LOCUS       NC_015657               5448 bp    DNA     circular BCT 16-JUN-2011
DEFINITION  Frankia symbiont of Datisca glomerata plasmid pFSYMDG02, complete
            sequence.
ACCESSION   NC_015657
VERSION     NC_015657.1  GI:336176136
DBLINK      Project: 46257
KEYWORDS    .
SOURCE      Frankia symbiont of Datisca glomerata
  ORGANISM  Frankia symbiont of Datisca glomerata
            Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales;
            Frankineae; Frankiaceae; Frankia.
REFERENCE   1  (bases 1 to 5448)
  AUTHORS   Lucas,S., Han,J., Lapidus,A., Cheng,J.-F., Goodwin,L., Pitluck,S.,
            Peters,L., Mikhailova,N., Chertkov,O., Teshima,H., Han,C.,
            Tapia,R., Land,M., Hauser,L., Kyrpides,N., Ivanova,N., Pagani,I.,
            Berry,A., Pawlowski,K., Persson,T., Vanden Heuvel,B., Benson,D. and
            Woyke,T.
  CONSRTM   US DOE Joint Genome Institute
  TITLE     Complete sequence of plasmid 2 of Frankia symbiont of Datisca
            glomerata
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5448)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (15-JUN-2011) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 5448)
  AUTHORS   Lucas,S., Han,J., Lapidus,A., Cheng,J.-F., Goodwin,L., Pitluck,S.,
            Peters,L., Mikhailova,N., Chertkov,O., Teshima,H., Han,C.,
            Tapia,R., Land,M., Hauser,L., Kyrpides,N., Ivanova,N., Pagani,I.,
            Berry,A., Pawlowski,K., Persson,T., Vanden Heuvel,B., Benson,D. and
            Woyke,T.
  CONSRTM   US DOE Joint Genome Institute
  TITLE     Direct Submission
  JOURNAL   Submitted (19-MAY-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 CP002803.
            URL -- http://www.jgi.doe.gov
            JGI Project ID: 4085684
            Source DNA and organism available from David Benson
            (david.benson@uconn.edu)
            Contacts: David Benson (david.benson@uconn.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           :: Frankia symbiont of Datisca glomerata
            collection_date        :: Missing
            lat_lon                :: Missing
            depth                  :: Missing
            alt_elev               :: Missing
            country                :: Missing
            environment            :: Host, Plant symbiont, Soil
            num_replicons          :: 3
            ref_biomaterial        :: Missing
            biotic_relationship    :: Symbiotic
            trophic_level          :: Chemoorganotroph
            rel_to_oxygen          :: Aerobe
            isol_growth_condt      :: Missing
            sequencing_meth        :: WGS
            assembly               :: Newbler v. 2.3 (pre-release)
            finishing_strategy     :: Finished
            GOLD Stamp ID          :: Gi04474
            Funding Program        :: DOE-CSP 2007
            Isolation Site         :: Datisca glomerata
            Host Name              :: Datisca glomerata
            Cell Shape             :: Filament-shaped
            Motility               :: Nonmotile
            Sporulation            :: Sporulating
            Temperature Range      :: Mesophile
            Gram Staining          :: Gram+
            Symbiotic Relationship :: Mutualistic
            Diseases               :: None
            Phenotypes             :: Non-Pathogen
            ##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/Illumina
            ##Genome-Assembly-Data-END##
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5448
                     /organism="Frankia symbiont of Datisca glomerata"
                     /mol_type="genomic DNA"
                     /strain="4085684"
                     /host="Datisca glomerata"
                     /db_xref="taxon:656024"
                     /plasmid="pFSYMDG02"
     gene            211..3903
                     /locus_tag="FsymDg_4560"
                     /db_xref="GeneID:10785245"
     CDS             211..3903
                     /locus_tag="FsymDg_4560"
                     /EC_number="3.1.26.4"
                     /inference="protein motif:PRIAM:3.1.26.4"
                     /note="KEGG: vpo:Kpol_1037p34 Tkp1 protein;
                     PFAM: Integrase, catalytic core"
                     /codon_start=1
                     /transl_table=11
                     /product="Ribonuclease H"
                     /protein_id="YP_004585717.1"
                     /db_xref="GI:336176137"
                     /db_xref="InterPro:IPR001584"
                     /db_xref="GeneID:10785245"
                     /translation="MASNDIISTNVPSKVPTTDTEEYPVQHGSAAKTPIVPSDNQASP
                     EESGSIDVEHKANADDEASGSHEGHHENFSKDSTKTGTPQDTLHKEPVDGSPVPNYAQ
                     QSWYYHTQPPPQFYPSPYANYGPGPYTPPWANMNMPIPGANTNPDKTGGHYQTTGPSG
                     DSSQYNPAYYFPYQLEPKPGLQSQTTTECTFGQLHNPRKTFTLSKVNSPHYYDSWVRE
                     MCQAMLEQNLGHLIPTEDNKTPETPEPAEKRYIEEIHIACVPEEKYPKWLKSSYDEGE
                     ALIDCFKEGIRRIKAEEDPEAIVLALAGLTLDYRESIPNFAKRLRKIHQRTVNAKFPM
                     AEKIVISRALKALPERYEKVDINFTKSNDQSFNNFINILLTTEPRMKSSNQYDNQPVS
                     VIYDKKLIHNFTSQSNQILVDVQQNEVAVKGEGNLELKFKGKRISLPAIYAPSTHTNI
                     ISVEDLTKSQAYLDLRRNCLLSKNGKTIAPTHKFAGLRWLSRKNAIELPNQTQSVYAI
                     TPRSVRSAPDKFSLTSIHNMFGHMNINYIRESFRKGLIQGVKEDDVDWTGVSSFQCQY
                     CMEGKAKRNNHYVNARKDYTKEYLPFEYLHTDVFGPVRVQRTRTTPRYFIAFIDEVTK
                     YIWTFPLLHKTAEEVAPTFKEVVMLIYTQFNTRVKTIQMDKGSEYLNTKVQKFLRERG
                     IVSRETTVADSKANGAIERQHYTLLNDCRTFLRQANLRPRLWYHAVVYSTVMRNSLLN
                     RSIGTSPRNRAGMSGLSFRDILPFGQPVIVHLPNPKSKLQARGVLGYALHPSTRSYGY
                     IIVVGKKKKIPIDTRNYRVLNYPPGATISEDEVQYMIDRMENNDAESQGDIESNFEPN
                     YTDMEQPIHHTADYFPNTTASNIETDQYNNDSFGLHYGGDSVPPESSSSEDELFPTDE
                     SENDSDSSDQSFNDDGDPMSPPYSGGEEQLVPTAAPIRRVPPMEPPSPVEDSPPPLSG
                     TDLDDLFGESNINNYIPEDTDLLALNHESVPEPDTAVPATTNIEQDNVLPLETNENSN
                     PPNDSSDQSGDESGEQSGEESGEESVDNRLKSIPIFNGNKHKDARIAEADLDSLYGGG
                     DNTENNNGPTLEEVFRSIEEDPFMLTQKRPRSRARYRESNQDSCDSGGDYESSSDSDG
                     SSDESPQKGRKIQRVNYVNAVQKPVSVIPLNMSLNYSQAISRNRNEEEKDAFQKAYQK
                     EIAQLTKMNTWNEELIDASTLPKKRF"
     misc_feature    1981..2340
                     /locus_tag="FsymDg_4560"
                     /note="Integrase core domain; Region: rve; cl01316"
                     /db_xref="CDD:194099"
     gene            3909..5333
                     /locus_tag="FsymDg_4561"
                     /db_xref="GeneID:10785244"
     CDS             3909..5333
                     /locus_tag="FsymDg_4561"
                     /EC_number="3.1.26.4"
                     /inference="protein motif:PRIAM:3.1.26.4"
                     /note="KEGG: sce:YDR210C-D Retrotransposon TYA Gag and TYB
                     Pol genes; transcribed/translated as one unit; polyprotein
                     is processed to make a nucleocapsid-like protein (Gag),
                     reverse transcriptase (RT), protease (PR), and integrase
                     (IN); similar to retroviral genes;
                     PFAM: Reverse transcriptase, RNA-dependent DNA polymerase"
                     /codon_start=1
                     /transl_table=11
                     /product="Ribonuclease H"
                     /protein_id="YP_004585718.1"
                     /db_xref="GI:336176138"
                     /db_xref="InterPro:IPR013103"
                     /db_xref="GeneID:10785244"
                     /translation="MFIFTTKRDNSKKCRLVARGDQQAADTYDTELKANTVDNLALMT
                     VLALTLDYNLTAFQLDISSAYLYADLKEELYIRAPPHMNAKNKVLRLNKSLYGLKQSG
                     ANWYELIRSFLIKKCDLIEDRMWKCVFRDKEPLKLIICLFVDDMLVVGNDVKYIKKFI
                     SKLSKRFDTKIVNDGSHRPEDGVNEYDILGIELEYKKKEYMKFGMQKSLEDKLPQLGI
                     PLLPNAKIRKVPGVPGDYIFSGKELKLNEREYKSKVKHLQRIVGLASYVGHKFRFDIL
                     YYVNILAQHQLYPSAKVLDRAAQLCQYLWDTRDKKLVWHYSGPKENNVTAVSDAAFAG
                     NQDFKSQSGTLYLRNNKPIAAKSRKIKLTCISSTEAEIYAISESLPILRGLEHLVNKL
                     QDIKATVKVKTDSQPSMAIINGTDDSACLKKHIGSRAMRIRDECDDLGLTLEYIPTKE
                     NNADVLTKPLSVKLFKLLTEDWIQ"
     misc_feature    3915..4532
                     /locus_tag="FsymDg_4561"
                     /note="Reverse transcriptase (RNA-dependent DNA
                     polymerase); Region: RVT_2; pfam07727"
                     /db_xref="CDD:149018"
     misc_feature    4884..5303
                     /locus_tag="FsymDg_4561"
                     /note="Ty1/Copia family of RNase HI in long-term repeat
                     retroelements; Region: RNase_HI_RT_Ty1; cd09272"
                     /db_xref="CDD:187696"
     misc_feature    order(4893..4904,5004..5012,5019..5021,5118..5120,
                     5199..5201,5280..5282)
                     /locus_tag="FsymDg_4561"
                     /note="RNA/DNA hybrid binding site [nucleotide binding];
                     other site"
                     /db_xref="CDD:187696"
     misc_feature    order(4893..4895,5019..5021,5118..5120,5256..5258)
                     /locus_tag="FsymDg_4561"
                     /note="active site"
                     /db_xref="CDD:187696"
ORIGIN      
        1 gctaaagcat ttgataattg atttgattcc aaaaagtata taagtagaag gtttcttcat
       61 ccaattccca ctttcgaatt gacaacttac ttactatcca attataagtc aagtcagaag
      121 aaaccaagga gaacaacagt aaatacttac ttatctagtg aatccaacaa ttcaattacc
      181 aattaattaa tccaacagct tcaagtcaaa atggcatcca acgacattat ttctactaac
      241 gtcccttcta aggtccctac taccgatact gaggaatatc cagtccaaca tggtagcgcc
      301 gctaagacac ctattgtccc ctcagacaat caggcaagtc cagaggaatc aggtagcatc
      361 gatgtcgagc ataaggccaa tgccgacgac gaagcgtccg gatcccacga aggtcatcat
      421 gaaaattttt caaaggattc aacaaaaacc ggaactccac aggacaccct acacaaagag
      481 cctgtggacg gttctcccgt tccaaattac gcccaacaaa gctggtacta ccatacacag
      541 ccaccgccac agttttatcc atctccttac gctaattatg ggcctggtcc ttacactcct
      601 ccgtgggcca acatgaatat gcccatccca ggagctaaca cgaacccaga taaaactgga
      661 ggacattatc aaacaacggg tccatctggg gacagctccc aatacaaccc tgcttactac
      721 ttcccgtacc aattggaacc aaaaccaggg ttgcaaagcc aaacaacgac cgaatgtact
      781 ttcggccaat tgcacaatcc cagaaaaaca tttactctgt caaaggtaaa ctcacctcac
      841 tattacgaca gctgggtaag agaaatgtgc caggcaatgc tcgagcaaaa cttgggccac
      901 ctcattccaa cagaggataa caaaacccca gaaaccccag aacctgcaga gaagaggtac
      961 atagaagaaa tccatatagc atgtgtgcct gaagaaaaat acccaaagtg gttaaagtcg
     1021 agttacgacg aaggtgaagc actaattgac tgcttcaagg aaggaattag aagaataaag
     1081 gcagaagaag atcctgaggc aatcgtgcta gccctagctg gactaacact agactacaga
     1141 gagtctattc ccaacttcgc caagagatta aggaaaatcc accagagaac ggtaaacgca
     1201 aaattcccaa tggcagaaaa gatcgtcatt tccagagcac taaaggctct accagaacga
     1261 tacgagaaag ttgatatcaa cttcaccaaa tcaaacgatc agagtttcaa taacttcata
     1321 aacatcctcc taacaactga gccaagaatg aaaagctcaa atcaatatga taatcaacca
     1381 gtctctgtga tatatgacaa aaagttaatt cacaatttta catctcaatc taatcaaatt
     1441 cttgtcgacg ttcaacaaaa cgaagtcgcc gttaaaggtg agggtaactt agaactcaag
     1501 tttaagggca aacgaatttc cctacccgcc atatatgcac catcaacaca caccaatatc
     1561 atcagtgtag aagatctaac aaaatcacag gcgtatctag atctaagaag gaactgcctg
     1621 ctatccaaga acgggaaaac catcgctccg acgcacaagt tcgcgggcct aaggtggtta
     1681 tctcgcaaaa atgctataga actaccaaac cagactcaat cagtctacgc aatcacaccc
     1741 agatcggtaa gatctgcgcc agacaagttc tctctgacaa gcatccacaa catgtttgga
     1801 catatgaata tcaattacat ccgagaatca ttcagaaaag gcttaattca aggtgtgaaa
     1861 gaagacgatg tagactggac aggagtaagc tcattccaat gccaatactg tatggaagga
     1921 aaagccaaac gtaataacca ttacgtgaac gctagaaaag attatacgaa ggaatatctt
     1981 cctttcgaat acttgcatac cgacgttttt ggaccagtaa gagtacaaag aacccgtact
     2041 actccaaggt acttcattgc attcatagac gaggtcacaa aatacatatg gaccttcccg
     2101 ttactacata aaacagcaga agaagtagcc ccgacattca aggaagtcgt catgctgatt
     2161 tatacacagt tcaacacgag agtgaaaacc atccaaatgg acaaaggatc ggaatacctg
     2221 aacactaagg tacagaaatt cctaagggaa agaggaattg tttcgagaga aacgaccgtt
     2281 gctgattcaa aagcaaatgg agccatagaa agacagcact atacactctt gaatgactgt
     2341 agaacgttct tgcgacaagc taacctacgc cctagattgt ggtatcatgc cgtcgtatac
     2401 tctacagtaa tgagaaattc actcctaaat agaagtatag gaacgtcccc gagaaacagg
     2461 gcggggatgt cgggactgtc attcagagac attcttccct tcggacaacc cgtgattgtc
     2521 cacttaccca acccaaaatc gaaactacaa gctcgaggag tcctaggcta tgctctccat
     2581 ccatccacta gatcatacgg ctacatcata gtcgtaggaa agaagaagaa aatacctatc
     2641 gacactcgaa actaccgagt cctgaactac ccaccaggtg caacaatctc agaagatgag
     2701 gtacagtaca tgatcgaccg tatggaaaat aacgacgcag aatctcaagg cgatatagag
     2761 tcgaactttg aaccaaatta tacggatatg gagcaaccca ttcaccacac agcggactat
     2821 ttcccgaaca caaccgcctc aaacatcgag acagaccaat acaataatga tagcttcggt
     2881 ctgcattacg ggggtgattc agtaccaccc gagtcgtcca gtagcgagga cgaactgttc
     2941 cccacagacg aatcagaaaa cgattcagac tcatcggacc aatcattcaa tgatgatgga
     3001 gaccccatgt cccctccata ttccgggggt gaggaacagt tagtaccgac agcagccccg
     3061 attagacgcg ttccaccaat ggaaccacca tctcctgtcg aggactctcc cccaccgtta
     3121 tctgggacag accttgacga cttatttgga gaatctaaca taaataatta catcccagaa
     3181 gatacagatc tactggcact aaaccatgaa tctgttccgg aacccgatac cgcggtacca
     3241 gcaacaacga acattgaaca agataatgtt ctaccattag aaactaacga aaactctaac
     3301 cctccaaatg atagctcgga ccagtcaggc gacgagtcag gcgaacagtc aggcgaagag
     3361 tccggcgagg agtcagtcga caacagactc aagtccatac ctattttcaa tggaaacaag
     3421 cacaaagatg caagaattgc tgaagcagat ttggattctt tgtacggggg tggagataat
     3481 acagaaaata acaatggacc aactttagaa gaggtgttca gatcgatcga agaagatcca
     3541 ttcatgctaa cacagaaaag accgagatca cgtgcccgat atcgagaatc taaccaagac
     3601 agttgcgatt ccgggggtga ctacgagtca agttcagact cagacgggtc atctgacgag
     3661 tcacctcaga agggaagaaa gatacaacgg gtaaactacg taaacgcggt tcagaaacct
     3721 gtgagtgtga tcccattgaa tatgtccttg aactattccc aggcaatatc tcggaacaga
     3781 aacgaagaag agaaggatgc tttccagaag gcataccaga aggaaatagc acagctaacc
     3841 aaaatgaaca catggaacga agaattaata gatgcctcta ctcttcctaa gaaaagattc
     3901 taaactcaat gttcattttc accactaaaa gagataactc caagaagtgc agactagtcg
     3961 ctagaggtga ccaacaagcc gcagacacgt atgacactga attaaaggca aatacagtgg
     4021 acaacctagc tctcatgaca gtcttagcac tgacactaga ctacaacctg accgcattcc
     4081 aacttgacat ctcatcagct tacctctacg ctgaccttaa ggaagaattg tacattagag
     4141 caccaccaca catgaatgcc aagaacaagg tactaagact aaataaatca ctctatgggc
     4201 taaaacagag tggagcaaat tggtacgaac taatcagatc gttcctaatt aagaaatgtg
     4261 acctgattga agatagaatg tggaagtgcg tttttagaga caaagaaccg ctgaaactta
     4321 ttatatgtct ttttgtcgat gacatgctgg ttgtaggaaa cgacgtcaag tatatcaaga
     4381 aattcatatc aaagctatct aagagatttg atacaaagat tgtaaatgat ggttcacaca
     4441 ggccagaaga tggagtaaac gagtatgaca ttttgggcat agaattagag tataagaaaa
     4501 aagaatacat gaagttcgga atgcagaagt ctctagagga caagctgcca caactgggaa
     4561 tacccctact cccaaacgct aaaatcagga aggttccggg ggtgcctgga gactacatct
     4621 tctcaggaaa ggaactgaaa ttaaatgaaa gagaatataa aagcaaagtt aaacacctgc
     4681 aaagaattgt aggactagcg tcctacgtag gacataagtt ccggtttgac atcttgtact
     4741 acgtgaacat cttagcacaa catcaactgt atcccagcgc caaggtccta gacagggctg
     4801 cacaattatg ccaatacttg tgggatacaa gagataagaa actagtttgg cattattctg
     4861 gtcccaagga aaacaacgtt accgctgtat cagatgcagc atttgcaggg aaccaagatt
     4921 ttaaatcaca atcaggaact ctttacctga gaaacaacaa gcccatagca gcaaaatcaa
     4981 gaaaaatcaa gttaacttgt atctcgtcca cagaagccga gatatacgca atcagtgaaa
     5041 gcctgccaat actacgtggg ttagaacacc tagtaaacaa gttacaagac ataaaagcaa
     5101 cagtaaaggt taaaacagac agtcaaccat caatggcaat aataaacggc acggatgact
     5161 cagcatgcct caagaaacac attggtagta gggcaatgag gataagagat gagtgcgatg
     5221 atctcggact tacactcgaa tatatcccca caaaagaaaa caatgctgac gttttaacca
     5281 aacccctatc cgtgaagcta ttcaaacttc tcacagagga ctggatacaa tagctttctc
     5341 ctagtagggg gtgtgttgat cctggacgtc ctacgacgtt gtctagggcg ccagatatta
     5401 taccaactat aaaagctaag gctaaagcct agatatacta ggatcaag
//
