Halogeometricum borinquense DSM 11551 plasmid pHBOR03, complete sequence.
Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Haloferacales; Haloferacaceae; Halogeometricum.
The complete plasmid3 of Halogeometricum borinquense DSM 11551
Submitted (10-AUG-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001693.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4082733\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Metadata-START##\nOrganism Display Name :: Halogeometricum borinquense PR3, DSM 11551\nCulture Collection ID :: DSM 11551, ATCC 700274, JCM 10706\nGOLD Stamp ID :: Gc01108\nFunding Program :: DOE-GEBA 2007\nNumber of Reads :: 2826 Sanger\nAssembly Method :: Newbler, PGA\nSequencing Depth :: 9.7x Sanger; 21.8x 454\nGene Calling Method :: GeneMark, GenePRIMP\nIsolation Site :: Solar salterns of Cabo Rojo Puerto Rico\nIsolation Country :: Puerto Rico\nLatitude :: 18.088189\nLongitude :: -67.147095\nOxygen Requirement :: Aerobe\nCell Shape :: Pleomorphic-shaped\nMotility :: Motile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 40C\nSalinity :: Halophile\nGram Staining :: gram-\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Solar saltern\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/24/2023 13:46:31\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,929\nCDSs (total) :: 3,869\nGenes (coding) :: 3,822\nCDSs (with protein) :: 3,822\nGenes (RNA) :: 60\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 2\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 27 of 47\nPseudo Genes (incomplete) :: 26 of 47\nPseudo Genes (internal stop) :: 11 of 47\nPseudo Genes (multiple problems) :: 14 of 47\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Halogeometricum borinquense
COORDINATES: similar to AA sequence:RefSeq:WP_006053354.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006053355.1
COORDINATES: protein motif:HMM:NF016831.2
helix-turn-helix domain-containing protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_006053357.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053358.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053359.1
COORDINATES: similar to AA sequence:RefSeq:WP_006430165.1
PotD/PotF family extracellular solute-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053361.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053362.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053363.1
COORDINATES: similar to AA sequence:RefSeq:WP_006430170.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053365.1
COORDINATES: similar to AA sequence:RefSeq:WP_008892679.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053367.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053368.1
right-handed parallel beta-helix repeat-containing protein
COORDINATES: protein motif:HMM:NF012791.2
COORDINATES: similar to AA sequence:RefSeq:WP_005536845.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053373.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053374.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053378.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053379.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053381.1
GO:0019290 - siderophore biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053382.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053384.1
IucA/IucC family siderophore biosynthesis protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053385.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053386.1
diaminobutyrate--2-oxoglutarate transaminase
COORDINATES: similar to AA sequence:RefSeq:WP_006053387.1
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053388.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053389.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322008.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006053392.1
COORDINATES: protein motif:HMM:TIGR01409.1
twin-arginine translocation signal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053394.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053395.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053396.1
COORDINATES: similar to AA sequence:RefSeq:WP_007276457.1
COORDINATES: similar to AA sequence:RefSeq:WP_008015529.1
COORDINATES: similar to AA sequence:RefSeq:WP_011222529.1
COORDINATES: similar to AA sequence:RefSeq:WP_004042300.1
proton-conducting transporter membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_006053401.1
COORDINATES: similar to AA sequence:RefSeq:WP_017344343.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053403.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014030762.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053405.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053406.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053408.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322016.1
COORDINATES: similar to AA sequence:RefSeq:WP_006650999.1
LysM peptidoglycan-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008322019.1
contractile injection system protein, VgrG/Pvc8 family
COORDINATES: similar to AA sequence:RefSeq:WP_006053416.1
COORDINATES: similar to AA sequence:RefSeq:WP_007542082.1
COORDINATES: similar to AA sequence:RefSeq:WP_006650995.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053419.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322021.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053422.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053423.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053424.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053425.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322031.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053427.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053428.1
COORDINATES: protein motif:HMM:NF025078.2
COORDINATES: similar to AA sequence:RefSeq:WP_006053430.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053431.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053432.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053433.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053434.1
GO:0005198 - structural molecule activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053435.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322036.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053437.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053438.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322038.1
COORDINATES: similar to AA sequence:RefSeq:WP_007542054.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008322325.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053442.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053444.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053445.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053446.1
COORDINATES: protein motif:HMM:NF024091.2
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053449.1
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012996418.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004216283.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006053453.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053454.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053455.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053456.1
COORDINATES: similar to AA sequence:RefSeq:WP_004595756.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053458.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053459.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053461.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053463.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053464.1
iron-containing alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053465.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053466.1
COORDINATES: similar to AA sequence:RefSeq:WP_006166289.1
GO:0043231 - intracellular membrane-bounded organelle [Evidence IEA]
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
CDGSH iron-sulfur domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053468.1
COORDINATES: similar to AA sequence:RefSeq:WP_004060624.1
COORDINATES: similar to AA sequence:RefSeq:WP_007540549.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053471.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053472.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053473.1
COORDINATES: similar to AA sequence:RefSeq:WP_004062408.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298763.1
zinc finger HIT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053475.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053476.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053477.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053478.1
COORDINATES: similar to AA sequence:RefSeq:WP_004056249.1
GO:0004514 - nicotinate-nucleotide diphosphorylase (carboxylating) activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF014719.2
COORDINATES: similar to AA sequence:RefSeq:WP_006053481.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053482.1
pantetheine-phosphate adenylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_006053483.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053484.1
orc1/cdc6 family replication initiation protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053485.1
GO:0005515 - protein binding [Evidence IEA]
fibronectin type III domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008324944.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053487.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053489.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053490.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053491.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053493.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053494.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053495.1
COORDINATES: similar to AA sequence:RefSeq:WP_008003984.1
COORDINATES: similar to AA sequence:RefSeq:WP_008321495.1
COORDINATES: similar to AA sequence:RefSeq:WP_006183554.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053498.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053499.1
COORDINATES: similar to AA sequence:RefSeq:WP_004056292.1
GO:0003987 - acetate-CoA ligase activity [Evidence IEA]
GO:0019427 - acetyl-CoA biosynthetic process from acetate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053316.1
bacterio-opsin activator domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004977978.1
COORDINATES: similar to AA sequence:RefSeq:WP_004064601.1
COORDINATES: similar to AA sequence:RefSeq:WP_008094190.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053320.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053321.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053322.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053323.1
COORDINATES: protein motif:HMM:NF024753.2
PQQ-binding-like beta-propeller repeat protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053325.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053326.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053327.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053328.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0051119 - sugar transmembrane transporter activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053329.1
COORDINATES: similar to AA sequence:RefSeq:WP_014050599.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053331.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053332.1
COORDINATES: similar to AA sequence:RefSeq:WP_011223062.1
COORDINATES: similar to AA sequence:RefSeq:WP_008321946.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053335.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053336.1
mechanosensitive ion channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006053337.1
COORDINATES: similar to AA sequence:RefSeq:WP_007740234.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053339.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053340.1
GO:0004047 - aminomethyltransferase activity [Evidence IEA]
GO:0019464 - glycine decarboxylation via glycine cleavage system [Evidence IEA]
glycine cleavage system aminomethyltransferase GcvT
COORDINATES: similar to AA sequence:RefSeq:WP_008387602.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008426906.1
GO:0004375 - glycine dehydrogenase (decarboxylating) activity [Evidence IEA]
GO:0006546 - glycine catabolic process [Evidence IEA]
aminomethyl-transferring glycine dehydrogenase subunit GcvPA
COORDINATES: similar to AA sequence:RefSeq:WP_008387600.1
aminomethyl-transferring glycine dehydrogenase subunit GcvPB
COORDINATES: similar to AA sequence:RefSeq:WP_006053344.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053345.1
GO:0004794 - L-threonine ammonia-lyase activity [Evidence IEA]
GO:0006549 - isoleucine metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012371.2
COORDINATES: similar to AA sequence:RefSeq:WP_006053347.1
GO:0004148 - dihydrolipoyl dehydrogenase activity [Evidence IEA]
GO:0045454 - cell redox homeostasis [Evidence IEA]; GO:0051068 - dihydrolipoamide metabolic process [Evidence IEA]; GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010903644.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0016992 - lipoate synthase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0009107 - lipoate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053349.1
GO:0019239 - deaminase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006053350.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053351.1
Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C-terminal domain
COORDINATES: similar to AA sequence:RefSeq:WP_007107699.1
COORDINATES: similar to AA sequence:RefSeq:WP_013446655.1