GenomeNet

Database: RefSeq
Entry: NC_017092
LinkDB: NC_017092
Original site: NC_017092 
LOCUS       NC_017092               8406 bp    DNA     linear   CON 28-MAY-2017
DEFINITION  Rahnella aquatilis CIP 78.65 = ATCC 33071 plasmid pRahaq203,
            partial sequence.
ACCESSION   NC_017092
VERSION     NC_017092.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02261385
            Assembly: GCF_000241955.1
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; Enterobacterales;
            Yersiniaceae; 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)
  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     REFSEQ INFORMATION: The reference sequence was derived from
            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).
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            
            ##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##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/28/2017 15:12:41
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS+
            Annotation Software revision      :: 4.2
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
                                                 repeat_region
            Genes (total)                     :: 5,031
            CDS (total)                       :: 4,923
            Genes (coding)                    :: 4,831
            CDS (coding)                      :: 4,831
            Genes (RNA)                       :: 108
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 76
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 92
            Pseudo Genes (ambiguous residues) :: 0 of 92
            Pseudo Genes (frameshifted)       :: 33 of 92
            Pseudo Genes (incomplete)         :: 52 of 92
            Pseudo Genes (internal stop)      :: 22 of 92
            Pseudo Genes (multiple problems)  :: 13 of 92
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
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_RS24585"
                     /old_locus_tag="Rahaq2_5114"
     CDS             167..598
                     /locus_tag="RAHAQ2_RS24585"
                     /old_locus_tag="Rahaq2_5114"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014440113.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF29 domain-containing protein"
                     /protein_id="WP_014440113.1"
                     /translation="MTARYETDFYGWTREQADLLRNGRFSELDTQNLLEEIEAMGTSA
                     ETELESRLEVLFIHMLKCQLLSEHQARSWKLTIEEQRRKIERSLRKSPSIRHKLPEII
                     GDAYGDAVIGAERETHIKRSVFPAECPWSFEQFMDPKFYPE"
     gene            complement(1524..1934)
                     /locus_tag="RAHAQ2_RS24590"
                     /old_locus_tag="Rahaq2_5115"
     CDS             complement(1524..1934)
                     /locus_tag="RAHAQ2_RS24590"
                     /old_locus_tag="Rahaq2_5115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014440114.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA-binding protein"
                     /protein_id="WP_014440114.1"
                     /translation="MAKISISEASRLTGKSRTTLHRLIKAGELSSCSGMKNTKLLDTS
                     ELLRVFGTLSSVQPAQLDGQVTGQRFTSETAQSEQVHQQLTQEVEHLRELVTAQQSHI
                     DSLKQAMLLLEHKKEIQPVAAASDNSPWWRFWKS"
     gene            complement(4109..4813)
                     /locus_tag="RAHAQ2_RS24595"
                     /old_locus_tag="Rahaq2_5116"
     CDS             complement(4109..4813)
                     /locus_tag="RAHAQ2_RS24595"
                     /old_locus_tag="Rahaq2_5116"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014440115.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="serine/threonine protein phosphatase"
                     /protein_id="WP_014440115.1"
                     /translation="MTVRMDFITSTGTRDRNLDRFLEVKTDFLSVFIMLDGFSQTDAN
                     PHYVDSLIDEMRDKILSGMGFEDVISVMENIQSSSVKCSGKSSIGVVLISDTEVKTMT
                     VGDVRIYFLIDGKRSLDDSLAQFLVSSGVSNPHFLNKHPYRNRLTKYLSKDSIHPIPA
                     FSSKRIINGEAIFMCTDGFWSNFEDREILEVTLDGKLTTMFNDVMHSNDENIDNASVA
                     LLRFNLADEEQQLALA"
     gene            complement(4823..5692)
                     /locus_tag="RAHAQ2_RS24600"
                     /old_locus_tag="Rahaq2_5117"
     CDS             complement(4823..5692)
                     /locus_tag="RAHAQ2_RS24600"
                     /old_locus_tag="Rahaq2_5117"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014440116.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nucleotidyl transferase AbiEii/AbiGii toxin
                     family protein"
                     /protein_id="WP_014440116.1"
                     /translation="MEFSIEEWVSLSPADRVVFRQSVHIVLSAIANSEYLKPKMIMKG
                     GMLLGIRYKSSRFTEDIDFSTKMKLSEIDQEEFRKELDDALVISSDELAYGVSCKVQS
                     LVIQPKKGYDKATFPSFNLTIGYARKNSAGEMDRLSRGQCPNTIKIDYSFNELSYSID
                     NIVMDDGSGVSAYGVTDLVAEKIRSIIQQPYRNRSRRQDVYDLDFIFDSICFDDGEKL
                     TILHSLLDKSTGRIPDGHITKDTLDREDIRDLSRRNYDTLHLEVEGDVKDFDFSFDRI
                     NEFYKSLPWDAVA"
     gene            complement(5705..6602)
                     /locus_tag="RAHAQ2_RS24715"
                     /old_locus_tag="Rahaq2_5118"
                     /pseudo
     CDS             complement(5705..6602)
                     /locus_tag="RAHAQ2_RS24715"
                     /old_locus_tag="Rahaq2_5118"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008110252.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
     gene            7127..7282
                     /locus_tag="RAHAQ2_RS25410"
     CDS             7127..7282
                     /locus_tag="RAHAQ2_RS25410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010251985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1508 domain-containing protein"
                     /protein_id="WP_072010247.1"
                     /translation="MNDKWEFYTDTANEWRWRRTASNGRIVGASSQGYVNRSDCVENA
                     RRNGYTG"
     gene            7684..7905
                     /locus_tag="RAHAQ2_RS24615"
                     /old_locus_tag="Rahaq2_5120"
     CDS             7684..7905
                     /locus_tag="RAHAQ2_RS24615"
                     /old_locus_tag="Rahaq2_5120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007373990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1471 domain-containing protein"
                     /protein_id="WP_014440119.1"
                     /translation="MKTIKTLVVAAALATVSFGSFAAEIGTVTATGNTLDGLESTFAA
                     KAAAAGATSYKIIEASGQNHLHGTAILYK"
     gene            complement(8112..8366)
                     /locus_tag="RAHAQ2_RS25415"
                     /old_locus_tag="Rahaq2_5121"
     CDS             complement(8112..8366)
                     /locus_tag="RAHAQ2_RS25415"
                     /old_locus_tag="Rahaq2_5121"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014440120.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_014440120.1"
                     /translation="MHNDAAADKPKEELGKKIPLSTVVMLSSRDKPRRQYETIKRGET
                     GVAVPEAGDGLVGPVWRRQPSLLAVRWISHAKSPFTGFGA"
CONTIG      join(CP003247.1:1..8406)
//
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