GenomeNet

Database: RefSeq
Entry: NC_017092
LinkDB: NC_017092
Original site: NC_017092 
LOCUS       NC_017092               8406 bp    DNA     linear   CON 11-JUN-2013
DEFINITION  Rahnella aquatilis CIP 78.65 = ATCC 33071 plasmid pRahaq203,
            complete sequence.
ACCESSION   NC_017092
VERSION     NC_017092.1  GI:383192418
DBLINK      Project: 86855
            BioProject: PRJNA86855
KEYWORDS    GSC:MIGS:2.1; RefSeq.
SOURCE      Rahnella aquatilis CIP 78.65 = ATCC 33071
  ORGANISM  Rahnella aquatilis CIP 78.65 = ATCC 33071
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
            Enterobacteriaceae; Rahnella.
REFERENCE   1  (bases 1 to 8406)
  AUTHORS   Martinez,R.J., Bruce,D., Detter,C., Goodwin,L.A., Han,J., Han,C.S.,
            Held,B., Land,M.L., Mikhailova,N., Nolan,M., Pennacchio,L.,
            Pitluck,S., Tapia,R., Woyke,T. and Sobecky,P.A.
  TITLE     Complete genome sequence of Rahnella aquatilis CIP 78.65
  JOURNAL   J. Bacteriol. 194 (11), 3020-3021 (2012)
   PUBMED   22582378
REFERENCE   2  (bases 1 to 8406)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (02-APR-2012) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 8406)
  AUTHORS   Lucas,S., Han,J., Lapidus,A., Cheng,J.-F., Goodwin,L., Pitluck,S.,
            Peters,L., Ovchinnikova,G., Held,B., Detter,J.C., Han,C., Tapia,R.,
            Land,M., Hauser,L., Kyrpides,N., Ivanova,N., Pagani,I., Sobecky,P.,
            Martinez,R. and Woyke,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-JAN-2012) 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 CP003247.
            URL -- http://www.jgi.doe.gov
            JGI Project ID: 4089211
            Source DNA and organism available from Robert Martinez
            (rmartinez@bama.ua.edu)
            Contacts: Robert Martinez (rmartinez@bama.ua.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        :: Rahnella aquatilis CIP 78.65
            collection_date     :: Missing
            lat_lon             :: Missing
            depth               :: Missing
            alt_elev            :: Missing
            country             :: Missing
            environment         :: Host
            num_replicons       :: 4
            ref_biomaterial     :: Missing
            biotic_relationship :: Missing
            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       :: Gi06369
            Type Strain         :: Yes
            Funding Program     :: DOE-CSP 2010
            Gene Calling Method :: Prodigal 1.4, GenePRIMP
            Isolation Site      :: drinking water
            Host Name           :: Water, humans
            Cell Shape          :: Rod-shaped
            Temperature Range   :: Mesophile
            Gram Staining       :: Gram-
            ##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..8406
                     /organism="Rahnella aquatilis CIP 78.65 = ATCC 33071"
                     /mol_type="genomic DNA"
                     /strain="CIP 78.65"
                     /isolation_source="drinking water"
                     /culture_collection="ATCC:33071"
                     /db_xref="taxon:745277"
                     /plasmid="pRahaq203"
     gene            167..598
                     /locus_tag="Rahaq2_5114"
                     /note="IMG reference gene:2506712136"
                     /db_xref="GeneID:11954049"
     CDS             167..598
                     /locus_tag="Rahaq2_5114"
                     /note="PFAM: Domain of unknown function DUF29;
                     manually curated"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005459729.1"
                     /db_xref="GI:383192419"
                     /db_xref="InterPro:IPR002636"
                     /db_xref="GeneID:11954049"
                     /translation="MTARYETDFYGWTREQADLLRNGRFSELDTQNLLEEIEAMGTSA
                     ETELESRLEVLFIHMLKCQLLSEHQARSWKLTIEEQRRKIERSLRKSPSIRHKLPEII
                     GDAYGDAVIGAERETHIKRSVFPAECPWSFEQFMDPKFYPE"
     misc_feature    176..592
                     /locus_tag="Rahaq2_5114"
                     /note="Domain of unknown function DUF29; Region: DUF29;
                     pfam01724"
                     /db_xref="CDD:250818"
     gene            complement(1524..1934)
                     /locus_tag="Rahaq2_5115"
                     /note="IMG reference gene:2506712137"
                     /db_xref="GeneID:11954042"
     CDS             complement(1524..1934)
                     /locus_tag="Rahaq2_5115"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005459730.1"
                     /db_xref="GI:383192420"
                     /db_xref="GeneID:11954042"
                     /translation="MAKISISEASRLTGKSRTTLHRLIKAGELSSCSGMKNTKLLDTS
                     ELLRVFGTLSSVQPAQLDGQVTGQRFTSETAQSEQVHQQLTQEVEHLRELVTAQQSHI
                     DSLKQAMLLLEHKKEIQPVAAASDNSPWWRFWKS"
     misc_feature    complement(1791..1925)
                     /locus_tag="Rahaq2_5115"
                     /note="Helix-turn-helix domain; Region: HTH_17; pfam12728"
                     /db_xref="CDD:257254"
     gene            complement(4109..4813)
                     /locus_tag="Rahaq2_5116"
                     /note="IMG reference gene:2506712138"
                     /db_xref="GeneID:11954043"
     CDS             complement(4109..4813)
                     /locus_tag="Rahaq2_5116"
                     /codon_start=1
                     /transl_table=11
                     /product="serine/threonine protein phosphatase"
                     /protein_id="YP_005459731.1"
                     /db_xref="GI:383192421"
                     /db_xref="InterPro:IPR001932"
                     /db_xref="GeneID:11954043"
                     /translation="MTVRMDFITSTGTRDRNLDRFLEVKTDFLSVFIMLDGFSQTDAN
                     PHYVDSLIDEMRDKILSGMGFEDVISVMENIQSSSVKCSGKSSIGVVLISDTEVKTMT
                     VGDVRIYFLIDGKRSLDDSLAQFLVSSGVSNPHFLNKHPYRNRLTKYLSKDSIHPIPA
                     FSSKRIINGEAIFMCTDGFWSNFEDREILEVTLDGKLTTMFNDVMHSNDENIDNASVA
                     LLRFNLADEEQQLALA"
     misc_feature    complement(4118..>4618)
                     /locus_tag="Rahaq2_5116"
                     /note="Serine/threonine phosphatases, family 2C, catalytic
                     domain; The protein architecture and deduced catalytic
                     mechanism of PP2C phosphatases are similar to the PP1,
                     PP2A, PP2B family of protein Ser/Thr phosphatases, with
                     which PP2C shares no sequence...; Region: PP2Cc; cl00120"
                     /db_xref="CDD:260203"
     gene            complement(4823..5692)
                     /locus_tag="Rahaq2_5117"
                     /note="IMG reference gene:2506712139"
                     /db_xref="GeneID:11954044"
     CDS             complement(4823..5692)
                     /locus_tag="Rahaq2_5117"
                     /note="PFAM: Domain of unknown function (DUF1814)"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005459732.1"
                     /db_xref="GI:383192422"
                     /db_xref="InterPro:IPR014942"
                     /db_xref="GeneID:11954044"
                     /translation="MEFSIEEWVSLSPADRVVFRQSVHIVLSAIANSEYLKPKMIMKG
                     GMLLGIRYKSSRFTEDIDFSTKMKLSEIDQEEFRKELDDALVISSDELAYGVSCKVQS
                     LVIQPKKGYDKATFPSFNLTIGYARKNSAGEMDRLSRGQCPNTIKIDYSFNELSYSID
                     NIVMDDGSGVSAYGVTDLVAEKIRSIIQQPYRNRSRRQDVYDLDFIFDSICFDDGEKL
                     TILHSLLDKSTGRIPDGHITKDTLDREDIRDLSRRNYDTLHLEVEGDVKDFDFSFDRI
                     NEFYKSLPWDAVA"
     misc_feature    complement(4868..5620)
                     /locus_tag="Rahaq2_5117"
                     /note="Nucleotidyl transferase of unknown function
                     (DUF1814); Region: DUF1814; pfam08843"
                     /db_xref="CDD:255068"
     gene            complement(5705..6602)
                     /locus_tag="Rahaq2_5118"
                     /note="IMG reference gene:2506712140"
                     /db_xref="GeneID:11954045"
     CDS             complement(join(5705..6196,6198..6602))
                     /locus_tag="Rahaq2_5118"
                     /artificial_location="low-quality sequence region"
                     /note="manually curated"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005459733.1"
                     /db_xref="GI:383192423"
                     /db_xref="GeneID:11954045"
                     /translation="MIKETISLREALKTIILERHAKPVINAYEIAWYLYELYRDKNFE
                     GVRLGKISAKEPDFRVIADVQHFLLSRGLISKCIDNTIYSINNRNPPTAQQVVCCMSP
                     CSYISHISAMEWHGITDRIPKILHITQSSSRFLRIFFSEKIKNTFSLVNDSHFLYPQN
                     ITGIDFFDGKEIIFHKKNNFKMKKEQYGSGGVRVTNIGETFLDMLKEPDLCGGFEHVF
                     SVFENYHEKFLPVILKEISKNGNSMDKARAGYILEEVIGIKNKVIESWKDDVKRGGSR
                     KLIPSNPYKNVFSETWCISINN"
     misc_feature    complement(6468..>6575)
                     /locus_tag="Rahaq2_5118"
                     /note="Protein of unknown function (DUF2419); Region:
                     DUF2419; pfam10343"
                     /db_xref="CDD:255922"
     misc_feature    complement(join(5987..6196,6198..6401))
                     /locus_tag="Rahaq2_5118"
                     /note="Domain of unknown function (DUF4095); Region:
                     DUF4095; pfam13338"
                     /db_xref="CDD:257668"
     gene            7164..7451
                     /locus_tag="Rahaq2_5119"
                     /note="IMG reference gene:2506712141"
                     /db_xref="GeneID:11954046"
     CDS             7164..7451
                     /locus_tag="Rahaq2_5119"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005459734.1"
                     /db_xref="GI:383192424"
                     /db_xref="GeneID:11954046"
                     /translation="MSGAGVERQAMVGSLEPPAKDMSTDLIVLKMLAAMAIPVKEVKF
                     SLKFQRIIIMSLKPGPKRIAESTGEPDKRQRDNKKTPGNTDKLKPSKSSEK"
     gene            7684..7905
                     /locus_tag="Rahaq2_5120"
                     /note="IMG reference gene:2506712142"
                     /db_xref="GeneID:11954047"
     CDS             7684..7905
                     /locus_tag="Rahaq2_5120"
                     /note="PFAM: Protein of unknown function (DUF1471);
                     manually curated"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005459735.1"
                     /db_xref="GI:383192425"
                     /db_xref="InterPro:IPR010854"
                     /db_xref="GeneID:11954047"
                     /translation="MKTIKTLVVAAALATVSFGSFAAEIGTVTATGNTLDGLESTFAA
                     KAAAAGATSYKIIEASGQNHLHGTAILYK"
     misc_feature    7684..7902
                     /locus_tag="Rahaq2_5120"
                     /note="Protein of unknown function (DUF1471); Region:
                     DUF1471; cl11507"
                     /db_xref="CDD:264403"
     sig_peptide     7684..7749
                     /locus_tag="Rahaq2_5120"
                     /note="Signal predicted by SignalP 3.0 HMM"
     gene            complement(8112..8366)
                     /locus_tag="Rahaq2_5121"
                     /note="IMG reference gene:2506712143"
                     /db_xref="GeneID:11954048"
     CDS             complement(8112..8366)
                     /locus_tag="Rahaq2_5121"
                     /note="IMG reference gene:2506712142_SP"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005459736.1"
                     /db_xref="GI:383192426"
                     /db_xref="GeneID:11954048"
                     /translation="MHNDAAADKPKEELGKKIPLSTVVMLSSRDKPRRQYETIKRGET
                     GVAVPEAGDGLVGPVWRRQPSLLAVRWISHAKSPFTGFGA"
CONTIG      join(CP003247.1:1..8406)
//
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