LOCUS AFM06067.1 680 aa PRT BCT 31-AUG-2017
DEFINITION Bernardetia litoralis DSM 6794 DNA ligase, NAD-dependent protein.
ACCESSION CP003345-3555
PROTEIN_ID AFM06067.1
SOURCE Bernardetia litoralis DSM 6794
ORGANISM Bernardetia litoralis DSM 6794
Bacteria; Bacteroidota; Cytophagia; Cytophagales; Bernardetiaceae;
Bernardetia.
REFERENCE 1 (bases 1 to 4919337)
AUTHORS Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E.,
Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Peters,L.,
Ovchinnikova,G., Lu,M., Kyrpides,N., Mavromatis,K., Ivanova,N.,
Brettin,T., Detter,J.C., Han,C., Larimer,F., Land,M., Hauser,L.,
Markowitz,V., Cheng,J.-F., Hugenholtz,P., Woyke,T., Wu,D.,
Spring,S., Lang,E., Kopitz,M., Brambilla,E., Klenk,H.-P. and
Eisen,J.A.
CONSRTM US DOE Joint Genome Institute (JGI-PGF)
TITLE The complete genome of Flexibacter litoralis DSM 6794
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 4919337)
AUTHORS Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E.,
Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Peters,L.,
Ovchinnikova,G., Lu,M., Kyrpides,N., Mavromatis,K., Ivanova,N.,
Brettin,T., Detter,J.C., Han,C., Larimer,F., Land,M., Hauser,L.,
Markowitz,V., Cheng,J.-F., Hugenholtz,P., Woyke,T., Wu,D.,
Spring,S., Lang,E., Kopitz,M., Brambilla,E., Klenk,H.-P. and
Eisen,J.A.
CONSRTM US DOE Joint Genome Institute (JGI-PGF)
TITLE Direct Submission
JOURNAL Submitted (05-JUN-2012) US DOE Joint Genome Institute, 2800
Mitchell Drive, Walnut Creek, CA 94598-1698, USA
COMMENT URL -- http://www.jgi.doe.gov
JGI Project ID: 4089456
Source DNA and organism available from Hans-Peter Klenk at the
German Collection of Microorganisms and Cell Cultures (DSMZ)
(hans-peter.klenk@dsmz.de)
Contacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)
David Bruce (microbe@cuba.jgi-psf.org)
Whole genome sequencing and draft assembly at JGI-PGF
Finishing done by JGI-LANL
Annotation by JGI-ORNL and JGI-PGF
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 :: Flexibacter litoralis DSM 6794
collection_date :: Missing
lat_lon :: 32.840 -117.258
depth :: Missing
alt_elev :: Missing
country :: USA
environment :: Marine
num_replicons :: 1
ref_biomaterial :: DSM 6794, ATCC 23117, IFO 15988, NBRC 15988
biotic_relationship :: Free living
trophic_level :: Missing
rel_to_oxygen :: Aerobe
isol_growth_condt :: Missing
sequencing_meth :: WGS
assembly :: Newbler v. 2.3 (pre-release)
finishing_strategy :: Finished
GOLD Stamp ID :: Gi04020
Type Strain :: Yes
Funding Program :: DOE-GEBA 2009
Gene Calling Method :: Prodigal, GenePRIMP
Isolation Site :: Sea water aquarium outflow, La Jolla,
California, U.S.A.
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##
FEATURES Qualifiers
source /organism="Bernardetia litoralis DSM 6794"
/mol_type="genomic DNA"
/strain="DSM 6794"
/isolation_source="sea water aquarium outflow"
/culture_collection="DSM:6794"
/type_material="type strain of Bernardetia litoralis"
/db_xref="taxon:880071"
/country="USA: La Jolla, CA"
/lat_lon="32.840 N 117.258 W"
protein /locus_tag="Fleli_3755"
/note="PFAM: NAD-dependent DNA ligase OB-fold domain;
NAD-dependent DNA ligase adenylation domain; BRCA1 C
Terminus (BRCT) domain; NAD-dependent DNA ligase C4 zinc
finger domain; TIGRFAM: DNA ligase, NAD-dependent"
/transl_table=11
/db_xref="InterPro:IPR001357"
/db_xref="InterPro:IPR001679"
/db_xref="InterPro:IPR004149"
/db_xref="InterPro:IPR004150"
/db_xref="InterPro:IPR010994"
/db_xref="InterPro:IPR012340"
/db_xref="InterPro:IPR013839"
/db_xref="InterPro:IPR016027"
/db_xref="InterPro:IPR018239"
BEGIN
1 MNLSAIKKRI NSLVEKLNHY NNQYYQNDIS EISDFEFDKL LEELKKLEKE NPQFKLPNSP
61 TLRVGGDITS NFETVVHRYP MLSLSNTYNE TELLEFDERI RKTVDNPIYV CELKFDGVAI
121 SLRYENGIFT QGVTRGDGEK GDDVTANVRT IRDIPLKIEG KNIDKNEVPS DFELRGEVYL
181 SKTQFEILNQ EIVERSKEKG VEEEKIPDLL LKNPRNAASG AIKMKDSKEM AKRKLSCFVY
241 DAYGTPFESH TSILENLEKY NFAVSPFHRK ANGIQEVLEF IKDWEEKRFT LPYETDGVVI
301 KINDLDQREE LGFTSKSPRW AIAYKYKAEE AQSKLKSVVF QVGRTGAITP VANLTPVQLS
361 GTTVKRATLH NEGEIKRLDL HEGDTVFVEK SGEIIPKVTR VVTEKRVKNA KPIIFIENCP
421 ECETKLVREE GEAAYYCLNQ DGCPPQILGK IEHFVCKNGM DIDSIGSKTA QNFLNAGIIK
481 SFADLYELDR EKLLALPNFK EKSVNNVFIG IENSKKRPFK NVLYSLGIKY VGRGVSEILT
541 DEFSSIDNII KASKEEISAV FGIGERIAEA VKAYFDEPKN IETIERLKTA GLQFEQAEKK
601 IVILDGILSG KTFVVSGTFQ NFEREELKEK IKGLGGKISS SVSKKLDYLL AGDKAGSSKI
661 EKAEKAGVAV ISEADFLKMI
//