LOCUS       NC_016903               5360 bp    DNA     circular CON 08-JUN-2013
DEFINITION  Escherichia coli KO11FL plasmid pEKO1102, complete sequence.
ACCESSION   NC_016903
VERSION     NC_016903.1  GI:378715370
DBLINK      Project: 52593
            BioProject: PRJNA52593
            BioSample: SRS084754
KEYWORDS    .
SOURCE      Escherichia coli KO11FL
  ORGANISM  Escherichia coli KO11FL
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5360)
  AUTHORS   Lucas,S., Copeland,A., Lapidus,A., Cheng,J.-F., Goodwin,L.,
            Pitluck,S., Munk,A.C., Detter,J.C., Han,C., Tapia,R., Land,M.,
            Hauser,L., Kyrpides,N., Ivanova,N., Ovchinnikova,G., Pagani,I.,
            Keating,D., Landick,R. and Woyke,T.
  CONSRTM   US DOE Joint Genome Institute
  TITLE     Complete sequence of plasmid2 of Escherichia coli KO11
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5360)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (21-FEB-2012) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 5360)
  AUTHORS   Lucas,S., Copeland,A., Lapidus,A., Cheng,J.-F., Goodwin,L.,
            Pitluck,S., Munk,A.C., Detter,J.C., Han,C., Tapia,R., Land,M.,
            Hauser,L., Kyrpides,N., Ivanova,N., Ovchinnikova,G., Pagani,I.,
            Keating,D., Landick,R. and Woyke,T.
  CONSRTM   US DOE Joint Genome Institute
  TITLE     Direct Submission
  JOURNAL   Submitted (07-FEB-2011) US DOE Joint Genome Institute, 2800
            Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence is identical to CP002518.
            URL -- http://www.jgi.doe.gov
            JGI Project ID: 4085738
            Source DNA and organism available from Robert Landick
            (landick@bact.wisc.edu)
            Contacts: Robert Landick (landick@bact.wisc.edu)
                      Tanja Woyke (microbe@cuba.jgi-psf.org)
            Annotation done by JGI-ORNL and JGI-PGF
            Finishing done by JGI-LANL
            The JGI and collaborators endorse the principles for the
            distribution and use of large scale sequencing data adopted by the
            larger genome sequencing community and urge users of this data to
            follow them. it is our intention to publish the work of this
            project in a timely fashion and we welcome collaborative
            interaction on the project and analysis.
            (http://www.genome.gov/page.cfm?pageID=10506376).
            
            ##MIGS-Data-START##
            investigation_type  :: bacteria_archaea
            project_name        :: Escherichia coli KO11
            collection_date     :: Missing
            lat_lon             :: Missing
            depth               :: Missing
            alt_elev            :: Missing
            country             :: Missing
            environment         :: Human intestinal microflora, Host
            num_replicons       :: 3
            ref_biomaterial     :: Missing
            biotic_relationship :: Free living
            trophic_level       :: Missing
            rel_to_oxygen       :: Facultative
            isol_growth_condt   :: Missing
            sequencing_meth     :: WGS
            assembly            :: Newbler v. 2.3 (pre-release)
            finishing_strategy  :: Finished
            GOLD Stamp ID       :: Gi04225
            Gene Calling Method :: JGI -ORNL annotation pipeline
            Cell Shape          :: Rod-shaped
            Motility            :: Motile
            Sporulation         :: Nonsporulating
            Temperature Range   :: Mesophile
            Temperature Optimum :: 37C
            Gram Staining       :: Gram-
            Diseases            :: None
            ##MIGS-Data-END##
            
            ##Genome-Assembly-Data-START##
            Finishing Goal           :: Finished
            Current Finishing Status :: Finished
            Assembly Method          :: Newbler v. 2.3
            Genome Coverage          :: 30x
            Sequencing Technology    :: 454-FLX, Illumina
            ##Genome-Assembly-Data-END##
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5360
                     /organism="Escherichia coli KO11FL"
                     /mol_type="genomic DNA"
                     /strain="KO11"
                     /db_xref="taxon:595495"
                     /plasmid="pEKO1102"
     gene            41..364
                     /locus_tag="EKO11_4770"
                     /db_xref="GeneID:11743927"
     CDS             41..364
                     /locus_tag="EKO11_4770"
                     /inference="protein motif:PFAM:PF05713"
                     /note="PFAM: mobilisation protein;
                     KEGG: eoj:ECO26_p3-3 putative mobilization protein 2"
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="YP_005280263.1"
                     /db_xref="GI:378715371"
                     /db_xref="InterPro:IPR008687"
                     /db_xref="GeneID:11743927"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPT
                     LAPPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQG
                     ARDDS"
     misc_feature    185..328
                     /locus_tag="EKO11_4770"
                     /note="Bacterial mobilisation protein (MobC); Region:
                     MobC; pfam05713"
                     /db_xref="CDD:218714"
     gene            354..1907
                     /locus_tag="EKO11_4771"
                     /db_xref="GeneID:11743921"
     CDS             354..1907
                     /locus_tag="EKO11_4771"
                     /inference="protein motif:PFAM:PF03432"
                     /note="PFAM: Relaxase/mobilization nuclease family
                     protein;
                     KEGG: eoj:ECO26_p3-4 mobilization protein MbeA"
                     /codon_start=1
                     /transl_table=11
                     /product="Relaxase/mobilization nuclease family protein"
                     /protein_id="YP_005280264.1"
                     /db_xref="GI:378715372"
                     /db_xref="InterPro:IPR005094"
                     /db_xref="GeneID:11743921"
                     /translation="MIVKFHARGKGGGSGPVDYLLGRERNREGATVLQGNPEEVRELI
                     DATPFAKKYTSGVLSFAEKELPPGGREKVMESFERVLMPGLEKNQYSILWVEHQDKGR
                     LELNFVIPNMELQTGKRLQPYYDRADRPRIDAWQTLVNHHYGLHDPNAPENRRTLILP
                     DNLPETKQALAESVTRGLEVLYHAGEIKGRQDVIQALTEVGLEVVRVTRSSISIADPN
                     GGRNIRLKGAFYEQSFTDGRGVREKAERESRIYRENAERRIQQARRICQRGCDLKRDE
                     NQRRYSPVYGLDGGIAEKTPGRGERGDDAAPEGHVKAGREFGHEVAGDSLSPVYREWR
                     DALVSRREDTDEPGRNQGTGRDIAETEREDMGCGVCSGRGKKISGHSARDVSRGDALS
                     GEGLDTTDGVIRNDRVGNTFAERLRAAATGLYAAAERMGERLRGIAEDVFAYATGQRD
                     AERAGHAVESAGTELERADRTLEPVIQRELEIREERLIQEREHALSLERERQPEIQER
                     TLDGPSLGW"
     misc_feature    <525..1064
                     /locus_tag="EKO11_4771"
                     /note="Relaxase/Mobilisation nuclease domain; Region:
                     Relaxase; pfam03432"
                     /db_xref="CDD:217554"
     gene            1983..2114
                     /locus_tag="EKO11_4772"
                     /pseudo
                     /db_xref="GeneID:11743922"
     gene            complement(2165..3145)
                     /locus_tag="EKO11_4773"
                     /db_xref="GeneID:11743926"
     CDS             complement(2165..3145)
                     /locus_tag="EKO11_4773"
                     /inference="similar to AA sequence:KEGG:Pcryo_2488"
                     /note="KEGG: pcr:Pcryo_2488 hypothetical protein"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005280265.1"
                     /db_xref="GI:378715373"
                     /db_xref="GeneID:11743926"
                     /translation="MDNNFTSYFTNPKYVTNYNFNGKGLIYIENERDYVFWESIFNAH
                     FDGMYEIKASIKNDGRRGKDALLELIPTLNKNCLLAIDGDFDYISECDYRFGKFMSNA
                     YVLHTHSYSRESAVFSKSKIDEVVSKLRLTLPCTFDVNKPIQIISKRYFKALVGFLYL
                     MKKNRDLAINIDIHKPIKKCEFRKYINNDFTSNDKIIQEMTSLLEPIENEIYSYIDER
                     SIEFSSFVEQANRKGLKEDSAYRFISGHVLNDNILLPMLARIKFLMERQSLRSIASED
                     TSRENKSNMISAIKNHYRDNCKVKTIITHLNLCANDEISKMIHSKVSAIH"
     gene            complement(3147..4154)
                     /locus_tag="EKO11_4774"
                     /db_xref="GeneID:11743923"
     CDS             complement(3147..4154)
                     /locus_tag="EKO11_4774"
                     /inference="similar to AA sequence:KEGG:Pcryo_2487"
                     /note="KEGG: pcr:Pcryo_2487 hypothetical protein"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005280266.1"
                     /db_xref="GI:378715374"
                     /db_xref="GeneID:11743923"
                     /translation="MSVKIKKLSIENLFDEYNVEWVLDDVNVLVGKNGKGKSVILNII
                     HSLLNKEESTEVNYCKKANIYLNDKRMISRRNDPSSSEFLKIIASQVLKGLSENKKEI
                     KKLAKIKNKEQEEKIKSEMELILEKLSSKDTDAPKGYFVEMGEKEKGKQEEKDKINTT
                     YISTINMSANSTNEIKKSSGEKVMVLDFEIKEEKDAALKKIASGSRSSEEKKTLLDVL
                     NGFFKDTKKEVVIEDDLIVFLEDKKTTIEIEKLSSGERQLIYTFLRVFNSERENQIIL
                     LDEPEISLHLSWQEILISSIKKIRDDCQIILVTHSPGIVMDGWMGAYKEIDSIITKAE
                     K"
     misc_feature    complement(<3924..4133)
                     /locus_tag="EKO11_4774"
                     /note="ATP-binding cassette transporter nucleotide-binding
                     domain; Region: ABC_ATPase; cl17201"
                     /db_xref="CDD:247755"
     misc_feature    complement(4041..4064)
                     /locus_tag="EKO11_4774"
                     /note="Walker A/P-loop; other site"
                     /db_xref="CDD:213179"
     misc_feature    complement(order(4038..4046,4050..4055))
                     /locus_tag="EKO11_4774"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:213179"
     misc_feature    complement(3210..>3647)
                     /locus_tag="EKO11_4774"
                     /note="AAA domain; Region: AAA_21; pfam13304"
                     /db_xref="CDD:222036"
     misc_feature    complement(3207..>3524)
                     /locus_tag="EKO11_4774"
                     /note="ATP-binding cassette transporter nucleotide-binding
                     domain; Region: ABC_ATPase; cd00267"
                     /db_xref="CDD:213179"
     misc_feature    complement(order(3225..3227,3318..3323,3405..3407,
                     3516..3524))
                     /locus_tag="EKO11_4774"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:213179"
     misc_feature    complement(3405..3410)
                     /locus_tag="EKO11_4774"
                     /note="Q-loop/lid; other site"
                     /db_xref="CDD:213179"
     misc_feature    complement(order(3372..3374,3378..3404))
                     /locus_tag="EKO11_4774"
                     /note="ABC transporter signature motif; other site"
                     /db_xref="CDD:213179"
     misc_feature    complement(3318..3335)
                     /locus_tag="EKO11_4774"
                     /note="Walker B; other site"
                     /db_xref="CDD:213179"
     misc_feature    complement(3300..3311)
                     /locus_tag="EKO11_4774"
                     /note="D-loop; other site"
                     /db_xref="CDD:213179"
     misc_feature    complement(3219..3239)
                     /locus_tag="EKO11_4774"
                     /note="H-loop/switch region; other site"
                     /db_xref="CDD:213179"
     gene            complement(4482..4922)
                     /locus_tag="EKO11_4775"
                     /db_xref="GeneID:11743924"
     CDS             complement(4482..4922)
                     /locus_tag="EKO11_4775"
                     /inference="similar to AA sequence:KEGG:NEMVE_v1g137021"
                     /note="KEGG: nve:NEMVE_v1g137021 hypothetical protein"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005280267.1"
                     /db_xref="GI:378715375"
                     /db_xref="GeneID:11743924"
                     /translation="MRYRIYSASSLTDSLRSVVRLRRAVPAYWRGGNILEDARKKLSR
                     EAIRPRQSRFSIGSAPLTSITKSDAQISGGETRQDLKIPGVSPWWLPRALSCSCLSVY
                     RCHSAVMAAVSHSTPDTRFREGSSLQAGLYARTPRSVRPQRLIR"
     gene            complement(5144..5335)
                     /locus_tag="EKO11_4776"
                     /db_xref="GeneID:11743925"
     CDS             complement(5144..5335)
                     /locus_tag="EKO11_4776"
                     /inference="protein motif:PFAM:PF01815"
                     /note="PFAM: regulatory protein Rop;
                     KEGG: rcu:RCOM_2091210 Regulatory protein rop, putative"
                     /codon_start=1
                     /transl_table=11
                     /product="regulatory protein Rop"
                     /protein_id="YP_005280268.1"
                     /db_xref="GI:378715376"
                     /db_xref="InterPro:IPR000769"
                     /db_xref="GeneID:11743925"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDH
                     ADELYRSCLSRFGDDGENM"
     misc_feature    complement(5153..5335)
                     /locus_tag="EKO11_4776"
                     /note="Rop protein; Region: Rop; pfam01815"
                     /db_xref="CDD:145136"
ORIGIN      
        1 ctgttcatgg ggggtaatga taccgatgaa acgagagagg atgctcacga tacgggttac
       61 tgatgatgaa catgcccggt tactggaacg ctgtgagggt aaacaactgg cggtatggat
      121 gcggcgggtc tgcctgggtg agccggttgc ccgctccggg aggctgccga cactggcacc
      181 gccgttactg cgtcagctgg ctgccatcgg gaataacctg aatcagacag cgaggaaggt
      241 gaacagcggg cagtggtctt ccggcgaccg ggttcaggtg gtggccgcac tgatggcgat
      301 cgagagagag ttgcgcagct tacggcaggt cgtcagggaa cagggagcgc gggatgatag
      361 ttaagtttca tgcccgggga aaaggtggtg gcagtggtcc ggttgattac cttctgggga
      421 gggagcgtaa ccgggaaggt gcaacggtac ttcagggtaa cccggaagaa gtccgggagc
      481 ttattgatgc cacgccattt gcgaagaaat acacgtccgg tgttctgtcg ttcgcagaga
      541 aggaactgcc gccgggagga cgtgaaaaag tgatggagag ctttgagcgc gtactgatgc
      601 ccggtctcga aaaaaatcag tacagcattc tgtgggtgga gcaccaggac aaggggcgtc
      661 ttgagctgaa ttttgtcatt ccgaacatgg agctacagac cggaaaacgc ctccagccgt
      721 actacgaccg ggcagacagg ccgagaattg atgcctggca gacactggtg aatcaccatt
      781 acgggctgca tgaccccaac gccccggaga accgcagaac gctgatcctc cctgataacc
      841 tgccggaaac gaaacaggcg cttgctgaga gcgttacacg aggcctggag gtgctttacc
      901 atgccgggga gataaaaggc cgtcaggatg tgattcaggc gctcacagag gtggggcttg
      961 aagtggtcag ggtgacgcga agcagtatca gcattgcaga cccgaacggc gggaggaata
     1021 tcagactgaa aggagcgttt tatgagcaat cttttacgga cgggcgcgga gttcgagaaa
     1081 aagctgaaag agagagccga atctacagag aaaatgctga acgacgaatt cagcaggctc
     1141 ggcgaatctg tcagcgaggc tgtgacctca aacgagacga aaatcaaagg cgctatagcc
     1201 cagtttacgg cctcgacgga ggaatcgctg aaaaaacacc gggaaggggt gaaagaggcg
     1261 atgatgcagc accggaagga catgttaaag ctggcaggga gttcgggcat gaggttgctg
     1321 gggatagtct ttctcctgtt taccgcgagt ggcgggacgc tctggtatct cggcgggagg
     1381 atacagacga acctggaaga aatcagggta caggaagaga cattgcggaa actgaacgcg
     1441 aagacatggg gtgtggagtt tgttcagggc gggggaagaa aatttctggt cattccgcaa
     1501 gggatgtcag cagaggtgac gcactatcag gggaaggact ggatacaact gacggagtga
     1561 tacggaatga cagagttgga aacacatttg ctgaacgcct tagagcagct gcaacaggac
     1621 tatatgcagc ggctgaacga atgggagagc gccttcgtgg aattgcagaa gatgttttcg
     1681 cttacgcaac aggacaacgc gatgctgaac gagcgggtca tgcagttgag tcagcaggta
     1741 cagaacttga gcgagcggac agaacacttg agccagttat acagcgagaa ctggagataa
     1801 gagaggaacg gttgatacag gagcgcgaac atgcgttatc cctggagcgt gagcgccagc
     1861 cggaaataca ggaacgcaca ctggatggtc cttcgctggg atggtgaaac tatgaaaaat
     1921 ggcaggttaa gtggattaag acgggctaat gtggtctgta ccatctggtt gcataggtat
     1981 tcatgcggtt aaaatttatc aggcgcgatc gcggcagttt ttcgggtggt ttgttgccat
     2041 ttttacctgt ctgctgccgt gatcgcaccg aacgcgtttc tgcggtgtgc gtaacagatg
     2101 ttatggtaaa ttaacaccgc atgactgatt cggacgccaa aaattcgtcc attgttccca
     2161 tcccttaatg tattgcagaa acctttgaat gtatcatttt gctgatttca tcattagcgc
     2221 aaagatttag gtgtgtaatt attgttttca ctttgcaatt gtctcgataa tggtttttta
     2281 ttgcagatat catgtttgac ttgttttctc tgctagtgtc ttcagatgct atagaacgga
     2341 gtgattgccg ctccattaaa aactttattc tggctagcat tggtagcaaa atgttatcat
     2401 taagaacatg ccctgatata aatctataag cgctatcctc ttttagtcct ttacggttag
     2461 cctgctctac aaaagaggaa aactctatag atctctcatc tatgtatgag taaatctcat
     2521 tttcgattgg ttcaagcaag gatgtcattt cttgaatgat cttatcattg ctagtgaagt
     2581 cgttgtttat gtactttctg aattcacatt tctttattgg tttatgtatg tcgatgttta
     2641 ttgctaggtc tctatttttt ttcatgaggt acaaaaaacc gacaagcgct ttgaaatatc
     2701 ttttagatat aatttgaatc ggtttgttta catcaaaggt gcaaggcaat gttagcctta
     2761 gtttgctaac aacttcatct atttttgatt ttgaaaaaac agcactttcc cgtgaataac
     2821 tgtgcgtatg caagacatac gcatttgaca taaacttacc aaatcggtag tcgcattctg
     2881 atatgtaatc aaaatcacca tcgatggcca aaagacaatt tttatttaat gttggaatca
     2941 attccagcaa tgcatcttta ccgcgccttc catcattctt aatggatgct ttaatttcat
     3001 acattccgtc aaagtgtgca ttgaatatag actcccaaaa gacgtaatct ctctcatttt
     3061 ctatgtaaat caagccctta ccattaaaat tgtagtttgt tacatatttt gggttggtaa
     3121 agtatgatgt gaagttgtta tccattttac ttctcggctt tagtaattat agaatcaatc
     3181 tctttgtatg cacccatcca cccgtccatt actattccag ggctgtgggt tactaatatt
     3241 atttggcaat catctcttat tttttttatt gatgaaatta gtatttcttg ccatgaaaga
     3301 tgtagagata tctcaggttc atccagaagt attatttggt tttctctctc agaattaaag
     3361 accctaagaa atgtataaat cagctgtctc tctccagatg ataatttttc tatttctata
     3421 gttgtttttt tatcttctag aaaaactatt aaatcatcct ctattaccac ctcttttttc
     3481 gtgtctttaa aaaaaccatt taaaacatca agtaatgttt tcttttcttc gctgctcctt
     3541 gagccgcttg ctattttttt taatgcggca tccttctcct cttttatttc aaagtctaat
     3601 accatcactt tttcgcctga acttttcttt atttcatttg ttgagttggc actcatgtta
     3661 atggttgata tgtaagttgt attgatttta tctttttctt cttgctttcc tttctctttt
     3721 tcccccatct caacgaaata tccttttgga gcgtcagtgt ctttggaaga tagcttttcc
     3781 aaaatcaact ccatttctga tttaatcttc tcctcttgct ctttgttttt tatttttgca
     3841 agctttttta tttctttttt attttcagac aggcctttaa gcacctggga tgctattatt
     3901 tttaaaaact cacttgaaga tgggtcgttt cttcttgata tcattcgttt atcatttaag
     3961 taaatattgg cctttttgca ataatttact tctgtggact cttctttatt tagtaggctg
     4021 tgaataatat tcaatattac agacttgcct ttcccattct tccccactaa tacattaaca
     4081 tcgtccaaaa cccattcaac attatattca tcgaagaggt tctctatact taattttttt
     4141 atttttacgc tcattaatct accgacctga taatccatta tgtttgatga gtaacactgt
     4201 agcttgattc tcgcttcaac ttaagcataa tgaagaagtt gaaaaaaaaa accaccgcta
     4261 ccaacggtgg tttttctaag gttctctgag ctaccaactc tttgaaccat ggtagcaggg
     4321 tgtacaagac cgctgaaacc aaattctgtc ctttcagttt agccgtagtt gggctgagaa
     4381 ttcaagaact ctgcatcagt aatctcttgt acaccctctt accaatggcc gcagccagtg
     4441 gcgttttgtt gtgtctttcc gggttggact caagtcgata gttaccggat aagacgctgc
     4501 ggtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact gccttcccgg
     4561 aaccgagtgt caggcgtgga atgagaaacc gcggccataa cagcggagtg acaccggtaa
     4621 accgaaaggc aggaacagga gagcgcacga gggagccacc agggggaaac gcctggtatc
     4681 tttaagtcct gtcgggtttc gccaccactg atttgagcgt cagatttcgt gatgcttgtc
     4741 aggggggcgg agcctatgga aaaacggctt tgccgtggcc ttatcgcttc cctgctaagt
     4801 ttcttcctgg catcttccag gatatttccg ccccgccagt aagccggtac cgctcgccgc
     4861 agccgaacga ccgagcgcag cgagtcagtg agcgaggaag cggaatatat cctgtatcgc
     4921 atattctgct gacgcgcctg tgccgccttt tttctcctgt cacatgaagc acttcactga
     4981 tttccgcatc catgccaaca tagtaagcca gtatacactc cgctatcgct acgtgactgg
     5041 ttcagggctt cgccccgaaa ccccctgacg cgccctgacg ggcttgtctg ctcccggcat
     5101 ccgctcacag gcaagctgtg accgtctccg ggagctacat gtgttacatg ttttcaccgt
     5161 catccccgaa gcgtgagagg cagctgcggt aaagctcatc agcgtggtcg tgaagcgatt
     5221 cacatatatc tgcctgttcg tccgcgtcca gctcgttgag tttctccaga agcgttaatg
     5281 tctggcttct gataaagcgg gccatgttaa gggcggtttt ttcctgttta gtcactgatg
     5341 cctccgtgta agggggattt
//
