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 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 179..586
/locus_tag="Rahaq2_5114"
/note="Domain of unknown function DUF29; Region: DUF29;
pfam01724"
/db_xref="CDD:216664"
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:205047"
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..>4540)
/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:241624"
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:220039"
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(<6219..6401)
/locus_tag="Rahaq2_5118"
/note="Domain of unknown function (DUF4095); Region:
DUF4095; pfam13338"
/db_xref="CDD:222054"
misc_feature complement(join(5711..6196,6198..>6293))
/locus_tag="Rahaq2_5118"
/note="Predicted transcriptional regulator
[Transcription]; Region: COG5340"
/db_xref="CDD:227645"
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"
sig_peptide 7684..7749
/locus_tag="Rahaq2_5120"
/note="Signal predicted by SignalP 3.0 HMM"
misc_feature 7753..7902
/locus_tag="Rahaq2_5120"
/note="Protein of unknown function (DUF1471); Region:
DUF1471; pfam07338"
/db_xref="CDD:219380"
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)
//
