTKKEVVIEDDLIVFLEDKKTTIEIEKLSSGERQLIYTFLRVFNSERENQIILLDEPE
                     ISLHLSWQEILISSIKKIRDDCQIILVTHSPGIVMDGWMGAYKEIDSIITKAEK"
                     /name="AAA family ATPase"
     gene            complement(4798..4989)
                     /locus_tag="ECSE_RS26020"
                     /old_locus_tag="ECSE_P5-0007"
     CDS             complement(4798..4989)
                     /locus_tag="ECSE_RS26020"
                     /old_locus_tag="ECSE_P5-0007"
                     /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_000165992.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLSRFGDDGENM"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4543..4716
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.857"
                     /coverage="100.0"
                     /evalue="2.61e-71"
     Typing          complement(4014..4619)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.475"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..1545
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.835"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          5022..5365
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.043"
                     /coverage="97.0"
                     /evalue="7.84e-62"
ORIGIN
        1 atgatagtta agtttcatgc ccggggaaaa ggtggtggca gtggtccggt tgattacctt
       61 ctggggaggg agcgtaaccg ggaaggtgca acggtacttc agggtaaccc ggaagaagtc
      121 cgggagctta ttgatgccac gccatttgcg aagaaataca cgtccggtgt tctgtcgttc
      181 gcagagaagg aactgccgcc gggaggacgt gaaaaagtga tggagagctt tgagcgcgta
      241 ctgatgcccg gtctcgaaaa aaatcagtac agcattctgt gggtggagca ccaggacaag
      301 gggcgtcttg agctgaattt tgtcattccg aacatggagc tacagaccgg aaaacgcctc
      361 cagccgtact acgaccgggc agacaggctg agaattgatg cctggcagac actggtgaat
      421 caccattacg ggctgcatga ccccaacgcc ccggagaacc gcagaacgct gatcctccct
      481 gataacctgc cggaaacgaa acaggcgctt gctgagagcg ttacacgagg cctggaggtg
      541 ctttaccatg ccggggagat aaaaggccgt caggatgtga ttcatgcgct cacagaggtg
      601 gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggcggg
      661 aggaatatca gactgaaagg agcgttttat gagcaatctt ttacggacgg gcgcggagtt
      721 cgagaaaaag ctgaaagaga gagccgaatc tacagagaaa atgctgaacg acgaattcag
      781 caggctcggc gaatctgtaa gcgaggctgt gacctcaaac gagacgaaaa tcaaaggcgc
      841 tatagcccag tttacggcct cgacggagga atcgctgaaa aaacaccggg aaggggtgaa
      901 agaggcgatg atgcagcacc ggaaggacat gttaaagctg gcagggagtt cgggcatgag
      961 gttgctgggg atagtctttc tcctgtttac cgcgagtggc gggacgctct ggtatctcgg
     1021 cgggaggata cagacgaacc tggaagaaat cagggtacag gaagagacat tgcggaaact
     1081 gaacgcgaag acatggggtg tggagtttgt tcagggcggg ggaagaaaat ttctggtcat
     1141 tccgcaaggg atgtcagcag aggtgacgca ctatcagggg aaggactgga tacaactgac
     1201 ggagtgatac ggaatgacag agctggaaac acatttgctg aacgccttag agcagctgca
     1261 acaggactat atgcagcggc tgaacgaatg ggagagcgcc ttcgtggaat tgcagaagat
     1321 gttttcgctt acgcaacggg acaacgcgat gctgaacgag cgggtcatgc agttgagtca
     1381 gcaggtacag cacttgagcg agcggacaga acacttgagc cagttataca gcgagaactg
     1441 gagataagag aggaacggct gatacaggag cgcgaacatg cgttatccct ggaacgggaa
     1501 cgccagctgg aaatacagga acgcacactg gatggtcctt cgttgtcgct gtgatggcga
     1561 aactataaaa aatggcagat tcagtggatt ttgacgggct aatgtagtct gcaccatctg
     1621 gttgcatagg tattcatgcg gttaaaattt atcaggcgcg atcgcggtag cttttcgggt
     1681 gatttgttgt tggttttggc tgactgccgc cccgttcgcg gcgaagctgt ccggggcggt
     1741 gcgggcaaca gatgttatgg taaattaaca ccgcatgact gattcggacg ccaaaaattc
     1801 gtccattgtt cccatccctt aatgtattgc agaaaccttt gaatgtatca ttttgctgat
     1861 ttcatcatta gcgcaaagat ttaggtgtgt aattattgtt ttcactttgc aattgtctcg
     1921 ataatggttt tttattgcag atatcatgtt tgacttgttt tctctgctag tgtcttcaga
     1981 tgctatagaa cggagtgatt gccgctccat taaaaacttt attctggcta gcattggtag
     2041 caaaatgtta tcattaagaa catgccctga tataaatcta taagcgctat cctcttttag
     2101 tcctttacgg ttagcctgct ctacaaaaga ggagaactct atagatctct catctatgta
     2161 tgagtaaatc tcattttcga ttggttcaag caaggatgtc atttcttgaa tgatcttatc
     2221 attgctagtg aagtcgttgt ttatgtactt tctgaattca cattttttta ttggtttatg
     2281 tatgtcgatg tttattgcta ggtctctatt ttttttcatg aggtacaaaa aaccgacaag
     2341 cgctttgaaa tatcttttag atataatttg aatcggtttg tttacatcaa aggtgcaagg
     2401 caatgttagc cttagtttgc taacaacttc atctattttt gattttgaaa aaacagcact
     2461 ttcccgcgaa taactgtgcg tatgcaagac atacgcattt gacataaact taccaaatcg
     2521 gtagtcgcat tctgatatgt aatcaaaatc accatcgatg gccaaaagac aatttttatt
     2581 taatgttgga atcaattcca gcaatgcatc tttaccgcgc cttccatcat tcttaatgga
     2641 tgctttaatt tcatacattc cgtcaaagtg tgcattgaat atagactccc aaaagacgta
     2701 atctctctca ttttctatgt aaatcaagcc cttaccatta aaattgtagt ttgttacata
     2761 ttttgggttg gtaaagtatg atgtgaagtt gttatccatt ttacttctcg gctttagtaa
     2821 ttatagaatc aatctctttg tatgcaccca tccacccgtc cattactatt ccagggctgt
     2881 gggttactaa tattatttgg caatcatctc ttattttttt tattgatgaa attagtattt
     2941 cttgccatga aagatgtaga gatatctcag gttcatccag aagtattatt tggttttctc
     3001 tctcagaatt aaagacccta agaaatgtat aaatcagctg tctctctcca gatgataatt
     3061 tttctatttc tatagttgtt tttttatctt ctagaaaaac tattaaatca tcctctatta
     3121 ccacctcttt tttcgtgtct ttaaaaaaac catttaaaac atcaagtaat gttttctttt
     3181 cttcgctgct ccttgagccg cttgctattt tttttaatgc ggcatccttc tcctctttta
     3241 tttcaaagtc taataccatc actttttcgc ctgaactttt ctttatttca tttgttgagt
     3301 tggcactcat gttaatggtt gatatgtaag ttgtattgat tttatctttt tcttcttgct
     3361 ttcctttctc tttttccccc atctcaacga aatatccttt tggagcgtca gtgtctttgg
     3421 aagatagctt ttccaaaatc aactccattt ctgatttaat cttctcctct tgctctttgt
     3481 tttttatttt tgcaagcttt tttatttctt ttttattttc agacaggcct ttaagcacct
     3541 gggatgctat tatttttaaa aactcacttg aagatgggtc gtttcttctt gatatcattc
     3601 gtttatcatt taagtaaatg ctggcctttt tgcaataatt tacttctgtg gactcttctt
     3661 tattcagtag gctgtgaata atattcaata ttacagactt gcctttccca ttcttcccca
     3721 ctaatacatt aacatcgtcc aaaatccatt caacattatg ttcatcgaag aggctctcta
     3781 tacttaattt ttttattttt acgctcatta atctaccgac ctgataatcc attatgtttg
     3841 atgagtaaca ctgtagcttg attctcgctt caacttaagc ataatgaaga agttgaaaaa
     3901 aaaaaccacc gctaccaacg gtggtttttc taaggttctc tgagctacca actctttgaa
     3961 ccatggtagc agggtgtaca agaccgctga aaccaaattc tgtcctttca gtttagccgt
     4021 agttgggctg agaattcaag aactctgcat cagtaatctc ttgtacaccc tcttaccaat
     4081 ggccgcagcc agtggcgttt tgttgtgtct ttccgggttg gactcaagtc gatagttacc
     4141 ggataagacg ctgcggtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg
     4201 aactgccttc ccggaaccga gtgtcaggcg tggaatgaga aaccgcggcc ataacagcgg
     4261 agtgacaccg gtaaaccgaa aggcaggaac aggagagcgc acgagggagc caccaggggg
     4321 aaacgcctgg tatctttaag tcctgtcggg tttcgccacc actgatttga gcgtcagatt
     4381 tcgtgatgct tgtcaggggg gcggagccta tggaaaaacg gctttgccgt ggccttatcg
     4441 cttccctgct aagtttcttc ctggcatctt ccaggatatt tccgccccgc cagtaagccg
     4501 gtaccgctcg ccgcagccga acgaccgagc gcagcgagtc agtgagcgag gaagcggaat
     4561 atatcctgta tcgcatattc tgctgacgcg cctgtgccgc cttttttctc ctgtcacatg
     4621 aagcacttca ctgatttccg catccatgcc aacatagtaa gccagtatac actccgctat
     4681 cgctacgtga ctggttcagg gcttcgcccc gaaaccccct gacgcgccct gacgggcttg
     4741 tctgctcccg gcatccgctc acaggcaagc tgtgaccgtc tccgggagct acatgtgtta
     4801 catgttttca ccgtcatccc cgaagcgtga gaggcagctg cggtaaagct catcggcgtg
     4861 gtcgtgaagc gattcacata tatctgcctg ttcgtccgcg tccagctcgt tgagtttctc
     4921 cagaagcgtt aatgtctggc ttctgataaa gcgggccatg ttaagggcgg ttttttcctg
     4981 tttagtcact gatgcctccg tgtaaggggg atttctgttc atgagggtaa tgataccgat
     5041 gaaacgagag aggatgctca cgatacgggt tactgatgat gaacatgccc ggttactgga
     5101 acgctgtgag ggtaaacaac tggcggtatg gatgcggcgg gtctgcctgg gtgagccggt
     5161 tgcccgctcc gggaggctgc cgacactggc accgccgtta ctgcgtcagc tggctgccat
     5221 cgggaataac ctgaatcaga cagcgaggaa ggtgaacagc gggcagtggt cttccggcga
     5281 ccgggttcag gtggtggccg cactgatggc catcgagaga gagttgcgca gcttacggca
     5341 ggtcgtcagg gaacagggag cgcggg
//
