Halostagnicola larsenii XH-48 plasmid unnamed4, 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\nCP007059.1.\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_006091059.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]; GO:0003979 - UDP-glucose 6-dehydrogenase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
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_006673523.1
GO:0016757 - glycosyltransferase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007109238.1
COORDINATES: similar to AA sequence:RefSeq:WP_006654407.1
COORDINATES: similar to AA sequence:RefSeq:WP_015320865.1
COORDINATES: similar to AA sequence:RefSeq:WP_005575644.1
NrfD/PsrC family molybdoenzyme membrane anchor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008426104.1
4Fe-4S ferredoxin N-terminal 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_006067658.1
GO:0009055 - electron transfer activity [Evidence IEA]
GO:0019646 - aerobic electron transport chain [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006182934.1
COORDINATES: similar to AA sequence:RefSeq:WP_004216283.1
COORDINATES: similar to AA sequence:RefSeq:WP_006067243.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007981429.1
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004216084.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
acetyl-CoA carboxylase biotin carboxylase subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004972396.1
COORDINATES: similar to AA sequence:RefSeq:WP_006089761.1
GO:0017168 - 5-oxoprolinase (ATP-hydrolyzing) activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006067239.1
GO:0009317 - acetyl-CoA carboxylase complex [Evidence IEA]
GO:0003989 - acetyl-CoA carboxylase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006431213.1
biotin-dependent carboxyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004216093.1
carboxyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008895565.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006090895.1
COORDINATES: similar to AA sequence:RefSeq:WP_008158942.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008895568.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
polysaccharide deacetylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006431438.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298928.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006650344.1
COORDINATES: similar to AA sequence:RefSeq:WP_005575957.1
COORDINATES: similar to AA sequence:RefSeq:WP_004215882.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024917.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006109673.1
COORDINATES: similar to AA sequence:RefSeq:WP_007142923.1
COORDINATES: similar to AA sequence:RefSeq:WP_015233823.1
GO:0004803 - transposase activity [Evidence IEA]
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004053736.1
DUF2080 family transposase-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_008158904.1
COORDINATES: similar to AA sequence:RefSeq:WP_006090917.1
COORDINATES: similar to AA sequence:RefSeq:WP_007261491.1
COORDINATES: similar to AA sequence:RefSeq:WP_006184432.1
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006827921.1
COORDINATES: similar to AA sequence:RefSeq:WP_006666380.1
MaoC/PaaZ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012945842.1
COORDINATES: similar to AA sequence:RefSeq:WP_004516850.1
COORDINATES: similar to AA sequence:RefSeq:WP_006432742.1
COORDINATES: similar to AA sequence:RefSeq:WP_007109774.1
COORDINATES: similar to AA sequence:RefSeq:WP_006180100.1
GO:0032559 - adenyl ribonucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005039491.1
COORDINATES: similar to AA sequence:RefSeq:WP_006665399.1
dicarboxylate/amino acid:cation symporter
COORDINATES: similar to AA sequence:RefSeq:WP_007142517.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009376303.1
GO:0018784 - (S)-2-haloacid dehalogenase activity [Evidence IEA]
GO:0006805 - xenobiotic metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014039995.1
COORDINATES: similar to AA sequence:RefSeq:WP_017597383.1
COORDINATES: similar to AA sequence:RefSeq:WP_006109864.1
GO:0008795 - NAD+ synthase activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004972245.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0071705 - nitrogen compound transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012945579.1
COORDINATES: similar to AA sequence:RefSeq:WP_007274611.1
COORDINATES: similar to AA sequence:RefSeq:WP_008427201.1
COORDINATES: similar to AA sequence:RefSeq:WP_006108098.1
COORDINATES: similar to AA sequence:RefSeq:WP_006649717.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_015299090.1
COORDINATES: similar to AA sequence:RefSeq:WP_008894725.1
COORDINATES: similar to AA sequence:RefSeq:WP_006664434.1
COORDINATES: protein motif:HMM:NF024948.2
COORDINATES: similar to AA sequence:RefSeq:WP_008895517.1
COORDINATES: similar to AA sequence:RefSeq:WP_007143097.1
COORDINATES: similar to AA sequence:RefSeq:WP_010902305.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006165231.1
GO:0004540 - ribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006165229.1
COORDINATES: similar to AA sequence:RefSeq:WP_008895583.1
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_049955228.1
IS200/IS605-like element ISHall1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_004971416.1
COORDINATES: similar to AA sequence:RefSeq:WP_007107559.1
COORDINATES: similar to AA sequence:RefSeq:WP_008414300.1
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_008526746.1
GO:0015075 - monoatomic ion transmembrane transporter activity [Evidence IEA]
GO:0034220 - monoatomic ion transmembrane transport [Evidence IEA]
monovalent cation/H+ antiporter complex subunit F
COORDINATES: similar to AA sequence:RefSeq:WP_006665922.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012659723.1
proton-conducting transporter membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012659722.1
COORDINATES: similar to AA sequence:RefSeq:WP_008012321.1
COORDINATES: similar to AA sequence:RefSeq:WP_006824888.1
COORDINATES: similar to AA sequence:RefSeq:WP_006667075.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008894288.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008006213.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
glycoside hydrolase family 2 TIM barrel-domain containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006109668.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006664876.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298644.1
twin-arginine translocation signal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006108298.1
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004971846.1
GO:0016853 - isomerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008308253.1
COORDINATES: similar to AA sequence:RefSeq:WP_014030959.1
COORDINATES: similar to AA sequence:RefSeq:WP_008308251.1
GO:0055085 - transmembrane transport [Evidence IEA]
energy-coupling factor transporter transmembrane component T
COORDINATES: similar to AA sequence:RefSeq:WP_006882280.1
GO:0050532 - 2-phosphosulfolactate phosphatase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007345514.1
COORDINATES: similar to AA sequence:RefSeq:WP_006087999.1
COORDINATES: similar to AA sequence:RefSeq:WP_007701933.1
COORDINATES: similar to AA sequence:RefSeq:WP_006827127.1
COORDINATES: protein motif:HMM:NF019928.2
COORDINATES: similar to AA sequence:RefSeq:WP_007981685.1
COORDINATES: similar to AA sequence:RefSeq:WP_008159854.1
COORDINATES: similar to AA sequence:RefSeq:WP_006885759.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:1905887 - autoinducer AI-2 transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006667205.1
quaternary ammonium compound efflux SMR transporter SugE
COORDINATES: similar to AA sequence:RefSeq:WP_007977859.1
COORDINATES: similar to AA sequence:RefSeq:WP_004059712.1
GO:0016831 - carboxy-lyase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0019752 - carboxylic acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006090871.1
COORDINATES: similar to AA sequence:RefSeq:WP_006067309.1
COORDINATES: similar to AA sequence:RefSeq:WP_004516371.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012941523.1
COORDINATES: similar to AA sequence:RefSeq:WP_006650338.1
COORDINATES: similar to AA sequence:RefSeq:WP_006090874.1
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_004214703.1
COORDINATES: similar to AA sequence:RefSeq:WP_007109215.1
COORDINATES: similar to AA sequence:RefSeq:WP_008158967.1
COORDINATES: similar to AA sequence:RefSeq:WP_006109658.1
GO:0008966 - phosphoglucosamine mutase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]; GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006179629.1
COORDINATES: similar to AA sequence:RefSeq:WP_014863628.1
GO:0004360 - glutamine-fructose-6-phosphate transaminase (isomerizing) activity [Evidence IEA]
GO:0006040 - amino sugar metabolic process [Evidence IEA]; GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
glutamine--fructose-6-phosphate transaminase (isomerizing)
COORDINATES: similar to AA sequence:RefSeq:WP_006168798.1
COORDINATES: similar to AA sequence:RefSeq:WP_006090961.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006168793.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014667.2