Halostagnicola larsenii XH-48 plasmid unnamed3, complete sequence.
Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Natrialbales; Natrialbaceae; Halostagnicola.
Submitted (10-JAN-2014) DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP007058.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 402803\nSource DNA and Organism available from Iain Anderson\n(IJAnderson@lbl.gov)\nSource DNA available from Iain Anderson (IJAnderson@lbl.gov)\nOrganism available from Iain Anderson (IJAnderson@lbl.gov)\nContacts: Iain Anderson (IJAnderson@lbl.gov)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nAnnotation by JGI-ORNL\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Halostagnicola larsenii XH-48, DSM\n 17691\nlat_lon :: 43.916 115.616\ncountry :: China\nref_biomaterial :: DSM 17691\nbiotic_relationship :: Free living\nrel_to_oxygen :: Obligate aerobe\nisol_growth_condt :: 16825623\nassembly :: ALLPATHS v. R37654\nenvironment :: Aquatic; Fresh water; Sediment\nsequencing_meth :: WGS\nGOLD Stamp ID :: Gi05997\nCurrent Finishing Status :: Level 6: Finished\nType Strain :: Yes\nFunding Program :: DOE-CSP 2010\nGene Calling Method :: Prodigal, GenePRIMP\nIsolation Site :: sediment of saline Lake Xilinhot, Inner\n Mongolia, China\nCell Shape :: Rod-shaped\nTemperature Range :: Mesophile\nTemperature Optimum :: 37\npH :: 7.0 - 8.0\nGram Staining :: Gram-\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: ALLPATHS v. R37654\nGenome Coverage :: Unknown\nSequencing Technology :: 454-GS-FLX-Titanium; Illumina HiSeq\n 2000\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/07/2023 02:25:20\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,095\nCDSs (total) :: 4,040\nGenes (coding) :: 3,947\nCDSs (with protein) :: 3,947\nGenes (RNA) :: 55\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 2\nPseudo Genes (total) :: 93\nCDSs (without protein) :: 93\nPseudo Genes (ambiguous residues) :: 0 of 93\nPseudo Genes (frameshifted) :: 29 of 93\nPseudo Genes (incomplete) :: 76 of 93\nPseudo Genes (internal stop) :: 18 of 93\nPseudo Genes (multiple problems) :: 25 of 93\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_006184412.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
orc1/cdc6 family replication initiation protein
COORDINATES: similar to AA sequence:RefSeq:WP_006673552.1
GO:0003825 - alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008895604.1
GO:0004805 - trehalose-phosphatase activity [Evidence IEA]
GO:0005992 - trehalose biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013880600.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006179647.1
bacterio-opsin activator domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007261525.1
COORDINATES: similar to AA sequence:RefSeq:WP_006168358.1
COORDINATES: similar to AA sequence:RefSeq:WP_008895611.1
GO:0003824 - catalytic activity [Evidence IEA]
GO:0009236 - cobalamin biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006091009.1
cob(I)yrinic acid a,c-diamide adenosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008895616.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006088474.1
COORDINATES: similar to AA sequence:RefSeq:WP_006654796.1
MaoC family dehydratase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007261400.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006823978.1
COORDINATES: protein motif:HMM:NF013757.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008419177.1
GO:0006096 - glycolytic process [Evidence IEA]
dihydrolipoamide acetyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007274703.1
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_006107361.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
alpha-ketoacid dehydrogenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_006824003.1
GO:0045250 - cytosolic pyruvate dehydrogenase complex [Evidence IEA]
GO:0004739 - pyruvate dehydrogenase (acetyl-transferring) activity [Evidence IEA]
GO:0006086 - acetyl-CoA biosynthetic process from pyruvate [Evidence IEA]
pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_006824002.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007260906.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006107357.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006667509.1
COORDINATES: similar to AA sequence:RefSeq:WP_007694493.1
COORDINATES: similar to AA sequence:RefSeq:WP_007260902.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007260901.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007260900.1
COORDINATES: similar to AA sequence:RefSeq:WP_008388370.1
GO:0032559 - adenyl ribonucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006823996.1
GO:0016790 - thiolester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006087712.1
GO:1903425 - fluoride transmembrane transporter activity [Evidence IEA]
GO:1903424 - fluoride transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006671939.1
COORDINATES: similar to AA sequence:RefSeq:WP_008574631.1
lysylphosphatidylglycerol synthase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004977766.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006825398.1
COORDINATES: similar to AA sequence:RefSeq:WP_006825705.1
COORDINATES: similar to AA sequence:RefSeq:WP_006166078.1
COORDINATES: similar to AA sequence:RefSeq:WP_008896855.1
COORDINATES: similar to AA sequence:RefSeq:WP_004595218.1
COORDINATES: similar to AA sequence:RefSeq:WP_007260913.1
COORDINATES: similar to AA sequence:RefSeq:WP_015233383.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF023899.2
GO:0004842 - ubiquitin-protein transferase activity [Evidence IEA]
GO:0006996 - organelle organization [Evidence IEA]; GO:0016567 - protein ubiquitination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014052229.1
GO:0033744 - L-methionine:thioredoxin-disulfide S-oxidoreductase activity [Evidence IEA]; GO:0008113 - peptide-methionine (S)-S-oxide reductase activity [Evidence IEA]
GO:0030091 - protein repair [Evidence IEA]; GO:0006979 - response to oxidative stress [Evidence IEA]
peptide-methionine (S)-S-oxide reductase MsrA
COORDINATES: similar to AA sequence:RefSeq:WP_006091041.1
2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_013880477.1
COORDINATES: similar to AA sequence:RefSeq:WP_012942085.1
COORDINATES: similar to AA sequence:RefSeq:WP_008896260.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013878952.1
COORDINATES: similar to AA sequence:RefSeq:WP_013878953.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946036.1
GO:0004152 - dihydroorotate dehydrogenase activity [Evidence IEA]
GO:0006222 - UMP biosynthetic process [Evidence IEA]
quinone-dependent dihydroorotate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_012946029.1
monovalent cation/H+ antiporter subunit E
COORDINATES: similar to AA sequence:RefSeq:WP_004267808.1
COORDINATES: similar to AA sequence:RefSeq:WP_008158802.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
GO:0098662 - inorganic cation transmembrane transport [Evidence IEA]; GO:1902600 - proton transmembrane transport [Evidence IEA]
monovalent cation/H(+) antiporter subunit G
COORDINATES: similar to AA sequence:RefSeq:WP_007109263.1
COORDINATES: similar to AA sequence:RefSeq:WP_006091090.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946024.1
COORDINATES: similar to AA sequence:RefSeq:WP_006663836.1
proton-conducting transporter membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_006654829.1
COORDINATES: similar to AA sequence:RefSeq:WP_004267815.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946020.1
COORDINATES: similar to AA sequence:RefSeq:WP_013035117.1
GO:0008869 - galactonate dehydratase activity [Evidence IEA]
GO:0009063 - amino acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008895305.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012942990.1
COORDINATES: similar to AA sequence:RefSeq:WP_008415216.1
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008895302.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: protein motif:HMM:NF024595.2
COORDINATES: similar to AA sequence:RefSeq:WP_008001139.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004957768.1
COORDINATES: similar to AA sequence:RefSeq:WP_014863326.1
COORDINATES: similar to AA sequence:RefSeq:WP_006184755.1
COORDINATES: similar to AA sequence:RefSeq:WP_006108110.1
COORDINATES: similar to AA sequence:RefSeq:WP_004050597.1
COORDINATES: similar to AA sequence:RefSeq:WP_008162587.1
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: similar to AA sequence:RefSeq:WP_008159558.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006166586.1
COORDINATES: similar to AA sequence:RefSeq:WP_007140917.1
GO:0042910 - xenobiotic transmembrane transporter activity [Evidence IEA]
GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006056857.1
MazG nucleotide pyrophosphohydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013879477.1
COORDINATES: similar to AA sequence:RefSeq:WP_013879476.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013879475.1
COORDINATES: similar to AA sequence:RefSeq:WP_013879474.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
GO:0009060 - aerobic respiration [Evidence IEA]
cbb3-type cytochrome c oxidase subunit I
COORDINATES: similar to AA sequence:RefSeq:WP_013879472.1
COORDINATES: similar to AA sequence:RefSeq:WP_008424597.1
COORDINATES: similar to AA sequence:RefSeq:WP_007741958.1
COORDINATES: similar to AA sequence:RefSeq:WP_013879469.1
COORDINATES: similar to AA sequence:RefSeq:WP_008895186.1
GO:0006813 - potassium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006430935.1
COORDINATES: similar to AA sequence:RefSeq:WP_006432930.1
COORDINATES: similar to AA sequence:RefSeq:WP_008895080.1
COORDINATES: similar to AA sequence:RefSeq:WP_007699155.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0015499 - formate transmembrane transporter activity [Evidence IEA]
GO:0015724 - formate transport [Evidence IEA]
formate/nitrite transporter family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013881901.1
COORDINATES: similar to AA sequence:RefSeq:WP_013881895.1
COORDINATES: similar to AA sequence:RefSeq:WP_006649725.1
COORDINATES: similar to AA sequence:RefSeq:WP_006430821.1
GO:0004849 - uridine kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006056174.1
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_006109461.1
COORDINATES: similar to AA sequence:RefSeq:WP_008894951.1
COORDINATES: similar to AA sequence:RefSeq:WP_013880498.1
COORDINATES: similar to AA sequence:RefSeq:WP_004043159.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008425301.1
COORDINATES: similar to AA sequence:RefSeq:WP_006666459.1
COORDINATES: similar to AA sequence:RefSeq:WP_007142607.1
COORDINATES: similar to AA sequence:RefSeq:WP_017343376.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006654786.1
COORDINATES: similar to AA sequence:RefSeq:WP_008159049.1
GO:0004765 - shikimate kinase activity [Evidence IEA]
GO:0009423 - chorismate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006067339.1
COORDINATES: similar to AA sequence:RefSeq:WP_008159046.1
COORDINATES: similar to AA sequence:RefSeq:WP_006663988.1
COORDINATES: similar to AA sequence:RefSeq:WP_006179725.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006180070.1
protein sorting system archaetidylserine decarboxylase
COORDINATES: similar to AA sequence:RefSeq:WP_015323191.1
COORDINATES: similar to AA sequence:RefSeq:WP_015322854.1
COORDINATES: similar to AA sequence:RefSeq:WP_004959160.1
GO:0016407 - acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007698453.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013880984.1
COORDINATES: similar to AA sequence:RefSeq:WP_012945356.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111112.1
COORDINATES: similar to AA sequence:RefSeq:WP_004266936.1
COORDINATES: similar to AA sequence:RefSeq:WP_014555977.1
GO:0046873 - metal ion transmembrane transporter activity [Evidence IEA]
GO:0030001 - metal ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013881957.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111127.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008849553.1
COORDINATES: similar to AA sequence:RefSeq:WP_012944290.1
COORDINATES: similar to AA sequence:RefSeq:WP_006652121.1
PQQ-binding-like beta-propeller repeat protein
COORDINATES: similar to AA sequence:RefSeq:WP_006652692.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006650950.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007140131.1
COORDINATES: similar to AA sequence:RefSeq:WP_008605661.1
COORDINATES: similar to AA sequence:RefSeq:WP_006179772.1
COORDINATES: similar to AA sequence:RefSeq:WP_006091046.1
COORDINATES: similar to AA sequence:RefSeq:WP_006431234.1
COORDINATES: similar to AA sequence:RefSeq:WP_006092896.1
COORDINATES: similar to AA sequence:RefSeq:WP_014863660.1
GO:0006750 - glutathione biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006106855.1
SMP-30/gluconolactonase/LRE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006883302.1
COORDINATES: similar to AA sequence:RefSeq:WP_020222076.1
GO:0008927 - mannonate dehydratase activity [Evidence IEA]
GO:0006064 - glucuronate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013879707.1
GO:0016853 - isomerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007261579.1
GO:0004038 - allantoinase activity [Evidence IEA]; GO:0050897 - cobalt ion binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0000256 - allantoin catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013880539.1
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006672734.1
COORDINATES: similar to AA sequence:RefSeq:WP_008011985.1
COORDINATES: similar to AA sequence:RefSeq:WP_006664222.1
COORDINATES: similar to AA sequence:RefSeq:WP_004214745.1
COORDINATES: similar to AA sequence:RefSeq:WP_008425351.1
COORDINATES: protein motif:HMM:NF019380.2
COORDINATES: similar to AA sequence:RefSeq:WP_006827941.1
COORDINATES: similar to AA sequence:RefSeq:WP_008895648.1
GO:0016746 - acyltransferase activity [Evidence IEA]; GO:0120225 - coenzyme A binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008895647.1
GO:0008483 - transaminase activity [Evidence IEA]
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_006827938.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006179583.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.